Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2181
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: 42553
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:565 original size:14 final size:13
Alignment explanation
Indices: 548--611 Score: 53
Period size: 14 Copynumber: 4.9 Consensus size: 13
538 AAAAAACAAA
548 AAATATAAAAAAT
1 AAATATAAAAAAT
561 CAAAT-T-AAAAAT
1 -AAATATAAAAAAT
*
573 AAATAATAAATAAT
1 AAAT-ATAAAAAAT
*
587 AAATAATTAAAAA-
1 AAAT-ATAAAAAAT
*
600 AAATTTAAAAAA
1 AAATATAAAAAA
612 GAGGGGAGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 4 0.10
12 12 0.29
13 6 0.14
14 20 0.48
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATATAAAAAAT
Found at i:590 original size:25 final size:24
Alignment explanation
Indices: 520--592 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 24
510 TATTCAATGT
*
520 AAAATATAATAATAAGTAA-AAA-A
1 AAAATA-AATAATAAATAATAAATA
*
543 ACAAA-AAAT-ATAAAAAATCAAATTA
1 A-AAATAAATAATAAATAAT-AAA-TA
568 AAAATAAATAATAAATAATAAATA
1 AAAATAAATAATAAATAATAAATA
592 A
1 A
593 TTAAAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
21 6 0.15
22 3 0.08
23 5 0.12
24 9 0.22
25 9 0.22
26 8 0.20
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.22
Consensus pattern (24 bp):
AAAATAAATAATAAATAATAAATA
Found at i:703 original size:43 final size:41
Alignment explanation
Indices: 642--724 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 41
632 AGGATTTGTA
* * * *
642 GCCACCTAATTGACTTAGGTGGCATTGCATTGCATTGCATGCT
1 GCCACCTAAATCAATTAGGTGGCAATGCA-TGCATT-CATGCT
685 GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATGC
1 GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATGC
725 ATGAAATTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 5 0.14
42 6 0.17
43 25 0.69
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (41 bp):
GCCACCTAAATCAATTAGGTGGCAATGCATGCATTCATGCT
Found at i:897 original size:20 final size:20
Alignment explanation
Indices: 872--912 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
862 TCATATGAAA
872 ATAAGATTGGTGTAAACAGC
1 ATAAGATTGGTGTAAACAGC
892 ATAAGATTGGTGTAAACAGC
1 ATAAGATTGGTGTAAACAGC
912 A
1 A
913 GCAAATAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (20 bp):
ATAAGATTGGTGTAAACAGC
Found at i:1392 original size:49 final size:48
Alignment explanation
Indices: 1301--1395 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 48
1291 AGTGACCACC
* *
1301 GCAACCTCCAGCAGCCCAGTAACTCCCACGACAGCCTTCAACAGCTAA
1 GCAACCTCCAGCAGCCCAGCAACTCCCACGACAGCCTCCAACAGCTAA
* * * * *
1349 GCAACTTCCAGTAGCTCCAGCAACTTCCATGGCAGCCTCCAACAGCT
1 GCAACCTCCAGCAGC-CCAGCAACTCCCACGACAGCCTCCAACAGCT
1396 CCTACGACAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 13 0.33
49 26 0.67
ACGTcount: A:0.28, C:0.40, G:0.16, T:0.16
Consensus pattern (48 bp):
GCAACCTCCAGCAGCCCAGCAACTCCCACGACAGCCTCCAACAGCTAA
Found at i:1515 original size:22 final size:22
Alignment explanation
Indices: 1489--1551 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
1479 TAGCAACTTT
*
1489 CAGCAGCCTCTAGCAGCTTCCA
1 CAGCAGCCTCCAGCAGCTTCCA
* * *
1511 CAGCAACCTCCAACAGCTCCCA
1 CAGCAGCCTCCAGCAGCTTCCA
*
1533 CAACAGCCTCCAGCAGCTT
1 CAGCAGCCTCCAGCAGCTT
1552 AACAATCCCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.44, G:0.14, T:0.14
Consensus pattern (22 bp):
CAGCAGCCTCCAGCAGCTTCCA
Found at i:1636 original size:31 final size:31
Alignment explanation
Indices: 1563--1652 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
1553 ACAATCCCAG
* * * * *
1563 GCAGCTCCCACAGCAACTTCCAACAGCTTCA
1 GCAGCTCCCACGGTAGCCTCCAGCAGCTTCA
*
1594 GCAGCTTCCACGGTAGCCTCCAGCAGCTTCA
1 GCAGCTCCCACGGTAGCCTCCAGCAGCTTCA
1625 GCAGCTCCCACGGTAGCCTCCAGCAGCT
1 GCAGCTCCCACGGTAGCCTCCAGCAGCT
1653 CCCACGACAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.22, C:0.41, G:0.20, T:0.17
Consensus pattern (31 bp):
GCAGCTCCCACGGTAGCCTCCAGCAGCTTCA
Found at i:1651 original size:22 final size:22
Alignment explanation
Indices: 1623--1689 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
1613 CCAGCAGCTT
**
1623 CAGCAGCTCCCACGGTAGCCTC
1 CAGCAGCTCCCACGACAGCCTC
1645 CAGCAGCTCCCACGACAGCCTC
1 CAGCAGCTCCCACGACAGCCTC
*
1667 TAGCAGCT--CA-G-CAGCCTC
1 CAGCAGCTCCCACGACAGCCTC
1685 CAGCA
1 CAGCA
1690 ACTTCCAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.27
19 1 0.02
20 2 0.05
22 27 0.66
ACGTcount: A:0.22, C:0.45, G:0.21, T:0.12
Consensus pattern (22 bp):
CAGCAGCTCCCACGACAGCCTC
Found at i:9952 original size:97 final size:97
Alignment explanation
Indices: 9817--10052 Score: 314
Period size: 97 Copynumber: 2.4 Consensus size: 97
9807 TTATTTATCG
* ** * *
9817 GGGATACTCCAACCTTATTCCTCCGAGGGGATACTCCAACCCCCCTTTTAAACACA-CTAAAGTT
1 GGGACACTCCAACCCCATTCCTCCGAGGGAATACTCCAACCCCACTTTTAAACACATC-AAAGTT
9881 TAAATCTTATTCTCACTTAAATTGTCACCATCA
65 TAAATCTTATTCTCACTTAAATTGTCACCATCA
* * * * *
9914 GGGACACTTCAACCCCATTCTTCCGAGGGAATATTCCAACCCGACTTTTAAACGCATCAAAGTTT
1 GGGACACTCCAACCCCATTCCTCCGAGGGAATACTCCAACCCCACTTTTAAACACATCAAAGTTT
* * *
9979 AAATTTTATTCTCACTTAAATTGTCATCATCG
66 AAATCTTATTCTCACTTAAATTGTCACCATCA
*
10011 GGGACACTCCAACCCCATTCCTCCGAAGGG-ATACTCTAACCC
1 GGGACACTCCAACCCCATTCCTCCG-AGGGAATACTCCAACCC
10053 TGTTTTTCAA
Statistics
Matches: 120, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
97 115 0.96
98 5 0.04
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.28
Consensus pattern (97 bp):
GGGACACTCCAACCCCATTCCTCCGAGGGAATACTCCAACCCCACTTTTAAACACATCAAAGTTT
AAATCTTATTCTCACTTAAATTGTCACCATCA
Found at i:22562 original size:101 final size:96
Alignment explanation
Indices: 22370--22549 Score: 220
Period size: 101 Copynumber: 1.8 Consensus size: 96
22360 TAAATTGGGC
* * *
22370 AAAATAAGATTTAAATATTGACAATTAAAAAAAAGTGGTTGGAATATCTCCTCAGAAGAATGAGG
1 AAAATAAGATTTAAATATTGACAATTAAAAAAAAG-GGTTGGAATATCCCCTCAAAAGAACGAGG
* *
22435 TTAGAGTACCCCTGACGACAATAATTTAAGTA
65 TTAGAGTACCCCCGACGACAAAAATTTAAGTA
*
22467 AAAATGAGATTTAAATATTGACAAATTTTTTAAAAAATAA-GGTTGGAATATCCCCTCAAAAGAA
1 AAAATAAGATTTAAATATTGAC-AA----TTAAAAAA-AAGGGTTGGAATATCCCCTCAAAAGAA
22531 CGAGG-TAGAAGTACCCCCG
60 CGAGGTTAG-AGTACCCCCG
22550 GTGAATAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
97 21 0.30
98 2 0.03
100 3 0.04
101 35 0.49
102 8 0.11
103 2 0.03
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (96 bp):
AAAATAAGATTTAAATATTGACAATTAAAAAAAAGGGTTGGAATATCCCCTCAAAAGAACGAGGT
TAGAGTACCCCCGACGACAAAAATTTAAGTA
Found at i:25989 original size:21 final size:22
Alignment explanation
Indices: 25950--25991 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
25940 AAGAACCTCT
25950 AAATCTCTCTAAGAATTGTACC
1 AAATCTCTCTAAGAATTGTACC
25972 AAAT-TCT-TAAGAGATTGTAC
1 AAATCTCTCTAAGA-ATTGTAC
25992 ACTAAGGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
AAATCTCTCTAAGAATTGTACC
Found at i:26418 original size:20 final size:20
Alignment explanation
Indices: 26393--26446 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
26383 ATTGGGCTTA
** *
26393 ATGTATCGATACATTTTACC
1 ATGTATCGATACAACTCACC
*
26413 ATGTATCGATACAACTCATC
1 ATGTATCGATACAACTCACC
26433 ATGTATCGATACAA
1 ATGTATCGATACAA
26447 TGTATTGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAACTCACC
Found at i:26531 original size:19 final size:20
Alignment explanation
Indices: 26507--26556 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
26497 CTTTTTAAGG
*
26507 TGTATCGATACTATG-AACA
1 TGTATCGATACTAAGCAACA
*
26526 TGTATCGATACTAAGCAATA
1 TGTATCGATACTAAGCAACA
26546 TGTATCGATAC
1 TGTATCGATAC
26557 ATCTGGGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
TGTATCGATACTAAGCAACA
Found at i:26686 original size:22 final size:22
Alignment explanation
Indices: 26656--26698 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
26646 ACTTTAGATT
26656 ATTTTTACTTG-AAAACATTTG
1 ATTTTTACTTGAAAAACATTTG
26677 ATTTATTACTTGAAAAACATTT
1 ATTT-TTACTTGAAAAACATTT
26699 ATGCTTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (22 bp):
ATTTTTACTTGAAAAACATTTG
Found at i:27610 original size:18 final size:18
Alignment explanation
Indices: 27587--27621 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27577 AGAGAAACAA
*
27587 AAAATGACTACTCCTATC
1 AAAATGACTAATCCTATC
27605 AAAATGACTAATCCTAT
1 AAAATGACTAATCCTAT
27622 GACTAATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAATGACTAATCCTATC
Found at i:33796 original size:15 final size:15
Alignment explanation
Indices: 33772--33803 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
33762 GTTAACTTCT
33772 TTATCATCATCATCA
1 TTATCATCATCATCA
*
33787 TTATCTTCATCATCA
1 TTATCATCATCATCA
33802 TT
1 TT
33804 GATAGTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATCATCATCATCA
Found at i:35978 original size:35 final size:33
Alignment explanation
Indices: 35906--35979 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 33
35896 TTTTTATTTT
*
35906 TAAATATTACGTTCAAAATATATAACAATATTT
1 TAAATATTACGTTCAAAATATATAACAATATTC
* *
35939 TAAAT-TTACGTTCAAAAATTCTATTATCAATATTC
1 TAAATATTACGTTC-AAAA-TATA-TAACAATATTC
35974 TAAATA
1 TAAATA
35980 ATTATTCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 8 0.24
33 9 0.26
34 3 0.09
35 14 0.41
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.41
Consensus pattern (33 bp):
TAAATATTACGTTCAAAATATATAACAATATTC
Found at i:39816 original size:19 final size:19
Alignment explanation
Indices: 39788--39825 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39778 TGAAATATTA
*
39788 CATTCACTTTTCATTGTTT
1 CATTCACTTTCCATTGTTT
*
39807 CATTCTCTTTCCATTGTTT
1 CATTCACTTTCCATTGTTT
39826 TAGCACTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.24, G:0.05, T:0.58
Consensus pattern (19 bp):
CATTCACTTTCCATTGTTT
Found at i:40073 original size:29 final size:28
Alignment explanation
Indices: 40033--40087 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
40023 GTCAATATTT
40033 TAAAATTTGTTAAGAATATAATATACGA
1 TAAAATTTGTTAAGAATATAATATACGA
*
40061 TAAAATATTGTTAATAATATAATATAC
1 TAAAAT-TTGTTAAGAATATAATATAC
40088 TTAAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (28 bp):
TAAAATTTGTTAAGAATATAATATACGA
Done.