Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2845
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 31751
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Found at i:1468 original size:30 final size:30
Alignment explanation
Indices: 1421--1477 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1411 TTTTTGAGCC
1421 TAGGGGAAAATCATAATTCTG-CAAAGGTT
1 TAGGGGAAAATCATAATTCTGTCAAAGGTT
** *
1450 TAGGGGTAAAATTGTAATTTTGTCAAAG
1 TAGGGG-AAAATCATAATTCTGTCAAAG
1478 TTTGAGTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 6 0.26
30 12 0.52
31 5 0.22
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.32
Consensus pattern (30 bp):
TAGGGGAAAATCATAATTCTGTCAAAGGTT
Found at i:2348 original size:54 final size:54
Alignment explanation
Indices: 2288--2711 Score: 492
Period size: 54 Copynumber: 7.9 Consensus size: 54
2278 TTGATAAGAT
* * **
2288 AAGGATATCATGTAAGACCATGACAAGGCATGGCATTGATAAGTTCTATAAGAT
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* * * * ** * *
2342 ATGGATATCATCTAAGAACATGCCAAGGCATGGCATTGATAAGTTAAATAGGGT
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* *
2396 AGGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAATTCTATAAGGC
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* *
2450 AAGGAAATCATGTAAGACCATGCCAAGGTAGGGCATTGATAAGTTCTATAAGGC
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* *
2504 AAGGAAATCATGTAAGACCATGCCAAGGCGTGGCATTGATAAGTTCTATAGGGC
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* * * *
2558 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTGTAAGGC
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTT-CTATAAGGC
*** * * *
2613 AAAGG-TCCCATGTAAGACCATGCTAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
* * * * * * * *
2666 AAGGATACCACGTAAGACCATGTCAAGACATGACAATGGTAAGTTC
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTC
2712 AAAAAGGAAA
Statistics
Matches: 320, Mismatches: 47, Indels: 7
0.86 0.13 0.02
Matches are distributed among these distances:
52 4 0.01
53 39 0.12
54 233 0.73
55 40 0.12
56 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (54 bp):
AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
Found at i:2532 original size:29 final size:29
Alignment explanation
Indices: 2445--2532 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 29
2435 TAAATTCTAT
2445 AAGGCAAGGAAATCATGTAAGACCATGCC
1 AAGGCAAGGAAATCATGTAAGACCATGCC
* ** * *
2474 AAGG-TAGGGCAT--TGATAAGTTCTAT---
1 AAGGCAAGGAAATCATG-TAAG-ACCATGCC
2499 AAGGCAAGGAAATCATGTAAGACCATGCC
1 AAGGCAAGGAAATCATGTAAGACCATGCC
2528 AAGGC
1 AAGGC
2533 GTGGCATTGA
Statistics
Matches: 41, Mismatches: 10, Indels: 16
0.61 0.15 0.24
Matches are distributed among these distances:
25 4 0.10
26 10 0.24
27 8 0.20
28 10 0.24
29 9 0.22
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18
Consensus pattern (29 bp):
AAGGCAAGGAAATCATGTAAGACCATGCC
Found at i:13255 original size:27 final size:27
Alignment explanation
Indices: 13224--13401 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
13214 TAAATTGTAC
13224 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
13251 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13277 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
13305 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
13333 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13360 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
13387 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
13402 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:13338 original size:82 final size:81
Alignment explanation
Indices: 13225--13380 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
13215 AAATTGTACA
* *
13225 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
13289 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
13306 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
13371 TGCGAGTTGA
65 TGCGAATTGA
13381 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:13392 original size:82 final size:81
Alignment explanation
Indices: 13221--13401 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
13211 GATTAAATTG
* *
13221 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
13286 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
13302 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
13366 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
13384 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
13402 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:21311 original size:27 final size:27
Alignment explanation
Indices: 21280--21457 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
21270 TAAATTGTAC
21280 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
21307 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21333 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
21361 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
21389 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
21416 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
21443 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
21458 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:21394 original size:82 final size:81
Alignment explanation
Indices: 21281--21436 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
21271 AAATTGTACA
* *
21281 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
21345 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
21362 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
21427 TGCGAGTTGA
65 TGCGAATTGA
21437 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:21448 original size:82 final size:81
Alignment explanation
Indices: 21277--21457 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
21267 GATTAAATTG
* *
21277 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
21342 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
21358 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
21422 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
21440 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
21458 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29316 original size:27 final size:27
Alignment explanation
Indices: 29285--29457 Score: 153
Period size: 27 Copynumber: 6.6 Consensus size: 27
29275 TAAATGTTAC
29285 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29312 TGCACT-AG-G-GCGA-ATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29334 ATGCAC-AAGTGTGCGAATATGACCATGC
1 A-GCACTAAGTGTGCG-ATTTGACTATGT
*
29362 GGCACTAAGTGTGCGAGTTTGACT-TGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
29389 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29416 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29443 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29458 GACTCAATAT
Statistics
Matches: 119, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
23 13 0.11
24 5 0.04
25 4 0.03
26 9 0.08
27 74 0.62
28 14 0.12
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Done.