Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 32 of 51
Found at i:6386001 original size:14 final size:14
Alignment explanation
Indices: 6385982--6386028 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
6385972 GGGAGAATGG
*
6385982 TTAGGGTTTACTGT
1 TTAGGGTTTAGTGT
*
6385996 TTAGGGTTTAGGGT
1 TTAGGGTTTAGTGT
*
6386010 TTAGGGTTTTGTGT
1 TTAGGGTTTAGTGT
6386024 TTAGG
1 TTAGG
6386029 ATTTTCAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.13, C:0.02, G:0.36, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTAGTGT
Found at i:6386004 original size:7 final size:7
Alignment explanation
Indices: 6385982--6386028 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
6385972 GGGAGAATGG
6385982 TTAGGGT
1 TTAGGGT
**
6385989 TTACTGT
1 TTAGGGT
6385996 TTAGGGT
1 TTAGGGT
6386003 TTAGGGT
1 TTAGGGT
6386010 TTAGGGT
1 TTAGGGT
* *
6386017 TTTGTGT
1 TTAGGGT
6386024 TTAGG
1 TTAGG
6386029 ATTTTCAACA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.13, C:0.02, G:0.36, T:0.49
Consensus pattern (7 bp):
TTAGGGT
Found at i:6386374 original size:22 final size:22
Alignment explanation
Indices: 6386348--6386389 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6386338 TTTAAAAAAA
6386348 ATAAAATCGACTAT-TTATAAAT
1 ATAAAATCGACT-TGTTATAAAT
*
6386370 ATAAATTCGACTTGTTATAA
1 ATAAAATCGACTTGTTATAA
6386390 GTTTAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (22 bp):
ATAAAATCGACTTGTTATAAAT
Found at i:6386469 original size:24 final size:24
Alignment explanation
Indices: 6386442--6386533 Score: 105
Period size: 24 Copynumber: 3.8 Consensus size: 24
6386432 TTTAAATATT
6386442 TAATCATTATTAAATAATTATTAG
1 TAATCATTATTAAATAATTATTAG
* *
6386466 TAATCATTTTTAAATTATTATTAG
1 TAATCATTATTAAATAATTATTAG
* * *
6386490 TAATTATTA-TAATTTAATTATTAC
1 TAATCATTATTAA-ATAATTATTAG
* *
6386514 TAATCATTACTAAATCATTA
1 TAATCATTATTAAATAATTA
6386534 ATATTAAATC
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 3 0.05
24 50 0.89
25 3 0.05
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (24 bp):
TAATCATTATTAAATAATTATTAG
Found at i:6386496 original size:13 final size:13
Alignment explanation
Indices: 6386458--6386499 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
6386448 TTATTAAATA
*
6386458 ATTATTAGTAATC
1 ATTATTAGTAATT
*
6386471 ATTTTTA--AATT
1 ATTATTAGTAATT
6386482 ATTATTAGTAATT
1 ATTATTAGTAATT
6386495 ATTAT
1 ATTAT
6386500 AATTTAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 9 0.38
13 15 0.62
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (13 bp):
ATTATTAGTAATT
Found at i:6386562 original size:21 final size:22
Alignment explanation
Indices: 6386522--6386565 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6386512 ACTAATCATT
* *
6386522 ACTAAATCATTAATATTAAATC
1 ACTAAATCAATAATAATAAATC
6386544 ACTAAAT-AATAATAATAAATC
1 ACTAAATCAATAATAATAAATC
6386565 A
1 A
6386566 TTATTAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (22 bp):
ACTAAATCAATAATAATAAATC
Found at i:6387809 original size:2 final size:2
Alignment explanation
Indices: 6387796--6387841 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
6387786 AATAATTAGC
6387796 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6387839 TA T
1 TA T
6387842 TAATTGTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6388578 original size:31 final size:31
Alignment explanation
Indices: 6388542--6388600 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
6388532 AACTTAAAAG
*
6388542 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
6388573 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
6388601 CCATACAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:6388631 original size:21 final size:22
Alignment explanation
Indices: 6388607--6388723 Score: 78
Period size: 22 Copynumber: 5.3 Consensus size: 22
6388597 TAATCCATAC
6388607 AAATACAAT-AATAAAT-TTTTA
1 AAATA-AATCAATAAATATTTTA
**
6388628 AAATAAATCAATCCATATTTTA
1 AAATAAATCAATAAATATTTTA
** *
6388650 AAATAAATCAATCCATATTTAA
1 AAATAAATCAATAAATATTTTA
** **
6388672 AAATAAAAT-TTTCCATATTTTA
1 AAAT-AAATCAATAAATATTTTA
**
6388694 AAATAAATCAATCCATATTTCTA
1 AAATAAATCAATAAATATTT-TA
6388717 ACAATAA
1 A-AATAA
6388724 TTTTTTTCCT
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
20 3 0.04
21 14 0.17
22 53 0.65
23 7 0.09
24 5 0.06
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATAAATCAATAAATATTTTA
Found at i:6388649 original size:22 final size:22
Alignment explanation
Indices: 6388623--6388723 Score: 141
Period size: 22 Copynumber: 4.5 Consensus size: 22
6388613 AATAATAAAT
6388623 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
6388645 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* **
6388667 TTTAAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
6388689 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
6388711 TTTCTAACAATAA
1 TTT-TAA-AATAA
6388724 TTTTTTTCCT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.06
22 53 0.77
23 7 0.10
24 5 0.07
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:6396068 original size:3 final size:3
Alignment explanation
Indices: 6396060--6396087 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6396050 TAAAGAAACC
6396060 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
6396088 GTAGCCGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6407175 original size:2 final size:2
Alignment explanation
Indices: 6407168--6407222 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
6407158 TACCCTAGAT
6407168 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6407210 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
6407223 GGCTGATGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6410587 original size:17 final size:17
Alignment explanation
Indices: 6410565--6410598 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6410555 ATGGTACTGA
*
6410565 ACTCGTATATACTTTGT
1 ACTCGTATATACGTTGT
6410582 ACTCGTATATACGTTGT
1 ACTCGTATATACGTTGT
6410599 CTTTGGTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (17 bp):
ACTCGTATATACGTTGT
Found at i:6412200 original size:20 final size:20
Alignment explanation
Indices: 6412106--6412474 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
6412096 GATTTTCCAT
* ** *
6412106 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
6412126 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
6412146 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6412166 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
6412186 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
6412206 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6412226 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
6412246 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
6412266 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
6412286 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6412306 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
6412326 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6412346 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
6412366 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
6412386 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
6412406 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
6412426 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
6412446 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
6412466 AATCACAAC
1 AATCGCAAC
6412475 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:6413195 original size:24 final size:24
Alignment explanation
Indices: 6413156--6413202 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6413146 AAATTTGGTC
6413156 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
6413180 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
6413203 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:6413394 original size:12 final size:12
Alignment explanation
Indices: 6413377--6413401 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6413367 ATATAATCCT
6413377 GAAGAAGAAAAA
1 GAAGAAGAAAAA
6413389 GAAGAAGAAAAA
1 GAAGAAGAAAAA
6413401 G
1 G
6413402 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:6415704 original size:19 final size:19
Alignment explanation
Indices: 6415682--6415988 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
6415672 CGGAAAATAC
*
6415682 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
6415701 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
6415715 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
6415735 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
6415749 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6415768 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
6415787 AATCGCAA--CG--AT-AG
1 AATCGCAATGCGAAATGAA
6415801 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6415820 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
6415839 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
6415853 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
6415872 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6415891 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6415910 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6415929 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
6415943 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6415962 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6415981 AATCGCAA
1 AATCGCAA
6415989 CGAGATAATC
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 47 0.19
15 3 0.01
16 16 0.06
17 14 0.06
18 4 0.02
19 155 0.62
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:6415797 original size:52 final size:52
Alignment explanation
Indices: 6415710--6415988 Score: 379
Period size: 52 Copynumber: 5.2 Consensus size: 52
6415700 AAATCCCAAC
6415710 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
6415763 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
6415815 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
6415867 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
6415924 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
6415976 ATGAAAATCGCAA
1 ATGAAAATCGCAA
6415989 CGAGATAATC
Statistics
Matches: 215, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
52 163 0.76
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:6415833 original size:71 final size:71
Alignment explanation
Indices: 6415749--6415988 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
6415739 GCAACGAGAG
6415749 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGA
6415814 AATGAA
66 AATGAA
* *
6415820 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-TAGAATCGCAA
6415880 TGCGAAATGAA
61 TGCGAAATGAA
*
6415891 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGA
6415956 AATGAA
66 AATGAA
6415962 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
6415989 CGAGATAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 4 0.03
70 1 0.01
71 122 0.79
72 1 0.01
73 4 0.03
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGA
AATGAA
Found at i:6415934 original size:142 final size:138
Alignment explanation
Indices: 6415682--6416026 Score: 518
Period size: 142 Copynumber: 2.5 Consensus size: 138
6415672 CGGAAAATAC
* * *
6415682 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAAC--GAAAATCGCAATGC-GAAATTAAAATCGCAATGCG
* *
6415745 -AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAA
63 AAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
6415809 TGCGAAATGAA
128 TGCGAAATGAA
6415820 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTAAAATCGCAATGCG-
6415885 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 AA-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
6415950 ATGCGAAATGAA
127 ATGCGAAATGAA
*
6415962 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGA-A-AATCGCAATGCGAAATTA-AAATCGCAATGCG
6416026 A
63 A
6416027 TTTTCATTTC
Statistics
Matches: 191, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 16 0.08
138 37 0.19
139 2 0.01
141 2 0.01
142 129 0.68
143 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (138 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAG
AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC
GAAATGAA
Found at i:6415989 original size:52 final size:55
Alignment explanation
Indices: 6415682--6416010 Score: 332
Period size: 52 Copynumber: 6.3 Consensus size: 55
6415672 CGGAAAATAC
* *
6415682 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-A
*
6415735 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
6415787 AATCGCAA--CG--AT-AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
* *
6415839 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
6415891 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
6415943 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
6415995 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
6416011 TATAAACGCA
Statistics
Matches: 255, Mismatches: 6, Indels: 31
0.87 0.02 0.11
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 180 0.71
53 24 0.09
54 6 0.02
55 6 0.02
57 26 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:6416126 original size:19 final size:19
Alignment explanation
Indices: 6416017--6416118 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
6416007 AAATTATAAA
6416017 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
6416036 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
6416056 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
6416072 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
6416089 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
6416108 CGCATTGCGAT
1 CGCATTGCGAT
6416119 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:6416244 original size:14 final size:14
Alignment explanation
Indices: 6416225--6416261 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6416215 CATCAATTAC
6416225 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
6416239 ACAAATCATCTTTT
1 ACAAATCAACTTTT
6416253 ACAAATCAA
1 ACAAATCAA
6416262 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:6418194 original size:20 final size:20
Alignment explanation
Indices: 6418166--6418228 Score: 85
Period size: 19 Copynumber: 3.2 Consensus size: 20
6418156 TTTACTTTCT
* *
6418166 CAACACGAAACTTAAAATCG
1 CAACGCGAAACTCAAAATCG
6418186 CAACGCGAAAC-CAAAATCG
1 CAACGCGAAACTCAAAATCG
*
6418205 CAACGCGAAA-TGAAAATCG
1 CAACGCGAAACTCAAAATCG
6418224 CAACG
1 CAACG
6418229 ACAGAATCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.10
Consensus pattern (20 bp):
CAACGCGAAACTCAAAATCG
Found at i:6418238 original size:14 final size:14
Alignment explanation
Indices: 6418219--6418275 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6418209 GCGAAATGAA
*
6418219 AATCGCAACGACAG
1 AATCGCAACGAAAG
6418233 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
6418250 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
6418266 AATCGCAACG
1 AATCGCAACG
6418276 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:6418246 original size:33 final size:33
Alignment explanation
Indices: 6418200--6418292 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
6418190 GCGAAACCAA
*
6418200 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
6418233 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
6418266 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
6418293 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:6418257 original size:19 final size:19
Alignment explanation
Indices: 6418179--6418297 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
6418169 CACGAAACTT
**
6418179 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
6418198 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
6418217 AAAATCGCAA--CGACA-G
1 AAAATCGCAACGCGAAATG
*
6418233 --AATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
6418250 AAAATCGCAA--CGAAA-G
1 AAAATCGCAACGCGAAATG
6418266 --AATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
6418283 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
6418298 TTTTGGTTTC
Statistics
Matches: 85, Mismatches: 5, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
14 16 0.19
16 11 0.13
17 11 0.13
19 47 0.55
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:6418315 original size:19 final size:19
Alignment explanation
Indices: 6418293--6418421 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
6418283 AAAATCGCAA
6418293 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
6418312 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
6418326 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
6418345 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
6418359 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
6418378 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
6418397 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
6418417 TGCGA
1 TGCGA
6418422 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:6418335 original size:33 final size:33
Alignment explanation
Indices: 6418293--6418384 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
6418283 AAAATCGCAA
6418293 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
6418326 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
6418359 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
6418385 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:6418624 original size:93 final size:93
Alignment explanation
Indices: 6418465--6419030 Score: 1107
Period size: 93 Copynumber: 6.1 Consensus size: 93
6418455 TTGAATGGAT
6418465 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6418530 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6418558 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
6418623 AGTTTAGCAGAATTGGTAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6418651 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6418716 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6418744 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6418809 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6418837 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
6418901 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6418929 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
6418994 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
6419022 AAATTTACT
1 AAATTTACT
6419031 AAGCAATCTA
Statistics
Matches: 469, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
92 92 0.20
93 377 0.80
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:6420754 original size:14 final size:14
Alignment explanation
Indices: 6420735--6420824 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
6420725 TTGAAATGAA
6420735 AATCGCAACGAGAG
1 AATCGCAACGAGAG
6420749 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
6420766 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
6420782 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
6420801 AATCGCAACGAGAG
1 AATCGCAACGAGAG
6420815 AATCGCAACG
1 AATCGCAACG
6420825 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:6420772 original size:33 final size:33
Alignment explanation
Indices: 6420727--6420841 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
6420717 TCTTTTGGTT
6420727 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
6420760 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6420793 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6420826 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
6420842 TGCGATTTTG
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:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:6420773 original size:19 final size:18
Alignment explanation
Indices: 6420734--6420846 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
6420724 GTTGAAATGA
6420734 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
6420749 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
6420766 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
6420782 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
6420799 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
6420815 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
6420832 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
6420847 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:6420877 original size:14 final size:14
Alignment explanation
Indices: 6420858--6420912 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
6420848 TTTGGTTTCG
6420858 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6420872 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
6420891 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6420905 CGTTGCGA
1 CGTTGCGA
6420913 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6420890 original size:33 final size:33
Alignment explanation
Indices: 6420842--6420912 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
6420832 AAAATCGCAA
**
6420842 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
6420875 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
6420908 TGCGA
1 TGCGA
6420913 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:6420920 original size:33 final size:33
Alignment explanation
Indices: 6420853--6420934 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
6420843 GCGATTTTGG
***
6420853 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
6420886 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
6420919 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
6420935 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:6420939 original size:20 final size:20
Alignment explanation
Indices: 6420865--6420953 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
6420855 TCGCGTTGCG
6420865 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
6420885 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
6420898 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
6420918 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
6420938 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
6420954 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:6421075 original size:33 final size:33
Alignment explanation
Indices: 6421033--6421103 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
6421023 AATACTAACT
*
6421033 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
6421066 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
6421099 TGAAA
1 TGAAA
6421104 TCTAAGTGAA
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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:6421337 original size:22 final size:22
Alignment explanation
Indices: 6421285--6421339 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
6421275 TGGTTGTGAG
**
6421285 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
6421307 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
6421329 GGATTTCTTCG
1 GGATTTCTTCG
6421340 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:6421510 original size:20 final size:20
Alignment explanation
Indices: 6421485--6421677 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
6421475 CTTTAAATAT
6421485 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
6421505 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
6421527 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6421546 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
6421566 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
6421586 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6421606 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
6421626 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
6421646 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
6421666 CGCGTTGCGATT
1 CGCGTTGCGATT
6421678 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:6421672 original size:60 final size:60
Alignment explanation
Indices: 6421485--6421677 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
6421475 CTTTAAATAT
**
6421485 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
6421546 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
6421606 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
6421666 CGCGTTGCGATT
1 CGCGTTGCGATT
6421678 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:6421758 original size:20 final size:20
Alignment explanation
Indices: 6421733--6421782 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
6421723 AAGAATCGCG
*
6421733 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
6421753 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
6421773 TTGCGATTCT
1 TTGCGATTCT
6421783 AGGGATCGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:6423781 original size:19 final size:19
Alignment explanation
Indices: 6423733--6423773 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
6423723 TTGATCTCCC
6423733 TCTCATCGTTGTCAACGCT
1 TCTCATCGTTGTCAACGCT
6423752 TCTCATCGTTGTCAACGCT
1 TCTCATCGTTGTCAACGCT
6423771 TCT
1 TCT
6423774 GCTTGTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.15, C:0.32, G:0.15, T:0.39
Consensus pattern (19 bp):
TCTCATCGTTGTCAACGCT
Found at i:6428492 original size:78 final size:80
Alignment explanation
Indices: 6428363--6428872 Score: 310
Period size: 83 Copynumber: 6.2 Consensus size: 80
6428353 AGCTGAATGA
* * *
6428363 AATCGAACTCGAAGGTCTTTGATGACAGATAACCCTTCTTGCCTTGAGTTATGTTGTAAATTTGA
1 AATCGAACTTGAAGGTCTTTGTTGACAGATAA-CCTTCTAGCCTTGAGTTATGTTGTAAATTTGA
6428428 TATGCC-T-A-AGTGT
65 TATGCCTTGAGAGTGT
*
6428441 AATCGAACTTGAAGGTCTTTGTTGACAGATAACTCTTCTAGCCTTGAGTTATGTTG-CAA-TTGA
1 AATCGAACTTGAAGGTCTTTGTTGACAGATAAC-CTTCTAGCCTTGAGTTATGTTGTAAATTTGA
6428504 TATGCCTTTGAGCTGAGTGT
65 TATGCC-TTGA---GAGTGT
* ** *
6428524 AGTTAAACTTGAAGGTCTTTGTCGGA-AGATAACCATTCTAGCCTTGAGTTATGTTGTAAA--TG
1 AATCGAACTTGAAGGTCTTTGT-TGACAGATAACC-TTCTAGCCTTGAGTTATGTTGTAAATTTG
* *
6428586 ATGTGCCTTGAAGCTGAGCGT
64 ATATGCCTTG-A---GAGTGT
* * ** * * * * *
6428607 AGTCTAACTCAAAAGTCTTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAA--TGA
1 AATCGAACTTGAAGGTCTTTGTTGACAGATAA-CCTTCTAGCCTTGAGTTATGTTGTAAATTTGA
* *
6428670 TGTGCCTTGGAGCTGAGCGT
65 TATGCCTT-GA---GAGTGT
** * * * ** * **
6428690 GGTCGAACTCGATGGTCTTTGGTTGGCAGATAACCCTTCTTTCCTTGAGTTATGCTACAAA--TG
1 AATCGAACTTGAAGGTCTTT-GTTGACAGATAA-CCTTCTAGCCTTGAGTTATGTTGTAAATTTG
*
6428753 ATGTGCCTTTGAGCTGAGTGT
64 ATATGCC-TTGA---GAGTGT
* * * * **
6428774 AATCGAACTCGAAGGTCTTGGTTGGCAAATAACTCTTCTAGCCTTGAGTTATGCCGTAAA--TGA
1 AATCGAACTTGAAGGTCTTTGTTGACAGATAAC-CTTCTAGCCTTGAGTTATGTTGTAAATTTGA
*
6428837 TGTGCCTTTGAGCTGAGTGT
65 TATGCC-TTGA---GAGTGT
*
6428857 AATCGAACTAGAAGGT
1 AATCGAACTTGAAGGT
6428873 TTTTTTATTA
Statistics
Matches: 371, Mismatches: 43, Indels: 31
0.83 0.10 0.07
Matches are distributed among these distances:
76 10 0.03
77 3 0.01
78 52 0.14
79 1 0.00
82 7 0.02
83 219 0.59
84 77 0.21
85 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (80 bp):
AATCGAACTTGAAGGTCTTTGTTGACAGATAACCTTCTAGCCTTGAGTTATGTTGTAAATTTGAT
ATGCCTTGAGAGTGT
Found at i:6428554 original size:83 final size:82
Alignment explanation
Indices: 6428436--6428921 Score: 483
Period size: 83 Copynumber: 5.8 Consensus size: 82
6428426 GATATGCCTA
* * * * * *
6428436 AGTGTAATCGAACTTGAAGGTCTTTGTTGACAGATAACTCTTCTAGCCTTGAGTTATGTTGCAAT
1 AGTGTAGTCGAACTCGAAGGTCTTTGTGGA-AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
*
6428501 TGATATGCCTTTGAGCTG
65 TGATGTGCCTTTGAGCTG
** * * * *
6428519 AGTGTAGTTAAACTTGAAGGTCTTTGTCGGAAGATAACCATTCTAGCCTTGAGTTATGTTGTAAA
1 AGTGTAGTCGAACTCGAAGGTCTTTGT-GGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
6428584 TGATGTGCC-TTGAAGCTG
65 TGATGTGCCTTTG-AGCTG
* * * * *
6428602 AGCGTAGTCTAACTCAAAAGTCTTTGAT-GACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAA
1 AGTGTAGTCGAACTCGAAGGTCTTTG-TGGA-AGATAACCCTTCTAGCCTTGAGTTATGCTGCAA
*
6428666 ATGATGTGCCTTGGAGCTG
64 ATGATGTGCCTTTGAGCTG
* * * * ** *
6428685 AGCGTGGTCGAACTCGATGGTCTTTGGTTGGCAGATAACCCTTCTTTCCTTGAGTTATGCTACAA
1 AGTGTAGTCGAACTCGAAGGTCTTT-G-TGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAA
6428750 ATGATGTGCCTTTGAGCTG
64 ATGATGTGCCTTTGAGCTG
* * * * *
6428769 AGTGTAATCGAACTCGAAGGTCTTGGTTGGCAA-ATAACTCTTCTAGCCTTGAGTTATGCCGTAA
1 AGTGTAGTCGAACTCGAAGGTCTTTG-TGG-AAGATAACCCTTCTAGCCTTGAGTTATGCTGCAA
6428833 ATGATGTGCCTTTGAGCTG
64 ATGATGTGCCTTTGAGCTG
* * * * * * * * *
6428852 AGTGTAATCGAACTAGAAGGTTTTTTTATTAGAAGATAGCCCTTCTTGCCTTGAGCTAAGCTGCA
1 AGTGTAGTCGAACTCGAAGG--TCTTT-GTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCA
6428917 AATGA
63 AATGA
6428922 GCACGATATC
Statistics
Matches: 336, Mismatches: 55, Indels: 22
0.81 0.13 0.05
Matches are distributed among these distances:
82 5 0.01
83 219 0.65
84 78 0.23
85 34 0.10
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (82 bp):
AGTGTAGTCGAACTCGAAGGTCTTTGTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
GATGTGCCTTTGAGCTG
Found at i:6428815 original size:250 final size:243
Alignment explanation
Indices: 6428368--6428853 Score: 593
Period size: 250 Copynumber: 2.0 Consensus size: 243
6428358 AATGAAATCG
* * * * *
6428368 AACTCGAAGGTCTTTGATGACAGATAACCCTTCTTGCCTTGAGTTATGTTGTAAATTTGATATGC
1 AACTCAAAAGTCTTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAA-TTGATATGC
* * * * *
6428433 CTAAGTGTAATCGAACTTGAAGGTCTTTGTTGACAGATAACTCTTCTAGCCTTGAGTTATGTTGC
65 CTAAGCGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTAC
* * * * *
6428498 AATTGATATGCCTTTGAGCTGAGTGTAGTTAAACTTGAAGGTCTTTGTCGGAAGATAACCATTCT
130 AAATGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTGGTCGGAAGATAACCATTCT
**
6428563 AGCCTTGAGTTATGTTGTAAATGATGTGCC-TTGAAGCTGAGCGTAGTCT
195 AGCCTTGAGTTATGCCGTAAATGATGTGCCTTTG-AGCTGAGCGTAGTCT
*
6428612 AACTCAAAAGTCTTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAA-TGATGTGCC
1 AACTCAAAAGTCTTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATTGATATGCC
** * * **
6428676 TTGGAGCTGAGCGTGGTCGAACTCGATGGTCTTTGGTTGGCAGATAACCCTTCTTTCCTTGAGTT
66 -T--A----AGCGTAATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGCCTTGAGTT
* * *
6428741 ATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGGCAA-ATA
123 ATGCTACAAATGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTGGTCGG-AAGATA
6428805 ACTC-TTCTAGCCTTGAGTTATGCCGTAAATGATGTGCCTTTGAGCTGAG
187 AC-CATTCTAGCCTTGAGTTATGCCGTAAATGATGTGCCTTTGAGCTGAG
6428854 TGTAATCGAA
Statistics
Matches: 204, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
242 8 0.04
243 1 0.00
244 50 0.25
245 1 0.00
249 20 0.10
250 118 0.58
251 6 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (243 bp):
AACTCAAAAGTCTTTGATGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATTGATATGCC
TAAGCGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTACA
AATGATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTGGTCGGAAGATAACCATTCTA
GCCTTGAGTTATGCCGTAAATGATGTGCCTTTGAGCTGAGCGTAGTCT
Found at i:6428820 original size:167 final size:166
Alignment explanation
Indices: 6428365--6428906 Score: 592
Period size: 167 Copynumber: 3.3 Consensus size: 166
6428355 CTGAATGAAA
* *
6428365 TCGAACTCGAAGGTCTTTGATGACAGATAACCCTTCTTGCCTTGAGTTATGTTGTAAAT--T-TG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGTTGTAAATGATGTG
* * * * *
6428427 -ATATG-CCTAAGTGTAATCGAACTTGAAGGTCTTTGTTGACAGATAACTCTTCTAGCCTTGAGT
66 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTAGCCTTGAGT
* * * *
6428490 TATGTTGCAATTGATATGCCTTTGAGCTGAGTGTAG
131 TATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAG
** * * * * *
6428526 TTAAACTTGAAGGTCTTTGTCGGAAGATAACCATTCTAGCCTTGAGTTATGTTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGTTGTAAATGATGTG
* * * * * * * *
6428591 CC-TTGAAGCTGAGCGTAGTCTAACTCAAAAGTCTTTGATGACAGATAACCCTTCTCGCCTTGAG
66 CCTTTG-AGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTAGCCTTGAG
* *
6428655 TTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTGG
130 TTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAG
* * * **
6428692 TCGAACTCGATGGTCTTTGGTTGGCAGATAACCCTTCTTTCCTTGAGTTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTTGCCTTGAGTTATGTTGTAAATGATGT
* * *
6428757 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGGCAAATAACTCTTCTAGCCTTGAG
65 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTAGCCTTGAG
* * * *
6428822 TTATGCCGTAAATGATGTGCCTTTGAGCTGAGTGTAA
130 TTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAG
* * * * * *
6428859 TCGAACTAGAAGGTTTTTTTATTAGAAGATAGCCCTTCTTGCCTTGAG
1 TCGAACTCGAAGG--TCTTTGTTGGCAGATAACCCTTCTTGCCTTGAG
6428907 CTAAGCTGCA
Statistics
Matches: 306, Mismatches: 65, Indels: 13
0.80 0.17 0.03
Matches are distributed among these distances:
161 50 0.16
163 1 0.00
164 4 0.01
166 91 0.30
167 130 0.42
168 26 0.08
169 4 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (166 bp):
TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGTTGTAAATGATGTG
CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTAGCCTTGAGT
TATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAG
Found at i:6429137 original size:121 final size:121
Alignment explanation
Indices: 6428923--6429143 Score: 336
Period size: 121 Copynumber: 1.8 Consensus size: 121
6428913 TGCAAATGAG
* * **
6428923 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGAATGACCCATTCATTGTGAAGTTGATCCTCGA
1 CACGATATCCTTCATCGTGAAGTTGAAATCGTGAATGACCCATTCATCGTGAAGTTGAAACTCGA
6428988 ATTGGATATCCTTCATCATGAAGTTGAAATCCAAGGGTTGCATTGTTGCTGGTGGA
66 ATTGGATATCCTTCATCATGAAGTTGAAATCCAAGGGTTGCATTGTTGCTGGTGGA
* * * * *
6429044 CACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAAACTTGA
1 CACGATATCCTTCATCGTGAAGTTGAAATCGTGAATGACCCATTCATCGTGAAGTTGAAACTCGA
*
6429109 ATTGGATATCCTTCGTCGA-GAAGTTGAAATCCAAG
66 ATTGGATATCCTTCATC-ATGAAGTTGAAATCCAAG
6429144 TTAAGTTGCA
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
121 88 0.99
122 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (121 bp):
CACGATATCCTTCATCGTGAAGTTGAAATCGTGAATGACCCATTCATCGTGAAGTTGAAACTCGA
ATTGGATATCCTTCATCATGAAGTTGAAATCCAAGGGTTGCATTGTTGCTGGTGGA
Found at i:6429355 original size:43 final size:43
Alignment explanation
Indices: 6429308--6429418 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
6429298 CGATTCCCTT
* * *
6429308 CGTCGTGAAGTTGAAACCGTGGATGTGTGGGCACGATATCCTC
1 CGTCGTGAAGTTGAAATCGTGGATGTATGGACACGATATCCTC
* * * *
6429351 CGTCGTGGAGTTGAAATCGTGGATCTATTGATACGATATCCTC
1 CGTCGTGAAGTTGAAATCGTGGATGTATGGACACGATATCCTC
* *
6429394 CATCGTGAAGTTGAAATCATGGATG
1 CGTCGTGAAGTTGAAATCGTGGATG
6429419 ACCCCTTCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (43 bp):
CGTCGTGAAGTTGAAATCGTGGATGTATGGACACGATATCCTC
Found at i:6429657 original size:332 final size:334
Alignment explanation
Indices: 6429045--6429750 Score: 1033
Period size: 332 Copynumber: 2.1 Consensus size: 334
6429035 GCTGGTGGAC
* * *
6429045 ACGATATCCTTCATCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAAACTTGAA
1 ACGATATCCTCCATCGTGAAGTTGAAATCGTGGATGACCCCTTCATCGTGAAGTTGAAACTTGAA
* *
6429110 TTGGATATCCTTCGTCGAGAAGTTGAAATCCAAGTTAAGTTGCATTGTTTTGAGGCCAATATCCT
66 TTGAATATCCTTCGTCGAGAAGTTGAAATCCAAGTT-AGTTG-ATTGTTTCGAGGCCAATATCC-
*
6429175 TTACCGTGAAGTTGAAATTGACTCTGAACTGAAAAGTTTATTGACAGACACTCTTTCTTTGAGTT
128 -TACCGTGAAGTTGAAATTGACTCTGAACTGAAAAGTTTATTGACAGACACTCATTCTTTGAGTT
* *
6429240 GGATATCATTCGTCGTGAAGTTGAAATCCAATCTAGAGATAGATGTTGCTTGTGTGTACGATTCC
192 GGATATCATTCGTCGTGAAGTTGAAATCCAATCTAGAGATAGATGTTGCTCGTGTATACGATTCC
* *
6429305 CTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCACGATATCCTCCGTCGTGGAGTTGAAATCG
257 CTTCGTCGTGAAGTTGAAACCGTGGATATGTGGGCACGATATCCTCCATCGTGGAGTTGAAATCG
*
6429370 TGGATCTATTGAT
322 TGGATCCATTGAT
* ** *
6429383 ACGATATCCTCCATCGTGAAGTTGAAATCATGGATGACCCCTTCATCGTGAAGTTGAGCCTTGAC
1 ACGATATCCTCCATCGTGAAGTTGAAATCGTGGATGACCCCTTCATCGTGAAGTTGAAACTTGAA
* * *
6429448 TTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTT-G-TG-TTGTTTCGAGTCCAATATCC-G
66 TTGAATATCCTTCGTCGAGAAGTTGAAATCCAAG-TTAGTTGATTGTTTCGAGGCCAATATCCTA
* * * *
6429509 CTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAGTTTATTGATAGACACTCATTCTTTGAGTTGG
130 CCGTGAAGTTGAAATTGACTCTG-AACTGAAAAGTTTATTGACAGACACTCATTCTTTGAGTTGG
* * * *
6429574 ATATCCTTCGTCGTGTAGTTGAAATCCAATCTAGAGATGGATGTTGCTCGTGTATACGATTCTCT
194 ATATCATTCGTCGTGAAGTTGAAATCCAATCTAGAGATAGATGTTGCTCGTGTATACGATTCCCT
* *
6429639 TCGTTGTGAAGTTGAAACCGTGGATATGTGGGCACGATATCCTCTATCGTGGAGTTGAAATCGTG
259 TCGTCGTGAAGTTGAAACCGTGGATATGTGGGCACGATATCCTCCATCGTGGAGTTGAAATCGTG
* *
6429704 GATCCGTTGGT
324 GATCCATTGAT
* * *
6429715 ACGATATCCTCCGTTGTGGAGTTGAAATCGTGGATG
1 ACGATATCCTCCATCGTGAAGTTGAAATCGTGGATG
6429751 TGTTGGTACG
Statistics
Matches: 332, Mismatches: 34, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
331 21 0.06
332 198 0.60
334 18 0.05
336 2 0.01
337 1 0.00
338 90 0.27
339 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (334 bp):
ACGATATCCTCCATCGTGAAGTTGAAATCGTGGATGACCCCTTCATCGTGAAGTTGAAACTTGAA
TTGAATATCCTTCGTCGAGAAGTTGAAATCCAAGTTAGTTGATTGTTTCGAGGCCAATATCCTAC
CGTGAAGTTGAAATTGACTCTGAACTGAAAAGTTTATTGACAGACACTCATTCTTTGAGTTGGAT
ATCATTCGTCGTGAAGTTGAAATCCAATCTAGAGATAGATGTTGCTCGTGTATACGATTCCCTTC
GTCGTGAAGTTGAAACCGTGGATATGTGGGCACGATATCCTCCATCGTGGAGTTGAAATCGTGGA
TCCATTGAT
Found at i:6429793 original size:43 final size:43
Alignment explanation
Indices: 6429648--6429793 Score: 202
Period size: 43 Copynumber: 3.4 Consensus size: 43
6429638 TTCGTTGTGA
* * * * **
6429648 AGTTGAAACCGTGGATATGTGGGCACGATATCCTCTATCGTGG
1 AGTTGAAATCGTGGATGTGTTGGTACGATATCCTCCGTCGTGG
** *
6429691 AGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTTGTGG
1 AGTTGAAATCGTGGATGTGTTGGTACGATATCCTCCGTCGTGG
6429734 AGTTGAAATCGTGGATGTGTTGGTACGATATCCTCCGTCGTGG
1 AGTTGAAATCGTGGATGTGTTGGTACGATATCCTCCGTCGTGG
*
6429777 AGTTGAAATCGCGGATG
1 AGTTGAAATCGTGGATG
6429794 ACCCCTTCAT
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (43 bp):
AGTTGAAATCGTGGATGTGTTGGTACGATATCCTCCGTCGTGG
Found at i:6429842 original size:34 final size:33
Alignment explanation
Indices: 6429798--6429881 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 33
6429788 CGGATGACCC
*
6429798 CTTCATCGTGAAGTTGAGCCTT-GACTT-GAATAT
1 CTTCGTCGTGAAGTTGAG-CTTCGACTTAG-ATAT
*
6429831 ACTTCGTCGTGAAGTTG-GCTTCGAGTTAGATAT
1 -CTTCGTCGTGAAGTTGAGCTTCGACTTAGATAT
6429864 CATTCGTCGTGAAGTTGA
1 C-TTCGTCGTGAAGTTGA
6429882 AATATACTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 4 0.09
33 24 0.55
34 16 0.36
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (33 bp):
CTTCGTCGTGAAGTTGAGCTTCGACTTAGATAT
Found at i:6430300 original size:32 final size:32
Alignment explanation
Indices: 6430232--6430301 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
6430222 TAGGATATTG
* * * *
6430232 AATCCCCAAATATGCCACAATATTCAATGTTG
1 AATCTCCAAATATACCACAACATTCAATGTTA
* * *
6430264 AATCTCCAAATATACCCCAACATTTACTGTTA
1 AATCTCCAAATATACCACAACATTCAATGTTA
6430296 AATCTC
1 AATCTC
6430302 TAAAGATGCC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (32 bp):
AATCTCCAAATATACCACAACATTCAATGTTA
Found at i:6430481 original size:22 final size:22
Alignment explanation
Indices: 6430447--6430508 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
6430437 CTTTTATTTT
*
6430447 CAAAAGTTATGAAAATGTATTAA
1 CAAAAGTTTTGAAAATGT-TTAA
*
6430470 -AAGAGTTTTGAAAAATGTTTAA
1 CAAAAGTTTTG-AAAATGTTTAA
6430492 TCAAAAGTTTTGAAAAT
1 -CAAAAGTTTTGAAAAT
6430509 ATTATCCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 12 0.36
23 12 0.36
24 9 0.27
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.34
Consensus pattern (22 bp):
CAAAAGTTTTGAAAATGTTTAA
Found at i:6437458 original size:14 final size:14
Alignment explanation
Indices: 6437441--6437474 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
6437431 CCCTACTTGT
6437441 TAATCCCTCTAATA
1 TAATCCCTCTAATA
6437455 TAATCCCTCTAATA
1 TAATCCCTCTAATA
6437469 TAATCC
1 TAATCC
6437475 ATGGACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATCCCTCTAATA
Found at i:6438789 original size:24 final size:24
Alignment explanation
Indices: 6438762--6438815 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
6438752 GTATTCGAAA
6438762 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
6438786 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
6438810 TTTGAT
1 TTTGAT
6438816 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:6441390 original size:33 final size:33
Alignment explanation
Indices: 6441333--6441533 Score: 213
Period size: 33 Copynumber: 5.8 Consensus size: 33
6441323 CTTAATGTCT
* **
6441333 ATCGCAATGCAGAAATTACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* * *
6441367 ATCGCAATACGAAATGAAAATCGCAACGTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
6441400 ATCGCAACGCGAATATGAATATTGCAATACGGAAATGA
1 ATCGCAATGCGAA-ATGAAAATCGC-A-AC-GAGA-GA
6441438 CTATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
6441473 ATCGCAATGCGAAATGAAAATTGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
6441506 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
6441534 CGAATTTAGT
Statistics
Matches: 139, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
33 86 0.62
34 18 0.13
35 3 0.02
36 5 0.04
37 4 0.03
38 2 0.01
39 9 0.06
40 12 0.09
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:6441400 original size:14 final size:14
Alignment explanation
Indices: 6441381--6441408 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6441371 CAATACGAAA
6441381 TGAAAATCGCAACG
1 TGAAAATCGCAACG
6441395 TGAAAATCGCAACG
1 TGAAAATCGCAACG
6441409 CGAATATGAA
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:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:6441418 original size:20 final size:19
Alignment explanation
Indices: 6441366--6441537 Score: 88
Period size: 19 Copynumber: 9.7 Consensus size: 19
6441356 GCAACGAGAG
**
6441366 AATCGCAATACGAAATGAA
1 AATCGCAACGCGAAATGAA
6441385 AATCGCAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
6441399 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* * *
6441419 TATTGCAATACG-GAAATGAC
1 AATCGC-A-ACGCGAAATGAA
* *
6441439 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
6441458 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
6441472 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* **
6441491 AATTGCAA--CG--A-GGG
1 AATCGCAACGCGAAATGAA
*
6441505 AATCGCAAAGCGAAATGAA
1 AATCGCAACGCGAAATGAA
6441524 AATCGCAACGCGAA
1 AATCGCAACGCGAA
6441538 TTTAGTTTCG
Statistics
Matches: 118, Mismatches: 16, Indels: 38
0.69 0.09 0.22
Matches are distributed among these distances:
14 30 0.25
15 2 0.02
16 6 0.05
17 6 0.05
18 4 0.03
19 46 0.39
20 17 0.14
21 4 0.03
22 3 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:6441453 original size:73 final size:66
Alignment explanation
Indices: 6441356--6441533 Score: 205
Period size: 73 Copynumber: 2.6 Consensus size: 66
6441346 AATTACTATC
* * *
6441356 GCAACG-AGAGAATCGCAATACGAAATGAAAATCGCAACGTGAAAATCGCAACGCGAATATGAAT
1 GCAACGAAG-GAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAA-ATGAAA
6441420 ATT
64 ATT
* * *
6441423 GCAATACGGAAATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 GC-A-AC-G-AAGGA--ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAAT
6441488 GAAAATT
60 GAAAATT
* *
6441495 GCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACG
1 GCAACGAAGGAATCGCAATGCGAAATGAAAATCGCAACG
6441534 CGAATTTAGT
Statistics
Matches: 95, Mismatches: 9, Indels: 15
0.80 0.08 0.13
Matches are distributed among these distances:
66 27 0.28
67 2 0.02
68 4 0.04
69 3 0.03
70 3 0.03
71 3 0.03
72 11 0.12
73 42 0.44
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (66 bp):
GCAACGAAGGAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAAAAT
T
Found at i:6441479 original size:106 final size:106
Alignment explanation
Indices: 6441326--6441523 Score: 290
Period size: 106 Copynumber: 1.9 Consensus size: 106
6441316 CAATCATCTT
* * **
6441326 AATGTCTATCGCAATGCAGAAATTACTATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGC
1 AATGACTATCGCAATGCAGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGC
* *
6441391 AACGTGAAAATCGCAACGCGAATATGAATATTGCAATACGGA
66 AACGAGAAAATCGCAAAGCGAA-ATGAATATTGCAATACGGA
* *
6441433 AATGACTATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATTGC
1 AATGACTATCGCAATGCAGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGC
**
6441497 AACGAGGGAATCGCAAAGCGAAATGAA
66 AACGAGAAAATCGCAAAGCGAAATGAA
6441524 AATCGCAACG
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
105 5 0.06
106 60 0.74
107 16 0.20
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (106 bp):
AATGACTATCGCAATGCAGAAATGAAAATCGCAACGAGAGAATCGCAATACGAAATGAAAATCGC
AACGAGAAAATCGCAAAGCGAAATGAATATTGCAATACGGA
Found at i:6441580 original size:33 final size:33
Alignment explanation
Indices: 6441543--6441622 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
6441533 GCGAATTTAG
* * *
6441543 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCAATTTTCA
* * *
6441576 TTTCGTATTGTGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCAATTTTCA
6441609 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
6441623 AGTCATTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.12, C:0.19, G:0.20, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCAATTTTCA
Found at i:6441748 original size:14 final size:14
Alignment explanation
Indices: 6441729--6441765 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6441719 CATCAATTAA
6441729 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
6441743 ACAAATCATCTTTT
1 ACAAATCAACTTTT
6441757 ACAAATCAA
1 ACAAATCAA
6441766 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:6443624 original size:94 final size:94
Alignment explanation
Indices: 6443510--6443869 Score: 605
Period size: 94 Copynumber: 3.8 Consensus size: 94
6443500 TGCATCAGAT
* *
6443510 AACAAAGACAAATACTAACTTCAAAGTATTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
1 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
6443575 GAACAAATTTACTTTCAACCAAAAGACAA
66 GAACAAATTTACTTTCAACCAAAAGACAA
6443604 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
1 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
6443669 GAACAAATTTACTTTCAACCAAAAGACAA
66 GAACAAATTTACTTTCAACCAAAAGACAA
* *
6443698 AACAAAGGCAAATACTTACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
1 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
*
6443763 GAATAAATTTAC-TTCAACCAAAAGACAA
66 GAACAAATTTACTTTCAACCAAAAGACAA
* * * *
6443791 AACAAAAGATAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATTGGTAGCAAC
1 AAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAC
* *
6443856 CAAATAAATTTACT
65 CGAACAAATTTACT
6443870 AAGCAATCTA
Statistics
Matches: 252, Mismatches: 12, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
93 19 0.08
94 233 0.92
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
GAACAAATTTACTTTCAACCAAAAGACAA
Found at i:6445605 original size:20 final size:20
Alignment explanation
Indices: 6445582--6445637 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
6445572 TGAAATGAAA
6445582 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
6445602 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
6445622 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
6445638 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:6445695 original size:19 final size:19
Alignment explanation
Indices: 6445662--6445706 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
6445652 AAAATCGCAA
**
6445662 TGCGATTTTGGTTTCACGT
1 TGCGATTTTAATTTCACGT
*
6445681 TGCGATTTTAATTTCGCGT
1 TGCGATTTTAATTTCACGT
*
6445700 TGTGATT
1 TGCGATT
6445707 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.13, C:0.13, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTAATTTCACGT
Found at i:6445731 original size:21 final size:20
Alignment explanation
Indices: 6445712--6445783 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
6445702 TGATTCTCTC
6445712 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
6445732 CGTTGCGATGGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
*
6445753 GTTGTGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
6445773 GTTGCGATTTT
1 GTTGCGATTTT
6445784 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.11, C:0.15, G:0.21, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:6446378 original size:20 final size:19
Alignment explanation
Indices: 6446345--6446594 Score: 177
Period size: 20 Copynumber: 12.4 Consensus size: 19
6446335 TAAAAATCGT
6446345 GTTGCGATTTTACGTATTGTC
1 GTTGCGA-TTTACGTATTG-C
* *
6446366 GTTGCGATTTACGGA-TAC
1 GTTGCGATTTACGTATTGC
6446384 GGATTGCGATTTACGTATT-C
1 -G-TTGCGATTTACGTATTGC
*
6446404 TTGTTGCGATTTACAG-ATACGC
1 --GTTGCGATTTAC-GTAT-TGC
*
6446426 GTTGCGATTTACGTATTCTC
1 GTTGCGATTTACGTATT-GC
* *
6446446 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGTAT-TGC
6446466 GTTGCGATTTTACGTATTGTC
1 GTTGCGA-TTTACGTATTG-C
* *
6446487 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGTAT-TGC
*
6446507 GTTGCGATTTTACGGATACT-C
1 GTTGCGA-TTTAC-G-TATTGC
* *
6446528 GTTGCGATAGT-CAGAATTGC
1 GTTGCGAT-TTAC-GTATTGC
6446548 GTTGCGATTTACGTAATTGC
1 GTTGCGATTTACGT-ATTGC
6446568 GTTGCGATTTACGTATTCGC
1 GTTGCGATTTACGTATT-GC
*
6446588 ATTGCGA
1 GTTGCGA
6446595 ATTAGGAAAA
Statistics
Matches: 184, Mismatches: 24, Indels: 43
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.01
19 10 0.05
20 129 0.70
21 41 0.22
22 2 0.01
23 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (19 bp):
GTTGCGATTTACGTATTGC
Found at i:6446397 original size:40 final size:41
Alignment explanation
Indices: 6446345--6446594 Score: 298
Period size: 40 Copynumber: 6.2 Consensus size: 41
6446335 TAAAAATCGT
*
6446345 GTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG-
1 GTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
* *
6446385 GATTGCGA-TTTACGTATTCTTGTTGCGATTTACAGATACGC
1 G-TTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
6446426 GTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGC
1 GTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
*
6446466 GTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGC
1 GTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
* * * * *
6446507 GTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-ATTGC
1 GTTGCGATTTTACGTATTCTCGTTGCGAT-TTACGGATA-CGC
* * *
6446548 GTTGCGA-TTTACGTAATT-GCGTTGCGATTTACGTATTCGC
1 GTTGCGATTTTACGT-ATTCTCGTTGCGATTTACGGATACGC
*
6446588 ATTGCGA
1 GTTGCGA
6446595 ATTAGGAAAA
Statistics
Matches: 181, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.01
40 100 0.55
41 79 0.44
42 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (41 bp):
GTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
Found at i:6446580 original size:81 final size:79
Alignment explanation
Indices: 6446345--6446594 Score: 256
Period size: 81 Copynumber: 3.1 Consensus size: 79
6446335 TAAAAATCGT
* ** * *
6446345 GTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG-GATTGCGATTTACGTATT-CTTGT
1 GTTGCGA-TTTACGGATACTCGTTGCGATTCACGAATACGCG-TTGCGATTTACGTATTGC--GT
*
6446408 TGCGATTTACAGATACGC
62 TGCGATTTACGGATACGC
* * * *
6446426 GTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTG
1 GTTGCGATTTACGGATACTCGTTGCGATTCACGAATACGCGTTGCGA-TTTACGTATTG-CGTTG
6446491 CGATTTACGGATACGC
64 CGATTTACGGATACGC
*
6446507 GTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAAT-TGCGTTGCGATTTACGTAATTGCGT
1 GTTGCGA-TTTACGGATACTCGTTGCGAT--TCACGAATACGCGTTGCGATTTACGT-ATTGCGT
* *
6446570 TGCGATTTACGTATTCGC
62 TGCGATTTACGGATACGC
*
6446588 ATTGCGA
1 GTTGCGA
6446595 ATTAGGAAAA
Statistics
Matches: 151, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
80 37 0.25
81 76 0.50
82 32 0.21
83 4 0.03
84 2 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (79 bp):
GTTGCGATTTACGGATACTCGTTGCGATTCACGAATACGCGTTGCGATTTACGTATTGCGTTGCG
ATTTACGGATACGC
Found at i:6446615 original size:21 final size:21
Alignment explanation
Indices: 6446591--6446678 Score: 113
Period size: 21 Copynumber: 4.2 Consensus size: 21
6446581 TATTCGCATT
*
6446591 GCGAATTAGGAAAACCGCAAC
1 GCGAATTTGGAAAACCGCAAC
6446612 GCGAATTTGGAAAACCGCAAC
1 GCGAATTTGGAAAACCGCAAC
* * *
6446633 GCGAATTTGGGAAATCGTAAC
1 GCGAATTTGGAAAACCGCAAC
* * *
6446654 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGAAAACCGCAAC
6446675 GCGA
1 GCGA
6446679 TAGTCAAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTTGGAAAACCGCAAC
Found at i:6456069 original size:25 final size:23
Alignment explanation
Indices: 6456041--6456091 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
6456031 ATTTTCCATT
6456041 ATGT-TGGCTTTTGAACTTTTCACAA
1 ATGTCTGGCTTTT--ACTTTTCA-AA
*
6456066 ATGTCTTGCTTTTACTTTTCAAA
1 ATGTCTGGCTTTTACTTTTCAAA
6456089 ATG
1 ATG
6456092 GACACATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 8 0.33
25 4 0.17
26 7 0.29
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.47
Consensus pattern (23 bp):
ATGTCTGGCTTTTACTTTTCAAA
Found at i:6456375 original size:20 final size:20
Alignment explanation
Indices: 6456352--6456403 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
6456342 AACGCGATCC
*
6456352 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAATTT
6456372 CCAGAATCGCAAATCAATTT
1 CCAGAATCGCAAATCAATTT
*
6456392 CCAAAATCGCAA
1 CCAGAATCGCAA
6456404 CGCGATTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAATTT
Found at i:6456420 original size:21 final size:20
Alignment explanation
Indices: 6456388--6456491 Score: 73
Period size: 21 Copynumber: 5.0 Consensus size: 20
6456378 TCGCAAATCA
*
6456388 ATTTCCAAAATCGCAACGCG
1 ATTTTCAAAATCGCAACGCG
* * *
6456408 ATTCTTGAAAATCGCGATGCG
1 ATT-TTCAAAATCGCAACGCG
* * * **
6456429 ATAGTACAAATTCGCATTGCG
1 AT-TTTCAAAATCGCAACGCG
6456450 ATTTTCCAAAATCGCAACGCG
1 ATTTT-CAAAATCGCAACGCG
* * *
6456471 AATATGAAAATCGCAACGCG
1 ATTTTCAAAATCGCAACGCG
6456491 A
1 A
6456492 ACACATAAAT
Statistics
Matches: 63, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
20 19 0.30
21 44 0.70
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATTTTCAAAATCGCAACGCG
Found at i:6456520 original size:20 final size:20
Alignment explanation
Indices: 6456458--6456651 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
6456448 CGATTTTCCA
* ** *
6456458 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
6456478 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
6456498 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
6456518 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
6456538 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
6456558 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
6456578 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
6456598 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
6456618 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
6456639 AAATCGCAACGCG
1 AAATCGCAACGCG
6456652 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:6456542 original size:60 final size:60
Alignment explanation
Indices: 6456458--6456651 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
6456448 CGATTTTCCA
* ** * *
6456458 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
6456518 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
6456578 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
6456639 AAATCGCAACGCG
1 AAATCGCAACGCG
6456652 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:6457071 original size:33 final size:33
Alignment explanation
Indices: 6457032--6457102 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
6457022 TTCACTTAGA
*
6457032 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
6457065 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
6457098 TTTCA
1 TTTCA
6457103 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:6457242 original size:14 final size:14
Alignment explanation
Indices: 6457223--6457277 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
6457213 AGAATGACTG
6457223 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
6457237 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
6457256 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
6457270 TCGCAACG
1 TCGCAACG
6457278 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:6457290 original size:33 final size:33
Alignment explanation
Indices: 6457223--6457293 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
6457213 AGAATGACTG
***
6457223 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
6457256 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
6457289 TCGCA
1 TCGCA
6457294 TTGCGATTTT
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:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:6457311 original size:19 final size:19
Alignment explanation
Indices: 6457289--6457386 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
6457279 GAAACCAAAA
*
6457289 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6457308 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
6457322 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6457341 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
6457355 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
6457374 TCGCGTTGCGATT
1 TCGCGTTGCGATT
6457387 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:6457330 original size:14 final size:14
Alignment explanation
Indices: 6457311--6457400 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
6457301 TTTCATTTCG
6457311 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6457325 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
6457344 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6457358 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
6457375 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
6457391 CGTTGCGATT
1 CGTTGCGATT
6457401 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6457336 original size:33 final size:33
Alignment explanation
Indices: 6457294--6457408 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
6457284 CAAAATCGCA
6457294 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
6457327 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
6457360 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
6457393 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
6457409 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:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:6459336 original size:185 final size:186
Alignment explanation
Indices: 6459106--6459487 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
6459096 TAGATTGCTT
6459106 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6459171 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
6459236 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
6459291 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6459356 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
6459421 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
6459477 AGTAAATTTAT
1 AGTAAATTTAT
6459488 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:6459420 original size:93 final size:93
Alignment explanation
Indices: 6459106--6459485 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
6459096 TAGATTGCTT
*
6459106 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6459171 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6459199 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6459263 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6459291 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6459356 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6459384 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6459449 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6459477 AGTAAATTT
1 AGTAAATTT
6459486 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:6459569 original size:19 final size:19
Alignment explanation
Indices: 6459529--6459657 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
6459519 TAGTTTACTT
* *
6459529 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
6459549 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
6459568 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
6459587 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
6459601 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
6459620 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
6459634 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
6459653 TCGCA
1 TCGCA
6459658 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:6459603 original size:33 final size:32
Alignment explanation
Indices: 6459565--6459657 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
6459555 CGCGAAACCA
**
6459565 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
6459597 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
6459630 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
6459658 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:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:6459655 original size:52 final size:52
Alignment explanation
Indices: 6459529--6459657 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
6459519 TAGTTTACTT
* **
6459529 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
*** *
6459581 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
6459634 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
6459658 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
51 3 0.05
52 47 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:6459675 original size:19 final size:19
Alignment explanation
Indices: 6459653--6459787 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
6459643 GAAACCAAAA
*
6459653 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6459672 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
6459688 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
6459705 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
6459721 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
6459738 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
6459757 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
6459777 TCGTGTTGCGA
1 TCGCGTTGCGA
6459788 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:6459694 original size:14 final size:14
Alignment explanation
Indices: 6459675--6459731 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6459665 TTTCATTTCG
6459675 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
6459689 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
6459706 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
6459722 CGTTGCGATT
1 CGTTGCGATT
6459732 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:6459700 original size:33 final size:33
Alignment explanation
Indices: 6459658--6459750 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
6459648 CAAAATCGCA
*
6459658 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
6459691 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
6459724 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
6459751 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:6461643 original size:38 final size:38
Alignment explanation
Indices: 6461600--6461672 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
6461590 AATTGATTGT
*
6461600 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
6461638 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
6461673 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:6461659 original size:19 final size:19
Alignment explanation
Indices: 6461595--6461659 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
6461585 AGTTTAATTG
*
6461595 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
6461614 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
6461632 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
6461652 ATTGATTT
1 ATTGATTT
6461660 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:6461673 original size:14 final size:14
Alignment explanation
Indices: 6461654--6461689 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6461644 ATTGTTTAAT
6461654 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
6461668 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
6461682 TGATTTGT
1 TGATTTGT
6461690 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:6461812 original size:19 final size:19
Alignment explanation
Indices: 6461796--6461897 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
6461786 AAAAATGACT
6461796 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
6461815 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6461834 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
6461848 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6461867 ATCGCAATGCGGAAATTAAA
1 ATCGCAATGC-GAAATGAAA
6461887 ATCGCAATGCG
1 ATCGCAATGCG
6461898 TTTATAATTT
Statistics
Matches: 74, Mismatches: 3, Indels: 12
0.83 0.03 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 40 0.54
20 18 0.24
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:6461946 original size:33 final size:36
Alignment explanation
Indices: 6461904--6462222 Score: 320
Period size: 33 Copynumber: 9.1 Consensus size: 36
6461894 TGCGTTTATA
*
6461904 ATTTCGCATTGCGA-TT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
6461937 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
6461973 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
6462008 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
6462046 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
6462082 -TCTCG--TTGCGATTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCG-ATTGCGATTTTC
*
6462116 ATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
6462149 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
6462185 -TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTT-CG-ATTGCGATTTTC
6462221 AT
1 AT
6462223 GTTGGGATTT
Statistics
Matches: 252, Mismatches: 10, Indels: 44
0.82 0.03 0.14
Matches are distributed among these distances:
32 18 0.07
33 85 0.34
34 13 0.05
35 29 0.12
36 28 0.11
37 7 0.03
38 72 0.29
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (36 bp):
ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
Found at i:6461950 original size:19 final size:19
Alignment explanation
Indices: 6461926--6462250 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
6461916 GATTATCTCG
6461926 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6461945 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6461964 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
6461978 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6461997 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6462016 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
6462035 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
6462054 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6462073 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
6462087 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6462105 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6462124 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
6462138 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6462157 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6462176 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
6462190 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
6462210 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
6462224 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
6462243 TTGCGATT
1 TTGCGATT
6462251 GTATTTTCCG
Statistics
Matches: 268, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
15 3 0.01
16 32 0.12
17 24 0.09
18 9 0.03
19 153 0.57
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:6461966 original size:52 final size:52
Alignment explanation
Indices: 6461904--6462222 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
6461894 TGCGTTTATA
*
6461904 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
6461956 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
6462008 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
6462065 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
6462116 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
6462168 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
6462221 AT
1 AT
6462223 GTTGGGATTT
Statistics
Matches: 255, Mismatches: 5, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
51 50 0.20
52 130 0.51
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:6464574 original size:12 final size:12
Alignment explanation
Indices: 6464557--6464581 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6464547 TCTTCGGGGA
6464557 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6464569 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6464581 C
1 C
6464582 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:6464790 original size:24 final size:24
Alignment explanation
Indices: 6464756--6464802 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6464746 CTGAAACATC
6464756 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
6464780 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
6464803 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:6465503 original size:20 final size:20
Alignment explanation
Indices: 6465475--6465843 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
6465465 AAATTTCAGT
* * * *
6465475 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6465495 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
6465515 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6465535 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6465555 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6465575 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6465595 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6465615 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6465635 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6465655 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
6465675 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6465695 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6465715 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
6465735 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
6465755 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
6465775 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
6465795 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
6465815 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
6465835 GTTGCGATT
1 GTTGCGATT
6465844 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:6469131 original size:6 final size:6
Alignment explanation
Indices: 6469120--6469183 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
6469110 AAGAGATAAT
6469120 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
6469168 TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTT
6469184 AGGGTAAACT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:6473376 original size:21 final size:21
Alignment explanation
Indices: 6473350--6473598 Score: 149
Period size: 21 Copynumber: 12.0 Consensus size: 21
6473340 GATTTACATA
*
6473350 TTCGCATTGCAATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
6473371 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* ** *
6473392 TTCGCGTTGCGATTTTCCAAA
1 TTCGCATTGCGATAGTCCAAG
*
6473413 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
6473432 TTCGCGTTGCGATGTATTCCAAA
1 TTCGCATTGCGA--TAGTCCAAG
*
6473455 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
6473474 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCCAAG
*
6473497 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
6473516 TTCGCGTTGTGATTTATTCCAAG
1 TTCGCATTGCGA--TAGTCCAAG
*
6473539 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* * * *
6473558 TTCACGTTGCGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCCAAG
6473581 TTCG--TTGCGATAGTCCAA
1 TTCGCATTGCGATAGTCCAA
6473599 AATCGCAACG
Statistics
Matches: 177, Mismatches: 35, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
19 52 0.29
21 85 0.48
23 40 0.23
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:6473465 original size:42 final size:42
Alignment explanation
Indices: 6473377--6473595 Score: 388
Period size: 42 Copynumber: 5.3 Consensus size: 42
6473367 CAAGTTCGCA
6473377 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
6473417 TTGCGATAGTCGAAGTTCGCGTTGCGATGTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
6473459 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
6473501 TTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
6473543 TTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
6473585 TTGCGATAGTC
1 TTGCGATAGTC
6473596 CAAAATCGCA
Statistics
Matches: 170, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
40 27 0.16
41 1 0.01
42 142 0.84
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:6475138 original size:37 final size:36
Alignment explanation
Indices: 6475084--6475184 Score: 134
Period size: 34 Copynumber: 2.8 Consensus size: 36
6475074 ATGCTTGTGA
* * * *
6475084 ATCCTATCTTTAAGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AACTCT
*
6475121 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAACTCT
6475155 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
6475185 TGACGAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
34 32 0.56
35 1 0.02
36 1 0.02
37 23 0.40
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAACTCT
Found at i:6475748 original size:22 final size:22
Alignment explanation
Indices: 6475722--6475798 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
6475712 TTGTGTTTGG
6475722 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
6475744 TCAAAGGTTTGGTATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
*
6475766 TCAAAGGTTTGTCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
6475788 TCAAAGGTTTG
1 TCAAAGGTTTG
6475799 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.40
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:6476427 original size:19 final size:18
Alignment explanation
Indices: 6476401--6476448 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
6476391 TTTTTGTCCC
6476401 TTTTTCTTTTTGATTTTG
1 TTTTTCTTTTTGATTTTG
**
6476419 TTCTTTCTTTTTTCTTTTG
1 TT-TTTCTTTTTGATTTTG
*
6476438 TTTCTCTTTTT
1 TTTTTCTTTTT
6476449 TCTTTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTTGATTTTG
Found at i:6476445 original size:18 final size:19
Alignment explanation
Indices: 6476414--6476453 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
6476404 TTCTTTTTGA
*
6476414 TTTTGTTCTTTCTTTTTTC
1 TTTTGTTCTCTCTTTTTTC
6476433 TTTTGTT-TCTCTTTTTTC
1 TTTTGTTCTCTCTTTTTTC
6476451 TTT
1 TTT
6476454 ATTTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTGTTCTCTCTTTTTTC
Found at i:6477628 original size:14 final size:15
Alignment explanation
Indices: 6477609--6477642 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
6477599 ATGAATGTAT
6477609 ATGCAAAATG-AAAA
1 ATGCAAAATGCAAAA
6477623 ATGCAAAATGCAAAA
1 ATGCAAAATGCAAAA
6477638 ATGCA
1 ATGCA
6477643 TGAGATGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (15 bp):
ATGCAAAATGCAAAA
Found at i:6479692 original size:19 final size:20
Alignment explanation
Indices: 6479670--6479721 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
6479660 TAGGATAAAG
6479670 ATAAAAAG-AAAATAGATAA
1 ATAAAAAGTAAAATAGATAA
* *
6479689 ATAAATGAGTAAAATATATAA
1 ATAAA-AAGTAAAATAGATAA
6479710 A-AAAAAGTAAAA
1 ATAAAAAGTAAAA
6479722 GCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 11 0.39
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (20 bp):
ATAAAAAGTAAAATAGATAA
Found at i:6479816 original size:2 final size:2
Alignment explanation
Indices: 6479799--6479853 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
6479789 AAAATAGGAA
* *
6479799 AT AT AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6479841 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
6479854 ATAACACTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6480574 original size:6 final size:6
Alignment explanation
Indices: 6480560--6480590 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
6480550 TCTCGTCTCG
*
6480560 GGTCGT GGTCAT GGTCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
6480591 TTAATACGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.16, G:0.48, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:6480746 original size:42 final size:42
Alignment explanation
Indices: 6480684--6480827 Score: 256
Period size: 42 Copynumber: 3.5 Consensus size: 42
6480674 TGCGATTTTG
*
6480684 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
6480726 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
6480766 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
6480808 GACTATCGCAACGAACTTTG
1 GACTATCGCAACGAA-TTTG
6480828 ACTATCACAA
Statistics
Matches: 98, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
40 39 0.40
41 2 0.02
42 53 0.54
43 4 0.04
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:6480795 original size:61 final size:57
Alignment explanation
Indices: 6480730--6480881 Score: 160
Period size: 59 Copynumber: 2.5 Consensus size: 57
6480720 AACTTCGACT
* * *
6480730 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTCGAAAATCGCAA--CGAACTTCGACTATCACAACGAATTTGG-A-AA
** *
6480791 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTTGACTATCACAACGAATTTGGAAA
1 ATCGCAA--CGAACTTCGAAAATCGCAACGAACTTCGACTATCACAACGAATTTGGAAA
**
6480850 ATCGCAACGCGAACTTCGACTATCGCAACGAA
1 ATCGCAA--CGAACTTCGAAAATCGCAACGAA
6480882 TTTGAAAAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
59 34 0.41
60 1 0.01
61 33 0.40
63 15 0.18
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (57 bp):
ATCGCAACGAACTTCGAAAATCGCAACGAACTTCGACTATCACAACGAATTTGGAAA
Found at i:6480831 original size:101 final size:100
Alignment explanation
Indices: 6480709--6480917 Score: 357
Period size: 101 Copynumber: 2.1 Consensus size: 100
6480699 CTTGGAATAA
*
6480709 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCG
1 ATCGCAAC-CGAACTTCGACTATCACAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCG
6480774 CAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
65 CAACGAATTT-GAA-AAATCGCAACGCGAACTTCGACT
*
6480812 ATCGCAA-CGAACTTTGACTATCACAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGC
1 ATCGCAACCGAACTTCGACTATCACAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGC
*
6480876 AACGAATTTGAAAAATCGCAACGCGAACTTGGACT
66 AACGAATTTGAAAAATCGCAACGCGAACTTCGACT
6480911 ATCGCAA
1 ATCGCAA
6480918 TGCGAATATG
Statistics
Matches: 103, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
99 29 0.28
100 3 0.03
101 64 0.62
103 7 0.07
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (100 bp):
ATCGCAACCGAACTTCGACTATCACAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGC
AACGAATTTGAAAAATCGCAACGCGAACTTCGACT
Found at i:6480875 original size:59 final size:61
Alignment explanation
Indices: 6480749--6480886 Score: 219
Period size: 59 Copynumber: 2.3 Consensus size: 61
6480739 AATTTGGAAA
* *
6480749 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTTGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
6480812 ATCGCAACGAACTTTGACTATCACAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTTGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
6480871 ATCGCAACGAA-TTTGA
1 ATCGCAACGAACTTTGA
6480887 AAAATCGCAA
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
58 5 0.07
59 34 0.47
60 1 0.01
61 26 0.36
63 7 0.10
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (61 bp):
ATCGCAACGAACTTTGACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:6480914 original size:40 final size:40
Alignment explanation
Indices: 6480812--6480917 Score: 162
Period size: 40 Copynumber: 2.7 Consensus size: 40
6480802 AACTTCGACT
* * *
6480812 ATCGCAA--CGAACTTTGACTATCACAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAA
6480850 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAA
*
6480890 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTCGACTATCGCAA
6480918 TGCGAATATG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 7 0.11
40 55 0.89
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (40 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAA
Found at i:6480957 original size:21 final size:21
Alignment explanation
Indices: 6480932--6480984 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
6480922 AATATGTAAA
6480932 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
6480953 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
6480974 TCGCGTTGCGA
1 TCGCATTGCGA
6480985 ATCTGGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:6484937 original size:13 final size:14
Alignment explanation
Indices: 6484913--6484941 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6484903 CCTTTGGTAT
6484913 CAATACCACATGAA
1 CAATACCACATGAA
6484927 CAATA-CACATGAA
1 CAATACCACATGAA
6484940 CA
1 CA
6484942 GTATCGATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14
Consensus pattern (14 bp):
CAATACCACATGAA
Found at i:6489807 original size:3 final size:3
Alignment explanation
Indices: 6489799--6489823 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6489789 CATTGATGTC
6489799 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
6489824 TAATAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:6494415 original size:3 final size:3
Alignment explanation
Indices: 6494401--6494446 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
6494391 CTTCTGGCTT
* * * *
6494401 TTG TTT TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG CTC TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
6494447 CATCTTTGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.02, C:0.04, G:0.26, T:0.67
Consensus pattern (3 bp):
TTG
Done.