Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005247.1 Hibiscus syriacus cultivar Beakdansim tig00011870_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: 232795
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:2257 original size:20 final size:20
Alignment explanation
Indices: 2232--2269 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2222 AATATATCTT
*
2232 ATAGCAATATGAATAAAATA
1 ATAGCAATAAGAATAAAATA
*
2252 ATAGCACTAAGAATAAAA
1 ATAGCAATAAGAATAAAA
2270 AAAATGAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.21
Consensus pattern (20 bp):
ATAGCAATAAGAATAAAATA
Found at i:2918 original size:57 final size:58
Alignment explanation
Indices: 2825--3104 Score: 397
Period size: 57 Copynumber: 4.9 Consensus size: 58
2815 TGATAAAAAA
* *
2825 TTTAAAAGGGTGCCTAATAAGTGATTAATTTATGTTAGGTGCTATTTTTGTAAATA-T
1 TTTAAAAGGGTGCCTAATAAGTAATTAATTTCTGTTAGGTGCTATTTTTGTAAATATT
*
2882 TTTAAAAGGGTGCCTAATAAGTAATTAATTTCTGTTAGGTGCAATTTTTGTAAATATT
1 TTTAAAAGGGTGCCTAATAAGTAATTAATTTCTGTTAGGTGCTATTTTTGTAAATATT
* *
2940 TTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAGGTGCTATTTTT-TACATA-T
1 TTTAAAAGGGTGCCTAATAAGTAATTAATTTCTGTTAGGTGCTATTTTTGTAAATATT
* * * * *
2996 TTTAAGA-GGTGCCTAATAGGTAATTAATTTTTTGCTAGGTGTTATTTTTGTAAATATT
1 TTTAAAAGGGTGCCTAATAAGTAATTAA-TTTCTGTTAGGTGCTATTTTTGTAAATATT
* * *
3054 TTTAAAAGGGTGCCTAATAGGTAATTAATTTCTGTAAGTGTGTTATTTTTG
1 TTTAAAAGGGTGCCTAATAAGTAATTAATTTCTGTTAG-GTGCTATTTTTG
3105 GAAAAGTTGA
Statistics
Matches: 201, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
55 19 0.09
56 25 0.12
57 63 0.31
58 62 0.31
59 32 0.16
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.45
Consensus pattern (58 bp):
TTTAAAAGGGTGCCTAATAAGTAATTAATTTCTGTTAGGTGCTATTTTTGTAAATATT
Found at i:4164 original size:19 final size:19
Alignment explanation
Indices: 4137--4173 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4127 TGTGATCTGT
4137 ACTGGTTTACCCCTTTCAA
1 ACTGGTTTACCCCTTTCAA
*
4156 ACTGTTTTACCCCTTTCA
1 ACTGGTTTACCCCTTTCA
4174 GATACTCTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.32, G:0.08, T:0.41
Consensus pattern (19 bp):
ACTGGTTTACCCCTTTCAA
Found at i:7670 original size:30 final size:28
Alignment explanation
Indices: 7617--7673 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
7607 GTATGGTTTT
*
7617 GAAACAAATGAAAGTTTATGTACTAAAC
1 GAAACAAATGAAAGTTTAGGTACTAAAC
*
7645 GAAACAAGATTGATAGTTTAGGTACTAAA
1 GAAACAA-A-TGAAAGTTTAGGTACTAAA
7674 TGCATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 1 0.04
30 17 0.68
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (28 bp):
GAAACAAATGAAAGTTTAGGTACTAAAC
Found at i:8132 original size:6 final size:6
Alignment explanation
Indices: 8121--8152 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
8111 GACACGTATT
8121 ACCACG ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG ACCACG AC
8153 GAGACGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:8674 original size:6 final size:6
Alignment explanation
Indices: 8663--8713 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
8653 TCTCGGGTTG
8663 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
8711 GGT
1 GGT
8714 AATACGTGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:8860 original size:41 final size:41
Alignment explanation
Indices: 8829--9068 Score: 385
Period size: 41 Copynumber: 5.9 Consensus size: 41
8819 GACATTGTAG
** *
8829 ACTATCGCAATACGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
8870 ACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ATTGT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG-CGATTTTCA
* *
8910 GACTATCGCAATGCGAAATGAAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
8952 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
8993 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
9034 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
9069 AATGGAAAAT
Statistics
Matches: 184, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
40 2 0.01
41 180 0.98
42 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:8901 original size:82 final size:82
Alignment explanation
Indices: 8805--9065 Score: 436
Period size: 82 Copynumber: 3.2 Consensus size: 82
8795 GCAACGAATT
* *
8805 TGGAAAATCACAACGACATTGTAGACTATCGCAATACGAAATGAAAAATCGCAACGCGATTTTCA
1 TGGAAAATCGCAACGACATTGTAGACTATCGCAATGCGAAATGAAAAATCGCAACGCGATTTTCA
8870 ACTATCGCAACGCGAAA
66 ACTATCGCAACGCGAAA
8887 TGGAAAATCGCAACGACATTGTAGACTATCGCAATGCGAAATGAAAAATCGCAACGCGATTTTCA
1 TGGAAAATCGCAACGACATTGTAGACTATCGCAATGCGAAATGAAAAATCGCAACGCGATTTTCA
8952 ACTATCGCAACGCGAAA
66 ACTATCGCAACGCGAAA
* * * *
8969 TGGAAAATCGCAACG-CGATTTTCA-ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTT
1 TGGAAAATCGCAACGAC-ATTGT-AGACTATCGCAATGCGAAATGAAAAATCGCAACGCGATTTT
9032 CAACTATCGCAACGCGAAA
64 CAACTATCGCAACGCGAAA
9051 TGGAAAATCGCAACG
1 TGGAAAATCGCAACG
9066 CGAAATGGAA
Statistics
Matches: 171, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
81 1 0.01
82 169 0.99
83 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (82 bp):
TGGAAAATCGCAACGACATTGTAGACTATCGCAATGCGAAATGAAAAATCGCAACGCGATTTTCA
ACTATCGCAACGCGAAA
Found at i:8938 original size:61 final size:61
Alignment explanation
Indices: 8873--9116 Score: 228
Period size: 61 Copynumber: 4.0 Consensus size: 61
8863 ATTTTCAACT
*
8873 ATCGCAACGCGAAATGGAAAATCGCAACG-ACATTGT-AGACTATCGCAATGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAAATCGCAACGCA-ATTGTCA-ACTATCGCAACGCGAAATGAAAA
** ** * * * * ** * **
8934 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG-GAA-AATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-AATCGCAACGC-AATTGTCAACTATCGCAACGCGA-AATGAAAA
* * * *
8996 ATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAAATCGCAACGCAATTGTCAACTATCGCAACGCGAAATGAAAA
*
9057 ATCGCAACGCGAAATGGAAAATCGCAACGCAATT-TCCAACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGGAAAATCGCAACGCAATTGT-CAACTATCGCAACGCGAAATGAAA
9117 CTCGAATTTG
Statistics
Matches: 141, Mismatches: 34, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
60 3 0.02
61 94 0.67
62 39 0.28
63 4 0.03
64 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.18
Consensus pattern (61 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCAATTGTCAACTATCGCAACGCGAAATGAAAA
Found at i:26445 original size:31 final size:31
Alignment explanation
Indices: 26410--26495 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
26400 TAAGTTTTAA
*
26410 AAAATTGAAAGTTTAGCTATTAAAACGAACT
1 AAAATTGAAAGTTTAGCTACTAAAACGAACT
26441 AAAATTGAAAGTTTAGCTACTAAAACGAACT
1 AAAATTGAAAGTTTAGCTACTAAAACGAACT
* * *
26472 AAAACTGATAGTTTAGGTACTAAA
1 AAAATTGAAAGTTTAGCTACTAAA
26496 CGCATTAAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (31 bp):
AAAATTGAAAGTTTAGCTACTAAAACGAACT
Found at i:28059 original size:20 final size:20
Alignment explanation
Indices: 28030--28078 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
28020 AACATCTTCG
*
28030 GTATCGATACCCATA-AATAA
1 GTATCAATACCC-TAGAATAA
*
28050 GTATCAATACCCTAGAATTA
1 GTATCAATACCCTAGAATAA
28070 GTATCAATA
1 GTATCAATA
28079 TTGCATGGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (20 bp):
GTATCAATACCCTAGAATAA
Found at i:28668 original size:21 final size:22
Alignment explanation
Indices: 28626--28673 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 22
28616 GTGACACTAT
28626 GCTTGTGAGTTCAACGTTCGTGTGC
1 GCTTGTGAGTTCAA---TCGTGTGC
28651 GCTTGTGAGTTCAA-CGTGTGC
1 GCTTGTGAGTTCAATCGTGTGC
28672 GC
1 GC
28674 AGGTTACTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.39
25 14 0.61
ACGTcount: A:0.12, C:0.21, G:0.33, T:0.33
Consensus pattern (22 bp):
GCTTGTGAGTTCAATCGTGTGC
Found at i:28884 original size:31 final size:30
Alignment explanation
Indices: 28818--28900 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
28808 AAGTATTCTT
*
28818 CTAATAATAAATATTGAAAAAATTGGGTTC
1 CTAATAATAAATATTGAAAAAATTGGATTC
*
28848 CTAATAATAAGTATTGAAAATAATTGGAATT-
1 CTAATAATAAATATTGAAAA-AATTGG-ATTC
* *
28879 TTAATAA-AAAAATT-AAAAAATT
1 CTAATAATAAATATTGAAAAAATT
28901 AGACACTTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
28 4 0.09
29 4 0.09
30 24 0.52
31 12 0.26
32 2 0.04
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.34
Consensus pattern (30 bp):
CTAATAATAAATATTGAAAAAATTGGATTC
Found at i:38194 original size:32 final size:32
Alignment explanation
Indices: 38150--38210 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
38140 CCAATGGACT
* *
38150 GGGGTTGTCGATGGTTACTGAGGCACCCGTCG
1 GGGGTTGCCGATGGTGACTGAGGCACCCGTCG
*
38182 GGGGTTGCCGATGGTGACTGAGGCTCCCG
1 GGGGTTGCCGATGGTGACTGAGGCACCCG
38211 CACCCAATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.11, C:0.23, G:0.43, T:0.23
Consensus pattern (32 bp):
GGGGTTGCCGATGGTGACTGAGGCACCCGTCG
Found at i:44304 original size:12 final size:12
Alignment explanation
Indices: 44287--44311 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44277 CCCGTGGATA
44287 TGTCAACCATTG
1 TGTCAACCATTG
44299 TGTCAACCATTG
1 TGTCAACCATTG
44311 T
1 T
44312 CTAGGCATAC
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:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTCAACCATTG
Found at i:58253 original size:31 final size:31
Alignment explanation
Indices: 58218--58293 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
58208 ACTTTGGAAT
**
58218 AAATATTAATTTAACCTATAAGTTTTAGATA
1 AAATATTAATTTAACCTATAAACTTTAGATA
* *
58249 AAATATTAATTTAACCTCTAAACTTTAGATG
1 AAATATTAATTTAACCTATAAACTTTAGATA
*
58280 AAACATTAATTTAA
1 AAATATTAATTTAA
58294 TCTTTGAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.39
Consensus pattern (31 bp):
AAATATTAATTTAACCTATAAACTTTAGATA
Found at i:58438 original size:21 final size:20
Alignment explanation
Indices: 58412--58452 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
58402 ATTTAACAAT
58412 TCAATAATCA-AAATGCATCAA
1 TCAATAA-CATAAATG-ATCAA
58433 TCAATAACATAAATGATCAA
1 TCAATAACATAAATGATCAA
58453 AATTTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.54, C:0.17, G:0.05, T:0.24
Consensus pattern (20 bp):
TCAATAACATAAATGATCAA
Found at i:60219 original size:19 final size:16
Alignment explanation
Indices: 60187--60229 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
60177 GGGTCATTCA
60187 ATTATTTTGTTTCAAAT
1 ATTATTTTGTTTC-AAT
60204 ATTATTTTACGTTTCAAT
1 ATTATTTT--GTTTCAAT
60222 -TTATTTTG
1 ATTATTTTG
60230 ATAATCCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
17 15 0.62
18 3 0.12
19 5 0.21
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (16 bp):
ATTATTTTGTTTCAAT
Found at i:62639 original size:29 final size:30
Alignment explanation
Indices: 62605--62668 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
62595 ATTATCTTTG
*
62605 TTTTTGTTTTAACTTATTAAATAT-TTTTA
1 TTTTTGTCTTAACTTATTAAATATATTTTA
* *
62634 TTTTTGTCTTAATTTATTAAATATATTTTG
1 TTTTTGTCTTAACTTATTAAATATATTTTA
62664 TTTTT
1 TTTTT
62669 ATTAAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (30 bp):
TTTTTGTCTTAACTTATTAAATATATTTTA
Found at i:62680 original size:29 final size:29
Alignment explanation
Indices: 62619--62680 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
62609 TGTTTTAACT
* * *
62619 TATTAAATATTTTTATTTTTGTCTTAATT
1 TATTAAATATTTTTATTTTTATCTAAATA
*
62648 TATTAAATATATTTTGTTTTTAT-TAAATA
1 TATTAAATAT-TTTTATTTTTATCTAAATA
62677 TATT
1 TATT
62681 CAGACATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (29 bp):
TATTAAATATTTTTATTTTTATCTAAATA
Found at i:63701 original size:20 final size:21
Alignment explanation
Indices: 63678--63718 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
63668 TATTATATGT
**
63678 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
63698 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
63719 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:64643 original size:27 final size:26
Alignment explanation
Indices: 64593--64662 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
64583 TGTTTTTTTT
* *
64593 TTTCTTTCTCTCCGGTTCTGTCTCTG
1 TTTCTGTCTCTCTGGTTCTGTCTCTG
64619 TTTCTGTCTCTCTTGGTTCTGTCTCTG
1 TTTCTGTCTCTC-TGGTTCTGTCTCTG
64646 -TTCTGTCTCTCCTGGTT
1 TTTCTGTCTCT-CTGGTT
64663 TTTTTCTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 26 0.65
27 14 0.35
ACGTcount: A:0.00, C:0.29, G:0.17, T:0.54
Consensus pattern (26 bp):
TTTCTGTCTCTCTGGTTCTGTCTCTG
Found at i:64650 original size:11 final size:11
Alignment explanation
Indices: 64607--64655 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 11
64597 TTTCTCTCCG
64607 GTTCTGTCTCT
1 GTTCTGTCTCT
64618 GTTTCTGTCTCTCTT
1 G-TTCTG--TCTC-T
64633 GGTTCTGTCTCT
1 -GTTCTGTCTCT
64645 GTTCTGTCTCT
1 GTTCTGTCTCT
64656 CCTGGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
11 12 0.36
12 6 0.18
13 4 0.12
14 4 0.12
15 6 0.18
16 1 0.03
ACGTcount: A:0.00, C:0.27, G:0.18, T:0.55
Consensus pattern (11 bp):
GTTCTGTCTCT
Found at i:65133 original size:3 final size:3
Alignment explanation
Indices: 65125--65186 Score: 97
Period size: 3 Copynumber: 20.3 Consensus size: 3
65115 AATATATATT
* *
65125 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
65171 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
65187 GGATAAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:65489 original size:113 final size:116
Alignment explanation
Indices: 65370--66053 Score: 767
Period size: 113 Copynumber: 6.2 Consensus size: 116
65360 TCTCTGGGAT
65370 GATGATCCATCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCT
1 GATGATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCT
* *
65434 TCTTCCTTCTTCAGATGACGAGTTCTTCTC-CATGAACTCTACCT-GCAAT
66 TCTTCCTTCTTCAGATGACGAGTTCTTCTCATATGAACTCTACCTGGCAAA
*
65483 GTTGATCCATCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCT
1 GATGATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCT
*
65547 TCTCCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAA
66 TCTTCCTTCTTCAGATGACGAGTTCTTCTCA-TATGAACTCTACCTGGCAAA
* * * *
65599 GATAATCCATTAACTTGATGAATTCAGGCAAAAGATTG-ACAAGTTCTTCTCATTATGAACTTCT
1 GATGATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCT
65663 TCTTCC-T-TTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAA
66 TCTTCCTTCTTCAGATGACGAGTTCTTCTCA-TATGAACTCTACCTGGCAAA
* * * * *
65713 GATAATCCATCAACTTGATGAATTC-AG-AAAAAAGGTGAACAAATTCTTCTCATTATGAACTTC
1 GATGATCCATCAACATGATGAATTCAAGCAAAAGA-TTGAACAAGTTCTTCTCATTATGAACTTC
*
65776 TTCTT-CTTCTTCAGAT-A--AGTTC-T-TC-TATGAA--CT--CTGGAAAA
65 TTCTTCCTTCTTCAGATGACGAGTTCTTCTCATATGAACTCTACCTGGCAAA
* ** * *
65817 GACTGATCCATCAA-ATGATGGATTCGGGTAAAAGGTTGAACAA--T-TTCTCATTATGAACTTC
1 GA-TGATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTC
* * *
65878 TTCTTCCTTC-TCA-A--ATGAG-T-TTCTCATATGAAC-CTTCTCTGGAAAA
65 TTCTTCCTTCTTCAGATGACGAGTTCTTCTCATATGAACTCTAC-CTGGCAAA
** * * * *
65924 GAT-ATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
1 GATGATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCT
* * *
65988 TCTTCCTTCTTCA-A--ATGAG-TCTTTTCATTATGAACTTTACCTGGCAAA
66 TCTTCCTTCTTCAGATGACGAGTTCTTCTCA-TATGAACTCTACCTGGCAAA
*
66036 GATAATCCATCAA-ATGAT
1 GATGATCCATCAACATGAT
66054 AGATTTGAAT
Statistics
Matches: 510, Mismatches: 31, Indels: 61
0.85 0.05 0.10
Matches are distributed among these distances:
100 1 0.00
101 3 0.01
102 29 0.06
103 11 0.02
104 20 0.04
105 27 0.05
106 33 0.06
107 10 0.02
108 7 0.01
109 27 0.05
110 12 0.02
111 6 0.01
112 31 0.06
113 107 0.21
114 98 0.19
115 21 0.04
116 45 0.09
117 22 0.04
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (116 bp):
GATGATCCATCAACATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCT
TCTTCCTTCTTCAGATGACGAGTTCTTCTCATATGAACTCTACCTGGCAAA
Found at i:65704 original size:114 final size:114
Alignment explanation
Indices: 65374--66053 Score: 779
Period size: 114 Copynumber: 6.1 Consensus size: 114
65364 TGGGATGATG
* *
65374 ATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
1 ATCCATCAATTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
* * * *
65439 CTTCTTCAGATGACGAGTTCTTCTC-CATGAACTCTACCT-GCAATGTTG
66 CTTCTTCAGAT-ACGAGTTCTTCTCATATGAACTCTACCTGGCAAAGATA
* * *
65487 ATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
1 ATCCATCAATTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
65552 CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
66 CTTCTTCAGAT-ACGAGTTCTTCTCA-TATGAACTCTACCTGGCAAAGATA
*
65603 ATCCATTAACTTGATGAATTCAGGCAAAAGATTG-ACAAGTTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAA-TTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
65667 CC-T-TTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATA
65 CCTTCTTCAGAT-ACGAGTTCTTCTCA-TATGAACTCTACCTGGCAAAGATA
** * *
65717 ATCCATCAACTTGATGAATTCAGAAAAAAG-GTGAACAAATTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAA-TTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
* *
65781 -CTTCTTCAGATA--AGTTC-T-TC-TATGAA--CT--CTGGAAAAGACTG
65 CCTTCTTCAGATACGAGTTCTTCTCATATGAACTCTACCTGGCAAAGA-TA
* * * * *
65822 ATCCATCAAATGATGGATTCGGGTAAAAGGTTGAACAA--T-TTCTCATTATGAACTTCTTCTTC
1 ATCCATCAATTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
* * *
65884 CTTC-TCA-A-ATGAG-T-TTCTCATATGAAC-CTTCTCTGGAAAAGAT-
66 CTTCTTCAGATACGAGTTCTTCTCATATGAACTCTAC-CTGGCAAAGATA
* * *
65927 ATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
1 ATCCATCAA-TTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
* * *
65992 CCTTCTTCA-A-ATGAG-TCTTTTCATTATGAACTTTACCTGGCAAAGATA
65 CCTTCTTCAGATACGAGTTCTTCTCA-TATGAACTCTACCTGGCAAAGATA
*
66040 ATCCATCAAATGAT
1 ATCCATCAATTGAT
66054 AGATTTGAAT
Statistics
Matches: 509, Mismatches: 30, Indels: 57
0.85 0.05 0.10
Matches are distributed among these distances:
100 1 0.00
101 3 0.01
102 29 0.06
103 11 0.02
104 26 0.05
105 26 0.05
106 29 0.06
107 10 0.02
108 7 0.01
109 27 0.05
110 12 0.02
111 6 0.01
112 26 0.05
113 103 0.20
114 105 0.21
115 21 0.04
116 45 0.09
117 22 0.04
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (114 bp):
ATCCATCAATTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
CTTCTTCAGATACGAGTTCTTCTCATATGAACTCTACCTGGCAAAGATA
Found at i:66887 original size:53 final size:59
Alignment explanation
Indices: 66789--66904 Score: 145
Period size: 53 Copynumber: 2.1 Consensus size: 59
66779 TAACTCAAAG
* **
66789 AACACTTCCATAAGATGCTATGAACACATTCATCTTTTAACTCAATGA-T-GTTCTGTCC
1 AACACTTCCAGAAGATGCTATG-ACACATTCATCTTCAAACTCAATGATTGGTTCTGTCC
*
66847 AACACTTCCAGAAGA-GCT-TG-CA-ATTCATCTTCAAATTCAATGATTGGTTCTGTCC
1 AACACTTCCAGAAGATGCTATGACACATTCATCTTCAAACTCAATGATTGGTTCTGTCC
66902 AAC
1 AAC
66905 CAGATCAGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
53 18 0.35
54 3 0.06
55 12 0.23
56 2 0.04
57 3 0.06
58 14 0.27
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (59 bp):
AACACTTCCAGAAGATGCTATGACACATTCATCTTCAAACTCAATGATTGGTTCTGTCC
Found at i:67012 original size:79 final size:79
Alignment explanation
Indices: 66866--67028 Score: 269
Period size: 79 Copynumber: 2.1 Consensus size: 79
66856 AGAAGAGCTT
66866 GCAATTCATCTTCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACCA
1 GCAATTCATCTTCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACCA
66931 GAAGATGCTATTGA
66 GAAGATGCTATTGA
*
66945 GCAATTCATCTTCTAAA-TCAATGATTGGTTTTG-CCAACCA-ATCAGATAACTCAAAGAACACT
1 GCAATTCATCTTC-AAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACAC-
67007 TCAGAAGATGCTATTGA
64 -CAGAAGATGCTATTGA
67024 GCAAT
1 GCAAT
67029 AATTTGTTCC
Statistics
Matches: 80, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
77 21 0.26
78 7 0.09
79 49 0.61
80 3 0.04
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (79 bp):
GCAATTCATCTTCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACCA
GAAGATGCTATTGA
Found at i:68157 original size:11 final size:10
Alignment explanation
Indices: 68138--68189 Score: 61
Period size: 10 Copynumber: 4.9 Consensus size: 10
68128 CCTTGACCCC
68138 CTTTCTTTTT
1 CTTTCTTTTT
68148 CTTCTCTTTTT
1 CTT-TCTTTTT
68159 -TTTCTTTTT
1 CTTTCTTTTT
68168 CATTTTTCTTTTT
1 C---TTTCTTTTT
68181 CTTTCTTTT
1 CTTTCTTTT
68190 CTTAAGCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
9 7 0.19
10 13 0.35
11 7 0.19
13 10 0.27
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:68173 original size:7 final size:6
Alignment explanation
Indices: 68139--68184 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
68129 CTTGACCCCC
*
68139 TTTCTT TTTCTT CTCTTTTT TTTCTT TTTCATT TTTCTT TTTCTT T
1 TTTCTT TTTCTT -T-TTCTT TTTCTT TTTC-TT TTTCTT TTTCTT T
68185 CTTTTCTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 23 0.66
7 8 0.23
8 4 0.11
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:68173 original size:13 final size:13
Alignment explanation
Indices: 68157--68181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68147 TCTTCTCTTT
68157 TTTTTCTTTTTCA
1 TTTTTCTTTTTCA
68170 TTTTTCTTTTTC
1 TTTTTCTTTTTC
68182 TTTCTTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTTTCA
Found at i:79419 original size:20 final size:21
Alignment explanation
Indices: 79396--79436 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
79386 TATTATATGT
**
79396 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
79416 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
79437 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:80351 original size:20 final size:18
Alignment explanation
Indices: 80327--80361 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
80317 GTTTGTTGTT
80327 GTTTTTTTTCTTTCTCTG
1 GTTTTTTTTCTTTCTCTG
*
80345 TTTTTTTTTCTTTCTCT
1 GTTTTTTTTCTTTCTCT
80362 CCGGTTCTGT
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:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (18 bp):
GTTTTTTTTCTTTCTCTG
Found at i:80381 original size:12 final size:12
Alignment explanation
Indices: 80366--80414 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
80356 TTCTCTCCGG
80366 TTCTGTCTCTGT
1 TTCTGTCTCTGT
*
80378 TTCTGTCTCTCTTGG
1 TTCTG--TCTC-TGT
*
80393 TTCTCTCTCTGT
1 TTCTGTCTCTGT
80405 TTCTGTCTCT
1 TTCTGTCTCT
80415 CCTGGTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 16 0.53
13 4 0.13
14 4 0.13
15 6 0.20
ACGTcount: A:0.00, C:0.29, G:0.14, T:0.57
Consensus pattern (12 bp):
TTCTGTCTCTGT
Found at i:80402 original size:27 final size:26
Alignment explanation
Indices: 80351--80421 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 26
80341 TCTGTTTTTT
* * *
80351 TTTCTTTCTCTCCGGTTCTGTCTCTG
1 TTTCTGTCTCTCTGGTTCTCTCTCTG
80377 TTTCTGTCTCTCTTGGTTCTCTCTCTG
1 TTTCTGTCTCTC-TGGTTCTCTCTCTG
80404 TTTCTGTCTCTCCTGGTT
1 TTTCTGTCTCT-CTGGTT
80422 TTTTTCTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 11 0.28
27 28 0.70
28 1 0.03
ACGTcount: A:0.00, C:0.30, G:0.15, T:0.55
Consensus pattern (26 bp):
TTTCTGTCTCTCTGGTTCTCTCTCTG
Found at i:80422 original size:16 final size:16
Alignment explanation
Indices: 80376--80422 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 16
80366 TTCTGTCTCT
*
80376 GTTTCTGTCTCTCTTG
1 GTTTCTGTCTCTCCTG
80392 G-TTC--TCTCT-CT-
1 GTTTCTGTCTCTCCTG
80403 GTTTCTGTCTCTCCTG
1 GTTTCTGTCTCTCCTG
80419 GTTT
1 GTTT
80423 TTTTCTTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 10
0.69 0.03 0.28
Matches are distributed among these distances:
11 1 0.04
12 4 0.16
13 5 0.20
14 5 0.20
15 5 0.20
16 5 0.20
ACGTcount: A:0.00, C:0.28, G:0.17, T:0.55
Consensus pattern (16 bp):
GTTTCTGTCTCTCCTG
Found at i:80899 original size:3 final size:3
Alignment explanation
Indices: 80891--80961 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
80881 AATATATATT
*
80891 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
80939 TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
80962 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:81315 original size:29 final size:30
Alignment explanation
Indices: 81277--81357 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 30
81267 TTCAAGCTGA
*
81277 AAAATAAAAACAAAATATATTTAATAAATT
1 AAAACAAAAACAAAATATATTTAATAAATT
* * *
81307 AAGACAAAAATAAAA-ATATTTAATAAGTT
1 AAAACAAAAACAAAATATATTTAATAAATT
81336 AAAACAAAAACAAAGATA-ATTT
1 AAAACAAAAACAAA-ATATATTT
81358 TAAAATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 25 0.58
30 17 0.40
31 1 0.02
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.26
Consensus pattern (30 bp):
AAAACAAAAACAAAATATATTTAATAAATT
Found at i:81590 original size:41 final size:41
Alignment explanation
Indices: 81553--81633 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
81543 CTATCGCATT
* * *
81553 GCGATTTTCCTAATTCACAATGCGAATACGTAAATCGCAAC
1 GCGAATTTCCAAAATCACAATGCGAATACGTAAATCGCAAC
** * *
81594 GCGAATTTGGAAAATCGCAATGCGATTACGTAAATCGCAA
1 GCGAATTTCCAAAATCACAATGCGAATACGTAAATCGCAA
81634 TGTGAATACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (41 bp):
GCGAATTTCCAAAATCACAATGCGAATACGTAAATCGCAAC
Found at i:81599 original size:20 final size:20
Alignment explanation
Indices: 81570--81656 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
81560 TCCTAATTCA
81570 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
* ** *
81590 CAACGCGAATTTGGAAAATCG
1 CAATGCGAA-TACGTAAATCG
*
81611 CAATGCGATTACGTAAATCG
1 CAATGCGAATACGTAAATCG
* *
81631 CAATGTGAATACATAAATCG
1 CAATGCGAATACGTAAATCG
81651 CAATGC
1 CAATGC
81657 AAATCTATAA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 38 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:81666 original size:20 final size:20
Alignment explanation
Indices: 81605--81673 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
81595 CGAATTTGGA
* * *
81605 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCAAATACAT
**
81625 AAATCGCAATGTGAATACAT
1 AAATCGCAATGCAAATACAT
81645 AAATCGCAATGCAAAT-CTAT
1 AAATCGCAATGCAAATAC-AT
81665 AAATCGCAA
1 AAATCGCAA
81674 CGAGATTCTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.23
Consensus pattern (20 bp):
AAATCGCAATGCAAATACAT
Found at i:85020 original size:20 final size:21
Alignment explanation
Indices: 84995--85088 Score: 124
Period size: 20 Copynumber: 4.7 Consensus size: 21
84985 GATATTCATT
84995 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAATA
*
85015 TGACTATCGCAACACGGAA-A
1 TGACTATCGCAACGCGGAATA
*
85035 TGACTATCGCAATGCGGAAT-
1 TGACTATCGCAACGCGGAATA
* *
85055 TGACTATCGCAACG-TGAAAA
1 TGACTATCGCAACGCGGAATA
85075 TGACTATCGCAACG
1 TGACTATCGCAACG
85089 AGAGAATCGC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.05
20 59 0.91
21 3 0.05
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.20
Consensus pattern (21 bp):
TGACTATCGCAACGCGGAATA
Found at i:85119 original size:33 final size:34
Alignment explanation
Indices: 85080--85155 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
85070 GAAAATGACT
85080 ATCGCAACGAGAGAATCGCAATGCG-AAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
*
85113 ATCGCAACGAGTGAATCGCAATGCGAAAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
85147 ATCGCAACG
1 ATCGCAACG
85156 CGAAATTAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 24 0.59
34 17 0.41
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATAAAA
Found at i:85190 original size:20 final size:18
Alignment explanation
Indices: 85165--85285 Score: 69
Period size: 20 Copynumber: 6.8 Consensus size: 18
85155 GCGAAATTAG
85165 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
*
85184 TTTTCGCATTGCGA-TTCA
1 -TTTCGCGTTGCGATTTCA
*
85202 ---CTCGTTGCGATTTTCA
1 TTTCGCGTTGCGA-TTTCA
*
85218 TTTCGCATTGCGA-TTC-
1 TTTCGCGTTGCGATTTCA
* *
85234 --TCTCGTTGCGATAGTCA
1 TTTCGCGTTGCGAT-TTCA
*
85251 TTTTCGCGTTGCGATAGTCA
1 -TTTCGCGTTGCGAT-TTCA
85271 TTTTCGCGTTGCGAT
1 -TTTCGCGTTGCGAT
85286 AGTCTGTTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
14 17 0.21
16 6 0.07
17 3 0.04
18 4 0.05
19 8 0.10
20 43 0.53
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTCA
Found at i:85227 original size:33 final size:34
Alignment explanation
Indices: 85170--85265 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
85160 ATTAGTTTCG
85170 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
85204 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** *
85237 CGTTGCGATAGTCATTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
85266 AGTCATTTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:85286 original size:20 final size:20
Alignment explanation
Indices: 85237--85289 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
85227 GCGATTCTCT
85237 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
85257 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
85277 CGTTGCGATAGTC
1 CGTTGCGATAGTC
85290 TGTTTTGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:85406 original size:14 final size:14
Alignment explanation
Indices: 85387--85423 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
85377 CATCAATTAA
85387 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
85401 ACAAATCATCTTTT
1 ACAAATCAACATTT
85415 ACAAATCAA
1 ACAAATCAA
85424 TTAAACAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:89731 original size:20 final size:20
Alignment explanation
Indices: 89657--89759 Score: 100
Period size: 20 Copynumber: 4.9 Consensus size: 20
89647 CAGAACCCCA
*
89657 GGGGGGTATCGATTCCC-CTGT
1 GGGGGG-ATCGATTCCCTC-AT
* *
89678 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGATT-CCC-TC-AT
* *
89702 GGGGGAATCGGTTCCCTCAT
1 GGGGGGATCGATTCCCTCAT
89722 GGGGGGATCGATTCCCTCAT
1 GGGGGGATCGATTCCCTCAT
89742 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
89760 TGCACCAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
20 37 0.53
21 14 0.20
22 6 0.09
23 7 0.10
24 6 0.09
ACGTcount: A:0.15, C:0.25, G:0.36, T:0.24
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAT
Found at i:93615 original size:22 final size:21
Alignment explanation
Indices: 93573--93612 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
93563 GAGTTTGTTT
*
93573 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
93594 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
93613 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:96348 original size:42 final size:41
Alignment explanation
Indices: 96284--96365 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
96274 TCTAGAATGT
* *
96284 TGGGAGGGACTCTTCAATGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGGACTCTTCAAGGATGACAGGGGCCTCTTGAACGG
* * *
96325 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACG
1 TGGGA-GGGACTCTTCAAGGATGACAGGGGCCTCTTGAACG
96366 ATAGGGGAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 5 0.14
42 30 0.86
ACGTcount: A:0.21, C:0.17, G:0.39, T:0.23
Consensus pattern (41 bp):
TGGGAGGGACTCTTCAAGGATGACAGGGGCCTCTTGAACGG
Found at i:96897 original size:20 final size:20
Alignment explanation
Indices: 96874--97047 Score: 142
Period size: 20 Copynumber: 9.3 Consensus size: 20
96864 GAAACTTAAA
*
96874 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
96894 ATCGCAATACGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
96914 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
*
96934 ATCGCAA--CG-AGA-GA--
1 ATCGCAATGCGAAAATGACT
**
96948 ATCGCAATGCG-AAATGAAA
1 ATCGCAATGCGAAAATGACT
96967 ATCGCAA--C-AACAA--A--
1 ATCGCAATGCGAA-AATGACT
* *
96981 ATGGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
97001 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
97021 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
97041 ATCGCAA
1 ATCGCAA
97048 CGAGAGAATC
Statistics
Matches: 127, Mismatches: 13, Indels: 28
0.76 0.08 0.17
Matches are distributed among these distances:
14 13 0.10
16 10 0.08
17 7 0.06
18 5 0.04
19 7 0.06
20 85 0.67
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:96957 original size:34 final size:34
Alignment explanation
Indices: 96873--97066 Score: 147
Period size: 40 Copynumber: 5.4 Consensus size: 34
96863 TGAAACTTAA
* * *
96873 AATCGCAACGCGAAAATGACTATCGCAATACGAAAATG
1 AATCGCAATGCGAATATGACTATCGC-A-ACG-AGA-G
*
96911 ACTATCGCAATGCGAATTTGACTATCGCAACGAGAG
1 A--ATCGCAATGCGAATATGACTATCGCAACGAGAG
** * * *
96947 AATCGCAATGCGAA-ATGAAAATCGCAACAACAA
1 AATCGCAATGCGAATATGACTATCGCAACGAGAG
* * * *
96980 AATGGCAACGCGAAAATGACTATCGCAATGCGAAAATG
1 AATCGCAATGCGAATATGACTATCGCAA--CG-AGA-G
*
97018 ACTATCGCAATGCGAATTTGACTATCGCAACGAGAG
1 A--ATCGCAATGCGAATATGACTATCGCAACGAGAG
97054 AATCGCAATGCGA
1 AATCGCAATGCGA
97067 TTTTCATTTC
Statistics
Matches: 125, Mismatches: 22, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
33 25 0.20
34 36 0.29
36 5 0.04
37 6 0.05
38 7 0.06
39 1 0.01
40 45 0.36
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (34 bp):
AATCGCAATGCGAATATGACTATCGCAACGAGAG
Found at i:97079 original size:107 final size:107
Alignment explanation
Indices: 96871--97066 Score: 374
Period size: 107 Copynumber: 1.8 Consensus size: 107
96861 TCTGAAACTT
96871 AAAATCGCAACGCGAAAATGACTATCGCAATACGAAAATGACTATCGCAATGCGAATTTGACTAT
1 AAAATCGCAACGCGAAAATGACTATCGCAATACGAAAATGACTATCGCAATGCGAATTTGACTAT
96936 CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACAAC
66 CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACAAC
* *
96978 AAAATGGCAACGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTAT
1 AAAATCGCAACGCGAAAATGACTATCGCAATACGAAAATGACTATCGCAATGCGAATTTGACTAT
97043 CGCAACGAGAGAATCGCAATGCGA
66 CGCAACGAGAGAATCGCAATGCGA
97067 TTTTCATTTC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 87 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.17
Consensus pattern (107 bp):
AAAATCGCAACGCGAAAATGACTATCGCAATACGAAAATGACTATCGCAATGCGAATTTGACTAT
CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACAAC
Found at i:97143 original size:54 final size:53
Alignment explanation
Indices: 97056--97177 Score: 181
Period size: 54 Copynumber: 2.3 Consensus size: 53
97046 AACGAGAGAA
* ** *
97056 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
**
97109 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATAGTCA-TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
97163 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
97178 AAACTATTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 14 0.23
54 48 0.77
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.39
Consensus pattern (53 bp):
TCGCATTGCGATAGTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
Found at i:97173 original size:20 final size:20
Alignment explanation
Indices: 97094--97177 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
97084 GATTCTTTCG
**
97094 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
97114 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
97134 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
97148 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
97168 TTGCGATAGT
1 TTGCGATAGT
97178 AAACTATTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.13
16 6 0.11
18 6 0.11
20 35 0.65
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:99110 original size:20 final size:20
Alignment explanation
Indices: 99055--99121 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
99045 ACTTTAAATT
* **
99055 GCAACACGAAAATGAAAATC
1 GCAACGCGAAAATGACTATC
*
99075 GCAACACGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
**
99095 GCAACGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
99115 GCAACGC
1 GCAACGC
99122 AAGAATCGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:99604 original size:22 final size:22
Alignment explanation
Indices: 99543--99604 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
99533 TGACCGTGAA
* *
99543 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
99565 TG-TTATCGTC---G-TGGGGAC
1 TGATT-TCGTCGGAGATGGGGAC
99583 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
99605 GGATGTCGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 13 0.41
19 3 0.09
21 3 0.09
22 13 0.41
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:99854 original size:21 final size:21
Alignment explanation
Indices: 99830--99875 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
99820 TATTCGCATT
99830 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
99851 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
99872 GCGA
1 GCGA
99876 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:104300 original size:4 final size:4
Alignment explanation
Indices: 104293--104359 Score: 79
Period size: 4 Copynumber: 17.2 Consensus size: 4
104283 ATATATATAT
104293 ATAC ATAC --AC ATAC ATAC AT-C TATAC ATAC ATAC AT-C TATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC -ATAC ATAC ATAC ATAC -ATAC ATAC
*
104339 ATAC ATAC ATGC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC A
104360 CATACACACA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
2 2 0.04
3 2 0.04
4 49 0.89
5 2 0.04
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:104322 original size:16 final size:16
Alignment explanation
Indices: 104301--104359 Score: 93
Period size: 16 Copynumber: 3.7 Consensus size: 16
104291 ATATACATAC
104301 ACATACATACATCTAT
1 ACATACATACATCTAT
104317 ACATACATACATCTAT
1 ACATACATACATCTAT
104333 ACATACATACATAC-AT
1 ACATACATACAT-CTAT
*
104349 GCATACATACA
1 ACATACATACA
104360 CATACACACA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
16 40 0.98
17 1 0.02
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (16 bp):
ACATACATACATCTAT
Found at i:104370 original size:2 final size:2
Alignment explanation
Indices: 104357--104433 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
104347 ATGCATACAT
*
104357 AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
104399 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
104434 TATATCGCTA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.48, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:107357 original size:21 final size:21
Alignment explanation
Indices: 107322--107371 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
107312 AAATTCATAA
107322 AACCCTAA-ACTTAAATCTCT
1 AACCCTAATACTTAAATCTCT
*
107342 AACCCTAATTCTTAAATCTCT
1 AACCCTAATACTTAAATCTCT
*
107363 AACCTTAAT
1 AACCCTAAT
107372 CTCAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (21 bp):
AACCCTAATACTTAAATCTCT
Found at i:109158 original size:71 final size:71
Alignment explanation
Indices: 109030--109164 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 71
109020 AAAAAAATTG
* * * * *
109030 AAAGTATCGATACTTTTCTATAAGTATTGATACTTTCGAATTTTTAAAAAAAAGGAAAATGAGAA
1 AAAGTATCAATACTTTTCCACAAGTATCGATACTTTCGAATATTTAAAAAAAAGGAAAATGAGAA
109095 GGTTAC
66 GGTTAC
* *
109101 AAAGTATCAATACTTTTCCACAAGTATCGATAC-TTCTAA-ATTTAAAATAATATGGAAAATGAG
1 AAAGTATCAATACTTTTCCACAAGTATCGATACTTTCGAATATTTAAAA-AA-AAGGAAAATGAG
109164 A
64 A
109165 TTATGCAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
69 7 0.13
70 7 0.13
71 41 0.75
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (71 bp):
AAAGTATCAATACTTTTCCACAAGTATCGATACTTTCGAATATTTAAAAAAAAGGAAAATGAGAA
GGTTAC
Found at i:109735 original size:75 final size:77
Alignment explanation
Indices: 109554--109723 Score: 238
Period size: 75 Copynumber: 2.2 Consensus size: 77
109544 TAAACTCTAT
* *
109554 TAACATTTTAGGTGCAACCTAAAATGTTAATAATATTTATAACATTCACCGTTTATAACTTATTT
1 TAACATTTTAGGTGCAACCTAAAATGTTAATAATATTAATAACATTCACCATTTATAACTTATTT
*
109619 TCTTATCGTTTA
66 TCTTATCATTTA
* ** * *
109631 TATCATTTTAGGCACAACCTAAAATGTTAA-AATATTAATAACATT-ATCATTTGTAACTTATTT
1 TAACATTTTAGGTGCAACCTAAAATGTTAATAATATTAATAACATTCACCATTTATAACTTATTT
109694 TCTTA-CAATTTA
66 TCTTATC-ATTTA
109706 TAACATTTTAGGTGCAAC
1 TAACATTTTAGGTGCAAC
109724 ATGTTATGTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
74 1 0.01
75 39 0.48
76 14 0.17
77 27 0.33
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (77 bp):
TAACATTTTAGGTGCAACCTAAAATGTTAATAATATTAATAACATTCACCATTTATAACTTATTT
TCTTATCATTTA
Found at i:110761 original size:20 final size:20
Alignment explanation
Indices: 110732--110784 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
110722 TGTTGAAGCC
* *
110732 AAAGTATCGAAACTTTAGGG
1 AAAGTTTCGAAACTTTAGAG
*
110752 AAAGTTTCGAAACTTTTGAG
1 AAAGTTTCGAAACTTTAGAG
*
110772 ATAGTTTCGAAAC
1 AAAGTTTCGAAAC
110785 ACTTGAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (20 bp):
AAAGTTTCGAAACTTTAGAG
Found at i:113490 original size:2 final size:2
Alignment explanation
Indices: 113483--113661 Score: 151
Period size: 2 Copynumber: 93.0 Consensus size: 2
113473 TGTAAAAATA
* *
113483 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
113525 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A- AT GT AA AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
113566 A- AT -T CT AT AT -T GT AT TT GAT AT AT -T AA AT A- AC AT -T AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
* *
113603 A- AT GT GA- AA 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 AT AT AT
*
113644 AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
113662 GGTCATAGAA
Statistics
Matches: 144, Mismatches: 22, Indels: 22
0.77 0.12 0.12
Matches are distributed among these distances:
1 9 0.06
2 134 0.93
3 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:124504 original size:12 final size:12
Alignment explanation
Indices: 124487--124520 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
124477 GGGTTTTCAA
124487 TGGTGAGCCAGC
1 TGGTGAGCCAGC
124499 TGGTGAGCCAGC
1 TGGTGAGCCAGC
124511 TGGTGAGCCA
1 TGGTGAGCCA
124521 ATGGAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.41, T:0.18
Consensus pattern (12 bp):
TGGTGAGCCAGC
Found at i:127790 original size:23 final size:23
Alignment explanation
Indices: 127760--127807 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
127750 CACTATTACC
127760 TTCTAGGGCTAATGAATGCATGT
1 TTCTAGGGCTAATGAATGCATGT
127783 TTCTAGGGCTAATGAATGCATGT
1 TTCTAGGGCTAATGAATGCATGT
127806 TT
1 TT
127808 TTGACAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (23 bp):
TTCTAGGGCTAATGAATGCATGT
Found at i:132056 original size:25 final size:25
Alignment explanation
Indices: 132008--132056 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
131998 TTTAGTTCTC
* *
132008 TATTTATTTATATGATATTTTTAAT
1 TATTTAATTATATGATATTATTAAT
132033 TATTTAATTATAT-ATATATATTAA
1 TATTTAATTATATGATAT-TATTAA
132057 AAAATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TATTTAATTATATGATATTATTAAT
Found at i:132445 original size:13 final size:12
Alignment explanation
Indices: 132405--132446 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
132395 GTTAATAATC
*
132405 AATTACGAAAAT
1 AATTAAGAAAAT
132417 AATTAA-AAAAT
1 AATTAAGAAAAT
*
132428 TATTAATGAAAAT
1 AATTAA-GAAAAT
132441 AATTAA
1 AATTAA
132447 AATTTTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 10 0.40
12 5 0.20
13 10 0.40
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (12 bp):
AATTAAGAAAAT
Found at i:133400 original size:18 final size:18
Alignment explanation
Indices: 133379--133421 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
133369 TGAGAATTAT
* *
133379 AAATAAAAATTTAATATA
1 AAATAAAAATTAAAAATA
133397 AAATAAAAATTAAAAATA
1 AAATAAAAATTAAAAATA
*
133415 TAATAAA
1 AAATAAA
133422 GTGGGTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAAAAATTAAAAATA
Found at i:133769 original size:23 final size:23
Alignment explanation
Indices: 133719--133768 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
133709 TTTCTGGTAC
*
133719 GTTTTCTTCTGTCTTTATGACAT
1 GTTTTCTTCTGCCTTTATGACAT
*
133742 GTTTTCTTTTGCCTTT-TGACAT
1 GTTTTCTTCTGCCTTTATGACAT
*
133764 ATTTT
1 GTTTT
133769 TGGTCATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.60
Consensus pattern (23 bp):
GTTTTCTTCTGCCTTTATGACAT
Found at i:133812 original size:26 final size:26
Alignment explanation
Indices: 133782--133831 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
133772 TCATATGGTC
133782 GGTTTTTATTTATCTTTTTCTAAGAA
1 GGTTTTTATTTATCTTTTTCTAAGAA
133808 GGTTTTTATTTATCTTTTTCTAAG
1 GGTTTTTATTTATCTTTTTCTAAG
133832 GATTAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.60
Consensus pattern (26 bp):
GGTTTTTATTTATCTTTTTCTAAGAA
Found at i:134334 original size:65 final size:65
Alignment explanation
Indices: 134260--134387 Score: 204
Period size: 65 Copynumber: 2.0 Consensus size: 65
134250 ATAAAAAAAA
* *
134260 AACCATTTATATGACTTAGTTTGAATAAAA-AGAAAGAACATATATTAATATTTTATATAATTAC
1 AACCATTTATATAACTTAGTTTCAA-AAAATAGAAAGAACATATATTAATATTTTATATAATTAC
134324 T
65 T
* *
134325 AACCATTTATATAACTTAGTTTCAAAAAATATAAAGAATATATATTAATATTTTATATAATTA
1 AACCATTTATATAACTTAGTTTCAAAAAATAGAAAGAACATATATTAATATTTTATATAATTA
134388 TTATTTTCAC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 4 0.07
65 54 0.93
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (65 bp):
AACCATTTATATAACTTAGTTTCAAAAAATAGAAAGAACATATATTAATATTTTATATAATTACT
Found at i:134392 original size:16 final size:17
Alignment explanation
Indices: 134362--134394 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
134352 AATATAAAGA
134362 ATATATATTAATATTTT
1 ATATATATTAATATTTT
*
134379 ATATA-ATTATTATTTT
1 ATATATATTAATATTTT
134395 CACATTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATATATTAATATTTT
Found at i:137429 original size:22 final size:22
Alignment explanation
Indices: 137401--137442 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
137391 CAGTTACAGA
*
137401 GTAATTATAAGAGTTACAAAAT
1 GTAATTACAAGAGTTACAAAAT
*
137423 GTAATTACATGAGTTACAAA
1 GTAATTACAAGAGTTACAAA
137443 CAGCAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (22 bp):
GTAATTACAAGAGTTACAAAAT
Found at i:141575 original size:20 final size:20
Alignment explanation
Indices: 141550--141600 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
141540 GGGGAGCTTC
141550 TTTCTTCTTCTTCTTGCCCG
1 TTTCTTCTTCTTCTTGCCCG
141570 TTTCTTCTTCTTCTTGCCCG
1 TTTCTTCTTCTTCTTGCCCG
141590 TTTCTTCTTCT
1 TTTCTTCTTCT
141601 GTCTGATTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.00, C:0.33, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTCTTCTTCTTCTTGCCCG
Found at i:142840 original size:21 final size:20
Alignment explanation
Indices: 142816--142863 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
142806 TCGTCATTTT
142816 ATTAATTTAATTAAGTAA-TAA
1 ATTAATTT-ATT-AGTAATTAA
*
142837 ATTATATTTATTATTAATTAA
1 ATTA-ATTTATTAGTAATTAA
142858 ATTAAT
1 ATTAAT
142864 AATGATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 6 0.25
21 14 0.58
22 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTAATTTATTAGTAATTAA
Found at i:143519 original size:25 final size:27
Alignment explanation
Indices: 143472--143522 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
143462 TCGAAGTTTA
*
143472 ATGAGTAAATCAAAAACTTGAAAGTATG
1 ATGAGTAAATCAAAAAC-AGAAAGTATG
143500 ATGAGTAAAT-AAAAA-AGAAAGTA
1 ATGAGTAAATCAAAAACAGAAAGTA
143523 AAGTTTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
27 5 0.23
28 10 0.45
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.22
Consensus pattern (27 bp):
ATGAGTAAATCAAAAACAGAAAGTATG
Found at i:145355 original size:20 final size:20
Alignment explanation
Indices: 145330--145424 Score: 113
Period size: 20 Copynumber: 4.8 Consensus size: 20
145320 TGTGATATTC
145330 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
*
145350 CAAATTTGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* *
145370 CAAATTCGCAACGAGAAAGT
1 CAAATTCGCAACGCGATAGT
* * *
145390 CAAATTCACAAC-TGA-ATTT
1 CAAATTCGCAACGCGATA-GT
145409 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
145425 ATTTAATTTC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
18 1 0.02
19 14 0.22
20 49 0.77
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:145428 original size:20 final size:20
Alignment explanation
Indices: 145228--145439 Score: 105
Period size: 20 Copynumber: 10.6 Consensus size: 20
145218 AAATGACCAA
* *
145228 CAAATTCGCAACGCTAATTC
1 CAAATTCGCAACGCGAATTT
* * *
145248 CAATTTCGCAAC-CCAGTTT
1 CAAATTCGCAACGCGAATTT
*
145267 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
** *
145290 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
*** * *
145308 CCAAATTCGCGTTGTGATATTC
1 -CAAATTCGCAACGCGA-ATTT
*
145330 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-TT
* *
145350 CAAATTTGCAACGCG-ATAGT
1 CAAATTCGCAACGCGAAT-TT
* **
145370 CAAATTCGCAACGAGAAAGT
1 CAAATTCGCAACGCGAATTT
* *
145390 CAAATTCACAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
145409 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
145429 -AATTTCGCAAC
1 CAAATTCGCAAC
145440 AGGTTTTAGT
Statistics
Matches: 150, Mismatches: 31, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
18 1 0.01
19 32 0.21
20 87 0.58
21 26 0.17
22 3 0.02
23 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:146387 original size:24 final size:24
Alignment explanation
Indices: 146336--146389 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
146326 GTATTCGAAA
* *
146336 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGGCAATACCCAGAC
* * *
146360 TTTGATCTTGGGGAATACTCAGAT
1 TTTGATCTTGGGCAATACCCAGAC
146384 TTTGAT
1 TTTGAT
146390 GATGTGATGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGGCAATACCCAGAC
Found at i:146582 original size:12 final size:12
Alignment explanation
Indices: 146564--146600 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
146554 ATATAACCCT
146564 GAAGAAGAAAAA
1 GAAGAAGAAAAA
* *
146576 TAAGAAGGAAAA
1 GAAGAAGAAAAA
146588 GAAGAAGAAAAA
1 GAAGAAGAAAAA
146600 G
1 G
146601 TCCCCGAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:147223 original size:232 final size:232
Alignment explanation
Indices: 146817--147275 Score: 855
Period size: 232 Copynumber: 2.0 Consensus size: 232
146807 CTAAAAGTTA
*
146817 ACAAATCAAGCAAAGATCGTTTCTAAACAAGGTGTATGATTGACAAAAACTGTGCGTGGCGTATG
1 ACAAATCAAGCAAAGATCGTTTCGAAACAAGGTGTATGATTGACAAAAACTGTGCGTGGCGTATG
*
146882 ATTGCAAAGAGGATAAAAGATTGTGAAATGTTTCAAGTTAGGACTTTTATTGATAAACATACATG
66 ATTGCAAAGAGGATAAAAGATTGTGAAATGTTTCAAGTTAAGACTTTTATTGATAAACATACATG
146947 TTCAAGAACCCAAGTTTTTCCTCACCATAGACAGACAAACAAAAAGGTGTTTGGTGGTTTTCTGG
131 TTCAAGAACCCAAGTTTTTCCTCACCATAGACAGACAAACAAAAAGGTGTTTGGTGGTTTTCTGG
147012 CTGAGTTAATGTTTTTGAATGGAAGGGTATATGATTG
196 CTGAGTTAATGTTTTTGAATGGAAGGGTATATGATTG
147049 ACAAATCAAGCAAAGATCGTTTCGAAACAAGGTGTATGATTGACAAAAACTGTGCGTGGCGTATG
1 ACAAATCAAGCAAAGATCGTTTCGAAACAAGGTGTATGATTGACAAAAACTGTGCGTGGCGTATG
*
147114 ATTGCAAAGAGGATAAAATATTGTGAAATGTTTCAAGTTAAGACTTTTATTGATAAACATACATG
66 ATTGCAAAGAGGATAAAAGATTGTGAAATGTTTCAAGTTAAGACTTTTATTGATAAACATACATG
* * *
147179 TTCAAGAACCCAAGTTTTTCCTCACCATAGATAGGCAAACAAAAATGTGTTTGGTGGTTTTCTGG
131 TTCAAGAACCCAAGTTTTTCCTCACCATAGACAGACAAACAAAAAGGTGTTTGGTGGTTTTCTGG
*
147244 CTGAGTTAATGTTTTTGAATTGAAGGGTATAT
196 CTGAGTTAATGTTTTTGAATGGAAGGGTATAT
147276 CAGGGACATA
Statistics
Matches: 220, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
232 220 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (232 bp):
ACAAATCAAGCAAAGATCGTTTCGAAACAAGGTGTATGATTGACAAAAACTGTGCGTGGCGTATG
ATTGCAAAGAGGATAAAAGATTGTGAAATGTTTCAAGTTAAGACTTTTATTGATAAACATACATG
TTCAAGAACCCAAGTTTTTCCTCACCATAGACAGACAAACAAAAAGGTGTTTGGTGGTTTTCTGG
CTGAGTTAATGTTTTTGAATGGAAGGGTATATGATTG
Found at i:148914 original size:18 final size:18
Alignment explanation
Indices: 148891--148926 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
148881 AAGAAAAAGG
148891 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
148909 AAATCAAAATCTCAATCA
1 AAATCAAAATCACAATCA
148927 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:154947 original size:20 final size:21
Alignment explanation
Indices: 154910--154970 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 21
154900 TATTGGTGCA
* **
154910 GAGGGAATCGATAACCCC-AT
1 GAGGGAACCGATTCCCCCTAT
*
154930 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTAT
154951 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
154971 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 15 0.44
21 2 0.06
22 1 0.03
23 16 0.47
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTAT
Found at i:157340 original size:20 final size:20
Alignment explanation
Indices: 157315--157391 Score: 136
Period size: 20 Copynumber: 3.9 Consensus size: 20
157305 ACCGAAAATT
*
157315 GCGTTGCGAATTTGGCTTTC
1 GCGTTGCGAATTTGACTTTC
157335 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
157355 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
*
157375 TCGTTGCGAATTTGACT
1 GCGTTGCGAATTTGACT
157392 ATCACAATGC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.40
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTC
Found at i:157876 original size:18 final size:18
Alignment explanation
Indices: 157855--157891 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
157845 GTAATTGGAG
157855 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
157873 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
157891 T
1 T
157892 ATAAATTTTG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:157898 original size:24 final size:24
Alignment explanation
Indices: 157847--157899 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
157837 TTTCATATGT
* * *
157847 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
157871 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
157895 AATTT
1 AATTT
157900 TGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:158245 original size:39 final size:39
Alignment explanation
Indices: 158202--158287 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
158192 TCCGATGCTC
158202 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
158241 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
158280 ATCAAAAT
1 ATCAAAAT
158288 TGTTGAAAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:160538 original size:21 final size:21
Alignment explanation
Indices: 160496--160539 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
160486 ACCCCGGTAG
*
160496 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
160517 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
160538 CT
1 CT
160540 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:161196 original size:31 final size:31
Alignment explanation
Indices: 161125--161204 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
161115 ATTTAACAAA
* * **
161125 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
161156 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
161187 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
161205 CAAAATCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:163594 original size:21 final size:21
Alignment explanation
Indices: 163552--163595 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
163542 ACCCCGGTAG
*
163552 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
163573 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
163594 CT
1 CT
163596 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:164250 original size:31 final size:31
Alignment explanation
Indices: 164179--164258 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
164169 ATTTAACAAA
* * **
164179 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
164210 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
164241 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
164259 CAAAATCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:166655 original size:21 final size:21
Alignment explanation
Indices: 166617--166656 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
166607 CGGCTAGCTC
*
166617 TTCTTCACGAGCTGCTCCTAG
1 TTCTTCACGAGCTCCTCCTAG
* *
166638 TTCTTCTCGTGCTCCTCCT
1 TTCTTCACGAGCTCCTCCT
166657 CCTCCTCCAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.07, C:0.38, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCTTCACGAGCTCCTCCTAG
Found at i:167310 original size:31 final size:31
Alignment explanation
Indices: 167239--167318 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
167229 ATTTAACAAA
* * **
167239 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
167270 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
167301 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
167319 CAAAATCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:169714 original size:21 final size:21
Alignment explanation
Indices: 169672--169715 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
169662 ACCCCGGTAG
*
169672 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
169693 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
169714 CT
1 CT
169716 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:170371 original size:31 final size:31
Alignment explanation
Indices: 170300--170379 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
170290 ATTTAACAAA
* * **
170300 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
170331 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
170362 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
170380 CAAAATCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:173422 original size:31 final size:31
Alignment explanation
Indices: 173384--173445 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
173374 AAAAATTTAA
*
173384 GATGTGCTATAGTAAGGGGGAGTAAGTTTTT
1 GATGTGCTATAGTAAGGGGGAATAAGTTTTT
173415 GATGTGCTATAGTAAGGGGGAATAAGTTTTT
1 GATGTGCTATAGTAAGGGGGAATAAGTTTTT
173446 CAAAATCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.03, G:0.34, T:0.35
Consensus pattern (31 bp):
GATGTGCTATAGTAAGGGGGAATAAGTTTTT
Found at i:174922 original size:28 final size:28
Alignment explanation
Indices: 174890--174943 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
174880 ATAATTCTTA
*
174890 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
* **
174918 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
174944 TTAATCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:174924 original size:14 final size:14
Alignment explanation
Indices: 174907--174943 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
174897 ATCAAATTAA
174907 ACAAATCAACTTTT
1 ACAAATCAACTTTT
174921 ACAAATCAACTTTT
1 ACAAATCAACTTTT
174935 ACAAATCAA
1 ACAAATCAA
174944 TTAATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:176398 original size:21 final size:21
Alignment explanation
Indices: 176337--176449 Score: 68
Period size: 21 Copynumber: 5.4 Consensus size: 21
176327 GTGAATCGGG
*
176337 CTCTTGAACGGTGGGCA-GGAC
1 CTCTTGAACGGTGGG-AGGGGC
* **
176358 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
176379 CTTTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* * * **
176400 TTCTTCG-ATGATGAAAGGGGC
1 CTCTT-GAACGGTGGGAGGGGC
* * * *
176421 CTCTTGAACGATAGGATGCGC
1 CTCTTGAACGGTGGGAGGGGC
176442 CTCTTGAA
1 CTCTTGAA
176450 TGATGATAGG
Statistics
Matches: 68, Mismatches: 21, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
20 2 0.03
21 65 0.96
22 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:176453 original size:42 final size:42
Alignment explanation
Indices: 176357--176455 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
176347 GTGGGCAGGA
* * * * * *
176357 CCTCTTGAACGATGACAGGGGCCTTTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAAAGGGGCCTCTTGAACGATAGGAGGCG
* *
176399 CTTCTTCG-ATGATGAAAGGGGCCTCTTGAACGATAGGATGCG
1 CCTCTT-GAATGATGAAAGGGGCCTCTTGAACGATAGGAGGCG
176441 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
176456 TAGGTGTATC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (42 bp):
CCTCTTGAATGATGAAAGGGGCCTCTTGAACGATAGGAGGCG
Found at i:179112 original size:20 final size:20
Alignment explanation
Indices: 179087--179252 Score: 160
Period size: 20 Copynumber: 8.3 Consensus size: 20
179077 GCGTAAAAAC
179087 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
179107 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
**
179127 ATTTGAC-TTCTGTATTGCGA
1 ATTTGACTTTC-GCGTTGCGA
* * *
179147 ATTTGACTTTTGTGTTACGA
1 ATTTGACTTTCGCGTTGCGA
* *
179167 ATTTGACTATCGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
179187 ATTTGACTTTTGTGTTGCG-
1 ATTTGACTTTCGCGTTGCGA
179206 ATTT-ACATATTCGCGTTGCGAA
1 ATTTGAC-T-TTCGCGTTGCG-A
* *
179228 ATTGGA-GTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
179247 ATTTGA
1 ATTTGA
179253 GATCGCATTA
Statistics
Matches: 122, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
18 2 0.02
19 13 0.11
20 101 0.83
21 2 0.02
22 3 0.02
23 1 0.01
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:179184 original size:60 final size:60
Alignment explanation
Indices: 179087--179252 Score: 203
Period size: 60 Copynumber: 2.8 Consensus size: 60
179077 GCGTAAAAAC
*
179087 ATTTGACTTTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTATTGCGA
1 ATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTATTGCGA
* * * * *
179147 ATTTGACTTTTGTGTTACGAATTTGACTATCGTGTTGCGAATTTGACTTTTGTGTTGCG-
1 ATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTATTGCGA
* * *
179206 ATTT-ACATATTCGCGTTGCGAAATTGGAGT-TCGCGTTGCGAATTTGA
1 ATTTGAC-T-TTCGCGTTACG-AATTTGACTATCGCGTTGCGAATTTGA
179253 GATCGCATTA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
58 2 0.02
59 5 0.05
60 77 0.85
61 7 0.08
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (60 bp):
ATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTATTGCGA
Found at i:180058 original size:15 final size:15
Alignment explanation
Indices: 180027--180060 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
180017 ATTAAAAATA
180027 TTTATATTTATATTT
1 TTTATATTTATATTT
*
180042 TTTATTATTTGTATTT
1 TTTA-TATTTATATTT
180058 TTT
1 TTT
180061 TGTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTATATTTATATTT
Found at i:182307 original size:17 final size:17
Alignment explanation
Indices: 182281--182313 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
182271 TGGAGGAACA
182281 TTTTAGA-TTTTATGAC
1 TTTTAGATTTTTATGAC
182297 TTTTAAGATTTTTATGA
1 TTTT-AGATTTTTATGA
182314 AAAAAATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 3 0.20
18 8 0.53
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (17 bp):
TTTTAGATTTTTATGAC
Found at i:188432 original size:27 final size:26
Alignment explanation
Indices: 188393--188444 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
188383 GACGTGATAC
*
188393 TTTTTATTATTAACATATCAAAATAT
1 TTTTTATTATTAACATATAAAAATAT
188419 TTTTCTATTATTAACATATAAAAATA
1 TTTT-TATTATTAACATATAAAAATA
188445 ATTTATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTTTATTATTAACATATAAAAATAT
Found at i:191536 original size:31 final size:33
Alignment explanation
Indices: 191478--191551 Score: 107
Period size: 31 Copynumber: 2.3 Consensus size: 33
191468 TTAAAAAAGC
*
191478 CCGACCCGAACCCGAAATTTTTATAAAAAAAAT
1 CCGACCCGATCCCGAAATTTTTATAAAAAAAAT
* *
191511 CTGACTCGATCCCGAAA-TTTT-TAAAAAAAAT
1 CCGACCCGATCCCGAAATTTTTATAAAAAAAAT
191542 CCGACCCGAT
1 CCGACCCGAT
191552 TACCAAAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 18 0.50
32 4 0.11
33 14 0.39
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.23
Consensus pattern (33 bp):
CCGACCCGATCCCGAAATTTTTATAAAAAAAAT
Found at i:192853 original size:18 final size:18
Alignment explanation
Indices: 192830--192864 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
192820 GTGTCCGAAG
192830 CGTGAGATTCGTCTGAAA
1 CGTGAGATTCGTCTGAAA
192848 CGTGAGATTCGTCTGAA
1 CGTGAGATTCGTCTGAA
192865 GCAAGTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (18 bp):
CGTGAGATTCGTCTGAAA
Found at i:196232 original size:14 final size:14
Alignment explanation
Indices: 196213--196305 Score: 84
Period size: 14 Copynumber: 6.6 Consensus size: 14
196203 CTCGAGTACA
196213 TATTTAATAATAAT
1 TATTTAATAATAAT
*
196227 TATTTAA-ATTTAAT
1 TATTTAATA-ATAAT
*
196241 TATTTAACT-TTAAT
1 TATTTAA-TAATAAT
*
196255 GATTTAATAATAAT
1 TATTTAATAATAAT
*
196269 TATTTAACT-TTAAT
1 TATTTAA-TAATAAT
*
196283 GATTTAATAATAAT
1 TATTTAATAATAAT
196297 TACTTTAAT
1 TA-TTTAAT
196306 GATTTAACTT
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
13 3 0.05
14 54 0.84
15 7 0.11
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (14 bp):
TATTTAATAATAAT
Found at i:196260 original size:8 final size:8
Alignment explanation
Indices: 196249--197311 Score: 957
Period size: 8 Copynumber: 138.8 Consensus size: 8
196239 ATTATTTAAC
196249 TTTAATGA
1 TTTAATGA
196257 TTTAAT-A
1 TTTAATGA
* *
196264 -ATAATTA
1 TTTAATGA
*
196271 TTTAA--C
1 TTTAATGA
196277 TTTAATGA
1 TTTAATGA
196285 TTTAAT-A
1 TTTAATGA
* *
196292 -ATAATTA
1 TTTAATGA
196299 CTTTAATGA
1 -TTTAATGA
*
196308 TTTAA--C
1 TTTAATGA
196314 TTTAATGA
1 TTTAATGA
196322 TTTAAT-A
1 TTTAATGA
* *
196329 -ATAATTA
1 TTTAATGA
196336 CTTTAATGA
1 -TTTAATGA
*
196345 TTTAA--C
1 TTTAATGA
196351 TTTAATGA
1 TTTAATGA
196359 TTTAAT-A
1 TTTAATGA
* *
196366 -ATAATTA
1 TTTAATGA
196373 CTTTAATGA
1 -TTTAATGA
196382 TTTAATGA
1 TTTAATGA
196390 TTTAATGA
1 TTTAATGA
196398 TTTAATGA
1 TTTAATGA
196406 TTTAATGA
1 TTTAATGA
*
196414 TTTAATTA
1 TTTAATGA
196422 TTTAATGA
1 TTTAATGA
196430 TTTAATGA
1 TTTAATGA
196438 TTTAAT-A
1 TTTAATGA
* *
196445 -ATAATTA
1 TTTAATGA
*
196452 CTTTAAAGA
1 -TTTAATGA
*
196461 TTTAA--C
1 TTTAATGA
196467 TTTAATGA
1 TTTAATGA
196475 TTTAAT-A
1 TTTAATGA
* *
196482 -ATAATTA
1 TTTAATGA
196489 CTTTAATGA
1 -TTTAATGA
196498 TTTAATGA
1 TTTAATGA
196506 TTTAATGA
1 TTTAATGA
196514 TTTAAT-A
1 TTTAATGA
* *
196521 -ATAATTA
1 TTTAATGA
196528 TTTTAATGA
1 -TTTAATGA
196537 TTTAATGA
1 TTTAATGA
196545 TTTAATGA
1 TTTAATGA
196553 TTTAATGA
1 TTTAATGA
196561 TTTAAT-A
1 TTTAATGA
* *
196568 -ATAATTA
1 TTTAATGA
196575 CTTTAATGA
1 -TTTAATGA
196584 TTTAATGA
1 TTTAATGA
196592 TTTAATGA
1 TTTAATGA
196600 TTTAATGA
1 TTTAATGA
196608 TTTAATGA
1 TTTAATGA
196616 TTTAAT-A
1 TTTAATGA
* *
196623 -ATAATTA
1 TTTAATGA
196630 CTTTAATGA
1 -TTTAATGA
196639 TTTAATGA
1 TTTAATGA
196647 TTTAATGA
1 TTTAATGA
196655 TTTAATGA
1 TTTAATGA
196663 TTTAATGA
1 TTTAATGA
196671 TTTAAT-A
1 TTTAATGA
* *
196678 -ATAATTA
1 TTTAATGA
196685 CTTTAATGA
1 -TTTAATGA
*
196694 TTTAA--C
1 TTTAATGA
196700 TTTAATGA
1 TTTAATGA
196708 TTTAAT-A
1 TTTAATGA
* *
196715 -ATAATTA
1 TTTAATGA
196722 CTTTAATGA
1 -TTTAATGA
196731 TTTAATGA
1 TTTAATGA
196739 TTTAATGA
1 TTTAATGA
196747 TTTAATGA
1 TTTAATGA
196755 TTTAATGA
1 TTTAATGA
196763 TTTAAT-A
1 TTTAATGA
* *
196770 -ATAATTA
1 TTTAATGA
196777 CTTTAATGA
1 -TTTAATGA
196786 TTTAATGA
1 TTTAATGA
196794 TTTAATGA
1 TTTAATGA
196802 TTTAATGA
1 TTTAATGA
196810 TTTAATGA
1 TTTAATGA
196818 TTTAATGA
1 TTTAATGA
196826 TTTAATGA
1 TTTAATGA
196834 TTTAATGA
1 TTTAATGA
196842 TTTAAT-A
1 TTTAATGA
* *
196849 -ATAATTA
1 TTTAATGA
196856 CTTTAATGA
1 -TTTAATGA
*
196865 TTTAA--C
1 TTTAATGA
196871 TTTAATGA
1 TTTAATGA
196879 TTTAAT-A
1 TTTAATGA
* *
196886 -ATAATTA
1 TTTAATGA
196893 CTTTAATGA
1 -TTTAATGA
196902 TTTAATGA
1 TTTAATGA
196910 TTTAAT-A
1 TTTAATGA
* *
196917 -ATAATTA
1 TTTAATGA
196924 CTTTAATGA
1 -TTTAATGA
196933 TTTAATGA
1 TTTAATGA
196941 TTTAATGA
1 TTTAATGA
196949 TTTAAT-A
1 TTTAATGA
* *
196956 -ATAATTA
1 TTTAATGA
196963 TTTTAATGA
1 -TTTAATGA
196972 TTTAATGA
1 TTTAATGA
196980 TTTAATGA
1 TTTAATGA
196988 TTTAATGA
1 TTTAATGA
196996 TTTAAT-A
1 TTTAATGA
* *
197003 -ATAATTA
1 TTTAATGA
197010 CTTTAATGA
1 -TTTAATGA
197019 TTTAATGA
1 TTTAATGA
197027 TTTAATGA
1 TTTAATGA
197035 TTTAATGA
1 TTTAATGA
197043 TTTAATGA
1 TTTAATGA
197051 TTTAAT-A
1 TTTAATGA
* *
197058 -ATAATTA
1 TTTAATGA
197065 CTTTAATGA
1 -TTTAATGA
197074 TTTAATGA
1 TTTAATGA
197082 TTTAATGA
1 TTTAATGA
197090 TTTAATGA
1 TTTAATGA
197098 TTTAATGA
1 TTTAATGA
197106 TTTAATGA
1 TTTAATGA
197114 -TTAAT-A
1 TTTAATGA
*
197120 -ATAAT-A
1 TTTAATGA
197126 CTTTAATGA
1 -TTTAATGA
*
197135 TTTAA--C
1 TTTAATGA
197141 TTTAATGA
1 TTTAATGA
197149 TTTAAT-A
1 TTTAATGA
* *
197156 -ATAATTA
1 TTTAATGA
197163 CTTTAATGA
1 -TTTAATGA
197172 TTTAATGA
1 TTTAATGA
197180 TTTAATGA
1 TTTAATGA
197188 TTTAAT-A
1 TTTAATGA
* *
197195 -ATAATTA
1 TTTAATGA
197202 TTTTAATGA
1 -TTTAATGA
197211 TTTAATGA
1 TTTAATGA
197219 TTTAATGA
1 TTTAATGA
197227 TTTAAT-A
1 TTTAATGA
* *
197234 -ATAATTA
1 TTTAATGA
197241 CTTTAATGA
1 -TTTAATGA
197250 TTTAAT--
1 TTTAATGA
*
197256 TTTAATAA
1 TTTAATGA
197264 TTTAAT-A
1 TTTAATGA
* *
197271 -ATAATTA
1 TTTAATGA
*
197278 CTTAAT--
1 TTTAATGA
197284 TTTAATGA
1 TTTAATGA
197292 TTTAAT--
1 TTTAATGA
197298 TTTAATGA
1 TTTAATGA
197306 TTTAAT
1 TTTAAT
197312 AATAATTACT
Statistics
Matches: 884, Mismatches: 84, Indels: 174
0.77 0.07 0.15
Matches are distributed among these distances:
6 146 0.17
7 49 0.06
8 589 0.67
9 100 0.11
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (8 bp):
TTTAATGA
Found at i:196457 original size:55 final size:55
Alignment explanation
Indices: 196314--197269 Score: 753
Period size: 55 Copynumber: 17.0 Consensus size: 55
196304 ATGATTTAAC
* *
196314 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAA-TA-ATAATTA
1 TTTAATGATTTAATAATAATTACTTTAATG-----A-TTTAATGATTTAATTATTTAATGA
* *
196373 CTTTAATGATTTAATGATTTAATGA-TTTAATGATTTAATGATTTAATTATTTAATGA
1 -TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGATTTAATTATTTAATGA
* * *
196430 TTTAATGATTTAATAATAATTACTTTAAAGATTTAA--CTTTAATGATTTAAT-A
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATTATTTAATGA
* * * * *
196482 -ATAATTACTTTAATGATTTAATGA-TTTAATGATTTAAT-A-ATAATTATTTTAATGA
1 TTTAATGA-TTTAAT-A-ATAATTACTTTAATGATTTAATGATTTAATTA-TTTAATGA
* *
196537 TTTAATGA--T--T--TAATGA-TTTAATGATTTAAT-A-ATAATTACTTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATTA-TTTAATGA
* * *
196584 TTTAATGATTTAATGATTTAATGA-TTTAATGATTTAAT-A-ATAATTACTTTAATGA
1 TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGATTTAATTA-TTTAATGA
* * *
196639 TTTAATGATTTAATGATTTAATGA-TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAA
1 TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGATTTAATTA-TTTAATG-----A
*
196699 CTTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTTAATGA
1 -TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATTATTTAATGA
*
196755 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATTATTTAATGA
* * *
196810 TTTAATGATTTAATGATTTAATGA-TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAA
1 TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGATTTAATTA-TTTAATG-----A
196870 CTTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATAATAATTACTTTAATGA
1 -TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA--T--T--TAATTA-TTTAATGA
* * * * *
196933 TTTAATGATTTAATGAT--TTAATAATAATTATTTTAATGATTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACT-TTAATGA-TTTAATGATTTAATTATTTAATGA
*
196988 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATTATTTAATGA
*
197043 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATTATTTAATGA
*
197098 TTTAATGATTTAATGATTAATAATAATACTTTAATGATTTAACTTTAATGATTTAA-TA-ATAAT
1 TTTAATGATTT-A--A-TAATAAT--TACTTTAATG-----A-TTTAATGATTTAATTATTTAAT
*
197161 TA
54 GA
* * * * *
197163 CTTTAATGATTTAATGATTTAATGA-TTTAAT-A-ATAATTATTTTAATGATTTAATGA
1 -TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGA-TTTAATTATTTAATGA
*
197219 TTTAATGATTTAATAATAATTACTTTAATGATTTAAT--TTTAATAATTTAAT
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATTATTTAAT
197270 AATAATTACT
Statistics
Matches: 770, Mismatches: 54, Indels: 151
0.79 0.06 0.15
Matches are distributed among these distances:
47 44 0.06
49 1 0.00
51 7 0.01
52 7 0.01
53 55 0.07
54 33 0.04
55 326 0.42
56 58 0.08
57 14 0.02
58 2 0.00
59 17 0.02
60 51 0.07
61 66 0.09
62 36 0.05
63 3 0.00
64 4 0.01
65 6 0.01
66 13 0.02
67 13 0.02
68 14 0.02
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.49
Consensus pattern (55 bp):
TTTAATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATTATTTAATGA
Found at i:196512 original size:39 final size:39
Alignment explanation
Indices: 196277--197322 Score: 1098
Period size: 39 Copynumber: 26.6 Consensus size: 39
196267 ATTATTTAAC
*
196277 TTTAATGATTTAATAATAATTACTTTAATGATTTAA--C
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
*
196314 TTTAATGATTTAATAATAATTACTTTAATGATTTAA--C
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
196351 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
* * *
196390 TTTAATGATTTAATGATTTAATGA-TTTAATTATTTAATGA
1 TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGA
* *
196430 TTTAATGATTTAATAATAATTACTTTAAAGATTTAA--C
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
196467 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
*
196506 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
* * * *
196545 TTTAATGATTTAATGAT--TTAATAATAATTACTTTAATGA
1 TTTAATGATTTAATAATAATTACT-TTAATGA-TTTAATGA
* *
196584 TTTAATGATTTAATGATTTAATGA-TTTAATGATTTAAT-A
1 TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGA
* * * *
196623 -ATAATTACTTTAATGATTTAATGA-TTTAATGATTTAATGA
1 TTTAATGA-TTTAAT-A-ATAATTACTTTAATGATTTAATGA
*
196663 TTTAATGATTTAATAATAATTACTTTAATGATTTAA--C
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
196700 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
* * * *
196739 TTTAATGATTTAATGATTTAATGA-TTTAAT-A-ATAATTA
1 TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGA
* *
196777 CTTTAATGATTTAATGATTTAATGA-TTTAATGATTTAATGA
1 -TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGA
* * * *
196818 TTTAATGATTTAATGATTTAATGA-TTTAAT-A-ATAATTA
1 TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGA
* * * *
196856 CTTTAATGATTTAACTTTAATGATTTAATAATAATTACTTTAATGA
1 -TTTAATGATTTAA---TAAT-AATTACT-TTAATGA-TTTAATGA
196902 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
*
196941 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGA
1 TTTAATGATTTAATAAT-A--A--TT-A--CTTTAATGATTTAATGA
196988 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
* * * *
197027 TTTAATGATTTAATGATTTAATGA-TTTAAT-A-ATAATTA
1 TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGA
* *
197065 CTTTAATGATTTAATGATTTAATGA-TTTAATGATTTAATGA
1 -TTTAATGATTTAAT-A-ATAATTACTTTAATGATTTAATGA
*
197106 TTTAATGA-TTAATAATAA-TACTTTAATGATTTAA--C
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
197141 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
*
197180 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGA
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
197219 TTTAATGATTTAATAATAATTACTTTAATGATTTAAT--
1 TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
*
197256 TTTAATAATTTAATAATAATTACTTAATTTTAATGATTTAAT--
1 TTTAATGATTTAATAATAATTAC-----TTTAATGATTTAATGA
197298 TTTAATGATTTAATAATAATTACTT
1 TTTAATGATTTAATAATAATTACTT
197323 GACTTTAATG
Statistics
Matches: 889, Mismatches: 63, Indels: 114
0.83 0.06 0.11
Matches are distributed among these distances:
35 8 0.01
36 11 0.01
37 204 0.23
38 36 0.04
39 371 0.42
40 104 0.12
41 46 0.05
42 46 0.05
43 6 0.01
44 4 0.00
45 14 0.02
46 6 0.01
47 33 0.04
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (39 bp):
TTTAATGATTTAATAATAATTACTTTAATGATTTAATGA
Found at i:198357 original size:18 final size:18
Alignment explanation
Indices: 198316--198360 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 18
198306 TTAATTAAAT
198316 AATTATAA-AAATCAACA
1 AATTATAATAAATCAACA
198333 AA-T-TAATAAAT-AACA
1 AATTATAATAAATCAACA
198348 ATATTATAATAAA
1 A-ATTATAATAAA
198361 CATAATATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 3 0.12
18 7 0.29
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (18 bp):
AATTATAATAAATCAACA
Found at i:199851 original size:172 final size:173
Alignment explanation
Indices: 199556--199903 Score: 556
Period size: 172 Copynumber: 2.0 Consensus size: 173
199546 CATCAAATAT
* *
199556 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
199621 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
* * *
199686 TTTTTATAATTTACTCTAATTTCTTAAATTCCTCAAATTTTGC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* *
199729 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * *
199793 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
* *
199857 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
199901 AAA
1 AAA
199904 TGGTCCCTAA
Statistics
Matches: 161, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
172 101 0.63
173 60 0.37
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (173 bp):
AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:200392 original size:23 final size:23
Alignment explanation
Indices: 200366--200409 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
200356 AGTTGCATGC
200366 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
200389 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
200410 CCTTGCAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:200454 original size:22 final size:22
Alignment explanation
Indices: 200426--200479 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
200416 AGGACCCAGG
200426 ACCCGTGATTTCTCCTTGCAGA
1 ACCCGTGATTTCTCCTTGCAGA
* *
200448 ACCCGTGCTCTCTCCTTGCAGA
1 ACCCGTGATTTCTCCTTGCAGA
200470 ACCCGTGATT
1 ACCCGTGATT
200480 CTCACGTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.35, G:0.19, T:0.30
Consensus pattern (22 bp):
ACCCGTGATTTCTCCTTGCAGA
Found at i:201109 original size:15 final size:16
Alignment explanation
Indices: 201089--201125 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
201079 TACGGTTGTG
201089 TTTAAATAAAAAAT-A
1 TTTAAATAAAAAATAA
201104 TTTAAATAAAAAATAA
1 TTTAAATAAAAAATAA
201120 TTTAAA
1 TTTAAA
201126 CAATACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTAAATAAAAAATAA
Found at i:202545 original size:15 final size:15
Alignment explanation
Indices: 202527--202555 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
202517 AAATTAAAAT
202527 AAATTATTAAATAAC
1 AAATTATTAAATAAC
202542 AAATTATTAAATAA
1 AAATTATTAAATAA
202556 TGATGTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTATTAAATAAC
Done.