Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5074.1
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: 34081
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3362 original size:30 final size:30
Alignment explanation
Indices: 3328--3385 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3318 ATTTTCGGGC
* *
3328 CTAGGGGTAAAAGGGTCATTTTATCAAAGT
1 CTAGGGGCAAAAGGGTCATTTTACCAAAGT
3358 CTAGGGGCAAAAGGGTCATTTTACCAAA
1 CTAGGGGCAAAAGGGTCATTTTACCAAA
3386 TATATGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (30 bp):
CTAGGGGCAAAAGGGTCATTTTACCAAAGT
Found at i:6548 original size:47 final size:47
Alignment explanation
Indices: 6488--6672 Score: 280
Period size: 47 Copynumber: 3.9 Consensus size: 47
6478 GATAATTGTG
**
6488 ATGTGAATGTGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* *
6535 ATGTGAACATGCATATATGTGATAAGGCCAAATGGCTAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* *
6582 ATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* * * *
6629 ATATGAACATGCATATATGTGGTAAAGCCGAATGGCTAATGTGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGA
6673 AATATATGTA
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 124 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (47 bp):
ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
Found at i:6579 original size:22 final size:22
Alignment explanation
Indices: 6504--6579 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
6494 ATGTGCATAT
* *
6504 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCAAATGGCTA
* **
6526 ATGTGATGAATGTGAACAT-GCATA
1 ATGTGAT-AAGGCCAA-ATGGC-TA
6550 TATGTGATAAGGCCAAATGGCTA
1 -ATGTGATAAGGCCAAATGGCTA
6573 ATGTGAT
1 ATGTGAT
6580 GAATGTGAGC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 14 0.34
23 10 0.24
24 10 0.24
25 7 0.17
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCAAATGGCTA
Found at i:6932 original size:37 final size:37
Alignment explanation
Indices: 6877--7026 Score: 246
Period size: 37 Copynumber: 4.1 Consensus size: 37
6867 GGAAATATAT
6877 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
6914 TCCGGGTAAGACCTGATGACTACGTGTGAAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
6951 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
6988 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
7025 TC
1 TC
7027 TGAGCTAAAG
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 106 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:8362 original size:40 final size:40
Alignment explanation
Indices: 8303--8710 Score: 699
Period size: 40 Copynumber: 10.2 Consensus size: 40
8293 AGTGGTATAC
*
8303 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* * *
8343 CCAGGCTAAGCCCCAAAGAGCATTCGTTCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
8383 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
8423 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
8463 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
8503 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
*
8543 CTGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
8583 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
8623 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
8663 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
8703 CCGGGCTA
1 CCGGGCTA
8711 GGTAAATAGC
Statistics
Matches: 345, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 345 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGCCCCGAAGAGCATTCGTGCTAGTGATGTAT
Found at i:14741 original size:15 final size:15
Alignment explanation
Indices: 14712--14751 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
14702 CAATCTGACC
14712 TTTTCTTTT-CTT-T
1 TTTTCTTTTCCTTCT
14725 TTTT-TTTTCCTTCT
1 TTTTCTTTTCCTTCT
14739 TTTTCTTTTCCTT
1 TTTTCTTTTCCTT
14752 TTACATGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.17
13 7 0.29
14 5 0.21
15 8 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTCCTTCT
Found at i:15382 original size:19 final size:19
Alignment explanation
Indices: 15355--15402 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
15345 ATTTTTTTCA
*
15355 ATAAAAATACA-AAAGATT
1 ATAAAAATACATAAAAATT
*
15373 TTATAAAATACATAAAAATT
1 ATA-AAAATACATAAAAATT
15393 ATAAAAATAC
1 ATAAAAATAC
15403 TTATAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.60
20 8 0.32
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (19 bp):
ATAAAAATACATAAAAATT
Found at i:16305 original size:12 final size:12
Alignment explanation
Indices: 16288--16319 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
16278 ACGACTCCTT
16288 GAAGAAAATCAA
1 GAAGAAAATCAA
16300 GAAGAAAATCAA
1 GAAGAAAATCAA
16312 GAAGAAAA
1 GAAGAAAA
16320 CTACTTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.69, C:0.06, G:0.19, T:0.06
Consensus pattern (12 bp):
GAAGAAAATCAA
Found at i:17496 original size:24 final size:24
Alignment explanation
Indices: 17442--17503 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
17432 TCACAAAGTT
* * *
17442 CACTATCATTATCATCATAGTTTG
1 CACTATTATTATCATCATAGCTCG
17466 CACTATTATTATCATCATAGCTCG
1 CACTATTATTATCATCATAGCTCG
*
17490 CACTATTACTATCA
1 CACTATTATTATCA
17504 ACTTTTTCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (24 bp):
CACTATTATTATCATCATAGCTCG
Found at i:20724 original size:17 final size:17
Alignment explanation
Indices: 20702--20753 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
20692 TGTCTGTGGG
20702 TTTTTAAAAAATATATT
1 TTTTTAAAAAATATATT
*
20719 TTTTTATAAAAT-TATT
1 TTTTTAAAAAATATATT
* * *
20735 GTTTTAATAAATAAATT
1 TTTTTAAAAAATATATT
20752 TT
1 TT
20754 ATGTTAGAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTTAAAAAATATATT
Found at i:20746 original size:16 final size:16
Alignment explanation
Indices: 20702--20753 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
20692 TGTCTGTGGG
*
20702 TTTTTAAAAAATATAT
1 TTTTTAATAAATATAT
*
20718 TTTTTTATAAA-ATTAT
1 TTTTTAATAAATA-TAT
*
20734 TGTTTTAATAAATAAAT
1 T-TTTTAATAAATATAT
20751 TTT
1 TTT
20754 ATGTTAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 1 0.03
16 15 0.52
17 12 0.41
18 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTTTAATAAATATAT
Found at i:22864 original size:9 final size:9
Alignment explanation
Indices: 22825--22903 Score: 56
Period size: 10 Copynumber: 8.7 Consensus size: 9
22815 ATATGTGACG
*
22825 AAAAATGAT
1 AAAAATTAT
22834 AAAATATTAT
1 AAAA-ATTAT
* *
22844 TATAATTAAT
1 AAAAATT-AT
22854 AAAAATTAT
1 AAAAATTAT
*
22863 AAAAA--AG
1 AAAAATTAT
*
22870 GAAAA-TAT
1 AAAAATTAT
22878 AAAAATTATT
1 AAAAATTA-T
22888 AAAAATTAT
1 AAAAATTAT
22897 AGAAAAT
1 A-AAAAT
22904 ATTTAAGATT
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.09
8 5 0.09
9 18 0.33
10 27 0.49
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:26139 original size:85 final size:84
Alignment explanation
Indices: 25974--26141 Score: 302
Period size: 84 Copynumber: 2.0 Consensus size: 84
25964 TAAATGTCAT
25974 GCATTTTTACGATATAATAAATAAAAATGGGGCCACCCTCTGCCAAATCTTCCCTGGCTTTGATG
1 GCATTTTTACGATATAATAAATAAAAATGGGGCCACCCTCTGCCAAATCTTCCCTGGCTTTGATG
26039 ATTCTTAAGCTAAAAAAAG
66 ATTCTTAAGCTAAAAAAAG
*
26058 NGCATTTTTACGATATAATAAATAAAAATGGGGCCA-CCTCTGCCAAATCTTCCCTGGCTTTGGT
1 -GCATTTTTACGATATAATAAATAAAAATGGGGCCACCCTCTGCCAAATCTTCCCTGGCTTTGAT
*
26122 GATTCTTAGGCTAAAAAAAG
65 GATTCTTAAGCTAAAAAAAG
26142 AAGAAAAAGT
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
84 46 0.57
85 35 0.43
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (84 bp):
GCATTTTTACGATATAATAAATAAAAATGGGGCCACCCTCTGCCAAATCTTCCCTGGCTTTGATG
ATTCTTAAGCTAAAAAAAG
Found at i:27124 original size:169 final size:168
Alignment explanation
Indices: 26671--27131 Score: 626
Period size: 166 Copynumber: 2.7 Consensus size: 168
26661 AAATAAATGA
* * * *
26671 AACTTAATAGGGACTAATTTGACTA-TTTTTTAGTAAAAGATGAAAAATGTAATTTGATTCCTAG
1 AACTTAATAGGGACTAATTTGCCTATTTTTTTAGTAAAAGATGAAAAATGAAATCTAATTCCTAG
* * *
26735 TATAAAGGCCTATATGTTACTTTTGTCTAATTCTACT-ATCCTTCAATTCCATGTCACTTACATA
66 TAT-AAGGCCTATATGGTACTTTTGTCTAATCCTACTCATCCTTAAATTCCATGTCACTTACATA
*
26799 ATTTTTTTTTAACAAAAAGGCGAGTTTGATCTTTGATCT
130 ATTTTTTTCTAACAAAAAGGCGAGTTTGATCTTTGATCT
26838 AACTT-ATAGGGACTAATTTGCCT-TTTTTTTAGTAAAAGATGAAAAATGAAATCTAATTCCTAG
1 AACTTAATAGGGACTAATTTGCCTATTTTTTTAGTAAAAGATGAAAAATGAAATCTAATTCCTAG
* * *
26901 TATAAGGGCCTATACGGTACTTTTATGTAATCCTAC-CATCCTTAAAATATTCCATGTCACTTAC
66 TATAA-GGCCTATATGGTACTTTTGTCTAATCCTACTCATCCTT--AA-ATTCCATGTCACTTAC
* * *
26965 ATAATTTTTTTCTAACAAAAGGGTGAGTTTGCTCTTTGATCT
127 ATAATTTTTTTCTAACAAAAAGGCGAGTTTGATCTTTGATCT
* * * * * *
27007 AACTTAATAAGAACTAATTTGCCTATTTTTTTAGTAAAAGAGGCAAAATGCAATCTAATTCCTAA
1 AACTTAATAGGGACTAATTTGCCTATTTTTTTAGTAAAAGATGAAAAATGAAATCTAATTCCTAG
* * *
27072 TATAAGGACCTTTATGGTACTTTTGTCTAACCCTACTCATCCTTTAATTCCATGTCACTT
66 TATAAGG-CCTATATGGTACTTTTGTCTAATCCTACTCATCCTTAAATTCCATGTCACTT
27132 GCACTTTTTT
Statistics
Matches: 258, Mismatches: 26, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
165 2 0.01
166 87 0.34
167 5 0.02
168 1 0.00
169 73 0.28
170 19 0.07
171 64 0.25
172 7 0.03
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (168 bp):
AACTTAATAGGGACTAATTTGCCTATTTTTTTAGTAAAAGATGAAAAATGAAATCTAATTCCTAG
TATAAGGCCTATATGGTACTTTTGTCTAATCCTACTCATCCTTAAATTCCATGTCACTTACATAA
TTTTTTTCTAACAAAAAGGCGAGTTTGATCTTTGATCT
Found at i:29532 original size:118 final size:118
Alignment explanation
Indices: 29324--29560 Score: 402
Period size: 118 Copynumber: 2.0 Consensus size: 118
29314 CGATTACAAG
* *
29324 TCCAATACATTAATATTATTTTGCACAGGACCTCACCTATAAAGAGCCCCTAAAACAATGAAGAG
1 TCCAACACATTAATATTATTCTGCACAGGACCTCACCTATAAAGAGCCCCTAAAACAATGAAGAG
* * *
29389 CGGACCAGCTCTTGAATATACTTGCCTATACTTTGCCAACTTACCTTCAGCAC
66 AGGACCAGCTCTTGAATATACTTGCCTATACTCTGCCAACTTACCTTCAACAC
* *
29442 TCCAACACATTAATATTATTCTGCACAGGACCTCACCTATAAAGAGCCCCTAAAACGATGAAGTG
1 TCCAACACATTAATATTATTCTGCACAGGACCTCACCTATAAAGAGCCCCTAAAACAATGAAGAG
*
29507 AGGACTAGCTCTTGAATATACTTGCCTATACTCTGCCAACTTACCTTCAACAC
66 AGGACCAGCTCTTGAATATACTTGCCTATACTCTGCCAACTTACCTTCAACAC
29560 T
1 T
29561 TAGTCTTCAT
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 111 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (118 bp):
TCCAACACATTAATATTATTCTGCACAGGACCTCACCTATAAAGAGCCCCTAAAACAATGAAGAG
AGGACCAGCTCTTGAATATACTTGCCTATACTCTGCCAACTTACCTTCAACAC
Found at i:31159 original size:12 final size:12
Alignment explanation
Indices: 31142--31166 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31132 TATTTATATT
31142 AAAAAAAAGAAA
1 AAAAAAAAGAAA
31154 AAAAAAAAGAAA
1 AAAAAAAAGAAA
31166 A
1 A
31167 CAACTTACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:33649 original size:65 final size:65
Alignment explanation
Indices: 33545--33675 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
33535 GTACAAGAGA
33545 TTCTTATATTAAAATTTTCTTAATTCGCTGTGGTTCTTTTATTTCTTAATTAAGTTAAAAAAATT
1 TTCTTATATTAAAATTTTCTTAATTCGCTGTGGTTCTTTTATTTCTTAATTAAGTTAAAAAAATT
33610 TTCTTATATTAAAATTTTCTTAATTCGCTGTGGTTCTTTTATTTCTTAATTAAGTTAAAAAAATT
1 TTCTTATATTAAAATTTTCTTAATTCGCTGTGGTTCTTTTATTTCTTAATTAAGTTAAAAAAATT
33675 T
1 T
33676 GGTATTTCAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.53
Consensus pattern (65 bp):
TTCTTATATTAAAATTTTCTTAATTCGCTGTGGTTCTTTTATTTCTTAATTAAGTTAAAAAAATT
Done.