Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3728
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: 104474
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5393 original size:22 final size:22
Alignment explanation
Indices: 5353--5394 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5343 AGAGAGGTAT
*
5353 GATGTGTATTGTATTTGATTCA
1 GATGTGTATTGGATTTGATTCA
5375 GATGT-TATTGGATTGTGATT
1 GATGTGTATTGGATT-TGATT
5395 TATCGATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.21, C:0.02, G:0.26, T:0.50
Consensus pattern (22 bp):
GATGTGTATTGGATTTGATTCA
Found at i:18778 original size:46 final size:46
Alignment explanation
Indices: 18665--18780 Score: 169
Period size: 46 Copynumber: 2.5 Consensus size: 46
18655 ATTTGAACAT
* * *
18665 CCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGT
1 CCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGC
* * *
18711 CTGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATTCAAACGC
1 CCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGC
*
18757 CCGAGCTCATTGAGTTGAGTCTGA
1 CCGAACTCATTGAGTTGAGTCTGA
18781 ATTTCGCTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (46 bp):
CCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCAAACGC
Found at i:32501 original size:40 final size:40
Alignment explanation
Indices: 32438--32695 Score: 360
Period size: 40 Copynumber: 6.5 Consensus size: 40
32428 AAGCCAAGTA
* * *
32438 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * * *
32477 CCTTCGGGACATAGCTCGGATATAGTAACTCGTACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
32517 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
32557 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCCCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
32597 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
32637 CCTTCGGGACTTAGCCTGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
32677 CCTTCGGAACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
32696 TTATTATCCA
Statistics
Matches: 197, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
39 13 0.07
40 184 0.93
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:36006 original size:25 final size:25
Alignment explanation
Indices: 35978--36028 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
35968 TAAGAAAACC
35978 ATCAATCTTTTTATTTAAGAGTTCT
1 ATCAATCTTTTTATTTAAGAGTTCT
36003 ATCAATCTTTTTATTTAAGAGTTCT
1 ATCAATCTTTTTATTTAAGAGTTCT
36028 A
1 A
36029 CCTGATTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (25 bp):
ATCAATCTTTTTATTTAAGAGTTCT
Found at i:38553 original size:46 final size:46
Alignment explanation
Indices: 38501--38860 Score: 322
Period size: 46 Copynumber: 7.8 Consensus size: 46
38491 ATTTGGGCAT
* *
38501 CCGAACTCGTTGATTTGAGTCTGAGTTCACTTATGGATGCGAATGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* * *
38547 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--GC
* *
38592 ATCCGAACTGGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* * * *
38640 CCGAACTCGTTGAGTTGAATCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--GC
* * ***
38685 ATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACAT
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* * * * *
38733 CCGAACTCGTTGAGTTGAGTCCAAGTTAACTTATGGATGTGAACGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* *
38779 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
* * * * *
38825 CTGAGCTCATTGAGTTGAGTCCAAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
38861 GTGGGTTACA
Statistics
Matches: 255, Mismatches: 41, Indels: 36
0.77 0.12 0.11
Matches are distributed among these distances:
42 4 0.02
43 10 0.04
45 8 0.03
46 163 0.64
47 51 0.20
48 6 0.02
50 9 0.04
51 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
Found at i:38607 original size:47 final size:47
Alignment explanation
Indices: 38547--38714 Score: 193
Period size: 47 Copynumber: 3.6 Consensus size: 47
38537 ATGCGAATGC
38547 CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCAT
* * * * *
38594 CCGAACTGGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAA-T--GC--
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCAT
*
38640 CCGAACTCGTTGAGTTGAATCCGAGTTCGTGAGATGTAACTAGGCAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCAT
* *
38687 CCGAGCTCATTGAGTTGAGTCCGAGTTC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC
38715 ACTTATGGAT
Statistics
Matches: 98, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 25 0.26
47 51 0.52
48 4 0.04
50 5 0.05
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (47 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCAT
Found at i:38655 original size:93 final size:93
Alignment explanation
Indices: 38496--38853 Score: 467
Period size: 93 Copynumber: 3.9 Consensus size: 93
38486 AGGATATTTG
* * *
38496 GGCATCCGAACTCGTTGATTTGAGTCTGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
38561 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCAAGTTCGTGAGATGTAACTA
* * *
38589 GGCATCCGAACTGGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
* *
38654 TTGAATCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCAAGTTCGTGAGATGTAACTA
* * **
38682 GGCATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
38747 TTGAGTCCAAGTTAAC-TTATGGATGTGAAC--
66 TTGAGTCCAAGTT--CGTGA--GATGT-AACTA
* * * *
38777 -G--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCTGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
38839 TTGAGTCCAAGTTCG
66 TTGAGTCCAAGTTCG
38854 CTTATGGGTG
Statistics
Matches: 236, Mismatches: 23, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
90 1 0.00
92 66 0.28
93 157 0.67
94 3 0.01
95 1 0.00
96 5 0.02
97 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCAAGTTCGTGAGATGTAACTA
Found at i:45079 original size:27 final size:27
Alignment explanation
Indices: 44996--45080 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
44986 TAGGAGTTTG
* *
44996 AGGCCTGACGAGCTAGTGTTCACTAGT
1 AGGCCTGAAGAGCTAGTGTTCTCTAGT
* * * *
45023 AGG-CTAGGCAA-A-CTACTATTCTCCAAT
1 AGGCCT--G-AAGAGCTAGTGTTCTCTAGT
45050 AGGCCTGAAGAGCTAGTGTTCTCTAGT
1 AGGCCTGAAGAGCTAGTGTTCTCTAGT
45077 AGGC
1 AGGC
45081 TTGGTGAGTT
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
25 2 0.05
26 4 0.10
27 31 0.74
28 4 0.10
29 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (27 bp):
AGGCCTGAAGAGCTAGTGTTCTCTAGT
Found at i:46627 original size:21 final size:20
Alignment explanation
Indices: 46599--46639 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
46589 TGTCCTAAGA
46599 CTTAGTTAT-TTATATGTTTT
1 CTTAGTTATATT-TATGTTTT
46619 CTTATGTTATATTTATGTTTT
1 CTTA-GTTATATTTATGTTTT
46640 TATTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 13 0.68
22 2 0.11
ACGTcount: A:0.20, C:0.05, G:0.10, T:0.66
Consensus pattern (20 bp):
CTTAGTTATATTTATGTTTT
Found at i:65474 original size:14 final size:15
Alignment explanation
Indices: 65425--65474 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
65415 GTATCTTGGG
*
65425 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
65440 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
65455 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
65469 TTTCTT
1 TTTCTT
65475 GTTATCTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.10, C:0.18, G:0.12, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:84168 original size:37 final size:37
Alignment explanation
Indices: 84115--84215 Score: 175
Period size: 37 Copynumber: 2.7 Consensus size: 37
84105 CGAATAGTCC
* *
84115 CCACACGTAGTTATCGGGTCTTACCCGGGCAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
84152 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
84189 CCACACGTAGTCATCGGGTCTTACCCG
1 CCACACGTAGTCATCGGGTCTTACCCG
84216 AAATATATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:84416 original size:48 final size:48
Alignment explanation
Indices: 84358--84542 Score: 334
Period size: 48 Copynumber: 3.9 Consensus size: 48
84348 ATATACACAC
*
84358 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
84406 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
84454 ATCTCATATATATTTCACAATAGCCATTCGGCTTCACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
84502 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACA
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACA
84543 CACATATATA
Statistics
Matches: 130, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 130 1.00
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.33
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:88352 original size:94 final size:94
Alignment explanation
Indices: 88185--88462 Score: 488
Period size: 94 Copynumber: 3.0 Consensus size: 94
88175 CGACATTCAG
* *
88185 ATCTGCACACATAGTGCCATTTAATTCCGCACAC--AGTGCCAATGTTAACTCATTATAATAAGG
1 ATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGG
88248 CAATTTACTTAATTCAAATAGCATATAAA
66 CAATTTACTTAATTCAAATAGCATATAAA
* * *
88277 ATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCTAATCTTAAATCATTATAATAAGG
1 ATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGG
*
88342 TAATTTACTTAATTCAAATAGCATATAAA
66 CAATTTACTTAATTCAAATAGCATATAAA
88371 ATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGG
1 ATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGG
88436 CAATTTACTTAATTCAAATAGCATATA
66 CAATTTACTTAATTCAAATAGCATATA
88463 CGGTCACATT
Statistics
Matches: 174, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
92 32 0.18
94 142 0.82
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (94 bp):
ATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAAGG
CAATTTACTTAATTCAAATAGCATATAAA
Found at i:95626 original size:24 final size:24
Alignment explanation
Indices: 95599--95659 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
95589 ACCGAATTCA
* * *
95599 CACACATAGTGCTA-ATTAAGCTCG
1 CACACATAGTGCCATACTAAAC-CG
95623 CACACATAGTGCCATACTAAACCG
1 CACACATAGTGCCATACTAAACCG
95647 CACACATAGTGCC
1 CACACATAGTGCC
95660 TGAAATTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.34, C:0.31, G:0.15, T:0.20
Consensus pattern (24 bp):
CACACATAGTGCCATACTAAACCG
Found at i:95808 original size:94 final size:94
Alignment explanation
Indices: 95688--95969 Score: 483
Period size: 94 Copynumber: 3.0 Consensus size: 94
95678 ATCGACATTC
* * *
95688 AAATTTGCACACATAGTGCCATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAA
1 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAA
95753 GGCAATTTACTTAATTCAAATAGCATATA
66 GGCAATTTACTTAATTCAAATAGCATATA
*
95782 AAATCTGCACACAAAGTGACATTTAATTCCGTACACATAGTGCCAATGTTAACTCATTATAATAA
1 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAA
* *
95847 GGCCATTTACTTAATTCAAAAAGCATATA
66 GGCAATTTACTTAATTCAAATAGCATATA
* *
95876 AAATCTACACACAAAGTGAAATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAA
1 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAA
*
95941 GGAAATTTACTTAATTCAAATAGCATATA
66 GGCAATTTACTTAATTCAAATAGCATATA
95970 CGGTCACATT
Statistics
Matches: 176, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 176 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.30
Consensus pattern (94 bp):
AAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAA
GGCAATTTACTTAATTCAAATAGCATATA
Found at i:98538 original size:40 final size:40
Alignment explanation
Indices: 98485--98765 Score: 415
Period size: 40 Copynumber: 7.0 Consensus size: 40
98475 GGGTTTAACC
* * * *
98485 GATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGCCTG
1 GATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
98525 GATATAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
98565 GATATAGTAACTCGCACCAATGCCTTCGGGACTTTAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGAC-TTAGCCCG
98606 GATATAGTAAC-CGCACAAATGCCTTCGGGACTTAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
98645 GATATAATAACTCGCACAAATGCCTTCGGGACTTAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
98685 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* * **
98725 GA-ACTAGTCACTAGTGCAAATGCCTTCGGGACTTAGCCCG
1 GATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
98765 G
1 G
98766 TTATCATCCA
Statistics
Matches: 226, Mismatches: 11, Indels: 8
0.92 0.04 0.03
Matches are distributed among these distances:
39 20 0.09
40 187 0.83
41 19 0.08
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
Found at i:100015 original size:5 final size:5
Alignment explanation
Indices: 99998--100036 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
99988 CATGAGAGCC
*
99998 TTTCT TTTTT TTTCT TTTCT TTCTCT TTTCT TTT-T TTTC
1 TTTCT TTTCT TTTCT TTTCT TT-TCT TTTCT TTTCT TTTC
100037 ATCATCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.13
5 21 0.70
6 5 0.17
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Done.