Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
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: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 37 of 52
Found at i:6117560 original size:27 final size:27
Alignment explanation
Indices: 6117504--6117598 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 27
6117494 ATATAAAAAA
*
6117504 TATATTAATATATGAATATATTAAATT
1 TATATAAATATATGAATATATTAAATT
* *
6117531 TATATAAATATAT-ATTATTTTAAATAT
1 TATATAAATATATGAATATATTAAAT-T
* * *
6117558 TAT-TATAATATGTAAAAAATATATAAATT
1 TATATA-AATATAT-GAATATAT-TAAATT
6117587 TAATATAAATAT
1 T-ATATAAATAT
6117599 TCATATTACT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
26 12 0.22
27 22 0.41
29 6 0.11
30 12 0.22
31 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TATATAAATATATGAATATATTAAATT
Found at i:6117778 original size:3 final size:3
Alignment explanation
Indices: 6117770--6117813 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
6117760 TATATCATAT
* *
6117770 TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6117814 TAAAAAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:6117835 original size:12 final size:12
Alignment explanation
Indices: 6117756--6117842 Score: 56
Period size: 12 Copynumber: 7.2 Consensus size: 12
6117746 GATAATTTTT
*
6117756 TAATTA-TATCA
1 TAATTATTATAA
* *
6117767 TATTTATTATTA
1 TAATTATTATAA
*
6117779 TTATTATTATTAA
1 TAATTATTA-TAA
*
6117792 T-ATTATTATTA
1 TAATTATTATAA
6117803 TAATTATTATTTAA
1 TAATTATTA--TAA
*
6117817 -AA-AATTATAA
1 TAATTATTATAA
6117827 TAATTATTAATAA
1 TAATTATT-ATAA
6117840 TAA
1 TAA
6117843 AAAATCAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
10 3 0.05
11 10 0.17
12 32 0.54
13 12 0.20
14 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (12 bp):
TAATTATTATAA
Found at i:6117844 original size:24 final size:24
Alignment explanation
Indices: 6117772--6117844 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
6117762 TATCATATTT
* **
6117772 ATTATTATTATTATTATTAATATT
1 ATTATTATAATTATTATTAATAAA
6117796 ATTATTATAATTATTATTTAA-AAA
1 ATTATTATAATTATTA-TTAATAAA
* *
6117820 ATTATAATAATTATTAATAATAAA
1 ATTATTATAATTATTATTAATAAA
6117844 A
1 A
6117845 AATCAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 3 0.07
24 35 0.83
25 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTATTATAATTATTATTAATAAA
Found at i:6123276 original size:18 final size:17
Alignment explanation
Indices: 6123226--6123292 Score: 61
Period size: 16 Copynumber: 4.1 Consensus size: 17
6123216 AATAGATATT
6123226 TTAAAAT-TTATATAATA
1 TTAAAATATTATA-AATA
* *
6123243 -TGAATTATTA-AAATA
1 TTAAAATATTATAAATA
6123258 TTAAAATATATATAAATA
1 TTAAAATAT-TATAAATA
*
6123276 -TAAAATATTTTAAATA
1 TTAAAATATTATAAATA
6123292 T
1 T
6123293 AATTATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 4 0.10
16 18 0.45
17 13 0.32
18 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (17 bp):
TTAAAATATTATAAATA
Found at i:6123291 original size:16 final size:17
Alignment explanation
Indices: 6123227--6123316 Score: 68
Period size: 15 Copynumber: 5.6 Consensus size: 17
6123217 ATAGATATTT
*
6123227 TAAAATTTATAT-AATA
1 TAAAATATATATAAATA
* *
6123243 TGAATTAT-TA-AAATA
1 TAAAATATATATAAATA
6123258 TTAAAATATATATAAATA
1 -TAAAATATATATAAATA
*
6123276 TAAAATAT-TTTAAATA
1 TAAAATATATATAAATA
* *
6123292 T-AATTATA-ATATA-A
1 TAAAATATATATAAATA
6123306 TAAAATATATA
1 TAAAATATATA
6123317 AATATAATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
14 2 0.04
15 20 0.35
16 20 0.35
17 10 0.18
18 5 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (17 bp):
TAAAATATATATAAATA
Found at i:6123306 original size:5 final size:5
Alignment explanation
Indices: 6123288--6123331 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
6123278 AAATATTTTA
*
6123288 AATAT AATTAT AATAT AATAA AATAT -ATA- AATAT AATAT AATAT
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
6123332 GAATGAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 6 0.18
5 23 0.68
6 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:6126139 original size:12 final size:12
Alignment explanation
Indices: 6126119--6126196 Score: 61
Period size: 12 Copynumber: 6.6 Consensus size: 12
6126109 GTATCAGTAA
6126119 TATTATAATAAT
1 TATTATAATAAT
*
6126131 TATTTTAATAAT
1 TATTATAATAAT
* **
6126143 T-TTAT-TTTTT
1 TATTATAATAAT
*
6126153 TATTATTAATATT
1 TATTA-TAATAAT
*
6126166 TATAATAATAAT
1 TATTATAATAAT
* *
6126178 TATAATAATATT
1 TATTATAATAAT
6126190 TATTATA
1 TATTATA
6126197 TTTATAATCA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
10 3 0.06
11 6 0.12
12 36 0.69
13 7 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATAATAAT
Found at i:6131690 original size:28 final size:27
Alignment explanation
Indices: 6131650--6131708 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
6131640 AATTAAATTT
*
6131650 ATTTATTAATAAAAAATATTTTTATTAA-
1 ATTTATTAAT-AAAAATAATTTT-TTAAC
6131678 ATTTAATT-ATAAAAATAATTTTTTAAC
1 ATTT-ATTAATAAAAATAATTTTTTAAC
6131705 ATTT
1 ATTT
6131709 TTGAATAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.14
27 15 0.54
28 6 0.21
29 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTATTAATAAAAATAATTTTTTAAC
Found at i:6131700 original size:29 final size:32
Alignment explanation
Indices: 6131641--6131702 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
6131631 CTTAATTTAA
*
6131641 ATTAAATTTATTTATTAATAAAAAATATTTTT
1 ATTAAATTTAATTATTAATAAAAAATATTTTT
*
6131673 ATTAAATTTAATTA-TAA-AAATAAT-TTTTT
1 ATTAAATTTAATTATTAATAAAAAATATTTTT
6131702 A
1 A
6131703 ACATTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 6 0.21
30 6 0.21
31 3 0.11
32 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTAAATTTAATTATTAATAAAAAATATTTTT
Found at i:6132173 original size:14 final size:14
Alignment explanation
Indices: 6132150--6132182 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
6132140 AACCAATATT
6132150 TGTA-ACACTTTTA
1 TGTATACACTTTTA
6132163 TGTATACACTTTTA
1 TGTATACACTTTTA
6132177 TGTATA
1 TGTATA
6132183 TTGAAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (14 bp):
TGTATACACTTTTA
Found at i:6135553 original size:20 final size:19
Alignment explanation
Indices: 6135525--6135576 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
6135515 CCTTTCAAAG
*
6135525 TTATATTTTATATAAATTAT
1 TTATATTTT-TAAAAATTAT
*
6135545 TTATTTTTTTAAAAATTAT
1 TTATATTTTTAAAAATTAT
* *
6135564 TTTTATATTTAAA
1 TTATATTTTTAAA
6135577 TATATATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATTTTTAAAAATTAT
Found at i:6136450 original size:193 final size:193
Alignment explanation
Indices: 6136104--6136475 Score: 419
Period size: 193 Copynumber: 1.9 Consensus size: 193
6136094 TATCAATTCG
* * * * *
6136104 TTTTGAATCCATGAATTTAGATTAATTTTAAAATAATTTTATAATTTGATATTTCATTCATGATG
1 TTTTGAATCAATAAATTTAGATCAATTTTAAAATAATCTTATAATTTGATATTTCATTCATGATC
* * * * *
6136169 TGAATCTTTTAGAATAGATATTTTTAAAATAGTCCACAATCTTAAGTGCATAACAACTCATCTCA
66 TAAATCTTTTAGAATAAATACTTTTAAAATAATCCACAATCTTAAATGCATAACAACTCATCTCA
* * * * * *
6136234 TATTAAAGTTTCGAATTGTAAAATTAAATTACGAGATTAATTTTTAAATCACAAATAATTTCA
131 GATTAAAGTCTCAAATCGTAAAATTAAATTACAAGATTAACTTTTAAATCACAAATAATTTCA
* * *
6136297 TTTTGAATCAATAAATTTAGATCAATTTTAAAATGATCTTGTAATTTGATATTTGATTCAT-AGT
1 TTTTGAATCAATAAATTTAGATCAATTTTAAAATAATCTTATAATTTGATATTTCATTCATGA-T
* * *** *
6136361 CTAAATCTTTTA-ATATAAATACTTTTAAGATAATTCTTGATCTTAAATGCATAACCA-TCCATC
65 CTAAATCTTTTAGA-ATAAATACTTTTAAAATAATCCACAATCTTAAATGCATAACAACT-CATC
** * *
6136424 TTGGATTGAAA-TCTCAAATCGTAAAATTGAATTGCAAGATTAACTTTTAAAT
128 TCAGATT-AAAGTCTCAAATCGTAAAATTAAATTACAAGATTAACTTTTAAAT
6136476 TGATGAATAA
Statistics
Matches: 146, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
192 3 0.02
193 140 0.96
194 3 0.02
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (193 bp):
TTTTGAATCAATAAATTTAGATCAATTTTAAAATAATCTTATAATTTGATATTTCATTCATGATC
TAAATCTTTTAGAATAAATACTTTTAAAATAATCCACAATCTTAAATGCATAACAACTCATCTCA
GATTAAAGTCTCAAATCGTAAAATTAAATTACAAGATTAACTTTTAAATCACAAATAATTTCA
Found at i:6138840 original size:12 final size:12
Alignment explanation
Indices: 6138803--6138854 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
6138793 ACAAATAAAC
6138803 ATAATAAATATT
1 ATAATAAATATT
* * *
6138815 TTTATAATTAATT
1 ATAATAAAT-ATT
6138828 ATAATAAATATT
1 ATAATAAATATT
*
6138840 AAAATAAA-ATT
1 ATAATAAATATT
6138851 ATAA
1 ATAA
6138855 AATTATAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
11 6 0.19
12 16 0.52
13 9 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATAAATATT
Found at i:6138846 original size:25 final size:24
Alignment explanation
Indices: 6138803--6138878 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 24
6138793 ACAAATAAAC
***
6138803 ATAATAAATATTTTTATAATTAATT
1 ATAATAAATATTAAAATAA-TAATT
6138828 ATAATAAATATTAAAATAA-AATT
1 ATAATAAATATTAAAATAATAATT
*
6138851 ATAA-AATTA-TAAAATAATAATT
1 ATAATAAATATTAAAATAATAATT
6138873 ATAATA
1 ATAATA
6138879 TTAACTTATC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.18
22 12 0.27
23 9 0.20
25 16 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAATAAATATTAAAATAATAATT
Found at i:6138875 original size:22 final size:23
Alignment explanation
Indices: 6138818--6138881 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
6138808 AAATATTTTT
*
6138818 ATAATTAATTATAATAAATATTAAA
1 ATAA-TAATTATAA-AATTATTAAA
6138843 ATAA-AATTATAAAATTA-TAAA
1 ATAATAATTATAAAATTATTAAA
*
6138864 ATAATAATTATAATATTA
1 ATAATAATTATAAAATTA
6138882 ACTTATCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 8 0.22
22 16 0.44
23 8 0.22
25 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAATAATTATAAAATTATTAAA
Found at i:6143622 original size:58 final size:56
Alignment explanation
Indices: 6143552--6143715 Score: 209
Period size: 48 Copynumber: 3.0 Consensus size: 56
6143542 CAAGCTGCAA
6143552 TGCACTCAATAAGAGAAAGGTGCTTGTAAATGCATTATAAGTAGATCAACAAAAACAT
1 TGCACTCAATAAGAGAAAGGTGCTTGTAAATGC-TTA-AAGTAGATCAACAAAAACAT
*
6143610 TGCACTCAATAAGAGAAAGGTGCTTGTAAATGC-----GT---TAAACAAAAACAT
1 TGCACTCAATAAGAGAAAGGTGCTTGTAAATGCTTAAAGTAGATCAACAAAAACAT
* *
6143658 TGCACTCAATAAGAGAAAGGTACTTGTAAATGCTTTAAAAGTAGATCAACCAAAACAT
1 TGCACTCAATAAGAGAAAGGTGCTTGTAAATGC-TT-AAAGTAGATCAACAAAAACAT
6143716 AACTAGCTTA
Statistics
Matches: 92, Mismatches: 4, Indels: 20
0.79 0.03 0.17
Matches are distributed among these distances:
48 44 0.48
51 2 0.02
55 2 0.02
58 44 0.48
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.24
Consensus pattern (56 bp):
TGCACTCAATAAGAGAAAGGTGCTTGTAAATGCTTAAAGTAGATCAACAAAAACAT
Found at i:6144989 original size:30 final size:30
Alignment explanation
Indices: 6144953--6145027 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
6144943 TAGCTAGGTG
6144953 TCAAACACTAGCAATAGAAAAGATCTTATC
1 TCAAACACTAGCAATAGAAAAGATCTTATC
*
6144983 TCAAACACTAGCAATAGCAAAGATCTTATC
1 TCAAACACTAGCAATAGAAAAGATCTTATC
*
6145013 TCAAATACTAGCAAT
1 TCAAACACTAGCAAT
6145028 GATAAGGGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.24
Consensus pattern (30 bp):
TCAAACACTAGCAATAGAAAAGATCTTATC
Found at i:6146338 original size:17 final size:18
Alignment explanation
Indices: 6146306--6146342 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6146296 AATATGTTGA
*
6146306 AAAAATAAGATAAAATAT
1 AAAAATAACATAAAATAT
6146324 AAAAATAACAT-AAATAT
1 AAAAATAACATAAAATAT
6146341 AA
1 AA
6146343 TATGAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAAATAACATAAAATAT
Found at i:6146357 original size:19 final size:22
Alignment explanation
Indices: 6146333--6146381 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
6146323 TAAAAATAAC
6146333 ATAAATATAATA-TG-A-ATAT
1 ATAAATATAATATTGAACATAT
*
6146352 ATAAAT-TTATATTGAACATAT
1 ATAAATATAATATTGAACATAT
6146373 ATAAATATA
1 ATAAATATA
6146382 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 4 0.17
19 8 0.33
20 1 0.04
21 10 0.42
22 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (22 bp):
ATAAATATAATATTGAACATAT
Found at i:6148439 original size:28 final size:28
Alignment explanation
Indices: 6148378--6148443 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
6148368 CACGATTACA
* *
6148378 ACATGAATAATACGAAAACATGATTAAG
1 ACATGAATTATACGAAAACATCATTAAG
*
6148406 ACATGAATTATACGAAAACA-CATTTAGG
1 ACATGAATTATACGAAAACATCA-TTAAG
*
6148434 ATATGAATTA
1 ACATGAATTA
6148444 CATGAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.26
Consensus pattern (28 bp):
ACATGAATTATACGAAAACATCATTAAG
Found at i:6148727 original size:20 final size:20
Alignment explanation
Indices: 6148702--6148746 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
6148692 GAAGCCACCT
6148702 ATTTAT-AAAATAAAAAAAA
1 ATTTATCAAAATAAAAAAAA
* *
6148721 CATTTATCAAAATCAAATAAA
1 -ATTTATCAAAATAAAAAAAA
6148742 ATTTA
1 ATTTA
6148747 ATAGTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
ATTTATCAAAATAAAAAAAA
Found at i:6151368 original size:21 final size:21
Alignment explanation
Indices: 6151338--6151384 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
6151328 ATATGTCATT
* *
6151338 TTAATTACAAAAGCACATGAA
1 TTAATCACAAAAGCACATAAA
6151359 TTAATCACAAAAGCACATAAA
1 TTAATCACAAAAGCACATAAA
6151380 TTAAT
1 TTAAT
6151385 GTGTAAGCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (21 bp):
TTAATCACAAAAGCACATAAA
Found at i:6153670 original size:18 final size:18
Alignment explanation
Indices: 6153645--6153687 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
6153635 AAAGTGAGCG
6153645 TATTTAATTTT-TATATTA
1 TATTTAATTTTATA-ATTA
*
6153663 TTTTTAATTTTATAATTA
1 TATTTAATTTTATAATTA
6153681 TATTTAA
1 TATTTAA
6153688 ATATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTAATTTTATAATTA
Found at i:6153746 original size:27 final size:27
Alignment explanation
Indices: 6153685--6153747 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
6153675 TAATTATATT
6153685 TAAATATATAAAAATTAATATATTAATA
1 TAAAT-TATAAAAATTAATATATTAATA
**
6153713 TTTATTATAAAAA-TAAT-TATTAAATA
1 TAAATTATAAAAATTAATATATT-AATA
6153739 TGAAATTAT
1 T-AAATTAT
6153748 TGACGCTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 4 0.14
26 9 0.31
27 13 0.45
28 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
TAAATTATAAAAATTAATATATTAATA
Found at i:6153989 original size:18 final size:18
Alignment explanation
Indices: 6153966--6154009 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6153956 TATATTTAAA
*
6153966 ATATTTTTAT-TATTTTT
1 ATATTTTTATCTATTTGT
*
6153983 ATCATTTATATCTATTTGT
1 AT-ATTTTTATCTATTTGT
6154002 ATATTTTT
1 ATATTTTT
6154010 TATCATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 2 0.09
18 12 0.55
19 8 0.36
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (18 bp):
ATATTTTTATCTATTTGT
Found at i:6156116 original size:14 final size:15
Alignment explanation
Indices: 6156085--6156115 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6156075 TGTGAAGATG
*
6156085 AATTTTTTTTAAAAA
1 AATTATTTTTAAAAA
6156100 AATTATTTTTAAAAA
1 AATTATTTTTAAAAA
6156115 A
1 A
6156116 TGTAGAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTATTTTTAAAAA
Found at i:6156675 original size:12 final size:12
Alignment explanation
Indices: 6156628--6156677 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
6156618 ATAAATTAAT
*
6156628 ATTTTAA-ATTT
1 ATTTTAATATTA
6156639 ATCTTTAAT-TTA
1 AT-TTTAATATTA
*
6156651 ATTATATATATTA
1 ATTTTA-ATATTA
6156664 ATTTTAATATTA
1 ATTTTAATATTA
6156676 AT
1 AT
6156678 ATATCCACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 5 0.16
12 19 0.59
13 8 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTTAATATTA
Found at i:6156754 original size:12 final size:12
Alignment explanation
Indices: 6156707--6156756 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
6156697 ATGAAATAAT
*
6156707 ATTTTAA-ATTT
1 ATTTTAATATTA
6156718 ATCTTTAAT-TTA
1 AT-TTTAATATTA
*
6156730 ATTATATATATTA
1 ATTTTA-ATATTA
6156743 ATTTTAATATTA
1 ATTTTAATATTA
6156755 AT
1 AT
6156757 ATATTATGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 5 0.16
12 19 0.59
13 8 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTTAATATTA
Found at i:6156759 original size:24 final size:24
Alignment explanation
Indices: 6156642--6156760 Score: 71
Period size: 24 Copynumber: 4.7 Consensus size: 24
6156632 TAAATTTATC
6156642 TTTAAT-TTAATTATATATATTAAT
1 TTTAATATTAA-TATATATATTAAT
** *
6156666 TTTAATATTAATATATCCACCTACAT
1 TTTAATATTAATATATATA-TTA-AT
* * * * *
6156692 TTTGTATGAAATAATATTTTAAATTTAT
1 TTT-AAT--ATTAATA-TATATATTAAT
6156720 CTTTAAT-TTAATTATATATATTAAT
1 -TTTAATATTAA-TATATATATTAAT
6156745 TTTAATATTAATATAT
1 TTTAATATTAATATAT
6156761 TATGCTATTT
Statistics
Matches: 70, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
24 23 0.33
25 21 0.30
26 7 0.10
27 2 0.03
28 4 0.06
29 10 0.14
30 3 0.04
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTAATATTAATATATATATTAAT
Found at i:6160382 original size:30 final size:31
Alignment explanation
Indices: 6160328--6160404 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 31
6160318 TAAAATTATT
*
6160328 TAATAAAAATAGTGTAAGTAATTTAATTTATTAA
1 TAATAAAAAT--T-TAAGTAATTTAATTTAATAA
6160362 TAATAAAAATTTAA-TAATTTAATTTAATAA
1 TAATAAAAATTTAAGTAATTTAATTTAATAA
6160392 -AATTAAAAATTTA
1 TAA-TAAAAATTTA
6160405 TGACTTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
29 2 0.05
30 25 0.61
31 3 0.07
32 1 0.02
34 10 0.24
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (31 bp):
TAATAAAAATTTAAGTAATTTAATTTAATAA
Found at i:6160711 original size:21 final size:20
Alignment explanation
Indices: 6160687--6160861 Score: 69
Period size: 20 Copynumber: 8.5 Consensus size: 20
6160677 AACGGAATAT
**
6160687 AAATATAAATATGATATTAA
1 AAATATAAATAAAATATTAA
6160707 AAA-ATAAATAAAATATTATA
1 AAATATAAATAAAATATTA-A
6160727 AAATATAAA-AATAAT-TTAA
1 AAATATAAATAA-AATATTAA
* *
6160746 ATATATTAAATATTTTAAATTTTAGA
1 AAATA-TAAATA----AAATATTA-A
* *
6160772 TAATATAAATTATTAATATATAA
1 AAATATAAA-TA-AAATAT-TAA
* * *
6160795 AAATTTATAT-AAATATAAA
1 AAATATAAATAAAATATTAA
* *
6160814 AAACATTAAAT-ATA-ATT-A
1 AAATA-TAAATAAAATATTAA
*
6160832 TAATAT-AATAAAATATTAA
1 AAATATAAATAAAATATTAA
6160851 AATATATAAAT
1 AA-ATATAAAT
6160862 TATTAAATTT
Statistics
Matches: 115, Mismatches: 21, Indels: 37
0.66 0.12 0.21
Matches are distributed among these distances:
16 3 0.03
17 3 0.03
18 7 0.06
19 27 0.23
20 31 0.27
21 12 0.10
22 1 0.01
23 12 0.10
24 5 0.04
25 8 0.07
26 6 0.05
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38
Consensus pattern (20 bp):
AAATATAAATAAAATATTAA
Found at i:6160736 original size:27 final size:26
Alignment explanation
Indices: 6160706--6160758 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
6160696 TATGATATTA
6160706 AAAAATAAATAAAATATTATAAAATAT
1 AAAAATAAATAAAATA-TATAAAATAT
* * *
6160733 AAAAATAATTTAAATATATTAAATAT
1 AAAAATAAATAAAATATATAAAATAT
6160759 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAAATAAATAAAATATATAAAATAT
Found at i:6160739 original size:18 final size:18
Alignment explanation
Indices: 6160700--6160860 Score: 64
Period size: 18 Copynumber: 8.6 Consensus size: 18
6160690 TATAAATATG
* *
6160700 ATATTAAAAAATAAATAAA
1 ATATTATAAAATATA-AAA
6160719 ATATTATAAAATATAAAA
1 ATATTATAAAATATAAAA
*
6160737 ATAATT-T-AAATATATTAA
1 AT-ATTATAAAATATA-AAA
* * *
6160755 ATATTTTAAATTTTAGATAA
1 ATATTATAAAATATA-A-AA
*
6160775 TATAAATTATTAATATATAAAA
1 -AT--ATTA-TAAAATATAAAA
6160797 AT-TTATATAAATATAAAA
1 ATATTATA-AAATATAAAA
* *
6160815 A-A-CATTAAATATAATTATA
1 ATATTATAAAATATAA--A-A
* *
6160834 ATATAATAAAATATTAAA
1 ATATTATAAAATATAAAA
6160852 ATA-TATAAA
1 ATATTATAAA
6160861 TTATTAAATT
Statistics
Matches: 108, Mismatches: 18, Indels: 34
0.68 0.11 0.21
Matches are distributed among these distances:
16 8 0.07
17 19 0.18
18 29 0.27
19 24 0.22
20 3 0.03
21 13 0.12
22 2 0.02
23 4 0.04
24 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38
Consensus pattern (18 bp):
ATATTATAAAATATAAAA
Found at i:6160782 original size:16 final size:15
Alignment explanation
Indices: 6160761--6160867 Score: 60
Period size: 17 Copynumber: 6.7 Consensus size: 15
6160751 TTAAATATTT
6160761 TAAATT-TTAGATAATA
1 TAAATTATTA-AT-ATA
6160777 TAAATTATTAATATA
1 TAAATTATTAATATA
6160792 TAAAAATTTATATAAATATA
1 T--AAA-TTAT-T-AATATA
* **
6160812 AAAAACATTAA-ATA
1 TAAATTATTAATATA
6160826 T-AATTA-TAATATAA
1 TAAATTATTAATAT-A
*
6160840 TAAAATATTAAAATATA
1 TAAATTATT--AATATA
6160857 TAAATTATTAA
1 TAAATTATTAA
6160868 ATTTACTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 25
0.68 0.08 0.24
Matches are distributed among these distances:
12 3 0.04
13 5 0.07
14 5 0.07
15 12 0.17
16 10 0.14
17 17 0.24
18 12 0.17
19 1 0.01
20 6 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (15 bp):
TAAATTATTAATATA
Found at i:6160869 original size:16 final size:16
Alignment explanation
Indices: 6160743--6160869 Score: 77
Period size: 18 Copynumber: 7.8 Consensus size: 16
6160733 AAAAATAATT
*
6160743 TAAATATATTAAATATTT
1 TAAAT-TATTAAATA-TA
*
6160761 TAAATT-TTAGATAATA
1 TAAATTATTAAAT-ATA
6160777 TAAATTATTAATATATA
1 TAAATTATTAA-ATATA
*
6160794 AAAATTTATATAAATATA
1 TAAA-TTAT-TAAATATA
* **
6160812 AAAAACATT-AA-ATA
1 TAAATTATTAAATATA
6160826 T-AATTA-T-AATATAA
1 TAAATTATTAAATAT-A
*
6160840 TAAAATATTAAAATATA
1 TAAATTATT-AAATATA
6160857 TAAATTATTAAAT
1 TAAATTATTAAAT
6160870 TTACTTACTT
Statistics
Matches: 87, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
12 3 0.03
13 5 0.06
14 5 0.06
15 6 0.07
16 18 0.21
17 22 0.25
18 25 0.29
19 3 0.03
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (16 bp):
TAAATTATTAAATATA
Found at i:6160870 original size:8 final size:8
Alignment explanation
Indices: 6160715--6160868 Score: 51
Period size: 8 Copynumber: 17.5 Consensus size: 8
6160705 AAAAAATAAA
6160715 TAAAATATT
1 TAAAATA-T
6160724 ATAAAATAT
1 -TAAAATAT
*
6160733 AAAAATAATT
1 TAAAAT-A-T
6160743 TAAATATAT
1 TAAA-ATAT
6160752 T-AAATATT
1 TAAAATA-T
* *
6160760 TTAAATTT
1 TAAAATAT
6160768 TAGATAATA-
1 TA-A-AATAT
*
6160777 TAAATTAT
1 TAAAATAT
*
6160785 TAATATAT
1 TAAAATAT
* *
6160793 AAAAATTT
1 TAAAATAT
6160801 ATATAAATAT
1 -TA-AAATAT
* *
6160811 AAAAAACAT
1 -TAAAATAT
6160820 TAAATATAAT
1 TAAA-AT-AT
*
6160830 TATAATATAA
1 TA-AA-ATAT
6160840 TAAAATAT
1 TAAAATAT
6160848 TAAAATAT
1 TAAAATAT
*
6160856 ATAAATTAT
1 -TAAAATAT
6160865 TAAA
1 TAAA
6160869 TTTACTTACT
Statistics
Matches: 110, Mismatches: 20, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
7 6 0.05
8 41 0.37
9 27 0.25
10 29 0.26
11 7 0.06
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (8 bp):
TAAAATAT
Found at i:6163253 original size:17 final size:18
Alignment explanation
Indices: 6163231--6163265 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6163221 TTTAATTTTT
*
6163231 TAAAA-TATTTTTAATTA
1 TAAAATTATTTTAAATTA
6163248 TAAAATTATTTTAAATTA
1 TAAAATTATTTTAAATTA
6163266 CTATCAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAAATTATTTTAAATTA
Found at i:6163874 original size:26 final size:27
Alignment explanation
Indices: 6163831--6163883 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
6163821 CATACACTTC
*
6163831 AATTAGAATATAACTTAATAATAATTT
1 AATTAGAATATAACTTAAAAATAATTT
6163858 AATTA-AATAGTAA-TTAAAAATAATTT
1 AATTAGAATA-TAACTTAAAAATAATTT
6163884 TAAGATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (27 bp):
AATTAGAATATAACTTAAAAATAATTT
Found at i:6165286 original size:2 final size:2
Alignment explanation
Indices: 6165279--6165304 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6165269 GGCAACCTTT
6165279 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6165305 AGAACACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6167461 original size:17 final size:17
Alignment explanation
Indices: 6167421--6167463 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
6167411 TTAATTTTTT
6167421 AAAATATT--TATTTAA
1 AAAATATTAATATTTAA
*
6167436 ATTAATATTAATATTTAA
1 A-AAATATTAATATTTAA
6167454 AAAATATTAA
1 AAAATATTAA
6167464 AATATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.04
16 6 0.26
17 8 0.35
18 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATATTAATATTTAA
Found at i:6167518 original size:21 final size:21
Alignment explanation
Indices: 6167494--6167535 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6167484 TTTATATATT
*
6167494 TTTATAAT-TAAATTTAAAAAA
1 TTTAT-ATCTAAATTAAAAAAA
6167515 TTTATATCTAAATTAAAAAAA
1 TTTATATCTAAATTAAAAAAA
6167536 ATAAAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTATATCTAAATTAAAAAAA
Found at i:6168926 original size:18 final size:18
Alignment explanation
Indices: 6168903--6168937 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6168893 TTAAATTATT
6168903 ATTTAAAATATATTTTTC
1 ATTTAAAATATATTTTTC
6168921 ATTTAAAATATATTTTT
1 ATTTAAAATATATTTTT
6168938 TAAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTAAAATATATTTTTC
Found at i:6169434 original size:16 final size:16
Alignment explanation
Indices: 6169415--6169465 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
6169405 TATGATTGAG
6169415 TTATTTTAAATTTAAA
1 TTATTTTAAATTTAAA
**
6169431 TTATTTTAAATTTTGA
1 TTATTTTAAATTTAAA
6169447 TT-TCTTTAAAATTTAAA
1 TTAT-TTT-AAATTTAAA
6169464 TT
1 TT
6169466 TATTCAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 1 0.03
16 19 0.66
17 9 0.31
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
TTATTTTAAATTTAAA
Found at i:6169771 original size:15 final size:16
Alignment explanation
Indices: 6169751--6169802 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
6169741 TTGAAGTTCG
6169751 AATTTTAATATTTTT-
1 AATTTTAATATTTTTA
**
6169766 AATTTTTTTATTTTTA
1 AATTTTAATATTTTTA
*
6169782 AATTATAA-ATTTTTTA
1 AATTTTAATA-TTTTTA
6169798 AATTT
1 AATTT
6169803 AAAAAATTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 14 0.48
16 15 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTTTAATATTTTTA
Found at i:6170608 original size:21 final size:20
Alignment explanation
Indices: 6170584--6170632 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
6170574 AGCATTATTC
6170584 AATTGATTAAAATCTAA-TAAA
1 AATTGATTAAAA--TAACTAAA
* *
6170605 AATTAAATAAAATAACTAAA
1 AATTGATTAAAATAACTAAA
6170625 AATTGATT
1 AATTGATT
6170633 TTAAATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 10 0.43
21 10 0.43
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (20 bp):
AATTGATTAAAATAACTAAA
Found at i:6170977 original size:4 final size:4
Alignment explanation
Indices: 6170968--6170995 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6170958 AAAATTAAAT
6170968 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
6170996 CAAGATGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:6171111 original size:28 final size:25
Alignment explanation
Indices: 6171080--6171144 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
6171070 TTAGGATTTT
*
6171080 TTTTATTATGTCATAATTTAATATTGGA
1 TTTTATTATGTCAT-ATTTAA-ATT-AA
*
6171108 TTTTATTAT-T-ATATTTTAATTAA
1 TTTTATTATGTCATATTTAAATTAA
6171131 TTTTATTATGTCAT
1 TTTTATTATGTCAT
6171145 TTTTTGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 10 0.30
24 4 0.12
25 7 0.21
26 2 0.06
27 1 0.03
28 9 0.27
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (25 bp):
TTTTATTATGTCATATTTAAATTAA
Found at i:6171154 original size:26 final size:26
Alignment explanation
Indices: 6171080--6171154 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 26
6171070 TTAGGATTTT
* *
6171080 TTTTATTATGTCATAATTTAATATTGGA
1 TTTTATTATGTCAT-ATTTTA-ATTGAA
6171108 TTTTATTAT-T-ATATTTTAATT-AA
1 TTTTATTATGTCATATTTTAATTGAA
*
6171131 TTTTATTATGTCATTTTTTGAATT
1 TTTTATTATGTCATATTTT-AATT
6171155 TTTACTGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.24
24 4 0.10
25 11 0.27
26 6 0.15
27 1 0.02
28 9 0.22
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.61
Consensus pattern (26 bp):
TTTTATTATGTCATATTTTAATTGAA
Found at i:6171536 original size:22 final size:23
Alignment explanation
Indices: 6171496--6171542 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
6171486 AACTATTAAT
6171496 ATATTTGTTATTAATATATGAAA
1 ATATTTGTTATTAATATATGAAA
*
6171519 ATATTT-TTATTTAA-ATATTAAA
1 ATATTTGTTA-TTAATATATGAAA
6171541 AT
1 AT
6171543 TAAAGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATATTTGTTATTAATATATGAAA
Found at i:6171669 original size:27 final size:27
Alignment explanation
Indices: 6171598--6171674 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
6171588 TCTTTTGATA
6171598 ATAT-TTATTATTAATATATTAAAAAT
1 ATATATTATTATTAATATATTAAAAAT
* *
6171624 ATATATTAATATTAAAATATTTAAAAA-
1 ATATATTATTATTAATATA-TTAAAAAT
*
6171651 ATACTACTTATTATTAATAAATTA
1 ATA-TA-TTATTATTAATATATTA
6171675 TTTATATTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
26 4 0.10
27 15 0.36
28 12 0.29
29 11 0.26
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
ATATATTATTATTAATATATTAAAAAT
Found at i:6173009 original size:20 final size:20
Alignment explanation
Indices: 6172986--6173023 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6172976 TTTAATTTAA
* *
6172986 AAATTTAAATTTTAAAAAAT
1 AAATTGAAAATTTAAAAAAT
6173006 AAATTGAAAATTTAAAAA
1 AAATTGAAAATTTAAAAA
6173024 GAATATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAATTGAAAATTTAAAAAAT
Found at i:6173164 original size:23 final size:23
Alignment explanation
Indices: 6173138--6173181 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6173128 TAAATAAATA
*
6173138 TTTATAAATTTAAAATTTATATT
1 TTTATAAATTTAAAATATATATT
* *
6173161 TTTATATATTTTAAATATATA
1 TTTATAAATTTAAAATATATA
6173182 ATAATAATAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTATAAATTTAAAATATATATT
Found at i:6173179 original size:21 final size:21
Alignment explanation
Indices: 6173127--6173181 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
6173117 TTTAAAATAA
*
6173127 TTAAATAAATATTTATAAATT
1 TTAAATATATATTTATAAATT
* * *
6173148 TAAAATTTATATTTTTATATATT
1 TTAAA--TATATATTTATAAATT
6173171 TTAAATATATA
1 TTAAATATATA
6173182 ATAATAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
21 9 0.35
23 17 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAATATATATTTATAAATT
Found at i:6176277 original size:17 final size:17
Alignment explanation
Indices: 6176257--6176293 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6176247 TTGAAATACT
6176257 CAAATAATTCAAATCAA
1 CAAATAATTCAAATCAA
* *
6176274 CAAATTATTCAAATCCA
1 CAAATAATTCAAATCAA
6176291 CAA
1 CAA
6176294 CATCCAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (17 bp):
CAAATAATTCAAATCAA
Found at i:6179782 original size:29 final size:28
Alignment explanation
Indices: 6179731--6179787 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
6179721 AAAATATAAA
* *
6179731 AATAATATATTAATTATTATATTTAATAT
1 AATAATATATTAATAAATATA-TTAATAT
6179760 AATAATATATT-ATAAATAGTATTAATAT
1 AATAATATATTAATAAATA-TATTAATAT
6179788 TAAAGGGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AATAATATATTAATAAATATATTAATAT
Found at i:6180201 original size:27 final size:27
Alignment explanation
Indices: 6180150--6180217 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
6180140 TAGATTTTGT
* * *
6180150 TAATATTT-TTATTTTAAGTAGTAATA
1 TAATATTTATTATTTAAAATAATAATA
6180176 TAATATTTATTATTTAAAATAATAATA
1 TAATATTTATTATTTAAAATAATAATA
*
6180203 AAATTATTTATTATT
1 TAA-TATTTATTATT
6180218 ATATTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 8 0.22
27 17 0.47
28 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
TAATATTTATTATTTAAAATAATAATA
Found at i:6182224 original size:7 final size:7
Alignment explanation
Indices: 6182212--6182236 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6182202 GACACGGAAA
6182212 TGAATGT
1 TGAATGT
6182219 TGAATGT
1 TGAATGT
6182226 TGAATGT
1 TGAATGT
6182233 TGAA
1 TGAA
6182237 CACAGCCCAA
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:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (7 bp):
TGAATGT
Found at i:6188604 original size:3 final size:3
Alignment explanation
Indices: 6188596--6188620 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6188586 AATCGCACTT
6188596 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
6188621 CATCTTGGAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6191030 original size:25 final size:25
Alignment explanation
Indices: 6191002--6191068 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
6190992 CATTTAATTT
6191002 TAATTTATTATTAAAATATTAAAAA
1 TAATTTATTATTAAAATATTAAAAA
*
6191027 TAATTT-TATATTAATAT-TTAAAAA
1 TAATTTAT-TATTAAAATATTAAAAA
* *
6191051 T--TTTAATAATAAAATATT
1 TAATTTATTATTAAAATATT
6191069 TAAGCTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
22 10 0.29
23 2 0.06
24 9 0.26
25 14 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATTTATTATTAAAATATTAAAAA
Found at i:6191084 original size:52 final size:51
Alignment explanation
Indices: 6191028--6191147 Score: 152
Period size: 52 Copynumber: 2.3 Consensus size: 51
6191018 TATTAAAAAT
* * *
6191028 AATTTTATATTAATATTTAAAA-ATTTTAATAATAAAATATTTAAGCTTTAAA
1 AATTTTATA-TAA-AATTAAAATATTTTAATAATAAAATATTTAAACCTTAAA
*
6191080 AATTTTGTATAAAATTAAAATTATTTTAATAATAAAATATTTAAACCTTAAA
1 AATTTTATATAAAATTAAAA-TATTTTAATAATAAAATATTTAAACCTTAAA
* *
6191132 AATTTTGTACAAAATT
1 AATTTTATATAAAATT
6191148 TGACTTCAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 7 0.11
51 3 0.05
52 51 0.84
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (51 bp):
AATTTTATATAAAATTAAAATATTTTAATAATAAAATATTTAAACCTTAAA
Found at i:6191844 original size:17 final size:17
Alignment explanation
Indices: 6191824--6191862 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
6191814 CATCACATGA
6191824 AATATTAACATT-TTTTT
1 AATATTAA-ATTGTTTTT
6191841 AATATTAAATTGTTTTT
1 AATATTAAATTGTTTTT
6191858 AATAT
1 AATAT
6191863 CCTCAACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
AATATTAAATTGTTTTT
Found at i:6192131 original size:19 final size:18
Alignment explanation
Indices: 6192109--6192155 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
6192099 GTATTTAAAA
6192109 ATATCATGTCATATTTATT
1 ATATCATGTCATATTT-TT
* *
6192128 ATATTATTTTCATATTTTT
1 ATATCA-TGTCATATTTTT
6192147 ATATCATGT
1 ATATCATGT
6192156 AAAAATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 2 0.09
19 12 0.52
20 9 0.39
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (18 bp):
ATATCATGTCATATTTTT
Found at i:6193553 original size:17 final size:16
Alignment explanation
Indices: 6193507--6193610 Score: 56
Period size: 16 Copynumber: 6.4 Consensus size: 16
6193497 TATGTTATAA
*
6193507 TTATATTTA-ACATATT
1 TTATATTTATATA-ATT
6193523 TTATATTTATATAATT
1 TTATATTTATATAATT
6193539 TTAATATATTA-ATAA-T
1 TT-ATAT-TTATATAATT
*
6193555 TCATA-TTATATAGATT
1 TTATATTTATATA-ATT
* * *
6193571 TTAAAATATATATTTATT
1 TT-ATATTTATA-TAATT
*
6193589 TTATATTT-TAATTATT
1 TTATATTTAT-ATAATT
6193605 TTATAT
1 TTATAT
6193611 ATCATATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
13 3 0.04
14 3 0.04
15 4 0.06
16 30 0.43
17 17 0.24
18 12 0.17
19 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (16 bp):
TTATATTTATATAATT
Found at i:6193564 original size:37 final size:36
Alignment explanation
Indices: 6193458--6193565 Score: 86
Period size: 37 Copynumber: 3.0 Consensus size: 36
6193448 CAATGTTACA
*
6193458 TTTA-AATTTTAA-AT-TTAATAATTCATGTATATAT
1 TTTATAATTTTAATATATTAATAATTCATAT-TATAT
*
6193492 TTTATTATGTTATAATTATATT--TAA--CATATTTTATAT
1 TTTATAAT-TT-TAA-TATATTAATAATTCATA--TTATAT
6193529 TTATATAATTTTAATATATTAATAATTCATATTATAT
1 TT-TATAATTTTAATATATTAATAATTCATATTATAT
6193566 AGATTTTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 23
0.69 0.04 0.27
Matches are distributed among these distances:
34 4 0.07
35 8 0.14
36 8 0.14
37 21 0.36
38 9 0.16
39 6 0.10
40 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (36 bp):
TTTATAATTTTAATATATTAATAATTCATATTATAT
Found at i:6193623 original size:15 final size:14
Alignment explanation
Indices: 6193603--6193633 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
6193593 ATTTTAATTA
6193603 TTTTATATATCATAT
1 TTTTATA-ATCATAT
6193618 TTTTATAATCATAT
1 TTTTATAATCATAT
6193632 TT
1 TT
6193634 AAAATTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTATAATCATAT
Found at i:6196233 original size:16 final size:16
Alignment explanation
Indices: 6196212--6196246 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
6196202 GTAGTTCATC
6196212 AATAACCTTTTGACTT
1 AATAACCTTTTGACTT
*
6196228 AATAACCTTTTGATTT
1 AATAACCTTTTGACTT
6196244 AAT
1 AAT
6196247 TACTAAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (16 bp):
AATAACCTTTTGACTT
Found at i:6196390 original size:2 final size:2
Alignment explanation
Indices: 6196385--6196434 Score: 54
Period size: 2 Copynumber: 26.0 Consensus size: 2
6196375 ATTATGTTAA
6196385 AT AT AT AT AT AT AT AT AT AT -T CA- AT CAT -T AT -T 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
6196425 AT AT AT AT AT
1 AT AT AT AT AT
6196435 TCCTAAAAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
1 4 0.10
2 36 0.86
3 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6197170 original size:17 final size:18
Alignment explanation
Indices: 6197148--6197187 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
6197138 ATATATTGTC
*
6197148 TTAATTTT-TTAAAAATT
1 TTAATTTTATTAAAAATA
6197165 TTAATTTTATTAAAAATA
1 TTAATTTTATTAAAAATA
6197183 TTAAT
1 TTAAT
6197188 AAAAACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTTTATTAAAAATA
Found at i:6198232 original size:20 final size:20
Alignment explanation
Indices: 6198209--6198247 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6198199 CCCCCACACG
**
6198209 TTTAAAAATTTTAAAAATAC
1 TTTAAAAAGGTTAAAAATAC
6198229 TTTAAAAAGGTTAAAAATA
1 TTTAAAAAGGTTAAAAATA
6198248 TATAAATCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (20 bp):
TTTAAAAAGGTTAAAAATAC
Found at i:6201591 original size:20 final size:20
Alignment explanation
Indices: 6201566--6201642 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
6201556 GTAAAAAGAC
6201566 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
6201586 AGAATGTATTGATACATTCA
1 AGAATGTATCGATACATTGA
* *
6201606 TA-CATGTTTCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
6201626 AAAATGTATCGACACAT
1 AGAATGTATCGATACAT
6201643 CTGGGTATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:6202178 original size:18 final size:21
Alignment explanation
Indices: 6202155--6202196 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6202145 TATAAATTGG
6202155 TATCT-AAA-ATG-TTAAAAA
1 TATCTAAAACATGTTTAAAAA
6202173 TATCTAAAACATGTTTAAAAA
1 TATCTAAAACATGTTTAAAAA
6202194 TAT
1 TAT
6202197 ATGAAATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 3 0.14
21 10 0.48
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (21 bp):
TATCTAAAACATGTTTAAAAA
Found at i:6203263 original size:19 final size:19
Alignment explanation
Indices: 6203225--6203263 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6203215 ATATATCACG
*
6203225 TCATATTTATTATATTTTT
1 TCATATTTATCATATTTTT
6203244 TCATATTT-TCATATTGTTT
1 TCATATTTATCATATT-TTT
6203263 T
1 T
6203264 TGTATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (19 bp):
TCATATTTATCATATTTTT
Found at i:6204707 original size:17 final size:16
Alignment explanation
Indices: 6204661--6204764 Score: 56
Period size: 16 Copynumber: 6.4 Consensus size: 16
6204651 TATGTTATAA
*
6204661 TTATATTTA-ACATATT
1 TTATATTTATATA-ATT
6204677 TTATATTTATATAATT
1 TTATATTTATATAATT
6204693 TTAATATATTA-ATAA-T
1 TT-ATAT-TTATATAATT
*
6204709 TCATA-TTATATAGATT
1 TTATATTTATATA-ATT
* * *
6204725 TTAAAATATATATTTATT
1 TT-ATATTTATA-TAATT
*
6204743 TTATATTT-TAATTATT
1 TTATATTTAT-ATAATT
6204759 TTATAT
1 TTATAT
6204765 ATCATATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 20
0.71 0.08 0.20
Matches are distributed among these distances:
13 3 0.04
14 3 0.04
15 4 0.06
16 30 0.43
17 17 0.24
18 12 0.17
19 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (16 bp):
TTATATTTATATAATT
Found at i:6204718 original size:37 final size:36
Alignment explanation
Indices: 6204612--6204719 Score: 86
Period size: 37 Copynumber: 3.0 Consensus size: 36
6204602 CAATGTTACA
*
6204612 TTTA-AATTTTAA-AT-TTAATAATTCATGTATATAT
1 TTTATAATTTTAATATATTAATAATTCATAT-TATAT
*
6204646 TTTATTATGTTATAATTATATT--TAA--CATATTTTATAT
1 TTTATAAT-TT-TAA-TATATTAATAATTCATA--TTATAT
6204683 TTATATAATTTTAATATATTAATAATTCATATTATAT
1 TT-TATAATTTTAATATATTAATAATTCATATTATAT
6204720 AGATTTTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 23
0.69 0.04 0.27
Matches are distributed among these distances:
34 4 0.07
35 8 0.14
36 8 0.14
37 21 0.36
38 9 0.16
39 6 0.10
40 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (36 bp):
TTTATAATTTTAATATATTAATAATTCATATTATAT
Found at i:6204777 original size:15 final size:14
Alignment explanation
Indices: 6204757--6204787 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
6204747 ATTTTAATTA
6204757 TTTTATATATCATAT
1 TTTTATA-ATCATAT
6204772 TTTTATAATCATAT
1 TTTTATAATCATAT
6204786 TT
1 TT
6204788 AAAATTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTATAATCATAT
Found at i:6207094 original size:21 final size:21
Alignment explanation
Indices: 6207048--6207105 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
6207038 AAAATGTATC
*
6207048 TTTGAATGAAATG-ATGCATTG
1 TTTGGATGAAA-GAATGCATTG
* *
6207069 GTTGGATGAAAGAATGCATTT
1 TTTGGATGAAAGAATGCATTG
* *
6207090 TTTGGATAAAAAAATG
1 TTTGGATGAAAGAATG
6207106 TAACTTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (21 bp):
TTTGGATGAAAGAATGCATTG
Found at i:6211056 original size:153 final size:156
Alignment explanation
Indices: 6210822--6211197 Score: 410
Period size: 153 Copynumber: 2.4 Consensus size: 156
6210812 TTTGTAACTT
* * * * *
6210822 TAAAAGACTCTAAAAATAATCAT-GAAAAGGTAAACCTATCTTAAATATACTCTTTTGGCATAAA
1 TAAAAGACTCTAAAAATAATCATAGATAA-GTGAACCTATCCTAAATATACACATTTGGCATAAA
* * *** *
6210886 AGTATCTCGATGATTATACC-AGACTTGGTTCTAAAAAAATTACCAAAAACCCTTAAGG-ACTAT
65 AGCATCCCGATGATTATACCGA-ACTCAATTCTAAAAAAATTACCAAAAACCCTTAAGGAACTAC
* * * *
6210949 CTTCATCTTAAAAGTATTCTAATGATCC
129 CTTCATCTTAAAAGCATCCCAATGACCC
*
6210977 T-AAAGACTCT-AAAATAATCATAGATTAGTGAACCTATCCTAAATATACACATTTGGCATAAAA
1 TAAAAGACTCTAAAAATAATCATAGATAAGTGAACCTATCCTAAATATACACATTTGGCATAAAA
* * * * * * *
6211040 GCATCCC-AGTGTTTATATCGAACTCAATTTTAGAAAAATTATCAAAAAGCCTTTAGGAACTACC
66 GCATCCCGA-TGATTATACCGAACTCAATTCTAAAAAAATTACCAAAAACCCTTAAGGAACTACC
*
6211104 TTCATCTTGAAAGCATCCCAATGACCC
130 TTCATCTTAAAAGCATCCCAATGACCC
* * * *
6211131 TAAAAGACT-TGAAAATAATCATAGATGAGTGAA-CTATCCTAAATACACACATATGGCAT-AAA
1 TAAAAGACTCTAAAAATAATCATAGATAAGTGAACCTATCCTAAATATACACATTTGGCATAAAA
6211193 GCATC
66 GCATC
6211198 TCAATGTCTA
Statistics
Matches: 188, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
152 1 0.01
153 92 0.49
154 66 0.35
155 29 0.15
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (156 bp):
TAAAAGACTCTAAAAATAATCATAGATAAGTGAACCTATCCTAAATATACACATTTGGCATAAAA
GCATCCCGATGATTATACCGAACTCAATTCTAAAAAAATTACCAAAAACCCTTAAGGAACTACCT
TCATCTTAAAAGCATCCCAATGACCC
Found at i:6211181 original size:154 final size:152
Alignment explanation
Indices: 6210920--6211197 Score: 398
Period size: 154 Copynumber: 1.8 Consensus size: 152
6210910 TTGGTTCTAA
* * * * *
6210920 AAAAATTACCAAAAACCCTTAAGGACTATCTTCATCTTAAAAGTATTCTAATGATCCTAAAGACT
1 AAAAATTACCAAAAACCCTTAAGGACTACCTTCATCTTAAAAGCATCCCAATGACCCTAAAGACT
* * *
6210985 CTAAAATAATCATAGATTAGTGAACCTATCCTAAATATACACATTTGGCATAAAAGCATCCCAGT
66 CTAAAATAATCATAGATGAGTGAACCTATCCTAAATACACACATATGGCAT-AAAGCATCCCAGT
6211050 GTTTATATCGAACTCAATTTTAG
130 GTTTATATCGAACTCAATTTTAG
* * * *
6211073 AAAAATTATCAAAAAGCCTTTAGGAACTACCTTCATCTTGAAAGCATCCCAATGACCCTAAAAGA
1 AAAAATTACCAAAAACCCTTAAGG-ACTACCTTCATCTTAAAAGCATCCCAATGACCCT-AAAGA
6211138 CT-TGAAAATAATCATAGATGAGTGAA-CTATCCTAAATACACACATATGGCATAAAGCATC
64 CTCT-AAAATAATCATAGATGAGTGAACCTATCCTAAATACACACATATGGCATAAAGCATC
6211198 TCAATGTCTA
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
153 29 0.26
154 53 0.48
155 28 0.25
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.28
Consensus pattern (152 bp):
AAAAATTACCAAAAACCCTTAAGGACTACCTTCATCTTAAAAGCATCCCAATGACCCTAAAGACT
CTAAAATAATCATAGATGAGTGAACCTATCCTAAATACACACATATGGCATAAAGCATCCCAGTG
TTTATATCGAACTCAATTTTAG
Found at i:6213734 original size:55 final size:55
Alignment explanation
Indices: 6213648--6213758 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
6213638 TTAAATAAGT
6213648 TATAAAAATATCAAATTCACATGACAAAAGTTAACTTTTATCAAGATAGCTATTA
1 TATAAAAATATCAAATTCACATGACAAAAGTTAACTTTTATCAAGATAGCTATTA
* *
6213703 TATAAAAATATCAAATTCACATGACAGAAGTTAACTTTTATCAAGATGGCTATTA
1 TATAAAAATATCAAATTCACATGACAAAAGTTAACTTTTATCAAGATAGCTATTA
6213758 T
1 T
6213759 GTTGGGGAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (55 bp):
TATAAAAATATCAAATTCACATGACAAAAGTTAACTTTTATCAAGATAGCTATTA
Found at i:6215841 original size:15 final size:15
Alignment explanation
Indices: 6215821--6215850 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6215811 ATTTTTTATA
6215821 AAAAATTTAATAAAT
1 AAAAATTTAATAAAT
*
6215836 AAAAATTTATTAAAT
1 AAAAATTTAATAAAT
6215851 CTTAATTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAATTTAATAAAT
Found at i:6216595 original size:14 final size:14
Alignment explanation
Indices: 6216551--6216595 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
6216541 ATTGATATTT
6216551 TAATCTGATTTAAC
1 TAATCTGATTTAAC
6216565 TAATACTGATATT--C
1 TAAT-CTGAT-TTAAC
6216579 TAATCTGATTTAAC
1 TAATCTGATTTAAC
6216593 TAA
1 TAA
6216596 GCTTGGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.07
13 5 0.19
14 13 0.48
15 5 0.19
16 2 0.07
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (14 bp):
TAATCTGATTTAAC
Found at i:6218754 original size:24 final size:22
Alignment explanation
Indices: 6218726--6218774 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
6218716 ATTATATATT
*
6218726 AAAATTTATAATTAAATTTAAATA
1 AAAATATATAATT--ATTTAAATA
*
6218750 AAAATATATTATTATTTAAATA
1 AAAATATATAATTATTTAAATA
6218772 AAA
1 AAA
6218775 TTTCACATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
24 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATATATAATTATTTAAATA
Found at i:6218906 original size:3 final size:3
Alignment explanation
Indices: 6218900--6218944 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
6218890 CTACAACACA
*
6218900 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6218945 GGATCAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6219839 original size:18 final size:18
Alignment explanation
Indices: 6219816--6219850 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6219806 ATTTGTTTAT
* *
6219816 TCGTATTATATTTATATA
1 TCGTATCATAATTATATA
6219834 TCGTATCATAATTATAT
1 TCGTATCATAATTATAT
6219851 TTAAAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (18 bp):
TCGTATCATAATTATATA
Found at i:6219889 original size:18 final size:17
Alignment explanation
Indices: 6219858--6219891 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6219848 TATTTAAAAT
*
6219858 ATTTTATATTTATATAG
1 ATTTTATATATATATAG
6219875 ATTTTGATATATATATA
1 ATTTT-ATATATATATA
6219892 TATTATCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
ATTTTATATATATATAG
Found at i:6220458 original size:19 final size:20
Alignment explanation
Indices: 6220417--6220460 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
6220407 GTTCACTATG
* * *
6220417 ATTTAAAATTTTATTTTATT
1 ATTTAAAATTATATTTAAAT
6220437 ATTTAAAA-TATATTTAAAT
1 ATTTAAAATTATATTTAAAT
6220456 ATTTA
1 ATTTA
6220461 TATAATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAAAATTATATTTAAAT
Found at i:6222473 original size:5 final size:5
Alignment explanation
Indices: 6222463--6222509 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
6222453 CTTTGGGTTT
* *
6222463 TTTTC TTTTC TTTTC TTTTC TTTTC TTTCC TTTT- TTTT- TTTTG TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
6222510 TTTATTTCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
4 8 0.21
5 31 0.79
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:6223627 original size:20 final size:21
Alignment explanation
Indices: 6223602--6223646 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
6223592 TAGTATAAAA
6223602 ATAATTAAAATATAATAT-AT
1 ATAATTAAAATATAATATAAT
6223622 ATAATTAAAATATAATATAAT
1 ATAATTAAAATATAATATAAT
6223643 ATAA
1 ATAA
6223647 AAATAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATTAAAATATAATATAAT
Found at i:6223641 original size:16 final size:17
Alignment explanation
Indices: 6223595--6223655 Score: 69
Period size: 16 Copynumber: 3.9 Consensus size: 17
6223585 ATAAACATAG
6223595 TATAAAA-ATAAT-TAA
1 TATAAAATATAATATAA
* *
6223610 AATATAATAT-ATATAA
1 TATAAAATATAATATAA
6223626 T-TAAAATATAATATAA
1 TATAAAATATAATATAA
6223642 TATAAAA-ATAATAT
1 TATAAAATATAATAT
6223656 TAAAATAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 14 0.37
16 19 0.50
17 5 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TATAAAATATAATATAA
Found at i:6223652 original size:11 final size:11
Alignment explanation
Indices: 6223585--6223669 Score: 64
Period size: 11 Copynumber: 7.5 Consensus size: 11
6223575 CAAATATGAC
* *
6223585 ATAAACATAGT
1 ATAAAAATAAT
6223596 ATAAAAATAAT
1 ATAAAAATAAT
6223607 -TAAAATATAAT
1 ATAAAA-ATAAT
* *
6223618 ATATATAATTAAA
1 ATA-A-AAATAAT
*
6223631 ATATAATATAAT
1 ATA-AAAATAAT
6223643 ATAAAAATAAT
1 ATAAAAATAAT
*
6223654 ATTAAAATAAT
1 ATAAAAATAAT
*
6223665 GTAAA
1 ATAAA
6223670 TGTATTAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
10 5 0.08
11 34 0.58
12 9 0.15
13 9 0.15
14 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:6223715 original size:2 final size:2
Alignment explanation
Indices: 6223708--6223733 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6223698 ACGTGTCAAA
6223708 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
6223734 GTATGCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6224055 original size:3 final size:3
Alignment explanation
Indices: 6224047--6224092 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
6224037 ATTTAGTATT
6224047 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6224093 GCATGATAAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6224170 original size:24 final size:23
Alignment explanation
Indices: 6224138--6224192 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
6224128 ATCCAAATTA
*
6224138 AATTATTATTTATATAATA-AAAAT
1 AATTTTTA-TTATA-AATATAAAAT
*
6224162 AATTTTTATTATAAATATTAATAT
1 AATTTTTATTATAAATA-TAAAAT
6224186 AATTTTT
1 AATTTTT
6224193 TTACCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 5 0.19
24 18 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTTTTATTATAAATATAAAAT
Found at i:6224594 original size:21 final size:19
Alignment explanation
Indices: 6224570--6224614 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
6224560 TTAAGAAATA
*
6224570 AAAAAGTATTTTTTAAATTTT
1 AAAAAGTAATTTTT-AA-TTT
*
6224591 AAAAATTAATTTTTAATTT
1 AAAAAGTAATTTTTAATTT
6224610 AAAAA
1 AAAAA
6224615 TGATTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 2 0.09
21 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
AAAAAGTAATTTTTAATTT
Found at i:6224873 original size:2 final size:2
Alignment explanation
Indices: 6224866--6224891 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6224856 CAAATGCCTT
6224866 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6224892 AAATGAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6225789 original size:18 final size:18
Alignment explanation
Indices: 6225750--6225791 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6225740 AAAGAAAATT
*
6225750 AAAATTAAAATATGAAAT
1 AAAATTAAAATATGAAAA
*
6225768 AAAATTAAAATATAATAAA
1 AAAATTAAAATATGA-AAA
6225787 AAAAT
1 AAAAT
6225792 ATATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAATTAAAATATGAAAA
Found at i:6225813 original size:19 final size:19
Alignment explanation
Indices: 6225791--6225849 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
6225781 AATAAAAAAA
6225791 TATATAATATTTTAAAATT
1 TATATAATATTTTAAAATT
**
6225810 TATATAA-A-AAT-AAA-T
1 TATATAATATTTTAAAATT
6225825 TAT-TAATATTTTAAAATT
1 TATATAATATTTTAAAATT
6225843 TATATAA
1 TATATAA
6225850 AATAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 3 0.10
15 5 0.16
16 4 0.13
17 4 0.13
18 5 0.16
19 10 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATAATATTTTAAAATT
Found at i:6225837 original size:33 final size:33
Alignment explanation
Indices: 6225777--6225851 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 33
6225767 TAAAATTAAA
6225777 ATATAATAAAAAAATATATAATATTTTAAAATTT
1 ATATAA-AAAAAAATATATAATATTTTAAAATTT
*
6225811 ATATAAAAATAAAT-TATTAATATTTTAAAATTT
1 ATATAAAAAAAAATATA-TAATATTTTAAAATTT
6225844 ATATAAAA
1 ATATAAAA
6225852 TAATTTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 2 0.05
33 31 0.79
34 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
ATATAAAAAAAAATATATAATATTTTAAAATTT
Found at i:6226868 original size:13 final size:13
Alignment explanation
Indices: 6226847--6226913 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
6226837 TCGTATTTAA
*
6226847 AATATTTTATATT
1 AATAATTTATATT
6226860 AATAATTTATATT
1 AATAATTTATATT
**
6226873 ATATAAATTT-TAAA
1 A-AT-AATTTATATT
6226887 ATATATATTTATATT
1 A-ATA-ATTTATATT
6226902 -AT-ATTTATATT
1 AATAATTTATATT
6226913 A
1 A
6226914 CTTTATTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
11 9 0.20
13 16 0.36
14 12 0.27
15 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATAATTTATATT
Found at i:6226906 original size:11 final size:11
Alignment explanation
Indices: 6226890--6226932 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
6226880 TTTTAAAATA
6226890 TATATTTATAT
1 TATATTTATAT
6226901 TATATTTATAT
1 TATATTTATAT
*
6226912 TA-CTTTATTAAT
1 TATATTTA-T-AT
6226924 TATATTTAT
1 TATATTTAT
6226933 GTAATCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.15
11 14 0.52
12 5 0.19
13 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:6227083 original size:14 final size:14
Alignment explanation
Indices: 6227064--6227093 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6227054 GATATCAAAC
6227064 AATTATTTGGAGTA
1 AATTATTTGGAGTA
6227078 AATTATTTGGAGTA
1 AATTATTTGGAGTA
6227092 AA
1 AA
6227094 GACCGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (14 bp):
AATTATTTGGAGTA
Found at i:6228218 original size:17 final size:19
Alignment explanation
Indices: 6228171--6228219 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
6228161 AAATAAAAAA
6228171 ATAATTTAAATTATTATTT
1 ATAATTTAAATTATTATTT
**
6228190 ATTAATAAAAATTATT-TTT
1 A-TAATTTAAATTATTATTT
6228209 A-AATTTAAATT
1 ATAATTTAAATT
6228220 TAATCATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 8 0.32
19 5 0.20
20 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAATTTAAATTATTATTT
Found at i:6228240 original size:22 final size:22
Alignment explanation
Indices: 6228214--6228255 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6228204 TTTTTAAATT
6228214 TAAAT-TTAATCATAAAAATATA
1 TAAATATTAAT-ATAAAAATATA
6228236 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
6228256 AATTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:6228985 original size:22 final size:23
Alignment explanation
Indices: 6228960--6229021 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
6228950 TACTATTTAA
* *
6228960 TAATAAAAAAATTATTTAAAT-T
1 TAATATAAAAATAATTTAAATAT
* *
6228982 TAATTATAAAAA-CATATAAATAT
1 TAA-TATAAAAATAATTTAAATAT
6229005 TAATATAAAAATAATTT
1 TAATATAAAAATAATTT
6229022 TTTATTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATATAAAAATAATTTAAATAT
Found at i:6230445 original size:22 final size:22
Alignment explanation
Indices: 6230420--6230461 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6230410 TTAAATTACT
6230420 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
6230442 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
6230462 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:6230691 original size:23 final size:24
Alignment explanation
Indices: 6230664--6230710 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
6230654 TGAAAGATTT
6230664 ATTGATAT-AATAAAA-ATATAAAA
1 ATTGATATAAATAAAATA-ATAAAA
6230687 ATTGATATAAATAAAATAATAAAA
1 ATTGATATAAATAAAATAATAAAA
6230711 TTTAAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.36
24 13 0.59
25 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
ATTGATATAAATAAAATAATAAAA
Found at i:6230712 original size:23 final size:23
Alignment explanation
Indices: 6230664--6230710 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
6230654 TGAAAGATTT
6230664 ATTGATATAATAAAAATATAAAA
1 ATTGATATAATAAAAATATAAAA
6230687 ATTGATATAA-ATAAAATAATAAAA
1 ATTGATATAATA-AAAAT-ATAAAA
6230711 TTTAAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.05
23 15 0.68
24 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
ATTGATATAATAAAAATATAAAA
Found at i:6232136 original size:23 final size:24
Alignment explanation
Indices: 6232109--6232155 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
6232099 TGAAAGATTT
6232109 ATTGATAT-AATAAAA-ATATAAAA
1 ATTGATATAAATAAAATA-ATAAAA
6232132 ATTGATATAAATAAAATAATAAAA
1 ATTGATATAAATAAAATAATAAAA
6232156 TTTAAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.36
24 13 0.59
25 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
ATTGATATAAATAAAATAATAAAA
Found at i:6232157 original size:23 final size:23
Alignment explanation
Indices: 6232109--6232155 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
6232099 TGAAAGATTT
6232109 ATTGATATAATAAAAATATAAAA
1 ATTGATATAATAAAAATATAAAA
6232132 ATTGATATAA-ATAAAATAATAAAA
1 ATTGATATAATA-AAAAT-ATAAAA
6232156 TTTAAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.05
23 15 0.68
24 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
ATTGATATAATAAAAATATAAAA
Found at i:6233354 original size:22 final size:22
Alignment explanation
Indices: 6233329--6233370 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6233319 TTAAATTACT
6233329 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
6233351 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
6233371 ATTTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:6233603 original size:23 final size:23
Alignment explanation
Indices: 6233576--6233622 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
6233566 AGATTTATTG
6233576 ATAT-AATAAAA-ATATAAAAATTT
1 ATATAAATAAAATA-AT-AAAATTT
6233599 ATATAAATAAAATAATAAAATTT
1 ATATAAATAAAATAATAAAATTT
6233622 A
1 A
6233623 AGAGTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.55
24 9 0.41
25 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
ATATAAATAAAATAATAAAATTT
Found at i:6234818 original size:22 final size:22
Alignment explanation
Indices: 6234793--6234834 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6234783 TTAAATTACT
6234793 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
6234815 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
6234835 ATTGTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:6235068 original size:23 final size:23
Alignment explanation
Indices: 6235041--6235087 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
6235031 AGATTTATTG
6235041 ATAT-AATAAAA-ATATAAAAATTT
1 ATATAAATAAAATA-AT-AAAATTT
6235064 ATATAAATAAAATAATAAAATTT
1 ATATAAATAAAATAATAAAATTT
6235087 A
1 A
6235088 AGAGTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.55
24 9 0.41
25 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
ATATAAATAAAATAATAAAATTT
Found at i:6237604 original size:74 final size:74
Alignment explanation
Indices: 6237468--6237688 Score: 406
Period size: 74 Copynumber: 3.0 Consensus size: 74
6237458 AAGGTTAAAT
* * *
6237468 AAACCGGACATAATGTTCCTTTTCCAGAAAAAAAAGCAGCAAAATAGTTATCATAGCATATTAGA
1 AAACCAGACATAATGTTCCTTTTCCAG-ATAAAAAGCAGCAAAATAGTTATTATAGCATATTAGA
6237533 AGTTCTGGAC
65 AGTTCTGGAC
6237543 AAACCAGACATAATGTTCCTTTTCCAGATAAAAAGCAGCAAAATAGTTATTATAGCATATTAGAA
1 AAACCAGACATAATGTTCCTTTTCCAGATAAAAAGCAGCAAAATAGTTATTATAGCATATTAGAA
6237608 GTTCTGGAC
66 GTTCTGGAC
6237617 AAACCAGACATAATGTTCCTTTTCCAGATAAAAAGCAGCAAAATAGTTATTATAGCATATTAGAA
1 AAACCAGACATAATGTTCCTTTTCCAGATAAAAAGCAGCAAAATAGTTATTATAGCATATTAGAA
6237682 GTTCTGG
66 GTTCTGG
6237689 CTTGCTGGAA
Statistics
Matches: 143, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
74 117 0.82
75 26 0.18
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (74 bp):
AAACCAGACATAATGTTCCTTTTCCAGATAAAAAGCAGCAAAATAGTTATTATAGCATATTAGAA
GTTCTGGAC
Found at i:6239608 original size:22 final size:22
Alignment explanation
Indices: 6239554--6239608 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
6239544 TTCGAAAAAA
6239554 ATTTAAAAT-T-T-AAATTTAG
1 ATTTAAAATATATAAAATTTAG
* *
6239573 ATTTAAATTTTATAAAATTTA-
1 ATTTAAAATATATAAAATTTAG
6239594 ATTTAATAATATATA
1 ATTTAA-AATATATA
6239609 TTTATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 8 0.28
20 1 0.03
21 7 0.24
22 13 0.45
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTTAAAATATATAAAATTTAG
Found at i:6239667 original size:21 final size:21
Alignment explanation
Indices: 6239642--6239681 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6239632 TTAAAAAAAT
6239642 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
6239663 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
6239682 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:6240216 original size:15 final size:16
Alignment explanation
Indices: 6240183--6240218 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6240173 TCATTCTCTT
*
6240183 AAAAAACTAATATTTA
1 AAAAAACTAATATTCA
6240199 AAAAAACTAATA-TCA
1 AAAAAACTAATATTCA
6240214 AAAAA
1 AAAAA
6240219 TTACTCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAACTAATATTCA
Found at i:6240261 original size:19 final size:18
Alignment explanation
Indices: 6240213--6240262 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
6240203 AACTAATATC
6240213 AAAAAATTACTCTATTAA
1 AAAAAATTACTCTATTAA
*
6240231 AAAACTATTACTCTATTAA
1 AAAA-AATTACTCTATTAA
*
6240250 ATAAAAACTACTC
1 A-AAAAATTACTC
6240263 ATATATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 20 0.74
20 3 0.11
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAAATTACTCTATTAA
Found at i:6240318 original size:14 final size:13
Alignment explanation
Indices: 6240297--6240342 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 13
6240287 TATTAAATAA
6240297 AAATTATTTATAT
1 AAATTATTTATAT
6240310 AAATATATTTATAT
1 AAAT-TATTTATAT
6240324 AAAATCTAATTTATAT
1 -AAAT-T-ATTTATAT
6240340 AAA
1 AAA
6240343 AAAATAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 4 0.14
14 9 0.31
15 8 0.28
16 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATTTATAT
Done.