Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 76 of 105
Found at i:13295621 original size:3 final size:3
Alignment explanation
Indices: 13295600--13295715 Score: 67
Period size: 3 Copynumber: 37.3 Consensus size: 3
13295590 AAAAGAAAAG
* *
13295600 ATA A-A ATA AAA ATTA ATA ATA ATA A-A ATAA ATA ATG ATA ATA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA
* * * * * *
13295645 ATAA ATA ATA AAA ATAA ATA ATAA ACA AAA AAA ACTA ATG CTA ATA ATA
1 AT-A ATA ATA ATA AT-A ATA AT-A ATA ATA ATA A-TA ATA ATA ATA ATA
*
13295694 ATA ATAA ATA AAA ATA A-A ATA A
1 ATA AT-A ATA ATA ATA ATA ATA A
13295716 AAAATATGGG
Statistics
Matches: 88, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
2 6 0.07
3 64 0.73
4 18 0.20
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:13295697 original size:49 final size:47
Alignment explanation
Indices: 13295603--13295711 Score: 148
Period size: 49 Copynumber: 2.3 Consensus size: 47
13295593 AGAAAAGATA
* * *
13295603 AAATAAAAATTAATAATAATAAAATAAATAATGATAATAATAATAA-
1 AAATAAAAATAAATAATAACAAAAAAAATAATGATAATAATAATAAT
*
13295649 ATAATAAAAATAAATAATAAACAAAAAAAACTAATGCTAATAATAATAAT
1 A-AATAAAAATAAATAAT-AACAAAAAAAA-TAATGATAATAATAATAAT
13295699 AAATAAAAATAAA
1 AAATAAAAATAAA
13295712 ATAAAAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
46 1 0.02
47 15 0.27
48 9 0.16
49 29 0.53
50 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.25
Consensus pattern (47 bp):
AAATAAAAATAAATAATAACAAAAAAAATAATGATAATAATAATAAT
Found at i:13303042 original size:2 final size:2
Alignment explanation
Indices: 13303035--13303070 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
13303025 TGATTTCTAG
* *
13303035 TA TA TA TA TT TA TA AA 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
13303071 CACACGTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13304223 original size:15 final size:16
Alignment explanation
Indices: 13304203--13304242 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
13304193 GACATAATAT
13304203 AATTAATATAT-TTAA
1 AATTAATATATATTAA
*
13304218 AATTAATTTATATTAA
1 AATTAATATATATTAA
13304234 AA-TAATATA
1 AATTAATATA
13304243 ACATAATACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAATATATATTAA
Found at i:13304270 original size:19 final size:19
Alignment explanation
Indices: 13304248--13304296 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
13304238 ATATAACATA
*
13304248 ATACGATTAATATGATTAT
1 ATACGATTAATATGATTAG
* *
13304267 ATACAAATAATATGATTAG
1 ATACGATTAATATGATTAG
*
13304286 ACACGATTAAT
1 ATACGATTAAT
13304297 TTATTTATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (19 bp):
ATACGATTAATATGATTAG
Found at i:13304359 original size:30 final size:29
Alignment explanation
Indices: 13304302--13304373 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 29
13304292 TTAATTTATT
13304302 TATTTAAATAAAAAATATCATTTAAATT-AA
1 TATTTAAAT--AAAATATCATTTAAATTAAA
*
13304332 TATTTAAATAAAATATTATTTAAAAATTAAA
1 TATTTAAATAAAATATCATTT--AAATTAAA
13304363 TATTTATAATA
1 TATTTA-AATA
13304374 TATTTAAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 11 0.30
30 14 0.38
31 8 0.22
32 4 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
TATTTAAATAAAATATCATTTAAATTAAA
Found at i:13304390 original size:27 final size:26
Alignment explanation
Indices: 13304338--13304399 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
13304328 TTAATATTTA
* *
13304338 AATAAAATATTATTTAAAAATTAAAT
1 AATATAATATTATTTAAAAATAAAAT
* *
13304364 ATTTATAATA-TATTTAAACATCAAAAT
1 A-ATATAATATTATTTAAAAAT-AAAAT
13304391 AATATAATA
1 AATATAATA
13304400 AATACGATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (26 bp):
AATATAATATTATTTAAAAATAAAAT
Found at i:13304678 original size:31 final size:31
Alignment explanation
Indices: 13304640--13304698 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
13304630 GAAGGAACGT
13304640 TTGAAACTATAAATGCAAAAATAAAATATTC
1 TTGAAACTATAAATGCAAAAATAAAATATTC
13304671 TTGAAACTATAAATGCAAAAATAAAATA
1 TTGAAACTATAAATGCAAAAATAAAATA
13304699 GAATATTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.58, C:0.08, G:0.07, T:0.27
Consensus pattern (31 bp):
TTGAAACTATAAATGCAAAAATAAAATATTC
Found at i:13304795 original size:3 final size:3
Alignment explanation
Indices: 13304787--13304816 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
13304777 TCATTGGACT
13304787 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
13304817 GTTTCTCAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:13308870 original size:220 final size:218
Alignment explanation
Indices: 13308469--13308907 Score: 781
Period size: 220 Copynumber: 2.0 Consensus size: 218
13308459 ACTTTATATC
13308469 TAGTCATAGTTGTAAAAACTTACTATTTTACTTGACATGGTTTCATATTTTGAAAACATTGCACG
1 TAGTCATAGTTGTAAAAACTTACTATTTTACTTGACATGGTTTCATATTTTGAAAACATTGCACG
*
13308534 ATAGATTTGTTATTAATTCTTTTGAACACATTTTCCAATGTACATAACTAATTTATCATTCAACC
66 ATAGATTTGTTATTAATACTTTTGAACACATTTTCCAATGTACATAACTAATTTATCATTCAACC
*
13308599 ATTAATTTCCAATTCAATTTCATAAACGAGTCTTCAAGATGCTCATTGTTGAAAATGCTCTCTAC
131 ATTAATTTCCAATTCAATTTCATAAACGAGTCTTCAAGATACTCATTGTTGAAAATGCTCTCTAC
13308664 CGTAACCATGGTATT-TGATAGAA
196 CGTAACCATGGT-TTATGATAGAA
*
13308687 TAGTCATAGTTGTAAAAAGTTTTACTATTTTACTTGACATGGTTTCATATTTTGAAAACATTGCA
1 TAGTCATAGTTGTAAAAA--CTTACTATTTTACTTGACATGGTTTCATATTTTGAAAACATTGCA
*
13308752 CGATAGGTTTGTTATTAATACTTTTGAACACATTTTCCAATGTACATAACTAATTTATCATTCAA
64 CGATAGATTTGTTATTAATACTTTTGAACACATTTTCCAATGTACATAACTAATTTATCATTCAA
* *
13308817 CCATTAATTTCCAATTCAATTTCATAAATGAGTCTTCAAGATATTCATTGTTGAAAATGCTCTCT
129 CCATTAATTTCCAATTCAATTTCATAAACGAGTCTTCAAGATACTCATTGTTGAAAATGCTCTCT
*
13308882 ACTGTAACCATGGTTTATGATAGAA
194 ACCGTAACCATGGTTTATGATAGAA
13308907 T
1 T
13308908 CAATACTAGT
Statistics
Matches: 211, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
218 18 0.09
219 2 0.01
220 191 0.91
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (218 bp):
TAGTCATAGTTGTAAAAACTTACTATTTTACTTGACATGGTTTCATATTTTGAAAACATTGCACG
ATAGATTTGTTATTAATACTTTTGAACACATTTTCCAATGTACATAACTAATTTATCATTCAACC
ATTAATTTCCAATTCAATTTCATAAACGAGTCTTCAAGATACTCATTGTTGAAAATGCTCTCTAC
CGTAACCATGGTTTATGATAGAA
Found at i:13313582 original size:23 final size:25
Alignment explanation
Indices: 13313556--13313639 Score: 68
Period size: 27 Copynumber: 3.4 Consensus size: 25
13313546 AAATATATAT
*
13313556 AATAATA-TAATTTT-TTCATTAAA
1 AATAATATTAATTTTATTAATTAAA
*
13313579 AAT-ATATTAATTTTAGTTAATTTAA
1 AATAATATTAATTTTA-TTAATTAAA
* * *
13313604 AATAATAATTTATATTATTTAATAAAA
1 AATAAT-ATTAATTTTA-TTAATTAAA
13313631 AAT-ATATTA
1 AATAATATTA
13313640 TAGGTATATA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
22 3 0.06
23 10 0.21
25 13 0.27
26 4 0.08
27 18 0.38
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
AATAATATTAATTTTATTAATTAAA
Found at i:13317634 original size:6 final size:6
Alignment explanation
Indices: 13317623--13317688 Score: 63
Period size: 6 Copynumber: 12.0 Consensus size: 6
13317613 ATTAATTAAT
* *
13317623 TTTATA TTTATA TATATA TTTATA -TAAT- TTTATA TTTATA --TATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
*
13317667 TTTATA -TAAT- TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA
13317689 CTAAAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
4 4 0.08
5 12 0.25
6 32 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTATA
Found at i:13317646 original size:10 final size:9
Alignment explanation
Indices: 13317621--13317683 Score: 60
Period size: 10 Copynumber: 7.0 Consensus size: 9
13317611 TGATTAATTA
13317621 ATTTTATAT
1 ATTTTATAT
*
13317630 -TTATATAT
1 ATTTTATAT
13317638 ATATTTATAT
1 AT-TTTATAT
*
13317648 AATTT-TAT
1 ATTTTATAT
13317656 A-TTTATAT
1 ATTTTATAT
13317664 ATATTTATAT
1 AT-TTTATAT
13317674 AATTTTATAT
1 -ATTTTATAT
13317684 TTATACTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
7 3 0.07
8 15 0.33
9 4 0.09
10 21 0.47
11 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTTTATAT
Found at i:13317669 original size:26 final size:26
Alignment explanation
Indices: 13317619--13317688 Score: 122
Period size: 26 Copynumber: 2.6 Consensus size: 26
13317609 TTTGATTAAT
13317619 TAATTTTATATTTATATATATATTTATA
1 TAATTTTATA-TT-TATATATATTTATA
13317647 TAATTTTATATTTATATATATTTATA
1 TAATTTTATATTTATATATATTTATA
13317673 TAATTTTATATTTATA
1 TAATTTTATATTTATA
13317689 CTAAAAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 30 0.71
27 2 0.05
28 10 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TAATTTTATATTTATATATATTTATA
Found at i:13317709 original size:25 final size:24
Alignment explanation
Indices: 13317621--13317728 Score: 94
Period size: 26 Copynumber: 4.3 Consensus size: 24
13317611 TGATTAATTA
**
13317621 ATTTTATATTTATATATATATTTATAT
1 ATTTTATATTTATATA-A-AAATA-AT
* **
13317648 AATTTTATATTTATATATATTTATAT
1 -ATTTTATATTTATATAAAAATA-AT
13317674 AATTTTATATTTATACTAAAAATAAT
1 -ATTTTATATTTATA-TAAAAATAAT
13317700 ATTTTATATTT-TA-AAAAATAAT
1 ATTTTATATTTATATAAAAATAAT
13317722 ATTTTAT
1 ATTTTAT
13317729 TAATTTTAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.21
24 2 0.03
25 11 0.15
26 25 0.33
27 5 0.07
28 16 0.21
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTATATTTATATAAAAATAAT
Found at i:13317719 original size:22 final size:22
Alignment explanation
Indices: 13317675--13317738 Score: 83
Period size: 22 Copynumber: 2.7 Consensus size: 22
13317665 TATTTATATA
13317675 ATTTTATATTTATACTAAAAATAAT
1 ATTTTATATTT-TA--AAAAATAAT
13317700 ATTTTATATTTTAAAAAATAAT
1 ATTTTATATTTTAAAAAATAAT
13317722 ATTTTATTAATTTTAAA
1 ATTTTA-T-ATTTTAAA
13317739 TCGAATCAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
22 15 0.41
23 1 0.03
24 10 0.27
25 11 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATTTTATATTTTAAAAAATAAT
Found at i:13318457 original size:11 final size:11
Alignment explanation
Indices: 13318438--13318474 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13318428 TCTGGAATAA
13318438 TTAAATTTAAT
1 TTAAATTTAAT
*
13318449 TTAATTTTAAT
1 TTAAATTTAAT
13318460 TTAAA--TAAT
1 TTAAATTTAAT
13318469 TTAAAT
1 TTAAAT
13318475 ATATAGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:13323434 original size:12 final size:12
Alignment explanation
Indices: 13323413--13323446 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13323403 TCAGTAAACC
*
13323413 ATTCAACATACG
1 ATTCAGCATACG
*
13323425 ATTTAGCATACG
1 ATTCAGCATACG
13323437 ATTCAGCATA
1 ATTCAGCATA
13323447 ACAATATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (12 bp):
ATTCAGCATACG
Found at i:13328904 original size:303 final size:303
Alignment explanation
Indices: 13328357--13328956 Score: 1074
Period size: 303 Copynumber: 2.0 Consensus size: 303
13328347 ACAAAATTCA
* *
13328357 AGAGTTATTGTCACTTCATCAACTACTAGCTATGCTAGTGCTAGGGACATAAACCTTTTAGAGGG
1 AGAGTTATTGTCACTTCATCAACTACTAGCTATGCTAGTGCTAGGGACATAAACCCTTTAGAGGA
* *
13328422 AAATATTGACTATTATGGCATGATTAATGACATCATTGAGTTGAATTATTATGACAAGTGGAAAG
66 AAATATTGACTATTATGACATGATTAATGACATCATTGAGTTGAATTATTATGACAAGTGAAAAG
* *
13328487 TTGTCTTATTTCGGTGTGATTGGGCTGATGAGAATAGTGTGAGGGATATTAAGAAAAATCAGTAT
131 TTATCTTATTTCGATGTGATTGGGCTGATGAGAATAGTGTGAGGGATATTAAGAAAAATCAGTAT
*
13328552 GGATTTACACTTGTGAATTTTTCTCGATTAATTCACATTAGGCAACAACTTATCGATGAACCTTA
196 GGATTTACACTTGTGAATTTTTCTCGATTAATTCACATTAGGCAACAACTTATCAATGAACCTTA
13328617 TGTTTTTTCATCTCAAGTCAAACAAATTTTTTATTCTGAAAAT
261 TGTTTTTTCATCTCAAGTCAAACAAATTTTTTATTCTGAAAAT
*
13328660 AGAGTTATTGTCACTTCATTAACTACTAGCTATGCTAGTGCTAGGGACATAAACCCTTTAGAGGA
1 AGAGTTATTGTCACTTCATCAACTACTAGCTATGCTAGTGCTAGGGACATAAACCCTTTAGAGGA
* *
13328725 AAATATTGACTATTATGACATGATTAATGACATCATTGAGTTGGATTATTATGGCAAGTGAAAAG
66 AAATATTGACTATTATGACATGATTAATGACATCATTGAGTTGAATTATTATGACAAGTGAAAAG
* *
13328790 TTATCTTATTTCGATGTGATTGGGCTGATGTGAATAGTGTGAGGGATATTAAGAAAAATTAGTAT
131 TTATCTTATTTCGATGTGATTGGGCTGATGAGAATAGTGTGAGGGATATTAAGAAAAATCAGTAT
13328855 GGATTTACACTTGTGAATTTTTCTCGATTAATTCACATTAGGCAACAACTTATCAATGAACCTTA
196 GGATTTACACTTGTGAATTTTTCTCGATTAATTCACATTAGGCAACAACTTATCAATGAACCTTA
* *
13328920 TGTTTTTTCATCTCAAGTCAAATAAGTTTTTTATTCT
261 TGTTTTTTCATCTCAAGTCAAACAAATTTTTTATTCT
13328957 AAAGATCCCA
Statistics
Matches: 283, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
303 283 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (303 bp):
AGAGTTATTGTCACTTCATCAACTACTAGCTATGCTAGTGCTAGGGACATAAACCCTTTAGAGGA
AAATATTGACTATTATGACATGATTAATGACATCATTGAGTTGAATTATTATGACAAGTGAAAAG
TTATCTTATTTCGATGTGATTGGGCTGATGAGAATAGTGTGAGGGATATTAAGAAAAATCAGTAT
GGATTTACACTTGTGAATTTTTCTCGATTAATTCACATTAGGCAACAACTTATCAATGAACCTTA
TGTTTTTTCATCTCAAGTCAAACAAATTTTTTATTCTGAAAAT
Found at i:13332334 original size:33 final size:33
Alignment explanation
Indices: 13332297--13332369 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
13332287 CATCTCAAAG
* * *
13332297 ATACAAACGCCGCTAATATAGTGGCGTTTTCAT
1 ATACAAACACCGCTAAAATAGTGGCGTCTTCAT
*
13332330 ATACAAACACCGCTAAAATAGTGGTGTCTTCAT
1 ATACAAACACCGCTAAAATAGTGGCGTCTTCAT
13332363 ATACAAA
1 ATACAAA
13332370 TGTCACTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (33 bp):
ATACAAACACCGCTAAAATAGTGGCGTCTTCAT
Found at i:13332449 original size:135 final size:134
Alignment explanation
Indices: 13332228--13332471 Score: 346
Period size: 135 Copynumber: 1.8 Consensus size: 134
13332218 CCTTTTTTTC
* * *
13332228 TATACAAATGCCACCAAAGCAACATAATTTTTTTTCATAAAATGTCACTAAATTAATGGCATCTC
1 TATACAAATGCCACCAAAGCAACATAATTTTTTCTCATAAAACGTCACTAAATTAACGGCATCTC
** *
13332293 AAAGATACAAACGCCGCTAATATAGTGGCGTTTTCATATACAAACACCGCTAAAATAGTGGTGTC
66 AAAGATACAAACGCCGCTAATATAACGGCGTTTTCAGATACAAACACCGCTAAAATAGTGGTGTC
13332358 TTCA
131 TTCA
* * * * *
13332362 TATACAAATGTCACTAAAGTAACATTA-TTTTTCTCATAAAAAACGTCACTAAATTAGCGGCATC
1 TATACAAATGCCACCAAAGCAACATAATTTTTTCTCAT--AAAACGTCACTAAATTAACGGCATC
* *
13332426 TCAAAGATACAAACGTCGTTAATATAACGGCGTTTTCAGATACAAA
64 TCAAAGATACAAACGCCGCTAATATAACGGCGTTTTCAGATACAAA
13332472 TGTCACTAAT
Statistics
Matches: 95, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
133 9 0.09
134 23 0.24
135 63 0.66
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.29
Consensus pattern (134 bp):
TATACAAATGCCACCAAAGCAACATAATTTTTTCTCATAAAACGTCACTAAATTAACGGCATCTC
AAAGATACAAACGCCGCTAATATAACGGCGTTTTCAGATACAAACACCGCTAAAATAGTGGTGTC
TTCA
Found at i:13334219 original size:16 final size:16
Alignment explanation
Indices: 13334198--13334235 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
13334188 ATTTTAAAAC
13334198 TTATTTTCA-TTTTATT
1 TTATTTTCACTTTTA-T
*
13334214 TTATTTTTACTTTTAT
1 TTATTTTCACTTTTAT
13334230 TTATTT
1 TTATTT
13334236 AGAATCGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCACTTTTAT
Found at i:13334964 original size:1 final size:1
Alignment explanation
Indices: 13334958--13334986 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
13334948 CAAAGACACC
13334958 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13334987 CCACCCACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13337519 original size:11 final size:11
Alignment explanation
Indices: 13337503--13337527 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13337493 TTTCCTTTAA
13337503 AAAAAAAAAAG
1 AAAAAAAAAAG
13337514 AAAAAAAAAAG
1 AAAAAAAAAAG
13337525 AAA
1 AAA
13337528 GAGAATTTTA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:13342491 original size:17 final size:19
Alignment explanation
Indices: 13342467--13342552 Score: 61
Period size: 19 Copynumber: 4.4 Consensus size: 19
13342457 GGACATGCAA
*
13342467 AAAAAAAAAAGTAAAAAG-G
1 AAAAAAAAGAG-AAAAAGAG
13342486 AAAAAAAAGAGAAAAAGAG
1 AAAAAAAAGAGAAAAAGAG
* *
13342505 AAAAGCAAGAAAAGAAAAA-TG
1 AAAA--AA-AAGAGAAAAAGAG
* *
13342526 AAAAGAAAGA-AAAAAAAGG
1 AAAAAAAAGAGAAAAAGA-G
13342545 AAAAAAAA
1 AAAAAAAA
13342553 AACTTTGCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
17 5 0.09
18 9 0.17
19 24 0.44
21 7 0.13
22 9 0.17
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.02
Consensus pattern (19 bp):
AAAAAAAAGAGAAAAAGAG
Found at i:13342660 original size:19 final size:19
Alignment explanation
Indices: 13342638--13342674 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
13342628 AAGTCCCAAA
13342638 CAAA-AAAAAAAGAAAACCG
1 CAAACAAAAAAA-AAAACCG
13342657 CAAACAAAAAAAAAAACC
1 CAAACAAAAAAAAAAACC
13342675 TTTTCTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.76, C:0.19, G:0.05, T:0.00
Consensus pattern (19 bp):
CAAACAAAAAAAAAAACCG
Found at i:13343022 original size:24 final size:23
Alignment explanation
Indices: 13342995--13343043 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
13342985 AAAGAAAAAG
13342995 AAAGGTAAAAGAAAA-AAAATTAAA
1 AAAGG-AAAAGAAAATAAAA-TAAA
*
13343019 AAAGGGAAAGAAAATAAAATAAA
1 AAAGGAAAAGAAAATAAAATAAA
13343042 AA
1 AA
13343044 GAATAAGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (23 bp):
AAAGGAAAAGAAAATAAAATAAA
Found at i:13343072 original size:7 final size:7
Alignment explanation
Indices: 13343060--13343103 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
13343050 GGAGAACAAA
13343060 AAAAAAT
1 AAAAAAT
13343067 AAAAAAT
1 AAAAAAT
13343074 AAAAAAT
1 AAAAAAT
*
13343081 AAAAGGA-
1 AAAA-AAT
13343088 AAAAAAT
1 AAAAAAT
13343095 AAAGAAAT
1 AAA-AAAT
13343103 A
1 A
13343104 GAAAGGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 1 0.03
7 25 0.78
8 6 0.19
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:13343113 original size:22 final size:21
Alignment explanation
Indices: 13343067--13343124 Score: 89
Period size: 23 Copynumber: 2.6 Consensus size: 21
13343057 AAAAAAAAAT
13343067 AAAAAATAAAAAATAAAAGGA
1 AAAAAATAAAAAATAAAAGGA
13343088 AAAAAATAAAGAAATAGAAAGGA
1 AAAAAATAAA-AAATA-AAAGGA
13343111 AAAAAATGAAAAAA
1 AAAAAAT-AAAAAA
13343125 AGGGGGGGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.29
22 5 0.15
23 16 0.47
24 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (21 bp):
AAAAAATAAAAAATAAAAGGA
Found at i:13343224 original size:81 final size:82
Alignment explanation
Indices: 13343082--13343259 Score: 295
Period size: 81 Copynumber: 2.2 Consensus size: 82
13343072 ATAAAAAATA
* *
13343082 AAAGGAAAAAAATAAAGAAATAGAAAGGAAAAAAATGAAAAAAAGGGGGGGGGAGAACAAAACAA
1 AAAGGAAAAAAA-AAAAAAATAGAAAGGAAAAAAATGAAAAAAAGGAGGGGGGAGAACAAAACAA
13343147 AAGAAAAGTGGAAAAGGG
65 AAGAAAAGTGGAAAAGGG
* * *
13343165 AAAGGAAAAAAAAAAAAAATAGAAAGGAAAAAGATGAAAAAAA-GATGGGGGATAACAAAACAAA
1 AAAGGAAAAAAAAAAAAAATAGAAAGGAAAAAAATGAAAAAAAGGAGGGGGGAGAACAAAACAAA
13343229 AGAAAAGTGGAAAAGGG
66 AGAAAAGTGGAAAAGGG
13343246 AAAGGAAAAAAAAA
1 AAAGGAAAAAAAAA
13343260 GAAATGAACG
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
81 49 0.54
82 29 0.32
83 12 0.13
ACGTcount: A:0.67, C:0.02, G:0.26, T:0.05
Consensus pattern (82 bp):
AAAGGAAAAAAAAAAAAAATAGAAAGGAAAAAAATGAAAAAAAGGAGGGGGGAGAACAAAACAAA
AGAAAAGTGGAAAAGGG
Found at i:13345680 original size:13 final size:13
Alignment explanation
Indices: 13345662--13345754 Score: 71
Period size: 13 Copynumber: 6.8 Consensus size: 13
13345652 CTAAACCTCC
13345662 AAACCCTAAAACT
1 AAACCCTAAAACT
**
13345675 AAACCCTAACCCTCT
1 AAACCCTAA--AACT
*
13345690 AAACCCTAAAATT
1 AAACCCTAAAACT
* *
13345703 AAACTCTAAACCCT
1 AAACCCTAAA-ACT
*
13345717 CCAAACCCTAAAACA
1 --AAACCCTAAAACT
13345732 AAACCCTAAAA-T
1 AAACCCTAAAACT
13345744 GAAACCCTAAA
1 -AAACCCTAAA
13345755 CCCTAAAAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
13 40 0.65
14 1 0.02
15 12 0.19
16 9 0.15
ACGTcount: A:0.49, C:0.33, G:0.01, T:0.16
Consensus pattern (13 bp):
AAACCCTAAAACT
Found at i:13345691 original size:21 final size:23
Alignment explanation
Indices: 13345644--13345692 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
13345634 AATCCTAAAA
13345644 TCTAAATACTAAACCTCCAAACC
1 TCTAAATACTAAACCTCCAAACC
* *
13345667 -CTAAA-ACTAAACC-CTAACCC
1 TCTAAATACTAAACCTCCAAACC
13345687 TCTAAA
1 TCTAAA
13345693 CCCTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
21 13 0.57
22 5 0.22
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (23 bp):
TCTAAATACTAAACCTCCAAACC
Found at i:13345709 original size:20 final size:20
Alignment explanation
Indices: 13345686--13345762 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
13345676 AACCCTAACC
13345686 CTCTAAACCCTAAAATTAAA
1 CTCTAAACCCTAAAATTAAA
**
13345706 CTCTAAACCCTCCAAACCCTAAA
1 CTCTAAACCCT--AAA-ATTAAA
* * *
13345729 -ACAAAACCCTAAAATGAAA
1 CTCTAAACCCTAAAATTAAA
*
13345748 CCCTAAACCCTAAAA
1 CTCTAAACCCTAAAA
13345763 ATGAAACCCT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
19 3 0.07
20 26 0.59
22 11 0.25
23 4 0.09
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.17
Consensus pattern (20 bp):
CTCTAAACCCTAAAATTAAA
Found at i:13345718 original size:57 final size:58
Alignment explanation
Indices: 13345607--13345741 Score: 177
Period size: 57 Copynumber: 2.3 Consensus size: 58
13345597 TTGTTTAAAT
* * *
13345607 CCTAAAATCTAAATCCTAAACCTTTCAAATCCTAAAATCTAAATACTAAACCTCCAAAC
1 CCTAAAA-CTAAACCCTAAACCTCTCAAACCCTAAAATCTAAATACTAAACCTCCAAAC
*
13345666 CCTAAAACTAAACCCTAACCCTCT-AAACCCTAAAAT-TAAACT-CTAAACCCTCCAAAC
1 CCTAAAACTAAACCCTAAACCTCTCAAACCCTAAAATCTAAA-TACTAAA-CCTCCAAAC
*
13345723 CCTAAAACAAAACCCTAAA
1 CCTAAAACTAAACCCTAAA
13345742 ATGAAACCCT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
56 9 0.13
57 38 0.56
58 14 0.21
59 7 0.10
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (58 bp):
CCTAAAACTAAACCCTAAACCTCTCAAACCCTAAAATCTAAATACTAAACCTCCAAAC
Found at i:13345735 original size:29 final size:29
Alignment explanation
Indices: 13345607--13345741 Score: 148
Period size: 29 Copynumber: 4.7 Consensus size: 29
13345597 TTGTTTAAAT
* * * *
13345607 CCTAAAATCTAAATCCTAAACCTTTCAAAT
1 CCTAAAA-CTAAACCCTAAACCCTCCAAAC
**
13345637 CCTAAAATCTAAATACTAAA-CCTCCAAAC
1 CCTAAAA-CTAAACCCTAAACCCTCCAAAC
*
13345666 CCTAAAACTAAACCCT-AACCCTCTAAAC
1 CCTAAAACTAAACCCTAAACCCTCCAAAC
* *
13345694 CCTAAAATTAAACTCTAAACCCTCCAAAC
1 CCTAAAACTAAACCCTAAACCCTCCAAAC
*
13345723 CCTAAAACAAAACCCTAAA
1 CCTAAAACTAAACCCTAAA
13345742 ATGAAACCCT
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
27 2 0.02
28 29 0.32
29 40 0.44
30 19 0.21
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (29 bp):
CCTAAAACTAAACCCTAAACCCTCCAAAC
Found at i:13345763 original size:21 final size:20
Alignment explanation
Indices: 13345732--13345775 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
13345722 CCCTAAAACA
13345732 AAACCCTAAAATGAAACCCT
1 AAACCCTAAAATGAAACCCT
13345752 AAACCCTAAAAATGAAACCCT
1 AAACCCT-AAAATGAAACCCT
13345773 AAA
1 AAA
13345776 ATTAAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.55, C:0.27, G:0.05, T:0.14
Consensus pattern (20 bp):
AAACCCTAAAATGAAACCCT
Found at i:13345783 original size:14 final size:14
Alignment explanation
Indices: 13345752--13345785 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13345742 ATGAAACCCT
*
13345752 AAACCCTAAAAATG
1 AAACCCTAAAAATA
*
13345766 AAACCCTAAAATTA
1 AAACCCTAAAAATA
13345780 AAACCC
1 AAACCC
13345786 CAAACCTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.26, G:0.03, T:0.15
Consensus pattern (14 bp):
AAACCCTAAAAATA
Found at i:13345804 original size:29 final size:29
Alignment explanation
Indices: 13345766--13345950 Score: 151
Period size: 29 Copynumber: 6.3 Consensus size: 29
13345756 CCTAAAAATG
*
13345766 AAACCCTAAAATTAAAACCCCAAACCTCC
1 AAACCCTAAAATCAAAACCCCAAACCTCC
* * **
13345795 AAACCTTAAAATCAATACCCCAAATTTCC
1 AAACCCTAAAATCAAAACCCCAAACCTCC
* * * **
13345824 AAA-CCTTAAA-CTAAACCCTAAACCCTTT
1 AAACCCTAAAATCAAAACCCCAAA-CCTCC
* * * *
13345852 AAACCTTAAAAAAT-GAAACCCAAAACCCTCT
1 AAACCCT--AAAATCAAAACCCCAAA-CCTCC
* *
13345883 GAACCCTAAAATCAAAACCCCAAACCTTC
1 AAACCCTAAAATCAAAACCCCAAACCTCC
* *
13345912 AAACCCTAAAATCAAAACCCCAAACTTTC
1 AAACCCTAAAATCAAAACCCCAAACCTCC
13345941 AAACCCTAAA
1 AAACCCTAAA
13345951 CCCCTTAACC
Statistics
Matches: 123, Mismatches: 27, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
27 9 0.07
28 9 0.07
29 74 0.60
30 9 0.07
31 22 0.18
ACGTcount: A:0.48, C:0.34, G:0.01, T:0.18
Consensus pattern (29 bp):
AAACCCTAAAATCAAAACCCCAAACCTCC
Found at i:13345917 original size:15 final size:15
Alignment explanation
Indices: 13345897--13345952 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
13345887 CCTAAAATCA
13345897 AAACCCCAAACCTTC
1 AAACCCCAAACCTTC
* *
13345912 AAACCCTAAA--ATC
1 AAACCCCAAACCTTC
*
13345925 AAAACCCCAAACTTTC
1 -AAACCCCAAACCTTC
*
13345941 AAACCCTAAACC
1 AAACCCCAAACC
13345953 CCTTAACCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
13 2 0.06
14 9 0.28
15 19 0.59
16 2 0.06
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.14
Consensus pattern (15 bp):
AAACCCCAAACCTTC
Found at i:13345931 original size:14 final size:14
Alignment explanation
Indices: 13345884--13345931 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
13345874 AAACCCTCTG
13345884 AACCCTAAAATCAA
1 AACCCTAAAATCAA
* *
13345898 AACCCCAAACCTTC-A
1 AACCCTAAA--ATCAA
13345913 AACCCTAAAATCAA
1 AACCCTAAAATCAA
13345927 AACCC
1 AACCC
13345932 CAAACTTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 2 0.07
14 14 0.52
15 9 0.33
16 2 0.07
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (14 bp):
AACCCTAAAATCAA
Found at i:13345996 original size:74 final size:75
Alignment explanation
Indices: 13345867--13346025 Score: 173
Period size: 74 Copynumber: 2.1 Consensus size: 75
13345857 TTAAAAAATG
* * *
13345867 AAACCCAAAACCCTCTGAACCCTAAAATCAAAACCCCAAACCTTCAAACCCTAAAA-TCAAAACC
1 AAACCCTAAACCCTCTGAACCCTAAAATCAAAACCCCAAACCTCCAAACCATAAAACT-AAAACC
*
13345931 CCAAA-CTTTC
65 CCAAACCCTTC
* * * *
13345941 AAACCCTAAACCC-CTTAACCCCTAAAATTAAAA-CCTAAATCCTCCAAATCATAAAACTAAAAC
1 AAACCCTAAACCCTCTGAA-CCCTAAAATCAAAACCCCAAA-CCTCCAAACCATAAAACTAAAAC
*
13346004 CCTAAACCCTTC
64 CCCAAACCCTTC
*
13346016 AAACCTTAAA
1 AAACCCTAAA
13346026 ATCAAAACCG
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
73 9 0.13
74 48 0.68
75 14 0.20
ACGTcount: A:0.47, C:0.35, G:0.01, T:0.18
Consensus pattern (75 bp):
AAACCCTAAACCCTCTGAACCCTAAAATCAAAACCCCAAACCTCCAAACCATAAAACTAAAACCC
CAAACCCTTC
Found at i:13346026 original size:30 final size:30
Alignment explanation
Indices: 13345941--13346067 Score: 97
Period size: 30 Copynumber: 4.3 Consensus size: 30
13345931 CCAAACTTTC
* *
13345941 AAACCCTAAACCCCTT-AACCCCTAAAATTA
1 AAACCCTAAA-CCCTTCAAACCCTAAAACTA
* * * *
13345971 AAA-CCTAAATCCTCCAAATCATAAAACTA
1 AAACCCTAAACCCTTCAAACCCTAAAACTA
*
13346000 AAACCCTAAACCCTTCAAACCTTAAAA-TCA
1 AAACCCTAAACCCTTCAAACCCTAAAACT-A
13346030 AAACCGC-AAA--CTTCAAAACCCTAAAACT-
1 AAACC-CTAAACCCTTC-AAACCCTAAAACTA
*
13346058 AAGCCCTAAA
1 AAACCCTAAA
13346068 ACCAAACCTA
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.01
28 14 0.18
29 30 0.38
30 32 0.41
31 1 0.01
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.18
Consensus pattern (30 bp):
AAACCCTAAACCCTTCAAACCCTAAAACTA
Found at i:13352897 original size:16 final size:18
Alignment explanation
Indices: 13352876--13352917 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
13352866 GCTAGAATTC
13352876 CAAAAAAAAA-TAAAA-A
1 CAAAAAAAAAGTAAAAGA
13352892 CAAAAAAAAAGTAAAAGA
1 CAAAAAAAAAGTAAAAGA
13352910 -AAAAAAAA
1 CAAAAAAAA
13352918 GAGAACATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.42
17 13 0.54
18 1 0.04
ACGTcount: A:0.86, C:0.05, G:0.05, T:0.05
Consensus pattern (18 bp):
CAAAAAAAAAGTAAAAGA
Found at i:13352918 original size:16 final size:17
Alignment explanation
Indices: 13352876--13352918 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
13352866 GCTAGAATTC
13352876 CAAAAAAAAA-TAAAAA
1 CAAAAAAAAAGTAAAAA
13352892 CAAAAAAAAAGT-AAAA
1 CAAAAAAAAAGTAAAAA
*
13352908 GAAAAAAAAAG
1 CAAAAAAAAAG
13352919 AGAACATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.84, C:0.05, G:0.07, T:0.05
Consensus pattern (17 bp):
CAAAAAAAAAGTAAAAA
Found at i:13354617 original size:37 final size:37
Alignment explanation
Indices: 13354566--13354682 Score: 121
Period size: 37 Copynumber: 3.2 Consensus size: 37
13354556 TTGATTCGTA
* * *
13354566 ATGTTATCCC-ATCGATTCTTTATTTTTTAACTTACG
1 ATGTTGTCCCGATCGATTATTTATTTTTTGACTTACG
* * *
13354602 GTGTTGTCCCGATCGATTATTTACTTTTTGACTCACG
1 ATGTTGTCCCGATCGATTATTTATTTTTTGACTTACG
* * * *
13354639 ATATTGCCCCGATC-ATTTTCTTATTTTTTGACTTACA
1 ATGTTGTCCCGATCGATTAT-TTATTTTTTGACTTACG
13354676 ATGTTGT
1 ATGTTGT
13354683 TCTAGTCAAT
Statistics
Matches: 64, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
36 12 0.19
37 52 0.81
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.48
Consensus pattern (37 bp):
ATGTTGTCCCGATCGATTATTTATTTTTTGACTTACG
Found at i:13354720 original size:22 final size:22
Alignment explanation
Indices: 13354690--13354806 Score: 101
Period size: 22 Copynumber: 5.3 Consensus size: 22
13354680 TGTTCTAGTC
13354690 AATTCTTTAAGACCTCTAAGCAT
1 AATT-TTTAAGACCTCTAAGCAT
*
13354713 AATTTTTAAGACCT-TCAAGCAC
1 AATTTTTAAGACCTCT-AAGCAT
* ****
13354735 AATTTGTAAGACCTAGGGGCAT
1 AATTTTTAAGACCTCTAAGCAT
* * *
13354757 GATTTCTAAGACCTCTAAGTAT
1 AATTTTTAAGACCTCTAAGCAT
* **
13354779 AATCTTTAAGACCTCCGAGCAT
1 AATTTTTAAGACCTCTAAGCAT
13354801 AATTTT
1 AATTTT
13354807 AATTTACGAT
Statistics
Matches: 72, Mismatches: 20, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
21 1 0.01
22 67 0.93
23 4 0.06
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (22 bp):
AATTTTTAAGACCTCTAAGCAT
Found at i:13354981 original size:132 final size:130
Alignment explanation
Indices: 13354753--13355176 Score: 403
Period size: 132 Copynumber: 3.2 Consensus size: 130
13354743 AGACCTAGGG
** * *
13354753 GCATGATTTCTAAGACCTCTAAGTATAATCTTTAAGACCTCCGAGCATAATTTTAATTTACG-A-
1 GCATGATTTCTAAGACCTCCGAGCATAATCTTTAGGACCTCCG-GCATAATTTTAA-TT-CGCAG
* * * *
13354816 TGTTATCCCAATCGATTTTTTATTTTTCGACTTACGATGTTATCTCGATCAATTTTATAAGACCT
63 TGTTATCCCGATCGA-TTCTTATTTTT-TACTTACGATGTTATCTCGATCGATTTTATAAGACCT
13354881 CTAGA
126 CTAGA
*
13354886 -CATGATTTCTAAGACCTCCGAGCATAATCTTTAGGACCTCCAGGCATAATTTTGATTCGCAGTG
1 GCATGATTTCTAAGACCTCCGAGCATAATCTTTAGGACCTCC-GGCATAATTTTAATTCGCAGTG
* * * *
13354950 TTATCCCGATCGATTCATTATTTTTTAACTTATGATGTTGTCCCGATCGATTTTATAAAACCT-T
65 TTATCCCGATCGATTC-TTATTTTTT-ACTTACGATGTTATCTCGATCGATTTTATAAGACCTCT
*
13355014 CGA
128 AGA
* * * * * * *
13355017 GCATGATTTCTAAGGCCT-CTAGGCGTAGTCTTT-GAGACCTCCGGATATAATTTCAATTCACAG
1 GCATGATTTCTAAGACCTCCGA-GCATAATCTTTAG-GACCTCCGG-CATAATTTTAATTCGCAG
* ** * * * *
13355080 TGTCATTTCGATCGATTCTTAATTTTTTACTTACGGTGTTATTTCGGTCGATTCTATAAGACCTC
63 TGTTATCCCGATCGATTCTT-ATTTTTTACTTACGATGTTATCTCGATCGATTTTATAAGACCTC
*
13355145 CA-A
127 TAGA
* * *
13355148 GCATGATTTCCAAGACTTTCGAGCATAAT
1 GCATGATTTCTAAGACCTCCGAGCATAAT
13355177 TTTGACTCGC
Statistics
Matches: 238, Mismatches: 41, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
130 2 0.01
131 64 0.27
132 171 0.72
133 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (130 bp):
GCATGATTTCTAAGACCTCCGAGCATAATCTTTAGGACCTCCGGCATAATTTTAATTCGCAGTGT
TATCCCGATCGATTCTTATTTTTTACTTACGATGTTATCTCGATCGATTTTATAAGACCTCTAGA
Found at i:13355294 original size:22 final size:22
Alignment explanation
Indices: 13355269--13355352 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
13355259 CAATCTCCAG
* *
13355269 GACCTCCA-AGCATGATTTCTGA
1 GACCT-CAGAGCATAATTTCTAA
13355291 GACCTCAGAGCATAATTTCTAA
1 GACCTCAGAGCATAATTTCTAA
* * *
13355313 GACCTTC-GGGCACAATCTCTAA
1 GACC-TCAGAGCATAATTTCTAA
* * *
13355335 GATCTCTGGGCATAATTT
1 GACCTCAGAGCATAATTT
13355353 TGACTTACGG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 4 0.08
22 45 0.88
23 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (22 bp):
GACCTCAGAGCATAATTTCTAA
Found at i:13357351 original size:29 final size:28
Alignment explanation
Indices: 13357286--13357734 Score: 294
Period size: 29 Copynumber: 15.3 Consensus size: 28
13357276 CCTAAAATTG
* * * **
13357286 AACCCTAACCCTTTAAACCTTAAAATTA
1 AACCCTAAACCTTCAAACCCTAAAACAA
* *
13357314 ATCTCTAAACCCTTCAAACCCTAAAACAA
1 AACCCTAAA-CCTTCAAACCCTAAAACAA
* * * *
13357343 AACCTTAAACTCTCCAAACTCTGAAACAA
1 AACCCTAAAC-CTTCAAACCCTAAAACAA
* ** *
13357372 AACCCTAAA-TTCTCTAAACTTTAAAAACGA
1 AACCCTAAACCT-TC-AAACCCT-AAAACAA
* * *
13357402 AACCTTAAACCTCCAAATCCTAAAATCAA
1 AACCCTAAACCTTCAAACCCTAAAA-CAA
* *
13357431 AACCCTAAACCTCCAAACCCTAAAACTA
1 AACCCTAAACCTTCAAACCCTAAAACAA
* * * *
13357459 AATCCTAAACCCTCTAAACCTTAAAAAAATGA
1 AACCCTAAACCTTC-AAACCCT-AAAACA--A
* *
13357491 AACCCTAAACCCTCTAAACCTTAAAATCAA
1 AACCCTAAACCTTC-AAACCCTAAAA-CAA
*
13357521 AAGCCC-AAACCTTCAAACCTTAAAATCAA
1 AA-CCCTAAACCTTCAAACCCTAAAA-CAA
*
13357550 AACCCTAAA-CTTCAAAACCCTAAAACTA
1 AACCCTAAACCTTC-AAACCCTAAAACAA
* * *
13357578 AACCCTAAACCTCCTAAACCTTAAAATCCA
1 AACCCTAAACCTTC-AAACCCTAAAA-CAA
* * * *
13357608 AACCCTAAATTCTCCAAATCATAAAACTAA
1 AACCCTAAA-CCTTCAAACCCTAAAAC-AA
13357638 AACCCTAAACCCTTCAAACCCTAAAATCAA
1 AACCCTAAA-CCTTCAAACCCTAAAA-CAA
* *
13357668 AATCCC-AAACCTCCAAACCCTAAAACTA
1 AA-CCCTAAACCTTCAAACCCTAAAACAA
* * *
13357696 AGCCCTAAAACCCTCTAAACCCTAAAACCA
1 AACCCT-AAACCTTC-AAACCCTAAAACAA
13357726 AACCCTAAA
1 AACCCTAAA
13357735 ACTCTTGAAA
Statistics
Matches: 337, Mismatches: 60, Indels: 47
0.76 0.14 0.11
Matches are distributed among these distances:
27 4 0.01
28 46 0.14
29 153 0.45
30 95 0.28
31 16 0.05
32 23 0.07
ACGTcount: A:0.47, C:0.33, G:0.01, T:0.20
Consensus pattern (28 bp):
AACCCTAAACCTTCAAACCCTAAAACAA
Found at i:13357516 original size:119 final size:118
Alignment explanation
Indices: 13357371--13357722 Score: 412
Period size: 119 Copynumber: 2.9 Consensus size: 118
13357361 CTCTGAAACA
* * *
13357371 AAACCCTAAATTCTCTAAACTTTAAAAACGAAACCTTAAACCTCCAAATCCTAAAATCAAAACCC
1 AAACCCTAAATTCTCTAAACCTTAAAAACAAAACC-TAAACCTTCAAA-CCTAAAATCAAAACCC
* *
13357436 TAAACCTCCAAACCCTAAAACTAAATCCTAAACCCTCTAAACCTTAAAAAAAT-G
64 TAAACCTCCAAACCCTAAAACTAAACCCTAAACCCTCTAAACCTTAAAAAAATCC
** * *
13357490 AAACCCTAAACCCTCTAAACCTTAAAATCAAAAGCCCAAACCTTCAAACCTTAAAATCAAAACCC
1 AAACCCTAAATTCTCTAAACCTTAAAAACAAAA-CCTAAACCTTCAAACC-TAAAATCAAAACCC
* *
13357555 TAAACTTCAAAACCCTAAAACTAAACCCTAAA-CCTCCTAAACCTT---AAAATCC
64 TAAACCTCCAAACCCTAAAACTAAACCCTAAACCCT-CTAAACCTTAAAAAAATCC
* * *
13357607 AAACCCTAAATTCTCCAAATCAT-AAAACTAAAACCCTAAACCCTTCAAACCCTAAAATCAAAAT
1 AAACCCTAAATTCTCTAAACCTTAAAAAC-AAAA-CCTAAA-CCTTCAAA-CCTAAAATCAAAA-
* *
13357671 CCC-AAACCTCCAAACCCTAAAACTAAGCCCTAAAACCCTCTAAACCCTAAAA
61 CCCTAAACCTCCAAACCCTAAAACTAAACCCT-AAACCCTCTAAACCTTAAAA
13357723 CCAAACCCTA
Statistics
Matches: 197, Mismatches: 23, Indels: 23
0.81 0.09 0.09
Matches are distributed among these distances:
116 9 0.05
117 27 0.14
118 49 0.25
119 106 0.54
120 5 0.03
122 1 0.01
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.19
Consensus pattern (118 bp):
AAACCCTAAATTCTCTAAACCTTAAAAACAAAACCTAAACCTTCAAACCTAAAATCAAAACCCTA
AACCTCCAAACCCTAAAACTAAACCCTAAACCCTCTAAACCTTAAAAAAATCC
Found at i:13359810 original size:13 final size:13
Alignment explanation
Indices: 13359782--13359820 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
13359772 GCAATTTTGC
**
13359782 TTTTCAGACTATA
1 TTTTCAGACTGCA
13359795 TTTTCAGACTGCA
1 TTTTCAGACTGCA
*
13359808 TTTTTAGACTGCA
1 TTTTCAGACTGCA
13359821 AAACATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (13 bp):
TTTTCAGACTGCA
Found at i:13362488 original size:10 final size:10
Alignment explanation
Indices: 13362473--13362498 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13362463 AAAATTATCT
13362473 TTTTAATAAA
1 TTTTAATAAA
13362483 TTTTAATAAA
1 TTTTAATAAA
13362493 TTTTAA
1 TTTTAA
13362499 GATTTTATTA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTTAATAAA
Found at i:13362521 original size:18 final size:17
Alignment explanation
Indices: 13362478--13362527 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
13362468 TATCTTTTTA
*
13362478 ATAAATTTTAATAAATT
1 ATAAATTTTAATAAAAT
* *
13362495 TTAAGATTTTATTAAAAAT
1 ATAA-ATTTTAAT-AAAAT
13362514 ATAAATTTTAATAA
1 ATAAATTTTAATAA
13362528 GTAATCAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 5 0.19
18 14 0.54
19 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
ATAAATTTTAATAAAAT
Found at i:13365338 original size:24 final size:23
Alignment explanation
Indices: 13365311--13365355 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
13365301 CTTTTGGATA
13365311 TTTATTTTCAAAAATTTTTAAAAT
1 TTTATTTT-AAAAATTTTTAAAAT
*
13365335 TTTATTTTTAAAATTTTTAAA
1 TTTATTTTAAAAATTTTTAAA
13365356 TCATACCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTATTTTAAAAATTTTTAAAAT
Found at i:13365353 original size:15 final size:14
Alignment explanation
Indices: 13365324--13365351 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13365314 ATTTTCAAAA
13365324 ATTTTTAAAATTTT
1 ATTTTTAAAATTTT
13365338 ATTTTTAAAATTTT
1 ATTTTTAAAATTTT
13365352 TAAATCATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTTAAAATTTT
Found at i:13373660 original size:2 final size:2
Alignment explanation
Indices: 13373655--13373695 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
13373645 CACACGAGTG
13373655 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13373696 GAATGCTGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13374988 original size:44 final size:44
Alignment explanation
Indices: 13374936--13375027 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
13374926 CCCTCTGCAC
13374936 AAGT-AAGTCCCATGAACTAATATTAAGGGATTGTACATAAGGA
1 AAGTCAAGTCCCATGAACTAATATTAAGGGATTGTACATAAGGA
13374979 AAGTCAAGTCCCATGAACTAATATTAAGGGATTGTACATAAGGA
1 AAGTCAAGTCCCATGAACTAATATTAAGGGATTGTACATAAGGA
13375023 AAGTC
1 AAGTC
13375028 TTGAACGAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 4 0.08
44 44 0.92
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (44 bp):
AAGTCAAGTCCCATGAACTAATATTAAGGGATTGTACATAAGGA
Found at i:13379446 original size:18 final size:17
Alignment explanation
Indices: 13379413--13379460 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
13379403 AAGAATATAA
13379413 AAAGAGAAAAAAGAAAG
1 AAAGAGAAAAAAGAAAG
* *
13379430 AAAGTGAAAATAAGAAAAA
1 AAAGAGAAAA-AAG-AAAG
13379449 AAATGAGAAAAA
1 AAA-GAGAAAAA
13379461 GTGAGCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 9 0.36
18 3 0.12
19 7 0.28
20 6 0.24
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (17 bp):
AAAGAGAAAAAAGAAAG
Found at i:13379821 original size:10 final size:11
Alignment explanation
Indices: 13379801--13379828 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
13379791 TTTTTAAATG
13379801 AAAAAGAAAAA
1 AAAAAGAAAAA
13379812 AAAAAGAAAAA
1 AAAAAGAAAAA
13379823 AAAAAG
1 AAAAAG
13379829 GAAAGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:13379994 original size:17 final size:17
Alignment explanation
Indices: 13379966--13380009 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
13379956 TAAATTAAAG
*
13379966 TATTAA-ATAATAAATT
1 TATTAATATAATAAATA
*
13379982 TATTAATATAATACATA
1 TATTAATATAATAAATA
*
13379999 TATAAATATAA
1 TATTAATATAA
13380010 AAGTAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TATTAATATAATAAATA
Found at i:13381059 original size:17 final size:17
Alignment explanation
Indices: 13381037--13381076 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
13381027 AAATAGGTCT
13381037 TAAAAAA-TATTAAAATA
1 TAAAAAATTATT-AAATA
13381054 TAAAAAATTATTAAATA
1 TAAAAAATTATTAAATA
13381071 TAAAAA
1 TAAAAA
13381077 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAAAATTATTAAATA
Found at i:13384782 original size:20 final size:20
Alignment explanation
Indices: 13384710--13384782 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
13384700 AAAATTTGAA
* *
13384710 ATTCACAATTGAAATTCAAGG
1 ATTCTCAATT-AAATTCAAAG
*
13384731 ATTCCCAACTTAAATCTCAAAG
1 ATTCTCAA-TTAAAT-TCAAAG
* *
13384753 -CTCTGTAATTAAATTCAAAG
1 ATTCT-CAATTAAATTCAAAG
13384773 ATTCTCAATT
1 ATTCTCAATT
13384783 TGAATTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
20 10 0.24
21 22 0.54
22 9 0.22
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (20 bp):
ATTCTCAATTAAATTCAAAG
Found at i:13384954 original size:38 final size:37
Alignment explanation
Indices: 13384898--13384996 Score: 101
Period size: 38 Copynumber: 2.6 Consensus size: 37
13384888 ATTCATAATA
* * *
13384898 TTCAAATTTTGCACAAGATTTAAAGGTTTGCGAAAAAT
1 TTCAAAATTTGCAAAAGATTTAAAGATTTGC-AAAAAT
* * **
13384936 TTCAAAATTCGCAAAAGATTTCAAGATTTGCAAAGGT
1 TTCAAAATTTGCAAAAGATTTAAAGATTTGCAAAAAT
*
13384973 TTCAAGATTTGC-AAAGAATTTAAA
1 TTCAAAATTTGCAAAAG-ATTTAAA
13384997 AAATTCATAA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
36 4 0.08
37 20 0.40
38 26 0.52
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (37 bp):
TTCAAAATTTGCAAAAGATTTAAAGATTTGCAAAAAT
Found at i:13384970 original size:18 final size:18
Alignment explanation
Indices: 13384905--13384989 Score: 89
Period size: 19 Copynumber: 4.6 Consensus size: 18
13384895 ATATTCAAAT
* *
13384905 TTTGCACAAGATTTAAAGG
1 TTTGCA-AAGATTTCAAGA
* *
13384924 TTTGCGAAAAATTTCAAAA
1 TTTGC-AAAGATTTCAAGA
*
13384943 TTCGCAAAAGATTTCAAGA
1 TTTGC-AAAGATTTCAAGA
*
13384962 TTTGCAAAGGTTTCAAGA
1 TTTGCAAAGATTTCAAGA
13384980 TTTGCAAAGA
1 TTTGCAAAGA
13384990 ATTTAAAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
18 21 0.39
19 32 0.59
20 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (18 bp):
TTTGCAAAGATTTCAAGA
Found at i:13385230 original size:18 final size:18
Alignment explanation
Indices: 13385170--13385231 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
13385160 TACCAAGATT
*
13385170 TTTTAG-TTTCGCAAGAA
1 TTTTAGATTTCACAAGAA
* *
13385187 TTTTCAGA-TTCAAAAGGA
1 TTTT-AGATTTCACAAGAA
**
13385205 TTAAAGATTTCACAAGAA
1 TTTTAGATTTCACAAGAA
13385223 TTTTAGATT
1 TTTTAGATT
13385232 CTTAAAAATT
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
17 7 0.21
18 26 0.79
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (18 bp):
TTTTAGATTTCACAAGAA
Found at i:13385290 original size:15 final size:16
Alignment explanation
Indices: 13385224--13385295 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 16
13385214 TCACAAGAAT
*
13385224 TTTAGATTCTTAAAAA
1 TTTAGATTCTCAAAAA
* *
13385240 TTTA-AAT-TCATAAGA
1 TTTAGATTCTCA-AAAA
* *
13385255 TTTCAGTTTCACAAAAA
1 TTT-AGATTCTCAAAAA
*
13385272 TTTA-ATTCTCAAAAT
1 TTTAGATTCTCAAAAA
13385287 TTTAGATTC
1 TTTAGATTC
13385296 GTAAAAACTC
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
14 2 0.05
15 20 0.49
16 10 0.24
17 7 0.17
18 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (16 bp):
TTTAGATTCTCAAAAA
Found at i:13385301 original size:16 final size:16
Alignment explanation
Indices: 13385221--13385301 Score: 58
Period size: 16 Copynumber: 5.1 Consensus size: 16
13385211 ATTTCACAAG
*
13385221 AATTTTAGATTCTTAA
1 AATTTTAGATTCATAA
* *
13385237 AAATTTAAATTCATAA
1 AATTTTAGATTCATAA
* * * *
13385253 GATTTCAGTTTCACAA
1 AATTTTAGATTCATAA
*
13385269 AAATTTA-ATTC-TCAA
1 AATTTTAGATTCAT-AA
*
13385284 AATTTTAGATTCGTAA
1 AATTTTAGATTCATAA
13385300 AA
1 AA
13385302 ACTCACATGA
Statistics
Matches: 47, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
15 11 0.23
16 35 0.74
17 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (16 bp):
AATTTTAGATTCATAA
Found at i:13385302 original size:31 final size:32
Alignment explanation
Indices: 13385221--13385302 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 32
13385211 ATTTCACAAG
*
13385221 AATTTTAGATTCTTAAAAATTTAAATTCATAA
1 AATTTTAGATTCATAAAAATTTAAATTCATAA
* * * *
13385253 GATTTCAGTTTCACAAAAATTT-AATTC-TCAA
1 AATTTTAGATTCATAAAAATTTAAATTCAT-AA
*
13385284 AATTTTAGATTCGTAAAAA
1 AATTTTAGATTCATAAAAA
13385303 CTCACATGAA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
30 1 0.03
31 21 0.54
32 17 0.44
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (32 bp):
AATTTTAGATTCATAAAAATTTAAATTCATAA
Found at i:13385741 original size:109 final size:107
Alignment explanation
Indices: 13385575--13385803 Score: 298
Period size: 109 Copynumber: 2.1 Consensus size: 107
13385565 CATTCGATAT
* * * *
13385575 TTCTCATTTAAAAATTTTAGGATTTCATATAAAATTTCAAAGCTTATCATTCGAGTTCAAAGATT
1 TTCTCATTTAAAAAATTTAGGAGTCCATATAAAATTTCAAAGCTTATCATTCAAGTTCAAAGATT
* *
13385640 CATATTGAATATATTTTAAAGTTTCACACCTAAATTCCAAA-G
66 CACATTGAATAGATTTTAAAGTTTCACACCTAAATT-CAAATG
* * * *
13385682 TTCTCATTCAAAAAATTTAGGGGTCCATATCCAAAATTTTAAAGCTTCTCATTCAAGTTCAAAGA
1 TTCTCATTTAAAAAATTTAGGAGTCCATAT--AAAATTTCAAAGCTTATCATTCAAGTTCAAAGA
* * * *
13385747 TTCACATTGGATAGATTTTAGAGTTTCATATCTAAATTCAAATG
64 TTCACATTGAATAGATTTTAAAGTTTCACACCTAAATTCAAATG
13385791 TTCTCATTTAAAA
1 TTCTCATTTAAAA
13385804 CTTCTTAAAG
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
107 25 0.24
108 4 0.04
109 75 0.72
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (107 bp):
TTCTCATTTAAAAAATTTAGGAGTCCATATAAAATTTCAAAGCTTATCATTCAAGTTCAAAGATT
CACATTGAATAGATTTTAAAGTTTCACACCTAAATTCAAATG
Found at i:13385818 original size:24 final size:24
Alignment explanation
Indices: 13385791--13385897 Score: 117
Period size: 24 Copynumber: 4.3 Consensus size: 24
13385781 AATTCAAATG
13385791 TTCTCATTTAAAACT-TCTTAAAGA
1 TTCTCATTTAAAACTCT-TTAAAGA
* *
13385815 TTCTCATTCAAAACTCTTTAAATA
1 TTCTCATTTAAAACTCTTTAAAGA
***
13385839 TTCTCATTTAAAACTAAAAAATAAAGA
1 TTCTCATTTAAAACT---CTTTAAAGA
13385866 TTCTCATTTAAAACTCTTTAAAGA
1 TTCTCATTTAAAACTCTTTAAAGA
*
13385890 TTATCATT
1 TTCTCATT
13385898 ATTTTTAACT
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
24 47 0.69
25 1 0.01
27 20 0.29
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (24 bp):
TTCTCATTTAAAACTCTTTAAAGA
Found at i:13387034 original size:9 final size:9
Alignment explanation
Indices: 13387022--13387131 Score: 130
Period size: 9 Copynumber: 13.1 Consensus size: 9
13387012 TCTCATTTCA
13387022 CATTTTTTT
1 CATTTTTTT
13387031 CA--TTTTT
1 CATTTTTTT
13387038 CATTTTTTT
1 CATTTTTTT
13387047 -ATTTTTTT
1 CATTTTTTT
13387055 -ATTTTTTT
1 CATTTTTTT
13387063 -ATTTTTTT
1 CATTTTTTT
13387071 -ATTTTTTT
1 CATTTTTTT
*
13387079 CACTTTTTT
1 CATTTTTTT
13387088 CATTTTTGTT
1 CATTTTT-TT
13387098 CA-TTTTTT
1 CATTTTTTT
*
13387106 CACTTTTTT
1 CATTTTTTT
13387115 CA--TTTTT
1 CATTTTTTT
13387122 CATTTTTTT
1 CATTTTTTT
13387131 C
1 C
13387132 TTCATTCATT
Statistics
Matches: 92, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
7 14 0.15
8 36 0.39
9 38 0.41
10 4 0.04
ACGTcount: A:0.12, C:0.11, G:0.01, T:0.76
Consensus pattern (9 bp):
CATTTTTTT
Found at i:13387044 original size:8 final size:8
Alignment explanation
Indices: 13387025--13387129 Score: 115
Period size: 8 Copynumber: 12.8 Consensus size: 8
13387015 CATTTCACAT
13387025 TTTTTTCA
1 TTTTTTCA
13387033 -TTTTTCA
1 TTTTTTCA
*
13387040 TTTTTTTA
1 TTTTTTCA
*
13387048 TTTTTTTA
1 TTTTTTCA
*
13387056 TTTTTTTA
1 TTTTTTCA
*
13387064 TTTTTTTA
1 TTTTTTCA
13387072 TTTTTTTCA
1 -TTTTTTCA
13387081 CTTTTTTCA
1 -TTTTTTCA
13387090 TTTTTGTTCA
1 -TTTT-TTCA
13387100 TTTTTTCA
1 TTTTTTCA
13387108 CTTTTTTCA
1 -TTTTTTCA
13387117 -TTTTTCA
1 TTTTTTCA
13387124 TTTTTT
1 TTTTTT
13387130 TCTTCATTCA
Statistics
Matches: 88, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
7 14 0.16
8 39 0.44
9 31 0.35
10 4 0.05
ACGTcount: A:0.11, C:0.10, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:13387052 original size:16 final size:17
Alignment explanation
Indices: 13387022--13387131 Score: 147
Period size: 16 Copynumber: 6.6 Consensus size: 17
13387012 TCTCATTTCA
13387022 CATTTTTTTCA-TTTTT
1 CATTTTTTTCATTTTTT
13387038 CATTTTTTT-ATTTTTT
1 CATTTTTTTCATTTTTT
*
13387054 TATTTTTTT-ATTTTTT
1 CATTTTTTTCATTTTTT
*
13387070 TATTTTTTTCACTTTTTT
1 CATTTTTTTCA-TTTTTT
13387088 CATTTTTGTTCATTTTTT
1 CATTTTT-TTCATTTTTT
*
13387106 CACTTTTTTCA-TTTTT
1 CATTTTTTTCATTTTTT
13387122 CATTTTTTTC
1 CATTTTTTTC
13387132 TTCATTCATT
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.01
16 52 0.60
17 5 0.06
18 24 0.28
19 4 0.05
ACGTcount: A:0.12, C:0.11, G:0.01, T:0.76
Consensus pattern (17 bp):
CATTTTTTTCATTTTTT
Found at i:13392531 original size:30 final size:28
Alignment explanation
Indices: 13392496--13392566 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 28
13392486 TGATTATAAC
*
13392496 TTAATTATAATATAATAATTGATTAGTTAA
1 TTAATTATAATATAATAATTG-GTAG-TAA
* *
13392526 TTAATTAGTAAATGTAATATTTGGTAGTAA
1 TTAATTA-T-AATATAATAATTGGTAGTAA
13392556 TTAAATTATAA
1 TT-AATTATAA
13392567 CTCCAATACC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
29 2 0.06
30 13 0.37
31 9 0.26
32 11 0.31
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (28 bp):
TTAATTATAATATAATAATTGGTAGTAA
Found at i:13392811 original size:21 final size:19
Alignment explanation
Indices: 13392772--13392817 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
13392762 AATAAAATAT
13392772 AATTATTTAATTTTATTAA
1 AATTATTTAATTTTATTAA
* *
13392791 ATTTATTTATGATTTTTTTAA
1 AATTATTTA--ATTTTATTAA
13392812 AATTAT
1 AATTAT
13392818 AAATCATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 8 0.36
21 14 0.64
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
AATTATTTAATTTTATTAA
Found at i:13393347 original size:13 final size:14
Alignment explanation
Indices: 13393329--13393357 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13393319 AATACATTCG
13393329 AAATAATT-TTAAT
1 AAATAATTATTAAT
13393342 AAATAATTATTAAT
1 AAATAATTATTAAT
13393356 AA
1 AA
13393358 GATTCAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATAATTATTAAT
Found at i:13403103 original size:24 final size:25
Alignment explanation
Indices: 13403076--13403128 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
13403066 ATCATAATTT
*
13403076 AAATTTAAATTTA-AATCAA-AGTTA
1 AAATTTAAAATTACAATCAACA-TTA
13403100 AAA-TTAAAATTACAATCAACATTA
1 AAATTTAAAATTACAATCAACATTA
13403124 AAATT
1 AAATT
13403129 GTGACCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 8 0.32
24 15 0.60
25 2 0.08
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (25 bp):
AAATTTAAAATTACAATCAACATTA
Found at i:13403106 original size:6 final size:6
Alignment explanation
Indices: 13403027--13403128 Score: 53
Period size: 6 Copynumber: 17.0 Consensus size: 6
13403017 ACTATTGACC
* * * * * * *
13403027 AAAATT AAAA-A AAAATC ATAATT ATAATT AAAATCC AAAATC ATAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT-T AAAATT AAAATT
* * * * * * * *
13403075 TAAATT TAAATT TAAATC AAAGTT AAAATT AAAATT ACAATC AACATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
13403123 AAAATT
1 AAAATT
13403129 GTGACCTTTT
Statistics
Matches: 73, Mismatches: 21, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
5 4 0.05
6 64 0.88
7 5 0.07
ACGTcount: A:0.59, C:0.08, G:0.01, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:13408309 original size:2 final size:2
Alignment explanation
Indices: 13408302--13408350 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
13408292 TCTTACGGCG
* * * * *
13408302 TA TA TA TA TG TA TA TA TA TA TT TA TG TT TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13408344 TA TA TA T
1 TA TA TA T
13408351 TCTCAGACTC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (2 bp):
TA
Found at i:13408327 original size:16 final size:16
Alignment explanation
Indices: 13408302--13408350 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
13408292 TCTTACGGCG
13408302 TATATATATGTATATA
1 TATATATATGTATATA
* *
13408318 TATATTTATGTTTATA
1 TATATATATGTATATA
13408334 TATATATATGTATATA
1 TATATATATGTATATA
13408350 T
1 T
13408351 TCTCAGACTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TATATATATGTATATA
Found at i:13410755 original size:11 final size:11
Alignment explanation
Indices: 13410739--13410763 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13410729 ACATTATTAT
13410739 ATTTATATATA
1 ATTTATATATA
13410750 ATTTATATATA
1 ATTTATATATA
13410761 ATT
1 ATT
13410764 GTCAAGTTAG
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTATATATA
Found at i:13416335 original size:4 final size:4
Alignment explanation
Indices: 13416326--13416373 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
13416316 ATCATAATTG
* * *
13416326 TTTA TTTA TTTA TTTA TTTG TTTG TTTA TTTG TTTA TTTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTT
13416374 GAATATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 35 0.90
5 4 0.10
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:13416929 original size:13 final size:14
Alignment explanation
Indices: 13416911--13416941 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
13416901 CAAATAGTAA
13416911 AAAATTT-AAAAAT
1 AAAATTTAAAAAAT
13416924 AAAATTTAAAAAAT
1 AAAATTTAAAAAAT
13416938 AAAA
1 AAAA
13416942 AATAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATTTAAAAAAT
Found at i:13417247 original size:32 final size:33
Alignment explanation
Indices: 13417196--13417269 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 33
13417186 TATAATATTA
13417196 AATTTAAAACCATTAGAATCAAGATCTTAGGAT
1 AATTTAAAACCATTAGAATCAAGATCTTAGGAT
13417229 AATTTAAAA-CATTAGAATCAAGATCTTAGGAT
1 AATTTAAAACCATTAGAATCAAGATCTTAGGAT
13417261 AATTTAAAA
1 AATTTAAAA
13417270 TAAAATAGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 32 0.78
33 9 0.22
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (33 bp):
AATTTAAAACCATTAGAATCAAGATCTTAGGAT
Found at i:13422561 original size:39 final size:42
Alignment explanation
Indices: 13422517--13422594 Score: 117
Period size: 39 Copynumber: 1.9 Consensus size: 42
13422507 TGTACGCATT
*
13422517 TAATTTTGTTTGAAATAATTT-ATATTT-A-TTTAATTTTTA
1 TAATTTTGTTTAAAATAATTTGATATTTAAGTTTAATTTTTA
*
13422556 TAATTTTGTTTAAAATAATTTGATTTTTAAGTTTAATTT
1 TAATTTTGTTTAAAATAATTTGATATTTAAGTTTAATTT
13422595 AAACATTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 20 0.59
40 5 0.15
41 1 0.03
42 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (42 bp):
TAATTTTGTTTAAAATAATTTGATATTTAAGTTTAATTTTTA
Found at i:13424523 original size:18 final size:18
Alignment explanation
Indices: 13424500--13424536 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
13424490 TGGTTTACTC
13424500 ATTGTATATTTATTTATT
1 ATTGTATATTTATTTATT
13424518 ATTGTATATTTATTTATT
1 ATTGTATATTTATTTATT
13424536 A
1 A
13424537 CAGTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
ATTGTATATTTATTTATT
Found at i:13430398 original size:16 final size:16
Alignment explanation
Indices: 13430379--13430416 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
13430369 AGAAAAAGTG
13430379 AAAAATGAAAAAAACAA
1 AAAAAT-AAAAAAACAA
*
13430396 AAAAATAGAAAAACAA
1 AAAAATAAAAAAACAA
13430412 AAAAA
1 AAAAA
13430417 GAGTGAAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.05
Consensus pattern (16 bp):
AAAAATAAAAAAACAA
Found at i:13433370 original size:45 final size:45
Alignment explanation
Indices: 13433265--13433379 Score: 126
Period size: 45 Copynumber: 2.5 Consensus size: 45
13433255 TATGTTTCCA
13433265 AAAGTTATAGAGCCTCTGATGAGAGGAGATTTTTAGATTAATTCTC
1 AAAGTTATA-AGCCTCTGATGAGAGGAGATTTTTAGATTAATTCTC
* * * * *
13433311 AAAGATGT-TAAGCCTCTAATGAGAGGAG-TTTTTATATTTATTGTT
1 AAAG-T-TATAAGCCTCTGATGAGAGGAGATTTTTAGATTAATTCTC
*
13433356 AAAGTTATGAAGCCTTTGATGAGA
1 AAAGTTAT-AAGCCTCTGATGAGA
13433380 AAAGTTTTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
43 1 0.02
44 2 0.03
45 30 0.52
46 21 0.36
47 3 0.05
48 1 0.02
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.37
Consensus pattern (45 bp):
AAAGTTATAAGCCTCTGATGAGAGGAGATTTTTAGATTAATTCTC
Found at i:13435456 original size:20 final size:21
Alignment explanation
Indices: 13435415--13435481 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 21
13435405 TAACCATTAA
* *
13435415 TTAGGCTTGACT-GAGAAGCT
1 TTAGGCCTGACTGGAGAAACT
13435435 TTAGGCCTGACTGGA-AAACT
1 TTAGGCCTGACTGGAGAAACT
* * *
13435455 TTAGACCTAACTGG-GAAGCT
1 TTAGGCCTGACTGGAGAAACT
*
13435475 TTGGGCC
1 TTAGGCC
13435482 CAATAGGATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 36 0.95
21 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.27
Consensus pattern (21 bp):
TTAGGCCTGACTGGAGAAACT
Found at i:13435526 original size:19 final size:19
Alignment explanation
Indices: 13435502--13435544 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
13435492 GAGCCTAAAA
*
13435502 TTTTTAATTTGATCTTGAT
1 TTTTTAATTTAATCTTGAT
* *
13435521 TTTTTATTTTAATTTTGAT
1 TTTTTAATTTAATCTTGAT
13435540 TTTTT
1 TTTTT
13435545 TTTAGATTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTTTAATTTAATCTTGAT
Found at i:13438610 original size:21 final size:21
Alignment explanation
Indices: 13438586--13438625 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13438576 TACAAGGCCA
*
13438586 AAGACATGGTAGA-AAAGGTTG
1 AAGA-ATGGAAGAGAAAGGTTG
13438607 AAGAATGGAAGAGAAAGGT
1 AAGAATGGAAGAGAAAGGT
13438626 GCCACCAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.47, C:0.03, G:0.35, T:0.15
Consensus pattern (21 bp):
AAGAATGGAAGAGAAAGGTTG
Found at i:13447906 original size:33 final size:32
Alignment explanation
Indices: 13447836--13447940 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 32
13447826 AGATGTAAGT
*
13447836 CCTCTAATTAGAAGAATTCTTCAAATACCATCA
1 CCTCTAATTAGAGGAA-TCTTCAAATACCATCA
* * **
13447869 CCTCTATTTAGAGGAATCATTCAAATACTATTG
1 CCTCTAATTAGAGGAATC-TTCAAATACCATCA
* * *
13447902 CCTCTAGTTAAAGGAATCTTCCAAGA-ATCATCA
1 CCTCTAATTAGAGGAATCTT-CAA-ATACCATCA
13447935 CCTCTA
1 CCTCTA
13447941 GTTAAATGTG
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
32 4 0.07
33 53 0.91
34 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (32 bp):
CCTCTAATTAGAGGAATCTTCAAATACCATCA
Found at i:13448076 original size:34 final size:34
Alignment explanation
Indices: 13448032--13448252 Score: 196
Period size: 34 Copynumber: 6.5 Consensus size: 34
13448022 TTGTTTTTTG
* * *
13448032 TTTTTAAAGTGTCATGGCCTCTAGTTAAAGGAGT
1 TTTTTAAAGTGTCATAGCCTCTGGTTAGAGGAGT
* * *
13448066 TTTTTCAAGTGTCATAGACTTTGGTTAGAGGAGT
1 TTTTTAAAGTGTCATAGCCTCTGGTTAGAGGAGT
*
13448100 TTTTTAAAGT-TACATAGCCTCTGGTTAGAGGAAT
1 TTTTTAAAGTGT-CATAGCCTCTGGTTAGAGGAGT
* * * *
13448134 TATTTAAAGTTTCATAGCCTTTGGTTAGAGAAGT
1 TTTTTAAAGTGTCATAGCCTCTGGTTAGAGGAGT
* * * * *
13448168 TTGCTTTAAAATGTCATAACTTTTGGTTAAAGGAGT
1 TT--TTTAAAGTGTCATAGCCTCTGGTTAGAGGAGT
* * * *
13448204 TTTTTTAAGTGCCA-AGTCT-TAGTTAGAGGAGT
1 TTTTTAAAGTGTCATAGCCTCTGGTTAGAGGAGT
* *
13448236 TTTTCAAAGTTTCATAG
1 TTTTTAAAGTGTCATAG
13448253 TTTTTGGTTA
Statistics
Matches: 149, Mismatches: 33, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
32 21 0.14
33 5 0.03
34 94 0.63
35 1 0.01
36 28 0.19
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.41
Consensus pattern (34 bp):
TTTTTAAAGTGTCATAGCCTCTGGTTAGAGGAGT
Found at i:13448105 original size:68 final size:68
Alignment explanation
Indices: 13448032--13448252 Score: 223
Period size: 68 Copynumber: 3.2 Consensus size: 68
13448022 TTGTTTTTTG
* * *
13448032 TTTTTAAAGTGTCATGGCCTCTAGTTAAAGGAGTTTTTTCAAGTGTCATAGACTTTGGTTAGAGG
1 TTTTTAAAGTGTCATAGCCTCTGGTTAAAGGAGTTTTTTAAAGTGTCATAGACTTTGGTTAGAGG
13448097 AGT
66 AGT
* * * * *
13448100 TTTTTAAAGT-TACATAGCCTCTGGTTAGAGGAATTATTTAAAGTTTCATAGCCTTTGGTTAGAG
1 TTTTTAAAGTGT-CATAGCCTCTGGTTAAAGGAGTTTTTTAAAGTGTCATAGACTTTGGTTAGAG
*
13448164 AAGT
65 GAGT
* * * * * * * *
13448168 TTGCTTTAAAATGTCATAACTTTTGGTTAAAGGAGTTTTTTTAAGTGCCA-AGTC-TTAGTTAGA
1 TT--TTTAAAGTGTCATAGCCTCTGGTTAAAGGAGTTTTTTAAAGTGTCATAGACTTTGGTTAGA
13448231 GGAGT
64 GGAGT
* *
13448236 TTTTCAAAGTTTCATAG
1 TTTTTAAAGTGTCATAG
13448253 TTTTTGGTTA
Statistics
Matches: 123, Mismatches: 26, Indels: 10
0.77 0.16 0.06
Matches are distributed among these distances:
66 11 0.09
67 1 0.01
68 73 0.59
69 3 0.02
70 34 0.28
71 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.41
Consensus pattern (68 bp):
TTTTTAAAGTGTCATAGCCTCTGGTTAAAGGAGTTTTTTAAAGTGTCATAGACTTTGGTTAGAGG
AGT
Found at i:13448252 original size:102 final size:104
Alignment explanation
Indices: 13448075--13448264 Score: 253
Period size: 102 Copynumber: 1.8 Consensus size: 104
13448065 TTTTTTCAAG
* * *
13448075 TGTCATAGACTTTGGTTAGAGGAGTTTTTTAAAGTTACATAGCCTCTGGTTAGAGGAATTATTTA
1 TGTCATAGACTTTGGTTAAAGGAGTTTTTTAAAGTGACATAGCCTCTAGTTAGAGGAATTATTTA
13448140 AAGTTTCATAGCCTTTGGTTAGAGAAGTTTGCTTTAAAA
66 AAGTTTCATAGCCTTTGGTTAGAGAAGTTTGCTTTAAAA
* * * *
13448179 TGTCATA-ACTTTTGGTTAAAGGAGTTTTTTTAAGTGCCA-AGTCT-TAGTTAGAGGAGTT-TTT
1 TGTCATAGAC-TTTGGTTAAAGGAGTTTTTTAAAGTGACATAGCCTCTAGTTAGAGGAATTATTT
**
13448240 CAAAGTTTCATAGTTTTTGGTTAGA
65 -AAAGTTTCATAGCCTTTGGTTAGA
13448265 AGAGCCTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
101 3 0.04
102 34 0.45
103 6 0.08
104 32 0.43
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (104 bp):
TGTCATAGACTTTGGTTAAAGGAGTTTTTTAAAGTGACATAGCCTCTAGTTAGAGGAATTATTTA
AAGTTTCATAGCCTTTGGTTAGAGAAGTTTGCTTTAAAA
Found at i:13448451 original size:36 final size:36
Alignment explanation
Indices: 13448399--13448506 Score: 114
Period size: 36 Copynumber: 3.0 Consensus size: 36
13448389 GTTAAAAGAG
*
13448399 TTATTT-AAGTTTTATAGCCTTTGGTTAGGGAAGTT
1 TTATTTAAAGTGTTATAGCCTTTGGTTAGGGAAGTT
13448434 TGT-TTTAAAGTGTTATAGCCTTTGGTTAGAGG-AGTT
1 T-TATTTAAAGTGTTATAGCCTTTGGTTAG-GGAAGTT
* ** * * *
13448470 TTATTTCAAGTGCCATAGCCTCTGATTAGAGAAGTT
1 TTATTTAAAGTGTTATAGCCTTTGGTTAGGGAAGTT
13448506 T
1 T
13448507 CTCAAAGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
35 6 0.10
36 53 0.87
37 2 0.03
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.44
Consensus pattern (36 bp):
TTATTTAAAGTGTTATAGCCTTTGGTTAGGGAAGTT
Found at i:13449293 original size:13 final size:14
Alignment explanation
Indices: 13449265--13449297 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13449255 TAAACTTTTA
*
13449265 AATTTTTATCTATT
1 AATTTTTACCTATT
13449279 AATTTTTACCT-TT
1 AATTTTTACCTATT
13449292 AATTTT
1 AATTTT
13449298 CTTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTTTTACCTATT
Found at i:13449308 original size:3 final size:3
Alignment explanation
Indices: 13449300--13449331 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
13449290 TTAATTTTCT
13449300 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13449332 TTACTGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13450252 original size:3 final size:3
Alignment explanation
Indices: 13450232--13450281 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
13450222 ATTTTTATGA
* * * *
13450232 TAT TAT TGT TAC TGT TAT TAT TAT TAT TAT T-T TA- TGT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13450278 TAT T
1 TAT T
13450282 CATCCTTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.08
3 34 0.92
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:13450272 original size:22 final size:24
Alignment explanation
Indices: 13450232--13450281 Score: 86
Period size: 22 Copynumber: 2.2 Consensus size: 24
13450222 ATTTTTATGA
13450232 TATTATTGTTACTGTTATTATTAT
1 TATTATTGTTACTGTTATTATTAT
13450256 TATTATT-TTA-TGTTATTATTAT
1 TATTATTGTTACTGTTATTATTAT
13450278 TATT
1 TATT
13450282 CATCCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 16 0.62
23 3 0.12
24 7 0.27
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (24 bp):
TATTATTGTTACTGTTATTATTAT
Found at i:13450856 original size:57 final size:55
Alignment explanation
Indices: 13450786--13450948 Score: 161
Period size: 54 Copynumber: 2.9 Consensus size: 55
13450776 TTATTATCAA
*
13450786 AAGAAATGATTTTTTTAGGATTTCATCAAATAGTCAGAATAATTCTAAAATCAATTC
1 AAGAAATGATTTTTTT-GGATTTCATCAAATAGT-AGGATAATTCTAAAATCAATTC
* * * * *
13450843 AAGAAATGA--TTTTTGGATTTCGTTAAATAGTTGTGATGATTCTAAAAATCAATTT
1 AAGAAATGATTTTTTTGGATTTCATCAAATAGTAG-GATAATTCT-AAAATCAATTC
* * *
13450898 AAGAAAAT-TTTTTTTTGGATTTTCACCAAATAGTTAGGATAATCCTAAAAT
1 AAG-AAATGATTTTTTTGGA-TTTCATCAAATAG-TAGGATAATTCTAAAAT
13450949 TAGCTCTATT
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
53 1 0.01
54 22 0.26
55 18 0.21
56 4 0.05
57 22 0.26
58 17 0.20
59 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (55 bp):
AAGAAATGATTTTTTTGGATTTCATCAAATAGTAGGATAATTCTAAAATCAATTC
Found at i:13452064 original size:448 final size:446
Alignment explanation
Indices: 13451231--13452064 Score: 1420
Period size: 448 Copynumber: 1.9 Consensus size: 446
13451221 GCTATACCTT
* *
13451231 ATCCACTCCTGATTTAGTAGATCAAAACATTTTTTTGTAAATCTTAATTAATTTTGAGATTTTAT
1 ATCCACTCCTGATTTAGTAGATCAAAACATTTTTTAGTAAATCTCAATTAATTTTGAGATTTTAT
* * *
13451296 TAAAAAATGATCTTTTAGATGACCAATCACATCCCTATAAAAAAATTTGTTGGTAACTCCATAAG
66 TAAAAAATGATCTTTTAGATGACCAATCACATCCCTACAAAAAAAATTATTGGTAACTCCATAAG
* ** *
13451361 TTTTTTTCAAGTCTAGCAATTAAGTCCCCTATGTAGACCATAATTTTGTTTGGGATATTTTATCA
131 TTTTTTTCAAGTCTAGCAATTAAGTCCCCTATATAGACCATAATTTTGTTCAGAATATTTTATCA
* ** * *
13451426 ATTAATCCAGGCATGGTTTTGTAATTAGACCCTAACCAAAATTTTTTTCGCTTGTTACATAATTT
196 ATTAATCCAGACACAGTTTTGTAATTAGACCCTAACCAAAATTTTTTTCGCCTGTTACATAATAT
*
13451491 ATTTTTAAATGTTCAAGGATAAGGTCAAATATGGGCCCTATAGTGAAGCTCATGCCACTAGCCCG
261 ATTTTTAAATGTTCAAGGATAAGGTCAAATATGAGCCCTATAGTGAAGCTCATGCCACTAGCCCG
*
13451556 AATAATATCTAACATAGCCCAATAAAAAGCTCGATAAAAGAATTATCCTTAAAGCCCATCATTCT
326 AATAATATCTAACATAGCCCAATAAAAAGCCCGATAAAAGAATTATCCTTAAAGCCCATCATTCT
13451621 TCAAACAGACGATGTGAGGGTGCTAATACCTTATCCACTCATAATTATACTCCTAA
391 TCAAACAGACGATGTGAGGGTGCTAATACCTTATCCACTCATAATTATACTCCTAA
13451677 ATCCACTCCTGATTTAGTAGATCAAAACATTTTTTAGTAAATCTCAATTAATTTTGAGATTTTAT
1 ATCCACTCCTGATTTAGTAGATCAAAACATTTTTTAGTAAATCTCAATTAATTTTGAGATTTTAT
* *
13451742 TAAAAAATGATCTTTTAGATGATCAATCACA-CTCCTACAAAAAAAATTATTGGTGACTCCATAA
66 TAAAAAATGATCTTTTAGATGACCAATCACATC-CCTACAAAAAAAATTATTGGTAACTCCATAA
13451806 GTTTTTTTCAAGTCTAGCAATTAAGTCCCCTATATAGA-CATCTAATTTTGTTCAGAATATTTTA
130 GTTTTTTTCAAGTCTAGCAATTAAGTCCCCTATATAGACCA--TAATTTTGTTCAGAATATTTTA
* * * *
13451870 TCAATTTAATCCAGACACAGTTTTGTAGTTAGACCCTAACTATAATTTTTTTTGCCTGTTACATA
193 TCAA-TTAATCCAGACACAGTTTTGTAATTAGACCCTAACCAAAATTTTTTTCGCCTGTTACATA
13451935 ATATATTTTTAAATGTTCAAGGATAAGGTCAAATATGAGCCCTATAGTGAAGCTCATGCCACTAG
257 ATATATTTTTAAATGTTCAAGGATAAGGTCAAATATGAGCCCTATAGTGAAGCTCATGCCACTAG
13452000 CCCGAATAATATCTAACATAGCCCAATAAAAAGCCCGATAAAAGAATTATCCTTAAAGCCCATCA
322 CCCGAATAATATCTAACATAGCCCAATAAAAAGCCCGATAAAAGAATTATCCTTAAAGCCCATCA
13452065 ATAGTCCGTT
Statistics
Matches: 362, Mismatches: 22, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
445 3 0.01
446 157 0.43
447 23 0.06
448 179 0.49
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (446 bp):
ATCCACTCCTGATTTAGTAGATCAAAACATTTTTTAGTAAATCTCAATTAATTTTGAGATTTTAT
TAAAAAATGATCTTTTAGATGACCAATCACATCCCTACAAAAAAAATTATTGGTAACTCCATAAG
TTTTTTTCAAGTCTAGCAATTAAGTCCCCTATATAGACCATAATTTTGTTCAGAATATTTTATCA
ATTAATCCAGACACAGTTTTGTAATTAGACCCTAACCAAAATTTTTTTCGCCTGTTACATAATAT
ATTTTTAAATGTTCAAGGATAAGGTCAAATATGAGCCCTATAGTGAAGCTCATGCCACTAGCCCG
AATAATATCTAACATAGCCCAATAAAAAGCCCGATAAAAGAATTATCCTTAAAGCCCATCATTCT
TCAAACAGACGATGTGAGGGTGCTAATACCTTATCCACTCATAATTATACTCCTAA
Found at i:13452334 original size:20 final size:20
Alignment explanation
Indices: 13452285--13452333 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
13452275 CTTCACGTGG
*
13452285 AAAAACAAAAGCAACAAACC
1 AAAAACAAAAGAAACAAACC
13452305 AAAAACAAAAGAAACAAACC
1 AAAAACAAAAGAAACAAACC
13452325 AAAAA-AAAA
1 AAAAACAAAA
13452334 AAAAAGGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.78, C:0.18, G:0.04, T:0.00
Consensus pattern (20 bp):
AAAAACAAAAGAAACAAACC
Found at i:13454518 original size:2 final size:2
Alignment explanation
Indices: 13454511--13454535 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13454501 TTATTATTAT
13454511 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
13454536 TATGGCTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13454826 original size:18 final size:19
Alignment explanation
Indices: 13454805--13454842 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
13454795 TTCAAATTAA
13454805 ATTAAATTATATAT-TTTT
1 ATTAAATTATATATATTTT
* *
13454823 ATTAATTTTTATATATTTT
1 ATTAAATTATATATATTTT
13454842 A
1 A
13454843 AAATTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTAAATTATATATATTTT
Found at i:13455283 original size:12 final size:11
Alignment explanation
Indices: 13455259--13455297 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
13455249 AATTTTTACA
*
13455259 TTTATAATTTT
1 TTTAAAATTTT
13455270 TTTAAAATTTT
1 TTTAAAATTTT
13455281 TTTAAAATTTT
1 TTTAAAATTTT
13455292 TTTAAA
1 TTTAAA
13455298 TTCATGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTAAAATTTT
Found at i:13457425 original size:23 final size:21
Alignment explanation
Indices: 13457387--13457432 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
13457377 GTACAAATTC
13457387 ATATTATATAATTTAAATAAAA
1 ATATTATATAATTTAAA-AAAA
*
13457409 ATATT-TATAATTATTAAAAAA
1 ATATTATATAATT-TAAAAAAA
13457430 ATA
1 ATA
13457433 GAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATTATATAATTTAAAAAAA
Found at i:13458134 original size:17 final size:17
Alignment explanation
Indices: 13458106--13458151 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
13458096 TACTAAAGTA
* *
13458106 TCATAGCTTCAAACGAT
1 TCATAACTTCAAACAAT
*
13458123 TTATAACTTCAAACAAT
1 TCATAACTTCAAACAAT
13458140 TCATAACTTCAA
1 TCATAACTTCAA
13458152 GCATAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (17 bp):
TCATAACTTCAAACAAT
Found at i:13464463 original size:23 final size:25
Alignment explanation
Indices: 13464410--13464463 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
13464400 AGAATCTTAT
* * *
13464410 AAAAATATATCACCAACAAATTTTA
1 AAAAATATATAACCAACAAATCTAA
*
13464435 ACAAATATATAACC-A-AAATCTAA
1 AAAAATATATAACCAACAAATCTAA
13464458 AAAAAT
1 AAAAAT
13464464 TTCAACAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 11 0.46
24 1 0.04
25 12 0.50
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAATATATAACCAACAAATCTAA
Found at i:13464563 original size:22 final size:24
Alignment explanation
Indices: 13464533--13464593 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 24
13464523 TTCAACAAAT
* *
13464533 AATTAACTAACAAAAACTC-AACA
1 AATTTACTAACAAAAACCCAAACA
* *
13464556 CA-TTACTAACCAAAACCCAAACA
1 AATTTACTAACAAAAACCCAAACA
13464579 AATTTA-TAACAAAAA
1 AATTTACTAACAAAAA
13464594 ATTAAACCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 13 0.43
23 14 0.47
24 3 0.10
ACGTcount: A:0.59, C:0.23, G:0.00, T:0.18
Consensus pattern (24 bp):
AATTTACTAACAAAAACCCAAACA
Found at i:13464582 original size:59 final size:59
Alignment explanation
Indices: 13464434--13464598 Score: 172
Period size: 59 Copynumber: 2.8 Consensus size: 59
13464424 AACAAATTTT
* * *
13464434 AACAAATATA-TAACCAAAATCTAAAAAAATTTCAACAAAT-ATAAAACCAACAAAAACTC
1 AACAAAT-TACTAACCAAAACCCAAAAAAATTTCAACAAATAAT-TAACCAACAAAAACTC
* * ** * *
13464493 AACAAATTAGTAACTAAAACTGAAATAAATTTCAACAAATAATTAACTAACAAAAACTC
1 AACAAATTACTAACCAAAACCCAAAAAAATTTCAACAAATAATTAACCAACAAAAACTC
* * * *
13464552 AACACATTACTAACCAAAACCCAAACAAATTTATAACAAAAAATTAA
1 AACAAATTACTAACCAAAACCCAAAAAAATTT-CAACAAATAATTAA
13464599 ACCCTAAACT
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 2 0.02
59 72 0.82
60 14 0.16
ACGTcount: A:0.60, C:0.18, G:0.01, T:0.21
Consensus pattern (59 bp):
AACAAATTACTAACCAAAACCCAAAAAAATTTCAACAAATAATTAACCAACAAAAACTC
Found at i:13465941 original size:2 final size:2
Alignment explanation
Indices: 13465936--13465965 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13465926 TATATCCATC
*
13465936 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13465966 GTTAAATACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13466767 original size:10 final size:10
Alignment explanation
Indices: 13466731--13466769 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
13466721 ATTTGAGTAC
13466731 ATAAATATAT
1 ATAAATATAT
13466741 ATATATATATAT
1 ATA-A-ATATAT
*
13466753 GTAAATATAT
1 ATAAATATAT
13466763 ATAAATA
1 ATAAATA
13466770 AATAGATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 15 0.60
11 2 0.08
12 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (10 bp):
ATAAATATAT
Found at i:13467183 original size:29 final size:30
Alignment explanation
Indices: 13467132--13467188 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
13467122 AAATCAATCA
*
13467132 TCAAATCAATTATTAATACAAAT-TTATAT
1 TCAAATCAATTAATAATACAAATATTATAT
*
13467161 TCAAATTAATTAATACATA-AAATATTAT
1 TCAAATCAATTAATA-ATACAAATATTAT
13467189 TTCTTTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (30 bp):
TCAAATCAATTAATAATACAAATATTATAT
Found at i:13468486 original size:2 final size:2
Alignment explanation
Indices: 13468479--13468514 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
13468469 TAAAAATCTA
*
13468479 AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13468515 ACAACATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13468639 original size:28 final size:28
Alignment explanation
Indices: 13468603--13468660 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
13468593 AAAAAATAAG
13468603 ATAGTTTCTTTTAATTACAAATTAGATA
1 ATAGTTTCTTTTAATTACAAATTAGATA
13468631 ATAGTTTCTTTTAATTACAAATTAGATA
1 ATAGTTTCTTTTAATTACAAATTAGATA
13468659 AT
1 AT
13468661 TTTAAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (28 bp):
ATAGTTTCTTTTAATTACAAATTAGATA
Found at i:13468787 original size:20 final size:20
Alignment explanation
Indices: 13468762--13468811 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
13468752 TGAAATATGG
13468762 ATTTTATTTTTTAAT-AAATA
1 ATTTTATTTTTT-ATCAAATA
*
13468782 ATTTTAGTTGTTTATCAAATA
1 ATTTTA-TTTTTTATCAAATA
*
13468803 ACTTTATTT
1 ATTTTATTT
13468812 AAAAAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (20 bp):
ATTTTATTTTTTATCAAATA
Found at i:13470498 original size:30 final size:29
Alignment explanation
Indices: 13470458--13470515 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
13470448 TTAGCTCATA
*
13470458 TTAAGGGATTATTTAAATACAAAATTAAAG
1 TTAAGAGATTATTTAAATA-AAAATTAAAG
* *
13470488 TTAAGAGATTATTTGAATATAAATTAAA
1 TTAAGAGATTATTTAAATAAAAATTAAA
13470516 AATTAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (29 bp):
TTAAGAGATTATTTAAATAAAAATTAAAG
Found at i:13477519 original size:20 final size:20
Alignment explanation
Indices: 13477494--13477533 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
13477484 TTAATAAATA
*
13477494 AATGTAT-ATATTTATTAATT
1 AATGTATCAT-TTTATGAATT
13477514 AATGTATCATTTTATGAATT
1 AATGTATCATTTTATGAATT
13477534 CCAAACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (20 bp):
AATGTATCATTTTATGAATT
Found at i:13477686 original size:20 final size:20
Alignment explanation
Indices: 13477657--13477695 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13477647 ATATGTAAAA
13477657 TTAAAAATAT-TAATGAAATT
1 TTAAAAATATAT-ATGAAATT
*
13477677 TTAAATATATATATGAAAT
1 TTAAAAATATATATGAAAT
13477696 CCAAATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TTAAAAATATATATGAAATT
Done.