Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 7 of 226
Found at i:2809534 original size:13 final size:13
Alignment explanation
Indices: 2809518--2809570 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
2809508 TTTAAACCAA
2809518 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
**
2809531 ACTTTTCAAAAGT
1 ACTTTTCAAAAAC
* *
2809544 ACTTTT-ACATAGC
1 ACTTTTCA-AAAAC
2809557 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
2809570 A
1 A
2809571 ATGAAGAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 1 0.03
13 30 0.94
14 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:2809547 original size:26 final size:26
Alignment explanation
Indices: 2809518--2809567 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2809508 TTTAAACCAA
2809518 ACTTTT-CAAAAACACTTTTCAAAAGT
1 ACTTTTAC-AAAACACTTTTCAAAAGT
* *
2809544 ACTTTTACATAGCACTTTTCAAAA
1 ACTTTTACAAAACACTTTTCAAAA
2809568 ACAATGAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (26 bp):
ACTTTTACAAAACACTTTTCAAAAGT
Found at i:2817672 original size:43 final size:43
Alignment explanation
Indices: 2817611--2817697 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
2817601 CGAATCAAAG
2817611 CATAATTAATCTCATACAAATTAAACTTGAAATAATTTAGAAT
1 CATAATTAATCTCATACAAATTAAACTTGAAATAATTTAGAAT
2817654 CATAATTAATCTCATACAAATTAAACTTGAAATAATTTAGAAT
1 CATAATTAATCTCATACAAATTAAACTTGAAATAATTTAGAAT
2817697 C
1 C
2817698 GAGATGATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (43 bp):
CATAATTAATCTCATACAAATTAAACTTGAAATAATTTAGAAT
Found at i:2817827 original size:16 final size:17
Alignment explanation
Indices: 2817800--2817847 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
2817790 TTAAAAAGTA
2817800 AAAATCAATCTAAAACT-
1 AAAAT-AATCTAAAACTC
2817817 AAAATAATCT-AAACTC
1 AAAATAATCTAAAACTC
*
2817833 AAAATTAATTTAAAA
1 AAAA-TAATCTAAAA
2817848 AAAGTAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.19
16 9 0.33
17 10 0.37
18 3 0.11
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAATCTAAAACTC
Found at i:2820981 original size:4 final size:4
Alignment explanation
Indices: 2820974--2820998 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2820964 TTGAAATACT
2820974 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
2820999 CCTCTTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:2834812 original size:14 final size:14
Alignment explanation
Indices: 2834790--2834822 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2834780 AAGGGATTGG
2834790 TTTTCTTTTTCCAT
1 TTTTCTTTTTCCAT
*
2834804 TTTTTTTTTTCCAT
1 TTTTCTTTTTCCAT
2834818 TTTTC
1 TTTTC
2834823 GGGTTTTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTCCAT
Found at i:2836735 original size:3 final size:3
Alignment explanation
Indices: 2836729--2836753 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2836719 ACAACACTCA
2836729 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2836754 TTGAGTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2853557 original size:31 final size:32
Alignment explanation
Indices: 2853522--2853583 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
2853512 AAAAAATTCA
2853522 AGTCTCAATGCGGGAAAAATTATCAA-GTTTT
1 AGTCTCAATGCGGGAAAAATTATCAATGTTTT
* * *
2853553 AGTCTCAATGTGGGAATAATTGTCAATGTTT
1 AGTCTCAATGCGGGAAAAATTATCAATGTTT
2853584 AGGACCTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.35
Consensus pattern (32 bp):
AGTCTCAATGCGGGAAAAATTATCAATGTTTT
Found at i:2853642 original size:92 final size:91
Alignment explanation
Indices: 2853424--2853642 Score: 228
Period size: 90 Copynumber: 2.4 Consensus size: 91
2853414 TGAAAATCTT
* * *
2853424 AAAGCTCAAGCCTCAATATGAGAATAATTGTCAAG-TTTAGGTCTCAATATGAGAACAATTGTCA
1 AAAGTTCAAGCCTCAATGTGAGAAAAATTGTCAAGTTTTAGGTCTCAATATGAGAACAATTGTCA
* *
2853488 ATTTTTGAGCTTAACTTGGATAAAAA
66 ATTTTGGAGCCTAACTTGGATAAAAA
* * * * * * * *
2853514 AAAATTCAAGTCTCAATGCGGGAAAAATTATCAAGTTTTA-GTCTCAATGTGGGAATAATTGTCA
1 AAAGTTCAAGCCTCAATGTGAGAAAAATTGTCAAGTTTTAGGTCTCAATATGAGAACAATTGTCA
**
2853578 ATGTTTAGGA-CCTAGTTTGGATAAAAGA
66 AT-TTT-GGAGCCTAACTTGGATAAAA-A
* * *
2853606 AAAGTTCAAACCTCAATGTGAAAAAAATTGTTAAGTT
1 AAAGTTCAAGCCTCAATGTGAGAAAAATTGTCAAGTT
2853643 CAGGCTCAAT
Statistics
Matches: 102, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
90 50 0.49
91 20 0.20
92 32 0.31
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (91 bp):
AAAGTTCAAGCCTCAATGTGAGAAAAATTGTCAAGTTTTAGGTCTCAATATGAGAACAATTGTCA
ATTTTGGAGCCTAACTTGGATAAAAA
Found at i:2857231 original size:14 final size:14
Alignment explanation
Indices: 2857212--2857243 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2857202 TCGTGCTTCA
2857212 GTTTTGCAAATTCT
1 GTTTTGCAAATTCT
*
2857226 GTTTTGCAACTTCT
1 GTTTTGCAAATTCT
2857240 GTTT
1 GTTT
2857244 CTTTTTGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (14 bp):
GTTTTGCAAATTCT
Found at i:2861764 original size:14 final size:14
Alignment explanation
Indices: 2861745--2861776 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2861735 TCGTGCTTCA
2861745 GTTTTGCAAATTCT
1 GTTTTGCAAATTCT
*
2861759 GTTTTGCAACTTCT
1 GTTTTGCAAATTCT
2861773 GTTT
1 GTTT
2861777 CTTTTTGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (14 bp):
GTTTTGCAAATTCT
Found at i:2864108 original size:15 final size:15
Alignment explanation
Indices: 2864090--2864121 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2864080 GAGCCGCTGC
2864090 AGCTAGTGGTTTTGG
1 AGCTAGTGGTTTTGG
*
2864105 AGCTGGTGGTTTTGG
1 AGCTAGTGGTTTTGG
2864120 AG
1 AG
2864122 ATGGTGGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.44, T:0.38
Consensus pattern (15 bp):
AGCTAGTGGTTTTGG
Found at i:2864126 original size:15 final size:15
Alignment explanation
Indices: 2864095--2864128 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2864085 GCTGCAGCTA
*
2864095 GTGGTTTTGGAGCTG
1 GTGGTTTTGGAGATG
2864110 GTGGTTTTGGAGATG
1 GTGGTTTTGGAGATG
2864125 GTGG
1 GTGG
2864129 AGATGATGGT
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:0.09, C:0.03, G:0.50, T:0.38
Consensus pattern (15 bp):
GTGGTTTTGGAGATG
Found at i:2864175 original size:21 final size:21
Alignment explanation
Indices: 2864151--2864191 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2864141 TGGTGGAGAC
*
2864151 GGTGGGGTCGACGGAGTTGAG
1 GGTGGGGTCGAAGGAGTTGAG
*
2864172 GGTGGGGTTGAAGGAGTTGA
1 GGTGGGGTCGAAGGAGTTGA
2864192 CGGAGGAGGG
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:0.17, C:0.05, G:0.56, T:0.22
Consensus pattern (21 bp):
GGTGGGGTCGAAGGAGTTGAG
Found at i:2868730 original size:20 final size:20
Alignment explanation
Indices: 2868705--2868774 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 20
2868695 ACTTCATGTT
2868705 AATTTTTAAAAATTTTTATG
1 AATTTTTAAAAATTTTTATG
* * *
2868725 AATTTTTTTAATATTTTTTTTG
1 AA--TTTTTAAAAATTTTTATG
* *
2868747 AGTTTTT-AATATTTTTAT-
1 AATTTTTAAAAATTTTTATG
2868765 AATTTTTAAA
1 AATTTTTAAA
2868775 TTTCTATTGA
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
18 6 0.16
19 9 0.24
20 7 0.18
22 16 0.42
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
AATTTTTAAAAATTTTTATG
Found at i:2869185 original size:26 final size:26
Alignment explanation
Indices: 2869154--2869203 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2869144 AAATTTATAT
*
2869154 TTATATTTATATTAAATAAAAAATCA
1 TTATATTGATATTAAATAAAAAATCA
*
2869180 TTATATTGATATTAAATATAAAAT
1 TTATATTGATATTAAATAAAAAAT
2869204 ACTCTCCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
TTATATTGATATTAAATAAAAAATCA
Found at i:2869373 original size:20 final size:21
Alignment explanation
Indices: 2869350--2869398 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
2869340 AATATAAATA
2869350 TAAATTTATTGTTAT-ATTTT
1 TAAATTTATTGTTATAATTTT
** *
2869370 TAAAAATATTTTTATAATTTT
1 TAAATTTATTGTTATAATTTT
2869391 TATAATTT
1 TA-AATTT
2869399 TTTTATTTCC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 12 0.55
21 7 0.32
22 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TAAATTTATTGTTATAATTTT
Found at i:2893512 original size:55 final size:55
Alignment explanation
Indices: 2893449--2893561 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
2893439 TGCGAATGTA
2893449 TACACACAAATAGAGAAATATATACATACATGTAAGGAAGAAGAAAGAGGAGACT
1 TACACACAAATAGAGAAATATATACATACATGTAAGGAAGAAGAAAGAGGAGACT
2893504 TACACACAAATAGAGAAATATATACATACATGTAAGGAAGAAGAAAGAGGAGACT
1 TACACACAAATAGAGAAATATATACATACATGTAAGGAAGAAGAAAGAGGAGACT
2893559 TAC
1 TAC
2893562 CACGCTTTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (55 bp):
TACACACAAATAGAGAAATATATACATACATGTAAGGAAGAAGAAAGAGGAGACT
Found at i:2903041 original size:19 final size:18
Alignment explanation
Indices: 2902981--2903054 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
2902971 TTAATACAGT
*
2902981 TTTAATATTAAATTTAATA
1 TTTAATATTTAATTTAA-A
* * *
2903000 CTTAAATTTTTTATCTT-AA
1 -TTTAATATTTAAT-TTAAA
*
2903019 TTTAGTATTTAAATTTAAA
1 TTTAATATTT-AATTTAAA
2903038 TTTAATATTTAATTTAA
1 TTTAATATTTAATTTAA
2903055 TACTCGAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
18 16 0.38
19 14 0.33
20 10 0.24
21 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (18 bp):
TTTAATATTTAATTTAAA
Found at i:2903056 original size:12 final size:13
Alignment explanation
Indices: 2902981--2903050 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
2902971 TTAATACAGT
2902981 TTTAATA-TTAAA
1 TTTAATATTTAAA
*
2902993 TTTAATACTTAAA
1 TTTAATATTTAAA
**
2903006 TTTTTTATCTT-AA
1 TTTAATAT-TTAAA
*
2903019 TTTAGTATTTAAA
1 TTTAATATTTAAA
2903032 TTTAA-ATTTAATA
1 TTTAATATTTAA-A
2903045 TTTAAT
1 TTTAAT
2903051 TTAATACTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
12 15 0.32
13 30 0.64
14 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (13 bp):
TTTAATATTTAAA
Found at i:2903239 original size:14 final size:14
Alignment explanation
Indices: 2903220--2903259 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2903210 TTGTTTGCCA
2903220 GTAAAATATTTTCT
1 GTAAAATATTTTCT
2903234 GTAAAATGA-TTTCT
1 GTAAAAT-ATTTTCT
*
2903248 GGAAAATATTTT
1 GTAAAATATTTT
2903260 ACTTTTCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (14 bp):
GTAAAATATTTTCT
Found at i:2903271 original size:34 final size:34
Alignment explanation
Indices: 2903228--2903293 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
2903218 CAGTAAAATA
*
2903228 TTTTCTGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCTGTAAAATGATTTAC-AGAAAATATTTTAC
2903262 TTTTCTGTAAAATGATTTACAGAAAATATTTT
1 TTTTCTGTAAAATGATTTACAGAAAATATTTT
2903294 CTAGTGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.47
Consensus pattern (34 bp):
TTTTCTGTAAAATGATTTACAGAAAATATTTTAC
Found at i:2904335 original size:73 final size:72
Alignment explanation
Indices: 2904232--2904376 Score: 238
Period size: 73 Copynumber: 2.0 Consensus size: 72
2904222 TTACGTATGA
2904232 TCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTC-TGATCAGATA
1 TCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGATA
2904296 AGTGTAG
66 AGTGTAG
* * *
2904303 TCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCTTGATCAGA
1 TCACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGA
2904368 TAAGTGTAG
64 TAAGTGTAG
2904377 CTAAAGCTAT
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
71 11 0.16
72 3 0.04
73 37 0.54
74 17 0.25
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.39
Consensus pattern (72 bp):
TCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGATA
AGTGTAG
Found at i:2904336 original size:37 final size:37
Alignment explanation
Indices: 2904233--2904377 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
2904223 TACGTATGAT
* *
2904233 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
2904268 CACCTATCACTTTGTTTC-TGATCAGATAAGTGTAGT
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
2904304 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
2904341 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
2904378 TAAAGCTATT
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
35 9 0.09
36 37 0.36
37 56 0.55
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:2904394 original size:46 final size:46
Alignment explanation
Indices: 2904341--2904702 Score: 333
Period size: 46 Copynumber: 7.6 Consensus size: 46
2904331 TAAGTGTAGC
** *
2904341 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* * * * *
2904387 TACTTATCACTTTGTCTCTTGATCAGATAGGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
2904433 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGT--C---A-CTTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCTGAAGC-TAT
* *
2904480 CACTT-TCCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTAT-CACTTT----GTC--ACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
2904532 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* *
2904578 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
* * *
2904624 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
*
2904676 CACTTATCACTTTTTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
2904703 AGTACTCAAA
Statistics
Matches: 266, Mismatches: 23, Indels: 54
0.78 0.07 0.16
Matches are distributed among these distances:
41 2 0.01
44 1 0.00
45 1 0.00
46 149 0.56
47 30 0.11
48 2 0.01
49 2 0.01
50 2 0.01
52 75 0.28
53 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
Found at i:2904673 original size:98 final size:97
Alignment explanation
Indices: 2904358--2904702 Score: 447
Period size: 98 Copynumber: 3.6 Consensus size: 97
2904348 CACTTTGTTT
* * *
2904358 CTTGATCAGATAAGTGTAGCTAAAGCTATTACTTATCACTTTGTCTCTTGATCAGATAGGTATAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
2904423 CCGAAGCTATCACTTATCACTTTTCACTTGTCA
66 CCGAAGCTATCACTTATCAC-TTTCACTTGTCA
* *
2904456 CTTGATCAGATAAGTGTCA-CTTATCA-CTTTCCACTT-TCCAC-TTGTCACTTGATCAGATAAG
1 CTTGATCAGATAAGTGT-AGC-TA-AAGCTAT-CACTTAT-CACTTTGTCACTTGATCAGATAAG
* *
2904517 TGTAGCTGAAGCTATCACTTATCAC--T---TTGTCA
61 TATAGCCGAAGCTATCACTTATCACTTTCACTTGTCA
* **
2904549 CTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
2904614 CCGAAGCTATTACTTATCACTTTCCACTTGTCA
66 CCGAAGCTATCACTTATCACTTT-CACTTGTCA
* *
2904647 CTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTTTCACTTGATCAGA
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGA
2904703 AGTACTCAAA
Statistics
Matches: 212, Mismatches: 20, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
91 9 0.04
92 47 0.22
93 23 0.11
94 1 0.00
96 1 0.00
98 75 0.35
99 48 0.23
100 8 0.04
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (97 bp):
CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
CCGAAGCTATCACTTATCACTTTCACTTGTCA
Found at i:2918629 original size:20 final size:20
Alignment explanation
Indices: 2918604--2918643 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2918594 CGTAAAATGA
*
2918604 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
2918624 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
2918644 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:2918633 original size:34 final size:35
Alignment explanation
Indices: 2918589--2918655 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2918579 CAGTAAAATA
*
2918589 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
2918623 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
2918656 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:2918659 original size:14 final size:15
Alignment explanation
Indices: 2918583--2918659 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2918573 GATTGCCAGT
* *
2918583 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
2918597 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
2918611 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
2918631 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
2918646 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
2918660 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:2920913 original size:215 final size:210
Alignment explanation
Indices: 2920647--2921073 Score: 737
Period size: 215 Copynumber: 2.0 Consensus size: 210
2920637 AATTGTTAGG
2920647 ATTTGGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCCTT
1 ATTTGGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCCTT
*
2920712 GGTATATAGCTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
66 GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
* * *
2920777 GCGGGACAAACTTAAAAGGAAACGAGGAAAAAAAAAAGAGCAATCAATTTATGGTTGTTGTTACC
131 GCGGGACAAACTTAAAAAGAAAAGAGG--AAAAAAAAGAGCAATCAATCTAT-G--GTTGTTACC
2920842 GCATGACGATGTATCTAACC
191 GCATGACGATGTATCTAACC
* *
2920862 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
1 ATTTGGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCCTT
2920927 GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
66 GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
* *
2920992 GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAGAGAGCAATCAATCTATGGTTGTTACGGCATG
131 GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAAAGAGCAATCAATCTATGGTTGTTACCGCATG
2921057 ACGATGTATCTAACC
196 ACGATGTATCTAACC
2921072 AT
1 AT
2921074 ATAACTAACA
Statistics
Matches: 204, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
210 30 0.15
212 1 0.00
213 21 0.10
215 152 0.75
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (210 bp):
ATTTGGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCCTT
GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAAAGAGCAATCAATCTATGGTTGTTACCGCATG
ACGATGTATCTAACC
Found at i:2924459 original size:2 final size:2
Alignment explanation
Indices: 2924454--2924485 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2924444 ATGCACACAC
2924454 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2924486 GTGTCTCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2928634 original size:2 final size:2
Alignment explanation
Indices: 2928627--2928662 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2928617 AAATATTTTA
2928627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2928663 GTTAGCAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2930449 original size:20 final size:21
Alignment explanation
Indices: 2930416--2930454 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2930406 TTTAAAATAC
2930416 TTTTAAAATAATTTTTTTATT
1 TTTTAAAATAATTTTTTTATT
2930437 TTTTAAAAT-ATTTTTTTA
1 TTTTAAAATAATTTTTTTA
2930455 ATGTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTAAAATAATTTTTTTATT
Found at i:2930461 original size:20 final size:21
Alignment explanation
Indices: 2930417--2930461 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2930407 TTAAAATACT
* *
2930417 TTTAAAATAATTTTTTTATTT
1 TTTAAAATAATTTTTTTAATG
2930438 TTTAAAAT-ATTTTTTTAATG
1 TTTAAAATAATTTTTTTAATG
2930458 TTTA
1 TTTA
2930462 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTAAAATAATTTTTTTAATG
Found at i:2931656 original size:2 final size:2
Alignment explanation
Indices: 2931651--2931681 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2931641 GTGCGTGTGA
*
2931651 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2931682 AGGATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2948980 original size:2 final size:2
Alignment explanation
Indices: 2948975--2949000 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2948965 ACAGAAAAAA
2948975 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
2949001 CCAAAGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2959700 original size:29 final size:27
Alignment explanation
Indices: 2959651--2959715 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
2959641 TATTTTGTAA
*
2959651 TTTTTATAAAAATTTTCAATTTTTATGT
1 TTTTTATTAAAATTTTCAATTTTTAT-T
2959679 TTTTTATTAAAATTTAAT-AATTTTTATT
1 TTTTTATTAAAATTT--TCAATTTTTATT
2959707 TTTTATATT
1 TTTT-TATT
2959716 TTTTGTCACA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 19 0.58
29 13 0.39
30 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTTATTAAAATTTTCAATTTTTATT
Found at i:2961022 original size:15 final size:15
Alignment explanation
Indices: 2960999--2961033 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2960989 CAATAACAAT
2960999 ATATATTTTTATAAA
1 ATATATTTTTATAAA
* *
2961014 ATATTTTTTTATAAT
1 ATATATTTTTATAAA
2961029 ATATA
1 ATATA
2961034 ACAGAAGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATTTTTATAAA
Found at i:2961067 original size:19 final size:19
Alignment explanation
Indices: 2961043--2961082 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2961033 AACAGAAGTA
2961043 ATTATTAACCACTAATTAT
1 ATTATTAACCACTAATTAT
*
2961062 ATTATTGACCACTAATTAT
1 ATTATTAACCACTAATTAT
2961081 AT
1 AT
2961083 CTTTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTATTAACCACTAATTAT
Found at i:2962792 original size:30 final size:31
Alignment explanation
Indices: 2962758--2962827 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
2962748 TTTTATTCTT
2962758 AGTTAAATTTAATT-TTAATATTTTAAAAAG
1 AGTTAAATTTAATTATTAATATTTTAAAAAG
* * *
2962788 AGTTAAACTTAATTATTAATTTTTTAAAAAT
1 AGTTAAATTTAATTATTAATATTTTAAAAAG
*
2962819 AGTCAAATT
1 AGTTAAATT
2962828 GTTATTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 13 0.38
31 21 0.62
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (31 bp):
AGTTAAATTTAATTATTAATATTTTAAAAAG
Found at i:2967864 original size:18 final size:18
Alignment explanation
Indices: 2967843--2967877 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2967833 AATTTAATTT
2967843 TTAAAAAATTATAAAAAC
1 TTAAAAAATTATAAAAAC
**
2967861 TTAAACTATTATAAAAA
1 TTAAAAAATTATAAAAA
2967878 TATACAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAAATTATAAAAAC
Found at i:2991279 original size:33 final size:34
Alignment explanation
Indices: 2991235--2991303 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
2991225 AATAAGAAAA
2991235 ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
1 ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
2991269 ATAAA-GTTTGATCCATTCTAAAAGTAATCTGCT
1 ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
2991302 AT
1 AT
2991304 CAACCTAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 30 0.86
34 5 0.14
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (34 bp):
ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
Found at i:3006604 original size:17 final size:17
Alignment explanation
Indices: 3006561--3006608 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
3006551 TATTAATATC
*
3006561 ATTTTTAAAAAGTACTT
1 ATTTTTAAAAAGAACTT
**
3006578 ATAATT--AAAGAACTT
1 ATTTTTAAAAAGAACTT
3006593 ATTTTTAAAAAGAACT
1 ATTTTTAAAAAGAACT
3006609 AAAACATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 12 0.50
17 12 0.50
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (17 bp):
ATTTTTAAAAAGAACTT
Found at i:3011499 original size:67 final size:67
Alignment explanation
Indices: 3011391--3011588 Score: 369
Period size: 67 Copynumber: 3.0 Consensus size: 67
3011381 TTTCCAATTC
* * *
3011391 AGAGAGCACACTCCCACGAACCTTATTTCTTATAGCGGGATTACCAGTCCAGGCTAAATCCCCTA
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTA
3011456 CA
66 CA
3011458 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTA
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTA
3011523 CA
66 CA
3011525 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCT
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCT
3011589 GTAATATAAA
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 128 1.00
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTA
CA
Found at i:3018221 original size:2 final size:2
Alignment explanation
Indices: 3018209--3018238 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3018199 TATGTTAGTT
3018209 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3018239 GTCGTGGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3019995 original size:19 final size:21
Alignment explanation
Indices: 3019950--3020002 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
3019940 CAAAAAGATG
*
3019950 AATTTTATATATACAAAT-AT
1 AATTTTATATATAAAAATAAT
* *
3019970 TATTTT-TATTTAAAAATAAT
1 AATTTTATATATAAAAATAAT
3019990 AATTTT-TAT-TAAA
1 AATTTTATATATAAA
3020003 TAAACTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTTATATATAAAAATAAT
Found at i:3037420 original size:16 final size:16
Alignment explanation
Indices: 3037401--3037434 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
3037391 TTTATTGTTT
3037401 TAATAAATTTTAAA-AA
1 TAAT-AATTTTAAATAA
3037417 TAATAATTTTAAATAA
1 TAATAATTTTAAATAA
3037433 TA
1 TA
3037435 TTATTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATTTTAAATAA
Found at i:3047441 original size:17 final size:18
Alignment explanation
Indices: 3047410--3047443 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3047400 TTATTATTTA
*
3047410 AGAGCAAAATTAACTAAT
1 AGAGCAAAATAAACTAAT
3047428 AGAG-AAAATAAACTAA
1 AGAGCAAAATAAACTAA
3047444 GGTAATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.18
Consensus pattern (18 bp):
AGAGCAAAATAAACTAAT
Found at i:3058233 original size:21 final size:21
Alignment explanation
Indices: 3058205--3058287 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 21
3058195 CGGGTGGATA
*
3058205 AGCTCTTACGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
*
3058226 AACTCTTATGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTC
* * *
3058247 AGCTCTTTTGAGCTTTTTTTC
1 AGCTCTTATGAGCTTCTGTTC
*
3058268 AGCTCTTATAAGCTTCTGTT
1 AGCTCTTATGAGCTTCTGTT
3058288 AGCGTTTTCG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.46
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTC
Found at i:3060181 original size:61 final size:61
Alignment explanation
Indices: 3060090--3060220 Score: 149
Period size: 61 Copynumber: 2.1 Consensus size: 61
3060080 ATACATTTTA
* * * * *
3060090 TATATATATGTGGTTCGAATATAGGTTACAAAG-TCATTGAGCTGAATTTAATGTTTTGAAC
1 TATATATATGAGGTTCGAATATAGATTAC-AAGTTCATTGAGCTAAAGTTAATGTTATGAAC
* * * *
3060151 TATACATATGAGGTTCGAATGTA-ATATACAAGTTCTTTGAGCTAAAGTTAATGTTATGAAT
1 TATATATATGAGGTTCGAATATAGAT-TACAAGTTCATTGAGCTAAAGTTAATGTTATGAAC
3060212 TATATATAT
1 TATATATAT
3060221 ATTCATGTGG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
60 4 0.07
61 54 0.93
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.40
Consensus pattern (61 bp):
TATATATATGAGGTTCGAATATAGATTACAAGTTCATTGAGCTAAAGTTAATGTTATGAAC
Found at i:3060490 original size:41 final size:41
Alignment explanation
Indices: 3060331--3060473 Score: 232
Period size: 41 Copynumber: 3.5 Consensus size: 41
3060321 GCTCTGTGCT
*
3060331 TAGCAGGCTTAATGCTAGTGAAATAATTCAGACTTTACATC
1 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACATC
* * *
3060372 TAGCAGCCTTAATGCCAGTGAAATAATTCAAACTTTACGTC
1 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACATC
* *
3060413 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACATC
1 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACATC
3060454 TAGCAGGCTTAATGCCAGTG
1 TAGCAGGCTTAATGCCAGTG
3060474 TTCTGAATCA
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACATC
Found at i:3060490 original size:82 final size:82
Alignment explanation
Indices: 3060331--3060516 Score: 241
Period size: 82 Copynumber: 2.3 Consensus size: 82
3060321 GCTCTGTGCT
*
3060331 TAGCAGGCTTAATGCTAGTGAAATAATTCAGACTTTACATCTAGCAGCCTTAATGCCAGTGAAAT
1 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACATCTAGCAGCCTTAATGCCAGTGAAAT
* *
3060396 AATTCAAACTTTACGTC
66 AATTCAAACTTTAAGCC
* * * ***
3060413 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACATCTAGCAGGCTTAATGCCAGTGTTCT
1 TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACATCTAGCAGCCTTAATGCCAGTGAAAT
**
3060478 GAA-TCAGGCTTTAAGCC
66 -AATTCAAACTTTAAGCC
3060495 TAGCAGGC-TACATGCCAGTGAA
1 TAGCAGGCTTA-ATGCCAGTGAA
3060517 TCATTTTAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 2 0.02
82 86 0.96
83 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (82 bp):
TAGCAGGCTTAATGCCAGTGAAATAATTCAGACTTTACATCTAGCAGCCTTAATGCCAGTGAAAT
AATTCAAACTTTAAGCC
Found at i:3063757 original size:23 final size:22
Alignment explanation
Indices: 3063714--3063757 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
3063704 TTCTAAGTCG
3063714 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
3063737 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
3063758 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:3063871 original size:45 final size:45
Alignment explanation
Indices: 3063803--3063890 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
3063793 ACAGATACTC
* * * * *
3063803 GGTGGATTCAGCACATAGTAACCACATTATTAATTAATGATGTCT
1 GGTGGAATCAGCACATAGCAACCACATTACTAATCAATCATGTCT
*
3063848 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATCATGT
1 GGTGGAATCAGCACATAGCAACCACATTACTAATCAATCATGT
3063891 TCGGTTCACA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACATTACTAATCAATCATGTCT
Found at i:3063959 original size:51 final size:50
Alignment explanation
Indices: 3063892--3064087 Score: 268
Period size: 51 Copynumber: 3.9 Consensus size: 50
3063882 CAATCATGTT
* *
3063892 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATC
* * * *
3063943 CGATACACGTAGTAGCCTGCACATAGTACTACACATGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATC
* * * *
3063994 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TC
3064044 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
3064088 CACTTTCACT
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
49 2 0.02
50 42 0.34
51 79 0.63
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCATC
Found at i:3064076 original size:101 final size:101
Alignment explanation
Indices: 3063899--3064083 Score: 318
Period size: 101 Copynumber: 1.8 Consensus size: 101
3063889 GTTCGGTTCA
*
3063899 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
3063964 CATAGTACTACACATGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACATGTGATCGAAACTATCCGGTACG
* *
3064001 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCA
3064065 CATAGTACTACACATGTGA
65 CATAGTACTACACATGTGA
3064084 CCATCACTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.52
102 34 0.43
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACATGTGATCGAAACTATCCGGTACG
Found at i:3067306 original size:23 final size:23
Alignment explanation
Indices: 3067275--3067330 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
3067265 ACCTACTTTC
* * *
3067275 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
3067298 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
*
3067321 TTACATTAGT
1 TTACAGTAGT
3067331 CTTATTGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.45
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:3089180 original size:25 final size:25
Alignment explanation
Indices: 3089149--3089198 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3089139 TAAGATTGCT
*
3089149 TTAAAA-TAATATTATAAATTAATAA
1 TTAAAATTAA-ATTATAAAATAATAA
*
3089174 TTAAAATTAAATTTTAAAATAATAA
1 TTAAAATTAAATTATAAAATAATAA
3089199 AATTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAAAATTAAATTATAAAATAATAA
Found at i:3091880 original size:20 final size:19
Alignment explanation
Indices: 3091857--3091902 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3091847 CAAACTTAAC
*
3091857 ATTTTTTAAAATTTTAATTT
1 ATTTTTTAAAA-TTCAATTT
3091877 ATTTTTATAAAATTCAATTT
1 ATTTTT-TAAAATTCAATTT
3091897 -TTTTTT
1 ATTTTTT
3091903 GCTAATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.04
19 5 0.21
20 13 0.54
21 5 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTTAAAATTCAATTT
Found at i:3096279 original size:47 final size:47
Alignment explanation
Indices: 3096226--3096370 Score: 158
Period size: 47 Copynumber: 3.1 Consensus size: 47
3096216 TCATGTAAGA
*
3096226 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
* **
3096273 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATT
* * *
3096317 ATATTTATTATCAAGAGTTTTATGAAATTATATATTATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
3096364 ATATTTA
1 ATATTTA
3096371 ATAATAATTA
Statistics
Matches: 79, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.30
45 8 0.10
46 8 0.10
47 33 0.42
48 3 0.04
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATAATTATTAAATT
Found at i:3096319 original size:91 final size:91
Alignment explanation
Indices: 3096211--3096426 Score: 324
Period size: 91 Copynumber: 2.4 Consensus size: 91
3096201 ATGATTTTAG
*
3096211 TAAATTCATGTAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
* * *
3096276 TTTAATATTAATTATTTTAAATTATA
66 TTTAATAATAATTATATTAAACTATA
* * *
3096302 TAAATTCATATAAGAATATTTATTATCAAGAGTTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
3096367 TTTAATAATAATTATATTAAACTATA
66 TTTAATAATAATTATATTAAACTATA
* * * * *
3096393 CAAATTCATTTAAGAAAATTTATTAGTAATAATT
1 TAAATTCATATAAGAATATTTATTATTAAGAATT
3096427 ATTTTAAATT
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 111 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATAATAATTATATTAAACTATA
Found at i:3096570 original size:121 final size:121
Alignment explanation
Indices: 3096424--3096964 Score: 1000
Period size: 121 Copynumber: 4.5 Consensus size: 121
3096414 ATTAGTAATA
3096424 ATTATTTTA-AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAA
1 ATTA-TTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAA
3096488 ATTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTG
65 ATTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTG
3096545 ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAA
1 ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAA
3096610 TTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTG
66 TTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTG
3096666 ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAA
1 ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAA
3096731 TTATATTTTATAGTATCATATATTATGATTTT-AGTAAATTCATATAAGAATATTG
66 TTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTG
*
3096786 ATTATTAAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AA
1 ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAA
*
3096850 ATTATATTTTATAGTATCATATATTATGA-TTTGAGTAAATTCATATAAGAATATTG
65 ATTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTG
* *
3096906 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT
3096965 GTTAAAATAT
Statistics
Matches: 415, Mismatches: 2, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
119 3 0.01
120 197 0.47
121 215 0.52
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (121 bp):
ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAA
TTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTG
Found at i:3096862 original size:241 final size:241
Alignment explanation
Indices: 3096424--3096964 Score: 998
Period size: 241 Copynumber: 2.2 Consensus size: 241
3096414 ATTAGTAATA
3096424 ATTATTTTA-AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAA
1 ATTA-TTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAA
*
3096488 ATTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTGATTATTTA
65 ATTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTGATTATTAA
3096553 GAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTT
130 GAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTT
3096618 TATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTG
195 TATAGTATCATATATTATGA-TTTAAGTAAATTCATATAAGAATATTG
3096666 ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAA
1 ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAA
3096731 TTATATTTTATAGTATCATATATTATGATTTT-AGTAAATTCATATAAGAATATTGATTATTAAG
66 TTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTGATTATTAAG
3096795 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
131 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT
*
3096859 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTG
195 TATAGTATCATATATTATGATTTAAGTAAATTCATATAAGAATATTG
* *
3096906 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT
3096965 GTTAAAATAT
Statistics
Matches: 293, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
240 83 0.28
241 116 0.40
242 94 0.32
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (241 bp):
ATTATTTAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAA
TTATATTTTATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTGATTATTAAG
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTAAGTAAATTCATATAAGAATATTG
Found at i:3096944 original size:18 final size:17
Alignment explanation
Indices: 3096916--3096950 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3096906 ATTATTAAGA
*
3096916 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3096933 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3096951 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3097195 original size:45 final size:40
Alignment explanation
Indices: 3097096--3097204 Score: 103
Period size: 45 Copynumber: 2.6 Consensus size: 40
3097086 TTTTCCATTA
*
3097096 TGCTATTACACCTCTATTCCATT-CAACCAAATACAAGAT
1 TGCTATTACACCTCTATTCCATTACAACCAAAAACAAGAT
* ** **
3097135 TACTATTACGTCTCTATTCCATTACATTCAACCAAACAATTGATT
1 TGCTATTACACCTCTATTCCATTACAACCAA--AAACAA--GA-T
*
3097180 TGCTATTACACCTCTATTTCATTAC
1 TGCTATTACACCTCTATTCCATTAC
3097205 GCCTCTATTC
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
39 20 0.37
40 5 0.09
42 5 0.09
44 2 0.04
45 22 0.41
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (40 bp):
TGCTATTACACCTCTATTCCATTACAACCAAAAACAAGAT
Found at i:3098096 original size:5 final size:5
Alignment explanation
Indices: 3098086--3098112 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3098076 TTTTTTCTTG
3098086 GATTT GATTT GATTT GATTT GATTT GA
1 GATTT GATTT GATTT GATTT GATTT GA
3098113 CTGTGTCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (5 bp):
GATTT
Found at i:3108791 original size:24 final size:24
Alignment explanation
Indices: 3108764--3108819 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
3108754 ATAAACACCA
*
3108764 AAAAATATTTTAAAATTAAAAATT
1 AAAAATATTTTAAAATTAAAAAAT
3108788 AAAAATATTTTAAAATTAAAAAAT
1 AAAAATATTTTAAAATTAAAAAAT
3108812 AAAAATAT
1 AAAAATAT
3108820 ATATTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AAAAATATTTTAAAATTAAAAAAT
Found at i:3110889 original size:12 final size:12
Alignment explanation
Indices: 3110872--3110897 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3110862 TCCATATGAG
3110872 ATGAATAAGAAT
1 ATGAATAAGAAT
3110884 ATGAATAAGAAT
1 ATGAATAAGAAT
3110896 AT
1 AT
3110898 CAAGCTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (12 bp):
ATGAATAAGAAT
Found at i:3123368 original size:2 final size:2
Alignment explanation
Indices: 3123363--3123398 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3123353 TATATATTAT
*
3123363 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3123399 TGAGGAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3125757 original size:22 final size:23
Alignment explanation
Indices: 3125729--3125772 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3125719 AGCTATCTAC
* *
3125729 AAAATCA-ATTTTTTAAGATTAT
1 AAAATCATATCTTCTAAGATTAT
3125751 AAAATCATATCTTCTAAGATTA
1 AAAATCATATCTTCTAAGATTA
3125773 CAAGTCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (23 bp):
AAAATCATATCTTCTAAGATTAT
Found at i:3128155 original size:13 final size:15
Alignment explanation
Indices: 3128137--3128169 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3128127 TAATTTCTTG
3128137 TATTTG-TTCT-TTT
1 TATTTGTTTCTGTTT
3128150 TATTTGTTTCTGTTT
1 TATTTGTTTCTGTTT
3128165 TATTT
1 TATTT
3128170 TGTCACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 4 0.22
15 8 0.44
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (15 bp):
TATTTGTTTCTGTTT
Found at i:3140629 original size:75 final size:75
Alignment explanation
Indices: 3140504--3140650 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 75
3140494 GATGAAAAGC
*
3140504 TTGGGGAAGTATCCTAGGTAGCGCATCATTTAAAAATTGTTTTACGTTTAACCACTCGATTTTTT
1 TTGGGGAAGTATCCTAGGTAGCGCATCATTTAAAAATTCTTTTACGTTTAACCACTCGATTTTTT
3140569 ATCTTAGAGG
66 ATCTTAGAGG
* * * *
3140579 TTGGGGAAGTATCCTAGGTAGCTCATCATTTAAAAATTCTTTTCCTTTTAACCACTCGGTTTTTT
1 TTGGGGAAGTATCCTAGGTAGCGCATCATTTAAAAATTCTTTTACGTTTAACCACTCGATTTTTT
3140644 ATCTTAG
66 ATCTTAG
3140651 TTGTTTGTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (75 bp):
TTGGGGAAGTATCCTAGGTAGCGCATCATTTAAAAATTCTTTTACGTTTAACCACTCGATTTTTT
ATCTTAGAGG
Found at i:3148850 original size:22 final size:21
Alignment explanation
Indices: 3148825--3148872 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
3148815 AAATTCATAA
3148825 TTATTCAAATTAAAATTTATTT
1 TTATTCAAATTAAAA-TTATTT
* * *
3148847 TTATTTAATTTATAATTATTT
1 TTATTCAAATTAAAATTATTT
3148868 TTATT
1 TTATT
3148873 TTTTATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTCAAATTAAAATTATTT
Found at i:3148865 original size:21 final size:19
Alignment explanation
Indices: 3148841--3148881 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
3148831 AAATTAAAAT
3148841 TTATTTTTATTTAATTTATAA
1 TTATTTTTATTT--TTTATAA
3148862 TTATTTTTATTTTTTATAA
1 TTATTTTTATTTTTTATAA
3148881 T
1 T
3148882 ATAAACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTTTATTTTTTATAA
Found at i:3156291 original size:46 final size:46
Alignment explanation
Indices: 3156223--3156468 Score: 336
Period size: 46 Copynumber: 5.6 Consensus size: 46
3156213 TTTGAGTACT
* *
3156223 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTA
* *
3156269 CCTGATCAAGTGACAAAATGATAAGTGGTAGCTCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTA
*
3156315 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTA
*
3156361 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CT---T---C--G
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTA
3156398 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTC-TAGCTACACTTA
*
3156444 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
3156469 ATCATACGTA
Statistics
Matches: 180, Mismatches: 11, Indels: 20
0.85 0.05 0.09
Matches are distributed among these distances:
37 33 0.18
38 1 0.01
39 1 0.01
41 1 0.01
42 1 0.01
44 13 0.07
45 6 0.03
46 124 0.69
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTAGCTACACTTA
Found at i:3156403 original size:37 final size:37
Alignment explanation
Indices: 3156361--3156432 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
3156351 GCTACACTTA
3156361 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTCG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTCG
3156398 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTT
3156433 AGCTACACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (37 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTCG
Found at i:3156407 original size:83 final size:81
Alignment explanation
Indices: 3156315--3156468 Score: 272
Period size: 83 Copynumber: 1.9 Consensus size: 81
3156305 GCTACACTTA
* *
3156315 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATC-AGGGAC-AAGT
3156380 GATAAGTGGTAGCCTTCG
64 GATAAGTGGTAGCCTTCG
3156398 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAGGGACAAGTGA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAGGGACAAGTGA
3156463 TAAGTG
66 TAAGTG
3156469 ATCATACGTA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
81 12 0.17
82 5 0.07
83 52 0.75
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (81 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAGGGACAAGTGA
TAAGTGGTAGCCTTCG
Found at i:3157106 original size:26 final size:27
Alignment explanation
Indices: 3157077--3157144 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 27
3157067 ATTTTCCATG
3157077 TCATATTTTA-GTATATCAAA-TAATT
1 TCATATTTTATGTATATCAAATTAATT
* *
3157102 ATCAT-TTCTATGTATTTCAAATTTAATT
1 -TCATATTTTATGTATATCAAA-TTAATT
3157130 TCATGATTTTATGTA
1 TCAT-ATTTTATGTA
3157145 CTTATCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 4 0.12
26 13 0.38
27 4 0.12
28 5 0.15
29 8 0.24
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (27 bp):
TCATATTTTATGTATATCAAATTAATT
Found at i:3161920 original size:22 final size:24
Alignment explanation
Indices: 3161870--3161920 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
3161860 TTGCAATGCT
3161870 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
3161895 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
3161916 TTTAT
1 TTTAT
3161921 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:3170330 original size:17 final size:17
Alignment explanation
Indices: 3170308--3170340 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3170298 GTAAGCAATC
3170308 ATCGCATTTTTTTTACT
1 ATCGCATTTTTTTTACT
3170325 ATCGCATTTTTTTTAC
1 ATCGCATTTTTTTTAC
3170341 CAACTGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.58
Consensus pattern (17 bp):
ATCGCATTTTTTTTACT
Found at i:3190901 original size:21 final size:21
Alignment explanation
Indices: 3190858--3190903 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3190848 ATACTTAATT
* *
3190858 TTAATTAATAATTTATATTTA
1 TTAATTAATAATTAAAATTTA
3190879 TTAATTAATAA-TAAAATTATA
1 TTAATTAATAATTAAAATT-TA
3190900 TTAA
1 TTAA
3190904 AATTTACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATTAATAATTAAAATTTA
Found at i:3191145 original size:2 final size:2
Alignment explanation
Indices: 3191138--3191174 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3191128 CACCTAATTA
*
3191138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3191175 TGTGAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3192931 original size:18 final size:18
Alignment explanation
Indices: 3192893--3192931 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3192883 ATCATCCATT
*
3192893 TCAATATATCATTATATA
1 TCAATATATCATTATACA
3192911 TCAATATATCA-TATACCA
1 TCAATATATCATTATA-CA
3192929 TCA
1 TCA
3192932 TTTTCATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (18 bp):
TCAATATATCATTATACA
Found at i:3207682 original size:20 final size:20
Alignment explanation
Indices: 3207659--3207704 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3207649 TGTTAATATT
3207659 TTGTTA-TTAATTCAAATAGG
1 TTGTTACTT-ATTCAAATAGG
* *
3207679 TTGTTACTTGTTTAAATAGG
1 TTGTTACTTATTCAAATAGG
3207699 TTGTTA
1 TTGTTA
3207705 AGATTTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.50
Consensus pattern (20 bp):
TTGTTACTTATTCAAATAGG
Found at i:3209315 original size:13 final size:14
Alignment explanation
Indices: 3209286--3209319 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3209276 ACAATTACTT
3209286 TATTCAAAAAAACA
1 TATTCAAAAAAACA
*
3209300 TATTCAAAATAA-A
1 TATTCAAAAAAACA
3209313 TATTCAA
1 TATTCAA
3209320 CATATTACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (14 bp):
TATTCAAAAAAACA
Found at i:3211745 original size:11 final size:12
Alignment explanation
Indices: 3211729--3211781 Score: 58
Period size: 11 Copynumber: 4.7 Consensus size: 12
3211719 TTAAATAGGG
3211729 ATTTGAGA-GAA
1 ATTTGAGAGGAA
3211740 ATTTGAGAGGAA
1 ATTTGAGAGGAA
* *
3211752 A-TTAAGAGCAA
1 ATTTGAGAGGAA
3211763 A-TTGAGAGGAA
1 ATTTGAGAGGAA
*
3211774 ATTAGAGA
1 ATTTGAGA
3211782 AAGGATTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 26 0.74
12 9 0.26
ACGTcount: A:0.47, C:0.02, G:0.28, T:0.23
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:3211767 original size:22 final size:22
Alignment explanation
Indices: 3211734--3211783 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
3211724 TAGGGATTTG
3211734 AGAGAAATTTGAGAGGAAATTA
1 AGAGAAATTTGAGAGGAAATTA
3211756 AGAGCAAA-TTGAGAGGAAATT-
1 AGAG-AAATTTGAGAGGAAATTA
3211777 AGAGAAA
1 AGAGAAA
3211784 GGATTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.11
21 4 0.15
22 17 0.63
23 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.28, T:0.18
Consensus pattern (22 bp):
AGAGAAATTTGAGAGGAAATTA
Found at i:3218070 original size:23 final size:24
Alignment explanation
Indices: 3218025--3218070 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3218015 TATAAAAAAT
* * *
3218025 AAATTATTTACTTAAATGTATTTG
1 AAATTATTTAATAAAATGAATTTG
3218049 AAATTATTTAATAAAAT-AATTT
1 AAATTATTTAATAAAATGAATTT
3218071 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTATTTAATAAAATGAATTTG
Found at i:3218482 original size:6 final size:6
Alignment explanation
Indices: 3218471--3218496 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3218461 CCCCTCCTTG
3218471 AGTCTC AGTCTC AGTCTC AGTCTC AG
1 AGTCTC AGTCTC AGTCTC AGTCTC AG
3218497 ATTTACCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (6 bp):
AGTCTC
Found at i:3223823 original size:29 final size:31
Alignment explanation
Indices: 3223788--3223857 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 31
3223778 ACTAAAAATT
**
3223788 TATTTTAAAAATTAAAAA-AAATTTAAAAA-
1 TATTTTAAAAATTAAAAAGAAATAAAAAAAG
*
3223817 TATTTT-AAAATTAAAAAGTAATAAAAAAAG
1 TATTTTAAAAATTAAAAAGAAATAAAAAAAG
3223847 TATTTTAAAAA
1 TATTTTAAAAA
3223858 AATTTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.31
29 14 0.40
30 6 0.17
31 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (31 bp):
TATTTTAAAAATTAAAAAGAAATAAAAAAAG
Found at i:3223885 original size:18 final size:17
Alignment explanation
Indices: 3223851--3223884 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3223841 AAAAAGTATT
3223851 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
3223868 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
3223885 AATAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:3223897 original size:19 final size:17
Alignment explanation
Indices: 3223852--3223890 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
3223842 AAAAGTATTT
*
3223852 TAAAAAAATTTTAAAAT
1 TAAAAAAATTTTAAAAA
3223869 TAAAAAAATTTTAAAAAA
1 TAAAAAAATTTT-AAAAA
3223887 TAAA
1 TAAA
3223891 TATAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAAATTTTAAAAA
Found at i:3232307 original size:125 final size:124
Alignment explanation
Indices: 3232084--3232358 Score: 415
Period size: 125 Copynumber: 2.2 Consensus size: 124
3232074 TTCCTCTCAA
* * * * *
3232084 TTTCCAGGACCCACTATAGCAAAAGCGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAAT
1 TTTCCAGGACCTACTATAGCAAAAGCGCGTCCACGAGGCCACGATTTCACAAATTATTATCAAAC
* * *
3232149 AACATCCTGCTATAAGTGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATT
66 AACATCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATT
*
3232208 TATTCCAGGACCTACTATAGCAAAAGCGCGTCCACGAGGCCGCGATTTCACAAATTATTATCAAA
1 T-TTCCAGGACCTACTATAGCAAAAGCGCGTCCACGAGGCCACGATTTCACAAATTATTATCAAA
* *
3232273 CAGCATCCTGCTAGAAGCGATTTTATACTATTTGCTTAGAAACATCAACTCGAAATTATT
65 CAACATCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATT
* * *
3232333 TTTTCAGGACCTACTGTAGTAAAAGC
1 TTTCCAGGACCTACTATAGCAAAAGC
3232359 ACGTAAACGT
Statistics
Matches: 136, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
124 23 0.17
125 113 0.83
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (124 bp):
TTTCCAGGACCTACTATAGCAAAAGCGCGTCCACGAGGCCACGATTTCACAAATTATTATCAAAC
AACATCCTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATT
Found at i:3233515 original size:10 final size:9
Alignment explanation
Indices: 3233476--3233667 Score: 88
Period size: 10 Copynumber: 20.0 Consensus size: 9
3233466 ACATGTGGCA
*
3233476 AAAAATGAT
1 AAAAATTAT
3233485 AAAAA--AT
1 AAAAATTAT
*
3233492 AAAAATCAAT
1 AAAAAT-TAT
*
3233502 AAAAGTTAT
1 AAAAATTAT
3233511 AAAAATTAT
1 AAAAATTAT
3233520 AAAAATTATT
1 AAAAATTA-T
*
3233530 AAAATTTAAT
1 AAAAATT-AT
*
3233540 AAAATAATAT
1 AAAA-ATTAT
*
3233550 AAAAATAATT
1 AAAAATTA-T
**
3233560 AAATTTTATT
1 AAAAATTA-T
*
3233570 AAAAATTAG
1 AAAAATTAT
3233579 AAAATATTTTAT
1 AAAA-A--TTAT
3233591 AAAAATCGTA-
1 AAAAAT--TAT
3233601 AAAAATTA-
1 AAAAATTAT
*
3233609 CAAAATATAT
1 AAAAAT-TAT
*
3233619 AGAAATATAT
1 AAAAAT-TAT
3233629 AAATAAATTAT
1 -AA-AAATTAT
3233640 AAAAAATGTA-
1 -AAAAAT-TAT
3233650 AAAAATTAT
1 AAAAATTAT
*
3233659 AAAAGTTAT
1 AAAAATTAT
3233668 CATACAGGAA
Statistics
Matches: 145, Mismatches: 20, Indels: 36
0.72 0.10 0.18
Matches are distributed among these distances:
7 7 0.05
8 9 0.06
9 46 0.32
10 58 0.40
11 14 0.10
12 11 0.08
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3233521 original size:18 final size:18
Alignment explanation
Indices: 3233476--3233667 Score: 88
Period size: 19 Copynumber: 10.0 Consensus size: 18
3233466 ACATGTGGCA
*
3233476 AAAAATGATAAAAA--AT
1 AAAAATTATAAAAATTAT
* *
3233492 AAAAATCAATAAAAGTTAT
1 AAAAAT-TATAAAAATTAT
3233511 AAAAATTATAAAAATTATT
1 AAAAATTATAAAAATTA-T
* *
3233530 AAAATTTAATAAAATAATAT
1 AAAAATT-ATAAAA-ATTAT
* **
3233550 AAAAATAATTAAATTTTATT
1 AAAAATTA-TAAAAATTA-T
*
3233570 AAAAATTAGAAAATATTTTAT
1 AAAAATTATAAAA-A--TTAT
3233591 AAAAATCGTA-AAAAATTA-
1 AAAAAT--TATAAAAATTAT
* *
3233609 CAAAATATATAGAAATATAT
1 AAAAAT-TATAAAAAT-TAT
3233629 AAATAAATTATAAAAAATGTA-
1 -AA-AAATTAT-AAAAAT-TAT
*
3233650 AAAAATTATAAAAGTTAT
1 AAAAATTATAAAAATTAT
3233668 CATACAGGAA
Statistics
Matches: 134, Mismatches: 22, Indels: 38
0.69 0.11 0.20
Matches are distributed among these distances:
16 6 0.04
17 10 0.07
18 24 0.18
19 33 0.25
20 26 0.19
21 15 0.11
22 18 0.13
23 2 0.01
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (18 bp):
AAAAATTATAAAAATTAT
Found at i:3234428 original size:3 final size:3
Alignment explanation
Indices: 3234420--3234450 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3234410 GAACCACCCT
3234420 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3234451 CATCAAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3252622 original size:24 final size:24
Alignment explanation
Indices: 3252602--3252647 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3252592 AAGATTTAGT
* *
3252602 ATTTATGAGTATAATATATTTATC
1 ATTTATGAGCACAATATATTTATC
*
3252626 ATTTATTAGCACAATATATTTA
1 ATTTATGAGCACAATATATTTA
3252648 ACTTTGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (24 bp):
ATTTATGAGCACAATATATTTATC
Found at i:3262289 original size:15 final size:16
Alignment explanation
Indices: 3262264--3262293 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3262254 GGCCCGTTTC
3262264 TATTATTTTAATTTAA
1 TATTATTTTAATTTAA
3262280 TATT-TTTTAATTTA
1 TATTATTTTAATTTA
3262294 TTAACCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTATTTTAATTTAA
Found at i:3263193 original size:30 final size:30
Alignment explanation
Indices: 3263136--3263193 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3263126 ATAGATTTAG
* * * *
3263136 TCTTAATACTAATCTATTTTATCAATTTCA
1 TCTTAATACTAAACAATTTAATAAATTTCA
*
3263166 TCTTAATTCTAAACAATTTAATAAATTT
1 TCTTAATACTAAACAATTTAATAAATTT
3263194 AATCGAGTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (30 bp):
TCTTAATACTAAACAATTTAATAAATTTCA
Found at i:3269632 original size:33 final size:34
Alignment explanation
Indices: 3269589--3269655 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 34
3269579 TGGTAAGGCC
*
3269589 TCGTAATCACCCAATTAATCTTATTCATTTTTAT
1 TCGTAATCACCCAATTAATCTTATTCATTGTTAT
3269623 TCGT-ATCACCCAATTAATCTTATTCATTGTTAT
1 TCGTAATCACCCAATTAATCTTATTCATTGTTAT
3269656 CGTGTCTGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.46
Consensus pattern (34 bp):
TCGTAATCACCCAATTAATCTTATTCATTGTTAT
Found at i:3281166 original size:24 final size:24
Alignment explanation
Indices: 3281139--3281191 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
3281129 TCAGAAAAGC
3281139 TGTTGAGTCATGTCCTTTAAAGTT
1 TGTTGAGTCATGTCCTTTAAAGTT
3281163 TGTTGAGTCATGTCCTTTAAAGTT
1 TGTTGAGTCATGTCCTTTAAAGTT
3281187 TGTTG
1 TGTTG
3281192 TCCTTTATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.19, C:0.11, G:0.23, T:0.47
Consensus pattern (24 bp):
TGTTGAGTCATGTCCTTTAAAGTT
Found at i:3281278 original size:24 final size:24
Alignment explanation
Indices: 3281251--3281315 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
3281241 TTATCTTTTG
*
3281251 TTAAAGTTTGTTGAGTCATGTCCT
1 TTAAAGTTTGATGAGTCATGTCCT
* *
3281275 TTAAAGTTTGCTGAGTAATGTCCT
1 TTAAAGTTTGATGAGTCATGTCCT
3281299 TT-AAGTTTGATGAGTCA
1 TTAAAGTTTGATGAGTCA
3281316 GGTAAAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 13 0.35
24 24 0.65
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.43
Consensus pattern (24 bp):
TTAAAGTTTGATGAGTCATGTCCT
Found at i:3284664 original size:594 final size:594
Alignment explanation
Indices: 3283525--3284715 Score: 1870
Period size: 594 Copynumber: 2.0 Consensus size: 594
3283515 GATTATGCAA
* *
3283525 CCGAGATGGAAAAGATACAGGCTGCTCAAGCCTATAAACTACAACTTATAAGGAGTACTTATGCT
1 CCGACATGGAAAAGATACAGGCTACTCAAGCCTATAAACTACAACTTATAAGGAGTACTTATGCT
* * *
3283590 GGATTCCAATAATAATAGAGTCCACTTTATATACCTGCCCTAATTGAGTGATTTGCAATGTGCCT
66 GGATTCCAATAATAATAGAGTCCACTTTATATACCTGCCCTAACTAAGTGATTTGCAATGTGCCC
* * * *
3283655 GTTCCTATAGCAAGGGTCCGATAGTACTAGCGACGCTATATCGTGAGCTTTGTCAGGGGAAAGGC
131 GTTCCTATAGCAAGGGTCCAACAGTACTAGCGACGCTATATCGTGAACTTTGTCAGGGGAAAAGC
* * *
3283720 GTAGAATTGTCGATATAGATGGTTGTTTGATATTGATACAATCTTGAGTACTATACAGGAAGCCA
196 ATAGAATTGTCGATATAGATGGTTGTTTGATACTGATACAATCTTGAGCACTATACAGGAAGCCA
* * *
3283785 TTTCTAGCATCAGTGGGTTATCAAGTACATGTGTTCCCACTTGTGAATATGTAAAAAAAAAATTA
261 TTTCTAGCATCAGTGGGTCATCAAGTACATGTGTTCCCACTTGCGAATATGTAAAAAAAAAATAA
*
3283850 AACTTTGATCAATATTTCTTTCACGAAAATATTTTCTAAAGAGCTTAGTTTATATTTTAGATGGA
326 AACTTGGATCAATATTTCTTTCACGAAAATATTTTCTAAAGAGCTTAGTTTATATTTTAGATGGA
* *
3283915 ATATTTGTCCGAACATTGGGAAGTCAAAAACTCTAATTGTATACCGACAGATGATCGAGGCATAC
391 ATACTTGTCCGAACATTGGGAAGTCAAAAACTCTAATTGTATACCAACAGATGATCGAGGCATAC
* * *
3283980 GTCGGGGATAGGGTAATTTATTTTCAAAAAATTAAATTATATTAATGTCATGTAATTAGTTTATT
456 GTCGGGGATAGGGTAATTTATTATCAAAAAATTAAATTATATTAATGTCATGTAATCAATTTATT
* *
3284045 TATTAAATTACATTGTAATTAGTATTTTAATCATGTTTTTAATTATGTAGTTCGTGTGGATGTTG
521 TATTAAATTACATTGTAATTAGTATTTTAATCATATGTTTAATTATGTAGTTCGTGTGGATGTTG
3284110 TATATCACG
586 TATATCACG
* * * * * *
3284119 CCGACATGGAGAAGATACAGGCTACTCGAGCCTATATACTACAACTTATAGGGGGTACTTATGTT
1 CCGACATGGAAAAGATACAGGCTACTCAAGCCTATAAACTACAACTTATAAGGAGTACTTATGCT
* *
3284184 GGATTCCAATAATAATAGAGTCCACTTTATATACCTGCCTTTACTAAGTGATTTGCAATGTGCCC
66 GGATTCCAATAATAATAGAGTCCACTTTATATACCTGCCCTAACTAAGTGATTTGCAATGTGCCC
* ** ** * *
3284249 GTTCTTATAGCTGGGGTTTAACAGTACTAGCGATGCTATATCGTGAACTTTGTCGGGGGACAAAG
131 GTTCCTATAGCAAGGGTCCAACAGTACTAGCGACGCTATATCGTGAACTTTGTCAGGGGA-AAAG
* * *
3284314 CATAGAATTGTCGATATAGGTGGTT-TTCTGATACT-ACTACAATCTTGAGCGCTATACAGGATG
195 CATAGAATTGTCGATATAGATGGTTGTT-TGATACTGA-TACAATCTTGAGCACTATACAGGAAG
*
3284377 CCTTTTCTAGCATCAGTGGGTCATCAAGTACATGTGTTCCCACTTGCGAATATGTGAAAAAAAAA
258 CCATTTCTAGCATCAGTGGGTCATCAAGTACATGTGTTCCCACTTGCGAATATGT-AAAAAAAAA
* *
3284442 A-AAAACTTGGATCAATATTTTTTTCACGAAAATATTTTCTAAAGAGTTTAGTTTATATTTTAGA
322 ATAAAACTTGGATCAATATTTCTTTCACGAAAATATTTTCTAAAGAGCTTAGTTTATATTTTAGA
3284506 TGGAATACTTGTCCGAACATTGGGAAGTCAGAAAA-TCTAATTGTATACCAACAGATGATCGAGG
387 TGGAATACTTGTCCGAACATTGGGAAGTCA-AAAACTCTAATTGTATACCAACAGATGATCGAGG
3284570 CATACGTC-GGGATAGGGTAATTTATTATCAAAAAATTAAATTATATTAATGTCATGTAATCAAT
451 CATACGTCGGGGATAGGGTAATTTATTATCAAAAAATTAAATTATATTAATGTCATGTAATCAAT
* * *
3284634 TTATTTATTAAATTACGTTGTAATTAGTATTTTAATCATATGTTTAATTGTGTAGTTTGTGTGGA
516 TTATTTATTAAATTACATTGTAATTAGTATTTTAATCATATGTTTAATTATGTAGTTCGTGTGGA
*
3284699 TGTTGTATATCATG
581 TGTTGTATATCACG
3284713 CCG
1 CCG
3284716 GATATTACTT
Statistics
Matches: 544, Mismatches: 48, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
594 299 0.55
595 231 0.42
596 14 0.03
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (594 bp):
CCGACATGGAAAAGATACAGGCTACTCAAGCCTATAAACTACAACTTATAAGGAGTACTTATGCT
GGATTCCAATAATAATAGAGTCCACTTTATATACCTGCCCTAACTAAGTGATTTGCAATGTGCCC
GTTCCTATAGCAAGGGTCCAACAGTACTAGCGACGCTATATCGTGAACTTTGTCAGGGGAAAAGC
ATAGAATTGTCGATATAGATGGTTGTTTGATACTGATACAATCTTGAGCACTATACAGGAAGCCA
TTTCTAGCATCAGTGGGTCATCAAGTACATGTGTTCCCACTTGCGAATATGTAAAAAAAAAATAA
AACTTGGATCAATATTTCTTTCACGAAAATATTTTCTAAAGAGCTTAGTTTATATTTTAGATGGA
ATACTTGTCCGAACATTGGGAAGTCAAAAACTCTAATTGTATACCAACAGATGATCGAGGCATAC
GTCGGGGATAGGGTAATTTATTATCAAAAAATTAAATTATATTAATGTCATGTAATCAATTTATT
TATTAAATTACATTGTAATTAGTATTTTAATCATATGTTTAATTATGTAGTTCGTGTGGATGTTG
TATATCACG
Found at i:3287440 original size:33 final size:33
Alignment explanation
Indices: 3287403--3287476 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
3287393 TGGTCCAACC
** ** *
3287403 ATGGTCTTATGTTTAATGTGCCATAACCCAGTT
1 ATGGTCTTATCATTAAAATGCCATAACCCAGCT
* *
3287436 ATGGTCTTTTCATTAAAATGCCATAGCCCAGCT
1 ATGGTCTTATCATTAAAATGCCATAACCCAGCT
3287469 ATGGTCTT
1 ATGGTCTT
3287477 GAGTGACAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (33 bp):
ATGGTCTTATCATTAAAATGCCATAACCCAGCT
Found at i:3292165 original size:14 final size:15
Alignment explanation
Indices: 3292139--3292168 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3292129 TGTTAGTTTT
3292139 CTGGGGAAAAAAAAG
1 CTGGGGAAAAAAAAG
3292154 CTGGGGAAAAAAAAG
1 CTGGGGAAAAAAAAG
3292169 TAAAAGTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.33, T:0.07
Consensus pattern (15 bp):
CTGGGGAAAAAAAAG
Found at i:3301052 original size:9 final size:9
Alignment explanation
Indices: 3301040--3301095 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
3301030 TTTTAGGTAA
3301040 TTTAAAATT
1 TTTAAAATT
3301049 TTTAAAA-T
1 TTTAAAATT
3301057 TTTAAAATT
1 TTTAAAATT
* ** *
3301066 TAATGTAATCC
1 T-TTAAAAT-T
3301077 TTTAAAATT
1 TTTAAAATT
3301086 TTTAAAATT
1 TTTAAAATT
3301095 T
1 T
3301096 AAAATTTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
8 8 0.22
9 19 0.53
10 8 0.22
11 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (9 bp):
TTTAAAATT
Found at i:3301061 original size:8 final size:8
Alignment explanation
Indices: 3301040--3301106 Score: 50
Period size: 7 Copynumber: 7.9 Consensus size: 8
3301030 TTTTAGGTAA
3301040 TTTAAAATT
1 TTTAAAA-T
3301049 TTTAAAAT
1 TTTAAAAT
3301057 TTTAAAA-
1 TTTAAAAT
3301064 TTTAATGTAAT
1 TTTAA---AAT
3301075 CCTTTAAAATT
1 --TTTAAAA-T
3301086 TTTAAAA-
1 TTTAAAAT
3301093 TTTAAAA-
1 TTTAAAAT
3301100 TTTAAAA
1 TTTAAAA
3301107 CCACCAGAGG
Statistics
Matches: 51, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
7 19 0.37
8 8 0.16
9 14 0.27
10 4 0.08
11 1 0.02
13 5 0.10
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (8 bp):
TTTAAAAT
Found at i:3306579 original size:12 final size:12
Alignment explanation
Indices: 3306562--3306594 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3306552 GAGATTAATT
3306562 TAATTTAAATAA
1 TAATTTAAATAA
*
3306574 TAATTTTAATAA
1 TAATTTAAATAA
3306586 -AATTTAAAT
1 TAATTTAAAT
3306595 GTATATTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATTTAAATAA
Found at i:3312733 original size:64 final size:65
Alignment explanation
Indices: 3312630--3312760 Score: 221
Period size: 64 Copynumber: 2.0 Consensus size: 65
3312620 TCCACGATGG
3312630 AACAGGAAAAAATGGATGACACCCATTCTTGATTACAATGTTC-TTTAAGGATAATTCGACAAAC
1 AACAGGAAAAAATGGATGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAAC
* *
3312694 AACAGGAAAAAAT-GATTGACACCCATTCTTGATTGCAATGTTCTTTTAGGGATAATTCGACAAA
1 AACAGGAAAAAATGGA-TGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAA
3312758 C
65 C
3312759 AA
1 AA
3312761 GGAGGAAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
63 2 0.03
64 39 0.62
65 22 0.35
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (65 bp):
AACAGGAAAAAATGGATGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAAC
Found at i:3314396 original size:18 final size:17
Alignment explanation
Indices: 3314363--3314399 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3314353 TTCGCTGCGA
3314363 TATTTTTTATTCATATT
1 TATTTTTTATTCATATT
*
3314380 TATTTTTTCATTTATATT
1 TATTTTTT-ATTCATATT
3314398 TA
1 TA
3314400 ATAGTCGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTTTATTCATATT
Found at i:3316061 original size:19 final size:19
Alignment explanation
Indices: 3316039--3316083 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3316029 TGTTAAATTC
*
3316039 ATGAATTATATATTGTA-TG
1 ATGAAATATATATT-TATTG
3316058 ATGAAATATATATTTATTG
1 ATGAAATATATATTTATTG
3316077 ATGAAAT
1 ATGAAAT
3316084 GAGAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (19 bp):
ATGAAATATATATTTATTG
Found at i:3316231 original size:46 final size:46
Alignment explanation
Indices: 3316164--3316319 Score: 273
Period size: 46 Copynumber: 3.5 Consensus size: 46
3316154 TGATCAGTGA
3316164 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
3316210 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
3316256 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
3316301 C-AGCGAC-AAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
3316320 ATCATACGTA
Statistics
Matches: 108, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
43 12 0.11
44 5 0.05
45 19 0.18
46 72 0.67
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:3317528 original size:16 final size:16
Alignment explanation
Indices: 3317507--3317545 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
3317497 TTAATTTAGT
3317507 GACTGCTGCGCAGGTG
1 GACTGCTGCGCAGGTG
3317523 GACTGCTGCGCAGGTG
1 GACTGCTGCGCAGGTG
3317539 GACTGCT
1 GACTGCT
3317546 TTATTGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.41, T:0.21
Consensus pattern (16 bp):
GACTGCTGCGCAGGTG
Found at i:3318333 original size:5 final size:5
Alignment explanation
Indices: 3318325--3318370 Score: 85
Period size: 5 Copynumber: 9.4 Consensus size: 5
3318315 GTTAAGTAAA
3318325 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-AT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
3318371 AATAAGAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.10
5 37 0.90
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:3319321 original size:41 final size:40
Alignment explanation
Indices: 3319276--3319411 Score: 118
Period size: 40 Copynumber: 3.5 Consensus size: 40
3319266 CGACCTCGAG
3319276 TCGATGAGACACTAGGTGTCAATCTATTACTTCGGATTAAT
1 TCGATGAGACACTAGGTGTCAA-CTATTACTTCGGATTAAT
* * * * *
3319317 TCGATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTAGT
1 TCGATGAGACACTAGGTGTCAACTATTACTTCGGATTAAT
** * *
3319355 T-GATGAGATGCTAAGTGTCAACTTATTACTTCGAATT-AT
1 TCGATGAGACACTAGGTGTCAAC-TATTACTTCGGATTAAT
* * *
3319394 CCGATTAGACACTGGGTG
1 TCGATGAGACACTAGGTG
3319412 CCAAACTGGT
Statistics
Matches: 71, Mismatches: 20, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
37 14 0.20
38 14 0.20
39 3 0.04
40 21 0.30
41 19 0.27
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (40 bp):
TCGATGAGACACTAGGTGTCAACTATTACTTCGGATTAAT
Found at i:3325549 original size:49 final size:49
Alignment explanation
Indices: 3325488--3325680 Score: 323
Period size: 49 Copynumber: 3.9 Consensus size: 49
3325478 ATGTGAACAT
3325488 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
3325538 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
3325587 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
3325636 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
3325681 AGAAAATGAA
Statistics
Matches: 137, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
49 133 0.97
50 4 0.03
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:3333705 original size:49 final size:49
Alignment explanation
Indices: 3333644--3333836 Score: 323
Period size: 49 Copynumber: 3.9 Consensus size: 49
3333634 ATGTGAACAT
3333644 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
3333694 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
3333743 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
3333792 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
3333837 AGAAAATGAA
Statistics
Matches: 137, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
49 133 0.97
50 4 0.03
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:3340014 original size:20 final size:20
Alignment explanation
Indices: 3339991--3340028 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3339981 TTTAATTAAT
*
3339991 TTAGCTTAATTAACTTAAAC
1 TTAGCTTAATTAAATTAAAC
*
3340011 TTAGTTTAATTAAATTAA
1 TTAGCTTAATTAAATTAA
3340029 GCTAACATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAGCTTAATTAAATTAAAC
Found at i:3346048 original size:2 final size:2
Alignment explanation
Indices: 3346041--3346096 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
3346031 GAAACGAAGC
* * * *
3346041 TA TA TA TA TA GA TA TA GA TA TA CA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3346083 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
3346097 CTGTTGGATC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:3355754 original size:38 final size:38
Alignment explanation
Indices: 3355703--3355780 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
3355693 CATCTCTTTG
3355703 AACATGGAAATTATGAAAGACCAAAAGTGAATGAAAAT
1 AACATGGAAATTATGAAAGACCAAAAGTGAATGAAAAT
3355741 AACATGGAAATTATGAAAGACCAAAAGTGAATGAAAAT
1 AACATGGAAATTATGAAAGACCAAAAGTGAATGAAAAT
3355779 AA
1 AA
3355781 AATCTCAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.56, C:0.08, G:0.18, T:0.18
Consensus pattern (38 bp):
AACATGGAAATTATGAAAGACCAAAAGTGAATGAAAAT
Done.