Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 42 of 206
Found at i:12019674 original size:2 final size:2
Alignment explanation
Indices: 12019667--12019691 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12019657 TATTTATGGA
12019667 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
12019692 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12023131 original size:3 final size:3
Alignment explanation
Indices: 12023109--12023160 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
12023099 ATAATGACAG
*
12023109 TAA TAA AAA T-A TAA TAAA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12023153 TAAA TAA T
1 T-AA TAA T
12023161 GGTAATTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12029957 original size:18 final size:19
Alignment explanation
Indices: 12029928--12029965 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
12029918 TAAATGAATA
*
12029928 ATTATATATTTTTAAAGAC
1 ATTATATATTTTGAAAGAC
12029947 ATTAT-TATTTTGAAAGAC
1 ATTATATATTTTGAAAGAC
12029965 A
1 A
12029966 CCTATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (19 bp):
ATTATATATTTTGAAAGAC
Found at i:12030559 original size:30 final size:30
Alignment explanation
Indices: 12030518--12030673 Score: 149
Period size: 30 Copynumber: 5.2 Consensus size: 30
12030508 GTGTTTTAAA
* *
12030518 AAAATTGTATTTTCACCCCTAAACTTTTTT
1 AAAATTATATTTTCACCCCTAAACTTTCTT
* * *
12030548 AAAATCATATTTTGACCCTTAAACTTTCTT
1 AAAATTATATTTTCACCCCTAAACTTTCTT
*
12030578 AAAATTACA-TTTCAACCCCTAAAC-TT-TT
1 AAAATTATATTTTC-ACCCCTAAACTTTCTT
* *
12030606 ATAAATTACT-TTTTAACCCCTAAACTTTCTC
1 A-AAATTA-TATTTTCACCCCTAAACTTTCTT
* * *
12030637 AAAATTATATTTTGACCCCTAAAATTTATT
1 AAAATTATATTTTCACCCCTAAACTTTCTT
*
12030667 GAAATTA
1 AAAATTA
12030674 CGTTTTAGTC
Statistics
Matches: 102, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
28 3 0.03
29 22 0.22
30 75 0.74
31 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.42
Consensus pattern (30 bp):
AAAATTATATTTTCACCCCTAAACTTTCTT
Found at i:12030641 original size:59 final size:59
Alignment explanation
Indices: 12030528--12030659 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 59
12030518 AAAATTGTAT
* * * *
12030528 TTTCACCCCTAAACTTTTTTAAAATCATATTTTGACCCTTAAACTTTCTTAAAATTACA
1 TTTCACCCCTAAACTTTTATAAAATCATATTTTAACCCCTAAACTTTCTCAAAATTACA
* *
12030587 TTTCAACCCCTAAACTTTTAT-AAATTACT-TTTTAACCCCTAAACTTTCTCAAAATTATA
1 TTTC-ACCCCTAAACTTTTATAAAATCA-TATTTTAACCCCTAAACTTTCTCAAAATTACA
*
12030646 TTTTGACCCCTAAA
1 -TTTCACCCCTAAA
12030660 ATTTATTGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 44 0.70
60 19 0.30
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (59 bp):
TTTCACCCCTAAACTTTTATAAAATCATATTTTAACCCCTAAACTTTCTCAAAATTACA
Found at i:12030691 original size:89 final size:89
Alignment explanation
Indices: 12030527--12030695 Score: 221
Period size: 89 Copynumber: 1.9 Consensus size: 89
12030517 AAAAATTGTA
* * * * * *
12030527 TTTTCACCCCTAAACTTTTTTAAAATCATATTTTGACCCTTAAACTTTCTTAAAATTACATTTCA
1 TTTTAACCCCTAAACTTTCTCAAAATCATATTTTGACCCCTAAAATTTATTAAAATTACATTTCA
*
12030592 ACCCCTAAACTTTTATAAATTACT
66 ACCCCAAAACTTTTATAAATTACT
* * * *
12030616 TTTTAACCCCTAAACTTTCTCAAAATTATATTTTGACCCCTAAAATTTATTGAAATTACGTTTTA
1 TTTTAACCCCTAAACTTTCTCAAAATCATATTTTGACCCCTAAAATTTATTAAAATTACATTTCA
**
12030681 GTCCCAAAACTTTTA
66 ACCCCAAAACTTTTA
12030696 CTGAGTTCAC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
89 67 1.00
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (89 bp):
TTTTAACCCCTAAACTTTCTCAAAATCATATTTTGACCCCTAAAATTTATTAAAATTACATTTCA
ACCCCAAAACTTTTATAAATTACT
Found at i:12031046 original size:14 final size:14
Alignment explanation
Indices: 12031029--12031059 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12031019 AAAAATAAAA
12031029 AAAAAACAGCAAAG
1 AAAAAACAGCAAAG
*
12031043 AAAAAAGAGCAAAG
1 AAAAAACAGCAAAG
12031057 AAA
1 AAA
12031060 GAAAAGAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.10, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAACAGCAAAG
Found at i:12031177 original size:24 final size:24
Alignment explanation
Indices: 12031149--12031221 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 24
12031139 GGGAAAGAAG
12031149 GAAAGGAAGAAA-AAAGAAGAAAAA
1 GAAA-GAAGAAAGAAAGAAGAAAAA
*
12031173 GAAAGAAGAAAGAAAGAAGAAAAGG
1 GAAAGAAGAAAGAAAGAAGAAAA-A
* * *
12031198 GGAAGAAGAAAGAAGGAAAAAAAA
1 GAAAGAAGAAAGAAAGAAGAAAAA
12031222 AGAATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 7 0.17
24 15 0.36
25 20 0.48
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (24 bp):
GAAAGAAGAAAGAAAGAAGAAAAA
Found at i:12031179 original size:4 final size:4
Alignment explanation
Indices: 12031141--12031194 Score: 51
Period size: 4 Copynumber: 14.0 Consensus size: 4
12031131 GGCTGATCGG
* * *
12031141 GAAA GAAG GAAA GGAA GAAA -AAA GAAGA AAAA GAAA G-AA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA
12031188 G-AA GAAA
1 GAAA GAAA
12031195 AGGGGAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
3 9 0.22
4 28 0.70
5 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:12031179 original size:32 final size:33
Alignment explanation
Indices: 12031141--12031225 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 33
12031131 GGCTGATCGG
*
12031141 GAAAGAAGGAAAGGAAGAA-AAAAGAAGAAAAA
1 GAAAGAAGGAAAGAAAGAAGAAAAGAAGAAAAA
** *
12031173 GAAAGAA-GAAAGAAAGAAGAAAAGGGGAAGAA
1 GAAAGAAGGAAAGAAAGAAGAAAAGAAGAAAAA
*
12031205 GAAAGAAGGAAA-AAAAAAGAA
1 GAAAGAAGGAAAGAAAGAAGAA
12031226 TAATTTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 10 0.22
32 32 0.70
33 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (33 bp):
GAAAGAAGGAAAGAAAGAAGAAAAGAAGAAAAA
Found at i:12031697 original size:12 final size:13
Alignment explanation
Indices: 12031680--12031708 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12031670 TTTATACATT
12031680 TTTATATTTTT-A
1 TTTATATTTTTAA
12031692 TTTATATTTTTAA
1 TTTATATTTTTAA
12031705 TTTA
1 TTTA
12031709 ATCCAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATATTTTTAA
Found at i:12031922 original size:38 final size:39
Alignment explanation
Indices: 12031858--12031960 Score: 93
Period size: 38 Copynumber: 2.7 Consensus size: 39
12031848 ATCGAAAATA
* * * *
12031858 TTCAAAAAAATTTGTGTTTTC-GAAAAAAATTCCCGTGT
1 TTCAAAAATATTCGTGTCTTCAAAAAAAAATTCCCGTGT
* * ** *
12031896 TTC-GAAATTTTCGTGTCTTCAAAAAAATTTTCTCGTGT
1 TTCAAAAATATTCGTGTCTTCAAAAAAAAATTCCCGTGT
*
12031934 TTCAAAAAATATTCGTGTTTTCAAAAA
1 TTC-AAAAATATTCGTGTCTTCAAAAA
12031961 TAAGGCAACG
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 12 0.24
38 19 0.38
40 19 0.38
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (39 bp):
TTCAAAAATATTCGTGTCTTCAAAAAAAAATTCCCGTGT
Found at i:12031925 original size:20 final size:19
Alignment explanation
Indices: 12031858--12031960 Score: 74
Period size: 20 Copynumber: 5.4 Consensus size: 19
12031848 ATCGAAAATA
12031858 TTCAAAAAAA-TTT-GTGTT
1 TTCAAAAAAATTTTCGTG-T
**
12031876 TTCGAAAAAAATTCCCGTGT
1 TTC-AAAAAAATTTTCGTGT
*
12031896 TTC---GAAATTTTCGTGT
1 TTCAAAAAAATTTTCGTGT
12031912 CTTCAAAAAAATTTTCTCGTGT
1 -TTCAAAAAAA-TTT-TCGTGT
*
12031934 TTC-AAAAAATATTCGTGTT
1 TTCAAAAAAATTTTCGTG-T
12031953 TTCAAAAA
1 TTCAAAAA
12031961 TAAGGCAACG
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
16 10 0.15
17 3 0.04
18 8 0.12
19 13 0.19
20 18 0.27
21 9 0.13
22 6 0.09
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (19 bp):
TTCAAAAAAATTTTCGTGT
Found at i:12031949 original size:18 final size:18
Alignment explanation
Indices: 12031858--12031960 Score: 61
Period size: 19 Copynumber: 5.4 Consensus size: 18
12031848 ATCGAAAATA
*
12031858 TTCAAAAAA-ATTTGTGTT
1 TTCAAAAAATATTCGTG-T
12031876 TTCGAAAAAA-ATTCCCGTGT
1 TTC-AAAAAATATT--CGTGT
* *
12031896 TTC--GAAATTTTCGTGT
1 TTCAAAAAATATTCGTGT
*
12031912 CTTCAAAAAAATTTTCTCGTGT
1 -TTC-AAAAAA-TAT-TCGTGT
12031934 TTCAAAAAATATTCGTGTT
1 TTCAAAAAATATTCGTG-T
12031953 TTCAAAAA
1 TTCAAAAA
12031961 TAAGGCAACG
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
16 5 0.07
17 6 0.09
18 10 0.14
19 20 0.29
20 13 0.19
21 9 0.13
22 6 0.09
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (18 bp):
TTCAAAAAATATTCGTGT
Found at i:12032118 original size:18 final size:18
Alignment explanation
Indices: 12032077--12032118 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12032067 AATTTGTGTA
*
12032077 AAAAAATCTTCGTGGTTT
1 AAAAAATATTCGTGGTTT
* *
12032095 CAAAAATATTCGTGTTTT
1 AAAAAATATTCGTGGTTT
12032113 AAAAAA
1 AAAAAA
12032119 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (18 bp):
AAAAAATATTCGTGGTTT
Found at i:12032173 original size:18 final size:17
Alignment explanation
Indices: 12032152--12032472 Score: 138
Period size: 18 Copynumber: 18.0 Consensus size: 17
12032142 TTTTTAAATT
*
12032152 TTTCATGTTTTCAAAAAA
1 TTTCGTGTTTTC-AAAAA
*
12032170 TTTCCGTGTTTTAAAAAAAA
1 TTT-CGTGTTTT--CAAAAA
* * *
12032190 TTCCAT-TTTTCAAAAT
1 TTTCGTGTTTTCAAAAA
12032206 TATTCGTGTTTTCAAAAA
1 T-TTCGTGTTTTCAAAAA
* * *
12032224 ATTCCTATGTTTCAAAAA
1 TTTCGTGT-TTTCAAAAA
* *
12032242 TCTTTGTGTTTTCAAAAG
1 T-TTCGTGTTTTCAAAAA
*
12032260 TTCCG-GTGTTTCAAAAA
1 TTTCGTGT-TTTCAAAAA
*
12032277 TTTTCATGTTTTCAAAAA
1 -TTTCGTGTTTTCAAAAA
*
12032295 TTCCCGTGTTTT-AAAAA
1 TT-TCGTGTTTTCAAAAA
12032312 TTTCCGTGTTTTCAAAAA
1 TTT-CGTGTTTTCAAAAA
*
12032330 TTT-GTGTTTT-AAAATT
1 TTTCGTGTTTTCAAAA-A
*
12032346 TTTCGTG-CTTCAAAAAGAAA
1 TTTCGTGTTTTC---AA-AAA
* *
12032366 ATTAGTGTTTTCAAAAAAAAAA
1 TTTCGTGTTTTC-----AAAAA
*
12032388 TTCTCGTG-TTTCAAAAT
1 TT-TCGTGTTTTCAAAAA
**
12032405 TTTCGTGTTTAAAAAAA
1 TTTCGTGTTTTCAAAAA
** * *
12032422 AATCATG-TTTCTAAAA
1 TTTCGTGTTTTCAAAAA
*
12032438 -TTCTGTTGTTTTAAAAAA
1 TTTC-G-TGTTTTCAAAAA
12032456 TTTCGTGTTTTCAAAAA
1 TTTCGTGTTTTCAAAAA
12032473 AAAAAGGTTG
Statistics
Matches: 226, Mismatches: 48, Indels: 59
0.68 0.14 0.18
Matches are distributed among these distances:
15 6 0.03
16 30 0.13
17 67 0.30
18 69 0.31
19 18 0.08
20 14 0.06
21 5 0.02
22 8 0.04
23 9 0.04
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (17 bp):
TTTCGTGTTTTCAAAAA
Found at i:12032277 original size:35 final size:34
Alignment explanation
Indices: 12032160--12032331 Score: 157
Period size: 35 Copynumber: 4.8 Consensus size: 34
12032150 TTTTTCATGT
* * *
12032160 TTTCAAAAAATTTCCGTGTTTTAAAAAAAATT-CCATT
1 TTTC-AAAAATTT-CGTGTTTT--CAAAAATTCCCGTG
* **
12032197 TTTCAAAATTATTCGTGTTTTCAAAAAATTCCTATG
1 TTTCAAAAAT-TTCGTGTTTTC-AAAAATTCCCGTG
* * *
12032233 TTTCAAAAATCTTTGTGTTTTCAAAAGTTCCGGTG
1 TTTCAAAAAT-TTCGTGTTTTCAAAAATTCCCGTG
*
12032268 TTTCAAAAATTTTCATGTTTTCAAAAATTCCCGTG
1 TTTCAAAAA-TTTCGTGTTTTCAAAAATTCCCGTG
*
12032303 TTTTAAAAATTTCCGTGTTTTCAAAAATT
1 TTTCAAAAATTT-CGTGTTTTCAAAAATT
12032332 TGTGTTTTAA
Statistics
Matches: 114, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
34 3 0.03
35 69 0.61
36 36 0.32
37 6 0.05
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (34 bp):
TTTCAAAAATTTCGTGTTTTCAAAAATTCCCGTG
Found at i:12032403 original size:21 final size:20
Alignment explanation
Indices: 12032347--12032403 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
12032337 TTTAAAATTT
*
12032347 TTCGTGCTTCAAAAAGAAAA
1 TTCGTGTTTCAAAAAGAAAA
* *
12032367 TTAGTGTTTTCAAAAAAAAAA
1 TTCGTG-TTTCAAAAAGAAAA
12032388 TTCTCGTGTTTCAAAA
1 -T-TCGTGTTTCAAAA
12032404 TTTTCGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.17
21 12 0.40
22 9 0.30
23 4 0.13
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
TTCGTGTTTCAAAAAGAAAA
Found at i:12032419 original size:16 final size:16
Alignment explanation
Indices: 12032383--12032419 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12032373 TTTTCAAAAA
12032383 AAAAATTCTCGTGTTT
1 AAAAATTCTCGTGTTT
* *
12032399 CAAAATTTTCGTGTTT
1 AAAAATTCTCGTGTTT
12032415 AAAAA
1 AAAAA
12032420 AAAATCATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (16 bp):
AAAAATTCTCGTGTTT
Found at i:12032473 original size:18 final size:18
Alignment explanation
Indices: 12032152--12032473 Score: 126
Period size: 17 Copynumber: 18.0 Consensus size: 18
12032142 TTTTTAAATT
*
12032152 TTTCATGTTTTCAAAAAA
1 TTTCGTGTTTTCAAAAAA
*
12032170 TTTCCGTGTTTTAAAAAAAA
1 TTT-CGTGTTTT-CAAAAAA
* * *
12032190 TTCCAT-TTTTC-AAAAT
1 TTTCGTGTTTTCAAAAAA
12032206 TATTCGTGTTTTCAAAAAA
1 T-TTCGTGTTTTCAAAAAA
* *
12032225 -TTCCTATGTTTC-AAAAA
1 TTTCGTGT-TTTCAAAAAA
* *
12032242 TCTTTGTGTTTTC-AAAAG
1 T-TTCGTGTTTTCAAAAAA
* *
12032260 TTCCG-GTGTTTCAAAAAT
1 TTTCGTGT-TTTCAAAAAA
*
12032278 TTTCATGTTTTC-AAAAA
1 TTTCGTGTTTTCAAAAAA
*
12032295 TTCCCGTGTTTT--AAAAA
1 TT-TCGTGTTTTCAAAAAA
12032312 TTTCCGTGTTTTC-AAAAA
1 TTT-CGTGTTTTCAAAAAA
**
12032330 TTT-GTGTTTT-AAAATT
1 TTTCGTGTTTTCAAAAAA
*
12032346 TTTCGTG-CTTCAAAAAGAAA
1 TTTCGTGTTTTC--AAA-AAA
* *
12032366 ATTAGTGTTTTCAAAAAAAAAA
1 TTTCGTGTTTTC----AAAAAA
*
12032388 TTCTCGTG-TTTC-AAAAT
1 TT-TCGTGTTTTCAAAAAA
*
12032405 TTTCGTG-TTTAAAAAAA
1 TTTCGTGTTTTCAAAAAA
** * *
12032422 AATCATG-TTTC-TAAAA
1 TTTCGTGTTTTCAAAAAA
12032438 -TTCTGTTGTTTT-AAAAAA
1 TTTC-G-TGTTTTCAAAAAA
12032456 TTTCGTGTTTTCAAAAAA
1 TTTCGTGTTTTCAAAAAA
12032474 AAAAGGTTGC
Statistics
Matches: 228, Mismatches: 45, Indels: 62
0.68 0.13 0.19
Matches are distributed among these distances:
15 2 0.01
16 34 0.15
17 68 0.30
18 65 0.29
19 25 0.11
20 14 0.06
21 3 0.01
22 8 0.04
23 9 0.04
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (18 bp):
TTTCGTGTTTTCAAAAAA
Found at i:12034655 original size:33 final size:31
Alignment explanation
Indices: 12034613--12034679 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 31
12034603 ATTTAATTAA
12034613 TTTTTAAATTTTTAAA-AAATTCTAAAAATATT
1 TTTTTAAATTTTTAAATAAATT-TAAAAAT-TT
*
12034645 TTTTATAAATTTTTAAATAAATTTAATAATTT
1 TTTT-TAAATTTTTAAATAAATTTAAAAATTT
12034677 TTT
1 TTT
12034680 AAAAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 9 0.28
33 18 0.56
34 5 0.16
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTTTAAATTTTTAAATAAATTTAAAAATTT
Found at i:12034662 original size:21 final size:21
Alignment explanation
Indices: 12034649--12034692 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
12034639 AATATTTTTT
12034649 ATAAATTTTTAAATAAATTTA
1 ATAAATTTTTAAATAAATTTA
* * *
12034670 ATAATTTTTTAAAAAAAATTA
1 ATAAATTTTTAAATAAATTTA
12034691 AT
1 AT
12034693 GTTTGTACGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAATTTTTAAATAAATTTA
Found at i:12035931 original size:18 final size:17
Alignment explanation
Indices: 12035904--12035948 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
12035894 AAAATATTTT
**
12035904 AAAAAATATTTTCAATA
1 AAAAAATATTTAAAATA
12035921 AAAAAACTATTTAAAATA
1 AAAAAA-TATTTAAAATA
12035939 AAAATAATAT
1 AAAA-AATAT
12035949 GAAAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 16 0.67
19 2 0.08
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAAATATTTAAAATA
Found at i:12037249 original size:16 final size:15
Alignment explanation
Indices: 12037229--12037269 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
12037219 AAATTAAGAG
12037229 TTATTTTTTAATTTA
1 TTATTTTTTAATTTA
* *
12037244 TGTATTATTTATTTTA
1 T-TATTTTTTAATTTA
12037260 TTATTTTTTA
1 TTATTTTTTA
12037270 CATATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (15 bp):
TTATTTTTTAATTTA
Found at i:12046606 original size:10 final size:10
Alignment explanation
Indices: 12046573--12046618 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
12046563 TAAAAACCAT
12046573 AAAAATTATA
1 AAAAATTATA
12046583 AACAAGATTTATA
1 AA-AA-A-TTATA
12046596 AAAAATTAT-
1 AAAAATTATA
12046605 -AAAATTATA
1 AAAAATTATA
12046614 AAAAA
1 AAAAA
12046619 ACTTTATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 8 0.26
10 10 0.32
11 3 0.10
12 3 0.10
13 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:12046609 original size:31 final size:31
Alignment explanation
Indices: 12046574--12046632 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
12046564 AAAAACCATA
*
12046574 AAAATTATAAACAAGA-TTTATAAAAAATTAT
1 AAAATTATAAA-AAAACTTTATAAAAAATTAT
*
12046605 AAAATTATAAAAAAACTTTATTAAAAAT
1 AAAATTATAAAAAAACTTTATAAAAAAT
12046633 AACAATATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (31 bp):
AAAATTATAAAAAAACTTTATAAAAAATTAT
Found at i:12053570 original size:11 final size:11
Alignment explanation
Indices: 12053553--12053582 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
12053543 ACCCATATTA
12053553 AATTTTTATAT
1 AATTTTTATAT
*
12053564 TATTTTTATAT
1 AATTTTTATAT
12053575 AATTTTTA
1 AATTTTTA
12053583 AATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
AATTTTTATAT
Found at i:12053752 original size:30 final size:30
Alignment explanation
Indices: 12053707--12053768 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
12053697 CTTAACAAGT
*
12053707 AAATTCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
*
12053737 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
12053767 AA
1 AA
12053769 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:12053823 original size:22 final size:22
Alignment explanation
Indices: 12053798--12053840 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12053788 TATCTAAATA
12053798 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
12053820 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
12053841 AATAGAGAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:12058440 original size:2 final size:2
Alignment explanation
Indices: 12058433--12058468 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
12058423 TTGCTTGTTT
*
12058433 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12058469 GTAACTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12070918 original size:12 final size:12
Alignment explanation
Indices: 12070901--12070926 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12070891 GTTTGGCATG
12070901 TACCTATCTAGT
1 TACCTATCTAGT
12070913 TACCTATCTAGT
1 TACCTATCTAGT
12070925 TA
1 TA
12070927 AGTCACTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (12 bp):
TACCTATCTAGT
Found at i:12073578 original size:25 final size:25
Alignment explanation
Indices: 12073550--12073612 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
12073540 ACAAGCACAT
*
12073550 TAACGGGAAGCTCTTCCGAGCCATA
1 TAACGGGAAGCTCATCCGAGCCATA
** *
12073575 TAACGGGAAGCTCATGTGAGCCATG
1 TAACGGGAAGCTCATCCGAGCCATA
12073600 TAACGGGAAGCTC
1 TAACGGGAAGCTC
12073613 GCAAGAACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.19
Consensus pattern (25 bp):
TAACGGGAAGCTCATCCGAGCCATA
Found at i:12073856 original size:21 final size:20
Alignment explanation
Indices: 12073806--12073856 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
12073796 TATGACAATT
*
12073806 TATACAATTCACACATATAA
1 TATACAAATCACACATATAA
*
12073826 TATTCAAAATCA-ATCATATAAA
1 TATAC-AAATCACA-CATAT-AA
12073848 TATACAAAT
1 TATACAAAT
12073857 TAGTTACACG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 5 0.20
21 14 0.56
22 6 0.24
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (20 bp):
TATACAAATCACACATATAA
Found at i:12077508 original size:23 final size:23
Alignment explanation
Indices: 12077478--12077524 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
12077468 ATTACAACTT
*
12077478 ATCTATACTTATATAGTAAAGTA
1 ATCTATACCTATATAGTAAAGTA
*
12077501 ATCTATACCTATATATTAAAGTA
1 ATCTATACCTATATAGTAAAGTA
12077524 A
1 A
12077525 GGTCCAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (23 bp):
ATCTATACCTATATAGTAAAGTA
Found at i:12078974 original size:29 final size:30
Alignment explanation
Indices: 12078939--12078997 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
12078929 TCTTGGTTGA
*
12078939 TGTGTAATTTTATATA-AAAACTTTGATTT
1 TGTGTAATTTTATACATAAAACTTTGATTT
*
12078968 TGTGTAATTTTATACATAAAATTTTGATTT
1 TGTGTAATTTTATACATAAAACTTTGATTT
12078998 GATTTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (30 bp):
TGTGTAATTTTATACATAAAACTTTGATTT
Found at i:12081427 original size:17 final size:17
Alignment explanation
Indices: 12081405--12081438 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12081395 AGATAATTGT
12081405 CATTTGGAAGCTTTAGA
1 CATTTGGAAGCTTTAGA
12081422 CATTTGGAAGCTTTAGA
1 CATTTGGAAGCTTTAGA
12081439 ACCTCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (17 bp):
CATTTGGAAGCTTTAGA
Found at i:12087154 original size:15 final size:16
Alignment explanation
Indices: 12087134--12087164 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12087124 AATAAAAAAG
12087134 AGAAAC-AAAAAGAGA
1 AGAAACAAAAAAGAGA
12087149 AGAAACAAAAAAGAGA
1 AGAAACAAAAAAGAGA
12087165 GAGAGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.74, C:0.06, G:0.19, T:0.00
Consensus pattern (16 bp):
AGAAACAAAAAAGAGA
Found at i:12092190 original size:26 final size:25
Alignment explanation
Indices: 12092154--12092205 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
12092144 TTCTAAAAAC
* *
12092154 GGGATGCTAGAAAATTTATGTTATTT
1 GGGATACTAGAAAAATTA-GTTATTT
12092180 GGGATACTAGAAAAATTAGTTATTT
1 GGGATACTAGAAAAATTAGTTATTT
12092205 G
1 G
12092206 AGTATTTACG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (25 bp):
GGGATACTAGAAAAATTAGTTATTT
Found at i:12102070 original size:19 final size:20
Alignment explanation
Indices: 12102034--12102071 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12102024 ATCAAAATCA
*
12102034 TTTTTTCTTGATTCAAAAGT
1 TTTTTTCTTGAATCAAAAGT
*
12102054 TTTTTTTTTGAAT-AAAAG
1 TTTTTTCTTGAATCAAAAG
12102072 CAATATTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTTTCTTGAATCAAAAGT
Found at i:12102755 original size:30 final size:29
Alignment explanation
Indices: 12102718--12102813 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
12102708 TATTCATAAC
*
12102718 AATAAAAA-CATATTAAAATTCTTAAAAACT
1 AATAAAAATCATA-TAAAATTATTAAAAA-T
*
12102748 TATAAAAATCATATAAAATTATTAAAAAT
1 AATAAAAATCATATAAAATTATTAAAAAT
* * *
12102777 AATAAAATTGATATAAACTTA-TAAAAATT
1 AATAAAAATCATATAAAATTATTAAAAA-T
*
12102806 ATTAAAAA
1 AATAAAAA
12102814 AACATAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 6 0.11
29 25 0.45
30 21 0.38
31 4 0.07
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (29 bp):
AATAAAAATCATATAAAATTATTAAAAAT
Found at i:12102765 original size:20 final size:20
Alignment explanation
Indices: 12102728--12102813 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
12102718 AATAAAAACA
* *
12102728 TATTAAAATTCTTA-AAAACT
1 TATTAAAAATCATATAAAA-T
12102748 TA-TAAAAATCATATAAAAT
1 TATTAAAAATCATATAAAAT
12102767 TATTAAAAAT-A-ATAAAAT
1 TATTAAAAATCATATAAAAT
* *
12102785 TGA-TATAAA-CTTATAAAAAT
1 T-ATTAAAAATCATAT-AAAAT
12102805 TATTAAAAA
1 TATTAAAAA
12102814 AACATAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
18 13 0.24
19 17 0.31
20 24 0.44
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (20 bp):
TATTAAAAATCATATAAAAT
Found at i:12103252 original size:9 final size:9
Alignment explanation
Indices: 12103240--12103465 Score: 93
Period size: 10 Copynumber: 23.8 Consensus size: 9
12103230 TTTTATGATT
12103240 TTTTTATAA
1 TTTTTATAA
12103249 TTTTTATAA
1 TTTTTATAA
*
12103258 GTTTATATCAA
1 -TTTTTAT-AA
*
12103269 -TTTTA-AT
1 TTTTTATAA
*
12103276 TTTTTATCAG
1 TTTTTAT-AA
*
12103286 TTTTTAAGAA
1 TTTTT-ATAA
*
12103296 TTTTAATACA
1 TTTTTATA-A
12103306 TTTTTATAAA
1 TTTTTAT-AA
* *
12103316 ATTTTAAATA
1 TTTTTATA-A
12103326 TATTTTATAA
1 T-TTTTATAA
**
12103336 AATTTATAA
1 TTTTTATAA
*
12103345 GTTTTTATCA
1 -TTTTTATAA
12103355 -TTTTATTATA
1 TTTTTA-TA-A
*
12103365 TTTTAATAA
1 TTTTTATAA
*
12103374 GTTTATATAA
1 -TTTTTATAA
* *
12103384 -GTTTATTA
1 TTTTTATAA
*
12103392 TTTTTAAAA
1 TTTTTATAA
12103401 TATTTT-TAA
1 T-TTTTATAA
12103410 TTTTTAATAA
1 TTTTT-ATAA
*
12103420 TTTTTTATACT
1 -TTTTTATA-A
*
12103431 TTTTTATGA
1 TTTTTATAA
*
12103440 TTTTTATATT
1 TTTTTATA-A
12103450 TTTTTATAA
1 TTTTTATAA
*
12103459 CTTTTAT
1 TTTTTAT
12103466 GAAAAAATAT
Statistics
Matches: 159, Mismatches: 36, Indels: 44
0.67 0.15 0.18
Matches are distributed among these distances:
7 1 0.01
8 19 0.12
9 47 0.30
10 73 0.46
11 19 0.12
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:12103287 original size:27 final size:27
Alignment explanation
Indices: 12103249--12103302 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
12103239 TTTTTTATAA
*
12103249 TTTTTATAAGTTTATATCAATTTTAAT
1 TTTTTATAAGTTTATAACAATTTTAAT
* * *
12103276 TTTTTATCAGTTTTTAAGAATTTTAAT
1 TTTTTATAAGTTTATAACAATTTTAAT
12103303 ACATTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (27 bp):
TTTTTATAAGTTTATAACAATTTTAAT
Found at i:12103330 original size:22 final size:21
Alignment explanation
Indices: 12103286--12103340 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
12103276 TTTTTATCAG
*
12103286 TTTTTA-AGAATTTTAATACA
1 TTTTTATAAAATTTTAATACA
*
12103306 TTTTTATAAAATTTTAA-ATA
1 TTTTTATAAAATTTTAATACA
12103326 TATTTTATAAAATTT
1 T-TTTTATAAAATTT
12103341 ATAAGTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTTATAAAATTTTAATACA
Found at i:12103374 original size:29 final size:28
Alignment explanation
Indices: 12103341--12103398 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
12103331 TATAAAATTT
* * *
12103341 ATAAGTTTTTATCATTTTATTATATTTTA
1 ATAAGTTTATATAAGTTTATTAT-TTTTA
12103370 ATAAGTTTATATAAGTTTATTATTTTTA
1 ATAAGTTTATATAAGTTTATTATTTTTA
12103398 A
1 A
12103399 AATATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (28 bp):
ATAAGTTTATATAAGTTTATTATTTTTA
Found at i:12103435 original size:29 final size:30
Alignment explanation
Indices: 12103403--12103463 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
12103393 TTTTAAAATA
12103403 TTTT-TAATTTTTAATAATTTTTTAT-ACTT
1 TTTTATAATTTTT-ATAATTTTTTATAACTT
* *
12103432 TTTTATGATTTTTATATTTTTTTATAACTT
1 TTTTATAATTTTTATAATTTTTTATAACTT
12103462 TT
1 TT
12103464 ATGAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (30 bp):
TTTTATAATTTTTATAATTTTTTATAACTT
Found at i:12103463 original size:19 final size:19
Alignment explanation
Indices: 12103422--12103465 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12103412 TTTAATAATT
* *
12103422 TTTTATACTTTTTTATGAT
1 TTTTATACTTTTTTATAAC
*
12103441 TTTTATATTTTTTTATAAC
1 TTTTATACTTTTTTATAAC
12103460 TTTTAT
1 TTTTAT
12103466 GAAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTATACTTTTTTATAAC
Found at i:12114262 original size:2 final size:2
Alignment explanation
Indices: 12114257--12114282 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12114247 AATCACACAC
12114257 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12114283 TCCCATGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12117672 original size:4 final size:4
Alignment explanation
Indices: 12117658--12117689 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
12117648 CTATTACCAT
12117658 AAAC AAAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC -AAAC AAAC AAAC AAAC AAAC AAAC AAA
12117690 TCGAATCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:12120138 original size:2 final size:2
Alignment explanation
Indices: 12120131--12120159 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12120121 ATGATGAACA
12120131 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12120160 ATCTACCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12120306 original size:2 final size:2
Alignment explanation
Indices: 12120301--12120353 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
12120291 AAAAGCTTTG
12120301 TC TC TC -C TC TC 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 TC TC TC TC TC TC
12120342 TC TC TC TC TC TC
1 TC TC TC TC TC TC
12120354 CTCCTCCTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:12121888 original size:2 final size:2
Alignment explanation
Indices: 12121881--12121911 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12121871 CTAAAAGGCT
12121881 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12121912 GTTATGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12132516 original size:34 final size:34
Alignment explanation
Indices: 12132478--12132597 Score: 145
Period size: 34 Copynumber: 3.6 Consensus size: 34
12132468 GCTATTGCAA
*
12132478 TGATCCATTATAAGCATGTTAATTGCTACCGTAT
1 TGATCTATTATAAGCATGTTAATTGCTACCGTAT
* **
12132512 TGATCTATTATAAGCATGATAATTGCTATTGTAT
1 TGATCTATTATAAGCATGTTAATTGCTACCGTAT
* *
12132546 CGA-CTTATTATAAACATGTT-ATTGCTACCGTAT
1 TGATC-TATTATAAGCATGTTAATTGCTACCGTAT
* *
12132579 TGATTTGTTATAAGCATGT
1 TGATCTATTATAAGCATGT
12132598 CATGTTGTAT
Statistics
Matches: 71, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
33 26 0.37
34 45 0.63
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (34 bp):
TGATCTATTATAAGCATGTTAATTGCTACCGTAT
Found at i:12132730 original size:21 final size:23
Alignment explanation
Indices: 12132704--12132754 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
12132694 GCAGTTTATT
12132704 TACAAC-GATT-AGTGGTTCATC
1 TACAACAGATTAAGTGGTTCATC
*
12132725 TACAACATATTACAGTGGTTCATC
1 TACAACAGATTA-AGTGGTTCATC
*
12132749 CACAAC
1 TACAAC
12132755 CTACTAGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.24
22 3 0.12
24 16 0.64
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (23 bp):
TACAACAGATTAAGTGGTTCATC
Found at i:12134305 original size:40 final size:40
Alignment explanation
Indices: 12134238--12134372 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 40
12134228 ACCAGTTTAG
* *
12134238 CACCTAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATCGGATAAATCGAAGTAATAAGTTGA
* * *
12134278 CACCCAGTGTCTCATCGGCTAAATCGAAGT-A-AA-TTGG
1 CACCCAGTGCCTCATCGGATAAATCGAAGTAATAAGTTGA
* * * *
12134315 CACCTAATGCCTCATCGAATTAATCCGAAGTAAT-AGATTGA
1 CACCCAGTGCCTCATCGGATAAAT-CGAAGTAATAAG-TTGA
*
12134356 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
12134373 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 21 0.28
38 8 0.11
39 3 0.04
40 26 0.35
41 17 0.23
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGGATAAATCGAAGTAATAAGTTGA
Found at i:12134871 original size:8 final size:8
Alignment explanation
Indices: 12134858--12134887 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
12134848 TTAATATTAT
12134858 TATAATAA
1 TATAATAA
12134866 TATAATAA
1 TATAATAA
12134874 TATAAT-A
1 TATAATAA
12134881 TATAATA
1 TATAATA
12134888 TACTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATAATAA
Found at i:12141575 original size:13 final size:13
Alignment explanation
Indices: 12141543--12141567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12141533 TTAATATTAT
12141543 TATAATAATATAA
1 TATAATAATATAA
12141556 TATAATAATATA
1 TATAATAATATA
12141568 TTTAAATATT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAATAATATAA
Found at i:12141584 original size:23 final size:23
Alignment explanation
Indices: 12141549--12141609 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 23
12141539 TTATTATAAT
12141549 AATATAATATAATA-ATATATTTA
1 AATATAATATAATACATAT-TTTA
12141572 AATATTAAT-TAATACATATTTT-
1 AATA-TAATATAATACATATTTTA
12141594 -AT-TAATAT-ATACATAT
1 AATATAATATAATACATAT
12141610 GTATATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
19 12 0.34
20 1 0.03
21 2 0.06
23 12 0.34
24 8 0.23
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (23 bp):
AATATAATATAATACATATTTTA
Found at i:12142551 original size:2 final size:2
Alignment explanation
Indices: 12142544--12142576 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12142534 ACATACATAC
12142544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12142577 ATCCAACCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12144250 original size:21 final size:21
Alignment explanation
Indices: 12144226--12144266 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12144216 TATAATTAAC
*
12144226 ATAATATTATTTATATTTATG
1 ATAATATTATATATATTTATG
* *
12144247 ATAATTTTATATATTTTTAT
1 ATAATATTATATATATTTAT
12144267 TTTCTTAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATAATATTATATATATTTATG
Found at i:12149668 original size:21 final size:19
Alignment explanation
Indices: 12149644--12149694 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
12149634 TGAATCAAGC
*
12149644 CGAGTGAAATGAAATCCGAGT
1 CGAGTGAAATG-AAT-CGAAT
*
12149665 CGAGTCAAATTGAATCGAAT
1 CGAGTGAAA-TGAATCGAAT
12149685 CGAGTGAAAT
1 CGAGTGAAAT
12149695 TGTTCAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 12 0.46
21 11 0.42
22 2 0.08
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (19 bp):
CGAGTGAAATGAATCGAAT
Found at i:12149901 original size:10 final size:10
Alignment explanation
Indices: 12149886--12149944 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
12149876 TTATTATTCT
12149886 AATTTTTTTA
1 AATTTTTTTA
12149896 AA-TTTTTTA
1 AATTTTTTTA
12149905 AATTTTTTTA
1 AATTTTTTTA
* *
12149915 TATACTTTTTA
1 AAT-TTTTTTA
* *
12149926 GAATATTTTTG
1 -AATTTTTTTA
12149937 AATTTTTT
1 AATTTTTT
12149945 ATAATATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 9 0.22
10 18 0.45
11 11 0.28
12 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:12149910 original size:8 final size:9
Alignment explanation
Indices: 12149889--12149945 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 9
12149879 TTATTCTAAT
12149889 TTTTTTAAA
1 TTTTTTAAA
12149898 TTTTTTAAA
1 TTTTTTAAA
12149907 TTTTTTTATATA
1 -TTTTTTA-A-A
*
12149919 CTTTTTAGAA
1 TTTTTTA-AA
*
12149929 TATTTTTGAA
1 T-TTTTTAAA
12149939 TTTTTTA
1 TTTTTTA
12149946 TAATATTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
9 14 0.36
10 11 0.28
11 13 0.33
12 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:12149990 original size:19 final size:19
Alignment explanation
Indices: 12149968--12150032 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
12149958 AACATATAAT
*
12149968 TTTTTAATTTTTATAAATA
1 TTTTGAATTTTTATAAATA
12149987 TTTTGAA-TTTTA-AAAT-
1 TTTTGAATTTTTATAAATA
* *
12150003 TCTTTTAATTTTTGATAATTA
1 T-TTTGAATTTTT-ATAAATA
12150024 TTTTGAATT
1 TTTTGAATT
12150033 ATTTTGTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.03
17 9 0.24
18 9 0.24
19 7 0.19
20 10 0.27
21 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTGAATTTTTATAAATA
Found at i:12149997 original size:18 final size:18
Alignment explanation
Indices: 12149976--12150032 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
12149966 ATTTTTTAAT
12149976 TTTTATAAATATTTTGAA
1 TTTTATAAATATTTTGAA
*
12149994 TTTTA-AAAT-TCTTTTAA
1 TTTTATAAATAT-TTTGAA
*
12150011 TTTTTGATAATTATTTTGAA
1 -TTTT-ATAAATATTTTGAA
12150031 TT
1 TT
12150033 ATTTTGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
16 1 0.03
17 9 0.29
18 9 0.29
19 3 0.10
20 8 0.26
21 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTATAAATATTTTGAA
Found at i:12150012 original size:17 final size:17
Alignment explanation
Indices: 12149965--12150014 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
12149955 AAAAACATAT
12149965 AATTTTTTAATTTTTATA
1 AATTTTTTAA-TTTTATA
*
12149983 AATATTTTGAATTTTA-A
1 AAT-TTTTTAATTTTATA
12150000 AATTCTTTTAATTTT
1 AATT-TTTTAATTTT
12150015 TGATAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
18 8 0.29
19 6 0.21
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
AATTTTTTAATTTTATA
Found at i:12152419 original size:2 final size:2
Alignment explanation
Indices: 12152412--12152441 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12152402 CTGAATATTC
12152412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12152442 TCCTCCTCCT
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):
AT
Found at i:12161982 original size:4 final size:4
Alignment explanation
Indices: 12161973--12162035 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
12161963 CGGATTTTTC
12161973 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
12162021 TATG TATG TATG TAT
1 TATG TATG TATG TAT
12162036 TAGTTTACTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:12180809 original size:20 final size:21
Alignment explanation
Indices: 12180786--12180826 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12180776 AATTTAAAAA
12180786 TAAAAAATAAAAAA-ATATTT
1 TAAAAAATAAAAAATATATTT
**
12180806 TAAAATTTAAAAAATATATTT
1 TAAAAAATAAAAAATATATTT
12180827 ATTATATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAAAATAAAAAATATATTT
Found at i:12180810 original size:19 final size:20
Alignment explanation
Indices: 12180788--12180827 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12180778 TTTAAAAATA
12180788 AAAAATAAAAAAATAT-TTT
1 AAAAATAAAAAAATATATTT
* *
12180807 AAAATTTAAAAAATATATTT
1 AAAAATAAAAAAATATATTT
12180827 A
1 A
12180828 TTATATACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATAAAAAAATATATTT
Found at i:12182488 original size:85 final size:85
Alignment explanation
Indices: 12182344--12182518 Score: 323
Period size: 85 Copynumber: 2.1 Consensus size: 85
12182334 GGGATAGCTA
*
12182344 ACACATAGTATGCTAACTCATATAACTATAATCTGTCAATTCTTGTACATGTATACTCACACGAG
1 ACACATAGTATGCTAACTCATATAACTATAATCCGTCAATTCTTGTACATGTATACTCACACGAG
12182409 CTGTGAAAATAGGTCTGCTC
66 CTGTGAAAATAGGTCTGCTC
* *
12182429 ACACATCGTATGCTAACTCATATAACTATAATCCGTCAATTCTTGTACATGTATGCTCACACGAG
1 ACACATAGTATGCTAACTCATATAACTATAATCCGTCAATTCTTGTACATGTATACTCACACGAG
12182494 CTGTGAAAATAGGTCTGCTC
66 CTGTGAAAATAGGTCTGCTC
12182514 ACACA
1 ACACA
12182519 AGCTGTGGGT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (85 bp):
ACACATAGTATGCTAACTCATATAACTATAATCCGTCAATTCTTGTACATGTATACTCACACGAG
CTGTGAAAATAGGTCTGCTC
Found at i:12183555 original size:24 final size:24
Alignment explanation
Indices: 12183521--12183590 Score: 122
Period size: 24 Copynumber: 2.9 Consensus size: 24
12183511 GAAACCAGTC
12183521 CCACAGCTCCTCTCTTCACCCTTT
1 CCACAGCTCCTCTCTTCACCCTTT
* *
12183545 CCACTGTTCCTCTCTTCACCCTTT
1 CCACAGCTCCTCTCTTCACCCTTT
12183569 CCACAGCTCCTCTCTTCACCCT
1 CCACAGCTCCTCTCTTCACCCT
12183591 ATCGATTGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.34
Consensus pattern (24 bp):
CCACAGCTCCTCTCTTCACCCTTT
Found at i:12187794 original size:33 final size:33
Alignment explanation
Indices: 12187742--12187816 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
12187732 AAGATGTAGA
* *
12187742 AAAATGTTTTGTAGGAGCCCCGCTTTTCAACTC
1 AAAAGGTTTAGTAGGAGCCCCGCTTTTCAACTC
*
12187775 AAAAGGTTTAGTAGGAGCCCTGCTTTTCAACTC
1 AAAAGGTTTAGTAGGAGCCCCGCTTTTCAACTC
12187808 AAAAGGTTT
1 AAAAGGTTT
12187817 CGTCTCAGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (33 bp):
AAAAGGTTTAGTAGGAGCCCCGCTTTTCAACTC
Found at i:12191666 original size:13 final size:13
Alignment explanation
Indices: 12191650--12191675 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12191640 ATTAATTTAG
12191650 TTAATTTAATTAA
1 TTAATTTAATTAA
12191663 TTAATTTAATTAA
1 TTAATTTAATTAA
12191676 GTAAATAATA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:12193308 original size:41 final size:41
Alignment explanation
Indices: 12193263--12193423 Score: 259
Period size: 41 Copynumber: 3.9 Consensus size: 41
12193253 ACTAGCTCTT
* * *
12193263 AGCCTGCTAGACATAATGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
* *
12193304 AGCCTGCTATACTTAAAGCCTGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
12193345 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
* *
12193386 AGCCTTCTAGACTTAAAGTCTGAAATGTTTCACTGGCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCA
12193424 ATAAACATGA
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 111 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
Found at i:12196235 original size:2 final size:2
Alignment explanation
Indices: 12196228--12196252 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12196218 TTGTTAATTA
12196228 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12196253 AATTAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12207108 original size:17 final size:17
Alignment explanation
Indices: 12207083--12207116 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12207073 TGTTTACACT
*
12207083 CTTTTTTTTCAGTTTTA
1 CTTTATTTTCAGTTTTA
*
12207100 CTTTATTTTTAGTTTTA
1 CTTTATTTTCAGTTTTA
12207117 AAATTTGAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.06, T:0.71
Consensus pattern (17 bp):
CTTTATTTTCAGTTTTA
Found at i:12207622 original size:30 final size:30
Alignment explanation
Indices: 12207574--12207679 Score: 110
Period size: 30 Copynumber: 3.5 Consensus size: 30
12207564 TTTTAGGTTA
*
12207574 CTTAAAAGTTGG-AAAAAAAATTTAAATCC
1 CTTAAAAGTTGGTAAAAAAAATTTAAAGCC
**
12207603 CTTAAAAGTTGGTAAAAAAAATTTTCAGCC
1 CTTAAAAGTTGGTAAAAAAAATTTAAAGCC
**
12207633 CTTAAAAGTT--TAAAAAAATATTTTTAGGGCTC
1 CTTAAAAGTTGGTAAAAAAA-A--TTTAAAGC-C
12207665 CTTAAAAGTTGGTAA
1 CTTAAAAGTTGGTAA
12207680 TTTTTTTTAC
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
28 8 0.12
29 13 0.20
30 24 0.38
31 5 0.08
32 11 0.17
34 3 0.05
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (30 bp):
CTTAAAAGTTGGTAAAAAAAATTTAAAGCC
Found at i:12209912 original size:21 final size:20
Alignment explanation
Indices: 12209888--12209934 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
12209878 AAATTAAATT
12209888 TTAAAATTTGAAATATAAAAA
1 TTAAAATTTGAAA-ATAAAAA
*
12209909 TTAAAAATTTTAAAATAAAAA
1 TT-AAAATTTGAAAATAAAAA
12209930 -TAAAA
1 TTAAAA
12209935 AATAAATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 1 0.04
21 9 0.38
22 10 0.42
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TTAAAATTTGAAAATAAAAA
Found at i:12209935 original size:21 final size:22
Alignment explanation
Indices: 12209890--12209937 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
12209880 ATTAAATTTT
*
12209890 AAAATTTGAAATATAAAAATTA
1 AAAATTTGAAATATAAAAATAA
*
12209912 AAAATTTTAAA-ATAAAAATAA
1 AAAATTTGAAATATAAAAATAA
12209933 AAAAT
1 AAAAT
12209938 AAATCTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATTTGAAATATAAAAATAA
Found at i:12210531 original size:17 final size:18
Alignment explanation
Indices: 12210509--12210550 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
12210499 AAACAAGCTT
12210509 AATATTATTA-TATTAAA
1 AATATTATTATTATTAAA
* *
12210526 AATATTTTTTATTTTTAAA
1 AATA-TTATTATTATTAAA
12210545 AATATT
1 AATATT
12210551 TAAAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATTATTATTATTAAA
Found at i:12214807 original size:6 final size:6
Alignment explanation
Indices: 12214798--12214823 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12214788 GATATATATA
12214798 ATACAC ATACAC ATACAC ATACAC AT
1 ATACAC ATACAC ATACAC ATACAC AT
12214824 CCATATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (6 bp):
ATACAC
Found at i:12252077 original size:2 final size:2
Alignment explanation
Indices: 12252070--12252112 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
12252060 ACAATGATAC
* *
12252070 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12252112 T
1 T
12252113 TTTGCTTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12258539 original size:36 final size:36
Alignment explanation
Indices: 12258490--12258579 Score: 144
Period size: 36 Copynumber: 2.4 Consensus size: 36
12258480 TCTGTAAGTG
*
12258490 GTGTATAGAGATGGATGGGTGTTTTATACCCATATGGT
1 GTGT-TAG-GATGGATGAGTGTTTTATACCCATATGGT
12258528 GTGTTAGGATGGATGAGTGTTTTATACCCATATGGT
1 GTGTTAGGATGGATGAGTGTTTTATACCCATATGGT
*
12258564 GTGTTGGGATGGATGA
1 GTGTTAGGATGGATGA
12258580 AGTTGGTGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
36 43 0.86
37 3 0.06
38 4 0.08
ACGTcount: A:0.22, C:0.07, G:0.34, T:0.37
Consensus pattern (36 bp):
GTGTTAGGATGGATGAGTGTTTTATACCCATATGGT
Found at i:12259540 original size:85 final size:87
Alignment explanation
Indices: 12259394--12259557 Score: 235
Period size: 85 Copynumber: 1.9 Consensus size: 87
12259384 TCAAATTTTT
* * * * *
12259394 TTTAAAAAAAAGAGTAATTAAGTCCTTATCTTTTTTTTTTGCACTCAATTAGGTACTTGAACTTT
1 TTTAAAAAAAAAAGTAATTAAGCCCCTAGCTTTTTGTTTTGCACTCAATTAGGTACTTGAACTTT
*
12259459 CAAAATGTATAAAAAATCTCAA
66 CAAAATATATAAAAAATCTCAA
*
12259481 TTTAAAAAAAAAAGTAATTAAGCCCCT-GC-TTTTGTTTTGCACTCAATTGGGTA-TATGAACTT
1 TTTAAAAAAAAAAGTAATTAAGCCCCTAGCTTTTTGTTTTGCACTCAATTAGGTACT-TGAACTT
12259543 TCAAAATATATAAAA
65 TCAAAATATATAAAA
12259558 TACCCTCGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 1 0.01
85 43 0.62
86 1 0.01
87 24 0.35
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (87 bp):
TTTAAAAAAAAAAGTAATTAAGCCCCTAGCTTTTTGTTTTGCACTCAATTAGGTACTTGAACTTT
CAAAATATATAAAAAATCTCAA
Found at i:12259811 original size:26 final size:26
Alignment explanation
Indices: 12259782--12259841 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
12259772 AATAGAAATT
*
12259782 ATAAAAAT-TATTAAATTTTAATAAAA
1 ATAAAAATGT-TTAAAATTTAATAAAA
*
12259808 ATAAAAATGTTTAAAATTTATTAAAA
1 ATAAAAATGTTTAAAATTTAATAAAA
12259834 ATTAAAAA
1 A-TAAAAA
12259842 AATTATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
ATAAAAATGTTTAAAATTTAATAAAA
Found at i:12259843 original size:20 final size:19
Alignment explanation
Indices: 12259820--12259894 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
12259810 AAAAATGTTT
12259820 AAAATTTATTAAAAATTAAA
1 AAAATTTA-TAAAAATTAAA
12259840 AAAA-TTATAAAAATCATAAA
1 AAAATTTATAAAAAT--TAAA
* **
12259860 AAAAATTATAAAAAATTGTA
1 AAAATTTAT-AAAAATTAAA
*
12259880 AAATTTTATAAAAAT
1 AAAATTTATAAAAAT
12259895 AGTAAGAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 7 0.15
19 9 0.19
20 21 0.45
21 4 0.09
22 6 0.13
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (19 bp):
AAAATTTATAAAAATTAAA
Found at i:12259851 original size:8 final size:9
Alignment explanation
Indices: 12259777--12260010 Score: 70
Period size: 9 Copynumber: 24.8 Consensus size: 9
12259767 AAACCAATAG
12259777 AAATTATAA
1 AAATTATAA
*
12259786 AAATTAT-T
1 AAATTATAA
*
12259794 AAATTTTAA
1 AAATTATAA
*
12259803 TAAA-AATAA
1 -AAATTATAA
*
12259812 AAATGTTTAA
1 AAAT-TATAA
*
12259822 AATTTATTAA
1 AAATTA-TAA
*
12259832 AAATTAAAA
1 AAATTATAA
12259841 AAATTATAA
1 AAATTATAA
*
12259850 AAATCATAAAAA
1 AAAT--T-ATAA
12259862 AAATTATAAA
1 AAATTAT-AA
*
12259872 AAATTGTAA
1 AAATTATAA
*
12259881 AATTTTATAA
1 AA-ATTATAA
12259891 AAA-TAGTAA
1 AAATTA-TAA
*
12259900 GAAA-TGT-A
1 -AAATTATAA
12259908 AAATATATAGA
1 AAAT-TATA-A
*
12259919 AAA-TAGAA
1 AAATTATAA
**
12259927 AAAAAATATA
1 AAATTATA-A
*
12259937 AAATTTTATA
1 AAATTATA-A
* *
12259947 AAGTCATAAGA
1 AAATTAT-A-A
12259958 AAATTATAA
1 AAATTATAA
12259967 ACAATGTA-AA
1 A-AAT-TATAA
12259977 GAAA-TATAA
1 -AAATTATAA
* *
12259986 AATTTGTAA
1 AAATTATAA
*
12259995 AAAATATAA
1 AAATTATAA
12260004 AAATTAT
1 AAATTAT
12260011 CGTAACAAAA
Statistics
Matches: 163, Mismatches: 38, Indels: 48
0.65 0.15 0.19
Matches are distributed among these distances:
7 3 0.02
8 20 0.12
9 61 0.37
10 57 0.35
11 15 0.09
12 7 0.04
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (9 bp):
AAATTATAA
Found at i:12259881 original size:10 final size:10
Alignment explanation
Indices: 12259820--12259893 Score: 62
Period size: 10 Copynumber: 7.4 Consensus size: 10
12259810 AAAAATGTTT
* *
12259820 AAAATTTATT
1 AAAAATTATA
12259830 AAAAATTA-A
1 AAAAATTATA
12259839 AAAAATTAT-
1 AAAAATTATA
*
12259848 AAAAATCATAAA
1 AAAAAT--TATA
12259860 AAAAATTATA
1 AAAAATTATA
*
12259870 AAAAATTGTA
1 AAAAATTATA
**
12259880 AAATTTTATA
1 AAAAATTATA
12259890 AAAA
1 AAAA
12259894 TAGTAAGAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
9 14 0.27
10 29 0.57
11 2 0.04
12 6 0.12
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:12259884 original size:18 final size:19
Alignment explanation
Indices: 12259861--12259899 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12259851 AATCATAAAA
*
12259861 AAAATTATA-AAAAATTGT
1 AAAATTATATAAAAATAGT
*
12259879 AAAATTTTATAAAAATAGT
1 AAAATTATATAAAAATAGT
12259898 AA
1 AA
12259900 GAAATGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAATTATATAAAAATAGT
Found at i:12259908 original size:28 final size:29
Alignment explanation
Indices: 12259869--12259948 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 29
12259859 AAAAAATTAT
*
12259869 AAAAAATTGTAAAATTTTATAAAAATAG-
1 AAAAAAATGTAAAATTTTATAAAAATAGA
* * *
12259897 TAAGAAATGTAAAA-TATATAGAAAATAGA
1 AAAAAAATGTAAAATTTTATA-AAAATAGA
*
12259926 AAAAAAATATAAAATTTTATAAA
1 AAAAAAATGTAAAATTTTATAAA
12259949 GTCATAAGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 5 0.12
28 18 0.44
29 13 0.32
30 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (29 bp):
AAAAAAATGTAAAATTTTATAAAAATAGA
Found at i:12259984 original size:19 final size:18
Alignment explanation
Indices: 12259957--12260005 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
12259947 AAGTCATAAG
*
12259957 AAAATTATAAACA-ATGTA
1 AAAAATATAAA-ATATGTA
*
12259975 AAGAAATATAAAATTTGTA
1 AA-AAATATAAAATATGTA
12259994 AAAAATATAAAA
1 AAAAATATAAAA
12260006 ATTATCGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (18 bp):
AAAAATATAAAATATGTA
Found at i:12260233 original size:30 final size:30
Alignment explanation
Indices: 12260194--12260256 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
12260184 TTTTATGCAT
*
12260194 TTTATAATTTTTT-TATGATTTTTATGAAAA
1 TTTACAATTTTTTATAT-ATTTTTATGAAAA
* *
12260224 TTTACAATTTTTTATATTTTTTTATTAAAA
1 TTTACAATTTTTTATATATTTTTATGAAAA
12260254 TTT
1 TTT
12260257 GATAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTACAATTTTTTATATATTTTTATGAAAA
Found at i:12264987 original size:30 final size:30
Alignment explanation
Indices: 12264953--12265015 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
12264943 ACTTAACAAG
12264953 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACCTTTAAAATAATAACAAAATTAA
*
12264983 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTTTAAAATAATAACAAAATTAA
12265013 CAA
1 CAA
12265016 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTTTAAAATAATAACAAAATTAA
Found at i:12265109 original size:11 final size:11
Alignment explanation
Indices: 12265095--12265125 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
12265085 TAAAATAGGG
12265095 AGAAAATAATA
1 AGAAAATAATA
12265106 AGAAAATAATA
1 AGAAAATAATA
12265117 AGAAAATAA
1 AGAAAATAA
12265126 CATTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (11 bp):
AGAAAATAATA
Found at i:12268812 original size:155 final size:154
Alignment explanation
Indices: 12268454--12269220 Score: 999
Period size: 155 Copynumber: 5.0 Consensus size: 154
12268444 AAAAATTGTA
12268454 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* * *
12268519 AAATTAGAAAAT-ATGATA-TTTTTTAAAGTAATAAAATGCGGAGAAAAAAATGCGAACAAATGG
66 AAATTAGAAAATAAT-ATATTTTTTTAAAGTAATAAAATTCGGA-AAAAAAATACGAACAAAGGG
* * *
12268582 CCGAAGTAAGGGTTTTTTACTAAAAT
129 CAGAAATAAGGGTTTTTTACTAAATT
** * * * * * *
12268608 TA-AAAAAAAACAGAATTAATTAATACATTTTAAACATAATGTACTAAAATAAAGTAAAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* *
12268672 AAA-TACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGAAAAAAAATACGAGCAAAGG
66 AAATTA-GAAAATAATATATTTTT-TT-AAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGG
* * *
12268736 GCAAAAATAATGGTTTTTT-TTAAATT
128 GCAGAAATAAGGGTTTTTTACTAAATT
*
12268762 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAGAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* * * *
12268827 AAATTAGAAAATAGTATA-TTTTTTAAAGTAATACAATTCGGGAAAAAAATACGAACAAAGGGCC
66 AAATTAGAAAATAATATATTTTTTTAAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGGGCA
12268891 GAAATAAGGGTTTTTTACTAAA-T
131 GAAATAAGGGTTTTTTACTAAATT
* * * * *
12268914 TA---AAAAAA-AGAATTAATTAATACATTTCAAACATAATGTACTAAAATAAAGTAAAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* * *
12268975 AAA-TACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCAGG-AAAAAAATACGAGCAAAT
66 AAATTA-GAAAATAATATATTTTT-TT-AAAGTAATAAAATTC-GGAAAAAAAATACGAACAAAG
*
12269038 GGCAGAAATAAGAGTTTTTT--TAAAATT
127 GGCAGAAATAAGGGTTTTTTACT-AAATT
12269065 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* *
12269130 AAATTAGAAAATAGTATATTTTTTTAAAGTAATACAATTCGGGAAAAAAAATACGAACAAAGGGT
66 AAATTAGAAAATAATATATTTTTTTAAAGTAATAAAATTC-GGAAAAAAAATACGAACAAAGGG-
12269195 C-GAAATAAGGGTTTTTTACTAAATT
129 CAGAAATAAGGGTTTTTTACTAAATT
12269220 T
1 T
12269221 TTTTTTGAAG
Statistics
Matches: 527, Mismatches: 62, Indels: 47
0.83 0.10 0.07
Matches are distributed among these distances:
147 2 0.00
148 60 0.11
149 11 0.02
150 5 0.01
151 51 0.10
152 57 0.11
153 87 0.17
154 60 0.11
155 172 0.33
156 22 0.04
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (154 bp):
TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
AAATTAGAAAATAATATATTTTTTTAAAGTAATAAAATTCGGAAAAAAAATACGAACAAAGGGCA
GAAATAAGGGTTTTTTACTAAATT
Found at i:12269026 original size:303 final size:305
Alignment explanation
Indices: 12268454--12269219 Score: 1326
Period size: 303 Copynumber: 2.5 Consensus size: 305
12268444 AAAAATTGTA
12268454 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* * * *
12268519 AAATTAGAAAATA-TGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATGCGAACAAATGGC
66 AAATTAGAAAATAGT-ATATTTTTTAAAGTAATACAATTCGG-GAAAAAAATACGAACAAAGGGC
* *
12268583 CGAAGTAAGGGTTTTTTACTAAAATTAAAAAAAAACAGAATTAATTAATACATTTTAAACATAAT
129 CGAAATAAGGGTTTTTTACT-AAATT-AAAAAAAACAGAATTAATTAATACATTTCAAACATAAT
12268648 GTACTAAAATAAAGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATT
192 GTACTAAAATAAAGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATT
*
12268713 CGGAAAAAAAATACGAGCAAAGGGCAAAAATAATG-GTTTTTTTTAAATT
257 CGGAAAAAAAATACGAGCAAAGGGCAAAAATAA-GAGTTTTTTTAAAATT
*
12268762 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAGAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
12268827 AAATTAGAAAATAGTATATTTTTTAAAGTAATACAATTCGGGAAAAAAATACGAACAAAGGGCCG
66 AAATTAGAAAATAGTATATTTTTTAAAGTAATACAATTCGGGAAAAAAATACGAACAAAGGGCCG
12268892 AAATAAGGGTTTTTTACTAAATT-AAAAAAA-AGAATTAATTAATACATTTCAAACATAATGTAC
131 AAATAAGGGTTTTTTACTAAATTAAAAAAAACAGAATTAATTAATACATTTCAAACATAATGTAC
12268955 TAAAATAAAGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCAGG
196 TAAAATAAAGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTC-GG
* *
12269020 -AAAAAAATACGAGCAAATGGCAGAAATAAGAGTTTTTTTAAAATT
260 AAAAAAAATACGAGCAAAGGGCAAAAATAAGAGTTTTTTTAAAATT
12269065 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
*
12269130 AAATTAGAAAATAGTATATTTTTTTAAAGTAATACAATTCGGGAAAAAAAATACGAACAAAGGGT
66 AAATTAGAAAATAGTATA-TTTTTTAAAGTAATACAATTCGGG-AAAAAAATACGAACAAAGGGC
12269195 CGAAATAAGGGTTTTTTACTAAATT
129 CGAAATAAGGGTTTTTTACTAAATT
12269220 TTTTTTTGAA
Statistics
Matches: 441, Mismatches: 12, Indels: 13
0.95 0.03 0.03
Matches are distributed among these distances:
302 1 0.00
303 216 0.49
304 33 0.07
305 45 0.10
306 5 0.01
307 39 0.09
308 101 0.23
309 1 0.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (305 bp):
TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
AAATTAGAAAATAGTATATTTTTTAAAGTAATACAATTCGGGAAAAAAATACGAACAAAGGGCCG
AAATAAGGGTTTTTTACTAAATTAAAAAAAACAGAATTAATTAATACATTTCAAACATAATGTAC
TAAAATAAAGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGA
AAAAAAATACGAGCAAAGGGCAAAAATAAGAGTTTTTTTAAAATT
Found at i:12270878 original size:12 final size:12
Alignment explanation
Indices: 12270858--12270894 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
12270848 TGATCCTAAA
12270858 CCAGAGCCCGAG
1 CCAGAGCCCGAG
*
12270870 CCGGAGCCCGAG
1 CCAGAGCCCGAG
*
12270882 CCAGATCCCGAG
1 CCAGAGCCCGAG
12270894 C
1 C
12270895 AGTCACATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.22, C:0.43, G:0.32, T:0.03
Consensus pattern (12 bp):
CCAGAGCCCGAG
Found at i:12271545 original size:124 final size:124
Alignment explanation
Indices: 12271325--12271576 Score: 468
Period size: 124 Copynumber: 2.0 Consensus size: 124
12271315 ATATAATGTT
12271325 AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
1 AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
* **
12271390 CTGAATTTAAGTTAATGGGTGTTTAAACAACATTGCAACATCTGAACATTACACATAAC
66 CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCCAAACATTACACATAAC
*
12271449 AATTATTCCGAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
1 AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
12271514 CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCCAAACATTACACATAAC
66 CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCCAAACATTACACATAAC
12271573 AATT
1 AATT
12271577 TGACAGCATT
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (124 bp):
AATTATTCCAAATGAATTATACTTTTTATAACTTAATTTGGATACAATTTAAGCATAAGCATAAG
CTGAATTTAAGTTAATGGGTGTTAAAACAACATTGCAACATCCAAACATTACACATAAC
Found at i:12274532 original size:37 final size:38
Alignment explanation
Indices: 12274448--12274534 Score: 108
Period size: 37 Copynumber: 2.3 Consensus size: 38
12274438 ACTAACACAA
* *
12274448 TAACAATAATAATAGTTTTATACTCAAAATAATACTAAC
1 TAACAATAATAATAGGTTTATACT-AAAATAATAATAAC
12274487 TAACAATAATAATTAGGGTTT-TACT-AAA-AATAATAAC
1 TAACAATAATAA-TA-GGTTTATACTAAAATAATAATAAC
12274524 TAACAATAATA
1 TAACAATAATA
12274535 TAATGTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
37 19 0.43
38 3 0.07
39 12 0.27
40 6 0.14
41 4 0.09
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (38 bp):
TAACAATAATAATAGGTTTATACTAAAATAATAATAAC
Found at i:12274566 original size:23 final size:23
Alignment explanation
Indices: 12274523--12274567 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12274513 AAAATAATAA
*
12274523 CTAACAATAATATAATGTAAAAC
1 CTAACAATAATATAATCTAAAAC
*
12274546 CTAACAATCATACTAA-CTAAAA
1 CTAACAATAATA-TAATCTAAAA
12274568 TAATAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.56, C:0.18, G:0.02, T:0.24
Consensus pattern (23 bp):
CTAACAATAATATAATCTAAAAC
Found at i:12282579 original size:16 final size:16
Alignment explanation
Indices: 12282558--12282588 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12282548 TAGATGCATC
*
12282558 TATCAAAATCATATAA
1 TATCAAAACCATATAA
12282574 TATCAAAACCATATA
1 TATCAAAACCATATA
12282589 CATGGTGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (16 bp):
TATCAAAACCATATAA
Found at i:12283904 original size:2 final size:2
Alignment explanation
Indices: 12283897--12283936 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
12283887 AACCATTTTC
*
12283897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12283937 ATCACTTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12285065 original size:41 final size:42
Alignment explanation
Indices: 12284967--12285070 Score: 133
Period size: 41 Copynumber: 2.5 Consensus size: 42
12284957 TCTGATTCAA
* * * *
12284967 TTCACCGGCAATT-AGCCTGCTAGACTTAAAGTCCGAATTAT
1 TTCACCGGCACTTAAGCCTGCTAGACATAAAGTCCGAATAAC
* *
12285008 TTCACCGACAC-AAAGCCTGCTAGACATAAAGTCCGAATAAC
1 TTCACCGGCACTTAAGCCTGCTAGACATAAAGTCCGAATAAC
12285049 TTCACCGGC-CTTAAGCCTGCTA
1 TTCACCGGCACTTAAGCCTGCTA
12285071 AGTTTTAAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 52 0.98
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (42 bp):
TTCACCGGCACTTAAGCCTGCTAGACATAAAGTCCGAATAAC
Found at i:12286759 original size:13 final size:13
Alignment explanation
Indices: 12286741--12286765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12286731 TCAAACTATC
12286741 AAATTTTCACACG
1 AAATTTTCACACG
12286754 AAATTTTCACAC
1 AAATTTTCACAC
12286766 ATATAACTTA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:12289077 original size:55 final size:56
Alignment explanation
Indices: 12289002--12289110 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 56
12288992 AAGAACTAAG
* * *
12289002 GATGATACTGGAATCGAACCAGAATCT-GGGGCTGAAACTGTAAATAAATAAGAAT
1 GATGATACTGGAATCAAACCAAAATCTGGGGGCTGAAACTATAAATAAATAAGAAT
*
12289057 GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAATAAGA
1 GATGATACTGGAATCAAACCAAAATCTGGGGGCTGAAACTATAAATAAATAAGA
12289111 GTCATTAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 24 0.49
56 25 0.51
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (56 bp):
GATGATACTGGAATCAAACCAAAATCTGGGGGCTGAAACTATAAATAAATAAGAAT
Found at i:12289974 original size:20 final size:19
Alignment explanation
Indices: 12289943--12289987 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
12289933 GTCATTATCC
12289943 TTTTTTGTCTTTTTCATTTGT
1 TTTTTTGTC-TTTT-ATTTGT
*
12289964 TTTTTTG-CTTTTGTTTGT
1 TTTTTTGTCTTTTATTTGT
12289982 TTTTTT
1 TTTTTT
12289988 CTGCCATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 4 0.17
20 1 0.04
21 7 0.30
ACGTcount: A:0.02, C:0.07, G:0.11, T:0.80
Consensus pattern (19 bp):
TTTTTTGTCTTTTATTTGT
Found at i:12290192 original size:18 final size:18
Alignment explanation
Indices: 12290157--12290194 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12290147 TAAAAATGTT
*
12290157 TTTAGTTTTGGGCTAGGG
1 TTTAGTTTTAGGCTAGGG
12290175 TTTAG-TTTAGGCTGAGGG
1 TTTAGTTTTAGGCT-AGGG
12290193 TT
1 TT
12290195 AATTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.13, C:0.05, G:0.37, T:0.45
Consensus pattern (18 bp):
TTTAGTTTTAGGCTAGGG
Found at i:12290847 original size:44 final size:46
Alignment explanation
Indices: 12290797--12290912 Score: 150
Period size: 45 Copynumber: 2.6 Consensus size: 46
12290787 TACTCCGCTG
* *
12290797 CAACTTTAGGGAGATAAGA-TTGG-TATCTTTAACTTGCTCCATTA
1 CAACTTTAGGGAGATAAGAGTTGGTTATCTTTAACCTGCTCCACTA
* *
12290841 CAACTTTAGGGAGATAA-AGTTGGTTATCTTTAGCCTGCTCCACTG
1 CAACTTTAGGGAGATAAGAGTTGGTTATCTTTAACCTGCTCCACTA
* *
12290886 CAACTTCAGGGAGATAAGACTT-GTTAT
1 CAACTTTAGGGAGATAAGAGTTGGTTAT
12290913 GGTAGATTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
43 1 0.02
44 21 0.33
45 38 0.60
46 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (46 bp):
CAACTTTAGGGAGATAAGAGTTGGTTATCTTTAACCTGCTCCACTA
Found at i:12290985 original size:44 final size:44
Alignment explanation
Indices: 12290739--12291044 Score: 135
Period size: 44 Copynumber: 6.9 Consensus size: 44
12290729 GATCCATCAT
** * *
12290739 TTTAATCCATTCCACTGTAACTTCAGGAAGATAGGA-T--TAGC
1 TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTAGTAGC
* ** * * * * *
12290780 TTCAATCTACTCCGCTGCAACTTTAGGGAGATAAGATTGGTATC
1 TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTAGTAGC
* * ** * * *
12290824 TTTAA-CTTGCTCCATTACAACTTTAGGGAGATA-AAGTTGGTTATC
1 TTTAATC-CGCTCCACTGTAACTTTAGGGAGATAGGA-TTAG-TAGC
* * * * *
12290869 TTT-AGCCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGA
1 TTTAATCC-GCTCCACTGTAACTTTAGGGAGATAGGA----TTA--GTAGC
* * * *
12290919 TTTAATCCGAC-CTACTGCAACTTTAGAGG-TATAGGATTCA-TTGC
1 TTTAATCCG-CTCCACTGTAACTTTAG-GGAGATAGGATT-AGTAGC
*
12290963 TTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTAGTAGC
1 TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTAGTAGC
* * * *
12291007 TTCAATCTGCTCCGCTGTAACTTTAGGGAGATAAGATT
1 TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATT
12291045 GGTATCTTCA
Statistics
Matches: 204, Mismatches: 40, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
41 28 0.14
42 1 0.00
43 6 0.03
44 101 0.50
45 30 0.15
46 3 0.01
47 1 0.00
49 3 0.01
50 24 0.12
51 7 0.03
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (44 bp):
TTTAATCCGCTCCACTGTAACTTTAGGGAGATAGGATTAGTAGC
Found at i:12291054 original size:44 final size:44
Alignment explanation
Indices: 12290783--12291052 Score: 181
Period size: 44 Copynumber: 6.0 Consensus size: 44
12290773 GATTAGCTTC
* *
12290783 AATCTACTCCGCTGCAACTTTAGGGAGATAAGATTGGTATCTTT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTATCTTT
* *
12290827 AA-CTTGCTCCATTACAACTTTAGGGAGATAA-AGTTGGTTATCTTT
1 AATC-TGCTCCACTGCAACTTTAGGGAGATAAGA-TTGG-TATCTTT
** * **
12290872 AGCCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTATGGTAGATTT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGA-----T-TGGTATCTTT
* * * * **
12290922 AATCCGAC-CTACTGCAACTTTAGAGG-TATAGGATTCAT-TGCTTT
1 AATCTG-CTCCACTGCAACTTTAG-GGAGATAAGATTGGTAT-CTTT
* * * * * * *
12290966 AATCCGCTCCACTGTAACTTCAGGGAGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTATCTTT
* *
12291010 AATCTGCTCCGCTGTAACTTTAGGGAGATAAGATTGGTATCTT
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTATCTT
12291053 CAGTCTAATT
Statistics
Matches: 174, Mismatches: 36, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
43 5 0.03
44 101 0.58
45 33 0.19
46 2 0.01
50 27 0.16
51 6 0.03
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTATCTTT
Found at i:12291197 original size:100 final size:100
Alignment explanation
Indices: 12291068--12291919 Score: 1034
Period size: 100 Copynumber: 8.5 Consensus size: 100
12291058 TAATTAACTA
** ** * * **
12291068 CAATGTCGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTCCCACTACACCGTTAGGGAAGT
1 CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
*
12291133 AAGATTCACCGTTGCGGCTTCAATCTTTTTAATTG
66 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * * * * *
12291168 CAATGTCGGGGAAGCAAGA-TCTGCCGTTGTAGCTTTAATCTGTTCCATTGCGCTGCCAGGGAAG
1 CAATGTCGGGGAAACAAGATTC-GCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAG
12291232 TAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
65 TAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * *
12291268 CAATGTCGGGGAAACAAGATTCACCATTGTAGCTTCAATCTGTTCCACTGTACCGCTAGGGAAGT
1 CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
** *
12291333 AAGATTTGCCGTTGTGGCTTCAATCTTTTTAATTA
66 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * *
12291368 CAATGTTGGGGAAACAAGATTC-AC-TGGGTTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAA
1 CAATGTCGGGGAAACAAGATTCGCCAT-TG-TAGCTTCAATCTGTTCCACTGCACCGCCAGGGAA
* *
12291431 GTAAGATTCACCGTTCTGGCTTCAATCTTTATAATTG
64 GTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* **
12291468 TAATGTCGGGGAAACAAGATT---CATTGGGTTAGCTTCAATCTGTTCCACTATACCGCCAGGGA
1 CAATGTCGGGGAAACAAGATTCGCCATT--G-TAGCTTCAATCTGTTCCACTGCACCGCCAGGGA
* * *
12291530 AGTAAGATTCGCCGTTCTGGCTTCAATCTTTATAATTG
63 AGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * * * * * *
12291568 TAATGTCGGGGAAACAAGATTAGCCATTGTAGCTTTAATCTATTCCACTGCACCACCTGAGAAGT
1 CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
12291633 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
66 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * * *
12291668 CAATGTCGGGGAAACAATATTCGCTATTGTAGCTTTAATCTGTTCTACTGCACCGCCAGGGAAGT
1 CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
* *
12291733 AAGATTCGCCGTTTTGGCTTCAATCTTTTTAATTG
66 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * * * *
12291768 CAATGTCGAGGAAATAAGATTCGCCGTTGTAGCTTCAATCTATTCCACTGCACCGCCAGGGGAGT
1 CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
** *
12291833 AAGATTTGCCATTGTGGCTTCAATCTTTTTAATTG
66 AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
* * * * * * ** *
12291868 AAATGTCAGAGAGACAAGATACGTC-GGGTTAGCTTCAATATGTTCCACTGCA
1 CAATGTCGGGGAAACAAGATTCGCCATTG-TAGCTTCAATCTGTTCCACTGCA
12291920 ATGCCAAATA
Statistics
Matches: 657, Mismatches: 84, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
98 2 0.00
99 6 0.01
100 642 0.98
101 3 0.00
103 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (100 bp):
CAATGTCGGGGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGT
AAGATTCACCGTTGTGGCTTCAATCTTTTTAATTG
Found at i:12292042 original size:89 final size:89
Alignment explanation
Indices: 12291943--12292294 Score: 508
Period size: 89 Copynumber: 4.0 Consensus size: 89
12291933 AGGACTAGTC
* *
12291943 TCTTCAATCTGCTTCACTGCCAGTATAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
1 TCTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
*
12292008 AAACTTAGGGAGGTCAGGCTGGTG
66 AAACTCAGGGAGGTCAGGCTGGTG
* * * * *
12292032 TCTTCGATCTGCTTCGCTACCAGTACAGGAAGACAAGATCTATAATCTTCAGTCTGCTCCGCTGC
1 TCTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
* *
12292097 AAACTCAAGGA-GACGAGGCTGGTG
66 AAACTCAGGGAGGTC-AGGCTGGTG
* * * *
12292121 TCTTCGATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTGCTCCACTAC
1 TCTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
*
12292186 AAACTCAGGGAGGTTAGGCTGGTG
66 AAACTCAGGGAGGTCAGGCTGGTG
* * * * *
12292210 TCTTCGATCTGCTTCACTGCCAGTGCAGGAAGATAAGATCTGCTATCTTTAGTCTGCTCCACTAC
1 TCTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
12292275 AAACTCAGGGAGGTCAGGCT
66 AAACTCAGGGAGGTCAGGCT
12292295 AGATATGACG
Statistics
Matches: 235, Mismatches: 26, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
88 2 0.01
89 232 0.99
90 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.27
Consensus pattern (89 bp):
TCTTCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTCAGTCTGCTCCACTAC
AAACTCAGGGAGGTCAGGCTGGTG
Found at i:12292132 original size:44 final size:44
Alignment explanation
Indices: 12292084--12292222 Score: 113
Period size: 44 Copynumber: 3.1 Consensus size: 44
12292074 TAATCTTCAG
*
12292084 TCTGCTCCGCTGCAAACTCAAGGAGACGAGGCTGGTGTCTTCGA
1 TCTGCTCCGCTGCAAACTCAAGGAGACAAGGCTGGTGTCTTCGA
* * * * *
12292128 TCTGCTTCGCTGCCAA-T-ACAGGAAGACAAGATCTGCTATCTTC-A
1 TCTGCTCCGCTGCAAACTCA-AGG-AGACAAG-GCTGGTGTCTTCGA
* * * ***
12292172 GTCTGCTCCACTACAAACTCAGGGAGGTTAGGCTGGTGTCTTCGA
1 -TCTGCTCCGCTGCAAACTCAAGGAGACAAGGCTGGTGTCTTCGA
12292217 TCTGCT
1 TCTGCT
12292223 TCACTGCCAG
Statistics
Matches: 71, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
42 1 0.01
43 4 0.06
44 36 0.51
45 26 0.37
46 3 0.04
47 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (44 bp):
TCTGCTCCGCTGCAAACTCAAGGAGACAAGGCTGGTGTCTTCGA
Found at i:12292177 original size:45 final size:45
Alignment explanation
Indices: 12292039--12292178 Score: 128
Period size: 45 Copynumber: 3.1 Consensus size: 45
12292029 GTGTCTTCGA
* *
12292039 TCTGCTTCGCTACCAGTACAGGAAGACAAGATCT-ATAATCTTCAG
1 TCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGAT-ATCTTCAG
* * * * * *
12292084 TCTGCTCCGCTGCAAACT-CAAGG-AGACGAG-GCTGGTGTCTTC-G
1 TCTGCTTCGCTGCCAA-TAC-AGGAAGACAAGATCTGATATCTTCAG
*
12292127 ATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAG
1 -TCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGATATCTTCAG
12292173 TCTGCT
1 TCTGCT
12292179 CCACTACAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
43 5 0.07
44 28 0.38
45 35 0.48
46 5 0.07
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (45 bp):
TCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGATATCTTCAG
Found at i:12293257 original size:10 final size:10
Alignment explanation
Indices: 12293242--12293275 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
12293232 TTTTTCGTTA
12293242 TTCTTTTTTT
1 TTCTTTTTTT
12293252 TTCTTTTTTT
1 TTCTTTTTTT
12293262 TTCGTTTCTTTT
1 TTC-TTT-TTTT
12293274 TT
1 TT
12293276 TAAGTGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.59
11 3 0.14
12 6 0.27
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:12293781 original size:9 final size:8
Alignment explanation
Indices: 12293744--12293780 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
12293734 TTTTATTTTA
12293744 TTTTTACT
1 TTTTTACT
**
12293752 TTTTGGCT
1 TTTTTACT
12293760 TTTTTACT
1 TTTTTACT
12293768 TTTTTACT
1 TTTTTACT
12293776 TTTTT
1 TTTTT
12293781 TGCCTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.76
Consensus pattern (8 bp):
TTTTTACT
Found at i:12295643 original size:24 final size:25
Alignment explanation
Indices: 12295615--12295667 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
12295605 GGGTTTTTCG
*
12295615 TGAAATTTAATGCAAATG-ATGCAA
1 TGAAATGTAATGCAAATGAATGCAA
* *
12295639 TGAAATGTAATGCAGATGAATGGAA
1 TGAAATGTAATGCAAATGAATGCAA
12295664 TGAA
1 TGAA
12295668 TGCAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (25 bp):
TGAAATGTAATGCAAATGAATGCAA
Found at i:12298137 original size:56 final size:56
Alignment explanation
Indices: 12298075--12298184 Score: 184
Period size: 56 Copynumber: 2.0 Consensus size: 56
12298065 AAGAACTAAG
* * * *
12298075 GATGATACTGGAATCGAACCAGAATTTGGGGGCTGAAACTGTAAATAAATAAGAAT
1 GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAACAAGAAT
12298131 GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAACAAGA
1 GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAACAAGA
12298185 GTCATTAAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.22
Consensus pattern (56 bp):
GATGATACTGGAATCAAACCAAAATTTGGGGGCTGAAACTATAAATAAACAAGAAT
Found at i:12299062 original size:23 final size:22
Alignment explanation
Indices: 12299010--12299066 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
12299000 TCGTTTGTCA
12299010 TTATTCTTTTTTGTCTTTTTCAT
1 TTATT-TTTTTTGTCTTTTTCAT
* *
12299033 TTGTTTTTTTTG-CTTTTGTTAGT
1 TTATTTTTTTTGTCTTTT-TCA-T
12299056 TTATTTTTTTT
1 TTATTTTTTTT
12299067 CTCTACCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.17
22 9 0.31
23 15 0.52
ACGTcount: A:0.07, C:0.07, G:0.09, T:0.77
Consensus pattern (22 bp):
TTATTTTTTTTGTCTTTTTCAT
Done.