Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2368
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: 123445
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1735 original size:31 final size:31
Alignment explanation
Indices: 1697--1773 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
1687 TATATTGTAC
1697 AATGTATCGATACATCTAGGTAAAATTCCCA
1 AATGTATCGATACATCTAGGTAAAATTCCCA
1728 AATGTATCGATACATCTAGGTAAAATTCCCA
1 AATGTATCGATACATCTAGGTAAAATTCCCA
1759 AATGTATCGATACAT
1 AATGTATCGATACAT
1774 GGAATAACGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (31 bp):
AATGTATCGATACATCTAGGTAAAATTCCCA
Found at i:1862 original size:13 final size:13
Alignment explanation
Indices: 1844--1868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1834 CAATCACTTG
1844 TGTATCGATACAT
1 TGTATCGATACAT
1857 TGTATCGATACA
1 TGTATCGATACA
1869 ACACTTATGT
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:1880 original size:32 final size:33
Alignment explanation
Indices: 1816--1887 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
1806 AGCTTTATAA
*
1816 CGATACATTGTATCGATACAATCACTTGTGTAT
1 CGATACATTGTATCGATACAATCACTTATGTAT
1849 CGATACATTGTATCGATACAA-CACTTATGTAT
1 CGATACATTGTATCGATACAATCACTTATGTAT
1881 CGATACA
1 CGATACA
1888 AATCGCTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 17 0.45
33 21 0.55
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (33 bp):
CGATACATTGTATCGATACAATCACTTATGTAT
Found at i:1881 original size:19 final size:18
Alignment explanation
Indices: 1823--1888 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
1813 TAACGATACA
1823 TTGTATCGATACAATCACT
1 TTGTATCGATACAA-CACT
1842 TGTGTATCGAT---ACA--
1 T-TGTATCGATACAACACT
1856 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
1874 TATGTATCGATACAA
1 T-TGTATCGATACAA
1889 ATCGCTGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
16 5 0.12
17 1 0.03
18 1 0.03
19 14 0.35
20 9 0.22
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (18 bp):
TTGTATCGATACAACACT
Found at i:1950 original size:21 final size:21
Alignment explanation
Indices: 1924--2000 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
1914 GTTGGGACCT
* *
1924 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
*
1945 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
*
1966 TATATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
1987 TGTATCGATACATT
1 TGTATCGATACATT
2001 TGGATAAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:2782 original size:26 final size:26
Alignment explanation
Indices: 2753--2839 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
2743 TGTGGGCTTC
2753 GAAAGGCGTCCTGCTCTTTGAGGACT
1 GAAAGGCGTCCTGCTCTTTGAGGACT
* ** * * *
2779 GAAAGGTGCTACCAACT-TGTGTGGGCTTT
1 GAAAGGCG-T-CCTGCTCTTTGAGGAC--T
*
2808 GAAAGGCGTCCTGCTCTTTGAGGATT
1 GAAAGGCGTCCTGCTCTTTGAGGACT
2834 GAAAGG
1 GAAAGG
2840 TGCCACCAAC
Statistics
Matches: 43, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
26 14 0.33
27 11 0.26
28 10 0.23
29 8 0.19
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (26 bp):
GAAAGGCGTCCTGCTCTTTGAGGACT
Found at i:2795 original size:55 final size:55
Alignment explanation
Indices: 2706--3617 Score: 1018
Period size: 55 Copynumber: 16.0 Consensus size: 55
2696 ATAAAGTGTA
* * * *
2706 TCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTCGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
2761 TCCTGCTCTTTGAGGACTGAAAGGTGCTACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
2816 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
2871 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
2926 TCCTGCTCTTTGGGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG------GCG
* *
2988 TCCTGCTCTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
3043 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
3098 TCCTGCTCCTTGGGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
3159 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
3214 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
3269 TCCTGCTCCTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* *
3330 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
3385 TCCTGCTCTTTGAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCG
* *
3446 TCCTGCTCTTTGAAGACTG-AAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* * *
3505 TCCTGCTCTTTGGGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
*
3566 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG
3618 AACAGGCATC
Statistics
Matches: 750, Mismatches: 59, Indels: 97
0.83 0.07 0.11
Matches are distributed among these distances:
54 14 0.02
55 406 0.54
56 36 0.05
59 35 0.05
60 81 0.11
61 130 0.17
62 48 0.06
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:3265 original size:171 final size:171
Alignment explanation
Indices: 2706--3617 Score: 1276
Period size: 171 Copynumber: 5.3 Consensus size: 171
2696 ATAAAGTGTA
* * * *
2706 TCCTACTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTCGAAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
* * *
2770 TTGAGGACTGAAAGGTGCTACCAACTTGTGTGGGCTTTG-AAAG-----GCGTCCTGCTCTTTGA
65 TTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGA
* *
2829 GGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
130 GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
2871 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
* * *
2936 TGGGGACTGAAAA-GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAAGCATCCTGCTCTTTA
66 TGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAAGCATCCTGCTCTTTG
*
3000 AGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
129 AGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
*
3043 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
3108 TGGGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
66 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
3173 GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
131 GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
*
3214 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
3279 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
66 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
* *
3344 GACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGCA
131 GACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGCG
*
3385 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGTGTCCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAGGTGTCCT
* * * * *
3450 GCTCTTTGAAGACT-GAAGGTGCCACTAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCTGCTC
60 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTC
* * * *
3513 TTTGGGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
125 TTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT---AAG---AGGCG
** *
3566 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
3618 AACAGGCATC
Statistics
Matches: 689, Mismatches: 34, Indels: 39
0.90 0.04 0.05
Matches are distributed among these distances:
165 86 0.12
166 11 0.02
171 270 0.39
172 162 0.24
174 4 0.01
175 57 0.08
176 28 0.04
177 24 0.03
180 26 0.04
181 21 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (171 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGCG
Found at i:3380 original size:28 final size:28
Alignment explanation
Indices: 3349--3435 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
3339 TTGAGGACTA
3349 GAAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAATGCCACCAACTTGTGTGGGCTTT
* ** * *
3377 G-AAA-GGCATCCTGCTCT-T-TGAGGATTG
1 GAAAATGCCA-CCAACT-TGTGTG-GGCTTT
3404 GAAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAATGCCACCAACTTGTGTGGGCTTT
3432 GAAA
1 GAAA
3436 GGAGAAGGTG
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
26 5 0.12
27 14 0.33
28 18 0.43
29 5 0.12
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (28 bp):
GAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:4623 original size:1 final size:1
Alignment explanation
Indices: 4607--4692 Score: 64
Period size: 1 Copynumber: 86.0 Consensus size: 1
4597 TAGATTCTTC
* * * * * * * * *
4607 TTTTTTCTTTTCTTTTTCTTTTGTTTTGTTTTTTGTTTTTTTTGTTTTTTTTTGTTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* **
4672 GTTTTTTTTTGGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
4693 AAAAGAATAT
Statistics
Matches: 63, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:4639 original size:22 final size:19
Alignment explanation
Indices: 4608--4681 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 19
4598 AGATTCTTCT
4608 TTTTTCTTTTCTTTTTCTTTTG
1 TTTTT-TTTT-TTTTT-TTTTG
4630 TTTTGTTTTTTGTTTTTTTTG
1 TTTT-TTTTTT-TTTTTTTTG
*
4651 TTTTTTTTTGTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTG
4670 TTGTTTTTTTTT
1 TT-TTTTTTTTT
4682 GGTTTTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 11 0.23
20 13 0.28
21 10 0.21
22 12 0.26
23 1 0.02
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.86
Consensus pattern (19 bp):
TTTTTTTTTTTTTTTTTTG
Found at i:4648 original size:10 final size:10
Alignment explanation
Indices: 4608--4692 Score: 91
Period size: 11 Copynumber: 7.9 Consensus size: 10
4598 AGATTCTTCT
*
4608 TTTTTCTTTTC
1 TTTTT-TTTTG
4619 TTTTTCTTTTG
1 TTTTT-TTTTG
4630 TTTTGTTTTT-
1 TTTT-TTTTTG
4640 TGTTTTTTTTG
1 T-TTTTTTTTG
4651 TTTTTTTTTG
1 TTTTTTTTTG
4661 TTTTTTTTGTTG
1 -TTTTTTT-TTG
4673 TTTTTTTTTGG
1 TTTTTTTTT-G
4684 TTTTTTTTT
1 TTTTTTTTT
4693 AAAAGAATAT
Statistics
Matches: 67, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
10 17 0.25
11 46 0.69
12 4 0.06
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:4687 original size:19 final size:17
Alignment explanation
Indices: 4619--4692 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
4609 TTTTCTTTTC
*
4619 TTTTTCTTTTGTTTTGT
1 TTTTTTTTTTGTTTTGT
*
4636 TTTTTGTTTT-TTTTGTT
1 TTTTTTTTTTGTTTTG-T
*
4653 TTTTTTTGTTTTTTTTGT
1 TTTTTTT-TTTGTTTTGT
4671 TGTTTTTTTTTGGTTTT-T
1 T-TTTTTTTTT-GTTTTGT
4689 TTTT
1 TTTT
4693 AAAAGAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
16 5 0.10
17 19 0.39
18 10 0.20
19 15 0.31
ACGTcount: A:0.00, C:0.01, G:0.12, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTGTTTTGT
Found at i:17218 original size:27 final size:27
Alignment explanation
Indices: 17157--17233 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
17147 ATAAAGCCGG
* *
17157 GGGTTGGAGTATCCCCTCGA-AAATAACG
1 GGGTTGGAGTAT-CCC-CGATGAATAACA
*
17185 GGGTTGGAGTATCCCCGATGATTAACA
1 GGGTTGGAGTATCCCCGATGAATAACA
17212 GGGTTGGAGTATCCCCGATGAA
1 GGGTTGGAGTATCCCCGATGAA
17234 AAATTGATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 3 0.07
27 29 0.66
28 12 0.27
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGATGAATAACA
Found at i:17284 original size:103 final size:104
Alignment explanation
Indices: 17072--17333 Score: 350
Period size: 103 Copynumber: 2.5 Consensus size: 104
17062 TTGGAGATAG
* * *
17072 TAACGGGGTTGGAGTATCCCCTTGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCA
1 TAACGGGGTTGGAGTATCCCC--GATGATTAACGGGGTTGGAGTATCCCCG---ATGAAAAATCA
* *
17136 ATATTTTAGGAATAAAGCCGGGGGTTGGAGTATCCCCTCGAAAA
61 ATATTTTAGAAATAAAACCGGGGGTTGGAGTATCCCCTCGAAAA
* ** *
17180 TAACGGGGTTGGAGTATCCCCGATGATTAACAGGGTTGGAGTATCCCCGATGAAAAATTGATGTT
1 TAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATGAAAAATCAATATT
* *
17245 TTAGAAATAAAACC-GGGGTTGGAGTGTTCCCTC-AGAAA
66 TTAGAAATAAAACCGGGGGTTGGAGTATCCCCTCGA-AAA
17283 TAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGAT
1 TAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGAT
17334 TGTGAAAATT
Statistics
Matches: 140, Mismatches: 12, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
102 1 0.01
103 70 0.50
104 24 0.17
106 2 0.01
107 22 0.16
108 21 0.15
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (104 bp):
TAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATGAAAAATCAATATT
TTAGAAATAAAACCGGGGGTTGGAGTATCCCCTCGAAAA
Found at i:17423 original size:51 final size:52
Alignment explanation
Indices: 17317--17438 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 52
17307 GATTAACGGG
* * * *
17317 GTTGGAGTATCCCCGATTGTGAAAATTTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAATTT-GAGTATTTTGAAAATAAAATCGGA
*
17370 GTTGGAGTATCCCCGATTATAGAAAA-TT-AGTATTTTGAAAATAAAATCTGA
1 GTTGGAGTATCCCCGATTAT-GAAAATTTGAGTATTTTGAAAATAAAATCGGA
*
17421 GTT-GAGATATCCTCGATT
1 GTTGGAG-TATCCCCGATT
17439 GCTGAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
50 3 0.05
51 32 0.52
53 21 0.34
54 5 0.08
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAAATTTGAGTATTTTGAAAATAAAATCGGA
Found at i:21385 original size:5 final size:5
Alignment explanation
Indices: 21377--21401 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
21367 TTAATTTGAA
21377 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
21402 TTAAATAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:30987 original size:2 final size:2
Alignment explanation
Indices: 30982--31011 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30972 ATTTTTTTCT
30982 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31012 CATGCACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33442 original size:20 final size:20
Alignment explanation
Indices: 33417--33480 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
33407 GATCAATTTT
33417 AAAATATTTCAAAAATTTGG
1 AAAATATTTCAAAAATTTGG
** *
33437 AAAATATTTC-ATGATTATGA
1 AAAATATTTCAAAAATT-TGG
* *
33457 AAAATATTTGAAAAATATGG
1 AAAATATTTCAAAAATTTGG
33477 AAAA
1 AAAA
33481 ATCATCTAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 4 0.12
20 27 0.79
21 3 0.09
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (20 bp):
AAAATATTTCAAAAATTTGG
Found at i:35941 original size:28 final size:28
Alignment explanation
Indices: 35852--37252 Score: 1499
Period size: 28 Copynumber: 48.8 Consensus size: 28
35842 CTAACTTGTA
* *
35852 TGGGCTTTGAAAAGAGTTGACACCGACTTGTG
1 TGGGCTTTGAAAAGA--TGCCACTGAC-T-TG
* *
35884 TGGGCTTTGAAAGGGTATGCCATTGACTTG
1 TGGGCTTTGAAA-AG-ATGCCACTGACTTG
* * * *
35914 TGGGTTTTGAAATGGTGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
35942 TGGGCTTTGAAAAGATGCCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* * *
35970 TCGACTTTGAAAAAATGCCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
*
35998 TAGGCTTTGAAAAGATGCCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36026 TCGGCTTTGAAAAAATGCCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36054 TAGGCTTTGAAAAGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
** * *
36082 CAGGCTTTGAAATGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36110 TGGGCTTT-AAAAGGATGCAACTAACTTG
1 TGGGCTTTGAAAA-GATGCCACTGACTTG
*
36138 TGAGCTTTGAAAAGATGCCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36166 TGGGCTTGGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
*
36194 TGGGCTTTGAAATA-ATGCCACTGATTTG
1 TGGGCTTTGAAA-AGATGCCACTGACTTG
* *
36222 TGGGCTTTGAAATGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
*
36250 TGGGCTTT-AAAAGGATGCCACTAACTTG
1 TGGGCTTTGAAAA-GATGCCACTGACTTG
* *
36278 TGGACTTTGAAAAGAGTTGCCACCGACTTGTG
1 TGGGCTTTGAAAAGA--TGCCACTGAC-T-TG
* *
36310 TGGGCTTTGAAAAGATGCTACTGACTTA
1 TGGGCTTTGAAAAGATGCCACTGACTTG
*
36338 TGGGCTTTGAAAATATGCCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36366 TGGGCTTTGAAATGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36394 TGGGCTTTGAAAGGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36422 TGGGCTTTGAAAGGATGCCATTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36450 TGGGCTTTGAAAGGATGCCATTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* * *
36478 TGGGATTTAAAAAGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
*
36506 TGGGCTTTGAAAAGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* **
36534 TGGGCTTTGAAATGAGTTGCCACCAACTTG
1 TGGGCTTTGAAA--AGATGCCACTGACTTG
**
36564 TGTGGACTTTGAAAAGAGTTGCCACCAACTTG
1 TG-GG-CTTTGAAAAGA--TGCCACTGACTTG
*
36596 TGTAGACTTTGAAAAGATGCCACTGACTTG
1 TG--GGCTTTGAAAAGATGCCACTGACTTG
36626 T-GGCTTT-AAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAA-GATGCCACTGACTTG
*
36653 GGGGCTTT-AAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAA-GATGCCACTGACTTG
* *
36681 TGGGCTTTGAAATGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
*
36709 TGGGCTTTGAAAAGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* * *
36737 TGGGCTTTGAAATGATGCCACTAACTTA
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36765 TGGGCTTTGAAAGGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* **
36793 CGAACTTTGAAAAGAGTTGCCA-TCGACTTGTG
1 TGGGCTTTGAAAAGA--TGCCACT-GAC-T-TG
36825 TGGGCTTTGAAAAGATGCCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* * *
36853 TGGACTTTGAAAAGATGCCATTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36881 CGGGCTTT-AAAAGAATGTCACTGACTTG
1 TGGGCTTTGAAAAG-ATGCCACTGACTTG
* *
36909 CGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* *
36937 TGGGCATTGAAAAGATGTCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* **
36965 TGGGCTTTGAAATGAATTGCCACCAACTTG
1 TGGGCTTTGAAAAG-A-TGCCACTGACTTG
*
36995 TGTGGACTTTGAAAAGAGTTGCCACCGACTTG
1 TG-GG-CTTTGAAAAGA--TGCCACTGACTTG
*
37027 TGTAGACTTTGAAAAGATGCCACTGACTTG
1 TG--GGCTTTGAAAAGATGCCACTGACTTG
* * *
37057 TGGGTTTTGAAATGATGCCACTAACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
*
37085 TGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGATGCCACTGACTTG
* **
37113 TGGGCTTTGAAATGAGTTGCCACCAACTTG
1 TGGGCTTTGAAA--AGATGCCACTGACTTG
37143 TGTGGACTTTGAAAAGAGTGCCA-TGACTTG
1 TG-GG-CTTTGAAAAGA-TGCCACTGACTTG
* * *
37173 TGGGCTTTGAAAGGAGTGCCACTAACTTA
1 TGGGCTTTGAAAAGA-TGCCACTGACTTG
37202 TGGGCTTT-AAAAGGGAATGCCACTGACTTG
1 TGGGCTTTGAAAA--G-ATGCCACTGACTTG
* **
37232 TGGACTTAAAAAAGATGCCAC
1 TGGGCTTTGAAAAGATGCCAC
37253 AAAGTTGTGG
Statistics
Matches: 1186, Mismatches: 137, Indels: 96
0.84 0.10 0.07
Matches are distributed among these distances:
26 4 0.00
27 31 0.03
28 823 0.69
29 36 0.03
30 141 0.12
31 21 0.02
32 126 0.11
33 3 0.00
34 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (28 bp):
TGGGCTTTGAAAAGATGCCACTGACTTG
Found at i:37260 original size:28 final size:27
Alignment explanation
Indices: 37219--37604 Score: 382
Period size: 28 Copynumber: 14.0 Consensus size: 27
37209 TAAAAGGGAA
* * *
37219 TGCCACTGACTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGACTT-AAAAAGG
** *
37247 TGCCACAAAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAAGG
37274 TGCCATC-GAGTTGTGGACTTTAAAAAGG
1 TGCCA-CGGAGTTGTGGAC-TTAAAAAGG
* * *
37302 TGCCACGAAGTTATGGACTTTAAAAGTG
1 TGCCACGGAGTTGTGGACTTAAAAAG-G
*
37330 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAAGG
** * *
37358 TGCCACAAAGTTGTGAACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAAGG
* * **
37386 TGCCATGGTGTTGTAAACTTTAAAAAGG
1 TGCCACGGAGTTGTGGAC-TTAAAAAGG
* *
37414 TACCACGGAGTTGTGGACTT-AAAAGCA
1 TGCCACGGAGTTGTGGACTTAAAAAG-G
**
37441 TGCCACAAAGTTGTGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAAGG
** *
37468 TGCCACTAAGTTGTGGACTTAAAACGGG
1 TGCCACGGAGTTGTGGACTTAAAA-AGG
* *
37496 TGCCACAGAGTTGTGAACTTAAAAAAGG
1 TGCCACGGAGTTGTGGACTT-AAAAAGG
*
37524 TGCCACTGAGTTGTGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAAGG
37551 TGCCACGGAGTTGTGGACTT-AAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAAGG
* *
37577 ATGCCACCGAGTTATGGACTTAAAAAGG
1 -TGCCACGGAGTTGTGGACTTAAAAAGG
37605 AATGTCATTG
Statistics
Matches: 303, Mismatches: 44, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
26 11 0.04
27 114 0.38
28 168 0.55
29 10 0.03
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.25
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAAGG
Found at i:37325 original size:56 final size:56
Alignment explanation
Indices: 37143--37604 Score: 424
Period size: 56 Copynumber: 8.3 Consensus size: 56
37133 CACCAACTTG
* * * * * * * *
37143 TGTGGACTTTGAAAAGAGTGCCA-TGACTTGTGGGCTTTGAAAGGAGTGCCACTAACT
1 TGTGGACTTT-AAAAGGGTGCCACAGAGTTGTGGACTTTAAAAAG-GTGCCACGAAGT
* * * * * * *
37200 TATGGGCTTTAAAAGGGAATGCCACTGACTTGTGGACTTAAAAAAGATGCCACAAAGT
1 TGTGGACTTTAAAAGGG--TGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
37258 TGTGGAC-TTAAAAGGGTGCCATC-GAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
1 TGTGGACTTTAAAAGGGTGCCA-CAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
* * * * *
37313 TATGGACTTTAAAAGTGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAAAGT
1 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
* ** * ** * *
37369 TGTGAACTTTAAAAGGGTGCCATGGTGTTGTAAACTTTAAAAAGGTACCACGGAGT
1 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
** * *
37425 TGTGGAC-TTAAAAGCATGCCACAAAGTTGTGGAC-TTAAAAAGGTGCCACTAAGT
1 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
* *
37479 TGTGGAC-TTAAAACGGGTGCCACAGAGTTGTGAACTTAAAAAAGGTGCCACTG-AGT
1 TGTGGACTTTAAAA-GGGTGCCACAGAGTTGTGGACTTTAAAAAGGTGCCAC-GAAGT
* *
37535 TGTGGAC-TTAAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGATGCCACCG-AGT
1 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAAGG-TGCCA-CGAAGT
* *
37589 TATGGACTTAAAAAGG
1 TGTGGACTTTAAAAGG
37605 AATGTCATTG
Statistics
Matches: 337, Mismatches: 56, Indels: 26
0.80 0.13 0.06
Matches are distributed among these distances:
53 6 0.02
54 46 0.14
55 101 0.30
56 131 0.39
57 17 0.05
58 19 0.06
59 17 0.05
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (56 bp):
TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAAGGTGCCACGAAGT
Found at i:37626 original size:83 final size:79
Alignment explanation
Indices: 37219--37601 Score: 354
Period size: 83 Copynumber: 4.6 Consensus size: 79
37209 TAAAAGGGAA
* * * * * *
37219 TGCCACTGACTTGTGGACTTAAAAAAGATGCCACAAAGTTGTGGACTTAAAAGGGTGCCATCGAG
1 TGCCACGGAGTTGTGGACTT--AAAAGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCA-CGAA
37284 TTGTGGACTTTAAAAAGG
63 TTGTGGAC-TTAAAAAGG
* * * * *
37302 TGCCACGAAGTTATGGACTTTAAAAGTGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAAA
1 TGCCACGGAGTTGTGGAC-TTAAAAG-GTGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACGAA
* *
37367 GTTGTGAACTTTAAAAGGG
63 -TTGTGGAC-TTAAAAAGG
* * ** * * * *
37386 TGCCATGGTGTTGTAAACTTTAAAAAGGTACCACGGAGTTGTGGACTTAAAAGCATGCCACAAAG
1 TGCCACGGAGTTGTGGAC-TT-AAAAGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGAA-
37451 TTGTGGACTTAAAAAGG
63 TTGTGGACTTAAAAAGG
** *
37468 TGCCACTAAGTTGTGGACTTAAAACGGGTGCCACAGAGTTGTGAACTTAAAAAAGG-TGCCACTG
1 TGCCACGGAGTTGTGGACTTAAAA--GGTGCCACAGAGTTGTGGACTT--AAAAGGATGCCAC-G
*
37532 AGTTGTGGACTTAAAAAGG
61 AATTGTGGACTTAAAAAGG
* *
37551 TGCCACGGAGTTGTGGACTTAAAAGGATGCCACCGAGTTATGGACTTAAAA
1 TGCCACGGAGTTGTGGACTTAAAAGG-TGCCACAGAGTTGTGGACTTAAAA
37602 AGGAATGTCA
Statistics
Matches: 250, Mismatches: 39, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
80 8 0.03
81 4 0.02
82 61 0.24
83 101 0.40
84 71 0.28
85 5 0.02
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.25
Consensus pattern (79 bp):
TGCCACGGAGTTGTGGACTTAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGAATTG
TGGACTTAAAAAGG
Found at i:49207 original size:76 final size:76
Alignment explanation
Indices: 49071--49300 Score: 243
Period size: 76 Copynumber: 3.0 Consensus size: 76
49061 TATTAGTTTG
* * * * * *
49071 TTCTTCAGCTCACTATCAATTTGTTTTGATCATTAATGGAAAATTTTAGGAACTACATATTCCCC
1 TTCTTCAGCTCATTATTAGTTTGTTTTGCT-ATTAATGGGAAATTTTAGAAAC-ACATATTCCCC
49136 ATCATGTT-TT-T
64 ATCATGTTCTTCT
* *
49147 TTCTTCAGCTCATTATTAGTTTGTTTATGCTATTAATGGGAAATTTTAGAAATCATATATTCCCT
1 TTCTTCAGCTCATTATTAGTTTGTTT-TGCTATTAATGGGAAATTTTAGAAA-CACATATTCCCC
49212 ATCATGTTCTTCT
64 ATCATGTTCTTCT
* * * **
49225 AT-TTCAGCTTATTATTAGTTTATTTTGACTATTAATGGGAAATTGCA-AAACCACATATTCCCC
1 TTCTTCAGCTCATTATTAGTTTGTTTTG-CTATTAATGGGAAATTTTAGAAA-CACATATTCCCC
* *
49288 ATCGTGATCTTCT
64 ATCATGTTCTTCT
49301 ACTTTAACCT
Statistics
Matches: 131, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
76 85 0.65
77 44 0.34
78 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.44
Consensus pattern (76 bp):
TTCTTCAGCTCATTATTAGTTTGTTTTGCTATTAATGGGAAATTTTAGAAACACATATTCCCCAT
CATGTTCTTCT
Found at i:49356 original size:75 final size:76
Alignment explanation
Indices: 49273--49450 Score: 207
Period size: 75 Copynumber: 2.3 Consensus size: 76
49263 GAAATTGCAA
* * * * *
49273 AACCACATATTCCCCATCGTGATCTTCTACTTTAACCTGTTATTA-ATTATTTCAACTATTGATG
1 AACCACATATTCCCCATCATGATCTTCTACTTCAACCTGTCATCAGATTATTTCAACCATTGATG
49337 GAAGATTACAG
66 GAAGATTACAG
* * *
49348 AACCACATATTCCCCATCATGATCTTCTACTTCAACTTGTCATCAGTTTGTTTCAACCATTGATG
1 AACCACATATTCCCCATCATGATCTTCTACTTCAACCTGTCATCAGATTATTTCAACCATTGATG
* *
49413 GAAAATGA-AG
66 GAAGATTACAG
* * *
49423 AAACTACATATTTCCCAATCATGTTCTT
1 -AACCACATA-TTCCCCATCATGATCTT
49451 AGTTTTTAGC
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
75 42 0.48
76 30 0.34
77 15 0.17
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (76 bp):
AACCACATATTCCCCATCATGATCTTCTACTTCAACCTGTCATCAGATTATTTCAACCATTGATG
GAAGATTACAG
Found at i:50506 original size:13 final size:13
Alignment explanation
Indices: 50488--50513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50478 ACATACAAGA
50488 TGTATCGATACAT
1 TGTATCGATACAT
50501 TGTATCGATACAT
1 TGTATCGATACAT
50514 GACCAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:50509 original size:32 final size:33
Alignment explanation
Indices: 50468--50535 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
50458 CCTTAACTGT
50468 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1 TTGTATCGATACATGACCAA-ATGTATCGATACA
*
50500 TTGTATCGATACATGACCAAATGTATTGATACA
1 TTGTATCGATACATGACCAAATGTATCGATACA
50533 TTG
1 TTG
50536 GCTTGTAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCGATACA
Found at i:52742 original size:36 final size:36
Alignment explanation
Indices: 52702--52775 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
52692 AGAGGAAAAA
52702 GAAAAATTTGAAAAGAAAATAAATGAATTACAAGTT
1 GAAAAATTTGAAAAGAAAATAAATGAATTACAAGTT
52738 GAAAAATTTGAAAAGAAAATAAATGAATTACAAGTT
1 GAAAAATTTGAAAAGAAAATAAATGAATTACAAGTT
52774 GA
1 GA
52776 TGTTAAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.58, C:0.03, G:0.15, T:0.24
Consensus pattern (36 bp):
GAAAAATTTGAAAAGAAAATAAATGAATTACAAGTT
Found at i:57724 original size:18 final size:17
Alignment explanation
Indices: 57697--57730 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
57687 CAAAAAAGGC
*
57697 TCGATTCCTCGAAACAT
1 TCGATTCCTCAAAACAT
57714 TCGAGTTCCTCAAAACA
1 TCGA-TTCCTCAAAACA
57731 AAGCCACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (17 bp):
TCGATTCCTCAAAACAT
Found at i:59317 original size:13 final size:13
Alignment explanation
Indices: 59299--59324 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59289 ACATACAAGA
59299 TGTATCGATACAT
1 TGTATCGATACAT
59312 TGTATCGATACAT
1 TGTATCGATACAT
59325 GACCAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:59340 original size:33 final size:32
Alignment explanation
Indices: 59279--59346 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
59269 CCTTAACTGT
59279 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
59311 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
59344 TTG
1 TTG
59347 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 17 0.50
34 3 0.09
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:61506 original size:28 final size:28
Alignment explanation
Indices: 61474--61593 Score: 102
Period size: 28 Copynumber: 4.3 Consensus size: 28
61464 GCCAAAGCTT
*
61474 AATTAAAAATTCTATATATAAAAAATCC
1 AATTAAAAATTCTATATATAAAAAGTCC
* * **
61502 AATTAAAAATTTTACA-AGTAAAAAGTTT
1 AATTAAAAATTCTATATA-TAAAAAGTCC
* * * **
61530 AATTGAAAATTTTATATCTAAAAAGTGT
1 AATTAAAAATTCTATATATAAAAAGTCC
*
61558 GATTAAAAATTC--TATATAAAAAGTCC
1 AATTAAAAATTCTATATATAAAAAGTCC
61584 AATTGAAAAA
1 AATT-AAAAA
61594 AAAAATAATT
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
26 14 0.19
27 6 0.08
28 53 0.73
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (28 bp):
AATTAAAAATTCTATATATAAAAAGTCC
Found at i:61790 original size:29 final size:29
Alignment explanation
Indices: 61756--61814 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
61746 AAAAAAAATC
61756 TAATTTAATCCCTATTAAAAATGGACTTT
1 TAATTTAATCCCTATTAAAAATGGACTTT
* *
61785 TAATTTAATCTCTATTAAAAGTGGACTTT
1 TAATTTAATCCCTATTAAAAATGGACTTT
61814 T
1 T
61815 CCAACTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (29 bp):
TAATTTAATCCCTATTAAAAATGGACTTT
Found at i:62008 original size:20 final size:19
Alignment explanation
Indices: 61963--62015 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
61953 TTGACTTAAT
*
61963 TTGATCAAAGTTGACCATG
1 TTGATCAAATTTGACCATG
*
61982 TTCGATCAAATTTGACCTTG
1 TT-GATCAAATTTGACCATG
*
62002 ATTGATCAAGTTTG
1 -TTGATCAAATTTG
62016 TCTGACTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (19 bp):
TTGATCAAATTTGACCATG
Found at i:64062 original size:17 final size:17
Alignment explanation
Indices: 64010--64066 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
64000 ATTAAAAATT
64010 AAATTATATTTATATTA
1 AAATTATATTTATATTA
* *
64027 AAATAATAAAATATATATTA
1 AAAT--T-ATATTTATATTA
64047 AAATTATATTTATATTA
1 AAATTATATTTATATTA
64064 AAA
1 AAA
64067 AATAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 17 0.52
18 1 0.03
19 1 0.03
20 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTATATTTATATTA
Found at i:64077 original size:20 final size:20
Alignment explanation
Indices: 64015--64089 Score: 79
Period size: 19 Copynumber: 4.0 Consensus size: 20
64005 AAATTAAATT
64015 ATATTTATATTAAAATAATAA
1 ATATTTATATTAAAA-AATAA
* *
64036 A-ATATATATT--AAAAT-T
1 ATATTTATATTAAAAAATAA
64052 ATATTTATATTAAAAAATAA
1 ATATTTATATTAAAAAATAA
*
64072 ATATTT-TTTTAAAAAATA
1 ATATTTATATTAAAAAATA
64090 GAGAGGTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.02
17 11 0.24
18 2 0.04
19 16 0.36
20 14 0.31
21 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTTATATTAAAAAATAA
Found at i:65187 original size:18 final size:18
Alignment explanation
Indices: 65164--65200 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
65154 ATAAATTTAA
65164 ATTAAAAAAATATTAAAT
1 ATTAAAAAAATATTAAAT
65182 ATTAAAAAAATATTAAAT
1 ATTAAAAAAATATTAAAT
65200 A
1 A
65201 AATAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTAAAAAAATATTAAAT
Found at i:65210 original size:18 final size:17
Alignment explanation
Indices: 65154--65212 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
65144 AGTTGAATCG
*
65154 ATAAAT-TTAAATTAAA
1 ATAAATATTAAATAAAA
65170 A-AAATATTAAATATTAAA
1 ATAAATATTAAATA--AAA
65188 A-AAATATTAAATAAATA
1 ATAAATATTAAATAAA-A
65205 ATAAATAT
1 ATAAATAT
65213 AATTAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
15 4 0.11
16 9 0.24
17 2 0.05
18 22 0.59
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAAATATTAAATAAAA
Found at i:65219 original size:13 final size:11
Alignment explanation
Indices: 65177--65231 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
65167 AAAAAAATAT
*
65177 TAAATATTAAA
1 TAAATAATAAA
* *
65188 AAAATATTAAA
1 TAAATAATAAA
65199 TAAATAATAAA
1 TAAATAATAAA
*
65210 T--ATAATTAA
1 TAAATAATAAA
*
65219 TAATTAATAAA
1 TAAATAATAAA
65230 TA
1 TA
65232 TATTATTTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 8 0.22
11 28 0.78
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:67461 original size:21 final size:22
Alignment explanation
Indices: 67430--67471 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
67420 ACTTACATGA
67430 TTAATATAATT-ATATTATTAAT
1 TTAATATAATTAATA-TATTAAT
67452 TTAA-ATAATTAATATATTAA
1 TTAATATAATTAATATATTAA
67472 AATATTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATATAATTAATATATTAAT
Found at i:68690 original size:3 final size:3
Alignment explanation
Indices: 68682--68719 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
68672 ACTCATACTT
*
68682 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
68720 CTGATTCCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:69102 original size:2 final size:2
Alignment explanation
Indices: 69095--69124 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
69085 CCTTTTCATA
69095 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
69125 AGCGCCTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:79559 original size:13 final size:13
Alignment explanation
Indices: 79527--79560 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
79517 CGACATGTTA
*
79527 TTAAACATCCAAC
1 TTAAACCTCCAAC
79540 TTAAACCTCCAAC
1 TTAAACCTCCAAC
79553 TTAAACCT
1 TTAAACCT
79561 AATTGGCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.26
Consensus pattern (13 bp):
TTAAACCTCCAAC
Found at i:81561 original size:20 final size:20
Alignment explanation
Indices: 81533--81607 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
81523 TTTTACCTAG
81533 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
81553 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
81573 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
81593 ATGTATCGATACATT
1 ATGTATCGATACATT
81608 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:81593 original size:40 final size:39
Alignment explanation
Indices: 81533--81610 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
81523 TTTTACCTAG
*
81533 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
81573 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
81611 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:82577 original size:13 final size:13
Alignment explanation
Indices: 82559--82584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
82549 TACACCTAGT
82559 ATGTATCGATACA
1 ATGTATCGATACA
82572 ATGTATCGATACA
1 ATGTATCGATACA
82585 TCAAAAAAAT
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:84229 original size:12 final size:12
Alignment explanation
Indices: 84197--84230 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
84187 AACCATCAAG
*
84197 GATGAAGAAGAT
1 GATGAAGATGAT
*
84209 GATGAAGATGTT
1 GATGAAGATGAT
84221 GATGAAGATG
1 GATGAAGATG
84231 GTGACTCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:88750 original size:13 final size:13
Alignment explanation
Indices: 88732--88770 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
88722 ACATCTTTCT
*
88732 TTGTATTGATACA
1 TTGTATCGATACA
*
88745 TTGTATCGATATA
1 TTGTATCGATACA
*
88758 CTGTATCGATACA
1 TTGTATCGATACA
88771 GGGGGTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:88916 original size:21 final size:19
Alignment explanation
Indices: 88892--88943 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
88882 AAATATTTTG
88892 CAAAATACTTGTTTTTCACT
1 CAAAATACTTGTTTTTCA-T
* *
88912 ACAAATTACATCGTTTTTCAT
1 -CAAAATAC-TTGTTTTTCAT
88933 CAAAATCACTT
1 CAAAAT-ACTT
88944 TTAAAAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
20 6 0.24
21 10 0.40
22 9 0.36
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (19 bp):
CAAAATACTTGTTTTTCAT
Found at i:89063 original size:13 final size:13
Alignment explanation
Indices: 89045--89069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89035 TTAGAAAGTG
89045 TTTTTGAACCAAA
1 TTTTTGAACCAAA
89058 TTTTTGAACCAA
1 TTTTTGAACCAA
89070 TCCTTTCCCA
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTTTGAACCAAA
Found at i:91364 original size:13 final size:13
Alignment explanation
Indices: 91346--91371 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
91336 TACACCAAGT
91346 ATGTATCGATACA
1 ATGTATCGATACA
91359 ATGTATCGATACA
1 ATGTATCGATACA
91372 TCAGAAAAAT
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:92208 original size:139 final size:139
Alignment explanation
Indices: 91958--92236 Score: 540
Period size: 139 Copynumber: 2.0 Consensus size: 139
91948 CTCGACAAGG
*
91958 AAGTGTCGAGGAGAGAGGATGTAGGTGCCGTGTTTGGACCGAACCTCTACAAATATCTTGTGTCA
1 AAGTGTCAAGGAGAGAGGATGTAGGTGCCGTGTTTGGACCGAACCTCTACAAATATCTTGTGTCA
92023 AGTTTTCCTTCCCTAATCTCTTTTCATTCCGAATTGTTTTGTTTCAAATTTGTACAAAACCCGAA
66 AGTTTTCCTTCCCTAATCTCTTTTCATTCCGAATTGTTTTGTTTCAAATTTGTACAAAACCCGAA
*
92088 AATTTGAAA
131 AATTCGAAA
92097 AAGTGTCAAGGAGAGAGGATGTAGGTGCCGTGTTTGGACCGAACCTCTACAAATATCTTGTGTCA
1 AAGTGTCAAGGAGAGAGGATGTAGGTGCCGTGTTTGGACCGAACCTCTACAAATATCTTGTGTCA
92162 AGTTTTCCTTCCCTAATCTCTTTTCATTCCGAATTGTTTTGTTTCAAATTTGTACAAAACCCGAA
66 AGTTTTCCTTCCCTAATCTCTTTTCATTCCGAATTGTTTTGTTTCAAATTTGTACAAAACCCGAA
92227 AATTCGAAA
131 AATTCGAAA
92236 A
1 A
92237 GAACCAATTC
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (139 bp):
AAGTGTCAAGGAGAGAGGATGTAGGTGCCGTGTTTGGACCGAACCTCTACAAATATCTTGTGTCA
AGTTTTCCTTCCCTAATCTCTTTTCATTCCGAATTGTTTTGTTTCAAATTTGTACAAAACCCGAA
AATTCGAAA
Found at i:97594 original size:34 final size:34
Alignment explanation
Indices: 97556--97628 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
97546 TGGTCCCTAC
97556 TACCCGAATGCACCTTACCCAAGCCCAGTCATAA
1 TACCCGAATGCACCTTACCCAAGCCCAGTCATAA
97590 TACCCGAATGCACCTTACCCAAGCCCAGTCATAA
1 TACCCGAATGCACCTTACCCAAGCCCAGTCATAA
97624 TACCC
1 TACCC
97629 TCTCAGCCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.32, C:0.40, G:0.11, T:0.18
Consensus pattern (34 bp):
TACCCGAATGCACCTTACCCAAGCCCAGTCATAA
Found at i:97791 original size:28 final size:28
Alignment explanation
Indices: 97736--99546 Score: 1871
Period size: 28 Copynumber: 65.0 Consensus size: 28
97726 CTAATGCCAT
* * *
97736 AACTCCATGGTACCC-TTTAATGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
97763 AACTCTGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* *
97791 AACTCCGTGGCATCGTTTT-AAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
97818 AACTCCGTGGCACCC-TTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
97845 AACTTCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * *
97873 AACTCCGTGGCATCGTTTTAAAGTCCAT
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
97901 AACTCCGTGGCAGCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * * * *
97929 AATTCTGTGGCATCGTTTT-AAGTCCAT
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
97956 AACTCCGTGGCACCC-TTTAAAGTCCGC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
97983 AACTCCGTGGTACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
98011 AACTCCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
98039 AACTTCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * * *
98067 AACTCCGTGACATCATTTT-AAGTCCAT
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * *
98094 AACTTCGTGGTACCC-TTTAAAGTCCAT
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
98121 AACTCCGTGGCACCCTTTTAAAGCCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * *
98149 AACTCCGTGACATCGTTTT-AAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
98176 AACTCCGTGGCACCC-TTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
98203 AACTCCGTGGCACCC-TTTAAAGTCCGC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
98230 AACTCCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* *
98258 AACTCCGTGGCATCCTTTTAAAGTCTAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* *
98286 AACTCCGTGGTACCC-ATTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* *
98313 AACTCTGTGGCACCCTTTTAAAGTCCAT
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * *
98341 AACTCCGTGGCA-TCGTTTAAAGTCTAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* *
98368 AACTCCGTGGTACCC-ATTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
98395 AACTCCGTGGCACCCTTTTAAAGTCCAT
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * *
98423 AACTCTGTGGCATCGTTTT-AAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
98450 AACTCCGTGGCACCC-TTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
98477 AACTCCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
98505 AACTCCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
98533 AACCCCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * *
98561 AACTCCGTGGCATCGTTTT-AAGTCCAT
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* *
98588 AACTCCGTGGTACAC-TTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
98615 AACTCCATGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * * *
98643 AACTCTGTGGCATCGTTTT-AAGTGCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
98670 AACTCTGTGGCACCC-TTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* *
98697 AACTCCGTGGCATCGTTTT-AAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
98724 AACTCTGTGGCACCC-TTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
98751 AACTCCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
98779 AACTCCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* *
98807 AACTCCGTGGCATCTTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
** *
98835 AACTCAATGGTACCC-TTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
98862 AACTCCGTGGCACTC-TTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
98889 AACTCCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
**
98917 AACTCCGTGGCACCCTTTTGCAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* *
98945 AACTTCGTGGCACCTTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * *
98973 AACTCCATGGCTTCAC-TTT-AAGTCCAC
1 AACTCCGTGGC-ACCCTTTTAAAGTCCAC
* *
99000 AACTCCGTGGTA-CCTTTTAAAGTCTAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
*
99027 AACTACGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* ***
99055 AACTCCATGGCATTGTTTT-AA-TCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
99081 AACTCCGTGGCACCCTTTTAAAGTCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * *
99109 AACTCCGTAGCACCCTTTT-CAGTTCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
** * * *
99136 AACTTTGTGGCATCCTTTTTAAGCCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* ** *
99164 AAGTTAGTGGCACCCTTTTAAAGCCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* ** * *
99192 ACATGTTGGTGGCAACCTATTTCAAAGCCCACAC
1 A-A-CTCCGTGGCACCCT-TTT-AAAG-TC-CAC
* * * *
99226 AAGTCGGTGGCAACCCATTTGAAAGCCCACAC
1 AACTCCGTGGC-ACCC-TTTTAAAG-TC-CAC
* ** * *
99258 AAGTTGGTGGCAACCCATTTCAAAGCCCAC
1 AACTCCGTGGC-ACCC-TTTTAAAGTCCAC
* * * *
99288 AAATCAGTGGCACCCTTTCAAAGCCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* ** * *
99316 AAGTTAGTGACACCCTTTTAAAGCCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* ** * * *
99344 AAGTGAGTGGAACCCTTTCAAAGCCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* ** * * *
99372 AAGTTAGTGGCATCCTTTCAAAGCCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * *
99400 ACGAGTCGGTGGCAACCCTTTTCAAAGCCCAC
1 A--ACTCCGTGGC-ACCCTTTT-AAAGTCCAC
* ** * * *
99432 AAGTTAGTGGCATCCTTTCAAAGCCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * * * * *
99460 GAGTCGGTGGCAACATTTTCAAAGCCCAC
1 AACTCCGTGGCACCCTTTT-AAAGTCCAC
* ** * *
99489 AAGTCAATGGCACCCTTTCAAAGCCCAC
1 AACTCCGTGGCACCCTTTTAAAGTCCAC
* * * * *
99517 AAGTCAGCGGCACTCTTTTCAAAGCCCAC
1 AACTCCGTGGCACCCTTTT-AAAGTCCAC
99546 A
1 A
99547 CGAGTTGGTG
Statistics
Matches: 1531, Mismatches: 211, Indels: 82
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.00
26 47 0.03
27 536 0.35
28 784 0.51
29 44 0.03
30 39 0.03
31 11 0.01
32 56 0.04
33 8 0.01
34 5 0.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (28 bp):
AACTCCGTGGCACCCTTTTAAAGTCCAC
Found at i:97873 original size:82 final size:82
Alignment explanation
Indices: 97736--99192 Score: 1739
Period size: 82 Copynumber: 17.7 Consensus size: 82
97726 CTAATGCCAT
* * * *
97736 AACTCCATGGTACCCTTTAATGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
1 AACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
* *
97801 CATCGTTTTAAGTCCAC
66 CACCCTTTTAAGTCCAC
*
97818 AACTCCGTGGCACCCTTTAAAGTCCACAACTTCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
1 AACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
* * *
97883 CATCGTTTTAAAGTCCAT
66 CACCCTTTT-AAGTCCAC
* * * * * *
97901 AACTCCGTGGCAGCCTTTTAAAGTCCACAATTCTGTGGCATCGTTTT-AAGTCCATAACTCCGTG
1 AACTCCGTGGCA-CCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
* *
97965 GCACCCTTTAAAGTCCGC
65 GCACCCTTTTAAGTCCAC
* *
97983 AACTCCGTGGTACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTTCGTG
1 AACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
98048 GCACCCTTTTAAAGTCCAC
65 GCACCCTTTT-AAGTCCAC
* * * * * * * *
98067 AACTCCGTGACATCATTTTAAGTCCATAACTTCGTGGTACCC-TTTAAAGTCCATAACTCCGTGG
1 AACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
*
98131 CACCCTTTTAAAGCCCAC
66 CACCCTTTT-AAGTCCAC
* * * *
98149 AACTCCGTGACATCGTTTTAAGTCCACAACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGG
1 AACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
* *
98213 CACCCTTTAAAGTCCGC
66 CACCCTTTTAAGTCCAC
* *
98230 AACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCTACAACTCCGTG
1 AACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
* * *
98295 GTACCCATTAAAGTCCAC
65 GCACCCTTTTAAGTCCAC
* * * * *
98313 AACTCTGTGGCACCCTTTTAAAGTCCATAACTCCGTGGCA-TCGTTTAAAGTCTACAACTCCGTG
1 AACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
* * *
98377 GTACCCATTAAAGTCCAC
65 GCACCCTTTTAAGTCCAC
* * * *
98395 AACTCCGTGGCACCCTTTTAAAGTCCATAACTCTGTGGCATCGTTTT-AAGTCCACAACTCCGTG
1 AACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
*
98459 GCACCCTTTAAAGTCCAC
65 GCACCCTTTTAAGTCCAC
*
98477 AACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACCCCGTG
1 AACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
98542 GCACCCTTTTAAAGTCCAC
65 GCACCCTTTT-AAGTCCAC
* * * * * * *
98561 AACTCCGTGGCATCGTTTTAAGTCCATAACTCCGTGGTACAC-TTTAAAGTCCACAACTCCATGG
1 AACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
98625 CACCCTTTTAAAGTCCAC
66 CACCCTTTT-AAGTCCAC
* * * * * *
98643 AACTCTGTGGCATCGTTTTAAGTGCACAACTCTGTGGCACCC-TTTAAAGTCCACAACTCCGTGG
1 AACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
* *
98707 CATCGTTTTAAGTCCAC
66 CACCCTTTTAAGTCCAC
*
98724 AACTCTGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
1 AACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
98789 CACCCTTTTAAAGTCCAC
66 CACCCTTTT-AAGTCCAC
** ** *
98807 AACTCCGTGGCATCTTTTTAAAGTCCACAACTCAATGGTACCC-TTTAAAGTCCACAACTCCGTG
1 AACTCCGTGGCA-CCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
* *
98871 GCACTCTTTAAAGTCCAC
65 GCACCCTTTTAAGTCCAC
** *
98889 AACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTGCAGTCCACAACTTCGTG
1 AACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
*
98954 GCACCTTTTTAAAGTCCAC
65 GCACCCTTTT-AAGTCCAC
* * * * * *
98973 AACTCCATGGCTTCACTTT-AAGTCCACAACTCCGTGGTA-CCTTTTAAAGTCTACAACTACGTG
1 AACTCCGTGGC-ACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
99036 GCACCCTTTTAAAGTCCAC
65 GCACCCTTTT-AAGTCCAC
* *** * *
99055 AACTCCATGGCATTGTTTTAA-TCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTAG
1 AACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
* *
99119 CACCCTTTTCAGTTCAC
66 CACCCTTTTAAGTCCAC
** * * * * ** *
99136 AACTTTGTGGCATCCTTTTTAAGCCCACAAGTTAGTGGCACCCTTTTAAAGCCCACA
1 AACTCCGTGGCA-CCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACA
99193 CATGTTGGTG
Statistics
Matches: 1207, Mismatches: 147, Indels: 41
0.87 0.11 0.03
Matches are distributed among these distances:
81 100 0.08
82 658 0.55
83 334 0.28
84 113 0.09
85 2 0.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (82 bp):
AACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGG
CACCCTTTTAAGTCCAC
Found at i:97999 original size:138 final size:137
Alignment explanation
Indices: 97751--99192 Score: 1867
Period size: 138 Copynumber: 10.5 Consensus size: 137
97741 CATGGTACCC
* * *
97751 TTTAATGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCGTTTT-AAGTC
1 TTTAA-GTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
*
97815 CACAACTCCGTGGCACCCTTTAAAGTCCACAACTTCGTGGCACCCTTTTAAAGTCCACAACTCCG
64 CACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCG
97880 TGGCATCGT
129 TGGCATCGT
* * * * *
97889 TTTAAAGTCCATAACTCCGTGGCAGCCTTTTAAAGTCCACAATTCTGTGGCATCGTTTT-AAGTC
1 TTT-AAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
* * *
97953 CATAACTCCGTGGCACCCTTTAAAGTCCGCAACTCCGTGGTACCCTTTTAAAGTCCACAACTCCG
64 CACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCG
* *
98018 TGGCACCCT
129 TGGCATCGT
* * * *
98027 TTTAAAGTCCACAACTTCGTGGCACCCTTTTAAAGTCCACAACTCCGTGACATCATTTT-AAGTC
1 TTT-AAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTC
* * * * *
98091 CATAACTTCGTGGTACCCTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAAGCCCACAACTCCG
64 CACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCG
*
98156 TGACATCGT
129 TGGCATCGT
* *
98165 TTTAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCC-TTTAAAGTCCG
1 TTTAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCA
* *
98229 CAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCTACAACTCCGT
66 CAACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
* * **
98294 GGTACCCA
130 GGCATCGT
* * * * * *
98302 TTAAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCATAACTCCGTGGCA-TCGTTTAAAGTCT
1 TTTAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCC
* * * *
98366 ACAACTCCGTGGTACCCATTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCATAACTCTGT
65 ACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
98431 GGCATCGT
130 GGCATCGT
*
98439 TTTAAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCA
1 TTTAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCA
*
98504 CAACTCCGTGGCACCCTTTTAAAGTCCACAACCCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
66 CAACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
98569 GGCATCGT
130 GGCATCGT
* * *
98577 TTTAAGTCCATAACTCCGTGGTACAC-TTTAAAGTCCACAACTCCATGGCACCCTTTTAAAGTCC
1 TTTAAGTCCACAACTCCGTGGCAC-CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCC
* * * * * *
98641 ACAACTCTGTGGCATCGTTTTAAGTGCACAACTCTGTGGCACCC-TTTAAAGTCCACAACTCCGT
65 ACAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
98705 GGCATCGT
130 GGCATCGT
* *
98713 TTTAAGTCCACAACTCTGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCA
1 TTTAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCA
* * **
98778 CAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCTTTTTAAAGTCCACAACTCAAT
66 CAACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
* * *
98843 GGTACCCT
130 GGCATCGT
*
98851 TTAAAGTCCACAACTCCGTGGCA-CTCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCC
1 TTTAAGTCCACAACTCCGTGGCACCT-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCC
** * * *
98915 ACAACTCCGTGGCACCCTTTTGCAGTCCACAACTTCGTGGCACCTTTTTAAAGTCCACAACTCCA
65 ACAACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCG
* **
98980 TGGCTTCAC
129 TGGCATCGT
* * *
98989 TTTAAGTCCACAACTCCGTGGTACCTTTTAAAGTCTACAACTACGTGGCACCCTTTTAAAGTCCA
1 TTTAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCA
* *** * *
99054 CAACTCCATGGCATTGTTTTAA-TCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTA
66 CAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
* *
99118 GCACCCT
131 GCATCGT
* * ** * * * ** *
99125 TTTCAGTTCACAACTTTGTGGCATCCTTTTTAAGCCCACAAGTTAGTGGCACCCTTTTAAAGCCC
1 TTTAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCC
99190 ACA
65 ACA
99193 CATGTTGGTG
Statistics
Matches: 1146, Mismatches: 144, Indels: 29
0.87 0.11 0.02
Matches are distributed among these distances:
135 4 0.00
136 229 0.20
137 269 0.23
138 639 0.56
139 5 0.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (137 bp):
TTTAAGTCCACAACTCCGTGGCACCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCA
CAACTCCGTGGCACCCTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
GCATCGT
Found at i:100184 original size:20 final size:20
Alignment explanation
Indices: 100156--100230 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
100146 TTTTACCTAG
100156 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
100176 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
100196 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
100216 ATGTATCGATACATT
1 ATGTATCGATACATT
100231 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:100216 original size:40 final size:39
Alignment explanation
Indices: 100156--100233 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
100146 TTTTACCTAG
*
100156 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
100196 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
100234 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:105190 original size:21 final size:21
Alignment explanation
Indices: 105164--105214 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
105154 AGCTATGCTA
*
105164 ATCAAGCATAATCGGGACAAC
1 ATCAAGCACAATCGGGACAAC
* *
105185 ATCAAGCACAATCGGGATAGC
1 ATCAAGCACAATCGGGACAAC
105206 ATCAAGCAC
1 ATCAAGCAC
105215 CTGGTCCCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (21 bp):
ATCAAGCACAATCGGGACAAC
Found at i:106782 original size:12 final size:12
Alignment explanation
Indices: 106765--106794 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
106755 ACCTAATCCT
*
106765 AAAAAAAGAAAA
1 AAAAAAACAAAA
106777 AAAAAAACAAAA
1 AAAAAAACAAAA
106789 AAAAAA
1 AAAAAA
106795 CCTTTTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.93, C:0.03, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:107911 original size:28 final size:28
Alignment explanation
Indices: 107837--110000 Score: 2409
Period size: 28 Copynumber: 77.6 Consensus size: 28
107827 AGTGGCATTT
* *
107837 CCTTTTAAAGTCCACAACTCTGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
107865 CCTTTT-AAGTCCATAACTCCATGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
107892 CCTTTTAAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
107920 CCTTTTAAAGTCCACAATTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
107948 CATTTT-AAGTCTATAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
107975 CC-TTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
108002 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
108030 CCTTTTAAAGTCCACAACAT-CGTGGCAC
1 CCTTTTAAAGTCCACAAC-TCCGTGGCAC
*
108058 CCTTTTAAAGTCCACAACTCCG-GAGCAT
1 CCTTTTAAAGTCCACAACTCCGTG-GCAC
* * * *
108086 CGTTTT-AAGTCCATAACTCCATGGTAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * **
108113 AC-TTTAAAGTCCATAACTCCGTGGTGC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108140 CCTTTTAAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
108168 CATTTT-AAGTCCACAACTTCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108195 CC-TTTGAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
108222 TCTTTTAAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
108250 CCTTTTAAAGTCCAAAACTCTGTGGTAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
108278 CC-TTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
108305 CCTTTTAAAGTCCACAACTCCGTAGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108333 CGTTTT-AAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
108360 CC-TTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
** *
108387 CCTTTTAAAGTCCACAACTTAGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108415 CATTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
108443 CCTTTTAAAGTCCACAATTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
108471 CGTTTT-AAGTCCATAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108498 CC-TTTAAAGTCCACAACTCCGTGCCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
108525 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108553 CCTTTTAAAGTCTACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
108581 CTTTTTAAAGTCCACAACTTCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
108609 CCTTTTAAAGTCCACAACTCCGAGACAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
108637 CGTTTT-AAGTCCATAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108664 CCTTTTAAAGTCCATAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108692 CCTTTTAAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
108720 CGTTTT-AAGTCCATAACTCCGTGGTAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
108747 CC-TTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
108774 CGTTTT-ATGTCCACAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
108801 CGTTTT-ATGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108828 CC-TTTAAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108855 CGTTTT-AAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108882 CC-TTTAAAGTCCACAACTACGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108909 CCTTTTAAAGTCCACAACTTCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
108937 CCTTTTAAAGTCCATAACTCCGTGGCGC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
108965 CCTTTTAAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
108993 CTTTTTAAAGTCCACAACTCCGTGGTAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
109021 CC-TTTAAAGTCCACAACTCCATGGTAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
109048 CC-TTTAATGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
109075 CCTTTTAAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
109103 CGTTTT-AAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
109130 CC-TTTAAAGTCCACAACTTCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
109157 CCTTTTAAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
109185 CGTTTTAAAGTCCATAACTCCGTGGCAG
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
109213 CCTTTTAAAGTACACAATTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
109241 CGTTTT-AAGTCCATAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
109268 CC-TTTAAAGTCCGCAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
109295 CCTTTTAAAGTTCGCAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
109323 CC-TTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
109350 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
109378 CCTTTTACAGTCCATAACTTCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
109406 CTTTTTAAAGTCCACAACTCCATGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
109434 CATTTT-AAGTCCACAACTCCGTGGTAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
109461 CC-TTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
109488 CCTTTTAAAGTCCACAATTTCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
**
109516 TGTTTT-AA-TCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
*
109542 CCTTTTAAAGGCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * *
109570 CCTTTT-AAGTTCACAACTTCGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * * *
109597 CCTTTTTAAGCCCACAAGTCAGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * * *
109625 CCTTTTAAAGCCAACACAAGTCGGTGGCAA
1 CCTTTTAAAGTC--CACAACTCCGTGGCAC
* * *
109655 CCTATTTCAAAGCCCACACAAGT-CGATGGCAA
1 CCT-TTT-AAAG-TC-CACAACTCCG-TGGCAC
* * *
109687 CCTATTTGAAAGCCCACACAAGTCGGTGGCAAC
1 CCT-TTT-AAAG-TC-CACAACTCCGTGGC-AC
* * * * *
109720 CCATTTCAGAGCCCACAAATCAGTGGCAC
1 CC-TTTTAAAGTCCACAACTCCGTGGCAC
* * * *
109749 CCTTTAAAAGCCCACAAGTCAGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * * *
109777 CCTTTTAAAGCCCACACAAATCGGTGGCAA
1 CCTTTTAAAG-TC-CACAACTCCGTGGCAC
* * **
109807 CCTATTTCAAAGCCCACACAAGTTGGTGGCAAC
1 CCT-TTT-AAAG-TC-CACAACTCCGTGGC-AC
* * * *
109840 CCATTTGAAAGCCCACACAAGTCGGTGGCAAC
1 CC-TTTTAAAG-TC-CACAACTCCGTGGC-AC
* * * *
109872 CCATTTCAAAGCCCACAAATCAGTGGCAC
1 CC-TTTTAAAGTCCACAACTCCGTGGCAC
* * * *
109901 CCTTTCAAAGCCCACAAGTCGGTGGCAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * * *
109929 CCTTTTAAAGCCCACAAGTCAGTGGAAC
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* * * ** *
109957 CCTTTCAAAGCCCACAAGTTAGTGGCAT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC
* *
109985 CCTTTCAAAGCCCACA
1 CCTTTTAAAGTCCACA
110001 CGAGTCGGTG
Statistics
Matches: 1866, Mismatches: 221, Indels: 98
0.85 0.10 0.04
Matches are distributed among these distances:
26 52 0.03
27 643 0.34
28 976 0.52
29 11 0.01
30 57 0.03
31 11 0.01
32 101 0.05
33 13 0.01
34 2 0.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
CCTTTTAAAGTCCACAACTCCGTGGCAC
Found at i:108086 original size:138 final size:139
Alignment explanation
Indices: 107837--110000 Score: 2384
Period size: 138 Copynumber: 15.5 Consensus size: 139
107827 AGTGGCATTT
* * * * *
107837 CCTTTTAAAGTCCACAACTCTGTGGCATCCTTTT-AAGTCCATAACTCCATGGCATCCTTTTAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * * * * *
107901 GTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAATTCCGTGGCATCATTTTAAGTCTATAACT
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
107966 CCGTGGCAC
131 CCGTGGCAC
107975 CC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * *
108039 GTCCACAACAT-CGTGGCACCCTTTTAAAGTCCACAACTCCG-GAGCATCGTTTTAAGTCCATAA
66 GTCCACAAC-TCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG-GCACCCTTTTAAGTCCACAA
* *
108102 CTCCATGGTAC
129 CTCCGTGGCAC
* * ** * *
108113 AC-TTTAAAGTCCATAACTCCGTGGTGCCCTTTTAAAGTCCACAACTCCGTGGCATCATTTT-AA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * * *
108176 GTCCACAACTTCGTGGCACCC-TTTGAAGTCCACAACTCCGTGGCACTCTTTTAAAGCCCACAAC
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAAC
108240 TCCGTGGCAC
130 TCCGTGGCAC
* * *
108250 CCTTTTAAAGTCCAAAACTCTGTGGTACCC-TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * * *
108314 GTCCACAACTCCGTAGCATCGTTTT-AAGTCCACAACTCCGTGGCACCCTTTAAAGTCCACAACT
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
108378 CCGTGGCAC
131 CCGTGGCAC
** * *
108387 CCTTTTAAAGTCCACAACTTAGTGGCATCATTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * * * *
108452 GTCCACAATTCCGTGGCATCGTTTT-AAGTCCATAACTCCGTGGCACCCTTTAAAGTCCACAACT
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
*
108516 CCGTGCCAC
131 CCGTGGCAC
* *
108525 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCTACAACTCCGTGGCACCTTTTTAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * * * * * *
108590 GTCCACAACTTCGTGGCATCCTTTTAAAGTCCACAACTCCGAGACATCGTTTTAAGTCCATAACT
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
108655 CCGTGGCAC
131 CCGTGGCAC
* * *
108664 CCTTTTAAAGTCCATAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCGTTTT-AA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * * *
108728 GTCCATAACTCCGTGGTACCC-TTTAAAGTCCACAACTCCGTGGCACCGTTTTATGTCCACAACT
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
*
108792 CCGTGGCAT
131 CCGTGGCAC
* * * *
108801 CGTTTT-ATGTCCACAACTCCGTGGCACCC-TTTAAAGTCCACAACTCCGTGGCATCGTTTT-AA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
*
108863 GTCCACAACTCCGTGGCACCC-TTTAAAGTCCACAACTACGTGGCACCCTTTTAAAGTCCACAAC
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAAC
*
108927 TTCGTGGCAC
130 TCCGTGGCAC
* * * *
108937 CCTTTTAAAGTCCATAACTCCGTGGCGCCCTTTTAAAGTCCACAACTCCGTGGCATCTTTTTAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * *
109002 GTCCACAACTCCGTGGTACCC-TTTAAAGTCCACAACTCCATGGTACCC-TTTAATGTCCACAAC
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAA-GTCCACAAC
109065 TCCGTGGCAC
130 TCCGTGGCAC
* *
109075 CCTTTTAAAGTCCACAACTCCGTGGCATCGTTTT-AAGTCCACAACTCCGTGGCACCC-TTTAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * * *
109138 GTCCACAACTTCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCGTTTTAAAGTCCATAAC
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAAC
*
109203 TCCGTGGCAG
130 TCCGTGGCAC
* * * * *
109213 CCTTTTAAAGTACACAATTCCGTGGCATCGTTTT-AAGTCCATAACTCCGTGGCACCC-TTTAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * * *
109276 GTCCGCAACTCCGTGGCACCCTTTTAAAGTTCGCAACTCCGTGGCACCCTTTAAAGTCCACAACT
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
109341 CCGTGGCAC
131 CCGTGGCAC
* * * *
109350 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTACAGTCCATAACTTCGTGGCACCTTTTTAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * * * *
109415 GTCCACAACTCCATGGCATCATTTT-AAGTCCACAACTCCGTGGTACCCTTTAAAGTCCACAACT
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
109479 CCGTGGCAC
131 CCGTGGCAC
* * ***
109488 CCTTTTAAAGTCCACAATTTCGTGGCATTGTTTT-AA-TCCACAACTCCGTGGCACCCTTTTAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
* * * * * *
109551 GGCCACAACTCCGTGGCACCCTTTT-AAGTTCACAACTTCGTGGCATCCTTTTTAAGCCCACAAG
66 GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAAC
*
109615 TCAGTGGCAC
130 TCCGTGGCAC
* * * * * * *
109625 CCTTTTAAAGCCAACACAAGTCGGTGGCAACCTATTTCAAAGCCCACACAAGT-CGATGGCAACC
1 CCTTTTAAAGTC--CACAACTCCGTGGCACCCT-TTT-AAAG-TC-CACAACTCCG-TGGCACCC
* * * * * * * *
109689 TATTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAGAGCCCACAAATCAGTGGCACCCTTT
59 T-TTT-AAAG-TC-CACAACTCCGTGGC-ACCC-TTTTAAAGTCCACAACTCCGTGGCACCCTTT
* * * *
109754 AAAAGCCCACAAGTCAGTGGCAC
118 -TAAGTCCACAACTCCGTGGCAC
* * * * * * **
109777 CCTTTTAAAGCCCACACAAATCGGTGGCAACCTATTTCAAAGCCCACACAAGTTGGTGGCAACCC
1 CCTTTTAAAG-TC-CACAACTCCGTGGCACCCT-TTT-AAAG-TC-CACAACTCCGTGGC-ACCC
* * * * * * * *
109842 ATTTGAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAATCAGTGGCACCCTTTC
59 -TTTTAAAG-TC-CACAACTCCGTGGC-ACCC-TTTTAAAGTCCACAACTCCGTGGCACCCTTT-
* * * *
109907 AAAGCCCACAAGTCGGTGGCAC
118 TAAGTCCACAACTCCGTGGCAC
* * * * * * * ** * *
109929 CCTTTTAAAGCCCACAAGTCAGTGGAACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAA
1 CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
*
109994 GCCCACA
66 GTCCACA
110001 CGAGTCGGTG
Statistics
Matches: 1786, Mismatches: 197, Indels: 82
0.86 0.10 0.04
Matches are distributed among these distances:
135 81 0.05
136 157 0.09
137 344 0.19
138 720 0.40
139 190 0.11
140 3 0.00
142 6 0.00
143 2 0.00
144 10 0.01
145 17 0.01
146 16 0.01
147 6 0.00
148 5 0.00
149 14 0.01
150 19 0.01
151 10 0.01
152 177 0.10
153 8 0.00
154 1 0.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (139 bp):
CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAA
GTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
CCGTGGCAC
Found at i:109674 original size:32 final size:31
Alignment explanation
Indices: 109609--110153 Score: 487
Period size: 32 Copynumber: 18.2 Consensus size: 31
109599 TTTTTAAGCC
* * *
109609 CACAAGTCAGTGGCACCCTTTT-AAAGCCAA
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
109639 CACAAGTCGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCT-TTTCAAAGCCCA
* *
109671 CACAAGTCGATGGCAACCTATTTGAAAGCCCA
1 CACAAGTCGGTGGCAACCT-TTTCAAAGCCCA
* *
109703 CACAAGTCGGTGGCAACCCATTTCAGAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
* * *
109735 CA-AA-TCAGTGGC-ACCCTTTAAAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
* *
109761 CACAAGTCAGTGGCACCCTTTT-AAAGCCCA
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
*
109791 CACAAATCGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCT-TTTCAAAGCCCA
* * *
109823 CACAAGTTGGTGGCAACCCATTTGAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
*
109855 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
* *
109887 CA-AA-TCAGTGGC-ACCCTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
*
109913 CACAAGTCGGTGGCACCCTTTT-AAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
* *
109941 CACAAGTCAGTGG-AACCCTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
** *
109969 CACAAGTTAGTGGCATCC-TTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
* *
109999 CACGAGTCGGTGGTAACCCTTTTCAAAG-CC-
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
** *
110029 CACAAGTTAGTGGCATCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
* *
110057 CACGAGTCGGTGGCAACATTTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
* *
110086 CACAAGTCAGCGGC-ACTCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAAC-CTTTTCAAAGCCCA
* * *
110117 CACGAGTTGGTGGCAATTCTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAA-CCTTTTCAAAGCCCA
110149 CACAA
1 CACAA
110154 TTAGTGGCAC
Statistics
Matches: 430, Mismatches: 59, Indels: 50
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.01
27 14 0.03
28 106 0.25
29 51 0.12
30 71 0.17
31 24 0.06
32 156 0.36
33 4 0.01
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (31 bp):
CACAAGTCGGTGGCAACCTTTTCAAAGCCCA
Found at i:109768 original size:152 final size:149
Alignment explanation
Indices: 109590--110153 Score: 712
Period size: 152 Copynumber: 3.8 Consensus size: 149
109580 TCACAACTTC
* ** *
109590 GTGGCATCCTTTTTAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCAACACAAGTCGGTGGCAA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCC--CACAAGTCAGTGGCAA
* *
109655 CCTATTTCAAAGCCCACACAAGTCGATGGCAACCTATTTGAAAGCCCACACAAGTCGGTGGCAAC
64 CCTATTTCAAAGCCCACACAAGTTGATGGCAACCT-TTTCAAAGCCCACACAAGTCGGTGGCAAC
*
109720 CCATTTCAGAGCCCACAAATCA
128 CCATTTCAAAGCCCACAAATCA
* * *
109742 GTGGCACCCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACACAAATCGGTGGCAA
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAG-CC-CACAAGTCAGTGGCAA
* * *
109807 CCTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTGAAAGCCCACACAAGTCGGTGGCAAC
64 CCTATTTCAAAGCCCACACAAGTTGATGGCAA-CCTTTTCAAAGCCCACACAAGTCGGTGGCAAC
109872 CCATTTCAAAGCCCACAAATCA
128 CCATTTCAAAGCCCACAAATCA
*
109894 GTGGCACCCTTTCAAAGCCCACAAGTCGGTGGCACCCTTTTAAAGCCCACAAGTCAGTGG-AACC
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCAACC
* * * *
109958 -CTTTCAAAG-CC-CACAAGTT-AGTGGCATCC-TTTCAAAGCCCACACGAGTCGGTGGTAACCC
66 TATTTCAAAGCCCACACAAGTTGA-TGGCAACCTTTTCAAAGCCCACACAAGTCGGTGGCAACCC
* * *
110018 TTTTCAAAGCCCACAAGTTA
130 ATTTCAAAGCCCACAAATCA
* * * * * *
110038 GTGGCATCCTTTCAAAGCCCACGAGTCGGTGGCAACATTTTCAAAGCCCACAAGTCAGCGGC-AC
1 GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCCACAAGTCAGTGGCAAC
* * *
110102 TCT-TTTCAAAGCCCACACGAGTTGGTGGCAATTCTTTTCAAAGCCCACACAA
65 -CTATTTCAAAGCCCACACAAGTTGATGGCAA-CCTTTTCAAAGCCCACACAA
110154 TTAGTGGCAC
Statistics
Matches: 369, Mismatches: 31, Indels: 26
0.87 0.07 0.06
Matches are distributed among these distances:
144 82 0.22
145 22 0.06
146 22 0.06
147 4 0.01
148 20 0.05
149 5 0.01
150 27 0.07
151 2 0.01
152 181 0.49
153 4 0.01
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.21
Consensus pattern (149 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCAACC
TATTTCAAAGCCCACACAAGTTGATGGCAACCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCA
TTTCAAAGCCCACAAATCA
Found at i:110754 original size:20 final size:20
Alignment explanation
Indices: 110726--110796 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
110716 TTTTACCTAG
110726 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
110746 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
110766 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
110786 ATGTATCGATA
1 ATGTATCGATA
110797 TATTATGTCT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:113887 original size:21 final size:21
Alignment explanation
Indices: 113861--113903 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
113851 AGTTCGGTCA
113861 CTTCGTAGTGACCGTGAAGAT
1 CTTCGTAGTGACCGTGAAGAT
113882 CTTCGTAGTGACCGTGAAGAT
1 CTTCGTAGTGACCGTGAAGAT
113903 C
1 C
113904 GATTAGATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTCGTAGTGACCGTGAAGAT
Found at i:119653 original size:23 final size:22
Alignment explanation
Indices: 119623--119667 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
119613 TTTCATTTTA
*
119623 CTCCCCTTTAATTAAAGAATTT
1 CTCCCCCTTAATTAAAGAATTT
119645 CTCCCCCTTAATTAAAGAATTT
1 CTCCCCCTTAATTAAAGAATTT
119667 C
1 C
119668 AAAGAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (22 bp):
CTCCCCCTTAATTAAAGAATTT
Done.