Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1326
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: 35101
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:36 original size:13 final size:13
Alignment explanation
Indices: 18--75 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
8 ACATAAATGT
18 TGTATCGATACAA
1 TGTATCGATACAA
31 TGTATCGATACATA
1 TGTATCGATACA-A
45 TTTTTTTGTATCGATACAA
1 ------TGTATCGATACAA
64 TGTATCGATACA
1 TGTATCGATACA
76 TATTTTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 24 0.63
14 1 0.03
19 1 0.03
20 12 0.32
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:56 original size:20 final size:20
Alignment explanation
Indices: 31--95 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
21 ATCGATACAA
31 TGTATCGATACATATTTTTT
1 TGTATCGATACATATTTTTT
51 TGTATCGATACA-A------
1 TGTATCGATACATATTTTTT
64 TGTATCGATACATATTTTTT
1 TGTATCGATACATATTTTTT
84 TGTATCGATACA
1 TGTATCGATACA
96 ATGTAAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 12 0.32
14 1 0.03
19 1 0.03
20 24 0.63
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATATTTTTT
Found at i:59 original size:33 final size:33
Alignment explanation
Indices: 17--100 Score: 168
Period size: 33 Copynumber: 2.5 Consensus size: 33
7 TACATAAATG
17 TTGTATCGATACAATGTATCGATACATATTTTT
1 TTGTATCGATACAATGTATCGATACATATTTTT
50 TTGTATCGATACAATGTATCGATACATATTTTT
1 TTGTATCGATACAATGTATCGATACATATTTTT
83 TTGTATCGATACAATGTA
1 TTGTATCGATACAATGTA
101 AGCTACTGCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (33 bp):
TTGTATCGATACAATGTATCGATACATATTTTT
Found at i:158 original size:13 final size:13
Alignment explanation
Indices: 140--164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
130 ATTACTCACA
140 TGTATCGATACAT
1 TGTATCGATACAT
153 TGTATCGATACA
1 TGTATCGATACA
165 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:229 original size:52 final size:52
Alignment explanation
Indices: 173--301 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
163 CACTGATCTT
*
173 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
225 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
277 TGTATCGATACATGCAAATAAATTT
1 TGTATCGATACATGCAGACAAATTT
302 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:7759 original size:20 final size:22
Alignment explanation
Indices: 7734--7775 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
7724 TTCTATAGTC
7734 TTTTTAT-T-TATAACATAATT
1 TTTTTATATATATAACATAATT
*
7754 TTTTTATATATATAAGATAATT
1 TTTTTATATATATAACATAATT
7776 AACACATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 1 0.05
22 11 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTTATATATATAACATAATT
Found at i:9603 original size:4 final size:4
Alignment explanation
Indices: 9587--9633 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
9577 TCTAAGGTAC
* *
9587 GTCT GTCT TTCT GTCT GT-T CGCCT GTCT GTCT GTCT GTCT GTCT GTC
1 GTCT GTCT GTCT GTCT GTCT -GTCT GTCT GTCT GTCT GTCT GTCT GTC
9634 ACAGCTCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 1 0.03
4 35 0.95
5 1 0.03
ACGTcount: A:0.00, C:0.28, G:0.23, T:0.49
Consensus pattern (4 bp):
GTCT
Found at i:12281 original size:2 final size:2
Alignment explanation
Indices: 12276--12323 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
12266 CACTATTGGG
12276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12318 AT AT AT
1 AT AT AT
12324 GCTTAACAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13210 original size:16 final size:16
Alignment explanation
Indices: 13162--13232 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
13152 TAAAGAAATT
13162 TAAATATTAAATAT-A
1 TAAATATTAAATATAA
*
13177 T-AAT-TTTAATAATAAA
1 TAAATATTAAAT-AT-AA
13193 TAAATATTAAATATAA
1 TAAATATTAAATATAA
* *
13209 TAAATATTTAATAAAA
1 TAAATATTAAATATAA
*
13225 TATATATT
1 TAAATATT
13233 TGATTAAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.11
14 5 0.11
15 1 0.02
16 25 0.54
17 5 0.11
18 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATATTAAATATAA
Found at i:13223 original size:20 final size:21
Alignment explanation
Indices: 13185--13228 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
13175 TATAATTTTA
*
13185 ATAATAAATAAAT-ATTAAAT
1 ATAATAAATAAATAATAAAAT
**
13205 ATAATAAATATTTAATAAAAT
1 ATAATAAATAAATAATAAAAT
13226 ATA
1 ATA
13229 TATTTGATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAATAAATAAATAATAAAAT
Found at i:13223 original size:31 final size:31
Alignment explanation
Indices: 13162--13232 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
13152 TAAAGAAATT
*
13162 TAAATATTAAATATATAATTTTAATAAT-AAA
1 TAAATATTAAATATATAATATT-ATAATAAAA
13193 TAAATATTAAATATAATAAATATT-TAATAAAA
1 TAAATATTAAATAT-AT-AATATTATAATAAAA
*
13225 TATATATT
1 TAAATATT
13233 TGATTAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 18 0.51
32 12 0.34
33 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TAAATATTAAATATATAATATTATAATAAAA
Found at i:13246 original size:17 final size:16
Alignment explanation
Indices: 13170--13247 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
13160 TTTAAATATT
13170 AAATATATAATTTTAATAA
1 AAATATAT-A-TTTAAT-A
* *
13189 TAAATAAATATTAAATA
1 -AAATATATATTTAATA
* *
13206 TAATAAATATTTAATA
1 AAATATATATTTAATA
* *
13222 AAATATATATTTGATT
1 AAATATATATTTAATA
13238 AAATGATATA
1 AAAT-ATATA
13248 ATCTATAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
16 30 0.61
17 6 0.12
18 5 0.10
19 1 0.02
20 7 0.14
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AAATATATATTTAATA
Found at i:13414 original size:21 final size:20
Alignment explanation
Indices: 13370--13414 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
13360 AATTTTATTG
* **
13370 ATTTTTTATTGATTCAATTA
1 ATTTTTTATCGATTCAAAAA
13390 ATTTTTTATCGATTCAAAAA
1 ATTTTTTATCGATTCAAAAA
13410 TATTT
1 -ATTT
13415 CAATTTAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTTTTATCGATTCAAAAA
Found at i:16069 original size:6 final size:6
Alignment explanation
Indices: 16058--16092 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
16048 TGAACCGTGG
* *
16058 GGGAAA GGGAAA AGGAAA GGAAAA GGGAAA GGGAA
1 GGGAAA GGGAAA GGGAAA GGGAAA GGGAAA GGGAA
16093 GAGTTTAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
GGGAAA
Found at i:18028 original size:2 final size:2
Alignment explanation
Indices: 18019--18049 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
18009 TATATACTCC
18019 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18050 CTATTTCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:19717 original size:15 final size:16
Alignment explanation
Indices: 19684--19717 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19674 ATGAGAAGAT
19684 TAATAATTTATAAACA
1 TAATAATTTATAAACA
*
19700 TAATAATTT-TAAATA
1 TAATAATTTATAAACA
19715 TAA
1 TAA
19718 CATAATTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATTTATAAACA
Found at i:22734 original size:4 final size:4
Alignment explanation
Indices: 22725--22749 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
22715 AATATTCCAC
22725 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
22750 CGAGCTCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:23459 original size:26 final size:27
Alignment explanation
Indices: 23417--23470 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
23407 ATTGACTTAT
*
23417 ATTAAAGACTTACTTAAATATAAATTA
1 ATTAAAGACTTACTTAAATACAAATTA
*
23444 ATTAAA-ACTTATTTAAATACAAATTA
1 ATTAAAGACTTACTTAAATACAAATTA
23470 A
1 A
23471 AATTTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (27 bp):
ATTAAAGACTTACTTAAATACAAATTA
Found at i:24621 original size:32 final size:35
Alignment explanation
Indices: 24570--24635 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 35
24560 CAATGTCAAT
*
24570 ATATATTTCAAAATCTATAT-AATATAAATTATTA
1 ATATATTTCAAAATCTATATAAATATAAAATATTA
*
24604 ATATA-TT-AAAATTTATATAAATATAAAATATT
1 ATATATTTCAAAATCTATATAAATATAAAATATT
24636 TTAAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.34
33 14 0.48
34 5 0.17
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (35 bp):
ATATATTTCAAAATCTATATAAATATAAAATATTA
Found at i:24630 original size:17 final size:17
Alignment explanation
Indices: 24579--24646 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
24569 TATATATTTC
*
24579 AAAATCTATAT-AATAT
1 AAAATTTATATAAATAT
24595 -AAA-TTAT-TAATATATT
1 AAAATTTATATAA-ATA-T
24611 AAAATTTATATAAATAT
1 AAAATTTATATAAATAT
*
24628 AAAATATTTTA-AAATAT
1 AAAAT-TTATATAAATAT
24645 AA
1 AA
24647 TTATAATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 6 0.14
16 1 0.02
17 17 0.40
18 11 0.26
19 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATTTATATAAATAT
Found at i:25832 original size:38 final size:38
Alignment explanation
Indices: 25780--25858 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
25770 GGTTTAGTGG
25780 TTTTTTATGGTTATGAGGCTGCTAATCAAGTGCAACCT
1 TTTTTTATGGTTATGAGGCTGCTAATCAAGTGCAACCT
* *
25818 TTTTTTATGTTTATGAGGCTGCTAATCAAGTGTAACCT
1 TTTTTTATGGTTATGAGGCTGCTAATCAAGTGCAACCT
25856 TTT
1 TTT
25859 ATTTGGCTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (38 bp):
TTTTTTATGGTTATGAGGCTGCTAATCAAGTGCAACCT
Done.