Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3806
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: 21516
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Found at i:1504 original size:40 final size:40
Alignment explanation
Indices: 1426--1648 Score: 292
Period size: 40 Copynumber: 5.5 Consensus size: 40
1416 ACCCAAGTAT
* * *
1426 CTTCGGGATTTAG-CCAGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
1465 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
1505 CTTCGGGACTTAGCCCGGATATAGTTACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1545 CTTCGGGACTTAGCCCGG-TATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
1587 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1627 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
1649 CATCCGAATA
Statistics
Matches: 163, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
39 20 0.12
40 106 0.65
41 1 0.01
42 28 0.17
43 8 0.05
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:1608 original size:82 final size:80
Alignment explanation
Indices: 1426--1648 Score: 308
Period size: 82 Copynumber: 2.8 Consensus size: 80
1416 ACCCAAGTAT
* * * * *
1426 CTTCGGGATTTAG-CCAGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
1490 CACTAGCATGAATGC
66 CACTAGCACAAATGC
*
1505 CTTCGGGACTTAGCCCGGATATAGTTACTAGCACAAATGCCTTCGGGACTTAGCCCGG-TATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1568 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
*
1587 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1649 CATCCGAATA
Statistics
Matches: 128, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
78 1 0.01
79 21 0.16
80 39 0.30
82 64 0.50
83 3 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:1640 original size:122 final size:119
Alignment explanation
Indices: 1426--1648 Score: 347
Period size: 122 Copynumber: 1.8 Consensus size: 119
1416 ACCCAAGTAT
* * *
1426 CTTCGGGATTTAGCCAGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTC
1 CTTCGGGACTTAGCCAGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
**
1491 ACTAGCATGAATGCCTTCGGGACTTAGCCCGGATATAGTTACTAGCACAAATGC
66 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTTACTAGCACAAATGC
* *
1545 CTTCGGGACTTAGCCCGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
1 CTTCGGGACTTAGCCAGATATAGC-A--ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATA
*
1610 GTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
63 GTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1649 CATCCGAATA
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
119 21 0.23
120 1 0.01
122 71 0.76
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (119 bp):
CTTCGGGACTTAGCCAGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTTACTAGCACAAATGC
Found at i:9628 original size:40 final size:40
Alignment explanation
Indices: 9550--9771 Score: 306
Period size: 40 Copynumber: 5.5 Consensus size: 40
9540 ACCCAAGTAT
* *
9550 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
9589 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
9629 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
9669 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
9712 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
9752 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGACTTAGCCCGGAT
9772 GTCATCCGAA
Statistics
Matches: 164, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 12 0.07
40 115 0.70
41 1 0.01
43 36 0.22
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:9746 original size:83 final size:80
Alignment explanation
Indices: 9550--9771 Score: 313
Period size: 83 Copynumber: 2.8 Consensus size: 80
9540 ACCCAAGTAT
* * * *
9550 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
9614 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* *
9629 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
9693 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
*
9712 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAT
9772 GTCATCCGAA
Statistics
Matches: 127, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
79 13 0.10
80 49 0.39
83 65 0.51
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:11270 original size:27 final size:27
Alignment explanation
Indices: 11240--11416 Score: 203
Period size: 27 Copynumber: 6.6 Consensus size: 27
11230 ATATTAAGTC
* * * *
11240 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
11267 CGCACACTTAGTGCCACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
11294 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
** * *
11321 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
11348 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
11375 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
11402 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
11417 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
27 128 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:11322 original size:54 final size:54
Alignment explanation
Indices: 11240--11416 Score: 239
Period size: 54 Copynumber: 3.3 Consensus size: 54
11230 ATATTAAGTC
* * *
11240 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * * *
11294 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
11348 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
11402 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
11417 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 106 0.99
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:11351 original size:81 final size:81
Alignment explanation
Indices: 11261--11415 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 81
11251 TGCTATATAA
* *
11261 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTG-CATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
11325 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
11342 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
11407 ACTTAGTGC
66 ACTTAGTGC
11416 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
80 2 0.03
81 65 0.97
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:19285 original size:27 final size:27
Alignment explanation
Indices: 19255--19431 Score: 203
Period size: 27 Copynumber: 6.6 Consensus size: 27
19245 ATATTGAGTC
* * * *
19255 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
19282 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
19309 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
** * *
19336 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
19363 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
19390 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
19417 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
19432 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
27 128 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:19393 original size:81 final size:81
Alignment explanation
Indices: 19276--19430 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 81
19266 TGCTATATAA
* * *
19276 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAACTCGCAC
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
19341 ACTTAGTGCCGCATGG
66 ACTTAGTGCCGCATGG
* * **
19357 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
19421 CACTTAGTGC
65 CACTTAGTGC
19431 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.02
81 65 0.98
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.