Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009189.1 Hibiscus syriacus cultivar Beakdansim tig00112762_pilon, whole genome shotgun sequence
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: 966119
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 1 of 4
Found at i:5162 original size:18 final size:18
Alignment explanation
Indices: 5139--5181 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
5129 GAACGCTGGA
5139 AACCGGTTTTGACCGTTT
1 AACCGGTTTTGACCGTTT
*
5157 AACCGGTTTTGACGGTTT
1 AACCGGTTTTGACCGTTT
*
5175 GACCGGT
1 AACCGGT
5182 CACGACCCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (18 bp):
AACCGGTTTTGACCGTTT
Found at i:5235 original size:13 final size:13
Alignment explanation
Indices: 5194--5224 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5184 CGACCCGTTT
*
5194 ACCCGTTTACCCG
1 ACCCGTTGACCCG
5207 ACCCGTTGACCCG
1 ACCCGTTGACCCG
5220 ACCCG
1 ACCCG
5225 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:13941 original size:21 final size:20
Alignment explanation
Indices: 13885--13942 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
13875 ATTTATCGTG
*
13885 ATTGCGGCCGTCGCGGGAGCT
1 ATTGCAGCCGTCGC-GGAGCT
* *
13906 ATTG-AGGTCGCCGCGGACGCT
1 ATTGCA-GCCGTCGCGGA-GCT
13927 ATTGCAGCCGTCGCGG
1 ATTGCAGCCGTCGCGG
13943 GTAACTCGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 3 0.10
21 25 0.86
22 1 0.03
ACGTcount: A:0.12, C:0.29, G:0.40, T:0.19
Consensus pattern (20 bp):
ATTGCAGCCGTCGCGGAGCT
Found at i:16464 original size:13 final size:13
Alignment explanation
Indices: 16445--16477 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
16435 ATTTTTAAAG
16445 CACACTTAAAACA
1 CACACTTAAAACA
*
16458 TACACTTAAAACA
1 CACACTTAAAACA
16471 CACACTT
1 CACACTT
16478 CTCCCCCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (13 bp):
CACACTTAAAACA
Found at i:18755 original size:21 final size:21
Alignment explanation
Indices: 18673--18756 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
18663 CAGAACCCCA
*
18673 GGGGGGTATCGATTCCC-C-T
1 GGGGGGGATCGATTCCCTCAT
* *
18692 GTGGGGGGAATCGGTTCCCCTTCAA
1 G-GGGGGG-ATCGATT-CCC-TCAT
* * *
18717 AGGGGGAATCGGTTCCCTCAT
1 GGGGGGGATCGATTCCCTCAT
18738 GGGGGGGATCGATTCCCTC
1 GGGGGGGATCGATTCCCTC
18757 TATACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 5 0.10
21 25 0.50
22 6 0.12
23 7 0.14
24 6 0.12
ACGTcount: A:0.14, C:0.25, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCTCAT
Found at i:24967 original size:32 final size:32
Alignment explanation
Indices: 24925--25008 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
24915 ATAGTGACTA
*
24925 TTTTGTTACAAATTAATAATGCTAATGACCAT
1 TTTTGTTACAAATTAATAATGCTAATGAACAT
* * *
24957 TTTTATTACAAATTAATAATGTTAATGAATAT
1 TTTTGTTACAAATTAATAATGCTAATGAACAT
*
24989 TTTTGTTATAAATTAATAAT
1 TTTTGTTACAAATTAATAAT
25009 ATCGGTGACT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.46
Consensus pattern (32 bp):
TTTTGTTACAAATTAATAATGCTAATGAACAT
Found at i:27985 original size:16 final size:17
Alignment explanation
Indices: 27964--28004 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
27954 CATAAAATTA
*
27964 TAAATAATTAA-TATAT
1 TAAATAATTAAGAATAT
27980 TAAAT-ATTAAGAATAT
1 TAAATAATTAAGAATAT
*
27996 AAAATAATT
1 TAAATAATT
28005 TAAATTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 13 0.62
17 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATAATTAAGAATAT
Found at i:33285 original size:15 final size:15
Alignment explanation
Indices: 33265--33295 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33255 CAACAGATAG
33265 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
33280 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
33295 A
1 A
33296 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:36667 original size:156 final size:156
Alignment explanation
Indices: 36434--36729 Score: 479
Period size: 156 Copynumber: 1.9 Consensus size: 156
36424 CATGTGGTTT
* * *
36434 AAATTTGGTAAATAACAAATTTAAAATAAATAACAAATTGAAGGAATAAGGATATTATGAAAAAT
1 AAATTTGGTAAATAACAAATTTAAAATAAATAACAAATTGAAGAAATAAGGAAATTATAAAAAAT
* *
36499 TGAAGGATTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAAGAATTGAAAGTACACATGTATT
66 TGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAG-AGAAATGAAAGTACACATGTATT
36564 CTACTATGGTTCAAGAGCGTGCGACTC
130 CTACTATGGTTCAAGAGCGTGCGACTC
* *
36591 AAATTTGGTAAA-AACAGATTTAAAATAAATGAA-GAATTGAAGAAATAAGGAAATTATAAAAAA
1 AAATTTGGTAAATAACAAATTTAAAATAAAT-AACAAATTGAAGAAATAAGGAAATTATAAAAAA
* *
36654 TTGAATGACTAAATTGAAAAATAAAAATTTGTTATCAAAAAGAGAAATGAAAGTACACATGTATT
65 TTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAGAAATGAAAGTACACATGTATT
36719 CTACTATGGTT
130 CTACTATGGTT
36730 TAGGAACTTG
Statistics
Matches: 129, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
155 33 0.26
156 82 0.64
157 14 0.11
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (156 bp):
AAATTTGGTAAATAACAAATTTAAAATAAATAACAAATTGAAGAAATAAGGAAATTATAAAAAAT
TGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAGAAATGAAAGTACACATGTATTC
TACTATGGTTCAAGAGCGTGCGACTC
Found at i:36760 original size:156 final size:157
Alignment explanation
Indices: 36426--36791 Score: 470
Period size: 156 Copynumber: 2.4 Consensus size: 157
36416 TATATGAGCA
* * * * * *
36426 TGTGGTTTAAATTTGGTAAATAACAAATTTAAAATAAAT-AACAAATTGAAGGAATAAGGATATT
1 TGTGGTTCAAATTTGGTAAAAAACAGATTTAAAATAAATGAA-GAATTGAAGAAATAAGGAAATT
* * *
36490 ATGAAAAATTGAAGGATTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAAGAATTGAAAGTAC
65 ATAAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAAGAAATGAAAGTAC
*
36555 ACATGTATTCTACTATGGTTCAAGAGCG
130 ACATGTATTCTACTATGGTTCAAGAACG
* **
36583 TGCGACTCAAATTTGGT-AAAAACAGATTTAAAATAAATGAAGAATTGAAGAAATAAGGAAATTA
1 TGTGGTTCAAATTTGGTAAAAAACAGATTTAAAATAAATGAAGAATTGAAGAAATAAGGAAATTA
* *
36647 TAAAAAATTGAATGACTAAATTGAAAAATAAAAATTTGTTATCAAAAAG-AGAAATGAAAGTACA
66 TAAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAAGAAATGAAAGTACA
* * *
36711 CATGTATTCTACTATGGTTTAGGAACT
131 CATGTATTCTACTATGGTTCAAGAACG
* ** * ** *
36738 TGTGGTTCAAATTTGTTAAAAAA-AGGCTTAAAATGAGGGAGGAATTGAAGAAAT
1 TGTGGTTCAAATTTGGTAAAAAACAGATTTAAAATAAATGAAGAATTGAAGAAAT
36792 GATAAATCAA
Statistics
Matches: 179, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
155 75 0.42
156 89 0.50
157 15 0.08
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.28
Consensus pattern (157 bp):
TGTGGTTCAAATTTGGTAAAAAACAGATTTAAAATAAATGAAGAATTGAAGAAATAAGGAAATTA
TAAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAAGAAATGAAAGTACA
CATGTATTCTACTATGGTTCAAGAACG
Found at i:36783 original size:155 final size:156
Alignment explanation
Indices: 36434--36791 Score: 443
Period size: 155 Copynumber: 2.3 Consensus size: 156
36424 CATGTGGTTT
* * * * * *
36434 AAATTTGGTAAATAACAA-ATTTAAAATAAA-TAACAAATTGAAGGAATAAGGATATTATGAAAA
1 AAATTTGGTAAA-AA-AAGACTTAAAATAAAGGAA-GAATTGAAGAAATAAGGAAATTATAAAAA
* *
36497 ATTGAAGGATTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAAGAATTGAAAGTACACATGTA
63 ATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAAGAAATGAAAGTACACATGTA
*
36562 TTCTACTATGGTTCAAGAGCGTGCGACTC
128 TTCTACTATGGTTCAAGAACGTGCGACTC
* * *
36591 AAATTTGGTAAAAACAGATTTAAAATAAATGAAGAATTGAAGAAATAAGGAAATTATAAAAAATT
1 AAATTTGGTAAAAAAAGACTTAAAATAAAGGAAGAATTGAAGAAATAAGGAAATTATAAAAAATT
* *
36656 GAATGACTAAATTGAAAAATAAAAATTTGTTATCAAAAAG-AGAAATGAAAGTACACATGTATTC
66 GAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAAGAAATGAAAGTACACATGTATTC
* * * * **
36720 TACTATGGTTTAGGAACTTGTGGTTC
131 TACTATGGTTCAAGAACGTGCGACTC
* * * * *
36746 AAATTTGTTAAAAAAAGGCTTAAAATGAGGGAGGAATTGAAGAAAT
1 AAATTTGGTAAAAAAAGACTTAAAATAAAGGAAGAATTGAAGAAAT
36792 GATAAATCAA
Statistics
Matches: 174, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
155 81 0.47
156 79 0.45
157 14 0.08
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (156 bp):
AAATTTGGTAAAAAAAGACTTAAAATAAAGGAAGAATTGAAGAAATAAGGAAATTATAAAAAATT
GAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAAGAAATGAAAGTACACATGTATTC
TACTATGGTTCAAGAACGTGCGACTC
Found at i:52065 original size:23 final size:21
Alignment explanation
Indices: 52007--52054 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
51997 CCTAATATTG
*
52007 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAAGTGCAA
52028 CAATGTCAAAATTAAGTGCAA
1 CAATGTCAAAATTAAGTGCAA
52049 CAATGT
1 CAATGT
52055 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
CAATGTCAAAATTAAGTGCAA
Found at i:58842 original size:30 final size:30
Alignment explanation
Indices: 58806--58899 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
58796 TTAATTACAA
58806 AATTTATCAAATTTTATAATCAAATCATTC
1 AATTTATCAAATTTTATAATCAAATCATTC
* * * *
58836 AATTTATTAAATTCTACAATCAAATCATTT
1 AATTTATCAAATTTTATAATCAAATCATTC
*
58866 AATTTATCAAATTTTATAATCAAATCACTC
1 AATTTATCAAATTTTATAATCAAATCATTC
58896 AATT
1 AATT
58900 GCAACTAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.43
Consensus pattern (30 bp):
AATTTATCAAATTTTATAATCAAATCATTC
Found at i:80153 original size:3 final size:3
Alignment explanation
Indices: 80147--80207 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
80137 TTCTTCTTCC
80147 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
80195 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
80208 CACTCTTCCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:81187 original size:17 final size:18
Alignment explanation
Indices: 81146--81180 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
81136 TTTGGTCTTT
81146 AAAA-TTTATCATATTTA
1 AAAATTTTATCATATTTA
81163 AAAATTTTATCA-ATTTA
1 AAAATTTTATCATATTTA
81180 A
1 A
81181 TCATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTTTATCATATTTA
Found at i:86554 original size:21 final size:21
Alignment explanation
Indices: 86503--86555 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
86493 ATTATGACTA
*
86503 TCGCAATGCGATTTTTCAATT
1 TCGCAATGCGATTTTCCAATT
**
86524 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
86545 TCGCAATGCGA
1 TCGCAATGCGA
86556 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:86587 original size:20 final size:20
Alignment explanation
Indices: 86564--86637 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
86554 GAATAAGTAA
86564 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* **
86584 ATCGCAATGCGA-ATTTGGAAA
1 ATCGCAATGCGATA-CT-GACT
*
86605 ATCGCAATGGGATACTGACT
1 ATCGCAATGCGATACTGACT
86625 ATCGCAATGCGAT
1 ATCGCAATGCGAT
86638 TTTCCTAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.02
20 27 0.63
21 14 0.33
22 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:86607 original size:41 final size:40
Alignment explanation
Indices: 86545--86636 Score: 139
Period size: 41 Copynumber: 2.3 Consensus size: 40
86535 TTTTCCCAAT
*
86545 TCGCAATGCGAATAAGTAAATCGCAATGCGATACTGACTA
1 TCGCAATGCGAATAAGAAAATCGCAATGCGATACTGACTA
** *
86585 TCGCAATGCGAATTTGGAAAATCGCAATGGGATACTGACTA
1 TCGCAATGCGAA-TAAGAAAATCGCAATGCGATACTGACTA
86626 TCGCAATGCGA
1 TCGCAATGCGA
86637 TTTTCCTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (40 bp):
TCGCAATGCGAATAAGAAAATCGCAATGCGATACTGACTA
Found at i:86651 original size:41 final size:41
Alignment explanation
Indices: 86565--86698 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
86555 AATAAGTAAA
** *
86565 TCGCAATGCGATACTGACTATCGCAATGCGAATTTGGA-AAA
1 TCGCAATGCGATACTGACTATCGCAATGCG-ATTTTCATAAT
* *
86606 TCGCAATGGGATACTGACTATCGCAATGCGATTTTCCTAAT
1 TCGCAATGCGATACTGACTATCGCAATGCGATTTTCATAAT
* * **
86647 TCGCATTGCGAT--TTACGTATTCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATACTGAC-TA-TCGCAATGCGATTTTCATAAT
86688 TCGCAATGCGA
1 TCGCAATGCGA
86699 ATACGTAAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 6 0.08
41 69 0.88
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
TCGCAATGCGATACTGACTATCGCAATGCGATTTTCATAAT
Found at i:86656 original size:21 final size:21
Alignment explanation
Indices: 86626--86698 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
86616 ATACTGACTA
*
86626 TCGCAATGCGATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
86647 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
86667 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
86688 TCGCAATGCGA
1 TCGCAATGCGA
86699 ATACGTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:86713 original size:20 final size:20
Alignment explanation
Indices: 86688--86799 Score: 156
Period size: 20 Copynumber: 5.5 Consensus size: 20
86678 TTTTCATAAT
86688 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTA-GTAAA
*
86708 TCGCAACGCGAATTAGTAAA
1 TCGCAATGCGAATTAGTAAA
*
86728 TCGCAACGCGAATTAGTAAA
1 TCGCAATGCGAATTAGTAAA
*
86748 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTA-GTAAA
86769 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTA-GTAAA
86789 TCGCAATGCGA
1 TCGCAATGCGA
86800 TTTACATAGC
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
20 67 0.79
21 18 0.21
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATTAGTAAA
Found at i:86732 original size:40 final size:41
Alignment explanation
Indices: 86688--86799 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 41
86678 TTTTCATAAT
* *
86688 TCGCAATGCGAATACGTAAATCGCAACGCGAATTA-GTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAA
*
86728 TCGCAACGCGAATTA-GTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAATCGCAATGCGAATTAGGAAAA
86769 TCGCAATGCGAATACGTAAATCGCAATGCGA
1 TCGCAATGCGAATACGTAAATCGCAATGCGA
86800 TTTACATAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
40 32 0.49
41 33 0.51
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATTAGGAAAA
Found at i:87382 original size:19 final size:19
Alignment explanation
Indices: 87343--87383 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
87333 GCAACGAGAG
*
87343 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
87362 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
87381 AAT
1 AAT
87384 TGCATTGCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:87434 original size:33 final size:34
Alignment explanation
Indices: 87388--87451 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
87378 CAAAATTGCA
**
87388 TTGCGATTTTCATTT-CGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTCTCG
87421 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
87452 ATTATCTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.42
Consensus pattern (34 bp):
TTGCGATAGTCATTTCCGCGTTGCGATTCTCTCG
Found at i:87453 original size:20 final size:19
Alignment explanation
Indices: 87388--87476 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 19
87378 CAAAATTGCA
*
87388 TTGCGATTTTCATTTCGCG
1 TTGCGATTCTCATTTCGCG
87407 TTGCGATTCTC---T--CG
1 TTGCGATTCTCATTTCGCG
**
87421 TTGCGATAGTCATTTCCGCG
1 TTGCGATTCTCATTT-CGCG
*
87441 TTGCGATTCTCATTATCTCG
1 TTGCGATTCTCATT-TCGCG
* *
87461 TTACGATTTTCATTTC
1 TTGCGATTCTCATTTC
87477 AACCAAAAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
14 11 0.20
16 1 0.02
17 1 0.02
19 12 0.22
20 29 0.53
21 1 0.02
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTCTCATTTCGCG
Found at i:88376 original size:24 final size:24
Alignment explanation
Indices: 88342--88395 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
88332 CTGAATCATC
*
88342 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
88366 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
88390 ATCAAA
1 ATCAAA
88396 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:89146 original size:20 final size:20
Alignment explanation
Indices: 89097--89148 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
89087 TTGCGAACTT
*
89097 TGAAAATCGCAATGAGATTC
1 TGAAAATCGCAACGAGATTC
***
89117 TGACTTTCGCAACGAGATTC
1 TGAAAATCGCAACGAGATTC
89137 TGAAAATCGCAA
1 TGAAAATCGCAA
89149 TCATCTTCAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (20 bp):
TGAAAATCGCAACGAGATTC
Found at i:89434 original size:20 final size:20
Alignment explanation
Indices: 89359--89426 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
89349 CAACGGGGAA
89359 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
89379 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
89399 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
89419 ATCGCAAC
1 ATCGCAAC
89427 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:89438 original size:34 final size:34
Alignment explanation
Indices: 89343--89446 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
89333 ATTCATTTGA
** *
89343 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
89377 CTATCGCAATTCGAAATGAAAAATCGCAACGCGAAAATGG
1 CTATCGCAA--C--AA-G-AAAATCGCAACGCGAAAATGG
* *
89417 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACAAGAAAATCGCAACGCGAAA
89447 TGAAAATCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
34 25 0.42
35 1 0.02
36 2 0.03
38 1 0.02
39 1 0.02
40 29 0.49
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
Found at i:89477 original size:14 final size:14
Alignment explanation
Indices: 89458--89511 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
89448 GAAAATCGCA
89458 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
89472 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
89489 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
89505 TTGCGAT
1 TTGCGAT
89512 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:89477 original size:33 final size:33
Alignment explanation
Indices: 89440--89510 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
89430 AAAATCGCAA
89440 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
89473 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
89506 TGCGA
1 TGCGA
89511 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:91562 original size:20 final size:20
Alignment explanation
Indices: 91539--91592 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
91529 GAAACTTAAA
91539 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
91559 ATCGCAACGC-AGAAATGGCT
1 ATCGCAACGCGA-AAATGACT
* *
91579 ATTGCAATGCGAAA
1 ATCGCAACGCGAAA
91593 TGCAAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:91654 original size:19 final size:19
Alignment explanation
Indices: 91632--91714 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
91622 GAAACACAAA
91632 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
91651 TCGCGTTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
*
91670 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
91686 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
91703 TCGCATTGCGAT
1 TCGCATTGCGAT
91715 AGCTATTTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 33 0.62
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:91742 original size:20 final size:19
Alignment explanation
Indices: 91687--91753 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
91677 GCGATTTTGT
**
91687 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
91706 CATTGCGATAG-CTATTTCCG
1 CGTTGCGATAGTC-ATTT-CG
91726 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
91746 TGTTGCGA
1 CGTTGCGA
91754 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.03
19 12 0.31
20 22 0.56
21 4 0.10
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:92261 original size:18 final size:18
Alignment explanation
Indices: 92235--92279 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
92225 GTCGATCAGA
*
92235 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
92253 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
92271 TGATGGCTC
1 TGATGGCTC
92280 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:93641 original size:20 final size:20
Alignment explanation
Indices: 93593--93651 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
93583 AATAGTTTCT
** *
93593 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
93613 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
93633 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
93652 AGAGAATCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:93941 original size:21 final size:21
Alignment explanation
Indices: 93906--93977 Score: 92
Period size: 22 Copynumber: 3.4 Consensus size: 21
93896 TCTGAGAGAT
* *
93906 GGAGATAGG-CGGATTTCGCC
1 GGAGATGGGACGGATTTCGTC
*
93926 GGAGATGGGACGGATTTTGTC
1 GGAGATGGGACGGATTTCGTC
93947 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GGGACGGATTTCGTC
*
93969 GGATATGGG
1 GGAGATGGG
93978 TGAGAGAGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 8 0.18
21 18 0.40
22 19 0.42
ACGTcount: A:0.19, C:0.12, G:0.44, T:0.24
Consensus pattern (21 bp):
GGAGATGGGACGGATTTCGTC
Found at i:94251 original size:20 final size:19
Alignment explanation
Indices: 94145--94279 Score: 108
Period size: 20 Copynumber: 6.7 Consensus size: 19
94135 CGCTTTGAAA
*
94145 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
94166 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGT-AGT
* *
94186 ATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATAG-TAGT
* * * *
94206 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
94227 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGT-AGT
94247 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
94267 ATCGCATTGCGAT
1 ATCGCATTGCGAT
94280 TTTCCCAATT
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.05
20 64 0.67
21 25 0.26
22 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:94251 original size:61 final size:61
Alignment explanation
Indices: 94145--94282 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
94135 CGCTTTGAAA
* * * * *
94145 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
94206 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
94267 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
94283 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:94298 original size:61 final size:61
Alignment explanation
Indices: 94145--94300 Score: 152
Period size: 61 Copynumber: 2.6 Consensus size: 61
94135 CGCTTTGAAA
* ** * * * * *
94145 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
94206 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
94267 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
94301 TTACTTATTC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 76 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:94390 original size:21 final size:21
Alignment explanation
Indices: 94350--94390 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
94340 ACTGTAGACC
** *
94350 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
94371 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
94391 GCGAATTTGC
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:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:94682 original size:2 final size:2
Alignment explanation
Indices: 94675--94717 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
94665 ATCGATTTAA
94675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94715 AT A
1 AT A
94718 ATAAATTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94724 original size:12 final size:13
Alignment explanation
Indices: 94672--94725 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 13
94662 TGGATCGATT
94672 TAAA-TATATATA
1 TAAATTATATATA
*
94684 TATA-TATATATA
1 TAAATTATATATA
*
94696 TATA-TATATATA
1 TAAATTATATATA
94708 T-AATTATATA-A
1 TAAATTATATATA
94719 TAAATTA
1 TAAATTA
94726 ATTATGAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
11 3 0.08
12 35 0.92
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAATTATATATA
Found at i:101962 original size:25 final size:25
Alignment explanation
Indices: 101933--101989 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
101923 TACCTAAATT
*
101933 AGGGTTTTTCTCTCTACCATTCCTA
1 AGGGTTTTTCTCTCTACCAGTCCTA
*
101958 AGGGTTTTTCTCTCTACCCGTCCTA
1 AGGGTTTTTCTCTCTACCAGTCCTA
101983 AGGGTTT
1 AGGGTTT
101990 CTGCCGCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.42
Consensus pattern (25 bp):
AGGGTTTTTCTCTCTACCAGTCCTA
Found at i:104927 original size:29 final size:29
Alignment explanation
Indices: 104878--104947 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
104868 ATGATTTGAT
** * **
104878 AAATTT-ATGACTATTTTATGACTTGTAA
1 AAATTTAATGACTAAGTGATGACTTCAAA
*
104906 AAATTTAATGACTAAGTGATGATTTCAAA
1 AAATTTAATGACTAAGTGATGACTTCAAA
104935 ATAATTTAATGAC
1 A-AATTTAATGAC
104948 CTCTAATGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 6 0.18
29 17 0.50
30 11 0.32
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.40
Consensus pattern (29 bp):
AAATTTAATGACTAAGTGATGACTTCAAA
Found at i:107051 original size:12 final size:12
Alignment explanation
Indices: 107025--107062 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
107015 CTGACCCGAT
107025 CCGACCCGTTGAC
1 CCGACCCG-TGAC
107038 CCGACCCGTGAC
1 CCGACCCGTGAC
107050 CCGACCCGGTGAC
1 CCGACCC-GTGAC
107063 ATTCTGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.16, C:0.47, G:0.26, T:0.11
Consensus pattern (12 bp):
CCGACCCGTGAC
Found at i:107124 original size:29 final size:29
Alignment explanation
Indices: 107091--107236 Score: 204
Period size: 30 Copynumber: 5.0 Consensus size: 29
107081 AAAAGGTAAT
107091 ATTCTGGGAAATATTTTGAAAAATGTGAC
1 ATTCTGGGAAATATTTTGAAAAATGTGAC
107120 ATTCTGGGAAATATTTTGAAAAATGTGAC
1 ATTCTGGGAAATATTTTGAAAAATGTGAC
** *
107149 ATTCTAAGAAATATTTTTGAAAAATATGAC
1 ATTCTGGGAAATA-TTTTGAAAAATGTGAC
**
107179 ATTCTGGGAAATATTTTGAAAAAAAATGAC
1 ATTCTGGGAAATATTTTG-AAAAATGTGAC
* *
107209 ATTCTAGGAATTATTTTGAAAAA-GTGAC
1 ATTCTGGGAAATATTTTGAAAAATGTGAC
107237 TTTGGAAATT
Statistics
Matches: 106, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
28 4 0.04
29 50 0.47
30 52 0.49
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (29 bp):
ATTCTGGGAAATATTTTGAAAAATGTGAC
Found at i:107179 original size:59 final size:59
Alignment explanation
Indices: 107098--107231 Score: 207
Period size: 59 Copynumber: 2.3 Consensus size: 59
107088 AATATTCTGG
* **
107098 GAAATATTTTGAAAAATGTGACATTCTGGGAAATATTTTG-AAAAATGTGACATTCTAA
1 GAAATATTTTGAAAAATATGACATTCTGGGAAATATTTTGAAAAAAAATGACATTCTAA
*
107156 GAAATATTTTTGAAAAATATGACATTCTGGGAAATATTTTGAAAAAAAATGACATTCTAG
1 GAAATA-TTTTGAAAAATATGACATTCTGGGAAATATTTTGAAAAAAAATGACATTCTAA
*
107216 GAATTATTTTGAAAAA
1 GAAATATTTTGAAAAA
107232 GTGACTTTGG
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
58 6 0.09
59 43 0.62
60 20 0.29
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (59 bp):
GAAATATTTTGAAAAATATGACATTCTGGGAAATATTTTGAAAAAAAATGACATTCTAA
Found at i:110727 original size:38 final size:39
Alignment explanation
Indices: 110665--110754 Score: 141
Period size: 38 Copynumber: 2.4 Consensus size: 39
110655 TTTTGTTCGG
110665 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTC-GA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCTGA
110702 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCTGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCTGA
*
110741 -TCGAGTTCGGGTTT
1 GTCG-GGTCGGGTTT
110755 AGGGTGGAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
37 11 0.22
38 27 0.55
39 11 0.22
ACGTcount: A:0.12, C:0.11, G:0.37, T:0.40
Consensus pattern (39 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCTGA
Found at i:110916 original size:255 final size:245
Alignment explanation
Indices: 110456--111001 Score: 739
Period size: 255 Copynumber: 2.2 Consensus size: 245
110446 ATTTTGTTCT
* * *
110456 GGTCGGGTC-GGTCGGG-TTTTTTAAGTGTGATATTAGGGTCG--G-GTTTGGGTTTAGGGTAAA
1 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGTCGAGTTCGGGTTTAGGGTAAA
* *
110516 AAAACGGACTGACCCGAAAAATATATATAATTCGGGTCGGGCCGGATTAAGTCACTGTTTTATTA
66 AAAACGGACCGACCCGAAAAATATATATAATTCGGGTCGGGCCGGATTAAGTCAATGTTTTATTA
* * *
110581 AATAAAAATAATTTTTTATTATTTCGGGTCGAATTTCTAATTCATATATTCGTGTCGGGTCGGAT
131 AATAAAAATAATTTATTATTATTTCGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTCAGAT
*
110646 GAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
196 AAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
110696 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCTGATCGAGTTCGGGTTTAGGGTG
1 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC-G-TCGAGTTCGGGTTTAGGGT-
* * * *
110761 GAAAAAACCGGACCGACTC-TAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCAATGTTTT
63 -AAAAAAACGGACCGACCCGAAAAATATATATAATTCGGGTCGGGCCGGATTAAGTCAATG-TTT
* * *
110825 TATTAAATAAAAATTA-TTATTATT-TCGGGTCGGGTCGGGTTGGATTTCTAATTCATATATTCG
126 TATTAAATAAAAATAATTTATTATTAT----T----TCGGGTCGAATTTCTAATTCATATATTCG
*
110888 GGTCGGGTCAGATAAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTTG
183 GGTCGGGTCAGATAAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
*
110951 GGTCAAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGAGT
1 GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC--GTCGAGT
111002 CAGGTTCTGG
Statistics
Matches: 268, Mismatches: 19, Indels: 23
0.86 0.06 0.07
Matches are distributed among these distances:
240 8 0.03
241 7 0.03
242 23 0.09
243 1 0.00
246 1 0.00
247 15 0.06
248 45 0.17
249 33 0.12
251 1 0.00
255 133 0.50
256 1 0.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (245 bp):
GGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGTCGAGTTCGGGTTTAGGGTAAA
AAAACGGACCGACCCGAAAAATATATATAATTCGGGTCGGGCCGGATTAAGTCAATGTTTTATTA
AATAAAAATAATTTATTATTATTTCGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTCAGAT
AAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCG
Found at i:110982 original size:38 final size:38
Alignment explanation
Indices: 110920--111007 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
110910 TTTTGTTCGG
*
110920 GTCGGGTCGGG-TTTTTTAAGTGTGATATTTGGGTCAA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
*
110957 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAG
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
* *
110995 GTCGAGTCAGGTT
1 GTCGGGTCGGGTT
111008 CTGGTTTAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 11 0.24
38 35 0.76
ACGTcount: A:0.15, C:0.10, G:0.36, T:0.39
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
Found at i:111417 original size:17 final size:16
Alignment explanation
Indices: 111382--111413 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
111372 AATAAAATAA
111382 AATTTTAATATTTTTT
1 AATTTTAATATTTTTT
111398 AATTTTAA-ATTTTTT
1 AATTTTAATATTTTTT
111413 A
1 A
111414 TAATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATTTTAATATTTTTT
Found at i:111614 original size:16 final size:18
Alignment explanation
Indices: 111593--111638 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
111583 TATAGAATTG
111593 AATTCCAATTCC-T-ACA
1 AATTCCAATTCCTTCACA
111609 AATTCCAATTCCTTCACA
1 AATTCCAATTCCTTCACA
*
111627 GATTCCAATTCC
1 AATTCCAATTCC
111639 CTCATAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 14 0.52
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.33
Consensus pattern (18 bp):
AATTCCAATTCCTTCACA
Found at i:115681 original size:19 final size:19
Alignment explanation
Indices: 115665--115705 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
115655 ATCACTATAT
115665 GCTTACCTGAACACTATTA
1 GCTTACCTGAACACTATTA
115684 GCTTACCTGAACACTATTA
1 GCTTACCTGAACACTATTA
115703 GCT
1 GCT
115706 AGCCATTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (19 bp):
GCTTACCTGAACACTATTA
Found at i:119382 original size:31 final size:31
Alignment explanation
Indices: 119347--119407 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
119337 TTGCGAGCCT
* *
119347 AAAATTTTCAAGCTCGACTCGAACTCGAAAG
1 AAAATATTCAAACTCGACTCGAACTCGAAAG
*
119378 AAAATATTGAAACTCGACTCGAACTCGAAA
1 AAAATATTCAAACTCGACTCGAACTCGAAA
119408 AGGCTCGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (31 bp):
AAAATATTCAAACTCGACTCGAACTCGAAAG
Found at i:119451 original size:11 final size:11
Alignment explanation
Indices: 119435--119583 Score: 64
Period size: 11 Copynumber: 12.6 Consensus size: 11
119425 AAATTTTAAG
119435 AGCTCGATTCA
1 AGCTCGATTCA
*
119446 AGCTCGAGACTCA
1 AGCTC--GATTCA
* *
119459 AGCTTGATTAA
1 AGCTCGATTCA
**
119470 AGCTCGATTTTG
1 AGCTCGA-TTCA
* *
119482 AGCTCAATTGAAA
1 AGCTCGATT--CA
* *
119495 AACTCGATGCA
1 AGCTCGATTCA
*
119506 AGCTCGATTGAGA
1 AGCTCGATT--CA
*
119519 AGCTCGATTAAAA
1 AGCTCGATT--CA
* *
119532 AACTCGATTTTA
1 AGCTCGA-TTCA
*
119544 AGCTCGTTTCA
1 AGCTCGATTCA
*
119555 AGCTCGTTTCA
1 AGCTCGATTCA
*
119566 AGCTCAATTCA
1 AGCTCGATTCA
119577 AGCTCGA
1 AGCTCGA
119584 AAACGGGTTA
Statistics
Matches: 103, Mismatches: 27, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
11 54 0.52
12 14 0.14
13 33 0.32
14 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:119533 original size:37 final size:36
Alignment explanation
Indices: 119469--119539 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
119459 AGCTTGATTA
** *
119469 AAGCTCGATTTTGAGCTCAATTGAAAAACTCGATGC
1 AAGCTCGATTGAGAGCTCAATTAAAAAACTCGATGC
*
119505 AAGCTCGATTGAGAAGCTCGATTAAAAAACTCGAT
1 AAGCTCGATTGAG-AGCTCAATTAAAAAACTCGAT
119540 TTTAAGCTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 11 0.37
37 19 0.63
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (36 bp):
AAGCTCGATTGAGAGCTCAATTAAAAAACTCGATGC
Found at i:136023 original size:64 final size:60
Alignment explanation
Indices: 135943--136082 Score: 226
Period size: 64 Copynumber: 2.3 Consensus size: 60
135933 AAGTTTGAGG
*
135943 ACTAATTTAAAATGAGAGTCATTGTTTATGGATGAAATTGAAATATTAAAAAAAAAATCTAAAA
1 ACTAATTTAAAATGAGAGTCATTGTTTATGGAAGAAATTGAAATATT----AAAAAATCTAAAA
*
136007 ACTAGTTTAAAATGAGAGTCATTGTTTATGGAAGAAATTGAAATATTAAAAAATCTAAAA
1 ACTAATTTAAAATGAGAGTCATTGTTTATGGAAGAAATTGAAATATTAAAAAATCTAAAA
136067 ACTAATTTAAAATGAG
1 ACTAATTTAAAATGAG
136083 GATCATAATT
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
60 28 0.38
64 45 0.62
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (60 bp):
ACTAATTTAAAATGAGAGTCATTGTTTATGGAAGAAATTGAAATATTAAAAAATCTAAAA
Found at i:136105 original size:60 final size:58
Alignment explanation
Indices: 135884--136118 Score: 168
Period size: 60 Copynumber: 3.9 Consensus size: 58
135874 AAGTTTGGGT
* * *** * * * * * **
135884 ACTAATTTAGAATGAGAGTCATAATTTGGGGTGAAACTAGAATATTCAAAAGTTTGAGG
1 ACTAATTTAAAATGAGAGTCATAATTTAGAAAGAAA-TTGAATATTAAAAAATCTAAAA
** * *
135943 ACTAATTTAAAATGAGAGTCATTGTTTATGGATGAAATTGAAATATTAAAAAAAAAATCTAAAA
1 ACTAATTTAAAATGAGAGTCATAATTTA-GAAAGAAATTG-AATATT----AAAAAATCTAAAA
* ** *
136007 ACTAGTTTAAAATGAGAGTCATTGTTTATGGAAGAAATTGAAATATTAAAAAATCTAAAA
1 ACTAATTTAAAATGAGAGTCATAATTTA-GAAAGAAATTG-AATATTAAAAAATCTAAAA
136067 ACTAATTTAAAATGAG-GATCATAATTTA-AAAGTAAAATTGAATATTAAAAAA
1 ACTAATTTAAAATGAGAG-TCATAATTTAGAAAG--AAATTGAATATTAAAAAA
136119 ATATGAGGAT
Statistics
Matches: 149, Mismatches: 18, Indels: 18
0.81 0.10 0.10
Matches are distributed among these distances:
58 3 0.02
59 39 0.26
60 55 0.37
64 52 0.35
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (58 bp):
ACTAATTTAAAATGAGAGTCATAATTTAGAAAGAAATTGAATATTAAAAAATCTAAAA
Found at i:136119 original size:60 final size:60
Alignment explanation
Indices: 135943--136120 Score: 184
Period size: 60 Copynumber: 2.9 Consensus size: 60
135933 AAGTTTGAGG
** * *
135943 ACTAATTTAAAATGAGAGTCATTGTTTATGGATGAAATTGAAATATTAAAAAAAAAATCTAAAA
1 ACTAATTTAAAATGAGAGTCATAATTTA-GAAAGAAATTGAAATATT---AAAAAAATCTAAAA
* ** *
136007 ACTAGTTTAAAATGAGAGTCATTGTTTATGGAAGAAATTGAAATATT-AAAAAATCTAAAA
1 ACTAATTTAAAATGAGAGTCATAATTTA-GAAAGAAATTGAAATATTAAAAAAATCTAAAA
136067 ACTAATTTAAAATGAG-GATCATAATTTA-AAAGTAAAATTG-AATATTAAAAAAAT
1 ACTAATTTAAAATGAGAG-TCATAATTTAGAAAG--AAATTGAAATATTAAAAAAAT
136121 ATGAGGATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
58 3 0.03
59 7 0.07
60 49 0.47
64 45 0.43
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (60 bp):
ACTAATTTAAAATGAGAGTCATAATTTAGAAAGAAATTGAAATATTAAAAAAATCTAAAA
Found at i:137988 original size:18 final size:17
Alignment explanation
Indices: 137965--138011 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
137955 TGTTTCTGAG
137965 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
137983 GGAATTAGAATCTGTCA
1 GGAATTGGAATCTGTAA
*
138000 TGAATTGGAATC
1 GGAATTGGAATC
138012 CAATTCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:140011 original size:14 final size:14
Alignment explanation
Indices: 139992--140034 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
139982 TGAGTCTGAA
139992 AAACATAAACGAAC
1 AAACATAAACGAAC
140006 AAACATAAACGAAC
1 AAACATAAACGAAC
* *
140020 AAACACAAACAAAC
1 AAACATAAACGAAC
140034 A
1 A
140035 GATTATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.67, C:0.23, G:0.05, T:0.05
Consensus pattern (14 bp):
AAACATAAACGAAC
Found at i:140557 original size:22 final size:22
Alignment explanation
Indices: 140505--140558 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
140495 GGTGGGGTTA
*
140505 ATAACTTAATAACTTGAATAAAT
1 ATAA-TTAATAAATTGAATAAAT
* *
140528 ATAGTTAATAAATTGAATACAT
1 ATAATTAATAAATTGAATAAAT
*
140550 GTAATTAAT
1 ATAATTAAT
140559 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 23 0.88
23 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (22 bp):
ATAATTAATAAATTGAATAAAT
Found at i:141121 original size:18 final size:19
Alignment explanation
Indices: 141084--141127 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
141074 TTATAACACT
*
141084 TAAAATAATGTATTTTTAA
1 TAAAATAATGTATCTTTAA
*
141103 TAAAATAATTTA-CTTTAA
1 TAAAATAATGTATCTTTAA
141121 TAAAATA
1 TAAAATA
141128 TTGACGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAAATAATGTATCTTTAA
Found at i:142028 original size:140 final size:139
Alignment explanation
Indices: 141750--142013 Score: 352
Period size: 140 Copynumber: 1.9 Consensus size: 139
141740 CTAGTTTAAG
* * *
141750 GACTAAAGTGAAATTAAACCTAAAATAGAGGCTCTAATTATTAATCCTAACCAATTTTATTCAAT
1 GACTAAAGTGAAAGTAAACCTAAAATAGAGACTCTAATTATTAATCCTAACCAATTTTAATCAAT
*
141815 TATTGAATTGAATAATTAAAATGGAACCCATACAAAAATGCAAGGACCAAATAAAAAAATTAACC
66 TATT-AATTGAATAATTAAAATGGAACCCAAACAAAAATGCAAGGACCAAATAAAAAAATTAACC
141880 AAAATTAAAT
130 AAAATTAAAT
** *
141890 GACTAAAGTGAAAGTAAACCTAAGGTGGAGACTCTAATTATTAATCCTAACCAATTTTAATCAAT
1 GACTAAAGTGAAAGTAAACCTAAAATAGAGACTCTAATTATTAATCCTAACCAATTTTAATCAAT
* * ** * *
141955 TATCT-ATTCGAATAATT-AATTAGGAACATCAAACATCAATGCGAGGACTAAATAAAAAA
66 TAT-TAATT-GAATAATTAAAAT-GGAAC-CCAAACAAAAATGCAAGGACCAAATAAAAAA
142014 TTTGCCTAAA
Statistics
Matches: 107, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
139 6 0.06
140 75 0.70
141 26 0.24
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (139 bp):
GACTAAAGTGAAAGTAAACCTAAAATAGAGACTCTAATTATTAATCCTAACCAATTTTAATCAAT
TATTAATTGAATAATTAAAATGGAACCCAAACAAAAATGCAAGGACCAAATAAAAAAATTAACCA
AAATTAAAT
Found at i:148357 original size:32 final size:32
Alignment explanation
Indices: 148290--148383 Score: 91
Period size: 32 Copynumber: 3.0 Consensus size: 32
148280 CAACCTAAGA
* * ** *
148290 GAGTACCTTGAGACTTTAGAGGTTATCCAATG
1 GAGTACCTTGAGACCTTAAAGCCTATCCAAGG
*
148322 GAGTACCTTGAGACCTTAAAGCCTATTCAAGG
1 GAGTACCTTGAGACCTTAAAGCCTATCCAAGG
* * * *
148354 GAGTACTTTGAG-CCTAAAAGCATACCCAAG
1 GAGTACCTTGAGACCTTAAAGCCTATCCAAG
148384 AGTCACCATA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 14 0.27
32 37 0.73
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (32 bp):
GAGTACCTTGAGACCTTAAAGCCTATCCAAGG
Found at i:148732 original size:53 final size:53
Alignment explanation
Indices: 148652--148760 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
148642 AAAGATCGGT
*
148652 CTAGGAGGTCTACTGAGCATCAGCCTCGCTACGCTCTACAGCACCACTCGAAC
1 CTAGGAAGTCTACTGAGCATCAGCCTCGCTACGCTCTACAGCACCACTCGAAC
*
148705 CTAGGAAGTCTACTGAGCATCAGCCTCGCTACGCTCTACCGCACCACTCGAAC
1 CTAGGAAGTCTACTGAGCATCAGCCTCGCTACGCTCTACAGCACCACTCGAAC
148758 CTA
1 CTA
148761 AACCATAATG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.25, C:0.37, G:0.19, T:0.19
Consensus pattern (53 bp):
CTAGGAAGTCTACTGAGCATCAGCCTCGCTACGCTCTACAGCACCACTCGAAC
Found at i:148743 original size:26 final size:26
Alignment explanation
Indices: 148660--148743 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
148650 GTCTAGGAGG
148660 TCTACTGAGCATCAGCCTCGCTACGC
1 TCTACTGAGCATCAGCCTCGCTACGC
* * * * * *
148686 TCTACAGCACCACTCGAACCTAG-GAAG-
1 TCTACTG-AGCA-TC-AGCCTCGCTACGC
148713 TCTACTGAGCATCAGCCTCGCTACGC
1 TCTACTGAGCATCAGCCTCGCTACGC
148739 TCTAC
1 TCTAC
148744 CGCACCACTC
Statistics
Matches: 41, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
24 5 0.12
25 4 0.10
26 14 0.34
27 9 0.22
28 4 0.10
29 5 0.12
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (26 bp):
TCTACTGAGCATCAGCCTCGCTACGC
Found at i:155550 original size:14 final size:14
Alignment explanation
Indices: 155531--155557 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
155521 AATCATATTT
155531 ACTTGCATGCTTTA
1 ACTTGCATGCTTTA
155545 ACTTGCATGCTTT
1 ACTTGCATGCTTT
155558 TTCTAATGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (14 bp):
ACTTGCATGCTTTA
Found at i:156301 original size:20 final size:19
Alignment explanation
Indices: 156274--156335 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
156264 CATTTTGGTG
156274 CAGAGGGAATCGATCCCCC
1 CAGAGGGAATCGATCCCCC
*
156293 CATGAGGGAACCGATTTCCCCC
1 CA-GAGGGAATCGA--TCCCCC
156315 ACAG-GGGAATCGATACCCCC
1 -CAGAGGGAATCGAT-CCCCC
156335 C
1 C
156336 TGGGGTACTG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
19 4 0.11
20 15 0.42
21 8 0.22
22 7 0.19
23 2 0.06
ACGTcount: A:0.26, C:0.37, G:0.24, T:0.13
Consensus pattern (19 bp):
CAGAGGGAATCGATCCCCC
Found at i:156334 original size:21 final size:20
Alignment explanation
Indices: 156275--156335 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
156265 ATTTTGGTGC
156275 AGAGGGAATCGATCCCCCCA
1 AGAGGGAATCGATCCCCCCA
* * *
156295 TGAGGGAACCGATTTCCCCCA
1 AGAGGGAATCGA-TCCCCCCA
156316 CAG-GGGAATCGATACCCCCC
1 -AGAGGGAATCGAT-CCCCCC
156336 TGGGGTACTG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 11 0.34
21 20 0.62
22 1 0.03
ACGTcount: A:0.26, C:0.36, G:0.25, T:0.13
Consensus pattern (20 bp):
AGAGGGAATCGATCCCCCCA
Found at i:156390 original size:3 final size:3
Alignment explanation
Indices: 156382--156413 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
156372 TTTTAAAACA
156382 TCT TCT TC- TCT TCT TCT TC- TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
156414 TCTGCCGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:156398 original size:11 final size:11
Alignment explanation
Indices: 156382--156416 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
156372 TTTTAAAACA
156382 TCTTCTTCTCT
1 TCTTCTTCTCT
156393 TCTTCTTCTCT
1 TCTTCTTCTCT
156404 TCTTCTTCT-T
1 TCTTCTTCTCT
156414 TCT
1 TCT
156417 GCCGTTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (11 bp):
TCTTCTTCTCT
Found at i:159274 original size:36 final size:36
Alignment explanation
Indices: 159236--159323 Score: 115
Period size: 37 Copynumber: 2.3 Consensus size: 36
159226 ATAATTTTAT
159236 AAATAAAATATTAAAATATTATATTTTTATTAAAATA
1 AAAT-AAATATTAAAATATTATATTTTTATTAAAATA
*
159273 AAATAAATATAAAATATATTA-ATTATTTATTAAAATA
1 AAATAAATATTAAA-ATATTATATT-TTTATTAAAATA
159310 AGAATAATATATTA
1 A-AATAA-ATATTA
159324 TTAGGTATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
36 12 0.27
37 23 0.51
38 5 0.11
39 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (36 bp):
AAATAAATATTAAAATATTATATTTTTATTAAAATA
Found at i:159277 original size:32 final size:33
Alignment explanation
Indices: 159208--159315 Score: 105
Period size: 36 Copynumber: 3.1 Consensus size: 33
159198 TCAATATTAT
159208 TATTAAAATATTATATCTATAATT-TTATAAATAAAA
1 TATTAAAATATTATAT-TAT--TTATTA-AAATAAAA
159244 TATTAAAATATTATATT-TTTATTAAAATAAAA
1 TATTAAAATATTATATTATTTATTAAAATAAAA
159276 TAAATATAAAATA-TATTAATTATTTATTAAAATAAGAA
1 T--AT-TAAAATATTA-T-ATTATTTATTAAAATAA-AA
159314 TA
1 TA
159316 ATATATTATT
Statistics
Matches: 64, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
32 11 0.17
33 3 0.05
34 5 0.08
35 9 0.14
36 20 0.31
37 13 0.20
38 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (33 bp):
TATTAAAATATTATATTATTTATTAAAATAAAA
Found at i:159359 original size:25 final size:26
Alignment explanation
Indices: 159330--159387 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
159320 ATTATTAGGT
* * *
159330 ATATTAATCATGTATT-AACATAATA
1 ATATTAATAAAGTATTAAAAATAATA
* *
159355 ATATTATTAAAGTATTAAAAATTATA
1 ATATTAATAAAGTATTAAAAATAATA
159381 ATATTAA
1 ATATTAA
159388 AATAAAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (26 bp):
ATATTAATAAAGTATTAAAAATAATA
Found at i:159547 original size:14 final size:13
Alignment explanation
Indices: 159483--159553 Score: 60
Period size: 13 Copynumber: 5.6 Consensus size: 13
159473 ATTAATTTTT
*
159483 TAATAATTTATTA
1 TAATAATATATTA
159496 T-AT-AT-TATTA
1 TAATAATATATTA
* *
159506 AAATAA-AAATATA
1 TAATAATATAT-TA
*
159519 TTATAATATATTA
1 TAATAATATATTA
159532 TAATAATATAATTA
1 TAATAATAT-ATTA
159546 TAATAATA
1 TAATAATA
159554 AAAATAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
10 5 0.11
11 4 0.09
12 5 0.11
13 17 0.37
14 15 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATAATATATTA
Found at i:163462 original size:34 final size:33
Alignment explanation
Indices: 163380--163463 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
163370 CGAGGGTGCA
** *
163380 CCGAGGCCGTACACACCAAGGGTGCACCTAAGG
1 CCGAGGCCGCGCACACCAAGGGCGCACCTAAGG
163413 CCGAGGCCGCGCACACCAAGGGCGCACCTAAGG
1 CCGAGGCCGCGCACACCAAGGGCGCACCTAAGG
163446 CCGAGGCCCGCGCACACC
1 CCGAGG-CCGCGCACACC
163464 GATAATGCAC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 36 0.77
34 11 0.23
ACGTcount: A:0.24, C:0.40, G:0.31, T:0.05
Consensus pattern (33 bp):
CCGAGGCCGCGCACACCAAGGGCGCACCTAAGG
Found at i:165654 original size:23 final size:23
Alignment explanation
Indices: 165580--165647 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
165570 AAATGCATCG
165580 AAGTGCCACGTAGAATTGCACCA
1 AAGTGCCACGTAGAATTGCACCA
* * *
165603 AAGTACCGCGTAAAATTGCACCA
1 AAGTGCCACGTAGAATTGCACCA
*
165626 AAGTGCCACATAGAATTGCACC
1 AAGTGCCACGTAGAATTGCACC
165648 GTAGTGCTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCA
Found at i:165911 original size:30 final size:31
Alignment explanation
Indices: 165877--165936 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
165867 TATCGTGTAG
*
165877 ACATATCA-TTTCCATACCTTTATCACATAA
1 ACATATAATTTTCCATACCTTTATCACATAA
165907 ACATATAATTTTCCATACCTTTATCACATA
1 ACATATAATTTTCCATACCTTTATCACATA
165937 GCTTATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.37, C:0.25, G:0.00, T:0.38
Consensus pattern (31 bp):
ACATATAATTTTCCATACCTTTATCACATAA
Found at i:168179 original size:81 final size:80
Alignment explanation
Indices: 168026--168180 Score: 184
Period size: 81 Copynumber: 1.9 Consensus size: 80
168016 ACCTAGAGCT
* * * * * * * * *
168026 GAGGCCAACGACGACAAGGTCAGCCGATGGCTCTAACCAGTAAGTAACGGGACATATTCGGGGTT
1 GAGGCCAACGACAACAAAGTCAGCCGATGGCTCTAACCAATAAGCAACAGGACACACTCAGGGTC
168091 AGGGCCAACACGATC
66 AGGGCCAACACGATC
* * *
168106 GAGGTCAACGCACAACAAAGTCAGCCGATGGCTTTAACCAATAAGCAACATGACACACTCAGGGT
1 GAGGCCAACG-ACAACAAAGTCAGCCGATGGCTCTAACCAATAAGCAACAGGACACACTCAGGGT
*
168171 CGGGGCCAAC
65 CAGGGCCAAC
168181 GCATACCAGG
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
80 9 0.15
81 52 0.85
ACGTcount: A:0.32, C:0.26, G:0.27, T:0.14
Consensus pattern (80 bp):
GAGGCCAACGACAACAAAGTCAGCCGATGGCTCTAACCAATAAGCAACAGGACACACTCAGGGTC
AGGGCCAACACGATC
Found at i:182199 original size:63 final size:63
Alignment explanation
Indices: 182082--182201 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
182072 GGGGTGAGGG
* ** * *
182082 TATTGCTATGATGAACATTAAATCACACAAGGAACGCAGAAAGTTAGATGGTGATGACGTAGC
1 TATTGCTACGATGAACATTAAATCACACAACAAACGCAGAAAGTCAGATAGTGATGACGTAGC
* * * *
182145 TATTGCTACGATGGAGATTAAATCACAGAACAAACGCAGAAAGTCGGATAGTGATGA
1 TATTGCTACGATGAACATTAAATCACACAACAAACGCAGAAAGTCAGATAGTGATGA
182202 AAATGATATT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (63 bp):
TATTGCTACGATGAACATTAAATCACACAACAAACGCAGAAAGTCAGATAGTGATGACGTAGC
Found at i:182212 original size:63 final size:63
Alignment explanation
Indices: 182082--182229 Score: 145
Period size: 63 Copynumber: 2.3 Consensus size: 63
182072 GGGGTGAGGG
* ** * * ** *
182082 TATTGCTATGATGAACATTAAATCACACAAGGAACGCAGAAAGTTAGATGGTGATGACGTAGC
1 TATTGCTACGATGAACATTAAATCACACAACAAACGCAGAAAGTCAGATAGTGATGAAATAGA
* * * *
182145 TATTGCTACGATGGAGATTAAATCACAGAACAAACGCAGAAAGTCGGATAGTGATGAAA-ATGA
1 TATTGCTACGATGAACATTAAATCACACAACAAACGCAGAAAGTCAGATAGTGATGAAATA-GA
** *
182208 TATTGCTATTACGAACATTAAA
1 TATTGCTACGATGAACATTAAA
182230 ACGAGGAGAA
Statistics
Matches: 67, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
62 1 0.01
63 66 0.99
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (63 bp):
TATTGCTACGATGAACATTAAATCACACAACAAACGCAGAAAGTCAGATAGTGATGAAATAGA
Found at i:182310 original size:63 final size:62
Alignment explanation
Indices: 182161--182330 Score: 180
Period size: 63 Copynumber: 2.7 Consensus size: 62
182151 TACGATGGAG
* * ** * * *
182161 ATTAAATCACAGAACAAACGCAGAAAGTCGGATAGTGATGAAAATGATATTGCTATTACGAAC
1 ATTAAATCACAGAACAAA-GCAGAAAGTTGGACAGTGATGAGGACGATATTGCTATAACAAAC
* * *
182224 ATTAAAACGAGGAGAA-AAAGCAGAAAGTTGGACAGTGATGAGGACGCTATTGCTATAACAAAC
1 ATTAAATC-A-CAGAACAAAGCAGAAAGTTGGACAGTGATGAGGACGATATTGCTATAACAAAC
* * *
182287 ATTAAATCACAAAACAAATGCAGAAAATTGGGCAGTGATGAGGA
1 ATTAAATCACAGAACAAA-GCAGAAAGTTGGACAGTGATGAGGA
182331 GAATACTGCT
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
61 3 0.03
62 4 0.05
63 73 0.83
64 4 0.05
65 4 0.05
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.19
Consensus pattern (62 bp):
ATTAAATCACAGAACAAAGCAGAAAGTTGGACAGTGATGAGGACGATATTGCTATAACAAAC
Found at i:203366 original size:20 final size:20
Alignment explanation
Indices: 203343--203414 Score: 51
Period size: 19 Copynumber: 3.7 Consensus size: 20
203333 TTAAATTTTA
203343 TATATATTATAATAATTGAT
1 TATATATTATAATAATTGAT
* * *
203363 TATAGA-TATAATTATATGAA
1 TATATATTATAATAAT-TGAT
* * *
203383 TGTA-ATTATAAT-TTTGTT
1 TATATATTATAATAATTGAT
*
203401 TATTTATTATAATA
1 TATATATTATAATA
203415 TTTATTTTGG
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
18 4 0.10
19 18 0.46
20 17 0.44
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (20 bp):
TATATATTATAATAATTGAT
Found at i:207106 original size:3 final size:3
Alignment explanation
Indices: 207100--207177 Score: 95
Period size: 3 Copynumber: 25.7 Consensus size: 3
207090 TATTATTTTT
*
207100 TAA TAA TAA TAA TAA T-A TATA TATA TAA TAA TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA
* * *
207146 TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
207178 TGGCTAGGGT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
2 2 0.03
3 56 0.86
4 7 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:207295 original size:3 final size:3
Alignment explanation
Indices: 207289--207378 Score: 128
Period size: 3 Copynumber: 30.0 Consensus size: 3
207279 TATTATTTTT
207289 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
207334 TAA TTA TAA TAA TAA TAT TTA TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
207379 AATGGGTAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.03
3 72 0.94
4 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:207308 original size:189 final size:194
Alignment explanation
Indices: 206988--207371 Score: 715
Period size: 189 Copynumber: 2.0 Consensus size: 194
206978 AGATGATGAG
206988 ATGGCTAGGGTTAGATCAAACCCTAATCTGTTAGGGTTTAGTTGGGCCATCTGAATTTGTAATTG
1 ATGGCTAGGGTTAGATCAAACCCTAATCTGTTAGGGTTTAGTTGGGCCATCTGAATTTGTAATTG
207053 GGCCAGATAATATGGGCCTGTTTGTAATTATTATTATTATTATTTTTTAATAATAATAAT-A-AT
66 GGCCAGATAATATGGGCCTGTTTGTAATTATTATTATTATTATTTTTTAATAATAATAATAATAT
*
207116 ATAT-AT-AT-ATAATAATAATAATAATAATTATAATAATAATATTTATAATAATTATAATAAT
131 ATATAATAATAATAATAATAATAATAATAATTATAATAATAATATTTATAATAATAATAATAAT
207177 ATGGCTAGGGTTAGATCAAACCCTAATCTGTTAGGGTTTAGTTGGGCCATCTGAATTTGTAATTG
1 ATGGCTAGGGTTAGATCAAACCCTAATCTGTTAGGGTTTAGTTGGGCCATCTGAATTTGTAATTG
207242 GGCCAGATAATATGGGCCTGTTTGTAATTATTATTATTATTATTTTTTAATAATAATAATAATAT
66 GGCCAGATAATATGGGCCTGTTTGTAATTATTATTATTATTATTTTTTAATAATAATAATAATAT
*
207307 ATATAATAATAATAATAATAATAATAATAATTATAATAATAATATTTATAATAATAATTATAAT
131 ATATAATAATAATAATAATAATAATAATAATTATAATAATAATATTTATAATAATAATAATAAT
207371 A
1 A
207372 ATAATAAAAT
Statistics
Matches: 188, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
189 125 0.66
190 1 0.01
191 6 0.03
192 2 0.01
193 2 0.01
194 52 0.28
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (194 bp):
ATGGCTAGGGTTAGATCAAACCCTAATCTGTTAGGGTTTAGTTGGGCCATCTGAATTTGTAATTG
GGCCAGATAATATGGGCCTGTTTGTAATTATTATTATTATTATTTTTTAATAATAATAATAATAT
ATATAATAATAATAATAATAATAATAATAATTATAATAATAATATTTATAATAATAATAATAAT
Found at i:207666 original size:122 final size:120
Alignment explanation
Indices: 207529--207800 Score: 352
Period size: 124 Copynumber: 2.2 Consensus size: 120
207519 TCTTCTCTTT
* * * * *
207529 CTTCAGATGAGTTCTTCTCATTATGAACTTTTCGCT-G-GGGATGATGTTGACCTATTTCCTTCT
1 CTTCAGATGAGTTCTTCTCATTATGAACTTTTCGCTAGAAGGATGATGCTAACATATCTCCTTCT
* *
207592 GTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTTCTC
66 GTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAA---CTT-TTTCTC
* * * *
207651 CTTCAGATGAGTTCTTCTCATTATGAAC-TTTCTCTAGAAAGGTTGATGCTAATATATCTGCTTC
1 CTTCAGATGAGTTCTTCTCATTATGAACTTTTCGCTAG-AAGGATGATGCTAACATATCTCCTTC
* * *
207715 TGTGATAGAATTATGCAAAAGGTTGAATAAGCTCTTCTCATTGTGAACTTTTTCTT
65 TGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTC
207771 CTTCAGATGAGTTCTTCTCATTATGAACTT
1 CTTCAGATGAGTTCTTCTCATTATGAACTT
207801 CTCTAAAAAA
Statistics
Matches: 132, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
120 33 0.25
121 10 0.08
122 29 0.22
124 60 0.45
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (120 bp):
CTTCAGATGAGTTCTTCTCATTATGAACTTTTCGCTAGAAGGATGATGCTAACATATCTCCTTCT
GTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTC
Found at i:207938 original size:116 final size:115
Alignment explanation
Indices: 207816--208337 Score: 685
Period size: 116 Copynumber: 4.5 Consensus size: 115
207806 AAAAAAACCG
* * *
207816 ATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
*
207881 CTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTA
66 CTTCTTCAGA-GATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGTTA
* * * *
207932 ATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTC
1 ATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
*
207997 CTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTA
66 CTTCTTCAGA-GATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGTTA
* * *
208048 ATCCATCAAATAATGAATTTAAACAAAACGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
* * * * * *
208113 CTTCTTC--AGATGAGTTCTTCTTATTATGAACTCGAAATGGTAATGCTG
66 CTTCTTCAGAGATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGTTA
** * *
208161 ATCCATTGAATGATGAATTCAAGCAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAAATGATGAATTTAAGC-AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
* * * * *
208226 CCTTCTTTAG-G-TGAGTTCTTCTCATTATGAACTCTAATTGGTACTGTTG
65 CCTTCTTCAGAGATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGTTA
* * * * *
208275 TTCCA-CTGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCT
1 ATCCATC-AAATGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
208338 GGAAAAGCTG
Statistics
Matches: 368, Mismatches: 34, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
113 90 0.24
114 98 0.27
115 1 0.00
116 179 0.49
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (115 bp):
ATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
CTTCTTCAGAGATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGTTA
Found at i:209616 original size:18 final size:17
Alignment explanation
Indices: 209595--209652 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
209585 TCTTGACCCC
*
209595 TTTTTTTCTTTTTCCTTT
1 TTTTTTTATTTTT-CTTT
209613 TTTTTTTATTTTT-TGTT
1 TTTTTTTATTTTTCT-TT
*
209630 TCTTTTTTATTTCTCTTT
1 T-TTTTTTATTTTTCTTT
209648 TTTTT
1 TTTTT
209653 CTCTTCAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 1 0.03
17 7 0.20
18 26 0.74
19 1 0.03
ACGTcount: A:0.03, C:0.10, G:0.02, T:0.84
Consensus pattern (17 bp):
TTTTTTTATTTTTCTTT
Found at i:209624 original size:11 final size:11
Alignment explanation
Indices: 209597--209654 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
209587 TTGACCCCTT
209597 TTTTTCTTTTTCC
1 TTTTT-TTTTT-C
*
209610 TTTTTTTTTTA
1 TTTTTTTTTTC
*
209621 TTTTTTGTTTC
1 TTTTTTTTTTC
*
209632 TTTTTTATTTC
1 TTTTTTTTTTC
*
209643 TCTTTTTTTTC
1 TTTTTTTTTTC
209654 T
1 T
209655 CTTCAAGAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 29 0.74
12 5 0.13
13 5 0.13
ACGTcount: A:0.03, C:0.12, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:217450 original size:69 final size:72
Alignment explanation
Indices: 217320--217464 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 72
217310 TTCTTTCCTT
217320 TCTCAAGGCTTTTGAGTAGACGGCTATTCTTTCCTTTTAGATCTTCAACTCGACTTTTCTCGATG
1 TCTCAAGGCTTTTGAGTAGACGGCTATTCTTTCC-TTTAGATCTTCAACTCGACTTTTCTCGATG
217385 TTCAA-TC
65 TTCAATTC
217392 TCTCAAGGC-TTTGAGTAGACGGCTATTCTTTCC-TTAGATCTTCAACTCGACTTTTCTCGATGT
1 TCTCAAGGCTTTTGAGTAGACGGCTATTCTTTCCTTTAGATCTTCAACTCGACTTTTCTCGATGT
217455 TCAATTC
66 TCAATTC
217462 TCT
1 TCT
217465 GGTCATCTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
69 34 0.47
70 5 0.07
71 24 0.33
72 9 0.12
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.41
Consensus pattern (72 bp):
TCTCAAGGCTTTTGAGTAGACGGCTATTCTTTCCTTTAGATCTTCAACTCGACTTTTCTCGATGT
TCAATTC
Found at i:221997 original size:12 final size:12
Alignment explanation
Indices: 221974--222088 Score: 180
Period size: 12 Copynumber: 9.6 Consensus size: 12
221964 TATTTATTTT
*
221974 TAATAATAATAA
1 TAATAATTATAA
221986 TAAT-ATATATAA
1 TAATAAT-TATAA
*
221998 TAATTA-TAGTAA
1 TAATAATTA-TAA
222010 TAATAATTATAA
1 TAATAATTATAA
222022 TAATAATTATAA
1 TAATAATTATAA
222034 TAATAATTATAA
1 TAATAATTATAA
222046 TAATAATTATAA
1 TAATAATTATAA
222058 TAATAATTATAA
1 TAATAATTATAA
222070 TAATAATTATAA
1 TAATAATTATAA
222082 TAATAAT
1 TAATAAT
222089 AAAATGGGTT
Statistics
Matches: 97, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
11 4 0.04
12 90 0.93
13 3 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (12 bp):
TAATAATTATAA
Found at i:225756 original size:21 final size:21
Alignment explanation
Indices: 225732--225780 Score: 91
Period size: 20 Copynumber: 2.4 Consensus size: 21
225722 GAGCCTTCAC
225732 CATTTTTCTTGGAAATTTATT
1 CATTTTTCTTGGAAATTTATT
225753 CA-TTTTCTTGGAAATTTATT
1 CATTTTTCTTGGAAATTTATT
225773 CATTTTTC
1 CATTTTTC
225781 ATTAGTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.57
Consensus pattern (21 bp):
CATTTTTCTTGGAAATTTATT
Found at i:228831 original size:26 final size:27
Alignment explanation
Indices: 228782--228833 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
228772 TGAAAAATAT
228782 AAATCTACATAAAAAAAACTATAATTAA
1 AAATCTACATAAAAAAAAC-ATAATTAA
228810 AAATC-ACATAAAACAAAA-ATAATT
1 AAATCTACATAAAA-AAAACATAATT
228834 TTTATACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.26
27 8 0.35
28 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (27 bp):
AAATCTACATAAAAAAAACATAATTAA
Found at i:230940 original size:20 final size:21
Alignment explanation
Indices: 230915--230960 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
230905 AACTTCGGGA
*
230915 TTTTTTCTTTAAAAA-AGTTT
1 TTTTTTCTTTAAAAATAATTT
*
230935 TTTTTTTTTTAAAAATAATTT
1 TTTTTTCTTTAAAAATAATTT
230956 TTTTT
1 TTTTT
230961 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTTCTTTAAAAATAATTT
Found at i:230956 original size:17 final size:17
Alignment explanation
Indices: 230936--230969 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
230926 AAAAAGTTTT
*
230936 TTTTTTTTTAAAAATAA
1 TTTTTTTTAAAAAATAA
230953 TTTTTTTTAAAAAATAA
1 TTTTTTTTAAAAAATAA
230970 AAATTCCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTTTTAAAAAATAA
Found at i:244149 original size:21 final size:21
Alignment explanation
Indices: 244097--244149 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
244087 ACTTTCTGCC
*
244097 TTCTCTACTTCTATTCTTCTT
1 TTCTCTACTTCTACTCTTCTT
244118 TTAC-CTACTTCTACTCTTCTT
1 TT-CTCTACTTCTACTCTTCTT
*
244139 TTCTCTTCTTC
1 TTCTCTACTTC
244150 CTGCCTTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.09, C:0.32, G:0.00, T:0.58
Consensus pattern (21 bp):
TTCTCTACTTCTACTCTTCTT
Found at i:244852 original size:27 final size:26
Alignment explanation
Indices: 244799--244852 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
244789 ACTTGCACTT
*
244799 CCATTTACCACATTAGGTTTCTCATA
1 CCATTTACCACATTAGGTTACTCATA
244825 CCATTTACCACATTCAGGTTGACT-ATA
1 CCATTTACCACATT-AGGTT-ACTCATA
244852 C
1 C
244853 TTCCGTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 14 0.56
27 9 0.36
28 2 0.08
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (26 bp):
CCATTTACCACATTAGGTTACTCATA
Found at i:259358 original size:25 final size:25
Alignment explanation
Indices: 259329--259378 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
259319 TAGACAGTTG
259329 ACCTGTAAGGTAACACAAGAGACAT
1 ACCTGTAAGGTAACACAAGAGACAT
259354 ACCTGTAAGGTAACACAAGAGACAT
1 ACCTGTAAGGTAACACAAGAGACAT
259379 CAATTAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (25 bp):
ACCTGTAAGGTAACACAAGAGACAT
Found at i:261884 original size:13 final size:13
Alignment explanation
Indices: 261868--261895 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
261858 GGGAAAAGAA
261868 CACCTTAAAAGTT
1 CACCTTAAAAGTT
261881 CACCTTAAAAGTT
1 CACCTTAAAAGTT
261894 CA
1 CA
261896 AAAATCAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.29
Consensus pattern (13 bp):
CACCTTAAAAGTT
Found at i:266804 original size:21 final size:21
Alignment explanation
Indices: 266730--266805 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
266720 CCGATAGAGC
*
266730 TCTACTTAAAATGTTATTTTT
1 TCTACCTAAAATGTTATTTTT
*
266751 TCTACATAAAATGTTATTTTT
1 TCTACCTAAAATGTTATTTTT
** * *
266772 TCTACCGGAAATGTTAATTTC
1 TCTACCTAAAATGTTATTTTT
*
266793 ACTACCTAAAATG
1 TCTACCTAAAATG
266806 AATATTTCCG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (21 bp):
TCTACCTAAAATGTTATTTTT
Found at i:272071 original size:8 final size:8
Alignment explanation
Indices: 272058--272093 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
272048 TGTCTTAATC
272058 AATTCTCA
1 AATTCTCA
272066 AATTCTCA
1 AATTCTCA
272074 AATTCTCA
1 AATTCTCA
272082 AATTCTCA
1 AATTCTCA
272090 AATT
1 AATT
272094 ATTAATCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (8 bp):
AATTCTCA
Found at i:276831 original size:25 final size:23
Alignment explanation
Indices: 276803--276856 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
276793 AATTTTATCT
*
276803 ACATTTAAATTTAGTCATTTTTAAA
1 ACATTTAAATGTA-T-ATTTTTAAA
* *
276828 ACATGTATATGTATATTTTTAAA
1 ACATTTAAATGTATATTTTTAAA
276851 A-ATTTA
1 ACATTTA
276857 TAGTTTAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 4 0.16
23 10 0.40
24 1 0.04
25 10 0.40
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (23 bp):
ACATTTAAATGTATATTTTTAAA
Found at i:291545 original size:372 final size:377
Alignment explanation
Indices: 290784--291547 Score: 1319
Period size: 389 Copynumber: 2.0 Consensus size: 377
290774 TGGTGGCGAC
290784 TCTTTGAACCGTATTTTTTCGATGGTAAAGGAAATTCAAAAATTTTCGAAACGAGAGGTTTTTAA
1 TCTTTGAACCGTATTTTTTCGATGGTAAAGGAAATTCAAAAATTTTCGAAACGAGAGGTTTTTAA
290849 ATCGCACTTATTTTTAAATTAAAAATCAATTGAAAGAGTAAATTAAAAATTAATGTGGTTTTCAA
66 ATCGCACTTATTTTTAAATTAAAAA-CAATTGAAAGAGTAAATTAAAAATTAATGTGGTTTTCAA
290914 AATCTCACCTTTAAGAAAAAATCGTTTCAACAGCTCGTTTATATATATATATATATATATAATTA
130 AATCTCACCTTTAAGAAAAAATCGTTTCAACAGCTCGTTTATATATATATATATATATATAATTA
290979 TAAATACGTATGTGCGTATAATGTTTTAATCGAACAAAGGACGAGGAAAGGTGGCAATGGTTCCA
195 TAAATACGTATGTGCGTATAATGTTTTAATCGAACAAAGGACGAGGAAAGGTGGCAATGGTTCCA
291044 TGATCACCAACACCAACACCACCACGACGGTTAAACAATCGTCTCCAAGTTTTCAACTGATTCAA
260 TG------------AACACCACCACGACGGTTAAACAATCGTCTCCAAGTTTTCAACTGATTCAA
291109 AACCTGTTTGTAAACGCCAATTCTTAAACCAGAAACGCTGACCATCACAGCTTTCCTTAGCTTCT
313 AACCTGTTTGTAAACGCCAATTCTTAAACCAGAAACGCTGACCATCACAGCTTTCCTTAGCTTCT
291174 TCTTTGAACCGTATTTTTTCGATGGTAAAGGAAATTCAAAAATTTTCGAAACGAGAGGTTTTTAA
1 TCTTTGAACCGTATTTTTTCGATGGTAAAGGAAATTCAAAAATTTTCGAAACGAGAGGTTTTTAA
291239 ATCGCACTTA-TTTTAAATT-AAAA-AATTGAAAGAGGTAAATTAAAAATTAATGTGGTTTTCAA
66 ATCGCACTTATTTTTAAATTAAAAACAATTGAAAGA-GTAAATTAAAAATTAATGTGGTTTTCAA
*
291301 AATCTCACCTTTAAGGAAAAATCGTTTCAACAGCTCGTTTATATATATATATATATATATATAAT
130 AATCTCACCTTTAAGAAAAAATCGTTTCAACAGCTCG-TT-TATATATATATATATATATATAAT
291366 TATAAATACGTATGTGCGTATAATGTTTTAATCGAACAAAGGACGAGGAAAGGTGGCAATGGTTC
193 TATAAATACGTATGTGCGTATAATGTTTTAATCGAACAAAGGACGAGGAAAGGTGGCAATGGTTC
291431 CATG-ACACCA-C-C-ACGGTTAAACAATCGTCTCCAAG-TTTCAACTGATTCAAAACCTGTTTG
258 CATGAACACCACCACGACGGTTAAACAATCGTCTCCAAGTTTTCAACTGATTCAAAACCTGTTTG
291491 TAAACGCCAATTCTTAAACCAGAAACGCTGACCATCACAGCTTTCCTTAGCTTCT
323 TAAACGCCAATTCTTAAACCAGAAACGCTGACCATCACAGCTTTCCTTAGCTTCT
291546 TC
1 TC
291548 AATTTTCTCC
Statistics
Matches: 370, Mismatches: 1, Indels: 24
0.94 0.00 0.06
Matches are distributed among these distances:
372 82 0.22
373 23 0.06
374 1 0.00
375 1 0.00
376 6 0.02
386 10 0.03
387 64 0.17
388 6 0.02
389 102 0.28
390 75 0.20
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (377 bp):
TCTTTGAACCGTATTTTTTCGATGGTAAAGGAAATTCAAAAATTTTCGAAACGAGAGGTTTTTAA
ATCGCACTTATTTTTAAATTAAAAACAATTGAAAGAGTAAATTAAAAATTAATGTGGTTTTCAAA
ATCTCACCTTTAAGAAAAAATCGTTTCAACAGCTCGTTTATATATATATATATATATATAATTAT
AAATACGTATGTGCGTATAATGTTTTAATCGAACAAAGGACGAGGAAAGGTGGCAATGGTTCCAT
GAACACCACCACGACGGTTAAACAATCGTCTCCAAGTTTTCAACTGATTCAAAACCTGTTTGTAA
ACGCCAATTCTTAAACCAGAAACGCTGACCATCACAGCTTTCCTTAGCTTCT
Found at i:292478 original size:121 final size:120
Alignment explanation
Indices: 292261--292490 Score: 291
Period size: 121 Copynumber: 1.9 Consensus size: 120
292251 AAATAATCAG
* * *
292261 TAAATTTATCAAACTTTATGATCATAAAAATGTTATGATAACCTAAAATGTAATTAAATAAGAGA
1 TAAATTTATCAAACTTTATGATCATAAAAATGTCACGATAACCTAAAATGTAATTAAATAAGAAA
* * * * *
292326 TATCAAGAGGAGAGAACAATGTGTAAATTATTTTTTGAAATAGTCCGAAATTACCT
66 CATCAACACGAAAGAACAA-GTGTAAATTATTTTTTAAAATAGTCCGAAATTACCT
* * *
292382 TAAATTTATCAAATTTTATGATCATAAAAATGTCACGATGACCTTCAAAATGTAATTAAATTAGA
1 TAAATTTATCAAACTTTATGATCATAAAAATGTCACGATAACC-T-AAAATGTAATTAAATAAGA
* * **
292447 AACATGAACACGAAAGAATAA-TGTATTTTATTTTTTAAAATAGT
64 AACATCAACACGAAAGAACAAGTGTAAATTATTTTTTAAAATAGT
292491 TTGAAGTGAT
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
121 59 0.64
122 1 0.01
123 32 0.35
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (120 bp):
TAAATTTATCAAACTTTATGATCATAAAAATGTCACGATAACCTAAAATGTAATTAAATAAGAAA
CATCAACACGAAAGAACAAGTGTAAATTATTTTTTAAAATAGTCCGAAATTACCT
Found at i:296534 original size:75 final size:75
Alignment explanation
Indices: 296395--296570 Score: 205
Period size: 75 Copynumber: 2.4 Consensus size: 75
296385 GGATCCACTG
* * * *
296395 GAATCAACATG-TTCGG-AACAAGCTTCTAAATTTCCTGAACCTGAATCACAAGCAATACAGTGT
1 GAATCAACATGTTTGGGAAACAAGCTTCTAAACTTCCTCAACCTGAACCACAAGCAATACAGTGT
296458 GAACCTACTA
66 GAACCTACTA
* * * **
296468 GAGTCAACATGTTTGGGAAACATGCTTCTAAACTTCCTCAACCTGAACCTCAAGTGATACCA-TG
1 GAATCAACATGTTTGGGAAACAAGCTTCTAAACTTCCTCAACCTGAACCACAAGCAATA-CAGTG
*
296532 TGAACCTACTG
65 TGAACCTACTA
* * *
296543 GAACCAACATGTTTGGAAAACAGGCTTC
1 GAATCAACATGTTTGGGAAACAAGCTTC
296571 CTAATTTTCC
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
73 10 0.12
74 4 0.05
75 70 0.81
76 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (75 bp):
GAATCAACATGTTTGGGAAACAAGCTTCTAAACTTCCTCAACCTGAACCACAAGCAATACAGTGT
GAACCTACTA
Found at i:307402 original size:729 final size:730
Alignment explanation
Indices: 304979--307649 Score: 3624
Period size: 729 Copynumber: 3.6 Consensus size: 730
304969 TCCGTGCGTA
* **
304979 ACTCTGAATAATGATTG-TCGATTTTGTTCTTAATTTAAGTAACAGCACACCTCTCCACCACCTT
1 ACTCTGAATAATGATTGCT-GATTTTGTTCTTAACTTAAGTAACAAAACACCTCTCCACCACCTT
* *
305043 TGCAGTTTCAGAACTGAAGTAATCAAT-ATTGTTAATTC-AACACTCTGGAAGAAGCCTTCTGAC
65 TGCAGTTTCATAAGTGAAGTAATCAATAATT-TTAATTCTAA-ACTCTGGAAGAAGCCTTCTGAC
* * * * * *
305106 ATCTTACAAGTGCAATCAG-CAGCAGTAGCTGCTTGAAAGGAAGACGCTCCTGCAATTGCTCAAA
128 ATCTTAAAATTGTAA-CTGCCAGCAGTAGCTGCATGAAAGGAAGATGCTCCTGCAATTGCTCAAA
* * * * *
305170 GCCATATGATTTTGTATAGTCTCAGATAAAACCACAACTGAAGCATACAAAAGAGAACT-TCTAG
192 -CCATATGCTTTGGTA-AAT-TC---T---A--A-GACTGAAGCATACAAATGAGAACTGT-TAG
* * * * ** *
305234 TAATCAAAT-AAGTAGACATTCAGGAGAAAACTAAGTACCTAAAAGCCTGCTTCGAGCAATTTGC
244 TAATCAAATAAATTAGATATTC---AGAAGACTAAGTACCAAAAAGCCTATTTCGAGAAATTTGC
* * * * * *
305298 CCTC-GAATAACCCTTTGAATTTCGATAGCTGCCAGTTTCTGCAAGTGAAATGCCTTCTGACATA
306 CCCCTG-ATAACCCTTTGAATCTCGATAGCAGCCAATTTCTGAAAATGAAATGCCTTCTGACATA
* * * * * * * * *
305362 TTAGGCGCCATATTGCTTTTTGGATCTTAATTGCAGCATCCCTTTTCAACAACA---CCTTCCGT
370 ATACGCACCGTATTGCTCTTTGGATCTTTATTGCAGCATCCCTTTCCGACAACAGCTCCTTCCTT
* *
305424 ACAAGCCAACCACGGCAATGTCTCTGATTTATAAGAAGAATAAAAAAAGAGAAGTCAATGTGATT
435 ACAAGCCAACCACGGCAATGTCTCTGATTTAT----A-AA-AAAAACA-AGAAGTCAGTGTGATT
* * * * * * * **
305489 TATGTATTGTTGCAAGTAAACACCATACAGAAATGTATGCTAGGGAATGCCAACGAGCATGATTC
493 TATGTATTGGTACAAGTAAACACCTTACGGAAATATATGCTAAGGAATGCCAACGGGTGTGATTC
* * * * * * *
305554 ATAAGAGCAAGTGGATGCTAAAAAGCAGTAAAGTTTAAGTGT--CA-TTTGCAAACGGCATCAAT
558 ATTAGAGCAAGTGGATGCTAAGAAGCAGAAAACTTTAAGTGTAGAAGTTTGCAAAAGGCATCATT
* * * * * **
305616 GATTGGAACTATATAAAGCTTAGCTGAAAATGGAGATATCATACTTGTATTACATCAATACATTG
623 TATTGGTACTATATAAAGCATAGCTGAAGA--GAGATATCATACTTGTATTACAACAATACAACG
* *
305681 CCTCTCTCTATGAGCTTTTTGCTTAGCAATCCACCCCCTTGCATG
686 CCTCTCTCTATGAGCTTTTTGCTTAGCAGTCCATCCCCTTGCATG
* * * * *
305726 ACTCTGAATAACGATTGATGATTTTGTTCTTAATTTAAGTAACATAACACCTTTCCACCACCTTT
1 ACTCTGAATAATGATTGCTGATTTTGTTCTTAACTTAAGTAACAAAACACCTCTCCACCACCTTT
* * * *
305791 GCAGTTTCACAAGTGAAGTAATCACTAAGTTTAATTCAAAACTTCT-GAAGAAGCCTTCTGACAT
66 GCAGTTTCATAAGTGAAGTAATCAATAATTTTAATTCTAAAC-TCTGGAAGAAGCCTTCTGACAT
* * *
305855 CTTACAATTGTAACAT-CCAGCAGTAGGTGCATGAAAGGAAGATGCTCCTGAAATTGCTCAAACC
130 CTTAAAATTGTAAC-TGCCAGCAGTAGCTGCATGAAAGGAAGATGCTCCTGCAATTGCTCAAACC
* * * * * * *
305919 ATACGCTTTGGT-GATTCTCAGA-TGGAACCACAACTAAAGAATACAGAACTTTTAGTAATCAAA
194 ATATGCTTTGGTAAATTCTAAGACT-GAA--GC-A-TACA-AAT-GAGAACTGTTAGTAATCAAA
* * *
305982 TAAGTT-GATATTCAGAAGAAAACAAAGTACCTAAAAGCCTATTTCGAGAAATTTGCCCCCTGAT
252 TAAATTAGATATTCAGAAG---ACTAAGTACCAAAAAGCCTATTTCGAGAAATTTGCCCCCTGAT
* * *
306046 AACCCTTTGGATCTCGATAGCAGCCAGTTTCTGAAAATGAAATGCCTTCGGACATAATACGCACC
314 AACCCTTTGAATCTCGATAGCAGCCAATTTCTGAAAATGAAATGCCTTCTGACATAATACGCACC
306111 GTATTGCTCTTTGGATCTTTATTGCAGCATCCCTTTCCGACAACAGCTCCTTCCTTACAAGCCAA
379 GTATTGCTCTTTGGATCTTTATTGCAGCATCCCTTTCCGACAACAGCTCCTTCCTTACAAGCCAA
*
306176 CCACGGCAATGTCTCTGATTTATAAGAAAAACAAGAAGTCAGTGTGATTTATGTATTGGTACAAG
444 CCACGGCAATGTCTCTGATTTATAAAAAAAACAAGAAGTCAGTGTGATTTATGTATTGGTACAAG
*
306241 TAAACACCTTACGGAAATATATGCTAAGGAATGCCAACGGGTGTGATTCATTAGAACAAGTGGAT
509 TAAACACCTTACGGAAATATATGCTAAGGAATGCCAACGGGTGTGATTCATTAGAGCAAGTGGAT
* *
306306 GCTAAGAAGCAGAAAACCTTAAGTGTAGACGTTTGCAAAAGGCATCATTTATTGGTACTATATAA
574 GCTAAGAAGCAGAAAACTTTAAGTGTAGAAGTTTGCAAAAGGCATCATTTATTGGTACTATATAA
306371 AGCATAGCTGAAGAGAGATATCATACTTGTATTACAACAATACAACGCCTCTCTCTATGAGCTTT
639 AGCATAGCTGAAGAGAGATATCATACTTGTATTACAACAATACAACGCCTCTCTCTATGAGCTTT
306436 TTGCTTAGCAGTCCATCCCCTTGCATG
704 TTGCTTAGCAGTCCATCCCCTTGCATG
*
306463 ACTCTGAATAATGATTGCTGATTTTGTTCTTAACTTGAGTAACAAAACACCTCTCCACCACCTTT
1 ACTCTGAATAATGATTGCTGATTTTGTTCTTAACTTAAGTAACAAAACACCTCTCCACCACCTTT
306528 GCAGTTTCATAAGTGAAGTAATCAATAATTTTAATTCTAAACTCTGGAAGAAGCCTTCTGACATC
66 GCAGTTTCATAAGTGAAGTAATCAATAATTTTAATTCTAAACTCTGGAAGAAGCCTTCTGACATC
* *
306593 TTAAAATTGTAACCGCCAGCAGTAGCTGCATGAAAGGAAGATGCTCCTGCAATTGCTCAAGCCAT
131 TTAAAATTGTAACTGCCAGCAGTAGCTGCATGAAAGGAAGATGCTCCTGCAATTGCTCAAACCAT
* * * * **
306658 ATGCTTTGGTAAATTCTAAGATTGAAGCATACGACTGAGAACTGTTCGTAATTGAATAAATTAG-
196 ATGCTTTGGTAAATTCTAAGACTGAAGCATACAAATGAGAACTGTTAGTAATCAAATAAATTAGA
* * *
306722 TATTCA-AAGAGTAAGTACCAAAAAGCCTATTTCGAGAATTTTGCCCCCTGATAACCCTTTGGAT
261 TATTCAGAAGACTAAGTACCAAAAAGCCTATTTCGAGAAATTTGCCCCCTGATAACCCTTTGAAT
*
306786 CTCGATAGCAGCCAATTTCTGAAAATGAAATGTCTTCTGACATAATACGCACCGTATTGCTCTTT
326 CTCGATAGCAGCCAATTTCTGAAAATGAAATGCCTTCTGACATAATACGCACCGTATTGCTCTTT
* *
306851 GGATCTTTATTGCTGCATCCCTTTCCGACAACAGTTCCTTCCTTACAAGCCAACCACGGCAATGT
391 GGATCTTTATTGCAGCATCCCTTTCCGACAACAGCTCCTTCCTTACAAGCCAACCACGGCAATGT
306916 CTCTGATTTATAAAAAAAACAAGAAGTCAGTGTGATTTATGTATTGGTACAAGTAAACACCTTAC
456 CTCTGATTTATAAAAAAAACAAGAAGTCAGTGTGATTTATGTATTGGTACAAGTAAACACCTTAC
306981 GGAAATATATGCTAAGGAATGCCAACGGGTGTGATTCATTAGAGCAAGTGGATGCTAAGAAGCAG
521 GGAAATATATGCTAAGGAATGCCAACGGGTGTGATTCATTAGAGCAAGTGGATGCTAAGAAGCAG
307046 AAAACTTTTAAGTGTAGAAGTTTGCAAAAGGCATCATTTATTGGTACTATATAAAGCATAGCTGA
586 AAAAC-TTTAAGTGTAGAAGTTTGCAAAAGGCATCATTTATTGGTACTATATAAAGCATAGCTGA
*
307111 AGAGAGATATCATACTTGTATTTCAACAATACAACGCCTCTCTCTATGAGCTTTTTGCTTAGCAG
650 AGAGAGATATCATACTTGTATTACAACAATACAACGCCTCTCTCTATGAGCTTTTTGCTTAGCAG
307176 TCCATCCCCTTGCATG
715 TCCATCCCCTTGCATG
*
307192 ACTCTGAATAATGATTGCTGATTTTGTTCTTAACTTGAGTAACAAAACACCTCTCCACCACCTTT
1 ACTCTGAATAATGATTGCTGATTTTGTTCTTAACTTAAGTAACAAAACACCTCTCCACCACCTTT
* *
307257 GCAATTTCATAAGTGATGTAATCAATAATTTTAATTCTAAACTCTGGAAGAAGCCTTCTGACATC
66 GCAGTTTCATAAGTGAAGTAATCAATAATTTTAATTCTAAACTCTGGAAGAAGCCTTCTGACATC
307322 TTAAAATTGTAACTGCCAGCAGTAGCTGCATGAAAGGAAGATGCTCCTGCAATTGCTCAAACCAT
131 TTAAAATTGTAACTGCCAGCAGTAGCTGCATGAAAGGAAGATGCTCCTGCAATTGCTCAAACCAT
* * **
307387 ATGCTTTGGTAAATTCTAAGACTGAAGCATACAACTGAGAACTGTTCGTAATTGAATAAATTAG-
196 ATGCTTTGGTAAATTCTAAGACTGAAGCATACAAATGAGAACTGTTAGTAATCAAATAAATTAGA
* * **
307451 TGTTCA-AAGAGTAAGTACCAAAAAGCCTATTTCGAGAAATTTGCCCCCTGATAAAACTTTGAAT
261 TATTCAGAAGACTAAGTACCAAAAAGCCTATTTCGAGAAATTTGCCCCCTGATAACCCTTTGAAT
* * *
307515 CTCGATAGCAGCCAATTTCTGAAAATGAAACGCCTTCTGACATAATACGCACCGTATCGCTCTCT
326 CTCGATAGCAGCCAATTTCTGAAAATGAAATGCCTTCTGACATAATACGCACCGTATTGCTCTTT
* * * * *
307580 GGATCTTTATTACAGCATCCATTTGC-AGCAAAAGCTCCTTCCTTACAAGCCAACCACGGTAATG
391 GGATCTTTATTGCAGCATCCCTTTCCGA-CAACAGCTCCTTCCTTACAAGCCAACCACGGCAATG
307644 TCTCTG
455 TCTCTG
307650 GTTTTCAATA
Statistics
Matches: 1747, Mismatches: 145, Indels: 82
0.89 0.07 0.04
Matches are distributed among these distances:
728 310 0.18
729 571 0.33
731 3 0.00
732 26 0.01
733 4 0.00
734 6 0.00
735 2 0.00
736 112 0.06
737 268 0.15
738 15 0.01
739 46 0.03
740 157 0.09
741 4 0.00
743 41 0.02
744 1 0.00
746 12 0.01
747 161 0.09
748 8 0.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (730 bp):
ACTCTGAATAATGATTGCTGATTTTGTTCTTAACTTAAGTAACAAAACACCTCTCCACCACCTTT
GCAGTTTCATAAGTGAAGTAATCAATAATTTTAATTCTAAACTCTGGAAGAAGCCTTCTGACATC
TTAAAATTGTAACTGCCAGCAGTAGCTGCATGAAAGGAAGATGCTCCTGCAATTGCTCAAACCAT
ATGCTTTGGTAAATTCTAAGACTGAAGCATACAAATGAGAACTGTTAGTAATCAAATAAATTAGA
TATTCAGAAGACTAAGTACCAAAAAGCCTATTTCGAGAAATTTGCCCCCTGATAACCCTTTGAAT
CTCGATAGCAGCCAATTTCTGAAAATGAAATGCCTTCTGACATAATACGCACCGTATTGCTCTTT
GGATCTTTATTGCAGCATCCCTTTCCGACAACAGCTCCTTCCTTACAAGCCAACCACGGCAATGT
CTCTGATTTATAAAAAAAACAAGAAGTCAGTGTGATTTATGTATTGGTACAAGTAAACACCTTAC
GGAAATATATGCTAAGGAATGCCAACGGGTGTGATTCATTAGAGCAAGTGGATGCTAAGAAGCAG
AAAACTTTAAGTGTAGAAGTTTGCAAAAGGCATCATTTATTGGTACTATATAAAGCATAGCTGAA
GAGAGATATCATACTTGTATTACAACAATACAACGCCTCTCTCTATGAGCTTTTTGCTTAGCAGT
CCATCCCCTTGCATG
Found at i:308413 original size:174 final size:174
Alignment explanation
Indices: 307985--308428 Score: 604
Period size: 173 Copynumber: 2.6 Consensus size: 174
307975 TTAGCCGTCT
** * * *
307985 AAAATTACTTTGAATGGTTATTATTGCTTGCTTCTGCTTGATAAAACTCCTCCTTAATTGCCAAC
1 AAAATTACTTTGAATTCTTATTATTGCTTGCTTCTGCTTCATAAAACTTCTCCTTAAATGCCAAC
* * * * * * *
308050 CACGGAAATGACTCTGAATTTTTGTTGCAGCAAATGTCTGATTTTGGAGGAATCTATGGGCAAAT
66 CCCGGAAATGGCTCTGAATTTTAGTTGCAGCAAATATCTGATTCTGGAGGAATCTACGGACAAAT
* * *
308115 TCCTTCTGAGCAACCTGGAAGGCCCTCCAACATTTCAGTTGTCG
131 TCCTTCTGAGCAACCTGAAAGGCCCACCAACATTTCAGTAGTCG
* * * *
308159 -AAATTACTTTGGATTTTTATTATAGCTTGCTTCTGTTTCATAAAACTTCTCCTTAAATGCCAAC
1 AAAATTACTTTGAATTCTTATTATTGCTTGCTTCTGCTTCATAAAACTTCTCCTTAAATGCCAAC
* * *
308223 CCCGGTAATGGCTCTGAATTTTAGTTGCTGCAAATATCTGATTCTGGA-GAGATTTACGGACAAA
66 CCCGGAAATGGCTCTGAATTTTAGTTGCAGCAAATATCTGATTCTGGAGGA-ATCTACGGACAAA
* *
308287 TTCCTTCTGAGCAATCTGAAAGGCCCACCAAGATTTCAGTAGTCG
130 TTCCTTCTGAGCAACCTGAAAGGCCCACCAACATTTCAGTAGTCG
* * *
308332 AAAATTACTTTGAATTCTTATTATTGCCTGCTTCTGCTTCATAAAACTTCTCCTTAAAAGCCAGC
1 AAAATTACTTTGAATTCTTATTATTGCTTGCTTCTGCTTCATAAAACTTCTCCTTAAATGCCAAC
* *
308397 CCCTGAAATGGCTCTGAATTTTAGTAGCAGCA
66 CCCGGAAATGGCTCTGAATTTTAGTTGCAGCA
308429 GAAGTCTGTT
Statistics
Matches: 234, Mismatches: 34, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
172 2 0.01
173 147 0.63
174 85 0.36
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (174 bp):
AAAATTACTTTGAATTCTTATTATTGCTTGCTTCTGCTTCATAAAACTTCTCCTTAAATGCCAAC
CCCGGAAATGGCTCTGAATTTTAGTTGCAGCAAATATCTGATTCTGGAGGAATCTACGGACAAAT
TCCTTCTGAGCAACCTGAAAGGCCCACCAACATTTCAGTAGTCG
Found at i:314252 original size:15 final size:15
Alignment explanation
Indices: 314228--314261 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
314218 GATTCAAGGA
*
314228 TTAATTTATTTTAAT
1 TTAATATATTTTAAT
314243 TTAATATATTTTAAT
1 TTAATATATTTTAAT
314258 TTAA
1 TTAA
314262 AAATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATATATTTTAAT
Found at i:315222 original size:21 final size:22
Alignment explanation
Indices: 315201--315242 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
315191 TACATTGATT
315201 AAATA-ACAATTTTTAAATATTA
1 AAATATAC-ATTTTTAAATATTA
*
315223 AAATATACTTTTTTAAATAT
1 AAATATACATTTTTAAATAT
315243 ATAATTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATATACATTTTTAAATATTA
Found at i:318066 original size:89 final size:89
Alignment explanation
Indices: 317957--318131 Score: 307
Period size: 89 Copynumber: 2.0 Consensus size: 89
317947 TTCGTTGAGG
*
317957 TTATCCTGGTGGTTCCGTTGCTGAAAAGATATAGTTCGTGATATTGAATATTGTTCGTTAGAATT
1 TTATCCTGGTGGTTCCGTTGCTGAAAAGATACAGTTCGTGATATTGAATATTGTTCGTTAGAATT
*
318022 AAAAT-ACCAAAATACGGATCAATT
66 AAAATGA-AAAAATACGGATCAATT
*
318046 TTATCCTGGTGGTTCCGTTGCTGCAAAGATACAGTTCGTGATATTGAATATTGTTCGTTAGAATT
1 TTATCCTGGTGGTTCCGTTGCTGAAAAGATACAGTTCGTGATATTGAATATTGTTCGTTAGAATT
318111 AAAATGAAAAAATACGGATCA
66 AAAATGAAAAAATACGGATCA
318132 GTTGAGACAT
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
89 81 0.99
90 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (89 bp):
TTATCCTGGTGGTTCCGTTGCTGAAAAGATACAGTTCGTGATATTGAATATTGTTCGTTAGAATT
AAAATGAAAAAATACGGATCAATT
Found at i:324692 original size:16 final size:16
Alignment explanation
Indices: 324671--324702 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
324661 AATCACGTGG
324671 GGAAAAGAAAGAGTTA
1 GGAAAAGAAAGAGTTA
324687 GGAAAAGAAAGAGTTA
1 GGAAAAGAAAGAGTTA
324703 TCTGGAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.31, T:0.12
Consensus pattern (16 bp):
GGAAAAGAAAGAGTTA
Found at i:331057 original size:13 final size:14
Alignment explanation
Indices: 331028--331058 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
331018 AACCATGCAA
331028 GTGATATGAACTAT
1 GTGATATGAACTAT
331042 GTGATATGAA-TAT
1 GTGATATGAACTAT
331055 GTGA
1 GTGA
331059 AATATGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (14 bp):
GTGATATGAACTAT
Found at i:338966 original size:27 final size:27
Alignment explanation
Indices: 338925--339021 Score: 169
Period size: 27 Copynumber: 3.6 Consensus size: 27
338915 TAAAGTTTTT
338925 GAGTTCGAGTCGAGCTCAGCAATACTC
1 GAGTTCGAGTCGAGCTCAGCAATACTC
*
338952 GAGTTCGAGTTGAGCTCAGCAATACTC
1 GAGTTCGAGTCGAGCTCAGCAATACTC
338979 GAGTTCGAGTCGAGCTCAGCAATACTC
1 GAGTTCGAGTCGAGCTCAGCAATACTC
*
339006 GAGTTCGACTCG-GCTC
1 GAGTTCGAGTCGAGCTC
339022 GTTTAACAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
26 4 0.06
27 63 0.94
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.24
Consensus pattern (27 bp):
GAGTTCGAGTCGAGCTCAGCAATACTC
Found at i:339390 original size:33 final size:32
Alignment explanation
Indices: 339348--339426 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 32
339338 ACCGCCGCCT
339348 TTTGAAATAAAATTTTTAAAAAGAAAACACAAA
1 TTTGAAATAAAATTTTTAAAAA-AAAACACAAA
** *
339381 TTTGAAATAATTTTTTTTTTAAAAAAAAACTCAAA
1 TTTGAAATAA---AATTTTTAAAAAAAAACACAAA
339416 TTTGAAATAAA
1 TTTGAAATAAA
339427 CCCAAAACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
33 10 0.26
35 19 0.49
36 10 0.26
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (32 bp):
TTTGAAATAAAATTTTTAAAAAAAAACACAAA
Found at i:341462 original size:423 final size:422
Alignment explanation
Indices: 340674--341516 Score: 1564
Period size: 423 Copynumber: 2.0 Consensus size: 422
340664 CAAGACTTTG
* * *
340674 CTGCTGCATGATTGGTTAATTAGGAACCTTCATAATGCACTTTTGTTTCCAGGTTGGTAAAATAT
1 CTGCTGCATGATTGGTCAATTAAGAACCTTCATAATGCACTTCTGTTTCCAGGTTGGTAAAATAT
340739 GACCATGATTCTCTTGGAGCATTTCGTTTCCACATGCTTGATATGTAAAGAATGTTTACATTTGG
66 GACCATGATTCTCTTGGAGCATTTCGTTTCCACATGCTTGATATGTAAAGAATGTTTACATTTGG
*
340804 GTCAAATTTCCATTTAATTTTAAAAATGTTTCTCTTAGTGGCTTCTTAGTTGTACCTGGATTAAA
131 GTCAAATTTCCATTTAATTTTAAAAATGTTTCTATTAGTGGCTTCTTAGTTGTACCTGGATTAAA
*
340869 GCAACAACAAGTGCTAAATTAAACATTCTTTAACATATCAAGCAACATTCTTTAAATTAAATGGA
196 GCAACAACAAGTGCTAAAGTAAACATTCTTTAACATATCAAGCAACATTCTTTAAATTAAATGGA
*
340934 AATTTGACCCAAATGTAAGTACTCTTTAACATATCAAGCACGTGGAAACGAAAGGCTCCAAGAGA
261 AATTTGACCCAAATGTAAGCACTCTTTAACATATCAAGCACGTGGAAACGAAAGGCTCCAAGAGA
340999 ATCATAGCCATATTAAATGTTTGCTATTAAATCACAAGTCGAGCATGGTTGCATTGGCCCACTCT
326 ATCATAGCCATATTAAATGTTTGCTATTAAATCACAAGTCGAGCATGGTTGCATTGGCCCACTCT
341064 AATATTCTAATTGAAGCTCCTCCTCCTGGTTA
391 AATATTCTAATTGAAGCTCCTCCTCCTGGTTA
341096 CTGCTGCATGATTGGTCAATTAAGAACCTTCATAATGCACTTCTGTTTCCAGGTTGGTAAAATAT
1 CTGCTGCATGATTGGTCAATTAAGAACCTTCATAATGCACTTCTGTTTCCAGGTTGGTAAAATAT
*
341161 GACCATGATTCTCTTGGAGCATTTCGTTTCCACATGCTTTATATGTTAAAGAATGTTTACATTTG
66 GACCATGATTCTCTTGGAGCATTTCGTTTCCACATGCTTGATATG-TAAAGAATGTTTACATTTG
341226 GGTCAAATTTCCATTTAA-TTTAAAGAATGTTTCTATTAGTGGCTTCTTAGTTGTACCTGGATTA
130 GGTCAAATTTCCATTTAATTTTAAA-AATGTTTCTATTAGTGGCTTCTTAGTTGTACCTGGATTA
341290 AAGCAACAACAAGTGCTAAAGTAAACATTCTTTAACATATCAAGCAACATTCTTTAAATTAAATG
194 AAGCAACAACAAGTGCTAAAGTAAACATTCTTTAACATATCAAGCAACATTCTTTAAATTAAATG
*
341355 GAAATTTGACCCAAATGTAAGCACTCTTTAACATATCAAGCATGTGGAAACGAAAGGCTCCAAGA
259 GAAATTTGACCCAAATGTAAGCACTCTTTAACATATCAAGCACGTGGAAACGAAAGGCTCCAAGA
*
341420 GAATCATAGCCATATTAAATGTTTGTTATTAAAT-ACCAAGTCGAGCATGGTTGCATTGGCCCAC
324 GAATCATAGCCATATTAAATGTTTGCTATTAAATCA-CAAGTCGAGCATGGTTGCATTGGCCCAC
341484 TCTAATATTCTAATTGAAGCTCCTCCTCCTGGT
388 TCTAATATTCTAATTGAAGCTCCTCCTCCTGGT
341517 CGATGTTCCC
Statistics
Matches: 409, Mismatches: 9, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
422 113 0.28
423 296 0.72
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (422 bp):
CTGCTGCATGATTGGTCAATTAAGAACCTTCATAATGCACTTCTGTTTCCAGGTTGGTAAAATAT
GACCATGATTCTCTTGGAGCATTTCGTTTCCACATGCTTGATATGTAAAGAATGTTTACATTTGG
GTCAAATTTCCATTTAATTTTAAAAATGTTTCTATTAGTGGCTTCTTAGTTGTACCTGGATTAAA
GCAACAACAAGTGCTAAAGTAAACATTCTTTAACATATCAAGCAACATTCTTTAAATTAAATGGA
AATTTGACCCAAATGTAAGCACTCTTTAACATATCAAGCACGTGGAAACGAAAGGCTCCAAGAGA
ATCATAGCCATATTAAATGTTTGCTATTAAATCACAAGTCGAGCATGGTTGCATTGGCCCACTCT
AATATTCTAATTGAAGCTCCTCCTCCTGGTTA
Found at i:341829 original size:72 final size:72
Alignment explanation
Indices: 341712--341854 Score: 286
Period size: 72 Copynumber: 2.0 Consensus size: 72
341702 CGTTGTGGAG
341712 TCTCATGCCCTGGAAGACGGTATCAGTATGGGTTTATTGGTTTCTAATGGGGCAAAAGGTGATTC
1 TCTCATGCCCTGGAAGACGGTATCAGTATGGGTTTATTGGTTTCTAATGGGGCAAAAGGTGATTC
341777 AATCTGC
66 AATCTGC
341784 TCTCATGCCCTGGAAGACGGTATCAGTATGGGTTTATTGGTTTCTAATGGGGCAAAAGGTGATTC
1 TCTCATGCCCTGGAAGACGGTATCAGTATGGGTTTATTGGTTTCTAATGGGGCAAAAGGTGATTC
341849 AATCTG
66 AATCTG
341855 GTTGCAGGGA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (72 bp):
TCTCATGCCCTGGAAGACGGTATCAGTATGGGTTTATTGGTTTCTAATGGGGCAAAAGGTGATTC
AATCTGC
Found at i:344404 original size:16 final size:17
Alignment explanation
Indices: 344364--344407 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
344354 CCCTACTTGA
344364 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** *
344381 TTGTATATTT-TTAAAT
1 TTAAATATTTAATAAAT
344397 TTAAATATTTA
1 TTAAATATTTA
344408 TTTATACATG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Done.