Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 105 of 186
Found at i:34510405 original size:9 final size:9
Alignment explanation
Indices: 34510393--34510448 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
34510383 AAAATTTAAA
34510393 AAAAATATT
1 AAAAATATT
34510402 AAAAATA-T
1 AAAAATATT
*
34510410 AAAAATTTT
1 AAAAATATT
* *
34510419 AAATAAAATA
1 AAA-AATATT
34510429 AAAAATAGTT
1 AAAAATA-TT
34510439 AAAAAT-TT
1 AAAAATATT
34510447 AA
1 AA
34510449 GTCAAGAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
8 11 0.29
9 14 0.37
10 13 0.34
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATATT
Found at i:34510407 original size:27 final size:26
Alignment explanation
Indices: 34510377--34510436 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
34510367 TTTCAATTTC
34510377 AAATAGAAAA-TTTAAAAAAAATATTAA
1 AAATAGAAAATTTTAAAAAAAATA--AA
* *
34510404 AAATATAAAAATTTTAAATAAAATAAA
1 AAATA-GAAAATTTTAAAAAAAATAAA
34510431 AAATAG
1 AAATAG
34510437 TTAAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 12 0.43
28 4 0.14
29 12 0.43
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (26 bp):
AAATAGAAAATTTTAAAAAAAATAAA
Found at i:34510426 original size:29 final size:28
Alignment explanation
Indices: 34510383--34510446 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
34510373 TTTCAAATAG
34510383 AAAA-TTTAAAAAAAATATTAAAAATA-TA
1 AAAATTTTAAAAAAAATA--AAAAATAGTA
*
34510411 AAAATTTTAAATAAAATAAAAAATAGTTA
1 AAAATTTTAAAAAAAATAAAAAATAG-TA
34510440 AAAATTT
1 AAAATTT
34510447 AAGTCAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 7 0.22
28 4 0.12
29 21 0.66
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (28 bp):
AAAATTTTAAAAAAAATAAAAAATAGTA
Found at i:34510440 original size:20 final size:18
Alignment explanation
Indices: 34510392--34510443 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
34510382 GAAAATTTAA
*
34510392 AAAAAATATTAAAAATAT
1 AAAAAATATTAAAAAAAT
*
34510410 -AAAAATTTTAAATAAAAT
1 AAAAAATATTAAA-AAAAT
34510428 AAAAAATAGTTAAAAA
1 AAAAAATA-TTAAAAA
34510444 TTTAAGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 11 0.39
18 4 0.14
19 8 0.29
20 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAAATATTAAAAAAAT
Found at i:34510447 original size:28 final size:28
Alignment explanation
Indices: 34510383--34510448 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
34510373 TTTCAAATAG
*
34510383 AAAATTTAAAAAAAATATTAAAAATATA
1 AAAATTTAAAAAAAATATAAAAAATATA
* *
34510411 AAAATTTTAAATAAA-ATAAAAAATAGTTA
1 AAAATTTAAAAAAAATATAAAAAATA--TA
34510440 AAAATTTAA
1 AAAATTTAA
34510449 GTCAAGAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 9 0.28
28 13 0.41
29 10 0.31
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAATTTAAAAAAAATATAAAAAATATA
Found at i:34514315 original size:16 final size:17
Alignment explanation
Indices: 34514284--34514316 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34514274 TTCATAAGTA
34514284 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
34514301 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
34514317 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:34514737 original size:46 final size:46
Alignment explanation
Indices: 34514602--34514738 Score: 181
Period size: 46 Copynumber: 3.0 Consensus size: 46
34514592 TTTGACATGA
* * * *
34514602 TGCCATAGTGTCTTTCAACTATGGTCTTACTA-ATTTTC-TGTCATG-T
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-ACA-TTTCATATCA-GAT
*
34514648 TGCCATGGTATCTTTCAAACATGGTCTTACACATTTCATATCAGAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAT
34514694 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGA
34514739 GAGTACACTC
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
45 6 0.07
46 76 0.93
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAT
Found at i:34516936 original size:30 final size:30
Alignment explanation
Indices: 34516869--34516936 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
34516859 CACCCTTAAA
* * *
34516869 ATATTTGCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
34516899 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
34516928 AGTATTTAC
1 A-TATTTAC
34516937 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:34519406 original size:16 final size:17
Alignment explanation
Indices: 34519375--34519407 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34519365 TTCATAAGTA
34519375 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
34519392 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
34519408 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:34519753 original size:46 final size:46
Alignment explanation
Indices: 34519693--34519961 Score: 414
Period size: 46 Copynumber: 5.8 Consensus size: 46
34519683 TTTGACATGA
* * * *
34519693 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGT
*
34519739 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
*
34519785 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* *
34519831 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
* * *
34519877 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
*
34519923 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
34519962 ATCAGAGAGC
Statistics
Matches: 213, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 4 0.02
46 209 0.98
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGT
Found at i:34526597 original size:12 final size:12
Alignment explanation
Indices: 34526580--34526610 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
34526570 CTCAAGTTTT
34526580 CACACGGCCTAG
1 CACACGGCCTAG
34526592 CACACGGCCTAG
1 CACACGGCCTAG
34526604 CACACGG
1 CACACGG
34526611 GTATATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.42, G:0.26, T:0.06
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:34533717 original size:7 final size:7
Alignment explanation
Indices: 34533707--34533733 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
34533697 GAGTTCTGGA
34533707 TTCAAGG
1 TTCAAGG
34533714 TTCAAGG
1 TTCAAGG
34533721 TTCAAGG
1 TTCAAGG
34533728 TTCAAG
1 TTCAAG
34533734 ATTCGAGTTT
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:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (7 bp):
TTCAAGG
Found at i:34533748 original size:7 final size:7
Alignment explanation
Indices: 34533738--34533776 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
34533728 TTCAAGATTC
34533738 GAGTTTG
1 GAGTTTG
34533745 GAGTTTG
1 GAGTTTG
34533752 GAGTTTAG
1 GAGTTT-G
34533760 G-GTTTG
1 GAGTTTG
*
34533766 GAGTTTA
1 GAGTTTG
34533773 GAGT
1 GAGT
34533777 AAAACAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.07
7 25 0.86
8 2 0.07
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (7 bp):
GAGTTTG
Found at i:34535151 original size:7 final size:7
Alignment explanation
Indices: 34535141--34535167 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
34535131 GAGTTCTGGA
34535141 TTCAAGG
1 TTCAAGG
34535148 TTCAAGG
1 TTCAAGG
34535155 TTCAAGG
1 TTCAAGG
34535162 TTCAAG
1 TTCAAG
34535168 ATTCGAGTTT
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:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (7 bp):
TTCAAGG
Found at i:34535182 original size:7 final size:7
Alignment explanation
Indices: 34535172--34535210 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
34535162 TTCAAGATTC
34535172 GAGTTTG
1 GAGTTTG
34535179 GAGTTTG
1 GAGTTTG
34535186 GAGTTTAG
1 GAGTTT-G
34535194 G-GTTTG
1 GAGTTTG
*
34535200 GAGTTTA
1 GAGTTTG
34535207 GAGT
1 GAGT
34535211 AAAACAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.07
7 25 0.86
8 2 0.07
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (7 bp):
GAGTTTG
Found at i:34537524 original size:27 final size:27
Alignment explanation
Indices: 34537494--34537667 Score: 160
Period size: 27 Copynumber: 6.4 Consensus size: 27
34537484 GTACGTTGCC
* **
34537494 AAGGCATTCCTTTCAGAGT-TTTCCATG
1 AAGGCATTCCTTTCAGA-TATTGCCACA
* *
34537521 AAGGCATTCCCTTT-AGAGTCTT-CCACG
1 AAGGCATT-CCTTTCAGA-TATTGCCACA
*
34537548 AAGGCATTCCCTTT-AGAGT-CTGCCACA
1 AAGGCATT-CCTTTCAGA-TATTGCCACA
*
34537575 AAGGCATTCCTTTCATATATTGCCACA
1 AAGGCATTCCTTTCAGATATTGCCACA
*
34537602 AAGGCATTCCTTTCATATATTGCCACA
1 AAGGCATTCCTTTCAGATATTGCCACA
* * * *
34537629 AAGGAATTCCTTTCATATATTTCCACT
1 AAGGCATTCCTTTCAGATATTGCCACA
34537656 AAGGCATTCCTT
1 AAGGCATTCCTT
34537668 CTCTAGCATG
Statistics
Matches: 133, Mismatches: 9, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
26 7 0.05
27 119 0.89
28 7 0.05
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (27 bp):
AAGGCATTCCTTTCAGATATTGCCACA
Found at i:34539680 original size:25 final size:26
Alignment explanation
Indices: 34539637--34539691 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
34539627 TGGTACAAAT
* *
34539637 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGATAAATATTCCA
34539663 TGATAAT-GGTTAGATAAATATTCCA
1 TGATAATGGGTTAGATAAATATTCCA
34539688 TGAT
1 TGAT
34539692 TCGCATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGATAAATATTCCA
Found at i:34548540 original size:21 final size:21
Alignment explanation
Indices: 34548496--34548545 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
34548486 TAATTATTAT
34548496 TATATAAATTAAAAAATCATAA
1 TATATAAATTAAAAAA-CATAA
*
34548518 TATATAATATTATAAAA-ATAA
1 TATATAA-ATTAAAAAACATAA
34548539 TATATAA
1 TATATAA
34548546 CCTACTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 7 0.27
23 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TATATAAATTAAAAAACATAA
Found at i:34553755 original size:24 final size:24
Alignment explanation
Indices: 34553730--34553773 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
34553720 GCATGTTATT
34553730 TTTTTGTTC-TGT-TTCTTCTTGG
1 TTTTTGTTCTTGTGTTCTTCTTGG
34553752 TTTTTGTTCTTGTGTTCTTCTT
1 TTTTTGTTCTTGTGTTCTTCTT
34553774 TTTGCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.00, C:0.14, G:0.16, T:0.70
Consensus pattern (24 bp):
TTTTTGTTCTTGTGTTCTTCTTGG
Found at i:34573553 original size:14 final size:14
Alignment explanation
Indices: 34573534--34573561 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34573524 TCTTTCCCTG
34573534 TTTTATAGATTATC
1 TTTTATAGATTATC
34573548 TTTTATAGATTATC
1 TTTTATAGATTATC
34573562 AAAGCAAGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTTATAGATTATC
Found at i:34578505 original size:25 final size:25
Alignment explanation
Indices: 34578473--34578528 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
34578463 AGGTTATTCT
* * *
34578473 AGATAATTTTCCCTAAATACTTTAC
1 AGATAATTTTCCATAAAGACCTTAC
34578498 AGATAATTTTCCATAAAGACCTTAC
1 AGATAATTTTCCATAAAGACCTTAC
34578523 AGATAA
1 AGATAA
34578529 CACGCCACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (25 bp):
AGATAATTTTCCATAAAGACCTTAC
Found at i:34579818 original size:16 final size:16
Alignment explanation
Indices: 34579794--34579842 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
34579784 CAAAACTCTA
34579794 AGGCGTACTCTTTCTT
1 AGGCGTACTCTTTCTT
*
34579810 AGTCGTACTCTTTCTT
1 AGGCGTACTCTTTCTT
*
34579826 AGGCGTAATCTTTCTT
1 AGGCGTACTCTTTCTT
34579842 A
1 A
34579843 ACTTGAAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.45
Consensus pattern (16 bp):
AGGCGTACTCTTTCTT
Found at i:34582010 original size:44 final size:42
Alignment explanation
Indices: 34581934--34582087 Score: 116
Period size: 43 Copynumber: 3.6 Consensus size: 42
34581924 TGATATGTGT
* ** *
34581934 TTTCATGTAAGACCACGTCTGGGATGTTGGCATCG-ACTTATGA
1 TTTCGTGTAAGACCACGTCTGGGACATCGGCATCGTA-TT-TGA
* *
34581977 TTTACGTGTAAGACCATGTTTGGGACATCGGCATCGTATTTGA
1 TTT-CGTGTAAGACCACGTCTGGGACATCGGCATCGTATTTGA
* * *
34582020 TTTCGTGTAAGACC-CTGTCTAGGACAGT-GGCATTGATATTTGG
1 TTTCGTGTAAGACCAC-GTCTGGGACA-TCGGCATCG-TATTTGA
* * * *
34582063 TTACATGTATGACCACGTTTGGGAC
1 TTTCGTGTAAGACCACGTCTGGGAC
34582088 GTTGGCATTG
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
42 25 0.28
43 34 0.38
44 29 0.33
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (42 bp):
TTTCGTGTAAGACCACGTCTGGGACATCGGCATCGTATTTGA
Found at i:34582052 original size:42 final size:42
Alignment explanation
Indices: 34581961--34582061 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 42
34581951 TCTGGGATGT
* *
34581961 TGGCATCG-ACTTATGATTTACGTGTAAGACCATGTTTGGGACA
1 TGGCATCGTA-TT-TGATTTACGTGTAAGACCATGTCTAGGACA
*
34582004 TCGGCATCGTATTTGATTT-CGTGTAAGACCCTGTCTAGGACA
1 T-GGCATCGTATTTGATTTACGTGTAAGACCATGTCTAGGACA
*
34582046 GTGGCATTGATATTTG
1 -TGGCATCG-TATTTG
34582062 GTTACATGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
42 26 0.52
43 14 0.28
44 9 0.18
45 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.35
Consensus pattern (42 bp):
TGGCATCGTATTTGATTTACGTGTAAGACCATGTCTAGGACA
Found at i:34582061 original size:43 final size:43
Alignment explanation
Indices: 34581939--34582045 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 43
34581929 TGTGTTTTCA
* * ** *
34581939 TGTAAGACCACGTCTGGGATGTTGGCATCG-ACTTATGATTTACG
1 TGTAAGACCATGTCTAGGACATCGGCATCGTA-TT-TGATTTACG
* *
34581983 TGTAAGACCATGTTTGGGACATCGGCATCGTATTTGATTT-CG
1 TGTAAGACCATGTCTAGGACATCGGCATCGTATTTGATTTACG
*
34582025 TGTAAGACCCTGTCTAGGACA
1 TGTAAGACCATGTCTAGGACA
34582046 GTGGCATTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 20 0.37
43 6 0.11
44 27 0.50
45 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACATCGGCATCGTATTTGATTTACG
Found at i:34593395 original size:21 final size:22
Alignment explanation
Indices: 34593359--34593409 Score: 86
Period size: 21 Copynumber: 2.3 Consensus size: 22
34593349 TTGAAAGCAA
34593359 AAATGAATAGTGTGTTTGAATAG
1 AAATGAATA-TGTGTTTGAATAG
34593382 AAATGAAT-TGTGTTTGAATAG
1 AAATGAATATGTGTTTGAATAG
34593403 AAATGAA
1 AAATGAA
34593410 AGGAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 20 0.71
23 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (22 bp):
AAATGAATATGTGTTTGAATAG
Found at i:34601400 original size:46 final size:48
Alignment explanation
Indices: 34601214--34601486 Score: 226
Period size: 46 Copynumber: 5.8 Consensus size: 48
34601204 AACGTGTAAT
* ** **
34601214 GCCGATGCCACGTCCCAGACATGGTCTTACACT-GACTAACGAAATCG-A
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTC-ATCTCGTA
* * *
34601262 GGCCGACGTCATGTCCTAGACATGGTCTTACACTAGCTCTCACATCTCTGT-
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT--CATCTC-GTA
* * *
34601313 GCCGATGCCATGCCCCAGACATGGTCTTACACT-G-GCACATCTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGTA
* * * *
34601359 GCCGGTG-CATGTCCTAGACAT-GTCTTACTCTAGCTCTCATCTC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGTA
* * * *
34601404 TGCCGATGCCATGTCCCAGACATGGTCTTGCACTGGCTCTCATAAT-GTG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-CTCGTA
34601453 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
34601487 GCACAAATGA
Statistics
Matches: 180, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
44 9 0.05
45 16 0.09
46 36 0.20
47 27 0.15
48 24 0.13
49 33 0.18
50 33 0.18
51 2 0.01
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCGTA
Found at i:34601477 original size:94 final size:95
Alignment explanation
Indices: 34601211--34601486 Score: 319
Period size: 94 Copynumber: 2.9 Consensus size: 95
34601201 CATAACGTGT
* * ** * *
34601211 AATGCCGATGCCACGTCCCAGACATGGTCTTACACTGACTAACGA-AATCGAGGCCGACGTCATG
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-ATAAT-GTGGCCGATG-CATG
34601275 TCCTAGACATGGTCTTACACTAGCTCTCACATCTC
63 TCCTAGACAT-GTCTTACACTAGCTCT-ACATCTC
** * * * * *
34601310 TGTGCCGATGCCATGCCCCAGACATGGTCTTACACTGGCACATC-T--CGTAGCCGGTGCATGTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATAATGTGGCCGATGCATGTC
*
34601372 CTAGACATGTCTTACTCTAGCTCT-CATCTC
65 CTAGACATGTCTTACACTAGCTCTACATCTC
*
34601402 AATGCCGATGCCATGTCCCAGACATGGTCTTGCACTGGCTCTCATAATGTGGCCGATGCATGTCC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCC
*
34601467 CAGACATGTCTTACACTAGC
66 TAGACATGTCTTACACTAGC
34601487 GCACAAATGA
Statistics
Matches: 148, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
91 2 0.01
92 43 0.29
94 48 0.32
95 14 0.09
96 6 0.04
99 34 0.23
100 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (95 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCATGTCC
TAGACATGTCTTACACTAGCTCTACATCTC
Found at i:34602821 original size:27 final size:27
Alignment explanation
Indices: 34602799--34603004 Score: 254
Period size: 27 Copynumber: 7.6 Consensus size: 27
34602789 TTAGTTTACC
34602799 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * * *
34602826 AAATTACCAAAATGCCCTTGGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTA
34602853 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* ** *
34602880 AAATTACTAAAATACCTTTTA-TTTATA
1 AAATTACCAAAATACC-CCTAGTTTGTA
*
34602907 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
34602934 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
34602961 AAATTATCAAAATACCCCT-GATTTGTG
1 AAATTACCAAAATACCCCTAG-TTTGTA
**
34602988 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
34603005 TCGACCTGTA
Statistics
Matches: 154, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.01
27 150 0.97
28 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTTTGTA
Found at i:34602858 original size:54 final size:54
Alignment explanation
Indices: 34602799--34603005 Score: 290
Period size: 54 Copynumber: 3.8 Consensus size: 54
34602789 TTAGTTTACC
*
34602799 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATGCCCTTGGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * **
34602853 AAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCTTTTATTTATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * *
34602907 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * **
34602961 AAATTATCAAAATACCCCT-GATTTGTGAAATTACTGAAATACCCT
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCT
34603006 CGACCTGTAA
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 1 0.01
54 134 0.99
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
Found at i:34602992 original size:81 final size:81
Alignment explanation
Indices: 34602799--34603074 Score: 288
Period size: 81 Copynumber: 3.4 Consensus size: 81
34602789 TTAGTTTACC
* * *
34602799 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATGCCCTTGGTTTATAAAATTACCAA
1 AAATTACCAAAATACCCCTGA-TTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAA
*
34602863 AATACCCCTAGTTTGTA
65 AATACCCCTGGTTTGTA
* ** * *
34602880 AAATTACTAAAATACCTTTTATTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
34602945 ATACCCCTGGTTTGTA
66 ATACCCCTGGTTTGTA
* * ** *** ***
34602961 AAATTATCAAAATACCCCTGATTTGTGAAATTACTGAAATA-CCCTCGACCTGTAAAATTATTGA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCCCT-GGTTTGTAAAATTACCAA
**
34603025 AATA-CCCTCGACTTGTA
65 AATACCCCT-GGTTTGTA
* * *
34603042 AAATTACCAAAGTACCCCTGATTTATAGAATTA
1 AAATTACCAAAATACCCCTGATTTGTAAAATTA
34603075 TCATTTTACC
Statistics
Matches: 162, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
80 8 0.05
81 153 0.94
82 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (81 bp):
AAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
ATACCCCTGGTTTGTA
Found at i:34603057 original size:27 final size:26
Alignment explanation
Indices: 34602799--34603074 Score: 228
Period size: 27 Copynumber: 10.2 Consensus size: 26
34602789 TTAGTTTACC
*
34602799 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCGA-TTTGTA
* * * *
34602826 AAATTACCAAAATGCCCTTGGTTTATA
1 AAATTACCAAAATACCC-CGATTTGTA
*
34602853 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCGA-TTTGTA
* *** *
34602880 AAATTACTAAAATACCTTTTATTTATA
1 AAATTACCAAAATACC-CCGATTTGTA
*
34602907 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCC-GATTTGTA
*
34602934 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCC-GATTTGTA
* *
34602961 AAATTATCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCC-GATTTGTA
** **
34602988 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCC-CGATTTGTA
*** *
34603015 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCC-CGATTTGTA
* *
34603042 AAATTACCAAAGTACCCCTGATTTATA
1 AAATTACCAAAATACCCC-GATTTGTA
*
34603069 GAATTA
1 AAATTA
34603075 TCATTTTACC
Statistics
Matches: 205, Mismatches: 38, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.00
27 201 0.98
28 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (26 bp):
AAATTACCAAAATACCCCGATTTGTA
Found at i:34603085 original size:81 final size:81
Alignment explanation
Indices: 34602933--34603113 Score: 188
Period size: 81 Copynumber: 2.2 Consensus size: 81
34602923 CCTGGTTTGT
* ** * * *
34602933 AAAATTACCAAAATACCC-CTGGTTTGTAAAATTATCAAAATACCCCTGATTTGTGAAATTACTG
1 AAAATTACCGAAATACCCTC-GACTTGTAAAATTACCAAAATACCCCTGATTTATGAAATTACTC
**
34602997 AAATACCCTCGACCTGT
65 AAATACCCTCGACCTAC
** *
34603014 AAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCTGATTTAT-AGAATTA-TC
1 AAAATTACCGAAATACCCTCGACTTGTAAAATTACCAAAATACCCCTGATTTATGA-AATTACTC
** *
34603077 ATTTTACCCTCGATCTAC
65 A-AATACCCTCGACCTAC
34603095 AAAATTACCGAAATACCCT
1 AAAATTACCGAAATACCCT
34603114 TGTAGGGTAG
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
80 3 0.04
81 77 0.95
82 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (81 bp):
AAAATTACCGAAATACCCTCGACTTGTAAAATTACCAAAATACCCCTGATTTATGAAATTACTCA
AATACCCTCGACCTAC
Found at i:34603130 original size:27 final size:27
Alignment explanation
Indices: 34603097--34603273 Score: 203
Period size: 27 Copynumber: 6.6 Consensus size: 27
34603087 CGATCTACAA
*
34603097 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
34603124 AAATACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*** *
34603151 AATTATAAAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
34603178 AATTACTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
34603205 -ATTACCGAAATACCCTTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
34603231 AAATACCGAAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
34603258 AATTACTGAGATACCC
1 AATTACCGAAATACCC
34603274 TTATGGGGTA
Statistics
Matches: 124, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
26 21 0.17
27 103 0.83
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:34603155 original size:54 final size:54
Alignment explanation
Indices: 34603097--34603275 Score: 225
Period size: 54 Copynumber: 3.3 Consensus size: 54
34603087 CGATCTACAA
*
34603097 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
*** * * * * * *
34603151 AATTATAAAAATACCCCTATAGGGTAGAATTACTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
* *
34603205 -ATTACCGAAATACCCTTGTAGGGTAAAAATACCGAAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
* *
34603258 AATTACTGAGATACCCTT
1 AATTACCGAAATACCCTT
34603276 ATGGGGTAAA
Statistics
Matches: 101, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
53 42 0.42
54 59 0.58
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (54 bp):
AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
Found at i:34603745 original size:6 final size:6
Alignment explanation
Indices: 34603736--34603833 Score: 85
Period size: 6 Copynumber: 15.8 Consensus size: 6
34603726 TTGCATTCAC
* * *
34603736 ATTCTG ATTCTG ACTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
*
34603786 ATTCTG ATTCTG ATTCT- ATTACCTG ATTCTG ATTTTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCT
34603834 AGTTCCGATA
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
5 6 0.08
6 56 0.75
7 7 0.09
8 6 0.08
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:34603767 original size:25 final size:25
Alignment explanation
Indices: 34603736--34603828 Score: 141
Period size: 25 Copynumber: 3.7 Consensus size: 25
34603726 TTGCATTCAC
*
34603736 ATTCTGATTCTGACTCTGTTACCTG
1 ATTCTGATTCTGATTCTGTTACCTG
* *
34603761 ATACTGATTCTGATTCTGTTACCTA
1 ATTCTGATTCTGATTCTGTTACCTG
*
34603786 ATTCTGATTCTGATTCTATTACCTG
1 ATTCTGATTCTGATTCTGTTACCTG
*
34603811 ATTCTGATTTTGATTCTG
1 ATTCTGATTCTGATTCTG
34603829 ATTCTAGTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTTACCTG
Found at i:34632617 original size:41 final size:40
Alignment explanation
Indices: 34632539--34632641 Score: 138
Period size: 41 Copynumber: 2.6 Consensus size: 40
34632529 AAACCAAGTA
* *
34632539 CCTTCGGGAATTAG-CCGGATATAGCTACTCGCTCAAATG
1 CCTTCGGGAATTAGCCCGGTTATAGCTACTCGCACAAATG
*
34632578 CCTTCGGGATTTAGCCCCGGTTATAG-TAACTCGCACAAATG
1 CCTTCGGGAATTAG-CCCGGTTATAGCT-ACTCGCACAAATG
*
34632619 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGAATTAGCCCGGTTAT
34632642 CATCCGAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
39 13 0.23
40 10 0.18
41 34 0.60
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
CCTTCGGGAATTAGCCCGGTTATAGCTACTCGCACAAATG
Found at i:34642053 original size:40 final size:40
Alignment explanation
Indices: 34641976--34642237 Score: 456
Period size: 40 Copynumber: 6.6 Consensus size: 40
34641966 AAACCAAGTA
* * *
34641976 CCTTCGGGAATTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
34642015 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
34642055 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
34642095 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
34642135 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
34642175 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
34642215 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
34642238 CATCCGAATA
Statistics
Matches: 216, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
39 14 0.06
40 202 0.94
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:34659667 original size:184 final size:184
Alignment explanation
Indices: 34659358--34659719 Score: 607
Period size: 184 Copynumber: 2.0 Consensus size: 184
34659348 GGATTTTCAA
* * *
34659358 AGGCACATGGCCGTATAGTCCACCTGTATGGGAGACCGTGTGGCCCTAAACCTACATAAAGTTTG
1 AGGCACATGGCCGTATAGTCCACCTGTATGGGAGACCGTATGGCCCTAAACCTACACAAAATTTG
* *
34659423 CCAAAATTTACTTGTAAAAGAACACACACCTTTCACCGAAGGTCTTATCGACGTTCCTCACGATC
66 CCAAAATTCACTTGCAAAAGAACACACACCTTTCACCGAAGGTCTTATCGACGTTCCTCACGATC
34659488 AAATCTAATCCAATTCACCTAAATCAAGTCCTTCAAACGACATTTTCACATCAG
131 AAATCTAATCCAATTCACCTAAATCAAGTCCTTCAAACGACATTTTCACATCAG
* * *
34659542 AGGCACATGGCCGTATGGTCCACCTGTGTGGGAGATCGTATGGCCCTAAACCTACACAAAATTTG
1 AGGCACATGGCCGTATAGTCCACCTGTATGGGAGACCGTATGGCCCTAAACCTACACAAAATTTG
* *
34659607 CCACAATTCACTTGCAAAAGAACACACACCTTTCACCGAAGGTCTTATCGACTTTCCTCACGATC
66 CCAAAATTCACTTGCAAAAGAACACACACCTTTCACCGAAGGTCTTATCGACGTTCCTCACGATC
** *
34659672 AAATCTAATCTGATTCACCTAAATCAGGTCCTTCAAACGACATTTTCA
131 AAATCTAATCCAATTCACCTAAATCAAGTCCTTCAAACGACATTTTCA
34659720 AATGAATTAA
Statistics
Matches: 165, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
184 165 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (184 bp):
AGGCACATGGCCGTATAGTCCACCTGTATGGGAGACCGTATGGCCCTAAACCTACACAAAATTTG
CCAAAATTCACTTGCAAAAGAACACACACCTTTCACCGAAGGTCTTATCGACGTTCCTCACGATC
AAATCTAATCCAATTCACCTAAATCAAGTCCTTCAAACGACATTTTCACATCAG
Found at i:34684856 original size:66 final size:66
Alignment explanation
Indices: 34684745--34684877 Score: 203
Period size: 66 Copynumber: 2.0 Consensus size: 66
34684735 GATAAGGTTA
* *
34684745 GATTGATTCTAGATCGTCTAAAAATGACTTCTGATAGACAAAAATCTTATGCAAACCTGAAAAGG
1 GATTGATTCTAGATCATCTAAAAATAACTTCTGATAGACAAAAATCTTATGCAAACCTGAAAAGG
34684810 C
66 C
* * * **
34684811 GATTGATTCTAGATCATTTAAAAATAACTTCTGATAGACAGAAATCTTATGCAGATTTGAAAAGG
1 GATTGATTCTAGATCATCTAAAAATAACTTCTGATAGACAAAAATCTTATGCAAACCTGAAAAGG
34684876 C
66 C
34684877 G
1 G
34684878 TGATATTGAG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (66 bp):
GATTGATTCTAGATCATCTAAAAATAACTTCTGATAGACAAAAATCTTATGCAAACCTGAAAAGG
C
Found at i:34688337 original size:23 final size:24
Alignment explanation
Indices: 34688305--34688351 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
34688295 CGTACCGCAC
*
34688305 ATGTTTCTTTT-TTAATAAA-ATTT
1 ATGTTCCTTTTATTAA-AAATATTT
34688328 ATGTTCCTTTTATTAAAAATATTT
1 ATGTTCCTTTTATTAAAAATATTT
34688352 TCTGGCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
ATGTTCCTTTTATTAAAAATATTT
Found at i:34698611 original size:6 final size:6
Alignment explanation
Indices: 34698600--34698632 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
34698590 TCCCACCACC
34698600 CCCATA CCCATA CCCATA CCCATA CCCATA CCC
1 CCCATA CCCATA CCCATA CCCATA CCCATA CCC
34698633 TCTCCCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.55, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCATA
Found at i:34698970 original size:3 final size:3
Alignment explanation
Indices: 34698962--34699075 Score: 60
Period size: 3 Copynumber: 38.0 Consensus size: 3
34698952 TGTACCCTCT
* * *
34698962 TTA TTA TTA TTA GTA TTA TTA TTA TTTA TT- TTA TTTC TTG TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA
* * *
34699007 TTA TT- TTA TTA TT- TTA TT- TTCT TTA CTGA TTA TT- TTT TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA TTA TTA TTA TTA -TTA
* *
34699051 TTA TCTT TTA CTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA
34699076 GTCATTTTAG
Statistics
Matches: 87, Mismatches: 12, Indels: 24
0.71 0.10 0.20
Matches are distributed among these distances:
2 12 0.14
3 61 0.70
4 14 0.16
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:34698995 original size:15 final size:14
Alignment explanation
Indices: 34698961--34699071 Score: 52
Period size: 16 Copynumber: 7.6 Consensus size: 14
34698951 TTGTACCCTC
*
34698961 TTTATTATTATTAGT
1 TTTATTATTTTTA-T
*
34698976 ATTATTATTATTTAT
1 TTTATTATT-TTTAT
* *
34698991 TTTA-T-TTCTTGT
1 TTTATTATTTTTAT
34699003 TTTATTATTTTATTAT
1 TTTATTA-TTT-TTAT
34699019 TTTATT-TTCTTTACT
1 TTTATTATT-TTTA-T
*
34699034 GATTATT-TTTTTA-
1 -TTTATTATTTTTAT
34699047 TTTATTATCTTTTACT
1 TTTATTAT-TTTTA-T
*
34699063 ATTATTATT
1 TTTATTATT
34699072 ATTAGTCATT
Statistics
Matches: 74, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
12 12 0.16
13 4 0.05
14 11 0.15
15 21 0.28
16 26 0.35
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTATTATTTTTAT
Found at i:34699050 original size:28 final size:29
Alignment explanation
Indices: 34698961--34699075 Score: 105
Period size: 29 Copynumber: 4.0 Consensus size: 29
34698951 TTGTACCCTC
* *
34698961 TTTATTAT-TATTAGTATTATTATTATTTAT
1 TTTATTATCTTTTACTATTATT-TTA-TTAT
*
34698991 TTTATT-TCTTGTT-TTATTATTTTATTAT
1 TTTATTATCTT-TTACTATTATTTTATTAT
* *
34699019 TTTATTTTC-TTTACTGATTATTTTTTTA-
1 TTTATTATCTTTTACT-ATTATTTTATTAT
34699047 TTTATTATCTTTTACTATTATTATTATTA
1 TTTATTATCTTTTACTATTATT-TTATTA
34699076 GTCATTTTAG
Statistics
Matches: 72, Mismatches: 6, Indels: 15
0.77 0.06 0.16
Matches are distributed among these distances:
27 2 0.03
28 26 0.36
29 28 0.39
30 14 0.19
31 2 0.03
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (29 bp):
TTTATTATCTTTTACTATTATTTTATTAT
Found at i:34700108 original size:13 final size:13
Alignment explanation
Indices: 34700090--34700122 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
34700080 GGTTGTTTAT
34700090 TAAACTAATTAAC
1 TAAACTAATTAAC
34700103 TAAACTAATTAAC
1 TAAACTAATTAAC
34700116 T-AACTAA
1 TAAACTAA
34700123 ACTAAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:34709152 original size:6 final size:6
Alignment explanation
Indices: 34709141--34709179 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
34709131 AGTTCATTTG
* *
34709141 TTTTAT TTTTAT TTTTAT GTTTAT GTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
34709180 GTTAGACTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:34711005 original size:19 final size:19
Alignment explanation
Indices: 34710983--34711026 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
34710973 CCATACAGCT
* *
34710983 TGGGCATTTCCATATGGGC
1 TGGGCATTTCCACAAGGGC
*
34711002 TGGGTATTTCCACAAGGGC
1 TGGGCATTTCCACAAGGGC
34711021 TGGGCA
1 TGGGCA
34711027 CACGCCCGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.27
Consensus pattern (19 bp):
TGGGCATTTCCACAAGGGC
Found at i:34727768 original size:22 final size:24
Alignment explanation
Indices: 34727721--34727769 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
34727711 TATTTGAAAT
*
34727721 ATTTTATAATATATGTTTTTTAAA
1 ATTTTATAATATATGATTTTTAAA
*
34727745 ATTTTA-AATATAT-ATTTTTGAA
1 ATTTTATAATATATGATTTTTAAA
34727767 ATT
1 ATT
34727770 AATTTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 7 0.30
24 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTTTATAATATATGATTTTTAAA
Found at i:34727940 original size:13 final size:13
Alignment explanation
Indices: 34727910--34727939 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
34727900 TTTAAATATT
34727910 TAAAATTTTTAAA
1 TAAAATTTTTAAA
34727923 TAAAATTTTT-AA
1 TAAAATTTTTAAA
34727935 TAAAA
1 TAAAA
34727940 ACTTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAAATTTTTAAA
Found at i:34727978 original size:10 final size:11
Alignment explanation
Indices: 34727954--34727983 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
34727944 TAAAATGGCT
34727954 AAATATATTTAA
1 AAATA-ATTTAA
34727966 AAATAATTTAA
1 AAATAATTTAA
34727977 AAATAAT
1 AAATAAT
34727984 AATTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATAATTTAA
Found at i:34727986 original size:14 final size:15
Alignment explanation
Indices: 34727963--34727995 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
34727953 TAAATATATT
34727963 TAAA-AATAATTTAA
1 TAAATAATAATTTAA
34727977 -AAATAATAATTTAA
1 TAAATAATAATTTAA
34727991 TAAAT
1 TAAAT
34727996 TCTATGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 10 0.59
15 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAATAATAATTTAA
Found at i:34728065 original size:13 final size:14
Alignment explanation
Indices: 34728038--34728070 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
34728028 TAAATTTTTT
*
34728038 AAATTTTTTTATAA
1 AAATTTTATTATAA
34728052 AAATTTTATT-TAA
1 AAATTTTATTATAA
34728065 AAATTT
1 AAATTT
34728071 CAATGTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATTTTATTATAA
Found at i:34728112 original size:20 final size:21
Alignment explanation
Indices: 34728076--34728244 Score: 87
Period size: 22 Copynumber: 8.3 Consensus size: 21
34728066 AATTTCAATG
34728076 TTTAAATATTATTAAAAAATATA
1 TTTAAA-ATT-TTAAAAAATATA
*
34728099 TTTAATA-TTTAAAAAATAATA
1 TTTAAAATTTTAAAAAAT-ATA
34728120 TTTAAAATTTTAAAAAATA-A
1 TTTAAAATTTTAAAAAATATA
* * *
34728140 TTTCAAA----AATATA-ATA
1 TTTAAAATTTTAAAAAATATA
* *
34728156 TTCAAAATTTAAAAAAAATA-A
1 TTTAAAATTT-TAAAAAATATA
* *
34728177 TTTC--A----AAAATATATA
1 TTTAAAATTTTAAAAAATATA
*
34728192 TTTAAAATTTTAGAAAATAATA
1 TTTAAAATTTTAAAAAAT-ATA
34728214 TTTAAAATTTTAAAAATTATATA
1 TTTAAAATTTTAAAAA--ATATA
34728237 TTATAAAA
1 TT-TAAAA
34728245 CATTTCAAAT
Statistics
Matches: 110, Mismatches: 16, Indels: 39
0.67 0.10 0.24
Matches are distributed among these distances:
14 7 0.06
15 5 0.05
16 10 0.09
17 1 0.01
19 1 0.01
20 16 0.15
21 23 0.21
22 30 0.27
23 10 0.09
24 7 0.06
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (21 bp):
TTTAAAATTTTAAAAAATATA
Found at i:34728120 original size:21 final size:22
Alignment explanation
Indices: 34728076--34728140 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
34728066 AATTTCAATG
34728076 TTTAAATATTATTAAAAAAT-ATA
1 TTTAAA-ATT-TTAAAAAATAATA
*
34728099 TTTAATA-TTTAAAAAATAATA
1 TTTAAAATTTTAAAAAATAATA
34728120 TTTAAAATTTTAAAAAATAAT
1 TTTAAAATTTTAAAAAATAAT
34728141 TTCAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 9 0.24
21 10 0.26
22 14 0.37
23 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAAATTTTAAAAAATAATA
Found at i:34728153 original size:14 final size:14
Alignment explanation
Indices: 34728125--34728198 Score: 56
Period size: 14 Copynumber: 5.7 Consensus size: 14
34728115 TAATATTTAA
*
34728125 AATTTTAAAAA-AT
1 AATTTCAAAAATAT
34728138 AATTTCAAAAATAT
1 AATTTCAAAAATAT
*
34728152 AATATTC-AAAATTT
1 AAT-TTCAAAAATAT
34728166 AA----AAAAA-AT
1 AATTTCAAAAATAT
34728175 AATTTCAAAAATAT
1 AATTTCAAAAATAT
34728189 ATATTT-AAAA
1 A-ATTTCAAAA
34728199 TTTTAGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
9 3 0.06
10 4 0.08
13 15 0.31
14 20 0.41
15 7 0.14
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (14 bp):
AATTTCAAAAATAT
Found at i:34728154 original size:36 final size:36
Alignment explanation
Indices: 34728105--34728212 Score: 159
Period size: 36 Copynumber: 3.1 Consensus size: 36
34728095 TATATTTAAT
34728105 ATTT-AAAAA-ATAATATTTAAAATTTTAAAAAATA
1 ATTTCAAAAATATAATATTTAAAATTTTAAAAAATA
* *
34728139 ATTTCAAAAATATAATATTCAAAATTTAAAAAAAATA
1 ATTTCAAAAATATAATATTTAAAATTT-TAAAAAATA
*
34728176 ATTTCAAAAATAT-ATATTTAAAATTTTAGAAAATA
1 ATTTCAAAAATATAATATTTAAAATTTTAAAAAATA
34728211 AT
1 AT
34728213 ATTTAAAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
34 4 0.06
35 14 0.21
36 27 0.41
37 21 0.32
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (36 bp):
ATTTCAAAAATATAATATTTAAAATTTTAAAAAATA
Found at i:34728161 original size:15 final size:13
Alignment explanation
Indices: 34728125--34728198 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 13
34728115 TAATATTTAA
*
34728125 AATTTTAAAAAAT
1 AATTTCAAAAAAT
34728138 AATTTCAAAAATAT
1 AATTTCAAAAA-AT
34728152 AATATTC--AAAAT
1 AAT-TTCAAAAAAT
**
34728164 --TTAAAAAAAAT
1 AATTTCAAAAAAT
34728175 AATTTCAAAAATAT
1 AATTTCAAAAA-AT
34728189 ATATTT-AAAA
1 A-ATTTCAAAA
34728199 TTTTAGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
9 1 0.02
10 1 0.02
11 5 0.10
12 2 0.04
13 20 0.42
14 12 0.25
15 7 0.15
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTTCAAAAAAT
Found at i:34728186 original size:23 final size:23
Alignment explanation
Indices: 34728138--34728184 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
34728128 TTTAAAAAAT
* *
34728138 AATTTCAAAAATATAATATTCAA
1 AATTTAAAAAAAATAATATTCAA
34728161 AATTTAAAAAAAATAAT-TTCAA
1 AATTTAAAAAAAATAATATTCAA
34728183 AA
1 AA
34728185 ATATATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (23 bp):
AATTTAAAAAAAATAATATTCAA
Found at i:34728208 original size:23 final size:22
Alignment explanation
Indices: 34728175--34728270 Score: 97
Period size: 22 Copynumber: 4.3 Consensus size: 22
34728165 TAAAAAAAAT
*
34728175 AATTTCAAAAATATATATTTAA
1 AATTTTAAAAATATATATTTAA
34728197 AATTTTAGAAAATA-ATATTTAA
1 AATTTTA-AAAATATATATTTAA
34728219 AATTTTAAAAATTATATATTATAA
1 AATTTTAAAAA-TATATATT-TAA
* * * *
34728243 AACATTT-CAAATATACATTTTA
1 AA-TTTTAAAAATATATATTTAA
34728265 AATTTT
1 AATTTT
34728271 TTAAAATTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
21 7 0.11
22 27 0.43
23 18 0.29
24 8 0.13
25 3 0.05
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (22 bp):
AATTTTAAAAATATATATTTAA
Found at i:34728334 original size:17 final size:17
Alignment explanation
Indices: 34728321--34728372 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
34728311 AATAAAACAA
34728321 AAAGAAAAAGAAAAAACT
1 AAAGAAAAAGAAAAAA-T
*
34728339 TAA-AAAAAGAAAAAAATT
1 AAAGAAAAAG-AAAAAA-T
34728357 AAAGAAAAAGAAAAAA
1 AAAGAAAAAGAAAAAA
34728373 GTTAAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 6 0.21
18 17 0.59
19 6 0.21
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.08
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAAT
Found at i:34728353 original size:19 final size:18
Alignment explanation
Indices: 34728325--34728396 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 18
34728315 AAACAAAAAG
*
34728325 AAAAAG-AAAAAACTTAA
1 AAAAAGAAAAAAAATTAA
34728342 AAAAAG-AAAAAAATTAA
1 AAAAAGAAAAAAAATTAA
*
34728359 AGAAAA-AGAAAAAAGTTAA
1 A-AAAAGA-AAAAAAATTAA
34728378 AAAGAAGTAAAAAAAATTA
1 AAA-AAG-AAAAAAAATTA
34728397 GAATTAGCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
17 17 0.37
18 6 0.13
19 13 0.28
20 9 0.20
21 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.12
Consensus pattern (18 bp):
AAAAAGAAAAAAAATTAA
Found at i:34728361 original size:36 final size:38
Alignment explanation
Indices: 34728321--34728392 Score: 121
Period size: 36 Copynumber: 1.9 Consensus size: 38
34728311 AATAAAACAA
34728321 AAAGAAAAAGAAAAAACTTAAAAA-AAG-AAAAAAATT
1 AAAGAAAAAGAAAAAACTTAAAAAGAAGTAAAAAAATT
*
34728357 AAAGAAAAAGAAAAAAGTTAAAAAGAAGTAAAAAAA
1 AAAGAAAAAGAAAAAACTTAAAAAGAAGTAAAAAAA
34728393 ATTAGAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 23 0.70
37 3 0.09
38 7 0.21
ACGTcount: A:0.78, C:0.01, G:0.11, T:0.10
Consensus pattern (38 bp):
AAAGAAAAAGAAAAAACTTAAAAAGAAGTAAAAAAATT
Found at i:34731686 original size:16 final size:15
Alignment explanation
Indices: 34731667--34731713 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
34731657 TAAGTAAGTG
*
34731667 ATATTTTATTTTAATT
1 ATATTTTATTAT-ATT
34731683 ATATTATTATTATATT
1 ATATT-TTATTATATT
34731699 ATA-TTTATTATATT
1 ATATTTTATTATATT
34731713 A
1 A
34731714 GTTATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.38
15 1 0.03
16 11 0.38
17 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATATTTTATTATATT
Found at i:34731694 original size:11 final size:10
Alignment explanation
Indices: 34731680--34731713 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
34731670 TTTTATTTTA
34731680 ATTATATTATT
1 ATTATATTA-T
34731691 ATTATATTAT
1 ATTATATTAT
34731701 ATT-TATTAT
1 ATTATATTAT
34731710 ATTA
1 ATTA
34731714 GTTATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 4 0.18
11 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTATATTAT
Found at i:34731712 original size:5 final size:5
Alignment explanation
Indices: 34731680--34731713 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
34731670 TTTTATTTTA
34731680 ATTAT ATTATT ATTAT ATTAT ATT-T ATTAT ATTA
1 ATTAT ATTA-T ATTAT ATTAT ATTAT ATTAT ATTA
34731714 GTTATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTAT
Found at i:34740840 original size:16 final size:17
Alignment explanation
Indices: 34740799--34740840 Score: 61
Period size: 15 Copynumber: 2.5 Consensus size: 17
34740789 ACGATTTTCA
34740799 TTTATTTATATTAAATTT
1 TTTATTT-TATTAAATTT
34740817 TTTA-TTTATT-AATTT
1 TTTATTTTATTAAATTT
34740832 TTTATTTTA
1 TTTATTTTA
34740841 AATAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
16 8 0.35
17 2 0.09
18 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTATTAAATTT
Found at i:34743518 original size:20 final size:22
Alignment explanation
Indices: 34743476--34743518 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
34743466 AAAATTAATT
34743476 AAGAATCCATAGACATTCATTA
1 AAGAATCCATAGACATTCATTA
* *
34743498 AAGAA-CCA-AGAGATTCTTTA
1 AAGAATCCATAGACATTCATTA
34743518 A
1 A
34743519 TTTAAAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.26
Consensus pattern (22 bp):
AAGAATCCATAGACATTCATTA
Found at i:34747753 original size:40 final size:40
Alignment explanation
Indices: 34747707--34747782 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
34747697 GCACACCATG
*
34747707 TGGGGATAAAATCGACCCACCCATCCCTACACACCAAATA
1 TGGGGATAAAATCGACCCACCCAACCCTACACACCAAATA
* *
34747747 TGGGGATAATATCGACCCATCCAACCCTACACACCA
1 TGGGGATAAAATCGACCCACCCAACCCTACACACCA
34747783 TAAGGTACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.36, C:0.36, G:0.13, T:0.16
Consensus pattern (40 bp):
TGGGGATAAAATCGACCCACCCAACCCTACACACCAAATA
Found at i:34748159 original size:18 final size:18
Alignment explanation
Indices: 34748136--34748170 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34748126 TGCCTATGTG
34748136 ACATGCCTGTATGGCCCT
1 ACATGCCTGTATGGCCCT
*
34748154 ACATGCCTGTGTGGCCC
1 ACATGCCTGTATGGCCC
34748171 ACACAGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (18 bp):
ACATGCCTGTATGGCCCT
Found at i:34754723 original size:30 final size:26
Alignment explanation
Indices: 34754663--34754715 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
34754653 ACAGTGAGTC
*
34754663 ACTTATTAGACCGAAATCAATTTTTA
1 ACTTATGAGACCGAAATCAATTTTTA
34754689 ACTTATGAGACCGAAATCAATTTTTA
1 ACTTATGAGACCGAAATCAATTTTTA
34754715 A
1 A
34754716 GTTACTTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (26 bp):
ACTTATGAGACCGAAATCAATTTTTA
Found at i:34756085 original size:27 final size:27
Alignment explanation
Indices: 34756038--34756096 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
34756028 AATTATATTT
* *
34756038 AAAATAAGATATATTATTTAATTTTTAA
1 AAAATAAGATATATTAATTAA-ATTTAA
*
34756066 AAAATAATATATA-TAATTAAATTTAA
1 AAAATAAGATATATTAATTAAATTTAA
34756092 AAAAT
1 AAAAT
34756097 TAATTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 10 0.36
27 6 0.21
28 12 0.43
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
AAAATAAGATATATTAATTAAATTTAA
Found at i:34759297 original size:13 final size:13
Alignment explanation
Indices: 34759245--34759297 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
34759235 AGTTTGGCAA
34759245 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
34759258 TGCTGTAGAAAAG
1 TGCTTTTGAAAAG
**
34759271 TGCTTTTGGGAAG
1 TGCTTTTGAAAAG
34759284 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
34759297 T
1 T
34759298 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:34760307 original size:20 final size:20
Alignment explanation
Indices: 34760282--34760324 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
34760272 ATTTAATGTT
34760282 TATCTACAAGATAAACATTC
1 TATCTACAAGATAAACATTC
34760302 TATCTACAAGATAAACATTC
1 TATCTACAAGATAAACATTC
34760322 TAT
1 TAT
34760325 TAATTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (20 bp):
TATCTACAAGATAAACATTC
Found at i:34761862 original size:46 final size:46
Alignment explanation
Indices: 34761809--34761908 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
34761799 CTTAAGGGTG
* *
34761809 TTACAGAATACGCCACACAGTCATCA-CAGAATACTCCACAAAGGCT
1 TTACAGAATACACCACACAGGCATCACCA-AATACTCCACAAAGGCT
* * *
34761855 TTACAGAATACACCACACAGGCTTTACCAAATACTCCACCAAGGCT
1 TTACAGAATACACCACACAGGCATCACCAAATACTCCACAAAGGCT
*
34761901 TTATAGAA
1 TTACAGAA
34761909 AATTACGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 45 0.96
47 2 0.04
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (46 bp):
TTACAGAATACACCACACAGGCATCACCAAATACTCCACAAAGGCT
Found at i:34761877 original size:23 final size:23
Alignment explanation
Indices: 34761809--34761908 Score: 105
Period size: 23 Copynumber: 4.3 Consensus size: 23
34761799 CTTAAGGGTG
* * *
34761809 TTACAGAATACGCCACACAGTCA
1 TTACAGAATACTCCACACAGGCT
* *
34761832 TCACAGAATACTCCACAAAGGCT
1 TTACAGAATACTCCACACAGGCT
*
34761855 TTACAGAATACACCACACAGGCT
1 TTACAGAATACTCCACACAGGCT
34761878 TTACCA-AATACTCCAC-CAAGGCT
1 TTA-CAGAATACTCCACAC-AGGCT
*
34761901 TTATAGAA
1 TTACAGAA
34761909 AATTACGTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
22 2 0.03
23 60 0.94
24 2 0.03
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (23 bp):
TTACAGAATACTCCACACAGGCT
Found at i:34763925 original size:21 final size:21
Alignment explanation
Indices: 34763899--34763948 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
34763889 ATTACTCCAA
*
34763899 AGAAGCCGATTGACCTATCTC
1 AGAAGCCGATTGACCCATCTC
*
34763920 AGAAGCCGATTGACCCATCTT
1 AGAAGCCGATTGACCCATCTC
34763941 AGAAGCCG
1 AGAAGCCG
34763949 GATTCATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
AGAAGCCGATTGACCCATCTC
Found at i:34771466 original size:41 final size:41
Alignment explanation
Indices: 34771409--34771489 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
34771399 TTAGCATGCC
* *
34771409 TACTATTACTTTTGAACCAG-ATACATGTTAAGCATGTCTAT
1 TACTACTACTATTGAA-CAGAATACATGTTAAGCATGTCTAT
*
34771450 TACTACTACTATTGAACTGAATACATGTTAAGCATGTCTA
1 TACTACTACTATTGAACAGAATACATGTTAAGCATGTCTA
34771490 CTGTTTTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.06
41 34 0.94
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.37
Consensus pattern (41 bp):
TACTACTACTATTGAACAGAATACATGTTAAGCATGTCTAT
Found at i:34773171 original size:40 final size:40
Alignment explanation
Indices: 34773108--34773187 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
34773098 GTTCATATTA
* *
34773108 TGACAAGAACCATGTGAGTGAGAGCTAGAAAGCGTTAGGT
1 TGACAAGAACCATATGAGCGAGAGCTAGAAAGCGTTAGGT
*
34773148 TGACAAGGACCATATGAGCGAGAGCTAGAAAGCGTTAGGT
1 TGACAAGAACCATATGAGCGAGAGCTAGAAAGCGTTAGGT
34773188 ACTTTTTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.33, T:0.19
Consensus pattern (40 bp):
TGACAAGAACCATATGAGCGAGAGCTAGAAAGCGTTAGGT
Found at i:34776124 original size:35 final size:35
Alignment explanation
Indices: 34776085--34776174 Score: 119
Period size: 35 Copynumber: 2.6 Consensus size: 35
34776075 GATATTTTGT
*
34776085 TTCGCATGTTGAGCATGAT-ATTATTCTAATTATGA
1 TTCGCATGTTAAGCATG-TCATTATTCTAATTATGA
* *
34776120 TTCGCATGTTAAGCATGTCATTATTCTGATTCTGA
1 TTCGCATGTTAAGCATGTCATTATTCTAATTATGA
* *
34776155 TTTGCATGTTAAACATGTCA
1 TTCGCATGTTAAGCATGTCA
34776175 CTGTGATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 1 0.02
35 48 0.98
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (35 bp):
TTCGCATGTTAAGCATGTCATTATTCTAATTATGA
Found at i:34776384 original size:30 final size:30
Alignment explanation
Indices: 34776350--34776414 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 30
34776340 ATCTAGTAGT
*
34776350 ATATTTACA-TTATCTGGTGGCTCAACCACA
1 ATATTTACAGTT-TCTGGTAGCTCAACCACA
* *
34776380 ATA-TT-CAGTTTCTGGTAGCTCGACTACA
1 ATATTTACAGTTTCTGGTAGCTCAACCACA
34776408 ATATTTA
1 ATATTTA
34776415 GTGGCTTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
28 20 0.69
29 6 0.21
30 3 0.10
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (30 bp):
ATATTTACAGTTTCTGGTAGCTCAACCACA
Found at i:34777480 original size:35 final size:35
Alignment explanation
Indices: 34777441--34777530 Score: 119
Period size: 35 Copynumber: 2.6 Consensus size: 35
34777431 GATATTTTGT
*
34777441 TTCGCATGTTGAGCATGAT-ATTATTCTAATTATGA
1 TTCGCATGTTAAGCATG-TCATTATTCTAATTATGA
* *
34777476 TTCGCATGTTAAGCATGTCATTATTCTGATTCTGA
1 TTCGCATGTTAAGCATGTCATTATTCTAATTATGA
* *
34777511 TTTGCATGTTAAACATGTCA
1 TTCGCATGTTAAGCATGTCA
34777531 CTGTGATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 1 0.02
35 48 0.98
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (35 bp):
TTCGCATGTTAAGCATGTCATTATTCTAATTATGA
Found at i:34777740 original size:30 final size:30
Alignment explanation
Indices: 34777706--34777770 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 30
34777696 ATCTAGTAGT
*
34777706 ATATTTACA-TTATCTGGTGGCTCAACCACA
1 ATATTTACAGTT-TCTGGTAGCTCAACCACA
* *
34777736 ATA-TT-CAGTTTCTGGTAGCTCGACTACA
1 ATATTTACAGTTTCTGGTAGCTCAACCACA
34777764 ATATTTA
1 ATATTTA
34777771 GTGGCTTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
28 20 0.69
29 6 0.21
30 3 0.10
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (30 bp):
ATATTTACAGTTTCTGGTAGCTCAACCACA
Found at i:34778906 original size:16 final size:16
Alignment explanation
Indices: 34778869--34778920 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
34778859 AATATAGATT
*
34778869 ACTATAGATTGTG--A
1 ACTATAGATTCTGAAA
*
34778883 ACTCTAGATTCTGAAA
1 ACTATAGATTCTGAAA
34778899 ACTATAGATTCT-AAA
1 ACTATAGATTCTGAAA
34778914 ACTATAG
1 ACTATAG
34778921 TGACAACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 11 0.33
15 10 0.30
16 12 0.36
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (16 bp):
ACTATAGATTCTGAAA
Found at i:34785015 original size:35 final size:35
Alignment explanation
Indices: 34784976--34785075 Score: 182
Period size: 35 Copynumber: 2.9 Consensus size: 35
34784966 ATTGACATTC
34784976 TGATTCGCATGTTGAGCATGCCATTATTCTGATTA
1 TGATTCGCATGTTGAGCATGCCATTATTCTGATTA
*
34785011 TGATTCGCAGGTTGAGCATGCCATTATTCTGATTA
1 TGATTCGCATGTTGAGCATGCCATTATTCTGATTA
*
34785046 TGATTCGCATGTTAAGCATGCCATTATTCT
1 TGATTCGCATGTTGAGCATGCCATTATTCT
34785076 AATTCTAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (35 bp):
TGATTCGCATGTTGAGCATGCCATTATTCTGATTA
Found at i:34788531 original size:48 final size:49
Alignment explanation
Indices: 34788455--34788584 Score: 147
Period size: 48 Copynumber: 2.7 Consensus size: 49
34788445 ACATCAAAGT
** * *
34788455 CGATGCCATGTCTTAGATAGGTCTTACACTGACTTTCATATATCGATGC
1 CGATGCCATGTCCCAAATAGGTCTTACACTGACTCTCATATATCGATGC
* * * * *
34788504 CGATGCCGTGTCCC-AGTAGGTCTTACACT-AGCTCTCATCTATCGGTGT
1 CGATGCCATGTCCCAAATAGGTCTTACACTGA-CTCTCATATATCGATGC
*
34788552 CGATGCCATGTCCCAAACAGGTCTTACACTGAC
1 CGATGCCATGTCCCAAATAGGTCTTACACTGAC
34788585 ACGCAACAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
47 1 0.02
48 39 0.59
49 25 0.38
50 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (49 bp):
CGATGCCATGTCCCAAATAGGTCTTACACTGACTCTCATATATCGATGC
Found at i:34788669 original size:141 final size:142
Alignment explanation
Indices: 34788402--34788719 Score: 348
Period size: 141 Copynumber: 2.2 Consensus size: 142
34788392 CATGGGATAA
* * * *
34788402 GATGCCGAAGCCATGTCCAAAACATGGTCTTACACTGGCTAGCACATCAAAGTCGATGCCATGTC
1 GATGCCGATGCCATGTCCCAAACA-GGTCTTACACTGACTAGCACATCAAAGTCGACGCCATGTC
* * * * * *
34788467 TTAGATAGGTCTTACACTGACTTTCATATATCGATGCCGATGCCGTGTCCCAGTAGGTCTTACAC
65 TCAGACAGGTCTTACACTGACTTTCATATATCGAGGCCGATGACATGTCCCAGCAGGTCTTACAC
34788532 TAGCTCTCATCTAT
130 TAGCTCTCATCT-T
* *
34788546 CGGTGTCGATGCCATGTCCCAAACAGGTCTTACACTGAC-ACGCA-A-C-AAG-CTGACGCCATG
1 -GATGCCGATGCCATGTCCCAAACAGGTCTTACACTGACTA-GCACATCAAAGTC-GACGCCATG
* *
34788606 TCTCAGACAGGTCTTACACT-AGCTTGT-ATATCTCGAGGCCGAT-ACATGTCCCAGACATGTCT
63 TCTCAGACAGGTCTTACACTGA-CTT-TCATATATCGAGGCCGATGACATGTCCCAG-CAGGTCT
34788668 TACACTAGCTCTCATCTT
125 TACACTAGCTCTCATCTT
* * *
34788686 TATGCCGATG-CATGTCCCAGACATGTCTTACACT
1 GATGCCGATGCCATGTCCCAAACAGGTCTTACACT
34788720 AGCTCTCATC
Statistics
Matches: 149, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
138 22 0.15
139 7 0.05
140 12 0.08
141 68 0.46
142 2 0.01
143 2 0.01
144 16 0.11
145 20 0.13
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (142 bp):
GATGCCGATGCCATGTCCCAAACAGGTCTTACACTGACTAGCACATCAAAGTCGACGCCATGTCT
CAGACAGGTCTTACACTGACTTTCATATATCGAGGCCGATGACATGTCCCAGCAGGTCTTACACT
AGCTCTCATCTT
Found at i:34788709 original size:46 final size:46
Alignment explanation
Indices: 34788602--34788814 Score: 291
Period size: 46 Copynumber: 4.6 Consensus size: 46
34788592 AAGCTGACGC
* * * * ** * *
34788602 CATGTCTCAGACAGGTCTTACACTAGCTTGTATATCTCGAGGCCGATA
1 CATGTCCCAGACATGTCTTACACTAGC-TCT-CATCTTTATGCCGATG
34788650 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCGATG
*
34788696 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCTATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCGATG
* *
34788742 CATATCCCAGACATGTCTTACACTAGCTCTCGTCTTTATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCGATG
* *
34788788 CATGTGCCAGACATGTCTTACTCTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
34788815 ATACATATCA
Statistics
Matches: 150, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 123 0.82
47 2 0.01
48 25 0.17
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCGATG
Found at i:34794769 original size:22 final size:23
Alignment explanation
Indices: 34794744--34794795 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
34794734 TATAAAACCT
34794744 AATAAAAA-TACG-CTTAAAGAAA
1 AATAAAAAGTA-GTCTTAAAGAAA
* *
34794766 AATAAAAAGTAGTCTTAAAGTAG
1 AATAAAAAGTAGTCTTAAAGAAA
34794789 AATAAAA
1 AATAAAA
34794796 GTGAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (23 bp):
AATAAAAAGTAGTCTTAAAGAAA
Found at i:34808135 original size:42 final size:42
Alignment explanation
Indices: 34808072--34808198 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
34808062 CTTCGTTTTC
** * *
34808072 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
34808115 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
34808156 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
34808197 TC
1 TC
34808199 TCACTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:34808260 original size:47 final size:46
Alignment explanation
Indices: 34808157--34808280 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
34808147 ATTCATATAT
* * * * *
34808157 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
34808203 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
*
34808250 CGATGCCATATCCCAGATATGGTTTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
34808281 GAAATCACTT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 27 0.40
47 40 0.60
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:34808340 original size:31 final size:31
Alignment explanation
Indices: 34808305--34808453 Score: 217
Period size: 31 Copynumber: 4.8 Consensus size: 31
34808295 CTTGTCACTT
*
34808305 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
34808336 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
34808367 GTAGCCGGAGCTACTACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
34808398 GTAGCAGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
34808429 GGAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
34808454 TGTCATTTGT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 107 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:34808528 original size:50 final size:50
Alignment explanation
Indices: 34808435--34808605 Score: 288
Period size: 50 Copynumber: 3.4 Consensus size: 50
34808425 TTAGGGAGCT
* * *
34808435 GAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGTGTAGCC
*
34808486 GAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCC
*
34808536 GAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCC
34808586 GAAGCTATCACTTATCACTT
1 GAAGCTATCACTTATCACTT
34808606 GTTGCCATGG
Statistics
Matches: 113, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 95 0.84
51 18 0.16
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (50 bp):
GAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCC
Found at i:34811875 original size:25 final size:25
Alignment explanation
Indices: 34811842--34811901 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
34811832 GAGTTGTAAA
*
34811842 CGGTAAGCTTATACGAGCTAAATAT
1 CGGTAAGCTCATACGAGCTAAATAT
** *
34811867 CGGTAAGCTCATGTGAGCTGAATAT
1 CGGTAAGCTCATACGAGCTAAATAT
34811892 CGGTAAGCTC
1 CGGTAAGCTC
34811902 TCTCGAGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (25 bp):
CGGTAAGCTCATACGAGCTAAATAT
Found at i:34811918 original size:25 final size:25
Alignment explanation
Indices: 34811842--34811922 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
34811832 GAGTTGTAAA
* *
34811842 CGGTAAGCTTATAC-GAGCTAAATAT
1 CGGTAAGCTCAT-CTGAGCTGAATAT
*
34811867 CGGTAAGCTCATGTGAGCTGAATAT
1 CGGTAAGCTCATCTGAGCTGAATAT
*
34811892 CGGTAAGCTC-TCTCGAGTTGAGA-AT
1 CGGTAAGCTCATCT-GAGCTGA-ATAT
34811917 CGGTAA
1 CGGTAA
34811923 CCCTAATGAC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
24 2 0.04
25 45 0.94
26 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (25 bp):
CGGTAAGCTCATCTGAGCTGAATAT
Found at i:34814204 original size:38 final size:38
Alignment explanation
Indices: 34814092--34814204 Score: 138
Period size: 38 Copynumber: 3.0 Consensus size: 38
34814082 ACACGGTCAT
* * * * *
34814092 GTAACCCTTTCACACAGCCTATAGCTTCGCACA-CCCGT
1 GTAACCCTTCCACACAACCTATAGCTTCACA-AGGCCGC
* *
34814130 GTAACCCTTCCATACAACCTATAGCTTCACATGGCCGC
1 GTAACCCTTCCACACAACCTATAGCTTCACAAGGCCGC
*
34814168 GTAACCCTTCCACACAATCTATAGCTTCACAAGGCCG
1 GTAACCCTTCCACACAACCTATAGCTTCACAAGGCCG
34814205 TGTGCCCCCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.27, C:0.37, G:0.13, T:0.23
Consensus pattern (38 bp):
GTAACCCTTCCACACAACCTATAGCTTCACAAGGCCGC
Found at i:34817589 original size:21 final size:21
Alignment explanation
Indices: 34817565--34817604 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34817555 CTACCTTTTT
34817565 TCGA-ATTAATATATTTATATG
1 TCGATATTAA-ATATTTATATG
*
34817586 TCGATTTTAAATATTTATA
1 TCGATATTAAATATTTATA
34817605 ATATTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (21 bp):
TCGATATTAAATATTTATATG
Found at i:34818964 original size:26 final size:26
Alignment explanation
Indices: 34818935--34819000 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
34818925 ATAGTTACCC
34818935 ATTTTTTAAATTTAT-TTTTATTTAAT
1 ATTTTTTAAATTTATATTTTA-TTAAT
**
34818961 ATTTAGT-AATTATATATTTTATTAAT
1 ATTTTTTAAATT-TATATTTTATTAAT
*
34818987 A-TTTTTAATTTTAT
1 ATTTTTTAAATTTAT
34819001 GATATTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
25 10 0.31
26 17 0.53
27 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTTTTTAAATTTATATTTTATTAAT
Found at i:34818999 original size:18 final size:17
Alignment explanation
Indices: 34818976--34819011 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34818966 GTAATTATAT
34818976 ATTTTATTAATATTTTTA
1 ATTTTA-TAATATTTTTA
*
34818994 ATTTTATGATATTTTTA
1 ATTTTATAATATTTTTA
34819011 A
1 A
34819012 ACATAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTATAATATTTTTA
Found at i:34820251 original size:30 final size:32
Alignment explanation
Indices: 34820215--34820280 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 32
34820205 AATTCAACTA
*
34820215 TTTTTT-A-AAAGATTAATTGTCGAATTTGAT
1 TTTTTTAATAAAGATTAATTGTCGAATTGGAT
34820245 TTTTTTAAAATAAAGATTAATTGTCGAATTGGAT
1 TTTTTT--AATAAAGATTAATTGTCGAATTGGAT
34820279 TT
1 TT
34820281 AGGCAGGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 6 0.19
33 1 0.03
34 24 0.77
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (32 bp):
TTTTTTAATAAAGATTAATTGTCGAATTGGAT
Found at i:34823209 original size:20 final size:20
Alignment explanation
Indices: 34823167--34823215 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
34823157 AGAACATAAT
**
34823167 AGAAAACGG-GAAAGAAAGGA
1 AGAAAA-GGAGAAAGAAAAAA
34823187 AGAAAAGGAGAAAGAAAAAA
1 AGAAAAGGAGAAAGAAAAAA
34823207 AGAAAAGGA
1 AGAAAAGGA
34823216 AAAACTAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAAAGGAGAAAGAAAAAA
Found at i:34824404 original size:18 final size:17
Alignment explanation
Indices: 34824381--34824492 Score: 80
Period size: 18 Copynumber: 6.2 Consensus size: 17
34824371 TAAATAAATG
*
34824381 TACTGAATGACTGACTGT
1 TACTGAATAACTGA-TGT
*
34824399 TACTGAATAATTGATCGT
1 TACTGAATAACTGAT-GT
*
34824417 TACTGAATAACTGATTGC
1 TACTGAATAACTGA-TGT
** * *
34824435 TACTGAGCAAATAATTGT
1 TACTGAATAACTGA-TGT
* *
34824453 TACTGAATAACTAATTGC
1 TACTGAATAACTGA-TGT
*
34824471 TACTGAATAATTGAATGT
1 TACTGAATAACTG-ATGT
34824489 TACT
1 TACT
34824493 AAGTGAAACT
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
17 1 0.01
18 72 0.96
19 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (17 bp):
TACTGAATAACTGATGT
Found at i:34824430 original size:36 final size:35
Alignment explanation
Indices: 34824381--34824492 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 35
34824371 TAAATAAATG
* * *
34824381 TACTGAATGACTGACTGTTACTGAATAATTGATCGT
1 TACTGAATAACTGATTGCTACTGAATAATTGAT-GT
** * *
34824417 TACTGAATAACTGATTGCTACTGAGCAAATAATTGT
1 TACTGAATAACTGATTGCTACTGAATAATTGA-TGT
*
34824453 TACTGAATAACTAATTGCTACTGAATAATTGAATGT
1 TACTGAATAACTGATTGCTACTGAATAATTG-ATGT
34824489 TACT
1 TACT
34824493 AAGTGAAACT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
36 60 0.97
37 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (35 bp):
TACTGAATAACTGATTGCTACTGAATAATTGATGT
Found at i:34830344 original size:17 final size:17
Alignment explanation
Indices: 34830322--34830364 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
34830312 AATTTAGGCT
34830322 GTGTAGGCCACATGGGC
1 GTGTAGGCCACATGGGC
34830339 GTGTAGGCCACATGGGC
1 GTGTAGGCCACATGGGC
34830356 GTGTAGGCC
1 GTGTAGGCC
34830365 CACACGGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.16, C:0.23, G:0.42, T:0.19
Consensus pattern (17 bp):
GTGTAGGCCACATGGGC
Found at i:34831320 original size:13 final size:13
Alignment explanation
Indices: 34831302--34831327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34831292 CACTTGATAA
34831302 GGTTTCCTAAAAG
1 GGTTTCCTAAAAG
34831315 GGTTTCCTAAAAG
1 GGTTTCCTAAAAG
34831328 TACTTTCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GGTTTCCTAAAAG
Found at i:34831779 original size:188 final size:188
Alignment explanation
Indices: 34831576--34831967 Score: 784
Period size: 188 Copynumber: 2.1 Consensus size: 188
34831566 TATTAAATTA
34831576 TTATTATTTATTATTATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATT
1 TTATTATTTATTATTATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATT
34831641 ATATTATGAAACAAATTAAAGTAAAGACAAATGTATGGTAATCAAAATATACATGTGTAATAATT
66 ATATTATGAAACAAATTAAAGTAAAGACAAATGTATGGTAATCAAAATATACATGTGTAATAATT
34831706 ATATTTGTACAATTGTGATATATTTATTTAATTACTTTTTATTTAAGTAAATCAATAT
131 ATATTTGTACAATTGTGATATATTTATTTAATTACTTTTTATTTAAGTAAATCAATAT
34831764 TTATTATTTATTATTATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATT
1 TTATTATTTATTATTATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATT
34831829 ATATTATGAAACAAATTAAAGTAAAGACAAATGTATGGTAATCAAAATATACATGTGTAATAATT
66 ATATTATGAAACAAATTAAAGTAAAGACAAATGTATGGTAATCAAAATATACATGTGTAATAATT
34831894 ATATTTGTACAATTGTGATATATTTATTTAATTACTTTTTATTTAAGTAAATCAATAT
131 ATATTTGTACAATTGTGATATATTTATTTAATTACTTTTTATTTAAGTAAATCAATAT
34831952 TTATTATTTATTATTA
1 TTATTATTTATTATTA
34831968 AGTAAAAGAT
Statistics
Matches: 204, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 204 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (188 bp):
TTATTATTTATTATTATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATT
ATATTATGAAACAAATTAAAGTAAAGACAAATGTATGGTAATCAAAATATACATGTGTAATAATT
ATATTTGTACAATTGTGATATATTTATTTAATTACTTTTTATTTAAGTAAATCAATAT
Found at i:34832065 original size:267 final size:267
Alignment explanation
Indices: 34831764--34832280 Score: 1034
Period size: 267 Copynumber: 1.9 Consensus size: 267
34831754 AAATCAATAT
34831764 TTATTATTTATTATTATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATT
1 TTATTATTTATTATTATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATT
34831829 ATATTATGAAACAAATTAAAGTAAAGACAAATGTATGGTAATCAAAATATACATGTGTAATAATT
66 ATATTATGAAACAAATTAAAGTAAAGACAAATGTATGGTAATCAAAATATACATGTGTAATAATT
34831894 ATATTTGTACAATTGTGATATATTTATTTAATTACTTTTTATTTAAGTAAATCAATATTTATTAT
131 ATATTTGTACAATTGTGATATATTTATTTAATTACTTTTTATTTAAGTAAATCAATATTTATTAT
34831959 TTATTATTAAGTAAAAGATATTTATTAATTAAATAATTATATTATAAGATTTTTAATATGTATAT
196 TTATTATTAAGTAAAAGATATTTATTAATTAAATAATTATATTATAAGATTTTTAATATGTATAT
34832024 TAAATTA
261 TAAATTA
34832031 TTATTATTTATTATTATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATT
1 TTATTATTTATTATTATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATT
34832096 ATATTATGAAACAAATTAAAGTAAAGACAAATGTATGGTAATCAAAATATACATGTGTAATAATT
66 ATATTATGAAACAAATTAAAGTAAAGACAAATGTATGGTAATCAAAATATACATGTGTAATAATT
34832161 ATATTTGTACAATTGTGATATATTTATTTAATTACTTTTTATTTAAGTAAATCAATATTTATTAT
131 ATATTTGTACAATTGTGATATATTTATTTAATTACTTTTTATTTAAGTAAATCAATATTTATTAT
34832226 TTATTATTAAGTAAAAGATATTTATTAATTAAATAATTATATTATAAGATTTTTA
196 TTATTATTAAGTAAAAGATATTTATTAATTAAATAATTATATTATAAGATTTTTA
34832281 TGTAATAAAT
Statistics
Matches: 250, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
267 250 1.00
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (267 bp):
TTATTATTTATTATTATGGTTTTATATTTGATATTTATTAATGTTATTTTTATTAAATTGATATT
ATATTATGAAACAAATTAAAGTAAAGACAAATGTATGGTAATCAAAATATACATGTGTAATAATT
ATATTTGTACAATTGTGATATATTTATTTAATTACTTTTTATTTAAGTAAATCAATATTTATTAT
TTATTATTAAGTAAAAGATATTTATTAATTAAATAATTATATTATAAGATTTTTAATATGTATAT
TAAATTA
Found at i:34833729 original size:18 final size:17
Alignment explanation
Indices: 34833706--34833817 Score: 89
Period size: 18 Copynumber: 6.2 Consensus size: 17
34833696 CAAATAAAGG
*
34833706 TACTGAATGACTGACTGT
1 TACTGAATAACTGA-TGT
*
34833724 TACTGAATAATTGATCGT
1 TACTGAATAACTGAT-GT
*
34833742 TACTGAATAACTGATTGC
1 TACTGAATAACTGA-TGT
** *
34833760 TACTGAGCAAATGATTGT
1 TACTGAATAACTGA-TGT
* *
34833778 TACTGAATAACTAATTGC
1 TACTGAATAACTGA-TGT
*
34833796 TACTGAATAATTGAATGT
1 TACTGAATAACTG-ATGT
34833814 TACT
1 TACT
34833818 AAGTGAAACT
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
17 1 0.01
18 72 0.96
19 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (17 bp):
TACTGAATAACTGATGT
Found at i:34833746 original size:36 final size:35
Alignment explanation
Indices: 34833706--34833817 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 35
34833696 CAAATAAAGG
* * *
34833706 TACTGAATGACTGACTGTTACTGAATAATTGATCGT
1 TACTGAATAACTGATTGCTACTGAATAATTGAT-GT
** *
34833742 TACTGAATAACTGATTGCTACTGAGCAAATGATTGT
1 TACTGAATAACTGATTGCTACTGAATAATTGA-TGT
*
34833778 TACTGAATAACTAATTGCTACTGAATAATTGAATGT
1 TACTGAATAACTGATTGCTACTGAATAATTG-ATGT
34833814 TACT
1 TACT
34833818 AAGTGAAACT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
36 62 0.97
37 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (35 bp):
TACTGAATAACTGATTGCTACTGAATAATTGATGT
Found at i:34835243 original size:339 final size:339
Alignment explanation
Indices: 34834623--34835299 Score: 1196
Period size: 339 Copynumber: 2.0 Consensus size: 339
34834613 GCACACGGGA
* *
34834623 GTGTGTCTTGGCTGTATGAAACTATTTTGTTCATAAGTAATTAGTCAGAGAGTTACACGGATAAA
1 GTGTGTCTTGGCAGTATGAAACTATTTTGTTCATAAGTAATAAGTCAGAGAGTTACACGGATAAA
*
34834688 GGACACGGGCATGTCCCCTAGACCACACGAGCGTGTGGGCACTGTTCAATAGGAAAATTTTGAAA
66 GGACACGGGCATGTCCCCTAGACCACACGAGCGTGTGGGCACTATTCAATAGGAAAATTTTGAAA
*
34834753 TTTTGAGAAAAATTCGTAGTGATTTTAAATTAGTCTCGAATTGATTTTACTATTCATATTGGACT
131 TTTTGAGAAAAATTCATAGTGATTTTAAATTAGTCTCGAATTGATTTTACTATTCATATTGGACT
34834818 TCGAGGGACCATTAAAGGGACGATACATTAAATTTAGGATAAGTGTAAACAATTATATTAATTAA
196 TCGAGGGACCATTAAAGGGACGATACATTAAATTTAGGATAAGTGTAAACAATTATATTAATTAA
*
34834883 TGTCCGTAATTGAACTGTATTGACTGGTAATGCCCCGCAATACTATT-TCGGGGATGAATAAGGG
261 TGTCCGTAATTGAACTGTATTGACTGGTAATGCCCCGCAATACTGTTCT-GGGGATGAATAAGGG
34834947 TTAGGGGATGTTACC
325 TTAGGGGATGTTACC
34834962 GTGTGTCTTGGCAGTATGAAACTATTTTGTTCATAAGTAATAAGTCAGAGAGTTACACGGATAAA
1 GTGTGTCTTGGCAGTATGAAACTATTTTGTTCATAAGTAATAAGTCAGAGAGTTACACGGATAAA
* * * *
34835027 GGACATGGGCGTGTCCCCTAGACCATACGAGCGTGTGGGTACTATTCAATAGGAAAATTTTGAAA
66 GGACACGGGCATGTCCCCTAGACCACACGAGCGTGTGGGCACTATTCAATAGGAAAATTTTGAAA
*
34835092 TTTTGAGAAAAATTCATAGTGATTTTAAATTAGT-TCCGAATTGATTTTACTGTTCATATTGGAC
131 TTTTGAGAAAAATTCATAGTGATTTTAAATTAGTCT-CGAATTGATTTTACTATTCATATTGGAC
*
34835156 TTCGAGGGCCCATTAAAGGGACGATACATTAAATTTAGGATAAGTGTAAACAATTATATTAATTA
195 TTCGAGGGACCATTAAAGGGACGATACATTAAATTTAGGATAAGTGTAAACAATTATATTAATTA
* * *
34835221 ATGTCCGTAGTTGAACTGTATTGACTGGTAATGCCCCGCAATCCTGTTCTGGGGATGGATAAGGG
260 ATGTCCGTAATTGAACTGTATTGACTGGTAATGCCCCGCAATACTGTTCTGGGGATGAATAAGGG
34835286 TTAGGGGATGTTAC
325 TTAGGGGATGTTAC
34835300 AGTAGGACTA
Statistics
Matches: 322, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
338 1 0.00
339 320 0.99
340 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (339 bp):
GTGTGTCTTGGCAGTATGAAACTATTTTGTTCATAAGTAATAAGTCAGAGAGTTACACGGATAAA
GGACACGGGCATGTCCCCTAGACCACACGAGCGTGTGGGCACTATTCAATAGGAAAATTTTGAAA
TTTTGAGAAAAATTCATAGTGATTTTAAATTAGTCTCGAATTGATTTTACTATTCATATTGGACT
TCGAGGGACCATTAAAGGGACGATACATTAAATTTAGGATAAGTGTAAACAATTATATTAATTAA
TGTCCGTAATTGAACTGTATTGACTGGTAATGCCCCGCAATACTGTTCTGGGGATGAATAAGGGT
TAGGGGATGTTACC
Found at i:34848130 original size:39 final size:40
Alignment explanation
Indices: 34848077--34848211 Score: 245
Period size: 40 Copynumber: 3.4 Consensus size: 40
34848067 GACTTATAGT
* *
34848077 CCGCAGACTTTGTGCTGGTAATAGATATCTGGGTTAAATC
1 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
34848117 CCGCAGGC-TTGTGCTGGTAATAGATATCCGGGTTAAATC
1 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
34848156 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
1 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
34848196 CCGCAGGCTTTGTGCT
1 CCGCAGGCTTTGTGCT
34848212 AGAAATTGGA
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
39 38 0.41
40 54 0.59
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (40 bp):
CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
Found at i:34848433 original size:20 final size:21
Alignment explanation
Indices: 34848401--34848445 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
34848391 ATGAGAAGTA
34848401 TATGTGAAAATCTCATATGTG
1 TATGTGAAAATCTCATATGTG
34848422 TATGTG-AAATCTCATATGTG
1 TATGTGAAAATCTCATATGTG
34848442 TATG
1 TATG
34848446 CGTGTATTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (21 bp):
TATGTGAAAATCTCATATGTG
Found at i:34854562 original size:39 final size:40
Alignment explanation
Indices: 34854509--34854641 Score: 241
Period size: 40 Copynumber: 3.4 Consensus size: 40
34854499 CTTATAGTCT
*
34854509 GCAGGCTTTGTGCTGGCAATAGATATCCGGGTTAAATCCC
1 GCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATCCC
34854549 GCAGGC-TTGTGCTGGTAATAGATATCCGGGTTAAATCCC
1 GCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATCCC
34854588 GCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATCCC
1 GCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATCCC
*
34854628 GTAGGCTTTGTGCT
1 GCAGGCTTTGTGCT
34854642 AGAAATTGGA
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
39 38 0.42
40 52 0.58
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATCCC
Found at i:34856462 original size:42 final size:41
Alignment explanation
Indices: 34856353--34856473 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 41
34856343 ATTTATATGC
*
34856353 CACACGGCCTGGACACACACCCATGTCCTTGCCCATGTAACT
1 CACAC-GCCTGGAGACACACCCATGTCCTTGCCCATGTAACT
* * * *
34856395 TACACGCCCT--AGACACATGCCCATGTCCTTGCTCGTGTGACT
1 CACACG-CCTGGAGACACA--CCCATGTCCTTGCCCATGTAACT
* *
34856437 CACACAGCCTGGAGACACACTCATGTCATCTGCCCAT
1 CACAC-GCCTGGAGACACACCCATGTCCT-TGCCCAT
34856474 ATGGTTCTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
40 6 0.10
41 1 0.02
42 42 0.68
43 6 0.10
44 7 0.11
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (41 bp):
CACACGCCTGGAGACACACCCATGTCCTTGCCCATGTAACT
Found at i:34859881 original size:19 final size:19
Alignment explanation
Indices: 34859844--34859882 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
34859834 GTCATTTAAT
*
34859844 ACATATCCCCTTTCCACAA
1 ACATATCCCCTTTACACAA
* *
34859863 ACATTTCCCCTTTAGACAA
1 ACATATCCCCTTTACACAA
34859882 A
1 A
34859883 ATTAGCTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (19 bp):
ACATATCCCCTTTACACAA
Found at i:34861424 original size:78 final size:79
Alignment explanation
Indices: 34861333--34861487 Score: 204
Period size: 79 Copynumber: 2.0 Consensus size: 79
34861323 TTAACAATAG
* * * * *
34861333 AAATCGAATAAATTCTATTGAATGACA-TAATAGAATCCTGAAACAGAATTGTTTAATTGATTTC
1 AAATCGAAAAAATTCTATTGAACGACAGGAATAAAATCCTGAAACAGAATTGTTCAATTGATTTC
34861397 TATTTAAAAACAAA
66 TATTTAAAAACAAA
* * * *
34861411 AAATCGAAAAAATTCTGTTGAACGATAGGAATAAAATCTTGAAATAGAATTGTTCAATTGATTTC
1 AAATCGAAAAAATTCTATTGAACGACAGGAATAAAATCCTGAAACAGAATTGTTCAATTGATTTC
* *
34861476 TGTTTACAAACA
66 TATTTAAAAACA
34861488 TAATACAATT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
78 23 0.35
79 42 0.65
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (79 bp):
AAATCGAAAAAATTCTATTGAACGACAGGAATAAAATCCTGAAACAGAATTGTTCAATTGATTTC
TATTTAAAAACAAA
Found at i:34862028 original size:203 final size:203
Alignment explanation
Indices: 34861679--34862080 Score: 579
Period size: 203 Copynumber: 2.0 Consensus size: 203
34861669 AATTGGATGA
* * *
34861679 AAATTGTGTACTCGTAGGTAAGAAAAAATCCAACTGGTAATTGAGGCCTGTTTGCACAGTTTCCT
1 AAATTGTGTACTCATAGGTAAGAAAAAATCCAACTGGTAATTGAAGCCTATTTGCACAGTTTCCT
* * *
34861744 TAAGAAAGATTTAGTAGCTCCTTTGGTGCTAGAGAAATGTTGGTCAACTGTCTCCTAGGATATAA
66 TAAGAAAGATTCAGTAGCTCCTTTGGTGCTAGAGAAACGTTGGTCAACTGTCTCCTAGGATACAA
*
34861809 CAAAAAGATGAGCACGGCTGCAGTAATCAATGAACTATAGCCTAGCTTTCTTCTATCACCGAAAA
131 CAAAAAGATGAGCACGGCTGCAGTAATCAACGAACTATAGCCTAGCTTTCTTCTATCACCGAAAA
34861874 CAGGATCG
196 CAGGATCG
* * * * * *
34861882 AAATTGTGTACTCATAGGTAGGCAGAAGTCCGACTGGTAATTGAAGCCTATTTTCACAGTTTCCT
1 AAATTGTGTACTCATAGGTAAGAAAAAATCCAACTGGTAATTGAAGCCTATTTGCACAGTTTCCT
* * * * * *
34861947 TAAGACAGATTCAGTCGTTCCTTTGGTGCTGGAGAAACGTTGGTCGATTGTCTCCTAGGATACAA
66 TAAGAAAGATTCAGTAGCTCCTTTGGTGCTAGAGAAACGTTGGTCAACTGTCTCCTAGGATACAA
** * ** *
34862012 CAACGAGATGAGCACGGCTGCAGTGATCAACGAACTATAGTGTAGCTTTCTTCTATCACTGAAAA
131 CAAAAAGATGAGCACGGCTGCAGTAATCAACGAACTATAGCCTAGCTTTCTTCTATCACCGAAAA
34862077 CAGG
196 CAGG
34862081 TTCGGAATAT
Statistics
Matches: 174, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
203 174 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (203 bp):
AAATTGTGTACTCATAGGTAAGAAAAAATCCAACTGGTAATTGAAGCCTATTTGCACAGTTTCCT
TAAGAAAGATTCAGTAGCTCCTTTGGTGCTAGAGAAACGTTGGTCAACTGTCTCCTAGGATACAA
CAAAAAGATGAGCACGGCTGCAGTAATCAACGAACTATAGCCTAGCTTTCTTCTATCACCGAAAA
CAGGATCG
Found at i:34873585 original size:12 final size:12
Alignment explanation
Indices: 34873568--34873600 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
34873558 TGGCCCGCCC
34873568 ATATTAATTTTT
1 ATATTAATTTTT
34873580 ATATT-ATTTTT
1 ATATTAATTTTT
34873591 ATA-TAATTTT
1 ATATTAATTTT
34873601 AAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:34873764 original size:29 final size:30
Alignment explanation
Indices: 34873722--34873781 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 30
34873712 ACTTAACAAG
34873722 CAAATGCTTCTAAAATAATAA-AAAATTAA
1 CAAATGCTTCTAAAATAATAACAAAATTAA
34873751 CAAATGTCTT-TAAAATAATAACAAAATTAA
1 CAAATG-CTTCTAAAATAATAACAAAATTAA
34873781 C
1 C
34873782 GATAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (30 bp):
CAAATGCTTCTAAAATAATAACAAAATTAA
Done.