Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 18 of 320
Found at i:5088561 original size:27 final size:27
Alignment explanation
Indices: 5088531--5088585 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5088521 TTGTATATAA
5088531 GCTTATGGTTGTGATTTGATATTTGAT
1 GCTTATGGTTGTGATTTGATATTTGAT
5088558 GCTTATGGTTGTGATTTGATATTTGAT
1 GCTTATGGTTGTGATTTGATATTTGAT
5088585 G
1 G
5088586 TTTGGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (27 bp):
GCTTATGGTTGTGATTTGATATTTGAT
Found at i:5090311 original size:21 final size:22
Alignment explanation
Indices: 5090285--5090333 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
5090275 CTATGCCTTG
5090285 AGACATAAATACC-ATGTCTCA
1 AGACATAAATACCAATGTCTCA
* * *
5090306 AGACATACATGCCAATGTCTCT
1 AGACATAAATACCAATGTCTCA
5090328 AGACAT
1 AGACAT
5090334 GCAACCCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (22 bp):
AGACATAAATACCAATGTCTCA
Found at i:5092431 original size:27 final size:25
Alignment explanation
Indices: 5092400--5092449 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
5092390 ATTTGAATAG
5092400 TAAAATATAGAAAAATAATATATAACC
1 TAAAATA-A-AAAAATAATATATAACC
*
5092427 TAAAATAAAATAATAATATATAA
1 TAAAATAAAAAAATAATATATAA
5092450 ATAAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.64
26 1 0.05
27 7 0.32
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAAATAAAAAAATAATATATAACC
Found at i:5093843 original size:14 final size:14
Alignment explanation
Indices: 5093770--5093853 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 14
5093760 GTATTTTATA
5093770 AAATTATAACAAAA-
1 AAATTATAA-AAAAT
** **
5093784 AAATTATATTATTT
1 AAATTATAAAAAAT
5093798 AAATTATAAAAAATTCT
1 AAATTATAAAAAA---T
5093815 AAATTTATGATAAAAATT
1 AAA-TTAT-A-AAAAA-T
5093833 AAATTATAAAAAAT
1 AAATTATAAAAAAT
5093847 AAATTAT
1 AAATTAT
5093854 GTGTTATAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
13 1 0.02
14 25 0.46
15 5 0.09
16 1 0.02
17 8 0.15
18 8 0.15
19 1 0.02
20 5 0.09
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (14 bp):
AAATTATAAAAAAT
Found at i:5102633 original size:18 final size:18
Alignment explanation
Indices: 5102610--5102653 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
5102600 CTCACAATGG
5102610 AGTAGTGAAAGTATGGAA
1 AGTAGTGAAAGTATGGAA
5102628 AGTAGTGAAAGTATGGAA
1 AGTAGTGAAAGTATGGAA
*
5102646 AGAAGTGA
1 AGTAGTGA
5102654 TCGGAACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.20
Consensus pattern (18 bp):
AGTAGTGAAAGTATGGAA
Found at i:5115259 original size:12 final size:13
Alignment explanation
Indices: 5115232--5115260 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5115222 AATAGACAAA
5115232 AAAACAGCACAGC
1 AAAACAGCACAGC
5115245 AAAACAGCA-AGC
1 AAAACAGCACAGC
5115257 AAAA
1 AAAA
5115261 GAATAGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.62, C:0.24, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAACAGCACAGC
Found at i:5116966 original size:28 final size:30
Alignment explanation
Indices: 5116902--5116966 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 30
5116892 GAGCATAGGT
* *
5116902 TTTTATATATATTAAAGTTAACTTTATTTTA
1 TTTTATATATATT-AAGTTAACCTTATATTA
*
5116933 -TATATATATATT-A-TTAACCTTATATTA
1 TTTTATATATATTAAGTTAACCTTATATTA
5116960 TTTTATA
1 TTTTATA
5116967 CATACGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
27 12 0.41
28 6 0.21
30 11 0.38
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTATATATATTAAGTTAACCTTATATTA
Found at i:5118354 original size:132 final size:131
Alignment explanation
Indices: 5117859--5118387 Score: 464
Period size: 131 Copynumber: 4.0 Consensus size: 131
5117849 TTCACAATTA
* * * * *
5117859 CTAAAAATCCC-TT-AAACGAAGGCGATA-TGCGATATTTGGCAATTCGCGGAATCGCGCCCTAA
1 CTAAAAA-CCCTTTAAAACGAAGGCAATACT-CGATGTTTGACAATTCG-GGAATAGTGCCCTAA
* * * * * * *
5117921 CGTGCTAGGTTGCAATTTTCCGTTTGCTT-AAAATAATCAAATATCCCTTCAAAATTTCACTCGT
63 CGTGCTGGGTTGCAATTTCCCGTTTG-TTCAAAACAATCGAATATTCTTTCGAAATTTCACTCGT
*
5117985 GTCTT
127 GTTTT
* * * * *
5117990 CTAAAAATCCTTTAAAACGAAGGCAATACTCGGTGTTTGATAATTCGAGAATCA-TGCCCTATCG
1 CTAAAAACCCTTTAAAACGAAGGCAATACTCGATGTTTGACAATTCGGGAAT-AGTGCCCTAACG
* ** * * * * **
5118054 TGCTGGTTTGTGACTTCTCGTTTGCTCAAAACAATCGAATATTCCTTTAG-GTTTTCACTCGTGT
65 TGCTGGGTTGCAATTTCCCGTTTGTTCAAAACAATCGAATATT-CTTTCGAAATTTCACTCGTGT
5118118 TTAT
129 TT-T
* * * * *
5118122 -TAAAAA-CCTTCCAAAACGAAGACAATACTCGGTGTTTGATAATTCGGGAATCGTGCCCTAACG
1 CTAAAAACCCTT-TAAAACGAAGGCAATACTCGATGTTTGACAATTCGGGAATAGTGCCCTAACG
* ** * * * **
5118185 TGTTGGGTTGTGATTTCTCGTTTTTTCAAAACAATCGAAGATTCTTTCGAAATTTCACTCACGTT
65 TGCTGGGTTGCAATTTCCCGTTTGTTCAAAACAATCGAATATTCTTTCGAAATTTCACTCGTGTT
5118250 TT
130 TT
* * * * **
5118252 CTAAAAACCCTTTAAAACGAAGGCGATATTCGATGTTTGGCAATTCGGGGAATAGTACCCTATTG
1 CTAAAAACCCTTTAAAACGAAGGCAATACTCGATGTTTGACAATTC-GGGAATAGTGCCCTAACG
* * *
5118317 TGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATAGCTCTTT-GAAATTTCACTCGTAT
65 TGCTGGGTTGCAATTTCCCGTTTGTTCAAAACAATCGAATA-TTCTTTCGAAATTTCACTCGTGT
5118381 TTT
129 TTT
5118384 CTAA
1 CTAA
5118388 GGTGAGGCAA
Statistics
Matches: 319, Mismatches: 65, Indels: 27
0.78 0.16 0.07
Matches are distributed among these distances:
130 13 0.04
131 198 0.62
132 102 0.32
133 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (131 bp):
CTAAAAACCCTTTAAAACGAAGGCAATACTCGATGTTTGACAATTCGGGAATAGTGCCCTAACGT
GCTGGGTTGCAATTTCCCGTTTGTTCAAAACAATCGAATATTCTTTCGAAATTTCACTCGTGTTT
T
Found at i:5124787 original size:16 final size:17
Alignment explanation
Indices: 5124752--5124785 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
5124742 GTCATGTGTC
5124752 TTATTTCTTTTACATAT
1 TTATTTCTTTTACATAT
5124769 TTATTT-TTTTA-ATAT
1 TTATTTCTTTTACATAT
5124784 TT
1 TT
5124786 TACTTTACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 5 0.29
17 6 0.35
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTCTTTTACATAT
Found at i:5126925 original size:17 final size:17
Alignment explanation
Indices: 5126892--5126925 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5126882 ACTTTTAAAA
*
5126892 TTTATATTATATTATTT
1 TTTATATTATATAATTT
*
5126909 TTTATATTATGTAATTT
1 TTTATATTATATAATTT
5126926 GTAAATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTATATTATATAATTT
Found at i:5129297 original size:14 final size:15
Alignment explanation
Indices: 5129272--5129306 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
5129262 TTTAATTTTC
5129272 AAAATTTCAAAAAAA
1 AAAATTTCAAAAAAA
*
5129287 AAAATTT-AAAAATA
1 AAAATTTCAAAAAAA
5129301 AAAATT
1 AAAATT
5129307 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTCAAAAAAA
Found at i:5129336 original size:30 final size:31
Alignment explanation
Indices: 5129302--5129403 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
5129292 TTAAAAATAA
*
5129302 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
5129332 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
5129362 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
5129392 AAATTTCATTTT
1 AAATTTCATTTT
5129404 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:5129776 original size:3 final size:3
Alignment explanation
Indices: 5129768--5129838 Score: 65
Period size: 3 Copynumber: 23.0 Consensus size: 3
5129758 GCTAGACTTT
*
5129768 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA
* *
5129815 GAAA GAA AAA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA
5129839 ATAATAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 4 0.07
3 40 0.70
4 13 0.23
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5129786 original size:10 final size:10
Alignment explanation
Indices: 5129771--5129799 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5129761 AGACTTTGAA
5129771 GAAGAAGAAG
1 GAAGAAGAAG
5129781 GAAGAAGAAG
1 GAAGAAGAAG
5129791 GAAGAAGAA
1 GAAGAAGAA
5129800 AAGAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:5129808 original size:28 final size:28
Alignment explanation
Indices: 5129772--5129838 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
5129762 GACTTTGAAG
* *
5129772 AAGAAGAAGGAAG-AAGAAGGAAGAAGAA
1 AAGAAGAA-GAAGAAAGAAAGAAAAAGAA
*
5129800 AAGAGGAAGAAGAAAGAAAGAAAAAGAAA
1 AAGAAGAAGAAGAAAGAAAGAAAAAG-AA
5129829 AAGAA-AAGAA
1 AAGAAGAAGAA
5129839 ATAATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.12
28 23 0.70
29 6 0.18
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (28 bp):
AAGAAGAAGAAGAAAGAAAGAAAAAGAA
Found at i:5129833 original size:34 final size:34
Alignment explanation
Indices: 5129771--5129837 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
5129761 AGACTTTGAA
* * *
5129771 GAAGAAGAAGGAAGAAGAAGGAAGAAGAAAAGAG
1 GAAGAAGAAGAAAGAAGAAAGAAAAAGAAAAGAG
5129805 GAAGAAGAAAGAAAGAA-AAAGAAAAAGAAAAGA
1 GAAGAAG-AAGAAAGAAGAAAGAAAAAGAAAAGA
5129838 AATAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (34 bp):
GAAGAAGAAGAAAGAAGAAAGAAAAAGAAAAGAG
Found at i:5129836 original size:17 final size:18
Alignment explanation
Indices: 5129769--5129839 Score: 60
Period size: 17 Copynumber: 4.0 Consensus size: 18
5129759 CTAGACTTTG
5129769 AAGAAG-AAGAAGGAAGAAGA
1 AAGAAGAAAGAA--AAGAA-A
* **
5129789 AGGAAG-AAGAAAAGAGG
1 AAGAAGAAAGAAAAGAAA
5129806 AAGAAGAAAG-AAAGAAA
1 AAGAAGAAAGAAAAGAAA
5129823 AAGAA-AAAGAAAAGAAA
1 AAGAAGAAAGAAAAGAAA
5129840 TAATAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
16 4 0.09
17 22 0.51
18 7 0.16
20 10 0.23
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (18 bp):
AAGAAGAAAGAAAAGAAA
Found at i:5130125 original size:13 final size:13
Alignment explanation
Indices: 5130104--5130158 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
5130094 CCAGCAGAGA
*
5130104 AAAAAAAGAAAAG
1 AAAAGAAGAAAAG
5130117 AAAAGAAGAAAAG
1 AAAAGAAGAAAAG
*
5130130 AGAAGGAA-AAAAG
1 A-AAAGAAGAAAAG
* *
5130143 -AAGGAAAAAAAG
1 AAAAGAAGAAAAG
5130155 AAAA
1 AAAA
5130159 AAAAGAGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 6 0.17
12 5 0.14
13 20 0.56
14 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAG
Found at i:5130138 original size:11 final size:11
Alignment explanation
Indices: 5130105--5130164 Score: 58
Period size: 10 Copynumber: 5.7 Consensus size: 11
5130095 CAGCAGAGAA
5130105 AAAAAAGAA--
1 AAAAAAGAAGG
5130114 AAGAAAAGAA-G
1 AA-AAAAGAAGG
*
5130125 AAAAGAGAAGG
1 AAAAAAGAAGG
5130136 AAAAAAGAAGG
1 AAAAAAGAAGG
5130147 AAAAAAAGAA--
1 -AAAAAAGAAGG
5130157 AAAAAAGA
1 AAAAAAGA
5130165 GGTTCAATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
9 10 0.22
10 13 0.29
11 13 0.29
12 9 0.20
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAGG
Found at i:5130141 original size:21 final size:18
Alignment explanation
Indices: 5130117--5130164 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 18
5130107 AAAAGAAAAG
5130117 AAAAGAAGAAAAGAGAAGGAA
1 AAAAGAAGAAAA-A-AA-GAA
5130138 AAAAGAAGGAAAAAAAGAA
1 AAAAGAA-GAAAAAAAGAA
5130157 AAAA-AAGA
1 AAAAGAAGA
5130165 GGTTCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.08
18 2 0.08
19 7 0.27
20 2 0.08
21 8 0.31
22 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAAGAAGAAAAAAAGAA
Found at i:5130330 original size:16 final size:17
Alignment explanation
Indices: 5130304--5130341 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5130294 TTATATTTAT
5130304 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
5130321 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
5130337 ATTTT
1 ATTTT
5130342 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:5130606 original size:72 final size:72
Alignment explanation
Indices: 5130504--5130677 Score: 192
Period size: 73 Copynumber: 2.4 Consensus size: 72
5130494 TCGTGCTTTT
* * * * *
5130504 AAAAATTCTCATGTTTCAAAAATCTT-CGTATTTTC-AAAATTC-TAGTGTTTCAAAAATTTTCT
1 AAAAATTATCGTGTTTCAAAAAT-TTCCGTATTTTCAAAAAATCAT-GTCTTTC-AAAATTTTCG
*
5130566 TGTTTTCAGA
63 TGTTTTCAAA
* * *
5130576 AAAAATTTTCGTGTTTTATAAATTTCCGTATTTTCAAAAAAATCATGTCTTTCAAAATTTTCGTG
1 AAAAATTATCGTGTTTCAAAAATTTCCGTATTTTC-AAAAAATCATGTCTTTCAAAATTTTCGTG
5130641 TTTTCAAA
65 TTTTCAAA
* *
5130649 AAAAATGACCGTGTTTCAAAAATTTCCGT
1 AAAAATTATCGTGTTTCAAAAATTTCCGT
5130678 GTTAAAAAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
71 2 0.02
72 28 0.33
73 42 0.49
74 12 0.14
75 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (72 bp):
AAAAATTATCGTGTTTCAAAAATTTCCGTATTTTCAAAAAATCATGTCTTTCAAAATTTTCGTGT
TTTCAAA
Found at i:5130650 original size:18 final size:18
Alignment explanation
Indices: 5130494--5131011 Score: 246
Period size: 17 Copynumber: 29.5 Consensus size: 18
5130484 TCTATAATCC
*
5130494 TCGTGCTTTT-AAAAATTC
1 TCGTG-TTTTCAAAAATTT
* *
5130512 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
* *
5130529 TCGTATTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTT
*
5130546 TAGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
5130563 TCTTGTTTTCAGAAAAAATTT
1 TCGTGTTTTC---AAAAATTT
*
5130584 TCGTGTTTT-ATAAATTT
1 TCGTGTTTTCAAAAATTT
* * **
5130601 CCGTATTTTCAAAAA-AA
1 TCGTGTTTTCAAAAATTT
*
5130618 TCATGTCTTTC-AAAATTT
1 TCGTGT-TTTCAAAAATTT
**
5130636 TCGTGTTTTCAAAAAAAATGA
1 TCGTGTTTTC---AAAAATTT
*
5130657 CCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* *** *
5130674 CCGTGTTAAAAAAAATCT
1 TCGTGTTTTCAAAAATTT
*
5130692 TCGTATTTTCAAAAAATTT
1 TCGTGTTTTC-AAAAATTT
*
5130711 TCGTG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
5130728 TCGTGTTTTCAAAAA-TT
1 TCGTGTTTTCAAAAATTT
*
5130745 TCG-GTGTTTCAAAGATTT
1 TCGTGT-TTTCAAAAATTT
* *
5130763 TCGTGTTTTCAAAAACTC
1 TCGTGTTTTCAAAAATTT
* * ***
5130781 TGGTGATTTTAAAAAAAAAA
1 TCGTG-TTTT-CAAAAATTT
*
5130801 TCGT-TTTCTAAAAAATTT
1 TCGTGTTT-TCAAAAATTT
*
5130819 CCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
5130836 TCGTGTTTT-AAAACTTT
1 TCGTGTTTTCAAAAATTT
* *
5130853 TCGTGTTTTTAAAAATTC
1 TCGTGTTTTCAAAAATTT
*
5130871 TCGTATTTT---AAATTT
1 TCGTGTTTTCAAAAATTT
** **
5130886 T--T-TTTAAGAAAAAAAT
1 TCGTGTTT-TCAAAAATTT
* *
5130902 T-GTG-TTTCAAAAAAATG
1 TCGTGTTTTC-AAAAATTT
* *
5130919 TCTTGTTTT-AAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
5130936 TCGTG-TTTCAAAAAATG
1 TCGTGTTTTCAAAAATTT
5130953 TCGTGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTT
**
5130970 TCGTG-TTTCTGAAATTT
1 TCGTGTTTTCAAAAATTT
* *
5130987 CCGTG-TTT-AAAAATTC
1 TCGTGTTTTCAAAAATTT
5131003 TCGTGTTTT
1 TCGTGTTTT
5131012 TTAAAAAAAA
Statistics
Matches: 375, Mismatches: 86, Indels: 79
0.69 0.16 0.15
Matches are distributed among these distances:
12 3 0.01
13 1 0.00
15 6 0.02
16 29 0.08
17 173 0.46
18 105 0.28
19 21 0.06
20 12 0.03
21 25 0.07
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:5130654 original size:73 final size:74
Alignment explanation
Indices: 5130551--5130724 Score: 194
Period size: 73 Copynumber: 2.4 Consensus size: 74
5130541 AATTCTAGTG
* * *** * * * *
5130551 TTTCAAAAATTTTCTTGTTTTCAGAAAAAATTTTCGTGTTTTATAAATTTCCGTATTTTCAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCG--TGTTAAAAAA
5130616 AATCAT-GT-C
64 AATCATCGTAC
5130625 TTTC-AAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
* *
5130689 TCTTCGTAT
66 TCATCGTAC
5130698 TTTCAAAAAATTTTCGTG-TTTCAAAAA
1 TTTC-AAAAATTTTCGTGTTTTCAAAAA
5130725 TCTTCGTGTT
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
71 13 0.15
72 2 0.02
73 45 0.53
74 13 0.15
75 12 0.14
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (74 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
TCATCGTAC
Found at i:5130867 original size:35 final size:35
Alignment explanation
Indices: 5130494--5131011 Score: 181
Period size: 35 Copynumber: 14.8 Consensus size: 35
5130484 TCTATAATCC
* * * * *
5130494 TCGTGCTTTTAAAAATTCTCATGTTTCAAAAATCT
1 TCGTGTTTTTAAAAATTTTCGTGTTTTAAAAATTT
* * * * *
5130529 TCGT-ATTTTCAAAATTCTAGTGTTTCAAAAATTT
1 TCGTGTTTTTAAAAATTTTCGTGTTTTAAAAATTT
* * *
5130563 TCTTGTTTTCAGAAAAAATTTTCGTGTTTTATAAATTT
1 TCGTGTTTT---TAAAAATTTTCGTGTTTTAAAAATTT
* * * ** * *
5130601 CCGTATTTTCAAAAA-AATCATGTCTTTCAAAATTT
1 TCGTGTTTTTAAAAATTTTCGTGT-TTTAAAAATTT
* *** *
5130636 TCGTGTTTTCAAAAAAAATGACCGTGTTTCAAAAATTT
1 TCGTGTTTT---TAAAAATTTTCGTGTTTTAAAAATTT
* *** * *
5130674 CCGTGTTAAAAAAAATCTTCGTATTTTCAAAAAATTT
1 TCGTGTTTTTAAAAATTTTCGTGTTTT--AAAAATTT
* *
5130711 TCGTG-TTTCAAAAATCTTCGTGTTTTCAAAAA-TT
1 TCGTGTTTTTAAAAATTTTCGTGTTTT-AAAAATTT
* * * *
5130745 TCG-GTGTTTCAAAGATTTTCGTGTTTTCAAAAACTC
1 TCGTGT-TTTTAAAAATTTTCGTGTTTT-AAAAATTT
* * ***
5130781 TGGTGATTTTAAAAAAAAAATCGT-TTTCTAAAAAATTT
1 TCGTG-TTTT-TAAAAATTTTCGTGTTT-T-AAAAATTT
* * *
5130819 CCGTG-TTTCAAAAATTTTCGTGTTTTAAAACTTT
1 TCGTGTTTTTAAAAATTTTCGTGTTTTAAAAATTT
* *
5130853 TCGTGTTTTTAAAAATTCTCGTATTTT--AAATTT
1 TCGTGTTTTTAAAAATTTTCGTGTTTTAAAAATTT
** ** * * *
5130886 T--T-TTTAAGAAAAAAATT-GTGTTTCAAAAAAATG
1 TCGTGTTT-TTAAAAATTTTCGTGTTT-TAAAAATTT
* * * * *
5130919 TCTTG-TTTTAAAAATTCTCGTGTTTCAAAAAATG
1 TCGTGTTTTTAAAAATTTTCGTGTTTTAAAAATTT
*
5130953 TCGTG-TTTTAAAAATTTTCGTGTTTCT-GAAATTT
1 TCGTGTTTTTAAAAATTTTCGTGTTT-TAAAAATTT
* *
5130987 CCGTG--TTTAAAAATTCTCGTGTTTT
1 TCGTGTTTTTAAAAATTTTCGTGTTTT
5131012 TTAAAAAAAA
Statistics
Matches: 363, Mismatches: 91, Indels: 61
0.70 0.18 0.12
Matches are distributed among these distances:
30 8 0.02
31 7 0.02
32 1 0.00
33 30 0.08
34 94 0.26
35 108 0.30
36 26 0.07
37 19 0.05
38 65 0.18
39 5 0.01
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (35 bp):
TCGTGTTTTTAAAAATTTTCGTGTTTTAAAAATTT
Found at i:5131032 original size:21 final size:20
Alignment explanation
Indices: 5131008--5131047 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
5130998 AATTCTCGTG
5131008 TTTTTTAAAAAAAAACTTTCA
1 TTTTTTAAAAAAAAA-TTTCA
5131029 TTTTTTAAAAAAAAATTTC
1 TTTTTTAAAAAAAAATTTC
5131048 GTGCTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTTTTAAAAAAAAATTTCA
Found at i:5145400 original size:29 final size:30
Alignment explanation
Indices: 5145355--5145411 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
5145345 GAAAATATAG
* *
5145355 AAATTCTAAAATGAATAATATGTAAAAAAT
1 AAATTCTAAAATAAATAATATATAAAAAAT
5145385 AAATT-TAAAATAAATAATATATAAAAA
1 AAATTCTAAAATAAATAATATATAAAAA
5145412 TATATAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (30 bp):
AAATTCTAAAATAAATAATATATAAAAAAT
Found at i:5145607 original size:25 final size:25
Alignment explanation
Indices: 5145563--5145647 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 25
5145553 ATAATATATA
* * *
5145563 TATAAAATGGTTTAAAATAAATAACG
1 TATAAAAT-ATTTAGAATAAATAATG
5145589 TATAAAATATTTAGAATAAATAATATG
1 TATAAAATATTTAGAATAAAT-A-ATG
* *
5145616 TA-AAAGAAATTTGGAATAAATAATG
1 TATAAA-ATATTTAGAATAAATAATG
5145641 TATAAAA
1 TATAAAA
5145648 ACCGTTTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
25 17 0.34
26 16 0.32
27 17 0.34
ACGTcount: A:0.56, C:0.01, G:0.11, T:0.32
Consensus pattern (25 bp):
TATAAAATATTTAGAATAAATAATG
Found at i:5145646 original size:27 final size:26
Alignment explanation
Indices: 5145573--5145648 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 26
5145563 TATAAAATGG
* * *
5145573 TTTAAAATAAATAACGTAT-AAAATA
1 TTTAGAATAAATAATGTATAAAAAAA
* *
5145598 TTTAGAATAAATAATATGTAAAAGAAA
1 TTTAGAATAAATAATGTATAAAA-AAA
*
5145625 TTTGGAATAAATAATGTATAAAAA
1 TTTAGAATAAATAATGTATAAAAA
5145649 CCGTTTAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
25 15 0.37
26 4 0.10
27 22 0.54
ACGTcount: A:0.58, C:0.01, G:0.09, T:0.32
Consensus pattern (26 bp):
TTTAGAATAAATAATGTATAAAAAAA
Found at i:5145700 original size:25 final size:24
Alignment explanation
Indices: 5145672--5145790 Score: 89
Period size: 24 Copynumber: 4.8 Consensus size: 24
5145662 AAAATATATG
*
5145672 TATATGAATAATCCAAAATAAATAA
1 TATAT-AATAATTCAAAATAAATAA
* *
5145697 TATATAA-AAGTTTAAAGTAAGA-AGA
1 TATATAATAA-TTCAAAATAA-ATA-A
5145722 TATATAAATAATTTCAAAATAAATAA
1 TATAT-AATAA-TTCAAAATAAATAA
* * **
5145748 GATATAATAGTTTGAAATAAATAA
1 TATATAATAATTCAAAATAAATAA
*
5145772 TATATGAAGAATTCAAAAT
1 TATAT-AATAATTCAAAAT
5145791 GAGTAATAGT
Statistics
Matches: 72, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
23 2 0.03
24 26 0.36
25 25 0.35
26 8 0.11
27 11 0.15
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.31
Consensus pattern (24 bp):
TATATAATAATTCAAAATAAATAA
Found at i:5145775 original size:50 final size:50
Alignment explanation
Indices: 5145672--5145790 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 50
5145662 AAAATATATG
* *
5145672 TATATGAATAATCCAAAATAAATAATATATAAAAGTTTAAAGTAAGAAGA
1 TATATGAATAATTCAAAATAAATAAGATATAAAAGTTTAAAGTAAGAAGA
* *
5145722 TATATAAATAATTTCAAAATAAATAAGATATAATAGTTTGAAA-TAA-ATA-A
1 TATATGAATAA-TTCAAAATAAATAAGATATAAAAGTTT-AAAGTAAGA-AGA
*
5145772 TATATGAAGAATTCAAAAT
1 TATATGAATAATTCAAAAT
5145791 GAGTAATAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
49 8 0.13
50 21 0.35
51 28 0.47
52 3 0.05
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.31
Consensus pattern (50 bp):
TATATGAATAATTCAAAATAAATAAGATATAAAAGTTTAAAGTAAGAAGA
Found at i:5147738 original size:93 final size:93
Alignment explanation
Indices: 5147569--5147739 Score: 243
Period size: 93 Copynumber: 1.8 Consensus size: 93
5147559 GCCCATAAGT
*****
5147569 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
5147634 CGAGCTCGGATGCCTAGTTACATCTCAC
66 AGAGCTCGGATGCCTAGTTACATCTCAC
* * *
5147662 GAACTCGGACTCAACTCAACGAGTTCAAACATTCGCATCCATAAGTGAACTCGGATTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
* *
5147727 AGAGTTTGGATGC
66 AGAGCTCGGATGC
5147740 TCAACCATCC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
93 67 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
AGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:5151188 original size:46 final size:44
Alignment explanation
Indices: 5151114--5151320 Score: 188
Period size: 46 Copynumber: 4.6 Consensus size: 44
5151104 GTCAATGCTG
* * *
5151114 TGTCCCAGACAGGTCTTACACT-GACACATGTAACCGT-GCTGACGCA
1 TGTCCCAGACATGTCTTACACTAG-CACATCT---CGTAGCCGACGCA
*
5151160 TGTCCTAGACATGTCTTACACTAGCACATCTCGTAGCCGACGCA
1 TGTCCCAGACATGTCTTACACTAGCACATCTCGTAGCCGACGCA
* * *
5151204 TGTCCCAGACATGTCTGACACTGGCTAACATCTCG-AGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTAGC--ACATCTCGTA-GCCGACGCA
* * * * *
5151250 TGTCCCAGACATGTCTTACACTGGCTC-TCATACTGTGGCTGATGCA
1 TGTCCCAGACATGTCTTACACTAGCACATC-T-C-GTAGCCGACGCA
5151296 TGTCCCAGACATGTCTTACACTAGC
1 TGTCCCAGACATGTCTTACACTAGC
5151321 CCTCGTCTCA
Statistics
Matches: 139, Mismatches: 13, Indels: 18
0.82 0.08 0.11
Matches are distributed among these distances:
43 5 0.04
44 32 0.23
45 2 0.01
46 99 0.71
47 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (44 bp):
TGTCCCAGACATGTCTTACACTAGCACATCTCGTAGCCGACGCA
Found at i:5151317 original size:92 final size:91
Alignment explanation
Indices: 5151157--5151373 Score: 231
Period size: 92 Copynumber: 2.4 Consensus size: 91
5151147 CCGTGCTGAC
* *
5151157 GCATGTCCTAGACATGTCTTACACTAG-CACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
1 GCATGTCCCAGACATGTCTTACACTGGCCACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
* * *
5151221 ACACTGGCTAACATCTCGAGGCCGAT
66 ACACTAGCCAACATCTCAAGGCCGAT
* * * *
5151247 GCATGTCCCAGACATGTCTTACACTGGCTCTCATACT-GTGGCTGATGCATGTCCCAGACATGTC
1 GCATGTCCCAGACATGTCTTACACTGGC-CACAT-CTCGTAGCCGACGCATGTCCCAGACATGTC
* ** * *
5151311 TTACACTAGCCCTCGTCTCAATGCCGAT
64 TGACACTAGCCAACATCTCAAGGCCGAT
* *
5151339 GCCATGTCTCATACATGGTCTTACACTGGCACACA
1 G-CATGTCCCAGACAT-GTCTTACACTGGC-CACA
5151374 AATCTCATGT
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
90 25 0.24
92 49 0.47
93 14 0.13
94 16 0.15
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (91 bp):
GCATGTCCCAGACATGTCTTACACTGGCCACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
ACACTAGCCAACATCTCAAGGCCGAT
Found at i:5151340 original size:46 final size:44
Alignment explanation
Indices: 5151157--5151365 Score: 172
Period size: 46 Copynumber: 4.6 Consensus size: 44
5151147 CCGTGCTGAC
* *
5151157 GCATGTCCTAGACATGTCTTACACTAGCACATC-TCGTA-GCCGAC
1 GCATGTCCCAGACATGTCTTACACTAGC-CATCATC-TATGCCGAT
* * * * *
5151201 GCATGTCCCAGACATGTCTGACACTGGCTAACATCTCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCATCATCT--ATGCCGAT
* * *
5151247 GCATGTCCCAGACATGTCTTACACTGGCTC-TCATACTGTGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTAGC-CATCAT-CTAT-GCCGAT
* *
5151293 GCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCATCATCT--ATGCCGAT
* *
5151339 GCCATGTCTCATACATGGTCTTACACT
1 G-CATGTCCCAGACAT-GTCTTACACT
5151366 GGCACACAAA
Statistics
Matches: 135, Mismatches: 18, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
43 3 0.02
44 27 0.20
45 4 0.03
46 76 0.56
47 15 0.11
48 10 0.07
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (44 bp):
GCATGTCCCAGACATGTCTTACACTAGCCATCATCTATGCCGAT
Found at i:5154196 original size:46 final size:46
Alignment explanation
Indices: 5154129--5154303 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
5154119 TGTAACCCGC
*
5154129 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
5154175 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
5154225 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* * *
5154268 CCATAAGTGAACTCGGATTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG
5154304 ATGCTCAATC
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 60 0.57
47 26 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:5154245 original size:93 final size:93
Alignment explanation
Indices: 5154137--5154307 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
5154127 GCCCATAAGT
* ** *
5154137 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
5154202 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* * *
5154230 GAACTCAGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGATTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
5154295 CGAGTTCGGATGC
66 CGAGCTCGGATGC
5154308 TCAATCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:5155904 original size:13 final size:14
Alignment explanation
Indices: 5155886--5155914 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5155876 TTTTTGTCGT
5155886 TTCTGCTTGG-TTC
1 TTCTGCTTGGCTTC
5155899 TTCTGCTTGGCTTC
1 TTCTGCTTGGCTTC
5155913 TT
1 TT
5155915 TTGTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.24, G:0.21, T:0.55
Consensus pattern (14 bp):
TTCTGCTTGGCTTC
Found at i:5157553 original size:17 final size:16
Alignment explanation
Indices: 5157525--5157577 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
5157515 TTTGGTTCGC
5157525 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5157541 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
5157558 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5157574 TGTA
1 TGTA
5157578 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:5157642 original size:44 final size:45
Alignment explanation
Indices: 5157558--5157648 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
5157548 GGATTAGAGG
* * *
5157558 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
5157603 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
5157647 TG
1 TG
5157649 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:5157844 original size:7 final size:7
Alignment explanation
Indices: 5157832--5157858 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5157822 AATTAAAATA
5157832 TATAATT
1 TATAATT
5157839 TATAATT
1 TATAATT
5157846 TATAATT
1 TATAATT
5157853 TATAAT
1 TATAAT
5157859 AAATTTTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATAATT
Found at i:5174712 original size:23 final size:25
Alignment explanation
Indices: 5174686--5174732 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5174676 ACGTTTGGTT
5174686 TGTTT-CTTTT-TTATATTT-CTTGC
1 TGTTTGCTTTTATTAT-TTTACTTGC
5174709 TGTTTGCTTTTATTATTTTACTTG
1 TGTTTGCTTTTATTATTTTACTTG
5174733 TTCCAGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 8 0.38
25 8 0.38
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.68
Consensus pattern (25 bp):
TGTTTGCTTTTATTATTTTACTTGC
Found at i:5186779 original size:173 final size:173
Alignment explanation
Indices: 5186334--5186889 Score: 735
Period size: 173 Copynumber: 3.2 Consensus size: 173
5186324 TTTAAAAGCT
* * * *
5186334 ATCTATTTAGCATTGCTTATGGCTCAATAAATTTAGGTCCAATATAAATATTATATAAAATACAT
1 ATCTATTTTGCATTGCTTATGACTCAATAAATTCAGATCCAATATAAATATTATATAAAAT-CAT
* * * **
5186399 TAAATTTTAAATAAGAGTTAAAAATAT-TCTGACTCCGAAAA-TGTTTTTTTTTTTAAAAAGGCA
65 TAAATTATAAATAAGAGTTAAAAATATCTTTGACTCC-AAAAGTG-TTTTTTTTTTACAAACACA
* *
5186462 ATAGTTTTTGGGTTTGGATTGAAAAACAATTTTAACTTCAAAAATG
128 ATAGCTTTTGGGTTTGGATTGAAAAACAATTTTAACTTCAAAAATA
* * * * * * * *
5186508 GTCTGTTTTACGTTGCTTATGGCTCAATAAATTCAGGTCCAATATAAATATTAGATAATAT-ATT
1 ATCTATTTTGCATTGCTTATGACTCAATAAATTCAGATCCAATATAAATATTATATAAAATCATT
* * *
5186572 AGATTAAAAATAAGAGTTAAAAATATCTTTGACTCCAAAAGTGTTTTTTTTTTACAAACATAATA
66 AAATTATAAATAAGAGTTAAAAATATCTTTGACTCCAAAAGTGTTTTTTTTTTACAAACACAATA
*
5186637 GCTTTTGGGTTTGGATTG-AAAACAATTTTAACTTTAAAAATA
131 GCTTTTGGGTTTGGATTGAAAAACAATTTTAACTTCAAAAATA
* *
5186679 ATCTATTTTGTATTGCTTATGACTCAATAAATTCAGATTCAATATAAATATTATATAAAATGCAT
1 ATCTATTTTGCATTGCTTATGACTCAATAAATTCAGATCCAATATAAATATTATATAAAAT-CAT
* *
5186744 TATATTATAAATAAGAGTTAAAAATATCTTTGACTCCAAAAGTGGTTTTTTTTT-CAAACACAAT
65 TAAATTATAAATAAGAGTTAAAAATATCTTTGACTCCAAAAGTGTTTTTTTTTTACAAACACAAT
* * *
5186808 AGCTATTGGGTTTGAATTGAAAAACAATTTTAACTTCACAAATA
130 AGCTTTTGGGTTTGGATTGAAAAACAATTTTAACTTCAAAAATA
* * * *
5186852 GTCTGTTCTGTATTGCTTATGACTCAATAAATTCAGAT
1 ATCTATTTTGCATTGCTTATGACTCAATAAATTCAGAT
5186890 AAAATACATT
Statistics
Matches: 337, Mismatches: 40, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
171 73 0.22
172 91 0.27
173 120 0.36
174 53 0.16
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.39
Consensus pattern (173 bp):
ATCTATTTTGCATTGCTTATGACTCAATAAATTCAGATCCAATATAAATATTATATAAAATCATT
AAATTATAAATAAGAGTTAAAAATATCTTTGACTCCAAAAGTGTTTTTTTTTTACAAACACAATA
GCTTTTGGGTTTGGATTGAAAAACAATTTTAACTTCAAAAATA
Found at i:5195509 original size:29 final size:29
Alignment explanation
Indices: 5195445--5195500 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
5195435 AAATTAATTT
* *
5195445 ATTTTTTTATTTTGAAGCAAATAGGATAC
1 ATTTTTTAATTTTGAAGCAAATAAGATAC
5195474 ATTTTTTAATTTTGAAGCAAATAAGAT
1 ATTTTTTAATTTTGAAGCAAATAAGAT
5195501 TAGTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (29 bp):
ATTTTTTAATTTTGAAGCAAATAAGATAC
Found at i:5195509 original size:30 final size:28
Alignment explanation
Indices: 5195446--5195510 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
5195436 AATTAATTTA
*
5195446 TTTTTTTATTTTGAAGCAAATAGGATAC
1 TTTTTTTATTTTGAAGCAAATAAGATAC
* *
5195474 ATTTTTTAATTTTGAAGCAAATAAGATTAG
1 -TTTTTTTATTTTGAAGCAAATAAGA-TAC
5195504 TTTTTTT
1 TTTTTTT
5195511 TTAGTTTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 29 0.94
30 2 0.06
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (28 bp):
TTTTTTTATTTTGAAGCAAATAAGATAC
Found at i:5197588 original size:23 final size:23
Alignment explanation
Indices: 5197551--5197594 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5197541 TTGCCTCAAC
5197551 ATGTACATATATTATACTTATAA
1 ATGTACATATATTATACTTATAA
*
5197574 ATGTACCATAT-TTATATTTAT
1 ATGTA-CATATATTATACTTAT
5197595 GAAACTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.48
Consensus pattern (23 bp):
ATGTACATATATTATACTTATAA
Found at i:5198709 original size:25 final size:25
Alignment explanation
Indices: 5198701--5198754 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
5198691 AAATAATTTT
5198701 AAAAATTATAAAAATAAAAAATTCA
1 AAAAATTATAAAAATAAAAAATTCA
*
5198726 AAAAATT-TAAAATTTATAAAAATTCA
1 AAAAATTATAAAA-ATA-AAAAATTCA
5198752 AAA
1 AAA
5198755 GAATAGAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 9 0.35
26 12 0.46
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAAATTATAAAAATAAAAAATTCA
Found at i:5198712 original size:9 final size:9
Alignment explanation
Indices: 5198689--5198749 Score: 58
Period size: 9 Copynumber: 7.0 Consensus size: 9
5198679 TGTTATGATA
5198689 ATAAATAATT
1 ATAAA-AATT
*
5198699 TTAAAAATT
1 ATAAAAATT
5198708 ATAAAAA-T
1 ATAAAAATT
5198716 A-AAAAATT
1 ATAAAAATT
5198724 CA-AAAAATT
1 -ATAAAAATT
*
5198733 -TAAAATTT
1 ATAAAAATT
5198741 ATAAAAATT
1 ATAAAAATT
5198750 CAAAAGAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
7 5 0.12
8 9 0.21
9 25 0.58
10 4 0.09
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:5198722 original size:16 final size:16
Alignment explanation
Indices: 5198701--5198748 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5198691 AAATAATTTT
5198701 AAAAATTATAAAAATA
1 AAAAATTATAAAAATA
*
5198717 AAAAATTCA-AAAAATTT
1 AAAAATT-ATAAAAA-TA
*
5198734 AAAATTTATAAAAAT
1 AAAAATTATAAAAAT
5198749 TCAAAAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATTATAAAAATA
Found at i:5199598 original size:33 final size:33
Alignment explanation
Indices: 5199561--5199624 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
5199551 TTAATTTTGT
5199561 TTTAATGTATAATTTGATAT-ATGAACTTTTAGC
1 TTTAATGTATAATTTGAT-TCATGAACTTTTAGC
* *
5199594 TTTAATGTATATTTTGATTCATGAATTTTTA
1 TTTAATGTATAATTTGATTCATGAACTTTTA
5199625 TTTTGTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.31, C:0.05, G:0.11, T:0.53
Consensus pattern (33 bp):
TTTAATGTATAATTTGATTCATGAACTTTTAGC
Found at i:5201548 original size:33 final size:33
Alignment explanation
Indices: 5201501--5201565 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
5201491 TTTATGTACC
* *
5201501 ATGTCTACAACAATACCATAAAATACAATAATT
1 ATGTATACAACAATACCATAAAACACAATAATT
*
5201534 ATGTATACAACAATACCGTAAAACACAATAAT
1 ATGTATACAACAATACCATAAAACACAATAAT
5201566 AATCTAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (33 bp):
ATGTATACAACAATACCATAAAACACAATAATT
Found at i:5202529 original size:78 final size:78
Alignment explanation
Indices: 5202400--5202556 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
5202390 GATCTAAGTC
5202400 GATTGACTATTTTATTTGATCTTTATGTAAAAAAAATAAAATTGTAGGAACATTCTTTTTAATTT
1 GATTGACTATTTTATTTGATCTTTATGTAAAAAAAATAAAATTGTAGGAACATTCTTTTTAATTT
5202465 ATATATATTTTAG
66 ATATATATTTTAG
5202478 GATTGACTATTTTATTTGATCTTTATGTAAAAAAAATAAAATTGTAGGAACATTCTTTTTAATTT
1 GATTGACTATTTTATTTGATCTTTATGTAAAAAAAATAAAATTGTAGGAACATTCTTTTTAATTT
5202543 ATATATATTTTAG
66 ATATATATTTTAG
5202556 G
1 G
5202557 TTGTTTGCAC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (78 bp):
GATTGACTATTTTATTTGATCTTTATGTAAAAAAAATAAAATTGTAGGAACATTCTTTTTAATTT
ATATATATTTTAG
Found at i:5205453 original size:32 final size:34
Alignment explanation
Indices: 5205417--5205485 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
5205407 GTGGCTAGGG
*
5205417 TTTCTTAGTT-TTTTTTTTTTGGGTTTGGT-TTT
1 TTTCTTAGTTCTTTTTTTTTTGGGTTAGGTATTT
**
5205449 TTTCTTTTTTCTTTTTTTTTTGGGTTAGGTATTT
1 TTTCTTAGTTCTTTTTTTTTTGGGTTAGGTATTT
5205483 TTT
1 TTT
5205486 GGGGGGGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 8 0.25
33 18 0.56
34 6 0.19
ACGTcount: A:0.04, C:0.04, G:0.16, T:0.75
Consensus pattern (34 bp):
TTTCTTAGTTCTTTTTTTTTTGGGTTAGGTATTT
Found at i:5206645 original size:74 final size:74
Alignment explanation
Indices: 5206354--5206690 Score: 527
Period size: 74 Copynumber: 4.6 Consensus size: 74
5206344 GTGATCTAAA
*
5206354 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAATTACCTCAGC
**
5206419 ATGTGAACCGAG
65 --GTGTCCCGAG
* *
5206431 GCTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTTGAAAACAGAAATTGAAATTACCTCAACG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCG
**
5206495 TGTCTTGAG
66 TGTCCCGAG
5206504 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCG
5206567 TGTCCCGAG
66 TGTCCCGAG
* *
5206576 GCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCG
*
5206641 TGTCCTGAG
66 TGTCCCGAG
*
5206650 GCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTTGAAA
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA
5206691 CAAAAATAAA
Statistics
Matches: 241, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
72 68 0.28
73 35 0.15
74 78 0.32
75 21 0.09
76 10 0.04
77 29 0.12
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (74 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCG
TGTCCCGAG
Found at i:5206650 original size:146 final size:147
Alignment explanation
Indices: 5206354--5206684 Score: 531
Period size: 146 Copynumber: 2.2 Consensus size: 147
5206344 GTGATCTAAA
5206354 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAGACAGAAATTGAAAATACCTCAGC
5206419 ATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAA
64 A-GTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAA
*
5206484 TTACCTCAACGTGTCTTGAG
128 TTACCTCAACGTGTCCTGAG
*
5206504 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-ACAGAAATTGAAATTACCTCAGC-G
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGACAGAAATTGAAAATACCTCAGCAG
** * * *
5206567 TGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATT
66 TGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTTGAAAACAGAAATTGAAATT
*
5206632 ACCTCAGCGTGTCCTGAG
130 ACCTCAACGTGTCCTGAG
*
5206650 GCTCAACTCACCTCTCGCAGTATGAGTTGATTTTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5206685 TTGAAACAAA
Statistics
Matches: 171, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
145 36 0.21
146 74 0.43
147 22 0.13
148 9 0.05
150 30 0.18
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (147 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAGACAGAAATTGAAAATACCTCAGCAG
TGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAATTA
CCTCAACGTGTCCTGAG
Found at i:5214760 original size:12 final size:12
Alignment explanation
Indices: 5214738--5214773 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5214728 TGGGATATGC
*
5214738 AATGAATGAATG
1 AATGCATGAATG
*
5214750 GATGCATGAATG
1 AATGCATGAATG
5214762 AATGCATGAATG
1 AATGCATGAATG
5214774 TTAAATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.28, T:0.25
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:5214760 original size:16 final size:17
Alignment explanation
Indices: 5214734--5214765 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5214724 AGTATGGGAT
5214734 ATGCAATGAATGAATGG
1 ATGCAATGAATGAATGG
5214751 ATGC-ATGAATGAATG
1 ATGCAATGAATGAATG
5214766 CATGAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.06, G:0.28, T:0.25
Consensus pattern (17 bp):
ATGCAATGAATGAATGG
Found at i:5220144 original size:15 final size:15
Alignment explanation
Indices: 5220106--5220151 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
5220096 AAAAAACTGT
* *
5220106 AAAATTAAATATTGA
1 AAAATTAAGTATTAA
*
5220121 AAAATTAAGTGTTAA
1 AAAATTAAGTATTAA
*
5220136 AAAATTAAGTAGTAA
1 AAAATTAAGTATTAA
5220151 A
1 A
5220152 TTTAAGTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (15 bp):
AAAATTAAGTATTAA
Found at i:5221956 original size:12 final size:12
Alignment explanation
Indices: 5221938--5221981 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
5221928 CTGAGAGTGG
5221938 TAAAGTAAATAA
1 TAAAGTAAATAA
*
5221950 AAAAGTAAATAA
1 TAAAGTAAATAA
*
5221962 TAAA-TAAAGAA
1 TAAAGTAAATAA
5221973 TAAAGTAAA
1 TAAAGTAAA
5221982 ATATATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (12 bp):
TAAAGTAAATAA
Found at i:5222886 original size:14 final size:14
Alignment explanation
Indices: 5222852--5222890 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
5222842 TTTTTTTCCC
* *
5222852 TTTTTTTATCTTAT
1 TTTTTTTATATAAT
5222866 TTATTTTTATATAAT
1 TT-TTTTTATATAAT
5222881 TTTTTTTATA
1 TTTTTTTATA
5222891 AATATATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTTATATAAT
Found at i:5232402 original size:34 final size:31
Alignment explanation
Indices: 5232346--5232454 Score: 121
Period size: 34 Copynumber: 3.3 Consensus size: 31
5232336 CACAAAATTA
5232346 TTTTTAAAAA-CTAAACCCTAATTTAATTAAT
1 TTTTTAAAAACCTAAA-CCTAATTTAATTAAT
*
5232377 TTTCTTAAAAACTCTAAACCTTAATTTAATTTAT
1 TTT-TTAAAAAC-CTAAACC-TAATTTAATTAAT
* *
5232411 TTATTTAAAACCCCTAAAAACTAATTTAATTAAT
1 TT-TTTAAAA-ACCT-AAACCTAATTTAATTAAT
5232445 TTTTTAAAAA
1 TTTTTAAAAA
5232455 AAATCTAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
31 3 0.05
32 7 0.11
33 9 0.14
34 41 0.62
35 6 0.09
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTTAAAAACCTAAACCTAATTTAATTAAT
Found at i:5233084 original size:18 final size:18
Alignment explanation
Indices: 5233061--5233108 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
5233051 TATTTATTTG
*
5233061 ATTAAAATTTTACTTTTA
1 ATTAAAATTATACTTTTA
*
5233079 ATTAAAGA-TATAGTTTTA
1 ATTAAA-ATTATACTTTTA
5233097 ATTATAAATTAT
1 ATTA-AAATTAT
5233109 TAAAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (18 bp):
ATTAAAATTATACTTTTA
Found at i:5236681 original size:13 final size:14
Alignment explanation
Indices: 5236655--5236684 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5236645 GTATGCTGAA
5236655 ATATTTTTATAAAT
1 ATATTTTTATAAAT
5236669 ATATTTTTA-AAAT
1 ATATTTTTATAAAT
5236682 ATA
1 ATA
5236685 AGATATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATTTTTATAAAT
Found at i:5242918 original size:68 final size:67
Alignment explanation
Indices: 5242845--5243042 Score: 223
Period size: 68 Copynumber: 3.0 Consensus size: 67
5242835 GTTTTAATAA
* *
5242845 ATTTAATATTAAATTTAATTTAATACTTATATTGATAGTATTTTATTAATTTAATATTAAAATAA
1 ATTTAATATTAAATTTAATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAAAATAA
5242910 TT
66 TT
** *
5242912 ATTTTAATATTAAATTTAATTTAATATTTATCTT-ATAGATAAATTATCT-A-TTACT-TT--AA
1 A-TTTAATATTAAATTTAATTTAATATTTATCTTGATAG-TATTTTAT-TAATTTAATATTAAAA
5242971 TAA--
63 TAATT
* * * *
5242974 ATTTAATACTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATATTAAAATG
1 ATTTAATATTAAATTTAATTTAATATTTATCTTGAT-AGTATTTTATTAATTTAATATTAAAATA
5243039 ATT
65 ATT
5243042 A
1 A
5243043 ATTTCAATCA
Statistics
Matches: 107, Mismatches: 12, Indels: 23
0.75 0.08 0.16
Matches are distributed among these distances:
61 31 0.29
62 9 0.08
63 6 0.06
64 7 0.07
66 6 0.06
67 9 0.08
68 38 0.36
69 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (67 bp):
ATTTAATATTAAATTTAATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAAAATAA
TT
Found at i:5245539 original size:16 final size:18
Alignment explanation
Indices: 5245507--5245541 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
5245497 AAAATAGAGG
5245507 GAAAAACAAAAGAGAAAA
1 GAAAAACAAAAGAGAAAA
5245525 GAAAAA-AAAAG-GAAAA
1 GAAAAACAAAAGAGAAAA
5245541 G
1 G
5245542 TTTAAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (18 bp):
GAAAAACAAAAGAGAAAA
Found at i:5245998 original size:31 final size:31
Alignment explanation
Indices: 5245963--5246025 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5245953 TTCGTTCTAG
5245963 TGAACCATGTTGTAATTGAATCAGGATGAAC
1 TGAACCATGTTGTAATTGAATCAGGATGAAC
5245994 TGAACCATGTTGTAATTGAATCAGGATGAAC
1 TGAACCATGTTGTAATTGAATCAGGATGAAC
5246025 T
1 T
5246026 AACTAGTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (31 bp):
TGAACCATGTTGTAATTGAATCAGGATGAAC
Found at i:5268085 original size:18 final size:18
Alignment explanation
Indices: 5268033--5268085 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
5268023 AAGAGGATTT
*
5268033 GCCAATATTGGTGTGTTC
1 GCCAATATTGGTGAGTTC
*
5268051 GCC-AT-TCTGGGGAAGTTC
1 GCCAATAT-TGGTG-AGTTC
5268069 GCCAATATTGGTGAGTT
1 GCCAATATTGGTGAGTT
5268086 TCCCAATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 6 0.21
18 14 0.50
19 6 0.21
20 1 0.04
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (18 bp):
GCCAATATTGGTGAGTTC
Found at i:5269621 original size:16 final size:15
Alignment explanation
Indices: 5269591--5269646 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
5269581 AACATAATAT
*
5269591 ATTATTAATTAATAAA
1 ATTATAAATT-ATAAA
5269607 ATTATAAATCTATAAA
1 ATTATAAAT-TATAAA
5269623 ATTGGATAAATTA-AAA
1 ATT--ATAAATTATAAA
*
5269639 ATAATAAA
1 ATTATAAA
5269647 AATTCAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 5 0.14
16 21 0.60
17 3 0.09
18 6 0.17
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (15 bp):
ATTATAAATTATAAA
Found at i:5283551 original size:20 final size:19
Alignment explanation
Indices: 5283528--5283572 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5283518 TAAAATCATT
*
5283528 TAAAAATAGAAAAAAAATTA
1 TAAAAATACAAAAAAAA-TA
* *
5283548 TAAAATTACAAAAACAATA
1 TAAAAATACAAAAAAAATA
5283567 TAAAAA
1 TAAAAA
5283573 ATCTAAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (19 bp):
TAAAAATACAAAAAAAATA
Found at i:5284260 original size:7 final size:7
Alignment explanation
Indices: 5284248--5284288 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
5284238 TAAGCCTTCT
5284248 TTTTTTC
1 TTTTTTC
5284255 TTTTTTC
1 TTTTTTC
5284262 TTTTTTC
1 TTTTTTC
5284269 TTTTTTC
1 TTTTTTC
5284276 TTTTTTC
1 TTTTTTC
5284283 TTTTTT
1 TTTTTT
5284289 TTTGTCTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:5290378 original size:21 final size:21
Alignment explanation
Indices: 5290352--5290392 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5290342 AGACGAGCAA
* *
5290352 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5290373 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5290393 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5298967 original size:18 final size:17
Alignment explanation
Indices: 5298944--5298979 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5298934 TCATTTAAAA
5298944 ATTAAAAAGATATAAATT
1 ATTAAAAAGATA-AAATT
*
5298962 ATTAAAATGATAAAATT
1 ATTAAAAAGATAAAATT
5298979 A
1 A
5298980 AATTTTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
ATTAAAAAGATAAAATT
Found at i:5299076 original size:20 final size:20
Alignment explanation
Indices: 5299051--5299090 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5299041 CTCTCCTATT
5299051 AACTAGAAACAACTATAATC
1 AACTAGAAACAACTATAATC
5299071 AACTAGAAACAACTATAATC
1 AACTAGAAACAACTATAATC
5299091 GTTTTGTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (20 bp):
AACTAGAAACAACTATAATC
Found at i:5301620 original size:21 final size:21
Alignment explanation
Indices: 5301594--5301644 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
5301584 AAAACAAAAA
5301594 CAAATTAAAAGAAAGGGCATG
1 CAAATTAAAAGAAAGGGCATG
5301615 CAAATTAAAAGAAAGGGCATG
1 CAAATTAAAAGAAAGGGCATG
5301636 CAAATTAAA
1 CAAATTAAA
5301645 GTAAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.55, C:0.10, G:0.20, T:0.16
Consensus pattern (21 bp):
CAAATTAAAAGAAAGGGCATG
Found at i:5301672 original size:14 final size:15
Alignment explanation
Indices: 5301648--5301676 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5301638 AATTAAAGTA
5301648 AAAAAGAAAAGAAAG
1 AAAAAGAAAAGAAAG
5301663 AAAAAG-AAAGAAAG
1 AAAAAGAAAAGAAAG
5301677 GGAGAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAGAAAG
Found at i:5315468 original size:13 final size:13
Alignment explanation
Indices: 5315450--5315492 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5315440 TTAATGTATT
5315450 ATATTTTTAAAAA
1 ATATTTTTAAAAA
5315463 ATATTTTTAAATAA
1 ATATTTTTAAA-AA
* *
5315477 AAATTAATTAAAAA
1 ATATT-TTTAAAAA
5315491 AT
1 AT
5315493 TAAATATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 11 0.44
14 9 0.36
15 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATTTTTAAAAA
Found at i:5318875 original size:13 final size:13
Alignment explanation
Indices: 5318859--5318883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5318849 AAATAATAAA
5318859 AAAATTTAAATTC
1 AAAATTTAAATTC
5318872 AAAATTTAAATT
1 AAAATTTAAATT
5318884 ATTTTTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTTAAATTC
Found at i:5318980 original size:11 final size:11
Alignment explanation
Indices: 5318942--5318980 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
5318932 AAATAAAATT
5318942 TTTAAATATAAA
1 TTTAAA-ATAAA
*
5318954 TTTAAAATACAT
1 TTTAAAATA-AA
5318966 TTTAAAATAAA
1 TTTAAAATAAA
5318977 TTTA
1 TTTA
5318981 TTGGTATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTAAAATAAA
Found at i:5322998 original size:6 final size:6
Alignment explanation
Indices: 5322942--5322980 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
5322932 AGAGTATCTT
5322942 AGATGC AGATGC AGATGC AGATGC AGATGC AGATGC AGA
1 AGATGC AGATGC AGATGC AGATGC AGATGC AGATGC AGA
5322981 ACATATAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.33, T:0.15
Consensus pattern (6 bp):
AGATGC
Found at i:5326643 original size:16 final size:16
Alignment explanation
Indices: 5326622--5326652 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5326612 CTGTTTGAAC
5326622 ATGAAAAAATAATTAA
1 ATGAAAAAATAATTAA
*
5326638 ATGAAAATATAATTA
1 ATGAAAAAATAATTA
5326653 CTAAGGTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
ATGAAAAAATAATTAA
Found at i:5332069 original size:3 final size:3
Alignment explanation
Indices: 5332061--5332288 Score: 103
Period size: 3 Copynumber: 74.3 Consensus size: 3
5332051 CTATTTTACC
* * *
5332061 ATT ATT ATT ATT -TGT ATC CTT ATT AAT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * *
5332105 ATT -TCCT CCT ATT ATT ATT AACCT ATT ATT ATT CTT ATT AGT A-T ATT
1 ATT AT--T ATT ATT ATT ATT -A-TT ATT ATT ATT ATT ATT ATT ATT ATT
*
5332152 ATT ATT -TCCT ATT CTT -TAT ATT ATT ATT ATT ATT CATGT ATAT ATT
1 ATT ATT AT--T ATT ATT AT-T ATT ATT ATT ATT ATT -AT-T AT-T ATT
* * * * * * *
5332198 ATT ATT GTT ATT ATT GTT ATT ATT AAT ATT CTT ATC GTT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
5332246 TTT ATT CCTT -TT ATT AGTT ATT ATC AAT A-T ATT ATT ATT ATT A
1 ATT ATT -ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT A
5332289 CCACCTTATT
Statistics
Matches: 170, Mismatches: 35, Indels: 40
0.69 0.14 0.16
Matches are distributed among these distances:
2 12 0.07
3 137 0.81
4 18 0.11
5 3 0.02
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:5332356 original size:23 final size:24
Alignment explanation
Indices: 5332330--5332384 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
5332320 TACTGTCACC
*
5332330 ATTATATTTTTTATT-TTATTATT
1 ATTATATTTTTTATTATCATTATT
5332353 ATTACTAATTTTTTATTATCATTATT
1 ATTA-T-ATTTTTTATTATCATTATT
*
5332379 ACTATA
1 ATTATA
5332385 GTATTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 4 0.15
24 2 0.07
25 11 0.41
26 10 0.37
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (24 bp):
ATTATATTTTTTATTATCATTATT
Found at i:5332365 original size:26 final size:23
Alignment explanation
Indices: 5332335--5332382 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
5332325 TCACCATTAT
*
5332335 ATTTTTTATTTTATTATTATTACTA
1 ATTTTTTA--TTATCATTATTACTA
5332360 ATTTTTTATTATCATTATTACTA
1 ATTTTTTATTATCATTATTACTA
5332383 TAGTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.64
25 8 0.36
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTTTATTATCATTATTACTA
Found at i:5332401 original size:20 final size:20
Alignment explanation
Indices: 5332346--5332404 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
5332336 TTTTTTATTT
* * **
5332346 TATTATTATTACTAATTTTT
1 TATTATTATTACTACTATAG
* *
5332366 TATTATCATTATTACTATAG
1 TATTATTATTACTACTATAG
5332386 TATTATTATTACTACTATA
1 TATTATTATTACTACTATA
5332405 TTTTCATCTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTATTATTACTACTATAG
Found at i:5332658 original size:14 final size:14
Alignment explanation
Indices: 5332612--5332663 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
5332602 TAATTTCAAA
5332612 TATTT-TTTTAGCT
1 TATTTATTTTAGCT
*
5332625 TATTTATTATT-TCT
1 TATTTATT-TTAGCT
*
5332639 TTTTTATTTTAGCT
1 TATTTATTTTAGCT
5332653 TATTTATTTTA
1 TATTTATTTTA
5332664 CCCATTTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 7 0.22
14 23 0.72
15 2 0.06
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (14 bp):
TATTTATTTTAGCT
Found at i:5342284 original size:27 final size:26
Alignment explanation
Indices: 5342245--5342295 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
5342235 CTTTTTTTTT
*
5342245 ACTTTTTTGAATTTAAACTTTTAAAATA
1 ACTTTATTGAATTT-AA-TTTTAAAATA
5342273 ACTTTATT-AATTTAATTTTAAAA
1 ACTTTATTGAATTTAATTTTAAAA
5342296 ATTAATGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 2 0.09
27 5 0.23
28 7 0.32
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (26 bp):
ACTTTATTGAATTTAATTTTAAAATA
Found at i:5342450 original size:13 final size:12
Alignment explanation
Indices: 5342428--5342474 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
5342418 ATATTGATTA
5342428 AAATATTTAAAT
1 AAATATTTAAAT
5342440 AAATATATTAAAT
1 AAATAT-TTAAAT
5342453 -AAT-TTTAAAAT
1 AAATATTT-AAAT
5342464 ATAATATTTAA
1 A-AATATTTAA
5342475 TTATGAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.07
11 5 0.17
12 9 0.30
13 11 0.37
14 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATATTTAAAT
Found at i:5343248 original size:28 final size:30
Alignment explanation
Indices: 5343177--5343250 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 30
5343167 TAGAAATAGA
* *
5343177 AAAATCATATATATATTAAAAATAAATAATT
1 AAAATTATATTTATATT-AAAATAAATAATT
* *
5343208 TAAAGTA-ATTTTATATT-AAAT-AATAATT
1 AAAATTATA-TTTATATTAAAATAAATAATT
5343236 AAAATTATATTTATA
1 AAAATTATATTTATA
5343251 ATAATAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
28 18 0.51
29 5 0.14
30 1 0.03
31 11 0.31
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (30 bp):
AAAATTATATTTATATTAAAATAAATAATT
Found at i:5343253 original size:21 final size:21
Alignment explanation
Indices: 5343217--5343275 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
5343207 TTAAAGTAAT
*
5343217 TTTATATTAAATAATAATTAAAA
1 TTTATATT-TATAATAA-TAAAA
5343240 -TTATATTTATAATAATAAAA
1 TTTATATTTATAATAATAAAA
5343260 TTTATATATT-TAATAA
1 TTTATAT-TTATAATAA
5343276 ATTATTGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.15
21 19 0.58
22 9 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTATATTTATAATAATAAAA
Found at i:5343275 original size:24 final size:24
Alignment explanation
Indices: 5343214--5343275 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 24
5343204 AATTTAAAGT
*
5343214 AATTTTATATTAAATAATAATTAA
1 AATTTTATATTTAATAATAATTAA
5343238 AA--TTATATTT-ATAATAA-TAA
1 AATTTTATATTTAATAATAATTAA
5343258 AATTTATATATTTAATAA
1 AATTT-TATATTTAATAA
5343276 ATTATTGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 5 0.15
21 7 0.21
22 8 0.24
23 7 0.21
24 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTTTATATTTAATAATAATTAA
Found at i:5343891 original size:19 final size:19
Alignment explanation
Indices: 5343849--5343887 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5343839 ATAAGCTAAG
*
5343849 TTAATTAAAATTTAATTAA
1 TTAATTAAGATTTAATTAA
5343868 TTAATTAAGATTT-ATTAA
1 TTAATTAAGATTTAATTAA
5343886 TT
1 TT
5343888 TAATCTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TTAATTAAGATTTAATTAA
Found at i:5345372 original size:15 final size:16
Alignment explanation
Indices: 5345352--5345381 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5345342 AATAATTTAA
5345352 AAATTG-TTGCATATT
1 AAATTGTTTGCATATT
5345367 AAATTGTTTGCATAT
1 AAATTGTTTGCATAT
5345382 GGTAAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGTTTGCATATT
Found at i:5345824 original size:19 final size:18
Alignment explanation
Indices: 5345793--5345846 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
5345783 ACAAGGATGA
5345793 GAAATGGATATGAAATGG
1 GAAATGGATATGAAATGG
*
5345811 GAAATGGAATATGAAATGAT
1 GAAATGG-ATATGAAATG-G
5345831 GAAATGAGATAT-AAAT
1 GAAATG-GATATGAAAT
5345847 ATTGAAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 7 0.22
19 14 0.44
20 10 0.31
21 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (18 bp):
GAAATGGATATGAAATGG
Found at i:5351734 original size:16 final size:16
Alignment explanation
Indices: 5351715--5351752 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5351705 TTTCATTAAG
5351715 TTTTTAAGACTT-ATTT
1 TTTTTAAGA-TTCATTT
5351731 TTTTTAAGATTCATTT
1 TTTTTAAGATTCATTT
*
5351747 GTTTTA
1 TTTTTA
5351753 CTTTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.63
Consensus pattern (16 bp):
TTTTTAAGATTCATTT
Found at i:5357427 original size:11 final size:11
Alignment explanation
Indices: 5357411--5357465 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 11
5357401 TTCAAAAAAT
5357411 AAATAAAA-GA
1 AAATAAAATGA
5357421 AAGATAAAATGA
1 AA-ATAAAATGA
*
5357433 AAATAAAGATAA
1 AAATAAA-ATGA
*
5357445 AAATAAAAATAA
1 AAAT-AAAATGA
5357457 AAATAAAAT
1 AAATAAAAT
5357466 AGATGGACTC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
10 2 0.05
11 16 0.40
12 19 0.47
13 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.16
Consensus pattern (11 bp):
AAATAAAATGA
Found at i:5357440 original size:17 final size:16
Alignment explanation
Indices: 5357411--5357466 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
5357401 TTCAAAAAAT
*
5357411 AAATAAAAGAAAGATA
1 AAATAAAATAAAGATA
5357427 AAATGAAAATAAAGATAA
1 AAAT-AAAATAAAGAT-A
*
5357445 AAATAAAAATAAAAATA
1 AAAT-AAAATAAAGATA
5357462 AAATA
1 AAATA
5357467 GATGGACTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.14
17 15 0.43
18 15 0.43
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (16 bp):
AAATAAAATAAAGATA
Found at i:5357444 original size:6 final size:6
Alignment explanation
Indices: 5357426--5357464 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
5357416 AAAGAAAGAT
* *
5357426 AAAATG AAAATA AAGATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
5357465 TAGATGGACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:5357447 original size:12 final size:11
Alignment explanation
Indices: 5357411--5357466 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
5357401 TTCAAAAAAT
*
5357411 AAATAAAAGAA
1 AAATAAAATAA
* *
5357422 AGATAAAATGA
1 AAATAAAATAA
5357433 AAATAAAGATAA
1 AAATAAA-ATAA
5357445 AAATAAAAATAA
1 AAAT-AAAATAA
5357457 AAATAAAATA
1 AAATAAAATA
5357467 GATGGACTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
11 20 0.53
12 15 0.39
13 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:5369454 original size:14 final size:14
Alignment explanation
Indices: 5369435--5369485 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
5369425 CATAACTTAT
5369435 ATTATATACATATA
1 ATTATATACATATA
* *
5369449 ATTATATACATTTT
1 ATTATATACATATA
5369463 ATTATTATAACATATA
1 ATTA-TAT-ACATATA
5369479 TATTATA
1 -ATTATA
5369486 CATATTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 16 0.53
15 3 0.10
16 7 0.23
17 4 0.13
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTATATACATATA
Found at i:5369482 original size:17 final size:17
Alignment explanation
Indices: 5369434--5369484 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
5369424 TCATAACTTA
5369434 TATTATATACATATA-AT
1 TATTATA-ACATATATAT
*
5369451 TA-TAT-ACAT-TTTAT
1 TATTATAACATATATAT
5369465 TATTATAACATATATAT
1 TATTATAACATATATAT
5369482 TAT
1 TAT
5369485 ACATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.04
14 8 0.29
15 3 0.11
16 7 0.25
17 9 0.32
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATAACATATATAT
Found at i:5370511 original size:78 final size:77
Alignment explanation
Indices: 5370342--5370573 Score: 347
Period size: 78 Copynumber: 3.0 Consensus size: 77
5370332 AGATGCTTTT
* * * *
5370342 GAGTAGTGTGATATATGTTTAAATGTTATGAGATTCTATGATATGGTGATATATGCTTGAATGTT
1 GAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGATATTGTGATATATGCTTGAATGTT
5370407 ATGTGATTATAC
66 ATGTGATTATAC
* * * *
5370419 AAGTGTTGTGATATATGCTTAAATGTTATGAGATTAAATGTATATTGTGACATATGCTTGAATGT
1 GAGTATTGTGATATATGCTTAAATGTTATGAGATTATATG-ATATTGTGATATATGCTTGAATGT
5370484 TATGTGATTATAC
65 TATGTGATTATAC
* *
5370497 GAGTATTGTCATATATGCTTAAATGTTATGTGATTATATGAGTATTGTGATATATGCTTGAATGT
1 GAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGA-TATTGTGATATATGCTTGAATGT
*
5370562 TAGGTGATTATA
65 TATGTGATTATA
5370574 TGTGTAATAG
Statistics
Matches: 138, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
77 35 0.25
78 103 0.75
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (77 bp):
GAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGATATTGTGATATATGCTTGAATGTT
ATGTGATTATAC
Found at i:5370574 original size:39 final size:39
Alignment explanation
Indices: 5370341--5370596 Score: 295
Period size: 39 Copynumber: 6.6 Consensus size: 39
5370331 AAGATGCTTT
* * * * *
5370341 TGAGTAGTGTGATATATGTTTAAATGTTATGAGATTCTA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
5370380 TGA-TATGGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
** * * * *
5370418 CAAGTGTTGTGATATATGCTTAAATGTTATGAGATTAAA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
5370457 TGTA-TATTGTGACATATGCTTGAATGTTATGTGATTATA
1 TG-AGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* * *
5370496 CGAGTATTGTCATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
5370535 TGAGTATTGTGATATATGCTTGAATGTTAGGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
5370574 TGTGTAATAG-GATATATG-TTGAA
1 TGAGT-ATTGTGATATATGCTTGAA
5370597 AAGTGAATAT
Statistics
Matches: 183, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
38 36 0.20
39 143 0.78
40 4 0.02
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:5387829 original size:37 final size:37
Alignment explanation
Indices: 5387765--5387909 Score: 148
Period size: 37 Copynumber: 3.9 Consensus size: 37
5387755 CCCCAATCGT
* * ** * *
5387765 TCATAAGAGCTAAACCATCTGAGAACACG-CTAATCGC
1 TCATAAGAGCTAATCCAACCAATAACACGCCAAAT-GC
*
5387802 TCATAAGAGCTAGTCCAACCAATAACACGCCAAATGC
1 TCATAAGAGCTAATCCAACCAATAACACGCCAAATGC
* * *
5387839 TTATAAGAGCTAATCCAACCGATAACACACCAAATGC
1 TCATAAGAGCTAATCCAACCAATAACACGCCAAATGC
* * * *
5387876 TCATAAAAGTTAATCCACCCGATAACACGCCAAA
1 TCATAAGAGCTAATCCAACCAATAACACGCCAAA
5387910 ATAGGTAGTA
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
37 87 0.96
38 4 0.04
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.18
Consensus pattern (37 bp):
TCATAAGAGCTAATCCAACCAATAACACGCCAAATGC
Found at i:5387866 original size:74 final size:74
Alignment explanation
Indices: 5387767--5387909 Score: 171
Period size: 74 Copynumber: 1.9 Consensus size: 74
5387757 CCAATCGTTC
* * * * * *
5387767 ATAAGAGCTAAACCATCTGAGAACAC-GCTAATCGCTCATAAGAGCTAGTCCAACCAATAACACG
1 ATAAGAGCTAAACCAACCGAGAACACACCAAAT-GCTCATAAAAGCTAATCCAACCAATAACACG
5387831 CCAAATGCTT
65 CCAAATGCTT
* * * * *
5387841 ATAAGAGCTAATCCAACCGATAACACACCAAATGCTCATAAAAGTTAATCCACCCGATAACACGC
1 ATAAGAGCTAAACCAACCGAGAACACACCAAATGCTCATAAAAGCTAATCCAACCAATAACACGC
5387906 CAAA
66 CAAA
5387910 ATAGGTAGTA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
74 53 0.93
75 4 0.07
ACGTcount: A:0.42, C:0.28, G:0.13, T:0.17
Consensus pattern (74 bp):
ATAAGAGCTAAACCAACCGAGAACACACCAAATGCTCATAAAAGCTAATCCAACCAATAACACGC
CAAATGCTT
Found at i:5393937 original size:9 final size:10
Alignment explanation
Indices: 5393919--5393948 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5393909 ACTATAAATT
5393919 TATAAAAAAA
1 TATAAAAAAA
*
5393929 TTTAAAAAAA
1 TATAAAAAAA
5393939 TATAAAAAAA
1 TATAAAAAAA
5393949 ACCTAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
TATAAAAAAA
Found at i:5394035 original size:17 final size:17
Alignment explanation
Indices: 5393989--5394038 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
5393979 GAATTTATAA
5393989 ATAAA-ATAAAAAAT-T
1 ATAAATATAAAAAATAT
*
5394004 ATAAATTTATGAAAAATAT
1 ATAAA--TATAAAAAATAT
5394023 ATAAATATAAAAAATA
1 ATAAATATAAAAAATA
5394039 ACTAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 5 0.17
17 10 0.34
18 8 0.28
19 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
ATAAATATAAAAAATAT
Found at i:5394044 original size:17 final size:16
Alignment explanation
Indices: 5393988--5394045 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
5393978 TGAATTTATA
5393988 AATAAA-ATAAAAAAT
1 AATAAATATAAAAAAT
* *
5394003 TATAAATTTATGAAAAAT
1 AATAAA--TATAAAAAAT
5394021 ATATAAATATAAAAAAT
1 A-ATAAATATAAAAAAT
5394038 AACTAAAT
1 AA-TAAAT
5394046 TTTTATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.15
16 1 0.03
17 15 0.44
18 8 0.24
19 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
AATAAATATAAAAAAT
Found at i:5396326 original size:15 final size:15
Alignment explanation
Indices: 5396285--5396328 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
5396275 GCAATTAGGG
5396285 TTAGGGTTTTGAGAATT
1 TTAGGGTTTT-A-AATT
* *
5396302 TTAAGTTTTTAAATT
1 TTAGGGTTTTAAATT
5396317 TTAGGGTTTTAA
1 TTAGGGTTTTAA
5396329 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.61
16 1 0.04
17 8 0.35
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.52
Consensus pattern (15 bp):
TTAGGGTTTTAAATT
Found at i:5396444 original size:97 final size:99
Alignment explanation
Indices: 5396316--5396522 Score: 262
Period size: 97 Copynumber: 2.1 Consensus size: 99
5396306 GTTTTTAAAT
* * ** *
5396316 TTTAGGG-TTTTAAGGAAAAAAATTAAATAAATTAAGGTTTAATGTTTGTTAATTAAATTAATTA
1 TTTAGGGTTTTTAAGGAAAAAAATCAAATAAATTAAGGTTTAAGGTTACTTAAGTAAATTAATTA
*
5396380 CT-AATTT-AAAAAAAATTAGATTATGG-TTTAGTG
66 -TAAATTTAAAAAAAAATTAGATTA-GGATTTAGGG
* * * *
5396413 TTTATGGTTTTTAAGG-AAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTA
1 TTTAGGGTTTTTAAGGAAAAAAATCAAATAAATTAAGGTTTAAGGTTACTTAAGTAAATTAATTA
5396477 TAAATTTAAAAAAAAATTAGATTAGGATTTTAGGG
66 TAAATTTAAAAAAAAATTAGATTAGGA-TTTAGGG
5396512 TTTAGGGTTTT
1 TTTAGGGTTTT
5396523 AGGGTATTTA
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
96 1 0.01
97 53 0.56
98 24 0.26
99 16 0.17
ACGTcount: A:0.41, C:0.01, G:0.17, T:0.41
Consensus pattern (99 bp):
TTTAGGGTTTTTAAGGAAAAAAATCAAATAAATTAAGGTTTAAGGTTACTTAAGTAAATTAATTA
TAAATTTAAAAAAAAATTAGATTAGGATTTAGGG
Found at i:5396522 original size:15 final size:15
Alignment explanation
Indices: 5396498--5396527 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5396488 AAAAATTAGA
5396498 TTAGGATTTTAGGGT
1 TTAGGATTTTAGGGT
*
5396513 TTAGGGTTTTAGGGT
1 TTAGGATTTTAGGGT
5396528 ATTTAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (15 bp):
TTAGGATTTTAGGGT
Found at i:5396826 original size:126 final size:126
Alignment explanation
Indices: 5396610--5397147 Score: 828
Period size: 126 Copynumber: 4.3 Consensus size: 126
5396600 AAAAGCTTCT
* * *
5396610 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTG-AAAAATAAATTTGAGATGACGTGTCTGCATAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
*
5396674 ATAGTGTCAAAAACGCTTCAAGCAGGATGTATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* **
5396735 ACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTGAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* *
5396800 ATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTTCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * * *
5396861 ATGTGGACGCTCTTTTGCTACAGTAGTCTCTAAAAAAATAATTTTGAGAAGCCGTGTCTGCGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * * *
5396926 ATAGTGGT-AAAAACGCTTCAAACAGGATGCATTTTCAGCAAAATTACTGGAAGAAGCTCCC
66 ATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * *
5396987 ACGTGGATGCTCTTTTGCTACAGTGGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCATAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* *
5397052 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAAAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * *
5397113 ACGTGGACGTTCTTTTGCTACAGTGGTTTCTGAAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
5397148 TAACTTGGGC
Statistics
Matches: 377, Mismatches: 33, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
125 33 0.09
126 342 0.91
127 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (126 bp):
ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
Found at i:5400558 original size:117 final size:116
Alignment explanation
Indices: 5400157--5400772 Score: 1092
Period size: 117 Copynumber: 5.3 Consensus size: 116
5400147 TTTATATTTT
* * **
5400157 ATTACATGAAATAATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTTTAATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
*
5400222 AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTATAT-T-
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTT-TATCTA
* *
5400272 ATCACATGAAATAATATAAAAATATTCAAAATGTTGTCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
5400337 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
*
5400388 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAACAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
5400453 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACC-TTTTATCTA
5400505 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
* *
5400570 AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACATTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
5400621 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATT-
5400686 AAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
65 AAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
*
5400738 ATTACATGAAATAATATAAAAAGATTCAAAATGTT
1 ATTACATGAAATAATATAAAAATATTCAAAATGTT
5400773 TGTACAAATA
Statistics
Matches: 481, Mismatches: 16, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
114 3 0.01
115 104 0.22
116 177 0.37
117 197 0.41
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.40
Consensus pattern (116 bp):
ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
Found at i:5400604 original size:233 final size:233
Alignment explanation
Indices: 5400157--5400772 Score: 1094
Period size: 233 Copynumber: 2.7 Consensus size: 233
5400147 TTTATATTTT
* * **
5400157 ATTACATGAAATAATATAAAAATATTCAAAATATTGCTTTATTTAAAATAATTTTAATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
* * *
5400222 AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTATAT-T-ATCACATGAAATA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTTATCTAATTACATGAAATA
*
5400285 ATATAAAAATATTCAAAATGTTGTCTTATTTAAAATAATTTCCATTTTATTAAAAATATAAAAGT
131 ATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTAAAAATATAAAAGT
*
5400350 AAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
196 AAATTACAATTACTTTATTTAAAACAACATTTTATCTA
*
5400388 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAACAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
5400453 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTTATCTAATTACATGAAATA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTTATCTAATTACATGAAATA
5400518 ATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTAAAAATATAAAAGT
131 ATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTAAAAATATAAAAGT
*
5400583 AAATTATAATTACTTTATTTAAAACAACATTTTATCTA
196 AAATTACAATTACTTTATTTAAAACAACATTTTATCTA
5400621 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATT-
5400686 AAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACC-TTTTATCTAATTACATGAAAT
65 AAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTTATCTAATTACATGAAAT
*
5400750 AATATAAAAAGATTCAAAATGTT
130 AATATAAAAATATTCAAAATGTT
5400773 TGTACAAATA
Statistics
Matches: 369, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
231 107 0.29
232 1 0.00
233 218 0.59
234 43 0.12
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.40
Consensus pattern (233 bp):
ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTA
AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTTATCTAATTACATGAAATA
ATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTATTAAAAATATAAAAGT
AAATTACAATTACTTTATTTAAAACAACATTTTATCTA
Found at i:5401189 original size:18 final size:18
Alignment explanation
Indices: 5401157--5401199 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5401147 GACTAGAAAA
* *
5401157 AGGAAACATATAAGGGCT
1 AGGATACATAAAAGGGCT
*
5401175 GGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
5401193 AGGATAC
1 AGGATAC
5401200 GTACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.30, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:5401294 original size:30 final size:30
Alignment explanation
Indices: 5401253--5401319 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
5401243 GTTGAACTGT
* * *
5401253 TGGGCCCGGTGACTGTGTAGGTC-CTGTTGC
1 TGGGCCTGGTGACTGTGT-GGGCACTGTTGA
*
5401283 TGGGCCTGGTGATTGTGTGGGCACTGTTGA
1 TGGGCCTGGTGACTGTGTGGGCACTGTTGA
5401313 TGGGCCT
1 TGGGCCT
5401320 ACGTCGTCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.07, C:0.19, G:0.42, T:0.31
Consensus pattern (30 bp):
TGGGCCTGGTGACTGTGTGGGCACTGTTGA
Found at i:5403018 original size:33 final size:30
Alignment explanation
Indices: 5402977--5403039 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
5402967 AGCTTTTTTG
*
5402977 AAAAAAATTAACGAGAGTTTTGAGAGGAATTT
1 AAAAAAATT--CGAGAGATTTGAGAGGAATTT
*
5403009 AAAAGAAATTTGAGAGATTTGAGAGGAATTT
1 AAAA-AAATTCGAGAGATTTGAGAGGAATTT
5403040 GAGAGAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 19 0.68
32 4 0.14
33 5 0.18
ACGTcount: A:0.46, C:0.02, G:0.24, T:0.29
Consensus pattern (30 bp):
AAAAAAATTCGAGAGATTTGAGAGGAATTT
Found at i:5403041 original size:11 final size:11
Alignment explanation
Indices: 5402995--5403044 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
5402985 TAACGAGAGT
5402995 TTTGAGAGGAA
1 TTTGAGAGGAA
* * *
5403006 TTTAAAAGAAA
1 TTTGAGAGGAA
5403017 TTTGAGA-G-A
1 TTTGAGAGGAA
5403026 TTTGAGAGGAA
1 TTTGAGAGGAA
5403037 TTTGAGAG
1 TTTGAGAG
5403045 AATATTGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
9 8 0.26
10 1 0.03
11 22 0.71
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (11 bp):
TTTGAGAGGAA
Found at i:5403052 original size:11 final size:10
Alignment explanation
Indices: 5402995--5403052 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
5402985 TAACGAGAGT
5402995 TTTGAGAGGAA
1 TTTGAGA-GAA
* *
5403006 TTTAAAAGAAA
1 TTTGAGAG-AA
5403017 TTTGAGAG-A
1 TTTGAGAGAA
5403026 TTTGAGAGGAA
1 TTTGAGA-GAA
5403037 TTTGAGAGAA
1 TTTGAGAGAA
5403047 TATTGA
1 T-TTGA
5403053 AAGATTGAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 8 0.21
10 6 0.15
11 25 0.64
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:5403058 original size:31 final size:31
Alignment explanation
Indices: 5402995--5403058 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
5402985 TAACGAGAGT
*
5402995 TTTGAGAGGAATTTAAAAGAAATTTGAGAGA
1 TTTGAGAGGAATTTAAAAGAAATTTGAAAGA
* *
5403026 TTTGAGAGGAATTTGAGAG-AATATTGAAAGA
1 TTTGAGAGGAATTTAAAAGAAAT-TTGAAAGA
5403057 TT
1 TT
5403059 GAAGATTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (31 bp):
TTTGAGAGGAATTTAAAAGAAATTTGAAAGA
Found at i:5404972 original size:18 final size:18
Alignment explanation
Indices: 5404949--5404984 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5404939 GAAAATATTT
5404949 ATCCTATTTGGTACTTAG
1 ATCCTATTTGGTACTTAG
5404967 ATCCTATTTGGTACTTAG
1 ATCCTATTTGGTACTTAG
5404985 GGGTGAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (18 bp):
ATCCTATTTGGTACTTAG
Done.