Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2490
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: 22326
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Found at i:4317 original size:79 final size:79
Alignment explanation
Indices: 4152--4353 Score: 219
Period size: 79 Copynumber: 2.6 Consensus size: 79
4142 GATAACAACA
* * * ** * *
4152 GGGTTGGAGTGTTCCCTT-GAAAATAATGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGAT
1 GGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGAT
*
4216 TAGAAAAAAAAATCG
65 TAGAAAAAAAAACCG
*
4231 GGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATT
1 GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA-T
* ** * *
4295 TTGGGAATAAAGCCG
65 TAGAAAAAAAAACCG
* * *
4310 GGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
4354 GATGAAATAA
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
78 7 0.07
79 96 0.93
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (79 bp):
GGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGATT
AGAAAAAAAAACCG
Found at i:4348 original size:28 final size:28
Alignment explanation
Indices: 4308--4379 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
4298 GGAATAAAGC
** *
4308 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
4336 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
4364 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
4380 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:4564 original size:28 final size:27
Alignment explanation
Indices: 4524--4594 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
4514 TAAAACCGGA
**
4524 GTTGGAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
4552 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
4579 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
4595 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.62
28 15 0.38
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:4628 original size:212 final size:212
Alignment explanation
Indices: 4301--5130 Score: 1366
Period size: 212 Copynumber: 3.9 Consensus size: 212
4291 TATTTTGGGA
* * * *
4301 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
* *
4366 AGGTTGGAGTATCCTCGATTGTGAA-AAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTAT
65 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTAT
4430 CCCCAATTAAAGGAAAATTGACGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGA
130 CCCCAATTAAAGGAAAATTGACGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGA
4495 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
4513 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGG
4578 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
* *
4643 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
131 CCCAATTAAAGGAAAATTGACGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
4708 AAATTAGTGTTTTAGCG
196 AAATTAGTGTTTTAGCG
4725 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGG
*
4790 GGTTCGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
* *
4855 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
131 CCCAATTAAAGGAAAATTGACGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
**
4920 AAATTAGCATTTTAGCG
196 AAATTAGTGTTTTAGCG
*
4937 ATAAAA-CGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGG
* * *
5001 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTAGATTA
66 GGTTGGAGTATCCCCGATTGTGAAGAAATT-G-GTATTTTTGGAAATAAAATCGGAGTTGGAGTA
* * * * *
5066 TCCCCGAA-TATA-GAAAATT-AGTGTTTTGAAAATAAAATC-GGAGTTGGAATATCCTCGATTG
129 TCCCC-AATTAAAGGAAAATTGA-CGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTG
5127 TGGA
191 TGGA
5131 GAATTGATAA
Statistics
Matches: 589, Mismatches: 23, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
211 118 0.20
212 433 0.74
213 37 0.06
214 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGG
GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
CCCAATTAAAGGAAAATTGACGTTTTGAAAATAAAACCAGGATTGGAGTATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:4776 original size:28 final size:27
Alignment explanation
Indices: 4736--4806 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
4726 TAAAACCGGA
**
4736 GTTGGAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
4764 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
*
4791 GTTCGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
4807 TTGTGAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:4923 original size:52 final size:52
Alignment explanation
Indices: 4368--4960 Score: 286
Period size: 52 Copynumber: 11.3 Consensus size: 52
4358 AAATAACGAG
* * * *
4368 GTTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGG-AGTTTTGAAAATAAAACCGGA
* **
4420 GTTGGAGTATCCCCAATTAAAGG-AAAATT-GACGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGGAAAAATTGGA-GTTTTGAAAATAAAACC-GGA
* * **
4473 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGA-AAATAAAACCGGA
* ** ** * *
4524 GTTGGAGTATCCCC---T-CGGAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGGAAA-AA-----TTGGAGT-T--TTGAAAATAAAACCGGA
* * *
4579 GTTGGAGTATCCCCGATTGT-GAAGAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAA-AAATTGG-AGTTTTGAAAATAAAACCGGA
** *
4632 GTTGGAGTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGGAAAAATTGGAGTTTTGAAAATAAAACC-GGA
* * **
4685 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGA-AAATAAAACCGGA
* ** ** * *
4736 GTTGGAGTATCCCC---T-CGGAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGGAAA-AA-----TTGGAGT-T--TTGAAAATAAAACCGGA
* * * *
4791 GTTCGAGTATCCCCGATTGT-GAAGAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAA-AAATTGG-AGTTTTGAAAATAAAACCGGA
** *
4844 GTTGGAGTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGGAAAAATTGGAGTTTTGAAAATAAAACC-GGA
* **
4897 -TTGGAGTATCCCCGATTGTGGAAAAATTAGCA-TTTT-AGCGATAAAA-CGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATT-GGAGTTTTGA-AAATAAAACCGGA
4947 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
4961 TCAGAAATAA
Statistics
Matches: 411, Mismatches: 73, Indels: 115
0.69 0.12 0.19
Matches are distributed among these distances:
48 10 0.02
49 6 0.01
50 3 0.01
51 36 0.09
52 194 0.47
53 82 0.20
54 17 0.04
55 37 0.09
56 4 0.01
57 6 0.01
58 14 0.03
59 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCGGA
Found at i:5006 original size:27 final size:28
Alignment explanation
Indices: 4941--5018 Score: 106
Period size: 27 Copynumber: 2.8 Consensus size: 28
4931 TTAGCGATAA
* *
4941 AACGGAGTTGGAGTATCCCCTCA-GAAAT
1 AACGGGGTTGGAGTATCCCC-GATGAAAT
*
4969 AACGGGGTTGGAGTATCCCCGATG-ATT
1 AACGGGGTTGGAGTATCCCCGATGAAAT
4996 AACGGGGTTGGAGTATCCCCGAT
1 AACGGGGTTGGAGTATCCCCGAT
5019 TGTGAAGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 26 0.57
28 20 0.43
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (28 bp):
AACGGGGTTGGAGTATCCCCGATGAAAT
Found at i:7497 original size:20 final size:20
Alignment explanation
Indices: 7470--7524 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
7460 TAAAATTTCC
*
7470 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
7490 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
7510 AAATGTATCGATACA
1 AAATGTATCGATACA
7525 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:7568 original size:19 final size:18
Alignment explanation
Indices: 7544--7643 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
7534 CAGTAGCTAA
7544 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
7563 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
7578 -T-TGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
7595 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
7610 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
7627 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
7644 TCGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:7584 original size:13 final size:13
Alignment explanation
Indices: 7566--7622 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
7556 ACAATACTTA
7566 TGTATCGATACAT
1 TGTATCGATACAT
7579 TGTATCGATACAATACTT
1 TGTATCGATAC---A--T
7597 ATGTATCGATACAT
1 -TGTATCGATACAT
7611 TGTATCGATACA
1 TGTATCGATACA
7623 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7588 original size:32 final size:32
Alignment explanation
Indices: 7547--7641 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
7537 TAGCTAATTA
7547 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
7579 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
*
7611 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAATACTTATGTATCGATACA
7642 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (32 bp):
TGTATCGATACAATACTTATGTATCGATACAT
Found at i:12269 original size:55 final size:55
Alignment explanation
Indices: 12201--13080 Score: 1178
Period size: 55 Copynumber: 15.8 Consensus size: 55
12191 GTAAAAAGTG
* * *
12201 CACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGC
1 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGATGC
* *
12256 CACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGC
1 CACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGATGC
** *
12311 CACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGC
1 CACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTGAAAGATGC
* * *
12372 CACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAA-ATGC
1 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGATGC
*
12427 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGC
1 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGATGC
** *
12482 CACCAACTTGTGTGGGCTTTGAAAAGAAAAG-CATCTGCTCTTTGAGGACTGAAAAATGC
1 CACCAACTTGTGTGGGCTTTG-AAAG--GTGTC--CTGCTCTTTGAGGACTGAAAGATGC
* * * *
12541 CACCAACCTGTGTGGGCTTTAAAAGGTGCCCTGCTCTTTGAGGATTGGAAA-ATGC
1 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGATGC
12596 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGC
1 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGATGC
*
12651 CACCAACTTATGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGC
1 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGATGC
*
12706 CACCAACTTATGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGC
1 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-GAAAGATGC
* *
12761 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCCTGCTC-TTGGGGACTGAAAGGTGC
1 CACCAACTTGTGTGGGCTTTGAAAGGTGT-CCTGCTCTTTGAGGACTGAAAGATGC
* *
12816 CACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGC
1 CACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGATGC
12871 CACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGC
1 CACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAGATGC
* *
12926 CACCAACTT-TGGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGC
1 CACCAACTTGT-GTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGATGC
* *
12981 CACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTACTC-TTGAGGACTGAAAGGTGC
1 CACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGATGC
13035 CACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACT
1 CACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACT
13081 AAAAAGCGGA
Statistics
Matches: 756, Mismatches: 41, Indels: 56
0.89 0.05 0.07
Matches are distributed among these distances:
54 78 0.10
55 550 0.73
56 29 0.04
57 4 0.01
58 5 0.01
59 42 0.06
60 4 0.01
61 44 0.06
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (55 bp):
CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGATGC
Found at i:12308 original size:26 final size:26
Alignment explanation
Indices: 12220--12309 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
12210 GTGTGGGCTT
* *
12220 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
12246 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
12273 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
12301 TGAAAGGTG
1 TGAAAGGTG
12310 CCACCAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:12333 original size:29 final size:29
Alignment explanation
Indices: 12246--12334 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
12236 CTTTGAGGAC
12246 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
12275 T-AAGAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAA-AGGTG-CCACCAACTTGTGTGGG-CTT
12301 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
12330 TGAAA
1 TGAAA
12335 AGAAAAAGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
25 3 0.07
26 9 0.20
27 8 0.18
28 8 0.18
29 14 0.31
30 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:12646 original size:27 final size:27
Alignment explanation
Indices: 12616--12756 Score: 74
Period size: 27 Copynumber: 5.1 Consensus size: 27
12606 TGTGGGCTTT
12616 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
12643 GAAA-ATG-CCACCAACTTATGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
12671 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
12698 GAAA-ATG-CCACCAACTTATGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
12726 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
12753 GAAA
1 GAAA
12757 ATGCCACCAA
Statistics
Matches: 76, Mismatches: 28, Indels: 20
0.61 0.23 0.16
Matches are distributed among these distances:
25 6 0.08
26 10 0.13
27 24 0.32
28 20 0.26
29 10 0.13
30 6 0.08
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:14094 original size:14 final size:14
Alignment explanation
Indices: 14076--14112 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
14066 TTTGTTTGTT
*
14076 TTTTTTGTTTTTTCC
1 TTTTTT-TTTTTGCC
14091 TTTTTTTTTTTGCC
1 TTTTTTTTTTTGCC
14105 TTTTTTTT
1 TTTTTTTT
14113 GAAGAGAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTTTGCC
Found at i:14094 original size:31 final size:31
Alignment explanation
Indices: 14044--14113 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 31
14034 CTTAAGTAGG
*
14044 TTTTTTCTTTTCTCTCTTTTTCTTTGTTTG-TT
1 TTTTTTGTTTTCTCTCTTTTT-TTT-TTTGCTT
*
14076 TTTTTTGTTTTTTC-CTTTTTTTTTTTGCCTT
1 TTTTTTGTTTTCTCTCTTTTTTTTTTTG-CTT
14107 TTTTTTG
1 TTTTTTG
14114 AAGAGAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 4 0.12
30 3 0.09
31 15 0.44
32 12 0.35
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (31 bp):
TTTTTTGTTTTCTCTCTTTTTTTTTTTGCTT
Done.