Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002790.1 Hibiscus syriacus cultivar Beakdansim tig00005749_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: 128006
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6470 original size:17 final size:17
Alignment explanation
Indices: 6448--6480 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6438 ATGATGATGA
*
6448 AAATGATTCTCATTTGG
1 AAATGATTCTAATTTGG
6465 AAATGATTCTAATTTG
1 AAATGATTCTAATTTG
6481 AATTGCATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (17 bp):
AAATGATTCTAATTTGG
Found at i:11435 original size:20 final size:20
Alignment explanation
Indices: 11395--11455 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
11385 ATGTGAAATT
*
11395 TGTCCCGAAAGACCTCATGTA
1 TGTCCTGAAAGACC-CATGTA
*
11416 TGTCCTGAAGGACCCATGTA
1 TGTCCTGAAAGACCCATGTA
* *
11436 TGTCCTGAATGACCTATGTA
1 TGTCCTGAAAGACCCATGTA
11456 ACACTCGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 24 0.67
21 12 0.33
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (20 bp):
TGTCCTGAAAGACCCATGTA
Found at i:11854 original size:30 final size:30
Alignment explanation
Indices: 11783--11842 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
11773 ACAATTTAAG
11783 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
11813 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
11843 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:11939 original size:8 final size:8
Alignment explanation
Indices: 11926--12054 Score: 65
Period size: 8 Copynumber: 18.0 Consensus size: 8
11916 GGTGTCAAAG
11926 TGCATCCA
1 TGCATCCA
11934 TGCATCCA
1 TGCATCCA
*
11942 TGCATCCC
1 TGCATCCA
*
11950 TGC-T--G
1 TGCATCCA
11955 TGCATCCA
1 TGCATCCA
*
11963 TGCATCCC
1 TGCATCCA
*
11971 TGCA---G
1 TGCATCCA
11976 TGCATCCA
1 TGCATCCA
*
11984 TGCATCCC
1 TGCATCCA
11992 TGCA---A
1 TGCATCCA
11997 TGCATCCA
1 TGCATCCA
12005 TGCAT-C-
1 TGCATCCA
*
12011 TGCA-CTAA
1 TGCATC-CA
* *
12019 TTCATCGA
1 TGCATCCA
12027 TGCAT-CA
1 TGCATCCA
12034 TGCA---A
1 TGCATCCA
12039 TGCATCCA
1 TGCATCCA
12047 TGCATCCA
1 TGCATCCA
12055 AACATCGAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 32
0.67 0.09 0.23
Matches are distributed among these distances:
5 16 0.17
6 5 0.05
7 7 0.08
8 63 0.68
9 1 0.01
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (8 bp):
TGCATCCA
Found at i:11960 original size:21 final size:21
Alignment explanation
Indices: 11934--12010 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
11924 AGTGCATCCA
*
11934 TGCATCCATGCATCCCTGCTG
1 TGCATCCATGCATCCCTGCAG
11955 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCATCCCTGCAG
*
11976 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCATCCCTGCAG
11997 TGCATCCATGCATC
1 TGCATCCATGCATC
12011 TGCACTAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.19, C:0.38, G:0.17, T:0.26
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAG
Found at i:12098 original size:20 final size:20
Alignment explanation
Indices: 12073--12147 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
12063 ATGCAATTAG
**
12073 TGCATCGATGCATCTTGATA
1 TGCATCGATGCATCTTGCCA
*
12093 TGCATCGATGCATCCTTTCCA
1 TGCATCGATGCAT-CTTGCCA
* *
12114 TGCATCGATGCATCCTGCGA
1 TGCATCGATGCATCTTGCCA
*
12134 TGCATCCATGCATC
1 TGCATCGATGCATC
12148 AAGGCTGCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 30 0.64
21 17 0.36
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATCTTGCCA
Found at i:13582 original size:14 final size:15
Alignment explanation
Indices: 13557--13585 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13547 TGATGGTAAA
13557 GGAAGATGAAGAAAG
1 GGAAGATGAAGAAAG
13572 GGAAGAT-AAGAAAG
1 GGAAGATGAAGAAAG
13586 AGGTAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (15 bp):
GGAAGATGAAGAAAG
Found at i:15436 original size:30 final size:30
Alignment explanation
Indices: 15365--15424 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
15355 ACAATTTAAG
*
15365 GCAAAATATTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
15395 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
15425 ATTCAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:15521 original size:8 final size:8
Alignment explanation
Indices: 15508--15607 Score: 55
Period size: 8 Copynumber: 14.0 Consensus size: 8
15498 GGTGTCAAAG
15508 TGCATCCA
1 TGCATCCA
*
15516 TGCATCCC
1 TGCATCCA
*
15524 TGCA---G
1 TGCATCCA
15529 TGCATCCA
1 TGCATCCA
*
15537 TGCATCCC
1 TGCATCCA
15545 TGCA---A
1 TGCATCCA
15550 TGCATCCA
1 TGCATCCA
15558 TGCAT-C-
1 TGCATCCA
*
15564 TGCA-CTAA
1 TGCATC-CA
*
15572 TGCATCGA
1 TGCATCCA
15580 TGCAT-CA
1 TGCATCCA
15587 TGCA---A
1 TGCATCCA
15592 TGCATCCA
1 TGCATCCA
15600 TGCATCCA
1 TGCATCCA
15608 AACATCGAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 26
0.68 0.08 0.25
Matches are distributed among these distances:
5 13 0.18
6 4 0.06
7 6 0.08
8 47 0.66
9 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:15532 original size:21 final size:21
Alignment explanation
Indices: 15508--15606 Score: 123
Period size: 21 Copynumber: 4.7 Consensus size: 21
15498 GGTGTCAAAG
*
15508 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCATCCCTGCAA
15529 TGCATCCATGCATCCCTGCAA
1 TGCATCCATGCATCCCTGCAA
15550 TGCATCCATGCAT--CTGCACTAA
1 TGCATCCATGCATCCCTG--C-AA
* *
15572 TGCATCGATGCAT-CATGCAA
1 TGCATCCATGCATCCCTGCAA
15592 TGCATCCATGCATCC
1 TGCATCCATGCATCC
15607 AAACATCGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
19 3 0.04
20 14 0.20
21 36 0.52
22 14 0.20
23 2 0.03
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.25
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAA
Found at i:15552 original size:13 final size:13
Alignment explanation
Indices: 15536--15603 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
15526 CAGTGCATCC
*
15536 ATGCATCCCTGCA
1 ATGCATCCATGCA
15549 ATGCATCCATGCA
1 ATGCATCCATGCA
* *
15562 TCTGCA-CTAATGCA
1 -ATGCATC-CATGCA
15576 TCGATGCAT-CATGCA
1 ---ATGCATCCATGCA
15591 ATGCATCCATGCA
1 ATGCATCCATGCA
15604 TCCAAACATC
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
12 6 0.14
13 19 0.44
14 9 0.21
15 5 0.12
16 4 0.09
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (13 bp):
ATGCATCCATGCA
Found at i:15669 original size:21 final size:21
Alignment explanation
Indices: 15626--15692 Score: 102
Period size: 20 Copynumber: 3.3 Consensus size: 21
15616 ATGCAATTAG
*
15626 TGCATCGATGCAT-CTTGCTA
1 TGCATCGATGCATCCTTGCCA
15646 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
*
15667 TGCATCGATGCATCC-TGCGA
1 TGCATCGATGCATCCTTGCCA
15687 TGCATC
1 TGCATC
15693 CTTGCCATGC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 23 0.52
21 21 0.48
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:15671 original size:13 final size:12
Alignment explanation
Indices: 15653--15705 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 12
15643 CTATGCATCG
15653 ATGCATCCTTGCC
1 ATGCATCC-TGCC
15666 ATGCAT-C-G--
1 ATGCATCCTGCC
*
15674 ATGCATCCTGCG
1 ATGCATCCTGCC
15686 ATGCATCCTTGCC
1 ATGCATCC-TGCC
15699 ATGCATC
1 ATGCATC
15706 GATGTATCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 6 0.18
9 1 0.03
10 2 0.06
12 9 0.26
13 16 0.47
ACGTcount: A:0.19, C:0.34, G:0.19, T:0.28
Consensus pattern (12 bp):
ATGCATCCTGCC
Found at i:15672 original size:33 final size:33
Alignment explanation
Indices: 15651--15726 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
15641 TGCTATGCAT
*
15651 CGATGCATCCTTGCCATGCATCGATGCATCCTG
1 CGATGCATCCTTGCCATGCATCGATGCATCATG
* *
15684 CGATGCATCCTTGCCATGCATCGATGTATCCTG
1 CGATGCATCCTTGCCATGCATCGATGCATCATG
*
15717 TGATGCATCC
1 CGATGCATCC
15727 ATGCATCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.18, C:0.32, G:0.21, T:0.29
Consensus pattern (33 bp):
CGATGCATCCTTGCCATGCATCGATGCATCATG
Found at i:15673 original size:41 final size:40
Alignment explanation
Indices: 15626--15733 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 40
15616 ATGCAATTAG
15626 TGCATCGATGCATCTTGCTATGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATC-TGCTATGCATCGATGCATCCTTGCCA
15667 TGCATCGATGCATC--C--TG---CGATGCATCCTTGCCA
1 TGCATCGATGCATCTGCTATGCATCGATGCATCCTTGCCA
* *
15700 TGCATCGATGTATCCTG-TGATGCATCCATGCATC
1 TGCATCGATGCAT-CTGCT-ATGCATCGATGCATC
15734 AAGGCTGCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
33 28 0.50
34 1 0.02
36 2 0.04
38 3 0.05
41 22 0.39
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.31
Consensus pattern (40 bp):
TGCATCGATGCATCTGCTATGCATCGATGCATCCTTGCCA
Found at i:15689 original size:12 final size:13
Alignment explanation
Indices: 15672--15705 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
15662 TGCCATGCAT
15672 CGATGCATCC-TG
1 CGATGCATCCTTG
15684 CGATGCATCCTTG
1 CGATGCATCCTTG
*
15697 CCATGCATC
1 CGATGCATC
15706 GATGTATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.18, C:0.35, G:0.21, T:0.26
Consensus pattern (13 bp):
CGATGCATCCTTG
Found at i:16820 original size:20 final size:19
Alignment explanation
Indices: 16795--16846 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
16785 AGTTTCAAAA
16795 ATGGTATCGATACTGACCTT
1 ATGGTATCGATACTG-CCTT
*
16815 ATGGTATCGGTAC--CC-T
1 ATGGTATCGATACTGCCTT
16831 -TGGTATCGATACTGCC
1 ATGGTATCGATACTGCC
16847 CTTCAGGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 11 0.39
16 1 0.04
17 4 0.14
20 12 0.43
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (19 bp):
ATGGTATCGATACTGCCTT
Found at i:18646 original size:156 final size:156
Alignment explanation
Indices: 18375--18711 Score: 489
Period size: 156 Copynumber: 2.2 Consensus size: 156
18365 TTTTATTGTC
* * * * *
18375 TGATATATCACTGAACTGAAGTGATATATTACTAAAAAGTTTTTGAAATGAAGTGATTGGGCACT
1 TGATATATCACTGAATTGAAGTGATATATCACTAAAAAGTTTCTAAAATAAAGTGATTGGGCACT
* * *
18440 AAAAAGTTTTTGTCATTGTGTATAAAATGGTATATGAGAAAATGATGTTTTTCATTAAAGGGATA
66 AAAAAGTTTTTGTAATTGTGTATAAAATGGTATATGAGAAAATGACGTTTTTCATTAAAGGGAAA
18505 CAAGTAAAAAAAATCATTCAATGGTA
131 CAAGTAAAAAAAATCATTCAATGGTA
* * *
18531 TGATATATCACTGAATTGAAGTGATATATCA-TTAAAAGTTTCTAAAATAAAGTGATTGTGTACT
1 TGATATATCACTGAATTGAAGTGATATATCACTAAAAAGTTTCTAAAATAAAGTGATTGGGCACT
* *
18595 GAAAAGTTTTTTGTAATTGTGTACT-AAATGGTCTATGAGAAAATGACGTTTTTCATTAAAGGGA
66 AAAAAG-TTTTTGTAATTGTGTA-TAAAATGGTATATGAGAAAATGACGTTTTTCATTAAAGGGA
* * *
18659 AATAAGTTAAAAACATCATTCAATGGTA
129 AACAAGTAAAAAAAATCATTCAATGGTA
*
18687 TGATAAATCACTGAATTGAAGTGAT
1 TGATATATCACTGAATTGAAGTGAT
18712 TCTTTCGCAG
Statistics
Matches: 162, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
155 32 0.20
156 129 0.80
157 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (156 bp):
TGATATATCACTGAATTGAAGTGATATATCACTAAAAAGTTTCTAAAATAAAGTGATTGGGCACT
AAAAAGTTTTTGTAATTGTGTATAAAATGGTATATGAGAAAATGACGTTTTTCATTAAAGGGAAA
CAAGTAAAAAAAATCATTCAATGGTA
Found at i:20819 original size:21 final size:21
Alignment explanation
Indices: 20795--20839 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
20785 TGAGTTGATT
*
20795 AAAATGTTTTTAAAG-TATTTA
1 AAAATGGTTTTAAAGCT-TTTA
20816 AAAATGGTTTTAAAGCTTTTA
1 AAAATGGTTTTAAAGCTTTTA
20837 AAA
1 AAA
20840 CATGAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.42
Consensus pattern (21 bp):
AAAATGGTTTTAAAGCTTTTA
Found at i:23756 original size:16 final size:16
Alignment explanation
Indices: 23735--23809 Score: 62
Period size: 16 Copynumber: 5.3 Consensus size: 16
23725 CGTTTATTTA
23735 TTTATTACATTTTTCT
1 TTTATTACATTTTTCT
*
23751 TTTA-T---TTTTT-A
1 TTTATTACATTTTTCT
23762 TTTATTACATTTTTCT
1 TTTATTACATTTTTCT
*
23778 TTTA-T---TTTTT-A
1 TTTATTACATTTTTCT
23789 TTTATTACATTTTTCT
1 TTTATTACATTTTTCT
23805 TTTAT
1 TTTAT
23810 ATTTATAGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 20
0.65 0.06 0.29
Matches are distributed among these distances:
11 8 0.18
12 12 0.27
15 12 0.27
16 13 0.29
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTACATTTTTCT
Found at i:23764 original size:27 final size:27
Alignment explanation
Indices: 23731--23809 Score: 158
Period size: 27 Copynumber: 2.9 Consensus size: 27
23721 GCAACGTTTA
23731 TTTATTTATTACATTTTTCTTTTATTT
1 TTTATTTATTACATTTTTCTTTTATTT
23758 TTTATTTATTACATTTTTCTTTTATTT
1 TTTATTTATTACATTTTTCTTTTATTT
23785 TTTATTTATTACATTTTTCTTTTAT
1 TTTATTTATTACATTTTTCTTTTAT
23810 ATTTATAGAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTATTTATTACATTTTTCTTTTATTT
Found at i:31633 original size:7 final size:7
Alignment explanation
Indices: 31613--31645 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
31603 TATCTATATG
31613 TAATAAA
1 TAATAAA
31620 TTAATAAA
1 -TAATAAA
31628 TAATAAA
1 TAATAAA
31635 TAATAAA
1 TAATAAA
31642 TAAT
1 TAAT
31646 TCATATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
TAATAAA
Found at i:34323 original size:29 final size:30
Alignment explanation
Indices: 34280--34346 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 30
34270 CCAAAGTATG
34280 ATTTTGGTTTCAGTTTAATG-CTTAACG-TTT
1 ATTTT-GTTTCAGTTTAATGTC-TAACGTTTT
**
34310 ATTTTGTTTCAGTTTGGTGTCTAACGTTTT
1 ATTTTGTTTCAGTTTAATGTCTAACGTTTT
34340 ATTTTGT
1 ATTTTGT
34347 AATTCAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.57
Consensus pattern (30 bp):
ATTTTGTTTCAGTTTAATGTCTAACGTTTT
Found at i:34448 original size:2 final size:2
Alignment explanation
Indices: 34443--34467 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34433 AAATTAAAAT
34443 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
34468 TAAAAAGAAA
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:35158 original size:2 final size:2
Alignment explanation
Indices: 35151--35175 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35141 GCAAAATTGA
35151 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
35176 CTAATGATTA
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:38747 original size:16 final size:17
Alignment explanation
Indices: 38709--38753 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
38699 TATTTATAAG
*
38709 AGAATTAGAATCTGTGAA
1 AGAATTAGAATATGT-AA
38727 AGAATTAGAATATGT-A
1 AGAATTAGAATATGTAA
38743 AGAATTAGAAT
1 AGAATTAGAAT
38754 CCAATTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (17 bp):
AGAATTAGAATATGTAA
Found at i:39356 original size:36 final size:37
Alignment explanation
Indices: 39315--39393 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 37
39305 TTCACCCTAA
39315 ACCCGAC-CCGACCCGAATATCACACTTAAAAAA-CCG
1 ACCCGACTCC-ACCCGAATATCACACTTAAAAAATCCG
39351 ACCCGACTCCACCCGAATATCACACTTAAAAAATCCG
1 ACCCGACTCCACCCGAATATCACACTTAAAAAATCCG
39388 ACCCGA
1 ACCCGA
39394 ATATATGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
36 30 0.73
37 11 0.27
ACGTcount: A:0.38, C:0.39, G:0.10, T:0.13
Consensus pattern (37 bp):
ACCCGACTCCACCCGAATATCACACTTAAAAAATCCG
Found at i:39598 original size:31 final size:32
Alignment explanation
Indices: 39530--39611 Score: 139
Period size: 33 Copynumber: 2.6 Consensus size: 32
39520 CTTAAACCCG
*
39530 AACCCGACCCGACCCGAATATCACGCTTAAAAA
1 AACCCGACCCGACCCGAATATCACACTT-AAAA
39563 AACCCGACCCGACCCGAATATCACACTT-AAA
1 AACCCGACCCGACCCGAATATCACACTTAAAA
39594 AACCCGACCCGACCCGAA
1 AACCCGACCCGACCCGAA
39612 CAAAATAAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 21 0.44
33 27 0.56
ACGTcount: A:0.38, C:0.40, G:0.12, T:0.10
Consensus pattern (32 bp):
AACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:39804 original size:220 final size:218
Alignment explanation
Indices: 39563--40127 Score: 796
Period size: 221 Copynumber: 2.6 Consensus size: 218
39553 CGCTTAAAAA
39563 AACCCGACCCGACCCGAATATCACACTT-AAAAACCCGACCCGACCCGAACAAAATAAAGTTTCA
1 AACCCGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCA
*
39627 TCCGACCCGACTCGACCCGAATATATGAATTAAAAATCCGACCCGACCCGAAATAATAAAAAATT
66 TCCGACCC-AC-CGACCCGAATATATGAATTAAAAACCCGACCCGACCCGAAATAATAAAAAATT
* *
39692 ATTTTTATTTAATAAAAACAGTGACTTAATTCGACCCGACCAGA-ATTATATATATTTTCGGGTC
129 ATTTTTATTTAATAAAAACAGTGACTTAATCCGA-CCGACCAGATA-TATATATATTTTCGGATC
*
39756 GGTCCGATTTTTTTCACCCTAAACCTG
192 GGTCCGATTTTTTTCACCCTAAACCCG
**
39783 AACCCGACCCGACCCGAATATCACACTTAAAAAACCCGACCTTACCCGAACAAAATAAAGTTTCA
1 AACCCGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCA
*
39848 TCTGA--C-CCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAA
66 TCCGACCCACCGACCCGAATATATGAATT--AAA---AACCCGACCCGACCCGAAATAATAAAAA
*
39910 ATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCGACCTGATATATATATATTTTCGGAT
126 ATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCGACCAGATATATATATATTTTCGGAT
*
39975 CGGTCCGGTTTTTTTCACCCTAAACCCG
191 CGGTCCGATTTTTTTCACCCTAAACCCG
* * * *
40003 -A----ACCCGACCCGATTATCACACTTAAAAAAACCCGATCCGACCCGACCAAAATAAAATTTC
1 AACCCGACCCGACCCGAATATCACACTT-AAAAAACCCGACCCGACCCGAACAAAATAAAGTTTC
* * *
40063 ACCCGACCCA---ACCCGAATATATGAATTAAAAACCCGACCCGATCCGAAATAAAAAAAAAATT
65 ATCCGACCCACCGACCCGAATATATGAATTAAAAACCCGACCCGACCCGAAAT-AATAAAAAATT
40125 ATT
129 ATT
40128 CAATATATGA
Statistics
Matches: 314, Mismatches: 19, Indels: 32
0.86 0.05 0.09
Matches are distributed among these distances:
211 19 0.06
212 13 0.04
214 3 0.01
215 21 0.07
216 71 0.23
217 1 0.00
218 4 0.01
219 2 0.01
220 78 0.25
221 102 0.32
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.23
Consensus pattern (218 bp):
AACCCGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCA
TCCGACCCACCGACCCGAATATATGAATTAAAAACCCGACCCGACCCGAAATAATAAAAAATTAT
TTTTATTTAATAAAAACAGTGACTTAATCCGACCGACCAGATATATATATATTTTCGGATCGGTC
CGATTTTTTTCACCCTAAACCCG
Found at i:44955 original size:21 final size:21
Alignment explanation
Indices: 44929--44984 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
44919 GGAGCGTGGG
44929 GGGAATCGGTTCCCCCTCATA
1 GGGAATCGGTTCCCCCTCATA
*
44950 GGGAATCGGTTCCTCCTCATA
1 GGGAATCGGTTCCCCCTCATA
44971 GGGAATCGGTTCCC
1 GGGAATCGGTTCCC
44985 TAAGTGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (21 bp):
GGGAATCGGTTCCCCCTCATA
Found at i:45498 original size:19 final size:19
Alignment explanation
Indices: 45474--45513 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
45464 ACACTTCTCT
45474 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
45493 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
45512 CA
1 CA
45514 CTTAAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
CATTTATCATTTTAAAACA
Found at i:50333 original size:3 final size:3
Alignment explanation
Indices: 50325--50359 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
50315 TAGGTGCTGA
50325 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
50360 AACCCAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:58542 original size:21 final size:21
Alignment explanation
Indices: 58516--58571 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
58506 TGGAGTGTGG
58516 GGGAATCGGTTCCCCCTCATA
1 GGGAATCGGTTCCCCCTCATA
* *
58537 GGGAATCAGTTCCTCCTCATA
1 GGGAATCGGTTCCCCCTCATA
58558 GGGAATCGGTTCCC
1 GGGAATCGGTTCCC
58572 TAAGTGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.25
Consensus pattern (21 bp):
GGGAATCGGTTCCCCCTCATA
Found at i:59736 original size:23 final size:23
Alignment explanation
Indices: 59706--59751 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
59696 CGAACAACTT
59706 TAATTTGATGGTTCCCACGCCAA
1 TAATTTGATGGTTCCCACGCCAA
*
59729 TAATTTGATGGTTCTCACGCCAA
1 TAATTTGATGGTTCCCACGCCAA
59752 CAATCTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (23 bp):
TAATTTGATGGTTCCCACGCCAA
Found at i:61676 original size:41 final size:41
Alignment explanation
Indices: 61581--62121 Score: 805
Period size: 41 Copynumber: 13.2 Consensus size: 41
61571 GATTCGTAAC
* * ** *
61581 GCGATAGTCGAAGTTCGCATTAAGATTTATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
*
61623 GCGATAGGCGAAGTTCGTGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
61664 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* * *
61705 GCGATAGGCGAAGTTCACATTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
61746 GCGACAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* * *
61787 GCGATAGTCAAAGTTCGTGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
61828 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* * * *
61869 GCGATAGCCGAAGTTCGCATTGCGATTCATTCCAATTTGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* * *
61910 GCGATAGGCGAAGTTTGCGTTGCGATTCATTTCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
61951 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
61992 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* * * *
62033 GCGATAGGTGAAGTTTGC-ATGTGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
62073 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
62115 GCGATAG
1 GCGATAG
62122 TCCAAATATT
Statistics
Matches: 450, Mismatches: 47, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
40 35 0.08
41 373 0.83
42 42 0.09
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (41 bp):
GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
Found at i:63051 original size:41 final size:41
Alignment explanation
Indices: 62993--63601 Score: 1002
Period size: 41 Copynumber: 14.8 Consensus size: 41
62983 TGGACTATCA
* *
62993 CAACGAATTTGGAATGAATCGCAACGTGAACTTCGCCTGTCG
1 CAACGAA-TTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
*
63035 CAACGAATTGGAATGAATCGCAATGCAAACTTCGCCTGTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
**
63076 CAACGAATTGGAATGAATCGCAATGCGAACTTTACCTGTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
63117 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
* * * *
63158 TAACGAATTGGAATGAATCGCAACGCGAACTTCGCTTCTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
* *
63199 CAACGAATTGGAATGAATCGCAATGCGAAATTCGTCTGTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
*
63240 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTATCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
* * *
63281 TAACAAATTGGAATGAATTGCAATGCGAACTTCGCCTGTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
* * *
63322 CAACGAATTAGAATGAATCGCAATACGAACTTCGCTTGTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
*
63363 CAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTGTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
63404 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
*
63445 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCT
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
*
63486 CAACGAATTGGAATGAATCGCAATGCGAACTTTGCCTGTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
*
63527 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTTG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
*
63568 CAACGAATTGGAATGAATCGCAACGCGAACTTCG
1 CAACGAATTGGAATGAATCGCAATGCGAACTTCG
63602 ACTATCGTGT
Statistics
Matches: 525, Mismatches: 42, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
41 518 0.99
42 7 0.01
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (41 bp):
CAACGAATTGGAATGAATCGCAATGCGAACTTCGCCTGTCG
Found at i:63404 original size:21 final size:21
Alignment explanation
Indices: 63380--63449 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
63370 TTGGAATGAA
63380 TCGCAACGCGAACTTCGCCTG
1 TCGCAACGCGAACTTCGCCTG
* **
63401 TCGCAA--CGAA-TTGGAATG
1 TCGCAACGCGAACTTCGCCTG
*
63419 AATCGCAATGCGAACTTCGCCTG
1 --TCGCAACGCGAACTTCGCCTG
63442 TCGCAACG
1 TCGCAACG
63450 AATTGGAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
18 5 0.14
19 4 0.11
20 6 0.16
21 13 0.35
22 4 0.11
23 5 0.14
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGCCTG
Found at i:68371 original size:6 final size:7
Alignment explanation
Indices: 68356--68404 Score: 62
Period size: 8 Copynumber: 6.6 Consensus size: 7
68346 CTAAAACAAT
68356 TATAATA
1 TATAATA
68363 TATTAATA
1 TA-TAATA
68371 TATATATA
1 TATA-ATA
68379 TATAATA
1 TATAATA
*
68386 TAAAATAA
1 TATAAT-A
68394 TATAATA
1 TATAATA
68401 TATA
1 TATA
68405 TAAATTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
7 17 0.46
8 20 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TATAATA
Found at i:85493 original size:39 final size:39
Alignment explanation
Indices: 85450--85525 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
85440 CTCATGATTT
85450 TATCAAAACAATGATAAACAATATCATACATAATAGTCA
1 TATCAAAACAATGATAAACAATATCATACATAATAGTCA
* * *
85489 TATCATAGCCATGATAAACAATATCATACATAATAGT
1 TATCAAAACAATGATAAACAATATCATACATAATAGT
85526 TGTATCATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.28
Consensus pattern (39 bp):
TATCAAAACAATGATAAACAATATCATACATAATAGTCA
Found at i:85532 original size:39 final size:39
Alignment explanation
Indices: 85460--85534 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
85450 TATCAAAACA
85460 ATGATAAACAATATCATACATAATAGTCATATCATAGCC
1 ATGATAAACAATATCATACATAATAGTCATATCATAGCC
**
85499 ATGATAAACAATATCATACATAATAGTTGTATCATA
1 ATGATAAACAATATCATACATAATAGTCATATCATA
85535 TTTTTTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.31
Consensus pattern (39 bp):
ATGATAAACAATATCATACATAATAGTCATATCATAGCC
Found at i:85704 original size:19 final size:19
Alignment explanation
Indices: 85682--85719 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
85672 AAATTCACAA
85682 CTTAATTTCATA-TTCATAG
1 CTTAATTTCA-AGTTCATAG
*
85701 CTTATTTTCAAGTTCATAG
1 CTTAATTTCAAGTTCATAG
85720 TCCAATGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (19 bp):
CTTAATTTCAAGTTCATAG
Found at i:87503 original size:30 final size:30
Alignment explanation
Indices: 87446--87503 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
87436 ATCAATCTCA
* *
87446 TAACTTTTCAAAATTTCTGAATAGGTCCCC
1 TAACTTTTCAAAATTACTAAATAGGTCCCC
*
87476 TAACTTTCTCAAAATTAC-AAATTGGTCC
1 TAACTTT-TCAAAATTACTAAATAGGTCC
87504 AAATAACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (30 bp):
TAACTTTTCAAAATTACTAAATAGGTCCCC
Found at i:89117 original size:36 final size:37
Alignment explanation
Indices: 89062--89141 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 37
89052 TCTCAAAAAA
* * *
89062 TCGGGTCAGGTTCGATGGAGGATGT-ATATTTTCGGG
1 TCGGGTCAAGTTCGATGGAGGATGTAAAATTTTCGAG
* *
89098 TCGGGTCAAG-TCGAGTGGAGGGTGTAAAATTTTTGAG
1 TCGGGTCAAGTTCGA-TGGAGGATGTAAAATTTTCGAG
89135 TCGGGTC
1 TCGGGTC
89142 GGCTTAGTCG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.11
36 18 0.49
37 15 0.41
ACGTcount: A:0.19, C:0.11, G:0.39, T:0.31
Consensus pattern (37 bp):
TCGGGTCAAGTTCGATGGAGGATGTAAAATTTTCGAG
Found at i:97203 original size:21 final size:21
Alignment explanation
Indices: 97179--97236 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
97169 AATTTTTAAT
97179 ATTTTATTTTAAAAAAATAAA
1 ATTTTATTTTAAAAAAATAAA
*
97200 ATTTTAATTTT-AAAAAATATA
1 ATTTT-ATTTTAAAAAAATAAA
*
97221 TTTTTATTATTAAAAA
1 ATTTTATT-TTAAAAA
97237 TTAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 3 0.09
21 20 0.62
22 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTTATTTTAAAAAAATAAA
Found at i:97236 original size:22 final size:22
Alignment explanation
Indices: 97180--97236 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
97170 ATTTTTAATA
97180 TTTTATTTTAAAAAAATAAAAT
1 TTTTATTTTAAAAAAATAAAAT
* *
97202 TTTAATTTT-AAAAAAT-ATAT
1 TTTTATTTTAAAAAAATAAAAT
97222 TTTTATTATTAAAAA
1 TTTTATT-TTAAAAA
97237 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 9 0.30
21 9 0.30
22 12 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTATTTTAAAAAAATAAAAT
Found at i:97633 original size:12 final size:13
Alignment explanation
Indices: 97611--97639 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
97601 TAATACAATA
97611 TATTAAAATAAAT
1 TATTAAAATAAAT
97624 TATT-AAATAAAT
1 TATTAAAATAAAT
97636 TATT
1 TATT
97640 CTTATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATTAAAATAAAT
Found at i:102879 original size:18 final size:18
Alignment explanation
Indices: 102853--102895 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
102843 ACAATTTCTT
*
102853 GAAACCCTCCACAAGTGG
1 GAAATCCTCCACAAGTGG
102871 GAAATCCTCCACAAGTGG
1 GAAATCCTCCACAAGTGG
102889 GAAATCC
1 GAAATCC
102896 ACCAATATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.35, C:0.30, G:0.21, T:0.14
Consensus pattern (18 bp):
GAAATCCTCCACAAGTGG
Found at i:106625 original size:183 final size:183
Alignment explanation
Indices: 106278--106626 Score: 425
Period size: 188 Copynumber: 1.9 Consensus size: 183
106268 TGAAAAAGAG
* * *
106278 GATTCCAATTTAACCCTCCATTAGCTTGCCAAGGTGATGCAGAAGACTAGGAGAAATCTAAAGCT
1 GATTCCAATTTAACCCTCCAGTAGCTGGCCAAGGTGATGCAGAAGACTAGGAGAAATCTAAAACT
*
106343 AACAATTAAGTGCTTACCCGTAAATCATTAGAATTCTGAAGGCACAGGAAACAATAAAAAAATAA
66 AACAATTAAGTGCTTACCCGTAAATCATTAGAA---TGAAGG-ACAGGAAACAATAAAAAAAGAA
*
106408 AAATCAAAGTTCAAAGGTTCAACCAAAGATCAAGGACTGATATAAAAAGCTAAACAA
127 AAATCAAAGTTCAAAGGTACAACCAAAGATCAAGGACTGATATAAAAAGCTAAACAA
* * * * *
106465 GATTCCAGTTTAAACCCTCCAGTAGCTGGCCAAGGTGGTGCAGAGGACTAGGAGAACTTTAAAAC
1 GATTCCAATTT-AACCCTCCAGTAGCTGGCCAAGGTGATGCAGAAGACTAGGAGAAATCTAAAAC
* * ** * * * * *
106530 TAACTATTACGTGCTTGTCC-TGAATCATTAGAA-GACAGG-CAGGAAACTATTAGAAACAGCAA
65 TAACAATTAAGTGCTTACCCGTAAATCATTAGAATGA-AGGACAGGAAAC-AATAAAAAAAGAAA
* *
106592 AATCAAAGTTCAAGGGTACAACCAAATATCAAGGA
128 AATCAAAGTTCAAAGGTACAACCAAAGATCAAGGA
106627 GCAACCATGT
Statistics
Matches: 138, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
182 8 0.06
183 43 0.31
184 3 0.02
187 22 0.16
188 62 0.45
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (183 bp):
GATTCCAATTTAACCCTCCAGTAGCTGGCCAAGGTGATGCAGAAGACTAGGAGAAATCTAAAACT
AACAATTAAGTGCTTACCCGTAAATCATTAGAATGAAGGACAGGAAACAATAAAAAAAGAAAAAT
CAAAGTTCAAAGGTACAACCAAAGATCAAGGACTGATATAAAAAGCTAAACAA
Found at i:108686 original size:16 final size:17
Alignment explanation
Indices: 108661--108694 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
108651 ATCCATTAAT
*
108661 ATTTTAAAATTCAAATA
1 ATTTTAAAATACAAATA
108678 ATTTT-AAATACAAATA
1 ATTTTAAAATACAAATA
108694 A
1 A
108695 AAAAAGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTTAAAATACAAATA
Found at i:108883 original size:24 final size:24
Alignment explanation
Indices: 108809--108890 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
108799 TCATTTAGTG
*
108809 TGTTCGTTTATATTCGTTTACAT-TC
1 TGTTCGTTTATGTTCG-TT-CATATC
* * *
108834 -GTTC-ATTGTGTTCGTTTATATC
1 TGTTCGTTTATGTTCGTTCATATC
* *
108856 TGTTCGTTTATGTTCGTTCATTTG
1 TGTTCGTTTATGTTCGTTCATATC
108880 TGTTCGTTTAT
1 TGTTCGTTTAT
108891 CACTTAAATG
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
21 2 0.04
22 4 0.09
23 11 0.24
24 28 0.62
ACGTcount: A:0.12, C:0.13, G:0.17, T:0.57
Consensus pattern (24 bp):
TGTTCGTTTATGTTCGTTCATATC
Found at i:111064 original size:22 final size:22
Alignment explanation
Indices: 111036--111079 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
111026 TATTTGTTTT
111036 CTATCTTTTTGCTATAAGGAAC
1 CTATCTTTTTGCTATAAGGAAC
111058 CTATCTTTTTGCTATAAGGAAC
1 CTATCTTTTTGCTATAAGGAAC
111080 TTATTCGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (22 bp):
CTATCTTTTTGCTATAAGGAAC
Found at i:113148 original size:123 final size:121
Alignment explanation
Indices: 112901--113148 Score: 313
Period size: 123 Copynumber: 2.0 Consensus size: 121
112891 TTAATATATA
* *
112901 AATAAGATATTTACTTATTTAAAAATATCAGAAAATGGCTTCTAGGTGCTTTAAGACAGCTCTTT
1 AATAAGATATTTACTTATTTAAAAATATCAGAAAATGGCTTCTAGGTGCCTTAAGACAACTCTTT
* ** * *
112966 TCTTTGATATTAATAATAAATAAATAACCAAAAGATTTTCTTAAATAAAATTTATTTT
66 TCTTTGATATTAATAATAAATAAATAA-CAAAAAAAATTCTAAAATAAAA-TTAATTT
* *
113024 AATAAGATATTTATTTATTTAAAAATATCAGAAAATGGCTTCTAGGTGCCTTAAGACAACTTTTT
1 AATAAGATATTTACTTATTTAAAAATATCAGAAAATGGCTTCTAGGTGCCTTAAGACAACTCTTT
* *
113089 TCTTTGATATTGATAAATAAATAACTAA-AAATGTAAAAATT-TAAAAGTAAAA-TAATTT
66 TCTTTGATATTAAT-AATAAATAAATAACAAA---AAAAATTCTAAAA-TAAAATTAATTT
113147 AA
1 AA
113149 GTAAAATTAA
Statistics
Matches: 109, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
122 3 0.03
123 81 0.74
124 16 0.15
125 9 0.08
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.38
Consensus pattern (121 bp):
AATAAGATATTTACTTATTTAAAAATATCAGAAAATGGCTTCTAGGTGCCTTAAGACAACTCTTT
TCTTTGATATTAATAATAAATAAATAACAAAAAAAATTCTAAAATAAAATTAATTT
Found at i:113313 original size:23 final size:24
Alignment explanation
Indices: 113269--113315 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
113259 AAAATTAATC
*
113269 AAATAATATATATTAATAAAAATA
1 AAATAATATATACTAATAAAAATA
*
113293 AAATAATA-ATACTAATTAAAATA
1 AAATAATATATACTAATAAAAATA
113316 TTAAACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATAATATATACTAATAAAAATA
Found at i:113332 original size:21 final size:20
Alignment explanation
Indices: 113305--113358 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 20
113295 ATAATAATAC
113305 TAATTAAAATA-TTAAACATA
1 TAATTAAAATATTTAAAC-TA
113325 TAAATTAAAATATATTTAAACTA
1 T-AATT-AAA-ATATTTAAACTA
113348 TAATTAAAATA
1 TAATTAAAATA
113359 AAATTAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.13
21 7 0.23
22 7 0.23
23 6 0.20
24 6 0.20
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATTAAAATATTTAAACTA
Found at i:113349 original size:11 final size:11
Alignment explanation
Indices: 113282--113367 Score: 63
Period size: 11 Copynumber: 7.8 Consensus size: 11
113272 TAATATATAT
*
113282 TAATAAAAATA
1 TAATTAAAATA
*
113293 -AAATAATAATA
1 TAATTAA-AATA
113304 CTAATT-AAA-A
1 -TAATTAAAATA
113314 T-ATTAAACATA
1 TAATTAAA-ATA
113325 TAAATTAAAATA
1 T-AATTAAAATA
* *
113337 TATTTAAACTA
1 TAATTAAAATA
113348 TAATTAAAATA
1 TAATTAAAATA
*
113359 AAATTAAAA
1 TAATTAAAA
113368 CTAAATATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
8 3 0.05
9 3 0.05
10 6 0.10
11 33 0.56
12 5 0.08
13 9 0.15
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATTAAAATA
Found at i:113368 original size:23 final size:22
Alignment explanation
Indices: 113282--113379 Score: 71
Period size: 23 Copynumber: 4.4 Consensus size: 22
113272 TAATATATAT
* *
113282 TAATAAAAATAAAATAATAA-TA
1 TAATTAAAATAAATTAA-AACTA
113304 CTAATTAAAAT--ATT-AAACATA
1 -TAATTAAAATAAATTAAAAC-TA
* *
113325 TAAATTAAAATATATTTAAACTA
1 T-AATTAAAATAAATTAAAACTA
113348 TAATTAAAATAAAATTAAAACTA
1 TAATTAAAAT-AAATTAAAACTA
113371 -AATATAAAA
1 TAAT-TAAAA
113380 AGTAATAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.03
20 2 0.03
21 13 0.21
22 12 0.19
23 30 0.48
24 4 0.06
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (22 bp):
TAATTAAAATAAATTAAAACTA
Found at i:114254 original size:21 final size:19
Alignment explanation
Indices: 114229--114284 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 19
114219 TCGTTGGTAG
114229 TTTTTCTTTTCTTTCGTTTTT
1 TTTTTCTTTTCTTTC--TTTT
114250 TTTTTCTTCTCTCTTTCTTTT
1 TTTTTCTT-T-TCTTTCTTTT
114271 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
114285 TTTCTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.15
20 1 0.03
21 20 0.61
22 1 0.03
23 6 0.18
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTCTTTCTTTT
Found at i:114292 original size:21 final size:21
Alignment explanation
Indices: 114229--114297 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
114219 TCGTTGGTAG
*
114229 TTTTTCTTTTCTTTCGTT-TTT
1 TTTTTCTTTTCTTT-TTTCTTT
* *
114250 TTTTTCTTCTC-TCTTTCTTTT
1 TTTTTCTTTTCTTTTTTC-TTT
114271 TTTTTCTTTTCTTTTTTCTTT
1 TTTTTCTTTTCTTTTTTCTTT
114292 TGTTTT
1 T-TTTT
114298 TCTCTGCTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 27 0.69
22 9 0.23
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (21 bp):
TTTTTCTTTTCTTTTTTCTTT
Found at i:114297 original size:5 final size:5
Alignment explanation
Indices: 114230--114285 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
114220 CGTTGGTAGT
* * *
114230 TTTTC TTTTC -TTTC GTTTTTT TTTTC TTCTC TCTTTC TTTTT TTTTC
1 TTTTC TTTTC TTTTC --TTTTC TTTTC TTTTC T-TTTC TTTTC TTTTC
114277 TTTTC TTTT
1 TTTTC TTTT
114286 TTCTTTTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
4 4 0.10
5 30 0.73
6 4 0.10
7 3 0.07
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:114300 original size:33 final size:33
Alignment explanation
Indices: 114228--114300 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
114218 ATCGTTGGTA
114228 GTTTTTC-TTTTCTTTCGTTTTTTTTTTCTTCT
1 GTTTTTCTTTTTCTTTCGTTTTTTTTTTCTTCT
* * * *
114260 CTCTTTCTTTTTTTTTC-TTTTCTTTTTTCTTTT
1 GTTTTTCTTTTTCTTTCGTTTT-TTTTTTCTTCT
114293 GTTTTTCT
1 GTTTTTCT
114301 CTGCTCTCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 9 0.27
33 24 0.73
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.79
Consensus pattern (33 bp):
GTTTTTCTTTTTCTTTCGTTTTTTTTTTCTTCT
Found at i:114719 original size:3 final size:3
Alignment explanation
Indices: 114711--114796 Score: 83
Period size: 3 Copynumber: 29.7 Consensus size: 3
114701 ATTTGGGCTT
*
114711 ATA ATA AT- ATA TTTA ATA ATA AT- ATA AT- ATA TATA AT- ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
* * *
114754 ATA ATA TTT ATA ATA ATA ATA ATA ATA AT- TTA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
114797 TTAAGTAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
2 9 0.13
3 54 0.79
4 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
ATA
Found at i:114737 original size:20 final size:21
Alignment explanation
Indices: 114711--114796 Score: 126
Period size: 20 Copynumber: 4.2 Consensus size: 21
114701 ATTTGGGCTT
114711 ATAATAATATATTTAATAATA
1 ATAATAATATATTTAATAATA
*
114732 AT-ATAATATATATAAT-ATA
1 ATAATAATATATTTAATAATA
114751 ATAATAATAT-TTATAATAATA
1 ATAATAATATATT-TAATAATA
114772 ATAATAATA-ATTTAATAATA
1 ATAATAATATATTTAATAATA
114792 ATAAT
1 ATAAT
114797 TTAAGTAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
19 6 0.10
20 37 0.63
21 16 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAATAATATATTTAATAATA
Found at i:115145 original size:76 final size:76
Alignment explanation
Indices: 114950--115888 Score: 1686
Period size: 76 Copynumber: 12.4 Consensus size: 76
114940 GAGGTCTTAA
* *
114950 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115015 AGGC-TTTTGG
66 AGGCTTTTTGG
*
115025 AAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115090 AGGCTTTTTGG
66 AGGCTTTTTGG
115101 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115166 AGGCTTTTTGG
66 AGGCTTTTTGG
115177 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115242 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
115253 AAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115318 AGGCTTTTTGG
66 AGGCTTTTTGG
115329 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115394 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
115405 AAACATCATGCACTGAAGGGCTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115470 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
115481 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115546 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
115557 AAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115622 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
115633 AAACATCATGCACTGAAGGGCTTACAGATGACCCGGAGGTTTTGAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115698 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
115709 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115774 AGGCTTTTTGG
66 AGGCTTTTTGG
115785 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
115849 AGGC-TTTTGG
66 AGGCTTTTTGG
*
115859 AAACATCATGCACTGAAAGGCTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
115889 TGGGAAATAG
Statistics
Matches: 835, Mismatches: 28, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
74 35 0.04
75 94 0.11
76 706 0.85
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:117040 original size:54 final size:54
Alignment explanation
Indices: 116958--117113 Score: 240
Period size: 54 Copynumber: 2.9 Consensus size: 54
116948 AGAATAGCAG
**** *
116958 GTTCGTAAAACATTTGACTGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCTCAGAT
* *
117012 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCTCAGAT
*
117066 GTTCGTAAAACATTTGACAACACATTCATCCTTTATTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGC
117114 CAAGATTTCT
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCTCAGAT
Found at i:119302 original size:114 final size:114
Alignment explanation
Indices: 119102--119324 Score: 347
Period size: 114 Copynumber: 2.0 Consensus size: 114
119092 GATCATGCAG
* * * * *
119102 TTCATCTTTCAATTTCAATGATTGGTTATGGGATTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGGGATTCATACCAAACCAAATCAGATAACTCAAAGA
* *
119167 ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* * *
119216 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGGGATTCATACCAAACCAAATCAGATAACTCAAAGA
*
119281 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
119325 TCACATGGCA
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTATGGGATTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:127195 original size:15 final size:16
Alignment explanation
Indices: 127165--127198 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
127155 AAATAATAAC
127165 TAAAATGTAAAAAATT
1 TAAAATGTAAAAAATT
*
127181 TAAAA-GTAAATAATT
1 TAAAATGTAAAAAATT
127196 TAA
1 TAA
127199 GTAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
TAAAATGTAAAAAATT
Found at i:127347 original size:23 final size:23
Alignment explanation
Indices: 127319--127364 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
127309 AAAATTAATC
* *
127319 AAATAATTATATTAATAAAAATA
1 AAATAATAATACTAATAAAAATA
*
127342 AAATAATAATACTAATTAAAATA
1 AAATAATAATACTAATAAAAATA
127365 TAAACTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATAATAATACTAATAAAAATA
Found at i:127361 original size:18 final size:18
Alignment explanation
Indices: 127340--127402 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
127330 TTAATAAAAA
127340 TAAAATAATAATACTAAT
1 TAAAATAATAATACTAAT
127358 TAAAAT-ATAA-ACTATAAAT
1 TAAAATAATAATAC--T-AAT
*
127377 TAAAATATTAACTA-TAAT
1 TAAAATAATAA-TACTAAT
127395 TAAAATAA
1 TAAAATAA
127403 ATTAAAACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
16 2 0.05
17 4 0.11
18 17 0.46
19 10 0.27
20 3 0.08
22 1 0.03
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATAATAATACTAAT
Found at i:127379 original size:19 final size:18
Alignment explanation
Indices: 127354--127401 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
127344 ATAATAATAC
127354 TAATTAAAATATAAACTA
1 TAATTAAAATATAAACTA
*
127372 TAAATTAAAATATTAACTA
1 T-AATTAAAATATAAACTA
127391 TAATTAAAATA
1 TAATTAAAATA
127402 AATTAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATTAAAATATAAACTA
Done.