Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2707
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: 28879
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:3068 original size:27 final size:28
Alignment explanation
Indices: 2984--3081 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
2974 CATGAGATTG
* * * *
2984 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
3013 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
3041 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
3068 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
3082 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:3092 original size:27 final size:27
Alignment explanation
Indices: 3012--3094 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
3002 TAAATTGTAC
* *
3012 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
3040 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
3067 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
3094 A
1 A
3095 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:3095 original size:29 final size:27
Alignment explanation
Indices: 2984--3095 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
2974 CATGAGATTG
** * *
2984 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
3013 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
3041 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
3068 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
3096 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:12106 original size:36 final size:36
Alignment explanation
Indices: 12048--12124 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
12038 CTATTACGAA
* *
12048 GTCTTACCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCGGACAAAATCTCCACACGAAGTCATCGG
*
12084 GTCTTACCCGGACAAAAT-TCCACACGTAGTCATCGG
1 GTCTTA-CCGGACAAAATCTCCACACGAAGTCATCGG
12120 GTCTT
1 GTCTT
12125 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 27 0.73
37 10 0.27
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (36 bp):
GTCTTACCGGACAAAATCTCCACACGAAGTCATCGG
Found at i:12405 original size:47 final size:47
Alignment explanation
Indices: 12244--12540 Score: 355
Period size: 46 Copynumber: 6.4 Consensus size: 47
12234 TGCCCTCGGA
* * * * * *
12244 CTTATCACAATTTATGCACTTTCACA-TCATCACGTTGGCCACTCGGC
1 CTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12291 C-TGTCACATA-ATACAC-TTCACATTCATCACAGTCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACA-TCGGCCATTAGGC
12335 C-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12381 CTTATCACATATATACACTTTCACATTCATCACATCGGCTA-TAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
12427 CTTATCACATATATACACTTTCACATTCATCACATCATCCATTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATT-AGGC
*
12474 TTTATCAC--ATAT-CACTTTCATCATTTCATTCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCA-CA-TTCA-TCACATCGGCCATTAGGC
12521 CTTATCACAATATATACACT
1 CTTATCAC-ATATATACACT
12541 GTCTTGGCTG
Statistics
Matches: 218, Mismatches: 16, Indels: 28
0.83 0.06 0.11
Matches are distributed among these distances:
43 6 0.03
44 35 0.16
45 21 0.10
46 77 0.35
47 70 0.32
48 1 0.00
50 4 0.02
51 4 0.02
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12433 original size:93 final size:94
Alignment explanation
Indices: 12244--12540 Score: 357
Period size: 93 Copynumber: 3.2 Consensus size: 94
12234 TGCCCTCGGA
* * * * * * *
12244 CTTATCACAATTTATGCACTTTCACA-TCATCACGTTGGCCACTCGGCC-TGTCACATA-ATACA
1 CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
12306 C-TTCACATTCATCACAGTCGGCATTAGGC
66 CTTTCACATTCATCACA-TCGGCATTAGGC
12335 C-TATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
12398 CTTTCACATTCATCACATCGGC-TATAGGC
66 CTTTCACATTCATCACATCGGCAT-TAGGC
** *
12427 CTTATCAC-ATATATACACTTTCACATTCATCACATCATCCATTCA-GCTTTATCAC--ATAT-C
1 CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATT-AGGCCTTATCACATATATAC
12487 ACTTTCATCATTTCATTCACATCGGCCATTAGGC
65 ACTTTCA-CA-TTCA-TCACATCGG-CATTAGGC
12521 CTTATCACAATATATACACT
1 CTTATCACAATATATACACT
12541 GTCTTGGCTG
Statistics
Matches: 183, Mismatches: 10, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
89 15 0.08
90 32 0.17
91 16 0.09
92 21 0.11
93 72 0.39
94 15 0.08
95 12 0.07
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
CTTTCACATTCATCACATCGGCATTAGGC
Found at i:12493 original size:22 final size:22
Alignment explanation
Indices: 12428--12508 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 22
12418 GCTATAGGCC
12428 TTATCACATATATACACTTTCACAT
1 TTATCAC--ATAT-CACTTTCACAT
* *
12453 TCATCACATCATC-CATTCAGC-T
1 TTATCACAT-ATCACTTTCA-CAT
12475 TTATCACATATCACTTTCATCAT
1 TTATCACATATCACTTTCA-CAT
12498 TTCATTCACAT
1 TT-A-TCACAT
12509 CGGCCATTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 3 0.07
22 20 0.44
23 7 0.16
24 3 0.07
25 12 0.27
ACGTcount: A:0.31, C:0.28, G:0.01, T:0.40
Consensus pattern (22 bp):
TTATCACATATCACTTTCACAT
Found at i:16183 original size:35 final size:36
Alignment explanation
Indices: 16063--16199 Score: 119
Period size: 35 Copynumber: 3.9 Consensus size: 36
16053 ATGCCCGGAT
16063 ACATCACTAGCACG-A-GCT-CTCGGACTTAGCCCAGA
1 ACATCACTAGCA-GAATGCTCCTCGGACTTAGCCC-GA
* *
16098 TA-TTCACTAGCACGAAGGCTCCTCGGACTTAGCCCGA
1 -ACATCACTAGCA-GAATGCTCCTCGGACTTAGCCCGA
** *
16135 TTATCAC-AG-AGAATGCTCCTACGGACTTAG-CGGA
1 ACATCACTAGCAGAATGCTCCT-CGGACTTAGCCCGA
16169 ACA-CACTAGCAGAATGCTCCTCGGAACTTAG
1 ACATCACTAGCAGAATGCTCCTCGG-ACTTAG
16200 TCCGGATATG
Statistics
Matches: 86, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
33 3 0.03
34 18 0.21
35 38 0.44
36 4 0.05
37 9 0.10
38 14 0.16
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (36 bp):
ACATCACTAGCAGAATGCTCCTCGGACTTAGCCCGA
Found at i:16697 original size:40 final size:42
Alignment explanation
Indices: 16599--16697 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 42
16589 TGCATTTCAA
16599 GCCCGCAACACTTAGTGCCAATCTCACAACCGATGAACACTTTAT
1 GCCCGC-ACACTTAGT-CCAATCTCACAACCGA-GAACACTTTAT
16644 -CCCGCACACTTAGT-CAATCTCACAACCG-GAACAC-TTATT
1 GCCCGCACACTTAGTCCAATCTCACAACCGAGAACACTTTA-T
16683 GCCCGCACACTTAGT
1 GCCCGCACACTTAGT
16698 GTGAAACACA
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
38 3 0.06
39 7 0.13
40 14 0.27
41 14 0.27
43 9 0.17
44 5 0.10
ACGTcount: A:0.29, C:0.35, G:0.13, T:0.22
Consensus pattern (42 bp):
GCCCGCACACTTAGTCCAATCTCACAACCGAGAACACTTTAT
Found at i:18916 original size:47 final size:47
Alignment explanation
Indices: 18720--19014 Score: 303
Period size: 47 Copynumber: 6.4 Consensus size: 47
18710 CCCTTCGGGA
* * * * * *
18720 CTTAGTCACATTTATGCACTTTCACATCCATCACGTTGGCCATCTCGGC
1 CTTA-TCACATATATACACTTTCACATTCATCACATCGGCCAT-TAGGC
* *
18769 CCTGTCACA-ATATACACTTTC-CATTCATCACAATAC-GCCATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCAC-AT-CGGCCATTAGGC
*
18814 CTTAATCACATAAAT-CAC-TTCACA-TCATCACATC-G-CATTAAGGC
1 CTT-ATCACATATATACACTTTCACATTCATCACATCGGCCATT-AGGC
* * *
18858 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
18905 CTTATCACATATATACACTTTCACTTTCATCACATCGGGCCATT-GGC
1 CTTATCACATATATACACTTTCACATTCATCACATC-GGCCATTAGGC
18952 CTTATCACATATATACAC-TTCACATT--TCATCATCGGCCATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCA-CATCGGCCATTAGGC
18996 CTTATCACATATATACACT
1 CTTATCACATATATACACT
19015 GCTCTATCTC
Statistics
Matches: 210, Mismatches: 20, Indels: 36
0.79 0.08 0.14
Matches are distributed among these distances:
42 4 0.02
43 14 0.07
44 36 0.17
45 24 0.11
46 39 0.19
47 77 0.37
48 14 0.07
49 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:24352 original size:28 final size:29
Alignment explanation
Indices: 24319--24376 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
24309 AACAAAAATT
*
24319 CCGAAAT-ACCCCCATAGGGGT-AAAATGA
1 CCGAAATGACCCCCATA-AGGTAAAAATGA
*
24347 CCGAAATGACCCCTATAAGGTAAAAATGA
1 CCGAAATGACCCCCATAAGGTAAAAATGA
24376 C
1 C
24377 GTAATCCCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (29 bp):
CCGAAATGACCCCCATAAGGTAAAAATGA
Found at i:24466 original size:28 final size:26
Alignment explanation
Indices: 24323--24469 Score: 131
Period size: 28 Copynumber: 5.5 Consensus size: 26
24313 AAAATTCCGA
* * *
24323 AATACCCCCATAGGGGTAAAATGACCGA
1 AATACCCCTATA-AGGTAAAATGA-CGT
24351 AATGACCCCTATAAGGTAAAAATGACGT
1 AAT-ACCCCTATAAGGT-AAAATGACGT
*
24379 AAT--CCCTGTAAGGTAAAA-GACTGT
1 AATACCCCTATAAGGTAAAATGAC-GT
* *
24403 AATACCCCTGTAGGGTAAAATGACGT
1 AATACCCCTATAAGGTAAAATGACGT
24429 AAATACCCCTATACAGGTAAAATGACAGT
1 -AATACCCCTATA-AGGTAAAATGAC-GT
24458 AATGA-CCCTATA
1 AAT-ACCCCTATA
24470 TAAATGACCG
Statistics
Matches: 102, Mismatches: 7, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
23 3 0.03
24 9 0.09
25 10 0.10
26 16 0.16
27 14 0.14
28 32 0.31
29 18 0.18
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.21
Consensus pattern (26 bp):
AATACCCCTATAAGGTAAAATGACGT
Done.