Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 96 of 193
Found at i:30947026 original size:18 final size:17
Alignment explanation
Indices: 30946992--30947027 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
30946982 CTTGAATTTC
*
30946992 ATTTAAAAGATAAATTA
1 ATTTAAAAAATAAATTA
30947009 ATTTAAAGAAATAAATTA
1 ATTTAAA-AAATAAATTA
30947027 A
1 A
30947028 AAGTAATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
ATTTAAAAAATAAATTA
Found at i:30958728 original size:18 final size:18
Alignment explanation
Indices: 30958705--30958749 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
30958695 CTTACGTTCA
30958705 CAAGTTAACTTCTTTCTG
1 CAAGTTAACTTCTTTCTG
*
30958723 CAAGTTTTTCACTTCTTTCTG
1 CAAG---TTAACTTCTTTCTG
30958744 CAAGTT
1 CAAGTT
30958750 TTTCTCACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 6 0.26
21 17 0.74
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.47
Consensus pattern (18 bp):
CAAGTTAACTTCTTTCTG
Found at i:30958760 original size:20 final size:21
Alignment explanation
Indices: 30958716--30958762 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
30958706 AAGTTAACTT
*
30958716 CTTTCTGCAAGTTTTTCACTT
1 CTTTCTGCAAGTTTTTCACTA
*
30958737 CTTTCTGCAAGTTTTTCTC-A
1 CTTTCTGCAAGTTTTTCACTA
30958757 CTTTCT
1 CTTTCT
30958763 TCTTCAGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.13, C:0.26, G:0.09, T:0.53
Consensus pattern (21 bp):
CTTTCTGCAAGTTTTTCACTA
Found at i:30958765 original size:23 final size:21
Alignment explanation
Indices: 30958712--30958753 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
30958702 TCACAAGTTA
30958712 ACTTCTTTCTGCAAGTTTTTC
1 ACTTCTTTCTGCAAGTTTTTC
30958733 ACTTCTTTCTGCAAGTTTTTC
1 ACTTCTTTCTGCAAGTTTTTC
30958754 TCACTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.24, G:0.10, T:0.52
Consensus pattern (21 bp):
ACTTCTTTCTGCAAGTTTTTC
Found at i:30974141 original size:80 final size:80
Alignment explanation
Indices: 30973998--30974162 Score: 251
Period size: 80 Copynumber: 2.1 Consensus size: 80
30973988 TCTTTACTTT
* * * *
30973998 CAACAAAATTCGTCAATTCATGGCACCCGGTGCCTAGCGGATAAACCGCGAAAAGTGAGCCCAGC
1 CAACGAAATCCGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACCGCGAAAAATGAGCCCAGC
30974063 TCTAGTTGGATTAAC
66 TCTAGTTGGATTAAC
* * *
30974078 CAACGAAATCCGTCAATTCTTGGCATCCAGTGCCTAGTGGATAAACCGC-AATAAATGAGCCCAG
1 CAACGAAATCCGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACCGCGAA-AAATGAGCCCAG
30974142 CTCTAGTTGGATTAAC
65 CTCTAGTTGGATTAAC
30974158 CAACG
1 CAACG
30974163 GTTTGCAGCC
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
79 2 0.03
80 75 0.97
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (80 bp):
CAACGAAATCCGTCAATTCATGGCACCCAGTGCCTAGCGGATAAACCGCGAAAAATGAGCCCAGC
TCTAGTTGGATTAAC
Found at i:30974175 original size:33 final size:34
Alignment explanation
Indices: 30974135--30974262 Score: 88
Period size: 33 Copynumber: 3.8 Consensus size: 34
30974125 GCAATAAATG
* *
30974135 AGCCCAGCTCTAGTTGGATTAACCAACGGTTTGC
1 AGCCAAGCTCTAGTTGGATAAACCAACGGTTTGC
* * *
30974169 AGCC-AGCGCTAGTTGGATAAATCAACGATTTTGGC
1 AGCCAAGCTCTAGTTGGATAAACCAACG-GTTT-GC
* *
30974204 ACCCAATGC-CTAG-TGGATAAATCGCAAAGG--TG-
1 AGCCAA-GCTCTAGTTGGATAAA-C-CAACGGTTTGC
* *
30974236 AGCCTAGCTCTAGTTGGATTAACCAAC
1 AGCCAAGCTCTAGTTGGATAAACCAAC
30974263 AAATATCCGT
Statistics
Matches: 74, Mismatches: 12, Indels: 19
0.70 0.11 0.18
Matches are distributed among these distances:
31 5 0.07
32 9 0.12
33 28 0.38
34 8 0.11
35 13 0.18
36 5 0.07
37 6 0.08
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (34 bp):
AGCCAAGCTCTAGTTGGATAAACCAACGGTTTGC
Found at i:30974466 original size:20 final size:20
Alignment explanation
Indices: 30974436--30974485 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
30974426 TCCATATGCC
*
30974436 ATTAA-TTAAATAAAAATTA
1 ATTAATTTAAATAAAAATCA
*
30974455 ATTAATTTAAATATAAATCA
1 ATTAATTTAAATAAAAATCA
30974475 A-T-ATTTAAATA
1 ATTAATTTAAATA
30974486 GCATAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 9 0.32
19 6 0.21
20 13 0.46
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAATTTAAATAAAAATCA
Found at i:30982817 original size:35 final size:35
Alignment explanation
Indices: 30982767--30982849 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
30982757 AGCTTAGCTA
* *
30982767 TAGTTGGATATACCAACAAATAT-TGCGCCCAGCAC
1 TAGTTGGATAAACCAACAAAT-TGTGCGCCCAACAC
* *
30982802 TAGTTGGATAAACCAACAAGTTGTGTGCCCAACAC
1 TAGTTGGATAAACCAACAAATTGTGCGCCCAACAC
*
30982837 TAGTTAGATAAAC
1 TAGTTGGATAAAC
30982850 TGACGATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 1 0.02
35 41 0.98
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (35 bp):
TAGTTGGATAAACCAACAAATTGTGCGCCCAACAC
Found at i:30985209 original size:28 final size:28
Alignment explanation
Indices: 30985164--30985323 Score: 173
Period size: 28 Copynumber: 5.7 Consensus size: 28
30985154 AACTGTGTGT
30985164 CCCTTATTCTTC-AGATTTTACAATTTTA
1 CCCTTATT-TTCTAGATTTTACAATTTTA
*
30985192 CCCTTATTTTCTATATTTTACAATTTTA
1 CCCTTATTTTCTAGATTTTACAATTTTA
* *
30985220 CCCCTATTTTCTAGATTTTACAATTTTG
1 CCCTTATTTTCTAGATTTTACAATTTTA
* * * * *
30985248 CAAC-TGTTTTCCAGATTTTACAGTTTTG
1 C-CCTTATTTTCTAGATTTTACAATTTTA
*
30985276 CCTTTATTTTCTAGATTTTACAATTTTA
1 CCCTTATTTTCTAGATTTTACAATTTTA
* *
30985304 CCCATACTTTT-AAGATTTTA
1 CCCTTA-TTTTCTAGATTTTA
30985324 TAACTTTGTC
Statistics
Matches: 111, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
27 3 0.03
28 103 0.93
29 5 0.05
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.51
Consensus pattern (28 bp):
CCCTTATTTTCTAGATTTTACAATTTTA
Found at i:30985349 original size:84 final size:83
Alignment explanation
Indices: 30985173--30985342 Score: 200
Period size: 84 Copynumber: 2.0 Consensus size: 83
30985163 TCCCTTATTC
* * *
30985173 TTCAGATTTTACAATTTTACCCTTATTTTCTATATTTTACAATTTTACCCCTATTTTCTAGATTT
1 TTCAGATTTTACAATTTTACCCTTATTTTCTAGATTTTACAATTTTACCCATATTTTCAAGATTT
* **
30985238 TACAATTTTGCAACTGTT
66 TACAATTTTCCAACAATT
* * *
30985256 TTCCAGATTTTACAGTTTTGCCTTTATTTTCTAGATTTTACAATTTTACCCATACTTTT-AAGAT
1 TT-CAGATTTTACAATTTTACCCTTATTTTCTAGATTTTACAATTTTACCCATA-TTTTCAAGAT
*
30985320 TTTATAACTTTGTCCAA-AATT
64 TTTACAA-TTT-TCCAACAATT
30985341 TT
1 TT
30985343 ATGATTTGTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
83 2 0.03
84 56 0.77
85 11 0.15
86 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (83 bp):
TTCAGATTTTACAATTTTACCCTTATTTTCTAGATTTTACAATTTTACCCATATTTTCAAGATTT
TACAATTTTCCAACAATT
Found at i:30985821 original size:45 final size:45
Alignment explanation
Indices: 30985764--30985857 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
30985754 GCAGCTTGTT
* * *
30985764 TGCACCATTTAGTGGTTTATCCACACCATATTAGCAGCTTTCATA
1 TGCACCATTTAGTGATTTACCCACACCATATTAGCAGCTTTAATA
*
30985809 TGCACCGA-TTAGTGATTTACCCACACCGTATTAGCAGCTTTAATA
1 TGCACC-ATTTAGTGATTTACCCACACCATATTAGCAGCTTTAATA
30985854 TGCA
1 TGCA
30985858 AATGTGTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 43 0.98
46 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (45 bp):
TGCACCATTTAGTGATTTACCCACACCATATTAGCAGCTTTAATA
Found at i:30987845 original size:19 final size:19
Alignment explanation
Indices: 30987803--30987845 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
30987793 CTTTATCAAC
*
30987803 CTTTATTATTTCTTCTCCT
1 CTTTATTATCTCTTCTCCT
* * *
30987822 ATTTATTGTCTCTTCTCTT
1 CTTTATTATCTCTTCTCCT
30987841 CTTTA
1 CTTTA
30987846 CTTGAAATTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.23, G:0.02, T:0.63
Consensus pattern (19 bp):
CTTTATTATCTCTTCTCCT
Found at i:30990591 original size:15 final size:16
Alignment explanation
Indices: 30990564--30990593 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30990554 GAAAAAATAA
30990564 TAATTTAAATATAAAG
1 TAATTTAAATATAAAG
30990580 TAATTT-AATATAAA
1 TAATTTAAATATAAA
30990594 ATTTAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
TAATTTAAATATAAAG
Found at i:30990929 original size:17 final size:17
Alignment explanation
Indices: 30990907--30990962 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
30990897 ATATAATTTT
30990907 ATTTTTACTAATTTAAA
1 ATTTTTACTAATTTAAA
* * **
30990924 ATTTTTAGTATAATT-CT
1 ATTTTTACTA-ATTTAAA
*
30990941 ATTTTTCCTAATTTAAA
1 ATTTTTACTAATTTAAA
30990958 ATTTT
1 ATTTT
30990963 AAAAATTTTA
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
16 3 0.11
17 22 0.79
18 3 0.11
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTTACTAATTTAAA
Found at i:30990944 original size:34 final size:34
Alignment explanation
Indices: 30990898--30990962 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
30990888 GAGATCAAAA
*
30990898 TATAATTTTATTTTTACTAATTTAAAATTTTTAG
1 TATAATTCTATTTTTACTAATTTAAAATTTTTAG
*
30990932 TATAATTCTATTTTTCCTAATTTAAAATTTT
1 TATAATTCTATTTTTACTAATTTAAAATTTT
30990963 AAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (34 bp):
TATAATTCTATTTTTACTAATTTAAAATTTTTAG
Found at i:30998498 original size:29 final size:29
Alignment explanation
Indices: 30998466--30998529 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
30998456 AGTCCCAAAA
* *
30998466 TTAT-TATTCTAGAATTTTTTTTAACATTT
1 TTATATATTCTAGAATTTCTTTGAA-ATTT
* *
30998495 TTATATTTTTTAGAATTTCTTTGAAATTT
1 TTATATATTCTAGAATTTCTTTGAAATTT
30998524 TTATAT
1 TTATAT
30998530 TTTTTAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (29 bp):
TTATATATTCTAGAATTTCTTTGAAATTT
Found at i:30998530 original size:29 final size:30
Alignment explanation
Indices: 30998475--30998535 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
30998465 ATTATTATTC
* *
30998475 TAGAATTTTTTTTAACATTTTTATATTTTT
1 TAGAATTTCTTTGAACATTTTTATATTTTT
30998505 TAGAATTTCTTTGAA-ATTTTTATATTTTT
1 TAGAATTTCTTTGAACATTTTTATATTTTT
30998534 TA
1 TA
30998536 AAATAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (30 bp):
TAGAATTTCTTTGAACATTTTTATATTTTT
Found at i:30998576 original size:19 final size:19
Alignment explanation
Indices: 30998547--30998596 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
30998537 AATAAAAAAA
30998547 TTTGAAGTTTTTATAAA-TAT
1 TTTGAA-TTTTTA-AAATTAT
*
30998567 TTTGAATTTTGAAAATTAT
1 TTTGAATTTTTAAAATTAT
30998586 TTTGAATTTTT
1 TTTGAATTTTT
30998597 TGTAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 18 0.67
20 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (19 bp):
TTTGAATTTTTAAAATTAT
Found at i:30999038 original size:14 final size:14
Alignment explanation
Indices: 30999016--30999053 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
30999006 ACTAAAAAAC
*
30999016 TTTTAAAAATTA-T
1 TTTTAAAAATCAGT
30999029 TTTCTAAAAATCAGT
1 TTT-TAAAAATCAGT
30999044 TTTTAAAAAT
1 TTTTAAAAAT
30999054 GTTTTTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 15 0.68
15 4 0.18
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (14 bp):
TTTTAAAAATCAGT
Found at i:31008497 original size:31 final size:33
Alignment explanation
Indices: 31008462--31008522 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 33
31008452 AAAATAGAAA
*
31008462 TAAAAGATAAAAACA-AATATTT-TTTGAAATT
1 TAAAAGATAAAAACAGAAGATTTCTTTGAAATT
* *
31008493 TAAAATATAGAAACAGAAGATTTCTTTGAA
1 TAAAAGATAAAAACAGAAGATTTCTTTGAA
31008523 GTTTTCTCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 13 0.52
32 6 0.24
33 6 0.24
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (33 bp):
TAAAAGATAAAAACAGAAGATTTCTTTGAAATT
Found at i:31009452 original size:45 final size:44
Alignment explanation
Indices: 31009388--31009486 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 44
31009378 TGAGATGGTA
* * * *
31009388 GCTTCAATTTGCCCTCTTGATTTAAGGGTAAAAGATTAGATTATG
1 GCTTCAATCTACCCTCTTGACTTAAGGGT-AAAGATTAGATGATG
*
31009433 GCTTCAATCTACCCTCTTGACTTAAGGGTAAAGATTGGATGATG
1 GCTTCAATCTACCCTCTTGACTTAAGGGTAAAGATTAGATGATG
*
31009477 TCTTCAATCT
1 GCTTCAATCT
31009487 GCCTCATGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 22 0.46
45 26 0.54
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (44 bp):
GCTTCAATCTACCCTCTTGACTTAAGGGTAAAGATTAGATGATG
Found at i:31009519 original size:39 final size:39
Alignment explanation
Indices: 31009474--31009739 Score: 234
Period size: 39 Copynumber: 6.6 Consensus size: 39
31009464 AGATTGGATG
* * * *
31009474 ATGTCTTCAATCTGCCTCATGATTGAGGTAAGGGAATGA
1 ATGTCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGA
* * *
31009513 AAGTCTTCAA-CATGCCCTATGAT-TAGGGTAAGAGATTGGA
1 ATGTCTTCAATC-TGCCCCATGATCGA-GGTAAGAGATT-GA
* *
31009553 TATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
1 -ATGTCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGA
* * *
31009593 ATGGCTTCAATCTACCCCATGATCGAGGTAAAAGATTGGA
1 ATGTCTTCAATCTGCCCCATGATCGAGGTAAGAGATT-GA
* * *
31009633 TGATGTCTTCAATCTGCCCTATGATC-AGGGTAAGAGGTTGG
1 --ATGTCTTCAATCTGCCCCATGATCGA-GGTAAGAGATTGA
* *
31009674 ATGGTCTT-AATCTGCCTCATGGTCGAGGTAAGAGATTGGA
1 AT-GTCTTCAATCTGCCCCATGATCGAGGTAAGAGATT-GA
*
31009714 TGATGTCTTCAGTCTGCCCCATGATC
1 --ATGTCTTCAATCTGCCCCATGATC
31009740 AGTGTAAAAG
Statistics
Matches: 181, Mismatches: 30, Indels: 29
0.75 0.12 0.12
Matches are distributed among these distances:
38 2 0.01
39 85 0.47
40 11 0.06
41 37 0.20
42 46 0.25
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (39 bp):
ATGTCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGA
Found at i:31009665 original size:81 final size:82
Alignment explanation
Indices: 31009430--31009746 Score: 326
Period size: 81 Copynumber: 3.9 Consensus size: 82
31009420 AGATTAGATT
* ** *
31009430 ATGGCTTCAATCTACCCTCTTGACTTAAGGGT-AAAGATTGGATGATGTCTTCAATCTGCCTCAT
1 ATGGCTTCAATCTACCC-CATGA-TCGAGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCAT
* * * *
31009494 GAT-TGAGGTAAGGGAATGA
64 GATCAG-GGTAAGAGATTGG
* * * * * *
31009513 AAGTCTTCAA-CATGCCCTATGAT-TAGGGTAAGAGATTGGAT-ATGTCTTCAATCTGCCCCATG
1 ATGGCTTCAATC-TACCCCATGATCGAGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATG
*
31009575 ATCGGGGTAAGAGATTGG
65 ATCAGGGTAAGAGATTGG
*
31009593 ATGGCTTCAATCTACCCCATGATCGA-GGTAAAAGATTGGATGATGTCTTCAATCTGCCCTATGA
1 ATGGCTTCAATCTACCCCATGATCGAGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGA
*
31009657 TCAGGGTAAGAGGTTGG
66 TCAGGGTAAGAGATTGG
* * * * *
31009674 ATGGTCTT-AATCTGCCTCATGGTCGA-GGTAAGAGATTGGATGATGTCTTCAGTCTGCCCCATG
1 ATGG-CTTCAATCTACCCCATGATCGAGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATG
*
31009737 ATCAGTGTAA
65 ATCAGGGTAA
31009747 AAGCCCATTT
Statistics
Matches: 199, Mismatches: 28, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
80 68 0.34
81 112 0.56
82 7 0.04
83 12 0.06
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (82 bp):
ATGGCTTCAATCTACCCCATGATCGAGGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGA
TCAGGGTAAGAGATTGG
Found at i:31010890 original size:15 final size:15
Alignment explanation
Indices: 31010861--31010889 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31010851 TTGTTTTAAA
31010861 AAAAAAGGGAATTTT
1 AAAAAAGGGAATTTT
31010876 AAAAAA-GGAATTTT
1 AAAAAAGGGAATTTT
31010890 TTTACCTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (15 bp):
AAAAAAGGGAATTTT
Found at i:31019316 original size:26 final size:26
Alignment explanation
Indices: 31019280--31019331 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
31019270 ATCTTTGTGA
31019280 AAGGCTCATTATCATTATTGGTTATT
1 AAGGCTCATTATCATTATTGGTTATT
31019306 AAGGCTCATTATCATTATTGGTTATT
1 AAGGCTCATTATCATTATTGGTTATT
31019332 TTAATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (26 bp):
AAGGCTCATTATCATTATTGGTTATT
Found at i:31023787 original size:38 final size:38
Alignment explanation
Indices: 31023742--31024461 Score: 445
Period size: 38 Copynumber: 18.7 Consensus size: 38
31023732 TCGATCATGG
*
31023742 GGCAGATTGAAGAACCCAATCTCTTACCTTAATCAGAA
1 GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAA
* ** * ** *
31023780 GGTAGATTGAAGATAGGCAATCTTTTACCTCGATCATG-G
1 GGCAGATTGAAGA-ATCCAATCTCTTACCTTAATCA-GAA
* * *
31023819 GGCAGATTGAAAAATCCAATCTTTTACATTAATCAGAA
1 GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAA
* * * * *
31023857 GGAAGATTGAATAATCCAATCTCTTACCCTAGTCAGAG
1 GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAA
* *** * *
31023895 GGCAGATTGAAAGCATCCAATCTCTTACCCCGATAATG-G
1 GGCAGATTG-AAGAATCCAATCTCTTACCTTAATCA-GAA
* * *
31023934 GGCAAATTGAAGAACCCAATATCTTACCTTAATCAGAA
1 GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAA
** * *** *
31023972 GGCAGATTGAAGACAGGCAATCTTTTACCCCGATCATG-G
1 GGCAGATTGAAGA-ATCCAATCTCTTACCTTAATCA-GAA
* * * *
31024011 GGTAGATTGAAGAATCTAATATTTTACCTTAATCAGAA
1 GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAA
* ** * *
31024049 GGCAGATTGAAGACATCCAATCTCTTATCTCGATCATAG
1 GGCAGATTGAAGA-ATCCAATCTCTTACCTTAATCAGAA
* * *
31024088 GGCAGATTGAAAGCATCAAATCTCTTACCCCT-ATCATG--
1 GGCAGATTG-AAGAATCCAATCTCTTA-CCTTAATCA-GAA
* *
31024126 GGACAGATTGAAAACACTTTCAATCTCTTACCTTAATCAG-A
1 GG-CAGATTGAAGA-A--TCCAATCTCTTACCTTAATCAGAA
* * *
31024167 GGCAGATTGAAGACATGCAATCTTTTA-CTCCAATCATCG-A
1 GGCAGATTGAAGA-ATCCAATCTCTTACCT-TAATCA--GAA
* * * *
31024207 -GTAGATTGAAGCATCCAATCTTTTACCTTAATTAGAA
1 GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAA
* * *
31024244 GGCAGATTGAAGAATCCAATCTCTTACCCTAGTCAGAG
1 GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAA
* * ** *** *
31024282 GGAAGATTAAAGATAAACAATCTCTTACCCCGATCATG-G
1 GGCAGATTGAAGA-ATCCAATCTCTTACCTTAATCA-GAA
* *
31024321 GGCAGATTGAAGAACCCAATCTCTTACCTTAATTAGAA
1 GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAA
* * *** * * * * *
31024359 GGAAAATTGAAGACAGATAATCTTTTACCCTGATCATAG
1 GGCAGATTGAAGA-ATCCAATCTCTTACCTTAATCAGAA
* * *
31024398 GGTAGATTGAAGAATCCAATCTTTTACCTTAATCAAAA
1 GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAA
*
31024436 GGTAGATTGAAGACATCCAATCTCTT
1 GGCAGATTGAAGA-ATCCAATCTCTT
31024462 GCCCCGATCA
Statistics
Matches: 523, Mismatches: 129, Indels: 59
0.74 0.18 0.08
Matches are distributed among these distances:
36 1 0.00
37 7 0.01
38 260 0.50
39 213 0.41
40 26 0.05
41 16 0.03
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (38 bp):
GGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAA
Found at i:31023913 original size:77 final size:76
Alignment explanation
Indices: 31023741--31024583 Score: 436
Period size: 77 Copynumber: 10.9 Consensus size: 76
31023731 CTCGATCATG
* * * ** *
31023741 GGGCAGATTGAAGAACCCAATCTCTTACCTTAATCAGAAGGTAGATTGAAGATAGGCAATCTTTT
1 GGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAGA-ATCCAATCTCTT
*
31023806 A-CCTCGATCATG-
65 ACCCT-AATCA-GA
** * * * *
31023818 GGGCAGATTGAAAAATCCAATCTTTTACATTAATCAGAAGGAAGATTGAATAATCCAATCTCTTA
1 GGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAGAATCCAATCTCTTA
*
31023883 CCCTAGTCAGA
66 CCCTAATCAGA
*** * * * * *
31023894 GGGCAGATTGAAAGCATCCAATCTCTTACCCCGATAATG-GGGCAAATTGAAGAACCCAATATCT
1 GGGCAGATTG-AAGCATCCAATCTCTTACCTTAATCA-GAAGGCAGATTGAAGAATCCAATCTCT
*
31023958 TACCTTAATCAGA
64 TACCCTAATCAGA
* ** * *** * * * * *
31023971 AGGCAGATTGAAGACAGGCAATCTTTTACCCCGATCATG-GGGTAGATTGAAGAATCTAATATTT
1 GGGCAGATTGAAG-CATCCAATCTCTTACCTTAATCA-GAAGGCAGATTGAAGAATCCAATCTCT
*
31024035 TACCTTAATCAGA
64 TACCCTAATCAGA
* * ** * * * *
31024048 AGGCAGATTGAAGACATCCAATCTCTTATCTCGATCATAGGGCAGATTGAAAGCATCAAATCTCT
1 GGGCAGATTGAAG-CATCCAATCTCTTACCTTAATCAGAAGGCAGATTG-AAGAATCCAATCTCT
31024113 TACCCCT-ATCATG-
64 TA-CCCTAATCA-GA
* * * *
31024126 GGACAGATTGAAAACACTTTCAATCTCTTACCTTAATCAG-AGGCAGATTGAAGACATGCAATCT
1 GGGCAGATTG-AAGCA--TCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAGA-ATCCAATCT
* **
31024190 TTTACTCC-AATCATC
62 CTTAC-CCTAATCAGA
* * * *
31024205 GAGTAGATTGAAGCATCCAATCTTTTACCTTAATTAGAAGGCAGATTGAAGAATCCAATCTCTTA
1 GGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAGAATCCAATCTCTTA
*
31024270 CCCTAGTCAGA
66 CCCTAATCAGA
* * * *** * *
31024281 GGGAAGATTAAAG-ATAAACAATCTCTTACCCCGATCATG-GGGCAGATTGAAGAACCCAATCTC
1 GGGCAGATTGAAGCAT--CCAATCTCTTACCTTAATCA-GAAGGCAGATTGAAGAATCCAATCTC
* *
31024344 TTACCTTAATTAGA
63 TTACCCTAATCAGA
* * * *** * * * * * * *
31024358 AGGAAAATTGAAGACAGATAATCTTTTACCCTGATCATAGGGTAGATTGAAGAATCCAATCTTTT
1 GGGCAGATTGAAG-CATCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAGAATCCAATCTCTT
* *
31024423 ACCTTAATCAAA
65 ACCCTAATCAGA
* * * *** * * * *
31024435 AGGTAGATTGAAGACATCCAATCTCTTGCCCCGATCATG-TGGCAGATTCAAAGCATCTAATCTC
1 GGGCAGATTGAAG-CATCCAATCTCTTACCTTAATCA-GAAGGCAGATT-GAAGAATCCAATCTC
*
31024499 TTACCCCT-ATCATA
63 TTA-CCCTAATCAGA
* * *** * *
31024513 GGACAGATTGAAGACA-CATCAATTTCTTACCCCGATCATG-GGGCAGATTGAAAGCATCCAATC
1 GGGCAGATTGAAG-CATC--CAATCTCTTACCTTAATCA-GAAGGCAGATTG-AAGAATCCAATC
31024576 TCTTACCC
61 TCTTACCC
31024584 CTATCATGGG
Statistics
Matches: 609, Mismatches: 127, Indels: 59
0.77 0.16 0.07
Matches are distributed among these distances:
75 5 0.01
76 71 0.12
77 359 0.59
78 72 0.12
79 85 0.14
80 17 0.03
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (76 bp):
GGGCAGATTGAAGCATCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAGAATCCAATCTCTTA
CCCTAATCAGA
Found at i:31023953 original size:115 final size:114
Alignment explanation
Indices: 31023745--31023984 Score: 293
Period size: 115 Copynumber: 2.1 Consensus size: 114
31023735 ATCATGGGGC
* * * * *
31023745 AGATTGAAGAACCCAATCTCTTACCTTAATCAGAAGGTAGATTGAAGATAGGCAATCTTTTACCT
1 AGATTGAAGAACCCAATCTCTTACCCTAATCAGAAGGCAGATTGAAGATA-CCAATCTCTTACCC
* * * * *
31023810 CGATCATGGGGCAGATTGAAAAATCCAATCTTTTACATTAATCAGAAGGA
65 CGATAATGGGGCAAATTGAAAAACCCAATATCTTACATTAATCAGAAGGA
* * * *
31023860 AGATTGAATAATCCAATCTCTTACCCTAGTCAGAGGGCAGATTGAAAGCAT-CCAATCTCTTACC
1 AGATTGAAGAACCCAATCTCTTACCCTAATCAGAAGGCAGATTG-AAG-ATACCAATCTCTTACC
* * *
31023924 CCGATAATGGGGCAAATTGAAGAACCCAATATCTTACCTTAATCAGAAGGC
64 CCGATAATGGGGCAAATTGAAAAACCCAATATCTTACATTAATCAGAAGGA
31023975 AGATTGAAGA
1 AGATTGAAGA
31023985 CAGGCAATCT
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
115 100 0.95
116 3 0.03
117 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (114 bp):
AGATTGAAGAACCCAATCTCTTACCCTAATCAGAAGGCAGATTGAAGATACCAATCTCTTACCCC
GATAATGGGGCAAATTGAAAAACCCAATATCTTACATTAATCAGAAGGA
Found at i:31024038 original size:115 final size:113
Alignment explanation
Indices: 31023745--31024038 Score: 286
Period size: 115 Copynumber: 2.5 Consensus size: 113
31023735 ATCATGGGGC
* ** * * * *
31023745 AGATTGAAGAACCCAATCTCTTACCTTAATCAGAAGGTAGATTGAAGATAGGCAATCTTTTACCT
1 AGATTGAAGAAGCCAATCTCTTACCCGAGTCAGAGGGTAGATTGAAGA-A-TCAATCTTTTACCC
* * * * *
31023810 CGATCATGGGGCAGATTGAAAAATCCAATCTTTTACATTAATCAGAAGGA
64 CGATAATGGGGCAAATTGAAAAACCCAATATCTTACATTAATCAGAAGGA
* * * * * *
31023860 AGATTGAATAATCCAATCTCTTACCCTAGTCAGAGGGCAGATTGAAAGCATCCAATCTCTTACCC
1 AGATTGAAGAAGCCAATCTCTTACCCGAGTCAGAGGGTAGATTG-AAGAAT-CAATCTTTTACCC
* * *
31023925 CGATAATGGGGCAAATTGAAGAACCCAATATCTTACCTTAATCAGAAGGC
64 CGATAATGGGGCAAATTGAAAAACCCAATATCTTACATTAATCAGAAGGA
* * *
31023975 AGATTGAAGACAGGCAATCTTTTACCCCGA-TCATG-GGGTAGATTGAAGAATCTAATATTTTAC
1 AGATTGAAGA-AGCCAATCTCTTA-CCCGAGTCA-GAGGGTAGATTGAAGAATC-AATCTTTTAC
31024038 C
62 C
31024039 TTAATCAGAA
Statistics
Matches: 146, Mismatches: 27, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
114 1 0.01
115 115 0.79
116 25 0.17
117 5 0.03
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (113 bp):
AGATTGAAGAAGCCAATCTCTTACCCGAGTCAGAGGGTAGATTGAAGAATCAATCTTTTACCCCG
ATAATGGGGCAAATTGAAAAACCCAATATCTTACATTAATCAGAAGGA
Found at i:31024340 original size:115 final size:114
Alignment explanation
Indices: 31024146--31024371 Score: 281
Period size: 115 Copynumber: 2.0 Consensus size: 114
31024136 AAAACACTTT
* * * ** * * *
31024146 CAATCTCTTACCTTAATCAGAGGCAGATTGAAGACATGCAATCTTTTACTCCAATCATCGAGTAG
1 CAATCTCTTACCCTAATCAGAGGAAGATTAAAGACAAACAATCTCTTACCCCAATCATCGAGCAG
* * * * *
31024211 ATTGAAGCATCCAATCTTTTACCTTAATTAGAAGGCAGATTGAAGAATC
66 ATTGAAGAACCCAATCTCTTACCTTAATTAGAAGGAAAATTGAAGAATC
* * * * *
31024260 CAATCTCTTACCCTAGTCAGAGGGAAGATTAAAGATAAACAATCTCTTACCCCGATCATGGGGCA
1 CAATCTCTTACCCTAATCAGA-GGAAGATTAAAGACAAACAATCTCTTACCCCAATCATCGAGCA
31024325 GATTGAAGAACCCAATCTCTTACCTTAATTAGAAGGAAAATTGAAGA
65 GATTGAAGAACCCAATCTCTTACCTTAATTAGAAGGAAAATTGAAGA
31024372 CAGATAATCT
Statistics
Matches: 93, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
114 19 0.20
115 74 0.80
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (114 bp):
CAATCTCTTACCCTAATCAGAGGAAGATTAAAGACAAACAATCTCTTACCCCAATCATCGAGCAG
ATTGAAGAACCCAATCTCTTACCTTAATTAGAAGGAAAATTGAAGAATC
Found at i:31024482 original size:39 final size:38
Alignment explanation
Indices: 31023723--31024642 Score: 444
Period size: 39 Copynumber: 23.7 Consensus size: 38
31023713 ATTTTACAAG
* * *
31023723 TCTCTTACCTCGATCATGGGGCAGATTGAAGA-ACCCAA
1 TCTCTTACCCCAATCAT-GGGCAGATTGAAGACATCCAA
** * * **
31023761 TCTCTTACCTTAATCA-GAAGGTAGATTGAAGATAGGCAA
1 TCTCTTACCCCAATCATG--GGCAGATTGAAGACATCCAA
* * * *
31023800 TCTTTTACCTCGATCATGGGGCAGATTGAA-AAATCCAA
1 TCTCTTACCCCAATCAT-GGGCAGATTGAAGACATCCAA
* *** * *
31023838 TCTTTTACATTAATCA-GAAGGAAGATTGAATA-ATCCAA
1 TCTCTTACCCCAATCATG--GGCAGATTGAAGACATCCAA
* * *
31023876 TCTCTTACCCTAGTCAGAGGGCAGATTGAA-AGCATCCAA
1 TCTCTTACCCCAATCA-TGGGCAGATTGAAGA-CATCCAA
* * * *
31023915 TCTCTTACCCCGATAATGGGGCAAATTGAAGA-ACCCAA
1 TCTCTTACCCCAATCAT-GGGCAGATTGAAGACATCCAA
* ** **
31023953 TATCTTACCTTAATCA-GAAGGCAGATTGAAGACAGGCAA
1 TCTCTTACCCCAATCATG--GGCAGATTGAAGACATCCAA
* * * *
31023992 TCTTTTACCCCGATCATGGGGTAGATTGAAGA-ATCTAA
1 TCTCTTACCCCAATCAT-GGGCAGATTGAAGACATCCAA
* * **
31024030 TATTTTACCTTAATCA-GAAGGCAGATTGAAGACATCCAA
1 TCTCTTACCCCAATCATG--GGCAGATTGAAGACATCCAA
* * * *
31024069 TCTCTTATCTCGATCATAGGGCAGATTGAA-AGCATCAAA
1 TCTCTTACCCCAATCAT-GGGCAGATTGAAGA-CATCCAA
* * *
31024108 TCTCTTACCCCTATCATGGGACAGATTGAAAACACTTTCAA
1 TCTCTTACCCCAATCATGGG-CAGATTGAAGACA--TCCAA
** *
31024149 TCTCTTACCTTAATCA-GAGGCAGATTGAAGACATGCAA
1 TCTCTTACCCCAATCATG-GGCAGATTGAAGACATCCAA
* * * *
31024187 TCTTTTACTCCAATCATCGAGTAGATTGAAG-CATCCAA
1 TCTCTTACCCCAATCAT-GGGCAGATTGAAGACATCCAA
* ** *
31024225 TCTTTTACCTTAATTA-GAAGGCAGATTGAAGA-ATCCAA
1 TCTCTTACCCCAATCATG--GGCAGATTGAAGACATCCAA
* * * * * * **
31024263 TCTCTTACCCTAGTCAGAGGGAAGATTAAAGATAAACAA
1 TCTCTTACCCCAATCA-TGGGCAGATTGAAGACATCCAA
* *
31024302 TCTCTTACCCCGATCATGGGGCAGATTGAAGA-ACCCAA
1 TCTCTTACCCCAATCAT-GGGCAGATTGAAGACATCCAA
** * * * ***
31024340 TCTCTTACCTTAATTA-GAAGGAAAATTGAAGACAGATAA
1 TCTCTTACCCCAATCATG--GGCAGATTGAAGACATCCAA
* ** *
31024379 TCTTTTACCCTGATCATAGGGTAGATTGAAGA-ATCCAA
1 TCTCTTACCCCAATCAT-GGGCAGATTGAAGACATCCAA
* ** ** *
31024417 TCTTTTACCTTAATCAAAAGGTAGATTGAAGACATCCAA
1 TCTCTTACCCCAATC-ATGGGCAGATTGAAGACATCCAA
* * * *
31024456 TCTCTTGCCCCGATCATGTGGCAGATTCAA-AGCATCTAA
1 TCTCTTACCCCAATCATG-GGCAGATTGAAGA-CATCCAA
* *
31024495 TCTCTTACCCCTATCATAGGACAGATTGAAGACA-CATCAA
1 TCTCTTACCCCAATCAT-GGGCAGATTGAAGACATC--CAA
* *
31024535 TTTCTTACCCCGATCATGGGGCAGATTGAA-AGCATCCAA
1 TCTCTTACCCCAATCAT-GGGCAGATTGAAGA-CATCCAA
* *
31024574 TCTCTTACCCCTATCATGGGACGGATTGAAGACA-CATCAA
1 TCTCTTACCCCAATCATGGG-CAGATTGAAGACATC--CAA
* * *
31024614 TTTCTTACCCCAAACGTAGGGCAGATTGA
1 TCTCTTACCCCAATCAT-GGGCAGATTGA
31024643 GGATGAATCG
Statistics
Matches: 678, Mismatches: 145, Indels: 116
0.72 0.15 0.12
Matches are distributed among these distances:
36 6 0.01
37 1 0.00
38 277 0.41
39 294 0.43
40 74 0.11
41 26 0.04
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (38 bp):
TCTCTTACCCCAATCATGGGCAGATTGAAGACATCCAA
Found at i:31024499 original size:387 final size:386
Alignment explanation
Indices: 31023723--31024543 Score: 1161
Period size: 387 Copynumber: 2.1 Consensus size: 386
31023713 ATTTTACAAG
* * * *
31023723 TCTCTTACCTCGATCATGGGGCAGATTGAAGAAC-C-CAATCTCTTACCTTAATCAGAAGGTAGA
1 TCTCTTACCCCTATCATGGGACAGATTGAA-AACACTCAATCTCTTACCTTAATCAGAAGGCAGA
* * * *
31023786 TTGAAGATAGGCAATCTTTTACCTCGATCATGGGGCAGATTGAAAAATCCAATCTTTTACATTAA
65 TTGAAGACAGGCAATCTTTTACCTCAATCATCGAGCAGATTGAAAAATCCAATCTTTTACATTAA
* * *
31023851 TCAGAAGGAAGATTGAATAATCCAATCTCTTACCCTAGTCAGAGGGCAGATTGAAAGCATCCAAT
130 TCAGAAGGAAGATTGAAGAATCCAATCTCTTACCCTAGTCAGAGGGAAGATTGAAAGCATACAAT
* *
31023916 CTCTTACCCCGATAATGGGGCAAATTGAAGAACCCAATATCTTACCTTAATCAGAAGGCAGATTG
195 CTCTTACCCCGATAATGGGGCAAATTGAAGAACCCAATATCTTACCTTAATCAGAAGGAAAATTG
* * *
31023981 AAGACAGGCAATCTTTTACCCCGATCATGGGGTAGATTGAAGAATCTAATATTTTACCTTAATCA
260 AAGACAGACAATCTTTTACCCCGATCATAGGGTAGATTGAAGAATCCAATATTTTACCTTAATCA
* * * *
31024046 GAAGGCAGATTGAAGACATCCAATCTCTTATCTCGATCATAGGGCAGATTGAAAGCATCAAA
325 AAAGGCAGATTGAAGACATCCAATCTCTTACCCCGATCATAGGGCAGATTCAAAGCATCAAA
31024108 TCTCTTACCCCTATCATGGGACAGATTGAAAACACTTTCAATCTCTTACCTTAATCAG-AGGCAG
1 TCTCTTACCCCTATCATGGGACAGATTGAAAACAC--TCAATCTCTTACCTTAATCAGAAGGCAG
* * ** *
31024172 ATTGAAGACATGCAATCTTTTA-CTCCAATCATCGAGTAGATTGAAGCATCCAATCTTTTACCTT
64 ATTGAAGACAGGCAATCTTTTACCT-CAATCATCGAGCAGATTGAAAAATCCAATCTTTTACATT
* *
31024236 AATTAGAAGGCAGATTGAAGAATCCAATCTCTTACCCTAGTCAGAGGGAAGATT-AAAG-ATAAA
128 AATCAGAAGGAAGATTGAAGAATCCAATCTCTTACCCTAGTCAGAGGGAAGATTGAAAGCAT--A
* * * *
31024299 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGAACCCAATCTCTTACCTTAATTAGAAGGAAA
191 CAATCTCTTACCCCGATAATGGGGCAAATTGAAGAACCCAATATCTTACCTTAATCAGAAGGAAA
* * *
31024364 ATTGAAGACAGATAATCTTTTACCCTGATCATAGGGTAGATTGAAGAATCCAATCTTTTACCTTA
256 ATTGAAGACAGACAATCTTTTACCCCGATCATAGGGTAGATTGAAGAATCCAATATTTTACCTTA
* * *
31024429 ATCAAAAGGTAGATTGAAGACATCCAATCTCTTGCCCCGATCAT-GTGGCAGATTCAAAGCATCT
321 ATCAAAAGGCAGATTGAAGACATCCAATCTCTTACCCCGATCATAG-GGCAGATTCAAAGCATCA
31024493 AA
385 AA
* * *
31024495 TCTCTTACCCCTATCATAGGACAGATTGAAGACACATCAATTTCTTACC
1 TCTCTTACCCCTATCATGGGACAGATTGAAAACAC-TCAATCTCTTACC
31024544 CCGATCATGG
Statistics
Matches: 387, Mismatches: 41, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
384 3 0.01
385 30 0.08
386 19 0.05
387 315 0.81
388 20 0.05
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (386 bp):
TCTCTTACCCCTATCATGGGACAGATTGAAAACACTCAATCTCTTACCTTAATCAGAAGGCAGAT
TGAAGACAGGCAATCTTTTACCTCAATCATCGAGCAGATTGAAAAATCCAATCTTTTACATTAAT
CAGAAGGAAGATTGAAGAATCCAATCTCTTACCCTAGTCAGAGGGAAGATTGAAAGCATACAATC
TCTTACCCCGATAATGGGGCAAATTGAAGAACCCAATATCTTACCTTAATCAGAAGGAAAATTGA
AGACAGACAATCTTTTACCCCGATCATAGGGTAGATTGAAGAATCCAATATTTTACCTTAATCAA
AAGGCAGATTGAAGACATCCAATCTCTTACCCCGATCATAGGGCAGATTCAAAGCATCAAA
Found at i:31027976 original size:42 final size:40
Alignment explanation
Indices: 31027894--31028277 Score: 449
Period size: 42 Copynumber: 9.6 Consensus size: 40
31027884 GGTTTTGACA
*
31027894 ATCGGGGTAAGAGATTGGATGG-GTTCAATCTGCCCCATG
1 ATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATG
* *
31027933 ATTGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCTCATG
1 ATCGGGGTAAGAGATTGGATG--GTCTTCAATCTGCCCCATG
31027975 ATCGGGGTAAGAGATTGGATGGTC-TCAATCTGCCCCATG
1 ATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATG
* * * *
31028014 GTCGGGGTAAGAGATTGTATGATGTCTTCAATCTGACCTATG
1 ATCGGGGTAAGAGATTGGATG--GTCTTCAATCTGCCCCATG
*
31028056 ATCGGGGTAAGAGATTTGATGGTC-TCAATCTGCCCCATG
1 ATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATG
*
31028095 ATCGGGGCAAGAGATTGGATGATGTCTTCAATCTGCCCCATG
1 ATCGGGGTAAGAGATTGGATG--GTCTTCAATCTGCCCCATG
* *
31028137 ATCGAGGTAAGAGATTGGATGGTCCTT-AATCTGCCTCATG
1 ATCGGGGTAAGAGATTGGATGGT-CTTCAATCTGCCCCATG
* **
31028177 ATCGGGGTAAGAGATTGG-TGTGTCTTCAATCTACCCTTTG
1 ATCGGGGTAAGAGATTGGATG-GTCTTCAATCTGCCCCATG
** * * *
31028217 ATTAGGGTAAAATATTGGAT-G-CTTCAATCTACCCCATG
1 ATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATG
* * *
31028255 ATCGGGTTATGAGATTGGGTGGT
1 ATCGGGGTAAGAGATTGGATGGT
31028278 AGCTTCGCTT
Statistics
Matches: 293, Mismatches: 37, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
38 28 0.10
39 92 0.31
40 62 0.21
41 11 0.04
42 100 0.34
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (40 bp):
ATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCCATG
Found at i:31027982 original size:81 final size:81
Alignment explanation
Indices: 31027894--31028272 Score: 509
Period size: 81 Copynumber: 4.7 Consensus size: 81
31027884 GGTTTTGACA
*
31027894 ATCGGGGTAAGAGATTGGATGGGT-TCAATCTGCCCCATGATTGGGGTAAGAGATTGGATGATGT
1 ATCGGGGTAAGAGATTGGAT-GGTCTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
31027958 CTTCAATCTGCCTCATG
65 CTTCAATCTGCCTCATG
* *
31027975 ATCGGGGTAAGAGATTGGATGGTCTCAATCTGCCCCATGGTCGGGGTAAGAGATTGTATGATGTC
1 ATCGGGGTAAGAGATTGGATGGTCTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTC
31028040 TTCAATCTGACCT-ATG
66 TTCAATCTG-CCTCATG
* *
31028056 ATCGGGGTAAGAGATTTGATGGTCTCAATCTGCCCCATGATCGGGGCAAGAGATTGGATGATGTC
1 ATCGGGGTAAGAGATTGGATGGTCTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTC
*
31028121 TTCAATCTGCCCCATG
66 TTCAATCTGCCTCATG
* * *
31028137 ATCGAGGTAAGAGATTGGATGGTCCTTAATCTGCCTCATGATCGGGGTAAGAGATTGG-TG-TGT
1 ATCGGGGTAAGAGATTGGATGGT-CTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT
* *
31028200 CTTCAATCTACC-CTTTG
65 CTTCAATCTGCCTC-ATG
** * * * * * *
31028217 ATTAGGGTAAAATATTGGATGCT-TCAATCTACCCCATGATCGGGTTATGAGATTGG
1 ATCGGGGTAAGAGATTGGATGGTCTCAATCTGCCCCATGATCGGGGTAAGAGATTGG
31028273 GTGGTAGCTT
Statistics
Matches: 267, Mismatches: 26, Indels: 13
0.87 0.08 0.04
Matches are distributed among these distances:
78 28 0.10
79 1 0.00
80 38 0.14
81 166 0.62
82 34 0.13
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (81 bp):
ATCGGGGTAAGAGATTGGATGGTCTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTC
TTCAATCTGCCTCATG
Found at i:31028487 original size:49 final size:49
Alignment explanation
Indices: 31028403--31028684 Score: 271
Period size: 49 Copynumber: 5.8 Consensus size: 49
31028393 CCTCATCTTC
* * * * * * *
31028403 AAGGTATGAGATTCGCCGTTACGGCCTCAATCTTTCCCTTCACATCTCT
1 AAGGTATAAGATTCACCGTTGCGGCTTCAACCTTTCCCTCCATATCTCT
* * * *
31028452 AAGGTATAAGGTTCACCGCTGCGGCTTCTACCTTTCCCTCCATATCTCC
1 AAGGTATAAGATTCACCGTTGCGGCTTCAACCTTTCCCTCCATATCTCT
* * ** *
31028501 ATGGTACAAGATTCGTCGTTGCGGCTTCAACCTTTCCCTCCATATCTCC
1 AAGGTATAAGATTCACCGTTGCGGCTTCAACCTTTCCCTCCATATCTCT
* * * *
31028550 ATGGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCCAT-CATGTCTTT
1 AAGGTATAAGATTCACCGTTGCGGCTTCAACCTTTCCC-TCCATATCTCT
* * * *
31028599 AAGGTACAAGGTTTGA-CGTTGCAGCTTCAACCTTTCCCTCCATATCTCT
1 AAGGTATAA-GATTCACCGTTGCGGCTTCAACCTTTCCCTCCATATCTCT
* * ** *
31028648 AGGGTATTAGATTTGCCGTTGCGGCTTCAATCTTTCC
1 AAGGTATAAGATTCACCGTTGCGGCTTCAACCTTTCC
31028685 GTTCAAACCT
Statistics
Matches: 188, Mismatches: 41, Indels: 8
0.79 0.17 0.03
Matches are distributed among these distances:
48 4 0.02
49 179 0.95
50 5 0.03
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (49 bp):
AAGGTATAAGATTCACCGTTGCGGCTTCAACCTTTCCCTCCATATCTCT
Found at i:31028672 original size:147 final size:147
Alignment explanation
Indices: 31028405--31028684 Score: 364
Period size: 147 Copynumber: 1.9 Consensus size: 147
31028395 TCATCTTCAA
* * * *
31028405 GGTATGAGATTCGCCGTTACGGCCTCAATCTTTCCCTTCACATCTCTAAGGTATAAGGTTCACCG
1 GGTATAAGATTCACCGTTACGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCACCG
* * * *
31028470 CTGCGGCTTCTACCTTTCCCTCCATATCTCCATGGTACAAGATTCGTCGTTGCGGCTTCAACCTT
66 CTGCAGCTTCAACCTTTCCCTCCATATCTCCAGGGTACAAGATTCGCCGTTGCGGCTTCAACCTT
31028535 TCCCTCCATATCTCCAT
131 TCCCTCCATATCTCCAT
* * ** * *
31028552 GGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCCATCATGTCTTTAAGGTACAAGGTTTGA-C
1 GGTATAAGATTCACCGTTACGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGG-TTCACC
* * ** * *
31028616 GTTGCAGCTTCAACCTTTCCCTCCATATCTCTAGGGTATTAGATTTGCCGTTGCGGCTTCAATCT
65 GCTGCAGCTTCAACCTTTCCCTCCATATCTCCAGGGTACAAGATTCGCCGTTGCGGCTTCAACCT
31028681 TTCC
130 TTCC
31028685 GTTCAAACCT
Statistics
Matches: 112, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
147 109 0.97
148 3 0.03
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.34
Consensus pattern (147 bp):
GGTATAAGATTCACCGTTACGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCACCG
CTGCAGCTTCAACCTTTCCCTCCATATCTCCAGGGTACAAGATTCGCCGTTGCGGCTTCAACCTT
TCCCTCCATATCTCCAT
Found at i:31029242 original size:106 final size:107
Alignment explanation
Indices: 31029100--31029292 Score: 318
Period size: 106 Copynumber: 1.8 Consensus size: 107
31029090 CGTCATTTTA
* *
31029100 ATGCAAAAATGCTTGAACAGGGGTTGTAAGGTGGATAAAATTGAATTTTATTGGA-AGCAAAGCT
1 ATGCAAAAATGCTTGAACAGAGGTTGTAAGGTGGATAAAATTGAATTTTATTGGAGA-AAAAGCT
*
31029164 GGCATGAATGAAAAGATTAAAAACCATTAGTCCACTAACTATT
65 CGCATGAATGAAAAGATTAAAAACCATTAGTCCACTAACTATT
**
31029207 ATGCAAACGTGCTTGAACA-AGGTTGTAAGGTGGATAAAATTGAATTTTATTGGAGAAAAAGCTC
1 ATGCAAAAATGCTTGAACAGAGGTTGTAAGGTGGATAAAATTGAATTTTATTGGAGAAAAAGCTC
31029271 GCATGAATGAAAAGATTAAAAA
66 GCATGAATGAAAAGATTAAAAA
31029293 TGACAAACAT
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
106 62 0.77
107 18 0.22
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.26
Consensus pattern (107 bp):
ATGCAAAAATGCTTGAACAGAGGTTGTAAGGTGGATAAAATTGAATTTTATTGGAGAAAAAGCTC
GCATGAATGAAAAGATTAAAAACCATTAGTCCACTAACTATT
Found at i:31029613 original size:5 final size:5
Alignment explanation
Indices: 31029603--31029649 Score: 58
Period size: 5 Copynumber: 8.8 Consensus size: 5
31029593 TCGGCCTCTC
*
31029603 CTTTT CTTTT CCTTTTT CTTTT CTTTT CTTTT CTTTT TTCTTT CTTT
1 CTTTT CTTTT -C-TTTT CTTTT CTTTT CTTTT CTTTT CT-TTT CTTT
31029650 CCCTTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 27 0.73
6 6 0.16
7 4 0.11
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
CTTTT
Found at i:31029625 original size:17 final size:17
Alignment explanation
Indices: 31029603--31029649 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
31029593 TCGGCCTCTC
31029603 CTTTTCTTTTCCTTTT-T
1 CTTTTCTTTT-CTTTTCT
31029620 CTTTTCTTTTCTTTTCT
1 CTTTTCTTTTCTTTTCT
*
31029637 TTTTTC-TTTCTTT
1 CTTTTCTTTTCTTT
31029650 CCCTTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
CTTTTCTTTTCTTTTCT
Found at i:31029628 original size:22 final size:21
Alignment explanation
Indices: 31029603--31029649 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
31029593 TCGGCCTCTC
31029603 CTTTTCTTTTCCTTTTTCTTTT
1 CTTTTCTTTTCCTTTTTC-TTT
*
31029625 CTTTTCTTTTCTTTTTTCTTT
1 CTTTTCTTTTCCTTTTTCTTT
31029646 CTTT
1 CTTT
31029650 CCCTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
CTTTTCTTTTCCTTTTTCTTT
Found at i:31029655 original size:17 final size:17
Alignment explanation
Indices: 31029604--31029662 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
31029594 CGGCCTCTCC
31029604 TTTTCTTTTCCTTT--TT
1 TTTTCTTTT-CTTTCCTT
*
31029620 CTTTTCTTTTCTTTTCTT
1 -TTTTCTTTTCTTTCCTT
*
31029638 TTTTC-TTTCTTTCCCT
1 TTTTCTTTTCTTTCCTT
*
31029654 TTTTATTTT
1 TTTTCTTTT
31029663 TTGGGTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 17 0.47
17 17 0.47
18 2 0.06
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTCTTTCCTT
Found at i:31029663 original size:22 final size:22
Alignment explanation
Indices: 31029603--31029656 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
31029593 TCGGCCTCTC
* *
31029603 CTTTTCTTTTCCTTTTTCTTTT
1 CTTTCCTTTTCTTTTTTCTTTT
*
31029625 CTTTTCTTTTCTTTTTTC-TTT
1 CTTTCCTTTTCTTTTTTCTTTT
31029646 CTTTCCCTTTT
1 CTTT-CCTTTT
31029657 TATTTTTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (22 bp):
CTTTCCTTTTCTTTTTTCTTTT
Found at i:31034927 original size:28 final size:29
Alignment explanation
Indices: 31034869--31034930 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
31034859 GGGATTAAAT
* *
31034869 TTAAAAAAAAAAAAGAATAATGGGTAAGA
1 TTAAAAAAAAAAAAGAATAACGGGAAAGA
*
31034898 TTAAAAAAAAAAAA-AA-AACGTGAAAGGA
1 TTAAAAAAAAAAAAGAATAACGGGAAA-GA
31034926 TTAAA
1 TTAAA
31034931 TTAAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 9 0.31
29 14 0.48
ACGTcount: A:0.68, C:0.02, G:0.15, T:0.16
Consensus pattern (29 bp):
TTAAAAAAAAAAAAGAATAACGGGAAAGA
Found at i:31037192 original size:55 final size:55
Alignment explanation
Indices: 31037116--31037238 Score: 174
Period size: 55 Copynumber: 2.2 Consensus size: 55
31037106 TGTTTTATTA
* * * * *
31037116 TTTTGAAGCACACGGGTTGACACACGGGCGTATGTCAGGGTGTGTGTGTATACTG
1 TTTTGAGGCACACGGGCTGACACACGAGCATATATCAGGGTGTGTGTGTATACTG
* *
31037171 TTTTGAGGCACACGGGCTGACACACGAGCATGTATCAGGGTGTGTGTGTATATTG
1 TTTTGAGGCACACGGGCTGACACACGAGCATATATCAGGGTGTGTGTGTATACTG
*
31037226 TTTTAAGGCACAC
1 TTTTGAGGCACAC
31037239 AGGCGTGTGT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (55 bp):
TTTTGAGGCACACGGGCTGACACACGAGCATATATCAGGGTGTGTGTGTATACTG
Found at i:31043244 original size:32 final size:31
Alignment explanation
Indices: 31043208--31043267 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
31043198 TACTCCATTC
*
31043208 TTAAGAATAGAAATCGAACCCTGACCACAAAA
1 TTAAGAATAGAAAT-GAACCATGACCACAAAA
* * *
31043240 TTAAGAGTTGAAATGAACCATGATCACA
1 TTAAGAATAGAAATGAACCATGACCACA
31043268 CCTAGTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 12 0.50
32 12 0.50
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (31 bp):
TTAAGAATAGAAATGAACCATGACCACAAAA
Found at i:31052261 original size:22 final size:22
Alignment explanation
Indices: 31052222--31052282 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
31052212 TAATCATATA
* *
31052222 ATAATTTATTAATATAATTAAT
1 ATAATTTATTATTTTAATTAAT
*
31052244 ATAATTTATTATTTTAATAAAT
1 ATAATTTATTATTTTAATTAAT
* *
31052266 -TATTTTA-TATTTCAATT
1 ATAATTTATTATTTTAATT
31052283 CTATTTTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 8 0.24
21 6 0.18
22 19 0.58
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
ATAATTTATTATTTTAATTAAT
Found at i:31052303 original size:13 final size:14
Alignment explanation
Indices: 31052285--31052326 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
31052275 TTTCAATTCT
31052285 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
31052298 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
31052313 ATTTTAAATAATAT
1 ATTTT-AATAATAT
31052327 TCTTAACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:31052311 original size:16 final size:16
Alignment explanation
Indices: 31052289--31052325 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
31052279 AATTCTATTT
31052289 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
31052306 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
31052321 TAATA
1 TAATA
31052326 TTCTTAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:31056273 original size:25 final size:25
Alignment explanation
Indices: 31056215--31056273 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
31056205 ACGAATCTGC
*
31056215 AAAAAAAAAAGGAAAGAAGATCAAG
1 AAAAAAAAAAGGAAACAAGATCAAG
* * *
31056240 AACACAAAAGGGAAACAAGATCAA-
1 AAAAAAAAAAGGAAACAAGATCAAG
*
31056264 ATAAAAAAAA
1 AAAAAAAAAA
31056274 TATTGTAAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.71, C:0.08, G:0.15, T:0.05
Consensus pattern (25 bp):
AAAAAAAAAAGGAAACAAGATCAAG
Found at i:31067476 original size:20 final size:20
Alignment explanation
Indices: 31067448--31067486 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31067438 CCATAACTTT
*
31067448 CATTATTAAGTTTAATTAAC
1 CATTATTAACTTTAATTAAC
*
31067468 CATTTTTAACTTTAATTAA
1 CATTATTAACTTTAATTAA
31067487 ACCTATTTAA
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:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (20 bp):
CATTATTAACTTTAATTAAC
Found at i:31067495 original size:20 final size:20
Alignment explanation
Indices: 31067453--31067496 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
31067443 ACTTTCATTA
* *
31067453 TTAAGTTTAATTAACCATTT
1 TTAACTTTAATTAACCATAT
31067473 TTAACTTTAATTAAACC-TAT
1 TTAACTTTAATT-AACCATAT
31067493 TTAA
1 TTAA
31067497 AAGTAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (20 bp):
TTAACTTTAATTAACCATAT
Found at i:31079516 original size:17 final size:16
Alignment explanation
Indices: 31079490--31079522 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
31079480 GGATTCCTAC
31079490 CATCGTGGACGGTGGT
1 CATCGTGGACGGTGGT
31079506 CATCAGTGGACGGTGGT
1 CATC-GTGGACGGTGGT
31079523 ATTCGACACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.18, G:0.42, T:0.24
Consensus pattern (16 bp):
CATCGTGGACGGTGGT
Found at i:31081730 original size:21 final size:21
Alignment explanation
Indices: 31081706--31081756 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
31081696 ATAGTGTAGA
* * *
31081706 CTTCTACCGATACAAGTGAAG
1 CTTCTACCGAAACAAATCAAG
*
31081727 CTTCTACCGAAACAAATCATG
1 CTTCTACCGAAACAAATCAAG
31081748 CTTCTACCG
1 CTTCTACCG
31081757 GTACTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.25
Consensus pattern (21 bp):
CTTCTACCGAAACAAATCAAG
Found at i:31082431 original size:28 final size:28
Alignment explanation
Indices: 31082390--31082445 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
31082380 GATATCCGAT
31082390 TTACTCCCTATTGACCCAAAGGTCATGC
1 TTACTCCCTATTGACCCAAAGGTCATGC
* *
31082418 TTACTCCTTGTTGACCCAAAGGTCATGC
1 TTACTCCCTATTGACCCAAAGGTCATGC
31082446 CTATTACCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.30
Consensus pattern (28 bp):
TTACTCCCTATTGACCCAAAGGTCATGC
Found at i:31084353 original size:20 final size:19
Alignment explanation
Indices: 31084308--31084354 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
31084298 AAAATGAAGA
*
31084308 AGTGCCCTTGTATGCACTC
1 AGTGCCCCTGTATGCACTC
*
31084327 CGATGCCCCTGTATGCACTC
1 AG-TGCCCCTGTATGCACTC
31084347 TAGTGCCC
1 -AGTGCCC
31084355 TTGATGGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.15, C:0.36, G:0.21, T:0.28
Consensus pattern (19 bp):
AGTGCCCCTGTATGCACTC
Found at i:31085874 original size:15 final size:16
Alignment explanation
Indices: 31085850--31085882 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
31085840 TTATAATTGG
*
31085850 TTGTTTTTTTAT-CTA
1 TTGTTATTTTATGCTA
31085865 TTGTTATTTTATGCTA
1 TTGTTATTTTATGCTA
31085881 TT
1 TT
31085883 TAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.70
Consensus pattern (16 bp):
TTGTTATTTTATGCTA
Found at i:31086053 original size:3 final size:3
Alignment explanation
Indices: 31086040--31086090 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
31086030 TTCCTAATTA
* * *
31086040 ATT AAT ATT ATT ATC ATT ATT ATT ATG ATT A-T ATT ATT ATT -TT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
31086087 ATT A
1 ATT A
31086091 CCATGATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:31086058 original size:9 final size:8
Alignment explanation
Indices: 31086044--31086090 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
31086034 TAATTAATTA
31086044 ATATTATT
1 ATATTATT
31086052 ATCATTATT
1 AT-ATTATT
*
31086061 ATTATGATT
1 A-TATTATT
31086070 ATATTATT
1 ATATTATT
*
31086078 ATTTTATT
1 ATATTATT
31086086 -TATTA
1 ATATTA
31086091 CCATGATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
7 4 0.12
8 15 0.45
9 13 0.39
10 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (8 bp):
ATATTATT
Found at i:31086062 original size:12 final size:12
Alignment explanation
Indices: 31086045--31086085 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
31086035 AATTAATTAA
31086045 TATTATTATCAT
1 TATTATTATCAT
*
31086057 TATTATTATGAT
1 TATTATTATCAT
*
31086069 TA-TATTATTAT
1 TATTATTATCAT
31086080 T-TTATT
1 TATTATT
31086086 TATTACCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 13 0.50
12 13 0.50
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTATTATCAT
Found at i:31086077 original size:29 final size:30
Alignment explanation
Indices: 31086045--31086110 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
31086035 AATTAATTAA
**
31086045 TATTATTATCA-TTATTATTATGATTATAT
1 TATTATTATCATTTATTACCATGATTATAT
* *
31086074 TATTATT-TTATTTATTACCATGATTATGT
1 TATTATTATCATTTATTACCATGATTATAT
31086103 TATT-TTAT
1 TATTATTAT
31086111 TTTATTGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (30 bp):
TATTATTATCATTTATTACCATGATTATAT
Found at i:31093141 original size:66 final size:65
Alignment explanation
Indices: 31092973--31093164 Score: 199
Period size: 66 Copynumber: 2.9 Consensus size: 65
31092963 GTGCAGGTCA
* * * * * * *
31092973 TACTTCGGTTTATCCGATGAGGTATTGGGTGTCAAATACATCGATGAGCATTGGGCGCAATTGAA
1 TACTTCGGTTTATCTGATGAGGCACT-GATGTCAAATACATCGATGAGCGTTGGGCACAATTAAA
31093038 T
65 T
* *
31093039 TACTTTGGTTTAT-TCGATGAGGCACTGA-GTACCAAATACATCGATGAGCGTTGGGCATAATTA
1 TACTTCGGTTTATCT-GATGAGGCACTGATGT--CAAATACATCGATGAGCGTTGGGCACAATTA
31093102 AAT
63 AAT
* * * * *
31093105 TACTTCGCTTTATCTGATGAGGCACTAGATGTCAAATATATTGATGAACGTTGGACACAA
1 TACTTCGGTTTATCTGATGAGGCACT-GATGTCAAATACATCGATGAGCGTTGGGCACAA
31093165 ACTAATATTT
Statistics
Matches: 104, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
64 2 0.02
65 1 0.01
66 96 0.92
67 3 0.03
68 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (65 bp):
TACTTCGGTTTATCTGATGAGGCACTGATGTCAAATACATCGATGAGCGTTGGGCACAATTAAAT
Found at i:31094639 original size:23 final size:22
Alignment explanation
Indices: 31094607--31094655 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
31094597 TAAACCCAAT
31094607 TTTAAATTATTTTAAGTTTAAA
1 TTTAAATTATTTTAAGTTTAAA
*
31094629 TTTAAACTTATTTTGAGTTTAAA
1 TTTAAA-TTATTTTAAGTTTAAA
31094652 TTTA
1 TTTA
31094656 TTTTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTAAATTATTTTAAGTTTAAA
Found at i:31094669 original size:18 final size:17
Alignment explanation
Indices: 31094629--31094673 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
31094619 TAAGTTTAAA
*
31094629 TTTAAACTTATTTTGAG
1 TTTAAATTTATTTTGAG
*
31094646 TTTAAATTTATTTTGAAT
1 TTTAAATTTATTTTG-AG
31094664 TTTAAATTTA
1 TTTAAATTTA
31094674 AGATTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTTTGAG
Found at i:31094709 original size:21 final size:20
Alignment explanation
Indices: 31094680--31094720 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
31094670 TTTAAGATTT
31094680 AATTAAAAGTCCAAAATTACA
1 AATTAAAAGTCC-AAATTACA
*
31094701 AATTCAAAGTCCAAATTACA
1 AATTAAAAGTCCAAATTACA
31094721 TTACCCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.54, C:0.17, G:0.05, T:0.24
Consensus pattern (20 bp):
AATTAAAAGTCCAAATTACA
Found at i:31096368 original size:29 final size:30
Alignment explanation
Indices: 31096335--31096631 Score: 249
Period size: 29 Copynumber: 10.1 Consensus size: 30
31096325 AAAAACCATG
*
31096335 TTTTTACCCCTGAACTTTTCAAAAATTACA
1 TTTTTACCCCTAAACTTTTCAAAAATTACA
* *
31096365 TTTTTACCCTTAAAC-TTCCAAAAATTACA
1 TTTTTACCCCTAAACTTTTCAAAAATTACA
* * *
31096394 TTTTTACCTCTAAAC-TTTCAAAAATCATA
1 TTTTTACCCCTAAACTTTTCAAAAATTACA
* * ** * *
31096423 CTTTTACCCCCAAACTACTCATAAATCACA
1 TTTTTACCCCTAAACTTTTCAAAAATTACA
* *
31096453 TTTTTACCCTTAAAC--TTCCAAAATTACA
1 TTTTTACCCCTAAACTTTTCAAAAATTACA
*
31096481 TTTTTGCCCCTAAAC-TTTCAAAAATTACA
1 TTTTTACCCCTAAACTTTTCAAAAATTACA
*
31096510 TTTTTACCCC-AAACTTCTC-AAAATTACA
1 TTTTTACCCCTAAACTTTTCAAAAATTACA
* *
31096538 TTTTTGA-CCCTAAACTCATCCAAAAATTATC-
1 TTTTT-ACCCCTAAACT-TTTCAAAAATTA-CA
* * * *
31096569 GTTTTACCCTTGAACTTCT-AAAAATTACA
1 TTTTTACCCCTAAACTTTTCAAAAATTACA
* *
31096598 -TTTTAACCCTAAA-TTTTCCTAAAATTACCA
1 TTTTTACCCCTAAACTTTT-CAAAAATTA-CA
31096628 TTTT
1 TTTT
31096632 GCCCTCGAAC
Statistics
Matches: 212, Mismatches: 41, Indels: 27
0.76 0.15 0.10
Matches are distributed among these distances:
27 3 0.01
28 54 0.25
29 94 0.44
30 39 0.18
31 21 0.10
32 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTTTACCCCTAAACTTTTCAAAAATTACA
Found at i:31096398 original size:59 final size:57
Alignment explanation
Indices: 31096335--31096694 Score: 277
Period size: 59 Copynumber: 6.2 Consensus size: 57
31096325 AAAAACCATG
*
31096335 TTTTTACCCCTGAACTTTTCAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTACA
1 TTTTTACCCCTAAAC-TTTCAAAAATTACATTTTTACCC-TAAACTTCCAAAAATTACA
* * * * * * * *
31096394 TTTTTACCTCTAAACTTTCAAAAATCATACTTTTACCCCCAAACTACTCATAAATCACA
1 TTTTTACCCCTAAACTTTCAAAAATTACATTTTTA-CCCTAAACTTC-CAAAAATTACA
* * * *
31096453 TTTTTACCCTTAAAC-TTCCAAAATTACATTTTTGCCCCTAAACTTTCAAAAATTACA
1 TTTTTACCCCTAAACTTTCAAAAATTACATTTTT-ACCCTAAACTTCCAAAAATTACA
31096510 TTTTTACCCC-AAACTTCTC-AAAATTACATTTTTGACCCTAAACTCATCCAAAAATTATC-
1 TTTTTACCCCTAAACTT-TCAAAAATTACATTTTT-ACCCTAAACT--TCCAAAAATTA-CA
* * * * * *
31096569 GTTTTACCCTTGAAC-TTCTAAAAATTACATTTTAACCCTAAATTTTCCTAAAATTACCA
1 TTTTTACCCCTAAACTTTC-AAAAATTACATTTTTACCCTAAA-CTTCCAAAAATTA-CA
* * * ** * *
31096628 -TTTT-GCCCTCGAACATAAAAAAATTACCATTTTTACCCTCGAACATCCAAAAATTAC-
1 TTTTTACCCCT-AAACTTTCAAAAATTA-CATTTTTACCCT-AAACTTCCAAAAATTACA
31096685 TATTTTACCC
1 T-TTTTACCC
31096695 TCGAGTGTCC
Statistics
Matches: 240, Mismatches: 41, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
56 4 0.02
57 46 0.19
58 77 0.32
59 91 0.38
60 22 0.09
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (57 bp):
TTTTTACCCCTAAACTTTCAAAAATTACATTTTTACCCTAAACTTCCAAAAATTACA
Found at i:31096574 original size:116 final size:116
Alignment explanation
Indices: 31096336--31096631 Score: 300
Period size: 116 Copynumber: 2.5 Consensus size: 116
31096326 AAAACCATGT
* * * *
31096336 TTTTACCCCTGAACTTTTCAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTACATTTTTAC
1 TTTTACCCTTAAACTTCT-AAAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTAC
* * *
31096401 CTCTAAACTTTCAAAAATCATACTTTTACCCCCAAACTACTCATAAATCACAT
65 CTCCAAACTTTCAAAAATCATA-TTTTACCCCCAAACTACTCAAAAATCACAG
* * *
31096454 TTTTACCCTTAAACTTC-CAAAATTACATTTTTGCCCCTAAACTTTCAAAAATTACATTTTTACC
1 TTTTACCCTTAAACTTCTAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTACC
* * *
31096518 -CCAAACTTCTCAAAATTACAT-TTTTGA-CCCTAAACT-CATCCAAAAATTATC-G
66 TCCAAACTT-TCAAAAAT-CATATTTT-ACCCCCAAACTAC-T-CAAAAATCA-CAG
* * * *
31096570 TTTTACCCTTGAACTTCTAAAAATTACA-TTTTAACCCTAAATTTTCCTAAAATTACCATTTT
1 TTTTACCCTTAAACTTCTAAAAATTACATTTTTACCCCTAAA-CTTCCAAAAATTA-CATTTT
31096632 GCCCTCGAAC
Statistics
Matches: 149, Mismatches: 20, Indels: 18
0.80 0.11 0.10
Matches are distributed among these distances:
114 1 0.01
115 20 0.13
116 85 0.57
117 23 0.15
118 20 0.13
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (116 bp):
TTTTACCCTTAAACTTCTAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTACC
TCCAAACTTTCAAAAATCATATTTTACCCCCAAACTACTCAAAAATCACAG
Found at i:31096592 original size:88 final size:86
Alignment explanation
Indices: 31096335--31096694 Score: 313
Period size: 88 Copynumber: 4.1 Consensus size: 86
31096325 AAAAACCATG
* *
31096335 TTTTTACCCCTGAACTTTTCAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTACATTTTTA
1 TTTTTACCCC-AAACTTCTC-AAAATTACATTTTTACCCTTAAACTTCCAAAAATTACATTTTTA
* *
31096400 -CCTCTAAACTTTCAAAAATCATA
64 CCCT-TAAACTTTCAAAAATTACA
* * * *
31096423 CTTTTACCCCCAAACTACTCATAAATCACATTTTTACCCTTAAACTTCC-AAAATTACATTTTTG
1 TTTTTA-CCCCAAACTTCTCA-AAATTACATTTTTACCCTTAAACTTCCAAAAATTACATTTTTA
*
31096487 CCCCTAAACTTTCAAAAATTACA
64 CCCTTAAACTTTCAAAAATTACA
*
31096510 TTTTTACCCCAAACTTCTCAAAATTACATTTTTGACCC-TAAACTCATCCAAAAATTATC-GTTT
1 TTTTTACCCCAAACTTCTCAAAATTACATTTTT-ACCCTTAAACT--TCCAAAAATTA-CATTTT
*
31096573 TACCCTTGAAC-TTCTAAAAATTACA
62 TACCCTTAAACTTTC-AAAAATTACA
* * * * ** * **
31096598 TTTTAACCCTAAA-TTTTCCTAAAATTACCA-TTTTGCCCTCGAACATAAAAAAATTACCATTTT
1 TTTTTACCCCAAACTTCT-C-AAAATTA-CATTTTTACCCTTAAACTTCCAAAAATTA-CATTTT
** * *
31096661 TACCCTCGAACATCCAAAAATTAC-
62 TACCCTTAAACTTTCAAAAATTACA
31096685 TATTTTACCC
1 T-TTTTACCC
31096695 TCGAGTGTCC
Statistics
Matches: 226, Mismatches: 30, Indels: 32
0.78 0.10 0.11
Matches are distributed among these distances:
85 18 0.08
86 17 0.08
87 57 0.25
88 111 0.49
89 21 0.09
90 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (86 bp):
TTTTTACCCCAAACTTCTCAAAATTACATTTTTACCCTTAAACTTCCAAAAATTACATTTTTACC
CTTAAACTTTCAAAAATTACA
Found at i:31096669 original size:30 final size:29
Alignment explanation
Indices: 31096618--31096698 Score: 117
Period size: 30 Copynumber: 2.8 Consensus size: 29
31096608 AAATTTTCCT
*
31096618 AAAATTACCATTTTGCCCTCGAACATAAA
1 AAAATTACCATTTTACCCTCGAACATAAA
**
31096647 AAAATTACCATTTTTACCCTCGAACATCCA
1 AAAATTACCA-TTTTACCCTCGAACATAAA
*
31096677 AAAATTACTATTTTACCCTCGA
1 AAAATTACCATTTTACCCTCGA
31096699 GTGTCCACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
29 22 0.47
30 25 0.53
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAACATAAA
Found at i:31096705 original size:29 final size:29
Alignment explanation
Indices: 31096554--31096738 Score: 135
Period size: 29 Copynumber: 6.4 Consensus size: 29
31096544 ACCCTAAACT
* * *
31096554 CATCCAAAAATTATCGTTTTACCCTTGAA
1 CATCCAAAAATTACCATTTTACCCTCGAA
* * *
31096583 CTTCTAAAAATTA-CATTTTAACCCT-AAA
1 CATCCAAAAATTACCATTTT-ACCCTCGAA
** * *
31096611 TTTTCCTAAAATTACCATTTTGCCCTCGAA
1 -CATCCAAAAATTACCATTTTACCCTCGAA
**
31096641 CATAAAAAAATTACCATTTTTACCCTCGAA
1 CATCCAAAAATTACCA-TTTTACCCTCGAA
* *
31096671 CATCCAAAAATTACTATTTTACCCTCGAG
1 CATCCAAAAATTACCATTTTACCCTCGAA
** * *
31096700 TGTCC-ACAATTACCATTTTGCCCTC-AA
1 CATCCAAAAATTACCATTTTACCCTCGAA
*
31096727 AATTCCAAAAAT
1 CA-TCCAAAAAT
31096739 CACACTTCCA
Statistics
Matches: 121, Mismatches: 28, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
27 1 0.01
28 27 0.22
29 60 0.50
30 33 0.27
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (29 bp):
CATCCAAAAATTACCATTTTACCCTCGAA
Found at i:31113769 original size:19 final size:20
Alignment explanation
Indices: 31113729--31113769 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
31113719 CTCACATGCC
*
31113729 AAAGTGAAAAATTATTATTTT
1 AAAGTGAAAAAGTA-TATTTT
31113750 AAAGTGAAAAAGTA-ATTTT
1 AAAGTGAAAAAGTATATTTT
31113769 A
1 A
31113770 TGCCCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
21 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (20 bp):
AAAGTGAAAAAGTATATTTT
Found at i:31113868 original size:47 final size:47
Alignment explanation
Indices: 31113814--31113924 Score: 168
Period size: 47 Copynumber: 2.4 Consensus size: 47
31113804 AAGGTGAAAG
* *
31113814 AAGTGACAGTTTATCTGCAAAAGTGATGGCTTGTCCATAATATTACA
1 AAGTGACAGTTTATCTACAAAAGTGATGGCTTGTCCACAATATTACA
* * **
31113861 AAGTGACAGTTTATCTACAAAAGTGGTGGCTTGTTCACAATATTATT
1 AAGTGACAGTTTATCTACAAAAGTGATGGCTTGTCCACAATATTACA
31113908 AAGTGACAGTTTATCTA
1 AAGTGACAGTTTATCTA
31113925 TGTTACTATA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (47 bp):
AAGTGACAGTTTATCTACAAAAGTGATGGCTTGTCCACAATATTACA
Found at i:31116497 original size:20 final size:20
Alignment explanation
Indices: 31116472--31116509 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31116462 GCAATTGACC
*
31116472 GTTGACTGTTGACTTTTTGG
1 GTTGACCGTTGACTTTTTGG
31116492 GTTGACCGTTGACTTTTT
1 GTTGACCGTTGACTTTTT
31116510 TCGAGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.13, G:0.26, T:0.50
Consensus pattern (20 bp):
GTTGACCGTTGACTTTTTGG
Found at i:31119933 original size:21 final size:19
Alignment explanation
Indices: 31119904--31119955 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
31119894 GAGTTTTTGG
*
31119904 TATCAGTAGATGCATGACTTA
1 TATCGGTAGAT-CAT-ACTTA
*
31119925 TATCGGTAGAAATCATACTTG
1 TATCGGTAG--ATCATACTTA
31119946 TATCGGTAGA
1 TATCGGTAGA
31119956 GCTAGCACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
21 21 0.78
22 3 0.11
23 2 0.07
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (19 bp):
TATCGGTAGATCATACTTA
Found at i:31131658 original size:20 final size:21
Alignment explanation
Indices: 31131611--31131664 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
31131601 ACCACAAGCC
*
31131611 AACCTAACCCAAATCCTTTTG
1 AACCAAACCCAAATCCTTTTG
*
31131632 AATCAAACCCAAA-CCTTTTG
1 AACCAAACCCAAATCCTTTTG
*
31131652 ACCCAAA-CCAAAT
1 AACCAAACCCAAAT
31131665 GAACCAAGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.18
20 12 0.43
21 11 0.39
ACGTcount: A:0.41, C:0.33, G:0.04, T:0.22
Consensus pattern (21 bp):
AACCAAACCCAAATCCTTTTG
Found at i:31131777 original size:20 final size:20
Alignment explanation
Indices: 31131752--31131789 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31131742 ACCGTTGATC
31131752 GTTAACCATTGACTTTTTGG
1 GTTAACCATTGACTTTTTGG
*
31131772 GTTAACCGTTGACTTTTT
1 GTTAACCATTGACTTTTT
31131790 CTAAGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.47
Consensus pattern (20 bp):
GTTAACCATTGACTTTTTGG
Found at i:31133236 original size:22 final size:21
Alignment explanation
Indices: 31133186--31133240 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
31133176 ACCTACAAAA
31133186 CATTATGTTTGTAACTCTCCT
1 CATTATGTTTGTAACTCTCCT
* *
31133207 CATAATGTTTAGTAACTCTCTT
1 CATTATGTTT-GTAACTCTCCT
*
31133229 TATTATGTTTGT
1 CATTATGTTTGT
31133241 TTTAAATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (21 bp):
CATTATGTTTGTAACTCTCCT
Found at i:31139130 original size:2 final size:2
Alignment explanation
Indices: 31139123--31139261 Score: 278
Period size: 2 Copynumber: 69.5 Consensus size: 2
31139113 TTTCATTCTT
31139123 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31139165 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31139207 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31139249 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
31139262 TTCTTTTTTT
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 137 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31144565 original size:24 final size:24
Alignment explanation
Indices: 31144529--31144603 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
31144519 ATAGACAACA
** * *
31144529 TTAGCTCACATGAGCCTAGAATGG
1 TTAGCTCTTATGAGCCCAAAATGG
31144553 TTAGCTCTTATGAGCCCAAAATGG
1 TTAGCTCTTATGAGCCCAAAATGG
**
31144577 TTAGCTCTTACAAGCCCAAAATGG
1 TTAGCTCTTATGAGCCCAAAATGG
31144601 TTA
1 TTA
31144604 ACCAGTATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (24 bp):
TTAGCTCTTATGAGCCCAAAATGG
Found at i:31154060 original size:41 final size:41
Alignment explanation
Indices: 31153980--31154087 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
31153970 TAGTAGCTTG
* * *** **
31153980 CTAAGTCGTAGCTTGAATTTCTATCATCAGTGTGTAGCCTA
1 CTAAGACGTAGCTTGAATTTCTATCACCAACATACAGCCTA
* *
31154021 CTAAGATGTAGCTTGAATTTCTATCACCAACATACAGCCTG
1 CTAAGACGTAGCTTGAATTTCTATCACCAACATACAGCCTA
* * *
31154062 CTAAGCCATAGCTTTAATTTCTATCA
1 CTAAGACGTAGCTTGAATTTCTATCA
31154088 ATGTAACTTA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (41 bp):
CTAAGACGTAGCTTGAATTTCTATCACCAACATACAGCCTA
Found at i:31154279 original size:39 final size:39
Alignment explanation
Indices: 31154225--31154304 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
31154215 ACAAAAATTA
* *
31154225 CTTGTAAGTTAAGAACTTACCTTTCCGATAATTGCGAGG
1 CTTGTAAGTTAAGAACTTACCTTTCCGACAACTGCGAGG
31154264 CTTGTAAGTTAAGAACTTACCTTTCCGACAACTGCGAGG
1 CTTGTAAGTTAAGAACTTACCTTTCCGACAACTGCGAGG
31154303 CT
1 CT
31154305 CGATGATGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (39 bp):
CTTGTAAGTTAAGAACTTACCTTTCCGACAACTGCGAGG
Found at i:31161106 original size:28 final size:29
Alignment explanation
Indices: 31161060--31161114 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
31161050 AAATTTTAAA
* *
31161060 TTATTTTTTCTATTCT-AAATATAAAATAT
1 TTATTTTTACTATTATAAAAT-TAAAATAT
31161089 TTATTTTTAC-ATTATAAAATTAAAAT
1 TTATTTTTACTATTATAAAATTAAAAT
31161115 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATTTTTACTATTATAAAATTAAAATAT
Found at i:31167279 original size:5 final size:5
Alignment explanation
Indices: 31167269--31167293 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31167259 TAATTCAGAA
31167269 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
31167294 CAACTAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:31168604 original size:17 final size:18
Alignment explanation
Indices: 31168573--31168606 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31168563 CAATGTAAGT
31168573 AAAAATTACATTTGAAAA
1 AAAAATTACATTTGAAAA
31168591 AAAAATTACA-TTGAAA
1 AAAAATTACATTTGAAA
31168607 CATGAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAAATTACATTTGAAAA
Found at i:31173150 original size:17 final size:17
Alignment explanation
Indices: 31173125--31173177 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
31173115 TACAATGAAA
*
31173125 AATGGAAATGCAATGAC
1 AATGTAAATGCAATGAC
*
31173142 AATGTAAATGCAGTGAC
1 AATGTAAATGCAATGAC
31173159 AAT-TAAAATGCAATGAC
1 AATGT-AAATGCAATGAC
31173176 AA
1 AA
31173178 AGGGAATGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 1 0.03
17 31 0.97
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (17 bp):
AATGTAAATGCAATGAC
Found at i:31183123 original size:2 final size:2
Alignment explanation
Indices: 31183116--31183140 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31183106 TATGGCAAAG
31183116 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
31183141 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31187432 original size:39 final size:39
Alignment explanation
Indices: 31187378--31187550 Score: 188
Period size: 39 Copynumber: 4.4 Consensus size: 39
31187368 CTGAAGTGGT
* *
31187378 AGTGACACTGTAAACACCACAATACGATACTAAACTGAC
1 AGTGACACTGTAAACACTACAATACAATACTAAACTGAC
* * * * *
31187417 AGTGACACTAG-AAACACTGCAATACGATATTGAACTGGC
1 AGTGACACT-GTAAACACTACAATACAATACTAAACTGAC
* * * *
31187456 AGTGACACTGGAAACATTACAATGCAATACTAAACTGGC
1 AGTGACACTGTAAACACTACAATACAATACTAAACTGAC
* * *
31187495 AGTGACACTGTAAACACTGCAATACAATACTGAATTGAC
1 AGTGACACTGTAAACACTACAATACAATACTAAACTGAC
31187534 -GTTGACACTGTAAACAC
1 AG-TGACACTGTAAACAC
31187551 CGTAATGTAT
Statistics
Matches: 113, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
38 2 0.02
39 110 0.97
40 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (39 bp):
AGTGACACTGTAAACACTACAATACAATACTAAACTGAC
Found at i:31187510 original size:78 final size:78
Alignment explanation
Indices: 31187366--31187551 Score: 223
Period size: 78 Copynumber: 2.4 Consensus size: 78
31187356 GTTATCAAAT
* * * *
31187366 TACTGAAGTGGTAGTGACACTGTAAACACCACAATACGATACTAAACTGACAGTGACACTAGAAA
1 TACTGAACTGGCAGTGACACTGGAAACACCACAATACAATACTAAACTGACAGTGACACTAGAAA
*
31187431 CACTGCAATACGA
66 CACTGCAATACAA
* ** * *
31187444 TATTGAACTGGCAGTGACACTGGAAACATTACAATGCAATACTAAACTGGCAGTGACACT-GTAA
1 TACTGAACTGGCAGTGACACTGGAAACACCACAATACAATACTAAACTGACAGTGACACTAG-AA
31187508 ACACTGCAATACAA
65 ACACTGCAATACAA
* * *
31187522 TACTGAATTGAC-GTTGACACTGTAAACACC
1 TACTGAACTGGCAG-TGACACTGGAAACACC
31187552 GTAATGTATA
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
77 2 0.02
78 88 0.98
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (78 bp):
TACTGAACTGGCAGTGACACTGGAAACACCACAATACAATACTAAACTGACAGTGACACTAGAAA
CACTGCAATACAA
Found at i:31188228 original size:17 final size:18
Alignment explanation
Indices: 31188206--31188242 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
31188196 TAAGCTCAAG
*
31188206 AAATCTAAGCTTG-GAAA
1 AAATCTAAACTTGAGAAA
31188223 AAATCTAAACTTGAGAAA
1 AAATCTAAACTTGAGAAA
31188241 AA
1 AA
31188243 TTTAAGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.22
Consensus pattern (18 bp):
AAATCTAAACTTGAGAAA
Found at i:31188996 original size:17 final size:19
Alignment explanation
Indices: 31188976--31189017 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
31188966 ATAAAATATC
*
31188976 TATAT-AAA-AATTTGTTT
1 TATATGAAACAATTTGTAT
31188993 TATATGAAACGAATTTGTAT
1 TATATGAAAC-AATTTGTAT
31189013 TATAT
1 TATAT
31189018 TATTATCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 3 0.14
20 13 0.62
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (19 bp):
TATATGAAACAATTTGTAT
Found at i:31189758 original size:92 final size:91
Alignment explanation
Indices: 31189654--31189881 Score: 246
Period size: 92 Copynumber: 2.5 Consensus size: 91
31189644 TTTTTCATTT
* *
31189654 AATTGAGTACTTGAACTTTCAAAATGCATCAAAAATA-CCTCAAATTTCTCCAAAAAAGCATTTA
1 AATTGAGTACTTGAACTTTCAAAATG-ATCAAAAAGACCCTCAAATTTCTCCAAAAAAGCAATTA
31189718 AGC-CCTTGCTTTTTTTTTTTTTACACAC
65 AGCTCC-TGC-TTTTTTTTTTTTACACAC
* * * * * * *
31189746 AATTGGGTACTTGAA-TATTCAAAATAGATAAAAAAGACCCTTAATTTTTTTCAAAAAGGCAATT
1 AATTGAGTACTTGAACT-TTCAAAAT-GATCAAAAAGACCCTCAAATTTCTCCAAAAAAGCAATT
* ***
31189810 AAGCTCCTGCTTTTTTTTTTTTGCATTT
64 AAGCTCCTGCTTTTTTTTTTTTACACAC
* * *
31189838 AATTGAGTACTTGAGCTTTCAAAATTATCAAAAAGGCCCTCAAA
1 AATTGAGTACTTGAACTTTCAAAATGATCAAAAAGACCCTCAAA
31189882 CTTAAAAGAA
Statistics
Matches: 111, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
91 15 0.14
92 65 0.59
93 29 0.26
94 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (91 bp):
AATTGAGTACTTGAACTTTCAAAATGATCAAAAAGACCCTCAAATTTCTCCAAAAAAGCAATTAA
GCTCCTGCTTTTTTTTTTTTACACAC
Found at i:31190097 original size:10 final size:9
Alignment explanation
Indices: 31190072--31190220 Score: 54
Period size: 10 Copynumber: 15.9 Consensus size: 9
31190062 AATGATAAAA
*
31190072 ATAAAAATCA
1 ATAAAAAT-T
*
31190082 ATAAAAGTT
1 ATAAAAATT
31190091 ATAAAAATT
1 ATAAAAATT
**
31190100 ATGAAATTTT
1 AT-AAAAATT
31190110 AATAAAAA-T
1 -ATAAAAATT
31190119 ATAAAATATT
1 ATAAAA-ATT
*
31190129 -TAAAATTT
1 ATAAAAATT
*
31190137 ATTATAAATT
1 A-TAAAAATT
31190147 -TGAAAGAATAT
1 AT-AAA-AAT-T
* *
31190158 ATATATATAT
1 ATAAAAAT-T
* *
31190168 ATATAAATC
1 ATAAAAATT
* *
31190177 GTAAAAAAT
1 ATAAAAATT
31190186 ATAAAAA-T
1 ATAAAAATT
*
31190194 ATAAAATGTT
1 ATAAAA-ATT
*
31190204 ATAAAAATC
1 ATAAAAATT
31190213 ATAAAAAT
1 ATAAAAAT
31190221 GCATCAAAAA
Statistics
Matches: 104, Mismatches: 23, Indels: 25
0.68 0.15 0.16
Matches are distributed among these distances:
8 16 0.15
9 39 0.38
10 43 0.41
11 5 0.05
12 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:31190134 original size:28 final size:29
Alignment explanation
Indices: 31190081--31190136 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
31190071 AATAAAAATC
* *
31190081 AATAAAAGTTATAAAAATTATGAAATTTT
1 AATAAAAGATATAAAAATTATAAAATTTT
31190110 AATAAAA-ATATAAAATATT-TAAAATTT
1 AATAAAAGATATAAAA-ATTATAAAATTT
31190137 ATTATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (29 bp):
AATAAAAGATATAAAAATTATAAAATTTT
Found at i:31190453 original size:39 final size:36
Alignment explanation
Indices: 31190408--31190509 Score: 98
Period size: 39 Copynumber: 2.7 Consensus size: 36
31190398 TGGTAAGATG
**
31190408 ATTTTTATAATTGTTTTACGAATTTTACATTTTTTGACA
1 ATTTTTATAATT-TTTTACGAATTTTA-AAATTTT-ACA
* *
31190447 TTTTTTATAATTTTCTTACG-CTTTATAAAATTTTACA
1 ATTTTTATAATTTT-TTACGAATTT-TAAAATTTTACA
*
31190484 ATTTTTATAATTTTTTTTCGAATTTT
1 ATTTTTATAA-TTTTTTACGAATTTT
31190510 TAATAAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
37 17 0.33
38 17 0.33
39 18 0.35
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.60
Consensus pattern (36 bp):
ATTTTTATAATTTTTTACGAATTTTAAAATTTTACA
Found at i:31199732 original size:17 final size:17
Alignment explanation
Indices: 31199680--31199740 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
31199670 CATTAATTTA
*
31199680 CAATGACACATGGAAATG
1 CAATGACA-ATGAAAATG
* *
31199698 CAATGACAATGCACATG
1 CAATGACAATGAAAATG
* *
31199715 CAGTGACAATTAAAATG
1 CAATGACAATGAAAATG
*
31199732 CAAAGACAA
1 CAATGACAA
31199741 AGGGAATGTG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 27 0.77
18 8 0.23
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Found at i:31208606 original size:12 final size:12
Alignment explanation
Indices: 31208589--31208618 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31208579 ACTTCTAATT
31208589 TTTACTAATTTC
1 TTTACTAATTTC
*
31208601 TTTACTAATTTG
1 TTTACTAATTTC
31208613 TTTACT
1 TTTACT
31208619 TTCTTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.60
Consensus pattern (12 bp):
TTTACTAATTTC
Found at i:31214287 original size:15 final size:15
Alignment explanation
Indices: 31214263--31214297 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31214253 TTACATTTTA
*
31214263 TTTTATTTGTTTCAC
1 TTTTACTTGTTTCAC
*
31214278 TTTTACTTGTTTCAT
1 TTTTACTTGTTTCAC
31214293 TTTTA
1 TTTTA
31214298 AATTTTATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTTACTTGTTTCAC
Found at i:31223749 original size:22 final size:22
Alignment explanation
Indices: 31223701--31223757 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
31223691 AAAAAAGAAA
* *
31223701 CTATTGTTTTGTTGTTGTTTTC
1 CTATTATTTTGTTGTTGATTTC
31223723 CTATTATTTTGTTGTT-ATTTC
1 CTATTATTTTGTTGTTGATTTC
* *
31223744 ATTATTATATTGTT
1 -CTATTATTTTGTT
31223758 ACTATCTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.14, C:0.07, G:0.12, T:0.67
Consensus pattern (22 bp):
CTATTATTTTGTTGTTGATTTC
Found at i:31224235 original size:14 final size:12
Alignment explanation
Indices: 31224211--31224250 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
31224201 AATTTTATAA
31224211 TTTTTATAATTT
1 TTTTTATAATTT
31224223 TCTTTTATAAATTT
1 T-TTTTAT-AATTT
*
31224237 TGTTTATAATTT
1 TTTTTATAATTT
31224249 TT
1 TT
31224251 ATGATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 7 0.29
13 11 0.46
14 6 0.25
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:31228995 original size:27 final size:26
Alignment explanation
Indices: 31228963--31229020 Score: 98
Period size: 27 Copynumber: 2.2 Consensus size: 26
31228953 TTAATTATTG
31228963 AAACCCAAACCATTTAGCCCAAAACCC
1 AAACCCAAACCATTTAGCCC-AAACCC
*
31228990 AAACCCAAACCATTTAGTCCAAACCC
1 AAACCCAAACCATTTAGCCCAAACCC
31229016 AAACC
1 AAACC
31229021 AAGTCAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 11 0.37
27 19 0.63
ACGTcount: A:0.45, C:0.40, G:0.03, T:0.12
Consensus pattern (26 bp):
AAACCCAAACCATTTAGCCCAAACCC
Found at i:31229054 original size:11 final size:11
Alignment explanation
Indices: 31229040--31229103 Score: 56
Period size: 11 Copynumber: 5.8 Consensus size: 11
31229030 CATTGAACAA
*
31229040 CCGTTGATCGG
1 CCGTTGACCGG
*
31229051 CCGTTGACCGA
1 CCGTTGACCGG
**
31229062 TTGTTGACCGG
1 CCGTTGACCGG
* * *
31229073 CCATTGATCGA
1 CCGTTGACCGG
31229084 CCGTTGACCGG
1 CCGTTGACCGG
*
31229095 TCGTTGACC
1 CCGTTGACC
31229104 ATTGACCATT
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.27
Consensus pattern (11 bp):
CCGTTGACCGG
Found at i:31229067 original size:22 final size:22
Alignment explanation
Indices: 31229042--31229107 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
31229032 TTGAACAACC
*
31229042 GTTGATCGGCCGTTGACCGATT
1 GTTGACCGGCCGTTGACCGATT
* * **
31229064 GTTGACCGGCCATTGATCGACC
1 GTTGACCGGCCGTTGACCGATT
*
31229086 GTTGACCGGTCGTTGACC-ATT
1 GTTGACCGGCCGTTGACCGATT
31229107 G
1 G
31229108 ACCATTGACT
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 2 0.06
22 32 0.94
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.29
Consensus pattern (22 bp):
GTTGACCGGCCGTTGACCGATT
Found at i:31229123 original size:21 final size:21
Alignment explanation
Indices: 31229097--31229178 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
31229087 TTGACCGGTC
*
31229097 GTTGACCATTGACCATTGACT
1 GTTGACCGTTGACCATTGACT
31229118 GTTGACCGTTGACCATTGACT
1 GTTGACCGTTGACCATTGACT
* * *
31229139 -TTGA-CTTTGATCGTTGA-T
1 GTTGACCGTTGACCATTGACT
*
31229157 CGTTGACCGTTGACCGTTGACT
1 -GTTGACCGTTGACCATTGACT
31229179 TTTTCAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
18 1 0.02
19 10 0.20
20 8 0.16
21 31 0.61
22 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (21 bp):
GTTGACCGTTGACCATTGACT
Found at i:31229155 original size:7 final size:7
Alignment explanation
Indices: 31229096--31229177 Score: 78
Period size: 7 Copynumber: 12.0 Consensus size: 7
31229086 GTTGACCGGT
31229096 CGTTGAC
1 CGTTGAC
*
31229103 CATTGAC
1 CGTTGAC
*
31229110 CATTGAC
1 CGTTGAC
*
31229117 TGTTGAC
1 CGTTGAC
31229124 CGTTGAC
1 CGTTGAC
*
31229131 CATTGA-
1 CGTTGAC
*
31229137 CTTTGA-
1 CGTTGAC
* *
31229143 CTTTGAT
1 CGTTGAC
*
31229150 CGTTGAT
1 CGTTGAC
31229157 CGTTGAC
1 CGTTGAC
31229164 CGTTGAC
1 CGTTGAC
31229171 CGTTGAC
1 CGTTGAC
31229178 TTTTTCAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
6 11 0.17
7 55 0.83
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.35
Consensus pattern (7 bp):
CGTTGAC
Found at i:31229163 original size:26 final size:27
Alignment explanation
Indices: 31229096--31229155 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
31229086 GTTGACCGGT
*
31229096 CGTTGACCATTGACCATTGACTGTTGAC
1 CGTTGACCATTGA-CTTTGACTGTTGAC
*
31229124 CGTTGACCATTGACTTTGACT-TTGAT
1 CGTTGACCATTGACTTTGACTGTTGAC
31229150 CGTTGA
1 CGTTGA
31229156 TCGTTGACCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 10 0.33
27 7 0.23
28 13 0.43
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (27 bp):
CGTTGACCATTGACTTTGACTGTTGAC
Found at i:31232220 original size:17 final size:19
Alignment explanation
Indices: 31232187--31232228 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
31232177 TTTAAAAGAT
31232187 TTGAGAGAGTTTGAGAAAA
1 TTGAGAGAGTTTGAGAAAA
31232206 TTGAGAGAG-TT-AGAAAA
1 TTGAGAGAGTTTGAGAAAA
31232223 -TGAGAG
1 TTGAGAG
31232229 TAAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
17 6 0.26
18 2 0.09
19 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24
Consensus pattern (19 bp):
TTGAGAGAGTTTGAGAAAA
Found at i:31236430 original size:16 final size:16
Alignment explanation
Indices: 31236409--31236448 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
31236399 TCATATTATA
31236409 TATTTTATAA-TATTTT
1 TATTTT-TAATTATTTT
31236425 TATTTTTAATTATTTT
1 TATTTTTAATTATTTT
31236441 TATGTTTT
1 TAT-TTTT
31236449 TTTAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 15 0.68
17 4 0.18
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TATTTTTAATTATTTT
Found at i:31236553 original size:7 final size:7
Alignment explanation
Indices: 31236541--31236579 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
31236531 ATGTCTCTCT
31236541 AAAATTA
1 AAAATTA
31236548 AAAATTA
1 AAAATTA
*
31236555 AAATTTA
1 AAAATTA
31236562 AAAATTA
1 AAAATTA
31236569 AAAATTA
1 AAAATTA
31236576 AAAA
1 AAAA
31236580 AAAAAGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATTA
Found at i:31258269 original size:4 final size:4
Alignment explanation
Indices: 31258256--31258308 Score: 65
Period size: 4 Copynumber: 13.2 Consensus size: 4
31258246 AACCGATATT
*
31258256 GAAA -AAA GAAA GAAA GAAAA GAAA GAAA GAAA G-GA GAAA GAGAA GAAA
1 GAAA GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA
31258304 GAAA G
1 GAAA G
31258309 GAGAAGGAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 5 0.12
4 30 0.70
5 8 0.19
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:31258277 original size:13 final size:13
Alignment explanation
Indices: 31258259--31258308 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
31258249 CGATATTGAA
31258259 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
31258272 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
*
31258285 -AAAG-GAGAAAG
1 AAAAGAAAGAAAG
*
31258296 AGAAGAAAGAAAG
1 AAAAGAAAGAAAG
31258309 GAGAAGGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 6 0.19
12 7 0.22
13 19 0.59
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:31258293 original size:24 final size:26
Alignment explanation
Indices: 31258266--31258318 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
31258256 GAAAAAAGAA
31258266 AGAAAGAAAAGAAAGAAA-GA-AAGG
1 AGAAAGAAAAGAAAGAAAGGAGAAGG
*
31258290 AGAAAGAGAAGAAAGAAAGGAGAAGG
1 AGAAAGAAAAGAAAGAAAGGAGAAGG
31258316 AGA
1 AGA
31258319 GAAAGGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 17 0.65
25 2 0.08
26 7 0.27
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (26 bp):
AGAAAGAAAAGAAAGAAAGGAGAAGG
Found at i:31258318 original size:20 final size:20
Alignment explanation
Indices: 31258261--31258323 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
31258251 ATATTGAAAA
31258261 AAGAAAGAAA-GA-AAAGA-
1 AAGAAAGAAAGGAGAAAGAG
31258278 AAGAAAGAAAGGAGAAAGAG
1 AAGAAAGAAAGGAGAAAGAG
*
31258298 AAGAAAGAAAGGAGAAGGAG
1 AAGAAAGAAAGGAGAAAGAG
31258318 -AGAAAG
1 AAGAAAG
31258324 GTAATGTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
17 10 0.24
18 2 0.05
19 11 0.26
20 19 0.45
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AAGAAAGAAAGGAGAAAGAG
Found at i:31258710 original size:4 final size:4
Alignment explanation
Indices: 31258701--31258752 Score: 61
Period size: 4 Copynumber: 13.0 Consensus size: 4
31258691 TTAAATATTA
* * *
31258701 AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAG GAAG AAGG AGAAT AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG
31258749 AAAG
1 AAAG
31258753 GAGAAGGAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
3 3 0.07
4 36 0.88
5 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:31258768 original size:20 final size:20
Alignment explanation
Indices: 31258725--31258762 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31258715 AGAAAGAAAG
31258725 AAAGAAGGAAGAAGGAGAAT
1 AAAGAAGGAAGAAGGAGAAT
31258745 AAAGAAAGG-AGAAGGAGA
1 AAAG-AAGGAAGAAGGAGA
31258763 GAAAAGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.03
Consensus pattern (20 bp):
AAAGAAGGAAGAAGGAGAAT
Found at i:31258944 original size:458 final size:444
Alignment explanation
Indices: 31258251--31259160 Score: 1508
Period size: 458 Copynumber: 2.0 Consensus size: 444
31258241 GGACCAACCG
*
31258251 ATATTGAAAAAAGAAAGAAAGAAAAGAAAGAAAGAAAGGAGAAAGAGAAGAAAGAAAGGAGAAGG
1 ATATTAAAAAAAGAAAGAAAGAAAAGAAAGAAAGAAAGGAGAAAGAGAAGAAAGAAAGGAGAAGG
* *
31258316 AGAGAAAGGTAATGTATTTATTTTTAAAATTTTTTAATTTGTTAGTTAGTAGTAGTAATTTTATT
66 AGAGAAAAGTAATGTATTTATTTTTAAAATTTTTTAATTTGTTAGTTAGTAGTAATAATTTTATT
*
31258381 TATTGTTTAATGTGATTGATTTGTATTATAATTTTATTTGTTTAGTAGATTGATTAAAAAATTAA
131 TATTGTTTAATGTGATTAATTTGTATTATAATTTTATTTGTTTAGTAGATTGATTAAAAAATTAA
*
31258446 AAGAAAGGAAGAAAGGTAAGTTTGATTATTATTGGTATTTATTATTTTAAGTTATTT-TTTTGTC
196 AAGAAAGGAAGAAAGGTAAGTTTGATTATTATTAGTATTTATTATTTTAAGTTATTTGTTTTGTC
31258510 TAATTTAATTTTTAATTAATTTGTTATTTAATGTTTTTATTTAGTTGAGTAAATTAAGAGGAGAA
261 TAATTTAATTTTTAA-TAATTTGTTATTTAATGTTTTTATTTAGTTGAGTAAATTAAGAGGAGAA
*
31258575 AAAAAGGTAAGTTTGGTTATTA-TTTATTATTAATTTACTTTAATTTAATTTTGATAGTAAGTAA
325 AAAAAGGTAAGTTTAGTTATTATTTTATTATTAATTTACTTTAATTTAATTTTGATAGTAAGTAA
*
31258639 TTTTTATTTTGTTAGTAGTAGTAAGTAAGTAATAATATAAATTAATTTAA-AATTAA
390 TTTTTATTTTGTTACTAGTAGTAAGTAAG--ATAATATAAATTAATTTAATAATTAA
* *
31258695 ATATTAAAAGAAAGAAAGAAAG-AAAGAAAGAAAG-AAGGAAGAAGGAGAATAAAGAAAGGAGAA
1 ATATTAAAA-AAAGAAAGAAAGAAAAGAAAGAAAGAAAGG-AGAAAGAGAAGAAAGAAAGGAGAA
31258758 GGAGAGAAAAGTAATGTATTTATTTTAAATTTATTTTTAAATTTCTTTAATTTGTTAGTTAGTAG
64 GGAGAGAAAAGTAATGTATTTA--TT---TTTA-----AAATTT-TTTAATTTGTTAGTTAGTAG
31258823 TAATAATTTTAATTTTATTGTTTAATGTGATTAATTTGTTATTATAATTTTATTTGTTTAGTAGA
118 TAATAATTTT-A-TTTATTGTTTAATGTGATTAATTTG-TATTATAATTTTATTTGTTTAGTAGA
31258888 TTGATTAAAAAATTAAAAGAAAGGAAGAAAGGTAAGTTTGATTATTATTAGTATTTATTATTTTA
180 TTGATTAAAAAATTAAAAGAAAGGAAGAAAGGTAAGTTTGATTATTATTAGTATTTATTATTTTA
*
31258953 AGTTATTTGTTTTGTTTAATTTAATTTTTAATAATTTGTTATTTAATGTTTTTATTTAGTTGAGT
245 AGTTATTTGTTTTGTCTAATTTAATTTTTAATAATTTGTTATTTAATGTTTTTATTTAGTTGAGT
*
31259018 AAATTAAGAGGAGAAAGAAAGGTAAGTTTAGTTATTATTTTATTATTAATTTACTTTAATTTAAT
310 AAATTAAGAGGAGAAAAAAAGGTAAGTTTAGTTATTATTTTATTATTAATTTACTTTAATTTAAT
31259083 TTTGATAGTAAGTAATTTTTATTTTGTTACTAGTAGTAAGTAAGATAATATAAATTAATTTAATA
375 TTTGATAGTAAGTAATTTTTATTTTGTTACTAGTAGTAAGTAAGATAATATAAATTAATTTAATA
31259148 ATTAA
440 ATTAA
31259153 ATA-TAAAA
1 ATATTAAAA
31259161 TAGGTTATTT
Statistics
Matches: 436, Mismatches: 11, Indels: 25
0.92 0.02 0.05
Matches are distributed among these distances:
443 4 0.01
444 63 0.14
445 12 0.03
446 2 0.00
449 4 0.01
454 6 0.01
455 29 0.07
456 1 0.00
457 48 0.11
458 176 0.40
459 91 0.21
ACGTcount: A:0.41, C:0.01, G:0.16, T:0.43
Consensus pattern (444 bp):
ATATTAAAAAAAGAAAGAAAGAAAAGAAAGAAAGAAAGGAGAAAGAGAAGAAAGAAAGGAGAAGG
AGAGAAAAGTAATGTATTTATTTTTAAAATTTTTTAATTTGTTAGTTAGTAGTAATAATTTTATT
TATTGTTTAATGTGATTAATTTGTATTATAATTTTATTTGTTTAGTAGATTGATTAAAAAATTAA
AAGAAAGGAAGAAAGGTAAGTTTGATTATTATTAGTATTTATTATTTTAAGTTATTTGTTTTGTC
TAATTTAATTTTTAATAATTTGTTATTTAATGTTTTTATTTAGTTGAGTAAATTAAGAGGAGAAA
AAAAGGTAAGTTTAGTTATTATTTTATTATTAATTTACTTTAATTTAATTTTGATAGTAAGTAAT
TTTTATTTTGTTACTAGTAGTAAGTAAGATAATATAAATTAATTTAATAATTAA
Found at i:31259472 original size:16 final size:16
Alignment explanation
Indices: 31259427--31259474 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
31259417 AAATACTCTA
31259427 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
31259443 -A-TAATATA--AAAAT
1 AATTAAT-TACCAAAAT
31259456 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
31259472 AAT
1 AAT
31259475 ATCCACATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 5 0.19
14 7 0.26
15 7 0.26
16 8 0.30
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AATTAATTACCAAAAT
Found at i:31261217 original size:45 final size:45
Alignment explanation
Indices: 31261128--31261217 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
31261118 GCCTAGCTCA
* *
31261128 TCAAGCCAAAGATATCAGCCTCAGTTTGACGAGCCACCGTAATAC
1 TCAAGCCAAAGATATCAGCCTCAGTTTGAAGAGCCACCGCAATAC
* *
31261173 TCAAGCCAAGGATATCAGCCTCAGTTTGAAGAGCCACTGCAATAC
1 TCAAGCCAAAGATATCAGCCTCAGTTTGAAGAGCCACCGCAATAC
31261218 CCTACTCCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAAGATATCAGCCTCAGTTTGAAGAGCCACCGCAATAC
Found at i:31264901 original size:30 final size:30
Alignment explanation
Indices: 31264867--31264929 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
31264857 TAGTCAAATA
*
31264867 AAATAAATAATTTTTGTATATTATTTTAGT
1 AAATAAATAATTTTTATATATTATTTTAGT
* * *
31264897 AAATAAATATTTTTTATATTTTATTTTGGT
1 AAATAAATAATTTTTATATATTATTTTAGT
31264927 AAA
1 AAA
31264930 AAACAAAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (30 bp):
AAATAAATAATTTTTATATATTATTTTAGT
Found at i:31264901 original size:35 final size:36
Alignment explanation
Indices: 31264831--31264903 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
31264821 TATTTTTATT
*
31264831 AAATTAATAATTTTTTAATATTACTTTAGTCAAATA
1 AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
*
31264867 AAATAAATAATTTTTGT-ATATTATTTTAGT-AAATA
1 AAATAAATAATTTTT-TAATATTACTTTAGTCAAATA
31264902 AA
1 AA
31264904 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 7 0.21
36 26 0.76
37 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (36 bp):
AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
Found at i:31272296 original size:274 final size:273
Alignment explanation
Indices: 31271763--31272306 Score: 998
Period size: 274 Copynumber: 2.0 Consensus size: 273
31271753 ATTACTGCTT
* * *
31271763 GCAGAAGCAAGTGGGCAGTCATTTTTCTTTTGTTCATCATTGAAAGAGAAATGATGCAAACGTCT
1 GCAGAAGCAAGTGGGCAGTCATTTTTCTTCTGTTCATCATTCAAAGAGAAATGATGCAAACATCT
31271828 ATTTGTCTCCATCACAAGATTTTCATTCTATTTTTTCAGTCTTCCTAAATATTTCAATGTTGTTT
66 ATTTGTCTCCATCACAAGATTTTCATTCTATTTTTTCAGTCTTCCTAAATATTTCAATGTTGTTT
*
31271893 AACACTGTACGACTGTCAGTAATTGTGCTCTAGAGCAAATATGTACATCTAGAGAATGTCAACTG
131 AACACTGCACGACTGTCAGTAATTGTGCTCTAGAGCAAATATGTACATCTAGAGAATGTCAACTG
* *
31271958 CTTTCTTTTGACCGTCATGTATCTCTTTCTGCTTAGTGAATGATTTTGTCTACTGTGCGTCCAGG
196 CTTTCTTCTGACCGTCATGTATCTCTTTCCGCTTAGTGAATGATTTTGTCTACTGTGCGTCCAGG
31272023 AAAGAGGAAGTGG
261 AAAGAGGAAGTGG
31272036 GCAGAAGCAAGTGGGCAGTCATTTTTCTTCTGTTCATCATTCAAAGAGAAATGATGCAAACATCT
1 GCAGAAGCAAGTGGGCAGTCATTTTTCTTCTGTTCATCATTCAAAGAGAAATGATGCAAACATCT
* *
31272101 ATTTGTCTCCATCACTAGATTTTCATTCTATTTTTTCTGTCTTCCTAAATATTTCAATGTTGTTT
66 ATTTGTCTCCATCACAAGATTTTCATTCTATTTTTTCAGTCTTCCTAAATATTTCAATGTTG-TT
31272166 TAACACTGCACGACTGTCAGTAATTGTGCTCTAGAGCAAATATGTACATCTAGAGAATGTCAACT
130 TAACACTGCACGACTGTCAGTAATTGTGCTCTAGAGCAAATATGTACATCTAGAGAATGTCAACT
*
31272231 GCTTTCTTCTGACTGTCATGTATCTCTTTCCGCTTAGTGAATGATTTTGTCTACTGTGCGTCCAG
195 GCTTTCTTCTGACCGTCATGTATCTCTTTCCGCTTAGTGAATGATTTTGTCTACTGTGCGTCCAG
31272296 GAAAGAGGAAG
260 GAAAGAGGAAG
31272307 CCTGATCCTG
Statistics
Matches: 261, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
273 122 0.47
274 139 0.53
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (273 bp):
GCAGAAGCAAGTGGGCAGTCATTTTTCTTCTGTTCATCATTCAAAGAGAAATGATGCAAACATCT
ATTTGTCTCCATCACAAGATTTTCATTCTATTTTTTCAGTCTTCCTAAATATTTCAATGTTGTTT
AACACTGCACGACTGTCAGTAATTGTGCTCTAGAGCAAATATGTACATCTAGAGAATGTCAACTG
CTTTCTTCTGACCGTCATGTATCTCTTTCCGCTTAGTGAATGATTTTGTCTACTGTGCGTCCAGG
AAAGAGGAAGTGG
Done.