Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1046
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: 41583
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:1611 original size:28 final size:28
Alignment explanation
Indices: 1530--1611 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1520 TTTTGGAGAT
*
1530 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
1558 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
1586 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
1612 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:1754 original size:51 final size:51
Alignment explanation
Indices: 1594--1763 Score: 196
Period size: 51 Copynumber: 3.3 Consensus size: 51
1584 GAAATAACGA
* * *
1594 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
1646 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
1699 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
1750 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
1764 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 38 0.40
52 16 0.17
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:1800 original size:26 final size:28
Alignment explanation
Indices: 1747--1820 Score: 93
Period size: 26 Copynumber: 2.8 Consensus size: 28
1737 AAAATAAAGT
1747 CGGGGTTGGAGTATCCCTC-A-GAAATAA
1 CGGGGTTGGAGTATCCC-CGATGAAATAA
*
1774 C-GGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1800 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1821 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 1 0.02
26 21 0.50
27 20 0.48
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:4302 original size:13 final size:13
Alignment explanation
Indices: 4284--4309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4274 ACAAAGATCC
4284 ATGTATCGATACA
1 ATGTATCGATACA
4297 ATGTATCGATACA
1 ATGTATCGATACA
4310 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4305 original size:33 final size:33
Alignment explanation
Indices: 4263--4329 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4253 AAAATTTCCA
***
4263 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
4296 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
4329 A
1 A
4330 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:4373 original size:19 final size:18
Alignment explanation
Indices: 4349--4416 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
4339 CAGTAGCTAA
4349 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
4368 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
4383 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4400 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
4417 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:4389 original size:13 final size:13
Alignment explanation
Indices: 4371--4395 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4361 ACAATACTTA
4371 TGTATCGATACAT
1 TGTATCGATACAT
4384 TGTATCGATACA
1 TGTATCGATACA
4396 AAACTTATGT
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:4393 original size:32 final size:32
Alignment explanation
Indices: 4352--4414 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4342 TAGCTAATTA
*
4352 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
4384 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
4415 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:4496 original size:21 final size:21
Alignment explanation
Indices: 4472--4528 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
4462 CATTTGTAGG
4472 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
4493 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
4514 ATGTATCGATACATT
1 ATGTATCGATACATT
4529 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:4557 original size:17 final size:17
Alignment explanation
Indices: 4535--4568 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4525 CATTTAAATT
4535 TTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTCAA
4552 TTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTCAA
4569 ACACTTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTTTTTCAA
Found at i:5329 original size:57 final size:56
Alignment explanation
Indices: 5121--5637 Score: 741
Period size: 55 Copynumber: 9.3 Consensus size: 56
5111 ATAAATTGTA
* * * * ** *
5121 TCCTGCTCATTGAGGAGT-AAAAAGTG-CACCAACGCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
5175 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCCACTTGTGTGGGCTTTGAA-AAGTG
1 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
5230 TCCTGCTCTTTGGGGAAT-G-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
5284 TCCTGCTCTTTGAGGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGA-GGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
5341 TCCTGCTCGTTGAGGACTGAAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGA-GGTG
5398 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
5454 TCCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 T-CCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
5510 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
5565 TCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGT-GGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
5620 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
5638 AAAAAGCGGA
Statistics
Matches: 432, Mismatches: 21, Indels: 19
0.92 0.04 0.04
Matches are distributed among these distances:
53 2 0.00
54 66 0.15
55 150 0.35
56 89 0.21
57 125 0.29
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (56 bp):
TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:5416 original size:113 final size:110
Alignment explanation
Indices: 5121--5637 Score: 751
Period size: 113 Copynumber: 4.7 Consensus size: 110
5111 ATAAATTGTA
* * * ** *
5121 TCCTGCTCATTGAGGAGTAAAAAGTG-CACCAACGCGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTT
* *
5185 TGAGGACT-GAAAGGTGCCACCCACTTGTGTGGGCTTTGAA-AAGTG
65 TGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
5230 TCCTGCTCTTTGGGGAATG-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTT
5294 TGAGGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
65 TGA-GGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
5341 TCCTGCTCGTTGAGGACTGAAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGGTGTCCTGCTC
1 TCCTGCTCTTTGAGGACTGAAAA-GTGCCACCAACTTGTGTGGGCTTTAA-A-GGTGTCCTGCTC
5406 TTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
63 TTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
5454 TCCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTC
1 T-CCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTC
* *
5518 TTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
63 TTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
5565 TCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGT-GGCTTTAAAAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCT
5629 TTGAGGACT
64 TTGAGGACT
5638 AAAAAGCGGA
Statistics
Matches: 378, Mismatches: 18, Indels: 23
0.90 0.04 0.05
Matches are distributed among these distances:
108 7 0.02
109 50 0.13
110 61 0.16
111 95 0.25
112 29 0.08
113 96 0.25
114 35 0.09
115 5 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (110 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTT
GAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:6622 original size:1 final size:1
Alignment explanation
Indices: 6618--6667 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
6608 CTTTTCTCTC
* * * * *
6618 TTTTTCTTTGTTTTGTTTTTTTTGTTTTTTTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6668 GAAGAGAAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:19312 original size:51 final size:51
Alignment explanation
Indices: 19152--19322 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
19142 GAAATAACGA
* * *
19152 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
19204 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
19257 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
19308 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
19323 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:19368 original size:27 final size:28
Alignment explanation
Indices: 19305--19380 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
19295 AAAATAAAGT
*
19305 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
19333 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
19360 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
19381 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:21867 original size:13 final size:13
Alignment explanation
Indices: 21849--21874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21839 ACAAAGATCC
21849 ATGTATCGATACA
1 ATGTATCGATACA
21862 ATGTATCGATACA
1 ATGTATCGATACA
21875 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21870 original size:33 final size:33
Alignment explanation
Indices: 21828--21894 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
21818 AAAATTTCCA
***
21828 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
21861 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
21894 A
1 A
21895 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:21938 original size:19 final size:18
Alignment explanation
Indices: 21914--21981 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
21904 CAGTAGCTAA
21914 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
21933 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
21948 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
21965 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
21982 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:21954 original size:13 final size:13
Alignment explanation
Indices: 21936--21960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21926 ACAATACTTA
21936 TGTATCGATACAT
1 TGTATCGATACAT
21949 TGTATCGATACA
1 TGTATCGATACA
21961 AAACTTATGT
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:21958 original size:32 final size:32
Alignment explanation
Indices: 21917--21979 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
21907 TAGCTAATTA
*
21917 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
21949 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
21980 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:22061 original size:21 final size:21
Alignment explanation
Indices: 22037--22093 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
22027 CATTTGTAGG
22037 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
22058 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
22079 ATGTATCGATACATT
1 ATGTATCGATACATT
22094 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:25355 original size:15 final size:15
Alignment explanation
Indices: 25335--25364 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25325 CATAAAAAAA
25335 TTATTAACTATTTTT
1 TTATTAACTATTTTT
*
25350 TTATTAATTATTTTT
1 TTATTAACTATTTTT
25365 AATAATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTAACTATTTTT
Found at i:25958 original size:21 final size:22
Alignment explanation
Indices: 25927--25980 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
25917 TTATAATCAC
*
25927 ATATT-TTATTATTAAT-TTTA
1 ATATTATTATTATTAATATTAA
*
25947 ATTTTATTATTA-TAATATTAA
1 ATATTATTATTATTAATATTAA
25968 ATATTATTATTAT
1 ATATTATTATTAT
25981 CATAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTATTATTATTAATATTAA
Found at i:26501 original size:15 final size:15
Alignment explanation
Indices: 26475--26513 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
26465 TGTATACATA
*
26475 TATTTT-ATTTTATT
1 TATTTTAATTTTAGT
26489 TATTTTAATTTTAGT
1 TATTTTAATTTTAGT
26504 TATTTTAATT
1 TATTTTAATT
26514 ATTTATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TATTTTAATTTTAGT
Found at i:26677 original size:21 final size:21
Alignment explanation
Indices: 26649--26706 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
26639 ATTTCGTAAT
26649 TAAT-TTTAATCTTATTATCA
1 TAATATTTAATCTTATTATCA
* * *
26669 TAATATTTAATCTCATCATTA
1 TAATATTTAATCTTATTATCA
* *
26690 TAATAATTAATTTTATT
1 TAATATTTAATCTTATT
26707 TTTATTACTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATATTTAATCTTATTATCA
Found at i:32318 original size:51 final size:51
Alignment explanation
Indices: 32158--32328 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
32148 GAAATAACGA
* * *
32158 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
32210 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
32263 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
32314 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
32329 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:32374 original size:27 final size:28
Alignment explanation
Indices: 32311--32386 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
32301 AAAATAAAGT
*
32311 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
32339 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
32366 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
32387 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:34875 original size:13 final size:13
Alignment explanation
Indices: 34857--34882 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34847 ACAAAGATCC
34857 ATGTATCGATACA
1 ATGTATCGATACA
34870 ATGTATCGATACA
1 ATGTATCGATACA
34883 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:34878 original size:33 final size:33
Alignment explanation
Indices: 34836--34902 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
34826 AAAATTTCCA
***
34836 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
34869 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
34902 A
1 A
34903 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:34946 original size:19 final size:18
Alignment explanation
Indices: 34922--34989 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
34912 CAGTAGCTAA
34922 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
34941 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
34956 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
34973 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
34990 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:34962 original size:13 final size:13
Alignment explanation
Indices: 34944--34968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34934 ACAATACTTA
34944 TGTATCGATACAT
1 TGTATCGATACAT
34957 TGTATCGATACA
1 TGTATCGATACA
34969 AAACTTATGT
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:34966 original size:32 final size:32
Alignment explanation
Indices: 34925--34987 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
34915 TAGCTAATTA
*
34925 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
34957 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
34988 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:35069 original size:21 final size:21
Alignment explanation
Indices: 35045--35101 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
35035 CATTTGTAGG
35045 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
35066 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
35087 ATGTATCGATACATT
1 ATGTATCGATACATT
35102 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:35803 original size:55 final size:55
Alignment explanation
Indices: 35719--36286 Score: 864
Period size: 55 Copynumber: 10.3 Consensus size: 55
35709 ATAAATTGTA
* * * * * *
35719 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
35774 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
35829 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
35884 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
35939 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
35994 TCCTGCTCTTTGAGGACTGGACAA--TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
36049 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
36104 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
36159 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
36214 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAACGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
36269 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
36287 AAAAAGCGGA
Statistics
Matches: 484, Mismatches: 20, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
53 2 0.00
54 6 0.01
55 464 0.96
56 10 0.02
57 2 0.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:37271 original size:1 final size:1
Alignment explanation
Indices: 37267--37320 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
37257 CTTTTCTCTC
* * * * * *
37267 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTTTCTTTCTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
37321 GAAGAGAAGG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (1 bp):
T
Found at i:37285 original size:31 final size:27
Alignment explanation
Indices: 37267--37320 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
37257 CTTTTCTCTC
* *
37267 TTTTTCTTTGTTTTGTTTTTTTGTTTT
1 TTTTTCTTTCTTTTGTTTTTTTTTTTT
37294 TTTTTCTTTCTTTT-TTTTTTTTTTTT
1 TTTTTCTTTCTTTTGTTTTTTTTTTTT
37320 T
1 T
37321 GAAGAGAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (27 bp):
TTTTTCTTTCTTTTGTTTTTTTTTTTT
Found at i:37306 original size:37 final size:35
Alignment explanation
Indices: 37252--37320 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 35
37242 TTAAGTAGGT
37252 TTTTTCTTTTCTCTCTTTTTCTTTGTTTTGTTTTTTTG
1 TTTTTCTTTTCTCTCTTTTT-TTT-TTTT-TTTTTTTG
*
37290 TTTTT-TTTTCTTTCTTTTTTTTTTTTTTTTT
1 TTTTTCTTTTCTCTCTTTTTTTTTTTTTTTTT
37321 GAAGAGAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 5 0.17
35 4 0.13
36 3 0.10
37 13 0.43
38 5 0.17
ACGTcount: A:0.00, C:0.10, G:0.04, T:0.86
Consensus pattern (35 bp):
TTTTTCTTTTCTCTCTTTTTTTTTTTTTTTTTTTG
Done.