Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013265.1 Kokia drynarioides strain JFW-HI SEQ_128286, 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: 200944
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 137 characters in sequence are not A, C, G, or T
Found at i:5045 original size:26 final size:26
Alignment explanation
Indices: 5009--5060 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
4999 AACGGTAGTA
5009 TAACCTTGATTAGGGGCTTTTTACCT
1 TAACCTTGATTAGGGGCTTTTTACCT
5035 TAACCTTGATTAGGGGCTTTTTACCT
1 TAACCTTGATTAGGGGCTTTTTACCT
5061 CAAGGTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (26 bp):
TAACCTTGATTAGGGGCTTTTTACCT
Found at i:6198 original size:6 final size:6
Alignment explanation
Indices: 6187--6222 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
6177 TACACCCCAG
*
6187 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA ATGGAA
1 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA
6223 TGGGATTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (6 bp):
AAGGAA
Found at i:7755 original size:15 final size:14
Alignment explanation
Indices: 7730--7759 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
7720 TTCCTAGGCT
7730 GCTGGTCAGCTTGA
1 GCTGGTCAGCTTGA
7744 GCTGGCTCAGCTTGA
1 GCTGG-TCAGCTTGA
7759 G
1 G
7760 ATTTGCTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (14 bp):
GCTGGTCAGCTTGA
Found at i:21954 original size:2 final size:2
Alignment explanation
Indices: 21947--21979 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21937 TTGTACTTTT
21947 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
21980 TTAACTCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:24129 original size:21 final size:21
Alignment explanation
Indices: 24105--24154 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
24095 TTGCACAATC
* *
24105 TCTTCTTCCTCCTCTTCCTCA
1 TCTTCTTCATACTCTTCCTCA
*
24126 TCTTCGTCATACTCTTCCTCA
1 TCTTCTTCATACTCTTCCTCA
*
24147 TCGTCTTC
1 TCTTCTTC
24155 GCCCATGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.08, C:0.42, G:0.04, T:0.46
Consensus pattern (21 bp):
TCTTCTTCATACTCTTCCTCA
Found at i:24283 original size:15 final size:15
Alignment explanation
Indices: 24246--24286 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
24236 TTTTTCCGCA
*
24246 GCTTCTGCAGCGGCT
1 GCTTCTGCTGCGGCT
**
24261 GCAGCTGCTGCGGCT
1 GCTTCTGCTGCGGCT
24276 GCTTCTGCTGC
1 GCTTCTGCTGC
24287 TTCTTGTGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.34, G:0.34, T:0.27
Consensus pattern (15 bp):
GCTTCTGCTGCGGCT
Found at i:26433 original size:31 final size:33
Alignment explanation
Indices: 26398--26459 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
26388 AAATATCATA
26398 ATATTAATTAATTTA-AATAT-TATTTAAATGC
1 ATATTAATTAATTTATAATATATATTTAAATGC
* *
26429 ATATTTATTACTTTATAATATAATATTTAAA
1 ATATTAATTAATTTATAATAT-ATATTTAAA
26460 ATAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 13 0.50
32 5 0.19
34 8 0.31
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (33 bp):
ATATTAATTAATTTATAATATATATTTAAATGC
Found at i:26468 original size:35 final size:31
Alignment explanation
Indices: 26397--26469 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 31
26387 AAAATATCAT
* *
26397 AATATTAATTAATTTAAATATTATTTAAATG
1 AATATTTATTAATTTAAATATTATTTAAATA
* *
26428 CATATTTATTACTTTATAATATAATATTTAAAATA
1 AATATTTATTAATTTA-AATAT--TATTT-AAATA
26463 AATATTT
1 AATATTT
26470 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
31 13 0.39
32 5 0.15
34 5 0.15
35 10 0.30
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (31 bp):
AATATTTATTAATTTAAATATTATTTAAATA
Found at i:27633 original size:33 final size:31
Alignment explanation
Indices: 27596--27665 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 31
27586 TCTGATTTCC
*
27596 TCTTTTGAACAATCATT-ATCTAATTGATTATAG
1 TCTTTTGAAC-ATCATTCAACTAATT--TTATAG
27629 TCTTTTGAACATCATTCAACTAATTTTATAG
1 TCTTTTGAACATCATTCAACTAATTTTATAG
*
27660 TTTTTT
1 TCTTTT
27666 TCTTAGAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 11 0.32
32 6 0.18
33 17 0.50
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (31 bp):
TCTTTTGAACATCATTCAACTAATTTTATAG
Found at i:31622 original size:21 final size:20
Alignment explanation
Indices: 31568--31625 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
31558 AGAAAAAACG
*
31568 AAATATTTTTATTTTTTAAA
1 AAATATTTTTATTATTTAAA
* *
31588 AGAA-AATTGTATTATTTAAA
1 A-AATATTTTTATTATTTAAA
31608 AAATATTTTTAATTATTT
1 AAATATTTTT-ATTATTT
31626 TATATCTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.07
20 19 0.63
21 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATATTTTTATTATTTAAA
Found at i:32691 original size:20 final size:20
Alignment explanation
Indices: 32663--32702 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
32653 CTCATTAACC
* *
32663 AATTTATTTTTTACTAATTA
1 AATTGATTTTGTACTAATTA
*
32683 AATTGATTTTGTATTAATTA
1 AATTGATTTTGTACTAATTA
32703 TTTGAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (20 bp):
AATTGATTTTGTACTAATTA
Found at i:35211 original size:20 final size:21
Alignment explanation
Indices: 35176--35215 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
35166 TAATAATTTG
*
35176 ATTGTTGAATTCTATAATATA
1 ATTGTTGAATTATATAATATA
35197 ATTGTT-AATTATATAATAT
1 ATTGTTGAATTATATAATAT
35216 TAAGTATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (21 bp):
ATTGTTGAATTATATAATATA
Found at i:35539 original size:19 final size:20
Alignment explanation
Indices: 35495--35539 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
35485 TTTAAATTTG
35495 TCATGATGTAAGGAACAAATA
1 TCAT-ATGTAAGGAACAAATA
*
35516 T-ATATGTAAGGAAC-ATTA
1 TCATATGTAAGGAACAAATA
35534 TCATAT
1 TCATAT
35540 TGAAATTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 15 0.68
20 2 0.09
21 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (20 bp):
TCATATGTAAGGAACAAATA
Found at i:49602 original size:28 final size:29
Alignment explanation
Indices: 49570--49629 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
49560 TTAATAAGTT
49570 TTTAAATTAATTTTTATAGATTTT-TA-TA
1 TTTAAATTAATTTTTATA-ATTTTCTATTA
*
49598 TTTAAATTACTTTTTATAATTTTCTATTA
1 TTTAAATTAATTTTTATAATTTTCTATTA
49627 TTT
1 TTT
49630 CTAAAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.17
28 19 0.66
29 5 0.17
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTAAATTAATTTTTATAATTTTCTATTA
Found at i:49824 original size:20 final size:20
Alignment explanation
Indices: 49760--49838 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
49750 TCCATTTCCC
* *
49760 ATTTTAATTATTTTATATAAT
1 ATTTTAATAATTTT-TATAAA
* * * *
49781 TTTTTTATCATTTCTA-AAA
1 ATTTTAATAATTTTTATAAA
49800 GATTTTAATAATTTTTATAAA
1 -ATTTTAATAATTTTTATAAA
* *
49821 ATTTTGAGAATTTTTATA
1 ATTTTAATAATTTTTATA
49839 TGATCCCTAC
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
19 2 0.04
20 30 0.67
21 13 0.29
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTTTAATAATTTTTATAAA
Found at i:49999 original size:12 final size:12
Alignment explanation
Indices: 49982--50015 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
49972 CCACGTTACT
49982 TATCATGTCATC
1 TATCATGTCATC
*
49994 TATCATGTCATT
1 TATCATGTCATC
*
50006 TGTCATGTCA
1 TATCATGTCA
50016 GCACTTAATG
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:0.24, C:0.21, G:0.12, T:0.44
Consensus pattern (12 bp):
TATCATGTCATC
Found at i:58856 original size:26 final size:26
Alignment explanation
Indices: 58813--58862 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
58803 ATTTTTTTCT
*
58813 AATCGAATCAAGTAAAATAAAATTCA
1 AATCGAATCAAATAAAATAAAATTCA
* *
58839 AATCGAATCAAATCAAATTAAATT
1 AATCGAATCAAATAAAATAAAATT
58863 ATTTAAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (26 bp):
AATCGAATCAAATAAAATAAAATTCA
Found at i:61684 original size:14 final size:14
Alignment explanation
Indices: 61665--61693 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
61655 TTAGCGTCGG
61665 ATTTTATTTTATTT
1 ATTTTATTTTATTT
61679 ATTTTATTTTATTT
1 ATTTTATTTTATTT
61693 A
1 A
61694 GGGTAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTTATTTTATTT
Found at i:72679 original size:20 final size:19
Alignment explanation
Indices: 72656--72696 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
72646 TTAATCTTTA
72656 TATTTTTATT-TTATAAAATT
1 TATTTTT-TTATT-TAAAATT
72676 TATTTTTTTATTTAAAATT
1 TATTTTTTTATTTAAAATT
72695 TA
1 TA
72697 AATTTAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TATTTTTTTATTTAAAATT
Found at i:73781 original size:15 final size:15
Alignment explanation
Indices: 73761--73791 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
73751 CTGCAAATCA
73761 AAACCTTCAACCGTG
1 AAACCTTCAACCGTG
73776 AAACCTTCAACCGTG
1 AAACCTTCAACCGTG
73791 A
1 A
73792 TTCTCTTGTC
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:0.35, C:0.32, G:0.13, T:0.19
Consensus pattern (15 bp):
AAACCTTCAACCGTG
Found at i:73928 original size:6 final size:6
Alignment explanation
Indices: 73917--73941 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
73907 AAATGAATAA
73917 GCGTGT GCGTGT GCGTGT GCGTGT G
1 GCGTGT GCGTGT GCGTGT GCGTGT G
73942 TGTGCGCGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GCGTGT
Found at i:75662 original size:84 final size:84
Alignment explanation
Indices: 75445--75671 Score: 357
Period size: 84 Copynumber: 2.7 Consensus size: 84
75435 GATGACACTA
*
75445 TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCGAAACGCCTATC
1 TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCGAAATGCCTATC
*
75510 ATTAGCTATGATGAAATCG
66 ATTAGCTATGATGAAACCG
*
75529 TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCAAAATGCAC-AT
1 TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCGAAATGC-CTAT
75593 CATTAGCTATGATGAAACCG
65 CATTAGCTATGATGAAACCG
* * * ** *
75613 TCACTAATGAAAGAAGCAATCAACCTAATATAGTTGATGTGGATGAGGGCTTCGAAATG
1 TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCGAAATG
75672 TCTTCTAACT
Statistics
Matches: 132, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
84 131 0.99
85 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (84 bp):
TCACTAATGAAAGAAGCAATCAACATAATATAGTTGTTGCGGAAAAGGGCATCGAAATGCCTATC
ATTAGCTATGATGAAACCG
Found at i:84336 original size:25 final size:26
Alignment explanation
Indices: 84289--84338 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
84279 ATTAAATATT
*
84289 TTCTTTTGTATTTTTTATTTTTCACA
1 TTCTTTTGTATTTTTTATCTTTCACA
84315 TTCTTTT-TATTTTTCT-TCTTTCAC
1 TTCTTTTGTATTTTT-TATCTTTCAC
84339 CAACTCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.70
Consensus pattern (26 bp):
TTCTTTTGTATTTTTTATCTTTCACA
Found at i:86487 original size:19 final size:19
Alignment explanation
Indices: 86465--86501 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
86455 TGTTGATACG
86465 ATTTGAAATTTTATTGTTT
1 ATTTGAAATTTTATTGTTT
* *
86484 ATTTGAATTTTTGTTGTT
1 ATTTGAAATTTTATTGTT
86502 GTTGTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.65
Consensus pattern (19 bp):
ATTTGAAATTTTATTGTTT
Found at i:91089 original size:15 final size:16
Alignment explanation
Indices: 91069--91102 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
91059 AACTCTTTAA
91069 AAATTA-TAAAAATAT
1 AAATTATTAAAAATAT
*
91084 AAATTATTAAAACTAT
1 AAATTATTAAAAATAT
91100 AAA
1 AAA
91103 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATTAAAAATAT
Found at i:105690 original size:13 final size:13
Alignment explanation
Indices: 105672--105705 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
105662 TTTAAAATTA
105672 TTAAAATTATTTT
1 TTAAAATTATTTT
105685 TTAAAAATTATTTT
1 TT-AAAATTATTTT
*
105699 TAAAAAT
1 TTAAAAT
105706 ACAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAAAATTATTTT
Found at i:105693 original size:14 final size:13
Alignment explanation
Indices: 105674--105705 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
105664 TAAAATTATT
105674 AAAATTATTTTTTA
1 AAAATTA-TTTTTA
105688 AAAATTATTTTTA
1 AAAATTATTTTTA
105701 AAAAT
1 AAAAT
105706 ACAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAAATTATTTTTA
Found at i:105698 original size:34 final size:34
Alignment explanation
Indices: 105655--105729 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
105645 TCACGTCACC
* *
105655 AAATAA-TTTTAAAATTATTAAAATTATTTTTTAA
1 AAATAATTTTTAAAAATA-CAAAATTATTTTTTAA
* **
105689 AAATTATTTTTAAAAATACAAAATTATTTTTTTT
1 AAATAATTTTTAAAAATACAAAATTATTTTTTAA
105723 AAATAAT
1 AAATAAT
105730 ATAATTATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 24 0.71
35 10 0.29
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (34 bp):
AAATAATTTTTAAAAATACAAAATTATTTTTTAA
Found at i:106857 original size:21 final size:22
Alignment explanation
Indices: 106832--106874 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
106822 AAAATTATTT
*
106832 AATAA-TTTAATTATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
106853 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
106875 TTATTTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:107555 original size:20 final size:20
Alignment explanation
Indices: 107500--107558 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
107490 AAAATGTGTA
107500 AATTAATTATTTAAAATT-AT
1 AATTAATTATTT-AAATTAAT
** *
107520 AATTCAAGGA-TCAAATTAAT
1 AATT-AATTATTTAAATTAAT
107540 AATTAATTATTTAAATTAA
1 AATTAATTATTTAAATTAA
107559 CATTTTATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 8 0.27
20 19 0.63
21 3 0.10
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AATTAATTATTTAAATTAAT
Found at i:109628 original size:15 final size:16
Alignment explanation
Indices: 109598--109636 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
109588 TATTAAAAAT
109598 ATAATTTTACTATTTTA
1 ATAA-TTTACTATTTTA
*
109615 ATAATTTA-TATTTTT
1 ATAATTTACTATTTTA
109630 ATAATTT
1 ATAATTT
109637 TTAAAGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAATTTACTATTTTA
Found at i:112806 original size:24 final size:23
Alignment explanation
Indices: 112736--112807 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
112726 CATAAGGCAG
* * * *
112736 AAGCGTGCTAAAATGCAGAGGAA
1 AAGCGTACCAAAAGGCAGAGAAA
* *
112759 AAGCGTACCACAAGGTAGAGAAA
1 AAGCGTACCAAAAGGCAGAGAAA
* *
112782 AAGCGTGCCATAAAGGCAGATAAA
1 AAGCGTACCA-AAAGGCAGAGAAA
112806 AA
1 AA
112808 TTAGAGGAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 26 0.68
24 12 0.32
ACGTcount: A:0.47, C:0.15, G:0.26, T:0.11
Consensus pattern (23 bp):
AAGCGTACCAAAAGGCAGAGAAA
Found at i:117716 original size:48 final size:48
Alignment explanation
Indices: 117660--117756 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
117650 AAAATAGCCA
117660 ATGGACCATCAGCTATTCCATCTGTTGGTAGTGTAGCTTCAGAAACTG
1 ATGGACCATCAGCTATTCCATCTGTTGGTAGTGTAGCTTCAGAAACTG
117708 ATGGACCATCAGCTATTCCATCTGTTGGTAGTGTAGCTTCAGAAACTG
1 ATGGACCATCAGCTATTCCATCTGTTGGTAGTGTAGCTTCAGAAACTG
117756 A
1 A
117757 CTTTGTCAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (48 bp):
ATGGACCATCAGCTATTCCATCTGTTGGTAGTGTAGCTTCAGAAACTG
Found at i:121536 original size:19 final size:20
Alignment explanation
Indices: 121501--121552 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
121491 CAAAATAATG
121501 TAAAATAATTT-TCAAAAATTC
1 TAAAAT-ATTTAT-AAAAATTC
121522 -AAAATATTTATAAAAATTC
1 TAAAATATTTATAAAAATTC
*
121541 TAAAATTTTTAT
1 TAAAATATTTAT
121553 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATATTTATAAAAATTC
Found at i:129524 original size:36 final size:36
Alignment explanation
Indices: 129484--129616 Score: 176
Period size: 36 Copynumber: 3.7 Consensus size: 36
129474 AATCCTACAT
* * * *
129484 TTATTGTAAAATTTTTCATTGCGTATGTATCACGAG
1 TTATTGTGAAACTCTTCATTGCGTAGGTATCACGAG
* * *
129520 TTATTGTGAAACTCTTCATTGCATAGGTATCTCGAA
1 TTATTGTGAAACTCTTCATTGCGTAGGTATCACGAG
*
129556 TTATTGTGAAACTCTTCATTGCGTAGGTATTACGAG
1 TTATTGTGAAACTCTTCATTGCGTAGGTATCACGAG
* *
129592 TTATGGTGAAGCTCTTCATTGCGTA
1 TTATTGTGAAACTCTTCATTGCGTA
129617 TGATAAAGTT
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 84 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (36 bp):
TTATTGTGAAACTCTTCATTGCGTAGGTATCACGAG
Found at i:129677 original size:36 final size:36
Alignment explanation
Indices: 129627--129707 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
129617 TGATAAAGTT
*
129627 TTCATTGCGTAGGTATCACGAATTATTGTAAAACTC
1 TTCATTGCGCAGGTATCACGAATTATTGTAAAACTC
* * *
129663 TTCATTGCGCAGGTATTACGAGTTATTGTGAAACTC
1 TTCATTGCGCAGGTATCACGAATTATTGTAAAACTC
*
129699 TTCACTGCG
1 TTCATTGCG
129708 TATGATAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (36 bp):
TTCATTGCGCAGGTATCACGAATTATTGTAAAACTC
Found at i:129694 original size:93 final size:93
Alignment explanation
Indices: 129528--130194 Score: 503
Period size: 93 Copynumber: 6.9 Consensus size: 93
129518 AGTTATTGTG
* * * * * *
129528 AAACTCTTCATTGCATAGGTATCTCGAATTATTGTGAAACTCTTCATTGCGTAGGTATTACGAGT
1 AAACTTTTCATTGCGTAGGTATCACGAGTTATTGTAAAACTCTTCATTGCGTAGGTATCACGAGT
* *
129593 TATGGTGAAGCTCTTCATTGCGTATGAT
66 TATTGTGAAACTCTTCATTGCGTATGAT
* * * *
129621 AAAGTTTTCATTGCGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGCAGGTATTACGAGT
1 AAACTTTTCATTGCGTAGGTATCACGAGTTATTGTAAAACTCTTCATTGCGTAGGTATCACGAGT
*
129686 TATTGTGAAACTCTTCACTGCGTATGAT
66 TATTGTGAAACTCTTCATTGCGTATGAT
* * * * * *
129714 AAACTTTTCATGGAGTAGATATCATC-AGTTATTGTGAAACTCTTCATTACATAGGTATCACGAG
1 AAACTTTTCATTGCGTAGGTATCA-CGAGTTATTGTAAAACTCTTCATTGCGTAGGTATCACGAG
129778 TTATTGT-AAACTCTTCATTGCGTAT-AT
65 TTATTGTGAAACTCTTCATTGCGTATGAT
* * * *
129805 ATCACGAGTTATTGTAAAACTCTTCACTGCGTATGTATCACGAATTATTGTAAAACTCTTCATTG
1 A--A--A-CT-TT-T----C-ATT----GCGTAGGTATCACGAGTTATTGTAAAACTCTTCATTG
* * * *
129870 CATAGGTATTACGAATTATTGTGAAACTCTTCATTACGTATGAT
50 CGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGCGTATGAT
* * * * * * *
129914 AAACTTTTCA-TGAAGTAGGTGTCATGAGTTATTGTGAAACTCTTCATTGCGTATG-ATAAAC-T
1 AAACTTTTCATTG-CGTAGGTATCACGAGTTATTGTAAAACTCTTCATTGCGTAGGTAT-CACGA
* ** * * ** * *
129976 TTTCACGGAGTAGGT-ATCA-TGAGTTATTG-T
64 GTT-ATTGTGAAACTCTTCATTGCG-TA-TGAT
* * **
130006 GAAACTCTTCATTACGTAGGTATCACGAGTTATTGTAAAACTCTTCATTGCGTAGGTATCATTAG
1 -AAACTTTTCATTGCGTAGGTATCACGAGTTATTGTAAAACTCTTCATTGCGTAGGTATCACGAG
130071 TTATTGTGAAACTCTTCATTGCGTAGGTATCACGAGTTAT
65 TTATTGTGAAACTCTTCATTGC----GTAT-----G--AT
*
130111 GAAACTCTTCATTGCGTAGGTATCACGAGTTA-TG--AAACTCTTCATTGCGTAGGTATCACGAG
1 -AAACTTTTCATTGCGTAGGTATCACGAGTTATTGTAAAACTCTTCATTGCGTAGGTATCACGAG
130173 TTATTGTGAAACTCTTCATTGC
65 TTATTGTGAAACTCTTCATTGC
130195 ATAGGTATAA
Statistics
Matches: 455, Mismatches: 76, Indels: 77
0.75 0.12 0.13
Matches are distributed among these distances:
91 5 0.01
92 28 0.06
93 239 0.53
94 9 0.02
95 3 0.01
96 2 0.00
97 3 0.01
98 4 0.01
99 1 0.00
102 51 0.11
103 3 0.01
104 3 0.01
105 33 0.07
106 1 0.00
107 50 0.11
108 17 0.04
109 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (93 bp):
AAACTTTTCATTGCGTAGGTATCACGAGTTATTGTAAAACTCTTCATTGCGTAGGTATCACGAGT
TATTGTGAAACTCTTCATTGCGTATGAT
Found at i:129946 original size:57 final size:57
Alignment explanation
Indices: 129885--130023 Score: 242
Period size: 57 Copynumber: 2.4 Consensus size: 57
129875 GTATTACGAA
* *
129885 TTATTGTGAAACTCTTCATTACGTATGATAAACTTTTCATGAAGTAGGTGTCATGAG
1 TTATTGTGAAACTCTTCATTACGTATGATAAACTTTTCACGAAGTAGGTATCATGAG
* *
129942 TTATTGTGAAACTCTTCATTGCGTATGATAAACTTTTCACGGAGTAGGTATCATGAG
1 TTATTGTGAAACTCTTCATTACGTATGATAAACTTTTCACGAAGTAGGTATCATGAG
129999 TTATTGTGAAACTCTTCATTACGTA
1 TTATTGTGAAACTCTTCATTACGTA
130024 GGTATCACGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 77 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (57 bp):
TTATTGTGAAACTCTTCATTACGTATGATAAACTTTTCACGAAGTAGGTATCATGAG
Found at i:130039 original size:293 final size:292
Alignment explanation
Indices: 129484--130493 Score: 940
Period size: 293 Copynumber: 3.4 Consensus size: 292
129474 AATCCTACAT
* * *
129484 TTATTGTAAAATTTTTCATTGCGTATGTATCACGAGTTATTGTGAAACTCTTCATTGCATAGGTA
1 TTATTGTAAAACTCTTCATTGCGTATGTATCACGAGTTATTGT-AAACTCTTCATTGCGTAGGTA
* * * *
129549 TCTCGAATTATTGTGAAACTCTTCATTGCGTAGGTATTACGAGTTATGGTGAAGCTCTTCATTGC
65 TCACGAATTATTGT-AAACTCTTCATTGCGTAGGTATTACGAGTTATTGTGAAACTCTTCATTAC
* * *
129614 GTATGATAAAGTTTTCATTGCGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGCAGGTAT
129 GTATGATAAACTTTTCATTGAGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGCAGATAT
* ** * * * *
129679 TACGAGTTATTGTGAAACTCTTCACTGCGTATGATAAACTTTTCATGGAGTAGATATCATCAGTT
194 AACGAGTTACGGAGAAACTCATCACTGAGTATGATAAACTCTTCATGGAGTAGATATCATCAGTT
*
129744 ATTGTGAAACTCTTCATTACATAGGTATCACGAG
259 ATTGTAAAACTCTTCATTACATAGGTATCACGAG
* * *
129778 TTATTGT-AAACTCTTCATTGCGTATATATCACGAGTTATTGTAAAACTCTTCACTGCGTATGTA
1 TTATTGTAAAACTCTTCATTGCGTATGTATCACGAGTTATTGT-AAACTCTTCATTGCGTAGGTA
* *
129842 TCACGAATTATTGTAAAACTCTTCATTGCATAGGTATTACGAATTATTGTGAAACTCTTCATTAC
65 TCACGAATTATTGT-AAACTCTTCATTGCGTAGGTATTACGAGTTATTGTGAAACTCTTCATTAC
* * * * *
129907 GTATGATAAACTTTTCA-TGAAGTAGGTGTCATGAGTTATTGTGAAACTCTTCATTGCGTATGAT
129 GTATGATAAACTTTTCATTG-AGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGCA-GAT
** * ** * *
129971 A-AAC-TTTTCACGGAGTAGGT-ATCA-TGAGTTATTG-TGAAACTCTTCAT-TACGTAGGTATC
192 ATAACGAGTT-ACGGAGAAACTCATCACTGAG-TA-TGAT-AAACTCTTCATGGA-GTAGATATC
* * **
130030 A-CGAGTTATTGTAAAACTCTTCATTGCGTAGGTATCATTAG
252 ATC-AGTTATTGTAAAACTCTTCATTACATAGGTATCACGAG
* *
130071 TTATTGTGAAACTCTTCATTGCGTAGGTATCACGAGTTA-TG-AAACTCTTCATTGCGTAGGTAT
1 TTATTGTAAAACTCTTCATTGCGTATGTATCACGAGTTATTGTAAACTCTTCATTGCGTAGGTAT
* *
130134 CACGAGTTA-TG-AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGCAT
66 CACGAATTATTGTAAACTCTTCATTGCGTAGGTATTACGAGTTATTGTGAAACTCTTCA-T---T
* *
130197 AGGTATAACGAGTTATTGTGAAACTCTTT-ATTGCGTAGGTATCACGAATTATTGTAAAACTCTT
127 ACGTAT-----G--A---T-AAACT-TTTCATTGAGTAGGTATCACGAATTATTGTAAAACTCTT
* * * ** * ** * * ** * **
130261 CATTGCGTAGGTATTACGAGTTATTGTGAAACTTTTCATTGCGTACAATAAACTTTTCATTTAGT
180 CATTGCGCAGATATAACGAGTTACGGAGAAACTCATCACTGAGTATGATAAACTCTTCATGGAGT
* * * * * * *
130326 AGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTAAGTATCACGAA
245 AGATATCATCAGTTATTGTAAAACTCTTCATTACATAGGTATCACGAG
* * * *
130374 TTATTATAAAACTCTTCATTGTGTAAGTATCAC--G--ATTGTAAAACTCTTCATTTCGTAGGTA
1 TTATTGTAAAACTCTTCATTGCGTATGTATCACGAGTTATTGT-AAACTCTTCATTGCGTAGGTA
* * * * *
130435 TCACGAGTTATTGTGAAACTCTTCATTGTGTAGGTATCATGAGTTATTGTAAAACTCTT
65 TCACGAATTATTGT-AAACTCTTCATTGCGTAGGTATTACGAGTTATTGTGAAACTCTT
130494 TATTGTGTAG
Statistics
Matches: 593, Mismatches: 84, Indels: 67
0.80 0.11 0.09
Matches are distributed among these distances:
288 43 0.07
289 1 0.00
290 2 0.00
291 31 0.05
292 18 0.03
293 228 0.38
294 39 0.07
297 1 0.00
299 2 0.00
300 2 0.00
301 1 0.00
302 34 0.06
303 132 0.22
304 15 0.03
305 44 0.07
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (292 bp):
TTATTGTAAAACTCTTCATTGCGTATGTATCACGAGTTATTGTAAACTCTTCATTGCGTAGGTAT
CACGAATTATTGTAAACTCTTCATTGCGTAGGTATTACGAGTTATTGTGAAACTCTTCATTACGT
ATGATAAACTTTTCATTGAGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGCAGATATAA
CGAGTTACGGAGAAACTCATCACTGAGTATGATAAACTCTTCATGGAGTAGATATCATCAGTTAT
TGTAAAACTCTTCATTACATAGGTATCACGAG
Found at i:130282 original size:174 final size:174
Alignment explanation
Indices: 129983--130508 Score: 634
Period size: 174 Copynumber: 3.1 Consensus size: 174
129973 ACTTTTCACG
*
129983 GAGTAGGTATCATGAGTTATTGTGAAACTCTTCATTACGTAGGTATCACGAGTTATTGTAAAACT
1 GAGTAGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTAGGTATCACGAGTTATTGTAAAACT
** *
130048 CTTCATTGCGTAGGTATCATTAGTTATTGTGAAACTCTTCATTGCGTAGGTATCACGAGTTA-TG
66 CTTCATTGCGTAGGTATCACGA-TTATTGTAAAACTCTTCATTGCGTAGGTATCACGAGTTATTG
130112 AAACTCTTCATTGCGTAGGTATCACGAGTTATGAAACTCTTCATT
130 AAACTCTTCATTGCGTAGGTATCACGAGTTATGAAACTCTTCATT
* * * * *
130157 GCGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGCATAGGTATAACGAGTTATTGTGAAACT
1 GAGTAGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTAGGTATCACGAGTTATTGTAAAACT
* *
130222 CTTTATTGCGTAGGTATCACGAATTATTGTAAAACTCTTCATTGCGTAGGTATTACGAGTTATTG
66 CTTCATTGCGTAGGTATCACG-ATTATTGTAAAACTCTTCATTGCGTAGGTATCACGAGTTA-T-
* *
130287 TGAAACTTTTCATTGC----G--T-AC-A---AT-AAACTTTTCATT
128 TGAAACTCTTCATTGCGTAGGTATCACGAGTTATGAAACTCTTCATT
* * * *
130322 TAGTAGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTAAGTATCACGAATTATTATAAAACT
1 GAGTAGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTAGGTATCACGAGTTATTGTAAAACT
* * *
130387 CTTCATTGTGTAAGTATCACG---ATTGTAAAACTCTTCATTTCGTAGGTATCACGAGTTATTGT
66 CTTCATTGCGTAGGTATCACGATTATTGTAAAACTCTTCATTGCGTAGGTATCACGAGTTA-T-T
* * *
130449 GAAACTCTTCATTGTGTAGGTATCATGAGTTATTGTAAAACTCTTTATT
129 GAAACTCTTCATTGCGTAGGTATCACGAGTTA-TG--AAACTCTTCATT
* *
130498 GTGTAGTTATC
1 GAGTAGGTATC
130509 GCAAGTTAAC
Statistics
Matches: 298, Mismatches: 35, Indels: 36
0.81 0.09 0.10
Matches are distributed among these distances:
161 52 0.17
165 86 0.29
166 2 0.01
167 1 0.00
168 1 0.00
169 2 0.01
170 2 0.01
171 1 0.00
172 1 0.00
173 2 0.01
174 114 0.38
175 1 0.00
176 18 0.06
177 15 0.05
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.38
Consensus pattern (174 bp):
GAGTAGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTAGGTATCACGAGTTATTGTAAAACT
CTTCATTGCGTAGGTATCACGATTATTGTAAAACTCTTCATTGCGTAGGTATCACGAGTTATTGA
AACTCTTCATTGCGTAGGTATCACGAGTTATGAAACTCTTCATT
Found at i:130303 original size:36 final size:36
Alignment explanation
Indices: 129714--130305 Score: 541
Period size: 36 Copynumber: 16.5 Consensus size: 36
129704 TGCGTATGAT
* * * *
129714 AAACTTTTCATGGAGTAGATATCATC-AGTTATTGTG
1 AAACTCTTCATTGCGTAGGTATCA-CGAGTTATTGTG
* *
129750 AAACTCTTCATTACATAGGTATCACGAGTTATTGT-
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
** *
129785 AAACTCTTCATTGCGTATATATCACGAGTTATTGTA
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
* * * *
129821 AAACTCTTCACTGCGTATGTATCACGAATTATTGTA
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
* * *
129857 AAACTCTTCATTGCATAGGTATTACGAATTATTGTG
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
* * * * *
129893 AAACTCTTCATTACGTATG-AT-A-AACTT-TTCATG
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATT-GTG
* * * * * **
129926 AAGTAGGT-GTCA-TGAGTTATTGTGA-AAC-TCTTCATTGCGTATG
1 AA--A-CTCTTCATTGCG-TA-GGT-ATCACGAGTT-ATT--G--TG
* ** * *
129969 ATAAACTTTTCACGGAGTAGGTATCATGAGTTATTGTG
1 --AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
* *
130007 AAACTCTTCATTACGTAGGTATCACGAGTTATTGTA
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
**
130043 AAACTCTTCATTGCGTAGGTATCATTAGTTATTGTG
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
130079 AAACTCTTCATTGCGTAGGTATCACGAGTTA---TG
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
130112 AAACTCTTCATTGCGTAGGTATCACGAGTTA---TG
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
130145 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
* *
130181 AAACTCTTCATTGCATAGGTATAACGAGTTATTGTG
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
* * *
130217 AAACTCTTTATTGCGTAGGTATCACGAATTATTGTA
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
*
130253 AAACTCTTCATTGCGTAGGTATTACGAGTTATTGTG
1 AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
*
130289 AAACTTTTCATTGCGTA
1 AAACTCTTCATTGCGTA
130306 CAATAAACTT
Statistics
Matches: 467, Mismatches: 63, Indels: 52
0.80 0.11 0.09
Matches are distributed among these distances:
32 2 0.00
33 73 0.16
34 3 0.01
35 40 0.09
36 315 0.67
38 7 0.01
40 3 0.01
41 2 0.00
42 7 0.01
43 10 0.02
44 3 0.01
45 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (36 bp):
AAACTCTTCATTGCGTAGGTATCACGAGTTATTGTG
Found at i:130328 original size:57 final size:57
Alignment explanation
Indices: 130253--130362 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
130243 AATTATTGTA
* * *
130253 AAACTCTTCATTGCGTAGGTATTACGAGTTATTGTGAAACTTTTCATTGCGTACAAT
1 AAACTCTTCATTGAGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGCGTACAAT
* * *
130310 AAACTTTTCATTTAGTAGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTA
1 AAACTCTTCATTGAGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGCGTA
130363 AGTATCACGA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (57 bp):
AAACTCTTCATTGAGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGCGTACAAT
Found at i:130357 original size:36 final size:35
Alignment explanation
Indices: 130310--130508 Score: 208
Period size: 36 Copynumber: 5.6 Consensus size: 35
130300 TGCGTACAAT
* * *
130310 AAACTTTTCATTTAGTAGGTATCATGAGTTATTGTG
1 AAACTCTTCATTT-GTAGGTATCACGAGTTATTGTA
* * * *
130346 AAACTCTTCATTGCGTAAGTATCACGAATTATTATA
1 AAACTCTTCATT-TGTAGGTATCACGAGTTATTGTA
*
130382 AAACTCTTCATTGTGTAAGTATCAC--G--ATTGTA
1 AAACTCTTCATT-TGTAGGTATCACGAGTTATTGTA
*
130414 AAACTCTTCATTTCGTAGGTATCACGAGTTATTGTG
1 AAACTCTTCATTT-GTAGGTATCACGAGTTATTGTA
*
130450 AAACTCTTCATTGTGTAGGTATCATGAGTTATTGTA
1 AAACTCTTCATT-TGTAGGTATCACGAGTTATTGTA
* *
130486 AAACTCTTTATTGTGTAGTTATC
1 AAACTCTTCATT-TGTAGGTATC
130509 GCAAGTTAAC
Statistics
Matches: 140, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
31 1 0.01
32 27 0.19
34 1 0.01
36 110 0.79
37 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (35 bp):
AAACTCTTCATTTGTAGGTATCACGAGTTATTGTA
Found at i:130425 original size:68 final size:68
Alignment explanation
Indices: 130340--130473 Score: 205
Period size: 68 Copynumber: 2.0 Consensus size: 68
130330 ATCATGAGTT
*
130340 ATTGTGAAACTCTTCATTGCGTAAGTATCACGAATTATTATAAAACTCTTCATTGTGTAAGTATC
1 ATTGTAAAACTCTTCATTGCGTAAGTATCACGAATTATTATAAAACTCTTCATTGTGTAAGTATC
130405 ACG
66 ACG
* * * * * *
130408 ATTGTAAAACTCTTCATTTCGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGTGTAGGTATC
1 ATTGTAAAACTCTTCATTGCGTAAGTATCACGAATTATTATAAAACTCTTCATTGTGTAAGTATC
130473 A
66 A
130474 TGAGTTATTG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (68 bp):
ATTGTAAAACTCTTCATTGCGTAAGTATCACGAATTATTATAAAACTCTTCATTGTGTAAGTATC
ACG
Found at i:130490 original size:104 final size:104
Alignment explanation
Indices: 130310--130502 Score: 305
Period size: 104 Copynumber: 1.9 Consensus size: 104
130300 TGCGTACAAT
* *
130310 AAACTTTTCATTTAGTAGGTATCATGAGTTATTGTGAAACTCTTCATTGCGTAAGTATCACGAAT
1 AAACTCTTCATTTAGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGCGTAAGTATCACGAAT
130375 TATTATAAAACTCTTCATTGTGTAAGTATCACGATTGTA
66 TATTATAAAACTCTTCATTGTGTAAGTATCACGATTGTA
* * * * *
130414 AAACTCTTCATTTCGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGTGTAGGTATCATGAGT
1 AAACTCTTCATTTAGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGCGTAAGTATCACGAAT
* *
130479 TATTGTAAAACTCTTTATTGTGTA
66 TATTATAAAACTCTTCATTGTGTA
130503 GTTATCGCAA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
104 80 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (104 bp):
AAACTCTTCATTTAGTAGGTATCACGAGTTATTGTGAAACTCTTCATTGCGTAAGTATCACGAAT
TATTATAAAACTCTTCATTGTGTAAGTATCACGATTGTA
Found at i:133973 original size:14 final size:14
Alignment explanation
Indices: 133954--133984 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
133944 TAAGTTTAAC
133954 AAATTTAATTAATT
1 AAATTTAATTAATT
*
133968 AAATTTATTTAATT
1 AAATTTAATTAATT
133982 AAA
1 AAA
133985 AATATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:134868 original size:17 final size:18
Alignment explanation
Indices: 134828--134873 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
134818 GTATTGCTTT
*
134828 TAAAAAATATTTTTAGAA
1 TAAAAAATATTTTGAGAA
134846 TAAAAAATACTTTTGAG-A
1 TAAAAAATA-TTTTGAGAA
134864 T-AAAAATATT
1 TAAAAAATATT
134874 GTTAAACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 7 0.27
18 11 0.42
19 6 0.23
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (18 bp):
TAAAAAATATTTTGAGAA
Found at i:140211 original size:2 final size:2
Alignment explanation
Indices: 140204--140233 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
140194 GCTTCCATGG
140204 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
140234 CATTACCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:142578 original size:27 final size:28
Alignment explanation
Indices: 142558--142645 Score: 78
Period size: 27 Copynumber: 3.2 Consensus size: 28
142548 ATTTAAATGT
* *
142558 TTTTTATATATTTTAT-AATTTATTATA
1 TTTTTATATATTTGATGAATTTATAATA
*
142585 TTTTTATATATTTGATGAATTT-TTATAA
1 TTTTTATATATTTGATGAATTTATAAT-A
*
142613 TTTTTATA-AGTTTATATGAATTT-TAAT-
1 TTTTTATATA-TTT-GATGAATTTATAATA
142640 TTTTTA
1 TTTTTA
142646 ATGTTTTAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
27 26 0.48
28 17 0.31
29 11 0.20
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (28 bp):
TTTTTATATATTTGATGAATTTATAATA
Found at i:142583 original size:19 final size:18
Alignment explanation
Indices: 142561--142620 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
142551 TAAATGTTTT
142561 TTATATATTTTATAATTTA
1 TTATAT-TTTTATAATTTA
142580 TTATATTTTTATATATTTGA
1 TTATATTTTTATA-ATTT-A
*
142600 TGA-ATTTTTATAATTT-
1 TTATATTTTTATAATTTA
142616 TTATA
1 TTATA
142621 AGTTTATATG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 2 0.06
17 1 0.03
18 11 0.31
19 19 0.53
20 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTATATTTTTATAATTTA
Found at i:142614 original size:9 final size:9
Alignment explanation
Indices: 142558--142636 Score: 65
Period size: 9 Copynumber: 8.4 Consensus size: 9
142548 ATTTAAATGT
142558 TTTTTAT-A
1 TTTTTATAA
142566 TATTTTATAA
1 T-TTTTATAA
142576 TTTATTAT-A
1 TTT-TTATAA
142585 TTTTTAT-A
1 TTTTTATAA
*
142593 TATTTGATGAA
1 T-TTTTAT-AA
142604 TTTTTATAA
1 TTTTTATAA
142613 TTTTTATAA
1 TTTTTATAA
*
142622 GTTTATATGAA
1 -TTTTTAT-AA
142633 TTTT
1 TTTT
142637 AATTTTTTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
8 7 0.12
9 28 0.47
10 20 0.34
11 4 0.07
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:143703 original size:17 final size:17
Alignment explanation
Indices: 143683--143752 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
143673 AAATTGCATC
*
143683 TATTTTAAAATTAAGTT
1 TATTTTAAAATTAAATT
* * *
143700 TATTTTAAATTTACATG
1 TATTTTAAAATTAAATT
143717 TA-TTTAAAATTTAAATT
1 TATTTTAAAA-TTAAATT
* *
143734 TATTATAAATTTAAATT
1 TATTTTAAAATTAAATT
143751 TA
1 TA
143753 AAATGTCCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
16 6 0.14
17 31 0.74
18 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTTAAAATTAAATT
Found at i:143874 original size:15 final size:15
Alignment explanation
Indices: 143797--143876 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
143787 TCTAAACAGT
*
143797 CCAATTACAGATGGC
1 CCAATTACAAATGGC
*
143812 CCAATTACAAATAGC
1 CCAATTACAAATGGC
* *
143827 CCAATT-CTTAACGGTC
1 CCAATTAC-AAATGG-C
* *
143843 CCAATTACAGATAGC
1 CCAATTACAAATGGC
**
143858 CCAATTTTAAATGGC
1 CCAATTACAAATGGC
143873 CCAA
1 CCAA
143877 GATTCCAAAC
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
14 1 0.02
15 38 0.78
16 9 0.18
17 1 0.02
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (15 bp):
CCAATTACAAATGGC
Found at i:144398 original size:15 final size:15
Alignment explanation
Indices: 144348--144398 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
144338 TAATTTTTTT
144348 ATTAATAATAATAAC
1 ATTAATAATAATAAC
* * *
144363 TGTTTA-AATAATAAT
1 -ATTAATAATAATAAC
*
144378 AGTAATAATAATAAC
1 ATTAATAATAATAAC
144393 ATTAAT
1 ATTAAT
144399 GACATTAATA
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
14 2 0.08
15 21 0.81
16 3 0.12
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (15 bp):
ATTAATAATAATAAC
Found at i:145624 original size:29 final size:29
Alignment explanation
Indices: 145592--145937 Score: 233
Period size: 29 Copynumber: 12.0 Consensus size: 29
145582 TTTACCTAAG
145592 AACTTCCAAAAAT-CCATTTTTGACCCCGA
1 AACTTCCAAAAATACCA-TTTTGACCCCGA
*
145621 AACTTCCAAAAATTACCA-TTTCACCCTCG-
1 AACTTCCAAAAA-TACCATTTTGACCC-CGA
* * *
145650 AACTTTCAAAAATCCCATTTTTGACCCTGA
1 AACTTCCAAAAATACCA-TTTTGACCCCGA
145680 AACTTCCAAAAATTACCATTTT-ACCCTCG-
1 AACTTCCAAAAA-TACCATTTTGACCC-CGA
* *
145709 AACTTCC-AAAATCCCATTTTTGA-CCCAA
1 AACTTCCAAAAATACCA-TTTTGACCCCGA
* *
145737 AACTTCTAAAAATTACCA-TTTCACTCCC-A
1 AACTTCCAAAAA-TACCATTTTGAC-CCCGA
* *
145766 AACTTCC-AAAATCCCATTTTTGACCTCGA
1 AACTTCCAAAAATACCA-TTTTGACCCCGA
* * *
145795 AACTTCTAAAAATTA-CA-CTTCACCCTCG-
1 AACTTCCAAAAA-TACCATTTTGACCC-CGA
145823 AACTTCCAAAAAT-CTCATTTTGA-CCCGA
1 AACTTCCAAAAATAC-CATTTTGACCCCGA
145851 AACTTCCAAAAATTACCATTTT-ACTCCCG-
1 AACTTCCAAAAA-TACCATTTTGAC-CCCGA
* * * *
145880 AACTTCAAAAAATCCCATTTTTAACCTCGA
1 AACTTCCAAAAATACCA-TTTTGACCCCGA
** *
145910 ATTTTCCCAAAATTACCATTTT-ACCCCG
1 AACTT-CCAAAAATACCATTTTGACCCCG
145938 TGCATCCGAG
Statistics
Matches: 250, Mismatches: 34, Indels: 66
0.71 0.10 0.19
Matches are distributed among these distances:
27 12 0.05
28 67 0.27
29 101 0.40
30 53 0.21
31 17 0.07
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (29 bp):
AACTTCCAAAAATACCATTTTGACCCCGA
Found at i:145661 original size:58 final size:58
Alignment explanation
Indices: 145571--145935 Score: 440
Period size: 57 Copynumber: 6.3 Consensus size: 58
145561 AAATTGTTCT
*
145571 AAAATTACCATTTTA-CCTAAGAACTTCCAAAAAT-CCATTTTTGACCCCGAAACTTCCA
1 AAAATTACCATTTTACCCT-CGAACTT-CAAAAATCCCATTTTTGACCCCGAAACTTCCA
* *
145629 AAAATTACCATTTCACCCTCGAACTTTCAAAAATCCCATTTTTGACCCTGAAACTTCCA
1 AAAATTACCATTTTACCCTCGAAC-TTCAAAAATCCCATTTTTGACCCCGAAACTTCCA
* * *
145688 AAAATTACCATTTTACCCTCGAACTTCCAAAATCCCATTTTTGA-CCCAAAACTTCTA
1 AAAATTACCATTTTACCCTCGAACTTCAAAAATCCCATTTTTGACCCCGAAACTTCCA
* * * * *
145745 AAAATTACCATTTCACTCC-CAAACTTCCAAAATCCCATTTTTGACCTCGAAACTTCTA
1 AAAATTACCATTTTAC-CCTCGAACTTCAAAAATCCCATTTTTGACCCCGAAACTTCCA
* * *
145803 AAAATTA-CACTTCACCCTCGAACTTCCAAAAATCTCA-TTTTGA-CCCGAAACTTCCA
1 AAAATTACCATTTTACCCTCGAACTT-CAAAAATCCCATTTTTGACCCCGAAACTTCCA
* * ** *
145859 AAAATTACCATTTTACTCC-CGAACTTCAAAAAATCCCATTTTTAACCTCGAATTTTCCC
1 AAAATTACCATTTTAC-CCTCGAACTTC-AAAAATCCCATTTTTGACCCCGAAACTTCCA
145918 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
145936 CGTGCATCCG
Statistics
Matches: 269, Mismatches: 26, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
56 21 0.08
57 90 0.33
58 82 0.30
59 76 0.28
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAACTTCAAAAATCCCATTTTTGACCCCGAAACTTCCA
Found at i:145922 original size:115 final size:114
Alignment explanation
Indices: 145591--145925 Score: 462
Period size: 115 Copynumber: 2.9 Consensus size: 114
145581 TTTTACCTAA
145591 GAACTTCCAAAAATCCATTTTTGACCCCGAAACTTCCAAAAATTACCATTTCAC-CCTCGAACTT
1 GAACTTCCAAAAATCCATTTTTGA-CCCGAAACTTCCAAAAATTACCATTTCACTCC-CGAAC-T
* *
145655 TCAAAAATCCCATTTTTGACC-CTGAAACTTCCAAAAATTACCATTTTACCCTC
63 TCAAAAATCCCATTTTTGACCTC-GAAACTTCCAAAAATTA-CACTTCACCCTC
* * *
145708 GAACTTCC-AAAATCCCATTTTTGACCCAAAACTTCTAAAAATTACCATTTCACTCCCAAACTTC
1 GAACTTCCAAAAAT-CCATTTTTGACCCGAAACTTCCAAAAATTACCATTTCACTCCCGAACTTC
* *
145772 CAAAATCCCATTTTTGACCTCGAAACTTCTAAAAATTACACTTCACCCTC
65 AAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTACACTTCACCCTC
*
145822 GAACTTCCAAAAATCTCA-TTTTGACCCGAAACTTCCAAAAATTACCATTTTACTCCCGAACTTC
1 GAACTTCCAAAAATC-CATTTTTGACCCGAAACTTCCAAAAATTACCATTTCACTCCCGAACTTC
* ** *
145886 AAAAAATCCCATTTTTAACCTCGAATTTTCCCAAAATTAC
65 -AAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTAC
145926 CATTTTACCC
Statistics
Matches: 195, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
114 61 0.31
115 77 0.39
116 37 0.19
117 20 0.10
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.30
Consensus pattern (114 bp):
GAACTTCCAAAAATCCATTTTTGACCCGAAACTTCCAAAAATTACCATTTCACTCCCGAACTTCA
AAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTACACTTCACCCTC
Found at i:147125 original size:29 final size:30
Alignment explanation
Indices: 147087--147156 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
147077 TTAAATAATT
* *
147087 TATATTTTTATAAATTTT-AAAAAATTAGA
1 TATAATTTTATAAATTTTAAAAAAATTAAA
*
147116 T-TAAATTTTAT-TATTTTAAAAAAATTAAA
1 TAT-AATTTTATAAATTTTAAAAAAATTAAA
147145 TATAATTTTATA
1 TATAATTTTATA
147157 TTTATTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 6 0.18
29 27 0.79
30 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
TATAATTTTATAAATTTTAAAAAAATTAAA
Found at i:163308 original size:16 final size:16
Alignment explanation
Indices: 163287--163319 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
163277 TTGGTGTTCC
163287 TGTTTCTTAATTCGCA
1 TGTTTCTTAATTCGCA
163303 TGTTTCTTAATTCGCA
1 TGTTTCTTAATTCGCA
163319 T
1 T
163320 TGCTTCTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (16 bp):
TGTTTCTTAATTCGCA
Found at i:168876 original size:12 final size:12
Alignment explanation
Indices: 168861--168921 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
168851 GTCGTCGTCT
*
168861 TCTTCAACTTCC
1 TCTTCTACTTCC
*
168873 TCTTCTACTTCA
1 TCTTCTACTTCC
* *
168885 ACTTCTTCTTCC
1 TCTTCTACTTCC
*
168897 ACTTCTACTTCC
1 TCTTCTACTTCC
*
168909 TCTTCCACTTCC
1 TCTTCTACTTCC
168921 T
1 T
168922 GTAGTTGCAG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.13, C:0.41, G:0.00, T:0.46
Consensus pattern (12 bp):
TCTTCTACTTCC
Found at i:168885 original size:18 final size:18
Alignment explanation
Indices: 168862--168919 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
168852 TCGTCGTCTT
*
168862 CTTCAACTTCCTCTTCTA
1 CTTCAACTTCCTCTTCCA
*
168880 CTTCAACTTCTTCTTCCA
1 CTTCAACTTCCTCTTCCA
*
168898 CTTCTACTTCCTCTTCCA
1 CTTCAACTTCCTCTTCCA
168916 CTTC
1 CTTC
168920 CTGTAGTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (18 bp):
CTTCAACTTCCTCTTCCA
Found at i:170563 original size:22 final size:24
Alignment explanation
Indices: 170515--170565 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
170505 TCATTCTCTA
*
170515 AATTAAAATTATATAAATTTTTAT
1 AATTAAAATTATACAAATTTTTAT
170539 AATTAAAA-T-TACAAATTATTT-T
1 AATTAAAATTATACAAATT-TTTAT
170561 AATTA
1 AATTA
170566 TGAACCCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 13 0.52
23 4 0.16
24 8 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTAAAATTATACAAATTTTTAT
Found at i:174708 original size:25 final size:25
Alignment explanation
Indices: 174667--174716 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
174657 AATAAAAACC
174667 TTATAATAGAATAAAATATTT-TCAT
1 TTATAATAGAATAAAAT-TTTCTCAT
*
174692 TTATAAGTATAAT-AAATTTTCTCAT
1 TTATAA-TAGAATAAAATTTTCTCAT
174717 CAAGTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 3 0.14
25 14 0.64
26 5 0.23
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (25 bp):
TTATAATAGAATAAAATTTTCTCAT
Found at i:174826 original size:19 final size:20
Alignment explanation
Indices: 174787--174829 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
174777 AAATCTTAAC
**
174787 AATAACAAAAAATTATTTAA
1 AATAACAAAAAATTAAATAA
174807 AATAAC-AAAAATTAAATAA
1 AATAACAAAAAATTAAATAA
174826 AATA
1 AATA
174830 TATTTAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (20 bp):
AATAACAAAAAATTAAATAA
Found at i:183315 original size:7 final size:7
Alignment explanation
Indices: 183305--183336 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
183295 TAAAAGACAA
183305 AAAAAAG
1 AAAAAAG
183312 AAAAAAG
1 AAAAAAG
183319 AAAAAAG
1 AAAAAAG
183326 AAAAAAG
1 AAAAAAG
183333 AAAA
1 AAAA
183337 GAAGCTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:183672 original size:127 final size:127
Alignment explanation
Indices: 183446--183701 Score: 476
Period size: 127 Copynumber: 2.0 Consensus size: 127
183436 TTAAAAAGAG
*
183446 AAAGAAAAGGCAGAGGTCACTTTCAGTAACAATATCTTTTACATTCACTTCAACCATTCACATTC
1 AAAGAAAAGGCAGAGGTCACTCTCAGTAACAATATCTTTTACATTCACTTCAACCATTCACATTC
183511 TTATACATGTTATTGCTTATTACCACAATCTTCACACTGCCCTTTTTCCTTTATTTTTTTTA
66 TTATACATGTTATTGCTTATTACCACAATCTTCACACTGCCCTTTTTCCTTTATTTTTTTTA
183573 AAAGAAAAGGCAGAGGTCACTCTCAGTAACAATATCTTTTACATTCACTTCAACCATTCACATTC
1 AAAGAAAAGGCAGAGGTCACTCTCAGTAACAATATCTTTTACATTCACTTCAACCATTCACATTC
* * *
183638 TTATACATGTTATTGCTTATTGCCACAATCTTCACACTTCCCTTTTTCCTTTCTTTTTTTTA
66 TTATACATGTTATTGCTTATTACCACAATCTTCACACTGCCCTTTTTCCTTTATTTTTTTTA
183700 AA
1 AA
183702 GAAGTTGGGT
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 125 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (127 bp):
AAAGAAAAGGCAGAGGTCACTCTCAGTAACAATATCTTTTACATTCACTTCAACCATTCACATTC
TTATACATGTTATTGCTTATTACCACAATCTTCACACTGCCCTTTTTCCTTTATTTTTTTTA
Found at i:192426 original size:30 final size:30
Alignment explanation
Indices: 192392--192448 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
192382 AGCAGCCCAA
*
192392 TGACTCAAATAAAAACTTTTGAATAGTCTG
1 TGACTCAAATAAAAACTTTCGAATAGTCTG
* **
192422 TGACTTAAATGGAAACTTTCGAATAGT
1 TGACTCAAATAAAAACTTTCGAATAGT
192449 TCAATGACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (30 bp):
TGACTCAAATAAAAACTTTCGAATAGTCTG
Done.