Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 126 of 163
Found at i:40601184 original size:17 final size:18
Alignment explanation
Indices: 40601158--40601193 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40601148 GCTTAGCTTA
40601158 ATTAAATATT-AAATATT
1 ATTAAATATTAAAATATT
*
40601175 ATTAATTATTAAAATATT
1 ATTAAATATTAAAATATT
40601193 A
1 A
40601194 AAATATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAAATATTAAAATATT
Found at i:40601492 original size:30 final size:30
Alignment explanation
Indices: 40601448--40601519 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
40601438 TAGCAATTAA
40601448 TTATTTTT-AAAAATA-ATTTTTATAATCT
1 TTATTTTTAAAAAATATATTTTTATAATCT
* *
40601476 TTAGTTTTTAAAAAATATATTTTTATATTTT
1 TTA-TTTTTAAAAAATATATTTTTATAATCT
40601507 TTATTTTTAAAAA
1 TTATTTTTAAAAA
40601520 TTTAATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 3 0.08
29 5 0.13
30 17 0.44
31 14 0.36
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
TTATTTTTAAAAAATATATTTTTATAATCT
Found at i:40601513 original size:29 final size:28
Alignment explanation
Indices: 40601448--40601520 Score: 101
Period size: 31 Copynumber: 2.5 Consensus size: 28
40601438 TAGCAATTAA
40601448 TTATTTTTAAAAATAATTTTTATAATCT
1 TTATTTTTAAAAATAATTTTTATAATCT
* *
40601476 TTAGTTTTTAAAAAATATATTTTTATATTTT
1 TTA-TTTTT-AAAAATA-ATTTTTATAATCT
40601507 TTATTTTTAAAAAT
1 TTATTTTTAAAAAT
40601521 TTAATTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 3 0.08
29 11 0.28
30 12 0.30
31 14 0.35
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (28 bp):
TTATTTTTAAAAATAATTTTTATAATCT
Found at i:40604957 original size:17 final size:17
Alignment explanation
Indices: 40604923--40604956 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
40604913 TTACATATTG
40604923 TGTAATTTGGTCTTTTT
1 TGTAATTTGGTCTTTTT
40604940 TGTAATTT-GTCTTTTT
1 TGTAATTTGGTCTTTTT
40604956 T
1 T
40604957 TTGTGACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.06, G:0.15, T:0.68
Consensus pattern (17 bp):
TGTAATTTGGTCTTTTT
Found at i:40605717 original size:6 final size:6
Alignment explanation
Indices: 40605706--40605730 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40605696 CTGGCCCGCA
40605706 CTGCCT CTGCCT CTGCCT CTGCCT C
1 CTGCCT CTGCCT CTGCCT CTGCCT C
40605731 GAGTAGTTTC
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:0.52, G:0.16, T:0.32
Consensus pattern (6 bp):
CTGCCT
Found at i:40612125 original size:10 final size:9
Alignment explanation
Indices: 40612094--40612118 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40612084 AATTGTAATT
40612094 TTAAAAAAA
1 TTAAAAAAA
40612103 TTAAAAAAA
1 TTAAAAAAA
40612112 TTAAAAA
1 TTAAAAA
40612119 TACTTAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:40633304 original size:266 final size:267
Alignment explanation
Indices: 40632819--40633352 Score: 1061
Period size: 266 Copynumber: 2.0 Consensus size: 267
40632809 AAATATATTT
40632819 TATAATTTATATTCGTTACTTAAAATTTTAAATTAGAAATAATTGTTAAGTTCTGAACTAACGTG
1 TATAATTTATATTCGTTACTTAAAATTTTAAATTAGAAATAATTGTTAAGTTCTGAACTAACGTG
40632884 AATAAAAAAATGTAATAATCAAATTGAAAAATTAAATGTGGCTTTGTCCCGTAAAATTATTTGGA
66 AATAAAAAAATGTAATAATCAAATTGAAAAATTAAATGTGGCTTTGTCCCGTAAAATTATTTGGA
40632949 GTTGTTTTTCAAAAATTAAGTTTGACGAAATAATTTGTTTGGTATTAAAAAGTATAATTTGCAAT
131 GTTGTTTTTCAAAAATTAAGTTTGACGAAATAATTTGTTTGGTATTAAAAAGTATAATTTGCAAT
40633014 GATTTATAAACAGAAAAAAATGGCAATGATCATTTCATGTTTTCATCCAACCTCTCAATTGTAAC
196 GATTTATAAACAGAAAAAAATGGCAATGATCATTTCATGTTTTCATCCAACCTCTCAATTGTAAC
40633079 ACCCCGA
261 ACCCCGA
40633086 TATAATTTAT-TTCGTTACTTAAAATTTTAAATTAGAAATAATTGTTAAGTTCTGAACTAACGTG
1 TATAATTTATATTCGTTACTTAAAATTTTAAATTAGAAATAATTGTTAAGTTCTGAACTAACGTG
40633150 AATAAAAAAATGTAATAATCAAATTGAAAAATTAAATGTGGCTTTGTCCCGTAAAATTATTTGGA
66 AATAAAAAAATGTAATAATCAAATTGAAAAATTAAATGTGGCTTTGTCCCGTAAAATTATTTGGA
40633215 GTTGTTTTTCAAAAATTAAGTTTGACGAAATAATTTGTTTGGTATTAAAAAGTATAATTTGCAAT
131 GTTGTTTTTCAAAAATTAAGTTTGACGAAATAATTTGTTTGGTATTAAAAAGTATAATTTGCAAT
40633280 GATTTATAAACAGAAAAAAATGGCAATGATCATTTCATGTTTTCATCCAACCTCTCAATTGTAAC
196 GATTTATAAACAGAAAAAAATGGCAATGATCATTTCATGTTTTCATCCAACCTCTCAATTGTAAC
40633345 ACCCCGA
261 ACCCCGA
40633352 T
1 T
40633353 TTTGGGACTA
Statistics
Matches: 267, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
266 257 0.96
267 10 0.04
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (267 bp):
TATAATTTATATTCGTTACTTAAAATTTTAAATTAGAAATAATTGTTAAGTTCTGAACTAACGTG
AATAAAAAAATGTAATAATCAAATTGAAAAATTAAATGTGGCTTTGTCCCGTAAAATTATTTGGA
GTTGTTTTTCAAAAATTAAGTTTGACGAAATAATTTGTTTGGTATTAAAAAGTATAATTTGCAAT
GATTTATAAACAGAAAAAAATGGCAATGATCATTTCATGTTTTCATCCAACCTCTCAATTGTAAC
ACCCCGA
Found at i:40634629 original size:50 final size:50
Alignment explanation
Indices: 40634574--40634701 Score: 132
Period size: 50 Copynumber: 2.6 Consensus size: 50
40634564 CATTGAGGTT
* ** *
40634574 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGTGTTGACACCGAG
1 ATGAGAGGTCCCATGTAAGACCATATCTAGGACATGGCATGGACACCGAG
* * * * * *
40634624 ATGAGAGGTCCTC-CGTAAGACTATATCTGGGACATGGCATGGGCACTGAT
1 ATGAGAGGTCC-CATGTAAGACCATATCTAGGACATGGCATGGACACCGAG
**
40634674 ATGAGAACTCCCATGTAAGACCATATCT
1 ATGAGAGGTCCCATGTAAGACCATATCT
40634702 GGGATATGAC
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
49 1 0.02
50 60 0.97
51 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATATCTAGGACATGGCATGGACACCGAG
Found at i:40634702 original size:50 final size:49
Alignment explanation
Indices: 40634638--40634759 Score: 138
Period size: 49 Copynumber: 2.5 Consensus size: 49
40634628 GAGGTCCTCC
* * *
40634638 GTAAGACTATATCTGGGACATGGCATGGGCACTGATATGAGAAC-TCCCAT
1 GTAAGACCATATCTGGGACATGGCATGGGCACT-ACAAGA-AACATCCCAT
* * * *
40634688 GTAAGACCATATCTGGGATATGACATTGGCAGTACAAGAAACATCCCAT
1 GTAAGACCATATCTGGGACATGGCATGGGCACTACAAGAAACATCCCAT
* *
40634737 GTAAGATCATGTCTGGGACATGG
1 GTAAGACCATATCTGGGACATGG
40634760 TTTTGGCATG
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
48 3 0.05
49 29 0.48
50 28 0.47
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (49 bp):
GTAAGACCATATCTGGGACATGGCATGGGCACTACAAGAAACATCCCAT
Found at i:40638334 original size:42 final size:42
Alignment explanation
Indices: 40638280--40638373 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
40638270 CCCTTCTAGG
* *
40638280 TTCAGTTCAGCTCTTTTGAGATTCA-ATTTAACCCTAATGGGT
1 TTCAGTTCAGCTCTTCTAAGATTCAGA-TTAACCCTAATGGGT
* * *
40638322 TTCAGTTTAGCTCTTCTAAGCTTCAGATTAACCCTTATGGGTT
1 TTCAGTTCAGCTCTTCTAAGATTCAGATTAACCCTAATGGG-T
40638365 TTC-GTTCAG
1 TTCAGTTCAG
40638374 TTCCTATGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
42 39 0.89
43 5 0.11
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.41
Consensus pattern (42 bp):
TTCAGTTCAGCTCTTCTAAGATTCAGATTAACCCTAATGGGT
Found at i:40641202 original size:19 final size:19
Alignment explanation
Indices: 40641172--40641214 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
40641162 TATACTTAAC
*
40641172 ATTAATTTAATTAAGATTTG
1 ATTAATTTAATTAAG-TTTA
40641192 ATTAA-TTAATTAAGTTTA
1 ATTAATTTAATTAAGTTTA
40641210 ATTAA
1 ATTAA
40641215 AGGTTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (19 bp):
ATTAATTTAATTAAGTTTA
Found at i:40656095 original size:3 final size:3
Alignment explanation
Indices: 40656087--40656124 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
40656077 AAATTAGTTA
40656087 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40656125 ACATAAAAGA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40658711 original size:15 final size:16
Alignment explanation
Indices: 40658691--40658728 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40658681 CTAAAAAATC
40658691 AAAAATAAT-AAATTA
1 AAAAATAATGAAATTA
* *
40658706 AAAAATAATGAACTTT
1 AAAAATAATGAAATTA
40658722 AAAAATA
1 AAAAATA
40658729 GAAAAGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAATAATGAAATTA
Found at i:40661708 original size:20 final size:19
Alignment explanation
Indices: 40661663--40661710 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
40661653 AGATCGAAGG
*
40661663 AAGAAAATAAAAGAGAGAA
1 AAGAAAAAAAAAGAGAGAA
*
40661682 AACAAAAAAAGAAGAGAGAA
1 AAGAAAAAAA-AAGAGAGAA
*
40661702 GAGAAAAAA
1 AAGAAAAAA
40661711 TATCATCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (19 bp):
AAGAAAAAAAAAGAGAGAA
Found at i:40676430 original size:13 final size:13
Alignment explanation
Indices: 40676412--40676446 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
40676402 CCGTGTGAGT
40676412 CACACGGCCTAGC
1 CACACGGCCTAGC
40676425 CACACGGCCTAGC
1 CACACGGCCTAGC
40676438 CACACGGCC
1 CACACGGCC
40676447 GTATGACCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.23, C:0.49, G:0.23, T:0.06
Consensus pattern (13 bp):
CACACGGCCTAGC
Found at i:40676944 original size:19 final size:20
Alignment explanation
Indices: 40676915--40676956 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
40676905 CAATCTCGGG
*
40676915 TTTTGATTCTCGGGTTCAAT
1 TTTTGATTCTCGAGTTCAAT
40676935 TTTTGA-TCTCGAGTTCAAT
1 TTTTGATTCTCGAGTTCAAT
40676954 TTT
1 TTT
40676957 CAAGTTCAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (20 bp):
TTTTGATTCTCGAGTTCAAT
Found at i:40693631 original size:18 final size:18
Alignment explanation
Indices: 40693608--40693646 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
40693598 ATACCAAGTG
*
40693608 CGTATCCTAGCCCTTATA
1 CGTATCCTAACCCTTATA
*
40693626 CGTATCTTAACCCTTATA
1 CGTATCCTAACCCTTATA
40693644 CGT
1 CGT
40693647 TTCATTTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.31, G:0.10, T:0.36
Consensus pattern (18 bp):
CGTATCCTAACCCTTATA
Found at i:40694090 original size:24 final size:23
Alignment explanation
Indices: 40694063--40694119 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
40694053 CATTTAATAA
*
40694063 AATAAAAGTTGTTTTTA-ATATTTT
1 AATAAAA-TTATTTTTATAT-TTTT
40694087 AATAGTAAATTATTTTTATATTTTT
1 AATA--AAATTATTTTTATATTTTT
40694112 AATAAAAT
1 AATAAAAT
40694120 AGAAGTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 4 0.14
25 16 0.55
26 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (23 bp):
AATAAAATTATTTTTATATTTTT
Found at i:40695321 original size:16 final size:16
Alignment explanation
Indices: 40695300--40695334 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
40695290 GAAGCACATT
40695300 TGAATCCATCTTGGGA
1 TGAATCCATCTTGGGA
40695316 TGAATCCATCTTGGGA
1 TGAATCCATCTTGGGA
40695332 TGA
1 TGA
40695335 TCTTGTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (16 bp):
TGAATCCATCTTGGGA
Found at i:40695918 original size:127 final size:127
Alignment explanation
Indices: 40695703--40696086 Score: 534
Period size: 127 Copynumber: 3.0 Consensus size: 127
40695693 ACTATTATAG
* *
40695703 AAAAAGCGTGTCCACGTGGGAGCTTTTTTCA-TCAATTTTGCTGACTGTGCATCCTACTTGAAGC
1 AAAAAGC--GTCCACGTGGGAGCTTTTTTCAGT-AATTTTGCTGACAGTGCATCCTGCTTGAAGC
* *
40695767 ATTTTTGACACCATTTGTTTAGAACCGTCTTCTCAAAATTATTTTTTCAAGAACTACTGTAGAAA
63 GTTTTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAAGAACTACTGTAGAAA
*
40695832 AAAAAGCGTCCACGTGGGAGCTTTTTTCAGTATTTTTGCTGACAGTGCATCCTGCTTGAAGCGTT
1 AAAAAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTT
*
40695897 TTTGACACCATTTGTTCAGAACCGTCTTTTCAAAATTATTTTTTC-AGAAACTACTGTAG--A
66 TTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAAG-AACTACTGTAGAAA
* *
40695957 AAAAA--GTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATCCTGTTTGAAGCGTT
1 AAAAAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTT
** * *
40696020 TTTGACATTATCTT-TTCAGAACCGTCTTC-CTAAAATTAATTTTTCTAA-AACTAATGTAGAAA
66 TTTGACACCAT-TTGTTCAGAACCGTCTTCTC-AAAATTATTTTTTC-AAGAACTACTGTAGAAA
40696082 AAAAA
1 AAAAA
40696087 CAAAATCCAT
Statistics
Matches: 233, Mismatches: 14, Indels: 20
0.87 0.05 0.07
Matches are distributed among these distances:
122 1 0.00
123 101 0.43
124 2 0.01
125 13 0.06
126 2 0.01
127 106 0.45
128 1 0.00
129 7 0.03
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (127 bp):
AAAAAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTT
TTTGACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCAAGAACTACTGTAGAAA
Found at i:40696216 original size:34 final size:32
Alignment explanation
Indices: 40696144--40696267 Score: 126
Period size: 34 Copynumber: 3.8 Consensus size: 32
40696134 CACAAAATCA
* *
40696144 TTTTAAAAA-ACTAAACCTTAA-TTAATTAATT
1 TTTTAAAAACTCTAAACCCTAATTTAATTAA-T
* *
40696175 TTCTTAAAAACTTTAAACCCTAATTTAATTTAT
1 TT-TTAAAAACTCTAAACCCTAATTTAATTAAT
* * *
40696208 TGATTTAAAACCCCTAAAACCTAATTTAATTAAT
1 T--TTTAAAAACTCTAAACCCTAATTTAATTAAT
*
40696242 TTTAAAAAACTCTAAACCCTAATTTA
1 TTTTAAAAACTCTAAACCCTAATTTA
40696268 TTTTTTAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
31 2 0.03
32 28 0.37
33 11 0.15
34 33 0.44
35 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.40
Consensus pattern (32 bp):
TTTTAAAAACTCTAAACCCTAATTTAATTAAT
Found at i:40696349 original size:15 final size:16
Alignment explanation
Indices: 40696316--40696355 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
40696306 TTATTTTAAC
*
40696316 AAAATCCTAAACCCTA
1 AAAATCCTAAACCCAA
*
40696332 AAAACCCTAAA-CCAA
1 AAAATCCTAAACCCAA
40696347 AAAATCCTA
1 AAAATCCTA
40696356 CGGACTCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAATCCTAAACCCAA
Found at i:40699413 original size:42 final size:41
Alignment explanation
Indices: 40699352--40699563 Score: 210
Period size: 42 Copynumber: 5.0 Consensus size: 41
40699342 CAGTGTTTAC
*
40699352 AAAAATAAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTT
1 AAAAA-AAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* *
40699394 GGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
1 -AAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
*
40699436 AAAAAAAA-GACGTCGCTAAATATCATGTTCTTTAGCGGCGCTTT
1 AAAAAAAATG-C--CGCTAAAGATCATGTTCTTTAGCGGCGC-TT
*** * * *
40699480 CTTCACAAATGCCGCTAACGATCATGTTCTTTAGCGGCGATT
1 -AAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * * * *
40699522 CAGAAAAAATGCCGGTAAAGAACATGATCTTTAGTGGCGCTT
1 -AAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
40699564 TTTTCACAAA
Statistics
Matches: 141, Mismatches: 22, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
40 1 0.01
41 8 0.06
42 68 0.48
43 56 0.40
44 2 0.01
45 5 0.04
46 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (41 bp):
AAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
Found at i:40699561 original size:85 final size:86
Alignment explanation
Indices: 40699400--40699603 Score: 250
Period size: 85 Copynumber: 2.4 Consensus size: 86
40699390 GCTTGGAAAA
* * * * *
40699400 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAAAAAAAGACGTCGCTAAATATCATGTT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGATTAAAAAAAAGACGCCGCTAAAGAACATGAT
40699465 CTTTAGCGGCGCTTTCTTCAC
66 CTTTAGCGGCGCTTTCTTCAC
* * * * * *
40699486 AAATGCCGCTAACGATCATGTTCTTTAGCGGCGATTCAGAAAAA-ATGCCGGTAAAGAACATGAT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGATTAAAAAAAAGACGCCGCTAAAGAACATGAT
* *
40699550 CTTTAGTGGCGCTTTTTTCAC
66 CTTTAGCGGCGCTTTCTTCAC
* *
40699571 AAACGGCGCTAAAAGA-AATGTTCTTTAGCGGCG
1 AAACGCCGCT-AAAGATCATGTTCTTTAGCGGCG
40699604 TTTTATTTTA
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
85 57 0.57
86 43 0.43
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (86 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGATTAAAAAAAAGACGCCGCTAAAGAACATGAT
CTTTAGCGGCGCTTTCTTCAC
Found at i:40699592 original size:128 final size:128
Alignment explanation
Indices: 40699358--40699603 Score: 291
Period size: 128 Copynumber: 1.9 Consensus size: 128
40699348 TTACAAAAAT
* * * * *
40699358 AAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTGGAAAAAAACGCCGCTAAAGATCATGTTC
1 AAATGCCGCTAAAGATCATGTTCTTTAGCGGCGATTAGAAAAAAACGCCGCTAAAGAACATGATC
* **
40699423 TTTAGCGGCGCTTAAAAAAAAGACGTCGCTAAATATCATGTTCTTTAGCGGCGCTTTCTTCAC
66 TTTAGCGGCGCTTAAAAAAAAGACGGCGCTAAATAAAATGTTCTTTAGCGGCGCTTTCTTCAC
* * *
40699486 AAATGCCGCTAACGATCATGTTCTTTAGCGGCGATTCAG-AAAAAATGCCGGTAAAGAACATGAT
1 AAATGCCGCTAAAGATCATGTTCTTTAGCGGCGATT-AGAAAAAAACGCCGCTAAAGAACATGAT
* **** *
40699550 CTTTAGTGGCGCTTTTTTCACAA-ACGGCGCTAAA-AGAAATGTTCTTTAGCGGCG
65 CTTTAGCGGCGC-TTAAAAAAAAGACGGCGCTAAATA-AAATGTTCTTTAGCGGCG
40699604 TTTTATTTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
127 1 0.01
128 91 0.93
129 6 0.06
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (128 bp):
AAATGCCGCTAAAGATCATGTTCTTTAGCGGCGATTAGAAAAAAACGCCGCTAAAGAACATGATC
TTTAGCGGCGCTTAAAAAAAAGACGGCGCTAAATAAAATGTTCTTTAGCGGCGCTTTCTTCAC
Found at i:40699617 original size:44 final size:44
Alignment explanation
Indices: 40699459--40699652 Score: 139
Period size: 43 Copynumber: 4.5 Consensus size: 44
40699449 CGCTAAATAT
* * * * *
40699459 CATGTTCTTTAGCGGCGCTTTCTTCACAAATGCCGCT-AACGAT
1 CATGATCTTTAGCGGCGCTTTTTTCACAAACGCCGCTAAAAGAA
* * **** * * *
40699502 CATGTTCTTTAGCGGCG-ATTCAGAAAAAATGCCGGT-AAAGAA
1 CATGATCTTTAGCGGCGCTTTTTTCACAAACGCCGCTAAAAGAA
* *
40699544 CATGATCTTTAGTGGCGCTTTTTTCACAAACGGCGCTAAAAGAA
1 CATGATCTTTAGCGGCGCTTTTTTCACAAACGCCGCTAAAAGAA
* * * *
40699588 -ATGTTCTTTAGCGGCGTTTTATTTTACAAACGCCGCT-ATAGAA
1 CATGATCTTTAGCGGCGCTTT-TTTCACAAACGCCGCTAAAAGAA
*
40699631 CATGA-CTTTTAGTGGCGCTTTT
1 CATGATC-TTTAGCGGCGCTTTT
40699653 ATAAAAAAAT
Statistics
Matches: 118, Mismatches: 28, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
42 32 0.27
43 51 0.43
44 35 0.30
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (44 bp):
CATGATCTTTAGCGGCGCTTTTTTCACAAACGCCGCTAAAAGAA
Found at i:40700062 original size:21 final size:21
Alignment explanation
Indices: 40700038--40700088 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
40700028 TTCTTTTGAA
*
40700038 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
* *
40700059 CCTCTGCTTCCCTTGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
40700080 CCTCTGCTT
1 CCTCTGCTT
40700089 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:40700123 original size:87 final size:87
Alignment explanation
Indices: 40699974--40700142 Score: 284
Period size: 87 Copynumber: 1.9 Consensus size: 87
40699964 TCTGCTCTGT
* *
40699974 TCTGCTTCTCTCGATGCCGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAAC
1 TCTGCTTCCCTCGATGCCGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAAC
40700039 CTCTGCTTCTCTCGCTGCAGCC
66 CTCTGCTTCTCTCGCTGCAGCC
* * * *
40700061 TCTGCTTCCCTTGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAAC
1 TCTGCTTCCCTCGATGCCGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAAC
40700126 CTCTGCTTCTCTCGCTG
66 CTCTGCTTCTCTCGCTG
40700143 TTTTATCCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.40
Consensus pattern (87 bp):
TCTGCTTCCCTCGATGCCGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAAC
CTCTGCTTCTCTCGCTGCAGCC
Found at i:40701961 original size:16 final size:16
Alignment explanation
Indices: 40701940--40702062 Score: 58
Period size: 16 Copynumber: 7.5 Consensus size: 16
40701930 TTCCATTTGC
*
40701940 TATGTAAGTTGTATT-T
1 TATGTAAGTTAT-TTAT
40701956 TATGTAAGTTATTTAT
1 TATGTAAGTTATTTAT
* *
40701972 TATGTAAGCTATGTAAGT
1 TATGTAAGTTAT-TTA-T
* *
40701990 TATGT-A-TTATGTAAGC
1 TATGTAAGTTAT-TTA-T
* * *
40702006 TATGTCA-TAAACTTTTT
1 TATGTAAGT-TA-TTTAT
*
40702023 TATGTAAGTTGTATT-T
1 TATGTAAGTTAT-TTAT
40702039 TATGTAAGTTATTTAT
1 TATGTAAGTTATTTAT
40702055 TATGTAAG
1 TATGTAAG
40702063 CTTCGTAAGT
Statistics
Matches: 85, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
15 4 0.05
16 58 0.68
17 13 0.15
18 9 0.11
19 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.50
Consensus pattern (16 bp):
TATGTAAGTTATTTAT
Found at i:40701967 original size:9 final size:9
Alignment explanation
Indices: 40701955--40702324 Score: 117
Period size: 9 Copynumber: 43.8 Consensus size: 9
40701945 AAGTTGTATT
40701955 TTATGTAAG
1 TTATGTAAG
*
40701964 TTAT-TTA-
1 TTATGTAAG
40701971 TTATGTAAG
1 TTATGTAAG
*
40701980 CTATGTAAG
1 TTATGTAAG
40701989 TTATGT-A-
1 TTATGTAAG
40701996 TTATGTAAG
1 TTATGTAAG
* *
40702005 CTATGTCA-
1 TTATGTAAG
* ** ***
40702013 TAAACTTTT
1 TTATGTAAG
40702022 TTATGTAAG
1 TTATGTAAG
**
40702031 -T-TGTATT
1 TTATGTAAG
40702038 TTATGTAAG
1 TTATGTAAG
*
40702047 TTAT-TTA-
1 TTATGTAAG
40702054 TTATGTAAG
1 TTATGTAAG
*
40702063 CTT-CGTAAG
1 -TTATGTAAG
*
40702072 TTATAT-A-
1 TTATGTAAG
*
40702079 TCATGTAAG
1 TTATGTAAG
*
40702088 CTATGTAAG
1 TTATGTAAG
**
40702097 -T-TGTATT
1 TTATGTAAG
40702104 TTATGTAAG
1 TTATGTAAG
*
40702113 TTAT-TTA-
1 TTATGTAAG
40702120 TTATGTAAG
1 TTATGTAAG
*
40702129 CTATGTAAG
1 TTATGTAAG
40702138 TTATGT-A-
1 TTATGTAAG
40702145 TTATGTAAG
1 TTATGTAAG
*
40702154 CTATGTCATAG
1 TTATGT-A-AG
40702165 ACTT-T-T---
1 --TTATGTAAG
40702171 TTATGTAAG
1 TTATGTAAG
*
40702180 TATTATGTATG
1 --TTATGTAAG
40702191 TTATGTAAG
1 TTATGTAAG
*
40702200 TTGTGT-AG
1 TTATGTAAG
*
40702208 -AATGTAAG
1 TTATGTAAG
*
40702216 CTATGTAAG
1 TTATGTAAG
*
40702225 TTATGTGAG
1 TTATGTAAG
40702234 TTA--T-A-
1 TTATGTAAG
40702239 -TATGTAAG
1 TTATGTAAG
40702247 TTATGTATAATG
1 TTATG--TAA-G
40702259 TTAAT-TAAG
1 TT-ATGTAAG
*
40702268 CTATGTAAG
1 TTATGTAAG
*
40702277 TTGTGT-A-
1 TTATGTAAG
*
40702284 TAATGTAAG
1 TTATGTAAG
*
40702293 TTATGAAAG
1 TTATGTAAG
40702302 TTATGT-A-
1 TTATGTAAG
40702309 TTATGTAAG
1 TTATGTAAG
40702318 TTATGTA
1 TTATGTA
40702325 TAATATTATT
Statistics
Matches: 258, Mismatches: 57, Indels: 92
0.63 0.14 0.23
Matches are distributed among these distances:
4 4 0.02
5 1 0.00
6 3 0.01
7 51 0.20
8 36 0.14
9 136 0.53
10 6 0.02
11 14 0.05
12 4 0.02
13 3 0.01
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:40701984 original size:25 final size:25
Alignment explanation
Indices: 40701956--40702112 Score: 129
Period size: 25 Copynumber: 6.0 Consensus size: 25
40701946 AGTTGTATTT
40701956 TATGTAAGTTATTTATTATGTAAGC
1 TATGTAAGTTATTTATTATGTAAGC
*
40701981 TATGTAAGTTATGTATTATGTAAGC
1 TATGTAAGTTATTTATTATGTAAGC
* * ***
40702006 TATGTCATAAACTTTTTTATGTAAGTTGTATTT
1 TATG---T-AAGTTATTTAT-T-A--TGTAAGC
40702039 TATGTAAGTTATTTATTATGTAAGC
1 TATGTAAGTTATTTATTATGTAAGC
* *
40702064 T-TCGTAAGTTATATATCATGTAAGC
1 TAT-GTAAGTTATTTATTATGTAAGC
*
40702089 TATGTAAGTTGTATT-TTATGTAAG
1 TATGTAAGTTAT-TTATTATGTAAG
40702113 TTATTTATTA
Statistics
Matches: 104, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
24 1 0.01
25 70 0.67
26 2 0.02
27 1 0.01
28 2 0.02
29 17 0.16
30 2 0.02
31 1 0.01
33 8 0.08
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (25 bp):
TATGTAAGTTATTTATTATGTAAGC
Found at i:40702085 original size:83 final size:83
Alignment explanation
Indices: 40701940--40702093 Score: 274
Period size: 83 Copynumber: 1.9 Consensus size: 83
40701930 TTCCATTTGC
* *
40701940 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTATGTATTATGTAAG
1 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTATATATCATGTAAG
40702005 CTATGTCATAAACTTTTT
66 CTATGTCATAAACTTTTT
40702023 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCT-TCGTAAGTTATATATCATGTAA
1 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTAT-GTAAGTTATATATCATGTAA
40702087 GCTATGT
65 GCTATGT
40702094 AAGTTGTATT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
82 1 0.01
83 67 0.99
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (83 bp):
TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTATATATCATGTAAG
CTATGTCATAAACTTTTT
Found at i:40702102 original size:66 final size:66
Alignment explanation
Indices: 40702023--40702321 Score: 240
Period size: 66 Copynumber: 4.4 Consensus size: 66
40702013 TAAACTTTTT
40702023 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCT-TCGTAAGTTATATATCATGTAA
1 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTAT-GTAAGTTATATATCATGTAA
40702087 GC
65 GC
* *
40702089 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTATGTATTATGTAAG
1 TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTATATATCATGTAAG
40702154 C
66 C
* * * **
40702155 TATGTCATAGACT-T-TTTTATGTAAG-TA-TTATGTATGT----TATGTAAGTTGTGTAGAATG
1 TATGT-A-AG-TTGTATTTTATGTAAGTTATTTAT-TATGTAAGCTATGTAAGTTATATATCATG
40702212 TAAGC
62 TAAGC
*
40702217 TATGTAAGTTATGTGAGTTATATATGTAAGTTATGTATAATGTTAAT-TAAGCTATGTAAGTTGT
1 TATGTAAG-T-TGT-A-TT-T-TATGTAAGTTAT-T-T-A--TT-ATGTAAGCTATGTAAGTTAT
* * *
40702281 GTATAATGTAAGT
54 ATATCATGTAAGC
* * * *
40702294 TATGAAAGTTATGTATTATGTAAGTTAT
1 TATGTAAGTTGTATTTTATGTAAGTTAT
40702322 GTATAATATT
Statistics
Matches: 195, Mismatches: 14, Indels: 43
0.77 0.06 0.17
Matches are distributed among these distances:
60 2 0.01
61 2 0.01
62 28 0.14
65 6 0.03
66 75 0.38
67 21 0.11
68 5 0.03
69 1 0.01
70 1 0.01
71 13 0.07
72 2 0.01
73 3 0.02
74 3 0.02
75 2 0.01
76 1 0.01
77 30 0.15
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.46
Consensus pattern (66 bp):
TATGTAAGTTGTATTTTATGTAAGTTATTTATTATGTAAGCTATGTAAGTTATATATCATGTAAG
C
Found at i:40702108 original size:16 final size:16
Alignment explanation
Indices: 40702089--40702128 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
40702079 TCATGTAAGC
*
40702089 TATGTAAGTTGTATT-T
1 TATGTAAGTTAT-TTAT
40702105 TATGTAAGTTATTTAT
1 TATGTAAGTTATTTAT
40702121 TATGTAAG
1 TATGTAAG
40702129 CTATGTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (16 bp):
TATGTAAGTTATTTAT
Found at i:40702126 original size:25 final size:25
Alignment explanation
Indices: 40702105--40702324 Score: 108
Period size: 25 Copynumber: 8.2 Consensus size: 25
40702095 AGTTGTATTT
*
40702105 TATGTAAGTTATTTATTATGTAAGC
1 TATGTAAGTTATGTATTATGTAAGC
40702130 TATGTAAGTTATGTATTATGTAAGC
1 TATGTAAGTTATGTATTATGTAAGC
*
40702155 TATGTCATAGACTT-T-T-TTATGTAAGTAT
1 TATGT-A-AG--TTATGTATTATGTAAG--C
* *
40702183 TATGTATGTTATGTAAGTTGTGT-AG-
1 TATGTAAGTTATGT-A-TTATGTAAGC
* * **
40702208 AATGTAAGCTATGTAAGTTATGTGAGTTATA
1 TATGTAAGTTATGT-A-TTATGT-A---AGC
*
40702239 TATGTAAGTTATGTATAATGTTAATTAAGC
1 TATGTAAGTTATGTATTATG-----TAAGC
* * *
40702269 TATGTAAGTTGTGTATAATGTAAGT
1 TATGTAAGTTATGTATTATGTAAGC
* *
40702294 TATGAAAGTTATGTATTATGTAAGT
1 TATGTAAGTTATGTATTATGTAAGC
40702319 TATGTA
1 TATGTA
40702325 TAATATTATT
Statistics
Matches: 153, Mismatches: 20, Indels: 44
0.71 0.09 0.20
Matches are distributed among these distances:
24 2 0.01
25 80 0.52
26 12 0.08
27 4 0.03
28 8 0.05
29 11 0.07
30 22 0.14
31 12 0.08
33 1 0.01
34 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (25 bp):
TATGTAAGTTATGTATTATGTAAGC
Found at i:40702129 original size:41 final size:41
Alignment explanation
Indices: 40702067--40702153 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
40702057 TGTAAGCTTC
* *
40702067 GTAAGTTATATATCATGTAAGCTATGTAAGTTGTATTTTAT
1 GTAAGTTATATATCATGTAAGCTATGTAAGTTATATATTAT
* * *
40702108 GTAAGTTATTTATTATGTAAGCTATGTAAGTTATGTATTAT
1 GTAAGTTATATATCATGTAAGCTATGTAAGTTATATATTAT
40702149 GTAAG
1 GTAAG
40702154 CTATGTCATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.46
Consensus pattern (41 bp):
GTAAGTTATATATCATGTAAGCTATGTAAGTTATATATTAT
Found at i:40702151 original size:16 final size:16
Alignment explanation
Indices: 40702130--40702325 Score: 72
Period size: 16 Copynumber: 13.0 Consensus size: 16
40702120 TTATGTAAGC
40702130 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
40702146 TATGTAAGCTATGTCA-
1 TATGTAAGTTATGT-AT
*
40702162 TA-G--ACTT-T-T-T
1 TATGTAAGTTATGTAT
40702172 TATGTAAGTATTATGTATGT
1 TATGTAAG--TTATGTA--T
* *
40702192 TATGTAAGTTGTGTAG
1 TATGTAAGTTATGTAT
* *
40702208 AATGTAAGCTATGTAAGT
1 TATGTAAGTTATGT-A-T
*
40702226 TATGTGAGTTA--TA-
1 TATGTAAGTTATGTAT
40702239 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
* * *
40702255 AATGTTAA-TTAAG--C
1 TATG-TAAGTTATGTAT
*
40702269 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
*
40702285 AATGTAAGTTATG---
1 TATGTAAGTTATGTAT
40702298 -A---AAGTTATGTAT
1 TATGTAAGTTATGTAT
40702310 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
40702326 AATATTATTT
Statistics
Matches: 129, Mismatches: 23, Indels: 56
0.62 0.11 0.27
Matches are distributed among these distances:
9 8 0.06
10 2 0.02
11 2 0.02
12 2 0.02
13 17 0.13
14 6 0.05
15 6 0.05
16 57 0.44
17 6 0.05
18 14 0.11
20 9 0.07
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:40702381 original size:19 final size:19
Alignment explanation
Indices: 40702357--40702398 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40702347 AATATTATCT
*
40702357 TAATATTATATAAGTTATG
1 TAATATTAAATAAGTTATG
**
40702376 TAATATTAAATTGGTTATG
1 TAATATTAAATAAGTTATG
40702395 TAAT
1 TAAT
40702399 TAGAAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (19 bp):
TAATATTAAATAAGTTATG
Found at i:40702574 original size:225 final size:225
Alignment explanation
Indices: 40702342--40702827 Score: 911
Period size: 225 Copynumber: 2.2 Consensus size: 225
40702332 ATTTATGTAA
*
40702342 TTAGAAATATTATCTTAATATTATATAAGTTATGTAATATTAAAT-TGGTTATGTAATTAGAAAT
1 TTAGAAATTTTATCTTAATATTATATAAGTTATGTAATATTAAATAT-GTTATGTAATTAGAAAT
40702406 TTTATCTTAATATTATATAAGTTATGAAGTGTCCTGCTAAAAGCTATGTAAGTTGTGAAAGTAGA
65 TTTATCTTAATATTATATAAGTTATGAAGTGTCCTGCTAAAAGCTATGTAAGTTGTGAAAGTAGA
40702471 TCTGAAATTACTGTTACTTAAGCTATGTAAGTTATATATTATGTAAGTTACATAAAATACATAAA
130 TCTGAAATTACTGTTACTTAAGCTATGTAAGTTATATATTATGTAAGTTACATAAAATACATAAA
40702536 TTATGAAATCTGATCGTAAGATTTTGCAAGT
195 TTATGAAATCTGATCGTAAGATTTTGCAAGT
*
40702567 TTAGAAATTTTATCTTAATATTATATAAGTTATGTAATATTATATATGTTATGTAATTAGAAATT
1 TTAGAAATTTTATCTTAATATTATATAAGTTATGTAATATTAAATATGTTATGTAATTAGAAATT
*
40702632 TTATCTTAATCTTATATAAGTTATGAAGTGTCCTGCTAAAAGCTATGTAAGTTGTGAAAGTAGAT
66 TTATCTTAATATTATATAAGTTATGAAGTGTCCTGCTAAAAGCTATGTAAGTTGTGAAAGTAGAT
40702697 CTGAAATTACTGTTACTTAAGCTATGTAAGTTATATATTATGTAAGTTACATAAAATACATAAAT
131 CTGAAATTACTGTTACTTAAGCTATGTAAGTTATATATTATGTAAGTTACATAAAATACATAAAT
40702762 TATGAAATCTGATCGTAAGATTTTGCAAGT
196 TATGAAATCTGATCGTAAGATTTTGCAAGT
* *
40702792 TTTGAAATTTTATCTTAATATTATATAAGTTTTGTA
1 TTAGAAATTTTATCTTAATATTATATAAGTTATGTA
40702828 TTAAGCAAGT
Statistics
Matches: 255, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
225 254 1.00
226 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.42
Consensus pattern (225 bp):
TTAGAAATTTTATCTTAATATTATATAAGTTATGTAATATTAAATATGTTATGTAATTAGAAATT
TTATCTTAATATTATATAAGTTATGAAGTGTCCTGCTAAAAGCTATGTAAGTTGTGAAAGTAGAT
CTGAAATTACTGTTACTTAAGCTATGTAAGTTATATATTATGTAAGTTACATAAAATACATAAAT
TATGAAATCTGATCGTAAGATTTTGCAAGT
Found at i:40702606 original size:19 final size:19
Alignment explanation
Indices: 40702582--40702623 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
40702572 AATTTTATCT
40702582 TAATATTATATAAGTTATG
1 TAATATTATATAAGTTATG
*
40702601 TAATATTATATATGTTATG
1 TAATATTATATAAGTTATG
40702620 TAAT
1 TAAT
40702624 TAGAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (19 bp):
TAATATTATATAAGTTATG
Found at i:40704389 original size:6 final size:6
Alignment explanation
Indices: 40704380--40704406 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40704370 TTTAGTTTTA
40704380 ATACAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATA
40704407 TATAAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:40704786 original size:19 final size:19
Alignment explanation
Indices: 40704762--40704803 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40704752 TGTTGGGTTT
*
40704762 GGGGAACTGTTAGGGATTA
1 GGGGAAATGTTAGGGATTA
* *
40704781 GGGGAAATTTTAGGGATTT
1 GGGGAAATGTTAGGGATTA
40704800 GGGG
1 GGGG
40704804 GAGATGAGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.45, T:0.29
Consensus pattern (19 bp):
GGGGAAATGTTAGGGATTA
Found at i:40705567 original size:26 final size:26
Alignment explanation
Indices: 40705532--40705583 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
40705522 ACGGCGTCAT
40705532 TTTCATGAATACAATTTAACATTAAA
1 TTTCATGAATACAATTTAACATTAAA
*
40705558 TTTCATGAATTCAATTTAACATTAAA
1 TTTCATGAATACAATTTAACATTAAA
40705584 CCATCCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
TTTCATGAATACAATTTAACATTAAA
Found at i:40706948 original size:118 final size:116
Alignment explanation
Indices: 40706826--40707065 Score: 435
Period size: 118 Copynumber: 2.1 Consensus size: 116
40706816 AATATAAAAT
*
40706826 AAAAATAACACGAAGCTAATAGTAAAATATAATAATATAATAAGGAATAAATGTAAAAAGGAAAA
1 AAAAATAACACAAAGCTAATAGTAAAATATAATAATATAATAAGGAATAAATGTAAAAAGGAAAA
*
40706891 ATACAAGCATGGTGATAAGTAGATCAATTAATAAGATAATAAAAATAACGATA
66 ATACAAGCATGGTAATAAGTAGATCAATTAATAAGATAATAAAAATAAC-A-A
*
40706944 AAAAAAAACACAAAGCTAATAGTAAAATATAATAATATAATAAGGAATAAATGTAAAAAGGAAAA
1 AAAAATAACACAAAGCTAATAGTAAAATATAATAATATAATAAGGAATAAATGTAAAAAGGAAAA
40707009 ATACAAGCATGGTAATAAGTAGATCAATTAATAAGATAATAAAAATAACAA
66 ATACAAGCATGGTAATAAGTAGATCAATTAATAAGATAATAAAAATAACAA
40707060 AAAAAT
1 AAAAAT
40707066 GGACTAATTT
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
116 6 0.05
117 1 0.01
118 111 0.94
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.21
Consensus pattern (116 bp):
AAAAATAACACAAAGCTAATAGTAAAATATAATAATATAATAAGGAATAAATGTAAAAAGGAAAA
ATACAAGCATGGTAATAAGTAGATCAATTAATAAGATAATAAAAATAACAA
Found at i:40707025 original size:61 final size:61
Alignment explanation
Indices: 40706842--40707025 Score: 206
Period size: 54 Copynumber: 3.1 Consensus size: 61
40706832 AACACGAAGC
40706842 TAATAGTAAAATATAATAATATAATAAGGAATAAATGTAAAAAGGAAAAATACAAGCATGG
1 TAATAGTAAAATATAATAATATAATAAGGAATAAATGTAAAAAGGAAAAATACAAGCATGG
* * * * *
40706903 TGATAAGTAGATCAAT-TAATAAGATAATAA-AAAT-AACG-ATAAAA--AAAAACACAA--A-G
1 TAAT-AGTA-A--AATATAATAATATAATAAGGAATAAATGTA-AAAAGGAAAAATACAAGCATG
*
40706959 C
61 G
40706960 TAATAGTAAAATATAATAATATAATAAGGAATAAATGTAAAAAGGAAAAATACAAGCATGG
1 TAATAGTAAAATATAATAATATAATAAGGAATAAATGTAAAAAGGAAAAATACAAGCATGG
40707021 TAATA
1 TAATA
40707026 AGTAGATCAA
Statistics
Matches: 97, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
53 3 0.03
54 13 0.13
55 4 0.04
56 11 0.11
57 5 0.05
58 10 0.10
60 10 0.10
61 10 0.10
62 11 0.11
63 4 0.04
64 13 0.13
65 3 0.03
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (61 bp):
TAATAGTAAAATATAATAATATAATAAGGAATAAATGTAAAAAGGAAAAATACAAGCATGG
Found at i:40707041 original size:61 final size:61
Alignment explanation
Indices: 40706858--40707041 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
40706848 TAAAATATAA
*
40706858 TAATATAATAAGGAATAAATGTAAAAAGGAAAAATACAAGCATGGTGATAAGTAGATCAAT
1 TAATATAATAAGGAATAAATGTAAAAAGGAAAAATACAAGCATGGTAATAAGTAGATCAAT
* * * *
40706919 TAATAAGATAATAA-AAAT-AACG-ATAAAA--AAAAACACAAAGCTAATAGTAA-AA-T--AT-
1 TAAT---ATAATAAGGAATAAATGTA-AAAAGGAAAAATAC-AAGC--ATGGTAATAAGTAGATC
40706974 AA-
59 AAT
40706976 TAATATAATAAGGAATAAATGTAAAAAGGAAAAATACAAGCATGGTAATAAGTAGATCAAT
1 TAATATAATAAGGAATAAATGTAAAAAGGAAAAATACAAGCATGGTAATAAGTAGATCAAT
40707037 TAATA
1 TAATA
40707042 AGATAATAAA
Statistics
Matches: 96, Mismatches: 9, Indels: 36
0.68 0.06 0.26
Matches are distributed among these distances:
54 7 0.07
55 9 0.09
56 9 0.09
57 10 0.10
58 9 0.09
59 4 0.04
60 9 0.09
61 15 0.16
62 9 0.09
63 8 0.08
64 7 0.07
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (61 bp):
TAATATAATAAGGAATAAATGTAAAAAGGAAAAATACAAGCATGGTAATAAGTAGATCAAT
Found at i:40707063 original size:61 final size:61
Alignment explanation
Indices: 40706880--40707063 Score: 190
Period size: 64 Copynumber: 3.1 Consensus size: 61
40706870 GAATAAATGT
*
40706880 AAAAAGGAAAAATACAAGCATGGTGATAAGTAGATCAATTAATAAGATAATAAAAATAACGA
1 AAAAAGGAAAAATACAAGCATGGTAATAAGTAGATCAATTAATAAGATAATAAAAATAAC-A
* * * * *
40706942 TAAAA--AAAAACACAA--A-GCTAAT-AGTA-A--AATATAATAATATAATAAGGAATAA-A
1 AAAAAGGAAAAATACAAGCATGGTAATAAGTAGATCAAT-TAATAAGATAATAA-AAATAACA
40706995 TGTAAAAAGGAAAAATACAAGCATGGTAATAAGTAGATCAATTAATAAGATAATAAAAATAACA
1 ---AAAAAGGAAAAATACAAGCATGGTAATAAGTAGATCAATTAATAAGATAATAAAAATAACA
40707059 AAAAA
1 AAAAA
40707064 ATGGACTAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 31
0.70 0.08 0.22
Matches are distributed among these distances:
53 4 0.04
54 13 0.14
55 6 0.06
56 8 0.08
57 4 0.04
58 10 0.10
60 10 0.10
61 10 0.10
62 8 0.08
63 6 0.06
64 14 0.15
65 3 0.03
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.20
Consensus pattern (61 bp):
AAAAAGGAAAAATACAAGCATGGTAATAAGTAGATCAATTAATAAGATAATAAAAATAACA
Found at i:40716191 original size:113 final size:113
Alignment explanation
Indices: 40715967--40716442 Score: 649
Period size: 112 Copynumber: 4.2 Consensus size: 113
40715957 ATTACTATTA
* ** * *
40715967 GCGGCGCTTCCTCA-AAAACGCCGCTAAAGGCCGGAGCATTAGTGGCGCTTTTTAAAAAACGCCG
1 GCGGCGCTT-TTCAGAAAACGCCGCTAAAGGCAAGAGCATTAGCGGCGCTTTTCAAAAAACGCCG
* **
40716031 CTATAGGCCCAAAAACTCAGAAAACGGCGTCGTTGGATTTAGGTTTTTT
65 CTACAGGCCCAAAAACTCAGAAAACGGCGTCGTTGGCCTTAGGTTTTTT
* *
40716080 GCGGCGCTTTTCAGAAAACGCCGCTAAAGGCAAGAGCATTTGCGGCGCTTTTC-AAAAACGCCGA
1 GCGGCGCTTTTCAGAAAACGCCGCTAAAGGCAAGAGCATTAGCGGCGCTTTTCAAAAAACGCCGC
*
40716144 TATAGGCCCAAAAACTCAGAAAACGGCGTCGTTGGCCTTAGGTTTTTT
66 TACAGGCCCAAAAACTCAGAAAACGGCGTCGTTGGCCTTAGGTTTTTT
* * *
40716192 GCTGCGCTTTTCAGAAAACGTCGCTAAAGGCAAGAGCATTAGCGGCGATTTTCAAAAAACGCCGC
1 GCGGCGCTTTTCAGAAAACGCCGCTAAAGGCAAGAGCATTAGCGGCGCTTTTCAAAAAACGCCGC
* * *
40716257 TACAGGCCCAAAAACTCAGAAAA---CGACATTGGCCTTAAGTTTTTT
66 TACAGGCCCAAAAACTCAGAAAACGGCGTCGTTGGCCTTAGGTTTTTT
* ** *
40716302 GCGGCGCTTTTCAGAAAACGCCGCT-AAGTCCCCCGAGCATTAGCGGCGCTTTTCAAAAAACGTC
1 GCGGCGCTTTTCAGAAAACGCCGCTAAAG--GCAAGAGCATTAGCGGCGCTTTTCAAAAAACGCC
* * *
40716366 GCTACAGGCCCAAAAACACAGAAAACAGCGTCGTTGGCCTTAGGTCTTTT
64 GCTACAGGCCCAAAAACTCAGAAAACGGCGTCGTTGGCCTTAGGTTTTTT
* *
40716416 GCGGCGCTTTTAATAAAACGCCGCTAA
1 GCGGCGCTTTTCAGAAAACGCCGCTAA
40716443 TGCTTATTAT
Statistics
Matches: 323, Mismatches: 32, Indels: 14
0.88 0.09 0.04
Matches are distributed among these distances:
109 3 0.01
110 42 0.13
111 53 0.16
112 108 0.33
113 75 0.23
114 41 0.13
115 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (113 bp):
GCGGCGCTTTTCAGAAAACGCCGCTAAAGGCAAGAGCATTAGCGGCGCTTTTCAAAAAACGCCGC
TACAGGCCCAAAAACTCAGAAAACGGCGTCGTTGGCCTTAGGTTTTTT
Found at i:40717761 original size:21 final size:21
Alignment explanation
Indices: 40717712--40717789 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 21
40717702 ATCTTCAAGG
*
40717712 ATATGTAATCGTAGATATG--
1 ATATGTAATCTTAGATATGAT
*
40717731 ATATGCAATCTTAGATATGAT
1 ATATGTAATCTTAGATATGAT
40717752 ATATGTAATCTTAGAAGATATGAT
1 ATATGTAATCTT---AGATATGAT
*
40717776 -TTTGTAATCTTAGA
1 ATATGTAATCTTAGA
40717790 GATTTTATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
19 17 0.34
20 3 0.06
21 11 0.22
23 10 0.20
24 9 0.18
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (21 bp):
ATATGTAATCTTAGATATGAT
Found at i:40717770 original size:24 final size:23
Alignment explanation
Indices: 40717724--40717789 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
40717714 ATGTAATCGT
*
40717724 AGATATGA-TATGCAATCTT---
1 AGATATGATTATGTAATCTTAGA
40717743 AGATATGATATATGTAATCTTAGA
1 AGATATGAT-TATGTAATCTTAGA
*
40717767 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
40717790 GATTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.20
21 10 0.25
23 13 0.32
24 9 0.22
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:40717785 original size:23 final size:24
Alignment explanation
Indices: 40717743--40717789 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
40717733 ATGCAATCTT
40717743 AGATATGATATATGTAATCTTAGA
1 AGATATGATATATGTAATCTTAGA
*
40717767 AGATATGAT-TTTGTAATCTTAGA
1 AGATATGATATATGTAATCTTAGA
40717790 GATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (24 bp):
AGATATGATATATGTAATCTTAGA
Found at i:40717802 original size:21 final size:21
Alignment explanation
Indices: 40717737--40717802 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
40717727 TATGATATGC
* *
40717737 AATCTTAGATATGA-TATATGT
1 AATCTTAGAGAT-ATTATTTGT
*
40717758 AATCTTAGAAGATATGATTTTGT
1 AATCTTAG-AGATATTA-TTTGT
*
40717781 AATCTTAGAGATTTTATTTGT
1 AATCTTAGAGATATTATTTGT
40717802 A
1 A
40717803 GATACCCTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 15 0.41
22 10 0.27
23 12 0.32
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
AATCTTAGAGATATTATTTGT
Found at i:40718033 original size:23 final size:23
Alignment explanation
Indices: 40717992--40718036 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
40717982 TCTTATTTTG
*
40717992 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTTATTTA
**
40718015 TTGATTTGTATATTTTTTATTT
1 TTGATTTGTATATAATTTATTT
40718037 CAAATCTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (23 bp):
TTGATTTGTATATAATTTATTTA
Found at i:40721929 original size:62 final size:62
Alignment explanation
Indices: 40721832--40721955 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 62
40721822 TTCGGCTTTC
40721832 GGTCGTCAATCCTCGGTGATGACTTCCTCGGCCATCCGCGGCGATTAGGGCTCGCAAATAGG
1 GGTCGTCAATCCTCGGTGATGACTTCCTCGGCCATCCGCGGCGATTAGGGCTCGCAAATAGG
* *
40721894 GGTCGTCAATCCTCGGTGCTGCCTTCCTCGGCCATCCGCGGCGATTAGGGCTCGCAAATAGG
1 GGTCGTCAATCCTCGGTGATGACTTCCTCGGCCATCCGCGGCGATTAGGGCTCGCAAATAGG
40721956 TTTTTCCTTC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.23
Consensus pattern (62 bp):
GGTCGTCAATCCTCGGTGATGACTTCCTCGGCCATCCGCGGCGATTAGGGCTCGCAAATAGG
Found at i:40722792 original size:44 final size:44
Alignment explanation
Indices: 40722743--40722927 Score: 108
Period size: 44 Copynumber: 4.2 Consensus size: 44
40722733 TATCTTGGAA
* *
40722743 AGATAAGATTCGCCGTCTTCGATCTACTCCACTACTGCTTAGAG
1 AGATAAGATTCGCCATCTTCAATCTACTCCACTACTGCTTAGAG
* * * * * * *
40722787 AGATAAGATCCACAATCTTCAACCTTCTCCACTACTGCTCAGGG
1 AGATAAGATTCGCCATCTTCAATCTACTCCACTACTGCTTAGAG
* * **** * *
40722831 AGACAAGGCTT-GGTGGC-TCAAATCTACTTCCCACTA-T-CTTGGAA
1 AGATAA-GATTCGCCATCTTC-AATCTAC-T-CCACTACTGCTTAGAG
** * * *
40722875 AGATAAGATTCGCCATCTTTGATCTGCTCCACTACTACTTAGGG
1 AGATAAGATTCGCCATCTTCAATCTACTCCACTACTGCTTAGAG
40722919 AGATAAGAT
1 AGATAAGAT
40722928 GTATAATCTT
Statistics
Matches: 98, Mismatches: 35, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
42 6 0.06
43 7 0.07
44 74 0.76
45 5 0.05
46 6 0.06
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
AGATAAGATTCGCCATCTTCAATCTACTCCACTACTGCTTAGAG
Found at i:40722867 original size:132 final size:132
Alignment explanation
Indices: 40722629--40722977 Score: 538
Period size: 132 Copynumber: 2.6 Consensus size: 132
40722619 AGATTGGATA
* * *
40722629 CGATCTGCTCCACTACTGCTTTA-AGGAAATAAGATCTACAATCTTCAACTTTCTCCGCTGCTAC
1 CGATCTGCTCCACTACTGC-TTAGA-GAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGC
* * *
40722693 TCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCG
64 TCAGGGAGACAAGGCTTGGTGGCTCAAATCTACTTCCCACTATCTTGGAAAGATAAGATTCGCCA
40722758 TCTT
129 TCTT
* * * *
40722762 CGATCTACTCCACTACTGCTTAGAGAGATAAGATCCACAATCTTCAACCTTCTCCACTACTGCTC
1 CGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
40722827 AGGGAGACAAGGCTTGGTGGCTCAAATCTACTTCCCACTATCTTGGAAAGATAAGATTCGCCATC
66 AGGGAGACAAGGCTTGGTGGCTCAAATCTACTTCCCACTATCTTGGAAAGATAAGATTCGCCATC
40722892 TT
131 TT
* * * * *
40722894 TGATCTGCTCCACTACTACTTAGGGAGATAAGATGTATAATCTTCAACCTTCTCCGCTGCTGCTC
1 CGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
40722959 AGGGAGACAAGGCTTGGTG
66 AGGGAGACAAGGCTTGGTG
40722978 TTTCACCGGT
Statistics
Matches: 196, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
132 177 0.90
133 19 0.10
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (132 bp):
CGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTC
AGGGAGACAAGGCTTGGTGGCTCAAATCTACTTCCCACTATCTTGGAAAGATAAGATTCGCCATC
TT
Found at i:40734838 original size:13 final size:12
Alignment explanation
Indices: 40734808--40734845 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
40734798 ATCGCATAAG
40734808 AATAATATAAACA
1 AATAA-ATAAACA
40734821 AATAAATAAACA
1 AATAAATAAACA
40734833 AGATAAA-AAACA
1 A-ATAAATAAACA
40734845 A
1 A
40734846 TAATCCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.16
Consensus pattern (12 bp):
AATAAATAAACA
Found at i:40737585 original size:19 final size:21
Alignment explanation
Indices: 40737548--40737586 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40737538 TGGAGGGGTT
*
40737548 GAAATTGTATAAATTGAAATC
1 GAAATTGTATAAATAGAAATC
40737569 GAAATTGTA-AAA-AGAAAT
1 GAAATTGTATAAATAGAAAT
40737587 AAAATTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.54, C:0.03, G:0.15, T:0.28
Consensus pattern (21 bp):
GAAATTGTATAAATAGAAATC
Found at i:40738334 original size:12 final size:12
Alignment explanation
Indices: 40738319--40738347 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40738309 ATTAAATCTA
40738319 AATAATAATCCT
1 AATAATAATCCT
40738331 AATAATAATCCT
1 AATAATAATCCT
40738343 AATAA
1 AATAA
40738348 AATTCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAATAATCCT
Found at i:40747102 original size:33 final size:34
Alignment explanation
Indices: 40747054--40747124 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
40747044 ATACAACATG
* * *
40747054 CAGTAACAGTCTGGGCCTGAGCCCTATTCAGTAT
1 CAGTAACAGTCTGGGCCTGAGCCCAATACAGTAA
* *
40747088 CAGT-ACAGTGTGGGCCTTAGCCCAATACAGTAA
1 CAGTAACAGTCTGGGCCTGAGCCCAATACAGTAA
40747121 CAGT
1 CAGT
40747125 GTAATAATGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (34 bp):
CAGTAACAGTCTGGGCCTGAGCCCAATACAGTAA
Found at i:40747497 original size:27 final size:27
Alignment explanation
Indices: 40747436--40747512 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
40747426 ATTTAATCTC
**
40747436 ATAGGGGTATAACAATCATTTTACCCT
1 ATAGGGGTATTTCAATCATTTTACCCT
*
40747463 AT-GAGGGTATTTCAATCATTTTGCCCT
1 ATAG-GGGTATTTCAATCATTTTACCCT
*
40747490 ATAGGGGTATTTCAGTCATTTTA
1 ATAGGGGTATTTCAATCATTTTA
40747513 TTAACCTCAC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
26 1 0.02
27 41 0.95
28 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (27 bp):
ATAGGGGTATTTCAATCATTTTACCCT
Found at i:40754625 original size:26 final size:26
Alignment explanation
Indices: 40754596--40754650 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
40754586 AACACACCAA
* *
40754596 TATCGCAGCAAAGCTGCCAGTATCAG
1 TATCGCAACAAAGCTGCCAGTAACAG
*
40754622 TATCGTAACAAAGCTGCCAGTAACAG
1 TATCGCAACAAAGCTGCCAGTAACAG
40754648 TAT
1 TAT
40754651 ATGTGCCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (26 bp):
TATCGCAACAAAGCTGCCAGTAACAG
Found at i:40754852 original size:27 final size:26
Alignment explanation
Indices: 40754813--40754953 Score: 104
Period size: 27 Copynumber: 5.2 Consensus size: 26
40754803 TAATCTCCTA
** * * *
40754813 GGGGTATAACAGTTATTTTAACTTAT
1 GGGGTATTTCAGTCATTTTACCATAT
40754839 GGGGATATTTCAGTCATTTTACCATAT
1 GGGG-TATTTCAGTCATTTTACCATAT
* * *
40754866 CAGGGTATTTCACTCATTTTACCCTAT
1 -GGGGTATTTCAGTCATTTTACCATAT
* * *
40754893 GGGGGTATTTCGGTTATTTTACCCTAT
1 -GGGGTATTTCAGTCATTTTACCATAT
* *
40754920 AAGGGTATTTC-GATCATTTTACCCTAT
1 -GGGGTATTTCAG-TCATTTTACCATAT
40754947 AGGGGTA
1 -GGGGTA
40754954 CTTCGATTAT
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
26 5 0.05
27 87 0.92
28 3 0.03
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (26 bp):
GGGGTATTTCAGTCATTTTACCATAT
Found at i:40754952 original size:54 final size:54
Alignment explanation
Indices: 40754839--40754967 Score: 170
Period size: 54 Copynumber: 2.4 Consensus size: 54
40754829 TTTAACTTAT
* * * *
40754839 GGGGATATTTCAGTCATTTTACCATATCAGGGTATTTCACTCATTTTACCCTATG
1 GGGG-TATTTCGGTTATTTTACCATATAAGGGTATTTCACTCATTTTACCCTATA
*
40754894 GGGGTATTTCGGTTATTTTACCCTATAAGGGTATTTCGA-TCATTTTACCCTATA
1 GGGGTATTTCGGTTATTTTACCATATAAGGGTATTTC-ACTCATTTTACCCTATA
* *
40754948 GGGGTACTTCGATTATTTTA
1 GGGGTATTTCGGTTATTTTA
40754968 TTGACCTCAC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
54 61 0.92
55 5 0.08
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (54 bp):
GGGGTATTTCGGTTATTTTACCATATAAGGGTATTTCACTCATTTTACCCTATA
Found at i:40754958 original size:27 final size:27
Alignment explanation
Indices: 40754839--40754967 Score: 138
Period size: 27 Copynumber: 4.7 Consensus size: 27
40754829 TTTAACTTAT
*
40754839 GGGGATATTTC-AGTCATTTTACCATATCA
1 GGGG-TATTTCGA-TCATTTTACCCTAT-A
*
40754868 -GGGTATTTC-ACTCATTTTACCCTATG
1 GGGGTATTTCGA-TCATTTTACCCTATA
* *
40754894 GGGGTATTTCGGTTATTTTACCCTATA
1 GGGGTATTTCGATCATTTTACCCTATA
*
40754921 AGGGTATTTCGATCATTTTACCCTATA
1 GGGGTATTTCGATCATTTTACCCTATA
* *
40754948 GGGGTACTTCGATTATTTTA
1 GGGGTATTTCGATCATTTTA
40754968 TTGACCTCAC
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
27 83 0.97
28 3 0.03
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (27 bp):
GGGGTATTTCGATCATTTTACCCTATA
Found at i:40775034 original size:28 final size:29
Alignment explanation
Indices: 40775001--40775055 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
40774991 ACCAAAAATT
40775001 TATTTTAAAAAT-AAAAAATAAAAAAAAG
1 TATTTTAAAAATAAAAAAATAAAAAAAAG
* *
40775029 TATTTTAAAATTAAAAAAATTAAAAAA
1 TATTTTAAAAATAAAAAAATAAAAAAA
40775056 TATATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (29 bp):
TATTTTAAAAATAAAAAAATAAAAAAAAG
Found at i:40778184 original size:42 final size:41
Alignment explanation
Indices: 40778030--40778185 Score: 147
Period size: 42 Copynumber: 3.7 Consensus size: 41
40778020 TGTGTTATCG
* *
40778030 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATT--GATTCA
* * * *
40778072 TGTATAAGACCATGTCTGGGACATCGACATC-ATATTTGATTTCG
1 TG--TAAGACCACGTCTGGGACATTGGCATCGATA-TTGA-TTCA
* *
40778116 TGTAAGACC-CTGTCTAGGACAGTGGCATCGATATTGATTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGATATTGATT-CA
40778158 TGTAAGACCACGTCTGGGACATTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
40778186 TGTACGAGTT
Statistics
Matches: 91, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
41 2 0.02
42 52 0.57
43 8 0.09
44 27 0.30
45 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATATTGATTCA
Found at i:40785007 original size:512 final size:508
Alignment explanation
Indices: 40784042--40785066 Score: 1727
Period size: 512 Copynumber: 2.0 Consensus size: 508
40784032 CAAAAGAAAA
40784042 TGAAATCTGAAAGTAAGAGATTCTCGAAATCTTTTTGTTCCTAAAACTTGTATTACATGGAGAAA
1 TGAAATCTGAAAGTAAGAGATTCTCGAAATCTTTTTGTTCCTAAAACTTGTATTACATGGAGAAA
*
40784107 AAAGAAAAGAAAAGTAGGTGTTTGTGCTCTTTTTTTAACGAGGTAGATTAAATGTTAAATCTAAA
66 AAAGAAAAGAAAAGTAGGTGTGTGTGCTCTTTTTTTAACGAGGTAGATTAAATGTTAAATCTAAA
40784172 ACTTAGATTTATTCATTTTGATCTAAATTTAAAAAAAATTAATTCTCATTATTCTCATTTTAAGA
131 ACTTAGATTTATTCATTTTGATCTAAATTTAAAAAAAATTAATTCTCATTATTCTCATTTTAAGA
* *
40784237 GTTTTGTGATTTACCCAATTCACTACGAATTTGTTGGTAAAACCAAAGGTTTCAGTCCCCGGCAA
196 GTTTTGTGATTTACCCAATTCACTACGAATTTGTTGGTAAAACCAAAGGTTTCAATCCCCAGCAA
*
40784302 CAACGCCAAAAAACTTGACTGTCTCTAAAAATGTTATCGTTTAGAGTATAAATATCACACCAAAA
261 CAACGCCAAAAAACTTGACTGTCTCTAAAAATGTTACCGTTTAGAGTATAAATATCACACCAAAA
* * ** *
40784367 ATATATAATTAAATCAGTGGTGTTTGCAAGTATATGGGTCAAATTATAGTATAGTAGTGTTACAA
326 ACATATAATTAAATCAGTAGTGTTCACAAGTATACGGGTCAAATTATAGTATAGTAGTGTTACAA
* * *
40784432 CAAAACATTGGTAAGTATTTTGAGGATCGTACCCAAGGAATTGCATTTTGGAGAATCTTATTATT
391 CAAAACACTGGTAAGTATTTTGAGGATCGTACCCAAGGAATTGCATATTGGAGAATCTTATTATG
* *
40784497 AAATTAATCACAGAAATAAATTACTAGTCTAATCGAGTCACAAGTTAGTTGTT
456 AAATTAATCACAGAAATAAATTACTAATCTAATCGAGTCACAAGTTAGTAGTT
40784550 TGAAATCTGAAAGTAAGAGATTCTCGAAATCTTTTTGTTCCTAAAACTTGTATTACATGGAGAAA
1 TGAAATCTGAAAGTAAGAGATTCTCGAAATCTTTTTGTTCCTAAAACTTGTATTACATGGAGAAA
40784615 AAAGAAAAGAAAAGTAGGTG-GTGTGCTCTTTATTTTAACGAGGTAGATTAAATGTTAAATCTAA
66 AAAGAAAAGAAAAGTAGGTGTGTGTGCTCTTT-TTTTAACGAGGTAGATTAAATGTTAAATCTAA
*
40784679 AACTTAGATTTATTCATTTTGATCTAAATTTTTTTTAAAAAAATTAATTCTCATTATTCTCATTT
130 AACTTAGATTTATTCATTTTGATCTAAA----TTTAAAAAAAATTAATTCTCATTATTCTCATTT
40784744 TAAGAGTTTTGTGATTTACCCAATTCACTACGAATATTTGTTGGTAAAACCAAAGGTTTCAATCC
191 TAAGAGTTTTGTGATTTACCCAATTCACTACG-A-ATTTGTTGGTAAAACCAAAGGTTTCAATCC
* * ** *
40784809 CCAGCAACAATGCC-AAAAACTTGGCTGTCTCTAAATGTGTTACCGTTTAGAGTTTAAATA-CTA
254 CCAGCAACAACGCCAAAAAACTTGACTGTCTCTAAAAATGTTACCGTTTAGAGTATAAATATC-A
40784872 CACCAAAAACATATAATTAAATCAGTAGTG-TCACAAGTATACGGGTTC-AATTATAGTATAGTA
318 CACCAAAAACATATAATTAAATCAGTAGTGTTCACAAGTATACGGG-TCAAATTATAGTATAGTA
* *
40784935 GTGTTACAACGAAACACTGGTAAGTATTTTGAGGATCGTACCCAAGGAATTTCATATTGGAGAAT
382 GTGTTACAACAAAACACTGGTAAGTATTTTGAGGATCGTACCCAAGGAATTGCATATTGGAGAAT
*
40785000 CTTATTATGAAATTAATCACAGAAATAAATTACTAATCTAATTGAGTCACAAGTTAGTAGTT
447 CTTATTATGAAATTAATCACAGAAATAAATTACTAATCTAATCGAGTCACAAGTTAGTAGTT
40785062 TGAAA
1 TGAAA
40785067 GCTATTAATG
Statistics
Matches: 485, Mismatches: 23, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
507 10 0.02
508 145 0.30
512 216 0.45
513 73 0.15
514 41 0.08
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (508 bp):
TGAAATCTGAAAGTAAGAGATTCTCGAAATCTTTTTGTTCCTAAAACTTGTATTACATGGAGAAA
AAAGAAAAGAAAAGTAGGTGTGTGTGCTCTTTTTTTAACGAGGTAGATTAAATGTTAAATCTAAA
ACTTAGATTTATTCATTTTGATCTAAATTTAAAAAAAATTAATTCTCATTATTCTCATTTTAAGA
GTTTTGTGATTTACCCAATTCACTACGAATTTGTTGGTAAAACCAAAGGTTTCAATCCCCAGCAA
CAACGCCAAAAAACTTGACTGTCTCTAAAAATGTTACCGTTTAGAGTATAAATATCACACCAAAA
ACATATAATTAAATCAGTAGTGTTCACAAGTATACGGGTCAAATTATAGTATAGTAGTGTTACAA
CAAAACACTGGTAAGTATTTTGAGGATCGTACCCAAGGAATTGCATATTGGAGAATCTTATTATG
AAATTAATCACAGAAATAAATTACTAATCTAATCGAGTCACAAGTTAGTAGTT
Found at i:40796143 original size:11 final size:11
Alignment explanation
Indices: 40796129--40796156 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40796119 TTTTTTTTTG
40796129 ATATTTTTATA
1 ATATTTTTATA
40796140 ATATTTTTATA
1 ATATTTTTATA
40796151 ATATTT
1 ATATTT
40796157 ATATTTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTTTTATA
Found at i:40797223 original size:16 final size:18
Alignment explanation
Indices: 40797202--40797235 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40797192 TTATTTGACA
40797202 AATTAA-ACT-AATTTAT
1 AATTAACACTAAATTTAT
40797218 AATTAACACTAAATTTAT
1 AATTAACACTAAATTTAT
40797236 TTTATTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTAACACTAAATTTAT
Found at i:40798891 original size:25 final size:24
Alignment explanation
Indices: 40798850--40798896 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
40798840 ATTTAATTCT
*
40798850 TTTTCTTTTACTTCTTTCATTTTCC
1 TTTTCTTTTACTCCTTT-ATTTTCC
40798875 TTTTCTTCTT-CTCCTTTATTTT
1 TTTTCTT-TTACTCCTTTATTTT
40798897 TCTCTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 13 0.65
26 2 0.10
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTCTTTTACTCCTTTATTTTCC
Found at i:40801704 original size:45 final size:45
Alignment explanation
Indices: 40801639--40801794 Score: 135
Period size: 45 Copynumber: 3.5 Consensus size: 45
40801629 GATCCACTCT
* * * *
40801639 ACTGCAACGTCAGAGAGATAAGATTCGTC-ATCTTCTGTCTGCCCC
1 ACTGCAACTTCA-AGGGATAAGATTCGTCAATCTTCAGTCTGCTCC
*
40801684 ACTGCAACTTCAAAGGGATAAGA--CCTGCAATCTTCAGTCTGCTCC
1 ACTGCAACTTC-AAGGGATAAGATTCGT-CAATCTTCAGTCTGCTCC
* * *
40801729 AC-GTAACTTC-AGGGACATAAGATTCG-CTATCTTCAGCCTGCTCC
1 ACTGCAACTTCAAGGG--ATAAGATTCGTCAATCTTCAGTCTGCTCC
*
40801773 ACTGCAACTTTAAGGAGATAAG
1 ACTGCAACTTCAAGG-GATAAG
40801795 GCTTGTAGCT
Statistics
Matches: 90, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
42 4 0.04
43 2 0.02
44 32 0.36
45 46 0.51
46 5 0.06
47 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (45 bp):
ACTGCAACTTCAAGGGATAAGATTCGTCAATCTTCAGTCTGCTCC
Found at i:40802451 original size:264 final size:264
Alignment explanation
Indices: 40801981--40802470 Score: 719
Period size: 264 Copynumber: 1.9 Consensus size: 264
40801971 TAATGCCAAA
** * *
40801981 GAGATAGGACTGGTGGTTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAAATTCATCGTCTTT
1 GAGATAGGACTGGTGACTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAAATTCACCGTATTT
* * * * *
40802046 GATCTGCTCCACTACTGCTTAAGGAGACAGTATCTACATTCTTCAACCTATTCCACTGCTGCTCA
66 GATCTGCTCCACTACTGCTTAAGGAGACAGGATCCACAATCCTCAACCTACTCCACTGCTGCTCA
* * *
40802111 AGGACATAGGACTGGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGATAATATTCGCCATCT
131 AGGACATAGGACTGGTGGCTTAAATATACTTCCCTACTACCTTGGGAAGATAAGATTCACCATCT
*
40802176 TCAATCTGCTCCACTACTGCTTAGGGAGACAAGATATACATTCTTCAACCTACTCCACTATTGCT
196 TCAATCTGCTCCACTAATGCTTAGGGAGACAAGATATACATTCTTCAACCTACTCCACTATTGCT
40802241 CAGG
261 CAGG
* *
40802245 GAGATAGGATTGGTGACTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTATTT
1 GAGATAGGACTGGTGACTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAAATTCACCGTATTT
** * * *
40802310 GATCTGCTCCACTACTTTTTAGGGAGACAGGATCCACAATCCTCAATCTACTCCACTGCTGCTGA
66 GATCTGCTCCACTACTGCTTAAGGAGACAGGATCCACAATCCTCAACCTACTCCACTGCTGCTCA
* * * * * * *
40802375 GGGAGATAGGATTGGTGGCTTAAATCTATTTCCCTACTACCTTGGGAAGATAAGATTTACCGTCT
131 AGGACATAGGACTGGTGGCTTAAATATACTTCCCTACTACCTTGGGAAGATAAGATTCACCATCT
* *
40802440 TCGATCTGCTCCACTAATGCTTAGGGGGACA
196 TCAATCTGCTCCACTAATGCTTAGGGAGACA
40802471 GGACTGGTGG
Statistics
Matches: 197, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
264 197 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (264 bp):
GAGATAGGACTGGTGACTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAAATTCACCGTATTT
GATCTGCTCCACTACTGCTTAAGGAGACAGGATCCACAATCCTCAACCTACTCCACTGCTGCTCA
AGGACATAGGACTGGTGGCTTAAATATACTTCCCTACTACCTTGGGAAGATAAGATTCACCATCT
TCAATCTGCTCCACTAATGCTTAGGGAGACAAGATATACATTCTTCAACCTACTCCACTATTGCT
CAGG
Found at i:40802472 original size:132 final size:132
Alignment explanation
Indices: 40801981--40802473 Score: 653
Period size: 132 Copynumber: 3.7 Consensus size: 132
40801971 TAATGCCAAA
* * * *
40801981 GAGATAGGACTGGTGGTTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAAATTCATCGTCTTT
1 GAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTCTTC
* * *
40802046 GATCTGCTCCACTACTGCTTAAGGAGACAGTATCTACATTCTTCAACCTATTCCACTGCTGCTCA
66 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACATTCTTCAACCTACTCCACTGCTGCTCA
*
40802111 AG
131 GG
* * * * * *
40802113 GACATAGGACTGGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGATAATATTCGCCATCTTC
1 GAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTCTTC
* * * **
40802178 AATCTGCTCCACTACTGCTTAGGGAGACAAGATATACATTCTTCAACCTACTCCACTATTGCTCA
66 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACATTCTTCAACCTACTCCACTGCTGCTCA
40802243 GG
131 GG
* * * *
40802245 GAGATAGGATTGGTGACTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTATTT
1 GAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTCTTC
** * * * * *
40802310 GATCTGCTCCACTACTTTTTAGGGAGACAGGATCCACAATCCTCAATCTACTCCACTGCTGCTGA
66 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACATTCTTCAACCTACTCCACTGCTGCTCA
40802375 GG
131 GG
* ** * *
40802377 GAGATAGGATTGGTGGCTTAAATCTATTTCCCTACTACCTTGGGAAGATAAGATTTACCGTCTTC
1 GAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTCTTC
* *
40802442 GATCTGCTCCACTAATGCTTAGGGGGACAGGA
66 GATCTGCTCCACTACTGCTTAGGGAGACAGGA
40802474 CTGGTGGCTT
Statistics
Matches: 310, Mismatches: 51, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
132 310 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (132 bp):
GAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTCTTC
GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACATTCTTCAACCTACTCCACTGCTGCTCA
GG
Found at i:40802509 original size:88 final size:88
Alignment explanation
Indices: 40802355--40802554 Score: 274
Period size: 88 Copynumber: 2.3 Consensus size: 88
40802345 ACAATCCTCA
* * * * * * * *
40802355 ATCTACTCCACTGCTGCTGAGGGAGATAGGATTGGTGGCTTAAATCTATTTCCCTACTACCTTGG
1 ATCTGCTCCACTACTGCTTAGGGGGACAGGACTGGTGGCTTAAATATACTTCCCTACTACCTTGG
*
40802420 GAAGATAAGATTTACCGTCTTCG
66 GAAGATAAGATTCACCGTCTTCG
* *
40802443 ATCTGCTCCACTAATGCTTAGGGGGACAGGACTGGTGGCTTAAATATGCTTCCCTACTACCTTGG
1 ATCTGCTCCACTACTGCTTAGGGGGACAGGACTGGTGGCTTAAATATACTTCCCTACTACCTTGG
**
40802508 GAAGATAAGATTCGTCGTCTTCG
66 GAAGATAAGATTCACCGTCTTCG
*
40802531 ATTTGCTCCACTACTGCTTAGGGG
1 ATCTGCTCCACTACTGCTTAGGGG
40802555 TACAAGATCT
Statistics
Matches: 97, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 97 1.00
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (88 bp):
ATCTGCTCCACTACTGCTTAGGGGGACAGGACTGGTGGCTTAAATATACTTCCCTACTACCTTGG
GAAGATAAGATTCACCGTCTTCG
Found at i:40802562 original size:132 final size:132
Alignment explanation
Indices: 40802437--40802783 Score: 444
Period size: 132 Copynumber: 2.6 Consensus size: 132
40802427 AGATTTACCG
* * * * *
40802437 TCTTCGATCTGCTCCACTAATGCTTAGGGGGACAGGACTGGTGGCTTAAATATGCTTCCCTACTA
1 TCTTCAATCTACTCCACTAATGCTCAGGGAGACAGGACTGGTGGCTTAAATCTGCTTCCCTACTA
** * * *
40802502 CCTTGGGAAGATAAGATTCGTCGTCTTCGATTTGCTCCACTACTGCTTAGGG-GTACAAGATCTA
66 CCTTGGGAAGATAAGATTCACCGTATTCGATCTACTCCACTACTGCTTAGGGAG-ACAAGATCTA
*
40802566 CAT
130 CAA
* * * * * * *
40802569 TCTTCAACCTACTCCACTATTGCTCATGGAGATAGGATTGGTGACTTAAATCTACTTCCCTACTA
1 TCTTCAATCTACTCCACTAATGCTCAGGGAGACAGGACTGGTGGCTTAAATCTGCTTCCCTACTA
* * * *
40802634 CCTTGGGAAGATAAGATTCACCGTATTTGATCTACTCCACTACTGTTTAGGGAGACAGGATCCAC
66 CCTTGGGAAGATAAGATTCACCGTATTCGATCTACTCCACTACTGCTTAGGGAGACAAGATCTAC
40802699 AA
131 AA
* ** *
40802701 TCCTCAATCTACTCCACTGCTGCTCAGGGAGACAGGACTGGTGGCTTAAATCTGTTTCCCTACTA
1 TCTTCAATCTACTCCACTAATGCTCAGGGAGACAGGACTGGTGGCTTAAATCTGCTTCCCTACTA
40802766 CCTTGGGAAGATAAGATT
66 CCTTGGGAAGATAAGATT
40802784 TTCCGTCTTC
Statistics
Matches: 182, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
132 181 0.99
133 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (132 bp):
TCTTCAATCTACTCCACTAATGCTCAGGGAGACAGGACTGGTGGCTTAAATCTGCTTCCCTACTA
CCTTGGGAAGATAAGATTCACCGTATTCGATCTACTCCACTACTGCTTAGGGAGACAAGATCTAC
AA
Found at i:40802610 original size:220 final size:220
Alignment explanation
Indices: 40802225--40802693 Score: 634
Period size: 220 Copynumber: 2.1 Consensus size: 220
40802215 ATTCTTCAAC
* * * * *
40802225 CTACTCCACTATTGCTCAGGGAGATAGGATTGGTGACTTAAATCTGCTTCCCTACTACCTTGGAA
1 CTACTCCACTAATGCTTAGGGAGACAGGACTGGTGACTTAAATATGCTTCCCTACTACCTTGGAA
* ** *
40802290 AGATAAGATTCACCGTATTTGATCTGCTCCACTACTTTTTAGGGAGACAGGATCCACAATCCTCA
66 AGATAAGATTCACCGTATTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCCACAATCCTCA
* * * * *
40802355 ATCTACTCCACTGCTGCTGAGGGAGATAGGATTGGTGGCTTAAATCTATTTCCCTACTACCTTGG
131 ACCTACTCCACTACTGCTCAGGGAGATAGGATTGGTGACTTAAATCTACTTCCCTACTACCTTGG
* *
40802420 GAAGATAAGATTTACCGTCTTCGAT
196 GAAGATAAGATTCACCGTATTCGAT
* * * *
40802445 CTGCTCCACTAATGCTTAGGGGGACAGGACTGGTGGCTTAAATATGCTTCCCTACTACCTTGGGA
1 CTACTCCACTAATGCTTAGGGAGACAGGACTGGTGACTTAAATATGCTTCCCTACTACCTTGGAA
** * * * * *
40802510 AGATAAGATTCGTCGTCTTCGATTTGCTCCACTACTGCTTAGGG-GTACAAGATCTACATTCTTC
66 AGATAAGATTCACCGTATTCGATCTGCTCCACTACTGCTTAGGGAG-ACAAGATCCACAATCCTC
* *
40802574 AACCTACTCCACTATTGCTCATGGAGATAGGATTGGTGACTTAAATCTACTTCCCTACTACCTTG
130 AACCTACTCCACTACTGCTCAGGGAGATAGGATTGGTGACTTAAATCTACTTCCCTACTACCTTG
*
40802639 GGAAGATAAGATTCACCGTATTTGAT
195 GGAAGATAAGATTCACCGTATTCGAT
* *
40802665 CTACTCCACTACTGTTTAGGGAGACAGGA
1 CTACTCCACTAATGCTTAGGGAGACAGGA
40802694 TCCACAATCC
Statistics
Matches: 214, Mismatches: 34, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
219 1 0.00
220 213 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (220 bp):
CTACTCCACTAATGCTTAGGGAGACAGGACTGGTGACTTAAATATGCTTCCCTACTACCTTGGAA
AGATAAGATTCACCGTATTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCCACAATCCTCA
ACCTACTCCACTACTGCTCAGGGAGATAGGATTGGTGACTTAAATCTACTTCCCTACTACCTTGG
GAAGATAAGATTCACCGTATTCGAT
Found at i:40802762 original size:352 final size:352
Alignment explanation
Indices: 40802118--40802801 Score: 1199
Period size: 352 Copynumber: 1.9 Consensus size: 352
40802108 TCAAGGACAT
*
40802118 AGGACTGGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGATAATATTCGCCATCTTCAATCT
1 AGGACTGGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCATCTTCAATCT
40802183 GCTCCACTACTGCTTAGGGAGACAAGATATACATTCTTCAACCTACTCCACTATTGCTCAGGGAG
66 GCTCCACTACTGCTTAGGGAGACAAGATATACATTCTTCAACCTACTCCACTATTGCTCAGGGAG
*
40802248 ATAGGATTGGTGACTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTATTTGAT
131 ATAGGATTGGTGACTTAAATCTACTTCCCTACTACCTTGGAAAGATAAGATTCACCGTATTTGAT
* * *
40802313 CTGCTCCACTACTTTTTAGGGAGACAGGATCCACAATCCTCAATCTACTCCACTGCTGCTGAGGG
196 CTACTCCACTACTGTTTAGGGAGACAGGATCCACAATCCTCAATCTACTCCACTGCTGCTCAGGG
* * *
40802378 AGATAGGATTGGTGGCTTAAATCTATTTCCCTACTACCTTGGGAAGATAAGATTTACCGTCTTCG
261 AGACAGGACTGGTGGCTTAAATCTATTTCCCTACTACCTTGGGAAGATAAGATTTACCGTCTTCA
40802443 ATCTGCTCCACTAATGCTTAGGGGGAC
326 ATCTGCTCCACTAATGCTTAGGGGGAC
* * * *
40802470 AGGACTGGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGATAAGATTCGTCGTCTTCGATTT
1 AGGACTGGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCATCTTCAATCT
* *
40802535 GCTCCACTACTGCTTAGGG-GTACAAGATCTACATTCTTCAACCTACTCCACTATTGCTCATGGA
66 GCTCCACTACTGCTTAGGGAG-ACAAGATATACATTCTTCAACCTACTCCACTATTGCTCAGGGA
*
40802599 GATAGGATTGGTGACTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTCACCGTATTTGA
130 GATAGGATTGGTGACTTAAATCTACTTCCCTACTACCTTGGAAAGATAAGATTCACCGTATTTGA
40802664 TCTACTCCACTACTGTTTAGGGAGACAGGATCCACAATCCTCAATCTACTCCACTGCTGCTCAGG
195 TCTACTCCACTACTGTTTAGGGAGACAGGATCCACAATCCTCAATCTACTCCACTGCTGCTCAGG
* *
40802729 GAGACAGGACTGGTGGCTTAAATCTGTTTCCCTACTACCTTGGGAAGATAAGATTTTCCGTCTTC
260 GAGACAGGACTGGTGGCTTAAATCTATTTCCCTACTACCTTGGGAAGATAAGATTTACCGTCTTC
40802794 AATCTGCT
325 AATCTGCT
40802802 TTGCTGTCAG
Statistics
Matches: 314, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
351 1 0.00
352 313 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (352 bp):
AGGACTGGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCATCTTCAATCT
GCTCCACTACTGCTTAGGGAGACAAGATATACATTCTTCAACCTACTCCACTATTGCTCAGGGAG
ATAGGATTGGTGACTTAAATCTACTTCCCTACTACCTTGGAAAGATAAGATTCACCGTATTTGAT
CTACTCCACTACTGTTTAGGGAGACAGGATCCACAATCCTCAATCTACTCCACTGCTGCTCAGGG
AGACAGGACTGGTGGCTTAAATCTATTTCCCTACTACCTTGGGAAGATAAGATTTACCGTCTTCA
ATCTGCTCCACTAATGCTTAGGGGGAC
Found at i:40807211 original size:21 final size:21
Alignment explanation
Indices: 40807165--40807211 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40807155 ATAAATATTG
40807165 ATAATGAAAATAACCATAACA
1 ATAATGAAAATAACCATAACA
* * * *
40807186 GTAATGATAATAACCATTATA
1 ATAATGAAAATAACCATAACA
40807207 ATAAT
1 ATAAT
40807212 CTAAATTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (21 bp):
ATAATGAAAATAACCATAACA
Found at i:40808261 original size:17 final size:17
Alignment explanation
Indices: 40808239--40808276 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
40808229 TATTCTTTCA
*
40808239 AAATAAAAAATATAAAT
1 AAATAAAAAATAAAAAT
40808256 AAATAAAAAATAAAAAT
1 AAATAAAAAATAAAAAT
40808273 AAAT
1 AAAT
40808277 TAATCAATAA
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAAAAATAAAAAT
Found at i:40808285 original size:25 final size:24
Alignment explanation
Indices: 40808238--40808287 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
40808228 TTATTCTTTC
*
40808238 AAAATAAAAAATATAAATAAATAA
1 AAAATAAAAAAAATAAATAAATAA
* *
40808262 AAAATAAAAATAAATTAATCAATAA
1 AAAATAAAAA-AAATAAATAAATAA
40808287 A
1 A
40808288 TAGACCGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (24 bp):
AAAATAAAAAAAATAAATAAATAA
Found at i:40809165 original size:28 final size:27
Alignment explanation
Indices: 40809133--40809186 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
40809123 TCCATATTCT
40809133 TTCTTATTCTCTCTTTCTCTCTTCCCCA
1 TTCTTATTCTCTCTTTCTCTC-TCCCCA
* *
40809161 TTCTTCTTCTCTCTTTCTGTCTCCCC
1 TTCTTATTCTCTCTTTCTCTCTCCCC
40809187 TTTTAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.04, C:0.41, G:0.02, T:0.54
Consensus pattern (27 bp):
TTCTTATTCTCTCTTTCTCTCTCCCCA
Found at i:40818810 original size:7 final size:7
Alignment explanation
Indices: 40818793--40818860 Score: 63
Period size: 6 Copynumber: 9.7 Consensus size: 7
40818783 ATTTATCAAC
40818793 TTTTTATA
1 TTTTTA-A
40818801 TTTTTAA
1 TTTTTAA
40818808 -TTTTAA
1 TTTTTAA
*
40818814 TATTGATTTA
1 T-TT--TTAA
40818824 -TTTTAA
1 TTTTTAA
40818830 TTTTTAA
1 TTTTTAA
40818837 TTTTTAA
1 TTTTTAA
40818844 -TTTTAA
1 TTTTTAA
40818850 -TTTTAA
1 TTTTTAA
40818856 TTTTT
1 TTTTT
40818861 TAATCTTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
6 21 0.40
7 18 0.35
8 10 0.19
10 3 0.06
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (7 bp):
TTTTTAA
Found at i:40818813 original size:6 final size:6
Alignment explanation
Indices: 40818802--40818859 Score: 66
Period size: 6 Copynumber: 9.7 Consensus size: 6
40818792 CTTTTTATAT
* *
40818802 TTTTAA TTTTAA TATTGA -TTT-A TTTTAA TTTTTAA TTTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA -TTTTAA TTTTAA
40818850 TTTTAA TTTT
1 TTTTAA TTTT
40818860 TTAATCTTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
4 1 0.02
5 5 0.11
6 27 0.59
7 13 0.28
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:40818861 original size:20 final size:20
Alignment explanation
Indices: 40818802--40818864 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 20
40818792 CTTTTTATAT
40818802 TTTTAATTTTAATATTGATTT-A
1 TTTTAATTTTAAT-TT--TTTAA
40818824 TTTTAATTTTTAA-TTTTTAA
1 TTTTAA-TTTTAATTTTTTAA
40818844 TTTTAATTTTAATTTTTTAA
1 TTTTAATTTTAATTTTTTAA
40818864 T
1 T
40818865 CTTGTTATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
19 9 0.24
20 15 0.39
21 2 0.05
22 6 0.16
23 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTAATTTTAATTTTTTAA
Found at i:40820706 original size:6 final size:6
Alignment explanation
Indices: 40820695--40820739 Score: 67
Period size: 6 Copynumber: 7.7 Consensus size: 6
40820685 CTTTTTATAT
40820695 TTTTAA TTTTAA TTTTAA -TTT-A TTTTAA TTTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA TTTTAA TTTT
40820740 TTAATCTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 1 0.03
5 6 0.17
6 23 0.64
7 6 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:40820719 original size:16 final size:17
Alignment explanation
Indices: 40820700--40820732 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40820690 TATATTTTTA
40820700 ATTTTAA-TTTTAATTT
1 ATTTTAATTTTTAATTT
40820716 ATTTTAATTTTTAATTT
1 ATTTTAATTTTTAATTT
40820733 TAATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTAATTTTTAATTT
Found at i:40820727 original size:23 final size:22
Alignment explanation
Indices: 40820695--40820738 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
40820685 CTTTTTATAT
40820695 TTTTAATTTTAATTTTAATTTA
1 TTTTAATTTTAATTTTAATTTA
40820717 TTTTAATTTTTAATTTTAATTT
1 TTTTAA-TTTTAATTTTAATTT
40820739 TTTAATCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTAATTTTAATTTTAATTTA
Found at i:40823154 original size:25 final size:24
Alignment explanation
Indices: 40823109--40823175 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 24
40823099 CTGATTAACA
*
40823109 ACTCTTATGAGC-TCCCAATATTTG
1 ACTC-TATGAGCTTCCCGATATTTG
*
40823133 GCTCGTATGAGCTTCCCGATATTTG
1 ACTC-TATGAGCTTCCCGATATTTG
40823158 ACTCTCATGAGCTTCCCG
1 ACTCT-ATGAGCTTCCCG
40823176 TTACTTAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 11 0.30
25 26 0.70
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.34
Consensus pattern (24 bp):
ACTCTATGAGCTTCCCGATATTTG
Found at i:40823191 original size:25 final size:25
Alignment explanation
Indices: 40823139--40823199 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
40823129 TTTGGCTCGT
* *
40823139 ATGAGCTTCCCGATATTTGACTCTC
1 ATGAGCTTCCCGATATTAGACTCAC
*
40823164 ATGAGCTTCCCGTTACTTAG-CTCAC
1 ATGAGCTTCCCGATA-TTAGACTCAC
*
40823189 ATGATCTTCCC
1 ATGAGCTTCCC
40823200 CTTATATGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 28 0.90
26 3 0.10
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCCGATATTAGACTCAC
Found at i:40827051 original size:9 final size:9
Alignment explanation
Indices: 40827037--40827077 Score: 82
Period size: 9 Copynumber: 4.6 Consensus size: 9
40827027 TTCAGATCAT
40827037 ATTTGTTAA
1 ATTTGTTAA
40827046 ATTTGTTAA
1 ATTTGTTAA
40827055 ATTTGTTAA
1 ATTTGTTAA
40827064 ATTTGTTAA
1 ATTTGTTAA
40827073 ATTTG
1 ATTTG
40827078 GTTTAACTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (9 bp):
ATTTGTTAA
Found at i:40836511 original size:30 final size:31
Alignment explanation
Indices: 40836470--40836529 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
40836460 AGGGGTGGGA
*
40836470 TGGGAAGGGAGTAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAGTAAAAATTTTAGGGGAAAAG
*
40836501 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAGTAAAAATTTTAGGGGAAAA
40836530 TAAAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAGTAAAAATTTTAGGGGAAAAG
Found at i:40837374 original size:14 final size:14
Alignment explanation
Indices: 40837355--40837408 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
40837345 CACATTGGGT
40837355 TCACACTAAGGGGC
1 TCACACTAAGGGGC
* *
40837369 TCACACCAA-GAGC
1 TCACACTAAGGGGC
* *
40837382 TCACACAAAAGGGGT
1 TCACAC-TAAGGGGC
40837397 TCACACTAAGGG
1 TCACACTAAGGG
40837409 CTCGTACATG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 9 0.28
14 15 0.47
15 8 0.25
ACGTcount: A:0.35, C:0.28, G:0.24, T:0.13
Consensus pattern (14 bp):
TCACACTAAGGGGC
Found at i:40838155 original size:18 final size:18
Alignment explanation
Indices: 40838132--40838169 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
40838122 CTACACTTGT
40838132 TTTGAAGACACAAAAACC
1 TTTGAAGACACAAAAACC
40838150 TTTGAAGACACAAAAACC
1 TTTGAAGACACAAAAACC
40838168 TT
1 TT
40838170 AGTTTTGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (18 bp):
TTTGAAGACACAAAAACC
Found at i:40839327 original size:17 final size:17
Alignment explanation
Indices: 40839304--40839349 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
40839294 TAGCTTATTG
40839304 ATAAAATATTAATATAA
1 ATAAAATATTAATATAA
* * *
40839321 TTAAAATTTTAATTTAA
1 ATAAAATATTAATATAA
*
40839338 ATATAATATTAA
1 ATAAAATATTAA
40839350 AATTATACAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAAAATATTAATATAA
Found at i:40843358 original size:20 final size:22
Alignment explanation
Indices: 40843319--40843359 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
40843309 CCTTTTTTAA
*
40843319 AATCGTAAATAAGTAAAAAAAT
1 AATCGTAAATAAGAAAAAAAAT
40843341 AATCG-AAA-AAGAAAAAAAA
1 AATCGTAAATAAGAAAAAAAA
40843360 CAGTAAGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.15
Consensus pattern (22 bp):
AATCGTAAATAAGAAAAAAAAT
Found at i:40843564 original size:23 final size:22
Alignment explanation
Indices: 40843521--40843578 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
40843511 AAATGGTATC
* *
40843521 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40843542 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
40843565 TACATATCATATCT
1 TACAAATCATATCT
40843579 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40843581 original size:19 final size:19
Alignment explanation
Indices: 40843534--40843612 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 19
40843524 AAATTAAATC
*
40843534 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
40843554 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
40843576 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
40843597 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
40843613 CTCGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.28
21 18 0.36
22 7 0.14
23 11 0.22
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:40843594 original size:21 final size:21
Alignment explanation
Indices: 40843568--40843611 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40843558 CTAAGATTAC
40843568 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
40843589 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
40843610 AT
1 AT
40843612 CCTCGAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:40844181 original size:132 final size:132
Alignment explanation
Indices: 40843985--40844302 Score: 492
Period size: 132 Copynumber: 2.4 Consensus size: 132
40843975 ATTTCAGGGG
* * *
40843985 GATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTTAGGGAGACAATGCTTGGTGGCTTAAA
1 GATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAA
* * * * *
40844050 TCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCTTATTCAATTTTCTCCACTACTGCTTAGA
66 TATGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTACTCAATCTACTCCACTACTGCTTAGA
40844115 GA
131 GA
*
40844117 GATAAGATCTACAATATTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAA
1 GATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAA
* * *
40844182 TATGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCCTCGATCTACTCCACTACTGCTTAGG
66 TATGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTACTCAATCTACTCCACTACTGCTTAGA
40844247 GA
131 GA
* * * *
40844249 GATAAGATCTACGATCCTCAACCTACTCCGCTGTTGCTCAAGGAGACAAGGCTT
1 GATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTT
40844303 AATGTTTCAC
Statistics
Matches: 169, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 169 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (132 bp):
GATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGACTTAAA
TATGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTACTCAATCTACTCCACTACTGCTTAGA
GA
Found at i:40851984 original size:44 final size:42
Alignment explanation
Indices: 40851934--40852492 Score: 246
Period size: 45 Copynumber: 12.9 Consensus size: 42
40851924 TAACAGATCG
*
40851934 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAGTAGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGT-GAGCAGATTAAGT-GGCA
* *
40851978 AGTCTTATC-CTCTTGAAGTTGCAGTGAGGCAGACTGAAGGTGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGA-GCAGA-TTAA-GTGGCA
* * * *
40852023 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGGTA
1 AGTCTTATCTCCCTGAAGTTGCAGT-GAGCAGATT-AAG-TGGCA
* * * *** *
40852068 A-TCCTATCTCGCTGAAGTTGCAGTGAGAAGATTAA-AACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGAGCAGATTAAGTGGC-A
* * * * ** *
40852109 AGATCTTATCTCTCTAAACTTGCAGAGAGCAGATCGCA-T--CT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGAGCAGAT-TAAGTGGCA
* *
40852150 AGTATTATCGT-CCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
1 AGTCTTATC-TCCCTGAAGTTGCAGTGA-GCAGA-TTAAG-TGGCA
* * * *
40852195 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCGGTA
1 AGTCTTATCTCCCTGAAGTTGCAGT-GAGCAGATT-AAG-TGGCA
* * * * *** *
40852240 A-CCCTATCTCGCTGAAGTTGTAGTGAGCAGATTAA-AACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGAGCAGATTAAGTGGC-A
* * * *
40852281 AGATCTTATCTCGCTGAAGTTGCAGAGAGCAGATCATA-T--CT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGAGCAGATTA-AGTGGCA
* *
40852322 AGTCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGA-GCAGA-TTAAG-TGGCA
* * * * * *
40852367 AATCTTATCTACCTGAAGTTGTAGTGGAGCGGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGT-GAGCAGATTAAGT-GGCA
* * *
40852411 AATCTTATC-CTCCTGAAGTTGCAGTGAAGTAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTG-AGCAGA-TTAAG-TGGCA
* * *
40852456 AATCTTATCTCCATGAAGTTGCAGTGGAGCAAATTAA
1 AGTCTTATCTCCCTGAAGTTGCAGT-GAGCAGATTAA
40852493 AGCCGGTAAT
Statistics
Matches: 393, Mismatches: 80, Indels: 84
0.71 0.14 0.15
Matches are distributed among these distances:
39 1 0.00
40 39 0.10
41 22 0.06
42 9 0.02
43 76 0.19
44 105 0.27
45 129 0.33
46 12 0.03
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (42 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGAGCAGATTAAGTGGCA
Found at i:40852084 original size:89 final size:88
Alignment explanation
Indices: 40851936--40852528 Score: 478
Period size: 89 Copynumber: 6.8 Consensus size: 88
40851926 ACAGATCGAG
* ** * * *
40851936 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAGTAGGCAAGTCTTATCCTCTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAA-TCCTAT-CTCCTGAAGTTGC
*
40852000 AGTGAGGCAGACTGAAGGTGGCAAA
64 AGTGAGGCAGACTGAAGATGGCAAA
*
40852025 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTC-CTGAAGTTGCA
* * * **** *
40852090 GTGA-GAAGA-TTAAAACCTTAGA
65 GTGAGGCAGACTGAAGATGGCAAA
* * * * *** * **
40852112 TCTTATCTCTCTAAACTTGCAG-AGAGCAGATCGCATCTAGT-AT--TATCGTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATC-TCCTGAAGTTGCA
40852173 GTGAGGCAGACTGAAGATGGCAAA
65 GTGAGGCAGACTGAAGATGGCAAA
* * *
40852197 TCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCGGTAACCCTATCTCGCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTC-CTGAAGTTGCA
* * **** *
40852262 GTGA-GCAGA-TTAAAACCTTAGA
65 GTGAGGCAGACTGAAGATGGCAAA
* * * * * * *
40852284 TCTTATCTCGCTGAAGTTGCAG-AGAGCAGATCATA-TC--TAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTAT-CTCCTGAAGTTGCA
*
40852345 GTGAGGCAGACTGAAGATGACAAA
65 GTGAGGCAGACTGAAGATGGCAAA
* * * * ** ** *
40852369 TCTTATCTACCTGAAGTTGTAGTGGAGCGGACT-AAGTAAGCAAATCTTATCCTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CCGGTAATCCTAT-CTCCTGAAGTTGC
* *
40852433 AGTGAAGTAGACTGAAGATGGCAAA
64 AGTGAGGCAGACTGAAGATGGCAAA
* * *
40852458 TCTTATCTCCATGAAGTTGCAGTGGAGCAAATTAAAGCCGGTAATCCTATCCCACTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTC-CTGAAGTTGCA
40852523 GT-AGGC
65 GTGAGGC
40852529 GGATTAAAAC
Statistics
Matches: 385, Mismatches: 99, Indels: 41
0.73 0.19 0.08
Matches are distributed among these distances:
83 39 0.10
84 14 0.04
85 54 0.14
86 38 0.10
87 53 0.14
88 18 0.05
89 159 0.41
90 10 0.03
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCCTGAAGTTGCAG
TGAGGCAGACTGAAGATGGCAAA
Found at i:40852119 original size:43 final size:43
Alignment explanation
Indices: 40852024--40852575 Score: 249
Period size: 43 Copynumber: 12.7 Consensus size: 43
40852014 AAGGTGGCAA
* * *
40852024 ATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGGTA-
1 ATCTTATCTCGCTGAAGTTGCAGT-GAGCAGATTAAAACC-GTAG
* * *
40852068 ATCCTATCTCGCTGAAGTTGCAGTGAGAAGATTAAAACCTTAG
1 ATCTTATCTCGCTGAAGTTGCAGTGAGCAGATTAAAACCGTAG
* * * * *** *
40852111 ATCTTATCTCTCTAAACTTGCAGAGAGCAGA-TCGCATC-TAG
1 ATCTTATCTCGCTGAAGTTGCAGTGAGCAGATTAAAACCGTAG
* * * ** * *
40852152 -TATTATCGTC-CTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAA
1 ATCTTATC-TCGCTGAAGTTGCAGTGA-GCAGA-TTAAAACCGTAG
* * *
40852196 ATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCGGTA-
1 ATCTTATCTCGCTGAAGTTGCAGT-GAGCAGATTAAAACC-GTAG
* * * *
40852240 ACCCTATCTCGCTGAAGTTGTAGTGAGCAGATTAAAACCTTAG
1 ATCTTATCTCGCTGAAGTTGCAGTGAGCAGATTAAAACCGTAG
* * * *
40852283 ATCTTATCTCGCTGAAGTTGCAGAGAGCAGA-TCATATC-TAG
1 ATCTTATCTCGCTGAAGTTGCAGTGAGCAGATTAAAACCGTAG
* * * * *
40852324 -TCTTATCCTC-CTGAAGTTGCAGTGAGGCAGACTGAAGA-TGACAA
1 ATCTTAT-CTCGCTGAAGTTGCAGTGA-GCAGA-TTAAAACCG-TAG
* * * * *
40852368 ATCTTATCTAC-CTGAAGTTGTAGTGGAGCGGACTAAGTAA--GCAA
1 ATCTTATCT-CGCTGAAGTTGCAGT-GAGCAGATTAA--AACCGTAG
* * * ** * *
40852412 ATCTTATCCTC-CTGAAGTTGCAGTGAAGTAGACTGAAGATGGCAA
1 ATCTTAT-CTCGCTGAAGTTGCAGTG-AGCAGA-TTAAAACCGTAG
* *
40852457 ATCTTATCTC-CATGAAGTTGCAGTGGAGCAAATTAAAGCCGGTA-
1 ATCTTATCTCGC-TGAAGTTGCAGT-GAGCAGATTAAAACC-GTAG
* * * * *
40852501 ATCCTATCCCACTGAAGTTGCAGT-AGGCGGATTAAAACCTTAG
1 ATCTTATCTCGCTGAAGTTGCAGTGA-GCAGATTAAAACCGTAG
* * *
40852544 ATCTTATCTCTCTGAAGTTGCAGAGAGTAGAT
1 ATCTTATCTCGCTGAAGTTGCAGTGAGCAGAT
40852576 CGCATTTAGT
Statistics
Matches: 387, Mismatches: 87, Indels: 69
0.71 0.16 0.13
Matches are distributed among these distances:
40 38 0.10
41 21 0.05
42 14 0.04
43 118 0.30
44 107 0.28
45 83 0.21
46 6 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (43 bp):
ATCTTATCTCGCTGAAGTTGCAGTGAGCAGATTAAAACCGTAG
Found at i:40852431 original size:172 final size:172
Alignment explanation
Indices: 40851978--40852396 Score: 685
Period size: 172 Copynumber: 2.4 Consensus size: 172
40851968 TAAGTAGGCA
* * *
40851978 AGTCTTATCCTCTTGAAGTTGCAGTGAGGCAGACTGAAGGTGGCAAATCTTATCTCCCTAAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
40852043 GCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGAGAAGATTAAAACCT
66 GCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGAGAAGATTAAAACCT
* *
40852108 TAGATCTTATCTCTCTAAACTTGCAGAGAGCAGATCGCATCT
131 TAGATCTTATCTCGCTAAACTTGCAGAGAGCAGATCACATCT
* *
40852150 AGTATTATCGTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* * * *
40852215 GCAGTGGAACAGATTAAAGCCGGTAACCCTATCTCGCTGAAGTTGTAGTGAGCAGATTAAAACCT
66 GCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGAGAAGATTAAAACCT
* * *
40852280 TAGATCTTATCTCGCTGAAGTTGCAGAGAGCAGATCATATCT
131 TAGATCTTATCTCGCTAAACTTGCAGAGAGCAGATCACATCT
* *
40852322 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTACCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
*
40852387 GTAGTGGAGC
66 GCAGTGGAGC
40852397 GGACTAAGTA
Statistics
Matches: 227, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
172 227 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (172 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAGATTAAAGCCGGTAATCCTATCTCGCTGAAGTTGCAGTGAGAAGATTAAAACCT
TAGATCTTATCTCGCTAAACTTGCAGAGAGCAGATCACATCT
Found at i:40855642 original size:24 final size:24
Alignment explanation
Indices: 40855614--40855665 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
40855604 TTTCTAGAAG
* *
40855614 ATTTAGTATTTA-TGAGTATAATAT
1 ATTTAGCATTTAGT-AGCATAATAT
40855638 ATTTAGCATTTAGTAGCATAATAT
1 ATTTAGCATTTAGTAGCATAATAT
40855662 ATTT
1 ATTT
40855666 GACTTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTAGTAGCATAATAT
Found at i:40858651 original size:28 final size:28
Alignment explanation
Indices: 40858586--40858641 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
40858576 CTATTTAGTG
*
40858586 ACAGT-ACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTCTGGGCCTTAGCCCAAT
40858613 ACAGTAACAGTCTGGGCCTTAGCCCAAT
1 ACAGTAACAGTCTGGGCCTTAGCCCAAT
40858641 A
1 A
40858642 TAGAATCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (28 bp):
ACAGTAACAGTCTGGGCCTTAGCCCAAT
Found at i:40859124 original size:27 final size:26
Alignment explanation
Indices: 40859068--40859612 Score: 425
Period size: 27 Copynumber: 20.4 Consensus size: 26
40859058 GGGCATAACA
*
40859068 GTCATTTTACC-TTATGGGGTATTTTG
1 GTCATTTTACCTTTA-GGGGTATTTCG
*
40859094 GTCATTTTACCTTATAGGGGTATTTCA
1 GTCATTTTACCTT-TAGGGGTATTTCG
*
40859121 GTCATTTTACC-CT--GGGTATTTCG
1 GTCATTTTACCTTTAGGGGTATTTCG
* * *
40859144 ATCATTTTACCATATAGGGGTA-TTCTA
1 GTCATTTTACC-TTTAGGGGTATTTC-G
* * * *
40859171 GCCATTTCACCTTTCGGGGGTATTTCA
1 GTCATTTTACCTTT-AGGGGTATTTCG
* *
40859198 GTCATTTTACCCTTCAAGGGTATTTCG
1 GTCATTTTA-CCTTTAGGGGTATTTCG
* *
40859225 GTCATTTTACCCTTCAGGGTTATTTCG
1 GTCATTTTA-CCTTTAGGGGTATTTCG
* *
40859252 GTCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCTTTAG-GGGTATTTCG
*
40859279 ATCATTTTACCCTTTAGGGGTATTTCG
1 GTCATTTTA-CCTTTAGGGGTATTTCG
* * *
40859306 ATCATTTTACCCTTTGGGGGTATTTCA
1 GTCATTTTA-CCTTTAGGGGTATTTCG
* * * *
40859333 GTAATTTTATCTTTTGGGGGTGTTTCG
1 GTCATTTTA-CCTTTAGGGGTATTTCG
* *
40859360 GTCATTTTATCCTTCAGGGATATTTCG
1 GTCATTTTA-CCTTTAGGGGTATTTCG
* *
40859387 ATCATTTTACCTTTTGGGGGTATTTCG
1 GTCATTTTACC-TTTAGGGGTATTTCG
* *
40859414 ATCATTTTACCCTTCAGGGGTATTTCG
1 GTCATTTTA-CCTTTAGGGGTATTTCG
* ** * *
40859441 GTAATTTTACCCATCGAGCGTATTTCG
1 GTCATTTTACCTTTAG-GGGTATTTCG
* *
40859468 GTCATTTTACCATTCAGGGATATTTCG
1 GTCATTTTACC-TTTAGGGGTATTTCG
* *
40859495 GTCATTTTACCCTTTGGGGGTATTTTG
1 GTCATTTTA-CCTTTAGGGGTATTTCG
* * * *
40859522 GTAATTTTACCTATCGAGGGTATTTTG
1 GTCATTTTACCTTTAG-GGGTATTTCG
** *
40859549 GTCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCTTTAG-GGGTATTTCG
* * * *
40859576 ATAATTTTACCCTTCGGGGTATTTCG
1 GTCATTTTACCTTTAGGGGTATTTCG
*
40859602 GTAATTTTACC
1 GTCATTTTACC
40859613 CATTGATGGT
Statistics
Matches: 426, Mismatches: 75, Indels: 36
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.04
25 2 0.00
26 50 0.12
27 336 0.79
28 19 0.04
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (26 bp):
GTCATTTTACCTTTAGGGGTATTTCG
Found at i:40859273 original size:81 final size:80
Alignment explanation
Indices: 40859068--40859633 Score: 499
Period size: 81 Copynumber: 7.1 Consensus size: 80
40859058 GGGCATAACA
* ** *
40859068 GTCATTTTA-CCTT-ATGGGGTATTTTGGTCATTTTA-CCTTATAGGGGTATTTCAGTCATTTTA
1 GTCATTTTACCCTTCA-GGGGTATTTCGGTCATTTTACCCTTCGA-GGGTATTTCGGTCATTTTA
40859130 CCC-T--GGGTATTTCG
64 CCCTTCAGGGTATTTCG
* * * * * * * *
40859144 ATCATTTTACCATAT-AGGGGTA-TTCTAGCCATTTCACCTTTCGGGGGTATTTCAGTCATTTTA
1 GTCATTTTACCCT-TCAGGGGTATTTC-GGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTA
40859207 CCCTTCAAGGGTATTTCG
64 CCCTTC-AGGGTATTTCG
* *
40859225 GTCATTTTACCCTTCAGGGTTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACC
1 GTCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACC
*
40859290 CTTTAGGGGTATTTCG
66 CTTCA-GGGTATTTCG
* ** * * * * * * * *
40859306 ATCATTTTACCCTTTGGGGGTATTTCAGTAATTTTATCTTTTGGGGGTGTTTCGGTCATTTTATC
1 GTCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACC
40859371 CTTCAGGGATATTTCG
66 CTTCAGGG-TATTTCG
* * ** * *
40859387 ATCATTTTACCTTTTGGGGGTATTTCGATCATTTTACCCTTC-AGGGGTATTTCGGTAATTTTAC
1 GTCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCCTTCGA-GGGTATTTCGGTCATTTTAC
* *
40859451 CCATCGAGCGTATTTCG
65 CCTTC-AGGGTATTTCG
* * * * * *
40859468 GTCATTTTACCATTCAGGGATATTTCGGTCATTTTACCCTTTGGGGGTATTTTGGTAATTTTA-C
1 GTCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACC
*
40859532 CTATCGAGGGTATTTTG
66 CT-TC-AGGGTATTTCG
* * * *
40859549 GTCATTTTACCCATC-GAGGGTATTTCGATAATTTTACCCTTCG-GGGTATTTCGGTAATTTTAC
1 GTCATTTTACCCTTCAG-GGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTAC
* * *
40859612 CCATTGATGGTATTTCA
65 CC-TTCAGGGTATTTCG
40859629 GTCAT
1 GTCAT
40859634 ACGAATCGCA
Statistics
Matches: 400, Mismatches: 71, Indels: 34
0.79 0.14 0.07
Matches are distributed among these distances:
76 10 0.03
77 37 0.09
78 6 0.01
80 39 0.10
81 301 0.75
82 7 0.02
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (80 bp):
GTCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACC
CTTCAGGGTATTTCG
Found at i:40863045 original size:24 final size:24
Alignment explanation
Indices: 40862983--40863034 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40862973 TTTCTAGAAG
* * *
40862983 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
40863007 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
40863031 ATTT
1 ATTT
40863035 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:40863606 original size:118 final size:119
Alignment explanation
Indices: 40863396--40863633 Score: 336
Period size: 118 Copynumber: 2.0 Consensus size: 119
40863386 TTTTTTTGAG
* * * * *
40863396 CTAAATATGGTCCTCAGCCTTTGAGAAAGAGTCAAAATAATGTTTTTTTAACGAGAATACTAACT
1 CTAAATATGGCCCTCAACCTTTGAAAAACAGTCAAAATAA-GTTTTTTTAACAAGAATACTAACT
* *
40863461 AAAATGTTAATTTTTAAACATTGCAGCTTCCGTGACAATTCAGATGTACTTCATT
65 AAAATGTTAATTTTTAAACATTGCAGCTTCCATGACAATTCACATGTACTTCATT
* * *
40863516 CTAAATATGGCCCTTAACCTTTGAAAAACAGTCCAAATGAA-TTTTTTTAACAATAATACT-ACT
1 CTAAATATGGCCCTCAACCTTTGAAAAACAGTCAAAAT-AAGTTTTTTTAACAAGAATACTAACT
* *
40863579 AAGATGTTAATTTTTAAACATTGCAGCTTGCATGACAATTCACATGTACTTCATT
65 AAAATGTTAATTTTTAAACATTGCAGCTTCCATGACAATTCACATGTACTTCATT
40863634 ATAATTTTTT
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
118 54 0.51
119 17 0.16
120 32 0.30
121 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (119 bp):
CTAAATATGGCCCTCAACCTTTGAAAAACAGTCAAAATAAGTTTTTTTAACAAGAATACTAACTA
AAATGTTAATTTTTAAACATTGCAGCTTCCATGACAATTCACATGTACTTCATT
Found at i:40863677 original size:8 final size:8
Alignment explanation
Indices: 40863665--40863712 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
40863655 AACTTCTTAT
*
40863665 ATTTTTTT
1 ATTTTTTA
40863673 A-TTTTTA
1 ATTTTTTA
40863680 ATTTTTTA
1 ATTTTTTA
40863688 ATTTTTATA
1 ATTTTT-TA
*
40863697 ATTTTTGA
1 ATTTTTTA
*
40863705 ATTATTTA
1 ATTTTTTA
40863713 TTGATATGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
7 6 0.18
8 20 0.59
9 8 0.24
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
ATTTTTTA
Found at i:40863685 original size:15 final size:15
Alignment explanation
Indices: 40863665--40863694 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40863655 AACTTCTTAT
*
40863665 ATTTTTTTATTTTTA
1 ATTTTTTAATTTTTA
40863680 ATTTTTTAATTTTTA
1 ATTTTTTAATTTTTA
40863695 TAATTTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
ATTTTTTAATTTTTA
Found at i:40863698 original size:17 final size:17
Alignment explanation
Indices: 40863661--40863713 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
40863651 TATGAACTTC
*
40863661 TTAT-ATTTTTTTA-TT
1 TTATAATTTTTTAATTT
40863676 TT-TAATTTTTTAATTT
1 TTATAATTTTTTAATTT
*
40863692 TTATAATTTTTGAATTAT
1 TTATAATTTTTTAATT-T
40863710 TTAT
1 TTAT
40863714 TGATATGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 1 0.03
15 10 0.31
16 4 0.12
17 12 0.38
18 5 0.16
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
TTATAATTTTTTAATTT
Found at i:40866571 original size:17 final size:17
Alignment explanation
Indices: 40866511--40866628 Score: 70
Period size: 17 Copynumber: 7.1 Consensus size: 17
40866501 TTGCATAAAT
*
40866511 ATAGGCTCGCATAAACC
1 ATAGGCTCGCATATACC
* *
40866528 -TAGGGCTCACA-A-ATC
1 ATA-GGCTCGCATATACC
*
40866543 ATATGCTCGCATATACC
1 ATAGGCTCGCATATACC
*
40866560 -TAGGGTTCGCATA-ACAC
1 ATA-GGCTCGCATATAC-C
* *
40866577 ATAGGCTCACATATTCC
1 ATAGGCTCGCATATACC
*
40866594 -TAGGGTTCGCATA-ACAC
1 ATA-GGCTCGCATATAC-C
40866611 ATAGGCTCGCATATACC
1 ATAGGCTCGCATATACC
40866628 A
1 A
40866629 ATGATTCACA
Statistics
Matches: 75, Mismatches: 14, Indels: 24
0.66 0.12 0.21
Matches are distributed among these distances:
15 8 0.11
16 13 0.17
17 47 0.63
18 7 0.09
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (17 bp):
ATAGGCTCGCATATACC
Found at i:40866596 original size:34 final size:34
Alignment explanation
Indices: 40866503--40866709 Score: 195
Period size: 34 Copynumber: 6.1 Consensus size: 34
40866493 ATCCAAGTTT
* ** *
40866503 GCATAA-ATATAGGCTCGCATAAACCTAGGGCTC
1 GCATAACACATAGGCTCGCATATTCCTAGGGTTC
* * * *
40866536 ACA-AA-TCATATGCTCGCATATACCTAGGGTTC
1 GCATAACACATAGGCTCGCATATTCCTAGGGTTC
*
40866568 GCATAACACATAGGCTCACATATTCCTAGGGTTC
1 GCATAACACATAGGCTCGCATATTCCTAGGGTTC
* * * *
40866602 GCATAACACATAGGCTCGCATATACCAATGATTC
1 GCATAACACATAGGCTCGCATATTCCTAGGGTTC
* * * *
40866636 ACATAACGCATAGGCTCACATATTCCTCGGGTTC
1 GCATAACACATAGGCTCGCATATTCCTAGGGTTC
* * *
40866670 GCATAACATATATAGGCTCGCATGTTCCTAGAGTTC
1 GCATAAC--ACATAGGCTCGCATATTCCTAGGGTTC
40866706 GCAT
1 GCAT
40866710 GCAATATACA
Statistics
Matches: 139, Mismatches: 31, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
32 26 0.19
33 4 0.03
34 84 0.60
36 25 0.18
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (34 bp):
GCATAACACATAGGCTCGCATATTCCTAGGGTTC
Found at i:40866916 original size:26 final size:27
Alignment explanation
Indices: 40866886--40866946 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
40866876 TCGCACAAAG
*
40866886 GGGATTCACACTAAGGGCTCGCAT-AA
1 GGGATTCACACTAAGGGCTCCCATAAA
* *
40866912 GGGATTCGCGCTAAGGGCTCCCATAAA
1 GGGATTCACACTAAGGGCTCCCATAAA
40866939 GGG-TTCAC
1 GGGATTCAC
40866947 GCACACTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.26, C:0.25, G:0.30, T:0.20
Consensus pattern (27 bp):
GGGATTCACACTAAGGGCTCCCATAAA
Found at i:40868701 original size:21 final size:21
Alignment explanation
Indices: 40868675--40868714 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
40868665 GTTAAGATAT
40868675 TATTTCAATAAATT-TTATAGG
1 TATTTCAAT-AATTATTATAGG
40868696 TATTTCAATAATTATTATA
1 TATTTCAATAATTATTATA
40868715 TTACCACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
TATTTCAATAATTATTATAGG
Found at i:40868870 original size:12 final size:12
Alignment explanation
Indices: 40868822--40868871 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
40868812 TTTATTGATA
40868822 AAATATAA-ATAT
1 AAATATAATAT-T
*
40868834 AAATATAATTTT
1 AAATATAATATT
* *
40868846 AATTTTAAT-TT
1 AAATATAATATT
40868857 AAATATAATATT
1 AAATATAATATT
40868869 AAA
1 AAA
40868872 ATTATAGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 9 0.29
12 21 0.68
13 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATATAATATT
Found at i:40870968 original size:140 final size:140
Alignment explanation
Indices: 40870716--40870995 Score: 560
Period size: 140 Copynumber: 2.0 Consensus size: 140
40870706 CCACATGCTT
40870716 CTTGATGGACACAAAGATGTGGAAATTTTGGTCAAATTCTTGACTTTTTTTAATTCAATTTAAGA
1 CTTGATGGACACAAAGATGTGGAAATTTTGGTCAAATTCTTGACTTTTTTTAATTCAATTTAAGA
40870781 CAAACATGTACAAATCTAAGAAATTTCAAACTTTCTTCAAAGTAATGAGAATTAACTTTTTATTT
66 CAAACATGTACAAATCTAAGAAATTTCAAACTTTCTTCAAAGTAATGAGAATTAACTTTTTATTT
40870846 ATTTGGAAAA
131 ATTTGGAAAA
40870856 CTTGATGGACACAAAGATGTGGAAATTTTGGTCAAATTCTTGACTTTTTTTAATTCAATTTAAGA
1 CTTGATGGACACAAAGATGTGGAAATTTTGGTCAAATTCTTGACTTTTTTTAATTCAATTTAAGA
40870921 CAAACATGTACAAATCTAAGAAATTTCAAACTTTCTTCAAAGTAATGAGAATTAACTTTTTATTT
66 CAAACATGTACAAATCTAAGAAATTTCAAACTTTCTTCAAAGTAATGAGAATTAACTTTTTATTT
40870986 ATTTGGAAAA
131 ATTTGGAAAA
40870996 ACGACTTCCA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (140 bp):
CTTGATGGACACAAAGATGTGGAAATTTTGGTCAAATTCTTGACTTTTTTTAATTCAATTTAAGA
CAAACATGTACAAATCTAAGAAATTTCAAACTTTCTTCAAAGTAATGAGAATTAACTTTTTATTT
ATTTGGAAAA
Found at i:40871049 original size:140 final size:137
Alignment explanation
Indices: 40870756--40871033 Score: 340
Period size: 140 Copynumber: 2.0 Consensus size: 137
40870746 GTCAAATTCT
40870756 TGACTTTTTTTAATTCAATTTAAGACAAACATGTACAAATCTAAGAAATTTCAAACTTTCTTCAA
1 TGACTTTTTTTAATTCAATTTAAGACAAACATGTACAAATCTAAGAAATTTCAAACTTTCTTCAA
* *** * * * ***** * *
40870821 AGTAATGAGAATTAACTTTTTATTTATTTGGAAAACTTGATGGACACAAAGATGTGGAAATTTTG
66 AGTAATGAGAATTAACTTTTTATTTATTTGGAAAACTTCAAAAAAAAAAAAAAAAAAAAACTTTC
* *
40870886 GTCAAATTCT
131 CTC--A-TCA
40870896 TGACTTTTTTTAATTCAATTTAAGACAAACATGTACAAATCTAAGAAATTTCAAACTTTCTTCAA
1 TGACTTTTTTTAATTCAATTTAAGACAAACATGTACAAATCTAAGAAATTTCAAACTTTCTTCAA
40870961 AGTAATGAGAATTAACTTTTTATTTATTTGGAAAAACGACTTCCAAAAAAAAAAAAAAAAAAAAA
66 AGTAATGAGAATTAACTTTTTATTTATTTGG--AAA--ACTT-CAAAAAAAAAAAAAAAAAAAAA
40871026 CTTTCCTC
126 CTTTCCTC
40871034 TCAATATTTT
Statistics
Matches: 118, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
140 96 0.81
142 3 0.03
144 4 0.03
145 15 0.13
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (137 bp):
TGACTTTTTTTAATTCAATTTAAGACAAACATGTACAAATCTAAGAAATTTCAAACTTTCTTCAA
AGTAATGAGAATTAACTTTTTATTTATTTGGAAAACTTCAAAAAAAAAAAAAAAAAAAAACTTTC
CTCATCA
Done.