Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2561
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: 33396
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Found at i:2471 original size:39 final size:39
Alignment explanation
Indices: 2385--2507 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
2375 TGTGAATATA
*
2385 TATACGCGAGAATTATATCCGGACTTCAGGT-CGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* * *
2423 TATAAGCGAGAATTATATCCGGACGTCATGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
* *
2462 TATATGCGAGAATTATATCCAGACTTTAGGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
*
2501 TACATGC
1 TATATGC
2508 TGGACATATA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 28 0.37
39 47 0.63
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (39 bp):
TATATGCGAGAATTATATCCGGACTTCAGGTCCGCAGGC
Found at i:16879 original size:28 final size:28
Alignment explanation
Indices: 16847--16909 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
16837 TCCCATATTA
*
16847 ATGGGGTATAGGAAAAGTCTCATAATTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
* * *
16875 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
16903 ATGGGGT
1 ATGGGGT
16910 TGATAATGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTCTCATAACTT
Found at i:23654 original size:47 final size:47
Alignment explanation
Indices: 23601--23910 Score: 442
Period size: 47 Copynumber: 6.6 Consensus size: 47
23591 AGGATTTAAG
*
23601 GTGATGAATGTGAACCTGCATATATGTGATAAGGCCGAATGGCCAAT
1 GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
* *
23648 GTGATGAATATGAACATGCATATATGAGATAAGGCCGAATGGCCAAT
1 GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
* * * *
23695 GTGATGAATGTGAGCATGCATATGTGTGATAAAGCCAAATGGCCAAT
1 GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
** *
23742 GTGATGAATGTGAATGTGCATATATGAGATAAGGCCGAATGGCCAAT
1 GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
* *
23789 GTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAAT
1 GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
** * *
23836 GTGATGAATGTGAATGTGCATATATGAGATAAGGCAGAATGGCCAAT
1 GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
* *
23883 GTGATGAACGTGAA-AGTGTATATATGTG
1 GTGATGAATGTGAACA-TGCATATATGTG
23911 GCGAAGCCGA
Statistics
Matches: 231, Mismatches: 31, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
47 231 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAAT
Found at i:23700 original size:94 final size:94
Alignment explanation
Indices: 23601--23910 Score: 487
Period size: 94 Copynumber: 3.3 Consensus size: 94
23591 AGGATTTAAG
* * **
23601 GTGATGAATGTGAACCTGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATATGAACATG
1 GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTG
23666 CATATATGAGATAAGGCCGAATGGCCAAT
66 CATATATGAGATAAGGCCGAATGGCCAAT
* * * *
23695 GTGATGAATGTGAGCATGCATATGTGTGATAAAGCCAAATGGCCAATGTGATGAATGTGAATGTG
1 GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTG
23760 CATATATGAGATAAGGCCGAATGGCCAAT
66 CATATATGAGATAAGGCCGAATGGCCAAT
* *
23789 GTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTG
1 GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTG
*
23854 CATATATGAGATAAGGCAGAATGGCCAAT
66 CATATATGAGATAAGGCCGAATGGCCAAT
* *
23883 GTGATGAACGTGAA-AGTGTATATATGTG
1 GTGATGAATGTGAACA-TGCATATATGTG
23911 GCGAAGCCGA
Statistics
Matches: 200, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
93 1 0.00
94 199 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (94 bp):
GTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAATGTG
CATATATGAGATAAGGCCGAATGGCCAAT
Found at i:23988 original size:46 final size:46
Alignment explanation
Indices: 23904--23992 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
23894 GAAAGTGTAT
* * *
23904 ATATGTGGCGAAGCCGAATGGCTAATGCGAAACGTGTATGAGACGG
1 ATATGTGGCAAAGCCAAATGGCTAATGCGAAACATGTATGAGACGG
* * * *
23950 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGA
1 ATATGTGGCAAAGCCAAATGGCTAATGCGAAACATGTATGAGA
23993 TGTGTATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.31, T:0.24
Consensus pattern (46 bp):
ATATGTGGCAAAGCCAAATGGCTAATGCGAAACATGTATGAGACGG
Found at i:25765 original size:61 final size:61
Alignment explanation
Indices: 25691--25822 Score: 255
Period size: 61 Copynumber: 2.2 Consensus size: 61
25681 CATCTAGCCT
25691 CTACACTCCATCTCCATCCAACCCTAAACTCCATGTGGGGATATAATCAACCCACCCATCC
1 CTACACTCCATCTCCATCCAACCCTAAACTCCATGTGGGGATATAATCAACCCACCCATCC
*
25752 CTACACTCCATCTCCATCCAACCCTACACTCCATGTGGGGATATAATCAACCCACCCATCC
1 CTACACTCCATCTCCATCCAACCCTAAACTCCATGTGGGGATATAATCAACCCACCCATCC
25813 CTACACTCCA
1 CTACACTCCA
25823 GAATCAGCAT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 70 1.00
ACGTcount: A:0.29, C:0.42, G:0.08, T:0.21
Consensus pattern (61 bp):
CTACACTCCATCTCCATCCAACCCTAAACTCCATGTGGGGATATAATCAACCCACCCATCC
Found at i:29375 original size:80 final size:80
Alignment explanation
Indices: 29242--29419 Score: 234
Period size: 80 Copynumber: 2.2 Consensus size: 80
29232 TGGATGATAA
* *
29242 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCCAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCCAAGGCATTCG
*
29307 TGCGAGTTA-CCATAT
66 AGCGAG-TAGCCATAT
* * * * *
29322 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTCCGGGCTATGTCCCGAAGGTATTCG
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCCAAGGCATTCG
*
29387 AGCGAGTAGCTATAT
66 AGCGAGTAGCCATAT
* *
29402 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29420 TACTTGGCTT
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
79 16 0.19
80 70 0.81
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCCAAGGCATTCG
AGCGAGTAGCCATAT
Found at i:29405 original size:40 final size:40
Alignment explanation
Indices: 29242--29380 Score: 208
Period size: 40 Copynumber: 3.5 Consensus size: 40
29232 TGGATGATAA
* * *
29242 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTT
* *
29282 CCGGGCTAAGTCCCCAAGGCATTTGTGCGAGTTACCA-TAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-T
29322 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTT
*
29362 CCGGGCTATGTCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29381 TATTCGAGCG
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.01
40 87 0.98
41 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTT
Found at i:31445 original size:39 final size:40
Alignment explanation
Indices: 31331--31512 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 40
31321 GCTACTCGTT
*
31331 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
31371 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
31411 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
31450 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
* *
31491 CAAA-ACCTTCGGAACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
31513 AGACATCATT
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 75 0.61
41 12 0.10
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:31500 original size:79 final size:79
Alignment explanation
Indices: 31337--31512 Score: 187
Period size: 79 Copynumber: 2.2 Consensus size: 79
31327 CGTTCAAATG
* * *
31337 CCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAG
1 CCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAG
* **
31402 TAACTCGCACCAATG
65 TAACTAGCACCAAAA
** *
31417 CCTTCGGGCTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATG
1 CCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATA
*
31480 GTCACTTAGCA-CAAAA
64 GTAAC-TAGCACCAAAA
*
31496 CCTTCGGAACTTAGCCC
1 CCTTCGG-GCTTAGCCC
31513 AGACATCATT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
78 4 0.05
79 57 0.70
80 20 0.25
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (79 bp):
CCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGT
AACTAGCACCAAAA
Found at i:32797 original size:22 final size:23
Alignment explanation
Indices: 32758--32810 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
32748 ATGGACACAT
*
32758 TTTTTTTTCT-TTTGTTTTCATCC
1 TTTTCTTTCTCTTTGTTTTC-TCC
32781 TTTTCTTTCTCTTT-TTTTCTCC
1 TTTTCTTTCTCTTTGTTTTCTCC
*
32803 ATTTCTTT
1 TTTTCTTT
32811 ATTACTAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 10 0.37
23 14 0.52
24 3 0.11
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTTCTTTCTCTTTGTTTTCTCC
Done.