diff --git a/Pipfile.lock b/Pipfile.lock
index ffff191..e378d44 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "089fff873ef627ba4da8943f369d35baf072b48b4421d4d025abb17d951ffce8"
+            "sha256": "6a9e94b9fb771cdbc70c29e68954211f6778ff1be83c9713a16fe72315bc5a16"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -16,131 +16,148 @@
         ]
     },
     "default": {
-        "appdirs": {
-            "hashes": [
-                "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41",
-                "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"
-            ],
-            "version": "==1.4.4"
+        "aligntools": {
+            "git": "git+https://github.com/cfe-lab/aligntools.git",
+            "ref": "94c65f42b8b2008de4259c837eda4e9378636cb3"
         },
         "biopython": {
             "hashes": [
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-                "sha256:3b36ba1bf6395c09a365c53530c9d71f3617763fa2c1d452b3d8948368c0f1de",
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-                "sha256:97cbdbed01b2512471f36c74b91658d1dfbdcbf39bc038f6ce5a41c3e60a8fc6",
-                "sha256:9ba33244f0eff830beaa7240065bdb5095d96fded6599b76bbb9ddab45cd2bbd",
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-                "sha256:ee51bb1cd7decffd24da6b76d5e01b7e2fd818ab85cf0c180226cbb5793a3abd",
-                "sha256:ef7c79b65b0b3f3c7dc59e20a7f8ae5758d8e852cb8b9cace590dc5617e348ba"
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+                "sha256:7b69d59f9a762c5bb5f77ed03f197dad05ebd702c34d2cae7be98f1f30e04089",
+                "sha256:7f4c746825721ec367c2f2d6a8cda3bc6495a1e084e5b2fbab26e9467706603f",
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             ],
-            "markers": "python_version >= '3.7'",
-            "version": "==1.81"
+            "markers": "python_version >= '3.9'",
+            "version": "==1.84"
         },
         "certifi": {
             "hashes": [
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             ],
             "markers": "python_version >= '3.6'",
-            "version": "==2023.7.22"
+            "version": "==2024.7.4"
+        },
+        "cfeintact": {
+            "git": "https://github.com/cfe-lab/CFEIntact",
+            "ref": "a6ea095998a894e795c89a896a5fdc83ed9bc715"
         },
         "charset-normalizer": {
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         "click": {
             "hashes": [
@@ -152,124 +169,17 @@
         },
         "gotoh": {
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@@ -300,6 +210,7 @@
                 "sha256:fd67b306320dcadea700a8f79b9e671e607f8696e98ec255915c0c6d6b818503"
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@@ -331,15 +242,16 @@
                 "sha256:f908a77cbeef9bbd646bd4b81214cbef9ac3dda4181d5092a4aa9797d1bc7774"
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@@ -350,10 +262,10 @@
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@@ -386,6 +298,7 @@
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@@ -409,6 +322,7 @@
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@@ -417,46 +331,47 @@
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@@ -468,87 +383,88 @@
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+                "sha256:65e528e2e921ba8fd67d9055e6b9f9e34b21ebd6768ae1c1723f4ea6ace1234d",
+                "sha256:6aae5cce399a0f065da65c7bb1e8abd5c7a3043da9dceb429ebe1b289bc07806",
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+                "sha256:c5986ee7ea0795a4095ac4d113cbb3448601efca7f158ec7f7087a6c705304e4",
+                "sha256:cdd31315fc20868c194130de9ee6bfd99755cc9565edff98ecc12585b90be882",
+                "sha256:cef4649ec906ea7ea5e9e796e68b987f83fa9a718514fe147f538cfeda76d7a7",
+                "sha256:d05c16cf4b4c2fc880cb12ba4c9b526e9e5d5bb1d81313d4d732a5b9fe2b9d53",
+                "sha256:d2e344d6adc8ef81c5a233d3a57b3c7d5181f40e79e05e1c143da143ccb6377d",
+                "sha256:d45d3cbd94159c468b9b8c5a556e3f6b81a8d1af2a92b77320e887c3e7a5d080",
+                "sha256:db14f552ac38f10758ad14dd7b983dbab424e731588d300c7db25b6f89e335b5",
+                "sha256:dbc5958cb471e5a5af41b0ddaea96a37e74ed289535e8deca404811f6cb0bc3d",
+                "sha256:ddbd2f9713a79e8e7242d7c51f1929611e991d855f414ca9996c20e44a895f7c",
+                "sha256:e16f3d6b491c48c5ae726308e6ab1e18ee830b4cdd6913f2d7f77354b33f91c8",
+                "sha256:e2afe743289273209c992075a5a4913e8d007d569a406ffed0bd080ea02b0633",
+                "sha256:e564c2cf45d2f44a9da56f4e3a26b2236504a496eb4cb0ca7221cd4cc7a9aca9",
+                "sha256:ed550e7442f278af76d9d65af48069f1fb84c9f745ae249c1a183c1e9d1b025c"
             ],
             "index": "pypi",
-            "version": "==7.3.1"
+            "markers": "python_version >= '3.8'",
+            "version": "==7.5.4"
         },
         "exceptiongroup": {
             "hashes": [
-                "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9",
-                "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3"
+                "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad",
+                "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"
             ],
             "markers": "python_version < '3.11'",
-            "version": "==1.1.3"
+            "version": "==1.2.1"
         },
         "iniconfig": {
             "hashes": [
@@ -560,27 +476,28 @@
         },
         "packaging": {
             "hashes": [
-                "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61",
-                "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"
+                "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002",
+                "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"
             ],
-            "markers": "python_version >= '3.7'",
-            "version": "==23.1"
+            "markers": "python_version >= '3.8'",
+            "version": "==24.1"
         },
         "pluggy": {
             "hashes": [
-                "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12",
-                "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"
+                "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1",
+                "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"
             ],
             "markers": "python_version >= '3.8'",
-            "version": "==1.3.0"
+            "version": "==1.5.0"
         },
         "pytest": {
             "hashes": [
-                "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002",
-                "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"
+                "sha256:c434598117762e2bd304e526244f67bf66bbd7b5d6cf22138be51ff661980343",
+                "sha256:de4bb8104e201939ccdc688b27a89a7be2079b22e2bd2b07f806b6ba71117977"
             ],
             "index": "pypi",
-            "version": "==7.4.2"
+            "markers": "python_version >= '3.8'",
+            "version": "==8.2.2"
         },
         "tomli": {
             "hashes": [