Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 10 of 29
Found at i:1366608 original size:199 final size:195
Alignment explanation
Indices: 1366386--1366755 Score: 587
Period size: 199 Copynumber: 1.9 Consensus size: 195
1366376 CATTAAGGCT
** * *
1366386 TTCATTCTTTTCCTTTTATATTTCACTCTCTTTATTATACTACAATATTAACGTTATCATCCTAA
1 TTCATTCTTTTCCTTCCATATTTCACTCTCTTTATCATACTACAATATTAACATTATCATCCTAA
* * * *
1366451 TTTATATATTAAATATATTTACGAGTTAAATTTTAATATGATCAAATTTAATATTTTTATTAAAA
66 TTTATACATGAAATATATTCACGACTTAAATTTTAATATGATCAAATTTAATATTTTTATTAAAA
1366516 TTTTTTTAAATATCAAATAAATTTTTAAATTTAAATTTAATAAATTGACTCCTAGACAAATCCAT
131 --TTTTT-AATATCAAATAAATTTTTAAATTTAAATTTAATAAATTGACTCCTAGACAAATCCAT
1366581 ATA
193 ATA
*
1366584 TTCATTCTTTTTCCTTCCATATTTCACTCTTTTTATCATACTACAATATTAACATTATCATCCTA
1 TTCATTC-TTTTCCTTCCATATTTCACTCTCTTTATCATACTACAATATTAACATTATCATCCTA
* * *
1366649 ATTTATACATGAGATATATTCACTACTTAAATTTTAATATGATCAAATTTGATATTTTTATTAAA
65 ATTTATACATGAAATATATTCACGACTTAAATTTTAATATGATCAAATTTAATATTTTTATTAAA
*
1366714 ATTTTTAATATCAATTAAATTTTTAAATTTAAATTTAATAAA
130 ATTTTTAATATCAAATAAATTTTTAAATTTAAATTTAATAAA
1366756 AATAAATCTT
Statistics
Matches: 158, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
196 35 0.22
197 5 0.03
198 7 0.04
199 111 0.70
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (195 bp):
TTCATTCTTTTCCTTCCATATTTCACTCTCTTTATCATACTACAATATTAACATTATCATCCTAA
TTTATACATGAAATATATTCACGACTTAAATTTTAATATGATCAAATTTAATATTTTTATTAAAA
TTTTTAATATCAAATAAATTTTTAAATTTAAATTTAATAAATTGACTCCTAGACAAATCCATATA
Found at i:1366747 original size:14 final size:14
Alignment explanation
Indices: 1366728--1366778 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1366718 TTAATATCAA
1366728 TTAAATTTTTAAAT
1 TTAAATTTTTAAAT
* *
1366742 TTAAATTTAATAAAA
1 TTAAATTT-TTAAAT
* *
1366757 ATAAATCTTTAAAT
1 TTAAATTTTTAAAT
1366771 TTAAATTT
1 TTAAATTT
1366779 AATAAATTGA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAAATTTTTAAAT
Found at i:1366762 original size:29 final size:29
Alignment explanation
Indices: 1366729--1366784 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1366719 TAATATCAAT
*
1366729 TAAATTTTTAAATTTAAATTTAATAAAAA
1 TAAATCTTTAAATTTAAATTTAATAAAAA
1366758 TAAATCTTTAAATTTAAATTTAATAAA
1 TAAATCTTTAAATTTAAATTTAATAAA
1366785 TTGACTCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAATCTTTAAATTTAAATTTAATAAAAA
Found at i:1371234 original size:21 final size:22
Alignment explanation
Indices: 1371194--1371234 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1371184 GAAAGAGGTA
*
1371194 TGATACATTCAATTATATTTAT
1 TGATACATTCAATCATATTTAT
*
1371216 TGATTCATT-AATCATATTT
1 TGATACATTCAATCATATTT
1371235 GTATTTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (22 bp):
TGATACATTCAATCATATTTAT
Found at i:1371985 original size:17 final size:20
Alignment explanation
Indices: 1371942--1371985 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 20
1371932 TGATTAATTT
1371942 TAATAATTATAAATAATAAA
1 TAATAATTATAAATAATAAA
*
1371962 TAA-AATTA-AAAT-CTAAA
1 TAATAATTATAAATAATAAA
1371979 -AATAATT
1 TAATAATT
1371986 TCGATCGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 2 0.09
17 8 0.36
18 4 0.18
19 5 0.23
20 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
TAATAATTATAAATAATAAA
Found at i:1372095 original size:8 final size:8
Alignment explanation
Indices: 1372082--1372116 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
1372072 GATTCTTGCT
1372082 TATTTATA
1 TATTTATA
1372090 TATTTATA
1 TATTTATA
1372098 TATATATATA
1 TAT-T-TATA
1372108 TATTTATA
1 TATTTATA
1372116 T
1 T
1372117 TAACTCACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.64
9 2 0.08
10 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTTATA
Found at i:1372210 original size:22 final size:22
Alignment explanation
Indices: 1372184--1372226 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1372174 TATAAAAAAA
* * *
1372184 TATAAATATATTAACATTTAAT
1 TATAAAAATATAAAAATTTAAT
1372206 TATAAAAATATAAAAATTTAA
1 TATAAAAATATAAAAATTTAA
1372227 ATGAATATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TATAAAAATATAAAAATTTAAT
Found at i:1373195 original size:16 final size:18
Alignment explanation
Indices: 1373149--1373197 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
1373139 GTAATTCGAT
1373149 TTGATATATAAATTAAAA
1 TTGATATATAAATTAAAA
* *
1373167 TTGATA-ATTAATT-CAA
1 TTGATATATAAATTAAAA
1373183 TTGATATA-AAATTAA
1 TTGATATATAAATTAA
1373198 TAAAGAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
16 12 0.48
17 7 0.28
18 6 0.24
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (18 bp):
TTGATATATAAATTAAAA
Found at i:1373365 original size:22 final size:21
Alignment explanation
Indices: 1373325--1373367 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1373315 TATATATAAA
1373325 AAATTATTAAATCGATCAATT
1 AAATTATTAAATCGATCAATT
* *
1373346 AAATTAATTGAATGGATCAATT
1 AAATT-ATTAAATCGATCAATT
1373368 CAAACTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (21 bp):
AAATTATTAAATCGATCAATT
Found at i:1373766 original size:19 final size:19
Alignment explanation
Indices: 1373744--1373796 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
1373734 AAATTAAAAA
1373744 ATAATTATAATATAATATT
1 ATAATTATAATATAATATT
*
1373763 ATAATTATAATAT-TTATT
1 ATAATTATAATATAATATT
1373781 ATTAATTATAAT-TAAT
1 A-TAATTATAATATAAT
1373797 TATAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 6 0.20
19 24 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATTATAATATAATATT
Found at i:1373794 original size:10 final size:10
Alignment explanation
Indices: 1373745--1373802 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 10
1373735 AATTAAAAAA
1373745 TAATTATAAT
1 TAATTATAAT
*
1373755 ATAA-TATTA-
1 -TAATTATAAT
1373764 TAATTATAA-
1 TAATTATAAT
* *
1373773 TATTTATTAT
1 TAATTATAAT
1373783 TAATTATAAT
1 TAATTATAAT
1373793 TAATTATAAT
1 TAATTATAAT
1373803 AATATTTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 3 0.08
9 11 0.28
10 22 0.56
11 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAATTATAAT
Found at i:1373805 original size:19 final size:19
Alignment explanation
Indices: 1373743--1373805 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
1373733 AAAATTAAAA
1373743 AATAATTATAATATAA-TAT
1 AATAATTATAAT-TAATTAT
* *
1373762 TATAATTATAA-TATTTATT
1 AATAATTATAATTAATTA-T
*
1373781 ATTAATTATAATTAATTAT
1 AATAATTATAATTAATTAT
1373800 AATAAT
1 AATAAT
1373806 ATTTATTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 26 0.74
20 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATAATTATAATTAATTAT
Found at i:1373808 original size:25 final size:24
Alignment explanation
Indices: 1373745--1373815 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
1373735 AATTAAAAAA
*
1373745 TAATTATAAT-ATAATATTATAAT
1 TAATTATAATAATATTATTATAAT
* * *
1373768 T-ATAATATTTATTATTAATTATAAT
1 TAATTATA-ATAATATT-ATTATAAT
1373793 TAATTATAATAATATTTATTATA
1 TAATTATAATAATA-TTATTATA
1373816 TTTTTAATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
22 5 0.14
23 2 0.06
24 3 0.08
25 19 0.53
26 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATTATAATAATATTATTATAAT
Found at i:1376272 original size:11 final size:11
Alignment explanation
Indices: 1376258--1376282 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1376248 ATAATTTTTA
1376258 AAAATTTAAAT
1 AAAATTTAAAT
1376269 AAAATTTAAAT
1 AAAATTTAAAT
1376280 AAA
1 AAA
1376283 TAAATTTTAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATTTAAAT
Found at i:1379409 original size:18 final size:19
Alignment explanation
Indices: 1379386--1379423 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1379376 AAAATTAAGT
1379386 AATATTAAT-TTAATTAAA
1 AATATTAATATTAATTAAA
**
1379404 AATATTTTTATTAATTAAA
1 AATATTAATATTAATTAAA
1379423 A
1 A
1379424 TAAAATGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATTAATATTAATTAAA
Found at i:1380437 original size:20 final size:20
Alignment explanation
Indices: 1380383--1380437 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
1380373 TAGGTTTTAG
1380383 AATTTTTTTTGGTTT-TAATT
1 AATTTTTTTT-GTTTGTAATT
*
1380403 -ATTTTTTTATATTTGTAATT
1 AATTTTTTT-TGTTTGTAATT
*
1380423 AATTATTTTTGTTTG
1 AATTTTTTTTGTTTG
1380438 GTAAAAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 11 0.38
20 11 0.38
21 7 0.24
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (20 bp):
AATTTTTTTTGTTTGTAATT
Found at i:1382401 original size:20 final size:21
Alignment explanation
Indices: 1382352--1382401 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
1382342 TATCTTGTTT
* *
1382352 TGTAATTATATAATATATTAA
1 TGTAATTTTTTAATATATTAA
*
1382373 T-TAAATTTTTAATATATT-A
1 TGTAATTTTTTAATATATTAA
1382392 TGTAATTTTT
1 TGTAATTTTT
1382402 ATCATATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.88
21 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TGTAATTTTTTAATATATTAA
Found at i:1385808 original size:3 final size:3
Alignment explanation
Indices: 1385800--1385828 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1385790 TTTGTGTCAG
1385800 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1385829 GGTTCAATTC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1386606 original size:22 final size:22
Alignment explanation
Indices: 1386581--1386623 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1386571 ATTTTAAAAA
1386581 ATATTTTTAT-ATTAATAATTAT
1 ATATTTTTATAATTAA-AATTAT
1386603 ATATTTTTATAATTAAAATTA
1 ATATTTTTATAATTAAAATTA
1386624 AATAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATATTTTTATAATTAAAATTAT
Found at i:1388712 original size:15 final size:15
Alignment explanation
Indices: 1388692--1388741 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
1388682 AATAAAAAAA
1388692 TAAAAATAAAATATT
1 TAAAAATAAAATATT
1388707 TAAAAATAAAATAATT
1 TAAAAATAAAAT-ATT
*
1388723 CAAAAA-AATTAATATT
1 TAAAAATAA--AATATT
1388739 TAA
1 TAA
1388742 TCTAACACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 14 0.47
16 13 0.43
17 3 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAATAAAATATT
Found at i:1389118 original size:25 final size:24
Alignment explanation
Indices: 1389084--1389135 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
1389074 TTTTTTATTT
1389084 TATTTTAAAATTATATTT-A-TATAA
1 TATTTTAAAA-TAT-TTTAACTATAA
1389108 TATTTATAAAATATTTTAACTATAA
1 TATTT-TAAAATATTTTAACTATAA
1389133 TAT
1 TAT
1389136 ATCACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.12
24 9 0.36
25 13 0.52
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTTAAAATATTTTAACTATAA
Found at i:1389150 original size:19 final size:18
Alignment explanation
Indices: 1389122--1389165 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1389112 TATAAAATAT
*
1389122 TTTAACTATAATATATCAC
1 TTTAATTATAATATAT-AC
* *
1389141 TTTAATTATATTATATAT
1 TTTAATTATAATATATAC
1389159 TTTAATT
1 TTTAATT
1389166 TTTTTATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTAATTATAATATATAC
Found at i:1389945 original size:17 final size:17
Alignment explanation
Indices: 1389907--1389948 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1389897 TAATTTTTAA
*
1389907 AAAAATAAT-ATTTATG
1 AAAAATTATGATTTATG
1389923 AAAAATTATGATTTATG
1 AAAAATTATGATTTATG
*
1389940 AGAAATTAT
1 AAAAATTAT
1389949 CTAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (17 bp):
AAAAATTATGATTTATG
Found at i:1390843 original size:15 final size:14
Alignment explanation
Indices: 1390825--1390876 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
1390815 TTTAACATAT
1390825 TTTTATTTATATAAA
1 TTTTA-TTATATAAA
*
1390840 TTTTAATATATTAATAA
1 TTTTATTATA-T-A-AA
1390857 TTTGTATTATATAAA
1 TTT-TATTATATAAA
1390872 TTTTA
1 TTTTA
1390877 GAATATGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 6 0.19
15 11 0.35
16 2 0.06
17 6 0.19
18 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TTTTATTATATAAA
Found at i:1392740 original size:14 final size:13
Alignment explanation
Indices: 1392723--1392759 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
1392713 AATTTAATTA
1392723 ATTTATATAATAAT
1 ATTTA-ATAATAAT
1392737 ATTTAATAAATAAT
1 ATTTAAT-AATAAT
1392751 ATTTAATAA
1 ATTTAATAA
1392760 ATTTAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTAATAATAAT
Found at i:1392740 original size:23 final size:23
Alignment explanation
Indices: 1392711--1392765 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1392701 TTAATTAAAT
* *
1392711 TAAATTTAATTAAT-TTATATAA
1 TAAATTTAATAAATAATATATAA
*
1392733 TAATATTTAATAAATAATATTTAA
1 TAA-ATTTAATAAATAATATATAA
1392757 TAAATTTAA
1 TAAATTTAA
1392766 AGTTAAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 16 0.57
24 9 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATTTAATAAATAATATATAA
Found at i:1392760 original size:14 final size:14
Alignment explanation
Indices: 1392731--1392761 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1392721 TAATTTATAT
1392731 AATAATATTTAATA
1 AATAATATTTAATA
1392745 AATAATATTTAATA
1 AATAATATTTAATA
1392759 AAT
1 AAT
1392762 TTAAAGTTAA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATAATATTTAATA
Found at i:1393026 original size:18 final size:18
Alignment explanation
Indices: 1393000--1393038 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1392990 AATTTACTTA
1393000 AAAAAATTAAAATAAAAT
1 AAAAAATTAAAATAAAAT
* *
1393018 AAAATATTAAAATAATAT
1 AAAAAATTAAAATAAAAT
1393036 AAA
1 AAA
1393039 CACAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAAATTAAAATAAAAT
Found at i:1393087 original size:22 final size:20
Alignment explanation
Indices: 1393040--1393094 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
1393030 TAATATAAAC
* *
1393040 ACAATATATATAAATATATT
1 ACAATTTATATAAATACATT
*
1393060 AAAATTTATATAACATACATT
1 ACAATTTATATAA-ATACATT
1393081 ATCAATTTAT-TAAA
1 A-CAATTTATATAAA
1393095 ATTTATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.41
21 10 0.34
22 7 0.24
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
ACAATTTATATAAATACATT
Found at i:1397518 original size:14 final size:13
Alignment explanation
Indices: 1397495--1397528 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
1397485 TTTAGGTTAA
1397495 AAATTTTAAATTT
1 AAATTTTAAATTT
1397508 AAATTTATAAATTT
1 AAATTT-TAAATTT
1397522 AAATTTT
1 AAATTTT
1397529 TTGTTTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AAATTTTAAATTT
Found at i:1397792 original size:21 final size:20
Alignment explanation
Indices: 1397725--1397803 Score: 72
Period size: 22 Copynumber: 3.8 Consensus size: 20
1397715 ATCGAAACAA
1397725 AAAATTTTAAATTCCTAAATCT
1 AAAATTTTAAATT--TAAATCT
* * *
1397747 AAACATTATAACTTTAAAATAT
1 AAA-ATTTTAAATTT-AAATCT
1397769 AAAATTTTAAAATTTAAATCT
1 AAAATTTT-AAATTTAAATCT
1397790 -AAA-TTTAAATTTAA
1 AAAATTTTAAATTTAA
1397804 GTTTCTAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
18 8 0.17
19 3 0.06
20 3 0.06
21 10 0.21
22 16 0.33
23 8 0.17
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTTTAAATTTAAATCT
Found at i:1400417 original size:20 final size:21
Alignment explanation
Indices: 1400366--1400409 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1400356 CAGAATATTG
1400366 AAAAAAA-TACAT-ATTTTTTT
1 AAAAAAACTAC-TCATTTTTTT
1400386 AAAAAAACTACTCATTTTTTT
1 AAAAAAACTACTCATTTTTTT
1400407 AAA
1 AAA
1400410 GAATTACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAAAAACTACTCATTTTTTT
Found at i:1402271 original size:32 final size:33
Alignment explanation
Indices: 1402232--1402293 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
1402222 AGATATAAAT
1402232 AAATATATTTAAA-TTTATAT-AATATAAATTTC
1 AAATATA-TTAAATTTTATATAAATATAAATTTC
*
1402264 AAATATATTAAATTTTATTTAAATATAAAT
1 AAATATATTAAATTTTATATAAATATAAAT
1402294 ATTTTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 5 0.19
32 13 0.48
33 9 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (33 bp):
AAATATATTAAATTTTATATAAATATAAATTTC
Found at i:1402277 original size:16 final size:15
Alignment explanation
Indices: 1402231--1402278 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1402221 GAGATATAAA
1402231 TAAATATATTTAAATT
1 TAAATATA-TTAAATT
*
1402247 TATATA-ATATAAATT
1 TAAATATAT-TAAATT
1402262 TCAAATATATTAAATT
1 T-AAATATATTAAATT
1402278 T
1 T
1402279 TATTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 1 0.04
15 8 0.30
16 16 0.59
17 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATATATTAAATT
Found at i:1405249 original size:124 final size:124
Alignment explanation
Indices: 1405108--1405331 Score: 324
Period size: 124 Copynumber: 1.8 Consensus size: 124
1405098 GAAACATGTA
** * * * *
1405108 ACCCATTCATTAGATTCAATCAACGCTCAATAAATACAAATATTAATTTAC-AGAAAAAAAAGTT
1 ACCCATTCATTAGATTCAATCAAAACTCAATAAA-ACAAAGATCAATTAACAAGAAAAAAAACTT
*
1405172 AAAAGTTTGAAACCCAATTATTACAATCTTATTATTTTCAAAACAGTGTGAAATACACAC
65 AAAAGTTTGAAACCCAATTATTACAATCCTATTATTTTCAAAACAGTGTGAAATACACAC
* * * *
1405232 ACCCATTCATTGGATTCAATCAAAACTCAATAAACCCAAGATCAATTAACAAGAAAAATAACTTA
1 ACCCATTCATTAGATTCAATCAAAACTCAATAAAACAAAGATCAATTAACAAGAAAAAAAACTTA
*
1405297 AAAGTTTGAAACCCGATTATTACAATCCTATTATT
66 AAAGTTTGAAACCCAATTATTACAATCCTATTATT
1405332 CTTGAAATAG
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 11 0.13
124 76 0.87
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (124 bp):
ACCCATTCATTAGATTCAATCAAAACTCAATAAAACAAAGATCAATTAACAAGAAAAAAAACTTA
AAAGTTTGAAACCCAATTATTACAATCCTATTATTTTCAAAACAGTGTGAAATACACAC
Found at i:1406352 original size:7 final size:7
Alignment explanation
Indices: 1406340--1406365 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1406330 TGAACCGCTC
1406340 AAATTTA
1 AAATTTA
1406347 AAATTTA
1 AAATTTA
1406354 AAATTTA
1 AAATTTA
1406361 AAATT
1 AAATT
1406366 CCTTTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:1406499 original size:15 final size:15
Alignment explanation
Indices: 1406479--1406542 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
1406469 CTCAAACAAA
1406479 AAATTTTAAATTTAT
1 AAATTTTAAATTTAT
* **
1406494 AAATTTGAAAAATAT
1 AAATTTTAAATTTAT
*
1406509 AAATTATAAATTT-T
1 AAATTTTAAATTTAT
* * *
1406523 AAATCTAAAATTTTT
1 AAATTTTAAATTTAT
1406538 AAATT
1 AAATT
1406543 CAAATCTAAA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
14 11 0.30
15 26 0.70
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
AAATTTTAAATTTAT
Found at i:1407043 original size:24 final size:24
Alignment explanation
Indices: 1407015--1407063 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1407005 TTTTAAAGTA
1407015 TAATTT-TTATTTATAAAATTAATT
1 TAATTTATT-TTTATAAAATTAATT
* *
1407039 TAATTTATTTTTATTAAATTTATT
1 TAATTTATTTTTATAAAATTAATT
1407063 T
1 T
1407064 TTACATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TAATTTATTTTTATAAAATTAATT
Found at i:1407185 original size:36 final size:36
Alignment explanation
Indices: 1407136--1407275 Score: 122
Period size: 39 Copynumber: 3.7 Consensus size: 36
1407126 AAGAAAAAAT
*
1407136 TTATTGTACATGTATTATTTTTATTAAAATTAATTA
1 TTATTGTATATGTATTATTTTTATTAAAATTAATTA
*
1407172 TTATTGCGTATGTAT-TATTACTTTTTATTTATAAATTATTTA
1 TTATT--GTA--TATGTATTA-TTTTTA-TTA-AAATTAATTA
* **
1407214 TAATT-TATTTATAAATTTATTTTTATTAAAATTAATTA
1 TTATTGTA--TATGTA-TTATTTTTATTAAAATTAATTA
*
1407252 ATATTGTATATGTATTATTTTTAT
1 TTATTGTATATGTATTATTTTTAT
1407276 AATTGATAGA
Statistics
Matches: 84, Mismatches: 10, Indels: 20
0.74 0.09 0.18
Matches are distributed among these distances:
36 15 0.18
37 4 0.05
38 15 0.18
39 16 0.19
40 15 0.18
41 6 0.07
42 13 0.15
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (36 bp):
TTATTGTATATGTATTATTTTTATTAAAATTAATTA
Found at i:1407212 original size:11 final size:11
Alignment explanation
Indices: 1407196--1407235 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
1407186 TTATTACTTT
1407196 TTATTTATAAA
1 TTATTTATAAA
*
1407207 TTATTTATAAT
1 TTATTTATAAA
1407218 TTATTTATAAA
1 TTATTTATAAA
1407229 TTTATTT
1 -TTATTT
1407236 TTATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 20 0.77
12 6 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:1407405 original size:289 final size:292
Alignment explanation
Indices: 1407070--1407717 Score: 1013
Period size: 296 Copynumber: 2.2 Consensus size: 292
1407060 ATTTTTACAT
*
1407070 ATTTTATTTTTCGGTAATGACTTAAATACGAGCTTTTCTTTATCTGTAAAATGACCAAGAAAAAA
1 ATTTTATTTTTCGGTAACGACTTAAATACGAGCTTTTCTTTATCTGTAAAATGACCAAGAAAAAA
* *
1407135 TTTATTGTACATGTATTATTTTTATTAAAATTAATTATTATTGCGTATGTATTATTACTTTTTAT
66 TTTATTGTACATGTATTATTTTTATTAAAATTAATTAATATTGCGCATGTATTATTAC--TTT-T
*
1407200 TTATAAATTA-TTT-A-TAATTTAT-TTAT-AAATTTATTTTTATTAAAATTAATTAATATTGTA
128 TTATAAATTATTTTAATTAATTTATATTATAAAATTTATTTTTATTAAAATTAATTAATATTCTA
**
1407260 TATGTATTATTTTTATAATTGATAG-ACTTAAATTTATGTTAGTCAACAATATTTTACCTTTTTT
193 TATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGTCAACAATAAATTACCTTTTTT
* * **
1407324 CGATAATGATTTATTTCGGATTTATAGATGCACAC
258 CGATAATGACTTATTTCGGATTTACAGACACACAC
* *
1407359 ATTTTATTTTTCGGTAACGACTTAAATACGAGCTTTTCTATATCTGTAAAATAACCAAGAAAAAA
1 ATTTTATTTTTCGGTAACGACTTAAATACGAGCTTTTCTTTATCTGTAAAATGACCAAGAAAAAA
* *
1407424 TTTATTGTATATGTATTATTTTTATTAAAATTAATTAATATTGTGCATGTATTATTACTTTTTTA
66 TTTATTGTACATGTATTATTTTTATTAAAATTAATTAATATTGCGCATGTATTATTACTTTTTTA
*
1407489 TAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTCT
131 TAAATTA-TTTTAATTAATTTAT--ATTATA-AAATTTATTTTTATTAAAATTAATTAATATTCT
* *
1407554 ATATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGTCAATAATAAATTACTTTTTT
192 ATATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGTCAACAATAAATTACCTTTTT
1407619 TCGATAATGACTTATTTCGGATTTACAGACACACAC
257 TCGATAATGACTTATTTCGGATTTACAGACACACAC
*
1407655 ATTTTATTTTTCGGTAACGACTTAAATACGAG-TTTTCTTTTATTTGTAAAATGACCAAGAAAA
1 ATTTTATTTTTCGGTAACGACTTAAATACGAGCTTTTC-TTTATCTGTAAAATGACCAAGAAAA
1407718 TTTTTTTCTC
Statistics
Matches: 328, Mismatches: 20, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
286 11 0.03
287 3 0.01
288 3 0.01
289 117 0.36
290 7 0.02
293 4 0.01
295 63 0.19
296 120 0.37
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (292 bp):
ATTTTATTTTTCGGTAACGACTTAAATACGAGCTTTTCTTTATCTGTAAAATGACCAAGAAAAAA
TTTATTGTACATGTATTATTTTTATTAAAATTAATTAATATTGCGCATGTATTATTACTTTTTTA
TAAATTATTTTAATTAATTTATATTATAAAATTTATTTTTATTAAAATTAATTAATATTCTATAT
GTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGTCAACAATAAATTACCTTTTTTCGA
TAATGACTTATTTCGGATTTACAGACACACAC
Found at i:1407518 original size:11 final size:11
Alignment explanation
Indices: 1407485--1407518 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1407475 TTATTACTTT
1407485 TTTATAAATTA
1 TTTATAAATTA
* *
1407496 TTTTTAATTTA
1 TTTATAAATTA
1407507 TTTATAAATTA
1 TTTATAAATTA
1407518 T
1 T
1407519 ACAAATTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTATAAATTA
Found at i:1411812 original size:182 final size:181
Alignment explanation
Indices: 1411433--1412272 Score: 980
Period size: 182 Copynumber: 4.7 Consensus size: 181
1411423 TAGTCTAACG
*
1411433 AAAAGAATCTGATTCTCAGATATAATTCATGCATTATTCTAA-TCTTTGCAGTCTAACATTTACA
1 AAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATTC-TTGCAGTCTAACATTTACA
* ** * * *
1411497 ATCAATCATTCTTTCTTTTTTTAATATAAAAAAGAATCTGATTTTCAGATATAATTCATGCGTTA
65 ATCAATCAGTCTTTCTTTTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAATTAATGCATTA
* * * * * * * *
1411562 GTTTAA-TCTTTGTAGTTTGATATTTACATTTAGTCAAC-TTTTTTTTCTATTA
130 GTCTAATTC-TTGCAGTCTGACATTTACAATCAATCAACTTTTTTTTTCCA-TA
* * * *
1411614 AAAAAAATCCGATTCTCAGATATAATTCGTGCATTAGTCTAATTCTTGCAGTCTGACATTTACAA
1 AAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATTCTTGCAGTCTAACATTTACAA
* ** *
1411679 TTAATTGGTCTTTCTTTTTTTTTTATATAAAAAGAATCTGATTCTTAGATATAATTAATGCATTA
66 TCAATCAGTCTTTCTTTTTTTTTTATA-AAAAAGAATCTGATTCTCAGATATAATTAATGCATTA
*
1411744 GTCTAA-TCTTTGCAGTCTGACATTTACAATCAATCAA-TTTTTTTTTCTATA
130 GTCTAATTC-TTGCAGTCTGACATTTACAATCAATCAACTTTTTTTTTCCATA
* * * *
1411795 ACAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTTTAACATTTAGA
1 A-AAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATTCTTGCAGTCTAACATTTACA
* *
1411860 ATCAATCAGTCTTTC--TTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTA
65 ATCAATCAGTCTTTCTTTTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAATTAATGCATTA
* *
1411923 GTCTAATTCTTACAGTCTGACATTTACAATCAATTAACTTTTTTTTTCCATA
130 GTCTAATTCTTGCAGTCTGACATTTACAATCAATCAACTTTTTTTTTCCATA
* * *
1411975 AAAA-AATTTGATTATCAGATATAATTTC-TGCATTAGTCTAATCCTTGCAGTCTAACATTTACA
1 AAAAGAATCTGATTCTCAGATATAA-TTCATGCATTAGTCTAATTCTTGCAGTCTAACATTTACA
* *
1412038 ATCAATCA-ACTTTTCTTTTTTTTTTCTATAAAAAAGAAT-TCAATTCTCAGATATAATTAATGC
65 ATCAATCAGTC-TTTC-TTTTTTTTT-TATAAAAAAGAATCT-GATTCTCAGATATAATTAATGC
*
1412101 ATTAGTCTAATTCTTGCATTCTGACATTTACAATCAATCAACTTTTCTTTATTTCCATAA
126 ATTAGTCTAATTCTTGCAGTCTGACATTTACAATCAATCAAC-TTT-TTT-TTTCCAT-A
* * ** * *
1412161 AAAAGAATCTGATTCTCAGATATAATTCATGCATCAATCTAA-TCTTTATAGTTTGACATTTACA
1 AAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATTC-TTGCAGTCTAACATTTACA
* * *
1412225 ATCAATCA-----AC-TTTTTTTTAATAAAAAA-AATCTAATTCTCAGATATAAT
65 ATCAATCAGTCTTTCTTTTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAAT
1412273 CACATTTATT
Statistics
Matches: 576, Mismatches: 62, Indels: 45
0.84 0.09 0.07
Matches are distributed among these distances:
177 1 0.00
178 81 0.14
179 82 0.14
180 34 0.06
181 88 0.15
182 216 0.38
183 3 0.01
184 3 0.01
185 7 0.01
186 9 0.02
187 52 0.09
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (181 bp):
AAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATTCTTGCAGTCTAACATTTACAA
TCAATCAGTCTTTCTTTTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAATTAATGCATTAG
TCTAATTCTTGCAGTCTGACATTTACAATCAATCAACTTTTTTTTTCCATA
Found at i:1412060 original size:273 final size:268
Alignment explanation
Indices: 1411433--1412272 Score: 1013
Period size: 273 Copynumber: 3.1 Consensus size: 268
1411423 TAGTCTAACG
* *
1411433 AAAAGAATCTGATTCTCAGATATAA-TTCATGCATTATTCTAATCTTTGCAGTCTAACATTTACA
1 AAAAAAATCTGATTCTCAGATATAATTTC-TGCATTAGTCTAATCTTTGCAGTCTAACATTTACA
* * *
1411497 ATCAATC-ATTCTTTCTTTTTTTAATATAAAAAAGAATCTGATTTTCAGATATAATTCATGCGTT
65 ATCAATCAATTCTTT-TTTTTTT-CTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATT
* * * * * * *
1411561 AGTTTAATCTTTGTAGTTTGATATTTACATTTAGTCAAC-TT-TTTTTTCTATTAAAAAA-AATC
128 AGTCTAATCCTTGCAGTTTGACATTTACAATCAATCAACTTTCTTTTTTCTA-TAAAAAAGAATC
* * * *
1411623 CGATTCTCAGATATAATTCGTGCATTAGTCTAATTCTTGCAGTCTGACATTTACAATTAATTGGT
192 TGATTCTCAGATATAATTCATGCATTAGTCTAATTCTTACAGTCTGACATTTACAATCAA----T
**
1411688 CTTTCTTTTTTTTTTATAT
253 -TAAC-TTTTTTTTTA-AT
* ** *
1411707 AAAAAGAATCTGATTCTTAGATATAATTAATGCATTAGTCTAATCTTTGCAGTCTGACATTTACA
1 AAAAA-AATCTGATTCTCAGATATAATTTCTGCATTAGTCTAATCTTTGCAGTCTAACATTTACA
*
1411772 ATCAATCAA----TTTTTTTTTCTATAACAAAGAATCTGATTCTCAGATATAATTCATGCATTAG
65 ATCAATCAATTCTTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAG
* * * *
1411833 TCTAATCCTTACAGTTTAACATTTAGAATCAATCAGTCTTTCTTTTTTCTATAAAAAAGAATCTG
130 TCTAATCCTTGCAGTTTGACATTTACAATCAATCA-ACTTTCTTTTTTCTATAAAAAAGAATCTG
1411898 ATTCTCAGATATAATTCATGCATTAGTCTAATTCTTACAGTCTGACATTTACAATCAATTAACTT
194 ATTCTCAGATATAATTCATGCATTAGTCTAATTCTTACAGTCTGACATTTACAATCAATTAACTT
*
1411963 TTTTTTTCCAT
259 TTTTTTT-AAT
* * *
1411974 AAAAAAATTTGATTATCAGATATAATTTCTGCATTAGTCTAATCCTTGCAGTCTAACATTTACAA
1 AAAAAAATCTGATTCTCAGATATAATTTCTGCATTAGTCTAATCTTTGCAGTCTAACATTTACAA
* *
1412039 TCAATCAACTTTTCTTTTTTTTTTCTATAAAAAAGAAT-TCAATTCTCAGATATAATTAATGCAT
66 TCAATCAA---TTCTTTTTTTTTTCTATAAAAAAGAATCT-GATTCTCAGATATAATTCATGCAT
* *
1412103 TAGTCTAATTCTTGCA-TTCTGACATTTACAATCAATCAACTTTTCTTTATTTCCATAAAAAAGA
127 TAGTCTAATCCTTGCAGTT-TGACATTTACAATCAATCAAC-TTTCTTT-TTTCTATAAAAAAGA
* * * *
1412167 ATCTGATTCTCAGATATAATTCATGCATCAATCTAA-TCTTTATAGTTTGACATTTACAATCAAT
189 ATCTGATTCTCAGATATAATTCATGCATTAGTCTAATTC-TTACAGTCTGACATTTACAATCAAT
*
1412231 CAAC-TTTTTTTTAAT
253 TAACTTTTTTTTTAAT
*
1412246 AAAAAAAATCTAATTCTCAGATATAAT
1 -AAAAAAATCTGATTCTCAGATATAAT
1412273 CACATTTATT
Statistics
Matches: 492, Mismatches: 53, Indels: 43
0.84 0.09 0.07
Matches are distributed among these distances:
266 61 0.12
267 16 0.03
268 2 0.00
269 1 0.00
270 64 0.13
271 8 0.02
272 17 0.03
273 184 0.37
274 78 0.16
275 59 0.12
276 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (268 bp):
AAAAAAATCTGATTCTCAGATATAATTTCTGCATTAGTCTAATCTTTGCAGTCTAACATTTACAA
TCAATCAATTCTTTTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGT
CTAATCCTTGCAGTTTGACATTTACAATCAATCAACTTTCTTTTTTCTATAAAAAAGAATCTGAT
TCTCAGATATAATTCATGCATTAGTCTAATTCTTACAGTCTGACATTTACAATCAATTAACTTTT
TTTTTAAT
Found at i:1412100 original size:361 final size:362
Alignment explanation
Indices: 1411433--1412272 Score: 1112
Period size: 361 Copynumber: 2.3 Consensus size: 362
1411423 TAGTCTAACG
* * *
1411433 AAAAGAATCTGATTCTCAGATATAATTCATGCATTATTCTAATCTTTGCAGTCTAACATTTACAA
1 AAAAGAATCTGATTCTCAGATATAATTCATGCATTAATCTAATCTTTACAGTTTAACATTTACAA
* *
1411498 TCAATCATTCTTTCTTTTTTTAATATAAAAAAGAATCTGATTTTCAGATATAATTCATGCGTTAG
66 TCAATCA-TCTTTC-TTTTTT--TATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAG
* ** * * * * * *
1411563 TTTAATCTTTGTAGTTTGATATTTACATTTAGTCAACTTTTTTTTCTATTAAAAAAAATCCGATT
127 TCTAATCTTTACAGTCTGACATTTACAATCAATCAACTTTTTTTTCCATTAAAAAAAATCCGATT
* * * * ***
1411628 CTCAGATATAATTCGTGCATTAGTCTAATTCTTGCAGTCTGACATTTACAATTAATTGGTCTTTC
192 ATCAGATATAATTCGTGCATTAGTCTAATCCTTGCAGTCTAACATTTACAATCAATAACTCTTTC
* *
1411693 TTTTTTTTTTATATAAAAAGAATCTGATTCTTAGATATAATTAATGCATTAGTCTAA-TCTTTGC
257 TTTTTTTTTTATATAAAAAGAATCTAATTCTCAGATATAATTAATGCATTAGTCTAATTC-TTGC
*
1411757 AGTCTGACATTTACAATCAATCAA-TTT-TTT-TTTCTATAA
321 AGTCTGACATTTACAATCAATCAACTTTCTTTATTTCCATAA
* * * *
1411796 CAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTTTAACATTTAGAA
1 AAAAGAATCTGATTCTCAGATATAATTCATGCATTAATCTAATCTTTACAGTTTAACATTTACAA
1411861 TCAATCAGTCTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTC
66 TCAATCA-TCTTTCTTTTTT-TATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTC
* **
1411926 TAAT-TCTTACAGTCTGACATTTACAATCAATTAACTTTTTTTTTCCA-T-AAAAAAATTTGATT
129 TAATCT-TTACAGTCTGACATTTACAATCAATCAAC-TTTTTTTTCCATTAAAAAAAATCCGATT
1411988 ATCAGATATAATTTC-TGCATTAGTCTAATCCTTGCAGTCTAACATTTACAATCAATCAACT-TT
192 ATCAGATATAA-TTCGTGCATTAGTCTAATCCTTGCAGTCTAACATTTACAATCAAT-AACTCTT
*
1412051 TCTTTTTTTTTTCTATAAAAAAGAAT-TCAATTCTCAGATATAATTAATGCATTAGTCTAATTCT
255 TCTTTTTTTTTTATAT-AAAAAGAATCT-AATTCTCAGATATAATTAATGCATTAGTCTAATTCT
*
1412115 TGCATTCTGACATTTACAATCAATCAACTTTTCTTTATTTCCATAA
318 TGCAGTCTGACATTTACAATCAATCAAC-TTTCTTTATTTCCATAA
* * *
1412161 AAAAGAATCTGATTCTCAGATATAATTCATGCATCAATCTAATCTTTATAGTTTGACATTTACAA
1 AAAAGAATCTGATTCTCAGATATAATTCATGCATTAATCTAATCTTTACAGTTTAACATTTACAA
* * *
1412226 TCAATCAAC-TT-TTTTTTAATAAAAAA-AATCTAATTCTCAGATATAAT
66 TCAATCATCTTTCTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAAT
1412273 CACATTTATT
Statistics
Matches: 422, Mismatches: 44, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
360 99 0.23
361 145 0.34
362 24 0.06
363 77 0.18
364 4 0.01
365 73 0.17
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (362 bp):
AAAAGAATCTGATTCTCAGATATAATTCATGCATTAATCTAATCTTTACAGTTTAACATTTACAA
TCAATCATCTTTCTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTA
ATCTTTACAGTCTGACATTTACAATCAATCAACTTTTTTTTCCATTAAAAAAAATCCGATTATCA
GATATAATTCGTGCATTAGTCTAATCCTTGCAGTCTAACATTTACAATCAATAACTCTTTCTTTT
TTTTTTATATAAAAAGAATCTAATTCTCAGATATAATTAATGCATTAGTCTAATTCTTGCAGTCT
GACATTTACAATCAATCAACTTTCTTTATTTCCATAA
Found at i:1413807 original size:26 final size:26
Alignment explanation
Indices: 1413778--1413871 Score: 140
Period size: 26 Copynumber: 3.7 Consensus size: 26
1413768 TAAATTAATT
*
1413778 TTAATAATTAAATAACATTATCAAGA
1 TTAATAATCAAATAACATTATCAAGA
*
1413804 TTAATAATCAAATCACATTATCAAGA
1 TTAATAATCAAATAACATTATCAAGA
*
1413830 TTAATAATCAAATCACATTATCAAGA
1 TTAATAATCAAATAACATTATCAAGA
1413856 TTAAT--T-AAATAACATT
1 TTAATAATCAAATAACATT
1413872 CATATTACTT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.14
24 1 0.02
26 55 0.85
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (26 bp):
TTAATAATCAAATAACATTATCAAGA
Found at i:1413826 original size:13 final size:13
Alignment explanation
Indices: 1413787--1413853 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
1413777 TTTAATAATT
*
1413787 AAATAACATTATC
1 AAATCACATTATC
* *
1413800 AAGATTA-ATAATC
1 AA-ATCACATTATC
1413813 AAATCACATTATC
1 AAATCACATTATC
* *
1413826 AAGATTA-ATAATC
1 AA-ATCACATTATC
1413839 AAATCACATTATC
1 AAATCACATTATC
1413852 AA
1 AA
1413854 GATTAATTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
12 6 0.14
13 30 0.71
14 6 0.14
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (13 bp):
AAATCACATTATC
Found at i:1413862 original size:13 final size:13
Alignment explanation
Indices: 1413794--1413862 Score: 70
Period size: 13 Copynumber: 5.3 Consensus size: 13
1413784 ATTAAATAAC
1413794 ATTATCAAGATTA
1 ATTATCAAGATTA
* *
1413807 ATAATCAA-ATCA
1 ATTATCAAGATTA
1413819 CATTATCAAGATTA
1 -ATTATCAAGATTA
* *
1413833 ATAATCAA-ATCA
1 ATTATCAAGATTA
1413845 CATTATCAAGATTA
1 -ATTATCAAGATTA
1413859 ATTA
1 ATTA
1413863 AATAACATTC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
12 6 0.14
13 32 0.73
14 6 0.14
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.33
Consensus pattern (13 bp):
ATTATCAAGATTA
Found at i:1416022 original size:27 final size:27
Alignment explanation
Indices: 1415951--1416029 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 27
1415941 CTCTATAGAG
* *
1415951 ATAAAATT-GATAAAGTTTAATTTTAT
1 ATAAAATTATATAAAGTTTAACTTTAT
* * *
1415977 CTGAGATTGATA-AAA-TTTAACTTTAT
1 ATAAAATT-ATATAAAGTTTAACTTTAT
1416003 ATAAAATTATATAAAGTTTAACTTTAT
1 ATAAAATTATATAAAGTTTAACTTTAT
1416030 CTAGGGTTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
25 3 0.07
26 23 0.56
27 14 0.34
28 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (27 bp):
ATAAAATTATATAAAGTTTAACTTTAT
Found at i:1417873 original size:34 final size:34
Alignment explanation
Indices: 1417827--1418044 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
1417817 GTAAAAACCA
*
1417827 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1417861 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
1417895 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1417929 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1417962 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1417996 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1418029 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1418045 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1417941 original size:68 final size:67
Alignment explanation
Indices: 1417825--1418044 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
1417815 TGGTAAAAAC
* * *
1417825 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1417890 AT
66 AT
* * *
1417892 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
1417957 AAT
65 AAT
* * * * * *
1417960 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1418025 AT
66 AT
1418027 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1418045 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:1422137 original size:19 final size:19
Alignment explanation
Indices: 1422110--1422172 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1422100 TCACGTGTAC
* *
1422110 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1422129 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1422148 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1422167 AGTACC
1 AGTACC
1422173 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1422523 original size:34 final size:34
Alignment explanation
Indices: 1422477--1422692 Score: 278
Period size: 34 Copynumber: 6.4 Consensus size: 34
1422467 GTAAAAACCA
*
1422477 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1422511 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
1422545 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1422579 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1422612 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1422646 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1422679 CCATTTAATCAACA
1 CCATTTAATCAACA
1422693 GGAACCTTGG
Statistics
Matches: 160, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 43 0.27
34 115 0.72
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1422591 original size:68 final size:67
Alignment explanation
Indices: 1422475--1422692 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
1422465 TGGTAAAAAC
* * *
1422475 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1422540 AT
66 AT
* * *
1422542 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
1422607 AAT
65 AAT
* * * * * *
1422610 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1422675 AT
66 AT
1422677 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1422693 GGAACCTTGG
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:1422817 original size:13 final size:14
Alignment explanation
Indices: 1422792--1422824 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1422782 ATTCGATTTA
1422792 AAATTTAATTTAAT
1 AAATTTAATTTAAT
*
1422806 TAATTT-ATTTAAT
1 AAATTTAATTTAAT
1422819 AAATTT
1 AAATTT
1422825 TTAAAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATTTAATTTAAT
Found at i:1423163 original size:16 final size:15
Alignment explanation
Indices: 1423137--1423170 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1423127 TTAAATTTAC
*
1423137 AATAAAAATAATTAA
1 AATAAAAATAATAAA
1423152 AATAAAATATAATAAA
1 AATAAAA-ATAATAAA
1423168 AAT
1 AAT
1423171 TAATATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAAAATAATAAA
Found at i:1423163 original size:22 final size:22
Alignment explanation
Indices: 1423138--1423179 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1423128 TAAATTTACA
1423138 ATAA-AAATAATTAAAATAAAAT
1 ATAATAAA-AATTAAAATAAAAT
*
1423160 ATAATAAAAATTAATATAAA
1 ATAATAAAAATTAAAATAAA
1423180 TACGATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
ATAATAAAAATTAAAATAAAAT
Found at i:1423187 original size:26 final size:25
Alignment explanation
Indices: 1423137--1423203 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
1423127 TTAAATTTAC
1423137 AATAAAAATAATTAAAATAAAATAT
1 AATAAAAATAATTAAAATAAAATAT
**
1423162 AATAAAAATTAA-TATAAATACGATAT
1 AATAAAAA-TAATTA-AAATAAAATAT
*
1423188 -ATAAATAT-ATTAAAAT
1 AATAAAAATAATTAAAAT
1423204 TTATATAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 5 0.14
24 3 0.08
25 16 0.44
26 12 0.33
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (25 bp):
AATAAAAATAATTAAAATAAAATAT
Found at i:1423246 original size:17 final size:17
Alignment explanation
Indices: 1423194--1423246 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1423184 ATATATAAAT
*
1423194 ATATTAAAATTTA-TATA
1 ATATCAAAATTTATTA-A
1423211 ATATC--AA-TTATTAA
1 ATATCAAAATTTATTAA
1423225 TATATCAAAATTTATTAA
1 -ATATCAAAATTTATTAA
1423243 ATAT
1 ATAT
1423247 ATAATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
17 10 0.33
18 7 0.23
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATCAAAATTTATTAA
Found at i:1423257 original size:19 final size:18
Alignment explanation
Indices: 1423191--1423248 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 18
1423181 ACGATATATA
*
1423191 AATATATTAAAATTTA-T
1 AATATATCAAAATTTATT
1423208 -ATAATATC--AA-TTATT
1 AAT-ATATCAAAATTTATT
1423223 AATATATCAAAATTTATT
1 AATATATCAAAATTTATT
1423241 AAATATAT
1 -AATATAT
1423249 AATATTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
14 3 0.09
15 8 0.24
16 4 0.12
17 6 0.18
18 5 0.15
19 7 0.21
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AATATATCAAAATTTATT
Found at i:1427372 original size:22 final size:22
Alignment explanation
Indices: 1427347--1427398 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
1427337 TAAAATTTAT
1427347 AAATCTAAAAATTATT-AATGTC
1 AAATCTAAAAATTATTAAAT-TC
*
1427369 AAATCT-AAAATTTTTAAATTC
1 AAATCTAAAAATTATTAAATTC
1427390 AAATCTAAA
1 AAATCTAAA
1427399 TTTAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATCTAAAAATTATTAAATTC
Found at i:1428072 original size:26 final size:25
Alignment explanation
Indices: 1428043--1428108 Score: 91
Period size: 26 Copynumber: 2.7 Consensus size: 25
1428033 AATTAATTTT
1428043 AATAATTAAATAACATTATCAAGATC
1 AATAATTAAATAACATTATCAAGA-C
* *
1428069 AATAATCAAATTACATTATCAAGAC
1 AATAATTAAATAACATTATCAAGAC
1428094 --TAATTAAATAACATT
1 AATAATTAAATAACATT
1428109 TATATTACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 13 0.36
25 1 0.03
26 22 0.61
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (25 bp):
AATAATTAAATAACATTATCAAGAC
Found at i:1429913 original size:28 final size:30
Alignment explanation
Indices: 1429858--1429915 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
1429848 ATATTAATTC
1429858 AATTTATAAATTATAAAAAAATAAAATAAA
1 AATTTATAAATTATAAAAAAATAAAATAAA
* *
1429888 AATTTAT-AA-TATCAAATAATAAAATAAA
1 AATTTATAAATTATAAAAAAATAAAATAAA
1429916 GTATTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 17 0.65
29 2 0.08
30 7 0.27
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (30 bp):
AATTTATAAATTATAAAAAAATAAAATAAA
Found at i:1429968 original size:22 final size:21
Alignment explanation
Indices: 1429943--1430006 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 21
1429933 TTTTTACATA
1429943 ATACTTTTTTTAAAAAATTTAC
1 ATACTTTTTTTAAAAAA-TTAC
1429965 ATAC--TTTTTAAAAAATTAC
1 ATACTTTTTTTAAAAAATTAC
*
1429984 TTACTCTTTTTTAAAAAAATTAC
1 ATACT-TTTTTT-AAAAAATTAC
1430007 TTGCATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 7 0.19
20 11 0.30
22 9 0.24
23 10 0.27
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (21 bp):
ATACTTTTTTTAAAAAATTAC
Found at i:1429977 original size:19 final size:20
Alignment explanation
Indices: 1429949--1430006 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
1429939 CATAATACTT
*
1429949 TTTTTAAAAAATTTACATAC
1 TTTTTAAAAAAATTACATAC
*
1429969 TTTTT-AAAAAATTACTTACTC
1 TTTTTAAAAAAATTACATA--C
1429990 TTTTTTAAAAAAATTAC
1 -TTTTTAAAAAAATTAC
1430007 TTGCATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 11 0.34
20 5 0.16
21 1 0.03
22 5 0.16
23 10 0.31
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTTAAAAAAATTACATAC
Found at i:1430007 original size:23 final size:23
Alignment explanation
Indices: 1429944--1430008 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1429934 TTTTACATAA
* *
1429944 TACT-TTTTTTAAAAAATTTACA
1 TACTCTTTTTTAAAAAAATTACT
1429966 TA--C-TTTTT-AAAAAATTACT
1 TACTCTTTTTTAAAAAAATTACT
1429985 TACTCTTTTTTAAAAAAATTACT
1 TACTCTTTTTTAAAAAAATTACT
1430008 T
1 T
1430009 GCATATAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 11 0.31
20 5 0.14
21 1 0.03
22 7 0.19
23 12 0.33
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (23 bp):
TACTCTTTTTTAAAAAAATTACT
Found at i:1431100 original size:24 final size:23
Alignment explanation
Indices: 1431073--1431131 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
1431063 TAATTTTATT
*
1431073 TATTTAATAATTTTTAAATAATAA
1 TATTTAATAATTTTAAAAT-ATAA
* *
1431097 TATTTAATAAATTTAAAATTTAA
1 TATTTAATAATTTTAAAATATAA
*
1431120 -ATTTCATAATTT
1 TATTTAATAATTT
1431132 ATTATCATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 17 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTAATAATTTTAAAATATAA
Found at i:1431406 original size:22 final size:21
Alignment explanation
Indices: 1431355--1431404 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1431345 AAATAATTTA
*
1431355 AATTAAATTTAATATTCAAAT
1 AATTAAATTTAATATTAAAAT
*
1431376 ATTTTAAATTT-ATATTAAAAAT
1 A-ATTAAATTTAATATT-AAAAT
1431398 AATTAAA
1 AATTAAA
1431405 ATAAAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTAAATTTAATATTAAAAT
Found at i:1431437 original size:20 final size:20
Alignment explanation
Indices: 1431402--1431447 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1431392 AAAAATAATT
*
1431402 AAAATAAAATATAATATA-A
1 AAAATAAAACATAATATATA
1431421 AAAATACAAACATAATATATA
1 AAAATA-AAACATAATATATA
1431442 AAAATA
1 AAAATA
1431448 TATTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 7 0.29
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATAAAACATAATATATA
Found at i:1431483 original size:32 final size:34
Alignment explanation
Indices: 1431444--1431506 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
1431434 AATATATAAA
1431444 AATATATTAAAATTTATAT-AATATA-AATAATT
1 AATATATTAAAATTTATATAAATATATAATAATT
*
1431476 AATATATTAAAATTTATTTAAATATATAATA
1 AATATATTAAAATTTATATAAATATATAATA
1431507 CTTTAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 18 0.64
33 6 0.21
34 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AATATATTAAAATTTATATAAATATATAATAATT
Found at i:1431506 original size:27 final size:31
Alignment explanation
Indices: 1431432--1431505 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
1431422 AAATACAAAC
*
1431432 ATAATAT-ATAA-AAATATATTAAAATTTAT
1 ATAATATAATAATTAATATATTAAAATTTAT
1431461 ATAATATAAATAATTAATATATTAAAATTTAT
1 ATAATAT-AATAATTAATATATTAAAATTTAT
*
1431493 TTAA-ATATATAAT
1 ATAATATA-ATAAT
1431506 ACTTTAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 7 0.18
30 1 0.03
31 11 0.28
32 20 0.51
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
ATAATATAATAATTAATATATTAAAATTTAT
Found at i:1431524 original size:27 final size:28
Alignment explanation
Indices: 1431444--1431524 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 28
1431434 AATATATAAA
1431444 AATATATTAAAATTTATATAATATAAATAATT
1 AATATATTAAAA--TATAT--TATAAATAATT
*
1431476 AATATATTAAAATTTATT-TAAAT-ATAT
1 AATATATTAAAATATATTATAAATAAT-T
1431503 AATACT-TTAAAA-ATATTATAAA
1 AATA-TATTAAAATATATTATAAA
1431525 AAAAATAACG
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
26 6 0.14
27 20 0.45
28 2 0.05
30 4 0.09
32 12 0.27
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
AATATATTAAAATATATTATAAATAATT
Found at i:1434192 original size:13 final size:13
Alignment explanation
Indices: 1434174--1434198 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1434164 TGACCACCTA
1434174 TCCTATGTTCCTG
1 TCCTATGTTCCTG
1434187 TCCTATGTTCCT
1 TCCTATGTTCCT
1434199 ACCTCAACAA
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:0.08, C:0.32, G:0.12, T:0.48
Consensus pattern (13 bp):
TCCTATGTTCCTG
Found at i:1439815 original size:52 final size:53
Alignment explanation
Indices: 1439681--1439817 Score: 197
Period size: 53 Copynumber: 2.6 Consensus size: 53
1439671 CATACTCGTT
*
1439681 ACCAAGGCGTCGCCTCACTAAGTGACACCAAGTCACTATTCTCCTTGATCGCC
1 ACCAAGGCGTCGACTCACTAAGTGACACCAAGTCACTATTCTCCTTGATCGCC
* *
1439734 ACCAAGGCGTCGACCCACTAAGTGACACCAAGTCACTATTCTTCTTGATCGCC
1 ACCAAGGCGTCGACTCACTAAGTGACACCAAGTCACTATTCTCCTTGATCGCC
* * *
1439787 -GCAAGGCGTTGTCTCACTAAGT-ATCACCAAG
1 ACCAAGGCGTCGACTCACTAAGTGA-CACCAAG
1439818 CCATTATGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
51 1 0.01
52 25 0.33
53 50 0.66
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (53 bp):
ACCAAGGCGTCGACTCACTAAGTGACACCAAGTCACTATTCTCCTTGATCGCC
Found at i:1439871 original size:104 final size:105
Alignment explanation
Indices: 1439683--1439874 Score: 228
Period size: 104 Copynumber: 1.8 Consensus size: 105
1439673 TACTCGTTAC
* ** * *
1439683 CAAGGCGTCGCCTCACTAAGTGACACCAAGTCACTATTCTCCTTGATCGCCACCAAGGCGTCGAC
1 CAAGGCGTCGCCTCACTAAGTGACACCAAGCCACTATGATCCTTGACCGCCACCAAGGCCTCGAC
1439748 CCACTAAGTGACACCAAGTCACTATTCTTCTTGATCGCCG
66 CCACTAAGTGACACCAAGTCACTATTCTTCTTGATCGCCG
* * * * *
1439788 CAAGGCGTTGTCTCACTAAGT-ATCACCAAGCCATTATGAT-CTTGACCGCCACTAAGGCCT-TA
1 CAAGGCGTCGCCTCACTAAGTGA-CACCAAGCCACTATGATCCTTGACCGCCACCAAGGCCTCGA
* * *
1439850 CCTCACTTAGTGACGCTAAGTCACT
65 CC-CACTAAGTGACACCAAGTCACT
1439875 TCGCAACTAA
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
103 3 0.04
104 37 0.51
105 32 0.44
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (105 bp):
CAAGGCGTCGCCTCACTAAGTGACACCAAGCCACTATGATCCTTGACCGCCACCAAGGCCTCGAC
CCACTAAGTGACACCAAGTCACTATTCTTCTTGATCGCCG
Found at i:1441588 original size:13 final size:14
Alignment explanation
Indices: 1441561--1441594 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
1441551 TGGAAGCATG
1441561 CAAGGCATCCCCAC
1 CAAGGCATCCCCAC
1441575 CAAGGCAT-CCCAC
1 CAAGGCATCCCCAC
1441588 CAAGGCA
1 CAAGGCA
1441595 ATACCATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.32, C:0.44, G:0.18, T:0.06
Consensus pattern (14 bp):
CAAGGCATCCCCAC
Found at i:1444078 original size:18 final size:18
Alignment explanation
Indices: 1444043--1444080 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1444033 AGTTTATAAT
1444043 TATTATTTTATAATTTTA
1 TATTATTTTATAATTTTA
*
1444061 TATT-TTTTATTATATTTA
1 TATTATTTTATAAT-TTTA
1444079 TA
1 TA
1444081 GTAATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTATTTTATAATTTTA
Found at i:1446096 original size:2 final size:2
Alignment explanation
Indices: 1446042--1446084 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
1446032 ATTATTTTCG
1446042 AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1446082 AT A
1 AT A
1446085 AAAAACATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1446468 original size:2 final size:2
Alignment explanation
Indices: 1446461--1446491 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1446451 GACCTTGCAT
1446461 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1446492 GCGCAAACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1449192 original size:2 final size:2
Alignment explanation
Indices: 1449185--1449224 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1449175 TCGGATCTCA
1449185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1449225 GCAGATGCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1451949 original size:2 final size:2
Alignment explanation
Indices: 1451942--1451971 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1451932 CTGATTGATG
1451942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1451972 TGTTTTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1452938 original size:16 final size:16
Alignment explanation
Indices: 1452919--1452952 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1452909 TTTACGAGGT
1452919 AAATT-TTTTTATATTA
1 AAATTATTTTT-TATTA
1452935 AAATTATTTTTTATTA
1 AAATTATTTTTTATTA
1452951 AA
1 AA
1452953 GAAGTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AAATTATTTTTTATTA
Found at i:1453842 original size:2 final size:2
Alignment explanation
Indices: 1453831--1453913 Score: 88
Period size: 2 Copynumber: 43.5 Consensus size: 2
1453821 TAGATCGTGA
1453831 AT AT -T AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1453871 AT AT AGT GT -T AT GA- AT -T AT GT -T AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1453911 AT A
1 AT A
1453914 GTGTTATGGA
Statistics
Matches: 71, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
1 6 0.08
2 63 0.89
3 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1453897 original size:38 final size:38
Alignment explanation
Indices: 1453854--1453930 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
1453844 TATATATATA
1453854 TATATATATATATATATATATAGTGTTATGAATTATGT
1 TATATATATATATATATATATAGTGTTATGAATTATGT
*
1453892 TATATATATATATATATATATAGTGTTATGGATTATGT
1 TATATATATATATATATATATAGTGTTATGAATTATGT
1453930 T
1 T
1453931 TGGGTTTTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.51
Consensus pattern (38 bp):
TATATATATATATATATATATAGTGTTATGAATTATGT
Found at i:1454016 original size:29 final size:28
Alignment explanation
Indices: 1453980--1454049 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
1453970 TTATATATTT
1453980 TTAA-ATTTTATA-AATATGTTTAAAATA
1 TTAATATTTTATATAA-ATGTTTAAAATA
* *
1454007 TTATATATTTTATATAAATTTTTAATATA
1 TTA-ATATTTTATATAAATGTTTAAAATA
*
1454036 TTAATAATTTATAT
1 TTAATATTTTATAT
1454050 TATATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.08
28 11 0.30
29 21 0.57
30 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATATTTTATATAAATGTTTAAAATA
Found at i:1454074 original size:25 final size:25
Alignment explanation
Indices: 1454043--1454092 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1454033 ATATTAATAA
1454043 TTTATATTATAT-ATATATTTATATT
1 TTTATATTATATCATAT-TTTATATT
1454068 TTTATATTATATCATATTTTATATT
1 TTTATATTATATCATATTTTATATT
1454093 ATATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTATATTATATCATATTTTATATT
Found at i:1454114 original size:23 final size:25
Alignment explanation
Indices: 1454084--1454136 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
1454074 TTATATCATA
*
1454084 TTTTATATTATATTT-T-TAATTAT
1 TTTTATATCATATTTATATAATTAT
1454107 TTTTATATCATATTTATATAATTAT
1 TTTTATATCATATTTATATAATTAT
*
1454132 ATTTA
1 TTTTA
1454137 AAATTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 14 0.54
24 1 0.04
25 11 0.42
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTTATATCATATTTATATAATTAT
Found at i:1454132 original size:42 final size:41
Alignment explanation
Indices: 1454004--1454134 Score: 119
Period size: 42 Copynumber: 3.1 Consensus size: 41
1453994 TATGTTTAAA
*
1454004 ATATTATATATTTTATATAAATTTTTA-ATATATTA-ATAATTT
1 ATATTATATATTTTA-AT-TATTTTTATATATATTATATAA-TT
* * *
1454046 ATATTATATATATATTTA-TATTTTTATATTATATCATAT-TTT
1 ATATTATATAT-T-TTAATTATTTTTATA-TATATTATATAATT
1454088 ATATTATAT-TTTTAATTATTTTTATATCATATTTATATAATT
1 ATATTATATATTTTAATTATTTTTATAT-ATA-TTATATAATT
1454130 ATATT
1 ATATT
1454135 TAAAATTAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
39 4 0.05
40 14 0.19
41 13 0.18
42 30 0.41
43 8 0.11
44 4 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (41 bp):
ATATTATATATTTTAATTATTTTTATATATATTATATAATT
Found at i:1454137 original size:35 final size:34
Alignment explanation
Indices: 1454054--1454137 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 34
1454044 TTATATTATA
*
1454054 TATATATTTATATTT--TTATATTATATCATATT
1 TATATAATTATATTTAATTATATTATATCATATT
*
1454086 T-TAT-ATTATATTTTTAATTATTTTTATATCATATT
1 TATATAATTATA--TTTAATTA-TATTATATCATATT
1454121 TATATAATTATATTTAA
1 TATATAATTATATTTAA
1454138 AATTAATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
30 5 0.12
31 3 0.07
32 4 0.09
34 3 0.07
35 19 0.44
36 3 0.07
37 6 0.14
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (34 bp):
TATATAATTATATTTAATTATATTATATCATATT
Found at i:1454142 original size:37 final size:35
Alignment explanation
Indices: 1454074--1454142 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1454064 TATTTTTATA
**
1454074 TTATATCATATTTTATATTATATTTTTAATTATTT
1 TTATATCATATTTTATATTATATTTAAAATTATTT
1454109 TTATATCATATTTATATAATTATATTTAAAATTA
1 TTATATCATATTT-TAT-ATTATATTTAAAATTA
1454143 ATAAATATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 13 0.43
36 3 0.10
37 14 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (35 bp):
TTATATCATATTTTATATTATATTTAAAATTATTT
Found at i:1454216 original size:2 final size:2
Alignment explanation
Indices: 1454209--1454243 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1454199 TTGTTGTGGC
*
1454209 CT CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1454244 CCTTTCCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1454515 original size:28 final size:28
Alignment explanation
Indices: 1454484--1454552 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 28
1454474 TAGTGGTTAT
* *
1454484 TTTGTGTTTGTCAAAAATGATAGTTTTC
1 TTTGTATTTGTCAAAAATGAAAGTTTTC
* *
1454512 TTTGTATTTGTTAAATATGAAAG-TTT-
1 TTTGTATTTGTCAAAAATGAAAGTTTTC
*
1454538 ATT-TATTTGTCAAAA
1 TTTGTATTTGTCAAAA
1454553 TTTGTGACTA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 10 0.29
26 2 0.06
27 3 0.09
28 19 0.56
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.51
Consensus pattern (28 bp):
TTTGTATTTGTCAAAAATGAAAGTTTTC
Found at i:1454650 original size:19 final size:20
Alignment explanation
Indices: 1454626--1454665 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
1454616 CCCTCTCAAG
1454626 CATCCCTCTCTT-TATCCCT
1 CATCCCTCTCTTGTATCCCT
1454645 CATCCCTCTCTTGTATCCCT
1 CATCCCTCTCTTGTATCCCT
1454665 C
1 C
1454666 TTCAATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.10, C:0.47, G:0.03, T:0.40
Consensus pattern (20 bp):
CATCCCTCTCTTGTATCCCT
Found at i:1455760 original size:2 final size:2
Alignment explanation
Indices: 1455753--1455790 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1455743 TTAATTTATC
1455753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1455791 TAGGTAATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1458058 original size:29 final size:29
Alignment explanation
Indices: 1458001--1458059 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
1457991 TAATGAGCAT
*
1458001 TTTAATTTTTATATTATTAAATTTAATAA
1 TTTAATTTTTATATTATTAAAATTAATAA
*
1458030 TTTAATTTTTATATTTTTATAAATT-ATAA
1 TTTAATTTTTATATTATTA-AAATTAATAA
1458059 T
1 T
1458060 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTAATTTTTATATTATTAAAATTAATAA
Found at i:1458777 original size:16 final size:16
Alignment explanation
Indices: 1458756--1458787 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1458746 TGTTAATGTT
*
1458756 TTTATTTAAAATATTA
1 TTTATTTAAAAAATTA
1458772 TTTATTTAAAAAATTA
1 TTTATTTAAAAAATTA
1458788 CCCAAGTTAC
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATTTAAAAAATTA
Found at i:1459489 original size:22 final size:22
Alignment explanation
Indices: 1459461--1459547 Score: 65
Period size: 22 Copynumber: 4.0 Consensus size: 22
1459451 TTAATATATT
1459461 TATAATTAAATTTAATTAAAAA
1 TATAATTAAATTTAATTAAAAA
** *
1459483 TATAATTTTATTTAA-TAAATA
1 TATAATTAAATTTAATTAAAAA
* *
1459504 -ATAATTCAGA-TTAAATAAAAA
1 TATAATT-AAATTTAATTAAAAA
*
1459525 TA-AATTAAACTTAAATTATAAAA
1 TATAATTAAA-TTTAATTA-AAAA
1459548 AAAAAATCCA
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
20 12 0.24
21 15 0.30
22 19 0.38
23 4 0.08
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (22 bp):
TATAATTAAATTTAATTAAAAA
Found at i:1459497 original size:18 final size:20
Alignment explanation
Indices: 1459471--1459509 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
1459461 TATAATTAAA
1459471 TTTAATTAA-AAAT-ATAAT
1 TTTAATTAATAAATAATAAT
*
1459489 TTTATTTAATAAATAATAAT
1 TTTAATTAATAAATAATAAT
1459509 T
1 T
1459510 CAGATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAATTAATAAATAATAAT
Found at i:1460724 original size:2 final size:2
Alignment explanation
Indices: 1460717--1460749 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1460707 CCTTATATTA
*
1460717 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1460750 AGGTTGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1462091 original size:20 final size:21
Alignment explanation
Indices: 1462052--1462102 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1462042 TGTATATCTA
**
1462052 ATAATTTATTTTTATCATATT
1 ATAATTTATTTTTAAAATATT
1462073 ATAA-TTATTTTTAAAATATT
1 ATAATTTATTTTTAAAATATT
*
1462093 TTATATTTAT
1 ATA-ATTTAT
1462103 ATAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 16 0.64
21 5 0.20
22 4 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATAATTTATTTTTAAAATATT
Found at i:1462850 original size:34 final size:34
Alignment explanation
Indices: 1462794--1463010 Score: 260
Period size: 34 Copynumber: 6.4 Consensus size: 34
1462784 TGGATATATT
*
1462794 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* **
1462827 TTGTTGATTAAATGGGTGATTTGGTAGTTTGTCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
*
1462861 TTGTTGATTAAAT-GGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* **
1462894 TTGTTGATTAAATGAGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
1462928 TTATTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* ** * **
1462962 TTGTTGACTAAAT-AATAGATTTGGTAGGTTGTCA
1 TTGTTGATTAAATGGGT-GATTTGGTAGCTTACCA
1462996 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
1463011 TGGTTTTTAC
Statistics
Matches: 157, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
33 43 0.27
34 114 0.73
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.42
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:1462902 original size:67 final size:67
Alignment explanation
Indices: 1462794--1463012 Score: 296
Period size: 67 Copynumber: 3.3 Consensus size: 67
1462784 TGGATATATT
* * *
1462794 TTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTAGTTTGT
1 TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGAGTGATTTGGTAGCTTGT
1462859 CA
66 CA
* ** **
1462861 TTGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAAATTTGGTAGCTTAC
1 TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGAGTGATTTGGTAGCTTGT
1462926 CA
66 CA
* * * * *
1462928 TTATTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAAT-AATAGATTTGGTAGGTT
1 TTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGAGT-GATTTGGTAGCTT
1462992 GTCA
64 GTCA
1462996 TTGTTGATTAAATGGTG
1 TTGTTGATTAAATGGTG
1463013 GTTTTTACCA
Statistics
Matches: 131, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
67 76 0.58
68 55 0.42
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.42
Consensus pattern (67 bp):
TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGAGTGATTTGGTAGCTTGT
CA
Found at i:1464880 original size:34 final size:34
Alignment explanation
Indices: 1464811--1465029 Score: 253
Period size: 34 Copynumber: 6.5 Consensus size: 34
1464801 AAGTGGGAGA
* *
1464811 ATTGTTGATTAAAT-GGTGATTTGATAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1464844 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1464878 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1464912 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1464946 ATTATTAATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * * *
1464980 ATTGTTGACTAAAT-GATAGATTTGGTAGATTGCT
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1465014 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1465030 TGGTTTTTAC
Statistics
Matches: 157, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
33 16 0.10
34 140 0.89
35 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1464959 original size:102 final size:101
Alignment explanation
Indices: 1464811--1465029 Score: 312
Period size: 102 Copynumber: 2.2 Consensus size: 101
1464801 AAGTGGGAGA
** * * * * *
1464811 ATTGTTGATTAAATGGTGATTTGATAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGATAGCTTACCATTATTAATTAAATGGGTGATTTGGTGGCTTA
* *
1464876 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGAGAGATTTGGTAGATTACC
*
1464912 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTAATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGATAGCTTACCATTATTAATTAAATGGGTGATTTGGTGGCTT
* * *
1464977 ACCATTGTTGACTAAATGATAGATTTGGTAGATTGCT
65 ACCATTGTTGACTAAATGAGAGATTTGGTAGATTACC
1465014 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1465030 TGGTTTTTAC
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 16 0.15
102 88 0.85
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGATAGCTTACCATTATTAATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGAGAGATTTGGTAGATTACC
Found at i:1465780 original size:26 final size:28
Alignment explanation
Indices: 1465750--1465807 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 28
1465740 ATTAATTTTA
1465750 AAATTA-TCTTTAA-TTACTATTA-AATT-
1 AAATTATTC-TTAAGTTA-TATTATAATTC
1465776 AAATTATTCTTAAGTTATATTATAATTC
1 AAATTATTCTTAAGTTATATTATAATTC
1465804 AAAT
1 AAAT
1465808 GTTTATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 15 0.54
27 9 0.32
28 4 0.14
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (28 bp):
AAATTATTCTTAAGTTATATTATAATTC
Found at i:1468690 original size:22 final size:22
Alignment explanation
Indices: 1468657--1468699 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1468647 TATTTTATTA
*
1468657 TTAAATAAAAATTTAAAAATTT
1 TTAAATAAAAATATAAAAATTT
*
1468679 TTAAA-AATAAATATAATAATT
1 TTAAATAA-AAATATAAAAATT
1468700 ATATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAATAAAAATATAAAAATTT
Found at i:1470146 original size:100 final size:98
Alignment explanation
Indices: 1469973--1470275 Score: 480
Period size: 100 Copynumber: 3.0 Consensus size: 98
1469963 TAACACGTCC
* * *
1469973 ATTACGAATTATGAACTATGTTACATACAGCAAACACTAAATTTTTATAATTTAATAATTTTAAA
1 ATTACGAATTATGAACTATGTTACATACAGCAAACACTAATTTTTTACAATCTAATAATTTTAAA
*
1470038 CATAATTCATCGATAAATACAAATACAAATTAAA
66 CATAATTCATCG-TAAATACAAATACAAATCAAA
1470072 ATTACGAAATTATGAACTATGTTACATACAGCAAACACTAATTTTTTACAATCTAATAATTTTAA
1 ATTACG-AATTATGAACTATGTTACATACAGCAAACACTAATTTTTTACAATCTAATAATTTTAA
* *
1470137 ACATGATTCATCGGTAAATATAAATACAAATCAAA
65 ACATAATTCATC-GTAAATACAAATACAAATCAAA
*
1470172 ATTACGGAATTATGAACTATGTTACATACAGCAAACACTAATTTTTTACAATCTAATAATTTTAG
1 ATTAC-GAATTATGAACTATGTTACATACAGCAAACACTAATTTTTTACAATCTAATAATTTTAA
* *
1470237 ACATAATTCATTTGTAAATACAAATACAAGTCAAA
65 ACATAATTCA-TCGTAAATACAAATACAAATCAAA
1470272 ATTA
1 ATTA
1470276 AACCAATTTG
Statistics
Matches: 189, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
99 6 0.03
100 180 0.95
101 3 0.02
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (98 bp):
ATTACGAATTATGAACTATGTTACATACAGCAAACACTAATTTTTTACAATCTAATAATTTTAAA
CATAATTCATCGTAAATACAAATACAAATCAAA
Found at i:1470937 original size:21 final size:21
Alignment explanation
Indices: 1470911--1470957 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1470901 ATTTACTATT
* *
1470911 AAATTTATTTATAAATTAATC
1 AAATTTAATTATAAATTAAAC
*
1470932 AAATTTAATTATAATTTAAAC
1 AAATTTAATTATAAATTAAAC
1470953 AAATT
1 AAATT
1470958 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTTAATTATAAATTAAAC
Found at i:1471054 original size:20 final size:20
Alignment explanation
Indices: 1471029--1471067 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1471019 ATATTAAAAA
1471029 ATATTTT-TAATTAATATTTT
1 ATATTTTATAATT-ATATTTT
1471049 ATATTTTATAATTATATTT
1 ATATTTTATAATTATATTT
1471068 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATTTTATAATTATATTTT
Found at i:1471933 original size:19 final size:19
Alignment explanation
Indices: 1471909--1471952 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1471899 GATTAAAATT
1471909 ATAATATAATTTA-ATTAAA
1 ATAATAT-ATTTATATTAAA
*
1471928 ATAATATATTTATATTTAA
1 ATAATATATTTATATTAAA
1471947 A-AATAT
1 ATAATAT
1471953 TCTTAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATATATTTATATTAAA
Found at i:1472409 original size:19 final size:20
Alignment explanation
Indices: 1472365--1472407 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1472355 ATGAACTAAT
* *
1472365 AAAATCAATTTAATTAATAA
1 AAAATTAATTAAATTAATAA
*
1472385 AAAATTAATTAAATTATTAA
1 AAAATTAATTAAATTAATAA
1472405 AAA
1 AAA
1472408 TTTATTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATTAATTAAATTAATAA
Found at i:1473280 original size:21 final size:23
Alignment explanation
Indices: 1473250--1473295 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
1473240 TATTTAAAAT
* *
1473250 TAATTTAATTTTATGT-TA-ATA
1 TAATTAAATTTCATGTATATATA
1473271 TAATTAAATTTCATGTATATATA
1 TAATTAAATTTCATGTATATATA
1473294 TA
1 TA
1473296 TCAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 2 0.10
23 5 0.24
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
TAATTAAATTTCATGTATATATA
Found at i:1474301 original size:12 final size:11
Alignment explanation
Indices: 1474276--1474323 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
1474266 TATATTTTAT
1474276 AAATATAATAA
1 AAATATAATAA
*
1474287 AAATATTAATTA
1 AAATA-TAATAA
*
1474299 AAATAAAAATAAA
1 AAAT-ATAAT-AA
1474312 AAATATAATAA
1 AAATATAATAA
1474323 A
1 A
1474324 TTTTTAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 8 0.27
12 16 0.53
13 6 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATATAATAA
Found at i:1474321 original size:18 final size:18
Alignment explanation
Indices: 1474276--1474323 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1474266 TATATTTTAT
**
1474276 AAATATAATAAAAATATT
1 AAATATAATAAAAATAAA
* *
1474294 AATTAAAATAAAAATAAA
1 AAATATAATAAAAATAAA
1474312 AAATATAATAAA
1 AAATATAATAAA
1474324 TTTTTAACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATATAATAAAAATAAA
Found at i:1475509 original size:10 final size:10
Alignment explanation
Indices: 1475494--1475540 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
1475484 AAAAGATAAA
1475494 ATATATTTTT
1 ATATATTTTT
1475504 ATATATTTTT
1 ATATATTTTT
1475514 AT-TA-TTTT
1 ATATATTTTT
1475522 AT-TATTATTT
1 ATATATT-TTT
1475532 -TA-ATTTTT
1 ATATATTTTT
1475540 A
1 A
1475541 ACTAATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 11 0.33
9 7 0.21
10 15 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATATATTTTT
Found at i:1475893 original size:29 final size:28
Alignment explanation
Indices: 1475861--1475923 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1475851 ACCTTTTTAA
1475861 TAAAATTAAATAAATATTTTATAA-ACATT
1 TAAAATTAAATAAAT-TTTTATAATA-ATT
* *
1475890 TAAAAATAAATATATTTTTATAATAATT
1 TAAAATTAAATAAATTTTTATAATAATT
1475918 TAAAAT
1 TAAAAT
1475924 AATTATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
TAAAATTAAATAAATTTTTATAATAATT
Found at i:1475918 original size:28 final size:28
Alignment explanation
Indices: 1475861--1475933 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
1475851 ACCTTTTTAA
* *
1475861 TAAAATTAAATAAATATTTTATAAACATT
1 TAAAAATAAATATAT-TTTTATAAACATT
1475890 TAAAAATAAATATATTTTTATAATA-ATT
1 TAAAAATAAATATATTTTTATAA-ACATT
*
1475918 T-AAAATAATTATATTT
1 TAAAAATAAATATATTT
1475934 GACCCAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
27 14 0.35
28 12 0.30
29 14 0.35
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
TAAAAATAAATATATTTTTATAAACATT
Found at i:1480089 original size:221 final size:220
Alignment explanation
Indices: 1479685--1480122 Score: 750
Period size: 221 Copynumber: 2.0 Consensus size: 220
1479675 TGAATGAAAG
* *
1479685 CCACATAAGGATACTTTTCTTGCAATCATAAACATCATTTTGATCTCCTTAACTGTACTTTCAGA
1 CCACATAAGGATACTTTTCTTGCAATCATAAACATCATTTTGATCACCTTAACTGTACCTTCAGA
* * *
1479750 CTGCTAAATTTAATGTTGTGTTTTCATTTCACTGGATATGAGAATAATGTGATGAGGGCATAACT
66 CTGCCAAATTTAATGTTGTGTTTTCATTTCACTGGATATGAGAATAATGTGATAAGGGCAGAACT
* *
1479815 TTGCATTTTTAGATAATAAAGTATTAGTCTTGATTATTAGTAATTGCTTTATGAACTTCTTTTAC
131 TGGCATTTTTAGATAATAAAGTATTAGTCTTGATTATTAATAATTGCTTTATGAACTTCTTTTAC
1479880 CACATGCAACTAAGCCCTGAAGGGT
196 CACATGCAACTAAGCCCTGAAGGGT
* * **
1479905 CCACATAAGGATGCTTTTCTCTGCAATCATAAACGTTTTTTTGATCACCTTAACTGTACCTTCAG
1 CCACATAAGGATACTTTTCT-TGCAATCATAAACATCATTTTGATCACCTTAACTGTACCTTCAG
*
1479970 ACTGCCAAATTTAATGTTGTGTTTTCATTTCACTGGATATGAGAATAATTTGATAAGGGCAGAAC
65 ACTGCCAAATTTAATGTTGTGTTTTCATTTCACTGGATATGAGAATAATGTGATAAGGGCAGAAC
*
1480035 TTGGCATTTTTAGATAATAAAGTATTAGTCTTGATTATTAATAATTGGTTTATGAACTTCTTTTA
130 TTGGCATTTTTAGATAATAAAGTATTAGTCTTGATTATTAATAATTGCTTTATGAACTTCTTTTA
1480100 CCACATGCAACTAAGCCCTGAAG
195 CCACATGCAACTAAGCCCTGAAG
1480123 TGTTGGCTCC
Statistics
Matches: 204, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
220 19 0.09
221 185 0.91
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (220 bp):
CCACATAAGGATACTTTTCTTGCAATCATAAACATCATTTTGATCACCTTAACTGTACCTTCAGA
CTGCCAAATTTAATGTTGTGTTTTCATTTCACTGGATATGAGAATAATGTGATAAGGGCAGAACT
TGGCATTTTTAGATAATAAAGTATTAGTCTTGATTATTAATAATTGCTTTATGAACTTCTTTTAC
CACATGCAACTAAGCCCTGAAGGGT
Found at i:1480414 original size:43 final size:43
Alignment explanation
Indices: 1480353--1480438 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1480343 TGACAGTGTT
1480353 CTTATCAAATGGTTATGAATGGTTAGTTCACTTATTAGTTATC
1 CTTATCAAATGGTTATGAATGGTTAGTTCACTTATTAGTTATC
*
1480396 CTTATCAAATGGTTATGAATGGTTAGTTCAGTTATTAGTTATC
1 CTTATCAAATGGTTATGAATGGTTAGTTCACTTATTAGTTATC
1480439 ACTGGAAGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.44
Consensus pattern (43 bp):
CTTATCAAATGGTTATGAATGGTTAGTTCACTTATTAGTTATC
Found at i:1480925 original size:118 final size:118
Alignment explanation
Indices: 1480728--1480959 Score: 347
Period size: 118 Copynumber: 2.0 Consensus size: 118
1480718 GTCTAAAACA
* * * * *
1480728 AACTTAACGTATGTTTTATGTGTTAGTACTATTTTTTGTTTTACAAATTTGTTTATCCATATATT
1 AACTTAACGTATGTTTTAGGTGTTAGTACCATTATTTGTTTGACAAATTTGTATATCCATATATT
**
1480793 TCTCATGTGCATGTCTTTTGCCGATTCCTTGGTGGAGATTACTGAAGGTGTCT
66 TCTCATGTGCATGTCTTTCACCGATTCCTTGGTGGAGATTACTGAAGGTGTCT
* *
1480846 AACTTAATGTGTGTTTTAGGTGTTAGTACCATTATTTGTTTGACAAATTTGTATATCCATATATT
1 AACTTAACGTATGTTTTAGGTGTTAGTACCATTATTTGTTTGACAAATTTGTATATCCATATATT
* * * *
1480911 TCTCTTGTGGATGTCTTTCACTGGTTCCTTGGTGGAGATTACTGAAGGT
66 TCTCATGTGCATGTCTTTCACCGATTCCTTGGTGGAGATTACTGAAGGT
1480960 CTTTAGAGGT
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 101 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (118 bp):
AACTTAACGTATGTTTTAGGTGTTAGTACCATTATTTGTTTGACAAATTTGTATATCCATATATT
TCTCATGTGCATGTCTTTCACCGATTCCTTGGTGGAGATTACTGAAGGTGTCT
Done.