Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 8 of 208
Found at i:2542260 original size:132 final size:132
Alignment explanation
Indices: 2542023--2542710 Score: 822
Period size: 132 Copynumber: 5.3 Consensus size: 132
2542013 TAGCAAATCT
* * * *
2542023 TGTCTCCCTAAACAGTAGTGGAGCAGATCGAGGACAGCAAATCTTATATTCCTAAGATAGTA-AT
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGA-
* * * *
2542087 GAAGCAGATTCAAGCCACCGGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAATATTGTAGA
65 GAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGA
2542152 TCC
130 TCC
2542155 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
* * * *
2542220 AAGTAGATTTAAGCCACCGGTCCTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAGATTATAGA-
66 AAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
2542284 CTC
131 C-C
* * ** * * *
2542287 TGTCTCCCTAAGCAGTAGCGGAGCAGGTCGAAGACGGTGAATCTTATCTTCTTAAGATAGCAGTG
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
* * *
2542352 AAGCAAATTTAAGCCACCAATCCTATCTCTCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
66 AAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
*
2542417 TC
131 CC
* * * ** * * * *
2542419 TGTCTCCCTAAGCAGTAGCGGAACAGGTCGAAGACGGTGAATTTTATCTTCCCAAGGTGGTAG-G
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
* *
2542483 AAAGC-GAATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAATGGAGTAGGTTGAAGAATGTAG
66 -AAGCAG-ATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAG
*
2542547 ATAC
129 ATCC
* * * * *
2542551 TGTTTCCCTAAGCAGTAGTGGAGCAGATC----A-TG--AATCTTATCTTCCCAAGGTAGTAGGG
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
** * * * *
2542609 AAGCAGATTTAAATCACTAGTCCTATCTCCCTGAGTAGCGGTGGAGTAGGTTGAAGATTGCAGAT
66 AAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
*
2542674 CA
131 CC
* *
2542676 TGTCTCCCTGAGCAGTAGTGGAGCAGATCTAAGAC
1 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
2542711 AGAGAATTTT
Statistics
Matches: 487, Mismatches: 57, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
125 104 0.21
126 2 0.00
127 1 0.00
128 1 0.00
129 1 0.00
131 2 0.00
132 375 0.77
133 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (132 bp):
TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCTAAGATAGTAGAG
AAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGAT
CC
Found at i:2543237 original size:19 final size:19
Alignment explanation
Indices: 2543213--2543266 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
2543203 CTTGAAAAAG
* *
2543213 GATATGCAGTCTTAGATAT
1 GATATGCAATCTTAGATAA
2543232 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
2543251 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
2543267 AGATAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:2543288 original size:23 final size:22
Alignment explanation
Indices: 2543226--2543289 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 22
2543216 ATGCAGTCTT
*
2543226 AGATATGATATGCAATCTT---
1 AGATAAGATATGCAATCTTAGA
2543245 AGATAAGATATGCAATCTTAGA
1 AGATAAGATATGCAATCTTAGA
* *
2543267 AGATAAGATTTTGTAATCTTAGA
1 AGATAAGA-TATGCAATCTTAGA
2543290 TATTTAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 18 0.47
22 8 0.21
23 12 0.32
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (22 bp):
AGATAAGATATGCAATCTTAGA
Found at i:2543758 original size:33 final size:33
Alignment explanation
Indices: 2543696--2543761 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2543686 TCTTATTTAC
2543696 ATATTGTTCATTCATTTAACCATTCTTATCATT
1 ATATTGTTCATTCATTTAACCATTCTTATCATT
2543729 ATATTGTTCATTCATTTAACCATTCTTATCATT
1 ATATTGTTCATTCATTTAACCATTCTTATCATT
2543762 CTTTTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.03, T:0.52
Consensus pattern (33 bp):
ATATTGTTCATTCATTTAACCATTCTTATCATT
Found at i:2544184 original size:24 final size:24
Alignment explanation
Indices: 2544156--2544270 Score: 87
Period size: 23 Copynumber: 4.9 Consensus size: 24
2544146 GTATTGTATA
*
2544156 TTATTATTTTAGATTTATCATGTT
1 TTATTATTTTAAATTTATCATGTT
* * * *
2544180 TTATTGTTTGT-GATTTATCA-ATA
1 TTATTATTT-TAAATTTATCATGTT
2544203 TTATTATTTTAAATTTAT--TGTT
1 TTATTATTTTAAATTTATCATGTT
**
2544225 AACATTATTTTAAATTTATCATG-T
1 -TTATTATTTTAAATTTATCATGTT
* *
2544249 ATATCTATTTCAAATTTATCAT
1 TTAT-TATTTTAAATTTATCAT
2544271 TAATATTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
22 2 0.03
23 34 0.47
24 34 0.47
25 3 0.04
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.57
Consensus pattern (24 bp):
TTATTATTTTAAATTTATCATGTT
Found at i:2544243 original size:11 final size:11
Alignment explanation
Indices: 2544206--2544243 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
2544196 ATCAATATTA
2544206 TTATTTTAAAT
1 TTATTTTAAAT
2544217 TTATTGTTAACA-
1 TTATT-TTAA-AT
2544229 TTATTTTAAAT
1 TTATTTTAAAT
2544240 TTAT
1 TTAT
2544244 CATGTATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.04
11 13 0.54
12 9 0.38
13 1 0.04
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (11 bp):
TTATTTTAAAT
Found at i:2544304 original size:24 final size:23
Alignment explanation
Indices: 2544157--2544304 Score: 99
Period size: 24 Copynumber: 6.4 Consensus size: 23
2544147 TATTGTATAT
* **
2544157 TATTATTTTAGATTTATCATGTTT
1 TATTATTTTAAATTTATCAT-TAC
* * * *
2544181 TATTGTTTGT-GATTTATCAATAT
1 TATTATTT-TAAATTTATCATTAC
**
2544204 TATTATTTTAAATTTATTGTTAAC
1 TATTATTTTAAATTTATCATT-AC
2544228 -ATTATTTTAAATTTATCATGTA-
1 TATTATTTTAAATTTATCAT-TAC
* *
2544250 TATCTATTTCAAATTTATCATTAA
1 TAT-TATTTTAAATTTATCATTAC
*
2544274 TA-T-TTTTAAATTTATTATATAC
1 TATTATTTTAAATTTATCAT-TAC
2544296 TATTATTTT
1 TATTATTTT
2544305 GAATCAAGTT
Statistics
Matches: 99, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
21 13 0.13
22 6 0.06
23 39 0.39
24 40 0.40
25 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (23 bp):
TATTATTTTAAATTTATCATTAC
Found at i:2544353 original size:20 final size:19
Alignment explanation
Indices: 2544323--2544381 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
2544313 TTTAATATAA
*
2544323 TTATATTAATAATATATTT
1 TTATTTTAATAATATATTT
* *
2544342 TTATTTTTAATATTATAATT
1 TTA-TTTTAATAATATATTT
* *
2544362 TTATTTTATTAATAAATTT
1 TTATTTTAATAATATATTT
2544381 T
1 T
2544382 AATAATTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTTTAATAATATATTT
Found at i:2544403 original size:26 final size:26
Alignment explanation
Indices: 2544325--2544405 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
2544315 TAATATAATT
* * *
2544325 ATATTAATAATATATTTTTATTTTTA
1 ATATTAATAATTTAATTTTATTTTAA
* *
2544351 ATATT-ATAATTTTATTTTATTAATAA
1 ATATTAATAATTTAATTTTATT-TTAA
* *
2544377 ATTTTAATAATTTAATTTAATTTTAA
1 ATATTAATAATTTAATTTTATTTTAA
2544403 ATA
1 ATA
2544406 ATGTTCTCAA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
25 13 0.30
26 16 0.37
27 14 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATTAATAATTTAATTTTATTTTAA
Found at i:2558160 original size:21 final size:21
Alignment explanation
Indices: 2558134--2558177 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2558124 CCCAAAATTG
2558134 GTACCAAATCGATTGTTTAAT
1 GTACCAAATCGATTGTTTAAT
2558155 GTACCAAATCGATTGTTTAAT
1 GTACCAAATCGATTGTTTAAT
2558176 GT
1 GT
2558178 CTTAGTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (21 bp):
GTACCAAATCGATTGTTTAAT
Found at i:2560393 original size:19 final size:19
Alignment explanation
Indices: 2560360--2560398 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2560350 AATAAAAGAA
*
2560360 AAAAAGAAAGCAAAGAATCG
1 AAAAAGAAAGAAAAG-ATCG
2560380 AAAAAGAAA-AAAAGATCG
1 AAAAAGAAAGAAAAGATCG
2560398 A
1 A
2560399 GAGCCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 9 0.50
ACGTcount: A:0.69, C:0.08, G:0.18, T:0.05
Consensus pattern (19 bp):
AAAAAGAAAGAAAAGATCG
Found at i:2564591 original size:17 final size:18
Alignment explanation
Indices: 2564548--2564593 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
2564538 TAAATATTTT
2564548 TAATAATATAAAACATAAA
1 TAATAAT-TAAAACATAAA
* *
2564567 AAAT-ATTAAAA-TTAAA
1 TAATAATTAAAACATAAA
2564583 TAATAATTAAA
1 TAATAATTAAA
2564594 TAATAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 2 0.09
19 3 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATAATTAAAACATAAA
Found at i:2564592 original size:11 final size:11
Alignment explanation
Indices: 2564576--2564600 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2564566 AAAATATTAA
2564576 AATTAAATAAT
1 AATTAAATAAT
2564587 AATTAAATAAT
1 AATTAAATAAT
2564598 AAT
1 AAT
2564601 ATATTTCTCA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTAAATAAT
Found at i:2570710 original size:15 final size:15
Alignment explanation
Indices: 2570667--2570716 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2570657 CATTTTTTCG
*
2570667 AATTGAGTCGAGTGA
1 AATTGAATCGAGTGA
*
2570682 AA-TGAAATTCGAGTCA
1 AATTG-AA-TCGAGTGA
2570698 AATTGAATCGAGTGA
1 AATTGAATCGAGTGA
2570713 AATT
1 AATT
2570717 ATTCAAGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.07
15 14 0.48
16 11 0.38
17 2 0.07
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (15 bp):
AATTGAATCGAGTGA
Found at i:2570906 original size:18 final size:19
Alignment explanation
Indices: 2570885--2570921 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2570875 AATTTAAAAT
*
2570885 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
2570903 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
2570922 ATATTAGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:2571481 original size:139 final size:139
Alignment explanation
Indices: 2571231--2571514 Score: 518
Period size: 139 Copynumber: 2.0 Consensus size: 139
2571221 GCTTGACACT
2571231 TGTTTTTATATTAGTCTATTTATCCTTTCAATGACAGTCTTATTACATTAAAAATTATCGTTCAA
1 TGTTTTTATATTAGTCTATTTATCCTTTCAATGACAGTCTTATTACATTAAAAATTATCGTTCAA
2571296 TTAAGCTTTGTATGTAATAATATGATAATAATAATTAAAATATAATGAAAGAATTTTTGTGTTAC
66 TTAAGCTTTGTATGTAATAATATGATAATAATAATTAAAATATAATGAAAGAATTTTTGTGTTAC
2571361 AATCTAGTA
131 AATCTAGTA
* *
2571370 TGTTTTTATATTAGTCTATTTATCCTTTCAATGATAGTCTTATTACGTTAAAAATTA-CTGTTCA
1 TGTTTTTATATTAGTCTATTTATCCTTTCAATGACAGTCTTATTACATTAAAAATTATC-GTTCA
2571434 ATTACA-CTTTGTATGTAATAATATGATAATAATAATTAAAATATAATGAAAGAATTTTTGTGTT
65 ATTA-AGCTTTGTATGTAATAATATGATAATAATAATTAAAATATAATGAAAGAATTTTTGTGTT
2571498 ACAATCTAGTA
129 ACAATCTAGTA
2571509 TGTTTT
1 TGTTTT
2571515 CCAATGTTAG
Statistics
Matches: 141, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
138 1 0.01
139 139 0.99
140 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.45
Consensus pattern (139 bp):
TGTTTTTATATTAGTCTATTTATCCTTTCAATGACAGTCTTATTACATTAAAAATTATCGTTCAA
TTAAGCTTTGTATGTAATAATATGATAATAATAATTAAAATATAATGAAAGAATTTTTGTGTTAC
AATCTAGTA
Found at i:2578888 original size:13 final size:13
Alignment explanation
Indices: 2578872--2578896 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2578862 TAAAAATATT
2578872 AAAATTAAATAAA
1 AAAATTAAATAAA
2578885 AAAATTAAATAA
1 AAAATTAAATAA
2578897 TAATATAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATTAAATAAA
Found at i:2579861 original size:18 final size:18
Alignment explanation
Indices: 2579838--2579875 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2579828 AATACTAACA
2579838 ATAAGTAATTTATGCATC
1 ATAAGTAATTTATGCATC
2579856 ATAAGTAATTTATGCATC
1 ATAAGTAATTTATGCATC
2579874 AT
1 AT
2579876 GACTAACAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
ATAAGTAATTTATGCATC
Found at i:2580627 original size:19 final size:19
Alignment explanation
Indices: 2580611--2580657 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2580601 AAAGTAAATA
2580611 AAAGAAAATAAAATAAAAG
1 AAAGAAAATAAAATAAAAG
* *
2580630 AAAGCAAATGAAATAAAAAG
1 AAAGAAAATAAAAT-AAAAG
*
2580650 AAACAAAA
1 AAAGAAAA
2580658 GAAGAACATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.77, C:0.04, G:0.11, T:0.09
Consensus pattern (19 bp):
AAAGAAAATAAAATAAAAG
Found at i:2581307 original size:22 final size:22
Alignment explanation
Indices: 2581282--2581323 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2581272 TTACGATTTG
2581282 TATTAC-TATAATTCAAATTATT
1 TATTACTTATAATT-AAATTATT
*
2581304 TATTACTTATTATTAAATTA
1 TATTACTTATAATTAAATTA
2581324 AAATTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTACTTATAATTAAATTATT
Found at i:2582568 original size:21 final size:21
Alignment explanation
Indices: 2582542--2582582 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2582532 GGGTTGCTAA
2582542 GTGCTGATTCCCCAAATCATC
1 GTGCTGATTCCCCAAATCATC
*
2582563 GTGCTGATTCTCCAAATCAT
1 GTGCTGATTCCCCAAATCAT
2582583 TGGTGGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (21 bp):
GTGCTGATTCCCCAAATCATC
Found at i:2582741 original size:27 final size:28
Alignment explanation
Indices: 2582702--2582755 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
2582692 GAATGTGCAA
*
2582702 AAGGAGGTTGCTAAGTGCTGATTCCCCC
1 AAGGAGGTTGCTAAGTGCTAATTCCCCC
2582730 AAGG-GGTTGCTAAGTGCTAATTCCCC
1 AAGGAGGTTGCTAAGTGCTAATTCCCC
2582756 GACTCACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (28 bp):
AAGGAGGTTGCTAAGTGCTAATTCCCCC
Found at i:2584120 original size:45 final size:45
Alignment explanation
Indices: 2584020--2584126 Score: 169
Period size: 45 Copynumber: 2.4 Consensus size: 45
2584010 TATGTGCCGA
2584020 CTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTG
1 CTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTG
* ** *
2584065 TTACCATTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTG
1 CTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTG
2584110 CTACTGTTACTGGTTAC
1 CTACTGTTACT-GTTAC
2584127 TGTTTATTAG
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 49 0.91
46 5 0.09
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (45 bp):
CTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTG
Found at i:2591637 original size:19 final size:19
Alignment explanation
Indices: 2591600--2591637 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2591590 CTACCTTTCT
*
2591600 TCTTTCTCTTCTCATCCTC
1 TCTTTCTCATCTCATCCTC
2591619 TCTTTCTCAATCTCA-CCTC
1 TCTTTCTC-ATCTCATCCTC
2591638 CCCGAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.11, C:0.42, G:0.00, T:0.47
Consensus pattern (19 bp):
TCTTTCTCATCTCATCCTC
Found at i:2595290 original size:16 final size:15
Alignment explanation
Indices: 2595245--2595287 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2595235 CATTTTTAAT
*
2595245 AAATATAAAACATAAA
1 AAATATTAAA-ATAAA
2595261 AAATATTAAAATAAA
1 AAATATTAAAATAAA
2595276 ATAATAATTAAA
1 A-AAT-ATTAAA
2595288 TAATGATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATATTAAAATAAA
Found at i:2598577 original size:217 final size:219
Alignment explanation
Indices: 2598202--2598652 Score: 658
Period size: 217 Copynumber: 2.1 Consensus size: 219
2598192 CCTTACTGAA
* * ** *
2598202 TTTCCAGAATTCATTAAAAGGCAACACAAGTTGGTTCACTTAGATCTTTCTAATAACCATACCCA
1 TTTCCAGAGTTCATCAAAACACAACACAAGTTGGTTCACTTAGATCTTTCTAACAACCATACCCA
* * * * **
2598267 TGGTTTTGTGCCCAATTGGTTGTGGAAGAGCAGTCTTTCATGGGTGGACCTTTCTTTCAATGTGA
66 TGGTGTTGTGCCCAATTGGTTCTGGAAGAGCAGCCTTTCAAGGGTAAACCTTTCTTTCAATGTGA
*
2598332 TTGATTTTCCAAAACAGCTTCCCTTAAATGATGCAAACTTCTCA-T-ATGTTGGC-AGACTTGGA
131 TTGATTTTCCAAAACAGCTTCCCTTAAATGATGCAAACTTCTCATTCATGTTGACAAGA-TTGGA
2598394 TTTGAGATCCTGCAACATAAGTGCG
195 TTTGAGATCCTGCAACATAAGTGCG
* * * *
2598419 TTTCCAGAGTTCATCAAAACACAAGACAAGTTGGTTGACTTAGATCTTTCTAACAATCATATCCA
1 TTTCCAGAGTTCATCAAAACACAACACAAGTTGGTTCACTTAGATCTTTCTAACAACCATACCCA
2598484 TGGTGTTGTGCCTC-ATTGGTTCTGGAAGAGCAGCCTTTCAAGGGTAAACCTTTCTTTCAATGTG
66 TGGTGTTGTGCC-CAATTGGTTCTGGAAGAGCAGCCTTTCAAGGGTAAACCTTTCTTTCAATGTG
*
2598548 ATTGATTTTCCAAAACAGCTTCCCTTAAATGATGCAAACTTCTTATTTCCAATGTTGACAAGATT
130 ATTGATTTTCCAAAACAGCTTCCCTTAAATGATGCAAACTTCTCA-TT-C-ATGTTGACAAGATT
* *
2598613 GGATTTGAGATCCTGTAATATAAGTGCG
192 GGATTTGAGATCCTGCAACATAAGTGCG
2598641 TTTCCAGAGTTC
1 TTTCCAGAGTTC
2598653 TTAAAGAGTC
Statistics
Matches: 208, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
217 156 0.75
218 1 0.00
219 1 0.00
222 47 0.23
223 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (219 bp):
TTTCCAGAGTTCATCAAAACACAACACAAGTTGGTTCACTTAGATCTTTCTAACAACCATACCCA
TGGTGTTGTGCCCAATTGGTTCTGGAAGAGCAGCCTTTCAAGGGTAAACCTTTCTTTCAATGTGA
TTGATTTTCCAAAACAGCTTCCCTTAAATGATGCAAACTTCTCATTCATGTTGACAAGATTGGAT
TTGAGATCCTGCAACATAAGTGCG
Found at i:2598807 original size:72 final size:72
Alignment explanation
Indices: 2598681--2598884 Score: 284
Period size: 72 Copynumber: 2.8 Consensus size: 72
2598671 TTTAGAAGAA
* * * * *
2598681 TTCGACGCATCTTATAAAAATTTGAGTGGCCCAATTTCAAATTGGTT-ATGCAATATGAGTCTAC
1 TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTTCAAATTGCTTGGT-CAATATGAGTCAAC
*
2598745 TTTACACT
65 TTGACACT
* *
2598753 TTCGATGCATCTTGTAACAATTTGAGTGGCTCAATTTCAAATTGCTTGGTCAATATGAGTCAACT
1 TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTTCAAATTGCTTGGTCAATATGAGTCAACT
2598818 TGACACT
66 TGACACT
* * * *
2598825 TTCGATGTATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTGGGGCAATATGAGT
1 TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTTCAAATTGCTTGGTCAATATGAGT
2598885 GCTCTGATTT
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
72 116 0.99
73 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (72 bp):
TTCGATGCATCTTATAACAATTTGAGTGGCCCAATTTCAAATTGCTTGGTCAATATGAGTCAACT
TGACACT
Found at i:2603041 original size:3 final size:3
Alignment explanation
Indices: 2603028--2603097 Score: 54
Period size: 3 Copynumber: 23.0 Consensus size: 3
2603018 AGAAAAATAG
* * * * *
2603028 ATT ATTT ATT ATT ATT GTT ATT ATT ATT GTT GTC ATT -TAT ATT ATC
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
2603074 ATT -TT CATT ATT ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT
2603098 TGTTTATGCA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 3 0.06
3 45 0.83
4 6 0.11
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2604625 original size:18 final size:16
Alignment explanation
Indices: 2604602--2604637 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
2604592 TTATTAGTTC
2604602 ATTATTATATGTTATATT
1 ATTATTATAT-TTAT-TT
2604620 ATTATTATATTTATTT
1 ATTATTATATTTATTT
2604636 AT
1 AT
2604638 ATGCGCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 4 0.22
18 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
ATTATTATATTTATTT
Found at i:2604981 original size:4 final size:4
Alignment explanation
Indices: 2604974--2605018 Score: 65
Period size: 4 Copynumber: 11.2 Consensus size: 4
2604964 TATATACATA
*
2604974 TATT TATT TATT TATT TATT TATT TATT TATT ATGTT TA-T TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT -TATT TATT TATT T
2605019 TTGTATACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 3 0.08
4 31 0.84
5 3 0.08
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:2611206 original size:21 final size:21
Alignment explanation
Indices: 2611168--2611224 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2611158 TTTTTATGAA
*
2611168 TATTTTG-A-ATTTTAAAAAT
1 TATTTTGAATATTTTGAAAAT
2611187 TATTTTGAATATTTTGAAAAT
1 TATTTTGAATATTTTGAAAAT
*
2611208 TATTTTAAATTATTTTG
1 TATTTTGAA-TATTTTG
2611225 TAATTTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 7 0.21
20 1 0.03
21 18 0.55
22 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
TATTTTGAATATTTTGAAAAT
Found at i:2623094 original size:50 final size:49
Alignment explanation
Indices: 2623040--2623203 Score: 155
Period size: 50 Copynumber: 3.4 Consensus size: 49
2623030 TGAAACCACA
* *
2623040 AATCTTATGCCCCTAAAGTTGTAGTGGGTCAGATTGAATCTACCATAGCG
1 AATCTTAT-CCCCTGAAGTTGCAGTGGGTCAGATTGAATCTACCATAGCG
* * *
2623090 AATCTTATCTCCCTGAAGTTACAGTGGAG-CAGATT-AA---AGC-TA-CA
1 AATCTTATC-CCCTGAAGTTGCAGTGG-GTCAGATTGAATCTACCATAGCG
*
2623134 AATCCTATTCCCCTGAAGTTGCAGTGGGTCA-AGTTGAATCTACCATAGCG
1 AATCTTA-TCCCCTGAAGTTGCAGTGGGTCAGA-TTGAATCTACCATAGCG
*
2623184 AGTCTTATCTCCCTGAAGTT
1 AATCTTATC-CCCTGAAGTT
2623204 CCAATAGTGA
Statistics
Matches: 91, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
43 2 0.02
44 27 0.30
45 6 0.07
46 2 0.02
48 2 0.02
49 7 0.08
50 44 0.48
51 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (49 bp):
AATCTTATCCCCTGAAGTTGCAGTGGGTCAGATTGAATCTACCATAGCG
Found at i:2623313 original size:123 final size:123
Alignment explanation
Indices: 2623084--2623318 Score: 330
Period size: 123 Copynumber: 1.9 Consensus size: 123
2623074 TGAATCTACC
* *
2623084 ATAGCGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCTACAAATCCTATTCCCCTG
1 ATAGCGAATCTTATCTCCCTGAAGTTACAATGGAGCAGATTAAAGCTACAAATCCTATACCCCTG
* * * * *
2623149 AAGTTGCAGTGGGTCAAGTTGAATCTACCATAGCGAGTCTTATCTCCCTGAAGTTCCA
66 AAGTTGCAGTGGGTCAAGTTGAATCTACCACAACAAATCTTAACTCCCTGAAGTTCCA
* * * *
2623207 ATAGTGAATCTTATCTCCCTGAAGTTGCAATGGAGCAAGA-TGAAGCTACAAATTCTATACCCCT
1 ATAGCGAATCTTATCTCCCTGAAGTTACAATGGAGC-AGATTAAAGCTACAAATCCTATACCCCT
*
2623271 GAAGTTGCAGTGGGTC-AGATTGAATTTACCACAACAAATCTTAACTCC
65 GAAGTTGCAGTGGGTCAAG-TTGAATCTACCACAACAAATCTTAACTCC
2623319 TTGAGGTTGC
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
122 2 0.02
123 93 0.95
124 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (123 bp):
ATAGCGAATCTTATCTCCCTGAAGTTACAATGGAGCAGATTAAAGCTACAAATCCTATACCCCTG
AAGTTGCAGTGGGTCAAGTTGAATCTACCACAACAAATCTTAACTCCCTGAAGTTCCA
Found at i:2625670 original size:106 final size:106
Alignment explanation
Indices: 2625474--2625686 Score: 311
Period size: 106 Copynumber: 2.0 Consensus size: 106
2625464 GAAATGAGCA
* * * *
2625474 TTCTTATTTTCGAGAATTCGAGACATCGTGCCCTAACTTATGAGGCATGATTTTCTTCTCGATTA
1 TTCTTATTTTCGAGAATTCGAGACATCATGCCCTAACTTACGAGACATGATTTTCTTCCCGATTA
* *
2625539 ACTTGAAATACGAAGACATTCTTCATAAAATTTGATTTAAT
66 ACTCGAAATACAAAGACATTCTTCATAAAATTTGATTTAAT
* * *
2625580 TTCTTATTTTTG-GAGATTTGAGACATTATGCCCTAACTTACGAGACATGATTTTCTTCCCGATT
1 TTCTTATTTTCGAGA-ATTCGAGACATCATGCCCTAACTTACGAGACATGATTTTCTTCCCGATT
* *
2625644 AACTCGAAATACAAAGGCATTTTTCATAAAATTTGATTTAAT
65 AACTCGAAATACAAAGACATTCTTCATAAAATTTGATTTAAT
2625686 T
1 T
2625687 AGCTGTATTT
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
105 2 0.02
106 93 0.98
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (106 bp):
TTCTTATTTTCGAGAATTCGAGACATCATGCCCTAACTTACGAGACATGATTTTCTTCCCGATTA
ACTCGAAATACAAAGACATTCTTCATAAAATTTGATTTAAT
Found at i:2627784 original size:10 final size:10
Alignment explanation
Indices: 2627767--2627801 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
2627757 TAAAAATCAG
2627767 AAAA-AAAAA
1 AAAAGAAAAA
2627776 AAAAGAAAAA
1 AAAAGAAAAA
2627786 AAAAGAAAAA
1 AAAAGAAAAA
*
2627796 GAAAGA
1 AAAAGA
2627802 TTTGATGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:2627786 original size:16 final size:16
Alignment explanation
Indices: 2627767--2627799 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2627757 TAAAAATCAG
2627767 AAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAGAA
*
2627783 AAAAAAAGAAAAAGAA
1 AAAAAAAAAAAAAGAA
2627799 A
1 A
2627800 GATTTGATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAA
Found at i:2628871 original size:19 final size:19
Alignment explanation
Indices: 2628847--2628957 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
2628837 AATTTTTGAG
*
2628847 GATATGCAATCTTATATAT
1 GATATGCAATCTTAGATAT
*
2628866 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
2628885 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2628904 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* ** *
2628923 GATGTATAATCTTTGATAT
1 GATATGCAATCTTAGATAT
2628942 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
2628958 AGATATGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2630148 original size:98 final size:98
Alignment explanation
Indices: 2630025--2630219 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
2630015 AAAAATCATG
*
2630025 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
2630090 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
* *
2630123 AAGGAAATATTCCGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTCTT
1 AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
*
2630188 AAATCTTGGATGAGTGGATGTTCTTTTAAAGT
66 AAATCTTGGATAAGTGGATGTTCTTTTAAAGT
2630220 TTTATTGTAT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (98 bp):
AAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTT
AAATCTTGGATAAGTGGATGTTCTTTTAAAGTA
Found at i:2634446 original size:72 final size:72
Alignment explanation
Indices: 2634348--2634546 Score: 238
Period size: 72 Copynumber: 2.8 Consensus size: 72
2634338 CGCATTTCAC
* *
2634348 TGCATCTCATAACAATTTGAGTGGCCCAATTCCAAATTGCTTATGCAATATGAGTCAACTCATTG
1 TGCATCTAATAACAATTTGAGTGGCCCAATTCCAAATTGCTTATGCAATATGAGTCAACTCAGTG
*
2634413 ACCTCGA
66 ACCTCAA
* * * * * *
2634420 TGTC-TCTAATAATAATTTGAGCGGCCCAATTCCAAATTGCTTATACAAAATGAGTCGACTTAGT
1 TG-CATCTAATAACAATTTGAGTGGCCCAATTCCAAATTGCTTATGCAATATGAGTCAACTCAGT
***
2634484 GGTTTCAA
65 GACCTCAA
* * **
2634492 TGCATCTTATAACAGTTTGAGTGGCCCAATTCCAAATTGCTTGGGCAATATGAGT
1 TGCATCTAATAACAATTTGAGTGGCCCAATTCCAAATTGCTTATGCAATATGAGT
2634547 GCTCTGAGTC
Statistics
Matches: 105, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
71 1 0.01
72 103 0.98
73 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (72 bp):
TGCATCTAATAACAATTTGAGTGGCCCAATTCCAAATTGCTTATGCAATATGAGTCAACTCAGTG
ACCTCAA
Found at i:2644384 original size:2 final size:2
Alignment explanation
Indices: 2644377--2644410 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2644367 AAAAAGCTAA
*
2644377 AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2644411 CTGTTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2648973 original size:31 final size:31
Alignment explanation
Indices: 2648916--2648978 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
2648906 TCTTTATAAC
* * *
2648916 TTTTAAAAGGTTAAATTAAAATTTTTATCAT
1 TTTTAAAAGATTAAAGTAAAATTTTTACCAT
*
2648947 TTTTGAAAAGATTAAAGTATAA-TTTTACCAT
1 TTTT-AAAAGATTAAAGTAAAATTTTTACCAT
2648978 T
1 T
2648979 ACTAATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (31 bp):
TTTTAAAAGATTAAAGTAAAATTTTTACCAT
Found at i:2653131 original size:27 final size:27
Alignment explanation
Indices: 2653099--2653152 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2653089 ACCCAACCTT
2653099 CAGGGATAGGACCAGGTGAGTCCTTGA
1 CAGGGATAGGACCAGGTGAGTCCTTGA
2653126 CAGGGATAGGACCAGGTGAGTCCTTGA
1 CAGGGATAGGACCAGGTGAGTCCTTGA
2653153 TGTCCTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.37, T:0.19
Consensus pattern (27 bp):
CAGGGATAGGACCAGGTGAGTCCTTGA
Found at i:2654282 original size:193 final size:194
Alignment explanation
Indices: 2653947--2654878 Score: 1462
Period size: 193 Copynumber: 4.8 Consensus size: 194
2653937 GTACACGGGG
* * * * *
2653947 TAGAAAAATTATGCCAATTTATTAAGATATAGTTTGTGACAAGAAATGAATCCTAATTTTAGGAT
1 TAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATTTTAGGAT
* * * *
2654012 GATTGACCTATTTAACCTAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGGAATGCATCTCACG
66 GATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAAGAGCTAAAGGAAATGCATCTCACG
* *
2654077 TGCACTAATTAGTGGGAATGAGAGGATTAATT-TCGGATCCCCAAGGACAAATGATTGATGCGA
131 TGCACCAATTAGTGGGAATGAGAGGATTAATTGTCGGATCCCCAAGGACAAATGATCGATGCGA
2654140 TAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATTTTAGGAT
1 TAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATTTTAGGAT
* *
2654205 GATTGACCTATTTAACCCAATCCATATAATGTCTTTTTCAAGAGCTAAAGGAAATGCATCTCACG
66 GATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAAGAGCTAAAGGAAATGCATCTCACG
* *
2654270 TGTACCAATTAGTGGGAATGAGAGGATTAA-TGTCGGATCCCCAAGGACAAATGATTGATGCGA
131 TGCACCAATTAGTGGGAATGAGAGGATTAATTGTCGGATCCCCAAGGACAAATGATCGATGCGA
*
2654333 TAGAAAAATTACGCCAATCTATTGAGATATGATTTGCGACAAGAAATGAATCCTAATTTTAGGAT
1 TAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATTTTAGGAT
* * *
2654398 GACTGACATGTTTAACCCAGTCCAAATAATGTCTTTTTCAAGAGCTAAAGGAAATGCATCTCACG
66 GATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAAGAGCTAAAGGAAATGCATCTCACG
* *
2654463 TGCACCAATTAGTGGGAATGACAGGATT-ATTGTCGGATCCCCAAGGACAAATGATCGATGCGG
131 TGCACCAATTAGTGGGAATGAGAGGATTAATTGTCGGATCCCCAAGGACAAATGATCGATGCGA
* * *
2654526 TAGAAAAATTACACCAATCTATTGAGGTATGGTTTACGACAAGAAATGAATCCTAATTTTAGGAT
1 TAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATTTTAGGAT
* * *
2654591 GACTGACATGTTTAACCCAGTCCATATAATGTCTTTTTCTAA-AGCTAAAGGAAATACATCTCAC
66 GATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTC-AAGAGCTAAAGGAAATGCATCTCAC
* * *
2654655 GTGCACCAATTAGTGGGAATGACAGGATT-ATTGTCAGATCCCCAAGGACAAATGATCAATGCGA
130 GTGCACCAATTAGTGGGAATGAGAGGATTAATTGTCGGATCCCCAAGGACAAATGATCGATGCGA
* * * * *
2654719 TAGAAAAATTATGTCAATCTATTGAGATATGGTTTGCAAAAATAAATGAATCCTAATTTTAGGAT
1 TAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATTTTAGGAT
* * *
2654784 GATTGACCTGTTTAACCC-TTCCATATAATATCTTTTTCAAGAGCTAAAAGAAATGCATCTCACG
66 GATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAAGAGCTAAAGGAAATGCATCTCACG
*
2654848 TGCACCAATTAGTGGGAATGCGAGGATTAAT
131 TGCACCAATTAGTGGGAATGAGAGGATTAAT
2654879 GTCAGATTCC
Statistics
Matches: 688, Mismatches: 46, Indels: 10
0.92 0.06 0.01
Matches are distributed among these distances:
191 2 0.00
192 67 0.10
193 617 0.90
194 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (194 bp):
TAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATTTTAGGAT
GATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAAGAGCTAAAGGAAATGCATCTCACG
TGCACCAATTAGTGGGAATGAGAGGATTAATTGTCGGATCCCCAAGGACAAATGATCGATGCGA
Found at i:2656163 original size:2 final size:2
Alignment explanation
Indices: 2656156--2656193 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2656146 CCCTAGTAGA
2656156 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2656194 GAAGTGGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2661513 original size:6 final size:6
Alignment explanation
Indices: 2661502--2661531 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2661492 ATATAAAAAA
2661502 AGTTTC AGTTTC AGTTTC AGTTTC AGTTTC
1 AGTTTC AGTTTC AGTTTC AGTTTC AGTTTC
2661532 CTTTTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
AGTTTC
Found at i:2667157 original size:6 final size:6
Alignment explanation
Indices: 2667103--2667143 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
2667093 CTCCTTCTCC
2667103 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTC
2667144 ATTCTCCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (6 bp):
TCCTCT
Found at i:2673870 original size:28 final size:28
Alignment explanation
Indices: 2673806--2673871 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
2673796 TAAATTTATG
2673806 ATTTTAAAATTTATTTTAATATGTAATT
1 ATTTTAAAATTTATTTTAATATGTAATT
**
2673834 ATTCGAAAATTTATAATTT-ATATG-AATT
1 ATTTTAAAATTTAT--TTTAATATGTAATT
2673862 ATTTTAAAAT
1 ATTTTAAAAT
2673872 GGTAGCAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 24 0.75
29 5 0.16
30 3 0.09
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (28 bp):
ATTTTAAAATTTATTTTAATATGTAATT
Found at i:2674003 original size:2 final size:2
Alignment explanation
Indices: 2673996--2674047 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2673986 TTAAAATTAG
2673996 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
2674038 TA TA TA TA TA
1 TA TA TA TA TA
2674048 AATCAAATGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2677232 original size:24 final size:25
Alignment explanation
Indices: 2677187--2677235 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2677177 TACTTATCTG
*
2677187 AATCAAATATTTTTTTTCAATTATT
1 AATCAAATATTTTTATTCAATTATT
*
2677212 AATCAATTATTTTTATT-AATTATT
1 AATCAAATATTTTTATTCAATTATT
2677236 TTTTATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (25 bp):
AATCAAATATTTTTATTCAATTATT
Found at i:2677234 original size:13 final size:14
Alignment explanation
Indices: 2677216--2677244 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2677206 ATTATTAATC
2677216 AATTA-TTTTTATT
1 AATTATTTTTTATT
2677229 AATTATTTTTTATT
1 AATTATTTTTTATT
2677243 AA
1 AA
2677245 ATTAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
AATTATTTTTTATT
Found at i:2677815 original size:39 final size:41
Alignment explanation
Indices: 2677762--2677841 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
2677752 AAAATTAATG
* * *
2677762 TTTTACTGTGAT-AAAAATAGAATTGAATATTTAAT-TTTA
1 TTTTACTGTAATAAAAAATAGAATTAAATAATTAATGTTTA
* *
2677801 TTTTATTGTAATAAAAAATATAATTAAATAATTAATGTTTA
1 TTTTACTGTAATAAAAAATAGAATTAAATAATTAATGTTTA
2677842 AGTTTATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 10 0.29
40 20 0.59
41 4 0.12
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (41 bp):
TTTTACTGTAATAAAAAATAGAATTAAATAATTAATGTTTA
Found at i:2679086 original size:24 final size:24
Alignment explanation
Indices: 2679036--2679087 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2679026 AATCAAAGTC
** **
2679036 AAATATATTATGTTAATAAATGTT
1 AAATATATTATACTAATAAATACT
*
2679060 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
2679084 AAAT
1 AAAT
2679088 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:2681757 original size:30 final size:30
Alignment explanation
Indices: 2681680--2681757 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
2681670 AACCCCTTTA
* *
2681680 TTTTTTGGACTTTAA-AATTTAGTCTCTTTAC
1 TTTTTT-GA-TTTAATAATTTAATCTCATTAC
*
2681711 --TTTTAATTTCAATAATTTAATCTCATTAC
1 TTTTTTGATTT-AATAATTTAATCTCATTAC
2681740 TTTTTTGATTTAATAATT
1 TTTTTTGATTTAATAATT
2681758 AAAGTTCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.08
28 3 0.08
29 18 0.46
30 7 0.18
31 8 0.21
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTTTTGATTTAATAATTTAATCTCATTAC
Found at i:2719203 original size:6 final size:7
Alignment explanation
Indices: 2719188--2719212 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2719178 TTTGACAACC
2719188 AAAAGAA
1 AAAAGAA
2719195 AAAAGAA
1 AAAAGAA
2719202 AAAAGAA
1 AAAAGAA
2719209 AAAA
1 AAAA
2719213 AATGAAGAAA
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:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:2719949 original size:63 final size:63
Alignment explanation
Indices: 2719878--2720004 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
2719868 AGACCCAAAA
2719878 ACTTAAATCCATTATCTTAAATTTGAGAGTTATTAATATTTATTTATAATAATTAATATTATT
1 ACTTAAATCCATTATCTTAAATTTGAGAGTTATTAATATTTATTTATAATAATTAATATTATT
2719941 ACTTAAATCCATTATCTTAAATTTGAGAGTTATTAATATTTATTTATAATAATTAATATTATT
1 ACTTAAATCCATTATCTTAAATTTGAGAGTTATTAATATTTATTTATAATAATTAATATTATT
2720004 A
1 A
2720005 TTAGTATTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (63 bp):
ACTTAAATCCATTATCTTAAATTTGAGAGTTATTAATATTTATTTATAATAATTAATATTATT
Found at i:2722304 original size:18 final size:18
Alignment explanation
Indices: 2722281--2722323 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
2722271 ATATATTTTA
*
2722281 ATTATATCATAATATTAC
1 ATTATATCATAATATAAC
*
2722299 ATTATAATCATATTATAAC
1 ATTAT-ATCATAATATAAC
2722318 -TTATAT
1 ATTATAT
2722324 TCTTGGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 9 0.41
19 11 0.50
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATATCATAATATAAC
Found at i:2723138 original size:29 final size:29
Alignment explanation
Indices: 2723080--2723141 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
2723070 TTTATATATT
*
2723080 AATTATTCATTAATAATCTTTCCTACAAA
1 AATTATTCATTAATAATCTTTCATACAAA
*
2723109 AATTATTCATTAGTAATCTTT-ATA-ATAA
1 AATTATTCATTAATAATCTTTCATACA-AA
2723137 AATTA
1 AATTA
2723142 CTATTTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 1 0.03
28 9 0.30
29 20 0.67
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (29 bp):
AATTATTCATTAATAATCTTTCATACAAA
Found at i:2733961 original size:16 final size:16
Alignment explanation
Indices: 2733940--2733978 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2733930 TGACCCACTC
2733940 TATAACAACCA-TTCGT
1 TATAACAA-CATTTCGT
*
2733956 TATAACAATATTTCGT
1 TATAACAACATTTCGT
2733972 TATAACA
1 TATAACA
2733979 GTCAAATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (16 bp):
TATAACAACATTTCGT
Found at i:2735255 original size:30 final size:29
Alignment explanation
Indices: 2735219--2735277 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2735209 TTATATTTTT
** *
2735219 AGTTAAATTTGACTTTCAGCCTTTTAAAAA
1 AGTTAAATTTGA-TCACAACCTTTTAAAAA
2735249 AGTTAAATTTGATCACAACCTTTTAAAAA
1 AGTTAAATTTGATCACAACCTTTTAAAAA
2735278 GAGCCAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (29 bp):
AGTTAAATTTGATCACAACCTTTTAAAAA
Found at i:2738492 original size:16 final size:16
Alignment explanation
Indices: 2738453--2738494 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2738443 AAATCATGGT
*
2738453 TATGTATATATGTGTG
1 TATGTATATATGTATG
**
2738469 TAAATATATATGTATG
1 TATGTATATATGTATG
2738485 TATGTATATA
1 TATGTATATA
2738495 CGTTGCTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.48
Consensus pattern (16 bp):
TATGTATATATGTATG
Found at i:2750909 original size:65 final size:65
Alignment explanation
Indices: 2750781--2750910 Score: 143
Period size: 65 Copynumber: 2.0 Consensus size: 65
2750771 CGACCTACGG
* * * *
2750781 GATTCGAACCAGTGACCTAAGGATTAGCTAAAGCTTACAACCGACTACAGCCCTCAGCCCTACCA
1 GATTCGAACCAGCGAACTAAGGATTAGCGAAAGCTTACAACCGACTACAGCCATCAGCCCTACCA
* * * * * * * * *
2750846 GATTTGAACCAGCGAACTGAGGATTAGCGGAAGGTTGCAACCTACTACAGTCATCCGCTCTACCA
1 GATTCGAACCAGCGAACTAAGGATTAGCGAAAGCTTACAACCGACTACAGCCATCAGCCCTACCA
2750911 ACTGAGCTAA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (65 bp):
GATTCGAACCAGCGAACTAAGGATTAGCGAAAGCTTACAACCGACTACAGCCATCAGCCCTACCA
Found at i:2758174 original size:22 final size:22
Alignment explanation
Indices: 2758145--2758204 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 22
2758135 CGCTAAATGC
2758145 AATTTAAATATTATGTGGAGCA
1 AATTTAAATATTATGTGGAGCA
* * *
2758167 TATTTAAA-A-TATATGGATCA
1 AATTTAAATATTATGTGGAGCA
2758187 AATTATAAATATATATGT
1 AATT-TAAATAT-TATGT
2758205 ATAATTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 12 0.41
21 5 0.17
22 8 0.28
24 4 0.14
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (22 bp):
AATTTAAATATTATGTGGAGCA
Found at i:2760521 original size:22 final size:22
Alignment explanation
Indices: 2760481--2760535 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2760471 AATGTATGAT
**
2760481 TAATTT-AAATAATTTTAATAA
1 TAATTTAAAATAATACTAATAA
*
2760502 TAATTTAAAATAATACTAATGA
1 TAATTTAAAATAATACTAATAA
2760524 TAAATTTTAAAA
1 T-AA-TTTAAAA
2760536 CGATGTTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 13 0.46
23 2 0.07
24 7 0.25
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
TAATTTAAAATAATACTAATAA
Found at i:2768237 original size:2 final size:2
Alignment explanation
Indices: 2768230--2768255 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2768220 TCAATATTTC
2768230 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
2768256 AGTATCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2770481 original size:19 final size:19
Alignment explanation
Indices: 2770457--2770493 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2770447 TATATCCATG
2770457 TGGTGAAATACTCGGATTT
1 TGGTGAAATACTCGGATTT
*
2770476 TGGTGAAATACTCTGATT
1 TGGTGAAATACTCGGATT
2770494 GTTTAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (19 bp):
TGGTGAAATACTCGGATTT
Found at i:2771880 original size:249 final size:249
Alignment explanation
Indices: 2771442--2771945 Score: 1008
Period size: 249 Copynumber: 2.0 Consensus size: 249
2771432 TAATTAGGAA
2771442 TTTTCAGTTTCATGGGATGCCAAGGATAGATTTTGATTATAGTATATATATTGTATCAACAGTAG
1 TTTTCAGTTTCATGGGATGCCAAGGATAGATTTTGATTATAGTATATATATTGTATCAACAGTAG
2771507 ATGCATCTAATTGTAGTGGGCTTCTCCTGTTCATTTGTCTGATGAAATGGTTCTAATTCAATGCC
66 ATGCATCTAATTGTAGTGGGCTTCTCCTGTTCATTTGTCTGATGAAATGGTTCTAATTCAATGCC
2771572 TTGGAACATCTTTTGATCTTAGTATTTTACTTGTCAGTGAGCCGATCTTTGTCCTGATTTTTGTA
131 TTGGAACATCTTTTGATCTTAGTATTTTACTTGTCAGTGAGCCGATCTTTGTCCTGATTTTTGTA
2771637 ATGTAAGATCCAGTGGCATTGCTTTTAATGCCTTTGCCTTGGTTTTGTTAATCC
196 ATGTAAGATCCAGTGGCATTGCTTTTAATGCCTTTGCCTTGGTTTTGTTAATCC
2771691 TTTTCAGTTTCATGGGATGCCAAGGATAGATTTTGATTATAGTATATATATTGTATCAACAGTAG
1 TTTTCAGTTTCATGGGATGCCAAGGATAGATTTTGATTATAGTATATATATTGTATCAACAGTAG
2771756 ATGCATCTAATTGTAGTGGGCTTCTCCTGTTCATTTGTCTGATGAAATGGTTCTAATTCAATGCC
66 ATGCATCTAATTGTAGTGGGCTTCTCCTGTTCATTTGTCTGATGAAATGGTTCTAATTCAATGCC
2771821 TTGGAACATCTTTTGATCTTAGTATTTTACTTGTCAGTGAGCCGATCTTTGTCCTGATTTTTGTA
131 TTGGAACATCTTTTGATCTTAGTATTTTACTTGTCAGTGAGCCGATCTTTGTCCTGATTTTTGTA
2771886 ATGTAAGATCCAGTGGCATTGCTTTTAATGCCTTTGCCTTGGTTTTGTTAATCC
196 ATGTAAGATCCAGTGGCATTGCTTTTAATGCCTTTGCCTTGGTTTTGTTAATCC
2771940 TTTTCA
1 TTTTCA
2771946 TTATGTTGAG
Statistics
Matches: 255, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
249 255 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.43
Consensus pattern (249 bp):
TTTTCAGTTTCATGGGATGCCAAGGATAGATTTTGATTATAGTATATATATTGTATCAACAGTAG
ATGCATCTAATTGTAGTGGGCTTCTCCTGTTCATTTGTCTGATGAAATGGTTCTAATTCAATGCC
TTGGAACATCTTTTGATCTTAGTATTTTACTTGTCAGTGAGCCGATCTTTGTCCTGATTTTTGTA
ATGTAAGATCCAGTGGCATTGCTTTTAATGCCTTTGCCTTGGTTTTGTTAATCC
Found at i:2773773 original size:39 final size:41
Alignment explanation
Indices: 2773728--2773833 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 41
2773718 TTTCCTTATG
* *
2773728 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
*
2773768 C-ATTACGCCTTAATTCCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCC-----TCTATTCCATTCAACCAAACAAAAGAATTAC
*
2773813 CTATTACGCCTCTATTTCATT
1 CTATTACGCCTCTATTCCATT
2773834 ACGCCTCTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
39 7 0.13
40 1 0.02
41 9 0.17
44 25 0.46
45 4 0.07
46 8 0.15
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:2773836 original size:16 final size:16
Alignment explanation
Indices: 2773815--2773851 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2773805 AGAATTACCT
*
2773815 ATTACGCCTCTATTTC
1 ATTACGCCTCTATTCC
2773831 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
2773847 ATTAC
1 ATTAC
2773852 AGTGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.32, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:2788165 original size:2 final size:2
Alignment explanation
Indices: 2788120--2788152 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2788110 TAAATATTTT
*
2788120 TA TA T- TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2788153 GCTCAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2794086 original size:23 final size:23
Alignment explanation
Indices: 2794059--2794132 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
2794049 TCTAAATATG
2794059 AAAATAGAAGAAATTAAAAAGAT
1 AAAATAGAAGAAATTAAAAAGAT
*** ** *
2794082 AAAAT-GATTTAATTCTAAATAT
1 AAAATAGAAGAAATTAAAAAGAT
*
2794104 GAAAATAAAAGAAATTAAAAAGAT
1 -AAAATAGAAGAAATTAAAAAGAT
2794128 AAAAT
1 AAAAT
2794133 GATTTTCTTG
Statistics
Matches: 36, Mismatches: 13, Indels: 4
0.68 0.25 0.08
Matches are distributed among these distances:
22 11 0.31
23 15 0.42
24 10 0.28
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.24
Consensus pattern (23 bp):
AAAATAGAAGAAATTAAAAAGAT
Found at i:2794100 original size:46 final size:46
Alignment explanation
Indices: 2794044--2794137 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
2794034 AAAATTAAAA
*
2794044 TTAATTCTAAATATGAAAATAGAAGAAATTAAAAAGATAAAATGAT
1 TTAATTCTAAATATGAAAATAAAAGAAATTAAAAAGATAAAATGAT
2794090 TTAATTCTAAATATGAAAATAAAAGAAATTAAAAAGATAAAATGAT
1 TTAATTCTAAATATGAAAATAAAAGAAATTAAAAAGATAAAATGAT
2794136 TT
1 TT
2794138 TCTTGTAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.30
Consensus pattern (46 bp):
TTAATTCTAAATATGAAAATAAAAGAAATTAAAAAGATAAAATGAT
Found at i:2795604 original size:30 final size:31
Alignment explanation
Indices: 2795568--2795643 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 31
2795558 CATTTTCATG
*
2795568 ACTAAAATTAATAATTTAGGAGTTTATTTA-
1 ACTAAAATTAATAATTTAAGAGTTTATTTAT
2795598 ACTAAAA--AA-AA--TAAGAGTTTATTTAT
1 ACTAAAATTAATAATTTAAGAGTTTATTTAT
2795624 AC-AAAATCTAATAATTTAAG
1 ACTAAAAT-TAATAATTTAAG
2795644 GGTATTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
25 17 0.45
26 2 0.05
27 2 0.05
28 4 0.11
29 2 0.05
30 7 0.18
31 4 0.11
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (31 bp):
ACTAAAATTAATAATTTAAGAGTTTATTTAT
Found at i:2796483 original size:27 final size:27
Alignment explanation
Indices: 2796448--2796514 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
2796438 GTAGTAATTC
*
2796448 AATTTGGTTAATTCGGTTAATTCAGG-T
1 AATTTGGTTAATTCGATTAATTC-GGTT
* *
2796475 AATTCGGTTGATTCGATTAATTCGGTT
1 AATTTGGTTAATTCGATTAATTCGGTT
2796502 AATTTGGTTAATT
1 AATTTGGTTAATT
2796515 TTTAACCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.46
Consensus pattern (27 bp):
AATTTGGTTAATTCGATTAATTCGGTT
Found at i:2796515 original size:9 final size:9
Alignment explanation
Indices: 2796448--2796514 Score: 82
Period size: 9 Copynumber: 7.4 Consensus size: 9
2796438 GTAGTAATTC
*
2796448 AATTTGGTT
1 AATTCGGTT
2796457 AATTCGGTT
1 AATTCGGTT
2796466 AATTCAGG-T
1 AATTC-GGTT
2796475 AATTCGGTT
1 AATTCGGTT
* *
2796484 GATTCGATT
1 AATTCGGTT
2796493 AATTCGGTT
1 AATTCGGTT
*
2796502 AATTTGGTT
1 AATTCGGTT
2796511 AATT
1 AATT
2796515 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
8 2 0.04
9 46 0.92
10 2 0.04
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.46
Consensus pattern (9 bp):
AATTCGGTT
Found at i:2802120 original size:15 final size:16
Alignment explanation
Indices: 2802089--2802121 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2802079 GGACTAGTTC
2802089 AAAACTGCTATTAGAA
1 AAAACTGCTATTAGAA
*
2802105 AAAAGTGCTATT-GAA
1 AAAACTGCTATTAGAA
2802120 AA
1 AA
2802122 GTGGTGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (16 bp):
AAAACTGCTATTAGAA
Found at i:2802564 original size:19 final size:19
Alignment explanation
Indices: 2802540--2802582 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
2802530 TGTTATTCAT
2802540 CACTTCTGCAGTGGAAAAA
1 CACTTCTGCAGTGGAAAAA
*
2802559 CACTTCTGCAGTGTAAAAA
1 CACTTCTGCAGTGGAAAAA
2802578 CACTT
1 CACTT
2802583 AACCCAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (19 bp):
CACTTCTGCAGTGGAAAAA
Found at i:2809311 original size:808 final size:793
Alignment explanation
Indices: 2807440--2809018 Score: 2105
Period size: 808 Copynumber: 1.9 Consensus size: 793
2807430 ATATTTTACA
*
2807440 ATCTAATAAATAAATTTTT-AATTAAATTCTCCATATTAAATCAAAATTTTAAAGCACTAAATCA
1 ATCTAATAAATAAATTTTTAAATT-AATTCTCCATATTAAATCAAAATTTCAAAGCACTAAATCA
* ** * ** * *
2807504 TTGCCCTAAAATTGTCAAAATACATCCTTTTGAATTTTAAAATTTATGAATTCCGAAACAGACTT
65 TT--CCTAAAATTGTCAAAATACATCATTTTGAA-TAAAAAATTAACAAATTACGAAAGAGACTT
* * * *
2807569 TCAGCA-TCTCAAATTCTCTATTTAAATTTCACCTACATAGTTTTTTTTTTTTTTTGGAAATTCT
127 TCAG-ATTCTCAAATTCTCTATTTAAATTTCACATACATAG-------TTATATTTGGCAATTCT
** * *
2807633 TCAAAA-TCTCATTTATTTAAATCATGGTTCTATTATAAGAA-AGAAAATTTTAAACTAAAAAAA
184 TCAAAACT-TCATGAATTTAAA-CAT-GTTCTATTATAA-AATACAAAATTTT--ATTAAAAAAA
*
2807696 TATTATTTTTATTTAAATCTAATGTGCATCTTTTTCTCTTTACAAAAATAAATTTTCAAAATTCA
243 TATTATTTTTATTTAAATCTAATGTGCATATTTTTCTCTTTACAAAAATAAATTTTCAAAATTCA
* *
2807761 AGTCTAACTATTAATATTGTTGAAATTATTTTATTAAATCCATGTTCATTACGTCATCTTTTAGT
308 AGTCTAACTATTAATACTATTGAAATTATTTTATTAAATCCATGTTCATTACGTCATCTTTTAGT
* *
2807826 TACATTGCTAACAAGTTCTTTTATTTCAAAATGTCAACACCAATAAATTATTTTTGAAAAATAAC
373 TACATTGCTAACAAGTTCTTTTATTTCAAAATGTCAACACCAATAAATTAATTTTAAAAAATAAC
* *
2807891 AATGTTAATAATTGAACTTGGATTTTGAAATTTAAAAAATAGAGGGATCAAATTCCCAAAAACAA
438 AATGTTAACAATTGAACTTGGATTTTGAAATTTAAAAAATAGAGGGA--AAATTCACAAAAACAA
2807956 AAATACAAGAATTAAATTACAAAAAAGTTAAATCACATTTTTTTAAACCAAAAAGTTAATAACAT
501 AAATACAAGAATTAAATTACAAAAAAGTTAAATCACATTTTTTTAAACCAAAAAGTTAATAACAT
2808021 GTGCATTTTGAAATTAATAAAAAAGTTTGAAAAAAAAGTTTAAGCACCTCAAAATGTAAGTTTAA
566 GTGCATTTTGAAATTAATAAAAAAGTTTGAAAAAAAAGTTTAAGCACCTCAAAATGTAAGTTTAA
2808086 ATTTCATAAAATTGAAGTTTTTTTTTTAAATTATTCAAAATTGAAATTTATTTATTTTTGGCCAA
631 ATTTCATAAAATTGAAGTTTTTTTTTTAAATTATTCAAAATTGAAATTTATTTATTTTTGGCCAA
* * * * *
2808151 AAAATGTCATTTATTTAACTCTAATATGTATTTTTATGTTTTATACTATTAAAAATATATGAAAT
696 AAAATGCCATTTAATTAACTCTAACATGTATTTTTATGTTTTATACCATT-AAAATATATCAAAT
*
2808216 TAAAATATAGTTATATTACATATTATAATATTTT
760 TAAAATATAGTTATATTACATATTATAAAATTTT
*
2808250 GCAATCTAATAAATAAATTTTTAAATTAAATTCTCCATATTAAATCAAAATTTTAAAGCACTAAA
1 ---ATCTAATAAATAAATTTTTAAATT-AATTCTCCATATTAAATCAAAATTTCAAAGCACTAAA
* ** * * *
2808315 TCATTGCCCTAAAATTGTCAAAATACATCCTTTTGAATTTTAAAATTTATAAATTCCGAAAGAGA
62 TCATT--CCTAAAATTGTCAAAATACATCATTTTGAA-TAAAAAATTAACAAATTACGAAAGAGA
* * * *
2808380 CTTTCAGCTTCTCAAATTCTCTATTTAAATTTCACCTACATAGTTTTTTTTGGCAATTCTTCAAA
124 CTTTCAGATTCTCAAATTCTCTATTTAAATTTCACATACATAGTTATATTTGGCAATTCTTCAAA
* ** * *
2808445 ATTTCATTTATTTAAATCATGGTTCTATTATAAAATAGAAAATTTTAAACTAAAAAAAATATTAT
189 ACTTCATGAATTTAAA-CAT-GTTCTATTATAAAATACAAAATTTT--A-TTAAAAAAATATTAT
*
2808510 TTTTATTTAAATCTAATGTGCATATTTTTCTCTTTACAAAAATAAATTTTCAAAATTCAGGTCTA
249 TTTTATTTAAATCTAATGTGCATATTTTTCTCTTTACAAAAATAAATTTTCAAAATTCAAGTCTA
2808575 ACTATTAATACTATTGAAATTATTTTATTAAATCCATGTTCATTACGTCATCTTTTAGTTACATT
314 ACTATTAATACTATTGAAATTATTTTATTAAATCCATGTTCATTACGTCATCTTTTAGTTACATT
* *
2808640 GCTACCAAGGTTTTTTTATTTCAAAATGTCAACACCAATAAATTAATTTTAAAAAATAACAATGT
379 GCTAACAA-GTTCTTTTATTTCAAAATGTCAACACCAATAAATTAATTTTAAAAAATAACAATGT
* * * *
2808705 TAACAATTGAACTTGGATTTT-AAATTTTAAAAAATAGAGGG-AAATTGACGAAAATAGAAATAC
443 TAACAATTGAACTTGGATTTTGAAA-TTTAAAAAATAGAGGGAAAATTCACAAAAACAAAAATAC
*
2808768 AAGAATTAAATTACAAATTCGTAAAGAGTACGTAGACCTATCACA-TTTTTTAAACCAAAAGGTT
507 AAGAATTAAATTAC-AA-----AAA-AGT---TA-A---ATCACATTTTTTTAAACCAAAAAGTT
* *
2808832 AATAACATGTGCATTTTGAAATTTAT-AAAAAGTTTGGAAAAAAAATTTTAAGCACCTCAAAATG
558 AATAACATGTGCATTTTGAAATTAATAAAAAAGTTT-GAAAAAAAAGTTTAAGCACCTCAAAATG
* *
2808896 TATGTTTAAATTTCATAAAATTGAAG-TTTTTTTTTAAATTATTCAAAATTGACATTTATTTATT
622 TAAGTTTAAATTTCATAAAATTGAAGTTTTTTTTTTAAATTATTCAAAATTGAAATTTATTTATT
* *
2808960 TTTGGCCAAAAAATGCCATTTAATTAACTCTAACGTGTATTTTTATGTTTTATGCCATT
687 TTTGGCCAAAAAATGCCATTTAATTAACTCTAACATGTATTTTTATGTTTTATACCATT
2809019 TATTTTACTC
Statistics
Matches: 713, Mismatches: 31, Indels: 39
0.91 0.04 0.05
Matches are distributed among these distances:
806 33 0.05
807 67 0.09
808 150 0.21
809 89 0.12
812 3 0.00
813 22 0.03
814 146 0.20
816 2 0.00
817 1 0.00
818 99 0.14
819 95 0.13
820 6 0.01
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (793 bp):
ATCTAATAAATAAATTTTTAAATTAATTCTCCATATTAAATCAAAATTTCAAAGCACTAAATCAT
TCCTAAAATTGTCAAAATACATCATTTTGAATAAAAAATTAACAAATTACGAAAGAGACTTTCAG
ATTCTCAAATTCTCTATTTAAATTTCACATACATAGTTATATTTGGCAATTCTTCAAAACTTCAT
GAATTTAAACATGTTCTATTATAAAATACAAAATTTTATTAAAAAAATATTATTTTTATTTAAAT
CTAATGTGCATATTTTTCTCTTTACAAAAATAAATTTTCAAAATTCAAGTCTAACTATTAATACT
ATTGAAATTATTTTATTAAATCCATGTTCATTACGTCATCTTTTAGTTACATTGCTAACAAGTTC
TTTTATTTCAAAATGTCAACACCAATAAATTAATTTTAAAAAATAACAATGTTAACAATTGAACT
TGGATTTTGAAATTTAAAAAATAGAGGGAAAATTCACAAAAACAAAAATACAAGAATTAAATTAC
AAAAAAGTTAAATCACATTTTTTTAAACCAAAAAGTTAATAACATGTGCATTTTGAAATTAATAA
AAAAGTTTGAAAAAAAAGTTTAAGCACCTCAAAATGTAAGTTTAAATTTCATAAAATTGAAGTTT
TTTTTTTAAATTATTCAAAATTGAAATTTATTTATTTTTGGCCAAAAAATGCCATTTAATTAACT
CTAACATGTATTTTTATGTTTTATACCATTAAAATATATCAAATTAAAATATAGTTATATTACAT
ATTATAAAATTTT
Found at i:2813834 original size:15 final size:16
Alignment explanation
Indices: 2813799--2813833 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2813789 TCATTTTTTG
2813799 TTTTATTCATGGAAAT
1 TTTTATTCATGGAAAT
2813815 TTTTATTCATGGAAAT
1 TTTTATTCATGGAAAT
2813831 TTT
1 TTT
2813834 ACTTCTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (16 bp):
TTTTATTCATGGAAAT
Found at i:2815858 original size:23 final size:23
Alignment explanation
Indices: 2815810--2815862 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
2815800 AACAACTCTA
*
2815810 AATTTTTCAACAGAAATGAATAT
1 AATTTTTCAACAGAAATCAATAT
2815833 AATTTTT-AACAGAATGATCAAT-T
1 AATTTTTCAACAGAA--ATCAATAT
2815856 AATTTTT
1 AATTTTT
2815863 TTTATCAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 7 0.26
23 15 0.56
24 5 0.19
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (23 bp):
AATTTTTCAACAGAAATCAATAT
Found at i:2815862 original size:24 final size:23
Alignment explanation
Indices: 2815810--2815863 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
2815800 AACAACTCTA
* *
2815810 AATTTTTCAACAGAAATGAATAT
1 AATTTTTTAACAGAAATCAATAT
2815833 AA-TTTTTAACAGAATGATCAAT-T
1 AATTTTTTAACAGAA--ATCAATAT
2815856 AATTTTTT
1 AATTTTTT
2815864 TTATCAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 11 0.42
23 5 0.19
24 10 0.38
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (23 bp):
AATTTTTTAACAGAAATCAATAT
Found at i:2825828 original size:35 final size:34
Alignment explanation
Indices: 2825784--2825898 Score: 122
Period size: 35 Copynumber: 3.3 Consensus size: 34
2825774 TAGTCTTGAC
* * *
2825784 TTGGCTTTATTAATGGAAAATTTAGGTCTTCATTT
1 TTGGTTTTATTAATGGAAATTTTAAGTCTTCA-TT
* * ** *
2825819 TTGGTTTTATTCATAGAAATTTTACTTCTTTGATT
1 TTGGTTTTATTAATGGAAATTTTAAGTC-TTCATT
*
2825854 TTGGTTTTATTAATGGAAATTTTAAGTCTTCAGT
1 TTGGTTTTATTAATGGAAATTTTAAGTCTTCATT
*
2825888 TTGCTTTTATT
1 TTGGTTTTATT
2825899 CTTGCACATT
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
34 14 0.22
35 48 0.74
36 3 0.05
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (34 bp):
TTGGTTTTATTAATGGAAATTTTAAGTCTTCATT
Found at i:2827449 original size:21 final size:24
Alignment explanation
Indices: 2827420--2827483 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 24
2827410 ATGCAATGTA
2827420 TATATTTATTTATTTTAAA-C-TT-
1 TATA-TTATTTATTTTAAATCGTTC
2827442 TATATTATTTATTTTAAATCGTTC
1 TATATTATTTATTTTAAATCGTTC
*
2827466 TATTACTATTTATTTTAA
1 TA-TATTATTTATTTTAA
2827484 GCCTTTTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 14 0.38
22 5 0.14
23 2 0.05
24 2 0.05
25 14 0.38
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (24 bp):
TATATTATTTATTTTAAATCGTTC
Found at i:2827475 original size:25 final size:21
Alignment explanation
Indices: 2827426--2827483 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 21
2827416 TGTATATATT
*
2827426 TATTTATTTTAAACTTTATAT
1 TATTTATTTTAAACTTTATAC
2827447 TATTTATTTTAAATCGTTCTATTAC
1 TATTTATTTTAAA-C-TT-TA-TAC
2827472 TATTTATTTTAA
1 TATTTATTTTAA
2827484 GCCTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 13 0.41
22 1 0.03
23 2 0.06
24 2 0.06
25 14 0.44
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTATTTTAAACTTTATAC
Found at i:2829427 original size:24 final size:25
Alignment explanation
Indices: 2829400--2829447 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
2829390 AGAGGAAAGT
2829400 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
2829424 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
2829448 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:2831051 original size:13 final size:12
Alignment explanation
Indices: 2831007--2831052 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
2830997 TATTTTAAAA
2831007 TTAAAAAA-ATT
1 TTAAAAAATATT
*
2831018 TAAAAAAAGTATT
1 TTAAAAAA-TATT
2831031 TT-AAAAATATT
1 TTAAAAAATATT
2831042 TTAAATAAATA
1 TTAAA-AAATA
2831053 CCAAAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 13 0.45
12 7 0.24
13 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:2831690 original size:19 final size:20
Alignment explanation
Indices: 2831666--2831710 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2831656 TGTTGTTCAT
*
2831666 CACTTCTGCA-GTGGAAAAA
1 CACTTCTCCAGGTGGAAAAA
*
2831685 CACTTCTCCATGGTGTAAAAA
1 CACTTCTCCA-GGTGGAAAAA
2831706 CACTT
1 CACTT
2831711 TTACCCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
21 13 0.59
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (20 bp):
CACTTCTCCAGGTGGAAAAA
Found at i:2842322 original size:23 final size:21
Alignment explanation
Indices: 2842255--2842330 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
2842245 TGCATATATA
* * *
2842255 TATATATAAATTATAAAAAATA
1 TATATGTATATTAT-AAAAATG
2842277 TATATG-ATATTATAAAAATG
1 TATATGTATATTATAAAAATG
*
2842297 TATGCATGTATATATATTAAAA-G
1 TAT--ATGTATAT-TATAAAAATG
2842320 TATATGTATAT
1 TATATGTATAT
2842331 GTGTATTTCG
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 9 0.20
21 14 0.30
22 8 0.17
23 8 0.17
24 7 0.15
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.41
Consensus pattern (21 bp):
TATATGTATATTATAAAAATG
Found at i:2842487 original size:20 final size:20
Alignment explanation
Indices: 2842450--2842488 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2842440 CACGTGTATA
* * *
2842450 TATGTATATATTAGAAAATG
1 TATGAATATATAACAAAATG
2842470 TATGAATATATAACAAAAT
1 TATGAATATATAACAAAAT
2842489 TTGGAATTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (20 bp):
TATGAATATATAACAAAATG
Found at i:2844638 original size:2 final size:2
Alignment explanation
Indices: 2844631--2844665 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2844621 AAAATCTCTA
*
2844631 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2844666 CATTTGCTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2846521 original size:30 final size:31
Alignment explanation
Indices: 2846469--2846537 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
2846459 TGGTTTCAAT
*
2846469 TCAGTCACTCAACTTTCAAAAAA-TAACAAA
1 TCAGTCACTCAACTTACAAAAAAGTAACAAA
* *
2846499 TCAGTCACT-AACGTTACCAAAAAGTGACAAA
1 TCAGTCACTCAAC-TTACAAAAAAGTAACAAA
*
2846530 TCAATCAC
1 TCAGTCAC
2846538 CCATTAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 17 0.52
31 13 0.39
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (31 bp):
TCAGTCACTCAACTTACAAAAAAGTAACAAA
Found at i:2846529 original size:31 final size:30
Alignment explanation
Indices: 2846469--2846537 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
2846459 TGGTTTCAAT
*
2846469 TCAGTCACTCAACTTTCAAAAAATAACAAA
1 TCAGTCACTCAACTTCCAAAAAATAACAAA
* *
2846499 TCAGTCACT-AACGTTACCAAAAAGTGACAAA
1 TCAGTCACTCAAC-TT-CCAAAAAATAACAAA
*
2846530 TCAATCAC
1 TCAGTCAC
2846538 CCATTAACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 11 0.33
31 19 0.58
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (30 bp):
TCAGTCACTCAACTTCCAAAAAATAACAAA
Found at i:2847278 original size:3 final size:3
Alignment explanation
Indices: 2847270--2847315 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
2847260 TTCCATTTTC
* *
2847270 TCT TCT TCT CCA T-T TCT TC- TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2847316 ACTGCCCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 3 0.08
3 34 0.92
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:2849717 original size:6 final size:7
Alignment explanation
Indices: 2849681--2849714 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
2849671 AATATGTTAT
2849681 GAAAAAA
1 GAAAAAA
2849688 GAAAAAA
1 GAAAAAA
2849695 GAAAAAA
1 GAAAAAA
2849702 GAAAAAA
1 GAAAAAA
2849709 GAAAAA
1 GAAAAA
2849715 GAAGAGAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:2855643 original size:20 final size:20
Alignment explanation
Indices: 2855620--2855664 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
2855610 AATATGAGTA
2855620 TTTTTTATTTATAAT-ATTAT
1 TTTTTTATTT-TAATAATTAT
*
2855640 TTTTTTATTTTTATAATTAT
1 TTTTTTATTTTAATAATTAT
2855660 TTTTT
1 TTTTT
2855665 ATCTCATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTATTTTAATAATTAT
Found at i:2857050 original size:21 final size:21
Alignment explanation
Indices: 2857008--2857050 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2856998 TTAAATTCTT
* **
2857008 AAAAATAAAAGTTGAAGGAAA
1 AAAAATAAAAGTTAAACAAAA
*
2857029 AAAAATAAAATTTAAACAAAA
1 AAAAATAAAAGTTAAACAAAA
2857050 A
1 A
2857051 CGAAAGTTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAGTTAAACAAAA
Found at i:2858775 original size:240 final size:242
Alignment explanation
Indices: 2858350--2858812 Score: 700
Period size: 240 Copynumber: 1.9 Consensus size: 242
2858340 GCACAAATAC
** *
2858350 TTATACCTTGGTTTGAGATGCTTTCAATGTTGTTGTAACTTAAATCCAAGTACTTCAAGTTTGTC
1 TTATACCTTGGTTTGAGATGCTTTCAATGTTGTTCCAACTTAAATCCAAGGACTTCAAGTTTGTC
* * * *
2858415 AAATTATTCCATTCTGATGAAATTCAATCCCAATGTTGATCAGTTATGTTTTCATGATAAGATAA
66 AAATTATTCAATTCTGA-GAAATTCAATCCCAATGTTGATCAGTTATATTTTCAGGACAAGATAA
* * * * *
2858480 AAGCAAATGAAATATTGCTATAGCTTTTTCTTAAACCAAATTGATTTTAAAGT-AAAAGGAAGCA
130 AAGCAAATGAAATATTGCAATAACTTTTCCTTAAACCAAATTGATTTTAAAGTAAAAAAGAAACA
* *
2858544 TGTAAAA-TAAGTCTACCTTGAATATGAAATAATATATAAATACTATAT
195 GGTAAAACCAA-TCTACCTTGAATATGAAATAATATATAAATACTATAT
* * *
2858592 TTATACCTTTGTTTGAGATGCTTTCAATTTTGTTCCCACTTAAATCCAAGGACTTCAAGTTTGTC
1 TTATACCTTGGTTTGAGATGCTTTCAATGTTGTTCCAACTTAAATCCAAGGACTTCAAGTTTGTC
2858657 AAATTATTCAATTCT-A-AAATTCAATCCCAAATGTTGATCAGTTATATTTTCAGGACAAGATAA
66 AAATTATTCAATTCTGAGAAATTCAATCCC-AATGTTGATCAGTTATATTTTCAGGACAAGATAA
*
2858720 AAGCAAATGACATATTGCAATAACTTTTCCTTAAACCAAATTGATTTTAAAGTAAAAAAGAAACA
130 AAGCAAATGAAATATTGCAATAACTTTTCCTTAAACCAAATTGATTTTAAAGTAAAAAAGAAACA
*
2858785 GGTAAAACCAATCTACCTTGAGTATGAA
195 GGTAAAACCAATCTACCTTGAATATGAA
2858813 TCAACTTTCC
Statistics
Matches: 199, Mismatches: 19, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
239 12 0.06
240 80 0.40
241 32 0.16
242 75 0.38
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.36
Consensus pattern (242 bp):
TTATACCTTGGTTTGAGATGCTTTCAATGTTGTTCCAACTTAAATCCAAGGACTTCAAGTTTGTC
AAATTATTCAATTCTGAGAAATTCAATCCCAATGTTGATCAGTTATATTTTCAGGACAAGATAAA
AGCAAATGAAATATTGCAATAACTTTTCCTTAAACCAAATTGATTTTAAAGTAAAAAAGAAACAG
GTAAAACCAATCTACCTTGAATATGAAATAATATATAAATACTATAT
Found at i:2860951 original size:31 final size:29
Alignment explanation
Indices: 2860913--2860972 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
2860903 AAATATCAAA
*
2860913 ATTATATATGAATTTTAATTTAATGTGTAAT
1 ATTATATATAAATTTTAATTT--TGTGTAAT
*
2860944 ATTATATATAAATTTTGATTTTGTGTAAT
1 ATTATATATAAATTTTAATTTTGTGTAAT
2860973 TTTAAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 8 0.30
31 19 0.70
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (29 bp):
ATTATATATAAATTTTAATTTTGTGTAAT
Found at i:2860968 original size:29 final size:30
Alignment explanation
Indices: 2860913--2860993 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 30
2860903 AAATATCAAA
* *
2860913 ATTATATATGAATTTTAATTTAATGTGTAAT
1 ATTATATATAAATTTTGATTT-ATGTGTAAT
2860944 ATTATATATAAATTTTGATTT-TGTGTAAT
1 ATTATATATAAATTTTGATTTATGTGTAAT
* *
2860973 TTTA-AAATGAAATTTTGATTT
1 ATTATATAT-AAATTTTGATTT
2860994 GATTTAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 3 0.07
29 23 0.51
31 19 0.42
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (30 bp):
ATTATATATAAATTTTGATTTATGTGTAAT
Found at i:2862747 original size:18 final size:17
Alignment explanation
Indices: 2862713--2862750 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
2862703 GTAAAAATGA
2862713 AATTTTATTATTTTAAT
1 AATTTTATTATTTTAAT
*
2862730 AA-TTTA-TATTTTTAT
1 AATTTTATTATTTTAAT
2862745 AATTTT
1 AATTTT
2862751 TAAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 10 0.53
16 7 0.37
17 2 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AATTTTATTATTTTAAT
Found at i:2864431 original size:24 final size:24
Alignment explanation
Indices: 2864344--2864436 Score: 60
Period size: 25 Copynumber: 3.7 Consensus size: 24
2864334 TAAAAAGCTC
* * *
2864344 TTTTATTATTATTTGTTTTAAGTTT
1 TTTTA-TATTATTTATTTAAAATTT
* * *
2864369 TTTATTTATCATTTACTTTAAACTGTT
1 TTT-TATATTATTTA-TTTAAAAT-TT
** *
2864396 TTACATACTATTTATTTAAAATTT
1 TTTTATATTATTTATTTAAAATTT
*
2864420 TTTTATATTATTCATTT
1 TTTTATATTATTTATTT
2864437 TAAACCATTA
Statistics
Matches: 50, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
24 15 0.30
25 17 0.34
26 14 0.28
27 4 0.08
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.63
Consensus pattern (24 bp):
TTTTATATTATTTATTTAAAATTT
Found at i:2865588 original size:3 final size:3
Alignment explanation
Indices: 2865580--2865672 Score: 114
Period size: 3 Copynumber: 29.7 Consensus size: 3
2865570 ATAGTAATGG
* * * *
2865580 TAA TAA TAA TAA TGA TAA TAA TAA TAA AAA TGA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2865628 TAA TAA TAA TAA TAA TAA TAA TAA TATA TGACA TAA TTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A T-A-A TAA -TAA TAA TA
2865673 TAAAAAACAA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
3 69 0.88
4 6 0.08
5 3 0.04
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2868608 original size:19 final size:19
Alignment explanation
Indices: 2868584--2868626 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
2868574 TGTTCTTCAT
2868584 CACTTCTGCAGTGGAAAAA
1 CACTTCTGCAGTGGAAAAA
*
2868603 CACTTCTGCAGTGTAAAAA
1 CACTTCTGCAGTGGAAAAA
2868622 CACTT
1 CACTT
2868627 TTAACCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (19 bp):
CACTTCTGCAGTGGAAAAA
Found at i:2875688 original size:515 final size:506
Alignment explanation
Indices: 2874709--2875720 Score: 1570
Period size: 515 Copynumber: 2.0 Consensus size: 506
2874699 AACCTCAGTA
2874709 GTGTTCCATCTATCATTGGAAGAAAATAATGAGTATAGTTAATATCATTCAAGATATAAATAGTT
1 GTGTTCCATCTATCATTGGAAGAAAATAATGAGTATAGTTAATATCATTCAAGATATAAATAGTT
*
2874774 AGGAAAAATGATTGTTTGAGAAGGAAGAGCCAGTTTACAAGCTTTCCCATGAATTGATAACTACA
66 AGGAAAAATGATTGTTTGAGAAGGAAGAGCCAATTTACAAGCTTTCCCATGAATTGATAACTACA
2874839 TTTTACAAGTAAAACTTAATTGATTCAATATATAAATACTTTGTTTGAGATACCTTCCTACTTTA
131 TTTTACAAGTAAAACTTAATTGATTCAATATATAAATACTTTGTTTGAGATACCTTCCTACTTTA
*
2874904 ATTACTCAATCCCAAATATTGATTACTTATATATATTCATGATATGATAAAAGCAAATGACTTAT
196 ATTACTCAATCCCAAATATTGATTACTTATATATATTCATGATATGACAAAAGCAAA-GACTTAT
** * * *
2874969 TAATTGCAACAGCTTTTCCTTCAACATGAATTTAATGCTATTCTTCAAATAATTCCAACTTATAT
260 TAATTGCAACAGAATTTACTTCAACATG----TAATGCTATTCTTCAAACAAATCCAACTTATAT
*
2875034 CAATAATCTCCAATCTAATGAGCCATTGAAAACCTGATTTATATATTATATAATTAGTTACTACA
321 CAATAATCTCCAATCTAATGAGCCACTGAAAACCTGATTTATATATTATATAATTAGTTACTACA
*
2875099 AAACATAAATAAATAATAATACTCCATTTTTGCAATAAAAATTCACTAAAGAAAATACATTTGAA
386 AAACATAAATAAATAACAATACTCCATTTTTGCAATAAAAATTCACTAAAGAAAATACATTTGAA
*
2875164 GTTTGTCATTGCCTTTTGGAATAAGAGTCGGTCAAGAAAGTTTGTTAGGCTTAATT
451 GTTTGTCATTGCCTTTTGAAATAAGAGTCGGTCAAGAAAGTTTGTTAGGCTTAATT
*
2875220 GTGTTCCATCTATGATTGGAAGAAAATAATGAGTATAGTTAATATCATTCAAGATATAAATAGTT
1 GTGTTCCATCTATCATTGGAAGAAAATAATGAGTATAGTTAATATCATTCAAGATATAAATAGTT
*
2875285 AGGAAAAATGATTGTTTGAGAAGGAAGAGCCAATTTAGAAGCTTTCCCATGAATTGATAACTACA
66 AGGAAAAATGATTGTTTGAGAAGGAAGAGCCAATTTACAAGCTTTCCCATGAATTGATAACTACA
2875350 TTTTACAAGTAAAAC-TAATTGATTCAATATATAAATACTTTGTTTGAGATACCTTCCTTCTTAA
131 TTTTACAAGTAAAACTTAATTGATTCAATATATAAATACTTTGTTTGAGATACCTT-C--C-T-A
* * *
2875414 TTTATTCAATTTTGAAATTCAATCCCAAATATTGATTACTTATATATATTCATGATATGACATAT
191 -CT-TT-AA--TT---ACTCAATCCCAAATATTGATTACTTATATATATTCATGATATGACA-AA
* ** * *
2875479 TGCAACA-ACTT-TTCCTT-CAACATGAATTTATTTTAA-A-G-AATGCTATTCTTCAAACAAAT
247 AGCAA-AGACTTATTAATTGCAACA-GAATTTACTTCAACATGTAATGCTATTCTTCAAACAAAT
* * *
2875538 CCAACTTATATCAATAATTTCCAATTTAATGAGCCACTGAAAACCTGATTTATATATTATATTAT
310 CCAACTTATATCAATAATCTCCAATCTAATGAGCCACTGAAAACCTGATTTATATATTATATAAT
2875603 TAGTTACTACAAAACATAAATAAATAACAATACTCCATTTTTGCAATAAAAATTCACTAAAGAAA
375 TAGTTACTACAAAACATAAATAAATAACAATACTCCATTTTTGCAATAAAAATTCACTAAAGAAA
*
2875668 ATACATTTGAAGTTTGTCATTGTCTTTTGAAATAAGAGTCGGTCAAGAAAGTT
440 ATACATTTGAAGTTTGTCATTGCCTTTTGAAATAAGAGTCGGTCAAGAAAGTT
2875721 ATGCACAAAT
Statistics
Matches: 461, Mismatches: 24, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
510 40 0.09
511 143 0.31
513 1 0.00
514 1 0.00
515 196 0.43
516 1 0.00
517 2 0.00
518 2 0.00
520 3 0.01
521 6 0.01
522 12 0.03
523 48 0.10
524 5 0.01
525 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (506 bp):
GTGTTCCATCTATCATTGGAAGAAAATAATGAGTATAGTTAATATCATTCAAGATATAAATAGTT
AGGAAAAATGATTGTTTGAGAAGGAAGAGCCAATTTACAAGCTTTCCCATGAATTGATAACTACA
TTTTACAAGTAAAACTTAATTGATTCAATATATAAATACTTTGTTTGAGATACCTTCCTACTTTA
ATTACTCAATCCCAAATATTGATTACTTATATATATTCATGATATGACAAAAGCAAAGACTTATT
AATTGCAACAGAATTTACTTCAACATGTAATGCTATTCTTCAAACAAATCCAACTTATATCAATA
ATCTCCAATCTAATGAGCCACTGAAAACCTGATTTATATATTATATAATTAGTTACTACAAAACA
TAAATAAATAACAATACTCCATTTTTGCAATAAAAATTCACTAAAGAAAATACATTTGAAGTTTG
TCATTGCCTTTTGAAATAAGAGTCGGTCAAGAAAGTTTGTTAGGCTTAATT
Found at i:2881911 original size:19 final size:19
Alignment explanation
Indices: 2881887--2881926 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2881877 CTTAAGCTTA
2881887 TATAGCCCCTACAATAATT
1 TATAGCCCCTACAATAATT
2881906 TATAGCCCCTACAATAATT
1 TATAGCCCCTACAATAATT
2881925 TA
1 TA
2881927 GGTTATGGAA
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:0.38, C:0.25, G:0.05, T:0.33
Consensus pattern (19 bp):
TATAGCCCCTACAATAATT
Found at i:2891263 original size:19 final size:19
Alignment explanation
Indices: 2891239--2891281 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2891229 TGTTCTTCAT
*
2891239 CACTTCTGGAGTGGAAAAA
1 CACTTCTGCAGTGGAAAAA
*
2891258 CACTTCTGCAGTGTAAAAA
1 CACTTCTGCAGTGGAAAAA
2891277 CACTT
1 CACTT
2891282 TTAATAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (19 bp):
CACTTCTGCAGTGGAAAAA
Found at i:2892123 original size:30 final size:30
Alignment explanation
Indices: 2892077--2892170 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
2892067 TTTTATTATG
* *
2892077 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATATTTGACTTT
*
2892108 CCAATATTTGATACCCATATTTTTGACTTT
1 CCAATATTTGATACCCATATATTTGACTTT
* * *
2892138 CTATTATTTGATACCCATATATTTGATTTT
1 CCAATATTTGATACCCATATATTTGACTTT
2892168 CCA
1 CCA
2892171 TAAATATGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 49 0.88
31 7 0.12
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.45
Consensus pattern (30 bp):
CCAATATTTGATACCCATATATTTGACTTT
Found at i:2892132 original size:15 final size:15
Alignment explanation
Indices: 2892087--2892164 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
2892077 CCAATATCTC
*
2892087 GATACCCATATCTTT
1 GATACCCATATATTT
**
2892102 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
*
2892117 GATACCCATATTTTT
1 GATACCCATATATTT
** *
2892132 GACTTTCTAT-TATTT
1 GA-TACCCATATATTT
2892147 GATACCCATATATTT
1 GATACCCATATATTT
2892162 GAT
1 GAT
2892165 TTTCCATAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
14 8 0.17
15 30 0.65
16 8 0.17
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (15 bp):
GATACCCATATATTT
Found at i:2896780 original size:30 final size:30
Alignment explanation
Indices: 2896741--2896852 Score: 188
Period size: 30 Copynumber: 3.7 Consensus size: 30
2896731 CCAATATCTC
*
2896741 GATATCCATATCTTTGACTTTCTAATATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
2896771 GATACCCATATCTTTGACTTTCCAATATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
2896801 GATACCCATATCTTTGACTTTCTATTATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
2896831 GATACCCATATCTTTGATTTTC
1 GATACCCATATCTTTGACTTTC
2896853 CATAAATATG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.47
Consensus pattern (30 bp):
GATACCCATATCTTTGACTTTCTAATATTT
Found at i:2896786 original size:15 final size:15
Alignment explanation
Indices: 2896768--2896848 Score: 67
Period size: 15 Copynumber: 5.4 Consensus size: 15
2896758 CTTTCTAATA
2896768 TTTGATACCCATATC
1 TTTGATACCCATATC
** *
2896783 TTTGACTTTCCA-ATA
1 TTTGA-TACCCATATC
2896798 TTTGATACCCATATC
1 TTTGATACCCATATC
** * *
2896813 TTTGACTTTCTAT-TA
1 TTTGA-TACCCATATC
2896828 TTTGATACCCATATC
1 TTTGATACCCATATC
2896843 TTTGAT
1 TTTGAT
2896849 TTTCCATAAA
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
14 8 0.17
15 32 0.67
16 8 0.17
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.47
Consensus pattern (15 bp):
TTTGATACCCATATC
Found at i:2906942 original size:35 final size:34
Alignment explanation
Indices: 2906891--2907005 Score: 131
Period size: 35 Copynumber: 3.3 Consensus size: 34
2906881 TAATCTTGAC
* * *
2906891 TTGGCTTTATTAATGGAAAATTTAGGTCTTCATTT
1 TTGGTTTTATTAATGGAAATTTTAAGTCTTCA-TT
* ** *
2906926 TTGGTTTTATTCATGGAAATTTTACTTCTTTGATT
1 TTGGTTTTATTAATGGAAATTTTAAGTC-TTCATT
*
2906961 TTGGTTTTATTAATGGAAATTTTAAGTCTTCATA
1 TTGGTTTTATTAATGGAAATTTTAAGTCTTCATT
*
2906995 TTGCTTTTATT
1 TTGGTTTTATT
2907006 CTTGCACGTT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
34 14 0.21
35 50 0.75
36 3 0.04
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (34 bp):
TTGGTTTTATTAATGGAAATTTTAAGTCTTCATT
Found at i:2907039 original size:70 final size:70
Alignment explanation
Indices: 2906896--2907032 Score: 161
Period size: 70 Copynumber: 2.0 Consensus size: 70
2906886 TTGACTTGGC
* * * * *
2906896 TTTATTAATGGAAAATTTAGGTCTTCATTTTTGGTTTTATTCATGGAAATTTTACTTCTTTGATT
1 TTTATTAATGGAAAATTTAAGTCTTCATTATTGCTTTTATTCATGCAAATTTTACGTCTTTGATT
*
2906961 TTGGT
66 TTGAT
* * ** *
2906966 TTTATTAATGGAAATTTTAAGTCTTCA-TATTGCTTTTATTCTTGCACGTTTTAGGT-TTTGATT
1 TTTATTAATGGAAAATTTAAGTCTTCATTATTGCTTTTATTCATGCAAATTTTACGTCTTTGATT
2907029 TTGA
66 TTGA
2907033 AATTTTAGTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
68 10 0.18
69 21 0.38
70 25 0.45
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (70 bp):
TTTATTAATGGAAAATTTAAGTCTTCATTATTGCTTTTATTCATGCAAATTTTACGTCTTTGATT
TTGAT
Found at i:2907565 original size:22 final size:22
Alignment explanation
Indices: 2907535--2907580 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2907525 CTTCAGGATC
2907535 AAAGATAAATAATA-AATTTTAT
1 AAAGATAAA-AATATAATTTTAT
* *
2907557 AAAGTTAAAACTATAATTTTAT
1 AAAGATAAAAATATAATTTTAT
2907579 AA
1 AA
2907581 TTATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
AAAGATAAAAATATAATTTTAT
Found at i:2911794 original size:10 final size:10
Alignment explanation
Indices: 2911779--2911804 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2911769 AGTAACGCAG
2911779 GAAAATGAAT
1 GAAAATGAAT
2911789 GAAAATGAAT
1 GAAAATGAAT
2911799 GAAAAT
1 GAAAAT
2911805 AAAGAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (10 bp):
GAAAATGAAT
Found at i:2913291 original size:31 final size:31
Alignment explanation
Indices: 2913239--2913298 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2913229 GCTATGAAAT
* *
2913239 CAAATTCAGGTACCAATTTGAATAAAAAAAC
1 CAAATTCAGATACCAATTTGAACAAAAAAAC
*
2913270 CAAATTTAGATACCTAA-TTGAACAAAAAA
1 CAAATTCAGATACC-AATTTGAACAAAAAA
2913299 TAATCTTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.23
Consensus pattern (31 bp):
CAAATTCAGATACCAATTTGAACAAAAAAAC
Found at i:2916625 original size:22 final size:22
Alignment explanation
Indices: 2916583--2916625 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2916573 AATTAGTTTC
**
2916583 TTTTAAAAATATTTATGAATAT
1 TTTTAAAAATATTTAAAAATAT
2916605 TTTTAAAAAT-TTTACAAAATA
1 TTTTAAAAATATTTA-AAAATA
2916626 ATATCCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTAAAAATATTTAAAAATAT
Found at i:2935818 original size:21 final size:21
Alignment explanation
Indices: 2935794--2935836 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2935784 GTTTTGTTAC
2935794 TTAGTTTGATTTGAACTAAGT
1 TTAGTTTGATTTGAACTAAGT
2935815 TTAGTTTGATTTGAACTAAGT
1 TTAGTTTGATTTGAACTAAGT
2935836 T
1 T
2935837 GTCAATGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.49
Consensus pattern (21 bp):
TTAGTTTGATTTGAACTAAGT
Found at i:2940087 original size:28 final size:28
Alignment explanation
Indices: 2940016--2940071 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
2940006 GTTGGTTCTA
*
2940016 CCGCTTGAATGATATATGATCGGCCTTG
1 CCGCTTGAATAATATATGATCGGCCTTG
2940044 CCGCTTGAATAATATATGATCGGCCTTG
1 CCGCTTGAATAATATATGATCGGCCTTG
2940072 TTGCCTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (28 bp):
CCGCTTGAATAATATATGATCGGCCTTG
Found at i:2941647 original size:26 final size:26
Alignment explanation
Indices: 2941611--2941665 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
2941601 CAAACATATC
*
2941611 CCATAGATACCACTTGATATCAAGCA
1 CCATAGATACCACTCGATATCAAGCA
2941637 CCATAGATACCACTCGATATCAAGCA
1 CCATAGATACCACTCGATATCAAGCA
2941663 CCA
1 CCA
2941666 CCATGAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.31, G:0.11, T:0.20
Consensus pattern (26 bp):
CCATAGATACCACTCGATATCAAGCA
Found at i:2947543 original size:13 final size:13
Alignment explanation
Indices: 2947525--2947558 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2947515 TAGGTGCCTG
2947525 AAAAAAATAAAAT
1 AAAAAAATAAAAT
*
2947538 AAAAAAATAACAT
1 AAAAAAATAAAAT
*
2947551 AATAAAAT
1 AAAAAAAT
2947559 GTTTGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:2950925 original size:7 final size:7
Alignment explanation
Indices: 2950913--2950956 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
2950903 GTAAGTCATT
2950913 TAATCAA
1 TAATCAA
2950920 TAATCAA
1 TAATCAA
2950927 TAAT-AA
1 TAATCAA
2950933 TAATCAA
1 TAATCAA
2950940 TAATCAA
1 TAATCAA
2950947 TAATCAA
1 TAATCAA
2950954 TAA
1 TAA
2950957 GATAGTACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (7 bp):
TAATCAA
Done.