Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 30
Found at i:5545561 original size:31 final size:30
Alignment explanation
Indices: 5545503--5545561 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
5545493 ATCGTTGGTG
*
5545503 CATATGATATGATTTGCACTTGGAGTGCAC
1 CATATGATATGATTTGCACTTGAAGTGCAC
*
5545533 CATATGTTGATGATTTGGCAC-TGAAGTGC
1 CATATGAT-ATGATTT-GCACTTGAAGTGC
5545562 CTAGTGCGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 14 0.56
32 4 0.16
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (30 bp):
CATATGATATGATTTGCACTTGAAGTGCAC
Found at i:5545696 original size:19 final size:19
Alignment explanation
Indices: 5545620--5545695 Score: 98
Period size: 19 Copynumber: 4.0 Consensus size: 19
5545610 ATGCATTGGA
*
5545620 CTATGAATTTGAAAATAAG
1 CTATGAATCTGAAAATAAG
* *
5545639 CTATGAATCTGACAGTAAG
1 CTATGAATCTGAAAATAAG
*
5545658 CTATGAGTCTGAAAATAAG
1 CTATGAATCTGAAAATAAG
* *
5545677 TTATGAATCTGGAAATAAG
1 CTATGAATCTGAAAATAAG
5545696 TACAAATTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (19 bp):
CTATGAATCTGAAAATAAG
Found at i:5547836 original size:4 final size:4
Alignment explanation
Indices: 5547827--5547851 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5547817 ATTGTTTTAC
5547827 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
5547852 GGAGTCCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:5548978 original size:3 final size:3
Alignment explanation
Indices: 5548970--5549043 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
5548960 TCATCCCAAA
5548970 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5549018 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
5549044 GTATATCTTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5549437 original size:23 final size:23
Alignment explanation
Indices: 5549404--5549474 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
5549394 GCTCGTATAA
*
5549404 ATGCACCGAAGTGCCACATAGA-
1 ATGCACTGAAGTGCCACATAGAG
* *
5549426 ATTGCACTGAAGTGTCGCATAGAG
1 A-TGCACTGAAGTGCCACATAGAG
* *
5549450 ATGCAATGAAGTGCCATATA-AG
1 ATGCACTGAAGTGCCACATAGAG
5549472 ATG
1 ATG
5549475 TCCCTAAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 6 0.15
23 33 0.82
24 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.21
Consensus pattern (23 bp):
ATGCACTGAAGTGCCACATAGAG
Found at i:5554444 original size:39 final size:39
Alignment explanation
Indices: 5554346--5554433 Score: 158
Period size: 39 Copynumber: 2.3 Consensus size: 39
5554336 CCCTTTCAGG
5554346 TTTCACTTTAGAATGTTTTTTCAAAACGCCGTTACGAGT
1 TTTCACTTTAGAATGTTTTTTCAAAACGCCGTTACGAGT
* *
5554385 TTTCACTTTAGAATGTTTTTTCAAAGCGTCGTTACGAGT
1 TTTCACTTTAGAATGTTTTTTCAAAACGCCGTTACGAGT
5554424 TTTCACTTTA
1 TTTCACTTTA
5554434 ATTCTTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (39 bp):
TTTCACTTTAGAATGTTTTTTCAAAACGCCGTTACGAGT
Found at i:5554454 original size:11 final size:10
Alignment explanation
Indices: 5554435--5554465 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
5554425 TTCACTTTAA
5554435 TTCTTTTTTT
1 TTCTTTTTTT
5554445 TTCTTTTTTT
1 TTCTTTTTTT
5554455 TTCTTTTTTT
1 TTCTTTTTTT
5554465 T
1 T
5554466 ATAATTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:5556819 original size:14 final size:14
Alignment explanation
Indices: 5556800--5556827 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5556790 AGTTAAAATT
5556800 AGATATTGATAGGC
1 AGATATTGATAGGC
5556814 AGATATTGATAGGC
1 AGATATTGATAGGC
5556828 GTTAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (14 bp):
AGATATTGATAGGC
Found at i:5558744 original size:21 final size:20
Alignment explanation
Indices: 5558658--5558815 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
5558648 AAATGACCAA
**
5558658 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
5558677 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
5558697 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
5558717 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
5558738 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
5558759 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
5558779 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
5558800 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
5558816 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:5558831 original size:40 final size:40
Alignment explanation
Indices: 5558782--5558936 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
5558772 CGATTTTCCA
* ** *
5558782 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
5558822 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
5558862 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
5558902 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
5558937 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:5558844 original size:20 final size:20
Alignment explanation
Indices: 5558782--5558935 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
5558772 CGATTTTCCA
* ** *
5558782 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
5558802 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
5558822 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5558842 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
5558862 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
5558882 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
5558902 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
5558923 AAATCGCAACGCG
1 AAATCGCAACGCG
5558936 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:5559357 original size:33 final size:33
Alignment explanation
Indices: 5559318--5559388 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5559308 TTCACTTAGA
*
5559318 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
5559351 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
5559384 TTTCA
1 TTTCA
5559389 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:5559512 original size:20 final size:20
Alignment explanation
Indices: 5559468--5559577 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
5559458 TGCAGAAGAG
*
5559468 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
5559489 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
5559509 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
5559530 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
5559544 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
5559563 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
5559578 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:5559525 original size:41 final size:38
Alignment explanation
Indices: 5559461--5559577 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
5559451 TTCAATTTGC
* *
5559461 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
5559499 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
5559540 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
5559573 AGAAT
1 AGAAT
5559578 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:5559547 original size:14 final size:14
Alignment explanation
Indices: 5559528--5559584 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5559518 GAGAAATGAA
5559528 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5559542 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5559561 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5559575 AATCGCAACG
1 AATCGCAACG
5559585 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5559560 original size:33 final size:33
Alignment explanation
Indices: 5559520--5559600 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
5559510 CGCAACGAGA
5559520 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
5559553 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
5559586 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
5559601 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:5559641 original size:14 final size:14
Alignment explanation
Indices: 5559622--5559707 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
5559612 ATTTCGCGTA
5559622 GCGATTCTCTCGTT
1 GCGATTCTCTCGTT
*
5559636 GCGATTTTCATTTCGCGTT
1 GCGA--TTC---TCTCGTT
*
5559655 GCGATTCTCTAGTT
1 GCGATTCTCTCGTT
*
5559669 GCGATTTTCATTTCGCGTT
1 GCGA--TTC---TCTCGTT
5559688 GCGATTCTCTCGTT
1 GCGATTCTCTCGTT
5559702 GCGATT
1 GCGATT
5559708 TTCATTTCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
14 25 0.45
16 6 0.11
17 6 0.11
19 19 0.34
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (14 bp):
GCGATTCTCTCGTT
Found at i:5559643 original size:33 final size:33
Alignment explanation
Indices: 5559601--5559715 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
5559591 CAAAATCGCA
* *
5559601 TTGCGATTTTAATTTCGCGTAGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
5559634 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5559667 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5559700 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
5559716 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:5559656 original size:19 final size:19
Alignment explanation
Indices: 5559596--5559693 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
5559586 GAAACCAAAA
* *
5559596 TCGCATTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
5559615 TCGCGTAGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5559629 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5559648 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
5559662 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5559681 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5559694 CTCTCGTTGC
Statistics
Matches: 59, Mismatches: 10, Indels: 20
0.66 0.11 0.22
Matches are distributed among these distances:
14 18 0.31
16 6 0.10
17 5 0.08
19 30 0.51
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5561572 original size:93 final size:93
Alignment explanation
Indices: 5561413--5561788 Score: 709
Period size: 93 Copynumber: 4.1 Consensus size: 93
5561403 TAGATTGCTT
*
5561413 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5561478 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5561506 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
5561571 TTTGTCTTTGTTTTGTCTTTTGGTTTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
5561599 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5561664 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
5561692 AGTAAATTTGTTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5561757 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5561784 AGTAA
1 AGTAA
5561789 TGCAATCCAT
Statistics
Matches: 277, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
92 6 0.02
93 271 0.98
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:5561860 original size:19 final size:19
Alignment explanation
Indices: 5561836--5561933 Score: 84
Period size: 19 Copynumber: 5.4 Consensus size: 19
5561826 TAGTTTACTT
* *
5561836 TCGCAACACGAACTTAAAA
1 TCGCAACGCGAACTCAAAA
5561855 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCG-AACTCAAAA
* *
5561874 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAACTCAAAA
*
5561893 TCGCAA--CG-A--CAGAA
1 TCGCAACGCGAACTCAAAA
5561907 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCG-AACTCAAAA
5561926 TCGCAACG
1 TCGCAACG
5561934 ACAAGATCGC
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.14
16 3 0.05
17 2 0.03
18 3 0.05
19 45 0.69
20 3 0.05
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAACTCAAAA
Found at i:5561914 original size:33 final size:32
Alignment explanation
Indices: 5561871--5561963 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
5561861 CGCGAAACCA
**
5561871 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
5561903 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
5561936 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
5561964 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:5561961 original size:52 final size:51
Alignment explanation
Indices: 5561851--5561963 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 51
5561841 ACACGAACTT
* *
5561851 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAAC-AC
* * *
5561903 AGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGATCGCAACGCGAAAC-C
1 AAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-AT-GAAAAGCGAAACAC
5561955 AAAATCGCA
1 AAAATCGCA
5561964 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
52 41 0.79
53 3 0.06
54 8 0.15
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (51 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAACAC
Found at i:5561963 original size:19 final size:19
Alignment explanation
Indices: 5561851--5561963 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
5561841 ACACGAACTT
5561851 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
5561870 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
5561889 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
5561903 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
5561922 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
5561936 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
5561955 AAAATCGCA
1 AAAATCGCA
5561964 TTGCGATTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 19 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 46 0.60
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:5561981 original size:19 final size:19
Alignment explanation
Indices: 5561959--5562112 Score: 141
Period size: 19 Copynumber: 8.6 Consensus size: 19
5561949 GAAACCAAAA
*
5561959 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5561978 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
5561994 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5562011 TCGCATTGCGA--TTC-TGT
1 TCGCGTTGCGATTTTCAT-T
5562028 T---GTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
5562044 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
5562063 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
5562082 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
5562102 TCGTGTTGCGA
1 TCGCGTTGCGA
5562113 AAGTAAACTA
Statistics
Matches: 114, Mismatches: 8, Indels: 25
0.78 0.05 0.17
Matches are distributed among these distances:
14 14 0.12
16 12 0.11
17 12 0.11
19 64 0.56
20 12 0.11
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5562000 original size:14 final size:14
Alignment explanation
Indices: 5561981--5562037 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 14
5561971 TTTCATTTCG
5561981 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
5561995 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
5562012 CGCATTGCGATTCTGTT
1 CG--TTGCGATTCT-TT
5562029 -GTTGCGATT
1 CGTTGCGATT
5562038 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 16 0.43
16 5 0.14
17 10 0.27
19 6 0.16
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:5562006 original size:33 final size:33
Alignment explanation
Indices: 5561964--5562094 Score: 165
Period size: 33 Copynumber: 3.8 Consensus size: 33
5561954 CAAAATCGCA
5561964 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
5561997 TTGCGATTTTCATTTCGCATTGCGATTCTGTT-G
1 TTGCGATTTTCATTTCGCGTTGCGATTCT-TTCG
*
5562030 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TT-CTTT--CG
**
5562068 TTGCGATTTTGGTTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
5562095 TTAAGTTTCG
Statistics
Matches: 86, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
33 53 0.62
34 2 0.02
35 4 0.05
36 3 0.03
38 24 0.28
ACGTcount: A:0.09, C:0.18, G:0.24, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:5562084 original size:38 final size:39
Alignment explanation
Indices: 5561959--5562112 Score: 145
Period size: 33 Copynumber: 4.3 Consensus size: 39
5561949 GAAACCAAAA
* *
5561959 TCGCATTGCGATTTTCATTTCGCGTTGCGA--TT--CTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTAAGTT
* *
5561994 T--CGTTGCGATTTTCATTTCGCATTGCGATTCT--G-T
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTAAGTT
*
5562028 T---GTTGCGATTTTCATTTCGCGTTGCGATTTT-GGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTAAGTT
**
5562063 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTAAGTT
*
5562102 TCGTGTTGCGA
1 TCGCGTTGCGA
5562113 AAGTAAACTA
Statistics
Matches: 101, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
33 53 0.52
34 3 0.03
35 4 0.04
38 28 0.28
39 13 0.13
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (39 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTAAGTT
Found at i:5564055 original size:14 final size:14
Alignment explanation
Indices: 5564036--5564071 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5564026 ATTGTTTAAT
5564036 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5564050 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5564064 TGATTTGT
1 TGATTTGT
5564072 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5564201 original size:19 final size:19
Alignment explanation
Indices: 5564177--5564274 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
5564167 CAAATTGACT
5564177 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5564196 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5564215 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5564229 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5564248 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
5564268 ATCGCAA
1 ATCGCAA
5564275 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5564306 original size:53 final size:53
Alignment explanation
Indices: 5564177--5564293 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
5564167 CAAATTGACT
5564177 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
5564229 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
5564282 ATCGCAATGCGA
1 ATCGCAATGCGA
5564294 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:5564311 original size:19 final size:19
Alignment explanation
Indices: 5564283--5564529 Score: 317
Period size: 19 Copynumber: 13.7 Consensus size: 19
5564273 AACGGGAGAA
* *
5564283 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
5564302 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
5564318 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5564335 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
5564354 TCGCATTGC-A-ATTC-TC
1 TCGCATTGCGATTTTCATT
5564370 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5564387 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5564406 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5564425 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
5564445 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5564464 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5564483 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
5564501 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
5564517 TCGCATTGCGATT
1 TCGCATTGCGATT
5564530 CTCTCGTTGC
Statistics
Matches: 201, Mismatches: 10, Indels: 34
0.82 0.04 0.14
Matches are distributed among these distances:
14 21 0.10
15 1 0.00
16 16 0.08
17 14 0.07
18 2 0.01
19 112 0.56
20 35 0.17
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5564346 original size:52 final size:52
Alignment explanation
Indices: 5564283--5564543 Score: 325
Period size: 52 Copynumber: 4.9 Consensus size: 52
5564273 AACGGGAGAA
* *
5564283 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
5564335 TCGCATTGCGATTTTCATTTCGCATTGCAATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
5564387 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
5564445 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
5564501 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
5564544 GTAATTTCCG
Statistics
Matches: 196, Mismatches: 7, Indels: 17
0.89 0.03 0.08
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.02
52 78 0.40
53 24 0.12
54 3 0.02
55 3 0.02
56 3 0.02
58 70 0.36
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:5564551 original size:33 final size:33
Alignment explanation
Indices: 5564289--5564543 Score: 194
Period size: 33 Copynumber: 7.2 Consensus size: 33
5564279 AGAATCGCAA
*
5564289 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
5564322 TGCGATTTTCATTTCGCATTGCGATT-T-TCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* * * * *
5564353 TTCGCA-TTGCAATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCG-ATTTTC-ATT-TCGCATTGCGA--TTC-TCTCG--T
*
5564393 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
5564432 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
*
5564470 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
5564504 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
5564537 TGCGATT
1 TGCGATT
5564544 GTAATTTCCG
Statistics
Matches: 191, Mismatches: 16, Indels: 30
0.81 0.07 0.13
Matches are distributed among these distances:
31 9 0.05
32 6 0.03
33 56 0.29
34 14 0.07
35 2 0.01
36 2 0.01
37 4 0.02
38 39 0.20
39 52 0.27
40 7 0.04
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:5566997 original size:24 final size:24
Alignment explanation
Indices: 5566963--5567009 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5566953 CTGAAACATC
5566963 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
5566987 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5567010 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:5567718 original size:20 final size:20
Alignment explanation
Indices: 5567690--5567939 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
5567680 AAATTTCAGT
* *
5567690 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
5567710 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
5567730 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
5567750 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
5567770 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
* *
5567790 GTTACGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
5567810 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
5567830 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
5567850 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
5567870 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* * *
5567890 GTTGCGATTTATGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
5567910 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
5567930 GTTGCGATTT
1 GTTGCGATTT
5567940 TCATATTCGT
Statistics
Matches: 203, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
20 202 1.00
21 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:5567948 original size:20 final size:19
Alignment explanation
Indices: 5567889--5567960 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
5567879 TACGGATACA
*
5567889 CGTTGCGA-TTTATGGATACG
1 CGTTGCGATTTTAT--ATTCG
* *
5567909 CGTTGCGATTTATGTGTTCG
1 CGTTGCGATTT-TATATTCG
5567929 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTT-ATATTCG
*
5567949 TGTTGCGATTTT
1 CGTTGCGATTTT
5567961 GGAAAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 38 0.88
21 2 0.05
22 2 0.05
ACGTcount: A:0.14, C:0.15, G:0.26, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTATATTCG
Found at i:5568996 original size:50 final size:50
Alignment explanation
Indices: 5568919--5569113 Score: 196
Period size: 51 Copynumber: 3.9 Consensus size: 50
5568909 AGATGTACAT
* * *
5568919 ACTTACATCTGTGTAAGTATGTATTAAGTACTAAACTTTTTTATTTTATTA
1 ACTTACACCGGTGTAAGTATGTATTAAGTACTACA-TTTTTTATTTTATTA
* ** * *
5568970 ACTTACACCGGTGT-AGTATGTGTTAAGTGTTACACTTTTTTGTTTTATTC
1 ACTTACACCGGTGTAAGTATGTATTAAGTACTACA-TTTTTTATTTTATTA
* * *
5569020 ACTTACACTGGTGTAAGCATGTATTAAGTGA-TACATTTATTTATTTTATTT
1 ACTTACACCGGTGTAAGTATGTATTAAGT-ACTACATTT-TTTATTTTATTA
* * * * *
5569071 ACTTATACCGGTATAAATATGTGTTAAGTGCTACATTTTTTAT
1 ACTTACACCGGTGTAAGTATGTATTAAGTACTACATTTTTTAT
5569114 AATATGAATT
Statistics
Matches: 119, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
50 51 0.43
51 68 0.57
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (50 bp):
ACTTACACCGGTGTAAGTATGTATTAAGTACTACATTTTTTATTTTATTA
Found at i:5569110 original size:101 final size:101
Alignment explanation
Indices: 5568919--5569111 Score: 259
Period size: 101 Copynumber: 1.9 Consensus size: 101
5568909 AGATGTACAT
* *
5568919 ACTTACATCTGTGTAAGTATGTATTAAGTACTAAACTTTTTTATTTTATTAACTTACACCGGTGT
1 ACTTACATCTGTGTAAGCATGTATTAAGTACTAAACTTTTTTATTTTATTAACTTACACCGGTAT
* *
5568984 AGTATGTGTTAAGTGTTACACTTTTTTGTTTTATTC
66 AATATGTGTTAAGTGCTACACTTTTTTGTTTTATTC
* * *
5569020 ACTTACA-CTGGTGTAAGCATGTATTAAGTGA-TACA-TTTATTTATTTTATTTACTTATACCGG
1 ACTTACATCT-GTGTAAGCATGTATTAAGT-ACTAAACTTT-TTTATTTTATTAACTTACACCGG
5569082 TATAAATATGTGTTAAGTGCTACA-TTTTTT
63 TAT-AATATGTGTTAAGTGCTACACTTTTTT
5569112 ATAATATGAA
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
100 5 0.06
101 57 0.70
102 19 0.23
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.47
Consensus pattern (101 bp):
ACTTACATCTGTGTAAGCATGTATTAAGTACTAAACTTTTTTATTTTATTAACTTACACCGGTAT
AATATGTGTTAAGTGCTACACTTTTTTGTTTTATTC
Found at i:5569701 original size:12 final size:12
Alignment explanation
Indices: 5569686--5569723 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
5569676 GTTATTTAAA
5569686 CGGGTATTGGGC
1 CGGGTATTGGGC
*
5569698 CGGGTATTGGGT
1 CGGGTATTGGGC
5569710 CGGGTATTGGGC
1 CGGGTATTGGGC
5569722 CG
1 CG
5569724 AGAATCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:5569713 original size:24 final size:24
Alignment explanation
Indices: 5569686--5569740 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
5569676 GTTATTTAAA
* * *
5569686 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
5569710 CGGGTATTGGGCCGAGAATCGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
5569734 CGGGTAT
1 CGGGTAT
5569741 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGT
Found at i:5569824 original size:32 final size:32
Alignment explanation
Indices: 5569739--5569840 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 32
5569729 CGGGTCGGGT
* *
5569739 ATATATATATATATATTTAAATTAAATATATAA
1 ATAT-TATATATATATTTAAATTAAATTTATTA
* *
5569772 ATA-TATATTTTTTATTTAAATTAAATTTATTA
1 ATATTATA-TATATATTTAAATTAAATTTATTA
*
5569804 ATATTATATATATATATAAA-TAATTATTT-TTA
1 ATATTATATATATATTTAAATTAA--ATTTATTA
5569836 ATATT
1 ATATT
5569841 TATCGGGTCG
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
31 7 0.12
32 40 0.69
33 11 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
ATATTATATATATATTTAAATTAAATTTATTA
Found at i:5569898 original size:13 final size:13
Alignment explanation
Indices: 5569842--5569885 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
5569832 TTTAATATTT
*
5569842 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
5569854 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
5569867 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
5569880 ATCGGG
1 ATCGGG
5569886 TAATCGGGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.14, C:0.16, G:0.52, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:5569920 original size:6 final size:6
Alignment explanation
Indices: 5569909--5569937 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5569899 GATTACCAAA
5569909 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
1 CCCGTC CCCGTC CCCGTC CCCGTC CCCGT
5569938 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.17, T:0.17
Consensus pattern (6 bp):
CCCGTC
Found at i:5570505 original size:31 final size:31
Alignment explanation
Indices: 5570470--5570536 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
5570460 TAATGTTTGA
* *
5570470 TCACTTTCGTTTTTATTTAATTAAGATGTTG
1 TCACTTTCGTTTTTATTTAATTAAGATATAG
*
5570501 TCACTTTTGTTTTTATTTAATTAAGATATAG
1 TCACTTTCGTTTTTATTTAATTAAGATATAG
5570532 TCACT
1 TCACT
5570537 ATAAGTTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.54
Consensus pattern (31 bp):
TCACTTTCGTTTTTATTTAATTAAGATATAG
Found at i:5571905 original size:52 final size:52
Alignment explanation
Indices: 5571827--5571970 Score: 202
Period size: 51 Copynumber: 2.8 Consensus size: 52
5571817 GAGATGTACA
*
5571827 TACTTACATCGGTGTAAGTATGTGTTAAGTGCTACATCTTTTTTATTTTATT
1 TACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATCTTTTTTATTTTATT
* * *
5571879 TACTTACACCGTTGTAAGTATGTGTTAATTGCTACA-CTTGTTTATTTTATT
1 TACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATCTTTTTTATTTTATT
* * * *
5571930 CACTTACACGGGTGTAAATATGTGTTAAGTGTTACAT-TTTT
1 TACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATCTTTT
5571971 GTAGTATGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
51 47 0.59
52 33 0.41
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.47
Consensus pattern (52 bp):
TACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATCTTTTTTATTTTATT
Found at i:5573810 original size:268 final size:268
Alignment explanation
Indices: 5573333--5573873 Score: 1082
Period size: 268 Copynumber: 2.0 Consensus size: 268
5573323 GATAACCCAA
5573333 AATCCTTTTGAAAGCCTGAAAATGCATGTCAAGTGGTGTCTGCATGAATTGGCGAACTCTATTAA
1 AATCCTTTTGAAAGCCTGAAAATGCATGTCAAGTGGTGTCTGCATGAATTGGCGAACTCTATTAA
5573398 CTGAGTAAGCAATGTCAAGATAATTTACTACAACATATTAAAGAACACCTACTATACTTCGATAC
66 CTGAGTAAGCAATGTCAAGATAATTTACTACAACATATTAAAGAACACCTACTATACTTCGATAC
5573463 TCTGCAATATTAGTTATGAAATCACCATTACGCGCTGACAACTTGCATGTAGAAACCATAGGAGT
131 TCTGCAATATTAGTTATGAAATCACCATTACGCGCTGACAACTTGCATGTAGAAACCATAGGAGT
5573528 TTGAAGTCCTTTTACATCATCAAAACCATATATCTGCAACAAGTCATGAATTTACTTTTGTTGAC
196 TTGAAGTCCTTTTACATCATCAAAACCATATATCTGCAACAAGTCATGAATTTACTTTTGTTGAC
5573593 TCAATATT
261 TCAATATT
5573601 AATCCTTTTGAAAGCCTGAAAATGCATGTCAAGTGGTGTCTGCATGAATTGGCGAACTCTATTAA
1 AATCCTTTTGAAAGCCTGAAAATGCATGTCAAGTGGTGTCTGCATGAATTGGCGAACTCTATTAA
5573666 CTGAGTAAGCAATGTCAAGATAATTTACTACAACATATTAAAGAACACCTACTATACTTCGATAC
66 CTGAGTAAGCAATGTCAAGATAATTTACTACAACATATTAAAGAACACCTACTATACTTCGATAC
5573731 TCTGCAATATTAGTTATGAAATCACCATTACGCGCTGACAACTTGCATGTAGAAACCATAGGAGT
131 TCTGCAATATTAGTTATGAAATCACCATTACGCGCTGACAACTTGCATGTAGAAACCATAGGAGT
5573796 TTGAAGTCCTTTTACATCATCAAAACCATATATCTGCAACAAGTCATGAATTTACTTTTGTTGAC
196 TTGAAGTCCTTTTACATCATCAAAACCATATATCTGCAACAAGTCATGAATTTACTTTTGTTGAC
5573861 TCAATATT
261 TCAATATT
5573869 AATCC
1 AATCC
5573874 ATCAGAATCA
Statistics
Matches: 273, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
268 273 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (268 bp):
AATCCTTTTGAAAGCCTGAAAATGCATGTCAAGTGGTGTCTGCATGAATTGGCGAACTCTATTAA
CTGAGTAAGCAATGTCAAGATAATTTACTACAACATATTAAAGAACACCTACTATACTTCGATAC
TCTGCAATATTAGTTATGAAATCACCATTACGCGCTGACAACTTGCATGTAGAAACCATAGGAGT
TTGAAGTCCTTTTACATCATCAAAACCATATATCTGCAACAAGTCATGAATTTACTTTTGTTGAC
TCAATATT
Found at i:5584077 original size:60 final size:60
Alignment explanation
Indices: 5583968--5584080 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
5583958 TTGAGTTATC
* * **
5583968 ATTTTATAACTTTTAATAGTTGAGAAACTCAATAAAATAATATTATATAATCAAATGATT
1 ATTTTATAACTTTTAATAGTTCAAAAACTCAATAAAATAATACGATATAATCAAATGATT
* *
5584028 ATTTTATAACTTTTAATAG-TCAAAATACTTAAT-AAATCAATACGCTATAATCA
1 ATTTTATAACTTTTAATAGTTCAAAA-ACTCAATAAAAT-AATACGATATAATCA
5584081 TGGGATCATT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 8 0.18
60 37 0.82
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTTCAAAAACTCAATAAAATAATACGATATAATCAAATGATT
Found at i:5585754 original size:14 final size:15
Alignment explanation
Indices: 5585737--5585765 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5585727 GTTTGTTTCA
5585737 TTGAAAA-TGTTTTT
1 TTGAAAAGTGTTTTT
5585751 TTGAAAAGTGTTTTT
1 TTGAAAAGTGTTTTT
5585766 CATAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (15 bp):
TTGAAAAGTGTTTTT
Found at i:5586113 original size:23 final size:24
Alignment explanation
Indices: 5586067--5586119 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
5586057 AGTATTATAT
5586067 TATATTTTAAAAATTATTAATTAA
1 TATATTTTAAAAATTATTAATTAA
* *
5586091 TATATTTTAAATA-TCTTAATTAA
1 TATATTTTAAAAATTATTAATTAA
*
5586114 AATATT
1 TATATT
5586120 ATTAGATTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATTTTAAAAATTATTAATTAA
Found at i:5586204 original size:27 final size:25
Alignment explanation
Indices: 5586181--5586230 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
5586171 ATAATATTAT
5586181 TTTTATGAAATTAATAAATTATATAAA
1 TTTTAT-AAA-TAATAAATTATATAAA
* *
5586208 TTTTATTAATAATATATTATATA
1 TTTTATAAATAATAAATTATATA
5586231 TTAATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 2 0.10
27 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTTATAAATAATAAATTATATAAA
Found at i:5586972 original size:32 final size:31
Alignment explanation
Indices: 5586911--5586972 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 31
5586901 ATTAAATGAA
*
5586911 AATTTTAAAAAATATATTAAAATTCTAAAATT
1 AATTTTAAAAAATATA-TAAAATTATAAAATT
5586943 AATTTTAAAAGAATATA-AAAATTTATAAAA
1 AATTTTAAAA-AATATATAAAA-TTATAAAA
5586973 ATGATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 17 0.63
33 6 0.22
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (31 bp):
AATTTTAAAAAATATATAAAATTATAAAATT
Found at i:5587042 original size:42 final size:43
Alignment explanation
Indices: 5586996--5587102 Score: 112
Period size: 48 Copynumber: 2.4 Consensus size: 43
5586986 TGTCATAAAG
*
5586996 ATCTAAAAAATAATAAAATTTAAT-GGATCAGTTCATATCATT
1 ATCTAAAAAATAAAAAAATTTAATAGGATCAGTTCATATCATT
*
5587038 ATCT-AAACATAAAAAAATTTAATAACAAGGGGATCAGTTCATATCATT
1 ATCTAAAAAATAAAAAAATTTAAT----A--GGATCAGTTCATATCATT
*
5587086 ATCT-AAACATAAAAAAA
1 ATCTAAAAAATAAAAAAA
5587103 ATTTGTCATT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
41 17 0.30
42 4 0.07
48 35 0.62
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.30
Consensus pattern (43 bp):
ATCTAAAAAATAAAAAAATTTAATAGGATCAGTTCATATCATT
Found at i:5592511 original size:24 final size:23
Alignment explanation
Indices: 5592472--5592517 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
5592462 GCTGATTAGC
**
5592472 TGTAACTGTTTTTGGTTAAGTTGT
1 TGTAACTGTTCCTGGTT-AGTTGT
5592496 TGTAACTGTTCCTGGTTAGTTG
1 TGTAACTGTTCCTGGTTAGTTG
5592518 GGCCGTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.15, C:0.09, G:0.26, T:0.50
Consensus pattern (23 bp):
TGTAACTGTTCCTGGTTAGTTGT
Found at i:5594457 original size:15 final size:15
Alignment explanation
Indices: 5594437--5594469 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5594427 TTAGTATCTG
5594437 CTGTTCCACAAGTTT
1 CTGTTCCACAAGTTT
*
5594452 CTGTTCCTCAAGTTT
1 CTGTTCCACAAGTTT
5594467 CTG
1 CTG
5594470 CAGCAACCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.27, G:0.15, T:0.42
Consensus pattern (15 bp):
CTGTTCCACAAGTTT
Found at i:5596196 original size:18 final size:19
Alignment explanation
Indices: 5596169--5596204 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5596159 CATTAACATC
*
5596169 ATCATTTTCACCA-AATAT
1 ATCATCTTCACCACAATAT
5596187 ATCATCTTCACCACAATA
1 ATCATCTTCACCACAATA
5596205 ACTCATCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCATCTTCACCACAATAT
Found at i:5596398 original size:18 final size:18
Alignment explanation
Indices: 5596375--5596433 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
5596365 TCATCACCAT
* *
5596375 CATCACTACCACCTTCAC
1 CATCACCACTACCTTCAC
5596393 CATCACCACTACCTTCAC
1 CATCACCACTACCTTCAC
5596411 CATCACCACTACCTTCAC
1 CATCACCACTACCTTCAC
5596429 CATCA
1 CATCA
5596434 TCATCATCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.29, C:0.49, G:0.00, T:0.22
Consensus pattern (18 bp):
CATCACCACTACCTTCAC
Found at i:5598239 original size:24 final size:23
Alignment explanation
Indices: 5598207--5598252 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
5598197 GCTGATTAGC
*
5598207 TGTAACTGTTTCTGGTTAAGTTGT
1 TGTAACTGTTCCTGGTT-AGTTGT
5598231 TGTAACTGTTCCTGGTTAGTTG
1 TGTAACTGTTCCTGGTTAGTTG
5598253 GGCCGTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.15, C:0.11, G:0.26, T:0.48
Consensus pattern (23 bp):
TGTAACTGTTCCTGGTTAGTTGT
Found at i:5598277 original size:20 final size:20
Alignment explanation
Indices: 5598242--5598291 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
5598232 GTAACTGTTC
5598242 CTGGTTAGTT-GGGCCGTTT
1 CTGGTTAGTTGGGGCCGTTT
5598261 CTGGTTAGTTGGGGCCGTTT
1 CTGGTTAGTTGGGGCCGTTT
5598281 CTGGTTAGTTG
1 CTGGTTAGTTG
5598292 AGCTAGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.06, C:0.14, G:0.38, T:0.42
Consensus pattern (20 bp):
CTGGTTAGTTGGGGCCGTTT
Found at i:5599145 original size:17 final size:19
Alignment explanation
Indices: 5599123--5599163 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
5599113 GTAAATTCTA
*
5599123 TTAATTTGA-TCA-TAATT
1 TTAATTTGATTCATTAAAT
5599140 TTAATTTGATTCATTAAAT
1 TTAATTTGATTCATTAAAT
5599159 TTAAT
1 TTAAT
5599164 CATCTATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 3 0.14
19 9 0.43
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAATTTGATTCATTAAAT
Found at i:5599676 original size:26 final size:26
Alignment explanation
Indices: 5599645--5599700 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
5599635 CGAAACGATT
5599645 TTTTCTTAAAAAGTGAAAAAATGAGA
1 TTTTCTTAAAAAGTGAAAAAATGAGA
*
5599671 TTTTCTTAAAGAGTGAAAAAATGAGA
1 TTTTCTTAAAAAGTGAAAAAATGAGA
5599697 TTTT
1 TTTT
5599701 GAAAACCACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.36
Consensus pattern (26 bp):
TTTTCTTAAAAAGTGAAAAAATGAGA
Found at i:5601685 original size:74 final size:76
Alignment explanation
Indices: 5601607--5601756 Score: 254
Period size: 76 Copynumber: 2.0 Consensus size: 76
5601597 TACAAATTTT
5601607 TTTTTGAATGTTCT-G-GAGAGTTTACAATACGC-CTCTTCTCCTTTTTTTTCTTGTC-GTCCAA
1 TTTTTGAATGTTCTGGAGAGAGTTTACAAT-CGCTCT-TTCTCCTTTTTTTTCTTGTCTGTCCAA
5601668 AAATTCTCTGTCC
64 AAATTCTCTGTCC
5601681 TTTTTGAATGTTCTGGAGAGAGTTTACAATCGCTCTTTCTCCTTTTTTTTCTTGTCTGTCCAAAA
1 TTTTTGAATGTTCTGGAGAGAGTTTACAATCGCTCTTTCTCCTTTTTTTTCTTGTCTGTCCAAAA
5601746 ATTCTCTGTCC
66 ATTCTCTGTCC
5601757 CCCTTCGTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
74 14 0.19
75 24 0.33
76 34 0.47
ACGTcount: A:0.17, C:0.22, G:0.14, T:0.47
Consensus pattern (76 bp):
TTTTTGAATGTTCTGGAGAGAGTTTACAATCGCTCTTTCTCCTTTTTTTTCTTGTCTGTCCAAAA
ATTCTCTGTCC
Found at i:5605231 original size:66 final size:65
Alignment explanation
Indices: 5605125--5605256 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 65
5605115 AGAGCATTGG
5605125 AAACTCAAGTGGGTCAAATTGCTACAATATTGCATGCACGCCCACAAGGCAGTTTGCCTAGTGAT
1 AAACTCAAGTGGGTCAAATTGCTACAATATTGCATGCACGCCCAC-AGGCAGTTTGCCTAGTGAT
5605190 A
65 A
5605191 AAACTCAAGTGGGTCAAATTGCTACAATATTGCATGCACGCCCACAGGCAGTTTGCCTAGTGATA
1 AAACTCAAGTGGGTCAAATTGCTACAATATTGCATGCACGCCCACAGGCAGTTTGCCTAGTGATA
5605256 A
1 A
5605257 TGTAGTCACT
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 21 0.32
66 45 0.68
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (65 bp):
AAACTCAAGTGGGTCAAATTGCTACAATATTGCATGCACGCCCACAGGCAGTTTGCCTAGTGATA
Found at i:5609751 original size:18 final size:17
Alignment explanation
Indices: 5609730--5609777 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
5609720 TAAAAAGAGG
5609730 TTTTTTAAAAAAATTTAT
1 TTTTTTAAAAAAATTT-T
*
5609748 TTTTTGATAAAAATATTTT
1 TTTTT--TAAAAAAATTTT
5609767 TATTTTTAAAA
1 T-TTTTTAAAA
5609778 TTTTAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 10 0.38
19 2 0.08
20 14 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTTTAAAAAAATTTT
Found at i:5613624 original size:40 final size:41
Alignment explanation
Indices: 5613574--5613652 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
5613564 CTCGAACTCC
5613574 AATTTCGCAACACAATTTCTAAATTC-CTAACGCGAATTTGG
1 AATTTCGCAACACAATTTCTAAATTCGC-AACGCGAATTTGG
* * *
5613615 AATTT-GCAACACAGTTTTTAAATTCGCAACTCGAATTT
1 AATTTCGCAACACAATTTCTAAATTCGCAACGCGAATTT
5613653 CCCAAATTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 28 0.82
41 6 0.18
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (41 bp):
AATTTCGCAACACAATTTCTAAATTCGCAACGCGAATTTGG
Found at i:5613643 original size:20 final size:20
Alignment explanation
Indices: 5613615--5613685 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
5613605 GCGAATTTGG
* * *
5613615 AATTTGCAACACAGTTTTTA
1 AATTCGCAACTCAGTTTTCA
* *
5613635 AATTCGCAACTCGAATTTCCCA
1 AATTCGCAACTC-AGTTT-TCA
5613657 AATTCGCAACTCAGTTTTCA
1 AATTCGCAACTCAGTTTTCA
*
5613677 AATTTGCAA
1 AATTCGCAA
5613686 TTTGAATTCG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 20 0.49
21 8 0.20
22 13 0.32
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.34
Consensus pattern (20 bp):
AATTCGCAACTCAGTTTTCA
Found at i:5613864 original size:22 final size:22
Alignment explanation
Indices: 5613839--5613884 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
5613829 TTCGCAACTC
*
5613839 AAATTGGCGCATTCGAGTTGCG
1 AAATTGGCGAATTCGAGTTGCG
5613861 AAATTGGCGAATTCGAGTTGCG
1 AAATTGGCGAATTCGAGTTGCG
5613883 AA
1 AA
5613885 TTTTTTCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (22 bp):
AAATTGGCGAATTCGAGTTGCG
Found at i:5613964 original size:20 final size:20
Alignment explanation
Indices: 5613941--5614000 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
5613931 CGAATTCGAA
5613941 TTGCGAATTTGAAAACTGAG
1 TTGCGAATTTGAAAACTGAG
** *
5613961 TTGCGAATTTTGGAAATTTGTG
1 TTGCGAA-TTT-GAAAACTGAG
*
5613983 TTGCGAATTTGGAAACTG
1 TTGCGAATTTGAAAACTG
5614001 TGTTTTCGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 12 0.38
21 6 0.19
22 14 0.44
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (20 bp):
TTGCGAATTTGAAAACTGAG
Found at i:5614004 original size:20 final size:20
Alignment explanation
Indices: 5613941--5614004 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
5613931 CGAATTCGAA
* *
5613941 TTGCGAATTTGAAAACTGAG
1 TTGCGAATTTGGAAACTGTG
*
5613961 TTGCGAATTTTGGAAATTTGTG
1 TTGCGAA-TTTGGAAA-CTGTG
5613983 TTGCGAATTTGGAAACTGTG
1 TTGCGAATTTGGAAACTGTG
5614003 TT
1 TT
5614005 TTCGAAATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.34
21 15 0.39
22 10 0.26
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGGAAACTGTG
Found at i:5614010 original size:21 final size:21
Alignment explanation
Indices: 5613941--5614016 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
5613931 CGAATTCGAA
* *
5613941 TTGCGAATTTGAAAACTGAG-
1 TTGCGAATTTGGAAACTGTGT
*
5613961 TTGCGAATTTTGGAAA-TTTGT
1 TTGCGAA-TTTGGAAACTGTGT
5613982 GTTGCGAATTTGGAAACTGTGT
1 -TTGCGAATTTGGAAACTGTGT
* *
5614004 TTTCGAAATTGGA
1 TTGCGAATTTGGA
5614017 GTTCGTCTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.20
21 26 0.57
22 11 0.24
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (21 bp):
TTGCGAATTTGGAAACTGTGT
Found at i:5617895 original size:21 final size:21
Alignment explanation
Indices: 5617871--5617911 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5617861 ATATGTTTCG
* *
5617871 CTCCCCCTAAATTTTAATTCT
1 CTCCACCTAAATTTAAATTCT
5617892 CTCCACCTAAATTTAAATTC
1 CTCCACCTAAATTTAAATTC
5617912 ACCCTCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (21 bp):
CTCCACCTAAATTTAAATTCT
Found at i:5624058 original size:46 final size:47
Alignment explanation
Indices: 5623971--5624060 Score: 137
Period size: 46 Copynumber: 1.9 Consensus size: 47
5623961 AGTAGAGCGT
*
5623971 TACCTAAAATGTTATTTTTTTTCTACCGGAAATATTAATATCGGGCGC
1 TACCTAAAATGTTA-TTTTTTTCTACCAGAAATATTAATATCGGGCGC
* *
5624019 TACCTAAAATGTTA-TTTTTTCTACCAGAAATGTTTATATCGG
1 TACCTAAAATGTTATTTTTTTCTACCAGAAATATTAATATCGG
5624061 AAATATTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
46 25 0.64
48 14 0.36
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (47 bp):
TACCTAAAATGTTATTTTTTTCTACCAGAAATATTAATATCGGGCGC
Found at i:5624817 original size:15 final size:15
Alignment explanation
Indices: 5624797--5624825 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5624787 ATTGAGGAAG
5624797 TAAAATGTTAGTTTC
1 TAAAATGTTAGTTTC
5624812 TAAAATGTTAGTTT
1 TAAAATGTTAGTTT
5624826 TTAGATTTCA
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:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (15 bp):
TAAAATGTTAGTTTC
Found at i:5630696 original size:19 final size:18
Alignment explanation
Indices: 5630657--5630704 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
5630647 AAAGAAGAAA
5630657 CATCGATTGCA-AATGGTG
1 CATCGA-TGCATAATGGTG
*
5630675 CATTGATGCATAATGAGTG
1 CATCGATGCATAATG-GTG
5630694 CATCGATGCAT
1 CATCGATGCAT
5630705 CCCTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 4 0.15
18 9 0.35
19 13 0.50
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (18 bp):
CATCGATGCATAATGGTG
Found at i:5630804 original size:20 final size:23
Alignment explanation
Indices: 5630756--5630811 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 23
5630746 GCATGGGTAG
5630756 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTT-AAGAA
*
5630780 TGCATCGATGCAC-TG-T-AGCA
1 TGCATCGATGCACATGTTAAGAA
5630800 TGCATCGATGCA
1 TGCATCGATGCA
5630812 GTTCAAGGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 2 0.06
24 13 0.42
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACATGTTAAGAA
Found at i:5631800 original size:31 final size:31
Alignment explanation
Indices: 5631762--5631857 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
5631752 AGAGTCGAGG
*
5631762 GTTTACCTAGGTTCTTCGGGACCTATGAACA
1 GTTTACCTAGGTTCTTCGGGACCTATGGACA
5631793 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGGGACCTATGGACA
*
5631824 GTTTACCTAGGTTCGTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGGGACCTATGGACA
5631855 GTT
1 GTT
5631858 GTCGAGGTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGGGACCTATGGACA
Found at i:5634949 original size:24 final size:20
Alignment explanation
Indices: 5634934--5634971 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5634924 CACATGTTAA
5634934 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
5634954 AGCATGCATCGATGCACT
1 AGAATGCATCGATGCACT
5634972 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:5635959 original size:31 final size:31
Alignment explanation
Indices: 5635921--5635985 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
5635911 AGAGTCGAGG
5635921 GTTTACCTAGGTTCT-TCGGGACCTATGAACA
1 GTTTACCTAGGTT-TGTCGGGACCTATGAACA
*
5635952 GTTTACCTAGGTTTGTCGGGACCTATGGACA
1 GTTTACCTAGGTTTGTCGGGACCTATGAACA
5635983 GTT
1 GTT
5635986 GCCGAGGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (31 bp):
GTTTACCTAGGTTTGTCGGGACCTATGAACA
Found at i:5636027 original size:29 final size:30
Alignment explanation
Indices: 5635971--5636042 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
5635961 GGTTTGTCGG
* * * *
5635971 GACCTATGGACAGTTGCCGAGGTTCTTTAT
1 GACCTCTGGATAGTTACCGAGGGTCTTTAT
*
5636001 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGGTCTTTAT
5636030 GACCTCTGGATAG
1 GACCTCTGGATAG
5636043 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGGTCTTTAT
Found at i:5638028 original size:25 final size:25
Alignment explanation
Indices: 5637987--5638036 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5637977 TATTTTAAAA
*
5637987 AATTATTTCTAAATTATAATATAAT
1 AATTATTTCAAAATTATAATATAAT
*
5638012 AATT-TTTCAAAATTTATAATTTAAT
1 AATTATTTCAAAA-TTATAATATAAT
5638037 TTCAAACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTATTTCAAAATTATAATATAAT
Found at i:5644934 original size:21 final size:20
Alignment explanation
Indices: 5644909--5644958 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
5644899 TTTCCATCCG
5644909 TTTGTAACTCAAGTAATTACA
1 TTTGTAACTCAAGTAATTA-A
* * *
5644930 TTTGTGACTCTAGTAATTAT
1 TTTGTAACTCAAGTAATTAA
5644950 TTTGTAACT
1 TTTGTAACT
5644959 GGCAGAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (20 bp):
TTTGTAACTCAAGTAATTAA
Found at i:5645437 original size:25 final size:26
Alignment explanation
Indices: 5645395--5645445 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
5645385 GATTTTGAAA
5645395 AATTATTTCTAAAATTATAATATAAT
1 AATTATTTCTAAAATTATAATATAAT
*
5645421 AATT-TTTC-AAAATTTATAATTTAAT
1 AATTATTTCTAAAA-TTATAATATAAT
5645446 TTCAAACTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 15 0.65
26 4 0.17
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (26 bp):
AATTATTTCTAAAATTATAATATAAT
Found at i:5646247 original size:146 final size:146
Alignment explanation
Indices: 5646087--5646383 Score: 522
Period size: 146 Copynumber: 2.0 Consensus size: 146
5646077 AATTTCTTAA
**
5646087 ATTATTTCACATTAATGTTCTAAATTATTTTTTAAAATATTTATTTTAACTTCAAAACATTTAAA
1 ATTATTTCACATTAACATTCTAAATTATTTTTTAAAATATTTATTTTAACTTCAAAACATTTAAA
5646152 AATTAATTGTATTACTTTATTTTAATTTTTAATAAAATTTATTTTCAATATATAATTTGAATTTT
66 AATTAATTGTATTACTTTATTTTAATTTTTAATAAAATTTATTTTCAATATATAATTTGAATTTT
5646217 TAAAATTTATGTGTGG
131 TAAAATTTATGTGTGG
*
5646233 ATTATTTCACATTAACATTCTAAATTATTTTTTAAAATATTTATTTTAACTTCAAAACATTTGAA
1 ATTATTTCACATTAACATTCTAAATTATTTTTTAAAATATTTATTTTAACTTCAAAACATTTAAA
* * * * *
5646298 ATTTAATTGTATTCCTTTATTTTAATTTTTAATAAATTTTATTTTCAATATGTATTTTGAATTTT
66 AATTAATTGTATTACTTTATTTTAATTTTTAATAAAATTTATTTTCAATATATAATTTGAATTTT
5646363 TAAAATTTATGTGTGG
131 TAAAATTTATGTGTGG
5646379 ATTAT
1 ATTAT
5646384 ATATATTACA
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
146 143 1.00
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (146 bp):
ATTATTTCACATTAACATTCTAAATTATTTTTTAAAATATTTATTTTAACTTCAAAACATTTAAA
AATTAATTGTATTACTTTATTTTAATTTTTAATAAAATTTATTTTCAATATATAATTTGAATTTT
TAAAATTTATGTGTGG
Found at i:5646575 original size:25 final size:27
Alignment explanation
Indices: 5646527--5646620 Score: 104
Period size: 27 Copynumber: 3.6 Consensus size: 27
5646517 TACATATATA
5646527 TTAATTTAAAAATACTTTTA-TATTAAC
1 TTAATTTAAAAATA-TTTTATTATTAAC
*
5646554 TT-A-TTAAATATATTTTATTATTAAC
1 TTAATTTAAAAATATTTTATTATTAAC
* * **
5646579 TTAATTTAAAAATATTGTATTTTTATT
1 TTAATTTAAAAATATTTTATTATTAAC
*
5646606 TTCATTTAAAAATAT
1 TTAATTTAAAAATAT
5646621 ATAATTTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
24 5 0.09
25 17 0.30
26 2 0.04
27 33 0.58
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (27 bp):
TTAATTTAAAAATATTTTATTATTAAC
Found at i:5646582 original size:22 final size:22
Alignment explanation
Indices: 5646523--5646582 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 22
5646513 ATTATACATA
*
5646523 TATATTAATTTAAAAATACTTT
1 TATATTAACTTAAAAATACTTT
5646545 TATATTAACTTATTAAATATA-TTT
1 TATATTAACTTA--AAA-ATACTTT
5646569 TATTATTAACTTAA
1 TA-TATTAACTTAA
5646583 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
22 11 0.33
23 1 0.03
24 8 0.24
25 13 0.39
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TATATTAACTTAAAAATACTTT
Found at i:5646633 original size:26 final size:27
Alignment explanation
Indices: 5646582--5646639 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
5646572 TATTAACTTA
* *
5646582 ATTTAAAAATATTGTATTTTTATTTTC
1 ATTTAAAAATATTGAATTTATATTTTC
5646609 ATTTAAAAATATAT-AATTTAT-TTTTC
1 ATTTAAAAATAT-TGAATTTATATTTTC
5646635 ATTTA
1 ATTTA
5646640 TTAAAAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 10 0.36
27 17 0.61
28 1 0.04
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (27 bp):
ATTTAAAAATATTGAATTTATATTTTC
Found at i:5648558 original size:14 final size:14
Alignment explanation
Indices: 5648539--5648589 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
5648529 TGAGTTGAAT
*
5648539 ATAAACGAACAAAC
1 ATAAACGAACGAAC
5648553 ATAAACGAACGAAC
1 ATAAACGAACGAAC
* *
5648567 ATAAATGAATGAAC
1 ATAAACGAACGAAC
5648581 ATAAACGAA
1 ATAAACGAA
5648590 TAAATAATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.61, C:0.16, G:0.12, T:0.12
Consensus pattern (14 bp):
ATAAACGAACGAAC
Found at i:5648590 original size:14 final size:14
Alignment explanation
Indices: 5648534--5648590 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
5648524 GAGATTGAGT
*
5648534 TGAATATAAACGAA
1 TGAACATAAACGAA
**
5648548 CAAACATAAACGAA
1 TGAACATAAACGAA
* *
5648562 CGAACATAAATGAA
1 TGAACATAAACGAA
5648576 TGAACATAAACGAA
1 TGAACATAAACGAA
5648590 T
1 T
5648591 AAATAATCGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (14 bp):
TGAACATAAACGAA
Found at i:5653987 original size:21 final size:21
Alignment explanation
Indices: 5653962--5654029 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
5653952 AACTAACAAT
5653962 CTAACTAATTAATAACAGCAA
1 CTAACTAATTAATAACAGCAA
5653983 CTAACTAATT-ATCAACAGC-A
1 CTAACTAATTAAT-AACAGCAA
* *
5654003 -TAACTAATCAAATAACAGAAAA
1 CTAACTAAT-TAATAACAG-CAA
5654025 CTAAC
1 CTAAC
5654030 ACTCCCCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 8 0.21
20 8 0.21
21 18 0.46
22 1 0.03
23 4 0.10
ACGTcount: A:0.53, C:0.21, G:0.04, T:0.22
Consensus pattern (21 bp):
CTAACTAATTAATAACAGCAA
Found at i:5658555 original size:22 final size:22
Alignment explanation
Indices: 5658529--5658573 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
5658519 GCCTAACTAA
5658529 CAATCTAACTAATTAAT-AACAG
1 CAATCTAACTAATT-ATCAACAG
5658551 CAATCTAACTAATTATCAACAG
1 CAATCTAACTAATTATCAACAG
5658573 C
1 C
5658574 CTAACTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (22 bp):
CAATCTAACTAATTATCAACAG
Found at i:5658579 original size:19 final size:20
Alignment explanation
Indices: 5658533--5658592 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
5658523 AACTAACAAT
5658533 CTAACTAATTAATAACAGCAA
1 CTAACTAATTAATAACAGC-A
5658554 TCTAACTAATT-ATCAACAGC-
1 -CTAACTAATTAAT-AACAGCA
*
5658574 CTAACTAATCAAATAACAG
1 CTAACTAAT-TAATAACAG
5658593 AAAACTAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 9 0.26
20 5 0.15
21 4 0.12
22 16 0.47
ACGTcount: A:0.48, C:0.22, G:0.05, T:0.25
Consensus pattern (20 bp):
CTAACTAATTAATAACAGCA
Found at i:5671264 original size:95 final size:96
Alignment explanation
Indices: 5671093--5671269 Score: 223
Period size: 95 Copynumber: 1.9 Consensus size: 96
5671083 TACCGATGAG
* * *
5671093 GTAGTATCGATACCATGATAAGGGGTATCGATACCAATAAACAACTAATCTAATTTTGGTATCGA
1 GTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCGA
* * *
5671158 TATCGGTAGGGGATATCGATACCCTAGTAAA
66 TACCCGAAGGGGATATCGATACCCTAGTAAA
* * * * *
5671189 GTAGTATCGATACCAT-AGTGA-GGGTATCGATACCAGGCAACATCGAACCTATTTTTGGTATCG
1 GTAGTATCGATACCATGA-TAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCG
*
5671252 ATACCCGAAGGGGGTATC
65 ATACCCGAAGGGGATATC
5671270 AGTACCATAG
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
95 50 0.74
96 18 0.26
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (96 bp):
GTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCGA
TACCCGAAGGGGATATCGATACCCTAGTAAA
Found at i:5671281 original size:95 final size:96
Alignment explanation
Indices: 5671093--5671290 Score: 222
Period size: 95 Copynumber: 2.1 Consensus size: 96
5671083 TACCGATGAG
* * *
5671093 GTAGTATCGATACCATGATAAGGGGTATCGATACCAATAAACAACTAATCTAATTTTGGTATCGA
1 GTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCGA
* * * *
5671158 TATCGGTAGGGGATATCGATACCCTAGTAAA
66 TACCCGAAGGGGATATCGATACCATAGTAAA
* * * * *
5671189 GTAGTATCGATACCAT-AGTGA-GGGTATCGATACCAGGCAACATCGAACCTATTTTTGGTATCG
1 GTAGTATCGATACCATGA-TAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCG
* *
5671252 ATACCCGAAGGGGGTATC-AGTACCATAGTATA
65 ATACCCGAAGGGGATATCGA-TACCATAGTAAA
*
5671284 GAAGTAT
1 GTAGTAT
5671291 TTGTACTAGG
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
94 1 0.01
95 66 0.78
96 18 0.21
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (96 bp):
GTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACAACGAACCTAATTTTGGTATCGA
TACCCGAAGGGGATATCGATACCATAGTAAA
Found at i:5671691 original size:58 final size:58
Alignment explanation
Indices: 5671629--5671802 Score: 206
Period size: 58 Copynumber: 3.0 Consensus size: 58
5671619 ATTACCAAAT
* ** *
5671629 GGCACTTCGTGTGCAAAATTTTAAGAAATTCATACTAAGTGTATGAATTGCCGTATAG
1 GGCACTTCGTGCGCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAG
* * * * *
5671687 GGCACTTCGTGCGCTAACATGATAAGAAATCCATACTAAATGTATGAATTTCTGTATTG
1 GGCACTTCGTGCGC-AAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAG
* * * *
5671746 GGCACCTT-GTGGGCTAAAGGATAAGAAATTCATACTAAGTGTATAAATTTCCGTATA
1 GGCA-CTTCGTGCGCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATA
5671803 AGAAATATAT
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
58 48 0.50
59 45 0.47
60 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (58 bp):
GGCACTTCGTGCGCAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAG
Found at i:5671725 original size:59 final size:58
Alignment explanation
Indices: 5671650--5671802 Score: 209
Period size: 59 Copynumber: 2.6 Consensus size: 58
5671640 TGCAAAATTT
* *
5671650 TAAGAAATTCATACTAAGTGTATGAATTGCCGTATAGGGCA-CTTCGTGCGCTAACATGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTT-GTGCGCTAA-AGGA
* * * * *
5671709 TAAGAAATCCATACTAAATGTATGAATTTCTGTATTGGGCACCTTGTGGGCTAAAGGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTTGTGCGCTAAAGGA
*
5671767 TAAGAAATTCATACTAAGTGTATAAATTTCCGTATA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATA
5671803 AGAAATATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
58 34 0.42
59 44 0.54
60 3 0.04
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (58 bp):
TAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACCTTGTGCGCTAAAGGA
Found at i:5672572 original size:136 final size:136
Alignment explanation
Indices: 5672172--5672563 Score: 615
Period size: 136 Copynumber: 2.9 Consensus size: 136
5672162 AAAGATCAGT
*
5672172 AGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTATGTGCCT
1 AGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
* * *
5672237 TTGAGGCCTAACTGTGCATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTG
66 TTGAGGCCTAACTGTGCATATGACAGAAAGTTGTCAATTATGCTAGTTAGATGAAAGACTAAGTG
5672302 TCTTGG
131 TCTTGG
* * * * *
5672308 AGGACTAACTGTGTATATGATAGAAAGGTGTCATTAATACCAGTTAGATGAAAGGCTTAGTGCCT
1 AGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
* *
5672373 TTGAAGCCTAATTGTGCATATGACAGAAA-TGTGTCAATTATGCTAGTTAGATGAAAGACTAAGT
66 TTGAGGCCTAACTGTGCATATGACAGAAAGT-TGTCAATTATGCTAGTTAGATGAAAGACTAAGT
*
5672437 GTCTTTG
130 GTCTTGG
* *
5672444 AGGCCTAACTGTGCATATGACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
* * *
5672509 TTGAGGCCAAACTGTGCGTATGATAGAAAGTTGTCAATTATGCTAGTTAGATGAA
66 TTGAGGCCTAACTGTGCATATGACAGAAAGTTGTCAATTATGCTAGTTAGATGAA
5672564 CGGTTAAGTA
Statistics
Matches: 230, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
136 229 1.00
137 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (136 bp):
AGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTGAGGCCTAACTGTGCATATGACAGAAAGTTGTCAATTATGCTAGTTAGATGAAAGACTAAGTG
TCTTGG
Found at i:5672581 original size:68 final size:68
Alignment explanation
Indices: 5672172--5672572 Score: 543
Period size: 68 Copynumber: 5.9 Consensus size: 68
5672162 AAAGATCAGT
* * *
5672172 AGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTATGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
5672237 TTG
66 TTG
* * *
5672240 AGGCCTAACTGTGCATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
5672305 TGG
66 TTG
* * * * *
5672308 AGGACTAACTGTGTATATGATAGAAAGGTGTC-ATTAATACCAGTTAGATGAAAGGCTTAGTGCC
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATT-ATGCCAGTTAGATGAAAGGCTAAGTGCC
5672372 TTTG
65 TTTG
* * * * * *
5672376 AAGCCTAATTGTGCATATGACAGAAATGTGTCAATTATGCTAGTTAGATGAAAGACTAAGTGTCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
5672441 TTG
66 TTG
* *
5672444 AGGCCTAACTGTGCATATGACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
5672509 TTG
66 TTG
* * * * * * *
5672512 AGGCCAAACTGTGCGTATGATAGAAAGTTGTCAATTATGCTAGTTAGATGAACGGTTAAGT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
5672573 ACGGTTGAGT
Statistics
Matches: 287, Mismatches: 44, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
67 3 0.01
68 281 0.98
69 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:5672655 original size:81 final size:81
Alignment explanation
Indices: 5672535--5673078 Score: 763
Period size: 81 Copynumber: 6.7 Consensus size: 81
5672525 CGTATGATAG
* *
5672535 AAAGTTGTCAATTATGCTAGTTAGATGAACGGTTAAGTACGGTTGAGTAAAAGAAAAATGGCCTA
1 AAAG-TGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTA
5672600 GCTGTGCAATTGGCAGA
65 GCTGTGCAATTGGCAGA
* *
5672617 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATTGTCTAG
1 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTAG
5672682 CTGTGCAATTGGCAGA
66 CTGTGCAATTGGCAGA
* * * *
5672698 AAGGTGTCGATTATGCTAGTTAGATGAACGGTTATGTACCGTTGAGTAAAAGAAAAATGG-CTAA
1 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCT-A
*
5672762 GCTGTGCAATTGGAAGA
65 GCTGTGCAATTGGCAGA
* * *
5672779 AATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAATAAAAATGGTCTAG
1 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTAG
5672844 CTGTGCAATTGGCAGA
66 CTGTGCAATTGGCAGA
* * * *
5672860 AATGTGTCAATTATGCCAGTTAGATGAACGATGAAGTACCGTTGAGTAAAAGGAAAATGGCCTAG
1 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTAG
* * *
5672925 TTGTGTAATTGGCATA
66 CTGTGCAATTGGCAGA
5672941 AACA-TGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTA
1 AA-AGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTA
* *
5673005 ACTGTGC-ATTGGCGGA
65 GCTGTGCAATTGGCAGA
* * * * * * * *
5673021 GAGGTGTCAATTATACCAGTTAGACGAAC-GTTAAATACTGTTGAATAAGAGAATAAAT
1 AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAA-AAAT
5673079 AAATTTTAAT
Statistics
Matches: 416, Mismatches: 41, Indels: 12
0.89 0.09 0.03
Matches are distributed among these distances:
79 20 0.05
80 37 0.09
81 353 0.85
82 6 0.01
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (81 bp):
AAAGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCCTAG
CTGTGCAATTGGCAGA
Found at i:5673350 original size:13 final size:14
Alignment explanation
Indices: 5673328--5673361 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5673318 ACTAAGAGAT
*
5673328 AAATGGAAAGGAA-
1 AAATGTAAAGGAAG
5673341 AAATGTAAAGGAAG
1 AAATGTAAAGGAAG
5673355 AAATGTA
1 AAATGTA
5673362 TGCTAGGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (14 bp):
AAATGTAAAGGAAG
Found at i:5676970 original size:601 final size:601
Alignment explanation
Indices: 5675878--5677079 Score: 2298
Period size: 601 Copynumber: 2.0 Consensus size: 601
5675868 CCAAATAGTA
5675878 GGTCAGTGACTAATTTGAAAGGAATTAAAAATTTAGAGGACTAAATTGAATAAAAGGTAGAGTAT
1 GGTCAGTGACTAATTTGAAAGGAATTAAAAATTTAGAGGACTAAATTGAATAAAAGGTAGAGTAT
*
5675943 AAGAAATTACTTAAGCAAGACCAATGTGTAAGTAATAGAATAATGAAAGGGCATTTTGGTCCTTT
66 AAGAAATTACTTAAGCAAGACCAATGTGTAAGTAATAGAATAATGAAAGGACATTTTGGTCCTTT
*
5676008 TAAGTGAAATGAATTTTAAAACCCATTGGATTTAGATAAAAAGGGGAAATGAAGTCAAAGAAGCT
131 TAAGTGAAATGAATTTTAAAACCCATTGGATCTAGATAAAAAGGGGAAATGAAGTCAAAGAAGCT
*
5676073 ATTTTTCTTCTTCTTCCTTCTTTCCTGTGGGTTTTGTTATCCTCCATAGCTCCAAAGGTAAACTT
196 ATTTTTCTTCTTCTTCCTTCTTTCCTGTGGGTTTTGCTATCCTCCATAGCTCCAAAGGTAAACTT
* *
5676138 TTATTATTTGATTTTTCCTTTCGATTATGGGTAGTTCTTGTAACCTTAAGTGGTATAAAAGCTTA
261 TTATTATTTGATTTTTCATTTCGATTATGGGTAGTTCTTGTAACCTTAAGTGATATAAAAGCTTA
5676203 AGGAAGGATTAAATGAGGTTAAAACTATGAACTGAAGGAAATATTGTAGATTTTAGAAAATGAGT
326 AGGAAGGATTAAATGAGGTTAAAACTATGAACTGAAGGAAATATTGTAGATTTTAGAAAATGAGT
5676268 TTTGAAATGATATGTTAGTATATTGTTTTTATTGATGGTTAATGGTAGATTTGACTTGTCAAAGA
391 TTTGAAATGATATGTTAGTATATTGTTTTTATTGATGGTTAATGGTAGATTTGACTTGTCAAAGA
* *
5676333 GGTAAATGAGAGAATAGAAGCATTATATAGAATTAAGAATATATTAGAAAAAGTGGTTTGATTCT
456 GGTAAATGAGAGAATAGAAGCATTATATAAAATTAAGAACATATTAGAAAAAGTGGTTTGATTCT
5676398 TAGAATTGAATGTTCATGAATGAGTTTAGATGTTCTAAAAGGCTAAATGAAGGAATGTTAGTATG
521 TAGAATTGAATGTTCATGAATGAGTTTAGATGTTCTAAAAGGCTAAATGAAGGAATGTTAGTATG
5676463 AATAGTTAAGGAAGAG
586 AATAGTTAAGGAAGAG
*
5676479 GGTCAGTGACTAATTTGAAAGGAATTAAAAATTTGGAGGACTAAATTGAATAAAAGGTAGAGTAT
1 GGTCAGTGACTAATTTGAAAGGAATTAAAAATTTAGAGGACTAAATTGAATAAAAGGTAGAGTAT
5676544 AAGAAATTACTTAAG-AAGACCAATGTGTAAGTAATAGAATAATGAAAGGACATTTTGGTCCTTT
66 AAGAAATTACTTAAGCAAGACCAATGTGTAAGTAATAGAATAATGAAAGGACATTTTGGTCCTTT
5676608 TAAGTGAAATGAATTTTAAAACCCATTGGATCTAGATAAAAAGGGGAAATGAAGTCAAAGAAGCT
131 TAAGTGAAATGAATTTTAAAACCCATTGGATCTAGATAAAAAGGGGAAATGAAGTCAAAGAAGCT
5676673 ATTTTTCTTCTTCTTCCTTCTTTCCTGTGGGTTTTGCTATCCTCCATAGCTCCAAAGGTAAACTT
196 ATTTTTCTTCTTCTTCCTTCTTTCCTGTGGGTTTTGCTATCCTCCATAGCTCCAAAGGTAAAC-T
5676738 TTTATTATTTGATTTTTCATTTCGATTATGGGTAGTTCTTGTAACCTTAAGTGATATAAAAGCTT
260 TTTATTATTTGATTTTTCATTTCGATTATGGGTAGTTCTTGTAACCTTAAGTGATATAAAAGCTT
*
5676803 AAGGAAGGATTAAATGAGGTTAAAACTGTGAACTGAAGGAAATATTGTAGATTTTAGAAAATGAG
325 AAGGAAGGATTAAATGAGGTTAAAACTATGAACTGAAGGAAATATTGTAGATTTTAGAAAATGAG
5676868 TTTTGAAATGATATGTTAGTATATTGTTTTTATTGATGGTTAATGGTAGATTTGACTTGTCAAAG
390 TTTTGAAATGATATGTTAGTATATTGTTTTTATTGATGGTTAATGGTAGATTTGACTTGTCAAAG
5676933 AGGTAAATGAGAGAATAGAAGCATTATATAAAATTAAGAACATATTAGAAAAAGTGGTTTGATTC
455 AGGTAAATGAGAGAATAGAAGCATTATATAAAATTAAGAACATATTAGAAAAAGTGGTTTGATTC
*
5676998 TTAGAATTGAATGTTCATGAATGATTTTAGATGTTCTAAAAGGCTAAATGAAGGAATGTTAGTAT
520 TTAGAATTGAATGTTCATGAATGAGTTTAGATGTTCTAAAAGGCTAAATGAAGGAATGTTAGTAT
5677063 GAATAGTTAAGGAAGAG
585 GAATAGTTAAGGAAGAG
5677080 TTTAATAGTA
Statistics
Matches: 590, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
600 174 0.29
601 416 0.71
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.35
Consensus pattern (601 bp):
GGTCAGTGACTAATTTGAAAGGAATTAAAAATTTAGAGGACTAAATTGAATAAAAGGTAGAGTAT
AAGAAATTACTTAAGCAAGACCAATGTGTAAGTAATAGAATAATGAAAGGACATTTTGGTCCTTT
TAAGTGAAATGAATTTTAAAACCCATTGGATCTAGATAAAAAGGGGAAATGAAGTCAAAGAAGCT
ATTTTTCTTCTTCTTCCTTCTTTCCTGTGGGTTTTGCTATCCTCCATAGCTCCAAAGGTAAACTT
TTATTATTTGATTTTTCATTTCGATTATGGGTAGTTCTTGTAACCTTAAGTGATATAAAAGCTTA
AGGAAGGATTAAATGAGGTTAAAACTATGAACTGAAGGAAATATTGTAGATTTTAGAAAATGAGT
TTTGAAATGATATGTTAGTATATTGTTTTTATTGATGGTTAATGGTAGATTTGACTTGTCAAAGA
GGTAAATGAGAGAATAGAAGCATTATATAAAATTAAGAACATATTAGAAAAAGTGGTTTGATTCT
TAGAATTGAATGTTCATGAATGAGTTTAGATGTTCTAAAAGGCTAAATGAAGGAATGTTAGTATG
AATAGTTAAGGAAGAG
Found at i:5677298 original size:21 final size:21
Alignment explanation
Indices: 5677272--5677324 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
5677262 GATGTGGTAT
5677272 TATCGATACCATGATAAGGGG
1 TATCGATACCATGATAAGGGG
5677293 TATCGATACCATGATAAGGGG
1 TATCGATACCATGATAAGGGG
*
5677314 TATAGATACCA
1 TATCGATACCA
5677325 AGAAACATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.25
Consensus pattern (21 bp):
TATCGATACCATGATAAGGGG
Found at i:5677413 original size:20 final size:20
Alignment explanation
Indices: 5677346--5677419 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 20
5677336 ATCTAATTTT
*
5677346 GGTATCGATACCGATAG--GG
1 GGTATCGATACC-ATAGTAAG
* *
5677365 GGTATCGATACCCTAGTAGG
1 GGTATCGATACCATAGTAAG
*
5677385 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGTAAG
5677407 GGTATCGATACCA
1 GGTATCGATACCA
5677420 GGCAACATTG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 3 0.06
19 12 0.26
20 15 0.32
22 17 0.36
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:5677428 original size:95 final size:96
Alignment explanation
Indices: 5677272--5677477 Score: 260
Period size: 95 Copynumber: 2.2 Consensus size: 96
5677262 GATGTGGTAT
5677272 TATCGATACCAT-GATAAGGG--GTATCGATACCATGATAAGGGGTATAGATACCAAGAAACATT
1 TATCGATACCATAG-T-AGGGTAGTATCGATACCATGATAAGGGGTATAGATACCAAGAAACATT
* *
5677334 GAATCTAATTTTGGTATCGATA-CCGATAGGGGG
64 GAACCTAATTTTGGTATCGATACCCGA-AAGGGG
* * * * *
5677367 TATCGATACCCTAGTAGGGTAGTATCGATACCATGGTAA-GGGTATCGATACCAGGCAACATTGA
1 TATCGATACCATAGTAGGGTAGTATCGATACCATGATAAGGGGTATAGATACCAAGAAACATTGA
* *
5677431 ACCTATTTTTGGTATTGATACCCGAAAGGGG
66 ACCTAATTTTGGTATCGATACCCGAAAGGGG
*
5677462 TATCGGTACCATAGTA
1 TATCGATACCATAGTA
5677478 TAGAAGTATC
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
94 4 0.04
95 70 0.73
96 22 0.23
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (96 bp):
TATCGATACCATAGTAGGGTAGTATCGATACCATGATAAGGGGTATAGATACCAAGAAACATTGA
ACCTAATTTTGGTATCGATACCCGAAAGGGG
Found at i:5677507 original size:95 final size:95
Alignment explanation
Indices: 5677292--5677512 Score: 230
Period size: 95 Copynumber: 2.3 Consensus size: 95
5677282 ATGATAAGGG
* * * * *
5677292 GTATCGATACCATGATAAGGGGTATAGATACCAAGAAACATTGAATCTAATTTTGGTATCGATAC
1 GTATCGATACCAGGGTAA-GAGTATCGATACCAAGAAACATTGAACCTAATTTTGGTATCGATAC
* * * *
5677357 CGATAGGGGGTATCGATACCCTAGTAGGGTA
65 CGATAAGGGGTATCGATACCATAGTAGAGAA
* * * * * *
5677388 GTATCGATACCATGGTAAGGGTATCGATACCAGGCAACATTGAACCTATTTTTGGTATTGATACC
1 GTATCGATACCAGGGTAAGAGTATCGATACCAAGAAACATTGAACCTAATTTTGGTATCGATA-C
* *
5677453 CGA-AAGGGGTATCGGTACCATAGTATAGAA
65 CGATAAGGGGTATCGATACCATAGTAGAGAA
* *
5677483 GTATCGGTACTAGGGT-AGTAGTATCGATAC
1 GTATCGATACCAGGGTAAG-AGTATCGATAC
5677513 TATCGAGCCA
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
94 2 0.02
95 83 0.78
96 21 0.20
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (95 bp):
GTATCGATACCAGGGTAAGAGTATCGATACCAAGAAACATTGAACCTAATTTTGGTATCGATACC
GATAAGGGGTATCGATACCATAGTAGAGAA
Found at i:5677922 original size:59 final size:57
Alignment explanation
Indices: 5677855--5678006 Score: 207
Period size: 57 Copynumber: 2.6 Consensus size: 57
5677845 CAAAATTTTG
* *
5677855 AGAAATTCATACTAAGTGTATGAATTTCTGTATAGGGCA-CTTCATGTGCTAACATGATA
1 AGAAATTCATACTAAGTGTATGAATTTCTATAT-GGGCACCTT-ATGTGCTAA-AGGATA
* *
5677914 AGAAATTCATACTAAGTGTATGAATTTCTATATTGGCACCTTGTGTGCTAAAGGATA
1 AGAAATTCATACTAAGTGTATGAATTTCTATATGGGCACCTTATGTGCTAAAGGATA
** *
5677971 AGAAATTCATTTTAAGTGTATGAATTTCCATATGGG
1 AGAAATTCATACTAAGTGTATGAATTTCTATATGGG
5678007 AAATATATGG
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
57 37 0.44
58 12 0.14
59 35 0.42
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.36
Consensus pattern (57 bp):
AGAAATTCATACTAAGTGTATGAATTTCTATATGGGCACCTTATGTGCTAAAGGATA
Found at i:5678462 original size:68 final size:69
Alignment explanation
Indices: 5678378--5678573 Score: 286
Period size: 68 Copynumber: 2.9 Consensus size: 69
5678368 AAATATCAAT
* * *
5678378 AGGCCTAACTGTGCATATTAAAGAAAGGTGTCATTTATGCCAGTTATATGAAAGGCTAAGTG-CC
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGTCC
*
5678442 TTTG
66 TTTC
* * **
5678446 AGGCCTAACTGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTTT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGTCC
5678511 TTTC
66 TTTC
* * *
5678515 AGGCCTAACTGTGCATATGACAGAAAAGTGTCATTGATGCCAGTTAGATGAAAAGCTAA
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAA
5678574 TTGTTGCATA
Statistics
Matches: 114, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
68 57 0.50
69 57 0.50
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (69 bp):
AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGTCC
TTTC
Found at i:5678597 original size:69 final size:69
Alignment explanation
Indices: 5678455--5678597 Score: 157
Period size: 69 Copynumber: 2.1 Consensus size: 69
5678445 GAGGCCTAAC
* *** * *
5678455 TGTGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTTTTTTCAGGCC
1 TGTGCATATGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTTGCATCAGACA
* *
5678520 TAAC
66 GAAA
*
5678524 TGTGCATATGACAGAAAAGTGTC-ATTGATGCCAGTTAGATGAAA-AGCTAATTGTTGCAT-ATG
1 TGTGCATATGACAGAAAAGTGTCAATT-ATGCCAGTTAGATGAAAGA-CTAAGTGTTGCATCA-G
5678586 ACAGAAA
63 ACAGAAA
5678593 TGTGC
1 TGTGC
5678598 CAATTATGGC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
68 5 0.08
69 57 0.92
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (69 bp):
TGTGCATATGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTTGCATCAGACA
GAAA
Found at i:5678683 original size:120 final size:121
Alignment explanation
Indices: 5678457--5678693 Score: 386
Period size: 120 Copynumber: 2.0 Consensus size: 121
5678447 GGCCTAACTG
* *
5678457 TGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGTTTTTTCAGGCCTA
1 TGCATATGACAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGACTAAGTGTTCTTTCAGGCCTA
5678522 ACTGTGCATATGACAGAAAAGTGTCATTGATGCCAGTTAGATGAAAAGCTAATTGT
66 ACTGTGCATATGACAGAAAAGTGTCATTGATGCCAGTTAGATGAAAAGCTAATTGT
* * *
5678578 TGCATATGACAGAAATGTGCCAATTATGGCAGTTAGATGAAAGACTAAGTG-TCTTTGAGGCCTA
1 TGCATATGACAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGACTAAGTGTTCTTTCAGGCCTA
* * * *
5678642 ACTGTGCATATGGCAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAA
66 ACTGTGCATATGACAGAAAAGTGTCATTGATGCCAGTTAGATGAAAAGCTAA
5678694 GTGCCTTTGA
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
120 59 0.55
121 48 0.45
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (121 bp):
TGCATATGACAGAAAGGTGCCAATTATGCCAGTTAGATGAAAGACTAAGTGTTCTTTCAGGCCTA
ACTGTGCATATGACAGAAAAGTGTCATTGATGCCAGTTAGATGAAAAGCTAATTGT
Found at i:5678687 original size:68 final size:69
Alignment explanation
Indices: 5678578--5678772 Score: 234
Period size: 68 Copynumber: 2.9 Consensus size: 69
5678568 AGCTAATTGT
* * * *
5678578 TGCATATGACAGAAATGTGCCAATTATGGCAGTTAGATGAAAGACTAAGTGTCTTTGAGGCCTAA
1 TGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTGAGGCCTAA
5678643 C-TG
66 CGTG
* * *
5678646 TGCATATGGCAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAA
1 TGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTGAGGCCTAA
5678711 CGGTG
66 C-GTG
* ** * * * *
5678716 TG-A-ATGATAGAAAGGAATCAATTATGCCAGTTAGATGAATGATTAAGTACCATTGAG
1 TGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTGAG
5678773 TAAAACAAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
68 103 0.95
69 1 0.01
70 4 0.04
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (69 bp):
TGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTGAGGCCTAA
CGTG
Found at i:5678858 original size:81 final size:81
Alignment explanation
Indices: 5678724--5679235 Score: 657
Period size: 81 Copynumber: 6.3 Consensus size: 81
5678714 TGTGAATGAT
** * * * *
5678724 AGAAAGGAATCAATTATGCCAGTTAGATGAATGATTAAGTACCATTGAGTAAAACAAAAATGGCC
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCC
* *
5678789 TATTTGTGCAATTAGC
66 TAGTTGTGCAATTGGC
* * * * * *
5678805 ATAAATGTGTCAATTATGTCAGTTAGATGAACGGTTAAATACCGTTGATTAAAAGAAAAATAGCC
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCC
*
5678870 TAGCTGTGCAATTGGC
66 TAGTTGTGCAATTGGC
* *
5678886 AGAAAGCTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTTAGTAAAAGAAAAATGGCC
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCC
* *
5678951 TAGCTGTGAAATTGGC
66 TAGTTGTGCAATTGGC
* * * * * * *
5678967 AGGAAGATGTCAATTATGCTAGTTAGATGAACGATTAAGTACCGTTGTGTTAAAGAAAAATGACC
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCC
5679032 TAGTTGTGCAATTGGC
66 TAGTTGTGCAATTGGC
* *
5679048 AGAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGTTGAGTAAAAGAAAAATAGCC
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCC
*
5679113 TAGTTGTGTAATTGGC
66 TAGTTGTGCAATTGGC
* * * * * * *
5679129 ATATAGGTGTTAATTATGCCAGTTAGATTAATGGTTATGTACCATTGAGTAAAAGAAAAATGGCC
1 AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCC
**
5679194 TAAATGTGC-ATTGGC
66 TAGTTGTGCAATTGGC
* *
5679209 ATAAAGGTGTCAATTATGTCAGTTAGA
1 AGAAAGGTGTCAATTATGCCAGTTAGA
5679236 CGATCGTTAA
Statistics
Matches: 374, Mismatches: 57, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
80 30 0.08
81 344 0.92
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (81 bp):
AGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAATGGCC
TAGTTGTGCAATTGGC
Found at i:5679308 original size:2 final size:2
Alignment explanation
Indices: 5679301--5679328 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5679291 TGAAGGGATG
5679301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5679329 TGTACAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5684738 original size:201 final size:197
Alignment explanation
Indices: 5684370--5684768 Score: 746
Period size: 201 Copynumber: 2.0 Consensus size: 197
5684360 AATTTGTTAA
5684370 ATGTTTTGTCGCAGCACCAAAAAGCTCTCGGGTGGAACATGGAAGATTTGAAAGGAATCAACCTA
1 ATGTTTTGTCGCAGCACCAAAAAGCTCTCGGGTGGAACATGGAAGATTTGAAAGGAATCAACCTA
5684435 CAATAAGCATGCACAAGATTAATTTATAAGATAGTCACAATATGTGGAACCACAAAGAAGACTAA
66 CAATAAGCATGCACAAGATTAATTTATAAGATAGTCACAATATGTGGAACCACAAAGAAGACTAA
5684500 ACCCGATCATGAAGAAAATTGTGATAAAGGAAATCATAAAATGGTTG-ATGCTAGAGTAATTTAT
131 ACCCGATCATGAAGAAAATTGTGATAAAGGAAATCATAAAATGGTTGAATGCTAGAGTAATTTAT
5684564 CC
196 CC
5684566 ATGTTTTGTCGCAGCACCAAAAAGCTCTCGGGTGGAACATGGAAGATTTGAAAGGAATCAACCCT
1 ATGTTTTGTCGCAGCACCAAAAAGCTCTCGGGTGGAACATGGAAGATTTGAAAGGAATCAA-CCT
5684631 ACAATAAGCATGCACAAGATTAATTTATAAGATAGTCATAGCAATTATGTGGAACCACAAAGAAG
65 ACAATAAGCATGCACAAGATTAATTTATAAGATAGTC--A-CAA-TATGTGGAACCACAAAGAAG
5684696 ACTAAACCCGATCATGAAGAAAATTGTGATAAAGGAAATCATAAAATGGTTGAATGCTAGAGTAA
126 ACTAAACCCGATCATGAAGAAAATTGTGATAAAGGAAATCATAAAATGGTTGAATGCTAGAGTAA
5684761 TTTATCC
191 TTTATCC
5684768 A
1 A
5684769 ATATCCGATA
Statistics
Matches: 197, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
196 61 0.31
197 40 0.20
199 1 0.01
200 3 0.02
201 72 0.37
202 20 0.10
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (197 bp):
ATGTTTTGTCGCAGCACCAAAAAGCTCTCGGGTGGAACATGGAAGATTTGAAAGGAATCAACCTA
CAATAAGCATGCACAAGATTAATTTATAAGATAGTCACAATATGTGGAACCACAAAGAAGACTAA
ACCCGATCATGAAGAAAATTGTGATAAAGGAAATCATAAAATGGTTGAATGCTAGAGTAATTTAT
CC
Found at i:5689076 original size:23 final size:23
Alignment explanation
Indices: 5689050--5689117 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
5689040 CCACACTATA
5689050 CCAGTTCCCGAACCTGACCAAAG
1 CCAGTTCCCGAACCTGACCAAAG
* * *
5689073 CCAG-TCTC-AA-C--ACTATA-
1 CCAGTTCCCGAACCTGACCAAAG
5689090 CCAGTTCCCGAACCTGACCAAAG
1 CCAGTTCCCGAACCTGACCAAAG
5689113 CCAGT
1 CCAGT
5689118 CTCAAGCAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
17 4 0.12
18 7 0.21
19 2 0.06
20 2 0.06
21 2 0.06
22 7 0.21
23 9 0.27
ACGTcount: A:0.31, C:0.38, G:0.15, T:0.16
Consensus pattern (23 bp):
CCAGTTCCCGAACCTGACCAAAG
Found at i:5689097 original size:40 final size:40
Alignment explanation
Indices: 5689042--5689122 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
5689032 CCGGATCGCC
5689042 ACACTATACCAGTTCCCGAACCTGACCAAAGCCAGTCTCA
1 ACACTATACCAGTTCCCGAACCTGACCAAAGCCAGTCTCA
5689082 ACACTATACCAGTTCCCGAACCTGACCAAAGCCAGTCTCA
1 ACACTATACCAGTTCCCGAACCTGACCAAAGCCAGTCTCA
5689122 A
1 A
5689123 GCAACACCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.37, G:0.12, T:0.17
Consensus pattern (40 bp):
ACACTATACCAGTTCCCGAACCTGACCAAAGCCAGTCTCA
Found at i:5693783 original size:24 final size:24
Alignment explanation
Indices: 5693751--5693798 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5693741 TTCCTAAGTT
5693751 TCTTAATTTCTGATTCACTTAAAA
1 TCTTAATTTCTGATTCACTTAAAA
5693775 TCTTAATTTCTGATTCACTTAAAA
1 TCTTAATTTCTGATTCACTTAAAA
5693799 GGGCTTGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (24 bp):
TCTTAATTTCTGATTCACTTAAAA
Found at i:5694622 original size:14 final size:14
Alignment explanation
Indices: 5694603--5694630 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5694593 AGAATTTTAG
5694603 GACTACTTCGTGAT
1 GACTACTTCGTGAT
5694617 GACTACTTCGTGAT
1 GACTACTTCGTGAT
5694631 ACGTAGTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
GACTACTTCGTGAT
Found at i:5697970 original size:21 final size:20
Alignment explanation
Indices: 5697945--5697994 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
5697935 TTTCCATCCG
5697945 TTTGTAACTCAAGTAATTACA
1 TTTGTAACTCAAGTAATTA-A
* * *
5697966 TTTGTGACTCTAGTAATTAT
1 TTTGTAACTCAAGTAATTAA
5697986 TTTGTAACT
1 TTTGTAACT
5697995 GGCAGAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (20 bp):
TTTGTAACTCAAGTAATTAA
Found at i:5699252 original size:137 final size:139
Alignment explanation
Indices: 5699101--5699383 Score: 423
Period size: 137 Copynumber: 2.0 Consensus size: 139
5699091 AATTTCTTAA
**
5699101 ATTATTTCACATTAATGTTCTAAATTATTTTTTAAAATATTTATTTAACTTCAAAACATTTAAAA
1 ATTATTTCACATTAACATTCTAAATTATTTTTTAAAA-ATTTATTTAACTTCAAAACATTTAAAA
5699166 ATTAA-TGTATAC-TTATTTT-TTTTT-TAAAATTTATTTTCAATATATAATTTGAATTTTTAAA
65 ATTAATTGTA-ACTTTATTTTATTTTTATAAAATTTATTTTCAATATAT-ATTTGAATTTTTAAA
5699227 ATTT-TGTGTGG
128 ATTTATGTGTGG
* *
5699238 ATTATTTCACATTAACATTCTAAATTATTTTTTAAAAATTTATTTAACTTCAAAACATTTGAAAT
1 ATTATTTCACATTAACATTCTAAATTATTTTTTAAAAATTTATTTAACTTCAAAACATTTAAAAA
* * *
5699303 TTAATTGTACCTTTATTTTAATTTTTAATAAATTTTATTTTCAATATGTATTTGAATTTTTAAAA
66 TTAATTGTAACTTTATTTT-ATTTTT-ATAAAATTTATTTTCAATATATATTTGAATTTTTAAAA
5699368 TTTATGTGTGG
129 TTTATGTGTGG
5699379 ATTAT
1 ATTAT
5699384 ATATTACAGA
Statistics
Matches: 132, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
136 31 0.23
137 46 0.35
139 5 0.04
140 19 0.14
141 31 0.23
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.52
Consensus pattern (139 bp):
ATTATTTCACATTAACATTCTAAATTATTTTTTAAAAATTTATTTAACTTCAAAACATTTAAAAA
TTAATTGTAACTTTATTTTATTTTTATAAAATTTATTTTCAATATATATTTGAATTTTTAAAATT
TATGTGTGG
Found at i:5699567 original size:23 final size:23
Alignment explanation
Indices: 5699517--5699573 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
5699507 TAATTATATA
* *
5699517 TATATTAATTTA-AAAATACTTT
1 TATATTAACTTATTAAATACTTT
5699539 TATATTAACTTATTAAATA-TTT
1 TATATTAACTTATTAAATACTTT
5699561 TATTATTAACTTA
1 TA-TATTAACTTA
5699574 ATTTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (23 bp):
TATATTAACTTATTAAATACTTT
Found at i:5701527 original size:14 final size:14
Alignment explanation
Indices: 5701508--5701558 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
5701498 TGAGTTGAAT
*
5701508 ATAAACGAACAAAC
1 ATAAACGAACGAAC
5701522 ATAAACGAACGAAC
1 ATAAACGAACGAAC
* *
5701536 ATAAATGAATGAAC
1 ATAAACGAACGAAC
5701550 ATAAACGAA
1 ATAAACGAA
5701559 TAAATAATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.61, C:0.16, G:0.12, T:0.12
Consensus pattern (14 bp):
ATAAACGAACGAAC
Done.