Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 140 of 172
Found at i:40237304 original size:15 final size:15
Alignment explanation
Indices: 40237284--40237342 Score: 75
Period size: 15 Copynumber: 3.7 Consensus size: 15
40237274 ATTTAACCGA
40237284 ATTTTTATTTTTTTT
1 ATTTTTATTTTTTTT
40237299 ATTTTTATTTATTGTTT
1 ATTTTTATTT-TT-TTT
40237316 ATTTTT-TTATTTTTT
1 ATTTTTATT-TTTTTT
40237331 ATTTTATATTTT
1 ATTTT-TATTTT
40237343 GTGTCCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
15 18 0.46
16 9 0.23
17 12 0.31
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (15 bp):
ATTTTTATTTTTTTT
Found at i:40242259 original size:15 final size:17
Alignment explanation
Indices: 40242239--40242272 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40242229 TATATTGCTA
40242239 ATATAA-AA-ATATATT
1 ATATAATAATATATATT
40242254 ATATAATAATATATATT
1 ATATAATAATATATATT
40242271 AT
1 AT
40242273 TTATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 2 0.12
17 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATAATATATATT
Found at i:40242581 original size:3 final size:3
Alignment explanation
Indices: 40242575--40242603 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40242565 TAATAATAAT
40242575 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
40242604 AACTAAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40243614 original size:6 final size:6
Alignment explanation
Indices: 40243577--40243601 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40243567 ATTTTCTATG
40243577 TGAAGT TGAAGT TGAAGT TGAAGT T
1 TGAAGT TGAAGT TGAAGT TGAAGT T
40243602 AAATTTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGAAGT
Found at i:40250130 original size:16 final size:16
Alignment explanation
Indices: 40250109--40250140 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40250099 GACATTTTTA
40250109 TAACAAAAGAAATAGT
1 TAACAAAAGAAATAGT
40250125 TAACAAAAGAAATAGT
1 TAACAAAAGAAATAGT
40250141 CACTCAGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (16 bp):
TAACAAAAGAAATAGT
Found at i:40256061 original size:21 final size:21
Alignment explanation
Indices: 40256034--40256117 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 21
40256024 ACATTTAATT
40256034 AATT-TTTT-AAAATTATTAA
1 AATTATTTTAAAAATTATTAA
*
40256053 AATTATTTTAAAAATTATGAA
1 AATTATTTTAAAAATTATTAA
* *
40256074 AATATATTTTTTAATATT-TTAA
1 AAT-TA-TTTTAAAAATTATTAA
*
40256096 AATT-TTTTAAAAAGTGATTAA
1 AATTATTTTAAAAA-TTATTAA
40256117 A
1 A
40256118 TGCTTACGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
19 11 0.21
20 5 0.10
21 19 0.37
22 8 0.15
23 9 0.17
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
AATTATTTTAAAAATTATTAA
Found at i:40256106 original size:10 final size:10
Alignment explanation
Indices: 40256034--40256107 Score: 51
Period size: 10 Copynumber: 7.2 Consensus size: 10
40256024 ACATTTAATT
40256034 AATTTTTTAA
1 AATTTTTTAA
*
40256044 AA-TTATTAA
1 AATTTTTTAA
40256053 AATTATTTTAA
1 AATT-TTTTAA
* * *
40256064 AAATTATGAA
1 AATTTTTTAA
**
40256074 AATATATTTTTT
1 AAT-T-TTTTAA
*
40256086 AATATTTTAA
1 AATTTTTTAA
40256096 AATTTTTTAA
1 AATTTTTTAA
40256106 AA
1 AA
40256108 AGTGATTAAA
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
9 8 0.17
10 24 0.52
11 9 0.20
12 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:40259275 original size:13 final size:13
Alignment explanation
Indices: 40259257--40259281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40259247 AAATTATCCA
40259257 ACCCAACCCAATT
1 ACCCAACCCAATT
40259270 ACCCAACCCAAT
1 ACCCAACCCAAT
40259282 AAAACTAAAA
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:40259362 original size:38 final size:39
Alignment explanation
Indices: 40259262--40259378 Score: 209
Period size: 39 Copynumber: 3.0 Consensus size: 39
40259252 ATCCAACCCA
40259262 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
40259301 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
* *
40259340 ACTCAATTA-CCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
40259378 A
1 A
40259379 ACTCTTAACT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
38 29 0.38
39 47 0.62
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.19
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:40259534 original size:17 final size:17
Alignment explanation
Indices: 40259514--40259576 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
40259504 TAATTTCAAG
40259514 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
40259531 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
40259549 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
40259568 AATTATGTA
1 AATTATGTA
40259577 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:40259557 original size:37 final size:37
Alignment explanation
Indices: 40259511--40259585 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
40259501 TGTTAATTTC
*
40259511 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
*
40259548 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
40259585 A
1 A
40259586 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:40259598 original size:9 final size:9
Alignment explanation
Indices: 40259584--40259614 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40259574 GTAGTGATTC
*
40259584 AATTCGGGT
1 AATTCGGTT
40259593 AATTCGGTT
1 AATTCGGTT
40259602 AATTCGGTT
1 AATTCGGTT
40259611 AATT
1 AATT
40259615 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:40260630 original size:14 final size:14
Alignment explanation
Indices: 40260611--40260638 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40260601 ATTCCAAAAT
40260611 ACCGATCCACCTCC
1 ACCGATCCACCTCC
40260625 ACCGATCCACCTCC
1 ACCGATCCACCTCC
40260639 GATCCTCCAC
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:0.21, C:0.57, G:0.07, T:0.14
Consensus pattern (14 bp):
ACCGATCCACCTCC
Found at i:40260847 original size:40 final size:41
Alignment explanation
Indices: 40260788--40260879 Score: 123
Period size: 44 Copynumber: 2.2 Consensus size: 41
40260778 GATTCCCTTC
* *
40260788 CATTTTCTGTCT-GTTTGTTTCTGGTTAATCCGGGTAACTT
1 CATTTTCTGTCTGGCTTGTTTCTAGTTAATCCGGGTAACTT
*
40260828 CATTTTCTGTTTGGCTGTTTGTTTCTAGTTAATCCGGGTAACTT
1 CATTTTCTGTCTGGC---TTGTTTCTAGTTAATCCGGGTAACTT
40260872 CATTTTCT
1 CATTTTCT
40260880 TCTTCTTCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
40 11 0.24
41 1 0.02
44 33 0.73
ACGTcount: A:0.13, C:0.17, G:0.18, T:0.51
Consensus pattern (41 bp):
CATTTTCTGTCTGGCTTGTTTCTAGTTAATCCGGGTAACTT
Found at i:40261612 original size:20 final size:21
Alignment explanation
Indices: 40261587--40261636 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
40261577 TTTAAAATAC
40261587 TTTAAAAATATTTTTT-TATT
1 TTTAAAAATATTTTTTGTATT
*
40261607 TTT-AAAATATTTTTTGTGTT
1 TTTAAAAATATTTTTTGTATT
40261627 TATTAAAAAT
1 T-TTAAAAAT
40261637 TGGGCCGGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 12 0.46
20 7 0.27
21 2 0.08
22 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTAAAAATATTTTTTGTATT
Found at i:40263982 original size:22 final size:23
Alignment explanation
Indices: 40263955--40264000 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
40263945 CCTTTTTTTA
*
40263955 TATTTT-TAAATTTAAATTATTT
1 TATTTTATAAATTTAAATGATTT
*
40263977 TATTTTATAATTTTAAATGATTT
1 TATTTTATAAATTTAAATGATTT
40264000 T
1 T
40264001 TAGCTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTTTATAAATTTAAATGATTT
Found at i:40266545 original size:63 final size:63
Alignment explanation
Indices: 40266476--40266602 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
40266466 CCACCAATCC
40266476 TTTTTGATAAGGTGTGATCGGATCACCTTGAAAAGTGGTTGTTTTTAATAAACGATTTGATTT
1 TTTTTGATAAGGTGTGATCGGATCACCTTGAAAAGTGGTTGTTTTTAATAAACGATTTGATTT
40266539 TTTTTGATAAGGTGTGATCGGATCACCTTGAAAAGTGGTTGTTTTTAATAAACGATTTGATTT
1 TTTTTGATAAGGTGTGATCGGATCACCTTGAAAAGTGGTTGTTTTTAATAAACGATTTGATTT
40266602 T
1 T
40266603 ATTAAAACAA
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:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (63 bp):
TTTTTGATAAGGTGTGATCGGATCACCTTGAAAAGTGGTTGTTTTTAATAAACGATTTGATTT
Found at i:40267716 original size:15 final size:16
Alignment explanation
Indices: 40267686--40267720 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
40267676 ATACATATAT
*
40267686 ATAAATAAGTATAATA
1 ATAAAAAAGTATAATA
40267702 ATAAAAAAG-ATAATA
1 ATAAAAAAGTATAATA
40267717 ATAA
1 ATAA
40267721 TAATACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
ATAAAAAAGTATAATA
Found at i:40284291 original size:38 final size:39
Alignment explanation
Indices: 40284214--40284291 Score: 90
Period size: 39 Copynumber: 2.0 Consensus size: 39
40284204 ATGATTAAAC
*
40284214 TATACATATATAAATTATTATATATTATAATAGTGCATG
1 TATACATATATAAATTATTATATATTATAATAATGCATG
* *
40284253 TATA-ATATATATATTGATT-TAATATTATATTAAT-CATG
1 TATACATATATAAATT-ATTAT-ATATTATAATAATGCATG
40284291 T
1 T
40284292 TTATAGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
38 16 0.47
39 18 0.53
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (39 bp):
TATACATATATAAATTATTATATATTATAATAATGCATG
Found at i:40289561 original size:31 final size:31
Alignment explanation
Indices: 40289511--40289592 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
40289501 CTAGCCTAAC
*
40289511 TTTAAAAAAAAAC-TT--AATAGGCCAATGA
1 TTTAAATAAAAACTTTCAAATAGGCCAATGA
*** *
40289539 TTTAAATAAAAACTTTCAAATAGTTTAGTGA
1 TTTAAATAAAAACTTTCAAATAGGCCAATGA
* *
40289570 CTTAAATGAAAACTTTCAAATAG
1 TTTAAATAAAAACTTTCAAATAG
40289593 TTCAATGACC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 12 0.27
29 2 0.05
31 30 0.68
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.32
Consensus pattern (31 bp):
TTTAAATAAAAACTTTCAAATAGGCCAATGA
Found at i:40292623 original size:16 final size:16
Alignment explanation
Indices: 40292602--40292644 Score: 63
Period size: 14 Copynumber: 2.8 Consensus size: 16
40292592 AACTTATAAA
*
40292602 ATATTATTTATTTTAT
1 ATATTATTTATATTAT
40292618 ATATTA--TATATTAT
1 ATATTATTTATATTAT
40292632 ATATTATTTATAT
1 ATATTATTTATAT
40292645 GAAATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.54
16 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATTATTTATATTAT
Found at i:40292636 original size:23 final size:23
Alignment explanation
Indices: 40292602--40292671 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
40292592 AACTTATAAA
*
40292602 ATATTATTTATTTTATATATTAT
1 ATATTATATATTTTATATATTAT
* *
40292625 ATATTATATATTATT-TATATGAA
1 ATATTATATATT-TTATATATTAT
* **
40292648 ATATTTTATATGCTATATA-TAT
1 ATATTATATATTTTATATATTAT
40292670 AT
1 AT
40292672 TTTTTATTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
22 4 0.11
23 31 0.84
24 2 0.05
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (23 bp):
ATATTATATATTTTATATATTAT
Found at i:40292651 original size:16 final size:16
Alignment explanation
Indices: 40292600--40292652 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
40292590 TTAACTTATA
*
40292600 AAATATTATTTATTTT
1 AAATATTATTTATATT
*
40292616 ATATATTA--TATATT
1 AAATATTATTTATATT
* *
40292630 ATATATTATTTATATG
1 AAATATTATTTATATT
40292646 AAATATT
1 AAATATT
40292653 TTATATGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 13 0.42
16 18 0.58
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
AAATATTATTTATATT
Found at i:40292658 original size:7 final size:7
Alignment explanation
Indices: 40292614--40292638 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40292604 ATTATTTATT
40292614 TTATATA
1 TTATATA
40292621 TTATATA
1 TTATATA
40292628 TTATATA
1 TTATATA
40292635 TTAT
1 TTAT
40292639 TTATATGAAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATATA
Found at i:40295698 original size:16 final size:16
Alignment explanation
Indices: 40295677--40295735 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 16
40295667 TTTCCATGTA
40295677 CATGTAACATCTATAC
1 CATGTAACATCTATAC
*
40295693 CATGTAATTCATGTAAATAC
1 CATGTAA--CATCT--ATAC
40295713 CATGTAACATCTATAC
1 CATGTAACATCTATAC
40295729 CATGTAA
1 CATGTAA
40295736 TTCATGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 18 0.49
18 8 0.22
20 11 0.30
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.32
Consensus pattern (16 bp):
CATGTAACATCTATAC
Found at i:40295714 original size:20 final size:20
Alignment explanation
Indices: 40295689--40295753 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
40295679 TGTAACATCT
40295689 ATACCATGTAATTCATGTAA
1 ATACCATGTAATTCATGTAA
*
40295709 ATACCATGTAA--CATCT--
1 ATACCATGTAATTCATGTAA
40295725 ATACCATGTAATTCATGTAA
1 ATACCATGTAATTCATGTAA
40295745 ATA-CATGTA
1 ATACCATGTA
40295754 CTAGTTCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 11 0.28
18 8 0.21
19 6 0.15
20 14 0.36
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (20 bp):
ATACCATGTAATTCATGTAA
Found at i:40295718 original size:36 final size:35
Alignment explanation
Indices: 40295675--40295753 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 35
40295665 AATTTCCATG
40295675 TACATGTAACATCTATACCATGTAATTCATGTAAA
1 TACATGTAACATCTATACCATGTAATTCATGTAAA
40295710 TACCATGTAACATCTATACCATGTAATTCATGTAAA
1 TA-CATGTAACATCTATACCATGTAATTCATGTAAA
40295746 TACATGTA
1 TACATGTA
40295754 CTAGTTCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 8 0.19
36 35 0.81
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (35 bp):
TACATGTAACATCTATACCATGTAATTCATGTAAA
Found at i:40295970 original size:25 final size:25
Alignment explanation
Indices: 40295885--40295972 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 25
40295875 GTACATGTAT
*
40295885 GCTCATACGAGCT-ATTAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* * * * ***
40295909 ACTCCTCCGAGTTGAATAATAATAA
1 GCTCATACGAGCTGAATAACGGTAA
* **
40295934 GCTCCTTTGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
40295959 GCTCATACGAGCTG
1 GCTCATACGAGCTG
40295973 GAATCGGTAA
Statistics
Matches: 45, Mismatches: 18, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
24 9 0.20
25 36 0.80
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:40298005 original size:19 final size:19
Alignment explanation
Indices: 40297983--40298032 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
40297973 TCTCAACAAA
40297983 AATTCTAAAAAATCAAAAT
1 AATTCTAAAAAATCAAAAT
* *
40298002 AATTTCCAAAAATTCAAAAT
1 AA-TTCTAAAAAATCAAAAT
* *
40298022 ATTTATAAAAA
1 AATTCTAAAAA
40298033 TTCCAAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTCTAAAAAATCAAAAT
Found at i:40298033 original size:19 final size:19
Alignment explanation
Indices: 40297988--40298046 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
40297978 ACAAAAATTC
* *
40297988 TAAAAAATCAAAATAATTTC
1 TAAAAATTCAAAAT-ATTTA
*
40298008 CAAAAATTCAAAATATTTA
1 TAAAAATTCAAAATATTTA
* *
40298027 TAAAAATTCCAAATTTTTA
1 TAAAAATTCAAAATATTTA
40298046 T
1 T
40298047 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAATTCAAAATATTTA
Found at i:40303012 original size:19 final size:20
Alignment explanation
Indices: 40302990--40303030 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
40302980 TTTATATCAA
40302990 TTTATAAATTT-TAAATTTT
1 TTTATAAATTTATAAATTTT
*
40303009 TTTATTAATTTAATAAATTTT
1 TTTATAAATTT-ATAAATTTT
40303030 T
1 T
40303031 AATTGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATAAATTTATAAATTTT
Found at i:40303570 original size:15 final size:16
Alignment explanation
Indices: 40303543--40303572 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40303533 TATTTAAGAG
40303543 TTAATATAAATATTTT
1 TTAATATAAATATTTT
40303559 TTAATA-AAATATTT
1 TTAATATAAATATTT
40303573 ACTAACTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATATAAATATTTT
Found at i:40304228 original size:26 final size:27
Alignment explanation
Indices: 40304190--40304253 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
40304180 TAAGTTTACC
*
40304190 TTTTAATAATTTTAATGA-TTTTT-AAT
1 TTTTAATAATTTT-ATAACTTTTTAAAT
**
40304216 TTTTAATTTTTTTATAACTTTTTAAAT
1 TTTTAATAATTTTATAACTTTTTAAAT
40304243 TTTTAA-AATTT
1 TTTTAATAATTT
40304254 AAAATATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 3 0.10
26 19 0.61
27 9 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTAATAATTTTATAACTTTTTAAAT
Found at i:40317341 original size:26 final size:26
Alignment explanation
Indices: 40317312--40317361 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
40317302 AAACTCTAAC
40317312 GCTTCCAATGGAACTGAACTATTATA
1 GCTTCCAATGGAACTGAACTATTATA
*
40317338 GCTTCCAGTGGAACTGAACTATTA
1 GCTTCCAATGGAACTGAACTATTA
40317362 CGATAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (26 bp):
GCTTCCAATGGAACTGAACTATTATA
Found at i:40329168 original size:4 final size:4
Alignment explanation
Indices: 40329159--40329183 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
40329149 TAATGAAAAC
40329159 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
40329184 GAGGATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:40347935 original size:30 final size:31
Alignment explanation
Indices: 40347901--40347960 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
40347891 AAACCTTTTA
*
40347901 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
40347931 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
40347961 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:40358374 original size:23 final size:23
Alignment explanation
Indices: 40358348--40358391 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40358338 GTAAGAAAAT
40358348 AATAAATATACATTTTTTAATTG
1 AATAAATATACATTTTTTAATTG
* * *
40358371 AATATATTTATATTTTTTAAT
1 AATAAATATACATTTTTTAAT
40358392 AAAAAAACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
AATAAATATACATTTTTTAATTG
Found at i:40358669 original size:18 final size:19
Alignment explanation
Indices: 40358646--40358695 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
40358636 TTAAAATTTA
40358646 TTTAATAATTTTATAT-AT
1 TTTAATAATTTTATATAAT
40358664 TTTAATAATATTT-TATAAT
1 TTTAATAAT-TTTATATAAT
40358683 TTT-ATAAATTTTA
1 TTTAAT-AATTTTA
40358696 AAGAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATAATTTTATATAAT
Found at i:40358675 original size:28 final size:28
Alignment explanation
Indices: 40358618--40358697 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
40358608 GGACTTAGAT
40358618 TTTAATTAATTTT-TAT-TTTTAAAATTTA
1 TTTAA-TAATTTTATATATTTTAAAA-TTA
40358646 TTTAATAATTTTATATATTTTAATAA-TA
1 TTTAATAATTTTATATATTTTAA-AATTA
* *
40358674 TTTTATAATTTTATAAATTTTAAA
1 TTTAATAATTTTATATATTTTAAA
40358698 GAAAAATAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
27 8 0.17
28 31 0.66
29 6 0.13
30 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTAATAATTTTATATATTTTAAAATTA
Found at i:40362546 original size:7 final size:7
Alignment explanation
Indices: 40362534--40362567 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
40362524 AAAATCAAGT
40362534 AGGAGGA
1 AGGAGGA
40362541 AGGAGGA
1 AGGAGGA
40362548 AGGAGGA
1 AGGAGGA
40362555 AGGAGGA
1 AGGAGGA
*
40362562 ATGAGG
1 AGGAGG
40362568 CAATAAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.56, T:0.03
Consensus pattern (7 bp):
AGGAGGA
Found at i:40365004 original size:12 final size:12
Alignment explanation
Indices: 40364987--40365012 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40364977 CAAAATTTAG
40364987 AAAAACTATAAA
1 AAAAACTATAAA
40364999 AAAAACTATAAA
1 AAAAACTATAAA
40365011 AA
1 AA
40365013 TTCCATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAACTATAAA
Found at i:40369834 original size:18 final size:17
Alignment explanation
Indices: 40369808--40369843 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
40369798 GTAAAGTAAT
40369808 AATACGATAATAAGAATA
1 AATACGATAATAA-AATA
*
40369826 AATATGATAATAAAATA
1 AATACGATAATAAAATA
40369843 A
1 A
40369844 CAATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (17 bp):
AATACGATAATAAAATA
Found at i:40370313 original size:19 final size:19
Alignment explanation
Indices: 40370279--40370315 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40370269 TACTCTAAAC
40370279 AGAAAAGAAAAGAAAAAAG
1 AGAAAAGAAAAGAAAAAAG
40370298 AGAAAGAGAAAA-AAAAAA
1 AGAAA-AGAAAAGAAAAAA
40370316 CCTAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AGAAAAGAAAAGAAAAAAG
Found at i:40372770 original size:6 final size:6
Alignment explanation
Indices: 40372759--40372788 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
40372749 GAGGAGTTGA
40372759 AAGTGG AAGTGG AAGTGG AAGTGG AAGTGG
1 AAGTGG AAGTGG AAGTGG AAGTGG AAGTGG
40372789 GGGATGACAT
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:0.33, C:0.00, G:0.50, T:0.17
Consensus pattern (6 bp):
AAGTGG
Found at i:40373559 original size:18 final size:18
Alignment explanation
Indices: 40373538--40373574 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40373528 ATTTATATTT
40373538 TTTAAAAAATTATAAAAA
1 TTTAAAAAATTATAAAAA
*
40373556 TTTAAAAAATTCTAAAAA
1 TTTAAAAAATTATAAAAA
40373574 T
1 T
40373575 ATATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAAAATTATAAAAA
Found at i:40373606 original size:8 final size:9
Alignment explanation
Indices: 40373538--40373603 Score: 55
Period size: 9 Copynumber: 6.9 Consensus size: 9
40373528 ATTTATATTT
40373538 TTTAAAAAA
1 TTTAAAAAA
40373547 -TTATAAAAA
1 TTTA-AAAAA
40373556 TTTAAAAAA
1 TTTAAAAAA
40373565 TTCTAAAAATA
1 TT-TAAAAA-A
40373576 TATATAAATAAA
1 T-T-TAAA-AAA
*
40373588 GTT-AAAAA
1 TTTAAAAAA
40373596 TTTAAAAA
1 TTTAAAAA
40373604 TTTTCTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
8 8 0.17
9 18 0.38
10 10 0.21
11 3 0.06
12 6 0.13
13 2 0.04
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:40378129 original size:3 final size:3
Alignment explanation
Indices: 40378121--40378145 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40378111 GAGGACATGG
40378121 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
40378146 TGAATGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:40379238 original size:23 final size:22
Alignment explanation
Indices: 40379204--40379254 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
40379194 CATGCAGATT
40379204 TTTTTTTATTAA-AACCATTTACA
1 TTTTTTTATTAATAACCA-TTA-A
* *
40379227 TTTTTTTGTTAATAATCATTAA
1 TTTTTTTATTAATAACCATTAA
40379249 TTTTTT
1 TTTTTT
40379255 ACATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.28
23 14 0.56
24 4 0.16
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTTTTATTAATAACCATTAA
Found at i:40379322 original size:5 final size:6
Alignment explanation
Indices: 40379307--40379331 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40379297 TAAATTAATG
40379307 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
40379332 ATGTGTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:40379625 original size:17 final size:16
Alignment explanation
Indices: 40379603--40379633 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40379593 AAAATTAATA
40379603 AAAAAAATTTAAAAAT
1 AAAAAAATTTAAAAAT
*
40379619 AACAAAATTTAAAAA
1 AAAAAAATTTAAAAA
40379634 AGTTGATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAAATTTAAAAAT
Found at i:40392822 original size:12 final size:13
Alignment explanation
Indices: 40392794--40392826 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
40392784 AATATTAGTC
40392794 TTTTTAAACATAT
1 TTTTTAAACATAT
40392807 TTTTTAAACATAT
1 TTTTTAAACATAT
40392820 TTTTTAA
1 TTTTTAA
40392827 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTTTAAACATAT
Found at i:40394226 original size:3 final size:3
Alignment explanation
Indices: 40394218--40394245 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40394208 TTGGTCTCTC
40394218 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
40394246 TACAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:40397593 original size:31 final size:31
Alignment explanation
Indices: 40397543--40397604 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
40397533 TTAATCGTGG
* * *
40397543 GTGACTAAAATTATAAAAGTATATAATGACA
1 GTGAATAAAATGATAAAAGTATATAACGACA
*
40397574 GTGAATAAAATGATTAAAGTATATAACGACA
1 GTGAATAAAATGATAAAAGTATATAACGACA
40397605 TTACTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (31 bp):
GTGAATAAAATGATAAAAGTATATAACGACA
Found at i:40398296 original size:109 final size:109
Alignment explanation
Indices: 40398121--40398517 Score: 645
Period size: 109 Copynumber: 3.7 Consensus size: 109
40398111 GTCAATCGAG
* * * *
40398121 AAATCGAAACCCAGCACATTAGGGCATG-TTCCTCGAATTTCCAAACGCAAAACATTGCCTTCTT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* *
40398185 TTAAATTTTTTAAAAGGATATTTAGCCATTTGGTTGAACGAGAA
66 TTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
* *
40398229 AAATCGACACCCA-AACCTTAGAGCATGTTTTCTCGAATTTCCCAAACGCAAAACATTGCCTTAT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTT-CCAAACGCAAAACATTGCCTTAT
* * *
40398293 TTTAAAATTTTTAAAACGATATTAAGTCATTTGGTTGAATGAGAA
65 TTTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
*
40398338 AAATCGACACCCAGCACCTTAGGGTATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
40398403 TTAAAATTTTTAAAAGGGTATTAAGCCATTTGGTTGAACGAGAA
66 TTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
40398447 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
40398512 TGAAAA
66 TTAAAA
40398518 AAAATTCGTT
Statistics
Matches: 266, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
107 11 0.04
108 23 0.09
109 208 0.78
110 24 0.09
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (109 bp):
AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTAAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGAGAA
Found at i:40400051 original size:26 final size:25
Alignment explanation
Indices: 40400012--40400060 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
40400002 TTTATGATAC
40400012 ATATACATACGCATGGCTTTTATAAT
1 ATATACATACGCAT-GCTTTTATAAT
* * *
40400038 ATATATATAGGCATTCTTTTATA
1 ATATACATACGCATGCTTTTATA
40400061 CAGTATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (25 bp):
ATATACATACGCATGCTTTTATAAT
Found at i:40401351 original size:15 final size:16
Alignment explanation
Indices: 40401318--40401356 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
40401308 TTTATGCAAG
*
40401318 TATGTATATACACGTT
1 TATGTATATACAAGTT
40401334 TATGTATATA-AAGTT
1 TATGTATATACAAGTT
*
40401349 TATATATA
1 TATGTATA
40401357 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (16 bp):
TATGTATATACAAGTT
Found at i:40401523 original size:21 final size:21
Alignment explanation
Indices: 40401459--40401525 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
40401449 ATGCGTATAT
* *
40401459 ATGTACATATTTAATA-AAAA
1 ATGTACATATATAATATGAAA
*
40401479 ACGTGTACATATATATTATGAAA
1 A--TGTACATATATAATATGAAA
* *
40401502 ATGTATATATATAGATATAAAA
1 ATGTACATATATA-ATATGAAA
40401524 AT
1 AT
40401526 AAAGCTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 11 0.30
22 21 0.57
23 4 0.11
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (21 bp):
ATGTACATATATAATATGAAA
Found at i:40403914 original size:30 final size:30
Alignment explanation
Indices: 40403873--40403937 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
40403863 ACTTATTTTA
40403873 TTGTTAATTTTGTTATTATCTTAGAGGCAT
1 TTGTTAATTTTGTTATTATCTTAGAGGCAT
* *
40403903 TTGTTATTTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATCTTAGAGGCAT
40403933 TTGTT
1 TTGTT
40403938 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.20, C:0.05, G:0.17, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATCTTAGAGGCAT
Found at i:40406678 original size:98 final size:98
Alignment explanation
Indices: 40406509--40406703 Score: 345
Period size: 98 Copynumber: 2.0 Consensus size: 98
40406499 ATACAATAAA
*
40406509 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTCAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTCAGGGCACAATC
40406574 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* * * *
40406607 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTATGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTCAGGGCACAATC
40406672 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTT
40406704 CATGATTTTT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTCAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:40407319 original size:106 final size:106
Alignment explanation
Indices: 40407209--40407423 Score: 430
Period size: 106 Copynumber: 2.0 Consensus size: 106
40407199 CAAATAAAAT
40407209 TTTGGGTTATAGAATTTATATATAAATACAATACATAATATACTTATGCAAATAAAGAAAAAATA
1 TTTGGGTTATAGAATTTATATATAAATACAATACATAATATACTTATGCAAATAAAGAAAAAATA
40407274 TAATTATACGTACATATATAAAATAATAATAAATAGGTATA
66 TAATTATACGTACATATATAAAATAATAATAAATAGGTATA
40407315 TTTGGGTTATAGAATTTATATATAAATACAATACATAATATACTTATGCAAATAAAGAAAAAATA
1 TTTGGGTTATAGAATTTATATATAAATACAATACATAATATACTTATGCAAATAAAGAAAAAATA
40407380 TAATTATACGTACATATATAAAATAATAATAAATAGGTATA
66 TAATTATACGTACATATATAAAATAATAATAAATAGGTATA
40407421 TTT
1 TTT
40407424 TTAAAAAGAA
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 109 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (106 bp):
TTTGGGTTATAGAATTTATATATAAATACAATACATAATATACTTATGCAAATAAAGAAAAAATA
TAATTATACGTACATATATAAAATAATAATAAATAGGTATA
Found at i:40408300 original size:19 final size:19
Alignment explanation
Indices: 40408276--40408407 Score: 210
Period size: 19 Copynumber: 6.8 Consensus size: 19
40408266 AATCATATAT
40408276 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
40408295 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
40408314 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40408333 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
40408354 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
40408373 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
40408392 TCTAATATTGCATATC
1 TCTAAGATTGCATATC
40408408 CTCAAAAATT
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
19 85 0.82
21 19 0.18
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40408360 original size:59 final size:59
Alignment explanation
Indices: 40408269--40408406 Score: 212
Period size: 59 Copynumber: 2.4 Consensus size: 59
40408259 ATTACAAAAT
*
40408269 CATAT-AT-TCTAAGATTGC--ATATCATATCTAAGATTATATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
* *
40408324 CATATCATATCTAAGATTGCATATATCATATCTAAGATTGCATATCATATCTAGGATTG
1 CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
*
40408383 CATATCATATCTAATATTGCATAT
1 CATATCATATCTAAGATTGCATAT
40408407 CCTCAAAAAT
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
55 5 0.07
56 2 0.03
57 11 0.15
59 57 0.76
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.39
Consensus pattern (59 bp):
CATATCATATCTAAGATTGCATATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:40417394 original size:8 final size:8
Alignment explanation
Indices: 40417381--40417413 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
40417371 AAAATTCTTT
40417381 AAAATTAA
1 AAAATTAA
40417389 AAAATTAA
1 AAAATTAA
*
40417397 AATA-TAA
1 AAAATTAA
40417404 AAAATTAA
1 AAAATTAA
40417412 AA
1 AA
40417414 TTCAATGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:40417406 original size:15 final size:14
Alignment explanation
Indices: 40417379--40417415 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
40417369 TAAAAATTCT
40417379 TTAAAATTAAAAAA
1 TTAAAATTAAAAAA
40417393 TTAAAATATAAAAAA
1 TTAAAAT-TAAAAAA
40417408 TTAAAATT
1 TTAAAATT
40417416 CAATGTTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TTAAAATTAAAAAA
Found at i:40425751 original size:22 final size:21
Alignment explanation
Indices: 40425723--40425766 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
40425713 AAAAACTAGA
40425723 AAAAAAAAATCAAAATGTTTAT
1 AAAAAAAAATCAAAAT-TTTAT
* *
40425745 AAAAAAAATTCCAAATTTTAT
1 AAAAAAAAATCAAAATTTTAT
40425766 A
1 A
40425767 TTTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAAAAAATCAAAATTTTAT
Found at i:40431823 original size:12 final size:13
Alignment explanation
Indices: 40431806--40431842 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
40431796 GAACCGGACA
40431806 CGAACCGAA-CTC
1 CGAACCGAAGCTC
40431818 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
40431830 CGAACCGTAGCTC
1 CGAACCGAAGCTC
40431843 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:40433693 original size:17 final size:17
Alignment explanation
Indices: 40433673--40433706 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40433663 ATTTTCACAC
*
40433673 TATAATGATTTTTTTAA
1 TATAATGATTATTTTAA
*
40433690 TATAATTATTATTTTAA
1 TATAATGATTATTTTAA
40433707 AAGAATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TATAATGATTATTTTAA
Found at i:40434328 original size:29 final size:29
Alignment explanation
Indices: 40434272--40434328 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
40434262 TCAGTTTGAA
* *
40434272 TTTAATTTTTAATATTTTAAATTGTTTAT
1 TTTAATTTTTAATATTTTAAAATATTTAT
*
40434301 TTTAGTTTTT-ATATTTTTAAAATATTTA
1 TTTAATTTTTAATA-TTTTAAAATATTTA
40434329 ATTAAATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (29 bp):
TTTAATTTTTAATATTTTAAAATATTTAT
Found at i:40438420 original size:15 final size:15
Alignment explanation
Indices: 40438377--40438482 Score: 83
Period size: 15 Copynumber: 7.1 Consensus size: 15
40438367 AATATCTCGG
*
40438377 TACCCATATCTTTGA
1 TACCCATATATTTGA
**
40438392 CTTTCCA-ATATTTGA
1 -TACCCATATATTTGA
*
40438407 TACCCATATCTTTGA
1 TACCCATATATTTGA
**
40438422 CTTTCCA-ATATTTGA
1 -TACCCATATATTTGA
40438437 TACCCATATATTTGA
1 TACCCATATATTTGA
** *
40438452 CTTTCTAT-TATTTGA
1 -TACCCATATATTTGA
40438467 TACCCATATATTTGA
1 TACCCATATATTTGA
40438482 T
1 T
40438483 TTTCTATAAA
Statistics
Matches: 68, Mismatches: 17, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
14 12 0.18
15 44 0.65
16 12 0.18
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.45
Consensus pattern (15 bp):
TACCCATATATTTGA
Found at i:40438489 original size:30 final size:30
Alignment explanation
Indices: 40438377--40438486 Score: 175
Period size: 30 Copynumber: 3.7 Consensus size: 30
40438367 AATATCTCGG
*
40438377 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATATTTGACTTTCCAATATTTGA
*
40438407 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATATTTGACTTTCCAATATTTGA
* *
40438437 TACCCATATATTTGACTTTCTATTATTTGA
1 TACCCATATATTTGACTTTCCAATATTTGA
*
40438467 TACCCATATATTTGATTTTC
1 TACCCATATATTTGACTTTC
40438487 TATAAATATG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.46
Consensus pattern (30 bp):
TACCCATATATTTGACTTTCCAATATTTGA
Found at i:40443106 original size:30 final size:30
Alignment explanation
Indices: 40443071--40443180 Score: 170
Period size: 30 Copynumber: 3.7 Consensus size: 30
40443061 AATATCTCGG
40443071 TACCCATATCTTTGACTTTTCAATATTTGA
1 TACCCATATCTTTGACTTTTCAATATTTGA
*
40443101 TACCCATATCTTTGACTTTCCAATATTTGA
1 TACCCATATCTTTGACTTTTCAATATTTGA
*
40443131 TACCCATATCTTTGAC-TTTCTATTATTTGA
1 TACCCATATCTTTGACTTTTC-AATATTTGA
*
40443161 TACCCATATATTTGA-TTTTC
1 TACCCATATCTTTGACTTTTC
40443181 CATAAATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
29 3 0.04
30 71 0.96
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.47
Consensus pattern (30 bp):
TACCCATATCTTTGACTTTTCAATATTTGA
Found at i:40443114 original size:15 final size:15
Alignment explanation
Indices: 40443093--40443176 Score: 73
Period size: 15 Copynumber: 5.6 Consensus size: 15
40443083 TGACTTTTCA
40443093 ATATTTGATACCCAT
1 ATATTTGATACCCAT
* **
40443108 ATCTTTGACTTTCCA-
1 ATATTTGA-TACCCAT
40443123 ATATTTGATACCCAT
1 ATATTTGATACCCAT
* ** *
40443138 ATCTTTGACTTTCTAT
1 ATATTTGA-TACCCAT
40443154 -TATTTGATACCCAT
1 ATATTTGATACCCAT
40443168 ATATTTGAT
1 ATATTTGAT
40443177 TTTCCATAAA
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
14 8 0.16
15 35 0.69
16 8 0.16
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.46
Consensus pattern (15 bp):
ATATTTGATACCCAT
Found at i:40447155 original size:15 final size:13
Alignment explanation
Indices: 40447118--40447159 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 13
40447108 TACCATGTAT
40447118 AAATGTTAGAATTA
1 AAAT-TTAGAATTA
40447132 AAA-TTAGAATTA
1 AAATTTAGAATTA
40447144 CAAATTTTAGAATTA
1 -AAA-TTTAGAATTA
40447159 A
1 A
40447160 GACTAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.36
13 3 0.12
14 4 0.16
15 9 0.36
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (13 bp):
AAATTTAGAATTA
Found at i:40447590 original size:19 final size:19
Alignment explanation
Indices: 40447568--40447630 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
40447558 ATTTTTTTAT
40447568 AAAAATCGTAAAAAATATA
1 AAAAATCGTAAAAAATATA
* **
40447587 AAAAATTGTAAAATTTCAT-
1 AAAAATCGTAAAAAAT-ATA
*
40447606 AAAAATCATAAAAAAATTATA
1 AAAAATCGT-AAAAAA-TATA
40447627 AAAA
1 AAAA
40447631 TGCATTAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 20 0.61
20 8 0.24
21 5 0.15
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAAATCGTAAAAAATATA
Found at i:40447641 original size:30 final size:28
Alignment explanation
Indices: 40447564--40447641 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 28
40447554 TAGAATTTTT
*
40447564 TTATAAAAAT-CGTAAAAAATATAAAAAA
1 TTATAAAAATGCAT-AAAAATATAAAAAA
* * *
40447592 TTGTAAAATTTCATAAAAATCATAAAAAAA
1 TTATAAAAATGCATAAAAAT-AT-AAAAAA
*
40447622 TTATAAAAATGCATTAAAAT
1 TTATAAAAATGCATAAAAAT
40447642 GCCCTTTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 14 0.35
29 4 0.10
30 22 0.55
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (28 bp):
TTATAAAAATGCATAAAAATATAAAAAA
Found at i:40482021 original size:51 final size:49
Alignment explanation
Indices: 40481891--40482083 Score: 208
Period size: 51 Copynumber: 3.8 Consensus size: 49
40481881 AGTTGCTAGG
* * *
40481891 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAAT-GATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAATAGAT-GA
* * * *
40481941 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAG-AT-GA
* * * *
40481992 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAT--AGATGA
* *
40482043 TCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGA
40482084 GTATCATTTA
Statistics
Matches: 118, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
49 4 0.03
50 35 0.30
51 77 0.65
52 1 0.01
53 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGATGA
Found at i:40482114 original size:102 final size:100
Alignment explanation
Indices: 40481893--40482083 Score: 267
Period size: 101 Copynumber: 1.9 Consensus size: 100
40481883 TTGCTAGGTC
* * *
40481893 ACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATGATAGGTCGCATGTGTAGTACTA
1 ACGTGTGTA-TACTATGTGCAGGCTACTACATGTACCGGAATGAAAGATCACATGTGTAGTACTA
* *
40481958 TGTGCAGGCTACTATGCGTACCGAATAGCTTCGATC
65 TGTGCAGGCTACTATGCGAACCGAATAGCTTCGATA
* *
40481994 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATGAAAATGATCACATGTGTAGTAC
1 ACGTGTGTA-TACTATGTGCAGGCTACTACATGTACCGGAATG-AAA-GATCACATGTGTAGTAC
*
40482058 TATGTGCAGGCTACTATGTGAACCGA
63 TATGTGCAGGCTACTATGCGAACCGA
40482084 GTATCATTTA
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
100 3 0.04
101 39 0.48
102 39 0.48
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (100 bp):
ACGTGTGTATACTATGTGCAGGCTACTACATGTACCGGAATGAAAGATCACATGTGTAGTACTAT
GTGCAGGCTACTATGCGAACCGAATAGCTTCGATA
Found at i:40484517 original size:17 final size:17
Alignment explanation
Indices: 40484495--40484529 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40484485 CACTTAATTT
*
40484495 ACATATATTACTGAAAC
1 ACATATATCACTGAAAC
*
40484512 ACATATATCACTGTAAC
1 ACATATATCACTGAAAC
40484529 A
1 A
40484530 TTTTCATCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (17 bp):
ACATATATCACTGAAAC
Found at i:40487685 original size:21 final size:20
Alignment explanation
Indices: 40487663--40487738 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 20
40487653 TTTTGTTTAG
*
40487663 CTCTTTCGAGCTTCTGTTCAG
1 CTCTTT-GAGCTTCTGTTCAA
* *
40487684 CTCTTAAGAGCTTATGTTCAA
1 CTCTT-TGAGCTTCTGTTCAA
40487705 CTCTTATGAGCTTCTGTTCAA
1 CTCTT-TGAGCTTCTGTTCAA
40487726 CT-TTTGAGCTTCT
1 CTCTTTGAGCTTCT
40487739 ATTGGCGTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 9 0.18
20 2 0.04
21 38 0.78
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (20 bp):
CTCTTTGAGCTTCTGTTCAA
Found at i:40487987 original size:10 final size:8
Alignment explanation
Indices: 40487972--40487998 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40487962 TGATGGCACA
40487972 TGATATAT
1 TGATATAT
40487980 TGATATAT
1 TGATATAT
40487988 TGATATAT
1 TGATATAT
40487996 TGA
1 TGA
40487999 AATGGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (8 bp):
TGATATAT
Found at i:40490290 original size:19 final size:22
Alignment explanation
Indices: 40490263--40490308 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
40490253 AGATAATCTC
40490263 AAAACAACAATATT-TAAATAAA
1 AAAAC-ACAATATTATAAATAAA
40490285 AAAACACAATATTATAAATAAA
1 AAAACACAATATTATAAATAAA
40490307 AA
1 AA
40490309 CTCAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAACACAATATTATAAATAAA
Found at i:40490317 original size:22 final size:21
Alignment explanation
Indices: 40490263--40490317 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
40490253 AGATAATCTC
40490263 AAAACAACAATATTTAAATAAA
1 AAAACAA-AATATTTAAATAAA
*
40490285 AAAACACAATATTATAAATAAA
1 AAAACAAAATATT-TAAATAAA
**
40490307 AACTCAAAATA
1 AAAACAAAATA
40490318 ACATATCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAACAAAATATTTAAATAAA
Found at i:40497931 original size:18 final size:18
Alignment explanation
Indices: 40497885--40497931 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
40497875 AATAAAGTAT
*
40497885 TATAAGCCCAATATATTT
1 TATAAGCCCAATATATTA
* *
40497903 TATAGGTCCAATATATTA
1 TATAAGCCCAATATATTA
*
40497921 TGTAAGCCCAA
1 TATAAGCCCAA
40497932 ACTAAATAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
TATAAGCCCAATATATTA
Found at i:40510039 original size:17 final size:17
Alignment explanation
Indices: 40510017--40510049 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40510007 CATGTGTCTC
40510017 TTTTTTT-TAAATATTTA
1 TTTTTTTCT-AATATTTA
40510034 TTTTTTTCTAATATTT
1 TTTTTTTCTAATATTT
40510050 TTCTATACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTTCTAATATTTA
Found at i:40511862 original size:9 final size:9
Alignment explanation
Indices: 40511838--40511880 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
40511828 CACATGAAGA
40511838 TTAAATTAT
1 TTAAATTAT
40511847 ATTAAATTAT
1 -TTAAATTAT
40511857 TTAAATTAT
1 TTAAATTAT
*
40511866 TCAAATTAT
1 TTAAATTAT
*
40511875 TCAAAT
1 TTAAAT
40511881 AATCGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 23 0.72
10 9 0.28
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAAATTAT
Found at i:40511889 original size:18 final size:18
Alignment explanation
Indices: 40511840--40511890 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
40511830 CATGAAGATT
* *
40511840 AAATTATATTAAATTATTT
1 AAATTA-ATCAAATTATTC
*
40511859 AAATTATTCAAATTATTC
1 AAATTAATCAAATTATTC
40511877 AAA-TAATCGAAATT
1 AAATTAATC-AAATT
40511891 GTACATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 17 0.63
19 6 0.22
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATTAATCAAATTATTC
Found at i:40516668 original size:23 final size:23
Alignment explanation
Indices: 40516639--40517278 Score: 362
Period size: 23 Copynumber: 24.4 Consensus size: 23
40516629 TAAAAACCCT
40516639 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
** * *
40516662 ATTCCTAACTTAACTTAATTAAAA
1 AACCCTAACCTAATTTAATT-AAA
*
40516686 AACCTAACCTAACTTAATTTAATTAAA
1 AA-C---CCTAACCTAATTTAATTAAA
*
40516713 AACCCTTACCCTAACCTAATTTAATTTAA
1 AA------CCCTAACCTAATTTAATTAAA
* *
40516742 AACCCTAACTTAACTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
40516765 AACCCTAACTTAATTTAATTTAATTAAA
1 AACCCTAAC-----CTAATTTAATTAAA
40516793 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
40516816 AACCCTAACCTAATTTAATTAAATTA
1 AACCCTAACCTAATTTAATT-AA--A
*
40516842 AACCCTAACCTAATTTAGTTAAA
1 AACCCTAACCTAATTTAATTAAA
*
40516865 AACCCTAACCCTAACCTATTTTACATGAAAA
1 AACCCTAA-CCT-A---A-TTTA-AT-TAAA
40516896 CCCTAACCCTAACCTAATTTAATTAAA
1 ----AACCCTAACCTAATTTAATTAAA
* *
40516923 AACTCTAACTTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
40516946 AACCCTAACCTAATTTAGTTAAA
1 AACCCTAACCTAATTTAATTAAA
*
40516969 AACCCTAACCCTAACCTATTTTACATGAAAA
1 AACCCTAA-CCT-A---A-TTTA-AT-TAAA
40517000 CCCTAACCCTAACCTAATTTAATTAAA
1 ----AACCCTAACCTAATTTAATTAAA
*
40517027 AACCCTAATCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
40517050 AACCCTAACCTAATTTAGTTAAA
1 AACCCTAACCTAATTTAATTAAA
*
40517073 AACCCTAACCCTAACCTATTTTACATGAAAA
1 AACCCTAA-CCT-A---A-TTTA-AT-TAAA
*
40517104 CCCTAACCCTAACCTAATTTAATCAAA
1 ----AACCCTAACCTAATTTAATTAAA
40517131 AACCCTAACCTAATTTAATTTAATTAAA
1 AACCCTAACC-----TAATTTAATTAAA
*
40517159 AACCCTTACCCTATTTTAATTTAATTAAA
1 AACCC-TAACC-----TAATTTAATTAAA
*
40517188 AACCCTTACCCTATTTTAATTTAATTAAA
1 AACCC-TAACC-----TAATTTAATTAAA
*
40517217 AACCCTTACCATATTTTAATTTAATTAAA
1 AACCCTAACC------TAATTTAATTAAA
* *
40517246 AACCCTAATCTAATTTAGTTAAA
1 AACCCTAACCTAATTTAATTAAA
40517269 AACCCTAACC
1 AACCCTAACC
40517279 CTAACCTATT
Statistics
Matches: 514, Mismatches: 42, Indels: 122
0.76 0.06 0.18
Matches are distributed among these distances:
23 216 0.42
24 15 0.03
25 5 0.01
26 20 0.04
27 14 0.03
28 67 0.13
29 125 0.24
30 6 0.01
31 9 0.02
32 1 0.00
33 3 0.01
34 9 0.02
35 24 0.05
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.33
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:40516668 original size:29 final size:28
Alignment explanation
Indices: 40516622--40517903 Score: 983
Period size: 29 Copynumber: 46.8 Consensus size: 28
40516612 TTTTGACATT
*
40516622 ATTTGATTAAAAACCCTAACCCTAACCTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* * *
40516651 ATTTAATTAAAATTCCTAA-CTTAACTTA
1 ATTTAATTAAAA-CCCTAACCCTAACCTA
*
40516679 A-TTAA--AAAA-CCTAA-CCTAACTTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
*
40516702 ATTTAATTAAAAACCCTTACCCTAACCTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* *
40516731 ATTTAATTTAAAACCCTAA-CTTAACTTA
1 ATTTAA-TTAAAACCCTAACCCTAACCTA
* **
40516759 A-TT-A--AAAACCCTAA-CTTAATTTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
40516782 ATTTAATT-AAA----AACCCTAACCTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
40516805 ATTTAATTAAAA----A-CCCTAACCTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
*
40516828 ATTTAATT-AAA--TTAAACCCTAACCTA
1 ATTTAATTAAAACCCT-AACCCTAACCTA
*
40516854 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* *
40516883 TTTTACATGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAACCCTAACCCTAACCTA
* *
40516912 ATTTAATT-AAA----AACTCTAACTTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
40516935 ATTTAATTAAAA----A-CCCTAACCTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
*
40516958 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* *
40516987 TTTTACATGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAACCCTAACCCTAACCTA
*
40517016 ATTTAATT-AAA----AACCCTAATCTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
40517039 ATTTAATTAAAA----A-CCCTAACCTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
*
40517062 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* *
40517091 TTTTACATGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAACCCTAACCCTAACCTA
* **
40517120 ATTTAATCAAAAACCCTAA-CCTAATTTA
1 ATTTAAT-TAAAACCCTAACCCTAACCTA
* ***
40517148 ATTTAATTAAAAACCCTTACCCTATTTTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* ***
40517177 ATTTAATTAAAAACCCTTACCCTATTTTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* * ***
40517206 ATTTAATTAAAAACCCTTACCATATTTTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
*
40517235 ATTTAATT-AAA----AACCCTAATCTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
*
40517258 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* *
40517287 TTTTACATGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAACCCTAACCCTAACCTA
*
40517316 TTTTAATTAAAATCCCTAACCCTAACCTAATTTA
1 ATTTAATTAAAA-CCCTAACCCTAACC-----TA
* ***
40517350 ATTTAATTAAAAACCCTTACCCTATTTTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
*
40517379 ATTTAATT-AAA----AACCCTTACCTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
*
40517402 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* *
40517431 TTTTACATGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAACCCTAACCCTAACCTA
* * *
40517460 TTTTAATTAAAATCCCTAACCGTTACCTA
1 ATTTAATTAAAA-CCCTAACCCTAACCTA
* **
40517489 ATTTAATTAAAAACTCTAA-CCTAATTTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* ***
40517517 ATTTAATTAAAAACCCTTACCCTATTTTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
40517546 ATTTAATT-AAA----AACCCTAACCTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
*
40517569 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* *
40517598 TTTTACATGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAACCCTAACCCTAACCTA
*
40517627 TTTTAATTAAAATCCCTAACCCTAACCTA
1 ATTTAATTAAAA-CCCTAACCCTAACCTA
**
40517656 ATTTAATTAAAAACCCTAA-CCTAATTTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
40517684 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* *
40517713 TTTTACATGAAAACCCTAACCCTAACCTA
1 ATTTA-ATTAAAACCCTAACCCTAACCTA
*
40517742 TTTTAATTAAAATCCCTAACCCTAACCTA
1 ATTTAATTAAAA-CCCTAACCCTAACCTA
* *
40517771 ATTTAATT-AAA----AACTCGAACCTA
1 ATTTAATTAAAACCCTAACCCTAACCTA
*
40517794 ATTTAGTTAAAAACCCTAACCCTAACCTA
1 ATTTAATT-AAAACCCTAACCCTAACCTA
* *
40517823 TTTTACATGAAAACCCTAACCCTAACCT-
1 ATTTA-ATTAAAACCCTAACCCTAACCTA
* *
40517851 ATCTTAATTAAAATACCGAACCCTAACCTA
1 AT-TTAATTAAAA-CCCTAACCCTAACCTA
* *
40517881 GTTTAATTGAAAACCCTTACCCT
1 ATTTAATT-AAAACCCTAACCCT
40517904 GATTTATCAT
Statistics
Matches: 1048, Mismatches: 116, Indels: 178
0.78 0.09 0.13
Matches are distributed among these distances:
22 5 0.00
23 194 0.19
24 26 0.02
25 18 0.02
26 21 0.02
27 25 0.02
28 140 0.13
29 571 0.54
30 25 0.02
34 19 0.02
35 4 0.00
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.32
Consensus pattern (28 bp):
ATTTAATTAAAACCCTAACCCTAACCTA
Found at i:40517276 original size:167 final size:163
Alignment explanation
Indices: 40516628--40517843 Score: 1017
Period size: 167 Copynumber: 7.4 Consensus size: 163
40516618 CATTATTTGA
* * * *
40516628 TTAAAAACCCTAACCCTAACCTAATTTAATT-AAAA---T-TCCTAACTTAACTTAATTAAAAAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAAC
* ** * *
40516688 CCTAACCTAACTTAATTTAATTAAAAACCCTTACCCTAACCTAATTTAATTTAAAACCCTAACTT
66 CCTAACCTAATTTAATTTAATTAAAAACCCTTACCCTATTCTAATTTAATTAAAAACCCTAACCT
* * * *
40516753 AACTTAATT--AAA-AACCCTAACTTAATTTAAT
131 AATTTAGTTAAAAACAACCCTAACCTAATTT-AC
** *
40516784 TTAATTAAA----AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAATT--AA
1 TTAA--AAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAA
* * ** * *
40516843 ACCCTAACC-----TAATTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAAC
64 ACCCTAACCTAATTTAATTTAATTAAAAACCCTTACCCTATTCTAATTTA-AT-TAAA----AAC
* * * *
40516903 CCTAACCTAATTTAATT--AAA-AACTCTAACTTAATTTAA
123 CCTAACCTAATTTAGTTAAAAACAACCCTAACCTAATTTAC
* * *
40516941 TT--AAA----AACCCTAACCTAATTTAGTTAAAAACCCTAACCCTAACCTATTTTACA-TGAAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAACCTAATTTA-ATTAAAA
**
40516999 ACCCTAACCCTAACCTAATTTAATTAAAAACCC-TA----A-TCTAATTTAATTAAAAACCCTAA
64 ACCCTAA-CCTAATTTAATTTAATTAAAAACCCTTACCCTATTCTAATTTAATTAAAAACCCTAA
*
40517058 CCTAATTTAGTTAAAAACCCTAACCCTAACCTATTTTAC
128 CCTAATTTAGTTAAAAA--C-AACCCTAACCTAATTTAC
* * * **
40517097 ATGAAAACCCTAACCCTAACCTAATTTAATCAAAAACCCTAACCTAATTTAATTTAATTAAAAAC
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAAC
* * * *
40517162 CCTTACCCTATTTTAATTTAATTAAAAACCCTTACCCTATTTTAATTTAATTAAAAACCCTTACC
66 CC-TAACCTAATTTAATTTAATTAAAAACCCTTACCCTATTCTAATTTAATTAAAAACCCTAACC
* * * *
40517227 ATATTTTAATTTAATTAAA-AACCCTAATCTAATTTAG
130 -TAATTT-AGTTAA--AAACAACCCTAACCTAATTTAC
* * *
40517264 TTAAAAACCCTAACCCTAACCTATTTTACA-TGAAAACCCTAACCCTAACCTATTTTAATTAAAA
1 TTAAAAACCCTAACCCTAACCTAATTTA-ATTAAAAACCCTAA-CCTAACCTAATTTAATT-AAA
*
40517328 TCCCTAACCCTAACCTAATTTAATTTAATTAAAAACCCTTACCCTATTTTAATTTAATTAAAAAC
63 -----AACCCTAACCTAATTTAATTTAATTAAAAACCCTTACCCTATTCTAATTTAATTAAAAAC
* *
40517393 CCTTACCTAATTTAGTTAAAAACCCTAACCCTAACCTATTTTAC
123 CCTAACCTAATTTAGTTAAAAA--C-AACCCTAACCTAATTTAC
* * * * *
40517437 ATGAAAACCCTAACCCTAACCTATTTTAATTAAAATCCCTAACCGTTACCTAATTTAATTAAAAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC-TAACCTAATTTAATTAAAAA
* *
40517502 CTCTAACCTAATTTAATTTAATTAAAAACCCTTACCCTATTTTAATTTAATTAAAAACCCTAACC
65 CCCTAACCTAATTTAATTTAATTAAAAACCCTTACCCTATTCTAATTTAATTAAAAACCCTAACC
*
40517567 TAATTTAGTTAAAAACCCTAACCCTAACCTATTTTAC
130 TAATTTAGTTAAAAA--C-AACCCTAACCTAATTTAC
* * * *
40517604 ATGAAAACCCTAACCCTAACCTATTTTAATTAAAATCCCTAACCCTAACCTAATTTAATTAAAAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAACCTAATTTAATTAAAAA
* ** * *
40517669 CCCTAACCTAATTTAATTTAATTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACC
65 CCCTAACCTAATTTAATTTAATTAAAAACCCTTACCCTATTCTAATTTA-AT-TAAA----AACC
* * * *
40517734 CTAACCTATTTTAATTAAAATCCCTAACCCTAACCTAATTTAA
124 CTAACCTAATTTAGTTAAAA--AC-AACCCTAACCTAATTTAC
* * * *
40517777 TTAAAAA--CT----CGAACCTAATTTAGTTAAAAACCCTAACCCTAACCTATTTTACA-TGAAA
1 TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAACCTAATTTA-ATTAAAA
40517835 ACCCTAACC
64 ACCCTAACC
40517844 CTAACCTATC
Statistics
Matches: 898, Mismatches: 91, Indels: 131
0.80 0.08 0.12
Matches are distributed among these distances:
150 19 0.02
152 36 0.04
153 35 0.04
154 36 0.04
155 7 0.01
156 35 0.04
157 16 0.02
158 43 0.05
159 14 0.02
160 1 0.00
161 42 0.05
162 50 0.06
166 1 0.00
167 329 0.37
168 25 0.03
169 14 0.02
171 10 0.01
172 11 0.01
173 169 0.19
174 5 0.01
ACGTcount: A:0.42, C:0.24, G:0.01, T:0.32
Consensus pattern (163 bp):
TTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAAC
CCTAACCTAATTTAATTTAATTAAAAACCCTTACCCTATTCTAATTTAATTAAAAACCCTAACCT
AATTTAGTTAAAAACAACCCTAACCTAATTTAC
Found at i:40517319 original size:144 final size:144
Alignment explanation
Indices: 40516793--40517888 Score: 843
Period size: 144 Copynumber: 7.9 Consensus size: 144
40516783 TTTAATTAAA
*
40516793 AACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAATTTAATTAAATT--AAACCCTAACCTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCTAA
40516855 TTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACC-----TAATT
66 TTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTATTTTAATT
40516915 TAATTAAAAA--CT
131 TAATTAAAAACCCT
* *
40516927 ----CTAACTTAATTTAATTAAAAACCCTAA-CCTAATTT-AGTTAA--AAACCCTAACCCTAAC
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAA----AACCCTAAC
* ** * * * *
40516984 CTATTTTACATGAAAACCCTAACCCTAACCTAATTTA-AT-TAAA----AACCCT-A---A-TCT
62 CTAATTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTATTTT
40517038 AATTTAATTAAAAACCCT
127 AATTTAATTAAAAACCCT
* ** * *
40517056 -A-----ACCTAATTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTA-AT-TAAA----AACCCTA
* * ** * * *
40517115 ACCTAATTTAATCAAAAACCCTAA-CCTAATTTAATTTA-AT-TAAA----AACCCTTACCCTAT
60 ACCTAATTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCC-TAACCTAT
40517173 TTTAATTTAATTAAAAACCCT
124 TTTAATTTAATTAAAAACCCT
* *** * * * *
40517194 TACCCTATTTTAATTTAATTAAAAACCCTTACCATATTTTAATTTAATTAAAAACCCTAATCTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCTAA
40517259 TTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTATTTTAATT
66 TTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTATTTTAATT
* ****
40517324 AAAATCCCTAACCCT
131 -TAATTAAAAACCCT
** * * *
40517339 AA-CCTAATTTAATTTAATTAAAAACCCTTACCCTATTTTAATTTAATTAAAAACCCTTACCTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCTAA
40517403 TTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTA---T--TT
66 TTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTATTTTAATT
*
40517463 TAATTAAAATCCCT
131 TAATTAAAAACCCT
* * * *
40517477 AACCGTTACCTAATTTAATTAAAAACTCTAA-CCTAATTTAATTTAATTAAAAACCCTTACCCTA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCC-TAACCTA
* * * ** *
40517541 TTTTAATTTAATTAAA----AACCCTAACCTAATTTAGTTAAAAACCCTAACCCTAACCTATTTT
65 ATTT-AGTTAA--AAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTATTTT
* *
40517602 -A---CA-TGAAAACCCT
127 AATTTAATTAAAAACCCT
* * **
40517615 AACCCTAACCTATTTTAATTAAAATCCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACC---
*
40517680 TTTAATTTAATTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTA---
63 --TAATTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTATTT
*
40517742 T--TTTAATTAAAATCCCT
126 TAATTTAATTAAAAACCCT
* * *
40517759 AACCCTAACCTAATTTAATTAAAAACTCGAA-CCTAATTT-AGTTAA--AAACCCTAACCCTAAC
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAA----AACCCTAAC
* ** * * * * * *
40517820 CTATTTTACATGAAAACCCTAACCCTAACCTATCTTA-ATTAAAATACCGAACCCTAACCTAGTT
62 CTAATTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAA-CCCTAACCCTAACCTATTT
40517884 TAATT
126 TAATT
40517889 GAAAACCCTT
Statistics
Matches: 782, Mismatches: 109, Indels: 132
0.76 0.11 0.13
Matches are distributed among these distances:
126 1 0.00
127 43 0.05
128 6 0.01
129 10 0.01
130 35 0.04
131 3 0.00
132 25 0.03
133 75 0.10
137 1 0.00
138 163 0.21
139 113 0.14
140 13 0.02
141 6 0.01
142 17 0.02
143 14 0.02
144 242 0.31
145 15 0.02
ACGTcount: A:0.41, C:0.25, G:0.02, T:0.32
Consensus pattern (144 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAATTTAATTTAATTAAAAACCCTAACCTAA
TTTAGTTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACCTATTTTAATT
TAATTAAAAACCCT
Found at i:40517670 original size:23 final size:23
Alignment explanation
Indices: 40517644--40517814 Score: 90
Period size: 23 Copynumber: 6.4 Consensus size: 23
40517634 TAAAATCCCT
40517644 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
40517667 AACCCTAACCTAATTTAATTTAATTAAA
1 AACCCTAACC-----TAATTTAATTAAA
*
40517695 AACCCTAACCCTAACCTATTTTACATGAAAA
1 AACCCTAA-CCT-A---A-TTTA-AT-TAAA
*
40517726 CCCTAACCCTAACCTATTTTAATTAAAA
1 ----AACCCTAACCTAATTTAATT-AAA
40517754 TCCCTAACCCTAACCTAATTTAATTAAA
1 -----AACCCTAACCTAATTTAATTAAA
* * *
40517782 AACTCGAACCTAATTTAGTTAAA
1 AACCCTAACCTAATTTAATTAAA
40517805 AACCCTAACC
1 AACCCTAACC
40517815 CTAACCTATT
Statistics
Matches: 120, Mismatches: 9, Indels: 38
0.72 0.05 0.23
Matches are distributed among these distances:
23 38 0.32
24 1 0.01
25 1 0.01
28 30 0.25
29 33 0.28
30 2 0.02
31 3 0.03
33 1 0.01
34 3 0.03
35 8 0.07
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.30
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:40521388 original size:125 final size:125
Alignment explanation
Indices: 40521168--40521547 Score: 649
Period size: 125 Copynumber: 3.1 Consensus size: 125
40521158 CCACGATGGC
* * * *
40521168 GCGATTTGACACTATTTGCTCAG-AAACGTC--AAAAAAATTATTTCCTACATGACCAACTGTAG
1 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAAATTATTTCTTACATGACC-ACTATAG
40521230 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
65 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
40521291 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAAATTATTTCTTACATGACCACTATAGC
1 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAAATTATTTCTTACATGACCACTATAGC
*
40521356 GAAATCGCGTCCACAAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
40521416 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAAATTATTTCTTACATGACCACTATAGC
1 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAAATTATTTCTTACATGACCACTATAGC
* * **
40521481 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
66 GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
40521541 GCGATTT
1 GCGATTT
40521548 CCCACTATTT
Statistics
Matches: 244, Mismatches: 10, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
123 21 0.09
124 7 0.03
125 193 0.79
126 23 0.09
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (125 bp):
GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAAATTATTTCTTACATGACCACTATAGC
GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
Found at i:40526815 original size:21 final size:22
Alignment explanation
Indices: 40526789--40526832 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
40526779 CAGAAATGTT
40526789 ATAAACTAAAAGA-AAT-ATAGA
1 ATAAAC-AAAAGAGAATAATAGA
*
40526810 ATAAACAAGAGAGAATAATAGA
1 ATAAACAAAAGAGAATAATAGA
40526832 A
1 A
40526833 AAATGGAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.66, C:0.05, G:0.14, T:0.16
Consensus pattern (22 bp):
ATAAACAAAAGAGAATAATAGA
Found at i:40528743 original size:37 final size:37
Alignment explanation
Indices: 40528673--40528818 Score: 224
Period size: 37 Copynumber: 4.0 Consensus size: 37
40528663 TACGTATGAT
* * *
40528673 CACTTATCAC-TTG-TCCCTGATCAGATAAATGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
40528708 CACCTATCACTTTGTTTCTTGATCACATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
40528745 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
40528782 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
40528819 TAAAGCTATC
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 89 0.88
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:40528883 original size:53 final size:53
Alignment explanation
Indices: 40528782--40529095 Score: 369
Period size: 46 Copynumber: 6.2 Consensus size: 53
40528772 TAAGTGTAGC
* * *
40528782 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG-CTAA---A--GC-TAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
40528828 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
40528881 CACTTTTCAC-TTGTCACTTGATCA-ATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
40528932 CACTT-TCCAC-TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
1 CACTTAT-CACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
*
40528984 --C--A--A-TTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
** *
40529030 CACTTTATCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CAC-TTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
40529083 CACTTTATCACTT
1 CAC-TTATCACTT
40529096 GATCAGAAGT
Statistics
Matches: 235, Mismatches: 13, Indels: 32
0.84 0.05 0.11
Matches are distributed among these distances:
46 76 0.32
47 3 0.01
48 1 0.00
50 3 0.01
51 49 0.21
52 40 0.17
53 62 0.26
54 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (53 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:40528974 original size:149 final size:151
Alignment explanation
Indices: 40528793--40529088 Score: 515
Period size: 149 Copynumber: 2.0 Consensus size: 151
40528783 ACTTATCACT
* * *
40528793 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAATTTGTCACTTGATCAGATAA
*
40528858 GTATAGCCGAAGCTATCACTTATCACTTT-TCACTTGTCACTTGATCA-ATAAGTGTAGCCGAAG
66 GTATAGCCGAAGCTATCACTTATCACTTTATCACTTGTCACTTGATCAGATAAGTGTAGCCAAAG
*
40528921 CTATCACTTATCACTTTCCAC
131 CTACCACTTATCACTTTCCAC
*
40528942 TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCAATTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAATTTGTCACTTGATCAGATAA
*
40529007 GTATAGCCGAAGCTATCACTTATCACTTTATCACTTGTCACTTGATCAGATAAGTGTAGCTAAAG
66 GTATAGCCGAAGCTATCACTTATCACTTTATCACTTGTCACTTGATCAGATAAGTGTAGCCAAAG
40529072 CTACCACTTATCACTTT
131 CTACCACTTATCACTTT
40529089 ATCACTTGAT
Statistics
Matches: 138, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
149 90 0.65
150 18 0.13
151 30 0.22
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (151 bp):
TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAATTTGTCACTTGATCAGATAA
GTATAGCCGAAGCTATCACTTATCACTTTATCACTTGTCACTTGATCAGATAAGTGTAGCCAAAG
CTACCACTTATCACTTTCCAC
Found at i:40529040 original size:15 final size:15
Alignment explanation
Indices: 40529020--40529054 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40529010 TAGCCGAAGC
40529020 TATCACTTATCACTT
1 TATCACTTATCACTT
*
40529035 TATCACTTGTCACTT
1 TATCACTTATCACTT
*
40529050 GATCA
1 TATCA
40529055 GATAAGTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (15 bp):
TATCACTTATCACTT
Found at i:40529096 original size:53 final size:53
Alignment explanation
Indices: 40528974--40529096 Score: 185
Period size: 53 Copynumber: 2.3 Consensus size: 53
40528964 TAGCTGAAGC
* *
40528974 TATCAC-TTATCAATTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTATC-ACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
** *
40529027 TATCACTTTATCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTATCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
40529080 TATCACTTTATCACTTG
1 TATCACTTTATCACTTG
40529097 ATCAGAAGTA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
53 59 0.92
54 5 0.08
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (53 bp):
TATCACTTTATCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:40531594 original size:86 final size:86
Alignment explanation
Indices: 40531446--40531622 Score: 300
Period size: 86 Copynumber: 2.1 Consensus size: 86
40531436 AAATACATTG
**
40531446 AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAGTCTAGGCT
1 AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAACCTAGGCT
*
40531511 ACAGTGATAACAAATTTAACT
66 ACAGTGATAACAAACTTAACT
* *
40531532 AACTAAAGTTAGAAATGTCATTACAACCAAAGTATAGAGATTGAAAGTGTATATAAACCTAGGCT
1 AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAACCTAGGCT
*
40531597 ACAGTGATAACTAACTTAACT
66 ACAGTGATAACAAACTTAACT
40531618 AACTA
1 AACTA
40531623 TAAGAACACC
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (86 bp):
AACTAAAGTTAGAAATGTCATTACAACCAAAGTACAGAGACTGAAAGTGTATATAAACCTAGGCT
ACAGTGATAACAAACTTAACT
Found at i:40532403 original size:24 final size:23
Alignment explanation
Indices: 40532354--40532408 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
40532344 TATGATTTTC
*
40532354 TTTAATAATATTTTTTTTATAAA
1 TTTAATAATATTTTTTTAATAAA
*
40532377 TTTATATAA-ATTTTATTTAATACA
1 TTTA-ATAATATTTT-TTTAATAAA
*
40532401 TTTGATAA
1 TTTAATAA
40532409 CTTTTAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAATAATATTTTTTTAATAAA
Found at i:40532470 original size:21 final size:22
Alignment explanation
Indices: 40532410--40532470 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 22
40532400 ATTTGATAAC
40532410 TTTTA-AAGAATTT-TAATATGT
1 TTTTATAA-AATTTATAATATGT
*
40532431 TTTTATAAAATTTAAAATATG-
1 TTTTATAAAATTTATAATATGT
* *
40532452 TTTTATTAATTTTATAATA
1 TTTTATAAAATTTATAATA
40532471 ATTTATTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 26 0.76
22 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTTATAAAATTTATAATATGT
Found at i:40535643 original size:14 final size:14
Alignment explanation
Indices: 40535624--40535654 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40535614 AGCGACGATT
40535624 AAACCACTGTTTGC
1 AAACCACTGTTTGC
40535638 AAACCACTGTTTGC
1 AAACCACTGTTTGC
40535652 AAA
1 AAA
40535655 ACATAAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (14 bp):
AAACCACTGTTTGC
Found at i:40542909 original size:24 final size:25
Alignment explanation
Indices: 40542882--40542928 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
40542872 CAAAATTTTA
*
40542882 AAATTTAAAAAATA-AAAAAAAATT
1 AAATTCAAAAAATACAAAAAAAATT
* *
40542906 AAATTCCAAATATACAAAAAAAA
1 AAATTCAAAAAATACAAAAAAAA
40542929 ATAGAGGACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.21
Consensus pattern (25 bp):
AAATTCAAAAAATACAAAAAAAATT
Found at i:40558932 original size:26 final size:26
Alignment explanation
Indices: 40558896--40558949 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
40558886 GACCTAAGTA
40558896 TACACATTAATCTCTGCATTACTTCT
1 TACACATTAATCTCTGCATTACTTCT
40558922 TACACATTAATCTCTGCATTACTTCT
1 TACACATTAATCTCTGCATTACTTCT
40558948 TA
1 TA
40558950 AGAAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.43
Consensus pattern (26 bp):
TACACATTAATCTCTGCATTACTTCT
Found at i:40563369 original size:3 final size:3
Alignment explanation
Indices: 40563361--40563406 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
40563351 CTTGTTTTTC
40563361 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40563407 CTAGGGAGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40568595 original size:25 final size:25
Alignment explanation
Indices: 40568561--40568666 Score: 81
Period size: 25 Copynumber: 4.3 Consensus size: 25
40568551 AGCTCTCTCT
*
40568561 CGAGCTATATAACAGGAAGCTCATG
1 CGAGCCATATAACAGGAAGCTCATG
* ** *
40568586 TGAGCCATATAATGGGAAGCTTAT-
1 CGAGCCATATAACAGGAAGCTCATG
* * * * *
40568610 CCAGGCTATATAACGGGAAACTCATA
1 CGA-GCCATATAACAGGAAGCTCATG
* *
40568636 AGAGCCATA-ATCAGGAAGCTCATG
1 CGAGCCATATAACAGGAAGCTCATG
40568660 CGAGCCA
1 CGAGCCA
40568667 ATACTCGGGT
Statistics
Matches: 60, Mismatches: 19, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
24 18 0.30
25 41 0.68
26 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGCTCATG
Found at i:40568634 original size:50 final size:53
Alignment explanation
Indices: 40568528--40568656 Score: 137
Period size: 50 Copynumber: 2.5 Consensus size: 53
40568518 TTTGGGAGTG
* * *
40568528 CTCATTAGA-CCATATAATCGGGAAGCTCTCTCTCGAGCTATATAACAGGAAG
1 CTCATAAGAGCCATATAATCGGGAAGCTCTATCTCGAGCTATATAACAGGAAA
** *
40568580 CTCATGTGAGCCATATAAT-GGGAAGCT-TATC-C-AGGCTATATAACGGGAAA
1 CTCATAAGAGCCATATAATCGGGAAGCTCTATCTCGA-GCTATATAACAGGAAA
*
40568630 CTCATAAGAGCC--ATAATCAGGAAGCTC
1 CTCATAAGAGCCATATAATCGGGAAGCTC
40568657 ATGCGAGCCA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
48 5 0.08
49 8 0.12
50 25 0.38
51 3 0.05
52 15 0.23
53 9 0.14
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (53 bp):
CTCATAAGAGCCATATAATCGGGAAGCTCTATCTCGAGCTATATAACAGGAAA
Found at i:40568708 original size:25 final size:25
Alignment explanation
Indices: 40568680--40568730 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
40568670 CTCGGGTAGC
40568680 TCTAAAGAGCCAT-TAATCGAGAAGT
1 TCTAAAGAGCCATAT-ATCGAGAAGT
* * *
40568705 TCTAGATAGTCATATATCGAGAAGT
1 TCTAAAGAGCCATATATCGAGAAGT
40568730 T
1 T
40568731 GAAGCGAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (25 bp):
TCTAAAGAGCCATATATCGAGAAGT
Found at i:40572940 original size:25 final size:25
Alignment explanation
Indices: 40572888--40572933 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
40572878 GTACTTTATT
40572888 TTAATAATTAAAAAAAATTAAATAA
1 TTAATAATTAAAAAAAATTAAATAA
*
40572913 TTAAT-ATTAAAAATAA-TAAAT
1 TTAATAATTAAAAAAAATTAAAT
40572934 TAAATTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TTAATAATTAAAAAAAATTAAATAA
Found at i:40579034 original size:20 final size:20
Alignment explanation
Indices: 40579009--40579048 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40578999 AATATTTTCT
*
40579009 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
40579029 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
40579049 TTATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:40579056 original size:34 final size:34
Alignment explanation
Indices: 40578997--40579062 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
40578987 CAAACAGCAG
* *
40578997 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
*
40579032 AAAACATTTTCCAG-AAATTATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
40579063 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 11 0.39
35 12 0.43
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:40579767 original size:21 final size:20
Alignment explanation
Indices: 40579743--40579786 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
40579733 ATAAATTTCC
*
40579743 TTTTAATATTCCAAAATTATA
1 TTTTAATATT-CAAAATTAAA
* *
40579764 TTTTATTATTTAAAATTAAA
1 TTTTAATATTCAAAATTAAA
40579784 TTT
1 TTT
40579787 ATCATGTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAATATTCAAAATTAAA
Found at i:40582019 original size:16 final size:16
Alignment explanation
Indices: 40582000--40582031 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40581990 ATACAAATCT
40582000 AAAAATTAAAAGAATA
1 AAAAATTAAAAGAATA
*
40582016 AAAAATTAAAATAATA
1 AAAAATTAAAAGAATA
40582032 TATTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (16 bp):
AAAAATTAAAAGAATA
Found at i:40584174 original size:19 final size:21
Alignment explanation
Indices: 40584123--40584175 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
40584113 TTTAATAGAA
*
40584123 TCAAGTGAAATGAAATTTGAGT
1 TCAAGTCAAAT-AAATTTGAGT
*
40584145 T-AAGTCGAATAAATTT-A-T
1 TCAAGTCAAATAAATTTGAGT
40584163 TCAAGTCAAATAA
1 TCAAGTCAAATAA
40584176 TTTCTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
20 6 0.22
21 7 0.26
22 1 0.04
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (21 bp):
TCAAGTCAAATAAATTTGAGT
Found at i:40593070 original size:103 final size:102
Alignment explanation
Indices: 40592858--40593061 Score: 272
Period size: 103 Copynumber: 2.0 Consensus size: 102
40592848 TTAATTCATC
*
40592858 TTTTTAATTAATAACTCTTTTACTTATATAAATAAAATAATAAACATGTAATTATAAAATAAAAA
1 TTTTTAATTAATAACTCTTTTACTTATACAAATAAAATAATAAACATGTAATTATAAAATAAAAA
* *
40592923 TATATATTTTTATGTATATACTATTATTTTAAAAATAT
66 TATATATTTATATGTATATA-TATTATGTTAAAAATAT
* * ** * * *
40592961 TTTTTAATTAATAACTCTTTTATTTATACAAATAAATTAATAAATTTTTAATTTTATAATAAAAA
1 TTTTTAATTAATAACTCTTTTACTTATACAAATAAAATAATAAACATGTAATTATAAAATAAAAA
*
40593026 TATAT-TTTATAT-T-TAT-TATTATGTTAAATATAT
66 TATATATTTATATGTATATATATTATGTTAAAAATAT
40593059 TTT
1 TTT
40593062 ATTTTTTAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
98 18 0.20
100 3 0.03
101 1 0.01
102 6 0.07
103 62 0.69
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (102 bp):
TTTTTAATTAATAACTCTTTTACTTATACAAATAAAATAATAAACATGTAATTATAAAATAAAAA
TATATATTTATATGTATATATATTATGTTAAAAATAT
Found at i:40593430 original size:72 final size:73
Alignment explanation
Indices: 40593354--40593514 Score: 202
Period size: 72 Copynumber: 2.2 Consensus size: 73
40593344 TATATTTATT
* * * * * *
40593354 AAAAATAATGATATTTGAAATAATTAATTGATTTTCTAATATTATAATTTATCATACTCACAATG
1 AAAAATAATGATATTTGAAATAATTAATTGATTTTATAATATTAAAAATCACCATACCCACAATG
40593419 TAGGT-GA
66 TAGGTGGA
** * *
40593426 AAAAATAATGATATTAAAAATAATTATTTGATTTTATAATATTAAAAATCACCATACCCGCAATG
1 AAAAATAATGATATTTGAAATAATTAATTGATTTTATAATATTAAAAATCACCATACCCACAATG
40593491 TAGGTGGA
66 TAGGTGGA
*
40593499 GAAAATAA--ATATTTGA
1 AAAAATAATGATATTTGA
40593515 CATATAAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
71 6 0.08
72 60 0.80
73 9 0.12
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (73 bp):
AAAAATAATGATATTTGAAATAATTAATTGATTTTATAATATTAAAAATCACCATACCCACAATG
TAGGTGGA
Found at i:40593740 original size:17 final size:17
Alignment explanation
Indices: 40593707--40593788 Score: 58
Period size: 17 Copynumber: 4.6 Consensus size: 17
40593697 ATTATTATTT
*
40593707 TATTTATATAAAT-AAAA
1 TATTTAT-TAATTAAAAA
40593724 TATTTATTAATTAAAAA
1 TATTTATTAATTAAAAA
* ** *
40593741 GATGAATTAAAATAAAAAA
1 TATTTATT--AATTAAAAA
40593760 TATGTTTATTAATTAAAAA
1 TA--TTTATTAATTAAAAA
*
40593779 TATTAATTAA
1 TATTTATTAA
40593789 AAATTTTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
16 4 0.08
17 23 0.46
19 19 0.38
21 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (17 bp):
TATTTATTAATTAAAAA
Found at i:40593754 original size:34 final size:36
Alignment explanation
Indices: 40593716--40593790 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 36
40593706 TTATTTATAT
40593716 AAAT-AAAATA-TTTATTAATTAAAAAGATGAATTA
1 AAATAAAAATAGTTTATTAATTAAAAAGATGAATTA
* *
40593750 AAATAAAAAATATGTTTATTAATTAAAAATATTAATTA
1 AAAT-AAAAATA-GTTTATTAATTAAAAAGATGAATTA
40593788 AAA
1 AAA
40593791 ATTTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 4 0.11
36 6 0.17
38 25 0.71
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (36 bp):
AAATAAAAATAGTTTATTAATTAAAAAGATGAATTA
Found at i:40593777 original size:19 final size:20
Alignment explanation
Indices: 40593725--40593781 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
40593715 TAAATAAAAT
*
40593725 ATTTATTAATTAAAAAGATG
1 ATTTATTAATTAAAAATATG
* * *
40593745 AATTA-AAATAAAAAATATG
1 ATTTATTAATTAAAAATATG
40593764 -TTTATTAATTAAAAATAT
1 ATTTATTAATTAAAAATAT
40593782 TAATTAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 3 0.10
19 22 0.76
20 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
ATTTATTAATTAAAAATATG
Found at i:40593784 original size:13 final size:13
Alignment explanation
Indices: 40593766--40593797 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40593756 AAAATATGTT
40593766 TATTAATTAAAAA
1 TATTAATTAAAAA
40593779 TATTAATTAAAAA
1 TATTAATTAAAAA
*
40593792 TTTTAA
1 TATTAA
40593798 AAAAAGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATTAATTAAAAA
Done.