Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1703
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: 34512
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:966 original size:18 final size:19
Alignment explanation
Indices: 943--978 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
933 GTTAGGAGAC
943 AGCCA-TCAATGCACTTCA
1 AGCCATTCAATGCACTTCA
*
961 AGCCATTCATTGCACTTC
1 AGCCATTCAATGCACTTC
979 TATCATCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (19 bp):
AGCCATTCAATGCACTTCA
Found at i:1478 original size:29 final size:30
Alignment explanation
Indices: 1394--1487 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 30
1384 TTAAACTAAA
*
1394 TGAGCTAAGCTTTAGCTCGTGAGCT-AAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * *
1423 TGAGCTGAGGCTAAACTC-TAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
*
1452 TGAG-TAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCTG-AAGT
1481 TGAGCTA
1 TGAGCTA
1488 GGAGGAGCTC
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
28 14 0.29
29 30 0.61
30 5 0.10
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:2598 original size:12 final size:11
Alignment explanation
Indices: 2580--2613 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
2570 AGTTATACAG
2580 CAAAAAAAATT
1 CAAAAAAAATT
2591 CAAAAAAAATT
1 CAAAAAAAATT
2602 CAAAAAAAATT
1 CAAAAAAAATT
2613 C
1 C
2614 GAAATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (11 bp):
CAAAAAAAATT
Found at i:3549 original size:5 final size:5
Alignment explanation
Indices: 3539--3592 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
3529 AAGAGAAAAT
3539 AAAGA AAAG- AAAGAA AAAGA AAAG- -AAGA AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AAA-GA AA-AGA
3583 AAAGA AAAGA
1 AAAGA AAAGA
3593 GAGGCAAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
3 3 0.07
4 5 0.12
5 25 0.60
6 8 0.19
7 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:3559 original size:15 final size:15
Alignment explanation
Indices: 3539--3592 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
3529 AAGAGAAAAT
3539 AAAGAAAAGAAAGAA
1 AAAGAAAAGAAAGAA
3554 AAAGAAAAG-AAG-A
1 AAAGAAAAGAAAGAA
*
3567 AAAGAAAATGAAATAA
1 AAAGAAAA-GAAAGAA
3583 AAAGAAAAGA
1 AAAGAAAAGA
3593 GAGGCAAGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
13 9 0.26
14 4 0.11
15 13 0.37
16 9 0.26
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (15 bp):
AAAGAAAAGAAAGAA
Found at i:3681 original size:12 final size:12
Alignment explanation
Indices: 3673--3697 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3663 TTTGAAAAGC
3673 AAAAAGAAAATG
1 AAAAAGAAAATG
3685 AAAAAGAAAATG
1 AAAAAGAAAATG
3697 A
1 A
3698 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:3694 original size:18 final size:18
Alignment explanation
Indices: 3667--3722 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
3657 AAAGCCTTTG
3667 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
3686 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
3704 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
3721 AA
1 AA
3723 TTGAGAGTGA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:3747 original size:29 final size:29
Alignment explanation
Indices: 3674--3755 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
3664 TTGAAAAGCA
* * *
3674 AAAAGAAAATGAAAAAGAAAATGAGATTG
1 AAAAGAAGATGAAAAAGAAATTGAGAGTG
*
3703 AAAA-AGAGAACG-AAAAGAAATTGAGAGTG
1 AAAAGA-AG-ATGAAAAAGAAATTGAGAGTG
3732 AAAAGAAGATGAAAAAGAAATTGA
1 AAAAGAAGATGAAAAAGAAATTGA
3756 AACAAAAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.63, C:0.01, G:0.23, T:0.12
Consensus pattern (29 bp):
AAAAGAAGATGAAAAAGAAATTGAGAGTG
Found at i:5891 original size:30 final size:31
Alignment explanation
Indices: 5857--5953 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
5847 AGCTCACTCC
*
5857 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
5887 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
5917 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
5947 TAGCTCA
1 TAGCTCA
5954 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:18464 original size:25 final size:25
Alignment explanation
Indices: 18389--18464 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
18379 ATGCATATAT
18389 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
18414 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
18436 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
18461 GTGA
1 GTGA
18465 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:18536 original size:48 final size:48
Alignment explanation
Indices: 18385--18609 Score: 223
Period size: 47 Copynumber: 4.7 Consensus size: 48
18375 GAACATGCAT
* * *
18385 ATATGTGATAAGGCCGAATGGCCAATGTG--ATGA-ATGTGAG-CATGC
1 ATATGTGGTAAAGCCGAATGGCCAATGTGAAAT-ATATATGAGACATGC
* *
18430 ATATGTGTGATAAGGCCGAATGGCCAATGTG--GTGA-ATATGA-ACATGC
1 ATATGTG-G-TAAAGCCGAATGGCCAATGTGAAAT-ATATATGAGACATGC
* *
18477 ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATGAGATATGC
1 ATATGTGGTAAAGCCGAATGGCCAATGTGAAATATATATGAGACATGC
** * *
18525 ATATGTGGTAAAGCCGAATGTTCAATGTGAAATATATATATGAGATATGT
1 ATATGTGGTAAAGCCGAATGGCCAATGTG-AA-ATATATATGAGACATGC
* *
18575 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 ATATGTGGTAAAGCCGAATGGCCAATGTGAAATAT
18610 GTAGGCATGT
Statistics
Matches: 158, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
45 26 0.16
46 2 0.01
47 48 0.30
48 37 0.23
49 4 0.03
50 41 0.26
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (48 bp):
ATATGTGGTAAAGCCGAATGGCCAATGTGAAATATATATGAGACATGC
Found at i:18902 original size:37 final size:37
Alignment explanation
Indices: 18757--18901 Score: 263
Period size: 37 Copynumber: 3.9 Consensus size: 37
18747 GGAAATATAT
18757 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
18794 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
18831 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
18868 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
18902 TCGTCTGAGC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:20525 original size:40 final size:40
Alignment explanation
Indices: 20166--20509 Score: 498
Period size: 40 Copynumber: 8.7 Consensus size: 40
20156 GAGAATTGAG
*
20166 AGTGATATATCTGGGCTAAGTCCCGAAGAG-ATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
20205 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
20245 AGTGATGTATCCGGGCTAGGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
20285 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
20325 AGTGATGTATCCGGACTAAGT-CCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
20364 AGTGATGTATCCGGACCAAGT-CCGAAGAGCATTCGTGGT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
20403 AGTGATGTATCCGGGCTAAGT-TCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* ** *
20442 AGTGATATATCCGTGCTAAACCCCAAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
20482 GGTGTTATATCCGGGCTAGGTCCCGAAG
1 AGTGATATATCCGGGCTAAGTCCCGAAG
20510 TGCAATCATG
Statistics
Matches: 277, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
39 136 0.49
40 141 0.51
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:23871 original size:28 final size:27
Alignment explanation
Indices: 23808--23959 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
23798 ATATTAAGTC
* * *
23808 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
23835 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
23863 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
23890 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
23918 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
23945 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
23960 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:23892 original size:55 final size:55
Alignment explanation
Indices: 23808--23959 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
23798 ATATTAAGTC
* * *
23808 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
23863 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
23918 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
23960 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:31916 original size:28 final size:27
Alignment explanation
Indices: 31853--31975 Score: 194
Period size: 27 Copynumber: 4.6 Consensus size: 27
31843 ATATTAAGTC
* *
31853 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
31880 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
31908 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
31935 CGCACACTTAGTGCTACATAGTCAA-T
1 CGCACACTTAGTGCTACATAATCAACT
31961 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31976 GCACAATTTA
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
26 16 0.17
27 50 0.54
28 26 0.28
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:31937 original size:55 final size:53
Alignment explanation
Indices: 31853--31975 Score: 192
Period size: 55 Copynumber: 2.3 Consensus size: 53
31843 ATATTAAGTC
* *
31853 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATC-AA-T
* *
31908 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAT
31961 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31976 GCACAATTTA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
53 16 0.25
54 2 0.03
55 46 0.72
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (53 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAT
Done.