Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 8 of 276
Found at i:2451303 original size:17 final size:17
Alignment explanation
Indices: 2451234--2451303 Score: 51
Period size: 17 Copynumber: 4.3 Consensus size: 17
2451224 TTATTAAAAT
* *
2451234 AAAATTGAAATATTATA
1 AAAATTTAAATATTTTA
2451251 AAAA-TTATAATATTTT-
1 AAAATTTA-AATATTTTA
* *
2451267 -ATA-TAAAAT-TTTTA
1 AAAATTTAAATATTTTA
2451281 ATAAATTTAAATATTTTA
1 A-AAATTTAAATATTTTA
2451299 AAAAT
1 AAAAT
2451304 AAAAATAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
13 4 0.10
14 3 0.07
15 4 0.10
16 4 0.10
17 20 0.49
18 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (17 bp):
AAAATTTAAATATTTTA
Found at i:2457121 original size:35 final size:35
Alignment explanation
Indices: 2457075--2457168 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
2457065 ATGGTCCATG
*
2457075 GTCCATAGTCCATAAGTAAAATCTTAGAAA-CTGTA
1 GTCCATAGTCCATAAGTAAAATCTTAGAAATC-ATA
*
2457110 GTCCATAGTCCATATGTAAAATCTTAGAAATCATA
1 GTCCATAGTCCATAAGTAAAATCTTAGAAATCATA
*
2457145 GTCCATGGTCCATATA-TAAAATCT
1 GTCCATAGTCCATA-AGTAAAATCT
2457169 ATTATATTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
35 52 0.98
36 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (35 bp):
GTCCATAGTCCATAAGTAAAATCTTAGAAATCATA
Found at i:2463939 original size:3 final size:3
Alignment explanation
Indices: 2463933--2463966 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2463923 CAACAACAAC
2463933 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2463967 GAGCTTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2464462 original size:27 final size:27
Alignment explanation
Indices: 2464424--2464476 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
2464414 TAGTTAATAA
*
2464424 TAAATAAGTTAT-TATAATATAAAAAG
1 TAAATAAGTTATATATAATAAAAAAAG
* *
2464450 TAAATAAATTTATATTTAATAAAAAAA
1 TAAAT-AAGTTATATATAATAAAAAAA
2464477 CTTAATTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 5 0.23
27 6 0.27
28 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (27 bp):
TAAATAAGTTATATATAATAAAAAAAG
Found at i:2465160 original size:2 final size:2
Alignment explanation
Indices: 2465153--2465180 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2465143 TAAAGAAAAT
2465153 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2465181 AATGTCACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2465576 original size:3 final size:3
Alignment explanation
Indices: 2465562--2465628 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
2465552 CTTTATTCCA
*
2465562 AAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2465610 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
2465629 TTGCATAATT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2465799 original size:4 final size:4
Alignment explanation
Indices: 2465790--2465816 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2465780 AAGCATAATC
2465790 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
2465817 GATAGACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:2469218 original size:19 final size:19
Alignment explanation
Indices: 2469194--2469232 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2469184 TGATTTATTC
2469194 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
*
2469213 TAAGATTTATCTACTTAAA
1 TAAGATTTATCTACCTAAA
2469232 T
1 T
2469233 GAATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:2470365 original size:9 final size:9
Alignment explanation
Indices: 2470351--2470389 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
2470341 GAAGATGAAA
2470351 AAAAAAAAG
1 AAAAAAAAG
2470360 AAAAAAAA-
1 AAAAAAAAG
2470368 AAGAAAAAAG
1 AA-AAAAAAG
*
2470378 AAAAAAGAG
1 AAAAAAAAG
2470387 AAA
1 AAA
2470390 GGATGCTCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
8 2 0.07
9 23 0.85
10 2 0.07
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:2470365 original size:11 final size:11
Alignment explanation
Indices: 2470349--2470381 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
2470339 AGGAAGATGA
2470349 AAAAAAAAAAG
1 AAAAAAAAAAG
2470360 AAAAAAAAAAG
1 AAAAAAAAAAG
2470371 AAAAAAGAAAA
1 AAAAAA-AAAA
2470382 AAGAGAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:2470369 original size:18 final size:18
Alignment explanation
Indices: 2470348--2470383 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2470338 GAGGAAGATG
2470348 AAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAGAAAAAA
*
2470366 AAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAGAAAAAA
2470384 GAGAAAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAAAAAA
Found at i:2471956 original size:434 final size:434
Alignment explanation
Indices: 2471148--2472883 Score: 3400
Period size: 434 Copynumber: 4.0 Consensus size: 434
2471138 AACATCATCT
2471148 AAACCCTGTATTAAGAGATAATTAATTTTTAGTAAAAAAAGGTGAAAGCTGTCAAACAGAAGAAT
1 AAACCCTGTATTAAGAGATAATTAATTTTTAGTAAAAAAAGGTGAAAGCTGTCAAACAGAAGAAT
2471213 AGGGATAAAATTGAAGATTTTACTGTATTTATTAGCTAAATTATAAATTTTGAAATTTTTATGGT
66 AGGGATAAAATTGAAGATTTTACTGTATTTATTAGCTAAATTATAAATTTTGAAATTTTTATGGT
2471278 AAAATATATTTGAGTCTAGTTTCAAAAACATCAAGCGGATCTTGATTTAAAATTCTGTAGCTCAA
131 AAAATATATTTGAGTCTAGTTTCAAAAACATCAAGCGGATCTTGATTTAAAATTCTGTAGCTCAA
*
2471343 GATATAAATAATTTAGTGACTATGACTCAAGTAGACAACTTTGATATGAACATATAAGTAAATAG
196 AATATAAATAATTTAGTGACTATGACTCAAGTAGACAACTTTGATATGAACATATAAGTAAATAG
*
2471408 TGGAATTTTAGATAATATTACATATAAGCATGTTATATACTAAAAGCTAAAGATTCTAACAAATA
261 TGAAATTTTAGATAATATTACATATAAGCATGTTATATACTAAAAGCTAAAGATTCTAACAAATA
2471473 TATACATAAAGGATGTGAAATGAAAAGGAGGAAGAGGAAAAATATATGAATATATATATATAGTA
326 TATACATAAAGGATGTGAAATGAAAAGGAGGAAGAGGAAAAATATATGAATATATATATATAGTA
2471538 GATGAATTTGAAATGTTTTGAAATGGTTGTAGGTGATGGAATGA
391 GATGAATTTGAAATGTTTTGAAATGGTTGTAGGTGATGGAATGA
2471582 AAACCCTGTATTAAGAGATAATTAATTTTTAGTAAAAAAAGGTGAAAGCTGTCAAACAGAAGAAT
1 AAACCCTGTATTAAGAGATAATTAATTTTTAGTAAAAAAAGGTGAAAGCTGTCAAACAGAAGAAT
2471647 AGGGATAAAATTGAAGATTTTACTGTATTTATTAGCTAAATTATAAATTTTGAAATTTTTATGGT
66 AGGGATAAAATTGAAGATTTTACTGTATTTATTAGCTAAATTATAAATTTTGAAATTTTTATGGT
2471712 AAAATATATTTGAGTCTAGTTTCAAAAACATCAAGCGGATCTTGATTTAAAATTCTGTAGCTCAA
131 AAAATATATTTGAGTCTAGTTTCAAAAACATCAAGCGGATCTTGATTTAAAATTCTGTAGCTCAA
*
2471777 GATATAAATAATTTAGTGACTATGACTCAAGTAGACAACTTTGATATGAACATATAAGTAAATAG
196 AATATAAATAATTTAGTGACTATGACTCAAGTAGACAACTTTGATATGAACATATAAGTAAATAG
*
2471842 TGGAATTTTAGATAATATTACATATAAGCATGTTATATACTAAAAGCTAAAGATTCTAACAAATA
261 TGAAATTTTAGATAATATTACATATAAGCATGTTATATACTAAAAGCTAAAGATTCTAACAAATA
*
2471907 TATACATAAAGGATGTGAAATGGAAAGGAGGAAGAGGAAAAATATATGAATATATATATATAGTA
326 TATACATAAAGGATGTGAAATGAAAAGGAGGAAGAGGAAAAATATATGAATATATATATATAGTA
2471972 GATGAATTTGAAATGTTTTGAAATGGTTGTAGGTGATGGAATGA
391 GATGAATTTGAAATGTTTTGAAATGGTTGTAGGTGATGGAATGA
2472016 AAACCCTGTATTAAGAGATAATTAATTTTTAGTAAAAAAAGGTGAAAGCTGTCAAACAGAAGAAT
1 AAACCCTGTATTAAGAGATAATTAATTTTTAGTAAAAAAAGGTGAAAGCTGTCAAACAGAAGAAT
2472081 AGGGATAAAATTGAAGATTTTACTGTATTTATTAGCTAAATTATAAATTTTGAAATTTTTATGGT
66 AGGGATAAAATTGAAGATTTTACTGTATTTATTAGCTAAATTATAAATTTTGAAATTTTTATGGT
2472146 AAAATATATTTGAGTCTAGTTTCAAAAACATCAAGCGGATCTTGATTTAAAATTCTGTAGCTCAA
131 AAAATATATTTGAGTCTAGTTTCAAAAACATCAAGCGGATCTTGATTTAAAATTCTGTAGCTCAA
2472211 AATATAAATAATTTAGTGACTATGACTCAAGTAGACAACTTTGATATGAACATATAAGTAAATAG
196 AATATAAATAATTTAGTGACTATGACTCAAGTAGACAACTTTGATATGAACATATAAGTAAATAG
2472276 TGAAATTTTAGATAATATTACATATAAGCATGTTATATACTAAAAGCTAAAGATTCTAACAAATA
261 TGAAATTTTAGATAATATTACATATAAGCATGTTATATACTAAAAGCTAAAGATTCTAACAAATA
2472341 TATACATAAAGGATGTGAAATGAAAAGGAGGAAGAGGAAAAATATATGAATATATATATATAGTA
326 TATACATAAAGGATGTGAAATGAAAAGGAGGAAGAGGAAAAATATATGAATATATATATATAGTA
2472406 GATGAATTTGAAATGTTTTGAAATGGTTGTAGGTGATGGAATGA
391 GATGAATTTGAAATGTTTTGAAATGGTTGTAGGTGATGGAATGA
**
2472450 AAACCCTGTATTAAGAGATAATTAATTTTTAGTCTAAAAAGGTGAAAGCTGTCAAACAGAAGAAT
1 AAACCCTGTATTAAGAGATAATTAATTTTTAGTAAAAAAAGGTGAAAGCTGTCAAACAGAAGAAT
2472515 AGGGATAAAATTGAAGATTTTACTGTATTTATTAGCTAAATTATAAATTTTGAAATTTTTATGGT
66 AGGGATAAAATTGAAGATTTTACTGTATTTATTAGCTAAATTATAAATTTTGAAATTTTTATGGT
2472580 AAAATATATTTGAGTCTAGTTTCAAAAACATCAAGCGGATCTTGATTTAAAATTCTGTAGCTCAA
131 AAAATATATTTGAGTCTAGTTTCAAAAACATCAAGCGGATCTTGATTTAAAATTCTGTAGCTCAA
2472645 AATATAAATAATTTAGTGACTATGACTCAAGTAGACAACTTTGATATGAACATATAAGTAAATAG
196 AATATAAATAATTTAGTGACTATGACTCAAGTAGACAACTTTGATATGAACATATAAGTAAATAG
2472710 TGAAATTTTAGATAATATTACATATAAGCATGTTATATACTAAAAGCTAAAGATTCTAACAAATA
261 TGAAATTTTAGATAATATTACATATAAGCATGTTATATACTAAAAGCTAAAGATTCTAACAAATA
*
2472775 TATACATAAAGGATGTGAAATGGAAAGGAGGAAGAGGAAAAATATATGAATATATATATATAGTA
326 TATACATAAAGGATGTGAAATGAAAAGGAGGAAGAGGAAAAATATATGAATATATATATATAGTA
2472840 GATGAATTTGAAATGTTTTGAAATGGTTGTAGGTGATGGAATGA
391 GATGAATTTGAAATGTTTTGAAATGGTTGTAGGTGATGGAATGA
2472884 TTGATACATA
Statistics
Matches: 1295, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
434 1295 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (434 bp):
AAACCCTGTATTAAGAGATAATTAATTTTTAGTAAAAAAAGGTGAAAGCTGTCAAACAGAAGAAT
AGGGATAAAATTGAAGATTTTACTGTATTTATTAGCTAAATTATAAATTTTGAAATTTTTATGGT
AAAATATATTTGAGTCTAGTTTCAAAAACATCAAGCGGATCTTGATTTAAAATTCTGTAGCTCAA
AATATAAATAATTTAGTGACTATGACTCAAGTAGACAACTTTGATATGAACATATAAGTAAATAG
TGAAATTTTAGATAATATTACATATAAGCATGTTATATACTAAAAGCTAAAGATTCTAACAAATA
TATACATAAAGGATGTGAAATGAAAAGGAGGAAGAGGAAAAATATATGAATATATATATATAGTA
GATGAATTTGAAATGTTTTGAAATGGTTGTAGGTGATGGAATGA
Found at i:2474719 original size:41 final size:41
Alignment explanation
Indices: 2474674--2474753 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
2474664 CAAGGCTTTC
* *
2474674 TAGGATACAAAGTAAGACATGAGATATTTGACAACATTTTT
1 TAGGATACAAAATAAGACATGAAATATTTGACAACATTTTT
*
2474715 TAGGATATAAAATAAGACATGAAATATTTGACAACATTT
1 TAGGATACAAAATAAGACATGAAATATTTGACAACATTT
2474754 CTAACACCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (41 bp):
TAGGATACAAAATAAGACATGAAATATTTGACAACATTTTT
Found at i:2492338 original size:17 final size:19
Alignment explanation
Indices: 2492305--2492348 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
2492295 TATTCTAAAT
2492305 AAAATGAATTAATAAGAA-
1 AAAATGAATTAATAAGAAG
2492323 AAAGATGAA-TAA-AAGAAG
1 AAA-ATGAATTAATAAGAAG
2492341 AAAATGAA
1 AAAATGAA
2492349 GGAGAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 10 0.42
18 9 0.38
19 5 0.21
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATGAATTAATAAGAAG
Found at i:2493714 original size:24 final size:23
Alignment explanation
Indices: 2493631--2493720 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 23
2493621 GTGAGGTTAT
*
2493631 GTGGCACTATGTGTGC-AAAAAC
1 GTGGCACTATGTGTGCGAGAAAC
* * *
2493653 TAGGTGGAATTATGTGTGCGAGATAC
1 ---GTGGCACTATGTGTGCGAGAAAC
* *
2493679 ATAGCACTATGTGTGCGAGGAAAC
1 GTGGCACTATGTGTGCGA-GAAAC
2493703 GTGGCACTATGTGTGCGA
1 GTGGCACTATGTGTGCGA
2493721 ATGAGTAAGA
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
23 14 0.27
24 20 0.38
25 14 0.27
26 4 0.08
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (23 bp):
GTGGCACTATGTGTGCGAGAAAC
Found at i:2495193 original size:5 final size:5
Alignment explanation
Indices: 2495183--2495214 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
2495173 CCATTCTTCC
2495183 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
2495215 TTTCACCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:2496328 original size:28 final size:28
Alignment explanation
Indices: 2496288--2496380 Score: 159
Period size: 28 Copynumber: 3.3 Consensus size: 28
2496278 ATGTACTAGA
2496288 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
2496316 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
* * *
2496344 ATACCCCTATGTATACAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATT
2496372 ATACCCCTA
1 ATACCCCTA
2496381 GGGTTAATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:2496544 original size:27 final size:27
Alignment explanation
Indices: 2496486--2496575 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
2496476 AGGAAGCGTC
2496486 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
2496514 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
2496541 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
2496570 CTGGTG
1 CTGGTG
2496576 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:2496594 original size:55 final size:56
Alignment explanation
Indices: 2496486--2496600 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
2496476 AGGAAGCGTC
* *
2496486 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
2496541 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
2496597 CTGG
1 CTGG
2496601 CAGCCATGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.58
56 21 0.40
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:2503108 original size:10 final size:10
Alignment explanation
Indices: 2503089--2503128 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
2503079 CTGGCCATTC
2503089 TTCC-TTCTT
1 TTCCTTTCTT
2503098 TTCCTTTCTT
1 TTCCTTTCTT
*
2503108 TTCTTTTCTT
1 TTCCTTTCTT
2503118 TT-CTTT-TT
1 TTCCTTTCTT
2503126 TTC
1 TTC
2503129 TCCATCTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 4 0.15
9 7 0.26
10 16 0.59
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (10 bp):
TTCCTTTCTT
Found at i:2503110 original size:5 final size:5
Alignment explanation
Indices: 2503093--2503124 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2503083 CCATTCTTCC
*
2503093 TTCTT TTCCT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
2503125 TTTCTCCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:2503944 original size:8 final size:8
Alignment explanation
Indices: 2503931--2503960 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2503921 CTAGATCGGC
2503931 AAAAGCCG
1 AAAAGCCG
2503939 AAAAGCCG
1 AAAAGCCG
*
2503947 AAATGCCG
1 AAAAGCCG
2503955 AAAAGC
1 AAAAGC
2503961 TGGTATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.23, G:0.23, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:2504249 original size:28 final size:28
Alignment explanation
Indices: 2504209--2504301 Score: 143
Period size: 28 Copynumber: 3.3 Consensus size: 28
2504199 ATGTACTAGA
2504209 ATACCCCTATGTATGAAAAATTACCATT
1 ATACCCCTATGTATGAAAAATTACCATT
*
2504237 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGAAAAATTACCATT
* *
2504265 ATACCCCTATGTAT-ACAAAATGACCTTT
1 ATACCCCTATGTATGA-AAAATTACCATT
2504293 ATACCCCTA
1 ATACCCCTA
2504302 GAGTTAATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGAAAAATTACCATT
Found at i:2504465 original size:27 final size:27
Alignment explanation
Indices: 2504407--2504496 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
2504397 AGGAAGCGTC
2504407 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
2504435 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
2504462 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
2504491 CTGGTG
1 CTGGTG
2504497 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:2507014 original size:14 final size:14
Alignment explanation
Indices: 2506995--2507059 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
2506985 ATCAAGACAC
2506995 AGTACCCTCTTACG
1 AGTACCCTCTTACG
* *
2507009 AGTACCCT-TCCATG
1 AGTACCCTCT-TACG
2507023 A-TACCCTCTTACGAG
1 AGTACCCTCTTAC--G
* *
2507038 AGTACCCTCCTACA
1 AGTACCCTCTTACG
2507052 AGTACCCT
1 AGTACCCT
2507060 TCTATGATAC
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
13 8 0.20
14 20 0.50
15 2 0.05
16 10 0.25
ACGTcount: A:0.25, C:0.37, G:0.12, T:0.26
Consensus pattern (14 bp):
AGTACCCTCTTACG
Found at i:2507123 original size:27 final size:28
Alignment explanation
Indices: 2507093--2507167 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 28
2507083 CCTCCAATAG
* *
2507093 TACCTTCCCATGAGTACCCTTTCACGA-
1 TACCTTCCCAAGAGTACCCTTCCACGAC
**
2507120 TACCTTCTTGTAAGAGTACCCTTCCACGAC
1 TACCTTC--CCAAGAGTACCCTTCCACGAC
*
2507150 TACC-TCCCACGAGTACCC
1 TACCTTCCCAAGAGTACCC
2507168 CACCCCAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
27 16 0.42
29 18 0.47
30 4 0.11
ACGTcount: A:0.23, C:0.39, G:0.12, T:0.27
Consensus pattern (28 bp):
TACCTTCCCAAGAGTACCCTTCCACGAC
Found at i:2509062 original size:46 final size:46
Alignment explanation
Indices: 2508994--2509261 Score: 360
Period size: 46 Copynumber: 5.8 Consensus size: 46
2508984 TTTCTGAAAT
* *
2508994 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* * * *
2509040 AAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAT
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* * * *
2509086 GAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACGTGACAT
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
*
2509132 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGA-AGGG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA--G
*
2509179 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* * *
2509224 GAGAACGAGTAAGACCATAGTTGAAAGATACTATGGCA
1 GA-AATGAGTAAGACCATGGTTGAAAGATACCATGGCA
2509262 TTGTAACACC
Statistics
Matches: 203, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
45 3 0.01
46 156 0.77
47 43 0.21
48 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (46 bp):
GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
Found at i:2510536 original size:43 final size:43
Alignment explanation
Indices: 2510488--2510666 Score: 295
Period size: 43 Copynumber: 4.2 Consensus size: 43
2510478 CCGGCATTAC
2510488 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
* *
2510531 GCCTGCTAGGCATGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
* * * * *
2510574 ACCTGCTAGGCACGAAGGCCCAAATATACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
2510617 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
2510660 GCCTGCT
1 GCCTGCT
2510667 GGATTTAACC
Statistics
Matches: 124, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 124 1.00
ACGTcount: A:0.31, C:0.34, G:0.23, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
Found at i:2515358 original size:20 final size:20
Alignment explanation
Indices: 2515333--2515476 Score: 107
Period size: 20 Copynumber: 7.2 Consensus size: 20
2515323 TTCATTCAAT
2515333 AACAGTAACTCATCCGTATA
1 AACAGTAACTCATCCGTATA
*
2515353 AACAGT-ACTTCATCCATATA
1 AACAGTAAC-TCATCCGTATA
*
2515373 AACAGTAA-TCCATCCGTAAA
1 AACAGTAACT-CATCCGTATA
* * * *
2515393 AACAGT-TCTTCGTTCATATA
1 AACAGTAAC-TCATCCGTATA
* *
2515413 AATAGTAATTCATCCGTATA
1 AACAGTAACTCATCCGTATA
* * *
2515433 AATAGT-ACTTCATTCATATA
1 AACAGTAAC-TCATCCGTATA
* *
2515453 AACAGTAATTCATCCGTATG
1 AACAGTAACTCATCCGTATA
2515473 AACA
1 AACA
2515477 CATAGCTTTT
Statistics
Matches: 94, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
19 4 0.04
20 87 0.93
21 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (20 bp):
AACAGTAACTCATCCGTATA
Found at i:2515387 original size:40 final size:40
Alignment explanation
Indices: 2515323--2515476 Score: 197
Period size: 40 Copynumber: 3.9 Consensus size: 40
2515313 TAAATAATAA
2515323 TTCATTCA-AT-AACAGTAA-CTCATCCGTATAAACAGTAC
1 TTCATTCATATAAACAGTAATC-CATCCGTATAAACAGTAC
* * *
2515361 TTCATCCATATAAACAGTAATCCATCCGTAAAAACAGTTC
1 TTCATTCATATAAACAGTAATCCATCCGTATAAACAGTAC
* * * *
2515401 TTCGTTCATATAAATAGTAATTCATCCGTATAAATAGTAC
1 TTCATTCATATAAACAGTAATCCATCCGTATAAACAGTAC
* *
2515441 TTCATTCATATAAACAGTAATTCATCCGTATGAACA
1 TTCATTCATATAAACAGTAATCCATCCGTATAAACA
2515477 CATAGCTTTT
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
38 7 0.07
39 2 0.02
40 89 0.90
41 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (40 bp):
TTCATTCATATAAACAGTAATCCATCCGTATAAACAGTAC
Found at i:2515699 original size:24 final size:23
Alignment explanation
Indices: 2515649--2515713 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
2515639 TGATGGACAG
**
2515649 TAAGCTCTATTGAGCTGAAACGA
1 TAAGCTCTAACGAGCTGAAACGA
2515672 TAAGCTCTAACGAGCTGCAAAC-A
1 TAAGCTCTAACGAGCTG-AAACGA
* *
2515695 TTAAGCTCTTACCAGCTGA
1 -TAAGCTCTAACGAGCTGA
2515714 TATATCGGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (23 bp):
TAAGCTCTAACGAGCTGAAACGA
Found at i:2519051 original size:17 final size:17
Alignment explanation
Indices: 2519029--2519095 Score: 80
Period size: 17 Copynumber: 3.7 Consensus size: 17
2519019 GACTCTCAAG
2519029 CACAAACTTATCATAAA
1 CACAAACTTATCATAAA
*
2519046 CACAAACTTATCCTATAAGTT
1 CACAAACTTAT-C-ATAA--A
*
2519067 TACAAACTTATCATAAA
1 CACAAACTTATCATAAA
2519084 CACAAACTTATC
1 CACAAACTTATC
2519096 CGATTTTGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 22 0.52
18 1 0.02
19 8 0.19
20 1 0.02
21 10 0.24
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.28
Consensus pattern (17 bp):
CACAAACTTATCATAAA
Found at i:2520220 original size:13 final size:12
Alignment explanation
Indices: 2520196--2520232 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2520186 ATTAAAAAGT
2520196 AAAATTATAAAA
1 AAAATTATAAAA
*
2520208 AAAATTATGAAA
1 AAAATTATAAAA
*
2520220 AAAATTGTAAAA
1 AAAATTATAAAA
2520232 A
1 A
2520233 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (12 bp):
AAAATTATAAAA
Found at i:2520503 original size:18 final size:18
Alignment explanation
Indices: 2520470--2520523 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
2520460 AATAGATTCT
2520470 ATATTTTTAAATATTTTTTC
1 ATATTTTT--ATATTTTTTC
*
2520490 ATATTTTTATATTTTTTG
1 ATATTTTTATATTTTTTC
*
2520508 TTATTTTTATTATTTT
1 ATATTTTTA-TATTTT
2520524 ATTACTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 17 0.55
19 6 0.19
20 8 0.26
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
ATATTTTTATATTTTTTC
Found at i:2520514 original size:9 final size:9
Alignment explanation
Indices: 2520491--2520542 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
2520481 TATTTTTTCA
2520491 TATTTTTA-
1 TATTTTTAT
*
2520499 TATTTTTTGT
1 TA-TTTTTAT
2520509 TATTTTTAT
1 TATTTTTAT
2520518 TA-TTTTAT
1 TATTTTTAT
*
2520526 TACTTTTAT
1 TATTTTTAT
2520535 TAATTTTT
1 T-ATTTTT
2520543 TGCAGCTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 10 0.27
9 20 0.54
10 7 0.19
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (9 bp):
TATTTTTAT
Found at i:2520532 original size:18 final size:17
Alignment explanation
Indices: 2520491--2520541 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
2520481 TATTTTTTCA
* *
2520491 TATTTTTATATTTTTTGT
1 TATTTTTAT-TATTTTAT
2520509 TATTTTTATTATTTTAT
1 TATTTTTATTATTTTAT
*
2520526 TACTTTTATTAATTTT
1 TATTTTTATT-ATTTT
2520542 TTGCAGCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (17 bp):
TATTTTTATTATTTTAT
Found at i:2526602 original size:16 final size:16
Alignment explanation
Indices: 2526581--2526612 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2526571 TTAAATTTAT
2526581 TAAATCTTTTTAAGGA
1 TAAATCTTTTTAAGGA
*
2526597 TAAATCTTTTTGAGGA
1 TAAATCTTTTTAAGGA
2526613 AAAGGAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (16 bp):
TAAATCTTTTTAAGGA
Found at i:2530005 original size:19 final size:19
Alignment explanation
Indices: 2529977--2530036 Score: 111
Period size: 19 Copynumber: 3.2 Consensus size: 19
2529967 ATCTAAGTTT
*
2529977 CTTTCAGAACGTCTAGAGC
1 CTTTCCGAACGTCTAGAGC
2529996 CTTTCCGAACGTCTAGAGC
1 CTTTCCGAACGTCTAGAGC
2530015 CTTTCCGAACGTCTAGAGC
1 CTTTCCGAACGTCTAGAGC
2530034 CTT
1 CTT
2530037 AAGTCAAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (19 bp):
CTTTCCGAACGTCTAGAGC
Found at i:2535810 original size:42 final size:42
Alignment explanation
Indices: 2535751--2535834 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
2535741 ATGGAATTGC
2535751 ATTGACATGTTTTAACCTTGATTGTGGATGCATTGGTTGTCT
1 ATTGACATGTTTTAACCTTGATTGTGGATGCATTGGTTGTCT
2535793 ATTGACATGTTTTAACCTTGATTGTGGATGCATTGGTTGTCT
1 ATTGACATGTTTTAACCTTGATTGTGGATGCATTGGTTGTCT
2535835 CAGTATGCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (42 bp):
ATTGACATGTTTTAACCTTGATTGTGGATGCATTGGTTGTCT
Found at i:2538268 original size:16 final size:15
Alignment explanation
Indices: 2538247--2538283 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2538237 CCACATAATA
*
2538247 TTTTTTTATTTTTTTC
1 TTTTTTTA-TATTTTC
2538263 TTTTTTTATATTTTC
1 TTTTTTTATATTTTC
2538278 TTTTTT
1 TTTTTT
2538284 CTGTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTATATTTTC
Found at i:2544820 original size:16 final size:17
Alignment explanation
Indices: 2544789--2544821 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2544779 TTCATAAGTA
2544789 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
2544806 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
2544822 GCACCATCAT
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:2545264 original size:92 final size:92
Alignment explanation
Indices: 2545107--2545327 Score: 334
Period size: 92 Copynumber: 2.4 Consensus size: 92
2545097 TTTGACATGA
* * * * *
2545107 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATTTTTCAAC
1 TGCCATGGTATCTTTCAACTATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
*
2545172 CATGGTCTTACACATTTCATGTCACGC
66 CATGGTCTTACACATTTCATATCACGC
* *
2545199 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACTATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
* *
2545264 CATGGTCTTACACATTTCATATCAGGT
66 CATGGTCTTACACATTTCATATCACGC
* *
2545291 TGCCATGGTATCTTTCAACTATAGTCTTACGCATTTC
1 TGCCATGGTATCTTTCAACTATGGTCTTACTCATTTC
2545328 ATATCAGAGA
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 115 1.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.40
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACTATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCACGC
Found at i:2545327 original size:46 final size:46
Alignment explanation
Indices: 2545107--2545334 Score: 278
Period size: 46 Copynumber: 5.0 Consensus size: 46
2545097 TTTGACATGA
* * * * *
2545107 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGTCAGGT
* * *
2545153 TGCCATGGTATTTTTCAACCATGGTCTTACACATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
** ** *
2545199 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
*
2545245 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
* * * *
2545291 TGCCATGGTATCTTTCAACTATAGTCTTACGCATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAG
2545335 AGAGCACACT
Statistics
Matches: 158, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 4 0.03
46 154 0.97
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCAGGT
Found at i:2555521 original size:47 final size:48
Alignment explanation
Indices: 2555470--2555684 Score: 171
Period size: 48 Copynumber: 4.6 Consensus size: 48
2555460 AGAGGTGAGT
*
2555470 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAT-GATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATAGATGATA
* * * *
2555517 GCCAGTGTAAGACGTGTCTCGGACATGCATC-GACT--A-AGTTTCG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATAG-AT-GATA
* ** * * * *
2555561 GCTAGCATAAGACATGTCTGGGACATGCATCAGCACT-TATACACGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGC-CTCGATAGATGATA
* * *
2555609 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGGA-GATA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGATAGATGATA
2555658 GCCAG-GTAAGACCATGTCTGGGACATG
1 GCCAGTGTAAGA-CATGTCTGGGACATG
2555685 ACAGCGGAAA
Statistics
Matches: 134, Mismatches: 22, Indels: 24
0.74 0.12 0.13
Matches are distributed among these distances:
44 28 0.21
45 3 0.02
46 7 0.05
47 31 0.23
48 32 0.24
49 23 0.17
50 10 0.07
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (48 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATAGATGATA
Found at i:2555541 original size:94 final size:91
Alignment explanation
Indices: 2555379--2555642 Score: 215
Period size: 94 Copynumber: 2.8 Consensus size: 91
2555369 GACGAGGGCT
* * * * * *
2555379 AGTGTAATACGTGTCTGGGATATGCATCAACCGCATCATGATAGCCCGTGTAAGACCACGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCGCATCATGATAGCCAGTGTAAGACCACGTCTCG
* **
2555444 GACATGGCATTGGTGTAGAGGTGAGTGCC
66 GACAT-GCA-TCGACTA-AGGTGAGTGCC
* * * **
2555473 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGATGATGTTAGCCAGTGTAAGA-CGTGTCTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCGC-ATCATGATAGCCAGTGTAAGACCACGTCTC
* ** *
2555537 GGACATGCATCGACTAAGTTTCGTGCT
65 GGACATGCATCGACTAAGGTGAGTGCC
** ** * * * *
2555564 AGCATAAGACATGTCTGGGACATGCATCAGCACTTATACACGAGAGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGC-CGCAT-CATGATAGCCAGTGTAAGACCACGTCT
*
2555629 GGGACATGGCATCG
64 CGGACAT-GCATCG
2555643 GCCTCGATGG
Statistics
Matches: 137, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
91 38 0.28
92 20 0.15
93 15 0.11
94 46 0.34
95 18 0.13
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (91 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCGCATCATGATAGCCAGTGTAAGACCACGTCTCG
GACATGCATCGACTAAGGTGAGTGCC
Found at i:2558175 original size:47 final size:47
Alignment explanation
Indices: 2558104--2558234 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 47
2558094 GGGTTATTGT
*
2558104 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCGCATT-ATGA-
1 GAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCGCATTGA-GAC
* *
2558150 GAGCCAGTGTAAAACCATGTTTGGGACATGGCATC-G--GCATTGAGAC
1 GAGCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCGCATTGAGAC
2558196 GAGTGCTAGTGTAAGACATGTTTGGGACATGCATCGGCC
1 GA--GCTAGTGTAAGACATGTTTGGGACATGCATCGGCC
2558235 TCGAGACGTA
Statistics
Matches: 71, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
45 7 0.10
46 20 0.28
47 29 0.41
48 15 0.21
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (47 bp):
GAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCGCATTGAGAC
Found at i:2558255 original size:46 final size:46
Alignment explanation
Indices: 2558104--2558325 Score: 177
Period size: 46 Copynumber: 4.8 Consensus size: 46
2558094 GGGTTATTGT
* * * *
2558104 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCGC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGA
* * * *
2558150 GAGCCAGTGTAAAACCATGTTTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGA
* * *
2558198 GTGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-A
* * * *
2558245 -AGCCAATGTAAGACATGTCTGAGG-CATGCATCGG-TTAC-A-AGGT
1 GAGCCAGTGTAAGACATGTCTG-GGACATGCATCGGCCT-CGAGACGA
* *
2558288 GTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
2558326 ACAGATATGC
Statistics
Matches: 142, Mismatches: 23, Indels: 21
0.76 0.12 0.11
Matches are distributed among these distances:
44 14 0.10
45 13 0.09
46 62 0.44
47 30 0.21
48 22 0.15
49 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGA
Found at i:2560248 original size:97 final size:96
Alignment explanation
Indices: 2560147--2560361 Score: 258
Period size: 97 Copynumber: 2.2 Consensus size: 96
2560137 TTTATTTTTT
* *
2560147 AATAAAAACAGGGGCTTAATTGCTTCTTCTTCTTCTTTTTT-TAA-GTTTGACGGTCTTTTTGAT
1 AATAAAAACAGGGGCTTAATTGCTTCTT-TT-TT-TTTTTTAAAAGGTTTGACGGCCTTTTT-AT
* * *
2560210 -CATTTTGAAAGTTCAAGTACCCAATTGAGT-GCAA
62 GCATTTTGAAAGTCCAAGTACCCAAAT-AATCGCAA
* * *
2560244 AATAAAAATAGGGGCTTATTTGCTTCTTTTTTTTTTTTGAAAAGGTTTGAGGGCCTTTTTATGCA
1 AATAAAAACAGGGGCTTAATTGCTTCTTTTTTTTTTTT-AAAAGGTTTGACGGCCTTTTTATGCA
2560309 TTTTGAAAGTCCAAGTACCCAAATAATCGCAA
65 TTTTGAAAGTCCAAGTACCCAAATAATCGCAA
* *
2560341 AAAAAAAACAGGGCCTTAATT
1 AATAAAAACAGGGGCTTAATT
2560362 TATTTTTTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
94 6 0.06
95 2 0.02
96 8 0.08
97 85 0.84
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (96 bp):
AATAAAAACAGGGGCTTAATTGCTTCTTTTTTTTTTTTAAAAGGTTTGACGGCCTTTTTATGCAT
TTTGAAAGTCCAAGTACCCAAATAATCGCAA
Found at i:2560484 original size:21 final size:20
Alignment explanation
Indices: 2560452--2560509 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
2560442 TCATAAACCT
2560452 TATTTATATTTTAATTAATCA
1 TATTT-TATTTTAATTAATCA
*
2560473 TATTTTAGTTTTAATTAATCT
1 TATTTTA-TTTTAATTAATCA
*
2560494 TAATTTA-TTTAATTAA
1 TATTTTATTTTAATTAA
2560510 GTTTAATTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.26
20 2 0.06
21 23 0.68
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTTTATTTTAATTAATCA
Found at i:2564950 original size:22 final size:22
Alignment explanation
Indices: 2564919--2564969 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2564909 CTGTTTGAAC
*
2564919 ATATTGTAGGAATATTCTGTAA
1 ATATTTTAGGAATATTCTGTAA
* *
2564941 ATATTTTAGGAATATTTTGTAG
1 ATATTTTAGGAATATTCTGTAA
2564963 ATATTTT
1 ATATTTT
2564970 TTTATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
ATATTTTAGGAATATTCTGTAA
Found at i:2568728 original size:22 final size:22
Alignment explanation
Indices: 2568700--2568744 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2568690 AGGGGGAGTG
2568700 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
2568722 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
2568744 T
1 T
2568745 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:2580545 original size:26 final size:26
Alignment explanation
Indices: 2580515--2580622 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
2580505 TGAAAGTCCC
2580515 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
2580541 ATCATGGGACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
2580567 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2580593 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2580619 ATCA
1 ATCA
2580623 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2581506 original size:6 final size:6
Alignment explanation
Indices: 2581349--2581490 Score: 284
Period size: 6 Copynumber: 23.7 Consensus size: 6
2581339 NNNNNNNNNN
2581349 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
2581397 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
2581445 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
2581491 CAGGATTTTT
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 136 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:2581508 original size:1 final size:1
Alignment explanation
Indices: 2581349--2581490 Score: 77
Period size: 1 Copynumber: 142.0 Consensus size: 1
2581339 NNNNNNNNNN
* * * * * * * * * * *
2581349 TTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTA
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * *
2581414 TTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
2581479 ATTTTTATTTTT
1 TTTTTTTTTTTT
2581491 CAGGATTTTT
Statistics
Matches: 95, Mismatches: 46, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 95 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (1 bp):
T
Found at i:2582069 original size:2 final size:2
Alignment explanation
Indices: 2582064--2582088 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2582054 GTTATATATA
2582064 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2582089 ATGAAACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2586598 original size:19 final size:20
Alignment explanation
Indices: 2586562--2586601 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2586552 TTTAAAATGA
2586562 TTTTAAATTCTCTCTAAAGT
1 TTTTAAATTCTCTCTAAAGT
* *
2586582 TTTTTAATTGTCT-TAAAGT
1 TTTTAAATTCTCTCTAAAGT
2586601 T
1 T
2586602 AGATAAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTAAATTCTCTCTAAAGT
Found at i:2587505 original size:81 final size:81
Alignment explanation
Indices: 2587410--2587586 Score: 354
Period size: 81 Copynumber: 2.2 Consensus size: 81
2587400 GATTTTAGGC
2587410 ACCAAAAATAAAAAAATTATCAAAGTTGGATGATTAACTTCGTAGTTTATCTTAAATCCTAATGT
1 ACCAAAAATAAAAAAATTATCAAAGTTGGATGATTAACTTCGTAGTTTATCTTAAATCCTAATGT
2587475 CGTTTAAATTTTTGTG
66 CGTTTAAATTTTTGTG
2587491 ACCAAAAATAAAAAAATTATCAAAGTTGGATGATTAACTTCGTAGTTTATCTTAAATCCTAATGT
1 ACCAAAAATAAAAAAATTATCAAAGTTGGATGATTAACTTCGTAGTTTATCTTAAATCCTAATGT
2587556 CGTTTAAATTTTTGTG
66 CGTTTAAATTTTTGTG
2587572 ACCAAAAATAAAAAA
1 ACCAAAAATAAAAAA
2587587 TTTTCATTTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 96 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (81 bp):
ACCAAAAATAAAAAAATTATCAAAGTTGGATGATTAACTTCGTAGTTTATCTTAAATCCTAATGT
CGTTTAAATTTTTGTG
Found at i:2588196 original size:11 final size:11
Alignment explanation
Indices: 2588180--2588214 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
2588170 GGTAAAATGG
2588180 TAATTAATTAA
1 TAATTAATTAA
2588191 TAATTAATTAA
1 TAATTAATTAA
2588202 TAAATTAAGTTAA
1 T-AATTAA-TTAA
2588215 AATAAAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.55
12 6 0.27
13 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (11 bp):
TAATTAATTAA
Found at i:2590257 original size:19 final size:19
Alignment explanation
Indices: 2590233--2590272 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2590223 AGTCATTAAC
2590233 TTATGGTTTTATTTACCAT
1 TTATGGTTTTATTTACCAT
2590252 TTATGGTTTTATTTACCAT
1 TTATGGTTTTATTTACCAT
2590271 TT
1 TT
2590273 TTGGGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (19 bp):
TTATGGTTTTATTTACCAT
Found at i:2591623 original size:41 final size:36
Alignment explanation
Indices: 2591541--2591705 Score: 174
Period size: 36 Copynumber: 4.5 Consensus size: 36
2591531 TCCTCATTGA
2591541 AATACCATACCTACATTTTTACAACTCGGTATGGGC
1 AATACCATACCTACATTTTTACAACTCGGTATGGGC
2591577 AATACCATACCTACATTTTTACAACTCGGTATGGGC
1 AATACCATACCTACATTTTTACAACTCGGTATGGGC
* * *
2591613 AATGCCATACCTACATTTCTT--AACTCAGTATGGATTTGAT
1 AATACCATACCTACATTT-TTACAACTCGGTATGG----G-C
* * * **
2591653 AATACCATACCTACA-TATCACAACTCAGTATGGAT
1 AATACCATACCTACATTTTTACAACTCGGTATGGGC
*
2591688 GATACCATACCTACATTT
1 AATACCATACCTACATTT
2591706 CACACTTTTC
Statistics
Matches: 111, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
35 26 0.23
36 54 0.49
37 2 0.02
38 1 0.01
39 2 0.02
40 26 0.23
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (36 bp):
AATACCATACCTACATTTTTACAACTCGGTATGGGC
Found at i:2595005 original size:40 final size:40
Alignment explanation
Indices: 2594936--2595061 Score: 182
Period size: 40 Copynumber: 3.2 Consensus size: 40
2594926 AACCCAAGTA
* *
2594936 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
2594975 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * * *
2595015 CCTTCGGGTCTTTGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
2595055 CCTTCGG
1 CCTTCGG
2595062 ATCTTAGTTC
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 13 0.16
40 66 0.84
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:2596407 original size:39 final size:39
Alignment explanation
Indices: 2596364--2596497 Score: 160
Period size: 39 Copynumber: 3.4 Consensus size: 39
2596354 ACTACTATAG
*
2596364 TGAATAATTGATAGTTACTGAATAACTAAATTACTGTAT
1 TGAATAATTGATAGTTACTGAATAACTAAATTACTGTAA
* * * *
2596403 TGAATAATTGATAGATATTGAATAACTAAACTACTGCAA
1 TGAATAATTGATAGTTACTGAATAACTAAATTACTGTAA
* * * * *
2596442 TGAATATTTTATAGTTACTGAATGACTAAATTACTATAC
1 TGAATAATTGATAGTTACTGAATAACTAAATTACTGTAA
* *
2596481 TGAATAACTGATTGTTA
1 TGAATAATTGATAGTTA
2596498 TTGATTGTTT
Statistics
Matches: 77, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (39 bp):
TGAATAATTGATAGTTACTGAATAACTAAATTACTGTAA
Found at i:2597257 original size:21 final size:21
Alignment explanation
Indices: 2597233--2597300 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 21
2597223 TACACGACCC
2597233 ATTATAAGAAAAACACCCAAG
1 ATTATAAGAAAAACACCCAAG
* *
2597254 ATTA-AAGTAAAAACCTACACGAACC
1 ATTATAAG-AAAAA-C-AC-CCAA-G
*
2597279 TTTATAAGAAAAACACCCAAG
1 ATTATAAGAAAAACACCCAAG
2597300 A
1 A
2597301 CATCTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
20 3 0.09
21 9 0.26
22 4 0.11
23 4 0.11
24 4 0.11
25 8 0.23
26 3 0.09
ACGTcount: A:0.54, C:0.21, G:0.09, T:0.16
Consensus pattern (21 bp):
ATTATAAGAAAAACACCCAAG
Found at i:2597259 original size:46 final size:46
Alignment explanation
Indices: 2597209--2597300 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
2597199 ATAATTTAAT
*
2597209 TTAAAGTAAAAACCTACACGACCCATTATAAGAAAAACACCCAAGA
1 TTAAAGTAAAAACCTACACGAACCATTATAAGAAAAACACCCAAGA
*
2597255 TTAAAGTAAAAACCTACACGAACCTTTATAAGAAAAACACCCAAGA
1 TTAAAGTAAAAACCTACACGAACCATTATAAGAAAAACACCCAAGA
2597301 CATCTAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.52, C:0.23, G:0.09, T:0.16
Consensus pattern (46 bp):
TTAAAGTAAAAACCTACACGAACCATTATAAGAAAAACACCCAAGA
Found at i:2597290 original size:25 final size:25
Alignment explanation
Indices: 2597209--2597292 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 25
2597199 ATAATTTAAT
*
2597209 TTAAAGTAAAAACCTACACGACCCA
1 TTAAAGTAAAAACCTACACGAACCA
* *
2597234 TTATAAG-AAAAA-C-AC-CCAA-GA
1 TTA-AAGTAAAAACCTACACGAACCA
*
2597255 TTAAAGTAAAAACCTACACGAACCT
1 TTAAAGTAAAAACCTACACGAACCA
2597280 TTATAAG-AAAAAC
1 TTA-AAGTAAAAAC
2597293 ACCCAAGACA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
20 3 0.07
21 9 0.20
22 3 0.07
23 4 0.09
24 4 0.09
25 17 0.37
26 6 0.13
ACGTcount: A:0.52, C:0.21, G:0.08, T:0.18
Consensus pattern (25 bp):
TTAAAGTAAAAACCTACACGAACCA
Found at i:2602472 original size:136 final size:136
Alignment explanation
Indices: 2602228--2602502 Score: 406
Period size: 136 Copynumber: 2.0 Consensus size: 136
2602218 TTCTGATACC
* * * *
2602228 ACTAAATGTAACACCCCTAATCCATATCTATTCATACTATAGACCATATAATAATATTAAAACAA
1 ACTAAATGTAAAACCCCTAACCCATATCTATTCATACTATAGACCATAAAATAATATGAAAACAA
* *
2602293 ATTTTCTTTTCGGGATCAGACTTGTGGTCCCGAAACCACTGTTCCAATTACTCTAAAAATGGGCT
66 ATTTTCTTTTCGAGATCAAACTTGTGGTCCCGAAACCACTGTTCCAATTACTCTAAAAATGGGCT
*
2602358 GTTACA
131 ATTACA
* * * *
2602364 ACTAAATGTAAAACTCCTAACCCATATCTATTCATACTGTATACCATAAAATAATATGAAAATAA
1 ACTAAATGTAAAACCCCTAACCCATATCTATTCATACTATAGACCATAAAATAATATGAAAACAA
* * * * *
2602429 GTTTTTTTTTCGAGATCAAATTTGTGGTCCCGAAACCACTGTTCCGATTTCTCTAAAAATGGGCT
66 ATTTTCTTTTCGAGATCAAACTTGTGGTCCCGAAACCACTGTTCCAATTACTCTAAAAATGGGCT
2602494 ATTACA
131 ATTACA
2602500 ACT
1 ACT
2602503 GGGCAGAAGT
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
136 123 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.33
Consensus pattern (136 bp):
ACTAAATGTAAAACCCCTAACCCATATCTATTCATACTATAGACCATAAAATAATATGAAAACAA
ATTTTCTTTTCGAGATCAAACTTGTGGTCCCGAAACCACTGTTCCAATTACTCTAAAAATGGGCT
ATTACA
Found at i:2623705 original size:3 final size:3
Alignment explanation
Indices: 2623697--2623722 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2623687 AACAAATAGG
2623697 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2623723 GAACTAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2629358 original size:17 final size:16
Alignment explanation
Indices: 2629314--2629360 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
2629304 TCTTTACAGA
*
2629314 AGAGTCTGCCAAACCTT
1 AGAGT-TGCCAAACCCT
2629331 AGAGTTCGCCAAACCCT
1 AGAGTT-GCCAAACCCT
2629348 AGAGTGTGCCAAA
1 AGAGT-TGCCAAA
2629361 TGGTGAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 1 0.04
17 25 0.93
18 1 0.04
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (16 bp):
AGAGTTGCCAAACCCT
Found at i:2629758 original size:30 final size:30
Alignment explanation
Indices: 2629724--2629783 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2629714 TAAATAAGGC
* *
2629724 CTTTAGGTCAA-TTTTATTTTTTAATTAGGA
1 CTTTAGATCAATTTTTA-ATTTTAATTAGGA
2629754 CTTTAGATCAATTTTTAATTTTAATTAGGA
1 CTTTAGATCAATTTTTAATTTTAATTAGGA
2629784 AAATAGGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.52
Consensus pattern (30 bp):
CTTTAGATCAATTTTTAATTTTAATTAGGA
Found at i:2643641 original size:47 final size:45
Alignment explanation
Indices: 2643586--2643773 Score: 175
Period size: 47 Copynumber: 4.0 Consensus size: 45
2643576 TACGTATTTA
*
2643586 TATT-AAAATATAAACATAATAAT-AGTATTAAAAAGTATATACATAG
1 TATTAAAAATATATACATAAT-ATGA-TATTAAAAA-TATATACATAG
* *
2643632 TATTAAAAATATATACATAATAATGATATTAAAAGTATGTACGTAATATAG
1 TATTAAAAATATATACATAAT-ATGATATTAAAA--ATATA--T-ACATAG
* * * *
2643683 TGTTAAAAATACATACATAATATAGTTATTAAAAATATATACATAA
1 TATTAAAAATATATACATAATAT-GATATTAAAAATATATACATAG
*
2643729 TATAATAAAATATATGA-ATAATATGATATTAAAAATATATACATA
1 TATTA-AAAATATAT-ACATAATATGATATTAAAAATATATACATA
2643774 ATATAATATT
Statistics
Matches: 119, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
46 31 0.26
47 42 0.35
48 5 0.04
49 5 0.04
50 3 0.03
51 33 0.28
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (45 bp):
TATTAAAAATATATACATAATATGATATTAAAAATATATACATAG
Found at i:2643644 original size:20 final size:21
Alignment explanation
Indices: 2643607--2643650 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2643597 AAACATAATA
2643607 ATAGTATTAAAAAGTATATAC
1 ATAGTATTAAAAAGTATATAC
2643628 ATAGTATTAAAAA-TATATAC
1 ATAGTATTAAAAAGTATATAC
2643648 ATA
1 ATA
2643651 ATAATGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (21 bp):
ATAGTATTAAAAAGTATATAC
Found at i:2643688 original size:25 final size:26
Alignment explanation
Indices: 2643586--2643778 Score: 159
Period size: 26 Copynumber: 7.9 Consensus size: 26
2643576 TACGTATTTA
*
2643586 TATT-AAAATATAAACATAATAATAG-
1 TATTAAAAATATATACATAAT-ATAGT
2643611 TATTAAAAAGTATATAC-----ATAG-
1 TATTAAAAA-TATATACATAATATAGT
*
2643632 TATTAAAAATATATACATAATA-ATGA
1 TATTAAAAATATATACATAATATA-GT
* * *
2643658 TATTAAAAGTATGTACGTAATATAG-
1 TATTAAAAATATATACATAATATAGT
* *
2643683 TGTTAAAAATACATACATAATATAGT
1 TATTAAAAATATATACATAATATAGT
2643709 TATTAAAAATATATACATAATATA--
1 TATTAAAAATATATACATAATATAGT
*
2643733 -A-T-AAAATATATGA-ATAATAT-GA
1 TATTAAAAATATAT-ACATAATATAGT
2643755 TATTAAAAATATATACATAATATA
1 TATTAAAAATATATACATAATATA
2643779 ATATTAATAT
Statistics
Matches: 138, Mismatches: 11, Indels: 37
0.74 0.06 0.20
Matches are distributed among these distances:
20 7 0.05
21 29 0.21
22 2 0.01
23 2 0.01
24 3 0.02
25 42 0.30
26 46 0.33
27 7 0.05
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (26 bp):
TATTAAAAATATATACATAATATAGT
Found at i:2643776 original size:97 final size:98
Alignment explanation
Indices: 2643590--2643778 Score: 260
Period size: 97 Copynumber: 1.9 Consensus size: 98
2643580 TATTTATATT
* * *
2643590 AAAATATAAACATAATAATAGTATTAAAAAGTATATACATAGTATTAAAAATATATACATAATAA
1 AAAATACAAACATAATAATAGTATTAAAAAGTATATACATAATATAAAAAATATATACATAATAA
* * *
2643655 TGATATTAAAAGTATGTACGTAATATAGTGTTA
66 TGATATTAAAAATATATACATAATATAGTGTTA
*
2643688 AAAATACATACATAAT-ATAGTTATTAAAAA-TATATACATAATATAATAAAATATATGA-ATAA
1 AAAATACAAACATAATAATAG-TATTAAAAAGTATATACATAATATAA-AAAATATAT-ACATAA
2643750 T-ATGATATTAAAAATATATACATAATATA
63 TAATGATATTAAAAATATATACATAATATA
2643779 ATATTAATAT
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
97 43 0.53
98 37 0.46
99 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (98 bp):
AAAATACAAACATAATAATAGTATTAAAAAGTATATACATAATATAAAAAATATATACATAATAA
TGATATTAAAAATATATACATAATATAGTGTTA
Found at i:2643802 original size:51 final size:50
Alignment explanation
Indices: 2643585--2643804 Score: 185
Period size: 51 Copynumber: 4.5 Consensus size: 50
2643575 ATACGTATTT
*
2643585 ATATT-AAAATATAAACATAATAAT-AGTATTAAAAAGTATATAC-----ATA
1 ATATTAAAAATATATACATAAT-ATGA-TATTAAAAA-TATATACATAATATA
* * * *
2643631 GTATTAAAAATATATACATAATAATGATATTAAAAGTATGTACGTAATATA
1 ATATTAAAAATATATACATAAT-ATGATATTAAAAATATATACATAATATA
* * * *
2643682 GTGTTAAAAATACATACATAATATAGTTATTAAAAATATATACATAATAT-
1 ATATTAAAAATATATACATAATAT-GATATTAAAAATATATACATAATATA
2643732 A-A-T-AAAATATATGA-ATAATATGATATTAAAAATATATACATAATATA
1 ATATTAAAAATATAT-ACATAATATGATATTAAAAATATATACATAATATA
* * *
2643779 ATATTAATATATATATGCGTAATATG
1 ATATTAA-AAATATATACATAATATG
2643805 GAGTATAATA
Statistics
Matches: 142, Mismatches: 17, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
46 34 0.24
47 42 0.30
48 4 0.03
49 1 0.01
50 3 0.02
51 58 0.41
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (50 bp):
ATATTAAAAATATATACATAATATGATATTAAAAATATATACATAATATA
Found at i:2645860 original size:24 final size:24
Alignment explanation
Indices: 2645833--2645880 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2645823 GAATTTAGCC
2645833 CATCTTGTAATGGCGTAAATTCAA
1 CATCTTGTAATGGCGTAAATTCAA
2645857 CATCTTGTAATGGCGTAAATTCAA
1 CATCTTGTAATGGCGTAAATTCAA
2645881 TGTTATCGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (24 bp):
CATCTTGTAATGGCGTAAATTCAA
Found at i:2650925 original size:24 final size:24
Alignment explanation
Indices: 2650898--2650948 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
2650888 TTTTGAGCAA
2650898 TTTAA-TTTT-TTTCTTTTATGTTAT
1 TTTAACTTTTCTTT-TTTTAT-TTAT
*
2650922 TTTAACTTTTCTTTTTTTCTTTAT
1 TTTAACTTTTCTTTTTTTATTTAT
2650946 TTT
1 TTT
2650949 CCATTCTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 12 0.50
25 9 0.38
26 3 0.12
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTAACTTTTCTTTTTTTATTTAT
Found at i:2651141 original size:25 final size:24
Alignment explanation
Indices: 2651112--2651158 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
2651102 ACAAATGGAA
2651112 AACATAAAA-AAAATAGAGTTAAAAG
1 AACATAAAAGAAAA-AGA-TTAAAAG
2651137 AACATAAAAGAAAAAGATTAAA
1 AACATAAAAGAAAAAGATTAAA
2651159 TTGCTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.15
Consensus pattern (24 bp):
AACATAAAAGAAAAAGATTAAAAG
Found at i:2651430 original size:15 final size:14
Alignment explanation
Indices: 2651402--2651446 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
2651392 TATCCTTTTT
2651402 TATTA-AATAATAA
1 TATTATAATAATAA
*
2651415 TATTTTAATAATTAA
1 TATTATAATAA-TAA
2651430 TATTATAATATATAA
1 TATTATAATA-ATAA
2651445 TA
1 TA
2651447 AAGAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.15
14 5 0.19
15 17 0.63
16 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTATAATAATAA
Found at i:2652258 original size:5 final size:5
Alignment explanation
Indices: 2652248--2652284 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
2652238 TGCTAATATC
2652248 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
2652285 TATGAATAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:2661796 original size:31 final size:31
Alignment explanation
Indices: 2661760--2661824 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
2661750 GTAAAAAGAC
* *
2661760 TAAATTCACAAATTTTATAAAATATATGA-AT
1 TAAATTCACAAATTTCACAAAATATA-GAGAT
* *
2661791 TAAATTTACAACTTTCACAAAATATAGAGAT
1 TAAATTCACAAATTTCACAAAATATAGAGAT
2661822 TAA
1 TAA
2661825 TAGTAGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (31 bp):
TAAATTCACAAATTTCACAAAATATAGAGAT
Found at i:2666705 original size:21 final size:22
Alignment explanation
Indices: 2666646--2666706 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 22
2666636 ATTATTTTAT
*
2666646 TTATATAAATAAAAGAGTTATTAA
1 TTAT-TAAATAAAA-ATTTATTAA
* *
2666670 TTA--AAATATATATTTA-TAA
1 TTATTAAATAAAAATTTATTAA
2666689 TTATTAAATAAAAATTTA
1 TTATTAAATAAAAATTTA
2666707 AAATGAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
19 6 0.20
20 4 0.13
21 17 0.57
24 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (22 bp):
TTATTAAATAAAAATTTATTAA
Found at i:2670714 original size:5 final size:5
Alignment explanation
Indices: 2670704--2670736 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
2670694 CTAAACAAAG
2670704 ACCAC ACCAC ACCAC ACCAC ACCAC ACTCAC AC
1 ACCAC ACCAC ACCAC ACCAC ACCAC AC-CAC AC
2670737 TCATTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.39, C:0.58, G:0.00, T:0.03
Consensus pattern (5 bp):
ACCAC
Found at i:2673062 original size:30 final size:30
Alignment explanation
Indices: 2673026--2673085 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2673016 ATGCTGATCC
*
2673026 GGATGACCTTGGCAAGGGGGGGCATGAGCT
1 GGATGACCTTGGCAAGGGGGGGCACGAGCT
2673056 GGATGACCTTGGCAAGGGGGGGCACGAGCT
1 GGATGACCTTGGCAAGGGGGGGCACGAGCT
2673086 TAGCAAAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.47, T:0.15
Consensus pattern (30 bp):
GGATGACCTTGGCAAGGGGGGGCACGAGCT
Found at i:2682112 original size:26 final size:26
Alignment explanation
Indices: 2682083--2682142 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
2682073 TCCCTTTGAA
* * *
2682083 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
2682109 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
2682137 CCATTC
1 TCATTC
2682143 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:2682128 original size:28 final size:28
Alignment explanation
Indices: 2682097--2682168 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
2682087 TCGATATTTT
*
2682097 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
2682125 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
2682153 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
2682169 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:2687082 original size:30 final size:30
Alignment explanation
Indices: 2687048--2687108 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2687038 TAAAGAACAC
*
2687048 ATAGATTTTTATGTGAAAACCCTTTCGGGA
1 ATAGATTTTTACGTGAAAACCCTTTCGGGA
2687078 ATAGATTTTTACGTGAAAACCCTTTCGGGA
1 ATAGATTTTTACGTGAAAACCCTTTCGGGA
2687108 A
1 A
2687109 AAAATTACGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (30 bp):
ATAGATTTTTACGTGAAAACCCTTTCGGGA
Found at i:2687443 original size:6 final size:7
Alignment explanation
Indices: 2687427--2687451 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2687417 TCTTTTTTTC
2687427 AAAAATA
1 AAAAATA
2687434 AAAAATA
1 AAAAATA
2687441 AAAAATA
1 AAAAATA
2687448 AAAA
1 AAAA
2687452 CAAATACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2693772 original size:16 final size:17
Alignment explanation
Indices: 2693751--2693782 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2693741 ATATTTAGTC
2693751 ATATAATAAAT-TATTA
1 ATATAATAAATATATTA
2693767 ATATAATAAATATATT
1 ATATAATAAATATATT
2693783 TTGTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATAAATATATTA
Found at i:2693835 original size:13 final size:14
Alignment explanation
Indices: 2693819--2693860 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
2693809 TTTCAATTTT
2693819 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
2693832 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
2693847 ATTTTAAATAATAT
1 ATTTT-AATAATAT
2693861 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:2693845 original size:16 final size:16
Alignment explanation
Indices: 2693823--2693859 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2693813 AATTTTATTT
2693823 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
2693840 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
2693855 TAATA
1 TAATA
2693860 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:2693912 original size:15 final size:15
Alignment explanation
Indices: 2693892--2693948 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
2693882 ATTCAATATT
2693892 AATATTTTAATAATA
1 AATATTTTAATAATA
*
2693907 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
2693926 AATATATTAATAATA
1 AATATTTTAATAATA
*
2693941 AATGTTTT
1 AATATTTT
2693949 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:2694419 original size:14 final size:14
Alignment explanation
Indices: 2694400--2694438 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2694390 CCGGAAAAGT
*
2694400 AAATCATTTTCTAG
1 AAATCATTTTCCAG
2694414 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
2694428 AAGTCATTTTC
1 AAATCATTTTC
2694439 AGTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:2694867 original size:13 final size:13
Alignment explanation
Indices: 2694849--2694909 Score: 95
Period size: 13 Copynumber: 4.7 Consensus size: 13
2694839 AGTTTGGCAA
2694849 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
2694862 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* * *
2694875 TGCTGTAGAAAAG
1 TGCTTTTGAGAAG
2694888 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
2694901 TGCTTTTGA
1 TGCTTTTGA
2694910 AAAATTTAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.25, C:0.08, G:0.30, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:2695146 original size:11 final size:11
Alignment explanation
Indices: 2695130--2695154 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2695120 TAATTAATAT
2695130 TAATTATTTCA
1 TAATTATTTCA
2695141 TAATTATTTCA
1 TAATTATTTCA
2695152 TAA
1 TAA
2695155 AATCAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TAATTATTTCA
Found at i:2695729 original size:17 final size:18
Alignment explanation
Indices: 2695689--2695723 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2695679 TTTATTTATG
*
2695689 ATATTTTTAATTTTAAAA
1 ATATTTTAAATTTTAAAA
2695707 ATATTTTAAATTTTAAA
1 ATATTTTAAATTTTAAA
2695724 TTATTTGCTA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTTTAAATTTTAAAA
Found at i:2696115 original size:17 final size:18
Alignment explanation
Indices: 2696079--2696117 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2696069 TCTTCAACTA
*
2696079 TTTTTAGGGTTTTAGAGT
1 TTTTTAGGGTTTAAGAGT
2696097 TTTTTAGGGTTTAAG-GT
1 TTTTTAGGGTTTAAGAGT
2696114 TTTT
1 TTTT
2696118 GTTTTTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (18 bp):
TTTTTAGGGTTTAAGAGT
Found at i:2696115 original size:25 final size:25
Alignment explanation
Indices: 2696081--2696139 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
2696071 TTCAACTATT
*
2696081 TTTAGGGTTTTAGAGTTTTT-TAGGG
1 TTTAAGGTTTTAG-GTTTTTGTAGGG
* *
2696106 TTTAAGGTTTTTGTTTTTTGTAGGG
1 TTTAAGGTTTTAGGTTTTTGTAGGG
2696131 TTTAAGGTT
1 TTTAAGGTT
2696140 GAAAATTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (25 bp):
TTTAAGGTTTTAGGTTTTTGTAGGG
Found at i:2698476 original size:57 final size:56
Alignment explanation
Indices: 2698327--2698464 Score: 168
Period size: 57 Copynumber: 2.4 Consensus size: 56
2698317 TATCATATAA
* * ** *
2698327 TAGGATTACCAGTTCAGGCTAAATTTTGTCTCCAACATATGATCACAAGAGCTTAAT
1 TAGGATTACCAGTCCAGGCTAAA-TATGTCTATAACATATGATCACAAGAGCTCAAT
* * ** *
2698384 TAGGATTACCAATCCAAGCTAAATATGTTCTATAACATATTCTCAGAAGAGCTCAAT
1 TAGGATTACCAGTCCAGGCTAAATATG-TCTATAACATATGATCACAAGAGCTCAAT
2698441 TAGGATTACCAGTCCAGGCTAAAT
1 TAGGATTACCAGTCCAGGCTAAAT
2698465 CCTAGCTATA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
56 3 0.04
57 65 0.96
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (56 bp):
TAGGATTACCAGTCCAGGCTAAATATGTCTATAACATATGATCACAAGAGCTCAAT
Found at i:2699977 original size:75 final size:75
Alignment explanation
Indices: 2699854--2700101 Score: 311
Period size: 75 Copynumber: 3.3 Consensus size: 75
2699844 ACAGAAAAGG
** * * * *
2699854 TTGCACCCAGCACTAGTCTGAT-TAACCGAC-AGTATTAAATGTGAGCCCAACTCTAGTTGGATA
1 TTGCACCCAGTGCTAGTCGGATAT-ACCGACGA-TAATAATTGTGAGCCCAGCTCTAGTTGGATA
* *
2699917 ACCCAACAATAT
64 AACCAACGATAT
* *
2699929 TTGCACCCAGTGCTAGTCGGATATATCGACGATAATAATTGTGAGCCCAGCTCTAGTGGGATAAA
1 TTGCACCCAGTGCTAGTCGGATATACCGACGATAATAATTGTGAGCCCAGCTCTAGTTGGATAAA
2699994 CCAACGATAT
66 CCAACGATAT
* * *
2700004 TTGCACCTAGTGCTAGTCGAATATACCGACGATAATAATTGTGAGCTCAGCTCTAGTTGGATAAA
1 TTGCACCCAGTGCTAGTCGGATATACCGACGATAATAATTGTGAGCCCAGCTCTAGTTGGATAAA
* *
2700069 CCAACGGTAA
66 CCAACGATAT
* *
2700079 TTGCACCCAATGCTAGTCAGATA
1 TTGCACCCAGTGCTAGTCGGATA
2700102 AACCCACAAT
Statistics
Matches: 150, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
75 148 0.99
76 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (75 bp):
TTGCACCCAGTGCTAGTCGGATATACCGACGATAATAATTGTGAGCCCAGCTCTAGTTGGATAAA
CCAACGATAT
Found at i:2699991 original size:40 final size:40
Alignment explanation
Indices: 2699941--2700066 Score: 120
Period size: 40 Copynumber: 3.3 Consensus size: 40
2699931 GCACCCAGTG
*
2699941 CTAGTCGGATATATCGACGATAATAATTGTGAGCCCAGCT
1 CTAGTCGGATATACCGACGATAATAATTGTGAGCCCAGCT
* * * * *
2699981 CTAGTGGGATAAACCAACGAT-AT--TTG-CA-CCTAG-T
1 CTAGTCGGATATACCGACGATAATAATTGTGAGCCCAGCT
* *
2700015 GCTAGTCGAATATACCGACGATAATAATTGTGAGCTCAGCT
1 -CTAGTCGGATATACCGACGATAATAATTGTGAGCCCAGCT
*
2700056 CTAGTTGGATA
1 CTAGTCGGATA
2700067 AACCAACGGT
Statistics
Matches: 64, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
34 1 0.02
35 21 0.33
36 3 0.05
37 3 0.05
38 3 0.05
39 3 0.05
40 29 0.45
41 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (40 bp):
CTAGTCGGATATACCGACGATAATAATTGTGAGCCCAGCT
Found at i:2700036 original size:35 final size:35
Alignment explanation
Indices: 2699925--2700037 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 35
2699915 TAACCCAACA
*
2699925 ATATTTGCACCCAGTGCTAGTCGGATATATCGACG
1 ATATTTGCACCCAGTGCTAGTCGGATATACCGACG
* * * *
2699960 ATAATAATTGTGAGCCCAGCT-CTAGTGGGATAAACCAACG
1 AT-AT--TTG-CA-CCCAG-TGCTAGTCGGATATACCGACG
* *
2700000 ATATTTGCACCTAGTGCTAGTCGAATATACCGACG
1 ATATTTGCACCCAGTGCTAGTCGGATATACCGACG
2700035 ATA
1 ATA
2700038 ATAATTGTGA
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
34 1 0.02
35 24 0.40
36 3 0.05
37 3 0.05
38 3 0.05
39 3 0.05
40 22 0.37
41 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (35 bp):
ATATTTGCACCCAGTGCTAGTCGGATATACCGACG
Found at i:2701472 original size:16 final size:16
Alignment explanation
Indices: 2701453--2701486 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2701443 TTTGCTAAAG
*
2701453 CAATGCTTTTATTTCT
1 CAATGCATTTATTTCT
*
2701469 CAATTCATTTATTTCT
1 CAATGCATTTATTTCT
2701485 CA
1 CA
2701487 TGTTAGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.53
Consensus pattern (16 bp):
CAATGCATTTATTTCT
Found at i:2705651 original size:40 final size:40
Alignment explanation
Indices: 2705602--2705769 Score: 126
Period size: 35 Copynumber: 4.5 Consensus size: 40
2705592 GCACCCAGTG
2705602 CTAGTTGGATATACCGACTATAATAATTGTGAGCCCAGCT
1 CTAGTTGGATATACCGACTATAATAATTGTGAGCCCAGCT
* * * * *
2705642 CTAGATGGATAAACCAACGAT-AT--TTG-CA-CCCA-CT
1 CTAGTTGGATATACCGACTATAATAATTGTGAGCCCAGCT
* *
2705676 GCTAGTAGGATATACCGA-TGATAATAATTGTGAGCTCAGCT
1 -CTAGTTGGATATACCGACT-ATAATAATTGTGAGCCCAGCT
* ** *
2705717 CTAGTTGGATAAACC-A--ACGATAATTGT--GCCCAGCA
1 CTAGTTGGATATACCGACTATAATAATTGTGAGCCCAGCT
*
2705752 CTAGTTGGATAAACCGAC
1 CTAGTTGGATATACCGAC
2705770 AATTGTGTGC
Statistics
Matches: 100, Mismatches: 18, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
34 2 0.02
35 40 0.40
36 4 0.04
37 12 0.12
38 3 0.03
39 4 0.04
40 33 0.33
41 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (40 bp):
CTAGTTGGATATACCGACTATAATAATTGTGAGCCCAGCT
Found at i:2705756 original size:75 final size:75
Alignment explanation
Indices: 2705560--2705769 Score: 280
Period size: 75 Copynumber: 2.8 Consensus size: 75
2705550 TAAATGCGAC
* * * *
2705560 CCCAACTCTAGTTGGATAAACCAACAATTTTTGCACCCAGTGCTAGTTGGATATACCGACTATAA
1 CCCAGCTCTAGTTGGATAAACCAACGATATTTGCACCCAGCGCTAGTTGGATATACCGACTATAA
2705625 TAATTGTGAG
66 TAATTGTGAG
* *
2705635 CCCAGCTCTAGATGGATAAACCAACGATATTTGCACCCA-CTGCTAGTAGGATATACCGA-TGAT
1 CCCAGCTCTAGTTGGATAAACCAACGATATTTGCACCCAGC-GCTAGTTGGATATACCGACT-AT
2705698 AATAATTGTGAG
64 AATAATTGTGAG
* * ** * *
2705710 CTCAGCTCTAGTTGGATAAACCAACGATAATTGTGCCCAGCACTAGTTGGATAAACCGAC
1 CCCAGCTCTAGTTGGATAAACCAACGATATTTGCACCCAGCGCTAGTTGGATATACCGAC
2705770 AATTGTGTGC
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
74 1 0.01
75 115 0.98
76 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (75 bp):
CCCAGCTCTAGTTGGATAAACCAACGATATTTGCACCCAGCGCTAGTTGGATATACCGACTATAA
TAATTGTGAG
Found at i:2705784 original size:34 final size:35
Alignment explanation
Indices: 2705701--2705790 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 35
2705691 CGATGATAAT
* * *
2705701 AATTGTGAGCTCAGCTCTAGTTGGATAAACCAACG
1 AATTGTGTGCCCAGCACTAGTTGGATAAACCAACG
* *
2705736 ATAAT-TGTGCCCAGCACTAGTTGGATAAACCGAC-
1 A-ATTGTGTGCCCAGCACTAGTTGGATAAACCAACG
2705770 AATTGTGTGCCCAGCACTAGT
1 AATTGTGTGCCCAGCACTAGT
2705791 CAGACAAGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
33 2 0.04
34 17 0.36
35 26 0.55
36 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (35 bp):
AATTGTGTGCCCAGCACTAGTTGGATAAACCAACG
Found at i:2707547 original size:21 final size:21
Alignment explanation
Indices: 2707523--2707570 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2707513 TGTACGAGTA
*
2707523 AATTTA-ACATCAATTTAATGT
1 AATTTATAC-TCAATTTAATCT
* *
2707544 AATTCATACTCAATTTAGTCT
1 AATTTATACTCAATTTAATCT
2707565 AATTTA
1 AATTTA
2707571 CAATTTAAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (21 bp):
AATTTATACTCAATTTAATCT
Found at i:2713082 original size:18 final size:18
Alignment explanation
Indices: 2713056--2713090 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2713046 GAGTTAAACG
2713056 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
*
2713074 AATCTAGTTATTCGAGT
1 AATCGAGTTATTCGAGT
2713091 CAACTCGAAT
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:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:2713291 original size:32 final size:30
Alignment explanation
Indices: 2713229--2713291 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
2713219 ACTTTTCCCT
* **
2713229 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCTTCCCACCTAACCCC
*
2713259 CAAAACTTTTACTCCTCTTCCATCCTAACCCC
1 CAAAACTTTTACTCCT-TCCCA-CCTAACCCC
2713291 C
1 C
2713292 CAATCTACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 16 0.59
31 4 0.15
32 7 0.26
ACGTcount: A:0.22, C:0.46, G:0.00, T:0.32
Consensus pattern (30 bp):
CAAAACTTTTACTCCTTCCCACCTAACCCC
Found at i:2716252 original size:75 final size:74
Alignment explanation
Indices: 2716051--2716260 Score: 251
Period size: 75 Copynumber: 2.8 Consensus size: 74
2716041 TCCGACAATA
* * * * * *
2716051 GATGTGCTCAGCACTAGTCAAACAAATTGACGAAAGTTGTGCCCAGCACTAGTCGGGTAAACCAA
1 GATGTGCCCAGCACTAGTCAAATAAATCGAC-AAAGTTGCGCCCAGCGCTAGTCGGATAAACCAA
2716116 CAAATATAAT
65 CAAATATAAT
* * * * *
2716126 GATGTGCCTAGCACTAGTCAGATAAA-CTGACAAAGGTTGCACCCGGCGCTAGTCGAATAAACCA
1 GATGTGCCCAGCACTAGTCAAATAAATC-GACAAA-GTTGCGCCCAGCGCTAGTCGGATAAACCA
*
2716190 ACAAGTATAAT
64 ACAAATATAAT
**
2716201 GATGTGCCCAGCACTAGTCAAATAAATCGACAAAGATTGCGCCCAATGCTAGTCGGATAA
1 GATGTGCCCAGCACTAGTCAAATAAATCGACAAAG-TTGCGCCCAGCGCTAGTCGGATAA
2716261 CCGACAATAG
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
74 4 0.04
75 107 0.96
76 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (74 bp):
GATGTGCCCAGCACTAGTCAAATAAATCGACAAAGTTGCGCCCAGCGCTAGTCGGATAAACCAAC
AAATATAAT
Found at i:2716705 original size:32 final size:32
Alignment explanation
Indices: 2716659--2716719 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
2716649 ATAGTTTCCA
* *
2716659 GTGATCGAGCTTAATTAATCGACGACTTTTCG
1 GTGATCAAGCTTAATTAATCGACAACTTTTCG
* *
2716691 GTGATCAAGGTTAATTATTCGACAACTTT
1 GTGATCAAGCTTAATTAATCGACAACTTT
2716720 CTCCTTCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (32 bp):
GTGATCAAGCTTAATTAATCGACAACTTTTCG
Found at i:2719534 original size:37 final size:37
Alignment explanation
Indices: 2719489--2719568 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 37
2719479 AGGCTAGGCA
* **
2719489 CGTGTTATTTGTTGGATTAGCTCTCATGATTGTTTGG
1 CGTGTTATTGGTTGGATTAGCTCTCATGAGCGTTTGG
*
2719526 CGTGTTATTGGTTGGATTAGCTCTTATGAGCGTTTGG
1 CGTGTTATTGGTTGGATTAGCTCTCATGAGCGTTTGG
*
2719563 TGTGTT
1 CGTGTT
2719569 TCCATTGAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.12, C:0.10, G:0.30, T:0.47
Consensus pattern (37 bp):
CGTGTTATTGGTTGGATTAGCTCTCATGAGCGTTTGG
Found at i:2720584 original size:30 final size:30
Alignment explanation
Indices: 2720541--2720605 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
2720531 AAGGTCTGCG
*
2720541 ACACGGTCATGTGTATCAAGTCAGAGAGTT
1 ACACGGCCATGTGTATCAAGTCAGAGAGTT
* * *
2720571 ACACGGCCGTGTGTATCAAGTTAGTGAGTT
1 ACACGGCCATGTGTATCAAGTCAGAGAGTT
2720601 ACACG
1 ACACG
2720606 AGCTGGGACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (30 bp):
ACACGGCCATGTGTATCAAGTCAGAGAGTT
Found at i:2728527 original size:18 final size:18
Alignment explanation
Indices: 2728490--2728527 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2728480 GAGTTAAATG
* *
2728490 AATCGAGTTATTCTATTT
1 AATCGAGTTATTCGAGTT
2728508 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
2728526 AA
1 AA
2728528 CTCAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:2729954 original size:47 final size:47
Alignment explanation
Indices: 2729846--2729972 Score: 164
Period size: 47 Copynumber: 2.7 Consensus size: 47
2729836 GAGTGATCCT
* * * *
2729846 TTGATTTGACTACGGGCCATGGTATAGGTATTTCAGTGAGGAGTTACC
1 TTGATTTGGCTACGGGCCATGGTATAGGTA-CTCAGGGAGAAGTTACC
* * * *
2729894 TTAATTTGGCTACGGGCCATGGTGTAGGTACTCCGGGATAAGTTACC
1 TTGATTTGGCTACGGGCCATGGTATAGGTACTCAGGGAGAAGTTACC
*
2729941 TTGATTTGGCTACGAGCCATGGTATAGGTACT
1 TTGATTTGGCTACGGGCCATGGTATAGGTACT
2729973 TATCAATTGA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 41 0.60
48 27 0.40
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (47 bp):
TTGATTTGGCTACGGGCCATGGTATAGGTACTCAGGGAGAAGTTACC
Found at i:2730676 original size:14 final size:14
Alignment explanation
Indices: 2730657--2730688 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2730647 AAATATAACC
2730657 ATTAAATATTTATA
1 ATTAAATATTTATA
2730671 ATTAAATATTTATA
1 ATTAAATATTTATA
2730685 ATTA
1 ATTA
2730689 GTATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTAAATATTTATA
Found at i:2734738 original size:51 final size:51
Alignment explanation
Indices: 2734655--2734797 Score: 180
Period size: 51 Copynumber: 2.8 Consensus size: 51
2734645 TCAACGATGG
* * * *
2734655 TTTCAGGGTGGGAT-TCATGCTTTCACTCCGGGGACTCAACCACTTGGCCAA
1 TTTCACGGTGGGATCT-ATGCTTCCACACCGGGGACTCAACCACTAGGCCAA
* * *
2734706 TTTCACGGTGGGATCTATGCTTCCACAGCGGGGACTCAACCACTAGGGCAG
1 TTTCACGGTGGGATCTATGCTTCCACACCGGGGACTCAACCACTAGGCCAA
* * *
2734757 CTTCACGGTGGGATCTTTGCTTCCACACCGGGGGCTCAACC
1 TTTCACGGTGGGATCTATGCTTCCACACCGGGGACTCAACC
2734798 GCAAGAGCTA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
51 79 0.99
52 1 0.01
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.24
Consensus pattern (51 bp):
TTTCACGGTGGGATCTATGCTTCCACACCGGGGACTCAACCACTAGGCCAA
Found at i:2737243 original size:62 final size:62
Alignment explanation
Indices: 2737169--2737294 Score: 182
Period size: 62 Copynumber: 2.0 Consensus size: 62
2737159 ATATTTTAAA
* * *
2737169 AAGAACTCGAAGATCTACAATTTAGACGA-AAGAATCATATATTAATAATAGTAGATTCCAGG
1 AAGAACTCGAAGATATACAATTTAGAC-ATAAGAACCACATATTAATAATAGTAGATTCCAGG
** *
2737231 AAGAACTCGAAGATATATTATTTAGACATAAGAACCACATATTAATAATAGTAGATTCTAGG
1 AAGAACTCGAAGATATACAATTTAGACATAAGAACCACATATTAATAATAGTAGATTCCAGG
2737293 AA
1 AA
2737295 AGTATTGCTC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 1 0.02
62 56 0.98
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (62 bp):
AAGAACTCGAAGATATACAATTTAGACATAAGAACCACATATTAATAATAGTAGATTCCAGG
Found at i:2742292 original size:14 final size:14
Alignment explanation
Indices: 2742273--2742301 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2742263 CTTTTTACTT
2742273 TGTTATATAGATTA
1 TGTTATATAGATTA
2742287 TGTTATATAGATTA
1 TGTTATATAGATTA
2742301 T
1 T
2742302 TATTTATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TGTTATATAGATTA
Found at i:2743329 original size:15 final size:15
Alignment explanation
Indices: 2743300--2743348 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
2743290 TTATTTTTTT
2743300 TTGTCTTCTT--C-G
1 TTGTCTTCTTGCCTG
* *
2743312 TTGTTTTCTTGCGTG
1 TTGTCTTCTTGCCTG
*
2743327 TTGGCTTCTTGCCTG
1 TTGTCTTCTTGCCTG
2743342 TTGTCTT
1 TTGTCTT
2743349 TGTCTTGCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 9 0.32
15 19 0.68
ACGTcount: A:0.00, C:0.20, G:0.22, T:0.57
Consensus pattern (15 bp):
TTGTCTTCTTGCCTG
Found at i:2745438 original size:20 final size:21
Alignment explanation
Indices: 2745402--2745446 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2745392 GAGTAGCATG
2745402 ATTTTACATGCATTTATAATT
1 ATTTTACATGCATTTATAATT
* *
2745423 ATTTTACCTG-ATTTATATTT
1 ATTTTACATGCATTTATAATT
2745443 ATTT
1 ATTT
2745447 AATATTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.29, C:0.09, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTTTACATGCATTTATAATT
Done.