Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 69 of 205
Found at i:20647367 original size:20 final size:20
Alignment explanation
Indices: 20647344--20647385 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
20647334 TTTTTAAAAA
* *
20647344 TTAAAAATCATTAAATTTAT
1 TTAAAAATCATAAAATATAT
*
20647364 TTAAAAATTATAAAATATAT
1 TTAAAAATCATAAAATATAT
20647384 TT
1 TT
20647386 TAAATATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAAAATCATAAAATATAT
Found at i:20647399 original size:49 final size:50
Alignment explanation
Indices: 20647314--20647408 Score: 124
Period size: 48 Copynumber: 1.9 Consensus size: 50
20647304 ATTTTAATAT
*
20647314 TTTAAAAATTCAAAAAATTATTTTTAAAAATTAAAAA-TCATTAAATTTA
1 TTTAAAAATTCAAAAAATTATTTTTAAAAATTAAAAAGTAATTAAATTTA
* *
20647363 TTTAAAAATT-ATAAAA-TATATTTTAAATATTAAAAAAGTAATTAAA
1 TTTAAAAATTCAAAAAATTAT-TTTTAAAAATT-AAAAAGTAATTAAA
20647409 CCTTGACATG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
47 3 0.08
48 15 0.38
49 15 0.38
50 7 0.17
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (50 bp):
TTTAAAAATTCAAAAAATTATTTTTAAAAATTAAAAAGTAATTAAATTTA
Found at i:20649102 original size:22 final size:23
Alignment explanation
Indices: 20649056--20649122 Score: 98
Period size: 25 Copynumber: 2.8 Consensus size: 23
20649046 TTTTTGCAAT
20649056 TTATTTATTTTAAAATTTTTATA
1 TTATTTATTTTAAAATTTTTATA
* *
20649079 TTATTTGTTTTAAATTATTTTATTA
1 TTATTTATTTTAAAAT-TTTTA-TA
20649104 TTATTTATTTTAAAATTTT
1 TTATTTATTTTAAAATTTT
20649123 CACATATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 14 0.37
24 8 0.21
25 16 0.42
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (23 bp):
TTATTTATTTTAAAATTTTTATA
Found at i:20649130 original size:25 final size:23
Alignment explanation
Indices: 20649056--20649142 Score: 93
Period size: 25 Copynumber: 3.6 Consensus size: 23
20649046 TTTTTGCAAT
*
20649056 TTATTTATTTTAAAATTTTTATA
1 TTATTTATTTTAAAATTTTAATA
* *
20649079 TTATTTGTTTTAAATTATTTTATTA
1 TTATTTATTTTAAA--ATTTTAATA
20649104 TTATTTATTTTAAAATTTTCACATA
1 TTATTTATTTTAAAATTTT-A-ATA
**
20649129 TTATGCATTTTAAA
1 TTATTTATTTTAAA
20649143 CTATATTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 18 0.34
24 1 0.02
25 34 0.64
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATTTATTTTAAAATTTTAATA
Found at i:20649409 original size:23 final size:22
Alignment explanation
Indices: 20649364--20649414 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
20649354 TCTTGGTTAT
* *
20649364 TTATTTTAATTTGCTTTGTATG
1 TTATTTTAATTTGCGTTGCATG
*
20649386 TTATTTGTATTTTGCGTTGCATG
1 TTATTT-TAATTTGCGTTGCATG
20649409 TTATTT
1 TTATTT
20649415 ACTTTGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.16, C:0.06, G:0.16, T:0.63
Consensus pattern (22 bp):
TTATTTTAATTTGCGTTGCATG
Found at i:20653534 original size:13 final size:12
Alignment explanation
Indices: 20653506--20653552 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
20653496 CTATGGTTTT
20653506 CAAAA-AAATAAA
1 CAAAATAAA-AAA
20653518 -AAAATAAAAAA
1 CAAAATAAAAAA
20653529 TCAAAATAAAAAA
1 -CAAAATAAAAAA
20653542 CAAAATCAAAA
1 CAAAAT-AAAA
20653553 TAATATTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.23
12 9 0.29
13 15 0.48
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.11
Consensus pattern (12 bp):
CAAAATAAAAAA
Found at i:20653557 original size:21 final size:22
Alignment explanation
Indices: 20653510--20653557 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 22
20653500 GGTTTTCAAA
20653510 AAAATAA-AAAAATAAAAAATC
1 AAAATAATAAAAATAAAAAATC
*
20653531 --AA-AATAAAAA-ACAAAATC
1 AAAATAATAAAAATAAAAAATC
20653549 AAAATAATA
1 AAAATAATA
20653558 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 8
0.71 0.03 0.26
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 2 0.09
21 4 0.18
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (22 bp):
AAAATAATAAAAATAAAAAATC
Found at i:20653601 original size:6 final size:5
Alignment explanation
Indices: 20653590--20653652 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 5
20653580 ATATTTCAAA
* *
20653590 AAAATG AAAATG AAAAT A-AAG AAAAG AAAAG AAAAAG AGAATG AAAAG
1 AAAA-G AAAA-G AAAAG AAAAG AAAAG AAAAG -AAAAG A-AAAG AAAAG
20653638 AAAAGG AAAAG AAAA
1 AAAA-G AAAAG AAAA
20653653 AGGCGAAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
4 3 0.06
5 22 0.45
6 24 0.49
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (5 bp):
AAAAG
Found at i:20653613 original size:9 final size:10
Alignment explanation
Indices: 20653607--20653652 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
20653597 AAATGAAAAT
20653607 AAAGAAAAGA
1 AAAGAAAAGA
20653617 AAAGAAAAAGA
1 AAAG-AAAAGA
*
20653628 GAATGAAAAGA
1 -AAAGAAAAGA
20653639 AAAGGAAAAGA
1 AAA-GAAAAGA
20653650 AAA
1 AAA
20653653 AGGCGAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 6 0.19
11 22 0.71
12 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:20653654 original size:6 final size:5
Alignment explanation
Indices: 20653607--20653652 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
20653597 AAATGAAAAT
*
20653607 AAAGA AAAGA AAAGAA AAAGA GAATGA AAAGA AAAGGA AAAGA AAA
1 AAAGA AAAGA AAAG-A AAAGA -AAAGA AAAGA AAA-GA AAAGA AAA
20653653 AGGCGAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 22 0.61
6 14 0.39
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:20654661 original size:45 final size:45
Alignment explanation
Indices: 20654589--20654676 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
20654579 AAGAAGAAGG
* * *
20654589 GACCAAGGTGAAAACTCACAAAGGGCGCCTTGAGTCCTAAAAAAA
1 GACCAAGGTGAAAACCCACAAAAGGCGCCTTGAGTCATAAAAAAA
* *
20654634 GACCAAGGTGAAAACCCGCAAAAGGCGCTTTGAGTCATAAAAA
1 GACCAAGGTGAAAACCCACAAAAGGCGCCTTGAGTCATAAAAA
20654677 TACAGTAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.14
Consensus pattern (45 bp):
GACCAAGGTGAAAACCCACAAAAGGCGCCTTGAGTCATAAAAAAA
Found at i:20656221 original size:44 final size:44
Alignment explanation
Indices: 20656153--20656518 Score: 160
Period size: 44 Copynumber: 7.8 Consensus size: 44
20656143 TATGGTGAAT
* * * *
20656153 CTTATCTTCTTGAAGTTGCGGTGGAGCAGATTGAAGCCACCAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGC
** * * **
20656197 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACCGAAGACAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CTAGC
* * * * * * * *
20656242 CTTATTTCCCGGATGTTGTAGTGGAACAAATTAAAGCTACAAGTTATGAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC--C-A-CTA-G-C
* *
20656292 GAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACTAGC
1 ----CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGC
* * * * **
20656340 CTTATCTCCTTGAAGTTGCAGTGGAGCAAATTGAAGACAACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CCACTAGC
* * * * * *
20656385 CTTATTTCCCTGGCA-TTGTAGTGGAACAGATT-AGAGTTACAAATTATGGC
1 CTTATCTCCCT-GAAGTTGCAGTGGAGCAGATTGA-AG---C-CACTA--GC
* * * *
20656435 GAATCTTATCTTCATGAAGTTGCAGTGGAGCAGATTGAAGCTACCAGC
1 ----CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGC
* *
20656483 CTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
20656519 ACAGCGAATC
Statistics
Matches: 234, Mismatches: 64, Indels: 48
0.68 0.18 0.14
Matches are distributed among these distances:
44 98 0.42
45 58 0.25
46 2 0.01
47 3 0.01
48 9 0.04
49 1 0.00
50 4 0.02
51 2 0.01
52 1 0.00
53 2 0.01
54 53 0.23
55 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGC
Found at i:20656265 original size:143 final size:143
Alignment explanation
Indices: 20655999--20657108 Score: 1354
Period size: 143 Copynumber: 7.8 Consensus size: 143
20655989 ATTACAGTAA
* *
20655999 TTATGGCGAATCTTATCTTCCTGGAGTTGCAGTGGAGCAGATTGAAGCCATCAGCCTTATCTCCC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * * * * * *
20656064 TGAAGTTACAATAGAGTAGACTGAAGACAGTGAATCTTATTTCTCGGACT-TTACAGTGGAACAA
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGA-TGTTGCAGTGGAACAG
20656128 ATTAAAGCTACAAG
130 ATTAAAGCTACAAG
* * *
20656142 TTATGGTGAATCTTATCTTCTTGAAGTTGCGGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * *
20656207 TGAAGTTGCAGTGGAGCAGACCGAAGACAGCGAATCTTATTTCCCGGATGTTGTAGTGGAACAAA
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGATGTTGCAGTGGAACAGA
20656272 TTAAAGCTACAAG
131 TTAAAGCTACAAG
* * * *
20656285 TTATGACGAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACTAGCCTTATCTCCT
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * * *
20656350 TGAAGTTGCAGTGGAGCAAATTGAAGACAACAAATCTTATTTCCCTGGCA--TTGTAGTGGAACA
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCC-GG-ATGTTGCAGTGGAACA
* * *
20656413 GATTAGAGTTACAAA
129 GATTAAAGCTACAAG
* *
20656428 TTATGGCGAATCTTATCTTCATGAAGTTGCAGTGGAGCAGATTGAAGCTACCAGCCTTATCTCCC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * * * *
20656493 TGAAGTTGTAGTGGAGCAGACTGAAGACAGCGAATCTTATTTTCC-TAGCGTTACACTGGAACAG
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGA-TGTTGCAGTGGAACAG
* *
20656557 ATTAGAGCTACAAA
130 ATTAAAGCTACAAG
* * ** * * * * * *
20656571 TTATGGC-AGATATTATCTTCCTGAAGTTGTAGTGTTGCATAATAAAACCATCATCCTTATCTCC
1 TTATGGCGA-ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * * * * * *
20656635 ATGATGTTGCAGTGGAGCAAACTGAAGAAAACGAATCTTATTTCCTTGG-CGTTACAATGGAACA
65 CTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCC-CGGATGTTGCAGTGGAACA
* *
20656699 GATTAAAACTACAGG
129 GATTAAAGCTACAAG
* * * * * *
20656714 TTATGGCAAATCTTATCTTCCTAAAGTTGCAGTCGAGCAGATTGAAGCCACCAGCCTTGTATCTC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * * * * *
20656779 TGAAGTTACAGCGGAGCAAACTGAAGACAGTGAATCTTATTTCCCTGAAGTTGCAGTGGAACATA
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGATGTTGCAGTGGAACAGA
20656844 TTAAAGCTACAAG
131 TTAAAGCTACAAG
* * *
20656857 TTATGGCGAATCTTATCTT-CTCGAAGTTGTAGTGGAGCAGATTGAAGCCACCAGACTTATCTCT
1 TTATGGCGAATCTTATCTTCCT-GAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * * *
20656921 CTGAAGTTACAGCGGAGCAGAATGAAGACAACGAATCTTATTTCCCTG-TGTTGCAGTGGAACAG
65 CTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGATGTTGCAGTGGAACAG
20656985 ATTAAAGCTACAAG
130 ATTAAAGCTACAAG
20656999 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
1 TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * *
20657064 TAAAGTTGTAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCC
66 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCC
20657109 TAGCGTTGCA
Statistics
Matches: 830, Mismatches: 124, Indels: 27
0.85 0.13 0.03
Matches are distributed among these distances:
140 1 0.00
142 132 0.16
143 693 0.83
144 3 0.00
145 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (143 bp):
TTATGGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCCCGGATGTTGCAGTGGAACAGA
TTAAAGCTACAAG
Found at i:20658595 original size:25 final size:23
Alignment explanation
Indices: 20658577--20658663 Score: 93
Period size: 24 Copynumber: 3.6 Consensus size: 23
20658567 TTTTTGCAAT
*
20658577 TTATTTATTTTAAACTTTTTTATA
1 TTATTTATTTTAAA-TTTTTAATA
*
20658601 TTATTTATTTTAAATTATTTTATTA
1 TTATTTATTTTAAA-T-TTTTAATA
*
20658626 TTATTTATTTTAAATTTTCACATA
1 TTATTTATTTTAAATTTTTA-ATA
**
20658650 TTATGCATTTTAAA
1 TTATTTATTTTAAA
20658664 CTATATTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 4 0.07
24 30 0.56
25 20 0.37
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (23 bp):
TTATTTATTTTAAATTTTTAATA
Found at i:20658617 original size:14 final size:14
Alignment explanation
Indices: 20658594--20658641 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
20658584 TTTTAAACTT
*
20658594 TTTTATATTATTTA
1 TTTTAAATTATTTA
20658608 TTTTAAATTATTT-
1 TTTTAAATTATTTA
*
20658621 TATT--ATTATTTA
1 TTTTAAATTATTTA
20658633 TTTTAAATT
1 TTTTAAATT
20658642 TTCACATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 7 0.25
12 3 0.11
13 3 0.11
14 15 0.54
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTAAATTATTTA
Found at i:20658917 original size:23 final size:23
Alignment explanation
Indices: 20658885--20658932 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
20658875 TGGTTATTTA
* *
20658885 TTTTAATTTGCTTTGCATGTTAT
1 TTTTAATTTGCGTTGCATATTAT
*
20658908 TTTTATTTTGCGTTGCATATTAT
1 TTTTAATTTGCGTTGCATATTAT
20658931 TT
1 TT
20658933 ACTTTGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.08, G:0.12, T:0.62
Consensus pattern (23 bp):
TTTTAATTTGCGTTGCATATTAT
Found at i:20665027 original size:14 final size:14
Alignment explanation
Indices: 20665008--20665050 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
20664998 TGCAGCAGGC
*
20665008 AAGGTGACCATGCA
1 AAGGTGGCCATGCA
20665022 AAGGTGGCCATGCA
1 AAGGTGGCCATGCA
20665036 AAGGTGGCCATGCA
1 AAGGTGGCCATGCA
20665050 A
1 A
20665051 GAAGAAAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.33, C:0.21, G:0.33, T:0.14
Consensus pattern (14 bp):
AAGGTGGCCATGCA
Found at i:20666998 original size:6 final size:6
Alignment explanation
Indices: 20666987--20667018 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
20666977 GCTTTAGCCC
20666987 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT AT
20667019 AATAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:20667026 original size:18 final size:18
Alignment explanation
Indices: 20666987--20667027 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20666977 GCTTTAGCCC
** *
20666987 ATTTTTATTTTTATTTTT
1 ATTTTTATTTTTATAATA
20667005 ATTTTTATTTTTATAATA
1 ATTTTTATTTTTATAATA
20667023 ATTTT
1 ATTTT
20667028 AAATATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTTATTTTTATAATA
Found at i:20667115 original size:30 final size:31
Alignment explanation
Indices: 20667077--20667222 Score: 133
Period size: 30 Copynumber: 4.9 Consensus size: 31
20667067 AGGCAAAAAA
**
20667077 TAAAATTTACATTTTAACCCCTGCACTTTT-
1 TAAAATTTACATTTTAACCCCTAAACTTTTC
* *
20667107 TGAAATTTACATTTTGA-CCCTAAACTTTTC
1 TAAAATTTACATTTTAACCCCTAAACTTTTC
*
20667137 TAAAATTTACATTTTAACCCC-AAAATTTTC
1 TAAAATTTACATTTTAACCCCTAAACTTTTC
* * ** *
20667167 TATAA-TTACATTTCAACCTTTAGAC-TTTC
1 TAAAATTTACATTTTAACCCCTAAACTTTTC
* *
20667196 TCAAAATTT-CACTTTGACCCCTAAACT
1 T-AAAATTTACATTTTAACCCCTAAACT
20667223 CTCAAGAAAT
Statistics
Matches: 90, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
29 27 0.30
30 58 0.64
31 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (31 bp):
TAAAATTTACATTTTAACCCCTAAACTTTTC
Found at i:20667710 original size:14 final size:14
Alignment explanation
Indices: 20667687--20667721 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20667677 AACCCAAAGG
20667687 AAAAAG-AGAGAAA
1 AAAAAGAAGAGAAA
20667700 AAAAAGAAGAGAAA
1 AAAAAGAAGAGAAA
*
20667714 AGAAAGAA
1 AAAAAGAA
20667722 AAAAGGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGAGAAA
Found at i:20667730 original size:22 final size:23
Alignment explanation
Indices: 20667688--20667734 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
20667678 ACCCAAAGGA
*
20667688 AAAAGAGAGAAAAAAAAGAAGAG
1 AAAAGAAAGAAAAAAAAGAAGAG
*
20667711 AAAAGAAAG-AAAAAAGGAAGAG
1 AAAAGAAAGAAAAAAAAGAAGAG
20667733 AA
1 AA
20667735 GGGGAGGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (23 bp):
AAAAGAAAGAAAAAAAAGAAGAG
Found at i:20668181 original size:18 final size:18
Alignment explanation
Indices: 20668143--20668180 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
20668133 CTTTTGGGTA
20668143 TTATTTTTTAAATATATT
1 TTATTTTTTAAATATATT
*
20668161 TTATTTTATTTAATATATT
1 TTATTTT-TTAAATATATT
20668180 T
1 T
20668181 AAATGGTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTTTTAAATATATT
Found at i:20668454 original size:16 final size:16
Alignment explanation
Indices: 20668426--20668531 Score: 95
Period size: 16 Copynumber: 6.2 Consensus size: 16
20668416 TCATATTTAA
20668426 AAAATTTCTCGTGTTTT
1 AAAA-TTCTCGTGTTTT
* *
20668443 AAAATCCTCGTGTTTC
1 AAAATTCTCGTGTTTT
*
20668459 AAAATTGTCGTGTTTT
1 AAAATTCTCGTGTTTT
* *
20668475 CAAAAATTTTAGTGTTTTT
1 --AAAATTCTCGTG-TTTT
* *
20668494 AAGAATTTTCGTGTCTCT
1 AA-AATTCTCGTGT-TTT
20668512 AAAATTCTCGTGTTTT
1 AAAATTCTCGTGTTTT
20668528 AAAA
1 AAAA
20668532 AATTTTCGTG
Statistics
Matches: 73, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
16 29 0.40
17 17 0.23
18 23 0.32
19 4 0.05
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (16 bp):
AAAATTCTCGTGTTTT
Found at i:20668481 original size:34 final size:36
Alignment explanation
Indices: 20668405--20668552 Score: 128
Period size: 35 Copynumber: 4.2 Consensus size: 36
20668395 AAATAAAAAA
* *
20668405 TTCAAAAATCCTCAT-ATTTAAAAAATTTCTCGTGTT
1 TTCAAAAATCCTCGTGTTTTAAAAAATTT-TCGTGTT
* *
20668441 TT--AAAATCCTCGTG-TTT-CAAAATTGTCGTGTT
1 TTCAAAAATCCTCGTGTTTTAAAAAATTTTCGTGTT
** * * *
20668473 TTCAAAAATTTTAGTGTTTTTAAGAATTTTCGTG-T
1 TTCAAAAATCCTCGTGTTTTAAAAAATTTTCGTGTT
* * *
20668508 CTCTAAAATTCTCGTGTTTTAAAAAATTTTCGTGTT
1 TTCAAAAATCCTCGTGTTTTAAAAAATTTTCGTGTT
*
20668544 CTCAAAAAT
1 TTCAAAAAT
20668553 AAAAAATGTT
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
32 9 0.10
33 6 0.07
34 22 0.24
35 32 0.36
36 21 0.23
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (36 bp):
TTCAAAAATCCTCGTGTTTTAAAAAATTTTCGTGTT
Found at i:20668526 original size:53 final size:51
Alignment explanation
Indices: 20668421--20668543 Score: 158
Period size: 53 Copynumber: 2.4 Consensus size: 51
20668411 AATCCTCATA
* *
20668421 TTTAAAAAATTTCTCGTG-TTTTAAAATCCTCGTGTTTCAAAATTGTCGTGT
1 TTTAAAAAATTT-TCGTGTTTTTAAAATCCTCGTGTCTCAAAATTCTCGTGT
* * **
20668472 TTTCAAAAATTTTAGTGTTTTTAAGAATTTTCGTGTCTCTAAAATTCTCGTGT
1 TTTAAAAAATTTTCGTGTTTTTAA-AATCCTCGTGTCTC-AAAATTCTCGTGT
20668525 TTTAAAAAATTTTCGTGTT
1 TTTAAAAAATTTTCGTGTT
20668544 CTCAAAAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 4 0.07
51 17 0.28
52 11 0.18
53 29 0.48
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (51 bp):
TTTAAAAAATTTTCGTGTTTTTAAAATCCTCGTGTCTCAAAATTCTCGTGT
Found at i:20668550 original size:18 final size:18
Alignment explanation
Indices: 20668425--20668552 Score: 113
Period size: 18 Copynumber: 7.3 Consensus size: 18
20668415 CTCATATTTA
20668425 AAAAATTTCTCGTGTTTT-
1 AAAAATTT-TCGTGTTTTC
**
20668443 -AAAATCCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
20668459 -AAAATTGTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
20668476 AAAAATTTTAGTGTTTTT
1 AAAAATTTTCGTGTTTTC
* *
20668494 AAGAATTTTCGTG-TCTC
1 AAAAATTTTCGTGTTTTC
* * *
20668511 TAAAATTCTCGTGTTTTA
1 AAAAATTTTCGTGTTTTC
*
20668529 AAAAATTTTCGTGTTCTC
1 AAAAATTTTCGTGTTTTC
20668547 AAAAAT
1 AAAAAT
20668553 AAAAAATGTT
Statistics
Matches: 86, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
15 3 0.03
16 15 0.17
17 21 0.24
18 47 0.55
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:20681132 original size:72 final size:72
Alignment explanation
Indices: 20680997--20681140 Score: 236
Period size: 72 Copynumber: 2.0 Consensus size: 72
20680987 TACCTGACAG
* *
20680997 TGTTTGAGAACTCAATGGGTTGCGTACTGGGACAACATGACGAGTCAGGGAGAAGAGAAAAGGCA
1 TGTTTGAGAACTCAATGGGTTGCGTACTGGGACAACATGACAAGTCAGGGAAAAGAGAAAAGGCA
20681062 ATTTACT
66 ATTTACT
* *
20681069 TGTTTGAGAACTCAATGGGTTGCGTACTGGGACAACATGATAAGTCGGGGAAAAGA-AAGAAGGC
1 TGTTTGAGAACTCAATGGGTTGCGTACTGGGACAACATGACAAGTCAGGGAAAAGAGAA-AAGGC
20681133 AATTTACT
65 AATTTACT
20681141 ACCTCAGCAA
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 2 0.03
72 65 0.97
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (72 bp):
TGTTTGAGAACTCAATGGGTTGCGTACTGGGACAACATGACAAGTCAGGGAAAAGAGAAAAGGCA
ATTTACT
Found at i:20682913 original size:10 final size:10
Alignment explanation
Indices: 20682898--20682970 Score: 107
Period size: 10 Copynumber: 7.5 Consensus size: 10
20682888 TATTATGCCT
*
20682898 AAAAAAAA-G
1 AAAAAAAACA
20682907 AAAAAAAACA
1 AAAAAAAACA
20682917 ACAAAAAAAC-
1 A-AAAAAAACA
20682927 -AAAAAAACA
1 AAAAAAAACA
20682936 AAAAAAAACA
1 AAAAAAAACA
20682946 AAAAAAAACA
1 AAAAAAAACA
20682956 AAAAAAAACA
1 AAAAAAAACA
20682966 AAAAA
1 AAAAA
20682971 GCAAAAAAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
8 8 0.14
9 8 0.14
10 35 0.59
11 8 0.14
ACGTcount: A:0.89, C:0.10, G:0.01, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:20682939 original size:28 final size:27
Alignment explanation
Indices: 20682899--20682991 Score: 109
Period size: 26 Copynumber: 3.4 Consensus size: 27
20682889 ATTATGCCTA
20682899 AAAAAAAGAAAAAAAACAACAAAAAAAC
1 AAAAAAA-AAAAAAAACAACAAAAAAAC
20682927 AAAAAAACAAAAAAAAACAA-AAAAAAAC
1 -AAAAAA-AAAAAAAAACAACAAAAAAAC
* * *
20682955 AAAAAAAAACAAAAA-AGCAAAAAAAG
1 AAAAAAAAAAAAAAACAACAAAAAAAC
*
20682981 TAAAAAAAAAA
1 AAAAAAAAAAA
20682992 GAAGAAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.02
26 24 0.42
27 6 0.11
28 8 0.14
29 17 0.30
30 1 0.02
ACGTcount: A:0.87, C:0.09, G:0.03, T:0.01
Consensus pattern (27 bp):
AAAAAAAAAAAAAAACAACAAAAAAAC
Found at i:20682991 original size:38 final size:38
Alignment explanation
Indices: 20682898--20682979 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
20682888 TATTATGCCT
*
20682898 AAAAAAAA-GAAAAAAAACAACAAAAAAACAAAAAAACA
1 AAAAAAAACAAAAAAAAACAA-AAAAAAACAAAAAAACA
*
20682936 AAAAAAAACAAAAAAAAACAAAAAAAAACAAAAAAGCA
1 AAAAAAAACAAAAAAAAACAAAAAAAAACAAAAAAACA
20682974 AAAAAA
1 AAAAAA
20682980 GTAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 30 0.73
39 11 0.27
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (38 bp):
AAAAAAAACAAAAAAAAACAAAAAAAAACAAAAAAACA
Found at i:20683000 original size:1 final size:1
Alignment explanation
Indices: 20682898--20682991 Score: 80
Period size: 1 Copynumber: 94.0 Consensus size: 1
20682888 TATTATGCCT
* * * * * * *
20682898 AAAAAAAAGAAAAAAAACAACAAAAAAACAAAAAAACAAAAAAAAACAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** **
20682963 ACAAAAAAGCAAAAAAAGTAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20682992 GAAGAAAAAT
Statistics
Matches: 71, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.87, C:0.09, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:20683000 original size:10 final size:9
Alignment explanation
Indices: 20682898--20682989 Score: 89
Period size: 9 Copynumber: 9.9 Consensus size: 9
20682888 TATTATGCCT
*
20682898 AAAAAAAAG
1 AAAAAAAAC
20682907 AAAAAAAAC
1 AAAAAAAAC
20682916 AACAAAAAA-
1 AA-AAAAAAC
20682925 ACAAAAAAAC
1 A-AAAAAAAC
20682935 AAAAAAAAAC
1 -AAAAAAAAC
20682945 AAAAAAAAAC
1 -AAAAAAAAC
20682955 AAAAAAAA-
1 AAAAAAAAC
*
20682963 ACAAAAAAGC
1 A-AAAAAAAC
**
20682973 AAAAAAAGT
1 AAAAAAAAC
20682982 AAAAAAAA
1 AAAAAAAA
20682990 AAGAAGAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
8 1 0.01
9 45 0.62
10 26 0.36
11 1 0.01
ACGTcount: A:0.87, C:0.09, G:0.03, T:0.01
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:20683000 original size:38 final size:35
Alignment explanation
Indices: 20682899--20683000 Score: 114
Period size: 38 Copynumber: 2.7 Consensus size: 35
20682889 ATTATGCCTA
*
20682899 AAAAAAAGAAAAAAAACAACAAAAAAACAAAAAAAC
1 AAAAAAAGAAAAAAAA-AAAAAAAAAACAAAAAAAC
* *
20682935 AAAAAAAAACAAAAAAAAACAAAAAAAAACAAAAAAGC
1 --AAAAAAAGAAAAAAAAA-AAAAAAAAACAAAAAAAC
*
20682973 AAAAAAAGTAAAAAAAAAAGAAGAAAAA
1 AAAAAAAG-AAAAAAAAAA-AAAAAAAA
20683001 TCAAGATGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
36 8 0.14
37 17 0.30
38 31 0.55
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.01
Consensus pattern (35 bp):
AAAAAAAGAAAAAAAAAAAAAAAAAACAAAAAAAC
Found at i:20684113 original size:81 final size:77
Alignment explanation
Indices: 20683862--20684435 Score: 490
Period size: 81 Copynumber: 7.4 Consensus size: 77
20683852 TCAAGAATTA
* * *
20683862 TATTTTTCAATTTTTGTTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAG
20683925 TCACG-CTGAGG
66 TCACGTCTGAGG
* * * *
20683936 TATTTTTAAATTGCTGCTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAG
20684000 TCA--TCTTGAGG
66 TCACGTC-TGAGG
* * * *
20684011 T-CTTTTCAATTTCTTTTTTTTCAAAAAAAAAAAATCAACTCATAATGCTAGAAGTGAGTTGAGC
1 TATTTTTCAATTTC-TGTTTTTC-----AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGC
20684075 CTCGAGTCACGTC-GAGG
60 CTCGAGTCACGTCTGAGG
* * * * * **
20684092 TATTTTTCAATTTTTGGTTTTCACAAAAATGAACTCATATTGCGAGAGGTGAGTTGAGCCTTAAG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAG
**
20684157 TCATATCCTGAGG
66 TCACGT-CTGAGG
* * * * * *
20684170 TATTTTTCAATTTCTATTTTTCAAAAAAATTCGACTCATATTGCGAGAGGTGAGTTAAGTCTCGG
1 TATTTTTCAATTTCTGTTTTTCAAAAAAA-TCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGA
* * *
20684235 GTCACATACCGATG
65 GTCACGT-CTGAGG
* * * * *
20684249 TATTTCTTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCCAGAGGTGAGTTGAACCTC
1 TA--T-TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
* * *
20684314 GGGTCACATATCGAGG
63 GAGTCACGTCT-GAGG
* * * * *
20684330 TATTTCTTTTAAATTTCTGTTTCTC--CAAAATCAACTCATAATGCGAGAGGCGAGTTGAGACTC
1 TA--T-TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
*
20684393 G-GATCATG-CTGAGG
63 GAG-TCACGTCTGAGG
*
20684407 TA-TTTTCAATTTCTATTTTTCAAGAAAAA
1 TATTTTTCAATTTCTGTTTTTCAA-AAAAA
20684436 ACGATAATAG
Statistics
Matches: 409, Mismatches: 67, Indels: 46
0.78 0.13 0.09
Matches are distributed among these distances:
73 16 0.04
74 28 0.07
75 55 0.13
76 44 0.11
77 7 0.02
78 31 0.08
79 76 0.19
81 117 0.29
82 33 0.08
83 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (77 bp):
TATTTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGAG
TCACGTCTGAGG
Found at i:20684280 original size:236 final size:229
Alignment explanation
Indices: 20683862--20684435 Score: 567
Period size: 236 Copynumber: 2.5 Consensus size: 229
20683852 TCAAGAATTA
* * **
20683862 TATTTTTCAATTTTTGTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTCAATTTTTGTTTTCCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCT-TAGTC
* * **
20683927 --A-CGCTGAGGTATTTTTAAATTGCTGCTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAG
65 ATATC-CTGAGGTATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAG
* * * **
20683988 TTGAGCCTCGGGTCATCTTGAGGTCTTTTCAATTTCTTTTTTTTCAAAAAAAAAAAATCAACTCA
129 TTAAGCCTCGGGTCATCATGAGGTCTTTTAAATTTCTTGCTTTTC----AAAAAAAATCAACTCA
* * *
20684053 TAATGCTAGAAGTGAGTTGAGCCTCGAGTCAC-GTCGAGG
190 TAATGCCAGAAGTGAGTTGAACCTCGAGTCACAATCGAGG
* *
20684092 TATTTTTCAATTTTTGGTTTTCACAAAAATGAACTCATATTGCGAGAGGTGAGTTGAGCCTTAAG
1 TATTTTTCAATTTTT-GTTTTC-CAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTT-AG
* *
20684157 TCATATCCTGAGGTATTTTTCAATTTCTATTTTTCAAAAAAATTCGACTCATATTGCGAGAGGTG
63 TCATATCCTGAGGTATTTTTCAATTTCTATTTTTCAAAAAAA-TCAACTCATAATGCGAGAGGTG
* **
20684222 AGTTAAGTCTCGGGTCACATACCGATGTATTTCTTTTAAATTTC-TGCTTTTC-AAAAAAATCAA
127 AGTTAAGCCTCGGGT--CAT--C-ATG-AGGTCTTTTAAATTTCTTGCTTTTCAAAAAAAATCAA
* * *
20684285 CTCATATTGCCAGAGGTGAGTTGAACCTCGGGTCACATATCGAGG
186 CTCATAATGCCAGAAGTGAGTTGAACCTCGAGTCACA-ATCGAGG
* * * * *
20684330 TATTTCTTTTAAATTTCTGTTTCTCC-AAAATCAACTCATAATGCGAGAGGCGAGTTGAGAC-TC
1 TA--T-TTTTCAATTTTTGTTT-TCCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTA
* *
20684393 G-GATCATGCTGAGGTA-TTTTCAATTTCTATTTTTCAAGAAAAA
62 GTCAT-ATCCTGAGGTATTTTTCAATTTCTATTTTTCAA-AAAAA
20684436 ACGATAATAG
Statistics
Matches: 287, Mismatches: 35, Indels: 37
0.80 0.10 0.10
Matches are distributed among these distances:
230 15 0.05
231 5 0.02
232 38 0.13
234 25 0.09
235 7 0.02
236 98 0.34
237 16 0.06
238 12 0.04
239 31 0.11
240 7 0.02
241 20 0.07
242 13 0.05
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (229 bp):
TATTTTTCAATTTTTGTTTTCCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTAGTCA
TATCCTGAGGTATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTT
AAGCCTCGGGTCATCATGAGGTCTTTTAAATTTCTTGCTTTTCAAAAAAAATCAACTCATAATGC
CAGAAGTGAGTTGAACCTCGAGTCACAATCGAGG
Found at i:20684332 original size:160 final size:154
Alignment explanation
Indices: 20683862--20684435 Score: 519
Period size: 160 Copynumber: 3.7 Consensus size: 154
20683852 TCAAGAATTA
* * *
20683862 TATTTTTCAATTTTTGTTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* * * *
20683925 TCACGCTGAGGTATTTTTAAATTGCTGCTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGT
66 TCACTCCGAGGTATTTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
20683989 TGAGCCTCGGGTCATC-T-T-GAGG
131 TGAGCCTCGGGTCA-CATATCGAGG
* * * *
20684011 T-CTTTTCAATTTCTTTTTTTTCAAAAAAAAAAAATCAACTCATAATGCTAGAAGTGAGTTGAGC
1 TATTTTTCAATTTC-TATTTTTC-----AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGC
* * * * * *
20684075 CTCGAGTCACGT-CGAGGTATTTTTCAATTTTTGGTTTTCACAAAAATGAACTCATATTGCGAGA
60 CTCGGGTCAC-TCCGAGGTATTTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGA
***
20684139 GGTGAGTTGAGCCTTAAGT--CATATCCTGAGG
124 GGTGAGTTGAGCCTCGGGTCACATAT-C-GAGG
* * * *
20684170 TATTTTTCAATTTCTATTTTTCAAAAAAATTCGACTCATATTGCGAGAGGTGAGTTAAGTCTCGG
1 TATTTTTCAATTTCTATTTTTCAAAAAAA-TCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
* *
20684235 GTCACATACCGATGTATTTCTTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCCAGAG
65 GTCAC-T-CCGAGGTA--T-TTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAG
*
20684300 GTGAGTTGAACCTCGGGTCACATATCGAGG
125 GTGAGTTGAGCCTCGGGTCACATATCGAGG
* * * * * *
20684330 TATTTCTTTTAAATTTCTGTTTCTC--CAAAATCAACTCATAATGCGAGAGGCGAGTTGAGACTC
1 TA--T-TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
* * * **
20684393 GGATCA-TGCTGAGGTA-TTTTCAATTTCTATTTTTCAAGAAAAA
63 GGGTCACT-CCGAGGTATTTTTAAATTTCTGCTTTTCAA-AAAAA
20684436 ACGATAATAG
Statistics
Matches: 341, Mismatches: 56, Indels: 50
0.76 0.13 0.11
Matches are distributed among these distances:
148 10 0.03
149 8 0.02
154 26 0.08
155 40 0.12
156 64 0.19
157 43 0.13
158 7 0.02
159 13 0.04
160 103 0.30
161 5 0.01
162 6 0.02
163 16 0.05
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (154 bp):
TATTTTTCAATTTCTATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
TCACTCCGAGGTATTTTTAAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
TGAGCCTCGGGTCACATATCGAGG
Found at i:20684737 original size:6 final size:6
Alignment explanation
Indices: 20684726--20684757 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
20684716 GCTTTAGCCC
20684726 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT AT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT AT
20684758 AATAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:20684765 original size:18 final size:18
Alignment explanation
Indices: 20684726--20684766 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20684716 GCTTTAGCCC
** *
20684726 ATTTTTATTTTTATTTTT
1 ATTTTTATTTTTATAATA
20684744 ATTTTTATTTTTATAATA
1 ATTTTTATTTTTATAATA
20684762 ATTTT
1 ATTTT
20684767 AAATATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTTATTTTTATAATA
Found at i:20684853 original size:30 final size:31
Alignment explanation
Indices: 20684815--20684960 Score: 133
Period size: 30 Copynumber: 4.9 Consensus size: 31
20684805 AGGCAAAAAA
* **
20684815 TAAAATTTACATTTTAACCCCTGTACTTTT-
1 TAAAATTTACATTTTGACCCCTAAACTTTTC
*
20684845 TGAAATTTACATTTTGA-CCCTAAACTTTTC
1 TAAAATTTACATTTTGACCCCTAAACTTTTC
*
20684875 TAAAATTTACATTTTGACCCC-AAAATTTTC
1 TAAAATTTACATTTTGACCCCTAAACTTTTC
* ** ** *
20684905 TATAA-TTACATTTCAACCTTTAGAC-TTTC
1 TAAAATTTACATTTTGACCCCTAAACTTTTC
*
20684934 TCAAAATTT-CACTTTGACCCCTAAACT
1 T-AAAATTTACATTTTGACCCCTAAACT
20684961 CTCAAGAAAT
Statistics
Matches: 90, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
29 26 0.29
30 59 0.66
31 5 0.06
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (31 bp):
TAAAATTTACATTTTGACCCCTAAACTTTTC
Found at i:20685447 original size:14 final size:14
Alignment explanation
Indices: 20685428--20685457 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20685418 CCAAAGGAAA
20685428 AAGAGAAAAAAAAG
1 AAGAGAAAAAAAAG
*
20685442 AAGAGAAAAGAAAG
1 AAGAGAAAAAAAAG
20685456 AA
1 AA
20685458 AAAGGAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAGAGAAAAAAAAG
Found at i:20685450 original size:21 final size:21
Alignment explanation
Indices: 20685426--20685469 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20685416 ACCCAAAGGA
20685426 AAAAGAGAA-AAAAAAGAAGAG
1 AAAAGA-AAGAAAAAAGAAGAG
*
20685447 AAAAGAAAGAAAAAGGAAGAG
1 AAAAGAAAGAAAAAAGAAGAG
20685468 AA
1 AA
20685470 GGAGAGGCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (21 bp):
AAAAGAAAGAAAAAAGAAGAG
Found at i:20685604 original size:12 final size:12
Alignment explanation
Indices: 20685577--20685619 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
20685567 AAAAAGAGAG
*
20685577 AAAAAGAAAGAGA
1 AAAAAGAAA-ATA
20685590 AAAAAGAAAATA
1 AAAAAGAAAATA
*
20685602 AAAAAGGAAATA
1 AAAAAGAAAATA
20685614 ATAAAA
1 A-AAAA
20685620 AATAAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 14 0.52
13 13 0.48
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAAGAAAATA
Found at i:20685902 original size:19 final size:19
Alignment explanation
Indices: 20685878--20685916 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20685868 CTTTTGGGTA
* *
20685878 TTATTTTTTTTAATCTATT
1 TTATTTTATTTAATATATT
20685897 TTATTTTATTTAATATATT
1 TTATTTTATTTAATATATT
20685916 T
1 T
20685917 AAATGGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTTATTTAATATATT
Found at i:20686454 original size:17 final size:17
Alignment explanation
Indices: 20686434--20686483 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
20686424 AAAAAAATTA
20686434 TGTTTTCAAAACTTTCG
1 TGTTTTCAAAACTTTCG
* *
20686451 TGTTTTCAAAATTTTTG
1 TGTTTTCAAAACTTTCG
20686468 TGTTTTCAAAACTTTC
1 TGTTTTCAAAACTTTC
20686484 ATGTGTTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (17 bp):
TGTTTTCAAAACTTTCG
Found at i:20686569 original size:17 final size:17
Alignment explanation
Indices: 20686549--20687089 Score: 89
Period size: 17 Copynumber: 30.6 Consensus size: 17
20686539 AAAAAATTCA
20686549 TGTTTTCAAAATTTTCG
1 TGTTTTCAAAATTTTCG
* *
20686566 TGTTTTTAAGATTTTTCG
1 TGTTTTCAA-AATTTTCG
*
20686584 TG---TCAAAATAATTCTCA
1 TGTTTTCAAAAT--TT-TCG
* *
20686601 TG-TATCGAAAATTTCCG
1 TGTTTTC-AAAATTTTCG
* *
20686618 TGTTTTCAAAAAATTTCC
1 TGTTTTC-AAAATTTTCG
* *
20686636 TCGTTTCCAAAA-ATTCAGG
1 T-GTTTTCAAAATTTTC--G
** *
20686655 TGATTTAAAAAATCTTCG
1 TG-TTTTCAAAATTTTCG
** *
20686673 TGTTTTCAAAAACTCCG
1 TGTTTTCAAAATTTTCG
*
20686690 -GTTTTCAAAATTTTCA
1 TGTTTTCAAAATTTTCG
*
20686706 TGTTTTTCAAAAAATTCTCG
1 TG-TTTTC--AAAATTTTCG
* *
20686726 TG-TTTCAAAAACTTCCG
1 TGTTTTC-AAAATTTTCG
* *
20686743 TGTTCTCAAAAATTCTCG
1 TGTTTTC-AAAATTTTCG
*
20686761 T-ATTTCAAAAATCTTT-G
1 TGTTTTC-AAAAT-TTTCG
* *
20686778 TGCTTTT-AAAACTTTCA
1 TG-TTTTCAAAATTTTCG
*
20686795 TG-TTTCAAAAATTTTCT
1 TGTTTTC-AAAATTTTCG
* *
20686812 TGTTTTCAAAAAATTCCG
1 TGTTTTC-AAAATTTTCG
* ***
20686830 ATGATCAAAGAAATTTTTCG
1 -TGTTTTCA-AAA-TTTTCG
* * * *
20686850 TGATTTCTAAAAACTTCCA
1 TG-TTT-TCAAAATTTTCG
20686869 TG-TTTCAAAAATTTTCG
1 TGTTTTC-AAAATTTTCG
* *
20686886 TGTTTT-AAGAGTTTTCT
1 TGTTTTCAA-AATTTTCG
*
20686903 TGCTTTCAACAATTCTT-G
1 TGTTTTCAA-AATT-TTCG
* *
20686921 T-ATTTCTTAAATTTTCG
1 TGTTTTC-AAAATTTTCG
* **
20686938 AG-TTTCAAAA-AATCG
1 TGTTTTCAAAATTTTCG
*
20686953 TGTTTTCAAAAAAAAAATTCTCG
1 TGTTTTC------AAAATTTTCG
**
20686976 TGTTTT-AAAATCCTCG
1 TGTTTTCAAAATTTTCG
*
20686992 TG-TTTCAAAATTGTCG
1 TGTTTTCAAAATTTTCG
*
20687008 TGTTTTCAAAAATTTTAG
1 TGTTTTC-AAAATTTTCG
*
20687026 TGTTTTTAAGAATTTTCG
1 TGTTTTCAA-AATTTTCG
* *
20687044 TG-TCTCTAAAATTCTCG
1 TGTTTTC-AAAATTTTCG
*
20687061 TGTTTTAAAAAAATTTT-G
1 TGTTTT--CAAAATTTTCG
*
20687079 TGTTCTCAAAA
1 TGTTTTCAAAA
20687090 ATAAAAAATG
Statistics
Matches: 378, Mismatches: 92, Indels: 109
0.65 0.16 0.19
Matches are distributed among these distances:
14 2 0.01
15 13 0.03
16 54 0.14
17 119 0.31
18 109 0.29
19 40 0.11
20 26 0.07
21 2 0.01
22 4 0.01
23 9 0.02
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (17 bp):
TGTTTTCAAAATTTTCG
Found at i:20686602 original size:52 final size:51
Alignment explanation
Indices: 20686504--20686634 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 51
20686494 GTTTTCAAAA
* * *
20686504 AAAATTCTCGTGTCTTTTAAAAAATTTCGTGTTAAAAAAAATTCATGTTTTC-
1 AAAATTTTCGTGT-TTTTAAAAAATTTCGTGTCAAAAAAAATTCATG-TATCG
* ** * *
20686556 AAAATTTTCGTGTTTTTAAGATTTTTCGTGTCAAAATAATTCTCATGTATCG
1 AAAATTTTCGTGTTTTTAAAAAATTTCGTGTCAAAAAAAAT-TCATGTATCG
* *
20686608 AAAATTTCCGTGTTTTCAAAAAATTTC
1 AAAATTTTCGTGTTTTTAAAAAATTTC
20686635 CTCGTTTCCA
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
51 25 0.39
52 39 0.61
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (51 bp):
AAAATTTTCGTGTTTTTAAAAAATTTCGTGTCAAAAAAAATTCATGTATCG
Found at i:20686767 original size:53 final size:52
Alignment explanation
Indices: 20686643--20686788 Score: 133
Period size: 53 Copynumber: 2.8 Consensus size: 52
20686633 TCCTCGTTTC
** *
20686643 CAAAAATTCAGGTGATTT-AAAAAATCTTCGTGTTTTCAAAAACTCCGGTTTT
1 CAAAAATTCTCGT-ATTTCAAAAAATCTTCGTGTTTTCAAAAACTCCGGTTCT
* *
20686695 C-AAAATTTTCATGTTTTTCAAAAAAT-TCTCGTG-TTTCAAAAACTTCCGTGTTCT
1 CAAAAATTCTC--GTATTTCAAAAAATCT-TCGTGTTTTCAAAAAC-TCCG-GTTCT
*
20686749 CAAAAATTCTCGTATTTC-AAAAATCTTTGTGCTTTT-AAAA
1 CAAAAATTCTCGTATTTCAAAAAATCTTCGTG-TTTTCAAAA
20686789 CTTTCATGTT
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
51 6 0.08
52 25 0.33
53 29 0.38
54 8 0.11
55 8 0.11
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (52 bp):
CAAAAATTCTCGTATTTCAAAAAATCTTCGTGTTTTCAAAAACTCCGGTTCT
Found at i:20686771 original size:18 final size:18
Alignment explanation
Indices: 20686502--20687090 Score: 113
Period size: 18 Copynumber: 33.3 Consensus size: 18
20686492 GTGTTTTCAA
*
20686502 AAAAAATTCTCGTGTCTTTT
1 AAAAAATTCTCGTG--TTTC
**
20686522 AAAAAATT-TCGTGTTAA
1 AAAAAATTCTCGTGTTTC
20686539 AAAAAATTCAT-GT-TTTC
1 AAAAAATTC-TCGTGTTTC
* *
20686556 --AAAATTTTCGTGTTTT
1 AAAAAATTCTCGTGTTTC
* * * *
20686572 TAAGATTTTTCGTG--TC
1 AAAAAATTCTCGTGTTTC
* *
20686588 AAAATAATTCTCATGTATC
1 AAAA-AATTCTCGTGTTTC
* *
20686607 GAAAATTTC-CGTGTTTTC
1 AAAAAATTCTCGTG-TTTC
*
20686625 AAAAAATT-TCCTCGTTTC
1 AAAAAATTCTCGT-GTTTC
* **
20686643 CAAAAATTCAGGTGATTT-
1 AAAAAATTCTCGTG-TTTC
20686661 AAAAAA-TCTTCGTGTTTTC
1 AAAAAATTC-TCGTG-TTTC
*
20686680 -AAAAACTC-CG-GTTTTC
1 AAAAAATTCTCGTG-TTTC
** *
20686696 AAAATTTTCAT-GTTTTTC
1 AAAAAATTC-TCGTGTTTC
20686714 AAAAAATTCTCGTGTTTC
1 AAAAAATTCTCGTGTTTC
*
20686732 AAAAACTTC-CGTGTTCTC
1 AAAAAATTCTCGTGTT-TC
*
20686750 -AAAAATTCTCGTATTTC
1 AAAAAATTCTCGTGTTTC
*
20686767 -AAAAA-TCTTTGTGCTTT-
1 AAAAAATTC-TCGTG-TTTC
* * *
20686784 TAAAACTT-TCATGTTTC
1 AAAAAATTCTCGTGTTTC
* *
20686801 -AAAAATTTTCTTGTTTTC
1 AAAAAATTCTCGTG-TTTC
*
20686819 AAAAAATTC-CGATG-ATC
1 AAAAAATTCTCG-TGTTTC
*
20686836 AAAGAAATTTTTCGTGATTTC
1 AAA-AAA-TTCTCGTG-TTTC
* *
20686857 TAAAAACTTC-CATGTTTC
1 -AAAAAATTCTCGTGTTTC
*
20686875 -AAAAATTTTCGTGTTT-
1 AAAAAATTCTCGTGTTTC
* * * * *
20686891 TAAGAGTTTTCTTGCTTTC
1 AAAAAATTCTCGTG-TTTC
* * *
20686910 -AACAATTCTTGTATTTC
1 AAAAAATTCTCGTGTTTC
** * *
20686927 -TTAAATTTTCGAGTTTC
1 AAAAAATTCTCGTGTTTC
20686944 AAAAAA---TCGTGTTTTC
1 AAAAAATTCTCGTG-TTTC
20686960 AAAAAAAAAATTCTCGTGTTT-
1 ----AAAAAATTCTCGTGTTTC
* *
20686981 -TAAAATCCTCGTGTTTC
1 AAAAAATTCTCGTGTTTC
*
20686998 --AAAATTGTCGTGTTTTC
1 AAAAAATTCTCGTG-TTTC
* * *
20687015 -AAAAATTTTAGTGTTTT
1 AAAAAATTCTCGTGTTTC
* * * *
20687032 TAAGAATTTTCGTGTCTC
1 AAAAAATTCTCGTGTTTC
* *
20687050 -TAAAATTCTCGTGTTTTA
1 AAAAAATTCTCGTG-TTTC
*
20687068 AAAAAATT-TTGTGTTCTC
1 AAAAAATTCTCGTGTT-TC
20687086 AAAAA
1 AAAAA
20687091 TAAAAAATGT
Statistics
Matches: 415, Mismatches: 95, Indels: 120
0.66 0.15 0.19
Matches are distributed among these distances:
14 1 0.00
15 12 0.03
16 57 0.14
17 116 0.28
18 155 0.37
19 41 0.10
20 18 0.04
21 4 0.01
22 6 0.01
23 5 0.01
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
AAAAAATTCTCGTGTTTC
Found at i:20686991 original size:16 final size:16
Alignment explanation
Indices: 20686966--20687070 Score: 102
Period size: 16 Copynumber: 6.2 Consensus size: 16
20686956 TTTCAAAAAA
20686966 AAAATTCTCGTGTTTT
1 AAAATTCTCGTGTTTT
* *
20686982 AAAATCCTCGTGTTTC
1 AAAATTCTCGTGTTTT
*
20686998 AAAATTGTCGTGTTTT
1 AAAATTCTCGTGTTTT
* *
20687014 CAAAAATTTTAGTGTTTTT
1 --AAAATTCTCGTG-TTTT
* *
20687033 AAGAATTTTCGTGTCTCT
1 AA-AATTCTCGTGT-TTT
20687051 AAAATTCTCGTGTTTT
1 AAAATTCTCGTGTTTT
20687067 AAAA
1 AAAA
20687071 AAATTTTGTG
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
16 33 0.45
17 13 0.18
18 23 0.32
19 4 0.05
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (16 bp):
AAAATTCTCGTGTTTT
Found at i:20688681 original size:9 final size:9
Alignment explanation
Indices: 20688670--20688772 Score: 143
Period size: 9 Copynumber: 11.4 Consensus size: 9
20688660 TTTGATTAAA
*
20688670 AATTAACCA
1 AATTAACCG
20688679 AATTAACCG
1 AATTAACCG
*
20688688 AAATAACCG
1 AATTAACCG
*
20688697 AATTACCCG
1 AATTAACCG
20688706 AATTAACCG
1 AATTAACCG
*
20688715 AATTACCCG
1 AATTAACCG
*
20688724 AATTACCCG
1 AATTAACCG
20688733 AATTAACCG
1 AATTAACCG
*
20688742 AATTACCCG
1 AATTAACCG
20688751 AATTAACCG
1 AATTAACCG
*
20688760 AATTAACCA
1 AATTAACCG
20688769 AATT
1 AATT
20688773 GAATCACTAC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 84 1.00
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTAACCG
Found at i:20691248 original size:12 final size:12
Alignment explanation
Indices: 20691231--20691263 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
20691221 GACACCACAC
20691231 GGCCATGTGCTA
1 GGCCATGTGCTA
*
20691243 GGCCATGTGGTA
1 GGCCATGTGCTA
20691255 GGCCATGTG
1 GGCCATGTG
20691264 AGCCAAACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.21, G:0.39, T:0.24
Consensus pattern (12 bp):
GGCCATGTGCTA
Found at i:20695594 original size:17 final size:17
Alignment explanation
Indices: 20695572--20695607 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
20695562 AAACCTGCAA
20695572 AGTATAATCAACCAACC
1 AGTATAATCAACCAACC
20695589 AGTATAATCAACCAACC
1 AGTATAATCAACCAACC
20695606 AG
1 AG
20695608 AATATCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.28, G:0.08, T:0.17
Consensus pattern (17 bp):
AGTATAATCAACCAACC
Found at i:20697856 original size:75 final size:75
Alignment explanation
Indices: 20697573--20698131 Score: 647
Period size: 77 Copynumber: 7.3 Consensus size: 75
20697563 AAATTATTTC
* * *
20697573 TTTCAATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTAGGTCGCAT
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCAGGTCGCAC
*
20697638 GCTAAGGTAT
66 GCTGAGGTAT
* * * *
20697648 TTTCAATTTATGTTTTTCAAAAAAATCAACTTATAATGCAAGAGGTGAGTTGAGCTTCAGGTCGC
1 TTTCAATTTATGTTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCAGGTCGC
20697713 ACGCTGAGGTAT
64 ACGCTGAGGTAT
*
20697725 TTTCAATTTATGTTTTTCAAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCAGGTCAC
1 TTTCAATTTATGTTTTTC--AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCAGGTCGC
* *
20697790 ACACTAAGGTAT
64 ACGCTGAGGTAT
* * *
20697802 TTTCAATTTATGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACAC
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCAGGTCGCAC
20697867 G-TAGAGGTATT
66 GCT-GAGGTA-T
* * *
20697878 TTTCAATTTATGTTTTTTTTTTAAAAAAATCAACTCATAAATACGAGAGG-GAGGTGAGCCTCGG
1 TTTCAATTTATG-----TTTTT-CAAAAATCAACTCAT-AATACGAGAGGTGAGTTGAGCCTCAG
*
20697942 GTCGCACTCTGAGGTATT
59 GTCGCACGCTGAGGTA-T
* * * * *
20697960 TTTCAATTTTTGTTTTTTCAAAAATCAACTCATAATCCGAGATGTGAGTTGAGCCTCGGGTTGCA
1 TTTCAATTTATG-TTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCAGGTCGCA
20698025 CGCTGAGGTAT
65 CGCTGAGGTAT
* * * * *
20698036 TTTCAATTTCTGTTTTTCAAAGATCAACTCATAATTA-GAAAGATGAGTTGAGCTTCAGGTCGCA
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATAA-TACGAGAGGTGAGTTGAGCCTCAGGTCGCA
* * * *
20698100 CACCGAGCTAG
65 CGCTGAGGTAT
* *
20698111 TTTCGATTTCTGTTTTTCAAA
1 TTTCAATTTATGTTTTTCAAA
20698132 TAAAAATAAA
Statistics
Matches: 427, Mismatches: 43, Indels: 28
0.86 0.09 0.06
Matches are distributed among these distances:
74 1 0.00
75 137 0.32
76 35 0.08
77 180 0.42
78 6 0.01
81 5 0.01
82 52 0.12
83 11 0.03
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (75 bp):
TTTCAATTTATGTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCAGGTCGCAC
GCTGAGGTAT
Found at i:20698015 original size:234 final size:228
Alignment explanation
Indices: 20697573--20698096 Score: 685
Period size: 234 Copynumber: 2.3 Consensus size: 228
20697563 AAATTATTTC
* * * *
20697573 TTTCAATTTATGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTAGGTCGCAT
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCACAC
* * *
20697638 GCTAAGGTATTTTCAATTTATGTTTTTCAAAAAAATCAACTTATAATGCAAGAGGTGAGTTGAGC
66 GCTAAGGTATTTTCAATTTATGTTTTTCAAAAAAATCAACTCATAATACAAGAGGTGAGGTGAGC
*
20697703 TTCAGGTCGCACGCTGAGGTATTTTCAATTTATGTTTTTCAAAAAAATCAACTCATAATACGAGA
131 CTCAGGTCGCACGCTGAGGTATTTTCAATTTATGTTTTTC-AAAAAATCAACTCATAATACGAGA
20697768 GGTGAGTTGAGCCTCAGGTCACACACTAAGGTAT
195 GGTGAGTTGAGCCTCAGGTCACACACTAAGGTAT
*
20697802 TTTCAATTTATGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCACAC
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCACAC
* *
20697867 G-TAGAGGTATTTTTCAATTTATGTTTTTTTTTTAAAAAAATCAACTCATAAATACGAGAGG-GA
66 GCTA-AGGTA-TTTTCAATTTATG----TTTTTCAAAAAAATCAACTCAT-AATACAAGAGGTGA
* * *
20697930 GGTGAGCCTCGGGTCGCACTCTGAGGTATTTTTCAATTTTTGTTTTTTC-AAAAATCAACTCATA
124 GGTGAGCCTCAGGTCGCACGCTGAGGTA-TTTTCAATTTATG-TTTTTCAAAAAATCAACTCATA
* * * ** * *
20697994 ATCCGAGATGTGAGTTGAGCCTCGGGTTGCACGCTGAGGTAT
187 ATACGAGAGGTGAGTTGAGCCTCAGGTCACACACTAAGGTAT
* * ** * * *
20698036 TTTCAATTTCTGTTTTTCAAAGATCAACTCATAATTAGAAAGATGAGTTGAGCTTCAGGTC
1 TTTCAATTTATGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTC
20698097 GCACACCGAG
Statistics
Matches: 257, Mismatches: 29, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
228 2 0.01
229 66 0.26
230 13 0.05
234 149 0.58
235 21 0.08
236 6 0.02
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (228 bp):
TTTCAATTTATGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCAGGTCACAC
GCTAAGGTATTTTCAATTTATGTTTTTCAAAAAAATCAACTCATAATACAAGAGGTGAGGTGAGC
CTCAGGTCGCACGCTGAGGTATTTTCAATTTATGTTTTTCAAAAAATCAACTCATAATACGAGAG
GTGAGTTGAGCCTCAGGTCACACACTAAGGTAT
Found at i:20698439 original size:30 final size:29
Alignment explanation
Indices: 20698376--20698476 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 29
20698366 AAAAAAATTT
* *
20698376 AAATTACATTTTGACCCAT-AACTTTTCA
1 AAATTACATTTTGACCCCTAAACTTTCCA
20698404 AAATTACATTTTGACCCCTAAACTTTCCTA
1 AAATTACATTTTGACCCCTAAACTTTCC-A
* *
20698434 AAATTACATTTTAACCCCTAAAATTTCCCA
1 AAATTACATTTTGACCCCTAAACTTT-CCA
*
20698464 AAATTACACTTTG
1 AAATTACATTTTG
20698477 GCTCCAAAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
28 18 0.28
29 7 0.11
30 37 0.58
31 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAACTTTCCA
Found at i:20701343 original size:15 final size:13
Alignment explanation
Indices: 20701323--20701356 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
20701313 TAACATAAAA
20701323 TATTTTATTATTTT
1 TATTTTATT-TTTT
20701337 GTATTTTATTTTTT
1 -TATTTTATTTTTT
20701351 TATTTT
1 TATTTT
20701357 CGGTTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 4 0.21
15 9 0.47
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TATTTTATTTTTT
Found at i:20703531 original size:3 final size:3
Alignment explanation
Indices: 20703523--20703562 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
20703513 CGGTTTCAAC
*
20703523 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
20703563 GTTAGTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20704158 original size:13 final size:15
Alignment explanation
Indices: 20704140--20704171 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20704130 ATAGTCTCAA
20704140 TAATTAA-A-AATAT
1 TAATTAATATAATAT
20704153 TAATTAATATAATAT
1 TAATTAATATAATAT
20704168 TAAT
1 TAAT
20704172 AGTTTAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATTAATATAATAT
Found at i:20704582 original size:21 final size:21
Alignment explanation
Indices: 20704556--20704598 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
20704546 GGTTCGCTGT
*
20704556 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
20704577 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
20704598 A
1 A
20704599 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:20704598 original size:16 final size:16
Alignment explanation
Indices: 20704579--20704611 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20704569 TGTATTGGAT
*
20704579 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
20704595 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
20704611 T
1 T
20704612 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:20704656 original size:45 final size:44
Alignment explanation
Indices: 20704590--20704684 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
20704580 GGATTAGAGG
* *
20704590 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
20704635 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
20704679 TGTAAT
1 TGTAAT
20704685 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:20704867 original size:18 final size:17
Alignment explanation
Indices: 20704846--20704880 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20704836 TTATTATTTA
*
20704846 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
20704864 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
20704881 GCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:20704874 original size:28 final size:27
Alignment explanation
Indices: 20704804--20704876 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
20704794 TTTATTATCA
*
20704804 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
20704832 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
20704859 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
20704877 AAATGCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:20704993 original size:144 final size:147
Alignment explanation
Indices: 20704765--20705036 Score: 478
Period size: 144 Copynumber: 1.9 Consensus size: 147
20704755 ATGATTATTG
20704765 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
20704830 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGC
20704895 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
20704914 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
*
20704976 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTA
20705037 ATATTCTTAT
Statistics
Matches: 120, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
144 91 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:20705011 original size:18 final size:17
Alignment explanation
Indices: 20704990--20705024 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20704980 TTATTATTAA
*
20704990 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
20705008 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
20705025 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:20718298 original size:3 final size:3
Alignment explanation
Indices: 20718290--20718322 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20718280 TACTAGCATA
20718290 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
20718323 AATAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:20718327 original size:3 final size:3
Alignment explanation
Indices: 20718321--20718365 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
20718311 GATGATGATG
20718321 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20718366 TGTGTACAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20718487 original size:18 final size:17
Alignment explanation
Indices: 20718435--20718487 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
20718425 TAAATAGATG
20718435 AGTAAATGATAATAAAAT
1 AGTAAAT-ATAATAAAAT
* * *
20718453 AATAATAGATGATAAAAT
1 AGTAA-ATATAATAAAAT
20718471 AGTAAATATAATGAAAA
1 AGTAAATATAAT-AAAA
20718488 CGTAAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 5 0.19
18 21 0.78
19 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.26
Consensus pattern (17 bp):
AGTAAATATAATAAAAT
Found at i:20719852 original size:24 final size:24
Alignment explanation
Indices: 20719808--20719853 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20719798 TTTTGGGTCT
*
20719808 GTTTGGGTTAGGTTTAGTTTGGTG
1 GTTTGGGTTAGGTTTAATTTGGTG
*
20719832 GTTTTGGTT-GGTTTGAATTTGG
1 GTTTGGGTTAGGTTT-AATTTGG
20719854 GTTGGGTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.09, C:0.00, G:0.39, T:0.52
Consensus pattern (24 bp):
GTTTGGGTTAGGTTTAATTTGGTG
Found at i:20720489 original size:239 final size:242
Alignment explanation
Indices: 20720049--20720531 Score: 760
Period size: 239 Copynumber: 2.0 Consensus size: 242
20720039 CCACTTCAGG
* *
20720049 GAAATAGGATCGTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGTAACTTCAACCTGC
1 GAAATAAGATCGTTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGACTCGTAACTT--ACC-GC
* * *
20720114 CCACTACAATTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCTCTACTATAACTTCAGAGAGAT
63 CCACTACAATTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCCCTACTACAACTTCAGAGAGAA
* * *
20720179 AAGATTCGCTATCTTCCAAGAGATAATATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGG
128 AAGATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGG
20720244 AGTTCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAAA
193 AGTTCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAAA
*
20720294 GAAATAAGATCGTTAGTCTGCTCCACTTCAACTTCAGGGAAATAAGACTCGTAAC-T-CC-CCCA
1 GAAATAAGATCGTTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGACTCGTAACTTACCGCCCA
* * *
20720356 CTACAACTTT-AGGGATATAAGGTTTATAGCTTTAATCTGCCCTACTACAACTTTAGAGAGAAAA
66 CTACAA-TTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCCCTACTACAACTTCAGAGAGAAAA
*
20720420 GATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTACAA-TTTCAGGAA
130 GATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGG-A
*
20720484 GTTCAGATTTGTAACTTATAGCCTTAATCTGTTCCACTGTAACTTCAA
194 GTTCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAA
20720532 GGTTGATGCT
Statistics
Matches: 222, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
238 6 0.03
239 158 0.71
240 3 0.01
241 2 0.01
244 1 0.00
245 52 0.23
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (242 bp):
GAAATAAGATCGTTAGTCTGCTCCACTGCAACTTCAGGGAAATAAGACTCGTAACTTACCGCCCA
CTACAATTTCAAGGAGATAAGGTTTATAGCTTTAATCTGCCCTACTACAACTTCAGAGAGAAAAG
ATTCGCTATATTCCAAAAGATAAAATTTGCTTTATTCAATCTGCTCCACTACAATTTTAAGGAGT
TCAGATTTGTAACTTATAGCCTTAATCTATTCCACTGTAACTTCAAA
Found at i:20720717 original size:11 final size:10
Alignment explanation
Indices: 20720703--20720768 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
20720693 GGCCTCTCCT
20720703 TTTTCTTTTTC
1 TTTT-TTTTTC
*
20720714 TTTTCTTTTCC
1 TTTT-TTTTTC
* *
20720725 TTATTTTTCC
1 TTTTTTTTTC
20720735 TTATTTTTTTC
1 TT-TTTTTTTC
*
20720746 TTATTTTTTC
1 TTTTTTTTTC
*
20720756 -TTATTTTTC
1 TTTTTTTTTC
20720765 TTTT
1 TTTT
20720769 ATGAAACATT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
9 7 0.16
10 17 0.38
11 21 0.47
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:20720741 original size:9 final size:10
Alignment explanation
Indices: 20720719--20720764 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
20720709 TTTTCTTTTC
20720719 TTTTCCTTAT
1 TTTTCCTTAT
20720729 TTTTCCTTATT
1 TTTTCCTTA-T
*
20720740 TTTTTCTTAT
1 TTTTCCTTAT
*
20720750 TTTTTCTTAT
1 TTTTCCTTAT
20720760 TTTTC
1 TTTTC
20720765 TTTTATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTCCTTAT
Found at i:20720743 original size:21 final size:21
Alignment explanation
Indices: 20720719--20720763 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
20720709 TTTTCTTTTC
20720719 TTTTCCTTATTTTTCCTTATT
1 TTTTCCTTATTTTTCCTTATT
* *
20720740 TTTTTCTTATTTTTTCTTATT
1 TTTTCCTTATTTTTCCTTATT
20720761 TTT
1 TTT
20720764 CTTTTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCCTTATTTTTCCTTATT
Found at i:20720762 original size:8 final size:9
Alignment explanation
Indices: 20720708--20720766 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 9
20720698 CTCCTTTTTC
*
20720708 TTTTTCTTT
1 TTTTTCTTA
20720717 TCTTTTCCTTA
1 T-TTTT-CTTA
20720728 TTTTTCCTTA
1 TTTTT-CTTA
20720738 TTTTTTTCTTA
1 --TTTTTCTTA
20720749 TTTTTTCTTA
1 -TTTTTCTTA
20720759 TTTTTCTT
1 TTTTTCTT
20720767 TTATGAAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
9 9 0.20
10 23 0.51
11 8 0.18
12 5 0.11
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTCTTA
Found at i:20720770 original size:21 final size:21
Alignment explanation
Indices: 20720708--20720770 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
20720698 CTCCTTTTTC
* *
20720708 TTTTTCTTTTCTTTTC-CTTAT
1 TTTTTCTTAT-TTTTCTTTTAT
*
20720729 TTTTCCTTATTTTT-TTCTTAT
1 TTTTTCTTATTTTTCTT-TTAT
20720750 TTTTTCTTATTTTTCTTTTAT
1 TTTTTCTTATTTTTCTTTTAT
20720771 GAAACATTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 4 0.11
21 29 0.83
22 2 0.06
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTCTTATTTTTCTTTTAT
Found at i:20727508 original size:44 final size:44
Alignment explanation
Indices: 20727458--20728387 Score: 662
Period size: 44 Copynumber: 20.6 Consensus size: 44
20727448 TTTGAACCTA
*
20727458 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* ** * * *
20727502 CCCCACTATAACTTCAGGGAGATAAGATTTTTAGCTTCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * *
20727546 TTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * *
20727590 CTCCACTGCAACTTTAGGGAGATAAGCTTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * *
20727634 CTCCACTGTAACTTCAGGGAGATAAGATTTTTAGCTTCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * *
20727678 TTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAACCCG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * * *
20727722 CTCCATTGTAACTTTAGGGAGATGAGGTTTGTAACTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGT-A----T--CTTCAATCTG
* * * *
20727773 TTCCATTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTG
* * * *
20727818 CTCCACTGCAACTTTAGGGAAATAAGATTTGTAGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * ** * *
20727862 ATCCACTGCAACTTCAGGGAGATAAGTTTTAAAACTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* ** *
20727906 CTCTACTGCAACTTCAAAGAGATAAGATTTGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTG
* *
20727951 CTCCACTGCAACTTTAGGGAGATAAGACTTGTATCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * *
20727995 CCCCACTACAACTTCAGGGGGATCCGATTGTAATTTGTAGCCTT-AATCTG
1 CTCCACTGCAACTTCAGGGAGAT---A-AG--ATTTGTA-TCTTCAATCTG
* * * * ** * * *
20728045 TTCCACTGCAACTTTAAGGAAATAAGATTCACTATATTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-TGTATCTTCAATCTG
* * * * * * * *
20728090 CTCCATTGCAACTTTAGGGAGATAAAACTTATAACTTAAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* ** * * *
20728134 C-CTCACTGCAACTTAAAGGG-GATCCGATTTGTATTTTGTAGCCTTGATATG
1 CTC-CACTGCAACTT-CAGGGAGATAAGATTTGTA-TCT-T---C--AATCTG
* * * ** **
20728185 TTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCCGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-TGTATCTTCAATCTG
* * * * *
20728230 CTCCATTGCAACTTCAGGGATATAAGACTTGTAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * * *
20728274 C-CCTACTGTAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTA
1 CTCC-ACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
* * * * *
20728318 CTCTAATACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCTG
* *
20728363 CTCCACTACAACTTTAGGGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAA
20728388 AATTCGTCAT
Statistics
Matches: 686, Mismatches: 167, Indels: 65
0.75 0.18 0.07
Matches are distributed among these distances:
43 3 0.00
44 414 0.60
45 167 0.24
46 2 0.00
47 4 0.01
48 1 0.00
50 33 0.05
51 58 0.08
52 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCTG
Found at i:20728035 original size:272 final size:271
Alignment explanation
Indices: 20727484--20728387 Score: 755
Period size: 272 Copynumber: 3.3 Consensus size: 271
20727474 GGGAGATAAG
* ** ** * * * * * *
20727484 ATTTGTATCTTTAATCTGCCCCACTATAACTTCAGGGAGATAAGATTTTTAGCTTCAATTTGTTC
1 ATTTGTAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTTCTATCTTCAATCTGCTC
* * *
20727549 CACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAACCTGCTCCACTGCAACTTTAGGGAGATA
66 CACTGCAACTTTAGGGAGATAAGATTTGTAGCTTCAACCTGATCCACTGCAACTTCAGGGAGATA
** * * ** * * *
20727614 AGCTTTGTAGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTTTAGCTTCAATTTGT
131 AGCTTTAAAACTTTAATCTGCTCCACTGCAACTTCAAAGAGATAAGATTTCTAGCTTCAATCTGC
* * * ** *
20727679 TCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAACCCGCTCCATTGTAACTTTAGGGAGA
196 TCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCCGCCCCACTACAACTTCAGGGAGA
* *
20727744 TGAGGTTTGTA
261 TGACGATTGTA
* *
20727755 ACTTGTAGCTTTAATCTGTTCCATTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAATCTGCT
1 ATTTGTAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTT-CTATCTTCAATCTGCT
* * *
20727820 CCACTGCAACTTTAGGGAAATAAGATTTGTAGCTTTAATCTGATCCACTGCAACTTCAGGGAGAT
65 CCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTCAACCTGATCCACTGCAACTTCAGGGAGAT
* * * *
20727885 AAGTTTTAAAACTTTAATCTGCTCTACTGCAACTTCAAAGAGATAAGATTTGCTATCTTCAGTCT
130 AAGCTTTAAAACTTTAATCTGCTCCACTGCAACTTCAAAGAGATAAGATTT-CTAGCTTCAATCT
* * * * *
20727950 GCTCCACTGCAACTTTAGGGAGATAAGACTTGTATCTTCAATCTGCCCCACTACAACTTCAGGGG
194 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCCGCCCCACTACAACTTCAGGGA
*
20728015 GAT-CCGATTGTA
259 GATGACGATTGTA
* * * * * *
20728027 ATTTGTAGCCTTAATCTGTTCCACTGCAACTTTAAGGAAATAAGATTCACTATATTTAGTCTGCT
1 ATTTGTAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATT-TCTATCTTCAATCTGCT
* * * * * * * *
20728092 CCATTGCAACTTTAGGGAGATAAAACTTATAACTTAAACCTG-CCTCACTGCAACTTAAAGGGGA
65 CCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTCAACCTGATC-CACTGCAACTT-CA-GGGA
** * ** * * * * * * ** * * *
20728156 TCCGATTTGTATTTTGTAGCCTTGATATGTTCCACCGCAACTTCAGGGAAATAAGATTCACTATC
127 ---GATAAG--CTTTAAAACTTTAATCTGCTCCACTGCAACTTCAAAGAGATAAGATT-TCTAGC
** * * * * * **
20728221 TTCCGTCTGCTCCATTGCAACTTCAGGGATATAAGACTTGTAACTTCAACCTGCCCTACTGTAAC
186 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCCGCCCCACTACAAC
20728286 TTCAGGGAGAT-A--A--G--
251 TTCAGGGAGATGACGATTGTA
* * ** * * * * * * *
20728300 GTTTATAGCTTTAATCTACTCTAATACAACTTCAGGGAGATAAGATTTGCTATCTTCAGTTTGCT
1 ATTTGTAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTT-CTATCTTCAATCTGCT
*
20728365 CCACTACAACTTTAGGGAGATAA
65 CCACTGCAACTTTAGGGAGATAA
20728388 AATTCGTCAT
Statistics
Matches: 513, Mismatches: 107, Indels: 24
0.80 0.17 0.04
Matches are distributed among these distances:
271 40 0.08
272 221 0.43
273 136 0.27
274 4 0.01
275 1 0.00
277 5 0.01
279 106 0.21
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (271 bp):
ATTTGTAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTTCTATCTTCAATCTGCTC
CACTGCAACTTTAGGGAGATAAGATTTGTAGCTTCAACCTGATCCACTGCAACTTCAGGGAGATA
AGCTTTAAAACTTTAATCTGCTCCACTGCAACTTCAAAGAGATAAGATTTCTAGCTTCAATCTGC
TCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCCGCCCCACTACAACTTCAGGGAGA
TGACGATTGTA
Found at i:20728232 original size:412 final size:404
Alignment explanation
Indices: 20727459--20728387 Score: 1027
Period size: 412 Copynumber: 2.3 Consensus size: 404
20727449 TTGAACCTAC
* * * * *
20727459 TCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTTAATCTGCCCCACTATAACTTCAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGATTTATAACTTTAATCTGCTCTACTACAACTTCAGGGAGA
* * * * * *
20727524 TAAGATTT-TTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAACC
66 TAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAGCTTCAACC
* * * * * * *
20727588 TGCTCCACTGCAACTTTAGGGAGATAAGCTTTGTAGCTTTAATCTGCTCCACTGTAACTTCAGGG
131 TGCCCCACTACAACTTCAGGGAGATAAGATTTGTAGCCTTAATCTGCTCCACTGCAACTTCAAGG
* ** * * * * * * * *
20727653 AGATAAGATTTTTAGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAA
196 AAATAAGATTACTAGATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAAACTTATAACTTAAA
* * * * * * * **
20727718 CCCGCTCCATTGTAACTTTAGGGAGATGAGGTTTGTAACTTGTAGCTTTAATCTGTTCCATTGCA
261 CCCGCTCCACTGCAACTTAAGGGAGATCAGATTTGTAACTTGTAGCCTTAATATGTTCCACCGCA
* ** * *
20727783 ACTTTAGGGAAATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTTAGGGAAATAAGATTT
326 ACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGACTT
* * *
20727848 GTAGCTTTAATCTG
391 GTAACTTCAACCTG
* * * **
20727862 ATCCACTGCAACTTCAGGGAGATAAGTTTTAAAACTTTAATCTGCTCTACTGCAACTTCAAAGAG
1 -TCCACTGCAACTTCAGGGAGATAAGATTTATAACTTTAATCTGCTCTACTACAACTTCAGGGAG
* * *
20727927 ATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTATCTTCAAT
65 ATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAGCTTCAAC
* * *
20727992 CTGCCCCACTACAACTTCAGGGGGATCCGATTGTAATTTGTAGCCTTAATCTGTTCCACTGCAAC
130 CTGCCCCACTACAACTTCAGGGAGAT---A-AG--ATTTGTAGCCTTAATCTGCTCCACTGCAAC
* * * * * *
20728057 TTTAAGGAAATAAGATTCACTATATTTAGTCTGCTCCATTGCAACTTTAGGGAGATAAAACTTAT
189 TTCAAGGAAATAAGATT-ACTAGATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAAACTTAT
* * ** *
20728122 AACTTAAACCTGC-CTCACTGCAACTTAAAGGG-GATCCGATTTGTATTTTGTAGCCTTGATATG
253 AACTTAAACCCGCTC-CACTGCAACTT-AAGGGAGATCAGATTTGTAACTTGTAGCCTTAATATG
** *
20728185 TTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCCGTCTGCTCCATTGCAACTTCAGGGA
316 TTCCACCGCAACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCACTGCAACTTCAGGGA
*
20728250 TATAAGACTTGTAACTTCAACCTG
381 AATAAGACTTGTAACTTCAACCTG
* * * * * *
20728274 CCCTACTGTAACTTCAGGGAGATAAGGTTTATAGCTTTAATCTACTCTAATACAACTTCAGGGAG
1 TCC-ACTGCAACTTCAGGGAGATAAGATTTATAACTTTAATCTGCTCTACTACAACTTCAGGGAG
*
20728339 ATAAGATTTGCTATCTTCAGTTTGCTCCACTACAACTTTAGGGAGATAA
65 ATAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAA
20728388 AATTCGTCAT
Statistics
Matches: 430, Mismatches: 84, Indels: 14
0.81 0.16 0.03
Matches are distributed among these distances:
404 63 0.15
405 68 0.16
408 1 0.00
409 1 0.00
411 43 0.10
412 250 0.58
413 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (404 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTATAACTTTAATCTGCTCTACTACAACTTCAGGGAGA
TAAGATTTGCTATCTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAGCTTCAACC
TGCCCCACTACAACTTCAGGGAGATAAGATTTGTAGCCTTAATCTGCTCCACTGCAACTTCAAGG
AAATAAGATTACTAGATTCAATCTGCTCCACTGCAACTTCAGGGAGATAAAACTTATAACTTAAA
CCCGCTCCACTGCAACTTAAGGGAGATCAGATTTGTAACTTGTAGCCTTAATATGTTCCACCGCA
ACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGACTT
GTAACTTCAACCTG
Found at i:20731368 original size:21 final size:23
Alignment explanation
Indices: 20731344--20731386 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20731334 CAACACAACT
20731344 TCTCA-ATT-AGTGAATATCTTG
1 TCTCACATTAAGTGAATATCTTG
*
20731365 TCTCACATTAAGTGAATTTCTT
1 TCTCACATTAAGTGAATATCTT
20731387 ACTGAGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (23 bp):
TCTCACATTAAGTGAATATCTTG
Found at i:20731922 original size:42 final size:42
Alignment explanation
Indices: 20731803--20731928 Score: 180
Period size: 43 Copynumber: 3.0 Consensus size: 42
20731793 GCCCCAAAAG
* *
20731803 TACATTTTGCTAGATTGAGCTTCAGTTGGAATTTTCTCAATC
1 TACATTTTGCTGGATTGAGCTTCAGCTGGAATTTTCTCAATC
* * *
20731845 TACATTTTTGTTGGATTAAGCTTCAGCTAGAATTTTCTCAATC
1 TACA-TTTTGCTGGATTGAGCTTCAGCTGGAATTTTCTCAATC
* *
20731888 TACATTTTACTGGAATGAGCTTCAGCTGGAATTTTCTCAAT
1 TACATTTTGCTGGATTGAGCTTCAGCTGGAATTTTCTCAAT
20731929 TTCAAGAACA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 36 0.49
43 37 0.51
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (42 bp):
TACATTTTGCTGGATTGAGCTTCAGCTGGAATTTTCTCAATC
Found at i:20738780 original size:30 final size:31
Alignment explanation
Indices: 20738741--20738800 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
20738731 AGAGGTGGGA
*
20738741 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
20738772 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
20738801 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:20739038 original size:18 final size:18
Alignment explanation
Indices: 20739015--20739049 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20739005 TAGTTTGATA
20739015 TTCGAGTTATTCGAATTG
1 TTCGAGTTATTCGAATTG
*
20739033 TTCGAGTTATTCTAATT
1 TTCGAGTTATTCGAATT
20739050 TGAAAACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (18 bp):
TTCGAGTTATTCGAATTG
Found at i:20747454 original size:41 final size:41
Alignment explanation
Indices: 20747397--20747544 Score: 183
Period size: 41 Copynumber: 3.6 Consensus size: 41
20747387 TTCCGAATCT
* **
20747397 ATGAAAAGGTTGAAAAGGA-AGTTATTTGAAAAGGATAACAA
1 ATGAAAAGGTTGAAAAGGACA-ATATCCGAAAAGGATAACAA
* *
20747438 ATGAAAAGGTTAAAAAGGACAATATCCGACAAA-GATACCAA
1 ATGAAAAGGTTGAAAAGGACAATATCCGA-AAAGGATAACAA
*
20747479 ATGAAAAGGTTGAAAAGGACAATATCCGAAAAGGATATCAA
1 ATGAAAAGGTTGAAAAGGACAATATCCGAAAAGGATAACAA
* * *
20747520 ATGAATAGGTTGAAAATGACGATAT
1 ATGAAAAGGTTGAAAAGGACAATAT
20747545 TTGAAGAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
40 3 0.03
41 87 0.93
42 4 0.04
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.20
Consensus pattern (41 bp):
ATGAAAAGGTTGAAAAGGACAATATCCGAAAAGGATAACAA
Found at i:20754591 original size:29 final size:29
Alignment explanation
Indices: 20754559--20754618 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
20754549 CTGAAGTAGG
20754559 AAAGTCTTATGGGACTATTTTATGAGTAC
1 AAAGTCTTATGGGACTATTTTATGAGTAC
20754588 AAAGTCTTATGGGACTATTTTATGAGTAC
1 AAAGTCTTATGGGACTATTTTATGAGTAC
20754617 AA
1 AA
20754619 GTATGCAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (29 bp):
AAAGTCTTATGGGACTATTTTATGAGTAC
Found at i:20770584 original size:14 final size:14
Alignment explanation
Indices: 20770565--20770613 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
20770555 TCATTTTTAA
20770565 AATTTTTACATTCT
1 AATTTTTACATTCT
20770579 AATTTTTACATTCT
1 AATTTTTACATTCT
*
20770593 AATTCTTT-TATTCT
1 AATT-TTTACATTCT
20770607 AATTTTT
1 AATTTTT
20770614 TTATTTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 3 0.09
14 27 0.82
15 3 0.09
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTTTTACATTCT
Found at i:20770615 original size:14 final size:14
Alignment explanation
Indices: 20770574--20770618 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
20770564 AAATTTTTAC
**
20770574 ATTCTAATTTTTAC
1 ATTCTAATTTTTTT
*
20770588 ATTCTAATTCTTTT
1 ATTCTAATTTTTTT
20770602 ATTCTAATTTTTTT
1 ATTCTAATTTTTTT
20770616 ATT
1 ATT
20770619 TTCTTCTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTCTAATTTTTTT
Found at i:20774322 original size:15 final size:15
Alignment explanation
Indices: 20774296--20774331 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
20774286 CCCTTTTACC
*
20774296 TTATTT-TTATTTGT
1 TTATTTATTATTTAT
20774310 TTATTTATTATTTAT
1 TTATTTATTATTTAT
20774325 TTATTTA
1 TTATTTA
20774332 GTTTCTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
TTATTTATTATTTAT
Found at i:20774657 original size:3 final size:3
Alignment explanation
Indices: 20774649--20774684 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
20774639 TTTTATTTTC
*
20774649 TAT TAT TAT TAT TAT TAT T-T TAT TAG TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
20774685 CTTCTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20774673 original size:17 final size:17
Alignment explanation
Indices: 20774651--20774684 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20774641 TTATTTTCTA
*
20774651 TTATTATTATTATTATT
1 TTATTAGTATTATTATT
20774668 TTATTAGTATTATTATT
1 TTATTAGTATTATTATT
20774685 CTTCTTTGTA
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:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATTAGTATTATTATT
Found at i:20775870 original size:6 final size:6
Alignment explanation
Indices: 20775859--20775922 Score: 56
Period size: 6 Copynumber: 9.8 Consensus size: 6
20775849 TTTGTTTCTC
* * *
20775859 TTTTTA TTTTTA TTTTTTTA TGTTTA TGTTTA ATTTTA TTTTTA GTTGTTTTA
1 TTTTTA TTTTTA --TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA --T-TTTTA
20775912 TTTTTA TTTTT
1 TTTTTA TTTTT
20775923 TTAGACTTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
6 36 0.73
7 1 0.02
8 7 0.14
9 5 0.10
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:20775920 original size:26 final size:25
Alignment explanation
Indices: 20775844--20775921 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 25
20775834 GGATCAGTGA
*
20775844 TTTTATTTGTTTCTCTTTTTATTTTTAT
1 TTTTA-TTGTTT-TATTTTTA-TTTTAT
* *
20775872 TTTT-TTATGTTTATGTTTAATTTTAT
1 TTTTATTGT-TTTAT-TTTTATTTTAT
20775898 TTTTAGTTGTTTTATTTTTATTTT
1 TTTTA-TTGTTTTATTTTTATTTT
20775922 TTTAGACTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 23 0.56
27 11 0.27
28 7 0.17
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (25 bp):
TTTTATTGTTTTATTTTTATTTTAT
Found at i:20783182 original size:8 final size:8
Alignment explanation
Indices: 20783171--20783201 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
20783161 ATGTATATAT
20783171 ATATTTTA
1 ATATTTTA
20783179 ATA-TTTA
1 ATATTTTA
20783186 ATATTTTA
1 ATATTTTA
20783194 ATATTTTA
1 ATATTTTA
20783202 CTATACCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATATTTTA
Found at i:20783191 original size:15 final size:15
Alignment explanation
Indices: 20783171--20783199 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20783161 ATGTATATAT
20783171 ATATTTTAATATTTA
1 ATATTTTAATATTTA
20783186 ATATTTTAATATTT
1 ATATTTTAATATTT
20783200 TACTATACCC
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTTAATATTTA
Found at i:20789659 original size:18 final size:17
Alignment explanation
Indices: 20789632--20789665 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20789622 ATTAGAATGT
*
20789632 AAAAATTAAATTAAAAC
1 AAAAATTAAAATAAAAC
20789649 AAAAATATAAAATAAAA
1 AAAAAT-TAAAATAAAA
20789666 TAAACAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATTAAAATAAAAC
Found at i:20796174 original size:31 final size:31
Alignment explanation
Indices: 20796115--20796174 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
20796105 TAATATATAA
20796115 AAAATATATAAATATTATTAAATATTAAATT
1 AAAATATATAAATATTATTAAATATTAAATT
* * *
20796146 AAAATAATATAATTTTTTTTAAAT-TTAAA
1 AAAAT-ATATAAATATTATTAAATATTAAA
20796175 AATAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
AAAATATATAAATATTATTAAATATTAAATT
Found at i:20797101 original size:15 final size:16
Alignment explanation
Indices: 20797072--20797105 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
20797062 TTTTTATTTT
*
20797072 TATTTTTAATCAAATA
1 TATTTTTAATAAAATA
20797088 TATTTTT-ATAAAATA
1 TATTTTTAATAAAATA
20797103 TAT
1 TAT
20797106 ATATTTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTTTAATAAAATA
Found at i:20807942 original size:18 final size:20
Alignment explanation
Indices: 20807909--20807945 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
20807899 TAAAATATTG
20807909 AAATTATTTCATGAAATAAA
1 AAATTATTTCATGAAATAAA
20807929 AAATTA-TT-ATGAAATAA
1 AAATTATTTCATGAAATAA
20807946 TATAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (20 bp):
AAATTATTTCATGAAATAAA
Found at i:20813045 original size:18 final size:18
Alignment explanation
Indices: 20813019--20813062 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
20813009 CACAATTTGG
*
20813019 CAAATTAATACAGTTCAC
1 CAAATTAATACAGATCAC
*
20813037 CATATTAATACAGATCAC
1 CAAATTAATACAGATCAC
20813055 CAAATTAA
1 CAAATTAA
20813063 CATAGTTAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.27
Consensus pattern (18 bp):
CAAATTAATACAGATCAC
Found at i:20820164 original size:16 final size:16
Alignment explanation
Indices: 20820143--20820175 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20820133 AAGGTTGTTG
20820143 AACTGAAATAGAGTTT
1 AACTGAAATAGAGTTT
20820159 AACTGAAATAGAGTTT
1 AACTGAAATAGAGTTT
20820175 A
1 A
20820176 CTCTTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (16 bp):
AACTGAAATAGAGTTT
Found at i:20822400 original size:19 final size:19
Alignment explanation
Indices: 20822378--20822520 Score: 117
Period size: 19 Copynumber: 7.4 Consensus size: 19
20822368 ATGCACCTCA
20822378 TGTGCCAATATGCACTTTG
1 TGTGCCAATATGCACTTTG
* *
20822397 TGTGCCAGTATGCGCTTTG
1 TGTGCCAATATGCACTTTG
** *
20822416 TGCACCAGGA-ATGCGCTTTG
1 TGTGCCA--ATATGCACTTTG
* *
20822436 TGTGCCAAGATGCACTTCG
1 TGTGCCAATATGCACTTTG
** *
20822455 TGTGCCAGGATGTACTTTG
1 TGTGCCAATATGCACTTTG
****
20822474 TGTGCCAATATATGTTTTG
1 TGTGCCAATATGCACTTTG
*
20822493 TGTGCCAATAATGCACTTCG
1 TGTGCCAAT-ATGCACTTTG
20822513 TGTGCCAA
1 TGTGCCAA
20822521 GTTGCACATT
Statistics
Matches: 98, Mismatches: 22, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
18 1 0.01
19 69 0.70
20 28 0.29
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.34
Consensus pattern (19 bp):
TGTGCCAATATGCACTTTG
Found at i:20822473 original size:58 final size:57
Alignment explanation
Indices: 20822378--20822519 Score: 151
Period size: 58 Copynumber: 2.5 Consensus size: 57
20822368 ATGCACCTCA
* * * * *
20822378 TGTGCCAATATGCACTTTGTGTGCCAGTATGCGCTTTGTGCACCAGGA-ATGCGCTTTG
1 TGTGCCAAAATGCACTTCGTGTGCCAGGATGCACTTTGTGCACCA--ATATACGCTTTG
* * ** * *
20822436 TGTGCCAAGATGCACTTCGTGTGCCAGGATGTACTTTGTGTGCCAATATATGTTTTG
1 TGTGCCAAAATGCACTTCGTGTGCCAGGATGCACTTTGTGCACCAATATACGCTTTG
20822493 TGTGCCAATAATGCACTTCGTGTGCCA
1 TGTGCCAA-AATGCACTTCGTGTGCCA
20822520 AGTTGCACAT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
56 1 0.01
57 15 0.21
58 55 0.77
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (57 bp):
TGTGCCAAAATGCACTTCGTGTGCCAGGATGCACTTTGTGCACCAATATACGCTTTG
Found at i:20822493 original size:77 final size:77
Alignment explanation
Indices: 20822362--20822536 Score: 179
Period size: 77 Copynumber: 2.3 Consensus size: 77
20822352 CACTTCATAC
* * * * *
20822362 GCCATGATGCACCTCATGTGCCAATATGCACTTTGTGTGCCAGTATGCGCTTTGTGCACCAGGAA
1 GCCAAGATGCACCTCATGTGCCAAGATGCACTTTGTGTGCCAATATACGCTTTGTGCACCAAGAA
* *
20822427 TGCGCTTTGTGT
66 TGCACTTCGTGT
* * * * * * ** *
20822439 GCCAAGATGCACTTCGTGTGCCAGGATGTACTTTGTGTGCCAATATATGTTTTGTGTGCCAATAA
1 GCCAAGATGCACCTCATGTGCCAAGATGCACTTTGTGTGCCAATATACGCTTTGTGCACCAAGAA
20822504 TGCACTTCGTGT
66 TGCACTTCGTGT
* * *
20822516 GCCAAGTTGCACATTATGTGC
1 GCCAAGATGCACCTCATGTGC
20822537 TAGTTACCCT
Statistics
Matches: 78, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (77 bp):
GCCAAGATGCACCTCATGTGCCAAGATGCACTTTGTGTGCCAATATACGCTTTGTGCACCAAGAA
TGCACTTCGTGT
Found at i:20823718 original size:27 final size:27
Alignment explanation
Indices: 20823680--20823736 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
20823670 GGCATTACAT
20823680 GGTTGCTGAAAAGTAAACGTGACCACG
1 GGTTGCTGAAAAGTAAACGTGACCACG
*
20823707 GGTTGCTGAAAAGTAAACGTGATCACG
1 GGTTGCTGAAAAGTAAACGTGACCACG
20823734 GGT
1 GGT
20823737 CATTCATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.21
Consensus pattern (27 bp):
GGTTGCTGAAAAGTAAACGTGACCACG
Found at i:20825701 original size:11 final size:11
Alignment explanation
Indices: 20825687--20825730 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
20825677 AGATAAATAT
20825687 TATTTTATTAA
1 TATTTTATTAA
*
20825698 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
20825711 TATTTTATTAT
1 TATTTTATTAA
20825722 TATTTTATT
1 TATTTTATT
20825731 TAGTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:20825898 original size:13 final size:13
Alignment explanation
Indices: 20825880--20825906 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20825870 AAAAGAATTT
20825880 CCATAGCTACCAA
1 CCATAGCTACCAA
20825893 CCATAGCTACCAA
1 CCATAGCTACCAA
20825906 C
1 C
20825907 AGTGTAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (13 bp):
CCATAGCTACCAA
Found at i:20826227 original size:21 final size:20
Alignment explanation
Indices: 20826189--20826251 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
20826179 ATTCAATTTC
20826189 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATAATATCATT
20826206 TCAATACCACAATAAT-TCATT
1 TCAAT-CCA-AATAATATCATT
*
20826227 T-AATTCAAATAATATCATT
1 TCAATCCAAATAATATCATT
20826246 TGCAAT
1 T-CAAT
20826252 TTCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATAATATCATT
Found at i:20826298 original size:16 final size:18
Alignment explanation
Indices: 20826261--20826298 Score: 55
Period size: 15 Copynumber: 2.3 Consensus size: 18
20826251 TTTCCATTTA
20826261 ATTCATGTACAGTTCAAT
1 ATTCATGTACAGTTCAAT
20826279 -TTCAT-TA-AGTTCAAT
1 ATTCATGTACAGTTCAAT
20826294 ATTCA
1 ATTCA
20826299 ATTCAATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (18 bp):
ATTCATGTACAGTTCAAT
Found at i:20826473 original size:51 final size:50
Alignment explanation
Indices: 20826413--20826651 Score: 234
Period size: 50 Copynumber: 4.7 Consensus size: 50
20826403 ATGTTCGGTT
*
20826413 CACATAGTAGCCTGCACATAGTACTACACACGTGA-TTGAA-ACTATCAGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCT-AACA-T-TCAGGTA
* * * * * * *
20826464 CGCATAGTAGCCTGCACATAGTTCTACAAATGCGACCTATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAACATTCAGGTA
* *
20826514 CACGTAGTAGCCTGCACATAGTACTACACACGTGA-TTGAA-ACTATCAGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCT-AACA-T-TCAGGTA
* * * * * * *
20826565 CGCATAGTAGCCTGCACATAGTTCTACAAATGCGACCTATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAACATTCAGGTA
*
20826615 CACGTAGTAGCCTGCACATAGTACTACACACGTGACC
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC
20826652 ATCACTTTCA
Statistics
Matches: 149, Mismatches: 32, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
49 2 0.01
50 74 0.50
51 69 0.46
52 4 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAACATTCAGGTA
Found at i:20826673 original size:101 final size:101
Alignment explanation
Indices: 20826408--20826649 Score: 466
Period size: 101 Copynumber: 2.4 Consensus size: 101
20826398 CAATGATGTT
* *
20826408 CGGTTCACATAGTAGCCTGCACATAGTACTACACACGTGATTGAAACTATCAGGTACGCATAGTA
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATTGAAACTATCAGGTACGCATAGTA
20826473 GCCTGCACATAGTTCTACAAATGCGACCTATCATTC
66 GCCTGCACATAGTTCTACAAATGCGACCTATCATTC
20826509 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATTGAAACTATCAGGTACGCATAGTA
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATTGAAACTATCAGGTACGCATAGTA
20826574 GCCTGCACATAGTTCTACAAATGCGACCTATCATTC
66 GCCTGCACATAGTTCTACAAATGCGACCTATCATTC
20826610 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA
20826650 CCATCACTTT
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 139 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (101 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATTGAAACTATCAGGTACGCATAGTA
GCCTGCACATAGTTCTACAAATGCGACCTATCATTC
Found at i:20832638 original size:13 final size:13
Alignment explanation
Indices: 20832620--20832657 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
20832610 TGCAAATGAA
20832620 TCATTTCTCATTT
1 TCATTTCTCATTT
20832633 TCATTTCT-ATTT
1 TCATTTCTCATTT
*
20832645 CCATTTC-CATTT
1 TCATTTCTCATTT
20832657 T
1 T
20832658 GAGAAAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 14 0.64
13 8 0.36
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (13 bp):
TCATTTCTCATTT
Found at i:20832709 original size:45 final size:46
Alignment explanation
Indices: 20832658--20832747 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 46
20832648 TTTCCATTTT
* *
20832658 GAGAAAACCACATTTATTTTCAAAT-TATTTCATTTCTCTATTTCG
1 GAGAAAACCACAATCATTTTCAAATGTATTTCATTTCTCTATTTCG
* * *
20832703 GAGAAAACCATAATCATTTTTAAATGTTTTTCATTTCTCTATTTC
1 GAGAAAACCACAATCATTTTCAAATGTATTTCATTTCTCTATTTC
20832748 TATTCATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.46
Consensus pattern (46 bp):
GAGAAAACCACAATCATTTTCAAATGTATTTCATTTCTCTATTTCG
Found at i:20835657 original size:20 final size:20
Alignment explanation
Indices: 20835632--20835672 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20835622 TAAGGTATAT
20835632 GTGTATGAAAACTAGTGAAA
1 GTGTATGAAAACTAGTGAAA
20835652 GTGTATGAAAACTAGTGAAA
1 GTGTATGAAAACTAGTGAAA
20835672 G
1 G
20835673 CATTTGGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.27, T:0.24
Consensus pattern (20 bp):
GTGTATGAAAACTAGTGAAA
Found at i:20836955 original size:18 final size:18
Alignment explanation
Indices: 20836928--20836969 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
20836918 ATACTTTATA
* *
20836928 ATTTTTTTTTGAAGTATT
1 ATTTTATTTTGAAGAATT
*
20836946 ATTTTATTTTTAAGAATT
1 ATTTTATTTTGAAGAATT
20836964 -TTTTAT
1 ATTTTAT
20836970 ATTTTTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (18 bp):
ATTTTATTTTGAAGAATT
Found at i:20837566 original size:22 final size:22
Alignment explanation
Indices: 20837522--20837561 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
20837512 ATAATTTAAA
20837522 ATATAAAATTTTATTAATATGT
1 ATATAAAATTTTATTAATATGT
20837544 ATAT-AAA-TTTATTAATAT
1 ATATAAAATTTTATTAATAT
20837562 ATGTAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 3 0.17
22 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (22 bp):
ATATAAAATTTTATTAATATGT
Found at i:20837697 original size:19 final size:20
Alignment explanation
Indices: 20837659--20837698 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20837649 AAATATTTTT
* *
20837659 AGTAAATTATTTTTTAAAAA
1 AGTAAATCATTTTCTAAAAA
20837679 AGTAAATCATTTTCTAAAAA
1 AGTAAATCATTTTCTAAAAA
20837699 TTATTTTCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (20 bp):
AGTAAATCATTTTCTAAAAA
Found at i:20843426 original size:40 final size:41
Alignment explanation
Indices: 20843373--20843519 Score: 161
Period size: 44 Copynumber: 3.5 Consensus size: 41
20843363 ACTCTACTGT
** * * * * *
20843373 AACTTCAAAGAGATAAGATC-ATTTTGATCCGCTCTACTGC
1 AACTTCAGGGAGATAGGATCTATTTTAATCCGCTCCAATAC
*
20843413 AACTTCAGGGAGATAGGATCTATTACTTCAATCCGCTCCAATAT
1 AACTTCAGGGAGATAGGATCTATT--TT-AATCCGCTCCAATAC
20843457 AACTTCAGGGAGATAGGATCTATTAGTTTAATCCGCTCCAATAC
1 AACTTCAGGGAGATAGGATCTA-T--TTTAATCCGCTCCAATAC
20843501 AACTTCAGGGAGATAGGAT
1 AACTTCAGGGAGATAGGAT
20843520 TATCGGCTTC
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
40 17 0.19
41 3 0.03
43 2 0.02
44 65 0.71
45 3 0.03
47 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (41 bp):
AACTTCAGGGAGATAGGATCTATTTTAATCCGCTCCAATAC
Found at i:20843461 original size:44 final size:44
Alignment explanation
Indices: 20843412--20843559 Score: 190
Period size: 44 Copynumber: 3.4 Consensus size: 44
20843402 CGCTCTACTG
20843412 CAACTTCAGGGAGATAGGATCTATTACTTCAATCCGCTCCAATA
1 CAACTTCAGGGAGATAGGATCTATTACTTCAATCCGCTCCAATA
* * *
20843456 TAACTTCAGGGAGATAGGATCTATTAGTTTAATCCGCTCCAATA
1 CAACTTCAGGGAGATAGGATCTATTACTTCAATCCGCTCCAATA
** ** * *
20843500 CAACTTCAGGGAGATAGGAT-TATCGGCTTCAATCTACTCCACTG
1 CAACTTCAGGGAGATAGGATCTAT-TACTTCAATCCGCTCCAATA
*
20843544 CAACCTCAGGGAGATA
1 CAACTTCAGGGAGATA
20843560 AGATTTGCCA
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 3 0.03
44 87 0.97
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (44 bp):
CAACTTCAGGGAGATAGGATCTATTACTTCAATCCGCTCCAATA
Found at i:20859065 original size:28 final size:27
Alignment explanation
Indices: 20859022--20859078 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
20859012 TAGTTCATGT
20859022 CTTCTCCAACAATCAAACAGTGGGAGGC
1 CTTCTCCAACAATCAAACA-TGGGAGGC
* *
20859050 CTTCTCCAACAGTCAAACATTGGAGGC
1 CTTCTCCAACAATCAAACATGGGAGGC
20859077 CT
1 CT
20859079 CGAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (27 bp):
CTTCTCCAACAATCAAACATGGGAGGC
Found at i:20873984 original size:60 final size:59
Alignment explanation
Indices: 20873867--20873984 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 59
20873857 TGTACTAGTA
*
20873867 GTCACTCAACTATTAGTAAATTTCTTTTTTGACACTCAATTATGAAAAGTTACAAAATG
1 GTCACCCAACTATTAGTAAATTTCTTTTTTGACACTCAATTATGAAAAGTTACAAAATG
* * * *
20873926 GTCACCCAATTATTAGTAAATTTCTTTTTTAGTCACTCAATTATTAAAAGTTATAAAAT
1 GTCACCCAACTATTAGTAAATTTCTTTTTT-GACACTCAATTATGAAAAGTTACAAAAT
20873985 TTTTACTCTA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
59 28 0.53
60 25 0.47
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.40
Consensus pattern (59 bp):
GTCACCCAACTATTAGTAAATTTCTTTTTTGACACTCAATTATGAAAAGTTACAAAATG
Done.