Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008528.1 Hibiscus syriacus cultivar Beakdansim tig00111403_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: 1199389
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:6163 original size:27 final size:27
Alignment explanation
Indices: 6125--6181 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
6115 TCTATTTAAG
* * *
6125 TTTGTCCCGAACTAGTTGACCATCCAC
1 TTTGTCCCGAACCAGATGAACATCCAC
6152 TTTGTCCCGAACCAGATGAACATCCAC
1 TTTGTCCCGAACCAGATGAACATCCAC
6179 TTT
1 TTT
6182 AATATGCTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.30
Consensus pattern (27 bp):
TTTGTCCCGAACCAGATGAACATCCAC
Found at i:11616 original size:31 final size:30
Alignment explanation
Indices: 11581--11641 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
11571 AATATTAATG
*
11581 AATTTGAAAATAA-TTTAAATTAATATATTTC
1 AATTT-AAAATAAGTTTAAAAT-ATATATTTC
*
11612 AATTTATAATAATGTTTAAAATATATATTT
1 AATTTAAAATAA-GTTTAAAATATATATTT
11642 ATTTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 6 0.23
31 13 0.50
32 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
AATTTAAAATAAGTTTAAAATATATATTTC
Found at i:11719 original size:12 final size:12
Alignment explanation
Indices: 11699--11758 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
11689 CAAACTTAAC
11699 TTTTCAAAATCA
1 TTTTCAAAATCA
*
11711 TTTTTAAAATCA
1 TTTTCAAAATCA
*
11723 CTTTCTAACAA-CGA
1 TTTTC-AA-AATC-A
*
11737 TTTTCAAAATCGC
1 TTTTCAAAATC-A
11750 TTTTCAAAA
1 TTTTCAAAA
11759 ACAATGTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 16 0.41
13 16 0.41
14 7 0.18
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.40
Consensus pattern (12 bp):
TTTTCAAAATCA
Found at i:12527 original size:7 final size:7
Alignment explanation
Indices: 12513--12630 Score: 107
Period size: 7 Copynumber: 16.9 Consensus size: 7
12503 TATGTGTTAA
12513 GGTTTAG
1 GGTTTAG
*
12520 GTTTTAG
1 GGTTTAG
12527 GGTTTA-
1 GGTTTAG
* *
12533 TGTGATAG
1 GGT-TTAG
* *
12541 GTTTTAA
1 GGTTTAG
12548 GGTTTAG
1 GGTTTAG
* *
12555 AGATTAG
1 GGTTTAG
12562 GGTTTAG
1 GGTTTAG
12569 GGTTTAG
1 GGTTTAG
12576 GGTTTAG
1 GGTTTAG
12583 GAG-TTAG
1 G-GTTTAG
*
12590 AGTTTAG
1 GGTTTAG
*
12597 AGTTTAG
1 GGTTTAG
12604 GAG-TTAG
1 G-GTTTAG
12611 GGTTTAG
1 GGTTTAG
12618 GGTTTAG
1 GGTTTAG
12625 GGTTTA
1 GGTTTA
12631 AGTTATGCAC
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
6 4 0.04
7 82 0.92
8 3 0.03
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:23593 original size:23 final size:23
Alignment explanation
Indices: 23567--23646 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
23557 CCCTTCTAGC
*
23567 TTGAATCTAGTTAAAAAACGAGT
1 TTGAATCGAGTTAAAAAACGAGT
* *
23590 TTGAATGGAGTTAAAAAAACAAGT
1 TTGAATCGAGTT-AAAAAACGAGT
* * *
23614 CTGAATCGAGCTCAAAAACGAGT
1 TTGAATCGAGTTAAAAAACGAGT
23637 TTGAATCGAG
1 TTGAATCGAG
23647 CTTATGAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 28 0.60
24 19 0.40
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.25
Consensus pattern (23 bp):
TTGAATCGAGTTAAAAAACGAGT
Found at i:23618 original size:24 final size:23
Alignment explanation
Indices: 23575--23642 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
23565 GCTTGAATCT
* *
23575 AGTTAAAAAACGAGTTTGAATGG
1 AGTTAAAAAACAAGTCTGAATGG
*
23598 AGTTAAAAAAACAAGTCTGAATCG
1 AGTT-AAAAAACAAGTCTGAATGG
* * * *
23622 AGCTCAAAAACGAGTTTGAAT
1 AGTTAAAAAACAAGTCTGAAT
23643 CGAGCTTATG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.24
Consensus pattern (23 bp):
AGTTAAAAAACAAGTCTGAATGG
Found at i:34753 original size:20 final size:20
Alignment explanation
Indices: 34702--34756 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
34692 TGGAGCGTGG
*
34702 GGGGAATCGGTACCCCTTAA
1 GGGGAATCGGTTCCCCTTAA
34722 GGGGAATCGGTTCCCCTTAA
1 GGGGAATCGGTTCCCCTTAA
34742 GGGGAATCGGTTCCC
1 GGGGAATCGGTTCCC
34757 TAAGTGTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.22
Consensus pattern (20 bp):
GGGGAATCGGTTCCCCTTAA
Found at i:46808 original size:23 final size:23
Alignment explanation
Indices: 46778--46876 Score: 101
Period size: 23 Copynumber: 4.3 Consensus size: 23
46768 CTATAGCTCG
46778 TATAATTGCACCGAAGTGCCACA
1 TATAATTGCACCGAAGTGCCACA
* *
46801 TATAATTGCACCGGAGTGCCACG
1 TATAATTGCACCGAAGTGCCACA
* * * *
46824 TAGAATTGCACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACA
* *
46847 TAGAATTGCACC-ATAGTGCCATA
1 TATAATTGCACCGA-AGTGCCACA
46870 TAATAAT
1 T-ATAAT
46877 GTCCATAAGG
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
23 61 0.94
24 4 0.06
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACA
Found at i:46854 original size:46 final size:46
Alignment explanation
Indices: 46776--46867 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
46766 CACTATAGCT
* * *
46776 CGTATAATTGCACCGAAGTGCCACATATAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCACATAGAATTGCACCAGAGTGCCA
* * * *
46822 CGTAGAATTGCACCGGAGTGCCGCGTAGAATTGCACCATAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCACATAGAATTGCACCAGAGTGCCA
46868 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (46 bp):
CGTAGAATTGCACCGAAGTGCCACATAGAATTGCACCAGAGTGCCA
Found at i:47045 original size:103 final size:101
Alignment explanation
Indices: 46892--47091 Score: 328
Period size: 103 Copynumber: 2.0 Consensus size: 101
46882 TAAGGATCAC
* *
46892 ATCATTCCTTAAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATG
1 ATCATTCCTTAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATG
46957 TTCCAAAGAATACATATATGTCCCGAAGGACCACAT
66 TTCCAAAGAATACATATATGTCCCGAAGGACCACAT
* *
46993 ATCATTCCTTAAGAATCATATACATGTGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACA
1 ATCATTCCTT-A-AATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACA
**
47058 TGTTCCAAAGAATACATATATGTCTTGAAGGACC
64 TGTTCCAAAGAATACATATATGTCCCGAAGGACC
47092 GCGTAGACCC
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 10 0.11
102 1 0.01
103 80 0.88
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (101 bp):
ATCATTCCTTAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATG
TTCCAAAGAATACATATATGTCCCGAAGGACCACAT
Found at i:48465 original size:20 final size:21
Alignment explanation
Indices: 48424--48479 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
48414 TTCGCTTGAG
*
48424 GGGTATCGATTTCCCATTGAAT
1 GGGTAACGA-TTCCCATTGAAT
48446 GGGTAACGATTCCC-TTGAAT
1 GGGTAACGATTCCCATTGAAT
*
48466 GGGTACCGATTCCC
1 GGGTAACGATTCCC
48480 CTTGCCCAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 19 0.59
21 5 0.16
22 8 0.25
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTAACGATTCCCATTGAAT
Found at i:49768 original size:23 final size:23
Alignment explanation
Indices: 49742--49833 Score: 107
Period size: 23 Copynumber: 4.0 Consensus size: 23
49732 CACCACAACT
*
49742 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
49765 CGTAGAATTGCACCGGAA-TGCCG
1 CGTAGAATTGCACC-GAAGTGCCA
* *
49788 CGTAGAATTGCACC-AGAGCGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
49811 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
49834 TATAATAATG
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 54 0.92
24 3 0.05
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:50014 original size:99 final size:100
Alignment explanation
Indices: 49857--50051 Score: 347
Period size: 99 Copynumber: 2.0 Consensus size: 100
49847 ATAAGGACCA
* * *
49857 CATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTTAC
1 CATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCAC
49922 ACATGTTCCAAAGAATACATAT-GTCCCGAAGGAC
66 ACATGTTCCAAAGAATACATATAGTCCCGAAGGAC
*
49956 CATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCAC
1 CATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCAC
50021 ACATGTTCCAAAGAATACATATAGTCCCGAA
66 ACATGTTCCAAAGAATACATATAGTCCCGAA
50052 AGACGCGTAG
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
99 83 0.91
100 8 0.09
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (100 bp):
CATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCAC
ACATGTTCCAAAGAATACATATAGTCCCGAAGGAC
Found at i:53151 original size:24 final size:24
Alignment explanation
Indices: 53119--53192 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 24
53109 TTTCTAAAAA
*
53119 ATAATAATAAAATATATATAATTT
1 ATAAAAATAAAATATATATAATTT
* * *
53143 ATAAAAATAGAATATTTATTTAATAT
1 ATAAAAATA-AA-ATATATATAATTT
* *
53169 AT-AAAAT-AAATAAATATTATTT
1 ATAAAAATAAAATATATATAATTT
53191 AT
1 AT
53193 TATATGACTT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
22 10 0.26
23 2 0.05
24 8 0.21
25 7 0.18
26 12 0.31
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (24 bp):
ATAAAAATAAAATATATATAATTT
Found at i:53215 original size:13 final size:13
Alignment explanation
Indices: 53181--53222 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
53171 AAAATAAATA
*
53181 AATATTA-TTTAT
1 AATATTACTTAAT
* *
53193 TATATGACTTAAT
1 AATATTACTTAAT
53206 AATATTACTTAAT
1 AATATTACTTAAT
53219 AATA
1 AATA
53223 ATTAAATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (13 bp):
AATATTACTTAAT
Found at i:53233 original size:23 final size:23
Alignment explanation
Indices: 53207--53271 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 23
53197 TGACTTAATA
*
53207 ATATTACTTAATAAT-AATTAAAT
1 ATATTAC-AAATAATAAATTAAAT
*
53230 ATATTGCAAATAATAAATT--A-
1 ATATTACAAATAATAAATTAAAT
53250 A-ATTA-AAATAATAAATTAAAT
1 ATATTACAAATAATAAATTAAAT
53271 A
1 A
53272 AAAATATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
18 12 0.34
19 3 0.09
20 2 0.06
21 2 0.06
22 6 0.17
23 10 0.29
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (23 bp):
ATATTACAAATAATAAATTAAAT
Found at i:53303 original size:13 final size:12
Alignment explanation
Indices: 53248--53304 Score: 52
Period size: 13 Copynumber: 5.0 Consensus size: 12
53238 AATAATAAAT
53248 TAAATTAAAATAA
1 TAAATT-AAATAA
53261 TAAATTAAATAA
1 TAAATTAAATAA
*
53273 -AAA-TATA-AA
1 TAAATTAAATAA
53282 TAAA-T-AATAA
1 TAAATTAAATAA
53292 CTAAATTAAATAA
1 -TAAATTAAATAA
53305 AATTAAAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 3 0.08
10 9 0.24
11 7 0.19
12 7 0.19
13 11 0.30
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
TAAATTAAATAA
Found at i:54628 original size:3 final size:3
Alignment explanation
Indices: 54620--54691 Score: 83
Period size: 3 Copynumber: 23.7 Consensus size: 3
54610 ATATTTATTA
**
54620 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT TTT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
**
54666 TTT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
54692 AACGAAATGA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:62392 original size:16 final size:16
Alignment explanation
Indices: 62371--62402 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
62361 TATAAATTAA
62371 TTTAATGATGTTCATC
1 TTTAATGATGTTCATC
*
62387 TTTAATTATGTTCATC
1 TTTAATGATGTTCATC
62403 CACACTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (16 bp):
TTTAATGATGTTCATC
Found at i:67138 original size:6 final size:7
Alignment explanation
Indices: 67112--67137 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
67102 GGTACCCGGT
67112 TTTTTTA
1 TTTTTTA
67119 TTTTTTA
1 TTTTTTA
67126 TTTTTTA
1 TTTTTTA
67133 TTTTT
1 TTTTT
67138 AAATTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:67257 original size:22 final size:22
Alignment explanation
Indices: 67213--67261 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
67203 ATATCCGAAC
*
67213 ATAAAATTTAAAAATTCGAAAT
1 ATAAAATTTAAAAATTCCAAAT
*
67235 ATAAAATTTAATAA-TCCATAAT
1 ATAAAATTTAAAAATTCCA-AAT
67257 ATAAA
1 ATAAA
67262 TAATTCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (22 bp):
ATAAAATTTAAAAATTCCAAAT
Found at i:69210 original size:29 final size:29
Alignment explanation
Indices: 69136--69211 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
69126 TTAACACTTC
69136 AGTGGTATAATTGAAATAAAAATCAAAGTTT
1 AGTGGTATAATTG--ATAAAAATCAAAGTTT
* * * *
69167 AGTGCTACAATTGATAAAATTGAAAGTTT
1 AGTGGTATAATTGATAAAAATCAAAGTTT
*
69196 AGTGGTATAAATGATA
1 AGTGGTATAATTGATA
69212 CAATGCCTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 27 0.71
31 11 0.29
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (29 bp):
AGTGGTATAATTGATAAAAATCAAAGTTT
Found at i:78013 original size:15 final size:15
Alignment explanation
Indices: 77993--78023 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
77983 ATATTTTGTC
77993 TCTAAAACTTATATA
1 TCTAAAACTTATATA
78008 TCTAAAACTTATATA
1 TCTAAAACTTATATA
78023 T
1 T
78024 TCTATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (15 bp):
TCTAAAACTTATATA
Found at i:94004 original size:17 final size:17
Alignment explanation
Indices: 93978--94015 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
93968 TATGGACCAT
93978 TTTTAAATTTTTTAATA
1 TTTTAAATTTTTTAATA
*
93995 TTTTAGATTTTTTAATA
1 TTTTAAATTTTTTAATA
94012 TTTT
1 TTTT
94016 TATTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTAAATTTTTTAATA
Found at i:96784 original size:11 final size:11
Alignment explanation
Indices: 96768--96797 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
96758 TGAGTTCCTT
96768 TTCTTTCATTC
1 TTCTTTCATTC
*
96779 TTCTTTCATTT
1 TTCTTTCATTC
96790 TTCTTTCA
1 TTCTTTCA
96798 AGAGTGGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (11 bp):
TTCTTTCATTC
Found at i:100497 original size:206 final size:206
Alignment explanation
Indices: 100141--100516 Score: 698
Period size: 206 Copynumber: 1.8 Consensus size: 206
100131 TATGGAAATG
100141 TCACAGGCCACTTGATTGAGTGAGACTAGAAATGCATGACCATGCTCGAATAAGTTGATATAAGA
1 TCACAGGCCACTTGATTGAGTGAGACTAGAAATGCATGACCATGCTCGAATAAGTTGATATAAGA
*
100206 TATCACAAATTATTTTGTTAATTATAGTCTACTCTAGATATCAAGAAACAATAGTTGGGCTATAA
66 TATCACAAATTATTTTGTTAATTATAGTCTACTCTAGATATCAAGAAACAATAGATGGGCTATAA
100271 AAGTGTGACTAATCCAAGACTTGTGCCTATTCTAGATATAAAGGACAAAAGAATGCAATGCATAA
131 AAGTGTGACTAATCCAAGACTTGTGCCTATTCTAGATATAAAGGACAAAAGAATGCAATGCATAA
100336 TAGGAAATATA
196 TAGGAAATATA
* * *
100347 TCACAGGCCACTTGATTGAGTGAGACTAGAAATGCATGGCCATGCTCGAATAAGTTGATGTGAGA
1 TCACAGGCCACTTGATTGAGTGAGACTAGAAATGCATGACCATGCTCGAATAAGTTGATATAAGA
*
100412 TATCACAAATTATTTTGTTAATTATAGTCTGCTCTAGATATCAAGAAACAATAGATGGGCTATAA
66 TATCACAAATTATTTTGTTAATTATAGTCTACTCTAGATATCAAGAAACAATAGATGGGCTATAA
*
100477 AAGTGTGACTAATGCAAGACTTGTGCCTATTCTAGATATA
131 AAGTGTGACTAATCCAAGACTTGTGCCTATTCTAGATATA
100517 CTATTGGCTT
Statistics
Matches: 164, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
206 164 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (206 bp):
TCACAGGCCACTTGATTGAGTGAGACTAGAAATGCATGACCATGCTCGAATAAGTTGATATAAGA
TATCACAAATTATTTTGTTAATTATAGTCTACTCTAGATATCAAGAAACAATAGATGGGCTATAA
AAGTGTGACTAATCCAAGACTTGTGCCTATTCTAGATATAAAGGACAAAAGAATGCAATGCATAA
TAGGAAATATA
Found at i:102302 original size:16 final size:15
Alignment explanation
Indices: 102277--102306 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
102267 TGTTCTTGTT
102277 ATATAAAAAGTACTA
1 ATATAAAAAGTACTA
102292 ATATCAAAAAGTACT
1 ATAT-AAAAAGTACT
102307 GAAGTTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.27
Consensus pattern (15 bp):
ATATAAAAAGTACTA
Found at i:107413 original size:21 final size:20
Alignment explanation
Indices: 107359--107420 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
107349 TGTCTAACGT
107359 ATATTTTATT-ATATT-TTTA
1 ATATTTTATTAAT-TTATTTA
107378 ATATTTTGTATTTAATTTATTTA
1 ATA-TTT-TA-TTAATTTATTTA
*
107401 ATATTTTACTTAATTAATTT
1 ATATTTTA-TTAATTTATTT
107421 TTTTGCAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 14 0.39
22 7 0.19
23 9 0.25
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
ATATTTTATTAATTTATTTA
Found at i:109658 original size:25 final size:25
Alignment explanation
Indices: 109617--109679 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
109607 AGATTTTGTT
* *
109617 TTTTTTATTATATTTG-TATTTAGTAC
1 TTTTTTATTGTAGTTGTTATTT-G-AC
109643 -TTTTTATTGTAGTTGTTTATTTGAC
1 TTTTTTATTGTAGTTG-TTATTTGAC
109668 TTTTTTATTGTA
1 TTTTTTATTGTA
109680 ATTTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 15 0.47
26 12 0.38
27 5 0.16
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (25 bp):
TTTTTTATTGTAGTTGTTATTTGAC
Found at i:120251 original size:2 final size:2
Alignment explanation
Indices: 120244--120280 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
120234 AAAGGGCTGT
120244 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
120281 CTATGATCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:122255 original size:2 final size:2
Alignment explanation
Indices: 122250--122276 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
122240 CATATGAATA
122250 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
122277 CTAATTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:122725 original size:18 final size:18
Alignment explanation
Indices: 122702--122736 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
122692 TTTAATGAAC
*
122702 GAATAAACACGAATAAAT
1 GAATAAACACCAATAAAT
122720 GAATAAACACCAATAAA
1 GAATAAACACCAATAAA
122737 AAATATTTTT
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:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (18 bp):
GAATAAACACCAATAAAT
Found at i:126486 original size:30 final size:30
Alignment explanation
Indices: 126452--126510 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
126442 TCCTCCAGAA
*
126452 GGGGTCATAAAACTC-TGTGACAGTGGCGGG
1 GGGGTCATAAAAC-CAGGTGACAGTGGCGGG
126482 GGGGTCATAAAACCAGGTGACAGTGGCGG
1 GGGGTCATAAAACCAGGTGACAGTGGCGG
126511 CGGCGGCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.25, C:0.17, G:0.41, T:0.17
Consensus pattern (30 bp):
GGGGTCATAAAACCAGGTGACAGTGGCGGG
Found at i:128276 original size:17 final size:19
Alignment explanation
Indices: 128256--128297 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
128246 ATTAATTAAA
128256 TAAAATA-TTAAA-AAATT
1 TAAAATACTTAAATAAATT
128273 T-AAATACTTAAATAAATT
1 TAAAATACTTAAATAAATT
*
128291 AAAAATA
1 TAAAATA
128298 AAACATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 6 0.29
18 5 0.24
19 5 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATACTTAAATAAATT
Found at i:128603 original size:51 final size:51
Alignment explanation
Indices: 128542--128638 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
128532 ATACTCCTAT
* * * * *
128542 GTGGCGCCAGATCAGCGTAAAGTGCGCTGCAGGGGGCGCGCCTTATCCCAC
1 GTGGCACCAGATCAGCATAAAGCGCGCTGCAGAGGGCGCACCTTATCCCAC
*
128593 GTGGCACCAGATCAGTATAAAGCGCGCTGCAGAGGGCGCACCTTAT
1 GTGGCACCAGATCAGCATAAAGCGCGCTGCAGAGGGCGCACCTTAT
128639 TGCAAAGGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (51 bp):
GTGGCACCAGATCAGCATAAAGCGCGCTGCAGAGGGCGCACCTTATCCCAC
Found at i:143172 original size:128 final size:128
Alignment explanation
Indices: 142944--143422 Score: 841
Period size: 128 Copynumber: 3.7 Consensus size: 128
142934 ACTATTCACA
*
142944 TGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
143009 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
143072 TGAAGGCGTGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * *
143137 TTATGTCATTCATGTCCCTCGGAGACACTATTCATATCAGTACATATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
143200 TGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
143265 TTATATCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTATCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
143328 TGAAGGCACGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCTGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
143393 TTATGTCACTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
143423 GATGGATTGT
Statistics
Matches: 332, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 332 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:143857 original size:34 final size:34
Alignment explanation
Indices: 143818--143924 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
143808 TAAGTTGAAA
* *
143818 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
143852 TTTAATTTTAAATTTCGATTAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
143886 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
143920 TTTAA
1 TTTAA
143925 AAACATTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:144471 original size:21 final size:21
Alignment explanation
Indices: 144445--144496 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
144435 TATGGTATAA
144445 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
144466 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
144487 AACCCTGCGG
1 AACCCTGCGG
144497 AGATGGCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:146339 original size:32 final size:34
Alignment explanation
Indices: 146278--146362 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 34
146268 AATTCTAAAT
146278 AAATAATAATTATATAAATATTATTTTAATAAAAA
1 AAATAATAATTATATAAATATTA-TTTAATAAAAA
* *
146313 AAATAATATTTATATAAATA-TA-TTAATATAAA
1 AAATAATAATTATATAAATATTATTTAATAAAAA
* * *
146345 ATATAATAACTATTTAAA
1 AAATAATAATTATATAAA
146363 AAAATACTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 23 0.52
34 2 0.05
35 19 0.43
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (34 bp):
AAATAATAATTATATAAATATTATTTAATAAAAA
Found at i:146346 original size:15 final size:15
Alignment explanation
Indices: 146312--146349 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
146302 TTTAATAAAA
*
146312 AAAATAATATTTATAT
1 AAAAT-ATATTAATAT
146328 -AAATATATTAATAT
1 AAAATATATTAATAT
146342 AAAATATA
1 AAAATATA
146350 ATAACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATATTAATAT
Found at i:146353 original size:35 final size:35
Alignment explanation
Indices: 146274--146360 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 35
146264 TAATAATTCT
*
146274 AAATAAATAATAATTATATAAATATTATTTTAATAA
1 AAATAAATAATATTTATATAAATATTA-TTTAATAA
146310 AAA-AAATAATATTTATATAAATA-TA-TTAATATA
1 AAATAAATAATATTTATATAAATATTATTTAATA-A
146343 AAATATAATAACTATTTA
1 AAATA-AATAA-TATTTA
146361 AAAAAATACT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
32 6 0.13
33 4 0.09
34 3 0.07
35 24 0.52
36 9 0.20
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (35 bp):
AAATAAATAATATTTATATAAATATTATTTAATAA
Found at i:146378 original size:34 final size:34
Alignment explanation
Indices: 146306--146383 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
146296 TATTATTTTA
* * * *
146306 ATAAAAAAAATAATATTTATATAAATATATTAAT
1 ATAAAAATAATAATATTTATATAAAAATACTAAC
146340 ATAAAATATAATAACTATTTA-A-AAAAATACTAAC
1 ATAAAA-ATAATAA-TATTTATATAAAAATACTAAC
146374 ATAAAAATAA
1 ATAAAAATAA
146384 ATTTCTTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 21 0.55
35 7 0.18
36 6 0.16
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (34 bp):
ATAAAAATAATAATATTTATATAAAAATACTAAC
Found at i:152959 original size:20 final size:20
Alignment explanation
Indices: 152936--153001 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
152926 GTTTCCAAAT
152936 TCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATCTGTAAA
*
152956 TCGCAACGCGAATCTGTAAA
1 TCGCAATGCGAATCTGTAAA
* *
152976 TCACAATGCGAATTTGTAAA
1 TCGCAATGCGAATCTGTAAA
152996 TCGCAA
1 TCGCAA
153002 CACAGAAGTC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATCTGTAAA
Found at i:153215 original size:14 final size:15
Alignment explanation
Indices: 153198--153235 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
153188 TTCCCATCTC
153198 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
153212 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
153228 TAATTTTT
1 TAATTTTT
153236 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:154028 original size:24 final size:24
Alignment explanation
Indices: 153977--154030 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
153967 GTATTCGAAA
*
153977 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
154001 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
154025 TTTGAT
1 TTTGAT
154031 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:156328 original size:3 final size:3
Alignment explanation
Indices: 156315--156348 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
156305 CTCCAGAGCT
*
156315 TTC TTC TTTC TTC TTC TTC TTC TTC TTA TTC TTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC
156349 ATACATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:157709 original size:31 final size:31
Alignment explanation
Indices: 157671--157735 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
157661 AGAGTCGAGG
*
157671 GTTTACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
** * *
157702 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
157733 GTT
1 GTT
157736 ACCGAGGATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGACA
Found at i:157766 original size:30 final size:30
Alignment explanation
Indices: 157721--157823 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
157711 GGTTCTTCGG
* *
157721 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
157751 GACATCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
157781 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
157811 GACCTCTGGATAG
1 GACCTCTGGATAG
157824 GTCCTTCGGG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:159377 original size:64 final size:64
Alignment explanation
Indices: 159276--159418 Score: 214
Period size: 64 Copynumber: 2.2 Consensus size: 64
159266 AATTTAAAAC
* * *
159276 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAAGTAAACAAGCAAAAAATAAGAATTAATTACACATAAATTA
*** * *
159340 AACAAATCAACTTTTACAAATCAAGTAAACAAGCAAAAAATAATTCTTAATTCCTCATAAATTA
1 AACAAATCAACTTTTACAAATCAAGTAAACAAGCAAAAAATAAGAATTAATTACACATAAATTA
159404 AACAAATCAACTTTT
1 AACAAATCAACTTTT
159419 CAACTTTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 71 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAAGTAAACAAGCAAAAAATAAGAATTAATTACACATAAATTA
Found at i:160766 original size:21 final size:20
Alignment explanation
Indices: 160737--160851 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 20
160727 GTGAATCGGG
* * *
160737 CTCTCGAACTGTGAGAGAGAC
1 CTCTTGAAC-GTGAGAGGGGC
*
160758 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACG-TGAGAGGGGC
*
160779 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAAC-GTGAGAGGGGC
* *
160800 CTCTTGAAGGATGATAGGGGC
1 CTCTTGAACG-TGAGAGGGGC
* *
160821 CTCTTGAACAAT-AGGAGAGGC
1 CTCTTGAAC-GTGA-GAGGGGC
160842 CTCTTGAACG
1 CTCTTGAACG
160852 ATGACAGGTG
Statistics
Matches: 75, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
20 3 0.04
21 71 0.95
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (20 bp):
CTCTTGAACGTGAGAGGGGC
Found at i:160819 original size:42 final size:42
Alignment explanation
Indices: 160751--160859 Score: 155
Period size: 42 Copynumber: 2.6 Consensus size: 42
160741 CGAACTGTGA
* ** *
160751 GAGAGACCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGG
1 GAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAATAG
* * *
160793 GAGGGGCCTCTTGAAGGATGATAGGGGCCTCTTGAACAATAG
1 GAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAATAG
160835 GAGAGGCCTCTTGAACGATGACAGG
1 GAGAGGCCTCTTGAACGATGACAGG
160860 TGAATCGAGC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (42 bp):
GAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAATAG
Found at i:161224 original size:21 final size:21
Alignment explanation
Indices: 161200--161247 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
161190 CACCATTGTT
161200 ATCACGTAA-AACCTCTACCTC
1 ATCACGTAAGAACC-CTACCTC
* * *
161221 ATCATGTAAGGACCGTACCTC
1 ATCACGTAAGAACCCTACCTC
161242 ATCACG
1 ATCACG
161248 CCATGCACCA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.31, C:0.33, G:0.12, T:0.23
Consensus pattern (21 bp):
ATCACGTAAGAACCCTACCTC
Found at i:161289 original size:21 final size:21
Alignment explanation
Indices: 161263--161312 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
161253 CACCATTTCT
* *
161263 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAGCACCGACCTCA
**
161284 TCACGTAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
161305 TCACGTAA
1 TCACGTAA
161313 CTTCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:162791 original size:20 final size:20
Alignment explanation
Indices: 162768--162810 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
162758 TCTGAAACTT
*
162768 AAAATCGCAATACGAAAATG
1 AAAATCGCAACACGAAAATG
*
162788 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACACGAAAATG
162808 AAA
1 AAA
162811 TCGAGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:163198 original size:20 final size:21
Alignment explanation
Indices: 163173--163236 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
163163 TTTGAGAGAT
163173 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
163193 GGAGATGGGACGGATTTCGTC
1 GGAGATGAGACGGATTTCGCC
* * *
163214 GGAAATGGGGACGGATGTCGCC
1 GGAGAT-GAGACGGATTTCGCC
163236 G
1 G
163237 TAGAGAGTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.16
21 17 0.46
22 14 0.38
ACGTcount: A:0.22, C:0.17, G:0.42, T:0.19
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:163206 original size:21 final size:22
Alignment explanation
Indices: 163180--163236 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
163170 GATGGAGATA
*
163180 GACGGATTTCGCCGGAGAT-GG
1 GACGGATTTCGCCGGAAATGGG
*
163201 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGCCGGAAATGGG
*
163223 GACGGATGTCGCCG
1 GACGGATTTCGCCG
163237 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAAATGGG
Found at i:163409 original size:20 final size:20
Alignment explanation
Indices: 163384--163430 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
163374 CTCGCTTTGA
163384 GAATTTGACTTCTGTGTTGC
1 GAATTTGACTTCTGTGTTGC
163404 GAATTTGACTTCTGTGTTGC
1 GAATTTGACTTCTGTGTTGC
163424 GAATTTG
1 GAATTTG
163431 GAATCTGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.45
Consensus pattern (20 bp):
GAATTTGACTTCTGTGTTGC
Found at i:163437 original size:20 final size:20
Alignment explanation
Indices: 163384--163446 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
163374 CTCGCTTTGA
*
163384 GAATTTGACTTCTGTGTTGC
1 GAATTTGACATCTGTGTTGC
*
163404 GAATTTGACTTCTGTGTTGC
1 GAATTTGACATCTGTGTTGC
*
163424 GAATTTGGA-ATCTGAGTTGC
1 GAATTT-GACATCTGTGTTGC
163444 GAA
1 GAA
163447 ATTAGAGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 38 0.95
21 2 0.05
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.40
Consensus pattern (20 bp):
GAATTTGACATCTGTGTTGC
Found at i:174507 original size:20 final size:20
Alignment explanation
Indices: 174469--174507 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
174459 AATAAAGTTA
* *
174469 AAATAATTTATTTTTTAATT
1 AAATAATTTAGTTTATAATT
*
174489 AAATAATTTGGTTTATAAT
1 AAATAATTTAGTTTATAAT
174508 GAAAAAGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
AAATAATTTAGTTTATAATT
Found at i:176875 original size:14 final size:14
Alignment explanation
Indices: 176856--176882 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
176846 ACCTTAACCA
176856 TCAAAGAGATTCCC
1 TCAAAGAGATTCCC
176870 TCAAAGAGATTCC
1 TCAAAGAGATTCC
176883 GACAACCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAAGAGATTCCC
Found at i:179365 original size:15 final size:14
Alignment explanation
Indices: 179338--179368 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
179328 TTCAAATTCA
179338 CTTTCTTTCTCTTC
1 CTTTCTTTCTCTTC
179352 CTTTCTTCTCTCTTC
1 CTTTCTT-TCTCTTC
179367 CT
1 CT
179369 CCATGCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
CTTTCTTTCTCTTC
Found at i:184820 original size:20 final size:20
Alignment explanation
Indices: 184797--184852 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
184787 ATATATTTTT
*
184797 TATTTTTTATTATTTTTAAA
1 TATTTTTTATTATTTTCAAA
** *
184817 TATTTTACATAATTTTCAAA
1 TATTTTTTATTATTTTCAAA
* *
184837 TATATTTTAATATTTT
1 TATTTTTTATTATTTT
184853 GAATTTTTAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTTATTATTTTCAAA
Found at i:184822 original size:9 final size:9
Alignment explanation
Indices: 184810--184865 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
184800 TTTTTATTAT
184810 TTTTAAATA
1 TTTTAAATA
*
184819 TTTTACATAA
1 TTTTAAAT-A
184829 TTTTCAAATA
1 TTTT-AAATA
*
184839 TATTTTAATA
1 T-TTTAAATA
*
184849 TTTTGAAT-
1 TTTTAAATA
184857 TTTTAAATA
1 TTTTAAATA
184866 AGTCATTAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
8 7 0.18
9 13 0.34
10 12 0.32
11 6 0.16
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (9 bp):
TTTTAAATA
Found at i:189430 original size:3 final size:3
Alignment explanation
Indices: 189414--189492 Score: 86
Period size: 3 Copynumber: 24.3 Consensus size: 3
189404 GATTTAAAAA
* *
189414 TAT TATT TATT TAT TAT TAC TAT TAC TAT TAT TATT TATT TATT TATT
1 TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TA-T
189462 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
189493 TTGTAGACCC
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
3 48 0.69
4 22 0.31
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:197961 original size:11 final size:11
Alignment explanation
Indices: 197945--197973 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
197935 TTATTCTATA
197945 ATATTTTCTTT
1 ATATTTTCTTT
197956 ATATTTTCTTT
1 ATATTTTCTTT
197967 ATATTTT
1 ATATTTT
197974 GTTTTTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (11 bp):
ATATTTTCTTT
Found at i:198086 original size:23 final size:23
Alignment explanation
Indices: 198053--198105 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
198043 GATACTATAC
198053 TTTATATATATATATATA-TTTCAT
1 TTTAT-TATATATAT-TAGTTTCAT
*
198077 TTTATTATATATATTAGTTTTAT
1 TTTATTATATATATTAGTTTCAT
198100 TTTATT
1 TTTATT
198106 GTCCATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 20 0.74
24 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTATTATATATATTAGTTTCAT
Found at i:198128 original size:26 final size:25
Alignment explanation
Indices: 198094--198153 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
198084 TATATATTAG
198094 TTTTATTTT-ATTGTCCATTATTTTT
1 TTTTATTTTCATTGT-CATTATTTTT
* * *
198119 TTATTATTTTCTTTGTTATTGTTTTT
1 TT-TTATTTTCATTGTCATTATTTTT
198145 TTTTATTTT
1 TTTTATTTT
198154 TAATCCTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 9 0.30
26 17 0.57
27 4 0.13
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (25 bp):
TTTTATTTTCATTGTCATTATTTTT
Found at i:198198 original size:11 final size:12
Alignment explanation
Indices: 198176--198208 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
198166 TATTTTCCTC
*
198176 TTTTGCTGTTAT
1 TTTTGCTTTTAT
198188 TTTTG-TTTTAT
1 TTTTGCTTTTAT
198199 TTTTGCTTTT
1 TTTTGCTTTT
198209 TTATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (12 bp):
TTTTGCTTTTAT
Found at i:198240 original size:5 final size:5
Alignment explanation
Indices: 198227--198305 Score: 50
Period size: 5 Copynumber: 14.6 Consensus size: 5
198217 TTTTTATTCC
* * * **
198227 TTTTG TTTTA TTTTA TTTTTA TTTAA TTTACTA TTTTA TCTTA TTTGG
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTT--TA TTTTA TTTTA TTTTA
*
198275 TTTTA TTTTTA TTTCTA TCTTTA TTCTA TTT
1 TTTTA -TTTTA TTT-TA T-TTTA TTTTA TTT
198306 GTGGTATTAC
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
5 35 0.61
6 16 0.28
7 6 0.11
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:198240 original size:10 final size:10
Alignment explanation
Indices: 198227--198305 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 10
198217 TTTTTATTCC
*
198227 TTTTGTTTTA
1 TTTTATTTTA
198237 TTTTATTTTTA
1 TTTTA-TTTTA
*
198248 TTTAATTTACTA
1 TTTTATTT--TA
*
198260 TTTTATCTTA
1 TTTTATTTTA
**
198270 TTTGGTTTTA
1 TTTTATTTTA
198280 TTTTTATTTCTA
1 -TTTTATTT-TA
*
198292 TCTTTATTCTA
1 T-TTTATTTTA
198303 TTT
1 TTT
198306 GTGGTATTAC
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
10 18 0.34
11 19 0.36
12 16 0.30
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:198298 original size:33 final size:32
Alignment explanation
Indices: 198243--198306 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
198233 TTTATTTTAT
198243 TTTTATTTAATTTACTATTTTA-TCTTATTTGG
1 TTTTATTTAATTTACTATTTTATTC-TATTTGG
*
198275 TTTTATTTTTATTT-CTATCTTTATTCTATTTG
1 TTTTA-TTTAATTTACTAT-TTTATTCTATTTG
198307 TGGTATTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 9 0.32
33 17 0.61
34 2 0.07
ACGTcount: A:0.19, C:0.08, G:0.05, T:0.69
Consensus pattern (32 bp):
TTTTATTTAATTTACTATTTTATTCTATTTGG
Found at i:201788 original size:16 final size:16
Alignment explanation
Indices: 201749--201788 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
201739 CAATGTGAAT
*
201749 ATAATTATTTTTTGTG
1 ATAATTATTTTTTGTA
201765 ATAA-TATTTTTTGTA
1 ATAATTATTTTTTGTA
201780 ATAATTATT
1 ATAATTATT
201789 AACACTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (16 bp):
ATAATTATTTTTTGTA
Found at i:203339 original size:20 final size:20
Alignment explanation
Indices: 203316--203373 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
203306 TTTACATTAT
203316 ATTTTTATTGAATTTTATT-C
1 ATTTTTATT-AATTTTATTGC
*
203336 ATTTTTAATTCATTTTATTGC
1 ATTTTT-ATTAATTTTATTGC
*
203357 ATTTTTATTTATTTTAT
1 ATTTTTATTAATTTTAT
203374 ATTTTTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 24 0.71
21 10 0.29
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.67
Consensus pattern (20 bp):
ATTTTTATTAATTTTATTGC
Found at i:203370 original size:10 final size:10
Alignment explanation
Indices: 203316--203376 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
203306 TTTACATTAT
*
203316 ATTTTTATTG
1 ATTTTTATTC
*
203326 AATTTTATTC
1 ATTTTTATTC
203336 ATTTTTAATTC
1 ATTTTT-ATTC
203347 A-TTTTATTGC
1 ATTTTTATT-C
*
203357 ATTTTTATTT
1 ATTTTTATTC
203367 ATTTTATATT
1 ATTTT-TATT
203377 TTTTATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
9 3 0.07
10 24 0.56
11 16 0.37
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:203396 original size:12 final size:12
Alignment explanation
Indices: 203379--203412 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
203369 TTTATATTTT
*
203379 TTATAATTAATA
1 TTATAAATAATA
203391 TTATAAATAATA
1 TTATAAATAATA
*
203403 TTTTAAATAA
1 TTATAAATAA
203413 AGAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTATAAATAATA
Found at i:209304 original size:19 final size:20
Alignment explanation
Indices: 209280--209323 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
209270 TACATATTCG
209280 CGTTGCGATAG-TCCAAGTT
1 CGTTGCGATAGCTCCAAGTT
209299 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
209320 CGTT
1 CGTT
209324 ATTGCATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.48
21 12 0.52
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCTCCAAGTT
Found at i:209906 original size:6 final size:6
Alignment explanation
Indices: 209895--209925 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
209885 TCGACTCGTC
209895 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
209926 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:210179 original size:21 final size:21
Alignment explanation
Indices: 210018--210173 Score: 230
Period size: 21 Copynumber: 7.5 Consensus size: 21
210008 TGCGATTTTG
*
210018 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
210039 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
210060 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
210081 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
* *
210102 GACTATCACAACGCACTTGGA
1 GACTATCGCAACGAACTTGGA
210123 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
210144 -A-AATCGCAACGCGAACTT-G-
1 GACTATCGCAA--CGAACTTGGA
210163 GACTATCGCAA
1 GACTATCGCAA
210174 TGCGAATATG
Statistics
Matches: 124, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
19 7 0.06
20 3 0.02
21 114 0.92
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (21 bp):
GACTATCGCAACGAACTTGGA
Found at i:210413 original size:17 final size:17
Alignment explanation
Indices: 210387--210436 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
210377 TAATTTAGTC
*
210387 TAAACAAAAAAATTATT
1 TAAACTAAAAAATTATT
*
210404 TAAACTAAAAAATGATT
1 TAAACTAAAAAATTATT
* **
210421 TCAACTTCAAAATTAT
1 TAAACTAAAAAATTAT
210437 AAACATAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAACTAAAAAATTATT
Found at i:211276 original size:3 final size:3
Alignment explanation
Indices: 211268--211332 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
211258 AACATTGTTT
211268 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
211316 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
211333 TATCGACATC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:212562 original size:18 final size:17
Alignment explanation
Indices: 212526--212589 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
212516 ATTACAAAAT
* *
212526 AAATTAAATAAATACTA
1 AAATTAAAAAAATAATA
212543 AAATTAAACAAAATAATAA
1 AAATTAAA-AAAATAAT-A
* *
212562 AAATTACAAATAATAAAGA
1 AAATTA-AAAAAAT-AATA
212581 AAATTAAAA
1 AAATTAAAA
212590 TACAAAGATC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 8 0.21
18 9 0.23
19 18 0.46
20 4 0.10
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (17 bp):
AAATTAAAAAAATAATA
Found at i:213888 original size:33 final size:33
Alignment explanation
Indices: 213846--213943 Score: 101
Period size: 33 Copynumber: 2.9 Consensus size: 33
213836 TCAATCTACT
*
213846 TCCTTATGTGATGAATTAAAATGTCGATCCAGC
1 TCCTCATGTGATGAATTAAAATGTCGATCCAGC
* *
213879 TCCTCATGTGAT-AGATTAAGATGTCGATCCATC
1 TCCTCATGTGATGA-ATTAAAATGTCGATCCAGC
* * *
213912 TCTTTC-TGTAATGGATTTAAAATGTCGATCCA
1 TC-CTCATGTGAT-GAATTAAAATGTCGATCCA
213944 CCTTCTTCTG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
32 1 0.02
33 35 0.65
34 17 0.31
35 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (33 bp):
TCCTCATGTGATGAATTAAAATGTCGATCCAGC
Found at i:213953 original size:34 final size:32
Alignment explanation
Indices: 213860--213960 Score: 103
Period size: 34 Copynumber: 3.0 Consensus size: 32
213850 TATGTGATGA
* * *
213860 ATTAAAATGTCGATCCAGCTCCTCATGTGATAG
1 ATTAAAATGTCGATCCACCTCTTC-TGTAATAG
* * *
213893 ATTAAGATGTCGATCCATCTCTTTCTGTAATGG
1 ATTAAAATGTCGATCCACCTC-TTCTGTAATAG
*
213926 ATTTAAAATGTCGATCCACCTTCTTCTGTGATAG
1 A-TTAAAATGTCGATCCACC-TCTTCTGTAATAG
213960 A
1 A
213961 ATCGAGCTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 26 0.46
34 28 0.50
35 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (32 bp):
ATTAAAATGTCGATCCACCTCTTCTGTAATAG
Found at i:214186 original size:133 final size:133
Alignment explanation
Indices: 213938--214906 Score: 1456
Period size: 133 Copynumber: 7.3 Consensus size: 133
213928 TTAAAATGTC
* * * * * *
213938 GATCCACCTTCTTCTGTGATAGAATCGAGCTAAAAGTTGACGTTGATCCAACTCCTTGTACGATG
1 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
* *
214003 GATTTGAGCGAAAATAAAAATGTCGATCAACCTCATTCTGTGATGGAATCGAACGAGATATCGAT
66 GATTTGAGCGAAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGAT
214068 GCT
131 GCT
* * *
214071 GATCTACCTCCTTCTGTGATAAAATCGATCAAAAAGTTGACGCTGATCCAACTCTTTCTGCGATG
1 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
* *
214136 GATTTGAGCGAAAATAAAAACGTCTATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGAT
66 GATTTGAGCGAAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGAT
214201 GCT
131 GCT
* * * *
214204 GATCTACCTCCTTATGTGATAAAATCGAGCAAGAAGTTGACGCTTATCCAACTCCTTCTGCGATG
1 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
* *
214269 GATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTATGATGGAATCGAACGAGATGTCGAT
66 GATTTGAGCGAAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGAT
*
214334 ACT
131 GCT
* * * *
214337 GATCTACCTCCTTATGTGATAGAATCGAGTAAAAAGTTGACGCTAATCCAACTCATTCTGCGATG
1 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
* * *
214402 TATTTGAGCAAAAATAAAAATGTCGATCCACCTCATTCTATGATGGAATCGAACGAGATGTCGAT
66 GATTTGAGCGAAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGAT
*
214467 GCC
131 GCT
* * ** **
214470 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAATGTTAACATTGATCCAACTCCTTCTATGATG
1 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
* * * * * *
214535 GATTTGAGTGAAAATAAAAATATCGATCAACTTCCTTTTGTGATGGAATCGAACGAGATGTCGAT
66 GATTTGAGCGAAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGAT
214600 GCT
131 GCT
*
214603 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGAGGCTGATCCAACTCCTTCTGCGATG
1 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
**
214668 GATTTGAGCGAAAATAAAAATGTCGATCCACCT-ACTTCTGTGATGGAATCGAATTAGATGTCGA
66 GATTTGAGCGAAAATAAAAATGTCGATCCACCTCA-TTCTGTGATGGAATCGAACGAGATGTCGA
*
214732 TGTT
130 TGCT
*
214736 GATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
1 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
* *
214801 GATTTGAGCGAGAAA-AAAAATATCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGA
66 GATTTGAGCGA-AAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGA
214865 TGCT
130 TGCT
** *
214869 GATCTACCTTATTTTGTGATAGAATCGAGCAAAAAGTT
1 GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTT
214907 TAACAAACTC
Statistics
Matches: 755, Mismatches: 78, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
133 752 1.00
134 3 0.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (133 bp):
GATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATG
GATTTGAGCGAAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGAT
GCT
Found at i:214503 original size:89 final size:89
Alignment explanation
Indices: 214407--214770 Score: 198
Period size: 89 Copynumber: 4.1 Consensus size: 89
214397 CGATGTATTT
*
214407 GAGCAAAAATAAAAATGTCGATCCACCTCATTCTATGATGGAATCGAACGAGATGTCGATGCCGA
1 GAGCAAAAATAAAAATGTCGATCCACCTCATTCTATGATGGAATCGAACGAAATGTCGATGCCGA
214472 TCTACCTCCTTCTGTGATAGAATC
66 TCTACCTCCTTCTGTGATAGAATC
* * * * * * * ** **** **
214496 GAGCAAAATGTTAACAT-T-GATCCAACTCCTTCTATGATGGATTTGAGTGAAAATAAAAATATC
1 GAGCAAAA-ATAAAAATGTCGATCCACCTCATTCTATGATGGAATCGAACG-AAATGTCGATGCC
* * * *
214559 GATCAACTTCCTTTTGTGATGGAATC
64 GATCTACCTCCTTCTGTGATAGAATC
* * * **** * * * * * * * * * *
214585 GAAC-GAGATGTCGATG-CTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGAGGCTG
1 GAGCAAAAATAAAAATGTC-GATCCACCTCATTCTATGATGGAATCGAACGAAATGTCGATGCCG
* * * * * *
214648 ATCCAACTCCTTCTGCGATGGATTT
65 ATCTACCTCCTTCTGTGATAGAATC
* * ** * **
214673 GAGCGAAAATAAAAATGTCGATCCACCT-ACTTCTGTGATGGAATCGAATTAGATGTCGATGTTG
1 GAGCAAAAATAAAAATGTCGATCCACCTCA-TTCTATGATGGAATCGAACGAAATGTCGATGCCG
*
214737 ATCTACCTCATTCTGTGATAGAATC
65 ATCTACCTCCTTCTGTGATAGAATC
214762 GAGCAAAAA
1 GAGCAAAAA
214771 GTTGACGCTG
Statistics
Matches: 189, Mismatches: 78, Indels: 16
0.67 0.28 0.06
Matches are distributed among these distances:
87 3 0.02
88 52 0.28
89 128 0.68
90 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (89 bp):
GAGCAAAAATAAAAATGTCGATCCACCTCATTCTATGATGGAATCGAACGAAATGTCGATGCCGA
TCTACCTCCTTCTGTGATAGAATC
Found at i:215705 original size:21 final size:21
Alignment explanation
Indices: 215679--215722 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
215669 TCTCCTCTCC
215679 TTTTTTTC-TTTCCTTTTTCT
1 TTTTTTTCTTTTCCTTTTTCT
*
215699 TTTTTTTCTTTTTCTTTTTCT
1 TTTTTTTCTTTTCCTTTTTCT
215720 TTT
1 TTT
215723 CAGGCGTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTTCTTTTCCTTTTTCT
Found at i:215711 original size:15 final size:17
Alignment explanation
Indices: 215681--215721 Score: 68
Period size: 15 Copynumber: 2.5 Consensus size: 17
215671 TCCTCTCCTT
215681 TTTTTCTTTCCTTTTTC
1 TTTTTCTTTCCTTTTTC
215698 TTTTT-TTT-CTTTTTC
1 TTTTTCTTTCCTTTTTC
215713 TTTTTCTTT
1 TTTTTCTTT
215722 TCAGGCGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.52
16 6 0.26
17 5 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCCTTTTTC
Found at i:215722 original size:11 final size:11
Alignment explanation
Indices: 215681--215723 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
215671 TCCTCTCCTT
*
215681 TTTTTCTTTCC
1 TTTTTCTTTTC
215692 TTTTTC-TTT-
1 TTTTTCTTTTC
215701 TTTTTCTTTTTC
1 TTTTTC-TTTTC
215713 TTTTTCTTTTC
1 TTTTTCTTTTC
215724 AGGCGTAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 14 0.50
12 6 0.21
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:228402 original size:3 final size:3
Alignment explanation
Indices: 228394--228431 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
228384 TGGGGATTAC
228394 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
228432 GAGACAAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:228768 original size:13 final size:13
Alignment explanation
Indices: 228750--228786 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
228740 TTTGTACATA
*
228750 TTTTGTATATTCC
1 TTTTGTTTATTCC
228763 TTTTGTTTATTCC
1 TTTTGTTTATTCC
228776 TTTTGTTTATT
1 TTTTGTTTATT
228787 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.11, C:0.11, G:0.08, T:0.70
Consensus pattern (13 bp):
TTTTGTTTATTCC
Found at i:228870 original size:28 final size:28
Alignment explanation
Indices: 228838--228900 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
228828 TACATCTCTT
228838 TAAAATTATATAAATTTGTCTCCTAATA
1 TAAAATTATATAAATTTGTCTCCTAATA
*
228866 TAAAATTATATAAATTTGTCTCTTAATA
1 TAAAATTATATAAATTTGTCTCCTAATA
228894 TAAAATT
1 TAAAATT
228901 TTGCTTGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (28 bp):
TAAAATTATATAAATTTGTCTCCTAATA
Found at i:229968 original size:29 final size:29
Alignment explanation
Indices: 229936--230015 Score: 124
Period size: 29 Copynumber: 2.8 Consensus size: 29
229926 AAGATCGGTG
*
229936 GTCAAAGTAAAAAAGGAAAATAATTAAGT
1 GTCAAAGTGAAAAAGGAAAATAATTAAGT
*
229965 GTCAAAGTGAAAAAGAAAAATAATTAAGT
1 GTCAAAGTGAAAAAGGAAAATAATTAAGT
* *
229994 GTCAAAGTGAAAATGGACAATA
1 GTCAAAGTGAAAAAGGAAAATA
230016 GTTATAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.56, C:0.05, G:0.19, T:0.20
Consensus pattern (29 bp):
GTCAAAGTGAAAAAGGAAAATAATTAAGT
Found at i:231050 original size:22 final size:22
Alignment explanation
Indices: 231022--231080 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
231012 AAATAACAAA
*
231022 AAAACGTGTCAAAAAATAGAGG
1 AAAACGTGTCAAAAAATAGAAG
*
231044 AAAACGTGTCAAAAGATAGAAG
1 AAAACGTGTCAAAAAATAGAAG
* *
231066 AAAATGTGTCTAAAA
1 AAAACGTGTCAAAAA
231081 GCCAAAGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.54, C:0.08, G:0.20, T:0.17
Consensus pattern (22 bp):
AAAACGTGTCAAAAAATAGAAG
Found at i:246690 original size:22 final size:22
Alignment explanation
Indices: 246662--246709 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
246652 AGGAGAGAGA
246662 GTAAATTTCAATGAATAAATTT
1 GTAAATTTCAATGAATAAATTT
246684 GTAAATTTCAATGAATAAATTT
1 GTAAATTTCAATGAATAAATTT
246706 GTAA
1 GTAA
246710 TTTACCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (22 bp):
GTAAATTTCAATGAATAAATTT
Found at i:248075 original size:102 final size:102
Alignment explanation
Indices: 247948--248144 Score: 394
Period size: 102 Copynumber: 1.9 Consensus size: 102
247938 TATTTTTTTC
247948 TCTTCATTTTAGTTTTATTTTATATTATAAATGAATCCGGTGTTTTATATTCAGAAAAATATTTT
1 TCTTCATTTTAGTTTTATTTTATATTATAAATGAATCCGGTGTTTTATATTCAGAAAAATATTTT
248013 ATATTTTATTCAGTTTAAATTTATGACATACTAATTT
66 ATATTTTATTCAGTTTAAATTTATGACATACTAATTT
248050 TCTTCATTTTAGTTTTATTTTATATTATAAATGAATCCGGTGTTTTATATTCAGAAAAATATTTT
1 TCTTCATTTTAGTTTTATTTTATATTATAAATGAATCCGGTGTTTTATATTCAGAAAAATATTTT
248115 ATATTTTATTCAGTTTAAATTTATGACATA
66 ATATTTTATTCAGTTTAAATTTATGACATA
248145 TTGATTTAAT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 95 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (102 bp):
TCTTCATTTTAGTTTTATTTTATATTATAAATGAATCCGGTGTTTTATATTCAGAAAAATATTTT
ATATTTTATTCAGTTTAAATTTATGACATACTAATTT
Found at i:257217 original size:24 final size:24
Alignment explanation
Indices: 257181--257231 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
257171 ATGCTGTCAC
257181 TATAACAACAATAAGTAATGATGT
1 TATAACAACAATAAGTAATGATGT
* * * *
257205 TATAAGAAGAATAAGTTATGGTGT
1 TATAACAACAATAAGTAATGATGT
257229 TAT
1 TAT
257232 CAATTTAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (24 bp):
TATAACAACAATAAGTAATGATGT
Found at i:259632 original size:50 final size:50
Alignment explanation
Indices: 259507--259616 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
259497 ATAGCAGTAA
* ** * * * *
259507 AGCGCGCCCCCTGAATCGCGTTACACGCTGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCATGCCTCGCGATATACGGTGATCTGGCGCCACGTGGGTAT
**
259557 AGCGCGCGTCATGCCTCGCGATATACGGTGATCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCATGCCTCGCGATATACGGTGATCTGGCGCCACGTGGGTAT
*
259607 AGCGTGCCCC
1 AGCGCGCCCC
259617 TTGATCCGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.15, C:0.32, G:0.32, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCATGCCTCGCGATATACGGTGATCTGGCGCCACGTGGGTAT
Found at i:259771 original size:10 final size:10
Alignment explanation
Indices: 259756--259794 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
259746 TTATCACACT
259756 AAATTCTCTC
1 AAATTCTCTC
259766 AAATTCTCT-
1 AAATTCTCTC
259775 AAATTTCTCTC
1 AAA-TTCTCTC
*
259786 AAATACTCT
1 AAATTCTCT
259795 ATCTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 20 0.77
11 3 0.12
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:259784 original size:20 final size:19
Alignment explanation
Indices: 259754--259795 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
259744 TTTTATCACA
*
259754 CTAAATTCTCTCAAATTCT
1 CTAAATTCTCTCAAATACT
259773 CTAAATTTCTCTCAAATACT
1 CTAAA-TTCTCTCAAATACT
259793 CTA
1 CTA
259796 TCTTTTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (19 bp):
CTAAATTCTCTCAAATACT
Found at i:260115 original size:111 final size:111
Alignment explanation
Indices: 259921--260142 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
259911 TGGAAATCAT
* *
259921 ATATCTCTACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAATAA
* *
259986 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
* *
260032 ATATCTCGACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAATAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAATAA
260097 TAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
260143 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAATAA
TAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
Found at i:261673 original size:18 final size:18
Alignment explanation
Indices: 261650--261689 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
261640 CCAGCAGCCA
261650 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
261668 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
261686 CCGC
1 CCGC
261690 CATCGCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:261712 original size:27 final size:27
Alignment explanation
Indices: 261682--261744 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
261672 AGCCATATAT
*
261682 GATGCCGCCATCGCCTTTCCATTACCA
1 GATGCCACCATCGCCTTTCCATTACCA
261709 GATGCCACCATCGCCTTTCCATTACCA
1 GATGCCACCATCGCCTTTCCATTACCA
261736 GATGCCACC
1 GATGCCACC
261745 GCCGCCTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.21, C:0.41, G:0.14, T:0.24
Consensus pattern (27 bp):
GATGCCACCATCGCCTTTCCATTACCA
Found at i:261750 original size:27 final size:27
Alignment explanation
Indices: 261682--261752 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
261672 AGCCATATAT
* *
261682 GATGCCGCCATCGCCTTTCCATTACCA
1 GATGCCACCACCGCCTTTCCATTACCA
*
261709 GATGCCACCATCGCCTTTCCATTACCA
1 GATGCCACCACCGCCTTTCCATTACCA
*
261736 GATGCCACCGCCGCCTT
1 GATGCCACCACCGCCTT
261753 CACCTGGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.18, C:0.42, G:0.15, T:0.24
Consensus pattern (27 bp):
GATGCCACCACCGCCTTTCCATTACCA
Found at i:262333 original size:35 final size:32
Alignment explanation
Indices: 262294--262377 Score: 80
Period size: 35 Copynumber: 2.5 Consensus size: 32
262284 ATATTTCAGT
262294 TAATTTTGTTTATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTTATTACCATTTAAT-TC--TTATTG
* *
262329 TAATTTGGTTATCATTTATCATTTAATTCTTATTG
1 TAATTTTGTT-T-A-TTACCATTTAATTCTTATTG
*
262364 TAAGTTTG-TTATTA
1 TAATTTTGTTTATTA
262378 GTTTGATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
31 3 0.07
32 1 0.02
33 1 0.02
34 1 0.02
35 21 0.50
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.56
Consensus pattern (32 bp):
TAATTTTGTTTATTACCATTTAATTCTTATTG
Found at i:262981 original size:2 final size:2
Alignment explanation
Indices: 262974--263013 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
262964 AAATAATTAT
262974 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
263014 TAATAAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:263017 original size:6 final size:7
Alignment explanation
Indices: 262966--263018 Score: 51
Period size: 6 Copynumber: 7.9 Consensus size: 7
262956 AATATTAAAA
262966 ATAAT-T
1 ATAATAT
*
262972 ATTATAT
1 ATAATAT
262979 AT-ATAT
1 ATAATAT
262985 AT-ATAT
1 ATAATAT
262991 ATATATAT
1 ATA-ATAT
262999 ATATATAT
1 ATA-ATAT
263007 ATAATAT
1 ATAATAT
263014 -TAATA
1 ATAATA
263019 AATTTAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
6 21 0.49
7 7 0.16
8 15 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
ATAATAT
Found at i:263058 original size:15 final size:15
Alignment explanation
Indices: 263036--263077 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
263026 TTTAATTAAA
263036 AAATATATATAATATT
1 AAATATATATAAT-TT
* *
263052 -TATATATTTAATTT
1 AAATATATATAATTT
263066 AAATATATATAA
1 AAATATATATAA
263078 CTGGCTCGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATATATATAATTT
Found at i:272554 original size:20 final size:19
Alignment explanation
Indices: 272506--272556 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
272496 AAATGACCAA
* *
272506 TAAAATCGCAACGCGATCT
1 TAAATTCGCAACGCGAACT
*
272525 TAAATTCGCATCGCGAACT
1 TAAATTCGCAACGCGAACT
*
272544 TCAACTTCGCAAC
1 T-AAATTCGCAAC
272557 TCAGTTTCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (19 bp):
TAAATTCGCAACGCGAACT
Found at i:272707 original size:41 final size:41
Alignment explanation
Indices: 272662--272883 Score: 365
Period size: 41 Copynumber: 5.4 Consensus size: 41
272652 AGTTTCTAAA
272662 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTTCAT
1 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTTCAT
*
272703 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTTCAT
* *
272744 TTCGCGTTGCGATAGTGCAAAATCGCATGGCGATTTTTCAT
1 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTTCAT
* *
272785 TTCGCGTTGCGATAGTCCAAATTCGCATTGC-AATTTTCTAT
1 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTTC-AT
*
272826 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTTCAT
*
272867 TTCTCGTTGCGATAGTC
1 TTCGCGTTGCGATAGTC
272884 TTGCTCTTGC
Statistics
Matches: 167, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 6 0.04
41 156 0.93
42 5 0.03
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTTCAT
Found at i:273159 original size:21 final size:21
Alignment explanation
Indices: 273135--273380 Score: 159
Period size: 21 Copynumber: 11.9 Consensus size: 21
273125 GCAATGGAAA
*
273135 ATCGCAATGCGATTTTGGACT
1 ATCGCAATGCGAATTTGGACT
** **
273156 ATCGCAA--CAGAAAATGGAAA
1 ATCGCAATGC-GAATTTGGACT
*
273176 ATCGCAATACGAATTTGGACT
1 ATCGCAATGCGAATTTGGACT
273197 ATCGCAAATGCGAATTTGGACT
1 ATCGC-AATGCGAATTTGGACT
* ** **
273219 ATCGGCAACGC-AAAATGGAAA
1 ATC-GCAATGCGAATTTGGACT
273240 ATCGCAATGCGAATTTGGACT
1 ATCGCAATGCGAATTTGGACT
* **
273261 ATCGTAACACGAATTTGGA--
1 ATCGCAATGCGAATTTGGACT
* * **
273280 AACTG-AGTTGCGAATTT--AAG
1 ATC-GCA-ATGCGAATTTGGACT
273300 ATCGCAATGCGAATTTGGACT
1 ATCGCAATGCGAATTTGGACT
* * **
273321 ATCGCAACGCGAA-ATGGAAA
1 ATCGCAATGCGAATTTGGACT
* *
273341 ATCGTAACGCGAATTTGGACT
1 ATCGCAATGCGAATTTGGACT
*
273362 ATCGCAACGCGAATTTGGA
1 ATCGCAATGCGAATTTGGA
273381 AACTGAGTTG
Statistics
Matches: 171, Mismatches: 40, Indels: 28
0.72 0.17 0.12
Matches are distributed among these distances:
18 1 0.01
19 14 0.08
20 46 0.27
21 85 0.50
22 23 0.13
23 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (21 bp):
ATCGCAATGCGAATTTGGACT
Found at i:273243 original size:64 final size:62
Alignment explanation
Indices: 273135--273279 Score: 211
Period size: 64 Copynumber: 2.3 Consensus size: 62
273125 GCAATGGAAA
*
273135 ATCGCAATGCGATTTTGGACTATCGCAACAGAAAATGGAAAATCGCAATACGAATTTGGACT
1 ATCGCAATGCGAATTTGGACTATCGCAACAGAAAATGGAAAATCGCAATACGAATTTGGACT
*
273197 ATCGCAAATGCGAATTTGGACTATCGGCAAC-GCAAAATGGAAAATCGCAATGCGAATTTGGACT
1 ATCGC-AATGCGAATTTGGACTATC-GCAACAG-AAAATGGAAAATCGCAATACGAATTTGGACT
* **
273261 ATCGTAACACGAATTTGGA
1 ATCGCAATGCGAATTTGGA
273280 AACTGAGTTG
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
62 5 0.07
63 31 0.41
64 39 0.52
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (62 bp):
ATCGCAATGCGAATTTGGACTATCGCAACAGAAAATGGAAAATCGCAATACGAATTTGGACT
Found at i:273356 original size:101 final size:103
Alignment explanation
Indices: 273127--273394 Score: 346
Period size: 101 Copynumber: 2.6 Consensus size: 103
273117 AAACAAATGC
* * ** * * *
273127 AATGGAAAATCGCAATGCGATTTTGGACTATCGCAACA-GAAAATGGAAAATCGCA-ATACGAAT
1 AATGGAAAATCGCAACGCGAATTTGGACTATCGCAACACGAATTTGGAAACT-G-AGTTGCGAAT
**
273190 TTGGACTATCGCAAATGCGAATTTGGACTATCGGCAACGCAA
64 TT--AAGATCGCAAATGCGAATTTGGACTATCGGCAACGCAA
* *
273232 AATGGAAAATCGCAATGCGAATTTGGACTATCGTAACACGAATTTGGAAACTGAGTTGCGAATTT
1 AATGGAAAATCGCAACGCGAATTTGGACTATCGCAACACGAATTTGGAAACTGAGTTGCGAATTT
*
273297 AAGATCGC-AATGCGAATTTGGACTATC-GCAACGCGA
66 AAGATCGCAAATGCGAATTTGGACTATCGGCAACGCAA
* *
273333 AATGGAAAATCGTAACGCGAATTTGGACTATCGCAACGCGAATTTGGAAACTGAGTTGCGAA
1 AATGGAAAATCGCAACGCGAATTTGGACTATCGCAACACGAATTTGGAAACTGAGTTGCGAA
273395 GTTAGAGTTC
Statistics
Matches: 147, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
101 66 0.45
102 19 0.13
103 6 0.04
104 1 0.01
105 45 0.31
106 10 0.07
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (103 bp):
AATGGAAAATCGCAACGCGAATTTGGACTATCGCAACACGAATTTGGAAACTGAGTTGCGAATTT
AAGATCGCAAATGCGAATTTGGACTATCGGCAACGCAA
Found at i:274865 original size:11 final size:11
Alignment explanation
Indices: 274849--274882 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
274839 ATTCATGTGT
274849 TATTTTTAATA
1 TATTTTTAATA
*
274860 TATTTTTAAAA
1 TATTTTTAATA
274871 TATTTGTTAATA
1 TATTT-TTAATA
274883 ATTATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
TATTTTTAATA
Found at i:277181 original size:23 final size:21
Alignment explanation
Indices: 277148--277193 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
277138 AAACTTAATT
277148 AAATAAAAAAATAAAATATCA
1 AAATAAAAAAATAAAATATCA
* *
277169 AAATAATATAAAATACAATTTCA
1 AAATAA-A-AAAATAAAATATCA
277192 AA
1 AA
277194 GATCAAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATAAAAAAATAAAATATCA
Found at i:281350 original size:12 final size:12
Alignment explanation
Indices: 281335--281369 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
281325 CTATATAATA
281335 AAATCGATAACT
1 AAATCGATAACT
281347 AAATCGATAACT
1 AAATCGATAACT
281359 AAATCGATAAC
1 AAATCGATAAC
281370 AACCAAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (12 bp):
AAATCGATAACT
Found at i:295922 original size:60 final size:57
Alignment explanation
Indices: 295827--295997 Score: 161
Period size: 55 Copynumber: 3.0 Consensus size: 57
295817 TATATCTCCA
* * * *
295827 AACTATGACTCTTATT-TTAAATTTGTTCTTAAACTTTTAAATGTTCCAATTTCATCTTC
1 AACTATGACTC-TATTCTT-AATTAGTCCTTAAACTTTTGAATATTCCAATTTCATC-TC
* * *
295886 AAGCTATGACTCTCATTCTTAATTAGTCCTTAAACTTCTGAACATTCTAATTTCATC-C
1 AA-CTATGACTCT-ATTCTTAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCTC
* * * *
295944 --CTATGAATCTATTTCTAAATTGGTCCTCAAACTTTTGAATATTCCAATTTCATC
1 AACTATGACTCTA-TTCTTAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATC
295998 CTCATTCACC
Statistics
Matches: 94, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
54 1 0.01
55 45 0.48
58 1 0.01
59 3 0.03
60 42 0.45
61 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.44
Consensus pattern (57 bp):
AACTATGACTCTATTCTTAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCTC
Found at i:296752 original size:27 final size:27
Alignment explanation
Indices: 296722--296777 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
296712 ATGAAGATCT
* *
296722 TGATGTTGTGTACTTTCAAGTTCAAAG
1 TGATGTTATGGACTTTCAAGTTCAAAG
*
296749 TGATGTTATGGAGTTTCAAGTTCAAAG
1 TGATGTTATGGACTTTCAAGTTCAAAG
296776 TG
1 TG
296778 GTGATGGCGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (27 bp):
TGATGTTATGGACTTTCAAGTTCAAAG
Found at i:297071 original size:2 final size:2
Alignment explanation
Indices: 297064--297088 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
297054 AAAAGAGTGT
297064 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
297089 TAATATTGCT
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:299056 original size:5 final size:5
Alignment explanation
Indices: 299046--299092 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
299036 ACGCGCCTTT
* *
299046 CCCTC CCCTC CCCTC CCCTC CCATC CCATC CCCTC CCCTC CCCTC CC
1 CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CCCTC CC
299093 TCACTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.04, C:0.77, G:0.00, T:0.19
Consensus pattern (5 bp):
CCCTC
Found at i:304762 original size:26 final size:27
Alignment explanation
Indices: 304703--304762 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
304693 CATAAGACCT
304703 TATAATACCATTAATGCTTATTATGAAA
1 TATAATACCATTAATGCTTATTAT-AAA
*
304731 TCATAATACTATTAAT-CATTATTAT-AA
1 T-ATAATACCATTAATGC-TTATTATAAA
304758 TATAA
1 TATAA
304763 AATTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
26 4 0.14
27 3 0.10
28 2 0.07
29 20 0.69
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (27 bp):
TATAATACCATTAATGCTTATTATAAA
Done.