Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1767
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: 52626
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:1138 original size:14 final size:15
Alignment explanation
Indices: 1110--1140 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1100 ACATAAATCG
1110 TAAACCCCTAACCCT
1 TAAACCCCTAACCCT
1125 TAAACCCC-AACCCT
1 TAAACCCCTAACCCT
1139 TA
1 TA
1141 TAATTGTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAACCCCTAACCCT
Found at i:2157 original size:41 final size:40
Alignment explanation
Indices: 2082--2265 Score: 224
Period size: 41 Copynumber: 4.5 Consensus size: 40
2072 TATGATAAAT
* * *
2082 CTGAGCATTAGCGGCCCTTTTCAACAAACACCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTTT-AAAAAACGCCGCTAAAGCC
* *
2123 CTGAGCATTAGCGGCGCTTATTAAAAAATGCCGCTAAATCC
1 CTGAGCATTAGCGGCGCTT-TTAAAAAACGCCGCTAAAGCC
* * * *
2164 CTAAACATTAGCGTCGCTTCTTTAAAAACGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTT-TTAAAAAACGCCGCTAAAGCC
*
2205 CTGAGCATTAGCGGCGCTTTTAAAAAACGCCGCTAAAACC
1 CTGAGCATTAGCGGCGCTTTTAAAAAACGCCGCTAAAGCC
** *
2245 CAAAACATTAGCGGCGCTTTT
1 CTGAGCATTAGCGGCGCTTTT
2266 TCAAAATCGC
Statistics
Matches: 122, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
40 37 0.30
41 83 0.68
42 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (40 bp):
CTGAGCATTAGCGGCGCTTTTAAAAAACGCCGCTAAAGCC
Found at i:2200 original size:82 final size:81
Alignment explanation
Indices: 2087--2281 Score: 277
Period size: 81 Copynumber: 2.4 Consensus size: 81
2077 TAAATCTGAG
* *
2087 CATTAGCGGC-CCTTTTCAACAAACACCGCTAAAGCCCTGAGCATTAGCGGCGCTTATTAAAAAA
1 CATTAGCGGCGCTTTTTCAA-AAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTT-TTAAAAAA
* * *
2151 TGCCGCTAAATCCCTAAA
64 CGCCGCTAAAACCCAAAA
*
2169 CATTAGCGTCGCTTCTTT-AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTTAAAAAAC
1 CATTAGCGGCGCTT-TTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTTAAAAAAC
2233 GCCGCTAAAACCCAAAA
65 GCCGCTAAAACCCAAAA
* *
2250 CATTAGCGGCGCTTTTTCAAAATCGCCACTAA
1 CATTAGCGGCGCTTTTTCAAAAACGCCGCTAA
2282 TGCCTCAAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
80 3 0.03
81 48 0.48
82 43 0.43
83 4 0.04
84 3 0.03
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (81 bp):
CATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTTAAAAAACG
CCGCTAAAACCCAAAA
Found at i:2410 original size:40 final size:40
Alignment explanation
Indices: 2360--2443 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
2350 CTAATGCTCA
* *
2360 TTTAGAAAGCGCCGCTAATACTTGATCTTTAGTGGCATTT
1 TTTAAAAAGCGCCGCTAATACTTGATCTTTAGCGGCATTT
* * * *
2400 TTTAAAAAGCGCCGTTAATGCTTGATTTTTAGCGGCGTTT
1 TTTAAAAAGCGCCGCTAATACTTGATCTTTAGCGGCATTT
2440 TTTA
1 TTTA
2444 TCCAAGCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (40 bp):
TTTAAAAAGCGCCGCTAATACTTGATCTTTAGCGGCATTT
Found at i:7134 original size:19 final size:19
Alignment explanation
Indices: 7110--7149 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
7100 ATGATTTATA
7110 TAAGTACTTAGATGATATT
1 TAAGTACTTAGATGATATT
7129 TAAGTACTTAGATGATATT
1 TAAGTACTTAGATGATATT
7148 TA
1 TA
7150 GGATGTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (19 bp):
TAAGTACTTAGATGATATT
Found at i:13820 original size:20 final size:21
Alignment explanation
Indices: 13797--13840 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
13787 GGTATGCAGT
13797 TTTTAG-ATGATTTA-AATGTG
1 TTTTAGTATG-TTTATAATGTG
*
13817 TTTTAGTTTGTTTATAATGTG
1 TTTTAGTATGTTTATAATGTG
13838 TTT
1 TTT
13841 GTAATGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.59
Consensus pattern (21 bp):
TTTTAGTATGTTTATAATGTG
Found at i:15934 original size:18 final size:16
Alignment explanation
Indices: 15907--15944 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
15897 ATGATGTGTA
*
15907 AATATAA-T-ATATTT
1 AATATAATTAATATAT
15921 AATATAATTAATATAT
1 AATATAATTAATATAT
15937 AATATAAT
1 AATATAAT
15945 AAGTGACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 1 0.05
16 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATAATTAATATAT
Found at i:17997 original size:21 final size:21
Alignment explanation
Indices: 17971--18013 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
17961 GTGATATTCT
*
17971 AACTTTTTATTGATTAAACTA
1 AACTTTTTATTCATTAAACTA
17992 AACTTTTTATTCATTAAACTA
1 AACTTTTTATTCATTAAACTA
18013 A
1 A
18014 GTGAGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (21 bp):
AACTTTTTATTCATTAAACTA
Found at i:20190 original size:18 final size:16
Alignment explanation
Indices: 20163--20200 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20153 ATGATGTGTA
*
20163 AATATAA-T-ATATTT
1 AATATAATTAATATAT
20177 AATATAATTAATATAT
1 AATATAATTAATATAT
20193 AATATAAT
1 AATATAAT
20201 AAGTGACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 1 0.05
16 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATAATTAATATAT
Found at i:22251 original size:21 final size:21
Alignment explanation
Indices: 22225--22267 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
22215 GTGATATTCT
*
22225 AACTTTTTATTGATTAAACTA
1 AACTTTTTATTCATTAAACTA
22246 AACTTTTTATTCATTAAACTA
1 AACTTTTTATTCATTAAACTA
22267 A
1 A
22268 GTGAGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (21 bp):
AACTTTTTATTCATTAAACTA
Found at i:24442 original size:18 final size:16
Alignment explanation
Indices: 24415--24452 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
24405 ATGATGTGTA
*
24415 AATATAA-T-ATATTT
1 AATATAATTAATATAT
24429 AATATAATTAATATAT
1 AATATAATTAATATAT
24445 AATATAAT
1 AATATAAT
24453 AAGTGACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 1 0.05
16 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATAATTAATATAT
Found at i:26503 original size:21 final size:21
Alignment explanation
Indices: 26477--26519 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
26467 GTGATATTCT
*
26477 AACTTTTTATTGATTAAACTA
1 AACTTTTTATTCATTAAACTA
26498 AACTTTTTATTCATTAAACTA
1 AACTTTTTATTCATTAAACTA
26519 A
1 A
26520 GTGAGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (21 bp):
AACTTTTTATTCATTAAACTA
Found at i:28618 original size:9 final size:9
Alignment explanation
Indices: 28600--28635 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
28590 ATGATGTGTA
28600 AATT-ATAT
1 AATTAATAT
28608 AATTAATAT
1 AATTAATAT
28617 AATTAATAT
1 AATTAATAT
28626 -A-TAATAT
1 AATTAATAT
28633 AAT
1 AAT
28636 AAGAGATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
7 6 0.24
8 6 0.24
9 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTAATAT
Found at i:30546 original size:21 final size:21
Alignment explanation
Indices: 30520--30562 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
30510 GTGATATTCT
*
30520 AACTTTTTATTGATTAAACTA
1 AACTTTTTATTCATTAAACTA
30541 AACTTTTTATTCATTAAACTA
1 AACTTTTTATTCATTAAACTA
30562 A
1 A
30563 GTGAGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (21 bp):
AACTTTTTATTCATTAAACTA
Found at i:32738 original size:18 final size:16
Alignment explanation
Indices: 32711--32748 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
32701 ATGATGTGTA
*
32711 AATATAA-T-ATATTT
1 AATATAATTAATATAT
32725 AATATAATTAATATAT
1 AATATAATTAATATAT
32741 AATATAAT
1 AATATAAT
32749 AAGTGACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 1 0.05
16 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATAATTAATATAT
Found at i:38979 original size:20 final size:21
Alignment explanation
Indices: 38956--39000 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
38946 AGGTGAGATT
*
38956 CTAAA-TTTTTATTGATTAAA
1 CTAAACTTTTTATTCATTAAA
38976 CTAAACTTTTTATTCATTAAA
1 CTAAACTTTTTATTCATTAAA
38997 CTAA
1 CTAA
39001 GTGAGTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (21 bp):
CTAAACTTTTTATTCATTAAA
Found at i:43804 original size:23 final size:23
Alignment explanation
Indices: 43772--43980 Score: 158
Period size: 22 Copynumber: 9.1 Consensus size: 23
43762 TATGTAAAGA
43772 GTAT-ATTGGTTGTGTTTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
43794 GTATAGTTGGTTGTGTTTGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
* * * * *
43817 TTATATATATGGTGGTATTTTGCA-A
1 GTATA-AT-TGGTTGT-GTTTGGAGG
* * * * **
43842 GTACATTTGATTATGTTCAGAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
43865 GTA-AATTGGTTGTGTTTGGAAG
1 GTATAATTGGTTGTGTTTGGAGG
* *
43887 GTATACTTGGTTGTGTTCGGAGG
1 GTATAATTGGTTGTGTTTGGAGG
*
43910 TTATATATATGGTTGTGTTTGGAGG
1 GTATA-AT-TGGTTGTGTTTGGAGG
* *
43935 GTA-AATTGGTTGTGTTTCGAGA
1 GTATAATTGGTTGTGTTTGGAGG
* *
43957 GTA-AATTGGTTTTGTTTGGGGG
1 GTATAATTGGTTGTGTTTGGAGG
43979 GT
1 GT
43981 GATAGCTTTA
Statistics
Matches: 142, Mismatches: 37, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
22 57 0.40
23 50 0.35
24 4 0.03
25 26 0.18
26 5 0.04
ACGTcount: A:0.19, C:0.03, G:0.34, T:0.44
Consensus pattern (23 bp):
GTATAATTGGTTGTGTTTGGAGG
Found at i:48196 original size:23 final size:23
Alignment explanation
Indices: 48150--48314 Score: 147
Period size: 23 Copynumber: 7.2 Consensus size: 23
48140 GATATGTTGA
*
48150 AGGGTAT-ATTGATTGTGTTTGG
1 AGGGTATAATTGGTTGTGTTTGG
* *
48172 AGGGTATAGTTGGTTGTGTTCGG
1 AGGGTATAATTGGTTGTGTTTGG
* * *
48195 AGGTTATATATATGGTTTTGTTTTG
1 AGGGTATA-AT-TGGTTGTGTTTGG
* * *
48220 AGGGTACATTTGGTTGTGTTCGG
1 AGGGTATAATTGGTTGTGTTTGG
*
48243 AGGGTA-AATTAGTTGTGTTTGG
1 AGGGTATAATTGGTTGTGTTTGG
* ** *
48265 AGGCTATGTTTTGTTGTGTTTGG
1 AGGGTATAATTGGTTGTGTTTGG
*
48288 AGGGTA-AATTGGTTGTATTTGG
1 AGGGTATAATTGGTTGTGTTTGG
*
48310 TGGGT
1 AGGGT
48315 GATAGATTTA
Statistics
Matches: 112, Mismatches: 27, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
22 41 0.37
23 53 0.47
24 2 0.02
25 16 0.14
ACGTcount: A:0.16, C:0.02, G:0.36, T:0.45
Consensus pattern (23 bp):
AGGGTATAATTGGTTGTGTTTGG
Found at i:48283 original size:45 final size:45
Alignment explanation
Indices: 48150--48314 Score: 170
Period size: 45 Copynumber: 3.6 Consensus size: 45
48140 GATATGTTGA
* *
48150 AGGGTATATTGATTGTGTTTGGAGGGTATAG-TTGGTTGTGTTCGG
1 AGGGTAAATTGGTTGTGTTTGGAGGGTAT-GTTTGGTTGTGTTCGG
* * * **
48195 AGGTTATATATATGGTTTTGTTTTGAGGGTACATTTGGTTGTGTTCGG
1 AGGGTA-A-AT-TGGTTGTGTTTGGAGGGTATGTTTGGTTGTGTTCGG
* * * *
48243 AGGGTAAATTAGTTGTGTTTGGAGGCTATGTTTTGTTGTGTTTGG
1 AGGGTAAATTGGTTGTGTTTGGAGGGTATGTTTGGTTGTGTTCGG
* *
48288 AGGGTAAATTGGTTGTATTTGGTGGGT
1 AGGGTAAATTGGTTGTGTTTGGAGGGT
48315 GATAGATTTA
Statistics
Matches: 96, Mismatches: 20, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
45 56 0.58
46 2 0.02
47 3 0.03
48 35 0.36
ACGTcount: A:0.16, C:0.02, G:0.36, T:0.45
Consensus pattern (45 bp):
AGGGTAAATTGGTTGTGTTTGGAGGGTATGTTTGGTTGTGTTCGG
Found at i:51377 original size:27 final size:27
Alignment explanation
Indices: 51333--51613 Score: 337
Period size: 27 Copynumber: 10.4 Consensus size: 27
51323 TGCGATTTGT
* * *
51333 GGGTAAAATGATCAAAATACCCTTGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
* *
51360 GGTTAAAATGACCGAAATACGCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
*
51387 GGGTAAAATAACCGAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
*
51414 GGGTAAAATAACCGAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
* *
51441 GGGTAAAATGATCGAAATACCCTCCAA
1 GGGTAAAATGACCGAAATACCCTCGAA
*** *
51468 GGGTAAAATGAATAAAACACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
51495 GGGTAAAATGACCGAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
**
51522 GGGTAAAATGATTGAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAA
* ** * *
51549 GAGTAAAATGATAGAAATACCCCCGAT
1 GGGTAAAATGACCGAAATACCCTCGAA
* * * *
51576 GTGTAAAATGATCGAATATACCCCCAAA
1 GGGTAAAATGACCGAA-ATACCCTCGAA
51604 GGGTAAAATG
1 GGGTAAAATG
51614 TCTGCTATAC
Statistics
Matches: 222, Mismatches: 31, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
27 204 0.92
28 18 0.08
ACGTcount: A:0.43, C:0.19, G:0.20, T:0.18
Consensus pattern (27 bp):
GGGTAAAATGACCGAAATACCCTCGAA
Found at i:51821 original size:23 final size:23
Alignment explanation
Indices: 51791--51834 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
51781 TTGCCACATA
51791 TACTGTTACCGGCAGCTTTGCGT
1 TACTGTTACCGGCAGCTTTGCGT
**
51814 TACTGTTATTGGCAGCTTTGC
1 TACTGTTACCGGCAGCTTTGC
51835 TGCGTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.39
Consensus pattern (23 bp):
TACTGTTACCGGCAGCTTTGCGT
Found at i:51857 original size:25 final size:25
Alignment explanation
Indices: 51823--51893 Score: 108
Period size: 25 Copynumber: 2.8 Consensus size: 25
51813 TTACTGTTAT
51823 TGGCAGCTTTGCTGCGTTATTATTC
1 TGGCAGCTTTGCTGCGTTATTATTC
51848 TGGCAGCTTT-CTTGCGTTATTATTC
1 TGGCAGCTTTGC-TGCGTTATTATTC
* *
51873 TGGTAGCTTTGCTGCGATATT
1 TGGCAGCTTTGCTGCGTTATT
51894 GGTGTGTTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.02
25 40 0.95
26 1 0.02
ACGTcount: A:0.13, C:0.18, G:0.24, T:0.45
Consensus pattern (25 bp):
TGGCAGCTTTGCTGCGTTATTATTC
Found at i:52259 original size:22 final size:22
Alignment explanation
Indices: 52231--52281 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
52221 ACAACTAAAC
*
52231 TAAACTAAAACTTTGTATTGAT
1 TAAACTAAAACTTTGTATTCAT
*
52253 TAAACT-AAACTTTTTATTCAT
1 TAAACTAAAACTTTGTATTCAT
52274 TAAACTAA
1 TAAACTAA
52282 GTGAGTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (22 bp):
TAAACTAAAACTTTGTATTCAT
Done.