Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold254
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: 33671
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:1507 original size:39 final size:40
Alignment explanation
Indices: 1362--1580 Score: 227
Period size: 39 Copynumber: 5.6 Consensus size: 40
1352 TTGAATGCTG
* * * * * *
1362 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
* * *
1402 TCC-GG-TAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
1440 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
1480 TCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTT-TTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
1518 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
1557 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
1581 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 14, Indels: 15
0.84 0.07 0.08
Matches are distributed among these distances:
38 45 0.28
39 71 0.45
40 42 0.27
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:1604 original size:78 final size:78
Alignment explanation
Indices: 1435--1615 Score: 204
Period size: 78 Copynumber: 2.3 Consensus size: 78
1425 GTGCGAGATA
* * *
1435 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCGAAGGC
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCGAAGGC
** **
1500 ATTCGTGCGAGTT
66 ATTCGAACGAGAG
* * * *
1513 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGT-CCGAAGG
*
1577 CATTTGAACGAGGAG
65 CATTCGAACGA-GAG
* *
1592 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
1616 TACGTGATTT
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
77 22 0.26
78 56 0.66
79 7 0.08
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (78 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCGAAGGC
ATTCGAACGAGAG
Found at i:9313 original size:40 final size:40
Alignment explanation
Indices: 9230--9492 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
9220 TTGAATGCTG
* * * * * *
9230 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
9270 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
9310 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
9350 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
9390 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
9430 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
9469 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
9493 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:9512 original size:79 final size:80
Alignment explanation
Indices: 9269--9527 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
9259 AAGTGAATAT
* * * * * *
9269 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
9333 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
9349 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
9414 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
9429 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
9493 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
9508 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
9528 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:13640 original size:43 final size:43
Alignment explanation
Indices: 13593--13686 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
13583 GTCCCGGATG
* *
13593 TGGTCTTACATGT-AAT-TCAATATCGATGCCTCTGTCCCAGACA
1 TGGTCTTACACGTAAATCTC-A-ATCGAGGCCTCTGTCCCAGACA
* *
13636 TGGTCTTATACGTAAATCTCAATCGAGGCCTGTGTCCCAGACA
1 TGGTCTTACACGTAAATCTCAATCGAGGCCTCTGTCCCAGACA
*
13679 CGGTCTTA
1 TGGTCTTA
13687 TACGATGTCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
43 38 0.86
44 4 0.09
45 2 0.05
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
TGGTCTTACACGTAAATCTCAATCGAGGCCTCTGTCCCAGACA
Found at i:16289 original size:29 final size:28
Alignment explanation
Indices: 16248--16302 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
16238 ATCTGAAGTA
16248 CTGATATCATGGCCCGAAGCCAAATCAG
1 CTGATATCATGGCCCGAAGCCAAATCAG
16276 CTGATATTCATGGCCCGAAGCCAAATC
1 CTGATA-TCATGGCCCGAAGCCAAATC
16303 GGTATAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (28 bp):
CTGATATCATGGCCCGAAGCCAAATCAG
Found at i:20422 original size:29 final size:30
Alignment explanation
Indices: 20352--20459 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 30
20342 ACCCCTACAT
* * *
20352 ACATGCATATGGCCCA-CTGGGCCCAA-TC
1 ACATTCATACGGCCCATCTAGGCCCAATTC
* * *
20380 TCATTCATATGGCCCATCT-GGCCTAATTC
1 ACATTCATACGGCCCATCTAGGCCCAATTC
* *
20409 ATATTCTTACGGCCCA-CTAGGCCCAATTC
1 ACATTCATACGGCCCATCTAGGCCCAATTC
*
20438 ACATTCATATGGCCCAT-TAGGC
1 ACATTCATACGGCCCATCTAGGC
20460 ACAAATCATA
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
28 22 0.34
29 43 0.66
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (30 bp):
ACATTCATACGGCCCATCTAGGCCCAATTC
Found at i:20469 original size:58 final size:57
Alignment explanation
Indices: 20362--20471 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 57
20352 ACATGCATAT
* * *
20362 GGCCCACTGGGCCCAATCTCATTCATATGGCCCATCTGGCCTAATTCATATTCTTAC
1 GGCCCACTAGGCCCAATCACATTCATATGGCCCATCTGGCCTAAATCATATTCTTAC
20419 GGCCCACTAGGCCCAATTCACATTCATATGGCCCAT-TAGGCAC-AAATCATATT
1 GGCCCACTAGGCCCAA-TCACATTCATATGGCCCATCT-GGC-CTAAATCATATT
20472 ATATTCATGC
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
57 16 0.34
58 30 0.64
59 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.27
Consensus pattern (57 bp):
GGCCCACTAGGCCCAATCACATTCATATGGCCCATCTGGCCTAAATCATATTCTTAC
Found at i:20766 original size:24 final size:23
Alignment explanation
Indices: 20708--20767 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
20698 TGTATCCCAA
* *
20708 CTTTTAGCTTTTTGGTATTTCGG
1 CTTTTGGCTTTTCGGTATTTCGG
* *
20731 CTTCTCGACTTTTCGGTATTTCGG
1 CTT-TTGGCTTTTCGGTATTTCGG
20755 CATTTTGGCTTTT
1 C-TTTTGGCTTTT
20768 GCCGATTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 3 0.10
24 24 0.83
25 2 0.07
ACGTcount: A:0.08, C:0.18, G:0.20, T:0.53
Consensus pattern (23 bp):
CTTTTGGCTTTTCGGTATTTCGG
Found at i:28887 original size:17 final size:17
Alignment explanation
Indices: 28844--28890 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
28834 ATATTAAAAA
* *
28844 ATTATTTAAACATAATT
1 ATTATATAAATATAATT
*
28861 A-AATATTAAATATAATT
1 ATTATA-TAAATATAATT
28878 ATTATATAAATAT
1 ATTATATAAATAT
28891 TAATAAATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 19 0.79
18 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTATATAAATATAATT
Found at i:28983 original size:7 final size:7
Alignment explanation
Indices: 28940--28973 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
28930 TTTGGGTCTT
28940 AAATTTA
1 AAATTTA
28947 AAATTTA
1 AAATTTA
*
28954 AGATTTA
1 AAATTTA
*
28961 GAATTTA
1 AAATTTA
28968 AAATTT
1 AAATTT
28974 TATAATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:28995 original size:10 final size:11
Alignment explanation
Indices: 28972--29041 Score: 58
Period size: 10 Copynumber: 6.6 Consensus size: 11
28962 AATTTAAAAT
28972 TTTATAATTTA
1 TTTATAATTTA
28983 TTTATAA-TTA
1 TTTATAATTTA
*
28993 TTTATTATTTA
1 TTTATAATTTA
*
29004 ATTAT-ATTTCA
1 TTTATAATTT-A
**
29015 -AAATAATTTA
1 TTTATAATTTA
*
29025 TTAAT-ATTTA
1 TTTATAATTTA
29035 TTTATAA
1 TTTATAA
29042 GCCCTTCATT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
10 25 0.52
11 23 0.48
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTATAATTTA
Found at i:29041 original size:21 final size:20
Alignment explanation
Indices: 28972--29041 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
28962 AATTTAAAAT
*
28972 TTTATAATTTATTTATAATTA
1 TTTATAATTTA-TTATATTTA
*
28993 TTTATTATTTAATTATATTTCA
1 TTTATAATTT-ATTATATTT-A
**
29015 -AAATAATTTATTAATATTTA
1 TTTATAATTTATT-ATATTTA
29035 TTTATAA
1 TTTATAA
29042 GCCCTTCATT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 4 0.11
21 32 0.84
22 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATAATTTATTATATTTA
Found at i:31186 original size:27 final size:27
Alignment explanation
Indices: 31156--31331 Score: 210
Period size: 27 Copynumber: 6.5 Consensus size: 27
31146 ATCGAGTCCA
* * * *
31156 CACACTCAGTGCTATATAATCAACTCG
1 CACACTTAGTGCTACATAGTCAAATCG
*
31183 CACACTTAGTGCTACATAATCAAATCG
1 CACACTTAGTGCTACATAGTCAAATCG
31210 CACACTTAGTGCTACATAGTCAAACTCG
1 CACACTTAGTGCTACATAGTCAAA-TCG
** * *
31238 CACACTTAGTGCCGCATGGTCAATTCG
1 CACACTTAGTGCTACATAGTCAAATCG
* **
31265 CACACTTAGTGC-ATCATATTCATTTCG
1 CACACTTAGTGCTA-CATAGTCAAATCG
*
31292 CACACTTAGTGCAACATAGTCAAATCG
1 CACACTTAGTGCTACATAGTCAAATCG
31319 CACACTTAGTGCT
1 CACACTTAGTGCT
31332 GTACAATTTA
Statistics
Matches: 130, Mismatches: 16, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (27 bp):
CACACTTAGTGCTACATAGTCAAATCG
Found at i:31293 original size:82 final size:81
Alignment explanation
Indices: 31175--31330 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
31165 TGCTATATAA
*
31175 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31240 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31257 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31321 CACTTAGTGC
65 CACTTAGTGC
31331 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.