Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008300.1 Hibiscus syriacus cultivar Beakdansim tig00110986_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: 255346
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7821 original size:12 final size:12
Alignment explanation
Indices: 7804--7864 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
7794 TTCAAAGAGG
7804 TTTTATATTTAA
1 TTTTATATTTAA
7816 TTTTATA-TT-A
1 TTTTATATTTAA
*
7826 TATTATA-TTATA
1 TTTTATATTTA-A
*
7838 TTTGAT-TTTAA
1 TTTTATATTTAA
7849 TTTTA-ATATTAA
1 TTTTATAT-TTAA
7861 TTTT
1 TTTT
7865 TTAAATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 9 0.22
11 8 0.20
12 23 0.57
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:7868 original size:14 final size:14
Alignment explanation
Indices: 7849--7897 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
7839 TTGATTTTAA
7849 TTTTAATATTAATT
1 TTTTAATATTAATT
7863 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
7873 ATTAAATATTAATT
1 TTTTAATATTAATT
7887 TTTTAATATTA
1 TTTTAATATTA
7898 TATTATAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 4 0.15
11 1 0.04
12 6 0.22
13 1 0.04
14 15 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:8493 original size:31 final size:31
Alignment explanation
Indices: 8435--8494 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
8425 TAGTTGTATG
* *
8435 AATTATTTAAATCTCAGTATTATAAAACTAA
1 AATTATTTAAATCTCAATATTAGAAAACTAA
*
8466 AATTATTTAAATCTCAATATTGGAAAACT
1 AATTATTTAAATCTCAATATTAGAAAACT
8495 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTAGAAAACTAA
Found at i:8797 original size:2 final size:2
Alignment explanation
Indices: 8792--8839 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
8782 TCCGTTTTAT
8792 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
8834 TA TA TA
1 TA TA TA
8840 AAAAGATTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9876 original size:2 final size:2
Alignment explanation
Indices: 9871--9895 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9861 AGCGGTAACA
9871 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9896 CTTATAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12708 original size:20 final size:20
Alignment explanation
Indices: 12683--12733 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
12673 GAGTACACTC
12683 GTGTCGGACACAACACAGAT
1 GTGTCGGACACAACACAGAT
12703 GTGTCGGACACAACACAGAT
1 GTGTCGGACACAACACAGAT
*
12723 GTGTCCGACAC
1 GTGTCGGACAC
12734 TTACTCCCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
GTGTCGGACACAACACAGAT
Found at i:12764 original size:33 final size:33
Alignment explanation
Indices: 12722--12784 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
12712 ACAACACAGA
** *
12722 TGTGTCCGACACTTACTCCCTGGTCTAGGTGAT
1 TGTGTCCGACACAAACTCCCTAGTCTAGGTGAT
12755 TGTGTCCGACACAAACTCCCTAGTCTAGGT
1 TGTGTCCGACACAAACTCCCTAGTCTAGGT
12785 AACATGGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.30
Consensus pattern (33 bp):
TGTGTCCGACACAAACTCCCTAGTCTAGGTGAT
Found at i:24610 original size:23 final size:23
Alignment explanation
Indices: 24563--24615 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
24553 AAGCGCAATG
* *
24563 GTAAA-GAGAGGAGAGAAATTAA
1 GTAAATGAGAGGAGAAAAATGAA
* *
24585 GTAGATGAGAGGAGAAAAATGGA
1 GTAAATGAGAGGAGAAAAATGAA
24608 GTAAATGA
1 GTAAATGA
24616 AGCGATTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.51, C:0.00, G:0.34, T:0.15
Consensus pattern (23 bp):
GTAAATGAGAGGAGAAAAATGAA
Found at i:25124 original size:20 final size:20
Alignment explanation
Indices: 25099--25251 Score: 112
Period size: 20 Copynumber: 7.3 Consensus size: 20
25089 CAACACGATC
25099 TCAAATTCGCAACGCGGAAG
1 TCAAATTCGCAACGCGGAAG
* *
25119 TCAAATTTGCAACGC-GAAT
1 TCAAATTCGCAACGCGGAAG
* * * *
25138 TTATAAATCGCAACACAGAAG
1 TCA-AATTCGCAACGCGGAAG
25159 TCAAATTCGCAACGC-GATAG
1 TCAAATTCGCAACGCGGA-AG
* *
25179 TCAAATTTGCAACGCGAAAG
1 TCAAATTCGCAACGCGGAAG
* *
25199 TCAAATTTGTAAATCGCAACACAGAAG
1 TCAAA----T---TCGCAACGCGGAAG
*
25226 TCAAATTCGCAACGCGAAAG
1 TCAAATTCGCAACGCGGAAG
25246 TCAAAT
1 TCAAAT
25252 GTTTTTACGC
Statistics
Matches: 103, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
19 7 0.07
20 73 0.71
21 6 0.06
23 1 0.01
24 1 0.01
27 15 0.15
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
TCAAATTCGCAACGCGGAAG
Found at i:25288 original size:67 final size:66
Alignment explanation
Indices: 25099--25251 Score: 210
Period size: 67 Copynumber: 2.4 Consensus size: 66
25089 CAACACGATC
* * *
25099 TCAAATTCGCAACGCGGAAGTCAAATTTGCAACGC----G--AATTTATAAATCGCAACACAGAA
1 TCAAATTCGCAACGCGAAAGTCAAATTTGCAACGCGAAAGCAAATATGTAAATCGCAACACAGAA
25158 G
66 G
* *
25159 TCAAATTCGCAACGCGATAGTCAAATTTGCAACGCGAAAGTCAAATTTGTAAATCGCAACACAGA
1 TCAAATTCGCAACGCGAAAGTCAAATTTGCAACGCGAAAG-CAAATATGTAAATCGCAACACAGA
25224 AG
65 AG
25226 TCAAATTCGCAACGCGAAAGTCAAAT
1 TCAAATTCGCAACGCGAAAGTCAAAT
25252 GTTTTTACGC
Statistics
Matches: 82, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
60 33 0.40
64 1 0.01
67 48 0.59
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (66 bp):
TCAAATTCGCAACGCGAAAGTCAAATTTGCAACGCGAAAGCAAATATGTAAATCGCAACACAGAA
G
Found at i:25407 original size:22 final size:22
Alignment explanation
Indices: 25381--25429 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
25371 GCGGCGACAA
25381 CCGTCCCCATCTCCGACGAAAT
1 CCGTCCCCATCTCCGACGAAAT
* * *
25403 TCGTCCCCATTTCTGACGAAAT
1 CCGTCCCCATCTCCGACGAAAT
25425 CCGTC
1 CCGTC
25430 TATCTCCATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.41, G:0.14, T:0.24
Consensus pattern (22 bp):
CCGTCCCCATCTCCGACGAAAT
Found at i:25660 original size:13 final size:13
Alignment explanation
Indices: 25642--25673 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
25632 AGTATTTGTC
*
25642 TTTGTTTTGTCTT
1 TTTGTTTTGTATT
25655 TTTGTTTTGTATT
1 TTTGTTTTGTATT
25668 TTTGTT
1 TTTGTT
25674 GAAGAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTGTTTTGTATT
Found at i:25742 original size:19 final size:20
Alignment explanation
Indices: 25702--25744 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
25692 AACACCAAAT
25702 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
25722 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
25741 TCGC
1 TCGC
25745 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:25782 original size:20 final size:20
Alignment explanation
Indices: 25741--25782 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
25731 GAAACTAAAA
* * *
25741 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTAAGTT
25761 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
25781 TC
1 TC
25783 AGAAACTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:27462 original size:20 final size:20
Alignment explanation
Indices: 27437--27636 Score: 133
Period size: 20 Copynumber: 10.0 Consensus size: 20
27427 TTACGAAATT
27437 AAATTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
*
27457 AAATTC-AGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
*
27476 AAATTC-AGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
**
27495 ACTTTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
* *
27515 -ACTATCGCGTTGCTAATTTG
1 AAAT-TCGCGTTGCGAATTTG
* * ***
27535 GAATATCACAACGCGAATTTGG
1 AAAT-TCGCGTTGCGAATTT-G
* **
27557 AAAATCGCAATGCG-ATTT-
1 AAATTCGCGTTGCGAATTTG
27575 ACATATTCGCGTTGCGAATTTG
1 A-A-ATTCGCGTTGCGAATTTG
* * * *
27597 GAA-GCTGGGTTGCGAAATTG
1 AAATTC-GCGTTGCGAATTTG
*
27617 GAATTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
27637 TTGGTCATTT
Statistics
Matches: 143, Mismatches: 27, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.01
19 38 0.27
20 74 0.52
21 27 0.19
22 3 0.02
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (20 bp):
AAATTCGCGTTGCGAATTTG
Found at i:27467 original size:19 final size:19
Alignment explanation
Indices: 27445--27515 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
27435 TTAAATTCGC
27445 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
27464 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
** *
27483 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTC-A
27503 GTTGCGAATTTGA
1 GTTGCGAATTTGA
27516 CTATCGCGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 35 0.73
20 13 0.27
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:27571 original size:21 final size:21
Alignment explanation
Indices: 27529--27571 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27519 TCGCGTTGCT
*
27529 AATTTGGAATATCACAACGCG
1 AATTTGGAAAATCACAACGCG
* *
27550 AATTTGGAAAATCGCAATGCG
1 AATTTGGAAAATCACAACGCG
27571 A
1 A
27572 TTTACATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (21 bp):
AATTTGGAAAATCACAACGCG
Found at i:28059 original size:2 final size:2
Alignment explanation
Indices: 28052--28076 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28042 AAAATAAATT
28052 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28077 TATTTCGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36780 original size:19 final size:19
Alignment explanation
Indices: 36756--36795 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
36746 TAAATAGTTA
36756 ATTATTTAACGATGCAATG
1 ATTATTTAACGATGCAATG
*
36775 ATTATTTAACGATGTAATG
1 ATTATTTAACGATGCAATG
36794 AT
1 AT
36796 AAAATAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (19 bp):
ATTATTTAACGATGCAATG
Found at i:36984 original size:21 final size:21
Alignment explanation
Indices: 36940--36984 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
36930 AAATTACGTG
*
36940 TTTAGTACCTAAACTATCAGT
1 TTTAGTACCTAAACTATCAAT
* *
36961 TTTAGTACCTAAACTTTTAAT
1 TTTAGTACCTAAACTATCAAT
36982 TTT
1 TTT
36985 TTAAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAAT
Found at i:41155 original size:15 final size:15
Alignment explanation
Indices: 41137--41175 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
41127 TAACCGGTTT
41137 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
41152 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
41167 CGATTTTAA
1 CGGTTTTAA
41176 TATTCCAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:41591 original size:13 final size:13
Alignment explanation
Indices: 41570--41624 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
41560 AAGTTCGATA
*
41570 AATTCAAATACTT
1 AATTGAAATACTT
41583 AATTGAAATACTT
1 AATTGAAATACTT
* *
41596 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
41610 AATTGAAATACTT
1 AATTGAAATACTT
41623 AA
1 AA
41625 ATACTTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:41655 original size:33 final size:33
Alignment explanation
Indices: 41610--41708 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
41600 AACTCAACAT
* * *
41610 AATTGAAATACTTAAATACTTTCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
*
41643 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
41676 AATTCAAATACTTAAAAAC-TTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
41708 A
1 A
41709 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 13 0.21
33 48 0.79
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTTCAAGTTCGATA
Found at i:41727 original size:21 final size:21
Alignment explanation
Indices: 41703--41742 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41693 ACTTCAAGTT
41703 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
41724 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
41743 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:44059 original size:11 final size:12
Alignment explanation
Indices: 44038--44069 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
44028 TCCGGATAAA
44038 AACCGGTTTTTT
1 AACCGGTTTTTT
44050 AACCGGTTTTTT
1 AACCGGTTTTTT
*
44062 ATCCGGTT
1 AACCGGTT
44070 AAAATACCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:52926 original size:14 final size:14
Alignment explanation
Indices: 52907--52937 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52897 AAATGAACAC
52907 AAATGAACGAATAT
1 AAATGAACGAATAT
*
52921 AAATGAACGAATGT
1 AAATGAACGAATAT
52935 AAA
1 AAA
52938 CTAACATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (14 bp):
AAATGAACGAATAT
Found at i:52972 original size:20 final size:20
Alignment explanation
Indices: 52926--52966 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
52916 AATATAAATG
* *
52926 AACGAATGTAAACTAACATA
1 AACGAACGTAAACAAACATA
52946 AACGAACGTAAACAAACATA
1 AACGAACGTAAACAAACATA
52966 A
1 A
52967 GTGAACACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.17, G:0.10, T:0.15
Consensus pattern (20 bp):
AACGAACGTAAACAAACATA
Found at i:63520 original size:3 final size:3
Alignment explanation
Indices: 63512--63573 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
63502 TGACGTCTCA
63512 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
63560 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
63574 GGGTAAATTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:65548 original size:17 final size:17
Alignment explanation
Indices: 65526--65566 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
65516 GTATTTTTAT
65526 ATCAAAATGAATATTAA
1 ATCAAAATGAATATTAA
65543 ATCAAAATGAATATTAA
1 ATCAAAATGAATATTAA
65560 ATCAAAA
1 ATCAAAA
65567 AATAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (17 bp):
ATCAAAATGAATATTAA
Found at i:67526 original size:6 final size:6
Alignment explanation
Indices: 67507--67543 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
67497 AAAGAAGCAA
*
67507 TTAT-T TTAT-T TTATTT TTATGT TTATGT TTATGT TTA
1 TTATGT TTATGT TTATGT TTATGT TTATGT TTATGT TTA
67544 CTAGAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (6 bp):
TTATGT
Found at i:72243 original size:12 final size:12
Alignment explanation
Indices: 72228--72271 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
72218 GCAGCAGCAG
*
72228 CAACAGCATCAT
1 CAACAGCATCAA
* *
72240 CAACAACAACAA
1 CAACAGCATCAA
72252 CAACAGCATCAA
1 CAACAGCATCAA
72264 CAACAGCA
1 CAACAGCA
72272 ACAGCAGGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.52, C:0.34, G:0.07, T:0.07
Consensus pattern (12 bp):
CAACAGCATCAA
Found at i:72264 original size:18 final size:18
Alignment explanation
Indices: 72243--72277 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
72233 GCATCATCAA
72243 CAACAACAACAACAGCAT
1 CAACAACAACAACAGCAT
*
72261 CAACAACAGCAACAGCA
1 CAACAACAACAACAGCA
72278 GGAGCAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.34, G:0.09, T:0.03
Consensus pattern (18 bp):
CAACAACAACAACAGCAT
Found at i:72275 original size:6 final size:6
Alignment explanation
Indices: 72219--72277 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
72209 AAAAATGCAG
* * * * * * *
72219 CAGCAG CAGCAA CAGCAT CATCAA CAACAA CAACAA CAGCAT CAACAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA
72267 CAGCAA CAGCA
1 CAGCAA CAGCA
72278 GGAGCAACAT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.49, C:0.34, G:0.12, T:0.05
Consensus pattern (6 bp):
CAGCAA
Found at i:73684 original size:5 final size:5
Alignment explanation
Indices: 73663--73709 Score: 78
Period size: 5 Copynumber: 9.4 Consensus size: 5
73653 AACAAAAGGA
73663 AAAAG AAGAAG -AAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
73710 GGGGGGGGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 3 0.08
5 34 0.85
6 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:79577 original size:2 final size:2
Alignment explanation
Indices: 79570--79595 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
79560 CCCTTTCTTC
79570 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
79596 TTCCTCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:80866 original size:14 final size:15
Alignment explanation
Indices: 80755--80872 Score: 139
Period size: 15 Copynumber: 7.5 Consensus size: 15
80745 TAATAAGGTT
80755 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
80770 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
80785 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
80800 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
80815 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
80834 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
80852 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
80866 ATTTATT
1 ATTTATT
80873 AGTATTGATT
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.13
15 58 0.64
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:80891 original size:22 final size:22
Alignment explanation
Indices: 80879--80919 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
80869 TATTAGTATT
80879 GATTGATTTATTTTGAAATATG
1 GATTGATTTATTTTGAAATATG
80901 GATTGATTTATTTT-AAATA
1 GATTGATTTATTTTGAAATA
80920 ATTTATTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (22 bp):
GATTGATTTATTTTGAAATATG
Found at i:80910 original size:69 final size:67
Alignment explanation
Indices: 80770--80984 Score: 210
Period size: 69 Copynumber: 3.2 Consensus size: 67
80760 TTTTAAAATA
80770 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
80835 TG
66 TG
* ** * * * * *
80837 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATTGATTGATTTATTTTGAAATATG
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATG
80901 GATTG
63 GATTG
* * * * *
80906 ATTTATTTT-AAATAATTTATTAGTATGTATTGATTTATTTT-AAAT-AA-T-TTAT-TAGTATG
1 ATTTATTTTAAAATAATTTATTA-TA--AAATAATTTATTTTAAAATAAATTATTATAAAATATG
80965 GATTG
63 GATTG
80970 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
80985 TGGATTGATT
Statistics
Matches: 122, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
64 19 0.16
65 8 0.07
66 14 0.11
67 23 0.19
68 15 0.12
69 32 0.26
70 2 0.02
72 9 0.07
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
TG
Found at i:80940 original size:32 final size:31
Alignment explanation
Indices: 80901--80981 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 31
80891 TTGAAATATG
80901 GATTGATTTATTTTAAATAATTTATTAGTAT
1 GATTGATTTATTTTAAATAATTTATTAGTAT
80932 GTATTGATTTATTTTAAATAATTTATTAGTAT
1 G-ATTGATTTATTTTAAATAATTTATTAGTAT
80964 GGATTGATTTATTTTAAA
1 -GATTGATTTATTTTAAA
80982 ATATGGATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
31 1 0.02
32 46 0.96
33 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (31 bp):
GATTGATTTATTTTAAATAATTTATTAGTAT
Found at i:80977 original size:22 final size:23
Alignment explanation
Indices: 80952--81025 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 23
80942 ATTTTAAATA
80952 ATTTAT-TAGTATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
80974 ATTT-TAAAATATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
80996 ATTATTGTAATTGTATGGATTGATTT
1 A-T-TTAT-ATAGTATGGATTGATTT
81022 ATTT
1 ATTT
81026 TAAATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.02
22 19 0.45
23 1 0.02
24 4 0.10
25 2 0.05
26 15 0.36
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (23 bp):
ATTTATATAGTATGGATTGATTT
Found at i:81012 original size:26 final size:23
Alignment explanation
Indices: 80959--81026 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 23
80949 ATAATTTATT
80959 AGTATGGATTGATTTA-TTTTAA
1 AGTATGGATTGATTTATTTTTAA
*
80981 AATATGGATTGATTTATTATTGTAA
1 AGTATGGATTGATTTATT-TT-TAA
*
81006 TTGTATGGATTGATTTATTTT
1 -AGTATGGATTGATTTATTTT
81027 AAATAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
22 15 0.38
23 1 0.03
24 2 0.05
25 5 0.13
26 16 0.41
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (23 bp):
AGTATGGATTGATTTATTTTTAA
Found at i:81083 original size:31 final size:31
Alignment explanation
Indices: 81008--81155 Score: 215
Period size: 31 Copynumber: 5.0 Consensus size: 31
80998 TATTGTAATT
81008 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
81040 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
81072 GTATGATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
81103 GTATGATTGATTTATTTT-AA-AA--TA-T-
1 GTATGATTGATTTATTTTAAATAATTTATTA
81128 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
81156 TTGTAGTTGT
Statistics
Matches: 109, Mismatches: 1, Indels: 16
0.87 0.01 0.13
Matches are distributed among these distances:
22 14 0.13
23 2 0.02
24 2 0.02
25 1 0.01
26 3 0.03
27 3 0.03
29 2 0.02
30 2 0.02
31 45 0.41
32 35 0.32
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (31 bp):
GTATGATTGATTTATTTTAAATAATTTATTA
Found at i:81087 original size:63 final size:56
Alignment explanation
Indices: 80852--81155 Score: 307
Period size: 54 Copynumber: 5.4 Consensus size: 56
80842 TTTTAAAATA
*
80852 ATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTGAAATATG---GATTG
1 ATTTATTTTAAATAATTTATTAGTA-TGATTGATTTATTTTAAAATATGTATGATTG
80906 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTT-AA-AA--TA-T-GTAT-GATTG
**
80970 ATTTATTTT-AA-AA--TA-T-G---GATTGATTTATTATTGTAAT-TGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTGATTTATT-TTAAAATATGTAT-GATTG
81018 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTAGTATGATTG
1 ATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTT-AA-AA--TA-T-GTATGATTG
81081 ATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATG---GATTG
1 ATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGTATGATTG
81134 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
81156 TTGTAGTTGT
Statistics
Matches: 216, Mismatches: 5, Indels: 59
0.77 0.02 0.21
Matches are distributed among these distances:
48 19 0.09
49 3 0.01
50 2 0.01
51 1 0.00
52 2 0.01
53 32 0.15
54 50 0.23
55 4 0.02
56 3 0.01
57 3 0.01
58 17 0.08
59 4 0.02
60 5 0.02
61 3 0.01
62 16 0.07
63 34 0.16
64 18 0.08
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (56 bp):
ATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAATATGTATGATTG
Found at i:87526 original size:44 final size:44
Alignment explanation
Indices: 87463--87553 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
87453 CTAAACTTTT
87463 AATATTTTTTCAAAACTTAATGTTAAATTTTATACAGCTATTCA
1 AATATTTTTTCAAAACTTAATGTTAAATTTTATACAGCTATTCA
87507 AATATTTTTTCAAAACTTAATGTTAAATTTTATACAGCTATTCA
1 AATATTTTTTCAAAACTTAATGTTAAATTTTATACAGCTATTCA
87551 AAT
1 AAT
87554 GAAACAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (44 bp):
AATATTTTTTCAAAACTTAATGTTAAATTTTATACAGCTATTCA
Found at i:88295 original size:6 final size:6
Alignment explanation
Indices: 88284--88309 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
88274 TAGCCATACA
88284 TTTCCT TTTCCT TTTCCT TTTCCT TT
1 TTTCCT TTTCCT TTTCCT TTTCCT TT
88310 ATTAGATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCCT
Found at i:89839 original size:6 final size:6
Alignment explanation
Indices: 89828--89854 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
89818 CTGAGACATA
89828 TGGATG TGGATG TGGATG TGGATG TGG
1 TGGATG TGGATG TGGATG TGGATG TGG
89855 TAAAATAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
TGGATG
Found at i:90903 original size:23 final size:23
Alignment explanation
Indices: 90883--90986 Score: 67
Period size: 23 Copynumber: 4.7 Consensus size: 23
90873 TATATTTGTC
90883 CCAAATGACCACATAGGTTTGCA
1 CCAAATGACCACATAGGTTTGCA
* * *
90906 CCGAGTGA-CACATA--ATTGTC-
1 CCAAATGACCACATAGGTTTG-CA
* * *
90926 TCGAATGACCACATATGTTTGCA
1 CCAAATGACCACATAGGTTTGCA
*
90949 CCAAAGTG-CCACATAGTTTTGCA
1 CCAAA-TGACCACATAGGTTTGCA
*
90972 CCGAAGTG-CCACATA
1 CC-AAATGACCACATA
90987 ATTATCCTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
20 9 0.14
21 7 0.11
22 7 0.11
23 36 0.57
24 4 0.06
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (23 bp):
CCAAATGACCACATAGGTTTGCA
Found at i:90906 original size:44 final size:44
Alignment explanation
Indices: 90856--90963 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 44
90846 TAACTCGTAA
* *
90856 TTTGCACCGAAGTGCCATATATTTGTCCCAAATGACCACATAGG
1 TTTGCACCGAAGTGCCACATAATTGTCCCAAATGACCACATAGG
* * * *
90900 TTTGCACCG-AGTGACACATAATTGTCTCGAATGACCACATATG
1 TTTGCACCGAAGTGCCACATAATTGTCCCAAATGACCACATAGG
*
90943 TTTGCACCAAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
90964 GTTTTGCACC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 36 0.65
44 19 0.35
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (44 bp):
TTTGCACCGAAGTGCCACATAATTGTCCCAAATGACCACATAGG
Found at i:91008 original size:21 final size:21
Alignment explanation
Indices: 90984--91024 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
90974 GAAGTGCCAC
*
90984 ATAATTATCCTGAAGGACCAT
1 ATAATTATCCCGAAGGACCAT
*
91005 ATAATTGTCCCGAAGGACCA
1 ATAATTATCCCGAAGGACCA
91025 CTTAGAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (21 bp):
ATAATTATCCCGAAGGACCAT
Found at i:92577 original size:8 final size:8
Alignment explanation
Indices: 92566--92595 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
92556 TTACTTATAA
92566 TTGAAGAG
1 TTGAAGAG
92574 TTGAAGAG
1 TTGAAGAG
92582 TTGAAGAG
1 TTGAAGAG
92590 TTGAAG
1 TTGAAG
92596 GGTAATGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (8 bp):
TTGAAGAG
Found at i:95272 original size:21 final size:21
Alignment explanation
Indices: 95233--95272 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
95223 CCCTCTATAT
*
95233 ATTATTTTTTTCAATTAAATC
1 ATTATTTTTTTCAAATAAATC
95254 ATTATTTTTATT-AAATAAA
1 ATTATTTTT-TTCAAATAAA
95273 AAATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATTTTTTTCAAATAAATC
Found at i:96089 original size:32 final size:30
Alignment explanation
Indices: 96053--96120 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
96043 GCATTAAGCA
*
96053 TTAATTGAATCAATTTTTTTCGATTTGAGAAT
1 TTAATTGAATCAA-TTTCTT-GATTTGAGAAT
* * *
96085 TTAATTGATTTAATTTCTTGATTTGAGAGT
1 TTAATTGAATCAATTTCTTGATTTGAGAAT
96115 TTAATT
1 TTAATT
96121 AGATGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 16 0.50
31 5 0.16
32 11 0.34
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.53
Consensus pattern (30 bp):
TTAATTGAATCAATTTCTTGATTTGAGAAT
Found at i:97433 original size:19 final size:19
Alignment explanation
Indices: 97381--97433 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
97371 TCTAGTTTCC
*
97381 TTTTTCATTTT-ATTACTA
1 TTTTTCATTTTAATTACGA
*
97399 TTTTTTATTTTAAATTA-GA
1 TTTTTCATTTT-AATTACGA
97418 TTTTTCATTTCTAATT
1 TTTTTCATTT-TAATT
97434 TCAAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 10 0.34
19 14 0.48
20 5 0.17
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTCATTTTAATTACGA
Found at i:100795 original size:44 final size:43
Alignment explanation
Indices: 100747--100830 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 43
100737 TACTAATTTA
* *
100747 TTAATAGATAATAAAAAAGA-TAAATTATTAATCTATTAATTTTT
1 TTAATAAATAA-AAAAAAGATTAAATTATTAAT-TAATAATTTTT
* *
100791 TTAATAAATAAAAAAAATATTGAATTATTAATTAATAATT
1 TTAATAAATAAAAAAAAGATTAAATTATTAATTAATAATT
100831 ATTATACCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 14 0.40
44 21 0.60
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.42
Consensus pattern (43 bp):
TTAATAAATAAAAAAAAGATTAAATTATTAATTAATAATTTTT
Found at i:101967 original size:2 final size:2
Alignment explanation
Indices: 101960--101995 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
101950 CAACCAACAA
101960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
101996 CACTTTTCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:108344 original size:29 final size:30
Alignment explanation
Indices: 108286--108365 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
108276 TTTCAGTAAG
* * *
108286 TTTAACGAGCACACGTCGAGTC-GAAGTTT
1 TTTAACGAGCACAAGTCGAGTCAAAATTTT
108315 TTTAACGAGCACAAGTCGAG-CAACAATTTT
1 TTTAACGAGCACAAGTCGAGTCAA-AATTTT
*
108345 TTTAACAAGCACGAA-TCGAGT
1 TTTAACGAGCAC-AAGTCGAGT
108366 ACTGCTCAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
28 1 0.02
29 19 0.44
30 21 0.49
31 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (30 bp):
TTTAACGAGCACAAGTCGAGTCAAAATTTT
Found at i:108434 original size:12 final size:12
Alignment explanation
Indices: 108417--108443 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
108407 GACCGGACAA
108417 AATAATAATAGC
1 AATAATAATAGC
108429 AATAATAATAGC
1 AATAATAATAGC
108441 AAT
1 AAT
108444 GAGATTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (12 bp):
AATAATAATAGC
Found at i:110804 original size:29 final size:29
Alignment explanation
Indices: 110750--110809 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
110740 AAATGAAATG
110750 AAAAACTAAAAATTAGGTATATAACA-GA
1 AAAAACTAAAAATTAGGTATATAACACGA
*
110778 AAAAACTAATAGATTAGGTACTA-AACACGA
1 AAAAACTAA-AAATTAGGTA-TATAACACGA
110808 AA
1 AA
110810 TTTACCCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.32
29 13 0.46
30 6 0.21
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (29 bp):
AAAAACTAAAAATTAGGTATATAACACGA
Found at i:118810 original size:14 final size:14
Alignment explanation
Indices: 118791--118833 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
118781 AACATGCTTG
118791 AATGAATAAAAATA
1 AATGAATAAAAATA
*
118805 AATGAACAAAAAGTA
1 AATGAATAAAAA-TA
118820 AA-G-ATAAAAATA
1 AATGAATAAAAATA
118832 AA
1 AA
118834 AATATACGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 4 0.15
13 6 0.23
14 12 0.46
15 4 0.15
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (14 bp):
AATGAATAAAAATA
Found at i:125008 original size:26 final size:27
Alignment explanation
Indices: 124950--125039 Score: 164
Period size: 27 Copynumber: 3.4 Consensus size: 27
124940 CAAAACAGTG
*
124950 TGAATGATTCAACACAGAAGTACATTA
1 TGAATGATTCAGCACAGAAGTACATTA
124977 TGAATGATTCAGCACAGAAGT-CATTA
1 TGAATGATTCAGCACAGAAGTACATTA
125003 TGAATGATTCAGCACAGAAGTACATTA
1 TGAATGATTCAGCACAGAAGTACATTA
125030 TGAATGATTC
1 TGAATGATTC
125040 GAGCCATTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
26 26 0.43
27 35 0.57
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (27 bp):
TGAATGATTCAGCACAGAAGTACATTA
Found at i:128293 original size:3 final size:3
Alignment explanation
Indices: 128281--128325 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
128271 AAAATGTTAG
128281 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATGA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
128326 TTAAATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:128531 original size:28 final size:28
Alignment explanation
Indices: 128487--128541 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
128477 AGAATAATAA
*
128487 AAAATAGAAATAAGTTAAATAAA-AAATG
1 AAAATAGAAAAAAGTTAAA-AAATAAATG
128515 AAAATA-AAAAAAGGTTAAAAAATAAAT
1 AAAATAGAAAAAA-GTTAAAAAATAAAT
128542 ATTAACAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (28 bp):
AAAATAGAAAAAAGTTAAAAAATAAATG
Found at i:129932 original size:32 final size:31
Alignment explanation
Indices: 129889--129963 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
129879 CAATATAGCG
* * *
129889 TATATAATATATAAAAAAATATTTTTTTAAAC
1 TATATATTATATAAAAAAAT-GTTTTTAAAAC
**
129921 TATATATTATATTTAAAAATGTTTTTAAAAC
1 TATATATTATATAAAAAAATGTTTTTAAAAC
129952 TATAT-TTATATA
1 TATATATTATATA
129964 GTTTTTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 6 0.16
31 14 0.38
32 17 0.46
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (31 bp):
TATATATTATATAAAAAAATGTTTTTAAAAC
Found at i:130006 original size:32 final size:34
Alignment explanation
Indices: 129936--130166 Score: 109
Period size: 34 Copynumber: 6.7 Consensus size: 34
129926 ATTATATTTA
* * * *
129936 AAAATGTTTTTAAAACTATATTTATATAGTTTTT
1 AAAATGTTTTTAAAAATATATATACATAGTTTTC
*
129970 AAAATGATTTTAAAAATATA-ATACA-AGTTTTC
1 AAAATGTTTTTAAAAATATATATACATAGTTTTC
* ** * *
130002 AAAATGTTTTTTAAGCTATATATTATATAAATTTTCC
1 AAAATGTTTTTAAAAATATATA-TACAT-AGTTTT-C
* *
130039 AAAAATGTTTTTTAAAA-A-CTAT--ATA-TTTTC
1 -AAAATGTTTTTAAAAATATATATACATAGTTTTC
** * * * *
130069 AAAATGACTTCAAAACTATATATTATATAATTTTC
1 AAAATGTTTTTAAAAATATATA-TACATAGTTTTC
* *
130104 AAAATG-TTTTAAAACTTATATATTGTATATAAGTTTTC
1 AAAATGTTTTTAAAA---ATATA-TATACAT-AGTTTTC
* *
130142 AAAAACGTTTTAAAAAATATATATA
1 -AAAATGTTTTTAAAAATATATATA
130167 TTTTTTCGGA
Statistics
Matches: 150, Mismatches: 28, Indels: 36
0.70 0.13 0.17
Matches are distributed among these distances:
29 11 0.07
30 2 0.01
31 6 0.04
32 24 0.16
33 6 0.04
34 30 0.20
35 12 0.08
36 10 0.07
37 16 0.11
38 21 0.14
39 5 0.03
40 7 0.05
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (34 bp):
AAAATGTTTTTAAAAATATATATACATAGTTTTC
Found at i:130163 original size:39 final size:36
Alignment explanation
Indices: 130058--130165 Score: 103
Period size: 35 Copynumber: 3.0 Consensus size: 36
130048 TTTTAAAAAC
* ** * *
130058 TATAT-ATTTTCAAAATGACTTCAAAACTATATA-T
1 TATATAATTTTCAAAACGTTTTAAAAAATATATATT
* **
130092 TATATAATTTTCAAAATGTTTTAAAACTTATATATT
1 TATATAATTTTCAAAACGTTTTAAAAAATATATATT
130128 GTATATAAGTTTTCAAAAACGTTTTAAAAAATATATAT
1 -TATATAA-TTTTC-AAAACGTTTTAAAAAATATATAT
130166 ATTTTTTCGG
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
34 5 0.08
35 23 0.38
36 1 0.02
37 7 0.11
38 5 0.08
39 20 0.33
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (36 bp):
TATATAATTTTCAAAACGTTTTAAAAAATATATATT
Found at i:130231 original size:2 final size:2
Alignment explanation
Indices: 130226--130265 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
130216 ATTTTAAAAA
*
130226 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
130266 ATAAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:137728 original size:5 final size:6
Alignment explanation
Indices: 137701--137734 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
137691 AATATTTTTT
137701 AAATAA ATAATTAA AAATAA AAATAA AAATAA AA
1 AAATAA A-AA-TAA AAATAA AAATAA AAATAA AA
137735 GATGGTCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 18 0.69
7 4 0.15
8 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:163333 original size:29 final size:31
Alignment explanation
Indices: 163280--163356 Score: 113
Period size: 29 Copynumber: 2.5 Consensus size: 31
163270 TGGTATTTAT
163280 TATATTCACAATACTATATTCTAAAATTATAAAA
1 TATATTCACAATAC-A-A-TCTAAAATTATAAAA
163314 TATA-TCA-AATACAATCTAAAATTATAAAA
1 TATATTCACAATACAATCTAAAATTATAAAA
163343 TATATTCACAATAC
1 TATATTCACAATAC
163357 TATATTCTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
29 19 0.46
30 4 0.10
31 6 0.15
32 5 0.12
33 3 0.07
34 4 0.10
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (31 bp):
TATATTCACAATACAATCTAAAATTATAAAA
Found at i:164660 original size:18 final size:16
Alignment explanation
Indices: 164622--164667 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
164612 TATGGAATTG
164622 GATTCCAATTCCTACA
1 GATTCCAATTCCTACA
*
164638 TATTCCAATTCCTTTACA
1 GATTCCAATTCC--TACA
164656 GATTCCAATTCC
1 GATTCCAATTCC
164668 CTCATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.30, G:0.04, T:0.37
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:188477 original size:259 final size:254
Alignment explanation
Indices: 188185--188800 Score: 748
Period size: 259 Copynumber: 2.4 Consensus size: 254
188175 CTCCATCCGA
* *
188185 GACCCGATCCGATCAAAATAAAGTTTAACCCGACCCGACCCGACCCGAATATATGAATTAGAAAC
1 GACCCGACCCGACCAAAATAAAGTTT-A-CCGACCCGACCCGACCCGAATATATGAATTAGAAAC
* *
188250 CCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGATTTAATTGGAAAAAAAAT
64 CCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAATGACTTAATT-GAAAAAAAAT
*
188315 ATATAGAGAGAGGG-CTA-T-TT-TTATTCCTAAATATATAAGGTAAAATTATATATTTTTTGGG
128 ATATAGAGAG-GGGACTATTGTTATTATTCCTAAATATATAAGGTAAAATTATATA-TATTT---
188376 TCGGGTCGGGTATTTTTCACCATAAACCCGAACCCGACCCGACCCAAATATCACACTTAAAAAAA
188 TCGGGTCGGGTATTTTTCACCATAAACCCGAACCCGACCCGACCCAAATATCACACTT-AAAAAA
*
188441 ATC
252 ACC
** *
188444 GATGCGACCCGACCAAAATAAAGTTT--C-ACCCGACCCGACTCGAATATATGAATTAGAAATCC
1 GACCCGACCCGACCAAAATAAAGTTTACCGACCCGACCCGACCCGAATATATGAATTAG-AA---
* *
188506 GACCCGACCCGAAATAATAACAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAGAAA
62 -ACCCGACCCGAAATAATAA-AAAATTATTTTTATTTAATAAAAACAATGACTTAATTGAAAAAA
* * *
188571 AATATATATATAGGGGTATTATTGTTATTATTCCTAAATATATAAGGTAAAATTATATATATTTT
125 AATATATAGAGAGGGG-ACTATTGTTATTATTCCTAAATATATAAGGTAAAATTATATATATTTT
* * * * *
188636 CGGGTCGGGTATTTTTCACCCTAAACCTGAACTCGACCCGACCCGAATATCATACTTAAAAAAAC
189 CGGGTCGGGTATTTTTCACCATAAACCCGAACCCGACCCGACCCAAATATCACACTTAAAAAAAC
188701 C
254 C
* * * *
188702 GACCCGATCCGACCAAAATAAAGTTT--C-ACTCGACACAACCCGAATATATGAATTAGAAACCC
1 GACCCGACCCGACCAAAATAAAGTTTACCGACCCGACCCGACCCGAATATATGAATTAGAAACCC
* ** * *
188764 GACTCGATCTGAAATAAAAAAATATTCTTATTTAATA
66 GACCCGAAAT--AATAAAAAATTATTTTTATTTAATA
188801 TATTGAATAA
Statistics
Matches: 312, Mismatches: 32, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
253 11 0.04
254 45 0.14
255 8 0.03
257 2 0.01
258 60 0.19
259 111 0.36
260 36 0.12
261 1 0.00
262 6 0.02
263 32 0.10
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (254 bp):
GACCCGACCCGACCAAAATAAAGTTTACCGACCCGACCCGACCCGAATATATGAATTAGAAACCC
GACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAATGACTTAATTGAAAAAAAATATA
TAGAGAGGGGACTATTGTTATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCG
GGTATTTTTCACCATAAACCCGAACCCGACCCGACCCAAATATCACACTTAAAAAAACC
Found at i:190455 original size:18 final size:20
Alignment explanation
Indices: 190416--190456 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
190406 CTTTTAAAAA
190416 TTTAAAATTATCTTACATAT
1 TTTAAAATTATCTTACATAT
*
190436 TTTAAAATT-T-TTATATAT
1 TTTAAAATTATCTTACATAT
190454 TTT
1 TTT
190457 TATATCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 1 0.05
20 9 0.45
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAAATTATCTTACATAT
Found at i:190710 original size:21 final size:20
Alignment explanation
Indices: 190643--190781 Score: 82
Period size: 21 Copynumber: 6.8 Consensus size: 20
190633 AAATGACCAA
***
190643 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
190663 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
190683 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
190704 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
190725 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
190745 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
190766 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
190782 ACACATAAAT
Statistics
Matches: 90, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.01
20 42 0.47
21 47 0.52
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:190810 original size:20 final size:20
Alignment explanation
Indices: 190748--190940 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
190738 CGATTTTCCA
* ** *
190748 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
190768 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
190788 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
190808 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
190828 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
190848 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
190868 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
190888 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
190908 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
190928 AAATCGCAACGCG
1 AAATCGCAACGCG
190941 ATATTTAAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 144 0.97
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:191363 original size:33 final size:33
Alignment explanation
Indices: 191323--191393 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
191313 TTCACTTAGA
*
191323 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
191356 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
191389 TTTCA
1 TTTCA
191394 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:191497 original size:21 final size:21
Alignment explanation
Indices: 191471--191547 Score: 95
Period size: 21 Copynumber: 3.8 Consensus size: 21
191461 TTTGCAGAAG
191471 AATCGCAACGAGATAAATGAA
1 AATCGCAACGAGATAAATGAA
* *
191492 AATCGCAACGA-A-GAATGAC
1 AATCGCAACGAGATAAATGAA
** *
191511 TGTCGCAACGAGAGAAATGAA
1 AATCGCAACGAGATAAATGAA
191532 AATCGCAACGAGATAA
1 AATCGCAACGAGATAA
191548 TCGCAACGCG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 14 0.31
20 2 0.04
21 29 0.64
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
AATCGCAACGAGATAAATGAA
Found at i:191551 original size:14 final size:14
Alignment explanation
Indices: 191529--191593 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
191519 CGAGAGAAAT
191529 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
191543 GATAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
191561 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
191576 GAGAATCGCAACGC
1 GAAAATCGCAACGA
191590 GAAA
1 GAAA
191594 CCAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:191564 original size:33 final size:33
Alignment explanation
Indices: 191469--191604 Score: 137
Period size: 33 Copynumber: 3.8 Consensus size: 33
191459 AATTTGCAGA
*
191469 AGAATCGCAACGAGATAAATGAAAATCGCAACGAAG
1 AGAATCGCAACGCG--AAATGAAAATCGCAACG-AG
* *
191505 AATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 -A-GA--ATCGCAAC--GCGAAATGAAAATCGCAACGAG
*
191544 ATAATCGCAACGCGAAATGAAAATCGCAACGAG
1 AGAATCGCAACGCGAAATGAAAATCGCAACGAG
**
191577 AGAATCGCAACGCGAAACCAAAATCGCA
1 AGAATCGCAACGCGAAATGAAAATCGCA
191605 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
33 46 0.53
35 7 0.08
37 2 0.02
38 3 0.03
39 2 0.02
40 24 0.28
42 3 0.03
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
AGAATCGCAACGCGAAATGAAAATCGCAACGAG
Found at i:191622 original size:19 final size:19
Alignment explanation
Indices: 191600--191697 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
191590 GAAACCAAAA
*
191600 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
191619 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
191633 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
191652 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
191666 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
191685 TCGCGTTGCGATT
1 TCGCGTTGCGATT
191698 CTCTCGTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
16 6 0.09
17 6 0.09
19 32 0.50
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:191641 original size:14 final size:14
Alignment explanation
Indices: 191622--191711 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
191612 TTTCATTTCG
191622 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
191636 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
191655 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
191669 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
191688 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
191702 CGTTGCGATT
1 CGTTGCGATT
191712 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
16 6 0.10
17 6 0.10
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:191647 original size:33 final size:33
Alignment explanation
Indices: 191605--191719 Score: 230
Period size: 33 Copynumber: 3.5 Consensus size: 33
191595 CAAAATCGCA
191605 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
191638 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
191671 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
191704 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
191720 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:193573 original size:93 final size:93
Alignment explanation
Indices: 193414--193789 Score: 709
Period size: 93 Copynumber: 4.0 Consensus size: 93
193404 TTGCTTAGTT
193414 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
193479 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
193507 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
193572 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
193600 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
193665 TCTTTGTTTTGTCTTTTGGTTGAAAGTAAATA
66 TCTTTGTTTTGTCTTTTGGTTGAAAG----TA
193697 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
193762 TCTTTGTTTTGTCTTTTGGTTG-AAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
193789 A
1 A
193790 TGCAATCCAT
Statistics
Matches: 279, Mismatches: 0, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
92 3 0.01
93 184 0.66
96 3 0.01
97 89 0.32
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTTGGTTGAAAGTA
Found at i:193877 original size:19 final size:19
Alignment explanation
Indices: 193837--194035 Score: 353
Period size: 19 Copynumber: 10.4 Consensus size: 19
193827 TAGTTTACTT
* *
193837 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
193857 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
193876 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
193895 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
193914 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
193933 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
193952 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
193971 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
193990 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
194009 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
194028 TCGCAACG
1 TCGCAACG
194036 ACAGAATCGC
Statistics
Matches: 174, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
19 162 0.93
20 12 0.07
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:194081 original size:19 final size:19
Alignment explanation
Indices: 194057--194102 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
194047 GCGATTCTGT
194057 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
**
194076 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTCATTTCG
*
194095 TGTTGCGA
1 CGTTGCGA
194103 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:196042 original size:14 final size:14
Alignment explanation
Indices: 196023--196058 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
196013 ATTGTTTAAT
196023 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
196037 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
196051 TGATTTGT
1 TGATTTGT
196059 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:196180 original size:19 final size:19
Alignment explanation
Indices: 196164--196270 Score: 107
Period size: 19 Copynumber: 6.4 Consensus size: 19
196154 AAAAATGACT
196164 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
196183 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
196202 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
196216 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
196234 ATCGCAA--CG--A-G--A
1 ATCGCAATGCGAAATGAAA
196246 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
196264 ATCGCAA
1 ATCGCAA
196271 CGAGAGAATC
Statistics
Matches: 75, Mismatches: 2, Indels: 23
0.75 0.02 0.23
Matches are distributed among these distances:
12 8 0.11
13 1 0.01
14 13 0.17
15 1 0.01
16 5 0.07
17 3 0.04
18 17 0.23
19 27 0.36
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:196241 original size:32 final size:32
Alignment explanation
Indices: 196182--196288 Score: 191
Period size: 30 Copynumber: 3.4 Consensus size: 32
196172 GCGAAATGAA
196182 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATG-AAATCGCAACGAGAG
196215 AATCGCAATGCGAAATGAAATCGCAAC--GAG
1 AATCGCAATGCGAAATGAAATCGCAACGAGAG
196245 AATCGCAATGCGAAATGAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAATCGCAACGAGAG
196277 AATCGCAATGCG
1 AATCGCAATGCG
196289 TTTATAATTT
Statistics
Matches: 72, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
30 30 0.42
32 25 0.35
33 17 0.24
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (32 bp):
AATCGCAATGCGAAATGAAATCGCAACGAGAG
Found at i:196341 original size:19 final size:19
Alignment explanation
Indices: 196317--196494 Score: 164
Period size: 19 Copynumber: 10.4 Consensus size: 19
196307 GATTCTCTCG
196317 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
196336 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
196355 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
196369 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
196388 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
196402 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
196421 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
*
196435 TTGCGATTTTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
196455 TTGCGA-TTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
196468 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
196487 TTGCGATT
1 TTGCGATT
196495 CTCTCGTTGC
Statistics
Matches: 131, Mismatches: 6, Indels: 44
0.72 0.03 0.24
Matches are distributed among these distances:
13 5 0.04
14 23 0.18
15 1 0.01
16 23 0.18
17 22 0.17
18 2 0.02
19 49 0.37
20 6 0.05
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:196351 original size:52 final size:51
Alignment explanation
Indices: 196295--196494 Score: 200
Period size: 52 Copynumber: 3.9 Consensus size: 51
196285 TGCGTTTATA
196295 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
196347 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TT-
1 ATTTCGCATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* * * * * *
196396 ATCTCG--TTGCGATTT-TCATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* *
196446 ATTTCCGCGTTGCGATTTCAT-GTTGGGATTTTCATTTCGCATTGCGATT
1 ATTT-CGCATTGCGATTTC-TCGTTGCGATTTTCATTTCGCATTGCGATT
196495 CTCTCGTTGC
Statistics
Matches: 122, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
45 9 0.07
46 5 0.04
47 17 0.14
49 7 0.06
50 5 0.04
51 2 0.02
52 57 0.47
53 13 0.11
54 6 0.05
55 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (51 bp):
ATTTCGCATTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:196373 original size:33 final size:33
Alignment explanation
Indices: 196336--196508 Score: 269
Period size: 33 Copynumber: 5.2 Consensus size: 33
196326 TCATTTCGCA
* *
196336 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
196369 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
196402 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
*
196435 TTGCGATTTTCATTTCCGCGTTGCGATT-TCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTATC-TCG
* *
196468 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
196501 TTGCGATT
1 TTGCGATT
196509 GTAATTTCCG
Statistics
Matches: 130, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
32 12 0.09
33 106 0.82
34 12 0.09
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCTCG
Found at i:198799 original size:12 final size:12
Alignment explanation
Indices: 198782--198806 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
198772 TCTTCGGGGA
198782 CTTTTTCTTCTT
1 CTTTTTCTTCTT
198794 CTTTTTCTTCTT
1 CTTTTTCTTCTT
198806 C
1 C
198807 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:199015 original size:24 final size:24
Alignment explanation
Indices: 198981--199027 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
198971 CTGAAACATC
198981 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
199005 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
199028 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:199735 original size:20 final size:20
Alignment explanation
Indices: 199707--199976 Score: 272
Period size: 20 Copynumber: 13.5 Consensus size: 20
199697 AAATTTCAGT
* * *
199707 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
199727 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
199747 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
199767 GTTGCGATTTATGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
199787 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
199807 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
199827 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
199847 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
199867 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
199887 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
199907 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
199927 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
199947 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
199967 GTTGCGATTT
1 GTTGCGATTT
199977 TGGAAAATCG
Statistics
Matches: 216, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
20 215 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:199767 original size:40 final size:40
Alignment explanation
Indices: 199707--199976 Score: 305
Period size: 40 Copynumber: 6.8 Consensus size: 40
199697 AAATTTCAGT
* *
199707 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* *
199747 GTTGCGATTTACAGATTCTCGTTGCGATTTATGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
199787 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* * *
199827 GTTGCGATTTACGGATACGCGTTGCGATATACGGA-TA-C
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
** * *
199865 GCATTGCGATTTACCCATACGCGTTGCGATTTACGGA-TACAC
1 G--TTGCGATTTACAGATTCGCGTTGCGATTTACGGATTA-TC
* * * **
199907 GTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACG-GATTATC
* *
199947 GTTGCGATTTTCATATTCGCGTTGCGATTT
1 GTTGCGATTTACAGATTCGCGTTGCGATTT
199977 TGGAAAATCG
Statistics
Matches: 205, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 197 0.96
41 2 0.01
42 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
Found at i:199993 original size:21 final size:21
Alignment explanation
Indices: 199963--200045 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
199953 ATTTTCATAT
*
199963 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
199984 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
200005 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
200026 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
200046 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:200036 original size:42 final size:43
Alignment explanation
Indices: 199943--200041 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
199933 ATTTATGTGT
* *
199943 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
199984 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
200026 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
200042 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:200842 original size:2 final size:2
Alignment explanation
Indices: 200835--200872 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
200825 GTTTCGTGTT
200835 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
200873 GAAGTAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:206277 original size:17 final size:18
Alignment explanation
Indices: 206243--206277 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
206233 CCTTGAAGTC
206243 ATTTCACTATCTTGGGTT
1 ATTTCACTATCTTGGGTT
*
206261 ATTTTACTATC-TGGGTT
1 ATTTCACTATCTTGGGTT
206278 TCTTTCTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (18 bp):
ATTTCACTATCTTGGGTT
Found at i:211481 original size:4 final size:4
Alignment explanation
Indices: 211472--211497 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
211462 GTGTCATTAC
211472 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
211498 TTCTATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:226223 original size:31 final size:31
Alignment explanation
Indices: 226188--226270 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
226178 AGAAAGTATA
226188 TGGATCATTTTGGTGATTTTTAAAAATAGTT
1 TGGATCATTTTGGTGATTTTTAAAAATAGTT
*
226219 TGGATCATTTTGGTGATTTTTAAAAATCGTT
1 TGGATCATTTTGGTGATTTTTAAAAATAGTT
* *
226250 TGGATCATTTTGATGACTTTT
1 TGGATCATTTTGGTGATTTTT
226271 GAATTGTACA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.49
Consensus pattern (31 bp):
TGGATCATTTTGGTGATTTTTAAAAATAGTT
Found at i:241492 original size:2 final size:2
Alignment explanation
Indices: 241485--241523 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
241475 GATCAATGCA
241485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
241524 AATCAGCCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:244226 original size:21 final size:22
Alignment explanation
Indices: 244201--244252 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
244191 ACACTTTACA
*
244201 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
244224 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
244247 ATATAA
1 ATATAA
244253 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:244237 original size:23 final size:23
Alignment explanation
Indices: 244211--244273 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
244201 ATATAACCAC
244211 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
244234 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
244257 TACCTATTACATCATAT
1 TACCTATTACATTATAT
244274 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:244651 original size:39 final size:39
Alignment explanation
Indices: 244597--244679 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
244587 TCAAGTTGTA
* *
244597 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
244636 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
244675 GATTT
1 GATTT
244680 TGATGAGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (39 bp):
GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:244965 original size:18 final size:18
Alignment explanation
Indices: 244942--244978 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
244932 CGAAATATAT
244942 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
244960 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
244978 A
1 A
244979 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:245255 original size:25 final size:25
Alignment explanation
Indices: 245227--245277 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
245217 TTAATCCAAA
*
245227 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
245252 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
245277 T
1 T
245278 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:245582 original size:23 final size:23
Alignment explanation
Indices: 245556--245618 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
245546 ATATAACCAC
245556 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* ** *
245579 TACCTATTTCATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
245602 TACCTATTACATCATAT
1 TACCTATTACATTATAT
245619 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:246036 original size:22 final size:23
Alignment explanation
Indices: 245975--246046 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
245965 AAACTTTACA
* *
245975 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
245998 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
246021 ATAT-AAGGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
246043 ATAT
1 ATAT
246047 GTTTACCTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 19 0.44
23 24 0.56
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:246394 original size:430 final size:431
Alignment explanation
Indices: 245312--247004 Score: 3229
Period size: 429 Copynumber: 3.9 Consensus size: 431
245302 GAATTATTTA
* * *
245312 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTA
1 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
* *
245377 GAATTTTTAATTTAATAATAATATATATCGCAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
** *
245442 ACTAAATTAATATCTTAAAACTCACTCAAAAGA-TAACCTTAAATTAATGTTTTCCACATTGAAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAA-ATTAATATTAAATTAATGTTTTCCACAGTGAAA
*
245506 AAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTAT
195 AAAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTAT
*
245571 ATAAACGATACCTATTTCATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTG
260 ATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTG
245636 AAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTC
325 AAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTC
245701 AA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
390 AATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
245742 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATA-TTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
245806 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
245871 ACTAAATTAATATCTTAAAACTCACTCAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAA
245936 AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
196 AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
246001 TAAACGATACCTATTACATTATATAA-GGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
246065 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
246130 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
391 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
246171 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
246236 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
246301 ACTAAATTAATATCTTAAAACTCACTCAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAA
246366 AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
196 AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
246431 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
*
246496 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATATTTCA
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
246561 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
391 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
246602 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
246667 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
246732 ACTAAATTAATATCTTAAAACTCACTCAAAAATTAATATT-AATTAATGTTTTCCACAGTG-AAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAA
246795 AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
196 AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
246860 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
246925 AAGTGTCCATAC-TTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
246989 ATTTTTTTAACAGTGT
391 ATTTTTTTAACAGTGT
247005 ACTGCGAATT
Statistics
Matches: 1247, Mismatches: 12, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
428 172 0.14
429 459 0.37
430 303 0.24
431 313 0.25
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (431 bp):
ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
ACTAAATTAATATCTTAAAACTCACTCAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAA
AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
Found at i:246430 original size:21 final size:22
Alignment explanation
Indices: 246405--246456 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
246395 AAACTTTACA
*
246405 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
246428 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
246451 ATATAA
1 ATATAA
246457 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:246441 original size:23 final size:23
Alignment explanation
Indices: 246415--246477 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
246405 ATATAACCAC
246415 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
246438 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
246461 TACCTATTACATCATAT
1 TACCTATTACATTATAT
246478 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:246859 original size:21 final size:22
Alignment explanation
Indices: 246834--246885 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
246824 AAACTTTACA
*
246834 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
246857 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
246880 ATATAA
1 ATATAA
246886 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:246870 original size:23 final size:23
Alignment explanation
Indices: 246844--246906 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
246834 ATATAACCAC
246844 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
246867 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
246890 TACCTATTACATCATAT
1 TACCTATTACATTATAT
246907 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:246970 original size:859 final size:859
Alignment explanation
Indices: 245312--247004 Score: 3223
Period size: 859 Copynumber: 2.0 Consensus size: 859
245302 GAATTATTTA
245312 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTA
*
245377 GAATTTTTAATTTAATAATAATATATATCGCAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGCAACGTAAAAAATAAATCATTAGACGCCTATAATT
* *
245442 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACATTGAAAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAA
*
245507 AAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATA
196 AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
*
245572 TAAACGATACCTATTTCATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
261 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
*
245637 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
326 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATATTTCA
245702 ATTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAGAAAA
391 ATTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAGAAAA
245767 AATTATTTGATTGTTTTTATATTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATAT
456 AATTATTTGATTGTTTTTATATTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATAT
245832 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
521 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
245897 CAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
586 CAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
245962 TAGAAACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAA
651 TAGAAACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAA
246027 GGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
716 GGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
246092 TCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTC
781 TCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTC
246157 CACCTACAATATTG
846 CACCTACAATATTG
* * *
246171 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTA
*
246236 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAATTTTTAATTTAATAATAATATATACCGCAACGTAAAAAATAAATCATTAGACGCCTATAATT
*
246301 ACTAAATTAATATCTTAAAACTCACTCAAAA-ATTAATATTAAATTAATGTTTTCCACAGTGAAA
131 ACTAAATTAATATCTTAAAACTCACTCAAAAGA-TAACATTAAATTAATGTTTTCCACAGTGAAA
246365 AAAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTAT
195 AAAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTAT
246430 ATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTG
260 ATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTG
246495 AAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATATTTC
325 AAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATATTTC
246560 AATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAGAA
390 AA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAGAA
246625 AAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATA
454 AAAATTATTTGATTGTTTTTATA-TTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATA
246690 TATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTC
518 TATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTC
246755 ACTCAAAAATTAATATT-AATTAATGTTTTCCACAGTG-AAAAAGTATGGACACTTTTATAAAAA
583 ACTCAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAA
246818 GGATAGAAACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATA
648 GGATAGAAACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATA
246883 TAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATAC-TTTTATAAAA
713 TAA-GGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAA
246947 AGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGT
777 AGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGT
247005 ACTGCGAATT
Statistics
Matches: 819, Mismatches: 11, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
858 1 0.00
859 540 0.66
860 155 0.19
861 123 0.15
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (859 bp):
ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTA
GAATTTTTAATTTAATAATAATATATACCGCAACGTAAAAAATAAATCATTAGACGCCTATAATT
ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAA
AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATATTTCA
ATTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCAGAAAA
AATTATTTGATTGTTTTTATATTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATAT
ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
CAAAAATTAATATTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
TAGAAACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAA
GGCTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
TCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTC
CACCTACAATATTG
Found at i:249792 original size:184 final size:184
Alignment explanation
Indices: 249483--250009 Score: 914
Period size: 184 Copynumber: 2.9 Consensus size: 184
249473 TTCAAATTAC
* **
249483 CGACACTTTTTTAAATGGTATCGACACATTTTTATTCCAATGGGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
249548 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
249613 ATATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTAAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTAAAATGT
*
249667 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
249732 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
249797 ATATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTAAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTAAAATGT
* *
249851 CGACAAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAC
1 CGAC-ACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAA
* * *
249915 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATTTATACCGGT
65 TATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGT
* * * *
249980 TATATTGCAAATTTACCTATT-TATTATAAT
130 TATATTACAAAATTATCTATTACATTATAAT
250010 ATGTTGAAAG
Statistics
Matches: 329, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
183 8 0.02
184 319 0.97
185 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTATTCCAATATGGACATAAAGTACCGACACAAT
ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTGCGATGTGTAAAATGT
Found at i:251478 original size:3 final size:3
Alignment explanation
Indices: 251470--251562 Score: 96
Period size: 3 Copynumber: 31.0 Consensus size: 3
251460 ACTTGTTTGG
* * * **
251470 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
251518 AGC TTC ATC GTC ATC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
251563 GTCAGCTTCA
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.25, C:0.34, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:251571 original size:12 final size:12
Alignment explanation
Indices: 251474--251574 Score: 94
Period size: 12 Copynumber: 8.4 Consensus size: 12
251464 GTTTGGATCA
* *
251474 TCATCTTCATCA
1 TCATCGTCATCT
* *
251486 TCATCATCATCA
1 TCATCGTCATCT
* *
251498 TCGTCATCATCT
1 TCATCGTCATCT
* *
251510 TCATCGCCAGCT
1 TCATCGTCATCT
*
251522 TCATCGTCATCA
1 TCATCGTCATCT
* *
251534 TCATCATCATCA
1 TCATCGTCATCT
251546 TCATCGTCATCT
1 TCATCGTCATCT
*
251558 TCATCGTCAGCT
1 TCATCGTCATCT
251570 TCATC
1 TCATC
251575 TTCTGCGACC
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 75 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:254068 original size:198 final size:199
Alignment explanation
Indices: 253030--254115 Score: 2027
Period size: 196 Copynumber: 5.5 Consensus size: 199
253020 TTTAAATTAG
253030 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
253095 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
253160 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTAATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
253224 AAAA
196 AAAA
253228 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
253293 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
253356 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
253420 AAAA
196 AAAA
253424 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
253489 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
253553 CGACAC--TTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
253615 AAAA
196 AAAA
253619 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
253684 A-T-TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGG-TCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
253746 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
253810 AAAA
196 AAAA
* *
253814 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
253879 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
253944 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
254008 AAAA
196 AAAA
*
254012 TATCGACACAAACTATATTAGTGTCGACACCTTATTTAGACATATCCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
254077 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTAT
254116 GGATCGACAC
Statistics
Matches: 870, Mismatches: 7, Indels: 22
0.97 0.01 0.02
Matches are distributed among these distances:
193 36 0.04
194 62 0.07
195 182 0.21
196 228 0.26
197 149 0.17
198 213 0.24
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATCCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:254307 original size:19 final size:19
Alignment explanation
Indices: 254261--254309 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
254251 AATTATTCAC
*
254261 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
254280 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
254299 ATACAAAATTA
1 ATACAAAATTA
254310 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Done.