Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 38 of 208
Found at i:10576622 original size:18 final size:19
Alignment explanation
Indices: 10576564--10576622 Score: 88
Period size: 18 Copynumber: 3.2 Consensus size: 19
10576554 GGGAAGAAAG
10576564 AAAATAGAAAGAAAAA-AA
1 AAAATAGAAAGAAAAAGAA
10576582 GAAAA-AGAAAGAAAAAGAA
1 -AAAATAGAAAGAAAAAGAA
10576601 AAAATAG-AAGAAAAAGAA
1 AAAATAGAAAGAAAAAGAA
10576619 AAAA
1 AAAA
10576623 ATAATAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 30 0.79
19 8 0.21
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAATAGAAAGAAAAAGAA
Found at i:10576818 original size:13 final size:13
Alignment explanation
Indices: 10576796--10576839 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
10576786 CCAATCTGCA
* *
10576796 AAAAAAAAAAAAC
1 AAAAAGAAAAAAG
10576809 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
*
10576822 AAAAAGAGAAAAG
1 AAAAAGAAAAAAG
10576835 AAAAA
1 AAAAA
10576840 AACAAAAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:10576846 original size:13 final size:12
Alignment explanation
Indices: 10576797--10576847 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
10576787 CAATCTGCAA
*
10576797 AAAAAAAAAAAC
1 AAAAAAAAAAAG
10576809 AAAAAGAAAAAAG
1 AAAAA-AAAAAAG
*
10576822 AAAAAGAGAAAAG
1 AAAAA-AAAAAAG
10576835 AAAAAAACAAAAG
1 AAAAAAA-AAAAG
10576848 GCCGGATTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
12 6 0.18
13 28 0.82
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:10576847 original size:20 final size:18
Alignment explanation
Indices: 10576797--10576847 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
10576787 CAATCTGCAA
*
10576797 AAAAAAAAAAACAAAAAG
1 AAAAAAAAAAAGAAAAAG
10576815 AAAAAAGAAAAAGAGAAAAG
1 AAAAAA-AAAAAGA-AAAAG
10576835 AAAAAAACAAAAG
1 AAAAAAA-AAAAG
10576848 GCCGGATTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
20 16 0.55
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAAAAAG
Found at i:10577356 original size:35 final size:35
Alignment explanation
Indices: 10577317--10577492 Score: 110
Period size: 35 Copynumber: 4.9 Consensus size: 35
10577307 AATTTGTCGT
*
10577317 TTTTCAAAAATTTCGAGTTTTAAAAAATAATCGAG
1 TTTTCAAAAATTTCGTGTTTTAAAAAATAATCGAG
* * * ** * *
10577352 TTTTCAAAAAAAAATTTTCGCG-TTTCATAAATTTTTGTG
1 TTTTC----AAAAA-TTTCGTGTTTTAAAAAATAATCGAG
* ** *
10577391 TTTTCAAAAATTCTCGTG-TTTCAAAAATTTTCGCG
1 TTTTCAAAAATT-TCGTGTTTTAAAAAATAATCGAG
10577426 TTTTCAAAAATTTTCGTGTTTTAAAAAA-AATTTC-A-
1 TTTTCAAAAA-TTTCGTGTTTTAAAAAATAA--TCGAG
10577461 TATTTCAAAAATATTCGTGTTTTAAAAAATAA
1 T-TTTCAAAAAT-TTCGTGTTTTAAAAAATAA
10577493 AAATAAAAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
34 2 0.02
35 45 0.40
36 35 0.31
37 4 0.04
39 21 0.19
40 6 0.05
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (35 bp):
TTTTCAAAAATTTCGTGTTTTAAAAAATAATCGAG
Found at i:10577395 original size:18 final size:18
Alignment explanation
Indices: 10577304--10577801 Score: 252
Period size: 18 Copynumber: 28.3 Consensus size: 18
10577294 TACTTTTAAA
10577304 AAAAATTTGTCGT-TTTTC
1 AAAAATTT-TCGTGTTTTC
* *
10577322 AAAAA-TTTCGAGTTTTA
1 AAAAATTTTCGTGTTTTC
** *
10577339 AAAAATAATCGAGTTTTC
1 AAAAATTTTCGTGTTTTC
*
10577357 AAAAAAAAATTTTCGCG-TTTC
1 ----AAAAATTTTCGTGTTTTC
* *
10577378 ATAAATTTTTGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
10577396 AAAAATTCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
10577413 AAAAATTTTCGCGTTTTC
1 AAAAATTTTCGTGTTTTC
*
10577431 AAAAATTTTCGTGTTTTAA
1 AAAAATTTTCGTGTTTT-C
* * *
10577450 AAAAAATTTCAT-ATTTC
1 AAAAATTTTCGTGTTTTC
*
10577467 AAAAATATTCGTGTTTT-
1 AAAAATTTTCGTGTTTTC
* ***** *
10577484 AAAAA--AT--AAAAATA
1 AAAAATTTTCGTGTTTTC
** * *
10577498 AAAAAGAATCCAT-TTTTC
1 AAAAA-TTTTCGTGTTTTC
*
10577516 -AAAATTCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
10577533 -AAAA--TTCCTGTGTTTC
1 AAAAATTTTCGTGT-TTTC
*
10577549 AAAAATTTTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
10577567 AAAAA-TTCCAATATTTT-
1 AAAAATTTTC-GTGTTTTC
* *
10577584 AAAAATTTCCGTATTTTC
1 AAAAATTTTCGTGTTTTC
*
10577602 AAAAA-TTTCTGTGTTTTA
1 AAAAATTTTC-GTGTTTTC
*
10577620 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* **
10577638 AAGAATCCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
10577656 -AAAA-TTCCGATG-TTTC
1 AAAAATTTTCG-TGTTTTC
*
10577672 AAAAATTTTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
**
10577690 AAAAATTCCCGTGTTTT-
1 AAAAATTTTCGTGTTTTC
*
10577707 AAAAATTTCCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
10577725 AAAAATTTTCGTATTTTTT
1 AAAAATTTTCGT-GTTTTC
* *
10577744 AAGAATTTTCGTG-TCTC
1 AAAAATTTTCGTGTTTTC
* * *
10577761 TAAAATTCTCGTGCTTT-
1 AAAAATTTTCGTGTTTTC
10577778 AAAAATTTTTCGTGTTTTC
1 AAAAA-TTTTCGTGTTTTC
10577797 AAAAA
1 AAAAA
10577802 AATAATTGTT
Statistics
Matches: 364, Mismatches: 81, Indels: 69
0.71 0.16 0.13
Matches are distributed among these distances:
13 1 0.00
14 5 0.01
15 6 0.02
16 15 0.04
17 127 0.35
18 157 0.43
19 39 0.11
21 4 0.01
22 10 0.03
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:10577624 original size:19 final size:17
Alignment explanation
Indices: 10577516--10577842 Score: 128
Period size: 17 Copynumber: 18.5 Consensus size: 17
10577506 TCCATTTTTC
*
10577516 AAAATTCTCGTGTTTT-C
1 AAAATT-TCGTGTTTTAA
* *
10577533 AAAATTCCTGTGTTTCAA
1 AAAATTTC-GTGTTTTAA
* * *
10577551 AAATTTTCATGTTTTCA
1 AAAATTTCGTGTTTTAA
* * *
10577568 AAAATTCCAATATTTT-A
1 AAAATTTC-GTGTTTTAA
* *
10577585 AAAATTTCCGTATTTTCA
1 AAAATTT-CGTGTTTTAA
10577603 AAAATTTCTGTGTTTTAA
1 AAAATTTC-GTGTTTTAA
*
10577621 AAAATCTTCGTGTTTTCA
1 AAAAT-TTCGTGTTTTAA
* * *
10577639 AGAATCCTCGTGTTTT-C
1 AAAAT-TTCGTGTTTTAA
* *
10577656 AAAATTCCGATGTTTCAA
1 AAAATTTCG-TGTTTTAA
* * *
10577674 AAATTTTCATGTTTTCA
1 AAAATTTCGTGTTTTAA
*
10577691 AAAATTCCCGTGTTTT-A
1 AAAATT-TCGTGTTTTAA
10577708 AAAATTTCCGTGTTTTCAA
1 AAAATTT-CGTGTTTT-AA
* *
10577727 AAATTTTCGTATTTTTTAA
1 AAAATTTCG--TGTTTTAA
* * *
10577746 GAATTTTCGTGTCTCT--
1 AAAATTTCGTGT-TTTAA
*
10577762 AAAATTCTCGTGCTTTAA
1 AAAATT-TCGTGTTTTAA
*
10577780 AAATTTTTCGTGTTTTCAA
1 AAA-ATTTCGTGTTTT-AA
* *** *
10577799 AAAAATAATTG-TTTCA
1 AAAATTTCGTGTTTTAA
10577815 AAAATCTTCGTGTTTTTAAA
1 AAAAT-TTCGTG-TTTT-AA
10577835 AAAATTTC
1 AAAATTTC
10577843 TCGTATTGTG
Statistics
Matches: 230, Mismatches: 55, Indels: 48
0.69 0.17 0.14
Matches are distributed among these distances:
16 14 0.06
17 86 0.37
18 86 0.37
19 33 0.14
20 11 0.05
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (17 bp):
AAAATTTCGTGTTTTAA
Found at i:10577670 original size:35 final size:34
Alignment explanation
Indices: 10577511--10577800 Score: 162
Period size: 35 Copynumber: 8.3 Consensus size: 34
10577501 AAGAATCCAT
* *
10577511 TTTTCAAAATTCTCGTGTTTTC-AAAA-TTCCTG
1 TTTTCAAAATTCCCGTGTTTTCAAAAATTTCGTG
** * * * *
10577543 TGTTTCAAAAATTTTCATGTTTTCAAAAATTCCAATA
1 T-TTTC-AAAATTCCCGTGTTTTCAAAAATTTC-GTG
* * *
10577580 TTTTAAAAATTTCCGTATTTTCAAAAATTTCTGTG
1 TTTTCAAAATTCCCGTGTTTTCAAAAATTTC-GTG
* * * * *
10577615 TTTTAAAAAATCTTCGTGTTTTCAAGAATCCTCGTG
1 TTTTCAAAATTC-CCGTGTTTTCAAAAAT-TTCGTG
*
10577651 TTTTCAAAATT-CCGATG-TTTCAAAAATTTTCATG
1 TTTTCAAAATTCCCG-TGTTTTCAAAAA-TTTCGTG
10577685 TTTTCAAAAATTCCCGTGTTTT-AAAAATTTCCGTG
1 TTTTC-AAAATTCCCGTGTTTTCAAAAATTT-CGTG
** * * *
10577720 TTTTCAAAAATTTTCGTATTTTTTAAGAATTTTCGTG
1 TTTTC-AAAATTCCCGT-GTTTTCAA-AAATTTCGTG
* * *
10577757 -TCTCTAAAATTCTCGTGCTTT-AAAAATTTTTCGTG
1 TTTTC-AAAATTCCCGTGTTTTCAAAAA--TTTCGTG
10577792 TTTTCAAAA
1 TTTTCAAAA
10577801 AAATAATTGT
Statistics
Matches: 202, Mismatches: 37, Indels: 35
0.74 0.14 0.13
Matches are distributed among these distances:
32 1 0.00
33 6 0.03
34 39 0.19
35 85 0.42
36 56 0.28
37 10 0.05
38 5 0.02
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (34 bp):
TTTTCAAAATTCCCGTGTTTTCAAAAATTTCGTG
Found at i:10577671 original size:123 final size:122
Alignment explanation
Indices: 10577511--10577732 Score: 374
Period size: 123 Copynumber: 1.8 Consensus size: 122
10577501 AAGAATCCAT
*
10577511 TTTTCAAAATTCTCGTGTTTTCAAAATTCCTGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCC
1 TTTTCAAAATCCTCGTGTTTTCAAAATTCCTGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCC
10577576 AATATTTTAAAAATTTCCGTATTTTCAAAAATTTCTGTGTTTTAAAAAATCTTCGTG
66 AATATTTTAAAAATTTCCGTATTTTCAAAAATTTCTGTGTTTTAAAAAATCTTCGTG
10577633 TTTTCAAGAATCCTCGTGTTTTCAAAATTCC-GATGTTTCAAAAATTTTCATGTTTTCAAAAATT
1 TTTTCAA-AATCCTCGTGTTTTCAAAATTCCTG-TGTTTCAAAAATTTTCATGTTTTCAAAAATT
** * *
10577697 CCCGTGTTTTAAAAATTTCCGTGTTTTCAAAAATTT
64 CCAATATTTTAAAAATTTCCGTATTTTCAAAAATTT
10577733 TCGTATTTTT
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
122 8 0.09
123 85 0.91
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (122 bp):
TTTTCAAAATCCTCGTGTTTTCAAAATTCCTGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCC
AATATTTTAAAAATTTCCGTATTTTCAAAAATTTCTGTGTTTTAAAAAATCTTCGTG
Found at i:10577772 original size:123 final size:122
Alignment explanation
Indices: 10577514--10577784 Score: 368
Period size: 123 Copynumber: 2.2 Consensus size: 122
10577504 AATCCATTTT
10577514 TCAAAATTCTCGTGTTTTCAAAATTCCTGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCCAAT
1 TCAAAATTCTCGTGTTTTCAAAATTCCTGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCCAAT
*
10577579 ATTTTAAAAATTTCCGTATTTTCAAAAATTTCTGTGTTTTAAAAAATCTTCGTGTTT
66 ATTTTAAAAATTTCCGTATTTTCAAAAATTTCTGTGTTTTAAAAAATCTTCGTGTTC
* *
10577636 TCAAGAATCCTCGTGTTTTCAAAATTCC-GATGTTTCAAAAATTTTCATGTTTTCAAAAATTCCC
1 TCAA-AATTCTCGTGTTTTCAAAATTCCTG-TGTTTCAAAAATTTTCATGTTTTCAAAAATTCCA
* * * * * * *
10577700 GTGTTTTAAAAATTTCCGTGTTTTCAAAAATTT-TCGTATTTTTTAAGAATTTTCGTG-TC
64 ATATTTTAAAAATTTCCGTATTTTCAAAAATTTCT-GT-GTTTTAAAAAATCTTCGTGTTC
* *
10577759 TCTAAAATTCTCGTGCTTTAAAAATT
1 TC-AAAATTCTCGTGTTTTCAAAATT
10577785 TTTCGTGTTT
Statistics
Matches: 131, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
122 6 0.05
123 108 0.82
124 17 0.13
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.45
Consensus pattern (122 bp):
TCAAAATTCTCGTGTTTTCAAAATTCCTGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCCAAT
ATTTTAAAAATTTCCGTATTTTCAAAAATTTCTGTGTTTTAAAAAATCTTCGTGTTC
Found at i:10586450 original size:21 final size:21
Alignment explanation
Indices: 10586388--10586457 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
10586378 AATTTGTAAT
* *
10586388 TGAGTTGGGGTAGCCTCCTAC
1 TGAGTTGGGGTAGCCTCTTGC
10586409 TGAGTTGGGGTA-CTCTCTTGC
1 TGAGTTGGGGTAGC-CTCTTGC
* *
10586430 TGATTTGGGGTAGCCTGTTGC
1 TGAGTTGGGGTAGCCTCTTGC
10586451 TGAGTTG
1 TGAGTTG
10586458 AGGCAACCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.36, T:0.36
Consensus pattern (21 bp):
TGAGTTGGGGTAGCCTCTTGC
Found at i:10588147 original size:15 final size:15
Alignment explanation
Indices: 10588129--10588171 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
10588119 TTATCCTATT
**
10588129 AGATACATCACTTTC
1 AGATACATCACTAAC
10588144 AGATACATCACTAAC
1 AGATACATCACTAAC
*
10588159 AGACACATCACTA
1 AGATACATCACTA
10588172 CCATACACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.28, G:0.07, T:0.23
Consensus pattern (15 bp):
AGATACATCACTAAC
Found at i:10588179 original size:15 final size:15
Alignment explanation
Indices: 10588133--10588183 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
10588123 CCTATTAGAT
** *
10588133 ACATCACTTTCAGAT
1 ACATCACTAACAGAC
10588148 ACATCACTAACAGAC
1 ACATCACTAACAGAC
* *
10588163 ACATCACTACCATAC
1 ACATCACTAACAGAC
10588178 ACATCA
1 ACATCA
10588184 AAATAAGACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.41, C:0.33, G:0.04, T:0.22
Consensus pattern (15 bp):
ACATCACTAACAGAC
Found at i:10589261 original size:21 final size:21
Alignment explanation
Indices: 10589235--10589275 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
10589225 CAACGTGGCA
10589235 AGTTAA-TTGGCCACATCAGCT
1 AGTTAACTT-GCCACATCAGCT
10589256 AGTTAACTTGCCACATCAGC
1 AGTTAACTTGCCACATCAGC
10589276 GATCCCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:10593649 original size:15 final size:16
Alignment explanation
Indices: 10593629--10593665 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
10593619 CGGATTCAGA
10593629 TAATTT-TAAA-ATTT
1 TAATTTATAAATATTT
10593643 CTAATTTATAAATATTT
1 -TAATTTATAAATATTT
10593660 TAATTT
1 TAATTT
10593666 CAAATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 10 0.50
17 4 0.20
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATTTATAAATATTT
Found at i:10593670 original size:15 final size:16
Alignment explanation
Indices: 10593629--10593672 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
10593619 CGGATTCAGA
10593629 TAATTTTAAA-ATTTC
1 TAATTTTAAATATTTC
10593644 TAATTTATAAATATTT-
1 TAATTT-TAAATATTTC
*
10593660 TAATTTCAAATAT
1 TAATTTTAAATAT
10593673 AATAATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 12 0.46
16 10 0.38
17 4 0.15
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTTTAAATATTTC
Found at i:10594219 original size:18 final size:17
Alignment explanation
Indices: 10594188--10594232 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
10594178 TATTATAATC
* *
10594188 TATAATATAATAATAGT
1 TATAATATATTAATACT
10594205 TATATATATATTAATACT
1 TATA-ATATATTAATACT
*
10594223 TATAAAATAT
1 TATAATATAT
10594233 ATTATTTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TATAATATATTAATACT
Found at i:10599178 original size:11 final size:11
Alignment explanation
Indices: 10599147--10599185 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
10599137 TATTTATTCA
10599147 TTTTTTTCTTT
1 TTTTTTTCTTT
* *
10599158 TTTCTCTCTTT
1 TTTTTTTCTTT
10599169 TTTTTTTCTTT
1 TTTTTTTCTTT
10599180 GTTTTT
1 -TTTTT
10599186 GAAAAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:10599650 original size:19 final size:20
Alignment explanation
Indices: 10599626--10599676 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
10599616 ATTTTCCTAC
*
10599626 AAAAATAAAATAA-AATAGT
1 AAAAATAAAATAATAATAGG
10599645 AAAAATAAATAATAATAATAGG
1 AAAAAT-AA-AATAATAATAGG
*
10599667 AAAATTAAAA
1 AAAAATAAAA
10599677 ATTTTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.22
20 4 0.15
21 7 0.26
22 10 0.37
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.22
Consensus pattern (20 bp):
AAAAATAAAATAATAATAGG
Found at i:10610881 original size:28 final size:27
Alignment explanation
Indices: 10610844--10610903 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
10610834 ATAACTTGTA
* *
10610844 ATAATTATTAATAATATTATTTAAATT
1 ATAATTATTAATAATAATATTTAAATC
* *
10610871 ATAATATATTAATATTAATATTTGAATC
1 ATAAT-TATTAATAATAATATTTAAATC
10610899 ATAAT
1 ATAAT
10610904 GAATTTTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATAATTATTAATAATAATATTTAAATC
Found at i:10619335 original size:29 final size:31
Alignment explanation
Indices: 10619261--10619348 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 31
10619251 ATTAAATCAA
** ** *
10619261 AATTAAAGTTTCAAATATATATTTGAACCAC
1 AATTAAAGTTTCATGTATATAACTGCACCAC
* *
10619292 AATTAGAGTTTCATGTGTATAACTGCACCA-
1 AATTAAAGTTTCATGTATATAACTGCACCAC
*
10619322 AATTAAAG-TTCATGTATATAATTGCAC
1 AATTAAAGTTTCATGTATATAACTGCAC
10619349 ATTAAACCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 17 0.36
30 7 0.15
31 23 0.49
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (31 bp):
AATTAAAGTTTCATGTATATAACTGCACCAC
Found at i:10621214 original size:12 final size:12
Alignment explanation
Indices: 10621197--10621221 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10621187 GAATTGATGA
10621197 GATGCTAACTTT
1 GATGCTAACTTT
10621209 GATGCTAACTTT
1 GATGCTAACTTT
10621221 G
1 G
10621222 GAATATAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (12 bp):
GATGCTAACTTT
Found at i:10624756 original size:151 final size:151
Alignment explanation
Indices: 10624463--10624735 Score: 411
Period size: 151 Copynumber: 1.8 Consensus size: 151
10624453 CTATTCCTTT
* * * * * *
10624463 TCACGGGTCTGCTCACACAAGCTGTCAGTCTTTTGTTACTACTCAGTGCTGGTCACACAAGCTAT
1 TCACGGGCCTACTCACACAAGCTGTAAGTCATTCGTTACTACTCAGTGCTGCTCACACAAGCTAT
* * *
10624528 CAGGTATCCACAACATATGCCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACTCGAGTT
66 CAAGTATCCACAACATATACCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACTCGAGTC
10624593 CACATTAATCACAGTTTTGCA
131 CACATTAATCACAGTTTTGCA
* *
10624614 TCACGGGCCTACTCACACAAGCTGTAAGTCATTCGTTACTACTCAGTGCTGCTCACACAAGTTGT
1 TCACGGGCCTACTCACACAAGCTGTAAGTCATTCGTTACTACTCAGTGCTGCTCACACAAGCTAT
* * * *
10624679 TAAGTATCCGCAACATATATCGGTATACCCAGCCACTGGTAGAACTTATGACCAGCA
66 CAAGTATCCACAACATATACCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCA
10624736 TCCGGATCCA
Statistics
Matches: 108, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
151 108 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (151 bp):
TCACGGGCCTACTCACACAAGCTGTAAGTCATTCGTTACTACTCAGTGCTGCTCACACAAGCTAT
CAAGTATCCACAACATATACCGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCACTCGAGTC
CACATTAATCACAGTTTTGCA
Found at i:10633904 original size:17 final size:17
Alignment explanation
Indices: 10633882--10633914 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10633872 TTCACTTTCT
*
10633882 TTTTTTTCTTGTTTTTA
1 TTTTTTTCTTCTTTTTA
10633899 TTTTTTTCTTCTTTTT
1 TTTTTTTCTTCTTTTT
10633915 CTCTCTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.09, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTTCTTTTTA
Found at i:10635171 original size:41 final size:41
Alignment explanation
Indices: 10635121--10635389 Score: 378
Period size: 41 Copynumber: 6.6 Consensus size: 41
10635111 TTAAATAGAT
* * * *
10635121 TCACTGGCACTTAGCTTGTTAGGCTTAAAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * * *
10635162 TCGCCGGCACTTAGCCTGCTAGGCTTATAGCCTAATCCAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* ** *
10635203 TCATCGGCACTTAGCCTATTAGGCTTATAGCCTAATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* *
10635244 TCACCGGCACTTAGCCTGCTAAGCTTATAGCCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
10635285 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCA-A
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* *
10635325 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTTAGA
1 -TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
10635367 TCACCGGCACTTAGCCTGCTAGG
1 TCACCGGCACTTAGCCTGCTAGG
10635390 TTTTAAAACC
Statistics
Matches: 203, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
40 1 0.00
41 201 0.99
42 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:10636350 original size:2 final size:2
Alignment explanation
Indices: 10636345--10636390 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
10636335 TTATATAAGC
* * * *
10636345 AT AT AT AT AT AT AC AC AC AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10636387 AT AT
1 AT AT
10636391 TGGAACACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:10646627 original size:22 final size:22
Alignment explanation
Indices: 10646599--10646751 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
10646589 TTTATTGTTC
*
10646599 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
10646621 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
10646643 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
10646665 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
10646687 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
10646709 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
10646731 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
10646752 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:10647317 original size:11 final size:11
Alignment explanation
Indices: 10647301--10647327 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
10647291 AGATAAATGT
10647301 TATTTAATTAA
1 TATTTAATTAA
10647312 TATTTAATTAA
1 TATTTAATTAA
10647323 TATTT
1 TATTT
10647328 TTAGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTAATTAA
Found at i:10649380 original size:26 final size:22
Alignment explanation
Indices: 10649328--10649370 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
10649318 TGGTATAATT
10649328 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
10649350 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
10649371 ACTATCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:10651586 original size:96 final size:96
Alignment explanation
Indices: 10651422--10651858 Score: 811
Period size: 96 Copynumber: 4.6 Consensus size: 96
10651412 NNNNNNNNNN
10651422 CATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGA
1 CATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGA
*
10651487 CTCGCCGTTGTATCTTCAATCTGTTCCGCTG
66 CTCGCCGTTGTAGCTTCAATCTGTTCCGCTG
* *
10651518 CATCGCCTGAAAGTAAGATTCGCTGTTGTGGCTTCGATCTTTTAAATTGCAATGGGAAAGTGAGA
1 CATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGA
10651583 CTCGCCGTTGTAGCTTCAATCTGTTCCGCTG
66 CTCGCCGTTGTAGCTTCAATCTGTTCCGCTG
10651614 CATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGA
1 CATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGA
*
10651679 CTCGCCGTTGTAGCTTCAATCTGTCCCGCTG
66 CTCGCCGTTGTAGCTTCAATCTGTTCCGCTG
* *
10651710 CATCGCCTAAAAGTAAGATTCGCCGCTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGA
1 CATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGA
10651775 CTCGCCGTTGTAGCTTCAATCTGTTCCGCTG
66 CTCGCCGTTGTAGCTTCAATCTGTTCCGCTG
*
10651806 CATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTTAATTGCAAT
1 CATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
10651859 CTATGGTTAC
Statistics
Matches: 329, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 329 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (96 bp):
CATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGA
CTCGCCGTTGTAGCTTCAATCTGTTCCGCTG
Found at i:10662737 original size:18 final size:17
Alignment explanation
Indices: 10662695--10662746 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
10662685 AAACAAAACA
*
10662695 CAATAAATCAGTACAAG
1 CAATAAATCAATACAAG
10662712 -AATAAAATCCAATACAAG
1 CAAT-AAAT-CAATACAAG
10662730 CAATAAAT-AATA-AAG
1 CAATAAATCAATACAAG
10662745 CA
1 CA
10662747 CCTATTTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 5 0.16
16 7 0.23
17 4 0.13
18 12 0.39
19 3 0.10
ACGTcount: A:0.60, C:0.15, G:0.08, T:0.17
Consensus pattern (17 bp):
CAATAAATCAATACAAG
Found at i:10664729 original size:3 final size:3
Alignment explanation
Indices: 10664658--10664717 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
10664648 AAATAAAGCC
* * *
10664658 AAT AAT AATT AAT AAT AGT AGT AAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
10664704 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
10664718 CACTATAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10664739 original size:20 final size:20
Alignment explanation
Indices: 10664684--10664729 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
10664674 AGTAGTAATG
*
10664684 ATAATAATAATAATAATA--
1 ATAATAATAATAATAACACT
10664702 ATAATAATAATAATAACACT
1 ATAATAATAATAATAACACT
10664722 ATAATAAT
1 ATAATAAT
10664730 CAATTAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.68
20 8 0.32
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATAATAATAATAACACT
Found at i:10666325 original size:50 final size:49
Alignment explanation
Indices: 10666161--10666327 Score: 131
Period size: 49 Copynumber: 3.4 Consensus size: 49
10666151 AATAAGATTT
* * *
10666161 GCCATTGTGGCCTCAATCTTTT-AATTGCAATGTCAGGGGAGTGAGATTC
1 GCCATTGTAGCCTCAATCTTTTAAATTGCAATGTTA-GGGAGTGAGATCC
* * * *** * * * *
10666210 GCTATTGTAGCTTCAATCTGTTACGCTGCATTGCTT-GGAAGTAAGATCT
1 GCCATTGTAGCCTCAATCTTTTAAATTGCAATG-TTAGGGAGTGAGATCC
* * * *
10666259 GCCGTCGTGGCCTCAATCTTTTAAATTACAATGTTGAGGGAGTGAGATCC
1 GCCATTGTAGCCTCAATCTTTTAAATTGCAATGTT-AGGGAGTGAGATCC
*
10666309 GCCATTGTAGCTTCAATCT
1 GCCATTGTAGCCTCAATCT
10666328 GTTCCTCTAG
Statistics
Matches: 83, Mismatches: 31, Indels: 7
0.69 0.26 0.06
Matches are distributed among these distances:
48 2 0.02
49 49 0.59
50 31 0.37
51 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (49 bp):
GCCATTGTAGCCTCAATCTTTTAAATTGCAATGTTAGGGAGTGAGATCC
Found at i:10666374 original size:49 final size:49
Alignment explanation
Indices: 10666241--10666390 Score: 126
Period size: 49 Copynumber: 3.0 Consensus size: 49
10666231 TACGCTGCAT
* *
10666241 TGCTTGGAAGTAAGATCTGCCGTCGTGGCCTCAATCTTTTAAATTACAA
1 TGCTTGGAAGTAAGATCCGCCGTCGTGGCCTCAATCTGTTAAATTACAA
* * * * * * ** *
10666290 TG-TTGAGGGAGTGAGATCCGCCATTGTAGCTTCAATCTGTT-CCTCTA-GA
1 TGCTT--GGAAGTAAGATCCGCCGTCGTGGCCTCAATCTGTTAAAT-TACAA
* *
10666339 TCGCTTGGAAGTAAGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAA
1 T-GCTTGGAAGTAAGATCCGCCGTCGTGGCCTCAATCTGTTAAATTACAA
10666389 TG
1 TG
10666391 GGGAAGTGAG
Statistics
Matches: 72, Mismatches: 22, Indels: 14
0.67 0.20 0.13
Matches are distributed among these distances:
48 2 0.03
49 35 0.49
50 33 0.46
51 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (49 bp):
TGCTTGGAAGTAAGATCCGCCGTCGTGGCCTCAATCTGTTAAATTACAA
Found at i:10666611 original size:96 final size:96
Alignment explanation
Indices: 10666097--10666863 Score: 998
Period size: 96 Copynumber: 8.0 Consensus size: 96
10666087 TAAAATGTCA
* * * * * * * * * *
10666097 GGGAAGCGAGATTCGCCATTGTAGCTTCAATTTGTTCCACTGTACCTGCTTAGGAA-TAAGATTT
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATC-GCCT-GAAAGTAAGATTC
* * *
10666161 GCCATTGTGGCCTCAATCTTTT-AATTGCAATG
64 GCCGTTGTGGCTTCGATCTTTTAAATTGCAATG
* * ** * * * *
10666193 TCAGGGGAGTGAGATTCGCTATTGTAGCTTCAATCTGTTACGCTGCATTGCTTGGAAGTAAGA-T
1 ---GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATT
* * * *
10666257 CTGCCGTCGTGGCCTCAATCTTTTAAATTACAATG
63 C-GCCGTTGTGGCTTCGATCTTTTAAATTGCAATG
* * * * *
10666292 TTGAGGGAGTGAGA-TCCGCCATTGTAGCTTCAATCTGTTCCTCTAG-ATCGCTTGGAAGTAAGA
1 --G-GGAAGTGAGACT-CGCCGTTGTAGCTTCAATCTGTTCCGCT-GCATCGCCTGAAAGTAAGA
* * * *
10666355 TCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAATG
61 TTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATG
*
10666391 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCAC
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
10666456 C---GT---TTCGATCTTTTAAATTGCAATG
66 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
* * *
10666481 GGGAAGTGAGCCTCACCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTGC
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
10666546 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
66 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
10666577 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
10666642 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
66 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
*
10666673 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTAAAAGTAAGATTCGC
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
10666738 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
66 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
10666769 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
*
10666834 CGTTGTGGCTTCGATCTTTTTAATTGCAAT
66 CGTTGTGGCTTCGATCTTTTAAATTGCAAT
10666864 CTATGGTTAC
Statistics
Matches: 613, Mismatches: 40, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
90 82 0.13
93 4 0.01
95 1 0.00
96 357 0.58
97 7 0.01
98 31 0.05
99 129 0.21
100 2 0.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.32
Consensus pattern (96 bp):
GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
CGTTGTGGCTTCGATCTTTTAAATTGCAATG
Found at i:10677626 original size:16 final size:17
Alignment explanation
Indices: 10677605--10677637 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
10677595 AAAAGGGTCC
10677605 TTAAAAAT-AAAAAAAA
1 TTAAAAATCAAAAAAAA
10677621 TTAAAAATCAAAAAAAA
1 TTAAAAATCAAAAAAAA
10677638 GAAAGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
TTAAAAATCAAAAAAAA
Found at i:10679255 original size:50 final size:49
Alignment explanation
Indices: 10679091--10679257 Score: 131
Period size: 49 Copynumber: 3.4 Consensus size: 49
10679081 AATAAGATTT
* * *
10679091 GCCATTGTGGCCTCAATCTTTT-AATTGCAATGTCAGGGGAGTGAGATTC
1 GCCATTGTAGCCTCAATCTTTTAAATTGCAATGTTA-GGGAGTGAGATCC
* * * *** * * * *
10679140 GCTATTGTAGCTTCAATCTGTTACGCTGCATTGCTT-GGAAGTAAGATCT
1 GCCATTGTAGCCTCAATCTTTTAAATTGCAATG-TTAGGGAGTGAGATCC
* * * *
10679189 GCCGTCGTGGCCTCAATCTTTTAAATTACAATGTTGAGGGAGTGAGATCC
1 GCCATTGTAGCCTCAATCTTTTAAATTGCAATGTT-AGGGAGTGAGATCC
*
10679239 GCCATTGTAGCTTCAATCT
1 GCCATTGTAGCCTCAATCT
10679258 GTTCCTCTAG
Statistics
Matches: 83, Mismatches: 31, Indels: 7
0.69 0.26 0.06
Matches are distributed among these distances:
48 2 0.02
49 49 0.59
50 31 0.37
51 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (49 bp):
GCCATTGTAGCCTCAATCTTTTAAATTGCAATGTTAGGGAGTGAGATCC
Found at i:10679304 original size:49 final size:49
Alignment explanation
Indices: 10679171--10679320 Score: 126
Period size: 49 Copynumber: 3.0 Consensus size: 49
10679161 TACGCTGCAT
* *
10679171 TGCTTGGAAGTAAGATCTGCCGTCGTGGCCTCAATCTTTTAAATTACAA
1 TGCTTGGAAGTAAGATCCGCCGTCGTGGCCTCAATCTGTTAAATTACAA
* * * * * * ** *
10679220 TG-TTGAGGGAGTGAGATCCGCCATTGTAGCTTCAATCTGTT-CCTCTA-GA
1 TGCTT--GGAAGTAAGATCCGCCGTCGTGGCCTCAATCTGTTAAAT-TACAA
* *
10679269 TCGCTTGGAAGTAAGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAA
1 T-GCTTGGAAGTAAGATCCGCCGTCGTGGCCTCAATCTGTTAAATTACAA
10679319 TG
1 TG
10679321 GGGAAGTGAG
Statistics
Matches: 72, Mismatches: 22, Indels: 14
0.67 0.20 0.13
Matches are distributed among these distances:
48 2 0.03
49 35 0.49
50 33 0.46
51 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (49 bp):
TGCTTGGAAGTAAGATCCGCCGTCGTGGCCTCAATCTGTTAAATTACAA
Found at i:10679387 original size:96 final size:96
Alignment explanation
Indices: 10679027--10679889 Score: 1174
Period size: 96 Copynumber: 9.0 Consensus size: 96
10679017 TAAAATGTCA
* * * * * * * * * *
10679027 GGGAAGCGAGATTCGCCATTGTAGCTTCAATTTGTTCCACTGTACCTGCTTAGGAA-TAAGATTT
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATC-GCCT-GAAAGTAAGATTC
* * *
10679091 GCCATTGTGGCCTCAATCTTTT-AATTGCAATG
64 GCCGTTGTGGCTTCGATCTTTTAAATTGCAATG
* * ** * * * *
10679123 TCAGGGGAGTGAGATTCGCTATTGTAGCTTCAATCTGTTACGCTGCATTGCTTGGAAGTAAGA-T
1 ---GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATT
* * * *
10679187 CTGCCGTCGTGGCCTCAATCTTTTAAATTACAATG
63 C-GCCGTTGTGGCTTCGATCTTTTAAATTGCAATG
* * * * *
10679222 TTGAGGGAGTGAGA-TCCGCCATTGTAGCTTCAATCTGTTCCTCTAG-ATCGCTTGGAAGTAAGA
1 --G-GGAAGTGAGACT-CGCCGTTGTAGCTTCAATCTGTTCCGCT-GCATCGCCTGAAAGTAAGA
* * * *
10679285 TCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAATG
61 TTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATG
10679321 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
10679386 CGTTGTGGCTTCGATC-TTTAAATTGCAATG
66 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
*
10679416 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAAGTAAGATTCA
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTG-AAAGTAAGATTCG
10679481 CC---GT---TTCGATCTTTTAAATTGCAATG
65 CCGTTGTGGCTTCGATCTTTTAAATTGCAATG
* * *
10679507 GGGAAGTGAGCCTCACCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTGC
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
10679572 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
66 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
10679603 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
10679668 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
66 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
*
10679699 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTAAAAGTAAGATTCGC
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
10679764 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
66 CGTTGTGGCTTCGATCTTTTAAATTGCAATG
10679795 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
1 GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
*
10679860 CGTTGTGGCTTCGATCTTTTTAATTGCAAT
66 CGTTGTGGCTTCGATCTTTTAAATTGCAAT
10679890 CTATGGTTAC
Statistics
Matches: 706, Mismatches: 41, Indels: 37
0.90 0.05 0.05
Matches are distributed among these distances:
90 20 0.03
91 63 0.09
93 4 0.01
95 66 0.09
96 384 0.54
97 7 0.01
98 31 0.04
99 129 0.18
100 2 0.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (96 bp):
GGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGC
CGTTGTGGCTTCGATCTTTTAAATTGCAATG
Found at i:10679388 original size:49 final size:49
Alignment explanation
Indices: 10679324--10679876 Score: 340
Period size: 49 Copynumber: 11.6 Consensus size: 49
10679314 TGCAATGGGG
*
10679324 AAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGA
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGA
* * * **** * *
10679373 AAGTAAGATTCGCCGTTGTGGCTTCGATCT-TTAAATTGCAAT-G--GGG
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTGA
*
10679419 AAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAA
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTG-A
* * * * **** * *
10679469 AAGTAAGATTCACC---GT---TTCGATCTTTTAAATTGCAAT-G--GGG
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTGA
* * *
10679510 AAGTGAGCCTCACCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGA
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGA
* * * * * **** * *
10679559 AAGTAAGATTTGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGG
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTGA
*
10679606 AAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGA
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGA
* * * * **** * *
10679655 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGG
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTGA
* *
10679702 AAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTAA
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGA
* * * * **** * *
10679751 AAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G--GGG
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTGA
*
10679798 AAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGA
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGA
* * *
10679847 AAGTAAGATTCGCCGTTGTGGCTTCGATCT
1 AAGTAAGACTCGCCGTTGTAGCTTCAATCT
10679877 TTTTAATTGC
Statistics
Matches: 358, Mismatches: 118, Indels: 56
0.67 0.22 0.11
Matches are distributed among these distances:
41 11 0.03
42 1 0.00
44 15 0.04
45 2 0.01
46 37 0.10
47 118 0.33
48 6 0.02
49 151 0.42
50 17 0.05
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.31
Consensus pattern (49 bp):
AAGTAAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGA
Found at i:10679852 original size:378 final size:380
Alignment explanation
Indices: 10679144--10679863 Score: 1189
Period size: 378 Copynumber: 1.9 Consensus size: 380
10679134 AGATTCGCTA
* * *
10679144 TTGTAGCTTCAATCTGTTACGCTGCATTGCTTGGAAGTAAGATCTGCCGTCGTGGCCTCAATCTT
1 TTGTAGCTTCAATCTGTTACGCTGCATCGCCTGAAAGTAAGATCTGCCGTCGTGGCCTCAATCTT
* * *
10679209 TTAAATTACAATGTTGAGGGAGTGAGATCCGCCATTGTAGCTTCAATCTGTTCCTCTAGATCGCT
66 TTAAATTACAATG-TGAGGAAGTGAGATCCGCCATTGTAGCTTCAATCTGTTCCGCTAGATCGCC
*
10679274 TGGAAGTAAGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCG
130 TGAAAGTAAGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCG
*
10679339 TTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTT
195 TTGTAGCTTCAATCTGTTCCGCTGCATCGCCTAAAAGTAAGATTCGCCGTTGTGGCTTCGATCTT
10679404 TAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAA
260 TAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAA
10679469 AAGTAAGATTCACCGTTTCGATCTTTTAAATTGCAATGGGGAAGTGAGCCTCACCG
325 AAGTAAGATTCACCGTTTCGATCTTTTAAATTGCAATGGGGAAGTGAGCCTCACCG
* * * * *
10679525 TTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAAGTAAGATTTGCCGTTGTGGCTTCGATCTT
1 TTGTAGCTTCAATCTGTTACGCTGCATCGCCTGAAAGTAAGATCTGCCGTCGTGGCCTCAATCTT
* *
10679590 TTAAATTGCAATG-G-GGAAGTGAGA-CTCGCCGTTGTAGCTTCAATCTGTTCCGCT-GCATCGC
66 TTAAATTACAATGTGAGGAAGTGAGATC-CGCCATTGTAGCTTCAATCTGTTCCGCTAG-ATCGC
* * * *
10679651 CTGAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCC
129 CTGAAAGTAAGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCC
10679716 GTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTAAAAGTAAGATTCGCCGTTGTGGCTTCGATCT
194 GTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTAAAAGTAAGATTCGCCGTTGTGGCTTCGATC-
10679781 TTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTG
258 TTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTG
*
10679846 -AAAGTAAGATTCGCCGTT
323 AAAAGTAAGATTCACCGTT
10679864 GTGGCTTCGA
Statistics
Matches: 316, Mismatches: 20, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
377 2 0.01
378 179 0.57
379 66 0.21
381 69 0.22
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (380 bp):
TTGTAGCTTCAATCTGTTACGCTGCATCGCCTGAAAGTAAGATCTGCCGTCGTGGCCTCAATCTT
TTAAATTACAATGTGAGGAAGTGAGATCCGCCATTGTAGCTTCAATCTGTTCCGCTAGATCGCCT
GAAAGTAAGATCCGCCGTCGTGGCCTCAATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGT
TGTAGCTTCAATCTGTTCCGCTGCATCGCCTAAAAGTAAGATTCGCCGTTGTGGCTTCGATCTTT
AAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGAAA
AGTAAGATTCACCGTTTCGATCTTTTAAATTGCAATGGGGAAGTGAGCCTCACCG
Found at i:10684696 original size:21 final size:21
Alignment explanation
Indices: 10684662--10684701 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
10684652 TCTTAACAAT
*
10684662 AATTCTAAAAAAATTTAAAAA
1 AATTCTAAAAAAATATAAAAA
10684683 AATTC-AAAATAAATATAAA
1 AATTCTAAAA-AAATATAAA
10684702 TTATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
AATTCTAAAAAAATATAAAAA
Found at i:10685480 original size:19 final size:19
Alignment explanation
Indices: 10685456--10685495 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
10685446 ATTTTTTATT
10685456 TAATA-TTTATTTAAAATAA
1 TAATATTTTA-TTAAAATAA
*
10685475 TAATATTTTATTAAAGTAA
1 TAATATTTTATTAAAATAA
10685494 TA
1 TA
10685496 TAATAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TAATATTTTATTAAAATAA
Found at i:10686577 original size:38 final size:38
Alignment explanation
Indices: 10686534--10686628 Score: 124
Period size: 38 Copynumber: 2.5 Consensus size: 38
10686524 ATACTATAAT
*
10686534 AGTCATCATTGTTGGGCAACTTGGGGTGAC-ATACTTTA
1 AGTCATCATTGTTGGGCAACTT-AGGTGACAATACTTTA
10686572 AGTCATCATTTGTT-GG-AACTTAGGTGACATATACTTTA
1 AGTCATCA-TTGTTGGGCAACTTAGGTGACA-ATACTTTA
*
10686610 AGTCATCATTTTTGGGCAA
1 AGTCATCATTGTTGGGCAA
10686629 TCCAAGGTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
36 6 0.12
37 9 0.18
38 28 0.56
39 7 0.14
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (38 bp):
AGTCATCATTGTTGGGCAACTTAGGTGACAATACTTTA
Found at i:10688125 original size:2 final size:2
Alignment explanation
Indices: 10688118--10688142 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10688108 CTTACAAACG
10688118 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
10688143 TCTATAATTT
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:10691572 original size:76 final size:72
Alignment explanation
Indices: 10691439--10691582 Score: 234
Period size: 76 Copynumber: 1.9 Consensus size: 72
10691429 AACATTATTA
*
10691439 ATTCGACCTGCTACAAAATTAAAAGCCAAGTCTATCTTCTCCGTCAATCCCCATTCCACAAGTTG
1 ATTCGACCTGCTACAAAATTAAAAGCCAAGTCTAACTTCTCCGTCAATCCCCATTCCACAAGTTG
10691504 GGGATTC
66 GGGATTC
*
10691511 ATTCGACTTGCTACAAAATTAAAAGCCAAGTAAGTCTAACTTCTCCGTCAATCCCCATTCCACAA
1 ATTCGACCTGCTACAAAATTAAAAGCC----AAGTCTAACTTCTCCGTCAATCCCCATTCCACAA
10691576 GTTGGGG
62 GTTGGGG
10691583 TCATCCACGT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
72 26 0.39
76 40 0.61
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (72 bp):
ATTCGACCTGCTACAAAATTAAAAGCCAAGTCTAACTTCTCCGTCAATCCCCATTCCACAAGTTG
GGGATTC
Found at i:10692004 original size:25 final size:25
Alignment explanation
Indices: 10691970--10692017 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
10691960 GTTGTCCATT
* *
10691970 GCTTGGGCCTTGAATAAAATTTTAA
1 GCTTGAGCCTGGAATAAAATTTTAA
*
10691995 GCTTGAGCCTGGCATAAAATTTT
1 GCTTGAGCCTGGAATAAAATTTT
10692018 GTCCAAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (25 bp):
GCTTGAGCCTGGAATAAAATTTTAA
Found at i:10692287 original size:22 final size:22
Alignment explanation
Indices: 10692250--10692306 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
10692240 ATAAAATAAT
* *
10692250 AACAACAAAATAGTAGCAATAC
1 AACAACAAAATGGTAGCAAAAC
* * *
10692272 AATAACGAAATGGTAGTAAAAC
1 AACAACAAAATGGTAGCAAAAC
10692294 AACAACAAAATGG
1 AACAACAAAATGG
10692307 CGGCAAACTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (22 bp):
AACAACAAAATGGTAGCAAAAC
Found at i:10693266 original size:21 final size:20
Alignment explanation
Indices: 10693218--10693266 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 20
10693208 TTAAATAAAT
10693218 AAATTTTAAAATTTTCACTA
1 AAATTTTAAAATTTTCACTA
10693238 AAATTTTAAAATTTT-ACATA
1 AAATTTTAAAATTTTCAC-TA
10693258 AATATTTTA
1 AA-ATTTTA
10693267 TGTAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.07
20 19 0.70
21 6 0.22
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTTTAAAATTTTCACTA
Found at i:10693320 original size:26 final size:26
Alignment explanation
Indices: 10693291--10693341 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
10693281 ATATATAAAA
10693291 TTATCATAAATG-TAAATATTATTTAG
1 TTATCATAAA-GATAAATATTATTTAG
* *
10693317 TTATCATTAAGATAAGTATTATTTA
1 TTATCATAAAGATAAATATTATTTA
10693342 TTGTAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (26 bp):
TTATCATAAAGATAAATATTATTTAG
Found at i:10696966 original size:41 final size:41
Alignment explanation
Indices: 10696909--10696993 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
10696899 CCCAAAGTCC
* *
10696909 TTTCCCAATTCATAAATAGGAGGATAGTGCATTTTAACGCA
1 TTTCCCAATCCATAAATAGGAGGATAGTACATTTTAACGCA
10696950 TTTCCCAATCCATAAATAGGAGGATAGTACATTTTAACGCA
1 TTTCCCAATCCATAAATAGGAGGATAGTACATTTTAACGCA
10696991 TTT
1 TTT
10696994 GAACTTACGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (41 bp):
TTTCCCAATCCATAAATAGGAGGATAGTACATTTTAACGCA
Found at i:10697723 original size:18 final size:19
Alignment explanation
Indices: 10697702--10697749 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 19
10697692 TATTTTTCTT
10697702 TTATAATTATTTT-TTAAC
1 TTATAATTATTTTATTAAC
10697720 TTATTAA--ATTTTATTAAC
1 TTA-TAATTATTTTATTAAC
10697738 TT-TAATT-TTTTA
1 TTATAATTATTTTA
10697750 AAATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.12
17 10 0.38
18 10 0.38
19 3 0.12
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATAATTATTTTATTAAC
Found at i:10702190 original size:28 final size:28
Alignment explanation
Indices: 10702158--10702229 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
10702148 TTTAATAAGT
* *
10702158 TCGCACACATAGTGCTTAATAATCAAAA
1 TCGCACACTTAGTGCTTAACAATCAAAA
* * * *
10702186 TCGCACACTTAGTCCTTCACAATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAA
10702214 TCGCACACTTAGTGCT
1 TCGCACACTTAGTGCT
10702230 AATCTCTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAA
Found at i:10707518 original size:4 final size:4
Alignment explanation
Indices: 10707501--10707572 Score: 58
Period size: 4 Copynumber: 16.8 Consensus size: 4
10707491 CAACCCAATT
*
10707501 TTTA TTTT TTTA TTTA TTGT- TTTA TTTTA TTTTA TTTA CTTTA TTTA
1 TTTA TTTA TTTA TTTA TT-TA TTTA -TTTA -TTTA TTTA -TTTA TTTA
10707548 CTTTA TTTA -TTA CTTTA TTTTA TTT
1 -TTTA TTTA TTTA -TTTA -TTTA TTT
10707573 TATTATTTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
3 4 0.07
4 29 0.50
5 25 0.43
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:10707529 original size:13 final size:12
Alignment explanation
Indices: 10707500--10707582 Score: 62
Period size: 13 Copynumber: 6.4 Consensus size: 12
10707490 GCAACCCAAT
10707500 TTTTATTTTTT-
1 TTTTATTTTTTA
10707511 TATTTATTGTTTTA
1 T-TTTATT-TTTTA
10707525 TTTTATTTTATTTA
1 TTTTA-TTT-TTTA
*
10707539 CTTTATTTACTTTA
1 TTTTATTT--TTTA
*
10707553 -TTTATTACTTTA
1 TTTTATT-TTTTA
10707565 TTTTATTTTATTA
1 TTTTATTTT-TTA
10707578 TTTTA
1 TTTTA
10707583 ATAATTATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
11 1 0.02
12 11 0.19
13 32 0.54
14 15 0.25
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:10707530 original size:5 final size:5
Alignment explanation
Indices: 10707520--10707576 Score: 55
Period size: 5 Copynumber: 11.4 Consensus size: 5
10707510 TTATTTATTG
* * *
10707520 TTTTA TTTTA TTTTA -TTTA CTTTA -TTTA CTTTA TTTATTA CTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA TTTTA TTTTA
10707570 TTTTA TT
1 TTTTA TT
10707577 ATTTTAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
4 8 0.18
5 32 0.71
6 2 0.04
7 3 0.07
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:10707543 original size:9 final size:9
Alignment explanation
Indices: 10707521--10707556 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
10707511 TATTTATTGT
*
10707521 TTTATTTTAT
1 TTTA-TTTAC
10707531 TTTATTTAC
1 TTTATTTAC
10707540 TTTATTTAC
1 TTTATTTAC
10707549 TTTATTTA
1 TTTATTTA
10707557 TTACTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 21 0.84
10 4 0.16
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTATTTAC
Found at i:10707555 original size:40 final size:39
Alignment explanation
Indices: 10707501--10707576 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 39
10707491 CAACCCAATT
* **
10707501 TTTATTTTTTTATTTATTGTTTTATTTTATTTTATTTAC
1 TTTATTTCTTTATTTATTACTTTATTTTATTTTATTTAC
10707540 TTTATTTACTTTATTTATTACTTTATTTTATTTTATT
1 TTTATTT-CTTTATTTATTACTTTATTTTATTTTATT
10707577 ATTTTAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 7 0.21
40 26 0.79
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (39 bp):
TTTATTTCTTTATTTATTACTTTATTTTATTTTATTTAC
Found at i:10708968 original size:16 final size:18
Alignment explanation
Indices: 10708951--10708992 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
10708941 CCTAAAGCAT
10708951 AAAAAATATAAAT-AATAA
1 AAAAAATA-AAATAAATAA
10708969 ATAAAAATCAAAATAAATAA
1 A-AAAAAT-AAAATAAATAA
10708989 AAAA
1 AAAA
10708993 GAAAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.05
19 13 0.62
20 7 0.33
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAAAATAAAATAAATAA
Found at i:10708997 original size:16 final size:16
Alignment explanation
Indices: 10708964--10708997 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10708954 AAATATAAAT
*
10708964 AATAAATAAAAATCAA
1 AATAAATAAAAAACAA
*
10708980 AATAAATAAAAAAGAA
1 AATAAATAAAAAACAA
10708996 AA
1 AA
10708998 AAGAAAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (16 bp):
AATAAATAAAAAACAA
Found at i:10709004 original size:23 final size:23
Alignment explanation
Indices: 10708958--10709004 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
10708948 CATAAAAAAT
* * *
10708958 ATAAATAATAAATAAAAATCAAA
1 ATAAATAAAAAAGAAAAAACAAA
*
10708981 ATAAATAAAAAAGAAAAAAGAAA
1 ATAAATAAAAAAGAAAAAACAAA
10709004 A
1 A
10709005 AGAAAAAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (23 bp):
ATAAATAAAAAAGAAAAAACAAA
Found at i:10709594 original size:15 final size:15
Alignment explanation
Indices: 10709569--10709603 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
10709559 GACTCTATTT
*
10709569 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
10709583 TAATTAATATTAAGA
1 TAATTAATATTAAGA
10709598 TAATTA
1 TAATTA
10709604 TTAACGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:10713379 original size:21 final size:20
Alignment explanation
Indices: 10713325--10713380 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
10713315 TAATAAAATA
10713325 AAAAAATAGAAAAAATGAAAG
1 AAAAAATA-AAAAAATGAAAG
* **
10713346 AACAACACCAAAAAATGAAGAG
1 AA-AAAATAAAAAAATGAA-AG
10713368 AAAAAATAAAAAA
1 AAAAAATAAAAAA
10713381 GAACCACCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.75, C:0.07, G:0.11, T:0.07
Consensus pattern (20 bp):
AAAAAATAAAAAAATGAAAG
Found at i:10716247 original size:33 final size:33
Alignment explanation
Indices: 10716205--10716271 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
10716195 AACATGTGTG
10716205 TCAATTGTACTAAATTGTAACAAATGAATAATT
1 TCAATTGTACTAAATTGTAACAAATGAATAATT
* *
10716238 TCAATTGTACTAAATTGTAATAAATTAATAATT
1 TCAATTGTACTAAATTGTAACAAATGAATAATT
10716271 T
1 T
10716272 TACTACCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (33 bp):
TCAATTGTACTAAATTGTAACAAATGAATAATT
Found at i:10718780 original size:30 final size:30
Alignment explanation
Indices: 10718734--10718822 Score: 125
Period size: 25 Copynumber: 3.1 Consensus size: 30
10718724 ATTTCTTATG
*
10718734 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
10718765 CCAATATTTGATACCCATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
10718794 ----TATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
10718820 CCA
1 CCA
10718823 TAAATATGGA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
25 23 0.43
26 2 0.04
29 2 0.04
30 19 0.36
31 7 0.13
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.42
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:10718789 original size:15 final size:15
Alignment explanation
Indices: 10718744--10718790 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
10718734 CCAATATCTC
10718744 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
10718759 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
10718774 GATACCCATATCTTT
1 GATACCCATATCTTT
10718789 GA
1 GA
10718791 CTTTATTTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:10719869 original size:22 final size:22
Alignment explanation
Indices: 10719841--10719919 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
10719831 TCATCTGAAA
10719841 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
10719863 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * * **
10719885 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAGC
10719907 CATGAGAGCTTAG
1 CATGAGAGCTTAG
10719920 CAAGTATACG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:10723436 original size:30 final size:30
Alignment explanation
Indices: 10723390--10723478 Score: 116
Period size: 25 Copynumber: 3.1 Consensus size: 30
10723380 ATTTCTTATG
*
10723390 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
*
10723421 CCAATATTTGATACCCATATCTTTGGC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
10723450 ----TATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
10723476 CCA
1 CCA
10723479 TAAATATAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
25 22 0.43
26 2 0.04
29 2 0.04
30 18 0.35
31 7 0.14
ACGTcount: A:0.25, C:0.26, G:0.08, T:0.42
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:10724358 original size:7 final size:7
Alignment explanation
Indices: 10724340--10724374 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
10724330 ATGTAAACAG
10724340 TTTATT-
1 TTTATTA
10724346 TTTATTA
1 TTTATTA
10724353 TTTATTA
1 TTTATTA
10724360 TTTATTA
1 TTTATTA
10724367 TTTATTA
1 TTTATTA
10724374 T
1 T
10724375 GAATTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTA
Found at i:10731556 original size:20 final size:19
Alignment explanation
Indices: 10731523--10731578 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
10731513 TCCAGCTTCA
*
10731523 TTTAGTTTTTAAAAAT-AT
1 TTTAATTTTTAAAAATAAT
*
10731541 TTTCTATTTTTAAAAAATAAT
1 TTT-AATTTTT-AAAAATAAT
10731562 TTTAATTTTTTAAAAAT
1 TTTAA-TTTTTAAAAAT
10731579 TAAAAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 3 0.10
19 5 0.16
20 13 0.42
21 10 0.32
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTAATTTTTAAAAATAAT
Found at i:10742363 original size:21 final size:21
Alignment explanation
Indices: 10742319--10742356 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10742309 TAACTTGTAA
10742319 TAAATTATTAATAATATTATT
1 TAAATTATTAATAATATTATT
10742340 TAAATTA-TAAT-ATATTA
1 TAAATTATTAATAATATTA
10742357 ATATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTATTAATAATATTATT
Found at i:10742378 original size:28 final size:28
Alignment explanation
Indices: 10742324--10742378 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
10742314 TGTAATAAAT
* *
10742324 TATTAATAATATTATTTAAATTATAATA
1 TATTAATAATAATATTTAAATCATAATA
* *
10742352 TATTAATATTAATATTTGAATCATAAT
1 TATTAATAATAATATTTAAATCATAAT
10742379 GAATTTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TATTAATAATAATATTTAAATCATAATA
Found at i:10743912 original size:1 final size:1
Alignment explanation
Indices: 10743902--10743953 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
10743892 AACCTATTAG
* * * * * *
10743902 TTTTTGTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10743954 GTGAATAAGT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (1 bp):
T
Found at i:10743918 original size:7 final size:7
Alignment explanation
Indices: 10743908--10743953 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
10743898 TTAGTTTTTG
10743908 TTTTTCT
1 TTTTTCT
10743915 TTTTTCT
1 TTTTTCT
10743922 TTTTTCT
1 TTTTTCT
10743929 TTTTTCT
1 TTTTTCT
10743936 TTTTTCT
1 TTTTTCT
10743943 TTTTT-T
1 TTTTTCT
10743949 TTTTT
1 TTTTT
10743954 GTGAATAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
6 6 0.15
7 33 0.85
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTCT
Found at i:10743926 original size:21 final size:20
Alignment explanation
Indices: 10743902--10743953 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 20
10743892 AACCTATTAG
*
10743902 TTTTTGTTTTTCTTTTTTCT
1 TTTTTTTTTTTCTTTTTTCT
10743922 TTTTTCTTTTTTCTTTTTTCT
1 TTTTT-TTTTTTCTTTTTTCT
10743943 TTTTTTTTTTT
1 TTTTTTTTTTT
10743954 GTGAATAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (20 bp):
TTTTTTTTTTTCTTTTTTCT
Found at i:10744400 original size:19 final size:19
Alignment explanation
Indices: 10744376--10744413 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
10744366 GATTGTACTA
10744376 GTCAAAATGCATCAGACAT
1 GTCAAAATGCATCAGACAT
*
10744395 GTCAAAATGTATCAGACAT
1 GTCAAAATGCATCAGACAT
10744414 AAGTGGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (19 bp):
GTCAAAATGCATCAGACAT
Found at i:10746529 original size:13 final size:13
Alignment explanation
Indices: 10746513--10746578 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
10746503 TTTAAACCAA
10746513 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
10746526 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
*
10746539 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
*
10746552 ACCTTTCAAAAGC
1 ACTTTTCAAAAGC
10746565 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
10746578 A
1 A
10746579 TTACCAAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 4 0.09
13 35 0.81
14 4 0.09
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.29
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:10747045 original size:47 final size:47
Alignment explanation
Indices: 10746993--10747091 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
10746983 AATTTCAACT
10746993 AAATGAATGTTTTCCATTTTAAGGAAATTTTAAGGAAATGAAAATGA
1 AAATGAATGTTTTCCATTTTAAGGAAATTTTAAGGAAATGAAAATGA
10747040 AAATGAATGTTTTCCATTTTAAGGAAATTTTAAGGAAATGAAAATGA
1 AAATGAATGTTTTCCATTTTAAGGAAATTTTAAGGAAATGAAAATGA
10747087 AAATG
1 AAATG
10747092 GCCTCTATCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.33
Consensus pattern (47 bp):
AAATGAATGTTTTCCATTTTAAGGAAATTTTAAGGAAATGAAAATGA
Found at i:10747315 original size:17 final size:18
Alignment explanation
Indices: 10747289--10747322 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10747279 AAATTAGAGA
10747289 ATAAAAAAATAA-AAATC
1 ATAAAAAAATAAGAAATC
*
10747306 ATAAATAAATAAGAAAT
1 ATAAAAAAATAAGAAAT
10747323 AAAAAGTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAAAAAATAAGAAATC
Found at i:10747760 original size:19 final size:20
Alignment explanation
Indices: 10747725--10747763 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10747715 TAAATAACTT
10747725 AAAATACGTAATAAATATAA
1 AAAATACGTAATAAATATAA
*
10747745 AAAATTCGTAAT-AATATAA
1 AAAATACGTAATAAATATAA
10747764 TAATAAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAATACGTAATAAATATAA
Found at i:10749336 original size:13 final size:13
Alignment explanation
Indices: 10749318--10749342 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10749308 CAATAACTCC
10749318 AAAAATATTTAAT
1 AAAAATATTTAAT
10749331 AAAAATATTTAA
1 AAAAATATTTAA
10749343 AGGTTCGGTT
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):
AAAAATATTTAAT
Found at i:10752541 original size:29 final size:30
Alignment explanation
Indices: 10752454--10752542 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 30
10752444 GATTAAATCA
** * *
10752454 AAATTAAAGTTTCAAATATACATTTGAACC
1 AAATTAAAGTTTCATGTATACAATTGCACC
* * * *
10752484 ACAATTAGAGTTTCATGTGTATAACTGCACC
1 A-AATTAAAGTTTCATGTATACAATTGCACC
10752515 AAATTAAAG-TTCATGTATACAATTGCAC
1 AAATTAAAGTTTCATGTATACAATTGCAC
10752543 ATTAAACCAA
Statistics
Matches: 46, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
29 16 0.35
30 8 0.17
31 22 0.48
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATACAATTGCACC
Found at i:10755877 original size:29 final size:28
Alignment explanation
Indices: 10755819--10755884 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
10755809 GATTTCGCTG
* *
10755819 AAAATGGCTCATTCCGGTAAATAATCAA
1 AAAATGGCCCATTCCGGTAAATAATAAA
* **
10755847 AAAATCGGCCCATTTCGGTAAATTTTAAAA
1 AAAAT-GGCCCATTCCGGTAAATAAT-AAA
10755877 AAAATGGC
1 AAAATGGC
10755885 TTTTTTTGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 5 0.16
29 19 0.61
30 7 0.23
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (28 bp):
AAAATGGCCCATTCCGGTAAATAATAAA
Found at i:10756331 original size:34 final size:34
Alignment explanation
Indices: 10756293--10756409 Score: 112
Period size: 35 Copynumber: 3.4 Consensus size: 34
10756283 AATTAAATTA
10756293 AAATTTTAAGTCTTGATTTTGTTTTTATTAATGG
1 AAATTTTAAGTCTTGATTTTGTTTTTATTAATGG
* ** *
10756327 AAATTTTAACTAATGATTTT-TCGTTTTATTCATGG
1 AAATTTTAAGTCTTGATTTTGT--TTTTATTAATGG
* * *
10756362 AATTTTTAGGTCACTT-ATTTTGGTTTTATTAATGG
1 AAATTTTAAGT--CTTGATTTTGTTTTTATTAATGG
*
10756397 AAAATTTAAGTCT
1 AAATTTTAAGTCT
10756410 CCTTTGTGTT
Statistics
Matches: 64, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
33 3 0.05
34 17 0.27
35 38 0.59
36 5 0.08
37 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (34 bp):
AAATTTTAAGTCTTGATTTTGTTTTTATTAATGG
Found at i:10766532 original size:12 final size:12
Alignment explanation
Indices: 10766517--10766542 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10766507 ATATGTAAAT
10766517 ATATATATATAC
1 ATATATATATAC
10766529 ATATATATATAC
1 ATATATATATAC
10766541 AT
1 AT
10766543 TTACGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATATATAC
Found at i:10766752 original size:3 final size:3
Alignment explanation
Indices: 10766744--10766771 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10766734 AAAATAAAAT
10766744 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
10766772 GATGATGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:10774396 original size:14 final size:14
Alignment explanation
Indices: 10774377--10774408 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
10774367 AAGTAGCAGG
10774377 AGAGAGCATCGAGC
1 AGAGAGCATCGAGC
*
10774391 AGAGAGCATCGGGC
1 AGAGAGCATCGAGC
10774405 AGAG
1 AGAG
10774409 GTGCTAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.41, T:0.06
Consensus pattern (14 bp):
AGAGAGCATCGAGC
Found at i:10778887 original size:15 final size:15
Alignment explanation
Indices: 10778867--10778895 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10778857 GAGGTCGGTA
10778867 TGTGTTTATATAAGT
1 TGTGTTTATATAAGT
10778882 TGTGTTTATATAAG
1 TGTGTTTATATAAG
10778896 CCTTAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTGTTTATATAAGT
Found at i:10782449 original size:24 final size:23
Alignment explanation
Indices: 10782410--10782455 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
10782400 AGGAATACAT
*
10782410 GCAAAAGAAGAAATAACAGCAAG
1 GCAAAAGAAGAAATAAAAGCAAG
10782433 GCAAGAAGAA-AAGATAAAAGCAA
1 GCAA-AAGAAGAA-ATAAAAGCAA
10782456 AAAATGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.63, C:0.11, G:0.22, T:0.04
Consensus pattern (23 bp):
GCAAAAGAAGAAATAAAAGCAAG
Found at i:10783543 original size:19 final size:19
Alignment explanation
Indices: 10783516--10783554 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
10783506 TAGTATTATA
* *
10783516 TTTATTATTACTTACTTAC
1 TTTACTATTAATTACTTAC
*
10783535 TTTACTATTAATTATTTAC
1 TTTACTATTAATTACTTAC
10783554 T
1 T
10783555 CATGGTGCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTACTATTAATTACTTAC
Found at i:10787539 original size:15 final size:15
Alignment explanation
Indices: 10787521--10787552 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
10787511 ACTTATTAAG
10787521 TTTTATTAAATTTAT
1 TTTTATTAAATTTAT
*
10787536 TTTTTTTAAATTTAT
1 TTTTATTAAATTTAT
10787551 TT
1 TT
10787553 ATTGAAGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATTAAATTTAT
Found at i:10789349 original size:11 final size:11
Alignment explanation
Indices: 10789333--10789374 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 11
10789323 TAAATTTTCT
10789333 TAAAAATAATTC
1 TAAAAA-AATTC
10789345 TAAAAAAATT-
1 TAAAAAAATTC
10789355 TAAAAAAATTC
1 TAAAAAAATTC
10789366 -AAAATAAAT
1 TAAAA-AAAT
10789375 ATAAATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 14 0.50
11 8 0.29
12 6 0.21
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAAAAATTC
Found at i:10789364 original size:21 final size:22
Alignment explanation
Indices: 10789332--10789379 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
10789322 TTAAATTTTC
10789332 TTAAAAATAATTCTAAAA-AAAT
1 TTAAAAATAATTC-AAAATAAAT
10789354 TTAAAAA-AATTCAAAATAAAT
1 TTAAAAATAATTCAAAATAAAT
*
10789375 ATAAA
1 TTAAA
10789380 TTATTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 13 0.54
22 7 0.29
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
TTAAAAATAATTCAAAATAAAT
Found at i:10789369 original size:9 final size:10
Alignment explanation
Indices: 10789332--10789379 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
10789322 TTAAATTTTC
10789332 TTAAAAATAAT
1 TTAAAAA-AAT
10789343 TCTAAAAAAAT
1 T-TAAAAAAAT
10789354 TTAAAAAAAT
1 TTAAAAAAAT
*
10789364 TCAAAATAAAT
1 TTAAAA-AAAT
*
10789375 ATAAA
1 TTAAA
10789380 TTATTAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 14 0.44
11 12 0.38
12 6 0.19
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:10789423 original size:11 final size:10
Alignment explanation
Indices: 10789383--10789422 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
10789373 ATATAAATTA
10789383 TTAAAATATG
1 TTAAAATATG
10789393 TTAAAATATG
1 TTAAAATATG
*
10789403 TTAAAATATTT
1 TTAAAATA-TG
10789414 TTAAAATAT
1 TTAAAATAT
10789423 TATAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (10 bp):
TTAAAATATG
Found at i:10789428 original size:21 final size:20
Alignment explanation
Indices: 10789379--10789428 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
10789369 ATAAATATAA
10789379 ATTATTAAAATATGTTAAAAT
1 ATTA-TAAAATATGTTAAAAT
*
10789400 ATGT-TAAAATATTTTTAAAAT
1 AT-TATAAAATA-TGTTAAAAT
10789421 ATTATAAA
1 ATTATAAA
10789429 TAAAAAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 8 0.32
21 16 0.64
22 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
ATTATAAAATATGTTAAAAT
Found at i:10789429 original size:20 final size:19
Alignment explanation
Indices: 10789376--10789430 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
10789366 AAAATAAATA
*
10789376 TAAATTATTA-AAATATGT
1 TAAAATATTATAAATATGT
*
10789394 TAAAATATGT-TAAAATATTTT
1 TAAAATAT-TAT-AAATA-TGT
10789415 TAAAATATTATAAATA
1 TAAAATATTATAAATA
10789431 AAAAATCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 7 0.23
19 1 0.03
20 11 0.37
21 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
TAAAATATTATAAATATGT
Found at i:10789798 original size:69 final size:69
Alignment explanation
Indices: 10789682--10789818 Score: 229
Period size: 69 Copynumber: 2.0 Consensus size: 69
10789672 CTATTCTAAC
**
10789682 TAATCCATATCTTTAGTGCAATTGGACAATGAATCAAGTGACTTGTGATCAAATAAAGAATCTAG
1 TAATCCATATCTTTAGTGCAATACGACAATGAATCAAGTGACTTGTGATCAAATAAAGAATCTAG
10789747 AAAA
66 AAAA
* * *
10789751 TAATTCATATCTTTAGTGCCATACGACAATGAATCAAGTGACTTGTGATCAAATAAAGAATCTGG
1 TAATCCATATCTTTAGTGCAATACGACAATGAATCAAGTGACTTGTGATCAAATAAAGAATCTAG
10789816 AAA
66 AAA
10789819 GGGTAGAGGA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (69 bp):
TAATCCATATCTTTAGTGCAATACGACAATGAATCAAGTGACTTGTGATCAAATAAAGAATCTAG
AAAA
Found at i:10790602 original size:19 final size:19
Alignment explanation
Indices: 10790578--10790617 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
10790568 ATTTTTTATT
10790578 TAATA-TTTATTTAAAATAA
1 TAATATTTTA-TTAAAATAA
*
10790597 TAATATTTTATTAAAGTAA
1 TAATATTTTATTAAAATAA
10790616 TA
1 TA
10790618 TAATAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TAATATTTTATTAAAATAA
Found at i:10792098 original size:31 final size:31
Alignment explanation
Indices: 10792005--10792100 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
10791995 GGCAAATTAC
*
10792005 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
10792036 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
10792068 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
10792099 AA
1 AA
10792101 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:10797307 original size:16 final size:17
Alignment explanation
Indices: 10797286--10797318 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
10797276 AAAAGGGTCC
10797286 TTAAAAAT-AAAAAAAA
1 TTAAAAATCAAAAAAAA
10797302 TTAAAAATCAAAAAAAA
1 TTAAAAATCAAAAAAAA
10797319 GAAAGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
TTAAAAATCAAAAAAAA
Found at i:10798655 original size:45 final size:45
Alignment explanation
Indices: 10798581--10798934 Score: 303
Period size: 45 Copynumber: 8.0 Consensus size: 45
10798571 CAGATCAGTG
* *
10798581 AAAATAGCAGATCTTGTCTTCCTGTATTGGTAGTGAAGTAAATCA
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* * ** * *
10798626 AAAACAGTAGATCTTGTCTTCCTGCATTGGCAGCGAAGTAGATCA
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* *
10798671 AAAATAGCAAATCTTGTCTTCCTATATTGGTAGCT-AAGTAGATCG
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAG-TGAAGTAGATCA
* * **
10798716 AAGATAACAGATCTTGTCTTCCTATATTGGCGGTGAAGTAGATCA
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
** * * ** * *
10798761 AATGTAGTAGATCTTTTCTTCCTATATTGGTAGCAAAATAGATCG
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* * * * * *
10798806 AAGATAACATATCTTGTTTTCTTATATTGGCAGTGAAGTAGATCA
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* * ** *
10798851 AAGATAGCAGA-----TC-T--TATCTTGGTAGCAAAGTAGATCG
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
* * * *
10798888 AAAACAGTAGATCTTATCTTCCTATATTGGCAGTGAAGTAGATCA
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
10798933 AA
1 AA
10798935 GACAGAAGTA
Statistics
Matches: 239, Mismatches: 60, Indels: 20
0.75 0.19 0.06
Matches are distributed among these distances:
37 26 0.11
39 1 0.00
40 1 0.00
42 2 0.01
43 1 0.00
44 1 0.00
45 207 0.87
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (45 bp):
AAAATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAGTAGATCA
Found at i:10798728 original size:90 final size:90
Alignment explanation
Indices: 10798581--10798934 Score: 375
Period size: 90 Copynumber: 4.0 Consensus size: 90
10798571 CAGATCAGTG
* * * * * **
10798581 AAAATAGCAGATCTTGTCTTCCTGTATTGGTAG-TGAAGTAAATCAAAAACAGTAGATCTTGTCT
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGCT-AAGTAGATCGAAGATAACAGATCTTGTCT
** *
10798645 TCCTGCATTGGCAGCGAAGTAGATCA
65 TCCTATATTGGCAGTGAAGTAGATCA
*
10798671 AAAATAGCAAATCTTGTCTTCCTATATTGGTAGCTAAGTAGATCGAAGATAACAGATCTTGTCTT
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGCTAAGTAGATCGAAGATAACAGATCTTGTCTT
*
10798736 CCTATATTGGCGGTGAAGTAGATCA
66 CCTATATTGGCAGTGAAGTAGATCA
** * * * * * *
10798761 AATGTAGTAGATCTTTTCTTCCTATATTGGTAGCAAAATAGATCGAAGATAACATATCTTGTTTT
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGCTAAGTAGATCGAAGATAACAGATCTTGTCTT
*
10798826 CTTATATTGGCAGTGAAGTAGATCA
66 CCTATATTGGCAGTGAAGTAGATCA
* * * * * ** *
10798851 AAGATAGCAGA-----TC-T--TATCTTGGTAGCAAAGTAGATCGAAAACAGTAGATCTTATCTT
1 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGCTAAGTAGATCGAAGATAACAGATCTTGTCTT
10798908 CCTATATTGGCAGTGAAGTAGATCA
66 CCTATATTGGCAGTGAAGTAGATCA
10798933 AA
1 AA
10798935 GACAGAAGTA
Statistics
Matches: 227, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
82 60 0.26
84 1 0.00
85 2 0.01
90 163 0.72
91 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (90 bp):
AAAATAGCAGATCTTGTCTTCCTATATTGGTAGCTAAGTAGATCGAAGATAACAGATCTTGTCTT
CCTATATTGGCAGTGAAGTAGATCA
Found at i:10798832 original size:135 final size:135
Alignment explanation
Indices: 10798588--10798870 Score: 343
Period size: 135 Copynumber: 2.1 Consensus size: 135
10798578 GTGAAAATAG
* * *
10798588 CAGATCTTGTCTTCCTGTATTGGTAGTGAAGTAAATCAAAAACAGTAGATCTTGTCTTCCTGCAT
1 CAGATCTTGTCTTCCTATATTGGCAGTGAAGTAAATCAAAAACAGTAGATCTTGTCTTCCTACAT
* * * * *
10798653 TGGCAGCGAAGTAGATCAAAAATAGCAAATCTTGTCTTCCTATATTGGTAGCT-AAGTAGATCGA
66 TGGCAGCAAAATAGATCAAAAATAACAAATCTTGTCTTCCTATATTGGCAG-TGAAGTAGATCAA
10798717 AGATAA
130 AGATAA
* * *** * *
10798723 CAGATCTTGTCTTCCTATATTGGCGGTGAAGTAGATCAAATGTAGTAGATCTTTTCTTCCTATAT
1 CAGATCTTGTCTTCCTATATTGGCAGTGAAGTAAATCAAAAACAGTAGATCTTGTCTTCCTACAT
* * * * * *
10798788 TGGTAGCAAAATAGATCGAAGATAACATATCTTGTTTTCTTATATTGGCAGTGAAGTAGATCAAA
66 TGGCAGCAAAATAGATCAAAAATAACAAATCTTGTCTTCCTATATTGGCAGTGAAGTAGATCAAA
*
10798853 GATAG
131 GATAA
*
10798858 CAGATCTTATCTT
1 CAGATCTTGTCTT
10798871 GGTAGCAAAG
Statistics
Matches: 124, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
134 1 0.01
135 123 0.99
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (135 bp):
CAGATCTTGTCTTCCTATATTGGCAGTGAAGTAAATCAAAAACAGTAGATCTTGTCTTCCTACAT
TGGCAGCAAAATAGATCAAAAATAACAAATCTTGTCTTCCTATATTGGCAGTGAAGTAGATCAAA
GATAA
Found at i:10799102 original size:44 final size:44
Alignment explanation
Indices: 10799039--10799136 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
10799029 ATCCAGTCTC
* ** * * * *
10799039 ATCTCCCCGAGATTACAGTGGAGGAGATTGAATAAGCCAATCTT
1 ATCTCCCTGAGATTACAGTGGAACAGATTAAAGAAACCAATCCT
*
10799083 ATCTCCCTGAGGTTACAGTGGAACAGATTAAAGAAACCAATCCT
1 ATCTCCCTGAGATTACAGTGGAACAGATTAAAGAAACCAATCCT
10799127 ATCTCCCTGA
1 ATCTCCCTGA
10799137 AGTCGCAGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (44 bp):
ATCTCCCTGAGATTACAGTGGAACAGATTAAAGAAACCAATCCT
Found at i:10799732 original size:19 final size:19
Alignment explanation
Indices: 10799686--10799741 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 19
10799676 AATCTTCAAG
10799686 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
10799705 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
10799726 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
10799742 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.46
21 19 0.54
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:10799763 original size:23 final size:22
Alignment explanation
Indices: 10799686--10799764 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 22
10799676 AATCTTCAAG
*
10799686 GATATGCAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
10799708 -ATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
10799726 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
10799748 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
10799765 GATTTAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.04
19 15 0.31
21 12 0.24
22 8 0.16
23 12 0.24
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:10800513 original size:23 final size:22
Alignment explanation
Indices: 10800484--10800527 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
10800474 ATAATTCACA
*
10800484 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
10800507 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
10800528 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:10802716 original size:76 final size:72
Alignment explanation
Indices: 10802583--10802726 Score: 234
Period size: 76 Copynumber: 1.9 Consensus size: 72
10802573 AACATTATTA
*
10802583 ATTCGACCTGCTACAAAATTAAAAGCCAAGTCTATCTTCTCCGTCAATCCCCATTCCACAAGTTG
1 ATTCGACCTGCTACAAAATTAAAAGCCAAGTCTAACTTCTCCGTCAATCCCCATTCCACAAGTTG
10802648 GGGATTC
66 GGGATTC
*
10802655 ATTCGACTTGCTACAAAATTAAAAGCCAAGTAAGTCTAACTTCTCCGTCAATCCCCATTCCACAA
1 ATTCGACCTGCTACAAAATTAAAAGCC----AAGTCTAACTTCTCCGTCAATCCCCATTCCACAA
10802720 GTTGGGG
62 GTTGGGG
10802727 TCATCCACGT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
72 26 0.39
76 40 0.61
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (72 bp):
ATTCGACCTGCTACAAAATTAAAAGCCAAGTCTAACTTCTCCGTCAATCCCCATTCCACAAGTTG
GGGATTC
Found at i:10803433 original size:22 final size:22
Alignment explanation
Indices: 10803396--10803452 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
10803386 ATAAAATAAT
* *
10803396 AACAACAAAATAGTAGCAATAC
1 AACAACAAAATGGTAGCAAAAC
* * *
10803418 AATAACGAAATGGTAGTAAAAC
1 AACAACAAAATGGTAGCAAAAC
10803440 AACAACAAAATGG
1 AACAACAAAATGG
10803453 CGGCAAACTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (22 bp):
AACAACAAAATGGTAGCAAAAC
Found at i:10804412 original size:21 final size:20
Alignment explanation
Indices: 10804364--10804412 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 20
10804354 TTAAATAAAT
10804364 AAATTTTAAAATTTTCACTA
1 AAATTTTAAAATTTTCACTA
10804384 AAATTTTAAAATTTT-ACATA
1 AAATTTTAAAATTTTCAC-TA
10804404 AATATTTTA
1 AA-ATTTTA
10804413 TGTAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.07
20 19 0.70
21 6 0.22
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTTTAAAATTTTCACTA
Found at i:10804466 original size:26 final size:26
Alignment explanation
Indices: 10804437--10804487 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
10804427 ATATATAAAA
10804437 TTATCATAAATG-TAAATATTATTTAG
1 TTATCATAAA-GATAAATATTATTTAG
* *
10804463 TTATCATTAAGATAAGTATTATTTA
1 TTATCATAAAGATAAATATTATTTA
10804488 TTGTAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (26 bp):
TTATCATAAAGATAAATATTATTTAG
Found at i:10808027 original size:22 final size:20
Alignment explanation
Indices: 10807983--10808029 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
10807973 TTATGTTAAA
10807983 TAAATAAAATCAAATAAATT
1 TAAATAAAATCAAATAAATT
* *
10808003 TAAATAATAATTAAATCCAATT
1 TAAATAA-AATCAAAT-AAATT
10808025 TAAAT
1 TAAAT
10808030 CGGATATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 7 0.30
22 9 0.39
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAATAAAATCAAATAAATT
Found at i:10814335 original size:24 final size:24
Alignment explanation
Indices: 10814308--10814354 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
10814298 ATATAATATT
*
10814308 TAATTTTATATTAAA-AATAAAAAG
1 TAATTATATATTAAATAA-AAAAAG
10814332 TAATTATATATTAAATAAAAAAA
1 TAATTATATATTAAATAAAAAAA
10814355 CAAAATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
TAATTATATATTAAATAAAAAAAG
Found at i:10814467 original size:16 final size:16
Alignment explanation
Indices: 10814428--10814472 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
10814418 ACTTTAGTTC
*
10814428 TGGTCAATTTTCGGTT
1 TGGTCAATTTTCGATT
10814444 TCGGTCAATTTTCGATT
1 T-GGTCAATTTTCGATT
10814461 TGGTCAACTTTT
1 TGGTCAA-TTTT
10814473 TTGCTCAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.49
Consensus pattern (16 bp):
TGGTCAATTTTCGATT
Found at i:10818524 original size:11 final size:11
Alignment explanation
Indices: 10818508--10818532 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10818498 ACGTTGTAAA
10818508 AAATTCAAATC
1 AAATTCAAATC
10818519 AAATTCAAATC
1 AAATTCAAATC
10818530 AAA
1 AAA
10818533 AAATAAAATC
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:0.16, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATTCAAATC
Found at i:10819162 original size:11 final size:11
Alignment explanation
Indices: 10819142--10819179 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
10819132 AAAGAGAAAG
*
10819142 TAAAATTAAAA
1 TAAAAATAAAA
10819153 TAAAAATAAAA
1 TAAAAATAAAA
10819164 T-AAAATAAAA
1 TAAAAATAAAA
10819174 TAAAAA
1 TAAAAA
10819180 CCCCAACACG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:10819179 original size:6 final size:5
Alignment explanation
Indices: 10819142--10819178 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
10819132 AAAGAGAAAG
10819142 TAAAA TTAAAA TAAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA -TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA
10819179 ACCCCAACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 20 0.67
6 10 0.33
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:10820391 original size:31 final size:31
Alignment explanation
Indices: 10820356--10820421 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
10820346 AATGTAATTT
* * * *
10820356 TTGGCCCTTGAACTTGATAAGTATGTTCACA
1 TTGGCCCTTAAACTTGACAACTAGGTTCACA
*
10820387 TTGGCCCTTAAACTTGACAACTAGGTTCACT
1 TTGGCCCTTAAACTTGACAACTAGGTTCACA
10820418 TTGG
1 TTGG
10820422 TACTTGTACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (31 bp):
TTGGCCCTTAAACTTGACAACTAGGTTCACA
Done.