Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 8 of 131
Found at i:1813772 original size:19 final size:19
Alignment explanation
Indices: 1813738--1813789 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 19
1813728 TATATTTATT
1813738 TAATTTTATATTATATTAAAAA
1 TAATTTT-TA-TAT-TTAAAAA
1813760 TAATATTTTATATTTAAAAA
1 TAAT-TTTTATATTTAAAAA
1813780 TAATTTTTAT
1 TAATTTTTAT
1813790 TAATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.21
20 11 0.38
21 3 0.10
22 6 0.21
23 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTTTTATATTTAAAAA
Found at i:1813778 original size:20 final size:18
Alignment explanation
Indices: 1813748--1813789 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 18
1813738 TAATTTTATA
1813748 TTATATTAAAAATAATATT
1 TTATATTAAAAATAAT-TT
1813767 TTATATTTAAAAATAATTT
1 TTATA-TTAAAAATAATTT
1813786 TTAT
1 TTAT
1813790 TAATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATATTAAAAATAATTT
Found at i:1813800 original size:20 final size:20
Alignment explanation
Indices: 1813682--1813802 Score: 59
Period size: 20 Copynumber: 5.7 Consensus size: 20
1813672 TAAATCCGAT
1813682 TTAATTTTATATATAATTTTTA
1 TTAATTTTA-A-ATAATTTTTA
* * *
1813704 TTTA-TTTAATTATTTATTTA
1 TTAATTTTAAATAATT-TTTA
**
1813724 TTTATATATTTATTTAATTTTATA
1 -TTA-AT-TTTAAATAATTTT-TA
**
1813748 TTATATTAAAAATAATATTTTA
1 TTA-ATTTTAAATAAT-TTTTA
*
1813770 -T-ATTTAAAAATAATTTTTA
1 TTAATTT-TAAATAATTTTTA
1813789 TTAATTTTAAATAA
1 TTAATTTTAAATAA
1813803 AATATAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
19 12 0.16
20 20 0.26
21 11 0.14
22 12 0.16
23 11 0.14
24 11 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAATTTTAAATAATTTTTA
Found at i:1813847 original size:21 final size:22
Alignment explanation
Indices: 1813801--1813846 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1813791 AATTTTAAAT
* *
1813801 AAAATATAATTTATATAATATC
1 AAAATATAATTTAAATAATATA
1813823 AAAAT-TAATTTAAAT-ATATA
1 AAAATATAATTTAAATAATATA
1813843 AAAA
1 AAAA
1813847 AAATCTTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATATAATTTAAATAATATA
Found at i:1815092 original size:61 final size:60
Alignment explanation
Indices: 1815022--1815146 Score: 205
Period size: 61 Copynumber: 2.1 Consensus size: 60
1815012 AATCTTCTAG
* *
1815022 CATCTTTCCATGAATAGTAAACATTGTAATAATATCTTTGTAAATTAAACAAGTTTCCAAA
1 CATCTTTCCATGAATAGAAAACATTGTAAGAATATCTTTGTAAATTAAACAAGTTTCC-AA
* *
1815083 CATCTTTCCATGAATAGAAAATATTGTAAGAATATCTTTGTAAATTAAACAAGTTTTCAA
1 CATCTTTCCATGAATAGAAAACATTGTAAGAATATCTTTGTAAATTAAACAAGTTTCCAA
1815143 CATC
1 CATC
1815147 AAATATGGTG
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
60 6 0.10
61 54 0.90
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (60 bp):
CATCTTTCCATGAATAGAAAACATTGTAAGAATATCTTTGTAAATTAAACAAGTTTCCAA
Found at i:1817331 original size:20 final size:22
Alignment explanation
Indices: 1817306--1817346 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
1817296 ACTATCATCT
1817306 AATTTAT-TAATAA-TATATAA
1 AATTTATATAATAATTATATAA
*
1817326 AATTTATATATTAATTATATA
1 AATTTATATAATAATTATATA
1817347 TTAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTATATAATAATTATATAA
Found at i:1819747 original size:21 final size:21
Alignment explanation
Indices: 1819722--1819762 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1819712 ATATAATATT
*
1819722 AAAATTTTAATTTTAATAATC
1 AAAATTTAAATTTTAATAATC
*
1819743 AAAATTTAAATTTTGATAAT
1 AAAATTTAAATTTTAATAAT
1819763 TTTAAATACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AAAATTTAAATTTTAATAATC
Found at i:1832483 original size:2 final size:2
Alignment explanation
Indices: 1832476--1832500 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1832466 TTCTAATTAA
1832476 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
1832501 GTGTTTACGA
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:1833508 original size:63 final size:64
Alignment explanation
Indices: 1833441--1833575 Score: 140
Period size: 63 Copynumber: 2.1 Consensus size: 64
1833431 ATTTAGTGAT
* *
1833441 TTATATATTTATATC-ATAT-AAACTAT-AAAATATTTGTATTATATTTTATATAAA-AATTATA
1 TTATATATTCATATCAATATAAAAATATAAAAATATTT-T-TT-TATTTTAT-TAAATAATTATA
1833502 T-A
62 TAA
* *
1833504 TTATA-ATTCGTATCAATATAAAAATATAAAAAATATTTTTTTATTTTATTAAATATTTATATAA
1 TTATATATTCATATCAATATAAAAATAT-AAAAATATTTTTTTATTTTATTAAATAATTATATAA
1833568 TTAT-TATT
1 TTATATATT
1833576 AAAGGTATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
62 11 0.18
63 24 0.39
64 16 0.26
65 1 0.02
66 9 0.15
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.50
Consensus pattern (64 bp):
TTATATATTCATATCAATATAAAAATATAAAAATATTTTTTTATTTTATTAAATAATTATATAA
Found at i:1837295 original size:30 final size:30
Alignment explanation
Indices: 1837259--1837364 Score: 108
Period size: 30 Copynumber: 3.6 Consensus size: 30
1837249 TTAAATATAA
* * *
1837259 TAAAAATTTATTTGAATGTAAATTAAAATT
1 TAAAAATTTATTTAAATGTAAAATAAAAAT
1837289 TAAAAATTTATTTAAATGTAAAATAAAAAT
1 TAAAAATTTATTTAAATGTAAAATAAAAAT
** *
1837319 TAATGATTTATTT-AAT-TATAATAAAAAT
1 TAAAAATTTATTTAAATGTAAAATAAAAAT
* * *
1837347 ATAGAGATTTATCTAAAT
1 -TAAAAATTTATTTAAAT
1837365 AAATCTAAAG
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
28 11 0.17
29 13 0.20
30 41 0.63
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.42
Consensus pattern (30 bp):
TAAAAATTTATTTAAATGTAAAATAAAAAT
Found at i:1843911 original size:49 final size:49
Alignment explanation
Indices: 1843854--1843949 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
1843844 CTTTTTTTTT
*
1843854 ATAGGCACTTTA-TAATAACTTATAACTTGTTTAGATCATGTAATGATTG
1 ATAGGCACTTTAGT-ATAACTTATAACTTGTTTAGATCATATAATGATTG
* *
1843903 ATAGGCACTTTAGTATAACTTATAACTTGTTTTGATTATATAATGAT
1 ATAGGCACTTTAGTATAACTTATAACTTGTTTAGATCATATAATGAT
1843950 GTATTCTCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 42 0.98
50 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (49 bp):
ATAGGCACTTTAGTATAACTTATAACTTGTTTAGATCATATAATGATTG
Found at i:1851592 original size:6 final size:6
Alignment explanation
Indices: 1851583--1851655 Score: 62
Period size: 6 Copynumber: 11.8 Consensus size: 6
1851573 ATTTTTTTTT
* *
1851583 TATAAA TATAAA TAT-AA TATATA TATACACA TATACA TATAAA TATAAA
1 TATAAA TATAAA TATAAA TATAAA TATA-A-A TATAAA TATAAA TATAAA
1851632 TA-AATA TGTATAAA -ATAAA TATAA
1 TATAA-A --TATAAA TATAAA TATAA
1851656 TGAGAACTAG
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
5 12 0.22
6 33 0.60
8 8 0.15
9 2 0.04
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (6 bp):
TATAAA
Found at i:1851654 original size:31 final size:31
Alignment explanation
Indices: 1851584--1851655 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1851574 TTTTTTTTTT
* *
1851584 ATAAATATAAATATAATATATATATACACAT
1 ATAAATATAAATATAATAAATATATACACAA
* * *
1851615 ATACATATAAATATAAATAAATATGTATA-AA
1 ATAAATATAAATAT-AATAAATATATACACAA
1851646 ATAAATATAA
1 ATAAATATAA
1851656 TGAGAACTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 23 0.68
32 11 0.32
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.33
Consensus pattern (31 bp):
ATAAATATAAATATAATAAATATATACACAA
Found at i:1852291 original size:29 final size:29
Alignment explanation
Indices: 1852259--1852314 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1852249 TATTTTTAAT
*
1852259 ATTATTTTAATATATTTAAATATAAAATA
1 ATTATTTTAATATATTAAAATATAAAATA
* * *
1852288 ATTATTTTATTTTATTAAAATTTAAAA
1 ATTATTTTAATATATTAAAATATAAAA
1852315 ATATGTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
ATTATTTTAATATATTAAAATATAAAATA
Found at i:1862604 original size:2 final size:2
Alignment explanation
Indices: 1862599--1862627 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1862589 AACCTAAAAA
1862599 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 A
1862628 AGAAAGGTTA
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1870453 original size:16 final size:14
Alignment explanation
Indices: 1870416--1870459 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
1870406 AAACTATTAT
*
1870416 TTTTAAAATATAAAA
1 TTTT-AAATATATAA
1870431 TTTTAAATATATAA
1 TTTTAAATATATAA
1870445 TTATATAAATATATA
1 TT-T-TAAATATATA
1870460 TAATAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 11 0.42
15 5 0.19
16 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTTAAATATATAA
Found at i:1870487 original size:19 final size:21
Alignment explanation
Indices: 1870450--1870490 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
1870440 TATAATTATA
1870450 TAAATATATATAATAAAAAAT
1 TAAATATATATAATAAAAAAT
*
1870471 TAAATA-AT-TAATTAAAAAT
1 TAAATATATATAATAAAAAAT
1870490 T
1 T
1870491 TTTTTGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 2 0.11
21 6 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATATATATAATAAAAAAT
Found at i:1871582 original size:22 final size:21
Alignment explanation
Indices: 1871541--1871585 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1871531 TATATCGTAC
*
1871541 TTAAAATTTTAAATAAAATAA
1 TTAAAATTATAAATAAAATAA
*
1871562 TTAAAATTATAATTTAAAATAA
1 TTAAAATTATAA-ATAAAATAA
1871584 TT
1 TT
1871586 TTAATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATTATAAATAAAATAA
Found at i:1871582 original size:27 final size:28
Alignment explanation
Indices: 1871493--1871583 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
1871483 AAAAAATTCA
* * * *
1871493 AAAATAAATAAATTTTAAAATTTTAAATT
1 AAAATAAA-ATATATTAAAATTATAATTT
*** * *
1871522 AAAATAAAATATATCGTACTTAAAATTT
1 AAAATAAAATATATTAAAATTATAATTT
*
1871550 TAAATAAAATA-ATTAAAATTATAATTT
1 AAAATAAAATATATTAAAATTATAATTT
1871577 AAAATAA
1 AAAATAA
1871584 TTTTAATAAA
Statistics
Matches: 46, Mismatches: 16, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
27 17 0.37
28 21 0.46
29 8 0.17
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.37
Consensus pattern (28 bp):
AAAATAAAATATATTAAAATTATAATTT
Found at i:1879306 original size:22 final size:23
Alignment explanation
Indices: 1879280--1879340 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1879270 TGTAATTTTT
1879280 TATTATAAT-TAAATAATTATA-A
1 TATTATAATATAAA-AATTATAGA
1879302 TATTATAATATAAAAATTATAGA
1 TATTATAATATAAAAATTATAGA
* * *
1879325 TAATATACTTTAAAAA
1 TATTATAATATAAAAA
1879341 ACGCCACTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 16 0.47
23 18 0.53
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TATTATAATATAAAAATTATAGA
Found at i:1900842 original size:25 final size:27
Alignment explanation
Indices: 1900813--1900863 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
1900803 TAGGACGAGT
1900813 ATAAATA-ATA-ATA-TTTATTATTATA
1 ATAAATACATATATAGTTTATT-TTATA
1900838 ATAAATACATATATAGTTTATTTTAT
1 ATAAATACATATATAGTTTATTTTAT
1900864 TTGGTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.30
26 3 0.13
27 7 0.30
28 6 0.26
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
ATAAATACATATATAGTTTATTTTATA
Found at i:1909304 original size:33 final size:35
Alignment explanation
Indices: 1909236--1909304 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 35
1909226 TATAATCAAA
*
1909236 ATTTTACACTAATAATATATCAAATATTAATTTTT
1 ATTTTACACTAATAATATATCAAATATTAAATTTT
* *
1909271 ATTTTA-ATTAAT-ATATAT-AATTATTTAAATTTT
1 ATTTTACACTAATAATATATCAAATA-TTAAATTTT
1909304 A
1 A
1909305 AAACTTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 4 0.13
33 15 0.50
34 5 0.17
35 6 0.20
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (35 bp):
ATTTTACACTAATAATATATCAAATATTAAATTTT
Found at i:1910313 original size:20 final size:20
Alignment explanation
Indices: 1910273--1910313 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1910263 AACCGAAACC
*
1910273 CAACTATCACAAGTTCACAA
1 CAACTATCACAAATTCACAA
1910293 CAACTATCATCAAATTC-CAA
1 CAACTATCA-CAAATTCACAA
1910313 C
1 C
1910314 TTTTTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (20 bp):
CAACTATCACAAATTCACAA
Found at i:1913549 original size:24 final size:24
Alignment explanation
Indices: 1913522--1913574 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
1913512 TGAATTTTTT
* *
1913522 TATTTAATTTAAATTAAATTTAAA
1 TATTAAATATAAATTAAATTTAAA
* *
1913546 TATTAAATATATATTAGATTT--A
1 TATTAAATATAAATTAAATTTAAA
1913568 TATTAAA
1 TATTAAA
1913575 ATACAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 8 0.32
24 17 0.68
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TATTAAATATAAATTAAATTTAAA
Found at i:1913693 original size:20 final size:22
Alignment explanation
Indices: 1913670--1913722 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
1913660 ATAATTATTT
1913670 TATATATAAATTTAT-TTAAA-
1 TATATATAAATTTATATTAAAG
*
1913690 TATAT-TAAAATTTTTATTAAAG
1 TATATAT-AAATTTATATTAAAG
1913712 TAATATATAAA
1 T-ATATATAAA
1913723 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.04
20 12 0.44
21 5 0.19
22 1 0.04
23 7 0.26
24 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATATATAAATTTATATTAAAG
Found at i:1913747 original size:22 final size:22
Alignment explanation
Indices: 1913719--1913767 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
1913709 AAGTAATATA
*
1913719 TAAAAAATAAAAAAATTAAAATT
1 TAAAAATTAAAAAAATT-AAATT
*
1913742 TAAAAATTAATAAAATTAAATT
1 TAAAAATTAAAAAAATTAAATT
1913764 TAAA
1 TAAA
1913768 TTAAATCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAAATTAAAAAAATTAAATT
Found at i:1913805 original size:33 final size:34
Alignment explanation
Indices: 1913753--1913816 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
1913743 AAAAATTAAT
*
1913753 AAAATTAAATTTAAATTAAATC-GATTTTAATAA
1 AAAATTAAATTTAAATTAAATCAAATTTTAATAA
1913786 AAAATT-AATTTAAATTTAAATCAAATTTTAA
1 AAAATTAAATTTAAA-TTAAATCAAATTTTAA
1913817 AATTTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 8 0.29
33 13 0.46
34 7 0.25
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (34 bp):
AAAATTAAATTTAAATTAAATCAAATTTTAATAA
Found at i:1917108 original size:4 final size:4
Alignment explanation
Indices: 1917099--1917124 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1917089 AATTAACATG
1917099 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
1917125 GTAATTAAAG
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:1917658 original size:6 final size:6
Alignment explanation
Indices: 1917631--1917672 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
1917621 AAATTTTAAA
1917631 TTATA- TTAT-T TTATATT TTATAT TTATAT TTATA- TTATAT TT
1 TTATAT TTATAT TTATA-T TTATAT TTATAT TTATAT TTATAT TT
1917673 TAAATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
5 13 0.39
6 14 0.42
7 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATAT
Found at i:1917664 original size:19 final size:17
Alignment explanation
Indices: 1917631--1917666 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
1917621 AAATTTTAAA
1917631 TTATATTATTTTATATT
1 TTATATTATTTTATATT
1917648 TTATATTTATATTTATATT
1 TTATA-TTAT-TTTATATT
1917667 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATATTATTTTATATT
Found at i:1917668 original size:17 final size:16
Alignment explanation
Indices: 1917623--1917672 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
1917613 TATTAATAAA
*
1917623 ATTTTAAATTATA-TT
1 ATTTTATATTATATTT
1917638 ATTTTATATTTTATATTT
1 ATTTTATA--TTATATTT
1917656 ATATTTATATTATATTT
1 AT-TTTATATTATATTT
1917673 TAAATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 7 0.23
17 13 0.43
18 4 0.13
19 6 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTATATTATATTT
Found at i:1917674 original size:12 final size:12
Alignment explanation
Indices: 1917623--1917680 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
1917613 TATTAATAAA
*
1917623 ATTTTAAATTAT
1 ATTTTATATTAT
*
1917635 A--TTATTTTAT
1 ATTTTATATTAT
1917645 ATTTTATATT-T
1 ATTTTATATTAT
1917656 ATATTTATATTAT
1 AT-TTTATATTAT
*
1917669 ATTTTAAATTAT
1 ATTTTATATTAT
1917681 TAAATTGACG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 8 0.21
11 3 0.08
12 24 0.63
13 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTTATATTAT
Found at i:1921229 original size:28 final size:27
Alignment explanation
Indices: 1921184--1921242 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1921174 AAATAATAAT
*
1921184 AAAAATTACTACAGTTATCATTGAAAAA
1 AAAAATTACTACAATTATCATT-AAAAA
* * *
1921212 AAAAATTATTATAATTATGATTAAAAA
1 AAAAATTACTACAATTATCATTAAAAA
1921239 AAAA
1 AAAA
1921243 TTTAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (27 bp):
AAAAATTACTACAATTATCATTAAAAA
Found at i:1927590 original size:2 final size:2
Alignment explanation
Indices: 1927583--1927617 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1927573 AAAATCAACC
1927583 AT AT AT AT AT AT AT AT -T 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
1927618 TCTTTTATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1927605 original size:17 final size:17
Alignment explanation
Indices: 1927583--1927615 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1927573 AAAATCAACC
1927583 ATATATATATATATATT
1 ATATATATATATATATT
1927600 ATATATATATATATAT
1 ATATATATATATATAT
1927616 ATTCTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:1930813 original size:8 final size:8
Alignment explanation
Indices: 1930800--1930829 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1930790 TATTGACTTG
1930800 AATTAACT
1 AATTAACT
1930808 AATTAACT
1 AATTAACT
*
1930816 AATTAATT
1 AATTAACT
1930824 AATTAA
1 AATTAA
1930830 ACCTCGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (8 bp):
AATTAACT
Found at i:1931358 original size:33 final size:33
Alignment explanation
Indices: 1931316--1931382 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
1931306 CATGCCTTTG
1931316 AGTGATTAGAGGGTTTTGTTTTG-AAATTTATTT
1 AGTGATTAGAGGGTTTTGTTTTGAAAATTT-TTT
1931349 AGTGATTAGAGGGTTTTGTTTTGAAAATTTTTT
1 AGTGATTAGAGGGTTTTGTTTTGAAAATTTTTT
1931382 A
1 A
1931383 AGGTAACCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (33 bp):
AGTGATTAGAGGGTTTTGTTTTGAAAATTTTTT
Found at i:1955395 original size:35 final size:35
Alignment explanation
Indices: 1955343--1955444 Score: 118
Period size: 36 Copynumber: 2.9 Consensus size: 35
1955333 TAAATTTATA
*
1955343 AAAAATTATAACACTTTTCAAAGATATATTTTTTTG
1 AAAAATTATAACACTTTTCAAA-AAATATTTTTTTG
* * **
1955379 AGAAA-TATAATACTTTT-AAAAAATACATTTTTG
1 AAAAATTATAACACTTTTCAAAAAATATTTTTTTG
*
1955412 AAAAATTATAACACTTCTCAAAAAAATATTTTT
1 AAAAATTATAACACTTTTC-AAAAAATATTTTT
1955445 AGAGTGAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
33 14 0.26
34 13 0.25
35 11 0.21
36 15 0.28
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (35 bp):
AAAAATTATAACACTTTTCAAAAAATATTTTTTTG
Found at i:1958350 original size:13 final size:14
Alignment explanation
Indices: 1958332--1958361 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1958322 AAAGTTGAAC
1958332 TTTCTTTTTTT-TT
1 TTTCTTTTTTTCTT
1958345 TTTCTTTTTTTCTT
1 TTTCTTTTTTTCTT
1958359 TTT
1 TTT
1958362 TTCTTGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTCTTTTTTTCTT
Found at i:1958352 original size:8 final size:8
Alignment explanation
Indices: 1958336--1958366 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
1958326 TTGAACTTTC
1958336 TTTTT-TT
1 TTTTTCTT
1958343 TTTTTCTT
1 TTTTTCTT
1958351 TTTTTCTT
1 TTTTTCTT
1958359 TTTTTCTT
1 TTTTTCTT
1958367 GAGTTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.22
8 18 0.78
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1961681 original size:2 final size:2
Alignment explanation
Indices: 1961669--1961704 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1961659 TGCACCCTTC
1961669 TA TA TA T- 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 TA TA T
1961705 TCCCTTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1967892 original size:17 final size:18
Alignment explanation
Indices: 1967848--1967897 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1967838 AAATGGGTTG
1967848 AATTGATTTAA-TTTAATT
1 AATT-ATTTAATTTTAATT
* *
1967866 AATTAATTAATTTTGATT
1 AATTATTTAATTTTAATT
1967884 AA-TATTTAAATTTT
1 AATTATTT-AATTTT
1967898 TTAAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
AATTATTTAATTTTAATT
Found at i:1968348 original size:21 final size:22
Alignment explanation
Indices: 1968318--1968369 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1968308 GATATTTTTA
1968318 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
1968338 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
1968360 AATATTTTAT
1 AATATTTTAT
1968370 TAATTTCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:1968580 original size:12 final size:13
Alignment explanation
Indices: 1968549--1968573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1968539 TTATATATGA
1968549 AAAATAAAATTTT
1 AAAATAAAATTTT
1968562 AAAATAAAATTT
1 AAAATAAAATTT
1968574 AATATAATAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATAAAATTTT
Found at i:1974034 original size:30 final size:29
Alignment explanation
Indices: 1973962--1974086 Score: 135
Period size: 30 Copynumber: 4.2 Consensus size: 29
1973952 TTGAACATAA
* * *
1973962 TAATTTTATTCAGATAAATTTTTATATTT
1 TAATTTTATTTAAATAAATTTTTAAATTT
* *
1973991 TTATTATATTTAAATAAATTTTTAAATTT
1 TAATTTTATTTAAATAAATTTTTAAATTT
*
1974020 TAATTTTAATTTAAATAAATTTTTAACTTT
1 TAATTTT-ATTTAAATAAATTTTTAAATTT
* *
1974050 TAA-TCTATGTTCAAATAAATTTTTAATTTCT
1 TAATTTTAT-TT-AAATAAATTTTTAAATT-T
1974081 TAATTT
1 TAATTT
1974087 GTACTTCTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.03
29 33 0.41
30 40 0.50
31 4 0.05
32 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (29 bp):
TAATTTTATTTAAATAAATTTTTAAATTT
Found at i:1974041 original size:59 final size:60
Alignment explanation
Indices: 1973962--1974086 Score: 157
Period size: 59 Copynumber: 2.1 Consensus size: 60
1973952 TTGAACATAA
* * *
1973962 TAATTTTATTCAGATAAATTTTTATA-TTTTTAT-TATATTTAAATAAATTTTTAAATT-T
1 TAATTTTATTCAAATAAATTTTTA-ACTTTTAATCTATATTCAAATAAATTTTTAAATTCT
* * *
1974020 TAATTTTAATTTAAATAAATTTTTAACTTTTAATCTATGTTCAAATAAATTTTTAATTTCT
1 TAATTTT-ATTCAAATAAATTTTTAACTTTTAATCTATATTCAAATAAATTTTTAAATTCT
1974081 TAATTT
1 TAATTT
1974087 GTACTTCTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
58 8 0.14
59 21 0.37
60 21 0.37
61 7 0.12
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (60 bp):
TAATTTTATTCAAATAAATTTTTAACTTTTAATCTATATTCAAATAAATTTTTAAATTCT
Found at i:1974181 original size:10 final size:10
Alignment explanation
Indices: 1974168--1974202 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1974158 AAATTTATTT
*
1974168 AAATATAATA
1 AAATATAAAA
1974178 AAATATAAAA
1 AAATATAAAA
*
1974188 AAATTTAAAA
1 AAATATAAAA
1974198 AAATA
1 AAATA
1974203 ATTCAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAATATAAAA
Found at i:1974190 original size:30 final size:29
Alignment explanation
Indices: 1974121--1974194 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
1974111 TATTTCCTTT
1974121 AAAAT-AAAAATTTATTTAAATTCAAATTA
1 AAAATAAAAAATTTATTTAAATT-AAATTA
*
1974150 AAAATTAAAAATTTATTTAAA-TATAA-TA
1 AAAATAAAAAATTTATTTAAATTA-AATTA
1974178 AAATATAAAAAAATTTA
1 AAA-AT-AAAAAATTTA
1974195 AAAAAATAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 6 0.15
29 10 0.25
30 24 0.60
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAATAAAAAATTTATTTAAATTAAATTA
Found at i:1977510 original size:8 final size:8
Alignment explanation
Indices: 1977497--1977591 Score: 54
Period size: 8 Copynumber: 11.6 Consensus size: 8
1977487 AATATTTTGA
1977497 TTAATATT
1 TTAATATT
1977505 TTAATA-T
1 TTAATATT
*
1977512 TAAATA-T
1 TTAATATT
1977519 TT-AT-TT
1 TTAATATT
*
1977525 AATAATATT
1 -TTAATATT
1977534 TTAATATT
1 TTAATATT
**
1977542 GTATTCTATT
1 -T-TAATATT
1977552 TTAATATT
1 TTAATATT
*
1977560 TTAATATA
1 TTAATATT
1977568 TTAATTATT
1 TTAA-TATT
*
1977577 AATTTATATT
1 --TTAATATT
1977587 TTAAT
1 TTAAT
1977592 GCATAATAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
6 3 0.05
7 9 0.14
8 35 0.53
9 7 0.11
10 9 0.14
11 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (8 bp):
TTAATATT
Found at i:1977514 original size:29 final size:29
Alignment explanation
Indices: 1977493--1977652 Score: 95
Period size: 29 Copynumber: 5.7 Consensus size: 29
1977483 TAAGAATATT
*
1977493 TTGATTAATATTTTAATATTAAATATTTA
1 TTGAATAATATTTTAATATTAAATATTTA
* *
1977522 TTTAATAATATTTTAATATT--GTATTCTA
1 TTGAATAATATTTTAATATTAAATATT-TA
* * *
1977550 TT--TTAATATTTTAATA-T-ATTAATTA
1 TTGAATAATATTTTAATATTAAATATTTA
* * *
1977575 TT-AATTTATATTTTAATGCATAATAATATCT-
1 TTGAA-TAATATTTTAAT--ATTA-AATATTTA
* *
1977606 TT-AATAATGTTTTAATATTAAATATTGA
1 TTGAATAATATTTTAATATTAAATATTTA
* *
1977634 TTTAATAAAATTTTAATAT
1 TTGAATAATATTTTAATAT
1977653 ATTATGTTTT
Statistics
Matches: 101, Mismatches: 19, Indels: 22
0.71 0.13 0.15
Matches are distributed among these distances:
25 5 0.05
26 16 0.16
27 20 0.20
28 9 0.09
29 33 0.33
30 10 0.10
31 4 0.04
32 4 0.04
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (29 bp):
TTGAATAATATTTTAATATTAAATATTTA
Found at i:1977689 original size:21 final size:21
Alignment explanation
Indices: 1977618--1977704 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
1977608 AATAATGTTT
*
1977618 TAATATTAAATATTGATTTAA
1 TAATATTAAATATTAATTTAA
* **
1977639 TAAAATTTTAATATATT-ATGTTTT
1 T--AATATTAA-ATATTAAT-TTAA
*
1977663 TTATATTAAATATTAATTTAA
1 TAATATTAAATATTAATTTAA
* *
1977684 TAATATAAAATAATAATTTAA
1 TAATATTAAATATTAATTTAA
1977705 CAAATTTTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
21 26 0.51
22 8 0.16
23 9 0.18
24 8 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TAATATTAAATATTAATTTAA
Found at i:1977762 original size:11 final size:11
Alignment explanation
Indices: 1977746--1977882 Score: 101
Period size: 11 Copynumber: 12.8 Consensus size: 11
1977736 ATAATATATC
1977746 ATTTTAATAAT
1 ATTTTAATAAT
*
1977757 ATTTTACT-AT
1 ATTTTAATAAT
*
1977767 A--TT-ATATT
1 ATTTTAATAAT
1977775 ATTTTAATAAT
1 ATTTTAATAAT
1977786 ATTTTAACTTAATT
1 ATTTTAA--TAA-T
1977800 ATATTT-A-AAT
1 AT-TTTAATAAT
* *
1977810 ATATT-ATCAT
1 ATTTTAATAAT
1977820 ATTTTAATAAT
1 ATTTTAATAAT
* *
1977831 ATTTTACT-TT
1 ATTTTAATAAT
* *
1977841 AATTTAATAAA
1 ATTTTAATAAT
*
1977852 ATTTTAATATT
1 ATTTTAATAAT
1977863 ATTTTAATAAT
1 ATTTTAATAAT
1977874 ATTTTAATA
1 ATTTTAATA
1977883 TTTACAAATA
Statistics
Matches: 97, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
7 1 0.01
8 4 0.04
9 3 0.03
10 21 0.22
11 58 0.60
13 3 0.03
14 4 0.04
15 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTTAATAAT
Found at i:1977787 original size:45 final size:45
Alignment explanation
Indices: 1977736--1977832 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
1977726 ATAATTTAAT
** * *
1977736 ATAATATATCATTTTAATAATATTTTACTATATTAT-ATTATTTTA
1 ATAATATATCAACTTAATAATATTTAAATATATTATCA-TATTTTA
* * *
1977781 ATAATATTTTAACTTAATTATATTTAAATATATTATCATATTTTA
1 ATAATATATCAACTTAATAATATTTAAATATATTATCATATTTTA
1977826 ATAATAT
1 ATAATAT
1977833 TTTACTTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 43 0.98
46 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (45 bp):
ATAATATATCAACTTAATAATATTTAAATATATTATCATATTTTA
Found at i:1977833 original size:45 final size:46
Alignment explanation
Indices: 1977748--1977880 Score: 161
Period size: 45 Copynumber: 3.0 Consensus size: 46
1977738 AATATATCAT
* * *
1977748 TTTAATAATATTTTACTATATTATATTATTTTAATAATATTTTAAC
1 TTTAATTATATTTAAATATATTATATTATTTTAATAATATTTTAAC
1977794 -TTAATTATATTTAAATATATTATCA-TATTTTAATAATATTTT-AC
1 TTTAATTATATTTAAATATATTAT-ATTATTTTAATAATATTTTAAC
* *
1977838 TTTAATT-TA-ATAAA-ATTTTAATATTATTTTAATAATATTTTAA
1 TTTAATTATATTTAAATATATT-ATATTATTTTAATAATATTTTAA
1977881 TATTTACAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
42 5 0.06
43 23 0.30
44 5 0.06
45 43 0.56
46 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (46 bp):
TTTAATTATATTTAAATATATTATATTATTTTAATAATATTTTAAC
Found at i:1977871 original size:22 final size:22
Alignment explanation
Indices: 1977737--1977884 Score: 116
Period size: 21 Copynumber: 6.8 Consensus size: 22
1977727 TAATTTAATA
*
1977737 TAATATATCATTTTAATAATATTT
1 TAATA-AT-ATTTTAATATTATTT
*
1977761 TACT-ATA--TT-ATATTATTT
1 TAATAATATTTTAATATTATTT
1977779 TAATAATATTTTAACTTAATTATATT
1 TAATAATATTTTAA--T-ATTAT-TT
*
1977805 T-A-AATATATT-ATCA-TATTT
1 TAATAATATTTTAAT-ATTATTT
* *
1977824 TAATAATATTTTACT-TTAATT
1 TAATAATATTTTAATATTATTT
*
1977845 TAATAAAATTTTAATATTATTT
1 TAATAATATTTTAATATTATTT
1977867 TAATAATATTTTAATATT
1 TAATAATATTTTAATATT
1977885 TACAAATACT
Statistics
Matches: 99, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
18 11 0.11
19 8 0.08
20 4 0.04
21 29 0.29
22 26 0.26
23 1 0.01
24 11 0.11
25 6 0.06
26 3 0.03
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAATATTTTAATATTATTT
Found at i:1977886 original size:29 final size:29
Alignment explanation
Indices: 1977548--1977886 Score: 109
Period size: 29 Copynumber: 11.5 Consensus size: 29
1977538 TATTGTATTC
*
1977548 TATTTTAATATTTTAATATATTAATTATTAATTTA
1 TATTTTAATA-TTT-A-ATATT-ATT-TTAA-TAA
*** *
1977583 TATTTTAATGCATAATAATATCTTTAATAA
1 TATTTTAATATTTAATATTAT-TTTAATAA
* *
1977613 TGTTTTAATATTAAATATTGA-TTTAATAA
1 TATTTTAATATTTAATATT-ATTTTAATAA
* *
1977642 AATTTTAATATATT-ATGTT-TTTTATATTAA
1 TATTTTAATAT-TTAATATTATTTTA-A-TAA
* * **
1977672 -ATATT-A-ATTTAATAATA-TAAAATAA
1 TATTTTAATATTTAATATTATTTTAATAA
* * * *
1977697 TAATTTAACAAATTTTAT-TGTAATTTAAT-A
1 T-ATTTTA-ATATTTAATAT-TATTTTAATAA
*
1977727 TAATTTAATA--TAATATATCATTTTAATAA
1 TATTTTAATATTTAATAT-T-ATTTTAATAA
*
1977756 TATTTTACTATATT-ATATTATTTTAATAA
1 TATTTTAATAT-TTAATATTATTTTAATAA
* *
1977785 TATTTT-A-ACTTAAT-TATATTTAAAT-A
1 TATTTTAATATTTAATAT-TATTTTAATAA
* * * *
1977811 TATTATCATATTTTAATAATATTTTACTTTAA
1 TATTTTAATA-TTTAATATTATTTTA--ATAA
* *
1977843 T-TTAATAAAATTTTAATATTATTTTAATAA
1 TATT-TTAATA-TTTAATATTATTTTAATAA
1977873 TATTTTAATATTTA
1 TATTTTAATATTTA
1977887 CAAATACTAA
Statistics
Matches: 224, Mismatches: 48, Indels: 70
0.65 0.14 0.20
Matches are distributed among these distances:
25 3 0.01
26 15 0.07
27 24 0.11
28 15 0.07
29 71 0.32
30 38 0.17
31 20 0.09
32 27 0.12
33 1 0.00
34 1 0.00
35 9 0.04
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (29 bp):
TATTTTAATATTTAATATTATTTTAATAA
Found at i:1986244 original size:10 final size:10
Alignment explanation
Indices: 1986229--1986280 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
1986219 AATTATTTTT
1986229 ATTAATTAAA
1 ATTAATTAAA
1986239 ATTAATTAATA
1 ATTAATTAA-A
*
1986250 ATCAATT-AA
1 ATTAATTAAA
* *
1986259 ATTGATTTAA
1 ATTAATTAAA
*
1986269 TTTAATTAAA
1 ATTAATTAAA
1986279 AT
1 AT
1986281 CAAATTTGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
9 6 0.18
10 20 0.61
11 7 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (10 bp):
ATTAATTAAA
Found at i:1988252 original size:2 final size:2
Alignment explanation
Indices: 1988245--1988299 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1988235 GGTATTTAAA
1988245 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1988287 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
1988300 TGGAAGAGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1988311 original size:12 final size:13
Alignment explanation
Indices: 1988249--1988315 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 13
1988239 TTTAAAAGAG
1988249 AGAGAGAGA-GAGA
1 AGAGAGAGATG-GA
1988262 GAGAGAGAGA-GAGA
1 -AGAGAGAGATG-GA
1988276 GAGAGAGAGA-GAGA
1 -AGAGAGAGATG-GA
1988290 GAGAGAGAGATGGA
1 -AGAGAGAGATGGA
1988304 AGAG-GAGATGGA
1 AGAGAGAGATGGA
1988316 GATAGAGCCA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
12 8 0.15
13 4 0.08
14 39 0.75
15 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.49, T:0.03
Consensus pattern (13 bp):
AGAGAGAGATGGA
Found at i:1992974 original size:27 final size:27
Alignment explanation
Indices: 1992936--1992993 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
1992926 CTGCACATGG
*
1992936 AATCTGTTGATATCCAACTCTACTAGA
1 AATCTGTTGATATCCAACTCTACCAGA
* *
1992963 AATCTGTTGATATGCAACTTTACCAGA
1 AATCTGTTGATATCCAACTCTACCAGA
1992990 AATC
1 AATC
1992994 AATCTTTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (27 bp):
AATCTGTTGATATCCAACTCTACCAGA
Found at i:1993561 original size:23 final size:23
Alignment explanation
Indices: 1993535--1993582 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1993525 CAGAAGGAGC
1993535 CTGCTCTGCATACTAGATCATTG
1 CTGCTCTGCATACTAGATCATTG
1993558 CTGCTCTGCATACTAGATCATTG
1 CTGCTCTGCATACTAGATCATTG
1993581 CT
1 CT
1993583 ACTGATGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (23 bp):
CTGCTCTGCATACTAGATCATTG
Found at i:2001228 original size:22 final size:22
Alignment explanation
Indices: 2001187--2001228 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2001177 CGAAAAGAGG
*
2001187 AAAAAAAAAGCCAAAAAAAATT
1 AAAAAAAAAGCAAAAAAAAATT
2001209 AAAAAAAAAG-AAAAAGAAAA
1 AAAAAAAAAGCAAAAA-AAAA
2001229 GAGAGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.83, C:0.05, G:0.07, T:0.05
Consensus pattern (22 bp):
AAAAAAAAAGCAAAAAAAAATT
Found at i:2011759 original size:19 final size:19
Alignment explanation
Indices: 2011717--2011764 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
2011707 AATCCGATCC
* *
2011717 AAATATAAA-ATTTTTTTT
1 AAATATAAATAATTATTTT
*
2011735 ACATATAAATAATTATTTT
1 AAATATAAATAATTATTTT
2011754 AAATATAAATA
1 AAATATAAATA
2011765 TGAACAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATATAAATAATTATTTT
Found at i:2011785 original size:29 final size:29
Alignment explanation
Indices: 2011742--2011797 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2011732 TTTACATATA
*
2011742 AATAATTATTTTAAAT-ATAAATATGAAC
1 AATAATTATTATAAATAATAAATATGAAC
*
2011770 AATAGATTATTATAAATAATATATATGA
1 AATA-ATTATTATAAATAATAAATATGA
2011798 GTAACAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 11 0.46
30 9 0.38
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (29 bp):
AATAATTATTATAAATAATAAATATGAAC
Found at i:2013394 original size:10 final size:11
Alignment explanation
Indices: 2013369--2013393 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2013359 CTAAAATTAA
2013369 AAAATATTATT
1 AAAATATTATT
2013380 AAAATATTATT
1 AAAATATTATT
2013391 AAA
1 AAA
2013394 TTCTTTTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATATTATT
Found at i:2023993 original size:2 final size:2
Alignment explanation
Indices: 2023986--2024014 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2023976 ACTATTCAGC
2023986 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2024015 GGGATGTTCC
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2026850 original size:29 final size:29
Alignment explanation
Indices: 2026805--2026879 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
2026795 TGGGTAAAAT
* * *
2026805 ATTCAAGACAGATTCTGCCGCAGTATAAAG
1 ATTCAAG-CAGACTCTGCAGCAGTACAAAG
2026835 ATTCAAGCAGACTCTGCAGCAGTACAAAG
1 ATTCAAGCAGACTCTGCAGCAGTACAAAG
* * *
2026864 CTTTAAGCAGGCTCTG
1 ATTCAAGCAGACTCTG
2026880 TAGTATTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 32 0.82
30 7 0.18
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (29 bp):
ATTCAAGCAGACTCTGCAGCAGTACAAAG
Found at i:2035044 original size:24 final size:24
Alignment explanation
Indices: 2035012--2035061 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2035002 GCGACTGTGA
2035012 TTGCCCTAGGATTGTAAGTTTTTT
1 TTGCCCTAGGATTGTAAGTTTTTT
2035036 TTGCCCTAGGATTGTAAGTTTTTT
1 TTGCCCTAGGATTGTAAGTTTTTT
2035060 TT
1 TT
2035062 TCCTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.52
Consensus pattern (24 bp):
TTGCCCTAGGATTGTAAGTTTTTT
Found at i:2040328 original size:23 final size:24
Alignment explanation
Indices: 2040298--2040343 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2040288 TTGACAGCAA
*
2040298 AGAAAAAG-GAGAATCTCATTGTT
1 AGAAAAAGAGAAAATCTCATTGTT
2040321 AGAAAAAGAGAAAATCTCATTGT
1 AGAAAAAGAGAAAATCTCATTGT
2040344 AAATTCACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (24 bp):
AGAAAAAGAGAAAATCTCATTGTT
Found at i:2044266 original size:13 final size:14
Alignment explanation
Indices: 2044242--2044271 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2044232 ATAGATAAAT
2044242 TTATATTTTTTTAA
1 TTATATTTTTTTAA
2044256 TTATA-TTTTTTAA
1 TTATATTTTTTTAA
2044269 TTA
1 TTA
2044272 CAAAAAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATATTTTTTTAA
Found at i:2048696 original size:50 final size:50
Alignment explanation
Indices: 2048635--2048731 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 50
2048625 ATTCGGTGAG
* * * *
2048635 TTCATCCAGAAAATATGCTGT-AAGCATTCTCGTGCTCTGAATTATCAGAC
1 TTCATCAAGAAAATATGCTGTGAA-CATTCTCATGCCCTGAAATATCAGAC
2048685 TTCATCAAGAAAATATGCTGTGAACATTCTCATGCCCTGAAATATCA
1 TTCATCAAGAAAATATGCTGTGAACATTCTCATGCCCTGAAATATCA
2048732 AATTTGTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 40 0.95
51 2 0.05
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (50 bp):
TTCATCAAGAAAATATGCTGTGAACATTCTCATGCCCTGAAATATCAGAC
Found at i:2054639 original size:34 final size:33
Alignment explanation
Indices: 2054597--2054676 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
2054587 TGTAATAAAA
2054597 AATATTTATATATAAAATT-GATAAAAAAAATATT
1 AATATTTATATATAAAATTAG-TAAAAAAAA-ATT
* *
2054631 TATATTTATAT-GAAAATTAGTAAAAAAAAATT
1 AATATTTATATATAAAATTAGTAAAAAAAAATT
*
2054663 AATCATTTTTATAT
1 AAT-ATTTATATAT
2054677 TTTTTATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
32 5 0.13
33 22 0.58
34 11 0.29
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (33 bp):
AATATTTATATATAAAATTAGTAAAAAAAAATT
Found at i:2054720 original size:17 final size:18
Alignment explanation
Indices: 2054697--2054747 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
2054687 AATGTAAATT
2054697 TTTTTTATTAATTTTACA
1 TTTTTTATTAATTTTACA
*
2054715 -TTTTTATTAACATTT-CA
1 TTTTTTATTAA-TTTTACA
2054732 TTTTTTATTAATTTTA
1 TTTTTTATTAATTTTA
2054748 TATATTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTATTAATTTTACA
Found at i:2054769 original size:15 final size:16
Alignment explanation
Indices: 2054736--2054771 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2054726 ATTTCATTTT
2054736 TTATTAATTTTATATA
1 TTATTAATTTTATATA
*
2054752 TTATTATTTTTATA-A
1 TTATTAATTTTATATA
2054767 TTATT
1 TTATT
2054772 TTTAATTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTAATTTTATATA
Found at i:2055287 original size:48 final size:52
Alignment explanation
Indices: 2055229--2055339 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 52
2055219 TAGTTAGAAA
2055229 TAATATTTATATTTTAAT-AAATATAA-TAATAATAATT-ATATATAAT-AT
1 TAATATTTATATTTTAATAAAATATAACTAATAATAATTAATATATAATAAT
* * * * *
2055277 TATTATTTATA-TTTATTAAAATATAACTATTATTTATTAATATATAATAAT
1 TAATATTTATATTTTAATAAAATATAACTAATAATAATTAATATATAATAAT
*
2055328 TAATCTTTATAT
1 TAATATTTATAT
2055340 AATAAAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
47 5 0.10
48 18 0.35
49 8 0.16
50 9 0.18
51 11 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (52 bp):
TAATATTTATATTTTAATAAAATATAACTAATAATAATTAATATATAATAAT
Found at i:2055329 original size:21 final size:21
Alignment explanation
Indices: 2055252--2055329 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
2055242 TTAATAAATA
*
2055252 TAATA-ATAATAATTATATA-
1 TAATATATAATAATTATTTAT
* *
2055271 TAATAT-TATTATTTATATTTAT
1 TAATATATAATA-AT-TATTTAT
*
2055293 TAAAATATAACT-ATTATTTAT
1 TAATATATAA-TAATTATTTAT
2055314 TAATATATAATAATTA
1 TAATATATAATAATTA
2055330 ATCTTTATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
19 9 0.20
20 2 0.04
21 25 0.56
22 6 0.13
23 2 0.04
24 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATATAATAATTATTTAT
Found at i:2055340 original size:18 final size:18
Alignment explanation
Indices: 2055316--2055366 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
2055306 TTATTTATTA
2055316 ATATATAATAATTAATCT
1 ATATATAATAATTAATCT
* **
2055334 TTATATAATAAAAAATCT
1 ATATATAATAATTAATCT
2055352 ATATATAA-AATTAAT
1 ATATATAATAATTAAT
2055367 AAAAAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATATAATAATTAATCT
Found at i:2055917 original size:30 final size:27
Alignment explanation
Indices: 2055883--2055937 Score: 74
Period size: 30 Copynumber: 1.9 Consensus size: 27
2055873 TTTTCTGATT
*
2055883 TAATGGTTTATTATGTAAATAGCCGATTCA
1 TAATGGTTTAAT-TGTAAA-A-CCGATTCA
2055913 TAATGGTTTAATTGTAAAACCGATT
1 TAATGGTTTAATTGTAAAACCGATT
2055938 TAATTACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 1 0.04
29 6 0.25
30 11 0.46
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (27 bp):
TAATGGTTTAATTGTAAAACCGATTCA
Found at i:2057851 original size:2 final size:2
Alignment explanation
Indices: 2057844--2057879 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2057834 GTTAAGGGCA
2057844 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
2057880 TAAAAAGGCT
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
Found at i:2060282 original size:30 final size:31
Alignment explanation
Indices: 2060235--2060296 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
2060225 TGAAGTAGTT
2060235 AGTTTATTTACTTTTATTAGTCTCCATGATTA
1 AGTTTATTTA-TTTTATTAGTCTCCATGATTA
*
2060267 AGTTTATTT-TTTTATTAGTCTCCGTGATTA
1 AGTTTATTTATTTTATTAGTCTCCATGATTA
2060297 TGAAGATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 20 0.69
32 9 0.31
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (31 bp):
AGTTTATTTATTTTATTAGTCTCCATGATTA
Found at i:2062609 original size:12 final size:12
Alignment explanation
Indices: 2062588--2062647 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
2062578 TAATTGTCTA
2062588 TTTATTTATTTG
1 TTTATTTATTTG
*
2062600 TTTGTTTA-TT-
1 TTTATTTATTTG
2062610 TTTATTTTATTTG
1 TTTA-TTTATTTG
* *
2062623 ATTATTTATGTG
1 TTTATTTATTTG
*
2062635 TTTATTTGTTTG
1 TTTATTTATTTG
2062647 T
1 T
2062648 AATATTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 3 0.08
11 6 0.16
12 26 0.68
13 3 0.08
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:2063061 original size:18 final size:20
Alignment explanation
Indices: 2063021--2063061 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
2063011 TTATATTTTT
*
2063021 AAAGAAAATCAATTTTTAGA
1 AAAGAAAATCAATTTTCAGA
*
2063041 AAAG-AAAT-AATTTTCATA
1 AAAGAAAATCAATTTTCAGA
2063059 AAA
1 AAA
2063062 TCCTACCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.58
19 4 0.21
20 4 0.21
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (20 bp):
AAAGAAAATCAATTTTCAGA
Found at i:2063088 original size:116 final size:122
Alignment explanation
Indices: 2062827--2063076 Score: 275
Period size: 122 Copynumber: 2.1 Consensus size: 122
2062817 CAAAAAGCTT
* ** *
2062827 TACCAACATATT-GCAAGGCAATTTGATTTTTAAAATAAAATTTTATTAACATATTGAAAAATTT
1 TACCAACATATTAG-AAGGTAATTTGATTTTTAAAATAAAATTTTACCAACATATTGAAAAATAT
* *
2062891 TATTAATTTTTTATAAAAAAAAAATTTCAAGAGAAAAATATAGTTTTTAATAAAATCT
65 TATTAATTTTTTATAAAAAAAAAATTTCAAGAGAAAAATATAGATTTTAATAAAATCC
* * *
2062949 TACTAACATATTAGAAGGTAATTTGATTTTTAAGAT-AAGTTTTACCAACATATTGAAAAATATT
1 TACCAACATATTAGAAGGTAATTTGATTTTTAAAATAAAATTTTACCAACATATTGAAAAATATT
** ** *
2063013 A-T-A-TTTTTA-AAGAAAATCAATTTTTAGA-AAAGAA-ATA-ATTTTCATAAAATCC
66 ATTAATTTTTTATAA-AAAAAAAATTTCAAGAGAAA-AATATAGATTTTAATAAAATCC
*
2063065 TACCAATATATT
1 TACCAACATATT
2063077 GGAGGATAAT
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
116 22 0.20
117 8 0.07
118 20 0.18
119 1 0.01
120 1 0.01
121 25 0.23
122 31 0.28
123 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (122 bp):
TACCAACATATTAGAAGGTAATTTGATTTTTAAAATAAAATTTTACCAACATATTGAAAAATATT
ATTAATTTTTTATAAAAAAAAAATTTCAAGAGAAAAATATAGATTTTAATAAAATCC
Found at i:2067401 original size:10 final size:10
Alignment explanation
Indices: 2067386--2067425 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
2067376 ATGAATGAAG
2067386 TGAAAAAAAA
1 TGAAAAAAAA
2067396 TGAAAAAAAA
1 TGAAAAAAAA
*
2067406 T-AATGAAAAA
1 TGAA-AAAAAA
2067416 TGAAAAAAAA
1 TGAAAAAAAA
2067426 AAATGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 2 0.08
10 22 0.85
11 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (10 bp):
TGAAAAAAAA
Found at i:2067442 original size:22 final size:20
Alignment explanation
Indices: 2067391--2067438 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2067381 TGAAGTGAAA
*
2067391 AAAAATGAAAAAAAATAATG
1 AAAAATGAAAAAAAAAAATG
2067411 AAAAATGAAAAAAAAAAATG
1 AAAAATGAAAAAAAAAAATG
*
2067431 AGAAATGA
1 AAAAATGA
2067439 GAAAGATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAAATGAAAAAAAAAAATG
Found at i:2067489 original size:13 final size:13
Alignment explanation
Indices: 2067473--2067497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2067463 AAGTAAAAAA
2067473 TGAAAACTCAAAT
1 TGAAAACTCAAAT
2067486 TGAAAACTCAAA
1 TGAAAACTCAAA
2067498 AAGATAATTT
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:0.16, G:0.08, T:0.20
Consensus pattern (13 bp):
TGAAAACTCAAAT
Found at i:2068328 original size:13 final size:13
Alignment explanation
Indices: 2068310--2068335 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2068300 TATTTATAAG
2068310 CATTGCATTCATA
1 CATTGCATTCATA
2068323 CATTGCATTCATA
1 CATTGCATTCATA
2068336 AATATTACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
CATTGCATTCATA
Found at i:2069240 original size:21 final size:22
Alignment explanation
Indices: 2069209--2069273 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
2069199 TAAGAGTTTT
2069209 AATTACGAATCTTTGAAATTT-A
1 AATTA-GAATCTTTGAAATTTCA
* *
2069231 AATATA-AATCTCTAAAATTTCCA
1 AAT-TAGAATCTTTGAAATTT-CA
*
2069254 AATTAGGATCTTTGAAATTT
1 AATTAGAATCTTTGAAATTT
2069274 TAGGTGTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
21 12 0.35
22 5 0.15
23 17 0.50
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (22 bp):
AATTAGAATCTTTGAAATTTCA
Found at i:2069481 original size:18 final size:18
Alignment explanation
Indices: 2069426--2069485 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
2069416 ATCTCTTGCA
*
2069426 AATCTTGAATATTTTATG
1 AATCTTGAATTTTTTATG
* * * *
2069444 AATTTTTTAA-TCTTTGTG
1 AA-TCTTGAATTTTTTATG
2069462 AATCTTGAATTTTTTATG
1 AATCTTGAATTTTTTATG
2069480 AATCTT
1 AATCTT
2069486 TGAAAATTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
17 5 0.16
18 21 0.68
19 5 0.16
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (18 bp):
AATCTTGAATTTTTTATG
Found at i:2069766 original size:22 final size:22
Alignment explanation
Indices: 2069722--2069767 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2069712 ACTTCTGAAC
*
2069722 TTCAAATTGAGAATTCTTTAAT
1 TTCAAATTGAGAATTCTTAAAT
*
2069744 TTCAAATTGTGAATGT-TTAAAT
1 TTCAAATTGAGAAT-TCTTAAAT
2069766 TT
1 TT
2069768 TTATTTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.48
Consensus pattern (22 bp):
TTCAAATTGAGAATTCTTAAAT
Found at i:2080054 original size:17 final size:19
Alignment explanation
Indices: 2080027--2080063 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
2080017 ATCAAGGATG
2080027 AAAGCAAAAGAAAA-AAAA
1 AAAGCAAAAGAAAAGAAAA
2080045 AAAG-AAAAGAAAAGAAAA
1 AAAGCAAAAGAAAAGAAAA
2080063 A
1 A
2080064 CAGATGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAGCAAAAGAAAAGAAAA
Found at i:2080170 original size:21 final size:21
Alignment explanation
Indices: 2080145--2080188 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2080135 GTATACATAC
2080145 ATGTATTTTTATGTACATTAT
1 ATGTATTTTTATGTACATTAT
2080166 ATGTATTTTTATGTACATTAT
1 ATGTATTTTTATGTACATTAT
2080187 AT
1 AT
2080189 AATAATATAA
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:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (21 bp):
ATGTATTTTTATGTACATTAT
Found at i:2081097 original size:29 final size:27
Alignment explanation
Indices: 2081041--2081101 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
2081031 ATTTTAAGAT
* *
2081041 AAATAAATTATTTAATTTTTTAAATTA
1 AAATAAAATATTTAATTTTATAAATTA
*
2081068 AAATAAAATATATTATATTTTATAATTTA
1 AAATAAAATAT-TTA-ATTTTATAAATTA
2081097 AAATA
1 AAATA
2081102 TATAATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 10 0.34
28 3 0.10
29 16 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AAATAAAATATTTAATTTTATAAATTA
Found at i:2081529 original size:27 final size:26
Alignment explanation
Indices: 2081491--2081546 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
2081481 GAAAATATTA
*
2081491 TATTTAGATATT-TGTATATATGAAATT
1 TATTTAGATATTATGT-T-TATAAAATT
*
2081518 TATTTAGTTATTATGTTTATAAAATT
1 TATTTAGATATTATGTTTATAAAATT
2081544 TAT
1 TAT
2081547 AAAGTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 11 0.42
27 12 0.46
28 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (26 bp):
TATTTAGATATTATGTTTATAAAATT
Found at i:2081705 original size:17 final size:17
Alignment explanation
Indices: 2081683--2081716 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2081673 TTGAAATTTG
2081683 AATTTTATTTTTTAAAA
1 AATTTTATTTTTTAAAA
*
2081700 AATTTTTTTTTTTAAAA
1 AATTTTATTTTTTAAAA
2081717 GTATATACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTATTTTTTAAAA
Found at i:2084113 original size:3 final size:3
Alignment explanation
Indices: 2084105--2084133 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2084095 CTTATCCGCT
2084105 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
2084134 TTACCACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:2100936 original size:15 final size:15
Alignment explanation
Indices: 2100913--2100959 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2100903 AATATATAAG
*
2100913 AATTTAAATTTTAAT
1 AATTAAAATTTTAAT
2100928 AATTAAAA-TTTAA-
1 AATTAAAATTTTAAT
*
2100941 AATCTAAAATTTTATT
1 AAT-TAAAATTTTAAT
2100957 AAT
1 AAT
2100960 AAATCACGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 3 0.11
14 10 0.37
15 11 0.41
16 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAAAATTTTAAT
Found at i:2101271 original size:19 final size:18
Alignment explanation
Indices: 2101249--2101284 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2101239 GAGCAAAAGT
2101249 ATAAACTAAAAAAAAAATC
1 ATAAA-TAAAAAAAAAATC
*
2101268 ATAAATATAAAAAAAAT
1 ATAAATAAAAAAAAAAT
2101285 TATATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (18 bp):
ATAAATAAAAAAAAAATC
Found at i:2101291 original size:16 final size:17
Alignment explanation
Indices: 2101243--2101293 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
2101233 ATTTAAGAGC
* *
2101243 AAAAGTATAAACTAAAAA
1 AAAAATATAAA-TATAAA
2101261 AAAAATCATAAATATAAA
1 AAAAAT-ATAAATATAAA
*
2101279 AAAAAT-TATATATAA
1 AAAAATATAAATATAA
2101294 TCCAAGTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 8 0.28
18 16 0.55
19 5 0.17
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAATATAAATATAAA
Found at i:2101487 original size:14 final size:14
Alignment explanation
Indices: 2101468--2101495 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2101458 ATTATAAATA
2101468 AAAAATATTTATTT
1 AAAAATATTTATTT
2101482 AAAAATATTTATTT
1 AAAAATATTTATTT
2101496 TTTTATGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAAATATTTATTT
Found at i:2102740 original size:45 final size:44
Alignment explanation
Indices: 2102691--2102785 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 44
2102681 TTAATAAGTA
**
2102691 AAAATA-AAAAATTAAGATGAGATTTTTTTATTATAAAATATTATT
1 AAAATATAAAAATTAAGAT-A-AAATTTTTATTATAAAATATTATT
* * *
2102736 AAAATTATTAATATTAATATAAAATTTTTATTATAAAATATTATT
1 AAAA-TATAAAAATTAAGATAAAATTTTTATTATAAAATATTATT
2102781 AAAAT
1 AAAAT
2102786 TATTAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 30 0.70
46 3 0.07
47 9 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (44 bp):
AAAATATAAAAATTAAGATAAAATTTTTATTATAAAATATTATT
Found at i:2102744 original size:9 final size:9
Alignment explanation
Indices: 2102720--2102792 Score: 53
Period size: 9 Copynumber: 8.0 Consensus size: 9
2102710 AGATTTTTTT
*
2102720 ATTATAAAA
1 ATTATTAAA
2102729 TATTATTAAA
1 -ATTATTAAA
*
2102739 ATTATTAAT
1 ATTATTAAA
2102748 ATTAATATAAA
1 ATT-AT-TAAA
*
2102759 ATT-TT--T
1 ATTATTAAA
*
2102765 ATTATAAAA
1 ATTATTAAA
2102774 TATTATTAAA
1 -ATTATTAAA
2102784 ATTATTAAA
1 ATTATTAAA
2102793 TTTTTTAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
6 3 0.06
7 1 0.02
8 1 0.02
9 21 0.42
10 18 0.36
11 6 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATTATTAAA
Found at i:2102805 original size:19 final size:19
Alignment explanation
Indices: 2102720--2102793 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 19
2102710 AGATTTTTTT
2102720 ATTATAAAATATTATTAAA
1 ATTATAAAATATTATTAAA
*
2102739 ATTAT-TAATATTAATATAAAA
1 ATTATAAAATATT-AT-T-AAA
2102760 TTTTTATTATAAAATATTATTAAA
1 -----ATTATAAAATATTATTAAA
*
2102784 ATTATTAAAT
1 ATTATAAAAT
2102794 TTTTTAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 18
0.67 0.05 0.28
Matches are distributed among these distances:
18 6 0.14
19 16 0.37
20 1 0.02
21 3 0.07
24 3 0.07
25 1 0.02
26 7 0.16
27 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTATAAAATATTATTAAA
Found at i:2102920 original size:14 final size:14
Alignment explanation
Indices: 2102879--2102927 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
2102869 TAATAAATAA
*
2102879 AAATTAATAAAATT
1 AAATTAATATAATT
* *
2102893 TAATT-ATTTAATT
1 AAATTAATATAATT
2102906 AAATTAATATAATT
1 AAATTAATATAATT
*
2102920 AAACTAAT
1 AAATTAAT
2102928 TTTATTCGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTAATATAATT
Found at i:2102921 original size:18 final size:18
Alignment explanation
Indices: 2102880--2102921 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2102870 AATAAATAAA
2102880 AATTAATAAAATTTAATT
1 AATTAATAAAATTTAATT
* *
2102898 ATTTAATTAAA-TTAATAT
1 AATTAATAAAATTTAAT-T
2102916 AATTAA
1 AATTAA
2102922 ACTAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAATAAAATTTAATT
Found at i:2103411 original size:14 final size:14
Alignment explanation
Indices: 2103392--2103420 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2103382 TAGTCATTTC
2103392 ATTTCATAAACTCT
1 ATTTCATAAACTCT
2103406 ATTTCATAAACTCT
1 ATTTCATAAACTCT
2103420 A
1 A
2103421 CATTCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTCATAAACTCT
Found at i:2104451 original size:33 final size:33
Alignment explanation
Indices: 2104394--2104468 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
2104384 GTTTTATAGC
* *
2104394 TTTTTATAAATAATTTTTTAAAAAATCATATAAT
1 TTTTTAGAAATAATATTTTAAAAAATCATA-AAT
*
2104428 TTTTTAGAAATAA-ATTTTCAAAAATCATAAAT
1 TTTTTAGAAATAATATTTTAAAAAATCATAAAT
2104460 TTTTT-GAAA
1 TTTTTAGAAA
2104469 ATTTTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 4 0.11
32 8 0.21
33 14 0.37
34 12 0.32
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (33 bp):
TTTTTAGAAATAATATTTTAAAAAATCATAAAT
Found at i:2104488 original size:32 final size:29
Alignment explanation
Indices: 2104408--2104502 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 29
2104398 TATAAATAAT
*
2104408 TTTTTAAAAAATCATATAATTTTTTAGAAATAA
1 TTTTTCAAAAATCATA-AATTTTTT-G-AA-AA
*
2104441 ATTTTCAAAAATCATAAATTTTTTGAAAA
1 TTTTTCAAAAATCATAAATTTTTTGAAAA
*
2104470 TTTTTCAGAAAAGTTCAT-AATATTTTGAAAA
1 TTTTTCA-AAAA--TCATAAATTTTTTGAAAA
2104501 TT
1 TT
2104503 CATTTTGGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
29 8 0.15
30 6 0.11
31 15 0.27
32 12 0.22
33 14 0.25
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (29 bp):
TTTTTCAAAAATCATAAATTTTTTGAAAA
Found at i:2107728 original size:2 final size:2
Alignment explanation
Indices: 2107721--2107752 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2107711 CAAATTTTGT
2107721 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2107753 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2110510 original size:27 final size:26
Alignment explanation
Indices: 2110465--2110519 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
2110455 ACTTGCTTGA
* **
2110465 GCCAACCCACTTGCTCACTTTCAACC
1 GCCAACCCACTTACTCACTGCCAACC
*
2110491 GCCAACCATACTTACTCACTGCCAACC
1 GCCAACC-CACTTACTCACTGCCAACC
2110518 GC
1 GC
2110520 AATTGTTACC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.25, C:0.45, G:0.09, T:0.20
Consensus pattern (26 bp):
GCCAACCCACTTACTCACTGCCAACC
Found at i:2112107 original size:11 final size:11
Alignment explanation
Indices: 2112087--2112117 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2112077 AAAATAAAAT
2112087 AATAATAAAGA
1 AATAATAAAGA
2112098 AATAATAAAGA
1 AATAATAAAGA
*
2112109 AAGAATAAA
1 AATAATAAA
2112118 AATTGACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (11 bp):
AATAATAAAGA
Found at i:2112340 original size:18 final size:20
Alignment explanation
Indices: 2112304--2112341 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
2112294 AAAATTATAT
2112304 TTTTAATAACTTTTAATTAA
1 TTTTAATAACTTTTAATTAA
*
2112324 TTTTAA-AA-TTTTTATTAA
1 TTTTAATAACTTTTAATTAA
2112342 AAGAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAATAACTTTTAATTAA
Found at i:2116698 original size:2 final size:2
Alignment explanation
Indices: 2116691--2116722 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2116681 TTTATCCTCC
2116691 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
2116723 AATAAAACGC
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:2121712 original size:27 final size:27
Alignment explanation
Indices: 2121677--2121728 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2121667 ATTTTGTTTT
*
2121677 TTATATTTTCTTA-TTTTCTTTATTAAG
1 TTATATTTT-TTAGTTTACTTTATTAAG
*
2121704 TTATCTTTTTTAGTTTACTTTATTA
1 TTATATTTTTTAGTTTACTTTATTA
2121729 TTTATTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67
Consensus pattern (27 bp):
TTATATTTTTTAGTTTACTTTATTAAG
Found at i:2121950 original size:16 final size:16
Alignment explanation
Indices: 2121924--2121967 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2121914 TTAAATTTGG
*
2121924 AAAAATAAAAAATAACC
1 AAAAAT-AAAAATAACA
**
2121941 AAAAATAAAAATATTA
1 AAAAATAAAAATAACA
2121957 AAAAATAAAAA
1 AAAAATAAAAA
2121968 ATTTTATCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAATAACA
Found at i:2122020 original size:26 final size:28
Alignment explanation
Indices: 2121991--2122051 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 28
2121981 ACGAGATTTT
2121991 AAAATATTCTAAG-TAATAATA-CTTTA
1 AAAATATTCTAAGATAATAATATCTTTA
* * * *
2122017 AAAA-ATTTTCAGATAATAATATTTTTT
1 AAAATATTCTAAGATAATAATATCTTTA
2122044 AAAATATT
1 AAAATATT
2122052 ATCAGTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 6 0.21
26 12 0.43
27 7 0.25
28 3 0.11
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (28 bp):
AAAATATTCTAAGATAATAATATCTTTA
Found at i:2122403 original size:14 final size:13
Alignment explanation
Indices: 2122366--2122413 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
2122356 ATTTTTCTTG
2122366 AATAAAAATGAAAT
1 AATAAAAA-GAAAT
2122380 AATAACAAAGAAAT
1 AATAA-AAAGAAAT
*
2122394 AATAGAAAAGGAAT
1 AATA-AAAAGAAAT
2122408 AA-AAAA
1 AATAAAA
2122414 TCGATAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 3 0.10
13 1 0.03
14 23 0.74
15 4 0.13
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (13 bp):
AATAAAAAGAAAT
Found at i:2129878 original size:27 final size:28
Alignment explanation
Indices: 2129846--2129911 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
2129836 AATTATTTAA
*
2129846 AATATTATTTATATT-TTAAA-TTTAATC
1 AATATT-TTTATATTATAAAAGTTTAATC
*
2129873 AATATTTTT-TAATTATAAAAGTTTTATC
1 AATATTTTTAT-ATTATAAAAGTTTAATC
2129901 AATATTTTTAT
1 AATATTTTTAT
2129912 TAGAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 1 0.03
26 6 0.18
27 10 0.30
28 15 0.45
29 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (28 bp):
AATATTTTTATATTATAAAAGTTTAATC
Found at i:2130448 original size:30 final size:30
Alignment explanation
Indices: 2130380--2130449 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
2130370 TAAATTAATT
*
2130380 AAATTTATTTAAATACAAATTAAATGATAA
1 AAATTTATTTAAATAAAAATTAAATGATAA
* * * *
2130410 AGACTTATTTAGATAAAAATTAAA-GTTTAA
1 AAATTTATTTAAATAAAAATTAAATG-ATAA
2130440 AAATTTATTT
1 AAATTTATTT
2130450 GAATGTAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (30 bp):
AAATTTATTTAAATAAAAATTAAATGATAA
Found at i:2136677 original size:132 final size:132
Alignment explanation
Indices: 2136438--2136700 Score: 355
Period size: 132 Copynumber: 2.0 Consensus size: 132
2136428 TTGGTGCAAC
* * * ** * * * **
2136438 CAAAGTTTTCTGCTTTGTAAGTTGTAAACATTTTTTTCTTAGAAACATAATGATATATCGCTTTT
1 CAAAGTCTCCTGCTTTATAAGTTGTAAACAACTCTTTCTTAGAAACACAATGATATACCGCTCAT
* * * *
2136503 GTATTTTCTATCCACTCAATGTCGGGATCACCAACATAATTACAATCACCATGTGTACAAATCAA
66 GTATCTACTATCCACTCAATATCAGGATCACCAACATAATTACAATCACCATGTGTACAAATCAA
2136568 AT
131 AT
2136570 CAAAGTCTCCTGCTTTATAAGTTGTAAACAACTCTTTCTTAGAAACACAATGATATACCGCTCAT
1 CAAAGTCTCCTGCTTTATAAGTTGTAAACAACTCTTTCTTAGAAACACAATGATATACCGCTCAT
* * * * *
2136635 GTGTCTACTATCCACTCAATATCATGATCACTAACATGATTACAATCACCATGTGTATAAATCAA
66 GTATCTACTATCCACTCAATATCAGGATCACCAACATAATTACAATCACCATGTGTACAAATCAA
2136700 A
131 A
2136701 GTAATTAAAT
Statistics
Matches: 112, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
132 112 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (132 bp):
CAAAGTCTCCTGCTTTATAAGTTGTAAACAACTCTTTCTTAGAAACACAATGATATACCGCTCAT
GTATCTACTATCCACTCAATATCAGGATCACCAACATAATTACAATCACCATGTGTACAAATCAA
AT
Done.