Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2762
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: 30594
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Found at i:8791 original size:39 final size:40
Alignment explanation
Indices: 8666--8851 Score: 202
Period size: 40 Copynumber: 4.7 Consensus size: 40
8656 GCTACTCACT
* *
8666 CAAATGCCTTCGGGACATAGCCCGGTCA-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-AATTAGTAACTCGCA
*
8706 CAAATGCCTTCGGGACTTAACCC-GAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAA-TTAGTAACTCGCA
*
8746 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
8785 CAAATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
* * *
8826 CAAAAGCCTTTGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
8852 TATCATTCGA
Statistics
Matches: 124, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
38 3 0.02
39 33 0.27
40 64 0.52
41 21 0.17
42 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:13811 original size:6 final size:6
Alignment explanation
Indices: 13747--13855 Score: 66
Period size: 6 Copynumber: 17.5 Consensus size: 6
13737 AGTGCATAAT
* *
13747 AAAAT- AAAATA AAACATA TAAATCCA GAAAAT- AAAATA AAGTAAAA
1 AAAATA AAAATA AAA-ATA AAAAT--A -AAAATA AAAATA AA--AATA
* *
13793 ACAAATA ACAATA AAAATA AAAA-A AAAAGTA AAAGTA AAAATA AAAAT-
1 A-AAATA AAAATA AAAATA AAAATA AAAA-TA AAAATA AAAATA AAAATA
13841 -AAATA AAACATA AAA
1 AAAATA AAA-ATA AAA
13856 CTGAATGGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
4 4 0.05
5 15 0.18
6 34 0.41
7 19 0.23
8 5 0.06
9 5 0.06
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:13812 original size:12 final size:11
Alignment explanation
Indices: 13747--13848 Score: 75
Period size: 10 Copynumber: 8.8 Consensus size: 11
13737 AGTGCATAAT
13747 AAAATAAAATA
1 AAAATAAAATA
13758 AAACATATAAATCCA
1 AAA-ATA-AAAT--A
13773 GAAAATAAAAT-
1 -AAAATAAAATA
*
13784 AAAGTAAAA-A
1 AAAATAAAATA
*
13794 CAAATAACAATA
1 AAAATAA-AATA
*
13806 AAAATAAAAAA
1 AAAATAAAATA
13817 AAAAGTAAAAGTA
1 AAAA-TAAAA-TA
13830 AAAATAAAA-A
1 AAAATAAAATA
*
13840 TAAATAAAA
1 AAAATAAAA
13849 CATAAAACTG
Statistics
Matches: 74, Mismatches: 7, Indels: 21
0.73 0.07 0.21
Matches are distributed among these distances:
10 22 0.30
11 12 0.16
12 20 0.27
13 9 0.12
14 4 0.05
15 4 0.05
16 3 0.04
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:13855 original size:17 final size:18
Alignment explanation
Indices: 13784--13855 Score: 64
Period size: 17 Copynumber: 4.1 Consensus size: 18
13774 AAAATAAAAT
*
13784 AAAGTAAAA-ACAAATAA
1 AAAGTAAAATAAAAATAA
*
13801 CAA-TAAAAATAAAAA-AA
1 AAAGT-AAAATAAAAATAA
13818 AAAGTAAAAGTAAAAATAA
1 AAAGTAAAA-TAAAAATAA
13837 AAA-T-AAATAAAACATAA
1 AAAGTAAAATAAAA-ATAA
13854 AA
1 AA
13856 CTGAATGGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
16 6 0.13
17 23 0.50
18 12 0.26
19 5 0.11
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (18 bp):
AAAGTAAAATAAAAATAA
Found at i:15224 original size:605 final size:601
Alignment explanation
Indices: 14044--15253 Score: 2073
Period size: 605 Copynumber: 2.0 Consensus size: 601
14034 TTGATCTGCT
* *
14044 CTAACTGTTGTTGCTTAAGGCGGTCTGCTCGGACTACTACTGCTACGTGCGATAGATGTCCCTAA
1 CTAACTGTTGTTCCTTAAGGCGGTCTGCTCGGACTACTACTACTACGTGCGATAGATGTCCCTAA
* * *
14109 GCATGACTGAATATGAGTAGTGGAGTGACTTAGAGGAGGAGAAGATCAGGCTGAGTCTGCATGTT
66 ACATGACTGAATATGAGCAGTGGAGTGACTCAGAGGAGGAGAAGATCAGGCTGAGTCTGCATGTT
*
14174 GAGGTGGGTCCTCTTCTGGGAGCTCCACATGCCCATTCTTAGGATTCGAGTGAAATAGTGTATAC
131 GAGATGGGTCCTCTTCTGGGAGCTCCACATGCCCATTCTTAGGATTCGAGTGAAATAGTGTATAC
* *
14239 CAATTTGGACCCACTTTGTTCTGACATTGAATCATCCACATGTGGTTCATAATAAATAACCCTTA
196 CAATTTGGACCCACTTTATGCTGACATTGAATCATCCACATGTGGTTCATAATAAATAACCCTTA
* *
14304 CGGGATCATCAGTCCCATTAGAATGAAGGATGAAGTCTATTCTGAAGTGTCGAGAAGCCCAAAGT
261 CAGGACCATCAGTCCCATTAGAATGAAGGATGAAGTCTATTCTGAAGTGTCGAGAAGCCCAAAGT
14369 ACCTCATTAGACGAGTCACGTAGGGACCCATACAGATAAGGCCCTTCCTGTTTCGATCGGGCTGG
326 ACCTCATTAGACGAGTCACGTAGGGACCCATACAGATAAGGCCCTTCCTGTTTCGATCGGGCTGG
14434 TGGCAACAACAGTGAACCATAAAGTAAGTGACATCGACTGGGTGGCATGTCTCCATACTCCATTA
391 TGGCAACAACAGTGAACCATAAAGTAAGTGACATCGACTGGGTGGCATGTCTCCATACTCCATTA
14499 GAAATAGGTGTCCGAAGTACTAACAACCCTCATTCTCTCCTTCCAACTAGTCAAATGTGTGGGCT
456 GAAATAGGTGTCCGAAGTACTAACAACCCTCATTCTCTCCTTCCAACTAGTCAAATGTGTGGGCT
* *
14564 AGAATGATATGAAAATAGCGCAAAGCTGAAGGTAAGCATATTGCCTTTGACTTACTTGGGTTATA
521 AGAATGATATGAAAATAGCGCAAAGCTAAAGGTAAGCATATTGCCTTTAACTTACTTGGGTTATA
* *
14629 TTGTGACTTAGACTCG
586 TTGTGACTCAGACTAG
* * * *
14645 CTAACTGTTGTTCCTTAAGGCGGTACATCTTCTCGGACTGCTACTATTATGTGCGATAGATGTCC
1 CTAACTGTTGTTCCTTAAGGCGG----TCTGCTCGGACTACTACTACTACGTGCGATAGATGTCC
* * *
14710 CTAAACATGACTGAATATGAGCAGTTGAGTGACTCAGAGGAGGAGAGGATTAGGCTGAGTCTGCA
62 CTAAACATGACTGAATATGAGCAGTGGAGTGACTCAGAGGAGGAGAAGATCAGGCTGAGTCTGCA
* *
14775 TGTTGAGATGGGTCCTCTTCTGGGAGCTCCACATGCCCATTCTT-GAGATTCGGGTGGAATAGTG
127 TGTTGAGATGGGTCCTCTTCTGGGAGCTCCACATGCCCATTCTTAG-GATTCGAGTGAAATAGTG
* *
14839 TATACCAATTTGGACCCACTTTATGCTTACATTGAATCATCCACATGTGGTTCATAATAGATAAC
191 TATACCAATTTGGACCCACTTTATGCTGACATTGAATCATCCACATGTGGTTCATAATAAATAAC
14904 CCTTACAGGACCATCAGTCCCATTAGAATGAAGGATGAAGTCTACTTC-GAAGTGTCGAGAAGCC
256 CCTTACAGGACCATCAGTCCCATTAGAATGAAGGATGAAGTCTA-TTCTGAAGTGTCGAGAAGCC
*
14968 CAAAGTACCTCATTAGATGAGTCACGTAGGGACCCATACAGATAAGGCCCTTCCTGTTTCGATCG
320 CAAAGTACCTCATTAGACGAGTCACGTAGGGACCCATACAGATAAGGCCCTTCCTGTTTCGATCG
*
15033 GGCTGGTGGCAACAACAGTGAACCATGAAGTAAGTGACATCGACTGGGTGGCATGTCTCCATACT
385 GGCTGGTGGCAACAACAGTGAACCATAAAGTAAGTGACATCGACTGGGTGGCATGTCTCCATACT
* * **
15098 CCATTAGAAATAGGTGTCCGAAGTACTAACGACCCTCGTTCTCTCCTTCTGACTAGTCAAATGTG
450 CCATTAGAAATAGGTGTCCGAAGTACTAACAACCCTCATTCTCTCCTTCCAACTAGTCAAATGTG
15163 TGGGCTAGAATGATATGAAAATAGCGCAAAGCTAAAGGTAAGCATATTGCCTTTAACTTACTTGG
515 TGGGCTAGAATGATATGAAAATAGCGCAAAGCTAAAGGTAAGCATATTGCCTTTAACTTACTTGG
15228 GTTATATTGTGACTCAGACTAG
580 GTTATATTGTGACTCAGACTAG
15250 CTAA
1 CTAA
15254 TGTGGGACCA
Statistics
Matches: 572, Mismatches: 31, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
601 22 0.04
604 1 0.00
605 546 0.95
606 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (601 bp):
CTAACTGTTGTTCCTTAAGGCGGTCTGCTCGGACTACTACTACTACGTGCGATAGATGTCCCTAA
ACATGACTGAATATGAGCAGTGGAGTGACTCAGAGGAGGAGAAGATCAGGCTGAGTCTGCATGTT
GAGATGGGTCCTCTTCTGGGAGCTCCACATGCCCATTCTTAGGATTCGAGTGAAATAGTGTATAC
CAATTTGGACCCACTTTATGCTGACATTGAATCATCCACATGTGGTTCATAATAAATAACCCTTA
CAGGACCATCAGTCCCATTAGAATGAAGGATGAAGTCTATTCTGAAGTGTCGAGAAGCCCAAAGT
ACCTCATTAGACGAGTCACGTAGGGACCCATACAGATAAGGCCCTTCCTGTTTCGATCGGGCTGG
TGGCAACAACAGTGAACCATAAAGTAAGTGACATCGACTGGGTGGCATGTCTCCATACTCCATTA
GAAATAGGTGTCCGAAGTACTAACAACCCTCATTCTCTCCTTCCAACTAGTCAAATGTGTGGGCT
AGAATGATATGAAAATAGCGCAAAGCTAAAGGTAAGCATATTGCCTTTAACTTACTTGGGTTATA
TTGTGACTCAGACTAG
Found at i:17200 original size:48 final size:48
Alignment explanation
Indices: 17129--17323 Score: 266
Period size: 48 Copynumber: 4.1 Consensus size: 48
17119 ACTCAGAAGT
* * ** *
17129 CTCGCACCCTAAGTGCCAATATCATGGCCCGAAGCTGAATCAAT-AAA
1 CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
*
17176 GCTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATTAATGTAA
1 -CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
*
17225 CTCGCACCCTAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
1 CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
* * * * *
17273 CTTGCACCTGAAGTACTAATATTATAGCCCGAAGCCAAATCAATGTAA
1 CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
17321 CTC
1 CTC
17324 ACAATAACAT
Statistics
Matches: 131, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
48 129 0.98
49 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.22
Consensus pattern (48 bp):
CTCGCACCCGAAGTGCTAATATCATGGCCCGAAGCCAAATCAATGTAA
Found at i:17663 original size:95 final size:94
Alignment explanation
Indices: 17489--17678 Score: 308
Period size: 95 Copynumber: 2.0 Consensus size: 94
17479 AAACTTACAT
*
17489 CGGATACAAAAACAGAAAAATGAGTCAATCAATCCAAAACTTGGTCCTTCCTCGAACTAAGTCCG
1 CGGATACAAAAACAGAAAAACGAGTCAATCAATCCAAAACTTGGTCCTTCCTCGAACTAAGTCCG
17554 AATTTCACTTTTCTTGATCTATATAATAC
66 AATTTCACTTTTCTTGATCTATATAATAC
** * * *
17583 CGGATACAAAAAGGGAAAAACGAGTCAATCAATCCAAAACCTTGGTCTTTCCTCGATCTAAGTCT
1 CGGATACAAAAACAGAAAAACGAGTCAATCAATCCAAAA-CTTGGTCCTTCCTCGAACTAAGTCC
*
17648 GAATTTCGCTTTTCTTGATCTATATAATAC
65 GAATTTCACTTTTCTTGATCTATATAATAC
17678 C
1 C
17679 AAATTTAGCT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
94 36 0.41
95 52 0.59
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.29
Consensus pattern (94 bp):
CGGATACAAAAACAGAAAAACGAGTCAATCAATCCAAAACTTGGTCCTTCCTCGAACTAAGTCCG
AATTTCACTTTTCTTGATCTATATAATAC
Found at i:19568 original size:46 final size:47
Alignment explanation
Indices: 19500--19624 Score: 157
Period size: 48 Copynumber: 2.7 Consensus size: 47
19490 TATGTGTGCT
* * *
19500 AGTGTAAGACATGTCTGAGACATACATC-GGCT-ACAT-TACGAGAGCC
1 AGTGTAAGACATGTCTGAGACATGCATCAGCCTCACATATAC-A-ACCC
* *
19546 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAACCC
1 AGTGTAAGACATGTCTGAGACATGCATCAGCCTC-ACATATACAACCC
19594 AGTGTAAGACATGTCTGAGACATGCATCAGC
1 AGTGTAAGACATGTCTGAGACATGCATCAGC
19625 ATTGAGACGA
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
46 26 0.38
47 3 0.04
48 33 0.48
49 4 0.06
50 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGAGACATGCATCAGCCTCACATATACAACCC
Found at i:19604 original size:94 final size:94
Alignment explanation
Indices: 19500--19710 Score: 246
Period size: 94 Copynumber: 2.2 Consensus size: 94
19490 TATGTGTGCT
* * * * *
19500 AGTGTAAGACATGTCTGAGACATACATCGGC-TACATTACGAGAGCCAGTGTAAGACATGTCTGG
1 AGTGTAAGACATGTCTGAGACATACATCAGCATACA-GACGAGAGCCAGTATAAGACATGCCTAG
*
19564 GACATGCATCAGCCTCGAGATATACAACCC
65 GACATACATCAGCCTCGAGATATACAACCC
* ** * *
19594 AGTGTAAGACATGTCTGAGACATGCATCAGCATTGAGACGAGATCTAGTATAAGACATGCCTAGG
1 AGTGTAAGACATGTCTGAGACATACATCAGCATACAGACGAGAGCCAGTATAAGACATGCCTAGG
** * *
19659 ATGTACATCAGCCTCGAGATATACAAGCT
66 ACATACATCAGCCTCGAGATATACAACCC
*
19688 AGTGTAAGA-ACTGTCTGGGACAT
1 AGTGTAAGACA-TGTCTGAGACAT
19711 GGCGTCAGCT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
93 1 0.01
94 96 0.97
95 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGAGACATACATCAGCATACAGACGAGAGCCAGTATAAGACATGCCTAGG
ACATACATCAGCCTCGAGATATACAACCC
Found at i:19608 original size:48 final size:48
Alignment explanation
Indices: 19544--19711 Score: 162
Period size: 48 Copynumber: 3.5 Consensus size: 48
19534 ATTACGAGAG
19544 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAAC
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAAC
* * * ** * *
19592 CCAGTGTAAGACATGTCTGAGACATGCATCAGCATTGAGA-CGA-GAT
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAAC
* * * * ** * *
19638 CTAGTATAAGACATGCCTAGGATGTACATCAGCCTCGAGATATACAAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAAC
*
19686 CTAGTGTAAGA-ACTGTCTGGGACATG
1 CCAGTGTAAGACA-TGTCTGGGACATG
19712 GCGTCAGCTT
Statistics
Matches: 90, Mismatches: 27, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
46 31 0.34
47 3 0.03
48 56 0.62
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (48 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATACAAC
Found at i:19819 original size:49 final size:49
Alignment explanation
Indices: 19730--19853 Score: 137
Period size: 49 Copynumber: 2.5 Consensus size: 49
19720 TTGTTGTATG
* *
19730 TCAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATATATGAGAAC
1 TCAGTGTAAGACCTGTCTGGGACATGACATCGACACCGATATATCA-AAC
* * *
19780 T-AGTGTAAGACCTTTTTGGGACATGACATC-AGC-CTCGATATATCAAAG
1 TCAGTGTAAGACCTGTCTGGGACATGACATCGA-CAC-CGATATATCAAAC
* *
19828 TCAGTGTAAGACTTGTCTAGGACATG
1 TCAGTGTAAGACCTGTCTGGGACATG
19854 GCATTGACTT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
48 5 0.08
49 56 0.90
50 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (49 bp):
TCAGTGTAAGACCTGTCTGGGACATGACATCGACACCGATATATCAAAC
Found at i:23511 original size:29 final size:27
Alignment explanation
Indices: 23493--23562 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
23483 ATATTAAGTC
23493 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
23520 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
23548 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
23563 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:23556 original size:28 final size:28
Alignment explanation
Indices: 23493--23590 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
23483 ATATTAAGTC
*
23493 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
23520 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
23548 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
23577 CGCACACTTAGTGC
1 CGCACACTTAGTGC
23591 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.