Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2131
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: 34166
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1432 original size:29 final size:28
Alignment explanation
Indices: 1400--1482 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 28
1390 GCAATCAAAT
* *
1400 ATGGTACTCAGTGTACGAAATATATGAGA
1 ATGGCACTCAATGTACGAAATAT-TGAGA
* * *
1429 ATGGCACTTAATGTGCGAGATATTGAGA
1 ATGGCACTCAATGTACGAAATATTGAGA
* * * * *
1457 ATGACACTTAGTGTGCAAAATATTGA
1 ATGGCACTCAATGTACGAAATATTGA
1483 ATGATTAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 27 0.60
29 18 0.40
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (28 bp):
ATGGCACTCAATGTACGAAATATTGAGA
Found at i:1459 original size:28 final size:28
Alignment explanation
Indices: 1417--1482 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
1407 TCAGTGTACG
* *
1417 AAATATATGAGAATGGCACTTAATGTGCG
1 AAATAT-TGAGAATGACACTTAATGTGCA
* *
1446 AGATATTGAGAATGACACTTAGTGTGCA
1 AAATATTGAGAATGACACTTAATGTGCA
1474 AAATATTGA
1 AAATATTGA
1483 ATGATTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAATGTGCA
Found at i:1686 original size:38 final size:39
Alignment explanation
Indices: 1555--1799 Score: 355
Period size: 39 Copynumber: 6.5 Consensus size: 39
1545 GACTTTATAA
*
1555 TGGTGTTATAT-CGGGCTAAGTCCT-AAGGCA-TC-TGT
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
1590 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
1629 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
*
1668 TGGTG-TATATTCC-GGCTAAGTCCCGAAGGCATTCGTGC
1 TGGTGTTATA-TCCGGGCTAAGTCCTGAAGGCATTCGTGC
*
1706 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
* *
1745 TGGTG-TATATCCGGGCTAAAGTCC-GCAGGC-TTTGTGC
1 TGGTGTTATATCCGGGCT-AAGTCCTGAAGGCATTCGTGC
*
1782 TGGTATTATATCCGGGCT
1 TGGTGTTATATCCGGGCT
1800 TAAAGTCCAT
Statistics
Matches: 196, Mismatches: 5, Indels: 15
0.91 0.02 0.07
Matches are distributed among these distances:
35 11 0.06
36 13 0.07
37 16 0.08
38 67 0.34
39 89 0.45
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (39 bp):
TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
Found at i:1688 original size:77 final size:77
Alignment explanation
Indices: 1555--1799 Score: 353
Period size: 77 Copynumber: 3.2 Consensus size: 77
1545 GACTTTATAA
*
1555 TGGTGTTATAT-CGGGCTAAGTCCT-AAGGCA-TC-TGTTGGTGT-TATATCCGGGCTAAGTCCT
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTATAT-TCCGGGCTAAGTCC-
1615 GAAGGCATTCGTGC
64 GAAGGCATTCGTGC
1629 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTATATTCC-GGCTAAGTCCCG
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTATATTCCGGGCTAAGT-CCG
1693 AAGGCATTCGTGC
65 AAGGCATTCGTGC
*
1706 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTATA-TCCGGGCTAAAGTCCG
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTATATTCCGGGCT-AAGTCCG
* *
1770 CAGGC-TTTGTGC
65 AAGGCATTCGTGC
*
1782 TGGTATTATATCCGGGCT
1 TGGTGTTATATCCGGGCT
1800 TAAAGTCCAT
Statistics
Matches: 158, Mismatches: 5, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
74 11 0.07
75 13 0.08
76 32 0.20
77 82 0.52
78 17 0.11
79 3 0.02
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (77 bp):
TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGTATATTCCGGGCTAAGTCCGA
AGGCATTCGTGC
Found at i:7991 original size:28 final size:28
Alignment explanation
Indices: 7958--8022 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
7948 CAGTGTACGG
* *
7958 AATATTGAAAATGGCACTTAATGTGCGA
1 AATATTGAAAATGACACTTAATGTGCAA
* * *
7986 GATATTGAGAATGACACTTAGTGTGCAA
1 AATATTGAAAATGACACTTAATGTGCAA
8014 AATATTGAA
1 AATATTGAA
8023 TGATTAAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (28 bp):
AATATTGAAAATGACACTTAATGTGCAA
Found at i:8138 original size:39 final size:39
Alignment explanation
Indices: 8094--8306 Score: 324
Period size: 39 Copynumber: 5.5 Consensus size: 39
8084 GACTTTATAA
* *
8094 TGGTGTTATATCTGGGCTAAGTCCTGAAGGCATTCGTGT
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
8133 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
*
8172 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
*
8211 TGGTGTTCTATCCGGGCTAAG-CCTCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCT-GAAGGCATTCGTGC
*
8250 TGGTGTTATATCCGGGCTAAAGTCCTGCAA-GC-TTTGTGC
1 TGGTGTTATATCCGGGCT-AAGTCCTG-AAGGCATTCGTGC
*
8289 TGGTATTATATCCGGGCT
1 TGGTGTTATATCCGGGCT
8307 TAAAGTCCCG
Statistics
Matches: 162, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
38 2 0.01
39 149 0.92
40 6 0.04
41 5 0.03
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.32
Consensus pattern (39 bp):
TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCGTGC
Found at i:10722 original size:49 final size:49
Alignment explanation
Indices: 10501--11100 Score: 935
Period size: 47 Copynumber: 12.6 Consensus size: 49
10491 CCCTTCGGGA
* * * * *
10501 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10548 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10595 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10642 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10689 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10738 CTTATCACATATATATACACTTTCACATTCATCAGATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10787 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10836 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10883 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10930 CTTATCATATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
10979 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
11028 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
11075 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
11101 CACAATTATC
Statistics
Matches: 518, Mismatches: 27, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 275 0.53
49 242 0.47
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:10897 original size:192 final size:192
Alignment explanation
Indices: 10501--11100 Score: 992
Period size: 192 Copynumber: 3.1 Consensus size: 192
10491 CCCTTCGGGA
* * * * * * * *
10501 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
10564 ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC--ATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
* * * *
10627 CATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGTCATTAGGC
131 CATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
10689 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
*
10754 ACACTTTCACATTCATCAGATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCAT
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCAT
10819 CACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 CACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
10883 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
10948 ACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
11013 CATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 CATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
11075 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
11101 CACAATTATC
Statistics
Matches: 387, Mismatches: 19, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
188 8 0.02
190 39 0.10
192 250 0.65
194 90 0.23
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (192 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
CATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:22653 original size:5 final size:5
Alignment explanation
Indices: 22643--22679 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
22633 TTGTGTGAAA
*
22643 AAAAT AAAAT AAAAT AAAAT -AAAG AAAA- AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
22680 CAACACACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
4 7 0.24
5 22 0.76
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:22658 original size:10 final size:10
Alignment explanation
Indices: 22643--22679 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
22633 TTGTGTGAAA
22643 AAAATAAAAT
1 AAAATAAAAT
22653 AAAATAAAAT
1 AAAATAAAAT
*
22663 -AAAGAAAA-
1 AAAATAAAAT
22671 AAAATAAAA
1 AAAATAAAA
22680 CAACACACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 14 0.58
10 10 0.42
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:25029 original size:79 final size:81
Alignment explanation
Indices: 24861--25045 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
24851 GCTACTCGTT
* *
24861 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
* *
24925 GATTTAGTAACTCGCAC
65 GATATAGTAACTAGCAC
* ** *
24942 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCA
* *
25004 GATATGGTCACTTAGCA-
65 GATATAGTAAC-TAGCAC
25021 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
25046 CATCATTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 25 0.28
81 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAG
ATATAGTAACTAGCAC
Found at i:25045 original size:40 final size:40
Alignment explanation
Indices: 24842--25045 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
24832 CGGAATTTAA
** *
24842 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
24882 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
24922 CCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
24961 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
25001 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
25041 CCGGA
1 CCGGA
25046 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:26237 original size:56 final size:56
Alignment explanation
Indices: 26169--26288 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
26159 TATTAGTTCA
26169 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
* *
26225 TTGCCGATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
26281 TTGCCCAT
1 TTGCCCAT
26289 CATCCCTTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:30207 original size:40 final size:39
Alignment explanation
Indices: 30165--30338 Score: 162
Period size: 40 Copynumber: 4.5 Consensus size: 39
30155 TACTCATTCA
*
30165 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCAC
1 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
*
30204 AAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCAC
1 -AATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCAC
* * *
30244 AATGCCGTCGGG-CTTAG-CCGG-AATTAGTATCTCGCAC
1 AATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCAC
* * * * **
30281 AATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTACAC
1 AATGCCTTCGGGA-CTTAGCCCGGTTATAGTAACTCGCAC
*
30320 AAAG-CTTCGGGACTTAGCC
1 AATGCCTTCGGGACTTAGCC
30339 GACATCATTC
Statistics
Matches: 111, Mismatches: 15, Indels: 18
0.77 0.10 0.12
Matches are distributed among these distances:
36 2 0.02
37 24 0.22
38 19 0.17
39 29 0.26
40 35 0.32
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
Found at i:30321 original size:76 final size:77
Alignment explanation
Indices: 30191--30339 Score: 169
Period size: 76 Copynumber: 1.9 Consensus size: 77
30181 AGCCCGGTTA
* * *
30191 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCGTCGGG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCACACAAAG-CGTCGGG
30256 -CTTAGCCGGAAT
65 ACTTAGCCGGAAT
* ** * * * *
30268 TAGTATCTCGCAC-AATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTACACAAAGCTTCGGG
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAACTCACACAAAGCGTCGGG
30331 ACTTAGCCG
65 ACTTAGCCG
30340 ACATCATTCA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
75 9 0.15
76 39 0.65
77 12 0.20
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (77 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTCACACAAAGCGTCGGGA
CTTAGCCGGAAT
Done.