Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 91 of 145
Found at i:30368108 original size:22 final size:22
Alignment explanation
Indices: 30368076--30368127 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
30368066 GGGTAGGAAA
* * *
30368076 CTGCATTTGTATTTGATTTGTT
1 CTGCATCTGTATCTGATATGTT
*
30368098 TTGCATCTGTATCTGATATGTT
1 CTGCATCTGTATCTGATATGTT
30368120 CTGCATCT
1 CTGCATCT
30368128 TATATGAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.52
Consensus pattern (22 bp):
CTGCATCTGTATCTGATATGTT
Found at i:30370157 original size:98 final size:98
Alignment explanation
Indices: 30370036--30370225 Score: 353
Period size: 98 Copynumber: 1.9 Consensus size: 98
30370026 ATATAAAAAT
*
30370036 TTTAAAAGAGCATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGAGCACGATCCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGAGCACGATCCC
30370101 TTTAGAATCCCAAACTCGGAATATTTCATTTAA
66 TTTAGAATCCCAAACTCGGAATATTTCATTTAA
* *
30370134 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGAGCACGATCCC
1 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGAGCACGATCCC
30370199 TTTAGAATCCCAAACTCGGAATATTTC
66 TTTAGAATCCCAAACTCGGAATATTTC
30370226 CTTCATGATT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGAGCACGATCCC
TTTAGAATCCCAAACTCGGAATATTTCATTTAA
Found at i:30382009 original size:17 final size:19
Alignment explanation
Indices: 30381986--30382030 Score: 67
Period size: 17 Copynumber: 2.4 Consensus size: 19
30381976 CCTGGATCAA
30381986 TTTTGGGCCACT-ATTTGG
1 TTTTGGGCCACTAATTTGG
30382004 -TTTGGGCCACTGAATTTGG
1 TTTTGGGCCACT-AATTTGG
30382023 TTTTGGGC
1 TTTTGGGC
30382031 TTTGTGGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.46
19 6 0.25
20 7 0.29
ACGTcount: A:0.11, C:0.16, G:0.31, T:0.42
Consensus pattern (19 bp):
TTTTGGGCCACTAATTTGG
Found at i:30382517 original size:25 final size:24
Alignment explanation
Indices: 30382474--30382525 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
30382464 ATGTTCAAGT
30382474 GAGCCATATCAGGAAGCTCATAAA
1 GAGCCATATCAGGAAGCTCATAAA
* *
30382498 GAGCCTATATCGGGATGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
30382523 GAG
1 GAG
30382526 TTGCGGTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:30383714 original size:192 final size:193
Alignment explanation
Indices: 30383387--30383769 Score: 759
Period size: 192 Copynumber: 2.0 Consensus size: 193
30383377 AATTAATCCC
30383387 CAAAATAGGTAGATTAGGCTTATGTATGAAATAATAGGTAGATTAGGTTACTAAAAACGGGACAA
1 CAAAATAGGTAGATTAGGCTTATGTATGAAATAATAGGTAGATTAGGTTACTAAAAACGGGACAA
30383452 GAATGATTACCCAATTAAGCCAATTTAGCTTGCTTGAACTCCTTTCTCTTAGCTAGGGTTTCCAT
66 GAATGATTACCCAATTAAGCCAATTTAGCTTGCTTGAACTCCTTTCTCTTAGCTAGGGTTTCCAT
30383517 GAAAATAATTTGGGGAAAGATGATGAAAAAGATTATATTTTCTTATTTAC-TTAATTATCAAT
131 GAAAATAATTTGGGGAAAGATGATGAAAAAGATTATATTTTCTTATTTACTTTAATTATCAAT
30383579 CAAAATAGGTAGATTAGGCTTATGTATGAAATAATAGGTAGATTAGGTTACTAAAAACGGGACAA
1 CAAAATAGGTAGATTAGGCTTATGTATGAAATAATAGGTAGATTAGGTTACTAAAAACGGGACAA
30383644 GAATGATTACCCAATTAAGCCAATTTAGCTTGCTTGAACTCCTTTCTCTTAGCTAGGGTTTCCAT
66 GAATGATTACCCAATTAAGCCAATTTAGCTTGCTTGAACTCCTTTCTCTTAGCTAGGGTTTCCAT
30383709 GAAAATAATTTGGGGAAAGATGATGAAAAAGATTATATTTTCTTATTTACTTTAATTATCA
131 GAAAATAATTTGGGGAAAGATGATGAAAAAGATTATATTTTCTTATTTACTTTAATTATCA
30383770 TCTTTTATTT
Statistics
Matches: 190, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
192 180 0.95
193 10 0.05
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (193 bp):
CAAAATAGGTAGATTAGGCTTATGTATGAAATAATAGGTAGATTAGGTTACTAAAAACGGGACAA
GAATGATTACCCAATTAAGCCAATTTAGCTTGCTTGAACTCCTTTCTCTTAGCTAGGGTTTCCAT
GAAAATAATTTGGGGAAAGATGATGAAAAAGATTATATTTTCTTATTTACTTTAATTATCAAT
Found at i:30386212 original size:3 final size:3
Alignment explanation
Indices: 30386204--30386234 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30386194 TTGTTATTTA
30386204 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
30386235 CTTGATCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:30387410 original size:18 final size:18
Alignment explanation
Indices: 30387387--30387421 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
30387377 TTATATTTTT
30387387 TTAATATTTTGATAATTA
1 TTAATATTTTGATAATTA
30387405 TTAATATTTTGATAATT
1 TTAATATTTTGATAATT
30387422 TATAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TTAATATTTTGATAATTA
Found at i:30387433 original size:19 final size:18
Alignment explanation
Indices: 30387389--30387432 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
30387379 ATATTTTTTT
*
30387389 AATATTTTGATAATTATT
1 AATATTTTGATAATTATA
30387407 AATATTTTGATAATTTATA
1 AATATTTTGATAA-TTATA
30387426 AAT-TTTT
1 AATATTTT
30387433 TTATACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
AATATTTTGATAATTATA
Found at i:30387593 original size:15 final size:17
Alignment explanation
Indices: 30387566--30387600 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
30387556 TAATATTTTG
30387566 TTTGAATTTTTTTA-TA
1 TTTGAATTTTTTTATTA
30387582 TTTGAA-TTTTTTATTA
1 TTTGAATTTTTTTATTA
30387598 TTT
1 TTT
30387601 TTAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTGAATTTTTTTATTA
Found at i:30390035 original size:25 final size:25
Alignment explanation
Indices: 30390007--30390059 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
30389997 TTTGTTATGT
* * *
30390007 TATGCCATGATCTGATTTGATATTA
1 TATGCCATGATCTAATCTGATATAA
* *
30390032 TATGCTATGGTCTAATCTGATATAA
1 TATGCCATGATCTAATCTGATATAA
30390057 TAT
1 TAT
30390060 ACTACGATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (25 bp):
TATGCCATGATCTAATCTGATATAA
Found at i:30397135 original size:29 final size:31
Alignment explanation
Indices: 30397075--30397144 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 31
30397065 TGTTATGATT
*
30397075 TGTATGAAAATATGTAAGTATGCATGCCATATGA
1 TGTATG-ATATATGTAAGTATGCA--CCATATGA
30397109 TGTATGATATATGTAAGTATG-A-CATATGA
1 TGTATGATATATGTAAGTATGCACCATATGA
30397138 T-TATGAT
1 TGTATGAT
30397145 TTGTTTGTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 6 0.17
29 8 0.23
32 1 0.03
33 14 0.40
34 6 0.17
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (31 bp):
TGTATGATATATGTAAGTATGCACCATATGA
Found at i:30397401 original size:5 final size:5
Alignment explanation
Indices: 30397392--30397486 Score: 52
Period size: 5 Copynumber: 19.0 Consensus size: 5
30397382 ATGTTATGCC
* * * * *
30397392 ATGAT TTGAT TTGAT ATGAT ATGAT ATGGT CTGAT CTGAT ATGAT AT-ACT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGA-T
* * * * *
30397442 ATGAT -TCGAC ATAAC ATGAG AT-ATT ATGAT ATGAT AAGAT ATGAT
1 ATGAT AT-GAT ATGAT ATGAT ATGA-T ATGAT ATGAT ATGAT ATGAT
30397487 CCGTATAAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
4 3 0.04
5 65 0.92
6 3 0.04
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (5 bp):
ATGAT
Found at i:30400422 original size:20 final size:20
Alignment explanation
Indices: 30400397--30400435 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30400387 TCAGAAATAG
*
30400397 TGGTTTTAGGACCACAATTT
1 TGGTTTCAGGACCACAATTT
*
30400417 TGGTTTCAGGACTACAATT
1 TGGTTTCAGGACCACAATT
30400436 CTGATGAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (20 bp):
TGGTTTCAGGACCACAATTT
Found at i:30404900 original size:19 final size:20
Alignment explanation
Indices: 30404876--30404917 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
30404866 ATATAAGTTT
30404876 AAAAACTAAAAA-AACACTA
1 AAAAACTAAAAAGAACACTA
*
30404895 AAAAACTAAAAAGAAGACTA
1 AAAAACTAAAAAGAACACTA
30404915 AAA
1 AAA
30404918 TGATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.74, C:0.12, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAAACTAAAAAGAACACTA
Found at i:30408214 original size:16 final size:16
Alignment explanation
Indices: 30408193--30408226 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
30408183 GCAAAGTTGA
30408193 AGAGACAGGCCAACAC
1 AGAGACAGGCCAACAC
30408209 AGAGACAGGCCAACAC
1 AGAGACAGGCCAACAC
30408225 AG
1 AG
30408227 TGAAGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.29, G:0.26, T:0.00
Consensus pattern (16 bp):
AGAGACAGGCCAACAC
Found at i:30413422 original size:18 final size:18
Alignment explanation
Indices: 30413399--30413436 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
30413389 GTTATTCTAA
30413399 AGAAGAAGAAGATAAGAG
1 AGAAGAAGAAGATAAGAG
30413417 AGAAGAAGAAGATAAGAG
1 AGAAGAAGAAGATAAGAG
30413435 AG
1 AG
30413437 CTCTACATAG
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:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (18 bp):
AGAAGAAGAAGATAAGAG
Found at i:30413974 original size:12 final size:12
Alignment explanation
Indices: 30413957--30413983 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
30413947 ACGGTGTAAT
30413957 TGACGTGTTAGA
1 TGACGTGTTAGA
30413969 TGACGTGTTAGA
1 TGACGTGTTAGA
30413981 TGA
1 TGA
30413984 TGTGGAGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (12 bp):
TGACGTGTTAGA
Found at i:30420601 original size:21 final size:20
Alignment explanation
Indices: 30420577--30420635 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
30420567 TATAGTGTGA
30420577 GTTACATAAATTATTCAATTT
1 GTTACATAAATTATT-AATTT
*
30420598 GTTACA-ATATTA-TAATATT
1 GTTACATAAATTATTAAT-TT
*
30420617 TTTA-ATAAATTATTGAATT
1 GTTACATAAATTATT-AATT
30420636 CCTTAGCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
18 4 0.13
19 11 0.35
20 7 0.23
21 9 0.29
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
GTTACATAAATTATTAATTT
Found at i:30420672 original size:20 final size:21
Alignment explanation
Indices: 30420642--30420682 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
30420632 AATTCCTTAG
30420642 CACATAAATTACTAAAATTCT
1 CACATAAATTACTAAAATTCT
*
30420663 CACA-AAATTACTCAAATTCT
1 CACATAAATTACTAAAATTCT
30420683 TTGTAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (21 bp):
CACATAAATTACTAAAATTCT
Found at i:30422848 original size:8 final size:8
Alignment explanation
Indices: 30422835--30422859 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
30422825 TATACTAAAC
30422835 AATAAAAT
1 AATAAAAT
30422843 AATAAAAT
1 AATAAAAT
30422851 AATAAAAT
1 AATAAAAT
30422859 A
1 A
30422860 TCATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:30426458 original size:27 final size:27
Alignment explanation
Indices: 30426421--30426481 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
30426411 AGAGGTCAAT
30426421 AAATGACCGAAATACCCCCATA-GAGTA
1 AAATGACCGAAATACCCCCATAGGA-TA
*
30426448 AAATGATCGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGATA
30426475 AAATGAC
1 AAATGAC
30426482 TGTTATACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.94
28 2 0.06
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.16
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGATA
Found at i:30426800 original size:28 final size:27
Alignment explanation
Indices: 30426768--30426825 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
30426758 ATACTGATAT
*
30426768 TGTATTAGGCTAAGGCCCACACTGTTAC
1 TGTATCAGGCTAAGGCCCACACTG-TAC
*
30426796 TGTATCGGGCTAAGGCCCACACTGTAC
1 TGTATCAGGCTAAGGCCCACACTGTAC
30426823 TGT
1 TGT
30426826 TACTGAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (27 bp):
TGTATCAGGCTAAGGCCCACACTGTAC
Found at i:30426825 original size:33 final size:34
Alignment explanation
Indices: 30426788--30426858 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
30426778 TAAGGCCCAC
* *
30426788 ACTGTTACTGTATCGGGCTAAGGCCCACACTG-T
1 ACTGTTACTGAATAGGGCTAAGGCCCACACTGTT
* *
30426821 ACTGTTACTGAATAGGGCTTAGGCCCAGACTGTT
1 ACTGTTACTGAATAGGGCTAAGGCCCACACTGTT
30426855 ACTG
1 ACTG
30426859 CATGTTGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 28 0.85
34 5 0.15
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (34 bp):
ACTGTTACTGAATAGGGCTAAGGCCCACACTGTT
Found at i:30429671 original size:15 final size:15
Alignment explanation
Indices: 30429627--30429672 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
30429617 AGGAATTTTG
30429627 AAAAAATTAAGAAAA
1 AAAAAATTAAGAAAA
*
30429642 AATAAAA-TAATAAAA
1 AA-AAAATTAAGAAAA
30429657 ATAAAAATTAA-AAAA
1 A-AAAAATTAAGAAAA
30429672 A
1 A
30429673 CCAAACTCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (15 bp):
AAAAAATTAAGAAAA
Found at i:30434652 original size:3 final size:3
Alignment explanation
Indices: 30434638--30434674 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
30434628 ATTAAGAAAT
*
30434638 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30434675 CAGTATTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30435097 original size:29 final size:28
Alignment explanation
Indices: 30435065--30435128 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
30435055 TAACATCTTC
*
30435065 AATTTATTTCAACTTATTTCAA-TATTGTT
1 AATTTATTCCAACTTATTTCAACT-TT-TT
* *
30435094 AATTTATTCCAATTTATTTTAACTTTTT
1 AATTTATTCCAACTTATTTCAACTTTTT
30435122 AATTTAT
1 AATTTAT
30435129 AGATATCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 9 0.29
29 21 0.68
30 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (28 bp):
AATTTATTCCAACTTATTTCAACTTTTT
Found at i:30435109 original size:10 final size:10
Alignment explanation
Indices: 30435062--30435112 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
30435052 TTTTAACATC
30435062 TTCAATTTAT
1 TTCAATTTAT
*
30435072 TTCAACTTAT
1 TTCAATTTAT
30435082 TTCAA--TAT
1 TTCAATTTAT
*
30435090 TGTTAATTTAT
1 T-TCAATTTAT
*
30435101 TCCAATTTAT
1 TTCAATTTAT
30435111 TT
1 TT
30435113 TAACTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
8 4 0.12
9 3 0.09
10 22 0.67
11 4 0.12
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (10 bp):
TTCAATTTAT
Found at i:30437873 original size:25 final size:24
Alignment explanation
Indices: 30437828--30437874 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
30437818 CATCGCAGGG
* *
30437828 CAAAAATCAAAACACATCCAAACC
1 CAAAAATCAAAACAAAACCAAACC
30437852 CAAAAATCAACAACAAAACCAAA
1 CAAAAATCAA-AACAAAACCAAA
30437875 AGAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.64, C:0.30, G:0.00, T:0.06
Consensus pattern (24 bp):
CAAAAATCAAAACAAAACCAAACC
Found at i:30438705 original size:32 final size:32
Alignment explanation
Indices: 30438669--30438735 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
30438659 GCCTACACGC
* * * **
30438669 CCAAATTGGCCTTGTCCATGTGGCCCACACAG
1 CCAAATCGGCCTAGGCCATGTAACCCACACAG
*
30438701 CCAAATCGGCCTAGGCCATGTAACCCACACGG
1 CCAAATCGGCCTAGGCCATGTAACCCACACAG
30438733 CCA
1 CCA
30438736 CACACACCCG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.37, G:0.21, T:0.16
Consensus pattern (32 bp):
CCAAATCGGCCTAGGCCATGTAACCCACACAG
Found at i:30440440 original size:385 final size:385
Alignment explanation
Indices: 30439730--30440501 Score: 1544
Period size: 385 Copynumber: 2.0 Consensus size: 385
30439720 CAAGCGGTTA
30439730 GTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTCAATTTCTATCATGAATCTCTTAATGACTGAAGT
1 GTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTCAATTTCTATCATGAATCTCTTAATGACTGAAGT
30439795 GGTAATGTTTTTTCTCTGCGATTTGGGCATAGGGGAGGCTCGGACTGGTGAATTCAGTATTCTCG
66 GGTAATGTTTTTTCTCTGCGATTTGGGCATAGGGGAGGCTCGGACTGGTGAATTCAGTATTCTCG
30439860 TTTTAACAATAGTTAAACAAAGGGTTATCGTTGGTGGTAAGTTGGGTTTCTATTCGTTCTTGGTT
131 TTTTAACAATAGTTAAACAAAGGGTTATCGTTGGTGGTAAGTTGGGTTTCTATTCGTTCTTGGTT
30439925 GTCAATTCACTTGTAAATCCATTAAATTAATGTTGAGTATCTTGATTATAGGCTTTGGAGTGCTC
196 GTCAATTCACTTGTAAATCCATTAAATTAATGTTGAGTATCTTGATTATAGGCTTTGGAGTGCTC
30439990 GAGGACTATTTTAGCATCAAACAAAACCAGGTGTGTACCCGAAACGGAAAAAAAAGGGATTAGGC
261 GAGGACTATTTTAGCATCAAACAAAACCAGGTGTGTACCCGAAACGGAAAAAAAAGGGATTAGGC
30440055 GAAAAGCCGAAATTGCTTGCTGTTTGGATAGCAGCAGTAGGCTAACTTTGAAAAATCTCC
326 GAAAAGCCGAAATTGCTTGCTGTTTGGATAGCAGCAGTAGGCTAACTTTGAAAAATCTCC
30440115 GTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTCAATTTCTATCATGAATCTCTTAATGACTGAAGT
1 GTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTCAATTTCTATCATGAATCTCTTAATGACTGAAGT
30440180 GGTAATGTTTTTTCTCTGCGATTTGGGCATAGGGGAGGCTCGGACTGGTGAATTCAGTATTCTCG
66 GGTAATGTTTTTTCTCTGCGATTTGGGCATAGGGGAGGCTCGGACTGGTGAATTCAGTATTCTCG
30440245 TTTTAACAATAGTTAAACAAAGGGTTATCGTTGGTGGTAAGTTGGGTTTCTATTCGTTCTTGGTT
131 TTTTAACAATAGTTAAACAAAGGGTTATCGTTGGTGGTAAGTTGGGTTTCTATTCGTTCTTGGTT
30440310 GTCAATTCACTTGTAAATCCATTAAATTAATGTTGAGTATCTTGATTATAGGCTTTGGAGTGCTC
196 GTCAATTCACTTGTAAATCCATTAAATTAATGTTGAGTATCTTGATTATAGGCTTTGGAGTGCTC
30440375 GAGGACTATTTTAGCATCAAACAAAACCAGGTGTGTACCCGAAACGGAAAAAAAAGGGATTAGGC
261 GAGGACTATTTTAGCATCAAACAAAACCAGGTGTGTACCCGAAACGGAAAAAAAAGGGATTAGGC
30440440 GAAAAGCCGAAATTGCTTGCTGTTTGGATAGCAGCAGTAGGCTAACTTTGAAAAATCTCC
326 GAAAAGCCGAAATTGCTTGCTGTTTGGATAGCAGCAGTAGGCTAACTTTGAAAAATCTCC
30440500 GT
1 GT
30440502 AAATTGTGGA
Statistics
Matches: 387, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
385 387 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (385 bp):
GTGCTCGCTTAGTTTCGGTAAGTGTTTCTCTCAATTTCTATCATGAATCTCTTAATGACTGAAGT
GGTAATGTTTTTTCTCTGCGATTTGGGCATAGGGGAGGCTCGGACTGGTGAATTCAGTATTCTCG
TTTTAACAATAGTTAAACAAAGGGTTATCGTTGGTGGTAAGTTGGGTTTCTATTCGTTCTTGGTT
GTCAATTCACTTGTAAATCCATTAAATTAATGTTGAGTATCTTGATTATAGGCTTTGGAGTGCTC
GAGGACTATTTTAGCATCAAACAAAACCAGGTGTGTACCCGAAACGGAAAAAAAAGGGATTAGGC
GAAAAGCCGAAATTGCTTGCTGTTTGGATAGCAGCAGTAGGCTAACTTTGAAAAATCTCC
Found at i:30444045 original size:13 final size:13
Alignment explanation
Indices: 30444027--30444051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30444017 TTCTGATTTA
30444027 CTGTATCTGCATT
1 CTGTATCTGCATT
30444040 CTGTATCTGCAT
1 CTGTATCTGCAT
30444052 CCTAATGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (13 bp):
CTGTATCTGCATT
Found at i:30447186 original size:20 final size:20
Alignment explanation
Indices: 30447149--30447186 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30447139 AAAGTTTCTC
*
30447149 AAAATTACTACATCTCTTGT
1 AAAATTACTAAATCTCTTGT
*
30447169 AAAATTACTAAATTTCTT
1 AAAATTACTAAATCTCTT
30447187 ACAACCATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATTACTAAATCTCTTGT
Found at i:30447271 original size:20 final size:19
Alignment explanation
Indices: 30447228--30447304 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 19
30447218 AAAATTTTAA
*
30447228 ATTACTAAATATCTTATTG
1 ATTACTAAATTTCTTATTG
30447247 AATTACTAAATTTCTTATTAG
1 -ATTACTAAATTTCTTATT-G
* * **
30447268 ATTATTATATTTCTTACGG
1 ATTACTAAATTTCTTATTG
30447287 ATTTACTAAATTTCTTAT
1 A-TTACTAAATTTCTTAT
30447305 GTTGAAGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 44 0.94
21 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTACTAAATTTCTTATTG
Found at i:30454049 original size:26 final size:28
Alignment explanation
Indices: 30454014--30454071 Score: 102
Period size: 26 Copynumber: 2.1 Consensus size: 28
30454004 ATTTGAATAG
30454014 TTATAATATTAAATGAATAA-TATTTGT
1 TTATAATATTAAATGAATAATTATTTGT
30454041 TTAT-ATATTAAATGAATAATTATTTGT
1 TTATAATATTAAATGAATAATTATTTGT
30454068 TTAT
1 TTAT
30454072 TTTAAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (28 bp):
TTATAATATTAAATGAATAATTATTTGT
Found at i:30454072 original size:23 final size:25
Alignment explanation
Indices: 30454013--30454077 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 25
30454003 TATTTGAATA
30454013 GTTATAATATTAAATGAATAATATTT
1 GTTAT-ATATTAAATGAATAATATTT
30454039 GTTTATATATTAAATGAATAATTATTT
1 G-TTATATATTAAATGAATAA-TATTT
*
30454066 GTT-TATTTTAAA
1 GTTATATATTAAA
30454078 AACATTATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 8 0.22
26 18 0.50
27 10 0.28
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (25 bp):
GTTATATATTAAATGAATAATATTT
Found at i:30457971 original size:21 final size:21
Alignment explanation
Indices: 30457945--30457997 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
30457935 CATCTTCAGC
*
30457945 AACTTCTTCTTCT-TCAGCAAA
1 AACTTCTTCTTCTAT-AACAAA
*
30457966 AACTTCCTCTTCTATAACAAA
1 AACTTCTTCTTCTATAACAAA
30457987 AACTTCCTTCT
1 AACTT-CTTCT
30457998 GAACAACAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.30, C:0.30, G:0.02, T:0.38
Consensus pattern (21 bp):
AACTTCTTCTTCTATAACAAA
Found at i:30475077 original size:51 final size:50
Alignment explanation
Indices: 30474945--30475139 Score: 203
Period size: 51 Copynumber: 3.9 Consensus size: 50
30474935 GAAGTTGCTA
* * *
30474945 GATCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGA-ATGATA
1 GATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GATT
* * * * *
30474995 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTT
1 GATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-ATT
* * * * * *
30475046 GATCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGATGAAAAT
1 GATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-AGATT
* * *
30475097 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 GATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
30475140 GTATCATTTA
Statistics
Matches: 116, Mismatches: 26, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
50 39 0.34
51 76 0.66
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (50 bp):
GATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGATT
Found at i:30475139 original size:102 final size:101
Alignment explanation
Indices: 30474945--30475139 Score: 293
Period size: 101 Copynumber: 1.9 Consensus size: 101
30474935 GAAGTTGCTA
* * *
30474945 GATCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATGATAGGTCGCATGTGTAGT
1 GATCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGAATGAAAGGTCACATGTGTAGT
*
30475010 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTT
66 ACTATGTGCAGGCTACTATGCGAACCGGATAGCTTT
* * *
30475046 GATCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAG-ATGAAAATGGTCACATGTGTA
1 GATCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGAATG-AAA-GGTCACATGTGTA
*
30475110 GTACTATGTGCAGGCTACTATGTGAACCGG
64 GTACTATGTGCAGGCTACTATGCGAACCGG
30475140 GTATCATTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
100 3 0.04
101 41 0.49
102 40 0.48
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (101 bp):
GATCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGAATGAAAGGTCACATGTGTAGT
ACTATGTGCAGGCTACTATGCGAACCGGATAGCTTT
Found at i:30475168 original size:102 final size:100
Alignment explanation
Indices: 30474949--30475139 Score: 258
Period size: 102 Copynumber: 1.9 Consensus size: 100
30474939 TTGCTAGATC
* * * *
30474949 ACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATGATAGGTCGCATGTGTAGTACTA
1 ACGTGTGTA-TACTATGTGTAGGCTACTACATGTACCAGAATGAAAGGTCACATGTGTAGTACTA
* *
30475014 TGTGCAGGCTACTATGCGTACCGGATAGCTTTGATC
65 TGTGCAGGCTACTATGCGAACCGGATAGCTTTGATA
* *
30475050 ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAG-ATGAAAATGGTCACATGTGTAGTAC
1 ACGTGTGTA-TACTATGTGTAGGCTACTACATGTACCAGAATG-AAA-GGTCACATGTGTAGTAC
*
30475114 TATGTGCAGGCTACTATGTGAACCGG
63 TATGTGCAGGCTACTATGCGAACCGG
30475140 GTATCATTTA
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 3 0.04
101 37 0.46
102 40 0.50
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (100 bp):
ACGTGTGTATACTATGTGTAGGCTACTACATGTACCAGAATGAAAGGTCACATGTGTAGTACTAT
GTGCAGGCTACTATGCGAACCGGATAGCTTTGATA
Found at i:30479291 original size:49 final size:49
Alignment explanation
Indices: 30479237--30479334 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
30479227 ATTATGAGAA
*
30479237 CACTCTTGATGGGATCTACCTATGTGAGTGAAAGTGTGGCCACTTCTAG
1 CACTCTTGATGGAATCTACCTATGTGAGTGAAAGTGTGGCCACTTCTAG
30479286 CACTCTTGATGGAATCTACCTATGTGAGTGAAAGTGTGGCCACTTCTAG
1 CACTCTTGATGGAATCTACCTATGTGAGTGAAAGTGTGGCCACTTCTAG
30479335 GAGTTCAAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (49 bp):
CACTCTTGATGGAATCTACCTATGTGAGTGAAAGTGTGGCCACTTCTAG
Found at i:30480832 original size:21 final size:22
Alignment explanation
Indices: 30480793--30480835 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
30480783 TAGAAAAGCT
*
30480793 AAAACAAAAATCAAGATTAAAA
1 AAAACAAAAATCAACATTAAAA
*
30480815 AAAACTAAAA-CAACATTAAAA
1 AAAACAAAAATCAACATTAAAA
30480836 TCCTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.72, C:0.12, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAACAAAAATCAACATTAAAA
Found at i:30488450 original size:18 final size:18
Alignment explanation
Indices: 30488416--30488464 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
30488406 CCAAAAAATA
*
30488416 TTGAAAATT-ATTTTACT
1 TTGAAAATTAAATTTACT
30488433 TTGAAAATTAAATTTACT
1 TTGAAAATTAAATTTACT
* *
30488451 TAGAAAATAAAATT
1 TTGAAAATTAAATT
30488465 GTTATATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (18 bp):
TTGAAAATTAAATTTACT
Found at i:30495907 original size:21 final size:21
Alignment explanation
Indices: 30495883--30495922 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30495873 CTTGAACTTA
*
30495883 AAACCTCGAACCTTGAACCAT
1 AAACCTCGAACCCTGAACCAT
* *
30495904 AAACTTTGAACCCTGAACC
1 AAACCTCGAACCCTGAACC
30495923 CTGAGGTTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.33, G:0.10, T:0.20
Consensus pattern (21 bp):
AAACCTCGAACCCTGAACCAT
Found at i:30495962 original size:21 final size:20
Alignment explanation
Indices: 30495932--30495996 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
30495922 CCTGAGGTTC
30495932 AAGGTTTGGGTTTAGAATTT
1 AAGGTTTGGGTTTAGAATTT
* *
30495952 AAGGTTTTGGG-TTCGAGGTTT
1 AAGG-TTTGGGTTTAGA-ATTT
*
30495973 AAGGTTTGAGGTTTAGGATTT
1 AAGGTTTG-GGTTTAGAATTT
30495994 AAG
1 AAG
30495997 AATTTGGGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
20 12 0.33
21 21 0.58
22 3 0.08
ACGTcount: A:0.23, C:0.02, G:0.34, T:0.42
Consensus pattern (20 bp):
AAGGTTTGGGTTTAGAATTT
Found at i:30496042 original size:34 final size:33
Alignment explanation
Indices: 30495933--30496042 Score: 78
Period size: 34 Copynumber: 3.2 Consensus size: 33
30495923 CTGAGGTTCA
* * ** *
30495933 AGGTTTGGGTTTAGAATTTAAGGTTTTGGGTTCG
1 AGGTTAGGGTTT-GAGTTTAAGGTTAAGGGTTTG
* **
30495967 AGGTTTAAGGTTTGAGGTTT-AGGATTTAAGAATTTG
1 AGG-TTAGGGTTTGA-GTTTAAGG--TTAAGGGTTTG
*
30496003 GGGTTAGGGTTTGAGTTTAAGGTTCAAGGGTTTG
1 AGGTTAGGGTTTGAGTTTAAGGTT-AAGGGTTTG
30496037 AGGTTA
1 AGGTTA
30496043 CGAATTACGA
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
33 2 0.04
34 24 0.42
35 23 0.40
36 8 0.14
ACGTcount: A:0.22, C:0.02, G:0.35, T:0.41
Consensus pattern (33 bp):
AGGTTAGGGTTTGAGTTTAAGGTTAAGGGTTTG
Found at i:30503875 original size:18 final size:18
Alignment explanation
Indices: 30503852--30503888 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30503842 CACCACCGGA
30503852 GAGCCTAATGGCTCTCCT
1 GAGCCTAATGGCTCTCCT
30503870 GAGCCTAATGGCTCTCCT
1 GAGCCTAATGGCTCTCCT
30503888 G
1 G
30503889 CCTCCGGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.24, T:0.27
Consensus pattern (18 bp):
GAGCCTAATGGCTCTCCT
Found at i:30504256 original size:151 final size:155
Alignment explanation
Indices: 30504031--30504390 Score: 438
Period size: 154 Copynumber: 2.4 Consensus size: 155
30504021 CTTTAAACAA
* * ** *
30504031 ATTTTTATTTTTCAAAATGTAAACTTT-T-TCATTTTATTAAAAAAACACTGTTTTTCTTAAAGA
1 ATTTTTATTATTCAAAATCTAAACTTTCTCTTTTTTTATTAAAAAAACACTATTTTTCTTAAAGA
* * *
30504094 TTAAAGCTTTTATTTTGAACTAGTT-AAAAAAATCAAAACTGTT-TTTTTAGAAATTTAAAATTT
66 TTAAAGCTTTTACTTTGAAATAGTTAAAAAAAATCAAAAC-GTTGTTTTTAAAAATTTAAAATTT
30504157 CCTTTAAAAT-A-ACTAAAAAAT-AG
130 CCTTTAAAATAATACTAAAAAATCAG
* *
30504180 ATTTTTATTATTCAAAATCTAAACTTTCTCTTTTTTCTTTTAAAAAAA-ATTATTTTTCTTAAAG
1 ATTTTTATTATTCAAAATCTAAACTTTCTCTTTTTT-TATTAAAAAAACACTATTTTTCTTAAAG
*
30504244 ATTAAAGCTTTTACTTTGAAATAGTTGAAAAAAAAATCAAAACGTTGTTTTTAAAAATTTAAACT
65 ATTAAAGCTTTTACTTTGAAATAGTT--AAAAAAAATCAAAACGTTGTTTTTAAAAATTTAAAAT
* *
30504309 TTCCTTTAAAATAAATATTAAAAAATCAT
128 TTCCTTTAAAAT-AATACTAAAAAATCAG
* **
30504338 ATTTTTATTTCTTCAAAATCTAAA-TTT-TCTCCTTTTA--AAAAAAACACTATTTT
1 ATTTTTA-TTATTCAAAATCTAAACTTTCTCTTTTTTTATTAAAAAAACACTATTTT
30504391 CCCAAAATCA
Statistics
Matches: 180, Mismatches: 18, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
149 25 0.14
150 1 0.01
151 42 0.23
152 10 0.06
153 3 0.02
154 49 0.27
155 7 0.04
156 2 0.01
157 15 0.08
158 11 0.06
159 15 0.08
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.44
Consensus pattern (155 bp):
ATTTTTATTATTCAAAATCTAAACTTTCTCTTTTTTTATTAAAAAAACACTATTTTTCTTAAAGA
TTAAAGCTTTTACTTTGAAATAGTTAAAAAAAATCAAAACGTTGTTTTTAAAAATTTAAAATTTC
CTTTAAAATAATACTAAAAAATCAG
Found at i:30505236 original size:42 final size:42
Alignment explanation
Indices: 30505188--30505551 Score: 509
Period size: 42 Copynumber: 8.7 Consensus size: 42
30505178 AGTAAACAGA
*
30505188 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGTAC
1 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
*
30505230 CTCCACACCTTGGTCTCTAAATGCAATGAAAAGTGAATGAAC
1 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
30505272 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAAT-AAC
1 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
* *
30505313 CTCCACACCTGGGTCTCTAGATGCAATGAAAAGTGAATGGAC
1 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
* * * *
30505355 CTTCACACCTGGGTCTTTAAATGTAATGAAAAGTGAATGGAC
1 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
* * * * *
30505397 CTTCACACCTGAGTCTTTAAATGTAATGAAAAGTGAATGGAC
1 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
* *
30505439 CTCCACACCTAGGTCTCTAGATGCAATGAAAAGTGAATCG-AC
1 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAAT-GAAC
** * * *
30505481 CTCCGTACCTAGGTTTCAAAATGCAATGAAAAGTGAAT-AAC
1 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
*
30505522 CTCCACACCTGGGTCTCTAGATGCAATGAA
1 CTCCACACCTGGGTCTCTAAATGCAATGAA
30505552 TGTTTTCCTT
Statistics
Matches: 292, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
41 66 0.23
42 225 0.77
43 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (42 bp):
CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
Found at i:30505362 original size:125 final size:126
Alignment explanation
Indices: 30505188--30505551 Score: 534
Period size: 125 Copynumber: 2.9 Consensus size: 126
30505178 AGTAAACAGA
* * *
30505188 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGTACCTCCACACCTTGGTCTCTAAATG
1 CTCCACACCTGGGTCTCTAGATGCAATGAAAAGTGAATGGACCTCCACACCTAGGTCTCTAAATG
30505253 CAATGAAAAGTGAATGAACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAAT-AAC
66 CAATGAAAAGTGAATGAACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
* * *
30505313 CTCCACACCTGGGTCTCTAGATGCAATGAAAAGTGAATGGACCTTCACACCTGGGTCTTTAAATG
1 CTCCACACCTGGGTCTCTAGATGCAATGAAAAGTGAATGGACCTCCACACCTAGGTCTCTAAATG
* * * * * * *
30505378 TAATGAAAAGTGAATGGACCTTCACACCTGAGTCTTTAAATGTAATGAAAAGTGAATGGAC
66 CAATGAAAAGTGAATGAACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
* * ** * *
30505439 CTCCACACCTAGGTCTCTAGATGCAATGAAAAGTGAATCGACCTCCGTACCTAGGTTTCAAAATG
1 CTCCACACCTGGGTCTCTAGATGCAATGAAAAGTGAATGGACCTCCACACCTAGGTCTCTAAATG
*
30505504 CAATGAAAAGTGAAT-AACCTCCACACCTGGGTCTCTAGATGCAATGAA
66 CAATGAAAAGTGAATGAACCTCCACACCTGGGTCTCTAAATGCAATGAA
30505552 TGTTTTCCTT
Statistics
Matches: 210, Mismatches: 28, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
125 138 0.66
126 72 0.34
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (126 bp):
CTCCACACCTGGGTCTCTAGATGCAATGAAAAGTGAATGGACCTCCACACCTAGGTCTCTAAATG
CAATGAAAAGTGAATGAACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGAAC
Found at i:30505369 original size:167 final size:167
Alignment explanation
Indices: 30505188--30505551 Score: 525
Period size: 167 Copynumber: 2.2 Consensus size: 167
30505178 AGTAAACAGA
*
30505188 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGTACCTCCACACCTTG-GTCTCTAAAT
1 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGGACCTCCACACC-TGAGTCTCTAAAT
*
30505252 GCAATGAAAAGTGAATGAACCTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAAT-AACCTC
65 GCAATGAAAAGTGAATGAACCTCCACACCTAGGTCTCTAAATGCAATGAAAAGTGAATCAACCTC
* * * *
30505316 CACACCTGGGTCTCTAGATGCAATGAAAAGTGAATGGAC
130 CACACCTAGGTCTCAAAATGCAATGAAAAGTGAAT-AAC
* * * * *
30505355 CTTCACACCTGGGTCTTTAAATGTAATGAAAAGTGAATGGACCTTCACACCTGAGTCTTTAAATG
1 CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGGACCTCCACACCTGAGTCTCTAAATG
* * * *
30505420 TAATGAAAAGTGAATGGACCTCCACACCTAGGTCTCTAGATGCAATGAAAAGTGAATCGACCTCC
66 CAATGAAAAGTGAATGAACCTCCACACCTAGGTCTCTAAATGCAATGAAAAGTGAATCAACCTCC
** *
30505485 GTACCTAGGTTTCAAAATGCAATGAAAAGTGAATAAC
131 ACACCTAGGTCTCAAAATGCAATGAAAAGTGAATAAC
*
30505522 CTCCACACCTGGGTCTCTAGATGCAATGAA
1 CTCCACACCTGGGTCTCTAAATGCAATGAA
30505552 TGTTTTCCTT
Statistics
Matches: 173, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
166 2 0.01
167 137 0.79
168 34 0.20
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (167 bp):
CTCCACACCTGGGTCTCTAAATGCAATGAAAAGTGAATGGACCTCCACACCTGAGTCTCTAAATG
CAATGAAAAGTGAATGAACCTCCACACCTAGGTCTCTAAATGCAATGAAAAGTGAATCAACCTCC
ACACCTAGGTCTCAAAATGCAATGAAAAGTGAATAAC
Found at i:30505978 original size:8 final size:8
Alignment explanation
Indices: 30505965--30506025 Score: 65
Period size: 8 Copynumber: 7.8 Consensus size: 8
30505955 ATTTTTTTGG
30505965 TTTCTTTT
1 TTTCTTTT
30505973 TTTC-TTT
1 TTTCTTTT
30505980 TTTC-TTT
1 TTTCTTTT
30505987 TTTCTTTT
1 TTTCTTTT
*
30505995 TGTCTTTT
1 TTTCTTTT
30506003 TGTT-TTTT
1 T-TTCTTTT
*
30506011 TTTTTGTTT
1 TTTCT-TTT
30506020 TTTCTT
1 TTTCTT
30506026 GATTTAAGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
7 16 0.35
8 22 0.48
9 8 0.17
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (8 bp):
TTTCTTTT
Found at i:30505982 original size:7 final size:7
Alignment explanation
Indices: 30505965--30506025 Score: 65
Period size: 7 Copynumber: 8.9 Consensus size: 7
30505955 ATTTTTTTGG
30505965 TTTCTTTT
1 TTTC-TTT
30505973 TTTCTTT
1 TTTCTTT
30505980 TTTCTTT
1 TTTCTTT
30505987 TTTCTTT
1 TTTCTTT
30505994 TTGTC-TT
1 TT-TCTTT
*
30506001 TTT-GTT
1 TTTCTTT
30506007 TTT-TTT
1 TTTCTTT
*
30506013 TTTGTTT
1 TTTCTTT
30506020 TTTCTT
1 TTTCTT
30506026 GATTTAAGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
6 11 0.23
7 31 0.65
8 6 0.12
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (7 bp):
TTTCTTT
Found at i:30505990 original size:22 final size:21
Alignment explanation
Indices: 30505965--30506025 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
30505955 ATTTTTTTGG
*
30505965 TTTCTTTTTTTCTTTTTTCTTT
1 TTTCTTTTTGTC-TTTTTCTTT
*
30505987 TTTCTTTTTGTCTTTTTGTTT
1 TTTCTTTTTGTCTTTTTCTTT
30506008 TTT-TTTTTGT-TTTTTCTT
1 TTTCTTTTTGTCTTTTTCTT
30506026 GATTTAAGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.19
20 7 0.19
21 11 0.31
22 11 0.31
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (21 bp):
TTTCTTTTTGTCTTTTTCTTT
Found at i:30508862 original size:50 final size:49
Alignment explanation
Indices: 30508746--30508937 Score: 215
Period size: 50 Copynumber: 3.8 Consensus size: 49
30508736 TGCCTATAAA
* * * * * * *
30508746 CACGTGTGTAGTACTAAGTGTAGGCTACTACGTTTATCGATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGAAAG-T-TTGGT
* *
30508797 CACATGTGTAGTACTATGTGCAAGCTACTATGTGTACCGAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGAAAG-TTTGGT
* * *
30508847 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAAAGTTTGAT
1 CACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCG-AAAGTTTGGT
*
30508897 CACGTGTGTAGTACTATGTG-AAGGCTACTACGTGTATCGAA
1 CACGTGTGTAGTACTATGTGCAA-GCTACTACGTGTACCGAA
30508938 TGATAATAAT
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
49 3 0.02
50 78 0.64
51 40 0.33
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
CACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCGAAAGTTTGGT
Found at i:30516621 original size:50 final size:50
Alignment explanation
Indices: 30516444--30516641 Score: 236
Period size: 51 Copynumber: 3.9 Consensus size: 50
30516434 TGCCTATAAA
* * * *
30516444 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAGAT-TTGGT
* * * *
30516495 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGAAGGCTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAAAGATTTGGT
* * *
30516546 CACGTGTGTAGTACTATGTCCAGGCTACTACGTGAACCGGAAAG-TTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAAAGATTTGGT
* * *
30516596 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAGATT
30516642 ATAATTACAC
Statistics
Matches: 125, Mismatches: 20, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
49 4 0.03
50 41 0.33
51 76 0.61
52 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAGATTTGGT
Found at i:30516631 original size:101 final size:102
Alignment explanation
Indices: 30516444--30516631 Score: 263
Period size: 101 Copynumber: 1.9 Consensus size: 102
30516434 TGCCTATAAA
* * * * *
30516444 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTAAGTCCAGGCTACTACGTGAACCGAAAGATAATGATCACATGTGTAGTAC
* *
30516509 TATGTGCAGGCTACTATGTGTACCAGAAGGCTTTGGT
66 TATGTGAAGGCTACTACGTGTACCAGAAGGCTTTGGT
* * *
30516546 CACGTGTGTAGTACTATGTCCAGGCTACTACGTGAACCGGAAAG-T-TTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTAAGTCCAGGCTACTACGTGAACC-GAAAGATAATGATCACATGTGTAGTA
30516609 CTATGTGAAGGCTACTACGTGTA
65 CTATGTGAAGGCTACTACGTGTA
30516632 TCGAATGATT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
101 36 0.48
102 35 0.47
103 4 0.05
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTAAGTCCAGGCTACTACGTGAACCGAAAGATAATGATCACATGTGTAGTAC
TATGTGAAGGCTACTACGTGTACCAGAAGGCTTTGGT
Found at i:30531026 original size:25 final size:25
Alignment explanation
Indices: 30530998--30531062 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
30530988 CTATTTTTGT
* *
30530998 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATACTGAAACTACTATAGG
* * *
30531023 TAGTGTATACTGAGACTACTATAGA
1 TAGTATATACTGAAACTACTATAGG
30531048 TAG-ACTATACTGAAA
1 TAGTA-TATACTGAAA
30531063 ACACTCAAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:30538428 original size:150 final size:144
Alignment explanation
Indices: 30538276--30538747 Score: 477
Period size: 150 Copynumber: 3.2 Consensus size: 144
30538266 TGGCAAATTT
* * * * *
30538276 TTTTTTTTTTTTGCAAAATC-AAAATTTTC-TATAGAAAAAATCATTACTTTTCTTAAAAATCAA
1 TTTTTTTTTTTT-CAAAATCTAAAATTTTCATTTAAAAAAAATCA-TATTTTTCTTAAAGATTAA
* *
30538339 AACCTTATTTCGAAGTAGTTAAAAGAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAA
64 AACTTTATTT-GAAGTAGTTAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAA
** *
30538404 AATGATTTTAAAAAAATAGA
128 AAT-A-ACTAAAAAAA-ACA
* * **
30538424 TTTTTATTTTTT-AAAATCTAAACATTCTCATTTTTTAAAAAATACA-ATTTTTCTTAAAGATTA
1 TTTTTTTTTTTTCAAAATCTAAA-ATTTTCA-TTTAAAAAAAAT-CATATTTTTCTTAAAGATTA
** *
30538487 AAGTTTTTATTTTGAAGTAGTTAAAAAAAATCAAAACTTTATTTTAAAAATTTAAACTTTCCTTT
63 AA-ACTTTA-TTTGAAGTAGTTAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTT
30538552 AAAATAACTAAAAAAAACAA
126 AAAATAACTAAAAAAAAC-A
* * * *
30538572 ATTTTTATTTTTCAAAATCTAAACTTTCTCATTTAAAAAAAAAACACTATTTTTCTTAAAGATTA
1 TTTTTTTTTTTTCAAAATCTAAAATTT-TCATTT-AAAAAAAATCA-TATTTTTCTTAAAGATTA
* * *
30538637 AAGCTTTTACTTTAAAATAGTTGAAAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCC
63 AAAC-TTTA-TTTGAAGTAGTT---AAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCC
30538702 TTTAAAATAACT-AAAAAAACA
123 TTTAAAATAACTAAAAAAAACA
* *
30538723 TATTTTTATTTCTTCAAAGTCTAAA
1 T-TTTTT-TTTTTTCAAAATCTAAA
30538748 CTTTCTCCCT
Statistics
Matches: 271, Mismatches: 34, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
146 6 0.02
147 4 0.01
148 41 0.15
149 36 0.13
150 100 0.37
151 6 0.02
152 13 0.05
153 65 0.24
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.41
Consensus pattern (144 bp):
TTTTTTTTTTTTCAAAATCTAAAATTTTCATTTAAAAAAAATCATATTTTTCTTAAAGATTAAAA
CTTTATTTGAAGTAGTTAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAAT
AACTAAAAAAAACA
Found at i:30538713 original size:153 final size:148
Alignment explanation
Indices: 30538354--30538781 Score: 561
Period size: 150 Copynumber: 2.8 Consensus size: 148
30538344 TATTTCGAAG
* **
30538354 TAGTTAAAAGAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATGATTTTAAAAAA
1 TAGTTAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAAT-A-ACTAAAAAA
* * * * ** *
30538419 ATAGATTTTTATTTTTTAAAATCTAAACATTCTCATTTTTTAAAAAATACAATTTTTCTTAAAGA
64 ACAAATTTTTATTTTTCAAAATCTAAACTTTCTCATTTTAAAAAAAAAACAATTTTTCTTAAAGA
* * * *
30538484 TTAAAGTTTTTATTTTGAAG
129 TTAAAGCTTTTACTTTAAAA
*
30538504 TAGTTAAAAAAAATCAAAACTTTATTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAAA
1 TAGTTAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACT-AAAAAAA
30538569 CAAATTTTTATTTTTCAAAATCTAAACTTTCTCA-TTTAAAAAAAAAACACTATTTTTCTTAAAG
65 CAAATTTTTATTTTTCAAAATCTAAACTTTCTCATTTTAAAAAAAAAACA--ATTTTTCTTAAAG
30538633 ATTAAAGCTTTTACTTTAAAA
128 ATTAAAGCTTTTACTTTAAAA
30538654 TAGTTGAAAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAA
1 TAGTT---AAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAA
* * *
30538719 AACATATTTTTATTTCTTCAAAGTCTAAACTTTCTCCCTTTTTAAAAGAGAAAAACTAATTTT
63 AACAAATTTTTATTT-TTCAAAATCTAAACTTTCT--CATTTTAAAA-A-AAAAAC-AATTTT
30538782 CCCAAAATGA
Statistics
Matches: 246, Mismatches: 19, Indels: 19
0.87 0.07 0.07
Matches are distributed among these distances:
148 13 0.05
149 38 0.15
150 86 0.35
152 19 0.08
153 69 0.28
155 1 0.00
156 7 0.03
157 6 0.02
158 6 0.02
159 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (148 bp):
TAGTTAAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAAC
AAATTTTTATTTTTCAAAATCTAAACTTTCTCATTTTAAAAAAAAAACAATTTTTCTTAAAGATT
AAAGCTTTTACTTTAAAA
Found at i:30539137 original size:9 final size:9
Alignment explanation
Indices: 30539123--30539157 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
30539113 TAATAGTATT
30539123 TAATAATAG
1 TAATAATAG
30539132 TAATAATAG
1 TAATAATAG
* *
30539141 TGATGATAG
1 TAATAATAG
30539150 TAATAATA
1 TAATAATA
30539158 ATTTGGGCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (9 bp):
TAATAATAG
Found at i:30546984 original size:17 final size:16
Alignment explanation
Indices: 30546954--30546988 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
30546944 AATAGGAAGA
*
30546954 AATATATATTAAATTG
1 AATATATATGAAATTG
30546970 AATATCATATGAAATTG
1 AATAT-ATATGAAATTG
30546987 AA
1 AA
30546989 GCAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (16 bp):
AATATATATGAAATTG
Found at i:30557848 original size:16 final size:15
Alignment explanation
Indices: 30557821--30557854 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
30557811 ATAACTAGTA
*
30557821 TATAATTATATTTAT
1 TATAATTATATTAAT
30557836 TATAATATATATTAAT
1 TATAAT-TATATTAAT
30557852 TAT
1 TAT
30557855 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:30558565 original size:25 final size:27
Alignment explanation
Indices: 30558523--30558576 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
30558513 TTCTCCTAAA
**
30558523 TTTCAATTTTATTTAATTATTAA-ATT
1 TTTCAATTTTATGGAATTATTAATATT
30558549 TTTCAA-TTTATGGAATTATTAATATT
1 TTTCAATTTTATGGAATTATTAATATT
30558575 TT
1 TT
30558577 ATACTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (27 bp):
TTTCAATTTTATGGAATTATTAATATT
Found at i:30570456 original size:34 final size:34
Alignment explanation
Indices: 30570413--30570482 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
30570403 TTCAAGAGGA
*
30570413 AAGTTAGAACACCAACACAAAAATCACAACTAAG
1 AAGTTAGAACACCAAAACAAAAATCACAACTAAG
* *
30570447 AAGTTAGAACACCAAAACGAGAATCACAACTAAG
1 AAGTTAGAACACCAAAACAAAAATCACAACTAAG
30570481 AA
1 AA
30570483 ATAAAAGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.11
Consensus pattern (34 bp):
AAGTTAGAACACCAAAACAAAAATCACAACTAAG
Found at i:30572188 original size:23 final size:23
Alignment explanation
Indices: 30572138--30572182 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
30572128 AAGGCAATGT
*
30572138 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
30572161 TGTAATACCCCGAAAATTACTA
1 TGTAATACCCCGAAAATTACTA
30572183 TAGTAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:30573692 original size:44 final size:44
Alignment explanation
Indices: 30573641--30573728 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
30573631 ATATGTGAGT
* *
30573641 CTAGTTTCAGATAAAATTTGTGGATCTTAATTTAGAGTTCTGTA
1 CTAGTTTCAGATAAAATTTGCGGATCTTAATTCAGAGTTCTGTA
30573685 CTAGTTTCAGATAAAATTTGCGGATCTTAATTCAGAGTTCTGTA
1 CTAGTTTCAGATAAAATTTGCGGATCTTAATTCAGAGTTCTGTA
30573729 GCTCAAGATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (44 bp):
CTAGTTTCAGATAAAATTTGCGGATCTTAATTCAGAGTTCTGTA
Found at i:30582480 original size:12 final size:13
Alignment explanation
Indices: 30582463--30582491 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
30582453 CTCATACATG
30582463 AATAAATAAA-GC
1 AATAAATAAATGC
30582475 AATAAATAAATGC
1 AATAAATAAATGC
30582488 AATA
1 AATA
30582492 GATATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:30590003 original size:7 final size:7
Alignment explanation
Indices: 30589991--30590046 Score: 112
Period size: 7 Copynumber: 8.0 Consensus size: 7
30589981 CAAAATTTCG
30589991 TTTCTTT
1 TTTCTTT
30589998 TTTCTTT
1 TTTCTTT
30590005 TTTCTTT
1 TTTCTTT
30590012 TTTCTTT
1 TTTCTTT
30590019 TTTCTTT
1 TTTCTTT
30590026 TTTCTTT
1 TTTCTTT
30590033 TTTCTTT
1 TTTCTTT
30590040 TTTCTTT
1 TTTCTTT
30590047 ATTTTACCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTCTTT
Found at i:30591401 original size:17 final size:17
Alignment explanation
Indices: 30591379--30591423 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
30591369 CGATGTTTGA
*
30591379 CTAAAATCACGGTTTTT
1 CTAAAAACACGGTTTTT
*
30591396 C-AAAAACAAAGGTTTTT
1 CTAAAAAC-ACGGTTTTT
30591413 CTAAAAACACG
1 CTAAAAACACG
30591424 AACTGGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.22
17 12 0.52
18 6 0.26
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (17 bp):
CTAAAAACACGGTTTTT
Found at i:30591812 original size:18 final size:20
Alignment explanation
Indices: 30591776--30591813 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
30591766 GGATAATATC
*
30591776 ATATTAAAATTAGATTAAAT
1 ATATTAAAATAAGATTAAAT
30591796 ATATT-AAATAAGA-TAAAT
1 ATATTAAAATAAGATTAAAT
30591814 TAAATAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
ATATTAAAATAAGATTAAAT
Found at i:30592011 original size:15 final size:15
Alignment explanation
Indices: 30591981--30592014 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30591971 TTAACTGCTT
**
30591981 AAAAATAAGTGTTGA
1 AAAAATAAGTACTGA
30591996 AAAAATAAGTACTGA
1 AAAAATAAGTACTGA
30592011 AAAA
1 AAAA
30592015 TTTAGTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.21
Consensus pattern (15 bp):
AAAAATAAGTACTGA
Found at i:30593670 original size:24 final size:24
Alignment explanation
Indices: 30593642--30593687 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
30593632 ACCAAAATGA
30593642 CCACATACATATATCAACATAAGG
1 CCACATACATATATCAACATAAGG
30593666 CCACATACATATATCAACATAA
1 CCACATACATATATCAACATAA
30593688 CAACCAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.26, G:0.04, T:0.22
Consensus pattern (24 bp):
CCACATACATATATCAACATAAGG
Found at i:30593697 original size:24 final size:24
Alignment explanation
Indices: 30593641--30593698 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
30593631 TACCAAAATG
*
30593641 ACCACATACATATATCAACATAAG
1 ACCACATACATATATCAACATAAA
*
30593665 GCCACATACATATATCAACATAACA
1 ACCACATACATATATCAACATAA-A
30593690 ACCA-ATACA
1 ACCACATACA
30593699 AAGCCAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.19
Consensus pattern (24 bp):
ACCACATACATATATCAACATAAA
Found at i:30598387 original size:90 final size:89
Alignment explanation
Indices: 30598332--30598665 Score: 632
Period size: 90 Copynumber: 3.7 Consensus size: 89
30598322 TGTAACTCAT
30598332 TATCAAAATTTTGATATATGGAATACAAATTCTAAACACTTTAAATAATTAATATTAATTATTTA
1 TATCAAAATTTTGATATATGGAATACAAATTCTAAACACTTTAAATAATTAATATT-ATTATTTA
30598397 AAGTGTTTAGAATTTGTATTCCATA
65 AAGTGTTTAGAATTTGTATTCCATA
30598422 TATCAAAATTTTGATATATGGAATACAAATTCTAAACACTTTAAATAATTAATATTAATTATTTA
1 TATCAAAATTTTGATATATGGAATACAAATTCTAAACACTTTAAATAATTAATATT-ATTATTTA
30598487 AAGTGTTTAGAATTTGTATTCCATA
65 AAGTGTTTAGAATTTGTATTCCATA
30598512 TATCAAAATTTTGATATATGGAATACAAATTCTAAACACTTTAAATAATTAATATTAATTATTTA
1 TATCAAAATTTTGATATATGGAATACAAATTCTAAACACTTTAAATAATTAATATT-ATTATTTA
30598577 AAGTGTTTAGAATTTGTATTCCATA
65 AAGTGTTTAGAATTTGTATTCCATA
30598602 TATCAAAATTTTGATATATGGAATACAAATTCTAAACACTTTAAATAATTAATATTAATTATTT
1 TATCAAAATTTTGATATATGGAATACAAATTCTAAACACTTTAAATAATTAATATT-ATTATTT
30598666 GTAAAATTTA
Statistics
Matches: 244, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 244 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (89 bp):
TATCAAAATTTTGATATATGGAATACAAATTCTAAACACTTTAAATAATTAATATTATTATTTAA
AGTGTTTAGAATTTGTATTCCATA
Found at i:30600976 original size:28 final size:28
Alignment explanation
Indices: 30600921--30600977 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
30600911 TAATTTAATA
*
30600921 AATTTATTAATATGATATTTGTACTTTT
1 AATTTATTAATATGATACTTGTACTTTT
*
30600949 AATTTATTTAATAT-AGTACTTGTATTTTT
1 AATTTA-TTAATATGA-TACTTGTACTTTT
30600978 CTTTTGGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.58
Consensus pattern (28 bp):
AATTTATTAATATGATACTTGTACTTTT
Found at i:30603836 original size:23 final size:23
Alignment explanation
Indices: 30603809--30603853 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
30603799 TTGAAGGACC
30603809 TTGAAAAGACCTTGAAAAAGATA
1 TTGAAAAGACCTTGAAAAAGATA
30603832 TTGAAAAGACCTTGAAAAAGAT
1 TTGAAAAGACCTTGAAAAAGAT
30603854 GTAGAATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (23 bp):
TTGAAAAGACCTTGAAAAAGATA
Found at i:30603852 original size:12 final size:11
Alignment explanation
Indices: 30603805--30603849 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
30603795 AAGTTTGAAG
30603805 GACCTTGAAAA
1 GACCTTGAAAA
30603816 GACCTTGAAAAA
1 GACCTTG-AAAA
**
30603828 GATATTGAAAA
1 GACCTTGAAAA
30603839 GACCTTGAAAA
1 GACCTTGAAAA
30603850 AGATGTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (11 bp):
GACCTTGAAAA
Found at i:30604384 original size:30 final size:30
Alignment explanation
Indices: 30604348--30604410 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
30604338 ACAAGAAAGA
30604348 AATGCATAACTTTCC-AGAACTCAATTTTCC
1 AATGCATAAC-TTCCAAGAACTCAATTTTCC
30604378 AATGCATAACTTCCAAGAACTCAATTTTCC
1 AATGCATAACTTCCAAGAACTCAATTTTCC
30604408 AAT
1 AAT
30604411 CTTTCTCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (30 bp):
AATGCATAACTTCCAAGAACTCAATTTTCC
Found at i:30610685 original size:15 final size:15
Alignment explanation
Indices: 30610665--30610694 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
30610655 AAAAGTAAAG
30610665 ATCTCTTAACTTTTA
1 ATCTCTTAACTTTTA
30610680 ATCTCTTAACTTTTA
1 ATCTCTTAACTTTTA
30610695 CTTGATTANN
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (15 bp):
ATCTCTTAACTTTTA
Found at i:30612407 original size:38 final size:39
Alignment explanation
Indices: 30612363--30612439 Score: 147
Period size: 38 Copynumber: 2.0 Consensus size: 39
30612353 TCTTGCCCAG
30612363 ATAGGAATTTTTGTTATTTATTTAGAAG-TAAATATATT
1 ATAGGAATTTTTGTTATTTATTTAGAAGTTAAATATATT
30612401 ATAGGAATTTTTGTTATTTATTTAGAAGTTAAATATATT
1 ATAGGAATTTTTGTTATTTATTTAGAAGTTAAATATATT
30612440 TTAATAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 28 0.74
39 10 0.26
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (39 bp):
ATAGGAATTTTTGTTATTTATTTAGAAGTTAAATATATT
Found at i:30612449 original size:39 final size:38
Alignment explanation
Indices: 30612367--30612449 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
30612357 GCCCAGATAG
*
30612367 GAATTTTTGTTATTTATTTAGAAGTAAATATATTATAG
1 GAATTTTTGTTATTTATTTAGAAGTAAATATATTATAA
*
30612405 GAATTTTTGTTATTTATTTAGAAGTTAAATATATTTTAA
1 GAATTTTTGTTATTTATTTAGAAG-TAAATATATTATAA
*
30612444 TAATTT
1 GAATTT
30612450 ATCTTGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 24 0.59
39 17 0.41
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (38 bp):
GAATTTTTGTTATTTATTTAGAAGTAAATATATTATAA
Found at i:30612984 original size:45 final size:45
Alignment explanation
Indices: 30612896--30613042 Score: 168
Period size: 45 Copynumber: 3.2 Consensus size: 45
30612886 TTATAAAATC
* * *
30612896 AAATAATTATTTCAAATATCATTATTATTTTTATATGTAAAATATTTT
1 AAATAATTATTCCAAATA-C--CATTATTTTTATATGTGAAATATTTT
* * *
30612944 AAATACTTATTCCAAATACCATTATTTTTATGTGTGAAATATTTC
1 AAATAATTATTCCAAATACCATTATTTTTATATGTGAAATATTTT
* * * * *
30612989 AATTAATTATTTCAAATATCACTATTATTATATGTGAAATATTTT
1 AAATAATTATTCCAAATACCATTATTTTTATATGTGAAATATTTT
30613034 AAATAATTA
1 AAATAATTA
30613043 ATTCACATAC
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
45 67 0.80
47 1 0.01
48 16 0.19
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (45 bp):
AAATAATTATTCCAAATACCATTATTTTTATATGTGAAATATTTT
Found at i:30614123 original size:27 final size:28
Alignment explanation
Indices: 30614071--30614123 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
30614061 AGTTAATAAA
**
30614071 TTCTCTTTGAGTTTTTCTTTTCAAGAAT
1 TTCTCTTTGAGTTTTTCTTTAAAAGAAT
30614099 TTCTC-TTGAGTATTTT-TTTAAAAGA
1 TTCTCTTTGAGT-TTTTCTTTAAAAGA
30614124 GTTTTAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (28 bp):
TTCTCTTTGAGTTTTTCTTTAAAAGAAT
Found at i:30616654 original size:26 final size:25
Alignment explanation
Indices: 30616601--30616677 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 25
30616591 ATGACCGTAA
* *
30616601 TGCCCCTAGAGGGTAAATGACT-ATTT
1 TGCCCCT-GAGGTTAAATGATTGA-TT
30616627 TGCCCCTCGAGGTTAAATGATTGATT
1 TGCCCCT-GAGGTTAAATGATTGATT
* *
30616653 TG--TCTGTGGTTAAATGATTGATT
1 TGCCCCTGAGGTTAAATGATTGATT
30616676 TG
1 TG
30616678 TCTGTGTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 19 0.42
24 2 0.04
26 23 0.51
27 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (25 bp):
TGCCCCTGAGGTTAAATGATTGATT
Found at i:30616667 original size:23 final size:23
Alignment explanation
Indices: 30616637--30616707 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
30616627 TGCCCCTCGA
30616637 GGTTAAATGATTGATTTGTCTGT
1 GGTTAAATGATTGATTTGTCTGT
30616660 GGTTAAATGATTGATTTGTCTGT
1 GGTTAAATGATTGATTTGTCTGT
* ** *
30616683 GTTTGGTATGACTGATTTGTCTGT
1 GGTT-AAATGATTGATTTGTCTGT
30616707 G
1 G
30616708 ATTTGAATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
23 26 0.60
24 17 0.40
ACGTcount: A:0.18, C:0.06, G:0.28, T:0.48
Consensus pattern (23 bp):
GGTTAAATGATTGATTTGTCTGT
Found at i:30616698 original size:24 final size:23
Alignment explanation
Indices: 30616642--30616723 Score: 101
Period size: 24 Copynumber: 3.5 Consensus size: 23
30616632 CTCGAGGTTA
* * *
30616642 AATGATTGATTTGTCTGTGGTTA
1 AATGACTGATTTGTCTGTGTTTG
*
30616665 AATGATTGATTTGTCTGTGTTTGG
1 AATGACTGATTTGTCTGTGTTT-G
*
30616689 TATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTGTG-TTTG
30616713 AATGACTGATT
1 AATGACTGATT
30616724 CTGAGCATGG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
23 21 0.40
24 28 0.54
25 3 0.06
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.48
Consensus pattern (23 bp):
AATGACTGATTTGTCTGTGTTTG
Found at i:30616969 original size:32 final size:32
Alignment explanation
Indices: 30616901--30616991 Score: 94
Period size: 32 Copynumber: 2.9 Consensus size: 32
30616891 ATGCTACTGT
* * * * *
30616901 TGGCTTTGTGCCGGTCATAGTACCGTTGCTAT
1 TGGCTTTGTGCCGATCATATTACCGTTACCAA
30616933 TGGCTTTGTGCCGATCATATTACCGTTACCAA
1 TGGCTTTGTGCCGATCATATTACCGTTACCAA
* * * *
30616965 TGGCTATGCGCCGA-CATTTTACTGTTA
1 TGGCTTTGTGCCGATCATATTACCGTTA
30616992 TTCATGGCTG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 11 0.22
32 39 0.78
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (32 bp):
TGGCTTTGTGCCGATCATATTACCGTTACCAA
Found at i:30617145 original size:22 final size:21
Alignment explanation
Indices: 30617120--30617184 Score: 51
Period size: 22 Copynumber: 3.0 Consensus size: 21
30617110 ATTACTATAC
30617120 TTATGGCTTGTAGTCATTCTGT
1 TTATGGCTT-TAGTCATTCTGT
* * *
30617142 TTATAGCTTATAG-CTATCCTAT
1 TTATGGCTT-TAGTC-ATTCTGT
*
30617164 TTATGACTCTTAGTCATTCTG
1 TTATGGCT-TTAGTCATTCTG
30617185 ACTACTAGCA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
21 1 0.03
22 29 0.91
23 2 0.06
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (21 bp):
TTATGGCTTTAGTCATTCTGT
Found at i:30623320 original size:18 final size:19
Alignment explanation
Indices: 30623297--30623333 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30623287 TTGACATATC
*
30623297 AAAATTAT-ATATAAATAA
1 AAAATTATCATAAAAATAA
30623315 AAAATTATCATAAAAATAA
1 AAAATTATCATAAAAATAA
30623334 GAAGTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATTATCATAAAAATAA
Found at i:30624608 original size:299 final size:299
Alignment explanation
Indices: 30624070--30624670 Score: 1121
Period size: 299 Copynumber: 2.0 Consensus size: 299
30624060 ATTAGGGACT
30624070 ATAACACCTTATACCTATCCCGGTCGCTGAGCCCGAATATAAGGATGCCATACCACCGTCTCATG
1 ATAACACCTTATACCTATCCCGGTCGCTGAGCCCGAATATAAGGATGCCATACCACCGTCTCATG
*
30624135 TCATACACAACAATTAAAAGCTCGTTCTCAATGAAACGTCTTCCATTTTAGTATTCGTATAGGTT
66 TCATACACAACAATTAAAAGCTCATTCTCAATGAAACGTCTTCCATTTTAGTATTCGTATAGGTT
30624200 TTAAGTCAATCTTACTTCTAAGTTATCATTGTTACATGCTAAACATGCATCAGATAGTCTTATAA
131 TTAAGTCAATCTTACTTCTAAGTTATCATTGTTACATGCTAAACATGCATCAGATAGTCTTATAA
30624265 CAATAGTTTAACATGCATAAGGTCTGTTTAGAAAAATCTCAAAACTGACTACATAGGTATTGGTA
196 CAATAGTTTAACATGCATAAGGTCTGTTTAGAAAAATCTCAAAACTGACTACATAGGTATTGGTA
30624330 CTAGAATATGGGTACCAATATTTCTCTCAAGTGGTATCG
261 CTAGAATATGGGTACCAATATTTCTCTCAAGTGGTATCG
* * * *
30624369 ATAACACCTTATACCTATCCCGGTCGCTGAGCCCGAATATCAGGATGGCATACTATCGTCTCATG
1 ATAACACCTTATACCTATCCCGGTCGCTGAGCCCGAATATAAGGATGCCATACCACCGTCTCATG
* * *
30624434 TTATACACAACAGTTAAAAGTTCATTCTCAATGAAACGTCTTCCATTTTAGTATTCGTATAGGTT
66 TCATACACAACAATTAAAAGCTCATTCTCAATGAAACGTCTTCCATTTTAGTATTCGTATAGGTT
*
30624499 TTAAGTCAATCTTACTTTTAAGTTATCATTGTTACATGCTAAACATGCATCAGATAGTCTTATAA
131 TTAAGTCAATCTTACTTCTAAGTTATCATTGTTACATGCTAAACATGCATCAGATAGTCTTATAA
30624564 CAATAGTTTAACATGCATAAGGTCTGTTTAGAAAAATCTCAAAACTGACTACATAGGTATTGGTA
196 CAATAGTTTAACATGCATAAGGTCTGTTTAGAAAAATCTCAAAACTGACTACATAGGTATTGGTA
30624629 CTAGAATATGGGTACCAATATTTCTCTCAAGTGGTATCG
261 CTAGAATATGGGTACCAATATTTCTCTCAAGTGGTATCG
30624668 ATA
1 ATA
30624671 CCGCTTGGAA
Statistics
Matches: 293, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
299 293 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (299 bp):
ATAACACCTTATACCTATCCCGGTCGCTGAGCCCGAATATAAGGATGCCATACCACCGTCTCATG
TCATACACAACAATTAAAAGCTCATTCTCAATGAAACGTCTTCCATTTTAGTATTCGTATAGGTT
TTAAGTCAATCTTACTTCTAAGTTATCATTGTTACATGCTAAACATGCATCAGATAGTCTTATAA
CAATAGTTTAACATGCATAAGGTCTGTTTAGAAAAATCTCAAAACTGACTACATAGGTATTGGTA
CTAGAATATGGGTACCAATATTTCTCTCAAGTGGTATCG
Found at i:30626560 original size:14 final size:14
Alignment explanation
Indices: 30626541--30626568 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30626531 TAAAATTATA
30626541 TTTAATAATTCATT
1 TTTAATAATTCATT
30626555 TTTAATAATTCATT
1 TTTAATAATTCATT
30626569 AATAAACTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:30645641 original size:21 final size:20
Alignment explanation
Indices: 30645617--30645656 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
30645607 AAGTGATGTG
*
30645617 AAAAATGAAAAGATGAAAATC
1 AAAAATGAAAA-AAGAAAATC
30645638 AAAAATGAAAAAAGAAAAT
1 AAAAATGAAAAAAGAAAAT
30645657 GGAGAGGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAAATGAAAAAAGAAAATC
Found at i:30646404 original size:51 final size:51
Alignment explanation
Indices: 30646324--30646424 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
30646314 AGAAAAGGCC
30646324 AAATCTTGTACTCTTGGGTTACAACGGGAAAAGATGGTACAAATTTTGCAG
1 AAATCTTGTACTCTTGGGTTACAACGGGAAAAGATGGTACAAATTTTGCAG
* *
30646375 AAATCTTTTACTCTTGGGTTACAATGGGAAAAGATGGTACAAATTTTGCA
1 AAATCTTGTACTCTTGGGTTACAACGGGAAAAGATGGTACAAATTTTGCA
30646425 TCCCATTGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.32
Consensus pattern (51 bp):
AAATCTTGTACTCTTGGGTTACAACGGGAAAAGATGGTACAAATTTTGCAG
Found at i:30646926 original size:100 final size:99
Alignment explanation
Indices: 30646739--30647006 Score: 414
Period size: 100 Copynumber: 2.7 Consensus size: 99
30646729 ACCATAGATT
* *
30646739 TTACTTCCTT-GCAATGCAGTGGAATAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGC-GTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
30646803 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
65 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
30646838 TTACTTCCTTAGCCGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAG-CGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
30646903 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
65 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * * * * *
30646938 TTACTTCCCTGAAG-GTGCGGTGGAACAGATTGAAGCTACGACAGCGAATCTGGTTTCCCCGACA
1 TTACTT-CCT-TAGCGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA
30647002 TTGCA
64 TTGCA
30647007 GTTGAACAAA
Statistics
Matches: 157, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
99 10 0.06
100 141 0.90
101 4 0.03
102 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (99 bp):
TTACTTCCTTAGCGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATT
GCAATTAAAAAGATTGAAGCCACAACGGCGGATC
Found at i:30646996 original size:50 final size:50
Alignment explanation
Indices: 30646753--30647022 Score: 220
Period size: 50 Copynumber: 5.4 Consensus size: 50
30646743 TTCCTTGCAA
* *
30646753 TGCAGTGGAATAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAG
* ** * * * *** * **
30646803 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGCCG
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-TAG
*
30646853 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAG
* ** * * * ***
30646903 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA-AGG
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA-G
* * * * * *
30646953 TGCGGTGGAACAGATTGAAGCTACGACAGCGAATCTGGTTTCCCCGACAT
1 TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAG
* *
30647003 TGCAGTTGAACAAATTGAAG
1 TGCAGTGGAACAGATTGAAG
30647023 ATTATAGATC
Statistics
Matches: 163, Mismatches: 53, Indels: 8
0.73 0.24 0.04
Matches are distributed among these distances:
49 5 0.03
50 153 0.94
51 5 0.03
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (50 bp):
TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAG
Found at i:30647187 original size:132 final size:132
Alignment explanation
Indices: 30647016--30648076 Score: 1225
Period size: 132 Copynumber: 8.0 Consensus size: 132
30647006 AGTTGAACAA
* * * **
30647016 ATTGAAGATTATAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGTGGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
*
30647081 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTA-TCTCCCTGGGCAGCAGTGGAA
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAA
30647145 TAG
130 TAG
* * * *
30647148 ATTAAAGATAACATATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
* *
30647213 CT-CCTCATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAG-AGCGGAA
66 CTCCCTGA-GGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAA
*
30647276 TGG
130 TAG
** * * * * *
30647279 ATTGAAGA-TAGCAGATCTTGCCTTCCTACA-TAGATAGCGAAGCAGATCGAAGATGGCAGATTT
1 ATTGAAGATTA-CAGATCTTATCTCCCTA-AGCAG-TAGTGGAGCAGATCAAAGATGGCAGATTT
* * * * *
30647342 TACCT-CCTCGTGGTTACAATGGAGTACATTGAAGCTAGTAATTCTACTTCCCTGGGCAACAGCG
63 TACCTCCCT-GAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTG
30647406 GAATAG
127 GAATAG
** * * *
30647412 ATTGAAGA-TAGCAGATCTTGCCTTCCT--GCA-TAGACATCGAAGCAGATCGAAGATGGCAGAT
1 ATTGAAGATTA-CAGATCTTATCTCCCTAAGCAGTAG---T-GGAGCAGATCAAAGATGGCAGAT
* * * * *
30647473 TTTACCT-CCTCGTGGTTACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTAGACAACAG
61 TTTACCTCCCT-GAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAG
*
30647537 TAGAATAG
125 TGGAATAG
* * * * * *
30647545 ATTGAAGATTTCAAATCTTGTCTTCCTAAGCAGTAGTGGGGCAGATCAAAGATGG-TGAATTTTA
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAG-ATTTTA
* * * *
30647609 CCTCCCTGTGGTTACAGTGGAGTACATTGAAACCGGTAATTTTACTTCCCTGGGCAGCAGTGGAA
65 CCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAA
30647674 TAG
130 TAG
* * * *
30647677 ATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAATGGAGCAGATCAAAGATGG-TGAATTTTA
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAG-ATTTTA
* * * *
30647741 CCTCCCTGTGGTTACAGTGGAGTACATTGAAACCGGTAATTTTACTTCCCTGGGCAGCAGTGGAA
65 CCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAA
30647806 TAG
130 TAG
* * * * *
30647809 ATTGAAGATTACAGGTCTTATCTCCCTAAGCAGTAGTGGAGCAGGTCGAAGATAGCGGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
* * * * * *
30647874 CTCCCTGAGATTACAGTGGAGTACATTGAAGCCCGTAGTTCTA-TCTCTCTAGGCAGTAGTGGAA
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAA
30647938 TAG
130 TAG
*
30647941 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGAAGCAGATCAAAGATGGCAGATTTTAC
1 ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
* * * * *
30648006 CTCCCTGAGGTTGCAGTGGAGTATATTGAAGCCAGTAATTC-AATTCCCCTGGTCGGCAGTGGAA
66 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTT-CCCTGGGCAGCAGTGGAA
*
30648070 TCG
130 TAG
30648073 ATTG
1 ATTG
30648077 GAAAAAGCAG
Statistics
Matches: 815, Mismatches: 92, Indels: 44
0.86 0.10 0.05
Matches are distributed among these distances:
129 3 0.00
130 1 0.00
131 40 0.05
132 612 0.75
133 152 0.19
134 1 0.00
135 3 0.00
136 3 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
ATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
AG
Found at i:30647847 original size:44 final size:44
Alignment explanation
Indices: 30647794--30647978 Score: 126
Period size: 44 Copynumber: 4.2 Consensus size: 44
30647784 ACTTCCCTGG
*
30647794 GCAGCAGTGGAATAGATTGAAGATTACAGGTCTTATCTCCCTAA
1 GCAGTAGTGGAATAGATTGAAGATTACAGGTCTTATCTCCCTAA
** * * * * *
30647838 GCAGTAGTGGAGCAGGTCGAAGA-TAGC-GGATTTTACCTCCCTGA
1 GCAGTAGTGGAATAGATTGAAGATTA-CAGG-TCTTATCTCCCTAA
* * * ***** * * *
30647882 G-ATTACAGTGGAGTACATTGAAGCCCGTAGTTC-TATCTCTCTAG
1 GCAGT--AGTGGAATAGATTGAAGATTACAGGTCTTATCTCCCTAA
*
30647926 GCAGTAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAA
1 GCAGTAGTGGAATAGATTGAAGATTACAGGTCTTATCTCCCTAA
30647970 GCAGTAGTG
1 GCAGTAGTG
30647979 AAGCAGATCA
Statistics
Matches: 99, Mismatches: 34, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
43 25 0.25
44 57 0.58
45 16 0.16
46 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
GCAGTAGTGGAATAGATTGAAGATTACAGGTCTTATCTCCCTAA
Found at i:30651904 original size:4 final size:4
Alignment explanation
Indices: 30651895--30651937 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
30651885 TTGAACTATT
*
30651895 TTTA TTTA TTTA TTTA TTTG TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
30651938 TTGTTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:30652235 original size:2 final size:2
Alignment explanation
Indices: 30652228--30652252 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30652218 TATACGCATT
30652228 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30652253 TATTGTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30658192 original size:20 final size:20
Alignment explanation
Indices: 30658167--30658272 Score: 81
Period size: 20 Copynumber: 5.3 Consensus size: 20
30658157 TAAATGCGTT
30658167 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * *
30658187 CAGGGGCA-CGTATGTGCAAT
1 CAGGGGTACCG-AAGTACAAA
* *
30658207 CATGGGTACCGAAGTATAAA
1 CAGGGGTACCGAAGTACAAA
** * *
30658227 CAAGGGG-ACATATGTGCAAA
1 C-AGGGGTACCGAAGTACAAA
*
30658247 CAGGGGTGCCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
30658267 CAGGGG
1 CAGGGG
30658273 CACGTATGTG
Statistics
Matches: 61, Mismatches: 21, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
19 7 0.11
20 48 0.79
21 6 0.10
ACGTcount: A:0.35, C:0.18, G:0.33, T:0.14
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:30658214 original size:40 final size:40
Alignment explanation
Indices: 30658170--30658290 Score: 181
Period size: 40 Copynumber: 3.0 Consensus size: 40
30658160 ATGCGTTCAG
30658170 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATCAT
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATCAT
* * * *
30658210 GGGTACCGAAGTATAAACAAGGGG-ACATATGTGCAAACAG
1 GGGTACCGAAGTACAAAC-AGGGGCACGTATGTGCAATCAT
*
30658250 GGGTGCCGAAGTACAAACAGGGGCACGTATGTGCAATCAT
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATCAT
30658290 G
1 G
30658291 CAATAATTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
39 5 0.07
40 60 0.86
41 5 0.07
ACGTcount: A:0.34, C:0.18, G:0.31, T:0.17
Consensus pattern (40 bp):
GGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATCAT
Found at i:30660717 original size:27 final size:27
Alignment explanation
Indices: 30660687--30660747 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
30660677 TTTAATAGTA
* *
30660687 ACAGTACCGTGTGGGCCTTAGCCCAAT
1 ACAGTACAGTGTGGGCCTAAGCCCAAT
* *
30660714 ACAGAAACAGTGTGGGCCTAAGCCCGAT
1 ACAG-TACAGTGTGGGCCTAAGCCCAAT
*
30660742 ATAGTA
1 ACAGTA
30660748 TCAATATGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.20
Consensus pattern (27 bp):
ACAGTACAGTGTGGGCCTAAGCCCAAT
Found at i:30660992 original size:32 final size:32
Alignment explanation
Indices: 30660937--30661331 Score: 531
Period size: 32 Copynumber: 12.4 Consensus size: 32
30660927 GAATGGCTAC
* *
30660937 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
30660968 AAGCCATCAGTAGCAGTGATATGATCGGCAGA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * * *
30661000 CAGCCATCAATAACGGTAATATGATTGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
30661032 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
**
30661064 AAGCCATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
30661096 AAGCCATCAGTAACGGTATTATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
30661128 AAGCCATCAGTAATAGTAATATAATTGGCACC
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
** *
30661160 AAGCCATCAGTAATGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
30661192 AAGCCATCAGTAACAGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
30661224 AAGCCATCAGTAACAGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
30661256 AAGCCATCAGTAACAGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* **
30661288 AAGCCATCAATAACAGTAATATGATTAGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
30661320 AAGCCATCAGTA
1 AAGCCATCAGTA
30661332 GCATTGCAGC
Statistics
Matches: 325, Mismatches: 38, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
31 10 0.03
32 315 0.97
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:30661351 original size:26 final size:26
Alignment explanation
Indices: 30661322--30661378 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
30661312 TTAGCACAAA
* * * *
30661322 GCCATCAGTAGCATTGCAGCAAAGCT
1 GCCAGCAGCAGCATCGCAACAAAGCT
*
30661348 GCCAGCAGCAGTATCGCAACAAAGCT
1 GCCAGCAGCAGCATCGCAACAAAGCT
30661374 GCCAG
1 GCCAG
30661379 TAATAGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.30, G:0.25, T:0.14
Consensus pattern (26 bp):
GCCAGCAGCAGCATCGCAACAAAGCT
Found at i:30661405 original size:27 final size:27
Alignment explanation
Indices: 30661375--30661430 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
30661365 AACAAAGCTG
30661375 CCAGTAATAGT-ATATGTGGCCA-AGCCA
1 CCAGTAATAGTGAT-TGTGG-CAGAGCCA
30661402 CCAGTAATAGTGATTGTGGCAGAGCCA
1 CCAGTAATAGTGATTGTGGCAGAGCCA
30661429 CC
1 CC
30661431 GGTACAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.85
28 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.21
Consensus pattern (27 bp):
CCAGTAATAGTGATTGTGGCAGAGCCA
Found at i:30661635 original size:27 final size:27
Alignment explanation
Indices: 30661594--30661747 Score: 193
Period size: 27 Copynumber: 5.7 Consensus size: 27
30661584 TTAACCTCGA
* *
30661594 GGGTGTTACGATCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
30661621 GGGCATTACAGTCATTTTACCTTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
30661648 GGGTATTACGGTCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
30661675 GGGCATTACGGTCATTTTACCATATAG
1 GGGTATTACGGTCATTTTACCCTACAG
* * *
30661702 GGGTATTACAGTCA-TTTACCTTACAA
1 GGGTATTACGGTCATTTTACCCTACAG
*
30661728 GGGTATTACGGTTATTTTAC
1 GGGTATTACGGTCATTTTAC
30661748 AACCTTTTCG
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
26 21 0.19
27 87 0.81
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (27 bp):
GGGTATTACGGTCATTTTACCCTACAG
Found at i:30663827 original size:30 final size:28
Alignment explanation
Indices: 30663793--30663848 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
30663783 TCATAATGAA
* *
30663793 ATATATTTAATATATTTTTATTATATAATT
1 ATATAATTAATAT-TTTAT-TTATATAATT
30663823 ATATAATTAATATTTTATTTATATAA
1 ATATAATTAATATTTTATTTATATAA
30663849 ATAAAAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 4 0.17
30 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATATAATTAATATTTTATTTATATAATT
Found at i:30666167 original size:50 final size:50
Alignment explanation
Indices: 30666110--30666443 Score: 334
Period size: 51 Copynumber: 6.6 Consensus size: 50
30666100 TTCGATACAG
* * *
30666110 TAGTAGCCTTCACATAGTACTACAAACGTGATCAAGTTTTTCGGTTCACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTTCGGTACACA
* * * * *
30666160 TATTAGCCTTCACATAGTACTACACACGTGATCAAATTTTAT-GGTTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTT-TCGGTACACA
*
30666210 TAGTAGCCTTCACATAGTACTACACACATGACCAAAGCTTTTT-GGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTTCGGTACACA
* * * * *
30666261 TAGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATCGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCA--AGTTTTTCGGTACACA
* * *
30666312 TAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGTTTTTCGGTACACA
** * * * * *
30666363 TTCTAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATCGATACACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCA--AGTTTTTCGGTACACA
* *
30666414 TAGTAGCCTTCACACAATACTACACACGTG
1 TAGTAGCCTTCACATAGTACTACACACGTG
30666444 TTCGTCGATA
Statistics
Matches: 236, Mismatches: 38, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
50 81 0.34
51 148 0.63
52 7 0.03
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (50 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTTCGGTACACA
Found at i:30666336 original size:102 final size:102
Alignment explanation
Indices: 30666101--30666443 Score: 471
Period size: 102 Copynumber: 3.4 Consensus size: 102
30666091 CTTTTATCAT
* * * * *
30666101 TCGATACA-GTAGTAGCCTTCACATAGTACTACAAACGTGATC-AAG-TTTTTCGGTTCACATAT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTT-GGTACACATAC
* * * *
30666163 TAGCCTTCACATAGTACTACACACGTGATCA-AATTTTA
65 TAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTA
* * * * *
30666201 T-GGTTCACGTAGTAGCCTTCACATAGTACTACACACATGACCAAAGCTTTTTGGTACACATAGT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTTGGTACACATACT
30666265 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
* * *
30666302 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTCT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTTGGTACACATACT
30666367 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
66 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
*
30666404 TCGATACACGTAGTAGCCTTCACACAATACTACACACGTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
30666444 TTCGTCGATA
Statistics
Matches: 218, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
99 4 0.02
100 32 0.15
101 45 0.21
102 137 0.63
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (102 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTTGGTACACATACT
AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
Found at i:30670075 original size:3 final size:3
Alignment explanation
Indices: 30670067--30670164 Score: 67
Period size: 3 Copynumber: 32.3 Consensus size: 3
30670057 TATTGCTATC
* * *
30670067 ATT ATT ATT ATT ATT -TAT ACT ACT ATT ATT ATT -TGT ACT ATT ATTT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT AT-T ATT ATT A-TT
* * * * *
30670113 ATT ATT ATT ATT ACT ACTT -TC ATT ATT ATT AGT AAT ATT ATT ACT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30670158 ATT ATT A
1 ATT ATT A
30670165 ATAATGTTTT
Statistics
Matches: 75, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
2 3 0.04
3 68 0.91
4 4 0.05
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:30670122 original size:43 final size:42
Alignment explanation
Indices: 30670067--30670164 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 42
30670057 TATTGCTATC
* *
30670067 ATTATTATTATTATTTA-TACTACT-ATTATTATTTGTACTATT
1 ATTATTATTATTA-TTACTACT-CTCATTATTATTAGTAATATT
*
30670109 ATTTATTATTATTATTACTACTTTCATTATTATTAGTAATATT
1 A-TTATTATTATTATTACTACTCTCATTATTATTAGTAATATT
*
30670152 ATTACTATTATTA
1 ATTATTATTATTA
30670165 ATAATGTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
42 16 0.33
43 33 0.67
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (42 bp):
ATTATTATTATTATTACTACTCTCATTATTATTAGTAATATT
Found at i:30670726 original size:27 final size:26
Alignment explanation
Indices: 30670672--30670727 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
30670662 TAATTTAAAA
* * * *
30670672 TTCATGTGTATTTTTATTTTTAAGTT
1 TTCATGTATATTTTTATCTTAAAATT
30670698 TTCATGTATATTATTTATCTTAAAATT
1 TTCATGTATATT-TTTATCTTAAAATT
30670725 TTC
1 TTC
30670728 TTTTATACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (26 bp):
TTCATGTATATTTTTATCTTAAAATT
Found at i:30683967 original size:3 final size:3
Alignment explanation
Indices: 30683959--30684038 Score: 66
Period size: 3 Copynumber: 28.0 Consensus size: 3
30683949 CACCCAACAA
*
30683959 AAT AAT AAT AA- AAGT AAT AAT AA- AA- AAT -AT GAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
30684001 AACT AAA AAT AAT AA- AAT AAT AAGT AA- AAT AA- AAT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
30684039 TAAATAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
2 14 0.22
3 43 0.66
4 8 0.12
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:30683984 original size:24 final size:26
Alignment explanation
Indices: 30683957--30684045 Score: 84
Period size: 25 Copynumber: 3.5 Consensus size: 26
30683947 ACCACCCAAC
30683957 AAAATAAT-AATAA-AAGTAATAAT-
1 AAAATAATAAATAATAAGTAATAATA
*
30683980 AAAA-AATATGATAATAA-TAATAACTA
1 AAAATAATA-AATAATAAGTAATAA-TA
30684006 AAAATAATAAAATAATAAGTAA-AAT-
1 AAAATAAT-AAATAATAAGTAATAATA
30684031 AAAATAATTAAATAA
1 AAAATAA-TAAATAA
30684046 AAATTAAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
22 3 0.05
23 4 0.07
24 10 0.18
25 16 0.29
26 6 0.11
27 12 0.22
28 4 0.07
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (26 bp):
AAAATAATAAATAATAAGTAATAATA
Found at i:30684014 original size:27 final size:24
Alignment explanation
Indices: 30683957--30684038 Score: 82
Period size: 27 Copynumber: 3.3 Consensus size: 24
30683947 ACCACCCAAC
30683957 AAAATAATAATAA-AAGTAATAAT
1 AAAATAATAATAATAAGTAATAAT
30683980 AAAA-AATATGATAATAA-TAATAACT
1 AAAATAATA--ATAATAAGTAATAA-T
30684005 AAAAATAATAAAATAATAAGTAA-AAT
1 -AAAATAAT--AATAATAAGTAATAAT
30684031 AAAATAAT
1 AAAATAAT
30684039 TAAATAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
22 4 0.08
23 4 0.08
24 10 0.20
25 11 0.22
26 5 0.10
27 12 0.24
28 3 0.06
29 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAATAATAATAATAAGTAATAAT
Found at i:30684254 original size:22 final size:23
Alignment explanation
Indices: 30684211--30684254 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
30684201 AGGGAAGAAT
*
30684211 GGGGAAGGTGGAGACGAGAGGAA
1 GGGGAAGGAGGAGACGAGAGGAA
*
30684234 GGGGAAGGAGG-GATGAGAGGA
1 GGGGAAGGAGGAGACGAGAGGA
30684255 GATCGAAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.34, C:0.02, G:0.59, T:0.05
Consensus pattern (23 bp):
GGGGAAGGAGGAGACGAGAGGAA
Found at i:30692522 original size:11 final size:12
Alignment explanation
Indices: 30692507--30692535 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
30692497 TATGTTTTTT
30692507 TTATTAACATTA
1 TTATTAACATTA
30692519 -TATTAACATTA
1 TTATTAACATTA
30692530 TTATTA
1 TTATTA
30692536 TTTTACTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATTAACATTA
Found at i:30695801 original size:21 final size:21
Alignment explanation
Indices: 30695775--30695827 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
30695765 CGCTGTTTCT
30695775 AATCTCACCGCTACAAT-ATCC
1 AATCTCACCGCTACAATAAT-C
** *
30695796 AATCTCACTACTACAATAATT
1 AATCTCACCGCTACAATAATC
30695817 AATCTCACCGC
1 AATCTCACCGC
30695828 CACCGCTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.36, C:0.34, G:0.04, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAATAATC
Found at i:30707589 original size:14 final size:15
Alignment explanation
Indices: 30707565--30707607 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
30707555 TTCCTATTAT
30707565 TATTATTTATTTTTAC
1 TATT-TTTATTTTTAC
**
30707581 TA-TTTTATTTTTTT
1 TATTTTTATTTTTAC
30707595 TATTTTTATTTTT
1 TATTTTTATTTTT
30707608 GCAGGAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 11 0.46
15 11 0.46
16 2 0.08
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (15 bp):
TATTTTTATTTTTAC
Found at i:30707600 original size:22 final size:23
Alignment explanation
Indices: 30707546--30707600 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
30707536 AAAAAAAAAC
* *
30707546 ATTTTAATTTTCCTATTATTATT
1 ATTTTTATTTTACTATTATTATT
*
30707569 ATTTAT-TTTTACTATT-TTATT
1 ATTTTTATTTTACTATTATTATT
*
30707590 TTTTTTATTTT
1 ATTTTTATTTT
30707601 TATTTTTGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTTTATTTTACTATTATTATT
Done.