Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 7 of 31
Found at i:1628348 original size:13 final size:13
Alignment explanation
Indices: 1628330--1628354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1628320 TTTAACTATA
1628330 AATATAAATATTG
1 AATATAAATATTG
1628343 AATATAAATATT
1 AATATAAATATT
1628355 TTAATAAAAA
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AATATAAATATTG
Found at i:1629521 original size:2 final size:2
Alignment explanation
Indices: 1629514--1629553 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1629504 TTGCTACTTG
1629514 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
1629554 CATGGACAAT
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:1635839 original size:35 final size:35
Alignment explanation
Indices: 1635793--1635862 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1635783 AATTGTAGTA
1635793 ATATTTTCTCTTAATATTACAATAACCTGAAAAGT
1 ATATTTTCTCTTAATATTACAATAACCTGAAAAGT
1635828 ATATTTTCTCTTAATATTACAATAACCTGAAAAGT
1 ATATTTTCTCTTAATATTACAATAACCTGAAAAGT
1635863 CCTAGAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (35 bp):
ATATTTTCTCTTAATATTACAATAACCTGAAAAGT
Found at i:1636624 original size:16 final size:16
Alignment explanation
Indices: 1636603--1636638 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1636593 TTAATTTTTT
*
1636603 ATATAAAAAAATATTA
1 ATATAAAAAAATATAA
*
1636619 ATATAAAAAATTATAA
1 ATATAAAAAAATATAA
1636635 ATAT
1 ATAT
1636639 TAATATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAAAAAATATAA
Found at i:1643151 original size:24 final size:24
Alignment explanation
Indices: 1643124--1643173 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1643114 GAAGTTCATA
*
1643124 AATGAGATCTATATAAGATATAAC
1 AATGAGATCTATATAAGATACAAC
1643148 AATGAGATCTATATAAGATACAAC
1 AATGAGATCTATATAAGATACAAC
1643172 AA
1 AA
1643174 GGTTTCCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (24 bp):
AATGAGATCTATATAAGATACAAC
Found at i:1643342 original size:25 final size:25
Alignment explanation
Indices: 1643313--1643365 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1643303 ATATAAAAAA
*
1643313 TTATT-ATTACATGTAAATATTTAAT
1 TTATTAATTA-ATATAAATATTTAAT
* *
1643338 TTATTAATTAATATATATTTTTAAT
1 TTATTAATTAATATAAATATTTAAT
1643363 TTA
1 TTA
1643366 ACAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TTATTAATTAATATAAATATTTAAT
Found at i:1644394 original size:34 final size:34
Alignment explanation
Indices: 1644347--1644412 Score: 82
Period size: 37 Copynumber: 1.9 Consensus size: 34
1644337 CGTGAGATTT
1644347 TTTTATTTTTATA-TAATTTTT-TAATAATTTTA
1 TTTTATTTTTATACTAATTTTTGTAATAATTTTA
*
1644379 TTTTATTAATTTATATCTTATTTTTGTAATAATT
1 TTTTATT--TTTATA-CTAATTTTTGTAATAATT
1644413 AATATCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 7 0.25
34 6 0.21
36 7 0.25
37 8 0.29
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (34 bp):
TTTTATTTTTATACTAATTTTTGTAATAATTTTA
Found at i:1652779 original size:2 final size:2
Alignment explanation
Indices: 1652772--1652802 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1652762 ACATACATGC
1652772 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1652803 ATTGAGGAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1653635 original size:2 final size:2
Alignment explanation
Indices: 1653623--1653662 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1653613 TTTTCAATAA
* * *
1653623 AT AT TT AT AT AT AT AC AT AC 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
1653663 TACGTGCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1656776 original size:2 final size:2
Alignment explanation
Indices: 1656769--1656793 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1656759 GGATTTATTT
1656769 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1656794 TGTTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1672433 original size:38 final size:38
Alignment explanation
Indices: 1672382--1672458 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
1672372 TTTTTACGTT
1672382 ATGCTATCAATAAAATGAATGTGACACATGGATTGTGA
1 ATGCTATCAATAAAATGAATGTGACACATGGATTGTGA
*
1672420 ATGCTATCAATAAAATGAATGTGATACATGGATTGTGA
1 ATGCTATCAATAAAATGAATGTGACACATGGATTGTGA
1672458 A
1 A
1672459 GATTTTACTA
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:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (38 bp):
ATGCTATCAATAAAATGAATGTGACACATGGATTGTGA
Found at i:1676180 original size:2 final size:2
Alignment explanation
Indices: 1676173--1676212 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1676163 CGCGTTTCGT
1676173 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1676213 TTTAACTAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1677493 original size:22 final size:24
Alignment explanation
Indices: 1677465--1677514 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1677455 TACATTGCTG
1677465 ATTTTAC-TCGAAAAAAT-TAATA
1 ATTTTACTTCGAAAAAATATAATA
* *
1677487 ATTTTACTTCTAATAAATATAATA
1 ATTTTACTTCGAAAAAATATAATA
1677511 ATTT
1 ATTT
1677515 ATCTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.29
23 8 0.33
24 9 0.38
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (24 bp):
ATTTTACTTCGAAAAAATATAATA
Found at i:1678355 original size:29 final size:29
Alignment explanation
Indices: 1678294--1678357 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 29
1678284 CTGATTTGAT
*
1678294 TTGATTTCTTTTTTTTTTAATTATAAAGC
1 TTGATTTCTTTTTTTTTTAATGATAAAGC
1678323 -TGATTTC-TTTTTTTTTAATGA-AAATGGC
1 TTGATTTCTTTTTTTTTTAATGATAAA--GC
1678351 TTGATTT
1 TTGATTT
1678358 GATTGAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 3 0.10
27 13 0.42
28 9 0.29
29 6 0.19
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.59
Consensus pattern (29 bp):
TTGATTTCTTTTTTTTTTAATGATAAAGC
Found at i:1681634 original size:20 final size:19
Alignment explanation
Indices: 1681575--1681634 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
1681565 GATGTATTTA
* *
1681575 AAATATAAAATATATTACAC
1 AAATATAAAATAT-TTAAAT
1681595 AAATACATAAAATA--TAAAT
1 AAAT--ATAAAATATTTAAAT
1681614 AAATATAAAATATTTTAAAT
1 AAATATAAAATA-TTTAAAT
1681634 A
1 A
1681635 TAATTATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
17 8 0.24
19 7 0.21
20 10 0.30
22 8 0.24
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATATAAAATATTTAAAT
Found at i:1710494 original size:20 final size:20
Alignment explanation
Indices: 1710469--1710535 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
1710459 TAAATTCTCA
*
1710469 AATTTATTAATCATTTGTAT
1 AATTTATTAATAATTTGTAT
*
1710489 AATTTACATATAA-AATTTGCA-
1 AATTT--AT-TAATAATTTGTAT
*
1710510 AATTTATTAATTATTTGTAT
1 AATTTATTAATAATTTGTAT
*
1710530 GATTTA
1 AATTTA
1710536 ACAGTAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
18 3 0.08
19 8 0.22
20 10 0.27
21 5 0.14
22 8 0.22
23 3 0.08
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (20 bp):
AATTTATTAATAATTTGTAT
Found at i:1711205 original size:16 final size:16
Alignment explanation
Indices: 1711165--1711211 Score: 69
Period size: 15 Copynumber: 2.9 Consensus size: 16
1711155 GATAAAGTCA
*
1711165 ATTTTATATTTAAATT
1 ATTTTAAATTTAAATT
1711181 ATTTT-AATTTAAATT
1 ATTTTAAATTTAAATT
1711196 ATTTTAAATTTTAAAT
1 ATTTTAAA-TTTAAAT
1711212 CTCTAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 14 0.50
16 7 0.25
17 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:1711533 original size:2 final size:2
Alignment explanation
Indices: 1711526--1711557 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1711516 ACATACATGC
1711526 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
1711558 GGAGTTGGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1712110 original size:20 final size:18
Alignment explanation
Indices: 1712061--1712112 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 18
1712051 TTTATTTATT
*
1712061 TAAAAATAATATAA-ACG
1 TAAAAATAATATAATAAG
1712078 TAAAAA-AAT-TAATAAG
1 TAAAAATAATATAATAAG
1712094 TAAAAAAATAATATAATAA
1 T--AAAAATAATATAATAA
1712113 AATGATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 3 0.10
16 6 0.21
17 6 0.21
18 5 0.17
19 3 0.10
20 6 0.21
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (18 bp):
TAAAAATAATATAATAAG
Found at i:1717942 original size:3 final size:3
Alignment explanation
Indices: 1717936--1717971 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1717926 GCTGTTGTTT
* *
1717936 TTC TTC TCC TTT TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1717972 CCATGGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1719764 original size:22 final size:24
Alignment explanation
Indices: 1719730--1719773 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1719720 ATCTAAATTA
1719730 TAAAATTTATAATTT-TTTTATTT
1 TAAAATTTATAATTTCTTTTATTT
1719753 TAAAA-TTATAATTTCTTTTAT
1 TAAAATTTATAATTTCTTTTAT
1719774 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TAAAATTTATAATTTCTTTTATTT
Found at i:1719779 original size:23 final size:23
Alignment explanation
Indices: 1719729--1719780 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1719719 TATCTAAATT
*
1719729 ATAAAATTTATAATTTTTTTATT
1 ATAAAATTTATAATTTTTTTATA
*
1719752 TTAAAA-TTATAATTTCTTTTATA
1 ATAAAATTTATAATTT-TTTTATA
1719775 ATAAAA
1 ATAAAA
1719781 AAATACCAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
ATAAAATTTATAATTTTTTTATA
Found at i:1727030 original size:4 final size:4
Alignment explanation
Indices: 1727021--1727046 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1727011 TTCTTATTGC
1727021 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
1727047 GAGTGTATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1727771 original size:21 final size:22
Alignment explanation
Indices: 1727747--1727788 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1727737 ATATATCAAA
1727747 AAATGT-TAATAACAATTTAAT
1 AAATGTGTAATAACAATTTAAT
* *
1727768 AAATGTGTATTAACAGTTTAA
1 AAATGTGTAATAACAATTTAA
1727789 CACCTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (22 bp):
AAATGTGTAATAACAATTTAAT
Found at i:1728065 original size:7 final size:6
Alignment explanation
Indices: 1728038--1728062 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1728028 TTATTTAAAC
1728038 TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT T
1728063 TAAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:1729566 original size:14 final size:15
Alignment explanation
Indices: 1729537--1729567 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1729527 AATTTAAAAA
1729537 ATACTTTTACTATAT
1 ATACTTTTACTATAT
1729552 ATACTTTTA-TATAT
1 ATACTTTTACTATAT
1729566 AT
1 AT
1729568 TTATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
ATACTTTTACTATAT
Found at i:1729728 original size:20 final size:20
Alignment explanation
Indices: 1729703--1729757 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
1729693 CACACGTAAC
* *
1729703 AAATATTAATTTTAAAATTT
1 AAATATTAATATAAAAATTT
1729723 AAATATTTAATATAAAAATTT
1 AAATA-TTAATATAAAAATTT
1729744 AAATATTAA-ATAAA
1 AAATATTAATATAAA
1729758 TAAGTATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 5 0.16
20 9 0.28
21 18 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATTAATATAAAAATTT
Found at i:1729738 original size:13 final size:15
Alignment explanation
Indices: 1729703--1729755 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 15
1729693 CACACGTAAC
1729703 AAATATT-AAT-TTT
1 AAATATTAAATATTT
1729716 AAA-ATTTAAATATTT
1 AAATA-TTAAATATTT
*
1729731 -AATA-TAAAAATTT
1 AAATATTAAATATTT
1729744 AAATATTAAATA
1 AAATATTAAATA
1729756 AATAAGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
12 1 0.03
13 13 0.41
14 9 0.28
15 9 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATATTAAATATTT
Found at i:1729767 original size:21 final size:20
Alignment explanation
Indices: 1729703--1729771 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
1729693 CACACGTAAC
* * *
1729703 AAATATTAATTTTAAAATTT
1 AAATATTAATATAAAAATAT
*
1729723 AAATATTTAATATAAAAATTT
1 AAATA-TTAATATAAAAATAT
1729744 AAATATTAA-ATAAATAAGTAT
1 AAATATTAATATAAA-AA-TAT
1729765 AAA-ATTA
1 AAATATTA
1729772 TTTTTTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
19 5 0.12
20 15 0.35
21 23 0.53
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (20 bp):
AAATATTAATATAAAAATAT
Found at i:1731966 original size:19 final size:20
Alignment explanation
Indices: 1731929--1731977 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1731919 AATATAAAAA
* *
1731929 AAATCTTTTAAATATATAAGT
1 AAAT-TTTTAAATAAATAAAT
1731950 AAATTTTTAAA-AAATAAAT
1 AAATTTTTAAATAAATAAAT
*
1731969 ATATTTTTA
1 AAATTTTTA
1731978 TTATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.56
20 7 0.28
21 4 0.16
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
AAATTTTTAAATAAATAAAT
Found at i:1733329 original size:11 final size:11
Alignment explanation
Indices: 1733310--1733360 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1733300 AATTTTAAAA
1733310 TATATTTATATT
1 TATA-TTATATT
1733322 TATATTATATT
1 TATATTATATT
*
1733333 T-TAATTATTTTT
1 TAT-ATTA-TATT
*
1733345 TATATTATAGT
1 TATATTATATT
1733356 TATAT
1 TATAT
1733361 AATTATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 1 0.03
11 19 0.58
12 12 0.36
13 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TATATTATATT
Found at i:1736405 original size:28 final size:28
Alignment explanation
Indices: 1736369--1736424 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1736359 CACACGAGTA
1736369 TATATTTTATATAAATATATTTAAAAAAT
1 TATATTTTATATAAATATA-TTAAAAAAT
**
1736398 TATA-TTTATATTCATATATTAAAAAAT
1 TATATTTTATATAAATATATTAAAAAAT
1736425 AAAAATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.36
28 12 0.48
29 4 0.16
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
TATATTTTATATAAATATATTAAAAAAT
Found at i:1737160 original size:20 final size:21
Alignment explanation
Indices: 1737135--1737175 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1737125 TACCTCTTTG
*
1737135 ATATATCTA-ATATTATATAT
1 ATATATATATATATTATATAT
1737155 ATATATATATTATATTATATA
1 ATATATATA-TATATTATATA
1737176 GGGTTTAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATATATATATATTATATAT
Found at i:1746574 original size:31 final size:32
Alignment explanation
Indices: 1746539--1746600 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1746529 TTGAGACAAG
*
1746539 AAATC-ATTAAAAATTACTTAGATGCTGCTTA
1 AAATCAATTAAAAATGACTTAGATGCTGCTTA
*
1746570 AAATCAATTAAAAATGACTTAGATGTTGCTT
1 AAATCAATTAAAAATGACTTAGATGCTGCTT
1746601 TTGTTTCAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (32 bp):
AAATCAATTAAAAATGACTTAGATGCTGCTTA
Found at i:1747970 original size:28 final size:27
Alignment explanation
Indices: 1747921--1748002 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 27
1747911 TAATACAAAT
* *
1747921 TAAAAATAAAAATATTACTTAAATATAA
1 TAAAAATAAAAA-CTTATTTAAATATAA
*
1747949 TAAAAATATAAAACTTATTTAAAAATAA
1 TAAAAATA-AAAACTTATTTAAATATAA
*
1747977 -AATAATTAAAAAACTT-TTTAATATAT
1 TAA-AAAT-AAAAACTTATTTAA-ATAT
1748003 TAGCTTAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
27 7 0.16
28 33 0.73
29 5 0.11
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (27 bp):
TAAAAATAAAAACTTATTTAAATATAA
Found at i:1753320 original size:17 final size:17
Alignment explanation
Indices: 1753298--1753337 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1753288 TCACTTACTT
1753298 TTTTAAAGTTTTTAAAA
1 TTTTAAAGTTTTTAAAA
**
1753315 TTTTAATTTTTTTAAAA
1 TTTTAAAGTTTTTAAAA
1753332 TTTTAA
1 TTTTAA
1753338 TTATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTAAAGTTTTTAAAA
Found at i:1753338 original size:17 final size:17
Alignment explanation
Indices: 1753306--1753345 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1753296 TTTTTTAAAG
1753306 TTTTTAAAATTTTAATT
1 TTTTTAAAATTTTAATT
1753323 TTTTTAAAATTTTAATT
1 TTTTTAAAATTTTAATT
*
1753340 ATTTTA
1 TTTTTA
1753346 TATTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTAAAATTTTAATT
Found at i:1753343 original size:26 final size:27
Alignment explanation
Indices: 1753296--1753350 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
1753286 TTTCACTTAC
*
1753296 TTTTTTAAAGTTTTTAAAATTTTA-AT
1 TTTTTTAAAGATTTTAAAATTTTATAT
*
1753322 TTTTTTAAA-ATTTTAATTATTTTATAT
1 TTTTTTAAAGATTTTAA-AATTTTATAT
1753349 TT
1 TT
1753351 AAATTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 15 0.60
27 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTTTAAAGATTTTAAAATTTTATAT
Found at i:1753451 original size:15 final size:18
Alignment explanation
Indices: 1753409--1753446 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1753399 TTCAACATTC
1753409 ATATTTATTTAAATTTAAA
1 ATATTTATTTAAATTT-AA
1753428 ATATTTATTTAAA-TTAA
1 ATATTTATTTAAATTTAA
1753445 AT
1 AT
1753447 TTATTAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 2 0.11
19 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTATTTAAATTTAA
Found at i:1754391 original size:20 final size:21
Alignment explanation
Indices: 1754346--1754394 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1754336 AATATTTTTT
* *
1754346 TAAAATAAGTTAATTATATAA
1 TAAATTAAGTAAATTATATAA
*
1754367 -GAATTAAGTAAATTATA-AA
1 TAAATTAAGTAAATTATATAA
1754386 TAAATTAAG
1 TAAATTAAG
1754395 AATATATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (21 bp):
TAAATTAAGTAAATTATATAA
Found at i:1754403 original size:2 final size:2
Alignment explanation
Indices: 1754396--1754420 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1754386 TAAATTAAGA
1754396 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1754421 AAGGCCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1754757 original size:21 final size:19
Alignment explanation
Indices: 1754723--1754774 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 19
1754713 AAACTCTTTG
1754723 TATTTTTATTATATTTAAA
1 TATTTTTATTATATTTAAA
1754742 TATTTTTAATTTATATTTATATA
1 TATTTTT-A-TTATATTTA-A-A
*
1754765 AATTTTTATT
1 TATTTTTATT
1754775 TTAAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 7 0.25
20 1 0.04
21 11 0.39
22 2 0.07
23 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTATTATATTTAAA
Found at i:1754849 original size:30 final size:31
Alignment explanation
Indices: 1754797--1754855 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1754787 TTGATATATG
* **
1754797 TTAAGAGTTTATTTAAGTATAAATTAAAAAT
1 TTAAGAGTTAATTTAAACATAAATTAAAAAT
1754828 TTAA-AGTTAATTTAAACATAAATTAAAA
1 TTAAGAGTTAATTTAAACATAAATTAAAA
1754856 GTTAATGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (31 bp):
TTAAGAGTTAATTTAAACATAAATTAAAAAT
Found at i:1756596 original size:7 final size:7
Alignment explanation
Indices: 1756582--1756611 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1756572 TTATTACTAA
1756582 TGAAGTT
1 TGAAGTT
*
1756589 TAAAGTT
1 TGAAGTT
1756596 TGAAGTT
1 TGAAGTT
1756603 TGAAGTT
1 TGAAGTT
1756610 TG
1 TG
1756612 GAGTGCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (7 bp):
TGAAGTT
Found at i:1757542 original size:52 final size:52
Alignment explanation
Indices: 1757481--1757586 Score: 142
Period size: 52 Copynumber: 2.0 Consensus size: 52
1757471 TGTAAAGCTT
* * * *
1757481 ATGTATTTTTAAAAATTGTATATAATAGTACTTTTCAATC-ATTTGTAAATAA
1 ATGTATTTTTAAAAAATGTACATAATAATACTTTTCAA-CGATTTGTAAACAA
* *
1757533 ATGTGTTTTTAAAAAATGTACATAGTAATACTTTTCAACGATTTGTAAACAA
1 ATGTATTTTTAAAAAATGTACATAATAATACTTTTCAACGATTTGTAAACAA
1757585 AT
1 AT
1757587 AACAAATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
51 1 0.02
52 46 0.98
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (52 bp):
ATGTATTTTTAAAAAATGTACATAATAATACTTTTCAACGATTTGTAAACAA
Found at i:1761488 original size:23 final size:24
Alignment explanation
Indices: 1761472--1761519 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1761462 ATAATTTATA
1761472 TATTATTAATAAAATAAATAATAT
1 TATTATTAATAAAATAAATAATAT
* *
1761496 TATT-TTATTAAAATAAAAAATAT
1 TATTATTAATAAAATAAATAATAT
1761519 T
1 T
1761520 TATATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTATTAATAAAATAAATAATAT
Found at i:1761516 original size:26 final size:25
Alignment explanation
Indices: 1761465--1761529 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 25
1761455 ATAATATATA
*
1761465 ATTTATATATTATTAATAAAATAAAT
1 ATTTATAT-TTATTAATAAAAAAAAT
1761491 AATATTAT-TTTATTAA-AATAAAAAAT
1 -AT-TTATATTTATTAATAA-AAAAAAT
1761517 ATTTATATTTATT
1 ATTTATATTTATT
1761530 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
24 4 0.12
25 10 0.29
26 13 0.38
27 3 0.09
28 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTATATTTATTAATAAAAAAAAT
Found at i:1762528 original size:2 final size:2
Alignment explanation
Indices: 1762521--1762549 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1762511 GTTCTTTAGC
1762521 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1762550 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1762554 original size:2 final size:2
Alignment explanation
Indices: 1762549--1762580 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1762539 TATATATATA
1762549 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1762581 CAAATGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1767192 original size:45 final size:46
Alignment explanation
Indices: 1767141--1767227 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 46
1767131 TTCTTTCGTT
* *
1767141 AATGTTAAATGGTTTTATTTTTTCAC-GAAAAAATTCAAAAAAATA
1 AATGTTAAATGGTTTTATTATTTCACAAAAAAAATTCAAAAAAATA
*
1767186 AATGTTACATGGTTTTATTATTTCACAAAAAAAATTCAAAAA
1 AATGTTAAATGGTTTTATTATTTCACAAAAAAAATTCAAAAA
1767228 TAAATTGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 24 0.63
46 14 0.37
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (46 bp):
AATGTTAAATGGTTTTATTATTTCACAAAAAAAATTCAAAAAAATA
Found at i:1767237 original size:45 final size:44
Alignment explanation
Indices: 1767141--1767238 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 44
1767131 TTCTTTCGTT
* * *
1767141 AATGTTAAATGGTTTTATTTTTTCACGAAAAAATTCAAAAAAATA
1 AATGTTACATGGTTTTATTATTTCACAAAAAAATTC-AAAAAATA
1767186 AATGTTACATGGTTTTATTATTTCACAAAAAAAATTC-AAAAATA
1 AATGTTACATGGTTTTATTATTTCAC-AAAAAAATTCAAAAAATA
1767230 AATTGTTAC
1 AA-TGTTAC
1767239 TAGAAAACTG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
44 9 0.19
45 30 0.62
46 9 0.19
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (44 bp):
AATGTTACATGGTTTTATTATTTCACAAAAAAATTCAAAAAATA
Found at i:1768118 original size:3 final size:3
Alignment explanation
Indices: 1768112--1768157 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1768102 TATGCATGGT
1768112 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
1768158 GAGGTTATAT
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:1768576 original size:2 final size:2
Alignment explanation
Indices: 1768571--1768602 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1768561 AAAAAAAATC
1768571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1768603 CCTGAATACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1771610 original size:23 final size:24
Alignment explanation
Indices: 1771558--1771628 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 24
1771548 AGTTGGACTC
*
1771558 ATTTTTAATTATATAATATATATT
1 ATTTTTAATTATATAATATATATA
* *
1771582 AGTTTTCATT-TAT-ATATTATATA
1 ATTTTTAATTATATAATA-TATATA
* *
1771605 ATTTTT-ATCATATAAAAATATATA
1 ATTTTTAATTATAT-AATATATATA
1771629 TTATATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
22 5 0.14
23 16 0.43
24 14 0.38
25 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (24 bp):
ATTTTTAATTATATAATATATATA
Found at i:1771742 original size:21 final size:22
Alignment explanation
Indices: 1771703--1771747 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1771693 ATATTAAATT
* *
1771703 ATAAAAATTAAAATTTAAA-AA
1 ATAAAAAATAAAATATAAATAA
*
1771724 ATAAAAAATATAATATAAATAA
1 ATAAAAAATAAAATATAAATAA
1771746 AT
1 AT
1771748 TTAGATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
ATAAAAAATAAAATATAAATAA
Found at i:1772027 original size:2 final size:2
Alignment explanation
Indices: 1772014--1772049 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1772004 TGTACACTGT
*
1772014 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1772050 AAAGCTACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1772424 original size:18 final size:16
Alignment explanation
Indices: 1772373--1772424 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 16
1772363 TTTATAATAA
*
1772373 TTATATTTAAAATATT
1 TTATATTTAATATATT
*
1772389 TTATATTTATATAAATT
1 TTATATTTA-ATATATT
1772406 TTAATATTATAATATATT
1 TT-ATATT-TAATATATT
1772424 T
1 T
1772425 ATTTTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 12 0.40
19 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTTAATATATT
Found at i:1772433 original size:16 final size:16
Alignment explanation
Indices: 1772361--1772433 Score: 55
Period size: 16 Copynumber: 4.6 Consensus size: 16
1772351 GTGTTATGTA
1772361 ATTTTATAATA-A-TT
1 ATTTTATAATATATTT
*
1772375 ATATTTAAAATAT-TTT
1 AT-TTTATAATATATTT
*
1772391 ATATTTAT-ATAAATTTT
1 AT-TTTATAATATA-TTT
*
1772408 AATATTATAATATATTT
1 -ATTTTATAATATATTT
1772425 ATTTTATAA
1 ATTTTATAA
1772434 ATTTTAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
14 2 0.04
15 11 0.24
16 17 0.37
17 10 0.22
18 6 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTATAATATATTT
Found at i:1772445 original size:33 final size:32
Alignment explanation
Indices: 1772383--1772460 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 32
1772373 TTATATTTAA
*
1772383 AATATTTTATATTTATATAAATTTTAATATTAT
1 AATATATTATATTTATATAAATTTTAATATT-T
1772416 AATATATT-TATTT-TATAAATTTTAAAATATTT
1 AATATATTATATTTATATAAATTTT--AATATTT
1772448 -ATATATTCATATT
1 AATATATT-ATATT
1772461 ATGTCAAGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
31 17 0.43
32 6 0.15
33 17 0.43
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (32 bp):
AATATATTATATTTATATAAATTTTAATATTT
Found at i:1776881 original size:22 final size:22
Alignment explanation
Indices: 1776856--1776907 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1776846 GAAATTAACC
* * *
1776856 TATCTTATATTTTATGAAAATA
1 TATCTTATATTTAATAAAAAAA
*
1776878 TATCATATATTTAATAAAAAAA
1 TATCTTATATTTAATAAAAAAA
*
1776900 TATGTTAT
1 TATCTTAT
1776908 GTACTTATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (22 bp):
TATCTTATATTTAATAAAAAAA
Found at i:1777499 original size:27 final size:28
Alignment explanation
Indices: 1777444--1777503 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1777434 TTTAGATACT
* *
1777444 AAATTTTAAATCTTAAATTTTTTATAAA
1 AAATTATAAATATTAAATTTTTTATAAA
* *
1777472 AAATTATAAATATTAATTTTTTTAAAAA
1 AAATTATAAATATTAAATTTTTTATAAA
1777500 AAAT
1 AAAT
1777504 GTAACAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
AAATTATAAATATTAAATTTTTTATAAA
Found at i:1780129 original size:2 final size:2
Alignment explanation
Indices: 1780122--1780159 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1780112 GGAAAGTTTG
1780122 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
1780160 TGATGCCAAA
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:1780748 original size:2 final size:2
Alignment explanation
Indices: 1780741--1780775 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1780731 AGAAGTCTTA
* *
1780741 AT AT AT AT AT AT AT AT AT AC AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1780776 AAAGAGGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1782838 original size:34 final size:34
Alignment explanation
Indices: 1782773--1782874 Score: 91
Period size: 34 Copynumber: 3.0 Consensus size: 34
1782763 TATGAGAATG
* * * * *
1782773 AAATAAAAAATTATAGTA-GTAATTTGATTTAATA
1 AAATAAAATATTATAATATTTAATTT-TTTTAAAA
1782807 AAATAAAATATTATAATATTTAATTTTTTTAAAA
1 AAATAAAATATTATAATATTTAATTTTTTTAAAA
* * *
1782841 AAATTAAAT-TTTTAATGATTTAAATCTTTTTAAA
1 AAATAAAATATTATAAT-ATTT-AATTTTTTTAAA
1782875 CAATTTCATA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
33 6 0.11
34 34 0.60
35 17 0.30
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (34 bp):
AAATAAAATATTATAATATTTAATTTTTTTAAAA
Found at i:1788801 original size:20 final size:19
Alignment explanation
Indices: 1788765--1788832 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
1788755 AATTAAAAAG
* *
1788765 AATAAAAAAATATTTTTAA
1 AATAAATAATTATTTTTAA
*
1788784 AATAAATAGTTAATTTTT--
1 AATAAATAATT-ATTTTTAA
*
1788802 AATGAATAATTATTTTTAAA
1 AATAAATAATTATTTTT-AA
1788822 AATAAATAATT
1 AATAAATAATT
1788833 TAAATAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
17 6 0.15
18 9 0.23
19 8 0.21
20 16 0.41
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
AATAAATAATTATTTTTAA
Found at i:1788891 original size:23 final size:23
Alignment explanation
Indices: 1788838--1788891 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
1788828 TAATTTAAAT
1788838 AATTTAATTTTTATTTTTTACTA
1 AATTTAATTTTTATTTTTTACTA
1788861 AACTTTTAATTTATTATTTTTTA-TA
1 AA--TTTAATTT-TTATTTTTTACTA
*
1788886 TATTTA
1 AATTTA
1788892 TAAAGAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 6 0.22
25 11 0.41
26 10 0.37
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
AATTTAATTTTTATTTTTTACTA
Found at i:1789198 original size:18 final size:17
Alignment explanation
Indices: 1789164--1789202 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1789154 ACTTTAGGTT
* *
1789164 TATTATTAATTATAATAA
1 TATTATTAATAACAAT-A
1789182 TATTATTAATAACAATA
1 TATTATTAATAACAATA
1789199 TATT
1 TATT
1789203 GTTTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTATTAATAACAATA
Found at i:1792572 original size:21 final size:23
Alignment explanation
Indices: 1792534--1792589 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
1792524 AGTATGAATT
*
1792534 ATAAATTAAAAAATTTA-TTTAA
1 ATAAAATAAAAAATTTATTTTAA
*
1792556 ATAAAATAAAAAA-TTATTTTGA
1 ATAAAATAAAAAATTTATTTTAA
*
1792578 ATAGAATAAAAA
1 ATAAAATAAAAA
1792590 GTGTAAAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (23 bp):
ATAAAATAAAAAATTTATTTTAA
Found at i:1792936 original size:12 final size:12
Alignment explanation
Indices: 1792921--1792953 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1792911 AAATAAATAA
1792921 AAATAATTATTT
1 AAATAATTATTT
*
1792933 AAATAAATATTT
1 AAATAATTATTT
1792945 AAA-AATTAT
1 AAATAATTAT
1792954 AGTTATCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATAATTATTT
Found at i:1793702 original size:21 final size:21
Alignment explanation
Indices: 1793676--1793737 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1793666 TACAGCATGC
1793676 GAGAAAGAGAGAGAAGAAAAG
1 GAGAAAGAGAGAGAAGAAAAG
* *
1793697 GAGAAAG-GAAGAAAAGAAAAA
1 GAGAAAGAG-AGAGAAGAAAAG
*
1793718 G-GAAAGAAAGAGAAGAAAAG
1 GAGAAAGAGAGAGAAGAAAAG
1793738 AAAGGAAAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
GAGAAAGAGAGAGAAGAAAAG
Found at i:1793715 original size:5 final size:5
Alignment explanation
Indices: 1793705--1793790 Score: 61
Period size: 5 Copynumber: 17.4 Consensus size: 5
1793695 AGGAGAAAGG
* * * * *
1793705 AAGAA AAGAAA AAGGA AAG-A AAGAG AAGAA AAGAA AGGAA AGGAA AGGAA
1 AAGAA AAG-AA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
* * *
1793755 AGGAA AA-AA AA-AA AAAAA AAGGA AAGAGA AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGA-A AAGAA AA
1793791 ATTTTGTAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
4 12 0.17
5 47 0.68
6 10 0.14
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:1793718 original size:15 final size:15
Alignment explanation
Indices: 1793688--1793731 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
1793678 GAAAGAGAGA
*
1793688 GAAGAAAAGGAGAAAG
1 GAAGAAAA-GAAAAAG
1793704 GAAGAAAAGAAAAAG
1 GAAGAAAAGAAAAAG
1793719 GAAAGAAAGAGAA
1 G-AAGAAA-AGAA
1793732 GAAAAGAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 14 0.56
17 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
GAAGAAAAGAAAAAG
Found at i:1793725 original size:24 final size:24
Alignment explanation
Indices: 1793698--1793791 Score: 90
Period size: 25 Copynumber: 3.8 Consensus size: 24
1793688 GAAGAAAAGG
1793698 AGAAAGGAAGAAAAGAAAAAGGAA
1 AGAAAGGAAGAAAAGAAAAAGGAA
1793722 AGAAAGAGAAGAAAAGAAAGGAAAGGAA
1 AGAAAG-GAAGAAAAG-AA--AAAGGAA
1793750 AGGAAAGGAA-AAAA-AAAAA--AA
1 A-GAAAGGAAGAAAAGAAAAAGGAA
1793771 A-AAAGGAAAGAGAAAGAAAAA
1 AGAAAGG-AAGA-AAAGAAAAA
1793792 TTTTGTAGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 19
0.76 0.00 0.24
Matches are distributed among these distances:
19 5 0.08
20 2 0.03
21 4 0.07
22 3 0.05
23 8 0.13
24 6 0.10
25 11 0.18
26 2 0.03
27 4 0.07
28 11 0.18
29 5 0.08
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (24 bp):
AGAAAGGAAGAAAAGAAAAAGGAA
Found at i:1793745 original size:10 final size:10
Alignment explanation
Indices: 1793693--1793790 Score: 53
Period size: 10 Copynumber: 9.9 Consensus size: 10
1793683 AGAGAGAAGA
1793693 AAAGGAGAAAG
1 AAAGGA-AAAG
*
1793704 GAA-GAAAAG
1 AAAGGAAAAG
1793713 AAAAAGG-AAAG
1 --AAAGGAAAAG
*
1793724 AAA-GAGAAG
1 AAAGGAAAAG
* *
1793733 AAAAGAAAGG
1 AAAGGAAAAG
*
1793743 AAAGGAAAGG
1 AAAGGAAAAG
1793753 AAAGGAAAA-
1 AAAGGAAAAG
** *
1793762 AAAAAAAAAA
1 AAAGGAAAAG
1793772 AAAGGAAAGAG
1 AAAGGAAA-AG
1793783 AAA-GAAAA
1 AAAGGAAAA
1793791 ATTTTGTAGT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
8 1 0.01
9 21 0.31
10 33 0.49
11 12 0.18
12 1 0.01
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAAGGAAAAG
Found at i:1793791 original size:19 final size:19
Alignment explanation
Indices: 1793713--1793791 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
1793703 GGAAGAAAAG
1793713 AAAAAGGAAAGA-AAGAGAA
1 AAAAAGGAAAGAGAA-AGAA
*
1793732 GAAAA-GAAAG-GAAAGGAA
1 AAAAAGGAAAGAGAAA-GAA
* * * *
1793750 AGGAAAGGAAAAAAAAAAAA
1 A-AAAAGGAAAGAGAAAGAA
1793770 AAAAAGGAAAGAGAAAGAA
1 AAAAAGGAAAGAGAAAGAA
1793789 AAA
1 AAA
1793792 TTTTGTAGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
17 1 0.02
18 10 0.22
19 24 0.53
20 7 0.16
21 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (19 bp):
AAAAAGGAAAGAGAAAGAA
Found at i:1793791 original size:29 final size:29
Alignment explanation
Indices: 1793708--1793791 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
1793698 AGAAAGGAAG
* *
1793708 AAAAGAAAAAGG-AA-AGAAAGAGAAGAAA
1 AAAAAAAAAAGGAAAGAGAAAGA-AAAAAA
* **
1793736 AGAAAGGAAAGGAAAG-GAAAGGAAAAAAA
1 AAAAAAAAAAGGAAAGAGAAA-GAAAAAAA
1793765 AAAAAAAAAAGGAAAGAGAAAGAAAAA
1 AAAAAAAAAAGGAAAGAGAAAGAAAAA
1793792 TTTTGTAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
28 8 0.18
29 30 0.68
30 6 0.14
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAGGAAAGAGAAAGAAAAAAA
Found at i:1794597 original size:22 final size:21
Alignment explanation
Indices: 1794557--1794599 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1794547 AATTATAATT
1794557 ATTTAATATAATTTAATTTAA
1 ATTTAATATAATTTAATTTAA
1794578 ATTT-ATATAATTATTAATTTAA
1 ATTTAATATAA-T-TTAATTTAA
1794600 CTAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATATAATTTAATTTAA
Found at i:1798125 original size:2 final size:2
Alignment explanation
Indices: 1798118--1798191 Score: 67
Period size: 2 Copynumber: 37.0 Consensus size: 2
1798108 TGTTCTAACA
* * * * * *
1798118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT GT GT GT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1798160 GT GT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1798192 TGTGACTGCA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1798437 original size:14 final size:15
Alignment explanation
Indices: 1798406--1798455 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
1798396 AATTTTTTTT
* *
1798406 TTTTTTGTAAATAAA
1 TTTTTTATAAATATA
1798421 TTTTTTATAAA-ATA
1 TTTTTTATAAATATA
1798435 TTTTTTA-AAATATA
1 TTTTTTATAAATATA
1798449 TATTTTT
1 T-TTTTT
1798456 TTACGAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 3 0.10
14 13 0.42
15 15 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTTTTATAAATATA
Found at i:1798806 original size:22 final size:22
Alignment explanation
Indices: 1798778--1798819 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1798768 ATTATTATTT
1798778 TTTTTTAA-TAAATTTAATTTAA
1 TTTTTTAAGT-AATTTAATTTAA
1798800 TTTTTTAAGTAATTTAATTT
1 TTTTTTAAGTAATTTAATTT
1798820 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTTAAGTAATTTAATTTAA
Found at i:1798835 original size:18 final size:18
Alignment explanation
Indices: 1798800--1798842 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1798790 TTTAATTTAA
** *
1798800 TTTTTTAAGTAATTTAAT
1 TTTTTTAAAAAATCTAAT
1798818 TTTTTTAAAAAATCTAAT
1 TTTTTTAAAAAATCTAAT
1798836 TTATTTT
1 TT-TTTT
1798843 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTTAAAAAATCTAAT
Found at i:1798843 original size:23 final size:22
Alignment explanation
Indices: 1798809--1798872 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 22
1798799 ATTTTTTAAG
*
1798809 TAATTTAATTTTTTTAAAAAAT
1 TAATTTATTTTTTTTAAAAAAT
*
1798831 CTAATTTATTTTTATTTTAAAAAT
1 -TAATTTATTTTT-TTTAAAAAAT
1798855 TAATTTAATTTATTTTTA
1 TAATTT-ATTT-TTTTTA
1798873 TGAAATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 17 0.49
24 16 0.46
25 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TAATTTATTTTTTTTAAAAAAT
Found at i:1798941 original size:22 final size:22
Alignment explanation
Indices: 1798897--1798938 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1798887 TATTTTATTA
* *
1798897 TATATAAATTTAAAATATTAAT
1 TATATAAAATTAAAAAATTAAT
1798919 TATA-AAAATTAAAAAATTAA
1 TATATAAAATTAAAAAATTAA
1798939 ATTTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TATATAAAATTAAAAAATTAAT
Found at i:1807956 original size:21 final size:21
Alignment explanation
Indices: 1807930--1807973 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1807920 CTAGAACATG
1807930 CTTGACTTAGACATGGGTATA
1 CTTGACTTAGACATGGGTATA
1807951 CTTGACTTAGACATGGGTATA
1 CTTGACTTAGACATGGGTATA
1807972 CT
1 CT
1807974 CAATGTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (21 bp):
CTTGACTTAGACATGGGTATA
Found at i:1808024 original size:15 final size:15
Alignment explanation
Indices: 1808000--1808049 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1807990 TTTTTATTTT
*
1808000 TTTAAAATATTTATA
1 TTTAATATATTTATA
1808015 TTTAATATATATATATA
1 TTTAATATAT-T-TATA
*
1808032 TTT--TATATTTATT
1 TTTAATATATTTATA
1808045 TTTAA
1 TTTAA
1808050 ATACGAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 6 0.21
14 1 0.03
15 14 0.48
16 1 0.03
17 7 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAATATATTTATA
Found at i:1808026 original size:17 final size:17
Alignment explanation
Indices: 1808006--1808045 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1807996 TTTTTTTAAA
1808006 ATATTTATATTTAATAT
1 ATATTTATATTTAATAT
* *
1808023 ATATATATATTTTATAT
1 ATATTTATATTTAATAT
*
1808040 TTATTT
1 ATATTT
1808046 TTAAATACGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTTATATTTAATAT
Found at i:1809226 original size:17 final size:17
Alignment explanation
Indices: 1809199--1809231 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1809189 AAACAGGTCT
1809199 TTATATATTACTATTTTA
1 TTATATATTACT-TTTTA
1809217 TTAT-TATTACTTTTT
1 TTATATATTACTTTTT
1809232 GGGTGCAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATATTACTTTTTA
Found at i:1809370 original size:2 final size:2
Alignment explanation
Indices: 1809363--1809388 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1809353 TTCTTTTTCT
1809363 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1809389 GATCGAAAGA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1811645 original size:14 final size:13
Alignment explanation
Indices: 1811610--1811648 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1811600 CAAGCAGGTT
*
1811610 TTTTTTTTTTTCC
1 TTTTTTTTTTTAC
*
1811623 TTCTTTTTTTTAC
1 TTTTTTTTTTTAC
1811636 TTTTTATTTTTTA
1 TTTTT-TTTTTTA
1811649 AGTTTTGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTTTAC
Found at i:1816131 original size:115 final size:112
Alignment explanation
Indices: 1815992--1816203 Score: 327
Period size: 115 Copynumber: 1.9 Consensus size: 112
1815982 TCAAACAAAA
*
1815992 AAATTCGACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGAT-GATTATGACGCCAGTCCCACCTCATT
1816057 -TTCTTTTGGGTAGACCCAAAATTGATGATAATCAATCAGCTTAAAATAAC
65 ATT-TTTT-GGTAGACCCAAAA-TGATGATAATCAATCAGCTTAAAATAAC
* * * *
1816107 AAATTCAACTCTCAGCTGCTTAAAATGTTTATTATGATGATTATGACGCCAGTCCCATCTCATTA
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGATTATGACGCCAGTCCCACCTCATTA
*
1816172 TTTTTTGGTAGACCCAAAATGATGATGATCAA
66 TTTTTTGGTAGACCCAAAATGATGATAATCAA
1816204 AAGCAGTTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
112 12 0.13
113 13 0.14
114 29 0.32
115 36 0.40
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (112 bp):
AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGATTATGACGCCAGTCCCACCTCATTA
TTTTTTGGTAGACCCAAAATGATGATAATCAATCAGCTTAAAATAAC
Found at i:1816215 original size:114 final size:115
Alignment explanation
Indices: 1815992--1816218 Score: 327
Period size: 114 Copynumber: 2.0 Consensus size: 115
1815982 TCAAACAAAA
*
1815992 AAATTCGACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
*
1816057 TTCTTTTGGGTAGACCCAAAATTGATGATAATCAATCAGCTTAAAATAAC
66 TTCTTTTGGGTAGACCCAAAATTGATGATAATCAAGCAGCTTAAAATAAC
* * * *
1816107 AAATTCAACTCTCAGCTGCTTAAAATGTTTATTATGAT-GATTATGACGCCAGTCCCATCTCATT
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
* *
1816171 ATT-TTTT-GGTAGACCCAAAA-TGATGATGATCAAAAGCAGTTTAAAATA
66 -TTCTTTTGGGTAGACCCAAAATTGATGATAATC--AAGCAGCTTAAAATA
1816219 TTGAATGTTG
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
112 10 0.10
113 13 0.13
114 42 0.42
115 36 0.36
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (115 bp):
AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
TTCTTTTGGGTAGACCCAAAATTGATGATAATCAAGCAGCTTAAAATAAC
Found at i:1816412 original size:2 final size:2
Alignment explanation
Indices: 1816405--1816433 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1816395 CTCGTTGCAA
1816405 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1816434 AAAAAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1819051 original size:21 final size:21
Alignment explanation
Indices: 1819025--1819068 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1819015 CTAGAACATG
1819025 CTTGACTTAGACATGGGTATA
1 CTTGACTTAGACATGGGTATA
1819046 CTTGACTTAGACATGGGTATA
1 CTTGACTTAGACATGGGTATA
1819067 CT
1 CT
1819069 CAATGTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (21 bp):
CTTGACTTAGACATGGGTATA
Found at i:1819121 original size:17 final size:16
Alignment explanation
Indices: 1819095--1819128 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1819085 TTTTTATTTT
1819095 TTTAAAATATATTTATA
1 TTTAAAATATA-TTATA
*
1819112 TTTAATATATATTATA
1 TTTAAAATATATTATA
1819128 T
1 T
1819129 GTATATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAAATATATTATA
Found at i:1820319 original size:17 final size:17
Alignment explanation
Indices: 1820292--1820324 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1820282 AAACAGGTCT
1820292 TTATATATTACTATTTTA
1 TTATATATTACT-TTTTA
1820310 TTAT-TATTACTTTTT
1 TTATATATTACTTTTT
1820325 GGGTGCAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATATTACTTTTTA
Found at i:1820464 original size:2 final size:2
Alignment explanation
Indices: 1820452--1820480 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1820442 AATTTCTTTT
1820452 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1820481 GATCGAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1822735 original size:14 final size:13
Alignment explanation
Indices: 1822700--1822738 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1822690 AAGCAGGTTT
*
1822700 TTTTTTTTTTTCC
1 TTTTTTTTTTTAC
*
1822713 TTCTTTTTTTTAC
1 TTTTTTTTTTTAC
1822726 TTTTTATTTTTTA
1 TTTTT-TTTTTTA
1822739 AGTTTTGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTTTAC
Found at i:1827225 original size:115 final size:112
Alignment explanation
Indices: 1827086--1827297 Score: 327
Period size: 115 Copynumber: 1.9 Consensus size: 112
1827076 TCAAACAAAA
*
1827086 AAATTCGACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGAT-GATTATGACGCCAGTCCCACCTCATT
1827151 -TTCTTTTGGGTAGACCCAAAATTGATGATAATCAATCAGCTTAAAATAAC
65 ATT-TTTT-GGTAGACCCAAAA-TGATGATAATCAATCAGCTTAAAATAAC
* * * *
1827201 AAATTCAACTCTCAGCTGCTTAAAATGTTTATTATGATGATTATGACGCCAGTCCCATCTCATTA
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGATTATGACGCCAGTCCCACCTCATTA
*
1827266 TTTTTTGGTAGACCCAAAATGATGATGATCAA
66 TTTTTTGGTAGACCCAAAATGATGATAATCAA
1827298 AAGCAGTTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
112 12 0.13
113 13 0.14
114 29 0.32
115 36 0.40
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (112 bp):
AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGATTATGACGCCAGTCCCACCTCATTA
TTTTTTGGTAGACCCAAAATGATGATAATCAATCAGCTTAAAATAAC
Found at i:1827309 original size:114 final size:115
Alignment explanation
Indices: 1827086--1827312 Score: 327
Period size: 114 Copynumber: 2.0 Consensus size: 115
1827076 TCAAACAAAA
*
1827086 AAATTCGACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
*
1827151 TTCTTTTGGGTAGACCCAAAATTGATGATAATCAATCAGCTTAAAATAAC
66 TTCTTTTGGGTAGACCCAAAATTGATGATAATCAAGCAGCTTAAAATAAC
* * * *
1827201 AAATTCAACTCTCAGCTGCTTAAAATGTTTATTATGAT-GATTATGACGCCAGTCCCATCTCATT
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
* *
1827265 ATT-TTTT-GGTAGACCCAAAA-TGATGATGATCAAAAGCAGTTTAAAATA
66 -TTCTTTTGGGTAGACCCAAAATTGATGATAATC--AAGCAGCTTAAAATA
1827313 TTGAATGTTG
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
112 10 0.10
113 13 0.13
114 42 0.42
115 36 0.36
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (115 bp):
AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
TTCTTTTGGGTAGACCCAAAATTGATGATAATCAAGCAGCTTAAAATAAC
Found at i:1827505 original size:2 final size:2
Alignment explanation
Indices: 1827498--1827526 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1827488 CCTCGTTGCA
1827498 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1827527 AAAAAAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1832304 original size:115 final size:112
Alignment explanation
Indices: 1832165--1832376 Score: 327
Period size: 115 Copynumber: 1.9 Consensus size: 112
1832155 TCAAACAAAA
*
1832165 AAATTCGACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGAT-GATTATGACGCCAGTCCCACCTCATT
1832230 -TTCTTTTGGGTAGACCCAAAATTGATGATAATCAATCAGCTTAAAATAAC
65 ATT-TTTT-GGTAGACCCAAAA-TGATGATAATCAATCAGCTTAAAATAAC
* * * *
1832280 AAATTCAACTCTCAGCTGCTTAAAATGTTTATTATGATGATTATGACGCCAGTCCCATCTCATTA
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGATTATGACGCCAGTCCCACCTCATTA
*
1832345 TTTTTTGGTAGACCCAAAATGATGATGATCAA
66 TTTTTTGGTAGACCCAAAATGATGATAATCAA
1832377 AAGCAGTTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
112 12 0.13
113 13 0.14
114 29 0.32
115 36 0.40
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (112 bp):
AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGATTATGACGCCAGTCCCACCTCATTA
TTTTTTGGTAGACCCAAAATGATGATAATCAATCAGCTTAAAATAAC
Found at i:1832388 original size:114 final size:115
Alignment explanation
Indices: 1832165--1832391 Score: 327
Period size: 114 Copynumber: 2.0 Consensus size: 115
1832155 TCAAACAAAA
*
1832165 AAATTCGACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
*
1832230 TTCTTTTGGGTAGACCCAAAATTGATGATAATCAATCAGCTTAAAATAAC
66 TTCTTTTGGGTAGACCCAAAATTGATGATAATCAAGCAGCTTAAAATAAC
* * * *
1832280 AAATTCAACTCTCAGCTGCTTAAAATGTTTATTATGAT-GATTATGACGCCAGTCCCATCTCATT
1 AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
* *
1832344 ATT-TTTT-GGTAGACCCAAAA-TGATGATGATCAAAAGCAGTTTAAAATA
66 -TTCTTTTGGGTAGACCCAAAATTGATGATAATC--AAGCAGCTTAAAATA
1832392 TTGAATGTTG
Statistics
Matches: 101, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
112 10 0.10
113 13 0.13
114 42 0.42
115 36 0.36
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (115 bp):
AAATTCAACTCTCAACTGCATAAAATGTTTATTACGATGGATTATGACGCCAGTCCCACCTCATT
TTCTTTTGGGTAGACCCAAAATTGATGATAATCAAGCAGCTTAAAATAAC
Found at i:1832584 original size:2 final size:2
Alignment explanation
Indices: 1832577--1832605 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1832567 CCTCGTTGCA
1832577 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1832606 AAAAAAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1838183 original size:2 final size:2
Alignment explanation
Indices: 1838176--1838202 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1838166 TCTTTTGCTT
1838176 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1838203 TTTATCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1838471 original size:2 final size:2
Alignment explanation
Indices: 1838464--1838488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1838454 CAACGCAAAA
1838464 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 T
1838489 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1838493 original size:2 final size:2
Alignment explanation
Indices: 1838488--1838519 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1838478 TCTCTCTCTC
1838488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1838520 CTTGGGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1847201 original size:77 final size:78
Alignment explanation
Indices: 1847096--1847247 Score: 209
Period size: 77 Copynumber: 1.9 Consensus size: 78
1847086 GGTTCAAGTA
*
1847096 AAAATCAATGGAATCAAATAGATACAAATAAATA-CTTATAAAATAAATCTAAATGTTATCTA-C
1 AAAATCAATGAAATCAAATAGATACAAATAAATATC-TATAAAATAAATCTAAATGTTATCTACC
1847159 ATATATGAATGGTT
65 ATATATGAATGGTT
* * * * * *
1847173 AAAATCAATTAAATTAAATAGATACAAATGAATATCTGTAAAATAAATTTATATGTTATCTATCC
1 AAAATCAATGAAATCAAATAGATACAAATAAATATCTATAAAATAAATCTAAATGTTATCTA-CC
1847238 ATATATGAAT
65 ATATATGAAT
1847248 ATATAAATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
77 53 0.82
78 1 0.02
79 11 0.17
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.34
Consensus pattern (78 bp):
AAAATCAATGAAATCAAATAGATACAAATAAATATCTATAAAATAAATCTAAATGTTATCTACCA
TATATGAATGGTT
Found at i:1848438 original size:15 final size:15
Alignment explanation
Indices: 1848420--1848475 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
1848410 TTAAATCGTA
*
1848420 TTTTTTAA-ATATAT
1 TTTTTTAACATAAAT
*
1848434 TTTTTTAACCTAAATT
1 TTTTTTAACATAAA-T
* *
1848450 TTTTTTAACTTAAGT
1 TTTTTTAACATAAAT
1848465 TTTTTTCAACA
1 TTTTTT-AACA
1848476 GTACTGCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 8 0.24
15 10 0.29
16 16 0.47
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (15 bp):
TTTTTTAACATAAAT
Found at i:1848452 original size:16 final size:16
Alignment explanation
Indices: 1848433--1848470 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1848423 TTTAAATATA
1848433 TTTTTTTAACCTAAAT
1 TTTTTTTAACCTAAAT
* *
1848449 TTTTTTTAACTTAAGT
1 TTTTTTTAACCTAAAT
1848465 TTTTTT
1 TTTTTT
1848471 CAACAGTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTTTTTAACCTAAAT
Found at i:1854846 original size:20 final size:20
Alignment explanation
Indices: 1854823--1854866 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1854813 AAAAATTTGC
*
1854823 TTAAGCCTATATAAATAAT-T
1 TTAAGCCTACA-AAATAATAT
*
1854843 TTAATCCTACAAAATAATAT
1 TTAAGCCTACAAAATAATAT
1854863 TTAA
1 TTAA
1854867 AAAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (20 bp):
TTAAGCCTACAAAATAATAT
Found at i:1869338 original size:21 final size:21
Alignment explanation
Indices: 1869312--1869353 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1869302 AATTCACCTC
**
1869312 ATAAAATCCCTATTGCATAGG
1 ATAAAATCCCTAGAGCATAGG
1869333 ATAAAATCCCTAGAGCATAGG
1 ATAAAATCCCTAGAGCATAGG
1869354 CCAAAAACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (21 bp):
ATAAAATCCCTAGAGCATAGG
Found at i:1869359 original size:21 final size:21
Alignment explanation
Indices: 1869314--1869359 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1869304 TTCACCTCAT
** *
1869314 AAAATCCCTATTGCATAGGAT
1 AAAATCCCTAGAGCATAGGAC
*
1869335 AAAATCCCTAGAGCATAGGCC
1 AAAATCCCTAGAGCATAGGAC
1869356 AAAA
1 AAAA
1869360 ACGTTTGCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAATCCCTAGAGCATAGGAC
Found at i:1879280 original size:2 final size:2
Alignment explanation
Indices: 1879273--1879312 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1879263 TTTCCAATAC
* *
1879273 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1879313 ATTTTTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1879782 original size:2 final size:2
Alignment explanation
Indices: 1879775--1879807 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1879765 ATCACCATGT
1879775 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1879808 TTGGCACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1880497 original size:24 final size:24
Alignment explanation
Indices: 1880454--1880506 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1880444 TTTGTTGGTA
* *
1880454 TAAAAAAATCCATAAAATTATATT
1 TAAAAAAATCCATAAAATTAAAAT
*
1880478 TAAAAAAAT-TATAAATATTAAAAT
1 TAAAAAAATCCATAAA-ATTAAAAT
1880502 TAAAA
1 TAAAA
1880507 GTTATGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
TAAAAAAATCCATAAAATTAAAAT
Found at i:1882827 original size:16 final size:16
Alignment explanation
Indices: 1882808--1882862 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
1882798 GTTTATGTTT
1882808 TAAAATTTATATAATA
1 TAAAATTTATATAATA
1882824 TAAAATATTA-AT-ATA
1 TAAAAT-TTATATAATA
1882839 TCAAAATTTATATAAATA
1 T-AAAATTTATAT-AATA
1882857 TAAAAT
1 TAAAAT
1882863 AATTTAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.21
16 15 0.44
17 8 0.24
18 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:1882857 original size:18 final size:17
Alignment explanation
Indices: 1882808--1882875 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 17
1882798 GTTTATGTTT
1882808 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
1882824 TAAAA--TAT-TAATATA
1 TAAAATTTATATAA-ATA
1882839 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
* *
1882857 TAAAA-TAATTTAAATA
1 TAAAATTTATATAAATA
1882873 TAA
1 TAA
1882876 TTATAATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 4 0.09
16 21 0.48
17 4 0.09
18 7 0.16
19 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1885643 original size:2 final size:2
Alignment explanation
Indices: 1885636--1885670 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1885626 TTCCTCTATT
*
1885636 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1885671 CTTCTGATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1887072 original size:20 final size:20
Alignment explanation
Indices: 1887031--1887074 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1887021 ATTTATCCAC
*
1887031 ATTTAAAAATATATATTTAA
1 ATTTAAAAATATATATTAAA
*
1887051 ATTTAAATATA-ATAATTAAA
1 ATTTAAAAATATAT-ATTAAA
1887071 ATTT
1 ATTT
1887075 TTTTATCGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAAAAATATATATTAAA
Found at i:1890087 original size:2 final size:2
Alignment explanation
Indices: 1890080--1890115 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1890070 AACATGCATA
1890080 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
1890116 TATGATCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.