Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 153 of 204
Found at i:46063309 original size:26 final size:26
Alignment explanation
Indices: 46063280--46063337 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
46063270 CTCGTTGCAT
*
46063280 AATAATTCTCACTCTATAGCTTATCA
1 AATAATTCTCACTCTATAGCTTATAA
*
46063306 AATAATTCTTACTCTATAGCTTATAA
1 AATAATTCTCACTCTATAGCTTATAA
46063332 AATAAT
1 AATAAT
46063338 ATAAATCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (26 bp):
AATAATTCTCACTCTATAGCTTATAA
Found at i:46063824 original size:16 final size:16
Alignment explanation
Indices: 46063803--46063833 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
46063793 CCAATTCAAA
46063803 TAGTATTATTTAATAC
1 TAGTATTATTTAATAC
46063819 TAGTATTATTTAATA
1 TAGTATTATTTAATA
46063834 TGGTTCCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
TAGTATTATTTAATAC
Found at i:46064628 original size:9 final size:9
Alignment explanation
Indices: 46064614--46064688 Score: 67
Period size: 9 Copynumber: 9.0 Consensus size: 9
46064604 TTAGAAATAA
46064614 TACATAACT
1 TACATAACT
46064623 TACATAA--
1 TACATAACT
46064630 TATC-TAACT
1 TA-CATAACT
46064639 TACATAACT
1 TACATAACT
46064648 TACATAA--
1 TACATAACT
*
46064655 TACACAACT
1 TACATAACT
46064664 TACATAA--
1 TACATAACT
46064671 TACATAACCT
1 TACATAA-CT
46064681 T-CATAACT
1 TACATAACT
46064689 CATATATACT
Statistics
Matches: 55, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
7 18 0.33
8 4 0.07
9 32 0.58
10 1 0.02
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:46064631 original size:16 final size:16
Alignment explanation
Indices: 46064610--46064678 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
46064600 AATTTTAGAA
46064610 ATAATACATAACTTAC
1 ATAATACATAACTTAC
46064626 ATAATATC-TAACTTAC
1 ATAATA-CATAACTTAC
46064642 -----A--TAACTTAC
1 ATAATACATAACTTAC
*
46064651 ATAATACACAACTTAC
1 ATAATACATAACTTAC
46064667 ATAATACATAAC
1 ATAATACATAAC
46064679 CTTCATAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
9 8 0.19
11 1 0.02
14 1 0.02
16 32 0.74
17 1 0.02
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATACATAACTTAC
Found at i:46064647 original size:25 final size:25
Alignment explanation
Indices: 46064614--46064677 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
46064604 TTAGAAATAA
*
46064614 TACATAACTTACATAATATC-TAACT
1 TACATAACTTACATAATA-CACAACT
46064639 TACATAACTTACATAATACACAACT
1 TACATAACTTACATAATACACAACT
46064664 TACATAA--TACATAA
1 TACATAACTTACATAA
46064678 CCTTCATAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
23 7 0.19
24 1 0.03
25 29 0.78
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (25 bp):
TACATAACTTACATAATACACAACT
Found at i:46064658 original size:41 final size:41
Alignment explanation
Indices: 46064610--46064688 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 41
46064600 AATTTTAGAA
*
46064610 ATAATACATAACTTACATAATATC-TAA-CTTACATAACTTAC
1 ATAATACACAACTTACATAATA-CATAACCTT-CATAACTTAC
46064651 ATAATACACAACTTACATAATACATAACCTTCATAACT
1 ATAATACACAACTTACATAATACATAACCTTCATAACT
46064689 CATATATACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
40 1 0.03
41 31 0.89
42 3 0.09
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.32
Consensus pattern (41 bp):
ATAATACACAACTTACATAATACATAACCTTCATAACTTAC
Found at i:46064686 original size:16 final size:16
Alignment explanation
Indices: 46064639--46064678 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
46064629 ATATCTAACT
46064639 TACATAACTTACATAA
1 TACATAACTTACATAA
*
46064655 TACACAACTTACATAA
1 TACATAACTTACATAA
46064671 TACATAAC
1 TACATAAC
46064679 CTTCATAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:46070411 original size:19 final size:20
Alignment explanation
Indices: 46070389--46070428 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
46070379 AAGAATAATA
* *
46070389 TGATTTTTATTTTAT-TTAT
1 TGATATTTATTATATATTAT
46070408 TGATATTTATTATATATTAT
1 TGATATTTATTATATATTAT
46070428 T
1 T
46070429 CGTTTAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TGATATTTATTATATATTAT
Found at i:46070650 original size:43 final size:43
Alignment explanation
Indices: 46070576--46070909 Score: 431
Period size: 43 Copynumber: 7.7 Consensus size: 43
46070566 GAAAAAGCAT
* * **
46070576 CGCTAAAAGGTCTTAGTCTTTTA-CGGCGTTTGTGAGAAAAGCGC
1 CGCT-AAAGGTCTTGGTC-TTTAGCGGCGTTTGTGTGGGAAGCGC
* * * *
46070620 CACTAAAGGTCTTGATCTTTAGCGGTGTTTGTCGT-GTAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGT-GTGGGAAGCGC
*
46070663 CGCTAAAAAGGTCATT-GTCTTTAGCGACGTTTGTGTGGGAAGCGC
1 CGCT--AAAGGTC-TTGGTCTTTAGCGGCGTTTGTGTGGGAAGCGC
* * *
46070708 TGCTCAAGGTCTTGGTCTTTAGCGGCGTTTGTGTGGGAAGCGT
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGTGGGAAGCGC
*
46070751 CGCTAAAAGTCTTGGTCTTTAGCGGCGTTTGTGTGGGAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGTGGGAAGCGC
*
46070794 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGTGGAAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGTGGGAAGCGC
* * *
46070837 CACTAAAGGTCTTGGTCTTTAACGGCGTTTGTGTTGGAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGTGGGAAGCGC
*
46070880 CGCTAAAGGTCTTGGCCTTTAGCGGCGTTT
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
46070910 TTTCCTAGAA
Statistics
Matches: 254, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
42 6 0.02
43 208 0.82
44 6 0.02
45 32 0.13
46 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.32
Consensus pattern (43 bp):
CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGTGGGAAGCGC
Found at i:46071031 original size:22 final size:22
Alignment explanation
Indices: 46071003--46071045 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
46070993 TAGCAGCGCT
*
46071003 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
46071025 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
46071046 GTTTTGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:46071851 original size:2 final size:2
Alignment explanation
Indices: 46071844--46071869 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46071834 TGGAATTATT
46071844 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
46071870 AAGTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46073010 original size:125 final size:125
Alignment explanation
Indices: 46072553--46073008 Score: 626
Period size: 125 Copynumber: 3.6 Consensus size: 125
46072543 GCAAAAAGCG
* * * *
46072553 CCGCAAACAATTAAGTAGAACGCCTTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCATTTAT
1 CCGCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTAT
* ** * *
46072618 CTGGAAACGCCGGTAAAGATCTAGCATTTGCGGCACTTATCAAAAAACGCCACTAATGCT
66 CTAGAAACGCCACTAAAGATCTAGCATTTGCGGCGCATATCAAAAAACGCCACTAATGCT
* *
46072678 CCTCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGACACTAGCGGCGTTTAT
1 CCGCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTAT
* * * * * *
46072743 CAAGAAATGCCGCCAAAGATCAAGCATTTGTGGCG-ATTATCAAAAAACGCCACTAATGCT
66 CTAGAAACGCCACTAAAGATCTAGCATTTGCGGCGCA-TATCAAAAAACGCCACTAATGCT
** * * *
46072803 CAACAAAAAATTAAGTAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCAGCGTTTAT
1 CCGCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTAT
* * * *
46072868 CTAAAAACGCCAGTAATGATCTAGCATTTGCGGCGCATACCAAAAAACGCCACTAATGCT
66 CTAGAAACGCCACTAAAGATCTAGCATTTGCGGCGCATATCAAAAAACGCCACTAATGCT
* *
46072928 CCGCAAATAATTAAGCAGAACGCTGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGTGTTTAT
1 CCGCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTAT
* *
46072993 CTGGAAATGCCACTAA
66 CTAGAAACGCCACTAA
46073009 TGCTCTGTAA
Statistics
Matches: 287, Mismatches: 42, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
125 286 1.00
126 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (125 bp):
CCGCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTAT
CTAGAAACGCCACTAAAGATCTAGCATTTGCGGCGCATATCAAAAAACGCCACTAATGCT
Found at i:46073294 original size:166 final size:168
Alignment explanation
Indices: 46073001--46073301 Score: 403
Period size: 166 Copynumber: 1.8 Consensus size: 168
46072991 ATCTGGAAAT
***
46073001 GCCACTAATGCTCTGTAAATAATTAAGCAGAATGATATCATTTAACTTTGATAATATTAATGGCA
1 GCCACTAATGCTCCACAAATAATTAAGCAGAATGATATCATTTAACTTTGATAATATTAATGGCA
* * * *
46073066 CTAGCGGCGTTTATATGAAAACGCCGGTAAAGATCTAGCATTTGTGACGCTTATAGAAAAACGCC
66 CTAGCGGCGTTTATATGAAAACACCAGTAAAAATCTAGCATTTGAGACGCTTATAGAAAAACGCC
*
46073131 GCTAAAGCTCGGTACATTAGCGACGCTACCATAAAAAC
131 ACTAAAGCTCGGTACATTAGCGACGCTACCATAAAAAC
* * * * ** *
46073169 GCCACTAATGCTCCACAAATAATTAAGCAGAATGCTGTCGTTTAGCTTTGA-CCT-TTAGTGGCA
1 GCCACTAATGCTCCACAAATAATTAAGCAGAATGATATCATTTAACTTTGATAATATTAATGGCA
* *
46073232 CTAGCGGCGTTTATATGGAAACACCAGTAAAAATCTAGCATTTGCAG-CGTTTATCA-AAAAACG
66 CTAGCGGCGTTTATATGAAAACACCAGTAAAAATCTAGCATTTG-AGACGCTTAT-AGAAAAACG
46073295 CCACTAA
129 CCACTAA
46073302 TGATCGATCT
Statistics
Matches: 114, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
166 67 0.59
167 3 0.03
168 44 0.39
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (168 bp):
GCCACTAATGCTCCACAAATAATTAAGCAGAATGATATCATTTAACTTTGATAATATTAATGGCA
CTAGCGGCGTTTATATGAAAACACCAGTAAAAATCTAGCATTTGAGACGCTTATAGAAAAACGCC
ACTAAAGCTCGGTACATTAGCGACGCTACCATAAAAAC
Found at i:46073736 original size:22 final size:24
Alignment explanation
Indices: 46073695--46073739 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
46073685 TCTTAGTTAT
46073695 TATTCATGGTTTAACAGGTTAGGC
1 TATTCATGGTTTAACAGGTTAGGC
*
46073719 TATT-ATGGTTTAA-GGGTTAGG
1 TATTCATGGTTTAACAGGTTAGG
46073740 GTTATTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.40
Consensus pattern (24 bp):
TATTCATGGTTTAACAGGTTAGGC
Found at i:46073745 original size:23 final size:24
Alignment explanation
Indices: 46073694--46073745 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
46073684 GTCTTAGTTA
46073694 TTATTCATGGTTTAACAGGTTAGG
1 TTATTCATGGTTTAACAGGTTAGG
* *
46073718 CTATT-ATGGTTTAA-GGGTTAGGG
1 TTATTCATGGTTTAACAGGTTA-GG
46073741 TTATT
1 TTATT
46073746 GATAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.23, C:0.06, G:0.27, T:0.44
Consensus pattern (24 bp):
TTATTCATGGTTTAACAGGTTAGG
Found at i:46073843 original size:13 final size:13
Alignment explanation
Indices: 46073825--46073869 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
46073815 TAGTGTTTAC
46073825 GGTTTATGGTGTA
1 GGTTTATGGTGTA
*
46073838 GGTTTATGGTTTA
1 GGTTTATGGTGTA
46073851 GTGTTTATGGTGTA
1 G-GTTTATGGTGTA
*
46073865 CGTTT
1 GGTTT
46073870 TCAATTTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.13, C:0.02, G:0.33, T:0.51
Consensus pattern (13 bp):
GGTTTATGGTGTA
Found at i:46073912 original size:21 final size:21
Alignment explanation
Indices: 46073888--46073954 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
46073878 CATGTTGAGT
*
46073888 GTTTAGGGGTGAGGGCTTAAG
1 GTTTAGGGGTTAGGGCTTAAG
*
46073909 GTTTAGGGGTTATAGGCTT-AG
1 GTTTAGGGGTTA-GGGCTTAAG
* *
46073930 GGTCAGGGGTTAGTGGCTTAAG
1 GTTTAGGGGTTAG-GGCTTAAG
46073952 GTT
1 GTT
46073955 ACGGGTTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
21 28 0.76
22 9 0.24
ACGTcount: A:0.18, C:0.06, G:0.43, T:0.33
Consensus pattern (21 bp):
GTTTAGGGGTTAGGGCTTAAG
Found at i:46073916 original size:14 final size:14
Alignment explanation
Indices: 46073899--46073988 Score: 58
Period size: 14 Copynumber: 6.3 Consensus size: 14
46073889 TTTAGGGGTG
46073899 AGGGCTTAAGGTTT
1 AGGGCTTAAGGTTT
* *
46073913 AGGGGTTATAGGCTT
1 AGGGCTTA-AGGTTT
* * *
46073928 AGGG-TCAGGGGTT
1 AGGGCTTAAGGTTT
46073941 AGTGGCTTAAGG-TT
1 AG-GGCTTAAGGTTT
*
46073955 ACGGGTTTAAGGGTTT
1 A-GGGCTTAA-GGTTT
* *
46073971 AGGGTTTAAGGTAT
1 AGGGCTTAAGGTTT
46073985 AGGG
1 AGGG
46073989 TATAAAAGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
13 6 0.10
14 28 0.46
15 24 0.39
16 3 0.05
ACGTcount: A:0.21, C:0.06, G:0.41, T:0.32
Consensus pattern (14 bp):
AGGGCTTAAGGTTT
Found at i:46073960 original size:21 final size:21
Alignment explanation
Indices: 46073901--46073961 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
46073891 TAGGGGTGAG
46073901 GGCTTAAGGTTTAGGGGTTATA
1 GGCTTAAGG-TTAGGGGTTATA
* *
46073923 GGCTTAGGGTCAGGGGTTAGT-
1 GGCTTAAGGTTAGGGGTTA-TA
*
46073944 GGCTTAAGGTTACGGGTT
1 GGCTTAAGGTTAGGGGTT
46073962 TAAGGGTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 24 0.73
22 9 0.27
ACGTcount: A:0.18, C:0.08, G:0.41, T:0.33
Consensus pattern (21 bp):
GGCTTAAGGTTAGGGGTTATA
Found at i:46074130 original size:14 final size:14
Alignment explanation
Indices: 46074048--46074131 Score: 57
Period size: 14 Copynumber: 6.1 Consensus size: 14
46074038 CTTATATAGT
46074048 GTTTACGATTTAGG
1 GTTTACGATTTAGG
* *
46074062 GTGTAC-ATTTACG
1 GTTTACGATTTAGG
* *
46074075 GTTTAAAGA-TTAAG
1 GTTT-ACGATTTAGG
* *
46074089 GTTTAGGATATA-G
1 GTTTACGATTTAGG
* *
46074102 TTTTAAGAGTTTAGG
1 GTTTACGA-TTTAGG
46074117 GTTTACGATTTAGG
1 GTTTACGATTTAGG
46074131 G
1 G
46074132 GTTAGTGGTT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
13 19 0.36
14 26 0.49
15 8 0.15
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.40
Consensus pattern (14 bp):
GTTTACGATTTAGG
Found at i:46074700 original size:23 final size:23
Alignment explanation
Indices: 46074611--46074708 Score: 83
Period size: 23 Copynumber: 4.2 Consensus size: 23
46074601 CCCAACTCAG
* * * *
46074611 ATTTCCCCAAATTGATTTCCCTA
1 ATTTCCCCGATTTCATTTCCCCA
46074634 ATTT-CCC-ATTTCATATTCTCCCA
1 ATTTCCCCGATTTCAT-TTC-CCCA
* **
46074657 ATTTCCCTGATTTCAAATCCCCA
1 ATTTCCCCGATTTCATTTCCCCA
*
46074680 ATTTCCCCGATATCATTTCCCCAA
1 ATTTCCCCGATTTCATTTCCCC-A
46074704 ATTTC
1 ATTTC
46074709 GAACTGAGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
21 5 0.08
22 6 0.10
23 33 0.55
24 10 0.17
25 6 0.10
ACGTcount: A:0.24, C:0.34, G:0.03, T:0.39
Consensus pattern (23 bp):
ATTTCCCCGATTTCATTTCCCCA
Found at i:46076425 original size:30 final size:31
Alignment explanation
Indices: 46076375--46076432 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
46076365 TATTTTAAAG
*
46076375 TTCAAATTTACATAACTTACATAATTTACGA
1 TTCAAATTTACATAAATTACATAATTTACGA
46076406 TTCAAATTT-CATAAATTACATAATTTA
1 TTCAAATTTACATAAATTACATAATTTA
46076433 AATATAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (31 bp):
TTCAAATTTACATAAATTACATAATTTACGA
Found at i:46076548 original size:12 final size:12
Alignment explanation
Indices: 46076531--46076630 Score: 53
Period size: 12 Copynumber: 9.1 Consensus size: 12
46076521 TACATAATGC
46076531 ATAACTTACATA
1 ATAACTTACATA
46076543 ATAACTTAC---
1 ATAACTTACATA
*
46076552 ATAACTTATAT-
1 ATAACTTACATA
*
46076563 ATAAACTTGC---
1 AT-AACTTACATA
46076573 ATAACTTACATA
1 ATAACTTACATA
46076585 AT-A---ACATA
1 ATAACTTACATA
46076593 ATAACTTACATA
1 ATAACTTACATA
* *
46076605 AT-ACATAGCCTA
1 ATAACTTA-CATA
46076617 CATAACTTACATA
1 -ATAACTTACATA
46076630 A
1 A
46076631 CTTACATGAT
Statistics
Matches: 67, Mismatches: 8, Indels: 26
0.66 0.08 0.26
Matches are distributed among these distances:
8 7 0.10
9 15 0.22
10 2 0.03
11 7 0.10
12 27 0.40
13 5 0.07
14 4 0.06
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:46076555 original size:9 final size:9
Alignment explanation
Indices: 46076543--46077017 Score: 297
Period size: 9 Copynumber: 53.9 Consensus size: 9
46076533 AACTTACATA
46076543 ATAACTTAC
1 ATAACTTAC
*
46076552 ATAACTTATAT
1 ATAAC-T-TAC
*
46076563 ATAAACTTGC
1 AT-AACTTAC
46076573 ATAACTTAC
1 ATAACTTAC
*
46076582 ATAA-TAAC
1 ATAACTTAC
46076590 ATAATAACTTAC
1 ---ATAACTTAC
46076602 ATAA--TAC
1 ATAACTTAC
* *
46076609 ATAGCCTAC
1 ATAACTTAC
46076618 ATAACTTAC
1 ATAACTTAC
46076627 ATAACTTAC
1 ATAACTTAC
*
46076636 ATGA--TAC
1 ATAACTTAC
*
46076643 ACAACTTATTAC
1 ATAAC---TTAC
*
46076655 ATAACTTAA
1 ATAACTTAC
46076664 ATAACTTAC
1 ATAACTTAC
46076673 ATAA--TAC
1 ATAACTTAC
*
46076680 ATAACTTTC
1 ATAACTTAC
46076689 ATAACTTAC
1 ATAACTTAC
*
46076698 ATTA--TAC
1 ATAACTTAC
*
46076705 ACAACTTAC
1 ATAACTTAC
46076714 ATAACTTA-
1 ATAACTTAC
* *
46076722 ATTAATATTAT
1 A-TAA-CTTAC
46076733 ATAGAACTTAC
1 AT--AACTTAC
46076744 ATAA--TAC
1 ATAACTTAC
* *
46076751 ATTACGTAC
1 ATAACTTAC
46076760 ATAACTTAC
1 ATAACTTAC
*
46076769 ATTA--TAC
1 ATAACTTAC
*
46076776 ACAACTTAC
1 ATAACTTAC
*
46076785 ATAACTTAT
1 ATAACTTAC
* *
46076794 TTAATATTATAC
1 AT-A-ACT-TAC
46076806 ATAACTTAC
1 ATAACTTAC
46076815 ATAA--TAC
1 ATAACTTAC
*
46076822 ATAACTTAT
1 ATAACTTAC
46076831 ATAACTTAC
1 ATAACTTAC
46076840 ATAACTTAC
1 ATAACTTAC
46076849 ATAACTTAC
1 ATAACTTAC
46076858 --AACTTAC
1 ATAACTTAC
*
46076865 ATAACTTAG
1 ATAACTTAC
*
46076874 ATACATTATAC
1 ATA-ACT-TAC
*
46076885 AGAACTTAC
1 ATAACTTAC
46076894 ATAACTTAC
1 ATAACTTAC
*
46076903 ATAGCTTAC
1 ATAACTTAC
*
46076912 AT-TC-TAC
1 ATAACTTAC
*
46076919 ATAACATAC
1 ATAACTTAC
*
46076928 ATAACATAC
1 ATAACTTAC
46076937 ATAA--TAC
1 ATAACTTAC
46076944 ATAACTTAC
1 ATAACTTAC
46076953 ATAA--TAC
1 ATAACTTAC
46076960 ATAGA-TTAC
1 ATA-ACTTAC
46076969 ATAA--TAC
1 ATAACTTAC
*
46076976 ACAACTTAC
1 ATAACTTAC
*
46076985 ATAGCTTAC
1 ATAACTTAC
46076994 ATAA--TAC
1 ATAACTTAC
46077001 ATAACTTAC
1 ATAACTTAC
*
46077010 ATAGCTTA
1 ATAACTTA
46077018 ATTATACTTA
Statistics
Matches: 367, Mismatches: 53, Indels: 92
0.72 0.10 0.18
Matches are distributed among these distances:
7 79 0.22
8 8 0.02
9 225 0.61
10 15 0.04
11 22 0.06
12 18 0.05
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:46076556 original size:21 final size:21
Alignment explanation
Indices: 46076530--46076678 Score: 115
Period size: 21 Copynumber: 6.8 Consensus size: 21
46076520 TTACATAATG
46076530 CATAACTTACATAATAACTTA
1 CATAACTTACATAATAACTTA
* *
46076551 CATAACTTATAT-ATAAACTTG
1 CATAACTTACATAAT-AACTTA
*
46076572 CATAACTTACATAATAACATA
1 CATAACTTACATAATAACTTA
*
46076593 -ATAACTTACATAATACATAGCCTA
1 CATAACTTACATAAT--A-A-CTTA
*
46076617 CATAACTTACATAACTTACATGATA
1 CATAACTTACATAA-TAAC-T--TA
* *
46076642 CACAACTTA-TTACATAACTTA
1 CATAACTTACATA-ATAACTTA
*
46076663 AATAACTTACATAATA
1 CATAACTTACATAATA
46076679 CATAACTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
20 16 0.16
21 43 0.43
22 6 0.06
23 3 0.03
24 8 0.08
25 24 0.24
26 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (21 bp):
CATAACTTACATAATAACTTA
Found at i:46076656 original size:37 final size:35
Alignment explanation
Indices: 46076585--46077004 Score: 162
Period size: 34 Copynumber: 12.6 Consensus size: 35
46076575 AACTTACATA
* * * *
46076585 ATAACATA-ATAACTTACATAATACATAGC-CTAC
1 ATAACTTACATAACTTACATAATACACAACTTTAC
*
46076618 ATAACTTACATAACTTACATGATACACAACTTATTAC
1 ATAACTTACATAACTTACATAATACACAAC-T-TTAC
* *
46076655 ATAACTTAAATAACTTACATAATACATAACTTT-C
1 ATAACTTACATAACTTACATAATACACAACTTTAC
46076689 ATAACTTAC---A--T---T-ATACACAAC-TTAC
1 ATAACTTACATAACTTACATAATACACAACTTTAC
* * *
46076714 ATAACTTA-ATTAATATTATATAGA-ACTTAC-A-TAATAC
1 ATAACTTACA-TAA-CTTACATA-ATAC--ACAACT-TTAC
* * *
46076751 ATTACGTACATAACTTACATTATACACAAC-TTAC
1 ATAACTTACATAACTTACATAATACACAACTTTAC
** * *
46076785 ATAACTTATTTAA--T--ATTATACATAAC-TTAC
1 ATAACTTACATAACTTACATAATACACAACTTTAC
* *
46076815 ATAA--TACATAACTTATATAACTTACATAAC-TTAC
1 ATAACTTACATAACTTACATAA--TACACAACTTTAC
* *
46076849 ATAACTTAC--AACTTACATAACTTAGA-TACATTATAC
1 ATAACTTACATAACTTACATAA--TACACAAC-TT-TAC
* * *
46076885 AGAACTTACATAACTTACATAGCT-TAC-A-TTCTAC
1 ATAACTTACATAACTTACATA-ATACACAACTT-TAC
* * *
46076919 ATAACATACATAACATACATAATACATAAC-TTAC
1 ATAACTTACATAACTTACATAATACACAACTTTAC
46076953 ATAA--TACATAGA-TTACATAATACACAAC-TTAC
1 ATAACTTACATA-ACTTACATAATACACAACTTTAC
*
46076985 ATAGCTTACATAA--TACATAA
1 ATAACTTACATAACTTACATAA
46077005 CTTACATAGC
Statistics
Matches: 300, Mismatches: 41, Indels: 93
0.69 0.09 0.21
Matches are distributed among these distances:
24 2 0.01
25 17 0.06
26 1 0.00
28 6 0.02
29 1 0.00
30 20 0.07
31 2 0.01
32 38 0.13
33 12 0.04
34 110 0.37
35 9 0.03
36 26 0.09
37 45 0.15
38 11 0.04
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (35 bp):
ATAACTTACATAACTTACATAATACACAACTTTAC
Found at i:46076659 original size:62 final size:61
Alignment explanation
Indices: 46076593--46077008 Score: 173
Period size: 62 Copynumber: 6.9 Consensus size: 61
46076583 TAATAACATA
* *
46076593 ATAACTTACATAA-TACATAGCCTACATAACTTACATAACTTACATGATACACAACTTATTAC
1 ATAACTTAAATAACTACATA--ATACATAACTTACATAACTTACATGATACACAACTTATTAC
* *
46076655 ATAACTTAAATAACTTACATAATACATAACTTTCATAACTTACATTATACACAAC---TTAC
1 ATAACTTAAATAAC-TACATAATACATAACTTACATAACTTACATGATACACAACTTATTAC
* * * * * *
46076714 ATAACTTAATTAA-T--ATTATATAGAACTTACATAA--TACATTACGTACATAACTTACATTAT
1 ATAACTTAAATAACTACATAATACATAACTTACATAACTTACATGA--TACACAACTT--A-T-T
46076774 AC
60 AC
* * * * * * *
46076776 ACAACTTACATAACT-TAT-TTA-AT-ATTATACATAACTTACATAATACATAACTTA-T--
1 ATAACTTAAATAACTACATAATACATAACT-TACATAACTTACATGATACACAACTTATTAC
* * *
46076831 ATAACTTACATAACTTACATAACTTAC--AACTTACATAACTTAGATACATTATACAGAAC---T
1 ATAACTTAAATAAC-TACATAA--TACATAACTTACATAAC-T---TACATGATACACAACTTAT
46076891 TAC
59 TAC
* * ** * * * *
46076894 ATAACTTACATAGCTTACATTCTACATAACATACATAACATACATAATACATAAC---TTAC
1 ATAACTTAAATAAC-TACATAATACATAACTTACATAACTTACATGATACACAACTTATTAC
* * * * * *
46076953 ATAA--TACATAGATTACATAATACACAACTTACATAGCTTACATAATACATAACTTA
1 ATAACTTAAATA-ACTACATAATACATAACTTACATAACTTACATGATACACAACTTA
46077009 CATAGCTTAA
Statistics
Matches: 280, Mismatches: 38, Indels: 74
0.71 0.10 0.19
Matches are distributed among these distances:
53 7 0.03
55 36 0.13
56 1 0.00
57 44 0.16
59 45 0.16
60 6 0.02
61 7 0.03
62 74 0.26
63 46 0.16
64 14 0.05
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.33
Consensus pattern (61 bp):
ATAACTTAAATAACTACATAATACATAACTTACATAACTTACATGATACACAACTTATTAC
Found at i:46076720 original size:71 final size:69
Alignment explanation
Indices: 46076543--46076972 Score: 311
Period size: 71 Copynumber: 6.2 Consensus size: 69
46076533 AACTTACATA
* * * *
46076543 ATAACTTACATAACTT--A-TATATA-AACTTGCATAACTTACATAATAA-CATAATAACTTACA
1 ATAACTTACATAACTTACATTATACACAACTTACATAACTTA-TTAATAATTA-AATAACTTACA
46076603 TAATAC
64 TAATAC
* * *** *
46076609 ATAGCCTACATAACTTACA-TA-ACTTACATGATACACAACTTATTACATAACTTAAATAACTTA
1 ATAACTTACATAACTTACATTATAC--ACAACTTACATAACTTATTA-ATAA-TTAAATAACTTA
46076672 CATAATAC
62 CATAATAC
* *
46076680 ATAACTTTCATAACTTACATTATACACAACTTACATAACTTAATTAAT-ATTATATAGAACTTAC
1 ATAACTTACATAACTTACATTATACACAACTTACATAACTT-ATTAATAATTA-A-ATAACTTAC
46076744 ATAATAC
63 ATAATAC
* *
46076751 ATTACGTACATAACTTACATTATACACAACTTACATAACTTATTTAAT-ATTATACATAACTTAC
1 ATAACTTACATAACTTACATTATACACAACTTACATAACTTA-TTAATAATTA-A-ATAACTTAC
46076815 ATAATAC
63 ATAATAC
* * * * * *
46076822 ATAACTTATATAACTTACATAACTTACATAACTTAC--AACTTA--CATAACTTAGATACATTAT
1 ATAACTTACATAACTTACATTA--TACACAACTTACATAACTTATTAATAA-TTAAATA-ACT-T
*
46076883 ACAGAACTTAC
61 ACATAA--TAC
* * * * *
46076894 ATAACTTACATAGCTTACATTCTACATAACATACATAAC--A-TACATAA-TACATAACTTACAT
1 ATAACTTACATAACTTACATTATACACAACTTACATAACTTATTA-ATAATTAAATAACTTACAT
46076955 AATAC
65 AATAC
46076960 ATAGA-TTACATAA
1 ATA-ACTTACATAA
46076973 TACACAACTT
Statistics
Matches: 295, Mismatches: 42, Indels: 54
0.75 0.11 0.14
Matches are distributed among these distances:
66 27 0.09
67 2 0.01
68 14 0.05
69 11 0.04
70 43 0.15
71 150 0.51
72 35 0.12
73 13 0.04
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (69 bp):
ATAACTTACATAACTTACATTATACACAACTTACATAACTTATTAATAATTAAATAACTTACATA
ATAC
Found at i:46077002 original size:32 final size:31
Alignment explanation
Indices: 46076924--46077004 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 31
46076914 TCTACATAAC
* *
46076924 ATACATAACATACATAATACATAACTTACATA
1 ATACAT-AGATACATAATACACAACTTACATA
46076956 ATACATAGATTACATAATACACAACTTACATA
1 ATACATAGA-TACATAATACACAACTTACATA
*
46076988 GCTTACATA-ATACATAA
1 --ATACATAGATACATAA
46077005 CTTACATAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 2 0.05
32 34 0.79
33 1 0.02
34 6 0.14
ACGTcount: A:0.51, C:0.19, G:0.02, T:0.28
Consensus pattern (31 bp):
ATACATAGATACATAATACACAACTTACATA
Found at i:46077012 original size:16 final size:16
Alignment explanation
Indices: 46076572--46076987 Score: 173
Period size: 16 Copynumber: 24.8 Consensus size: 16
46076562 TATAAACTTG
46076572 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
46076589 CATAATAACTTACATAATA
1 C---ATAACTTACATAATA
* *
46076608 CATAGCCTACATAACTTA
1 CATAACTTACATAA--TA
*
46076626 CATAACTTACATGATA
1 CATAACTTACATAATA
*
46076642 CACAACTT--AT--TA
1 CATAACTTACATAATA
*
46076654 CATAACTTAAATAACTTA
1 CATAACTTACATAA--TA
*
46076672 CATAA--TACATAACTTT
1 CATAACTTACATAA--TA
*
46076688 CATAACTTACATTATA
1 CATAACTTACATAATA
*
46076704 CACAACTTACAT-A-A
1 CATAACTTACATAATA
*
46076718 CTTAA-TTA-ATATTATA
1 CATAACTTACATA--ATA
* *
46076734 TAGAACTTACATAATA
1 CATAACTTACATAATA
* *
46076750 CATTACGTACATAACTTA
1 CATAACTTACATAA--TA
* *
46076768 CATTA--TACACAACTTA
1 CATAACTTACATAA--TA
*
46076784 CATAACTTATTTAATATTATA
1 CATAACTTA---CATA--ATA
46076805 CATAACTTACATAATA
1 CATAACTTACATAATA
*
46076821 CATAACTTATATAACTTA
1 CATAACTTACATAA--TA
46076839 CATAACTTACATAACTTA
1 CATAACTTACATAA--TA
46076857 C--AACTTACATAACTTA
1 CATAACTTACATAA--TA
* * *
46076873 GATACATTATACAGAACTTA
1 CATA-ACT-TACATAA--TA
*
46076893 CATAACTTACATAGCTTA
1 CATAACTTACATA--ATA
*
46076911 CAT-TC-TACATAACATA
1 CATAACTTACAT-A-ATA
*
46076927 CATAACATACATAATA
1 CATAACTTACATAATA
46076943 CATAACTTACATAATA
1 CATAACTTACATAATA
46076959 CATAGA-TTACATAATA
1 CATA-ACTTACATAATA
*
46076975 CACAACTTACATA
1 CATAACTTACATA
46076988 GCTTACATAA
Statistics
Matches: 318, Mismatches: 40, Indels: 83
0.72 0.09 0.19
Matches are distributed among these distances:
12 11 0.03
13 3 0.01
14 8 0.03
15 3 0.01
16 160 0.50
17 9 0.03
18 77 0.24
19 6 0.02
20 27 0.08
21 13 0.04
23 1 0.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:46077017 original size:25 final size:25
Alignment explanation
Indices: 46076543--46077004 Score: 189
Period size: 25 Copynumber: 17.9 Consensus size: 25
46076533 AACTTACATA
*
46076543 ATAACTTACATAACTT--AT-ATAT
1 ATAACTTACATAACTTACATAATAC
*
46076565 A-AACTTGCATAACTTACATAATAAC
1 ATAACTTACATAACTTACATAAT-AC
*
46076590 ATAATAACTTACATAA--TACATAGCCTAC
1 ---ATAACTTACATAACTTACATA--ATAC
*
46076618 ATAACTTACATAACTTACATGATAC
1 ATAACTTACATAACTTACATAATAC
* *
46076643 ACAACTTATTACATAACTTAAATAACTTAC
1 ATAAC---TTACATAACTTACATAA--TAC
*
46076673 ATAA--TACATAACTTTCATAACTTAC
1 ATAACTTACATAACTTACATAA--TAC
* *
46076698 ATTA--TACACAACTTACATAACTTA-
1 ATAACTTACATAACTTACATAA--TAC
* *
46076722 ATTAATATTATATAGAACTTACATAATAC
1 A-TAA-CTTACAT--AACTTACATAATAC
* * *
46076751 ATTACGTACATAACTTACATTATAC
1 ATAACTTACATAACTTACATAATAC
* *
46076776 ACAACTTACATAACTTATTTAATATTATAC
1 ATAACTTACATAACTTA---CATA--ATAC
*
46076806 ATAACTTACATAA--TACATAACTTAT
1 ATAACTTACATAACTTACATAA--TAC
46076831 ATAACTTACATAACTTACATAACTTAC
1 ATAACTTACATAACTTACATAA--TAC
*
46076858 --AACTTACATAACTTAGATACATTATAC
1 ATAACTTACATAAC-T---TACATAATAC
* *
46076885 AGAACTTACATAACTTACATAGCTTAC
1 ATAACTTACATAACTTACATA--ATAC
* *
46076912 AT-TC-TACATAACATACATAACATAC
1 ATAACTTACATAACTTACAT-A-ATAC
46076937 ATAA--TACATAACTTACATAATAC
1 ATAACTTACATAACTTACATAATAC
*
46076960 ATAGA-TTACATAA--TACACAACTTAC
1 ATA-ACTTACATAACTTACATAA--TAC
*
46076985 ATAGCTTACATAA--TACATAA
1 ATAACTTACATAACTTACATAA
46077005 CTTACATAGC
Statistics
Matches: 348, Mismatches: 44, Indels: 93
0.72 0.09 0.19
Matches are distributed among these distances:
21 13 0.04
22 1 0.00
23 16 0.05
24 5 0.01
25 184 0.53
26 3 0.01
27 33 0.09
28 30 0.09
29 30 0.09
30 33 0.09
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (25 bp):
ATAACTTACATAACTTACATAATAC
Found at i:46082622 original size:21 final size:21
Alignment explanation
Indices: 46082597--46082647 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
46082587 GGCAGCAAGG
*
46082597 GAAGCAGAGGC-AGTAGTGAGA
1 GAAGCAGAGGCTA-CAGTGAGA
*
46082618 GAAGCAGAGGCTACAGTGAGG
1 GAAGCAGAGGCTACAGTGAGA
46082639 GAAGCAGAG
1 GAAGCAGAG
46082648 CAGAGCAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.12, G:0.43, T:0.08
Consensus pattern (21 bp):
GAAGCAGAGGCTACAGTGAGA
Found at i:46083046 original size:43 final size:43
Alignment explanation
Indices: 46082980--46083393 Score: 318
Period size: 43 Copynumber: 9.6 Consensus size: 43
46082970 GAAACACCAT
* * * * *
46082980 TAAAAGTCATGGTCTTTCGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCTTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * * * **
46083023 CAAAGGTCTTGGCCTATAGCGGCGTTTTTGGAAAAAGTGTTGC
1 TAAAGGTCTTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * * * **
46083066 TAAAGGTCATGGTCTATAGCAGCGTTTGT-AAACAAAGCGTCAA
1 TAAAGGTCTTGGTCTATAGCGGCGTTTGTGGAA-AAAGCGCCGC
* * **
46083109 TAAAGGTCTTGAG-CTATAGCGGCGTTTGT-AAACAAAGCGTCAA
1 TAAAGGTCTTG-GTCTATAGCGGCGTTTGTGGAA-AAAGCGCCGC
* *
46083152 TAAAGGTCTTGAG-CTATAGCGGCGTTTGTGGAAAAAGCACAGC
1 TAAAGGTCTTG-GTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * * * *
46083195 CAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAAAGGCACCGC
1 TAAAGGTCTTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * * *
46083238 TAAAGGTCTTGATCTATAGCGGCATTTTTGGAAAAAAGTGCCGC
1 TAAAGGTCTTGGTCTATAGCGGCGTTTGTGG-AAAAAGCGCCGC
* * ** * *
46083282 TACAGATCTTGAG-CTATAATGGCGTTTGT-GTAAAAGCGCCCC
1 TAAAGGTCTTG-GTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * * * *
46083324 TAAAGGTCCTGATCTATAGCGGCGTTTCTGGAAGAAGCACCGC
1 TAAAGGTCTTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * *
46083367 TAAAGGTCATGATCTATAGTGGCGTTT
1 TAAAGGTCTTGGTCTATAGCGGCGTTT
46083394 ATTTCTAAAA
Statistics
Matches: 299, Mismatches: 64, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
42 32 0.11
43 235 0.79
44 32 0.11
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (43 bp):
TAAAGGTCTTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
Found at i:46084037 original size:16 final size:16
Alignment explanation
Indices: 46084016--46084071 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
46084006 CGTTTGGTTC
46084016 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
46084032 GCTGTAATTGAAGAGA
1 GCTGTAATGGAATAGA
46084048 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
46084064 GTTGTAAT
1 GCTGTAAT
46084072 AAGTAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:46084146 original size:44 final size:46
Alignment explanation
Indices: 46084053--46084146 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 46
46084043 AGAGAGCTGT
** *
46084053 AATGGAATAGAGTTGTAATAAGTAATTCAATTGTTTGGTTGAATTG
1 AATGGAATAGAACTGTAATAAGTAATTCAATTGTTTGGTTGAATGG
*
46084099 AATGGAATAGAACTGTAAT-AGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAAGTAATTCAAT-TGTTTGGTTGAATGG
46084143 AATG
1 AATG
46084147 ATGTTGTACT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.51
45 3 0.07
46 17 0.40
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (46 bp):
AATGGAATAGAACTGTAATAAGTAATTCAATTGTTTGGTTGAATGG
Found at i:46084364 original size:57 final size:56
Alignment explanation
Indices: 46084248--46084381 Score: 153
Period size: 57 Copynumber: 2.3 Consensus size: 56
46084238 AATAAGATTA
* * *
46084248 TTAATAAAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAAT-AAAATAATATATAATTTAATAAAATTTTAACATAATTATTATT-AATATAAT
* *
46084306 TTAATAAAATAATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATATATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
46084363 TTACTAAAATCATAATATA
1 TTAATAAAATAAT-ATATA
46084382 TAATACTATA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
56 4 0.06
57 37 0.56
58 25 0.38
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (56 bp):
TTAATAAAATAATATATAATTTAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:46084389 original size:21 final size:21
Alignment explanation
Indices: 46084364--46084406 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
46084354 TATATGAATT
46084364 TACTA-AAATCATAATATATAA
1 TACTATAAA-CATAATATATAA
*
46084385 TACTATAAAGATAATATATAA
1 TACTATAAACATAATATATAA
46084406 T
1 T
46084407 CTACTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (21 bp):
TACTATAAACATAATATATAA
Found at i:46085074 original size:24 final size:24
Alignment explanation
Indices: 46085041--46085091 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
46085031 AATACAAGCA
46085041 TCAAGACAATAGTTTAATACATCC
1 TCAAGACAATAGTTTAATACATCC
*
46085065 TCAAGGCAATAGTTTAATACATCC
1 TCAAGACAATAGTTTAATACATCC
46085089 TCA
1 TCA
46085092 TGATACTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (24 bp):
TCAAGACAATAGTTTAATACATCC
Found at i:46089214 original size:24 final size:24
Alignment explanation
Indices: 46089187--46089249 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
46089177 ATAATTTAGC
*
46089187 CATTTTTATTTTTATTATAATTTT
1 CATTTTTATTTTAATTATAATTTT
* * *
46089211 CATTTTTAGTTTAATTTTTATTTT
1 CATTTTTATTTTAATTATAATTTT
46089235 CTAATTTTTATTTTA
1 C--ATTTTTATTTTA
46089250 TTTGCTTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 21 0.66
26 11 0.34
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.70
Consensus pattern (24 bp):
CATTTTTATTTTAATTATAATTTT
Found at i:46089215 original size:18 final size:18
Alignment explanation
Indices: 46089188--46089234 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
46089178 TAATTTAGCC
46089188 ATTTTTATTTTTA-TTATA
1 ATTTTTATTTTTAGTT-TA
*
46089206 ATTTTCATTTTTAGTTTA
1 ATTTTTATTTTTAGTTTA
46089224 ATTTTTATTTT
1 ATTTTTATTTT
46089235 CTAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTATTTTTAGTTTA
Found at i:46089230 original size:7 final size:6
Alignment explanation
Indices: 46089188--46089252 Score: 60
Period size: 6 Copynumber: 10.7 Consensus size: 6
46089178 TAATTTAGCC
* * * * *
46089188 ATTTTT ATTTTT ATTATA ATTTTC ATTTTT AGTTTA ATTTTT ATTTTCT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT-T
46089237 AATTTTT A-TTTT ATTT
1 -ATTTTT ATTTTT ATTT
46089253 GCTTCTGGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
5 5 0.11
6 35 0.74
7 2 0.04
8 5 0.11
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (6 bp):
ATTTTT
Found at i:46089241 original size:14 final size:14
Alignment explanation
Indices: 46089222--46089248 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46089212 ATTTTTAGTT
46089222 TAATTTTTATTTTC
1 TAATTTTTATTTTC
46089236 TAATTTTTATTTT
1 TAATTTTTATTTT
46089249 ATTTGCTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (14 bp):
TAATTTTTATTTTC
Found at i:46091926 original size:6 final size:6
Alignment explanation
Indices: 46091917--46091955 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
46091907 TTCGTTTTAG
* * *
46091917 TTATTT TTATTT TTATCT TTATTT TTAATT TTGTTT TTA
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTA
46091956 GCTGCTTCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:46097785 original size:26 final size:26
Alignment explanation
Indices: 46097702--46097774 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 26
46097692 CCAATATCGT
*
46097702 AGCAAAGCTGCCAGTAATAG-AGATGC
1 AGCAAAGCTGCCAGTAACAGTA-ATGC
46097728 A-CTAAAGCTGCCAGTAACAGTAATGC
1 AGC-AAAGCTGCCAGTAACAGTAATGC
46097754 AGCAAAGCTGCCAGT-ACAGTA
1 AGCAAAGCTGCCAGTAACAGTA
46097775 TATGTGGCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 7 0.16
26 34 0.79
27 2 0.05
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.16
Consensus pattern (26 bp):
AGCAAAGCTGCCAGTAACAGTAATGC
Found at i:46097977 original size:27 final size:27
Alignment explanation
Indices: 46097947--46098142 Score: 220
Period size: 27 Copynumber: 7.3 Consensus size: 27
46097937 GGGTATAATA
* *
46097947 GTCATTTCACCCTAT-AGGGGTATTTCG
1 GTCATTTTACCCT-TCAGGGGTAATTCG
* * *
46097974 GTCATTTTATCCTTC-GAGGGTACTTCA
1 GTCATTTTACCCTTCAG-GGGTAATTCG
* *
46098001 GTAATTTTACCCTTC-GGAGCTAATTCG
1 GTCATTTTACCCTTCAGG-GGTAATTCG
*
46098028 GTCATTTTACCCTTCGGGGGTAATTCG
1 GTCATTTTACCCTTCAGGGGTAATTCG
*
46098055 ATCATTTTACCCTTCAGGGGTAATTCG
1 GTCATTTTACCCTTCAGGGGTAATTCG
* *
46098082 ATCATTTTACCCTTCGGGGGTAATTCG
1 GTCATTTTACCCTTCAGGGGTAATTCG
46098109 GTCATTTTACCCTTC-GAGGGTAATTCG
1 GTCATTTTACCCTTCAG-GGGTAATTCG
*
46098136 ATCATTT
1 GTCATTT
46098143 GCCCATGATT
Statistics
Matches: 148, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
26 4 0.03
27 142 0.96
28 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCCTTCAGGGGTAATTCG
Found at i:46098089 original size:81 final size:81
Alignment explanation
Indices: 46097963--46098142 Score: 256
Period size: 81 Copynumber: 2.2 Consensus size: 81
46097953 TCACCCTATA
* * * *
46097963 GGGGTATTTCGGTCATTTTATCCTTCGAGGGTACTTCAGTAATTTTACCCTTCGGAGCTAATTCG
1 GGGGTAATTCGATCATTTTACCCTTCGAGGGTAATTCAGTAATTTTACCCTTCGGAGCTAATTCG
46098028 GTCATTTTACCCTTCG
66 GTCATTTTACCCTTCG
* * *
46098044 GGGGTAATTCGATCATTTTACCCTTC-AGGGGTAATTC-GATCATTTTACCCTTCGGGGGTAATT
1 GGGGTAATTCGATCATTTTACCCTTCGA-GGGTAATTCAG-TAATTTTACCCTTCGGAGCTAATT
46098107 CGGTCATTTTACCCTTCG
64 CGGTCATTTTACCCTTCG
*
46098125 AGGGTAATTCGATCATTT
1 GGGGTAATTCGATCATTT
46098143 GCCCATGATT
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
80 2 0.02
81 87 0.98
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (81 bp):
GGGGTAATTCGATCATTTTACCCTTCGAGGGTAATTCAGTAATTTTACCCTTCGGAGCTAATTCG
GTCATTTTACCCTTCG
Found at i:46102635 original size:25 final size:24
Alignment explanation
Indices: 46102615--46102662 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
46102605 ACAAAATATT
*
46102615 AATAATTCAAT-AAATTGAAAACTTA
1 AATAATTAAATAAAATT-AAAA-TTA
46102640 AATAATTAAATAAAATTAAAATT
1 AATAATTAAATAAAATTAAAATT
46102663 TAGGAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.10
25 14 0.67
26 5 0.24
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAATTAAATAAAATTAAAATTA
Found at i:46119958 original size:17 final size:18
Alignment explanation
Indices: 46119936--46119974 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
46119926 AAACATGATT
*
46119936 CTTAAGT-ATGTCATACA
1 CTTAAGTCATGTCAAACA
46119953 CTTAAGTCCATGTCAAACA
1 CTTAAGT-CATGTCAAACA
46119972 CTT
1 CTT
46119975 CATTGGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
19 12 0.63
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (18 bp):
CTTAAGTCATGTCAAACA
Found at i:46121430 original size:77 final size:77
Alignment explanation
Indices: 46121291--46121612 Score: 310
Period size: 77 Copynumber: 4.1 Consensus size: 77
46121281 TTTAAATTTT
* ** * ** * * *
46121291 GAAACAAAATCAAAATTAGTTCTGTTAAATGGCAAGATTAAATCTCGATACA-AAGTTATTTAAT
1 GAAACAAAATCAAAATAAAATCTGTTAAACGGTGAGAATAAATCCCGAAACAGAA-TTATTTAAT
*
46121355 AAAATCTTGTTTG
65 TAAATCTTGTTTG
* *
46121368 GAAACAAAATCAAAATAAAATCTGTTAAACGGTGAGAATAAATCCCGAAATAGAATTCTTTAATT
1 GAAACAAAATCAAAATAAAATCTGTTAAACGGTGAGAATAAATCCCGAAACAGAATTATTTAATT
*
46121433 AAATATTGTTTG
66 AAATCTTGTTTG
* * * * * *
46121445 AAAACAAAACCAAAATGAAATCTGTTAAATGGTGGGAATAAATCCC-ATAACACAATTATTTAAT
1 GAAACAAAATCAAAATAAAATCTGTTAAACGGTGAGAATAAATCCCGA-AACAGAATTATTTAAT
*
46121509 TAAATCTTCATTTG
65 TAAATCTT-GTTTG
* *
46121523 GAAACAAAATCAAAATCAAATCAAACCTGTTAAACGGT-AGGAATAAATCCCGATACAG-ATTAT
1 GAAACAAAATCAAAAT---A--AAATCTGTTAAACGGTGA-GAATAAATCCCGAAACAGAATTAT
* **
46121586 TCAATTATTTCTTGTTTG
60 TTAATTAAATCTTGTTTG
46121604 GAAACAAAA
1 GAAACAAAA
46121613 AAAAGGAATA
Statistics
Matches: 200, Mismatches: 35, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
76 1 0.00
77 122 0.61
78 20 0.10
81 13 0.06
82 15 0.08
83 28 0.14
84 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (77 bp):
GAAACAAAATCAAAATAAAATCTGTTAAACGGTGAGAATAAATCCCGAAACAGAATTATTTAATT
AAATCTTGTTTG
Found at i:46121472 original size:154 final size:156
Alignment explanation
Indices: 46121288--46121575 Score: 363
Period size: 154 Copynumber: 1.8 Consensus size: 156
46121278 GAATTTAAAT
* * ** * *
46121288 TTTGAAACAAAATCAAAATTAGTTCTGTTAAATGGCAAGATTAAATCTCGAT-ACA-AAGTTATT
1 TTTGAAACAAAACCAAAATGAAATCTGTTAAATGGCAAGAATAAATC-CCATAACACAA-TTATT
* *
46121351 TAATAAAATCTT-GTTTGGAAACAAAATCAAAAT-A-AAATCTGTTAAACGGT-GAGAATAAATC
64 TAATAAAATCTTCATTTGGAAACAAAATCAAAATAACAAACCTGTTAAACGGTAG-GAATAAATC
46121412 CCGAAATAGAATTCTTTAATTAAATATTG
128 CCGAAATAGAATTCTTTAATTAAATATTG
***
46121441 TTTGAAAACAAAACCAAAATGAAATCTGTTAAATGGTGGGAATAAATCCCATAACACAATTATTT
1 TTTG-AAACAAAACCAAAATGAAATCTGTTAAATGGCAAGAATAAATCCCATAACACAATTATTT
*
46121506 AATTAAATCTTCATTTGGAAACAAAATCAAAATCAAATCAAACCTGTTAAACGGTAGGAATAAAT
65 AATAAAATCTTCATTTGGAAACAAAATCAAAAT--AA-CAAACCTGTTAAACGGTAGGAATAAAT
46121571 CCCGA
127 CCCGA
46121576 TACAGATTAT
Statistics
Matches: 113, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
153 7 0.06
154 54 0.48
155 22 0.19
158 1 0.01
160 28 0.25
161 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (156 bp):
TTTGAAACAAAACCAAAATGAAATCTGTTAAATGGCAAGAATAAATCCCATAACACAATTATTTA
ATAAAATCTTCATTTGGAAACAAAATCAAAATAACAAACCTGTTAAACGGTAGGAATAAATCCCG
AAATAGAATTCTTTAATTAAATATTG
Found at i:46121627 original size:83 final size:83
Alignment explanation
Indices: 46121456--46121627 Score: 188
Period size: 83 Copynumber: 2.1 Consensus size: 83
46121446 AAACAAAACC
* * * * *
46121456 AAAATGAAATCTGTTAAATGGTGGGAATAAATCCCATAACACAATTATTTAATTAAATCTTCATT
1 AAAATCAAACCTGTTAAACGGTAGGAATAAATCCCATAACACAATTATTCAATTAAATCTTCATT
**
46121521 TGGAAACAAAATCAAAAT
66 TGGAAACAAAAAAAAAAT
* * ** *
46121539 CAAATCAAACCTGTTAAACGGTAGGAATAAATCCCGAT-ACA-GATTATTCAATTATTTCTT-GT
1 AAAATCAAACCTGTTAAACGGTAGGAATAAATCCC-ATAACACAATTATTCAATTAAATCTTCAT
46121601 TTGGAAACAAAAAAAAGGAAT
65 TTGGAAACAAAAAAAA--AAT
46121622 AAAATC
1 AAAATC
46121628 CATTGAACAG
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
81 15 0.21
82 15 0.21
83 41 0.56
84 2 0.03
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.28
Consensus pattern (83 bp):
AAAATCAAACCTGTTAAACGGTAGGAATAAATCCCATAACACAATTATTCAATTAAATCTTCATT
TGGAAACAAAAAAAAAAT
Found at i:46122372 original size:32 final size:32
Alignment explanation
Indices: 46122331--46122394 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
46122321 ATGAGCATTT
*
46122331 AAATCAATTTGAATAAAATCAAATCAAATTGA
1 AAATCAATTTGAATAAAATAAAATCAAATTGA
* **
46122363 AAATCAATTTGATTGGAATAAAATCAAATTGA
1 AAATCAATTTGAATAAAATAAAATCAAATTGA
46122395 GATATTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (32 bp):
AAATCAATTTGAATAAAATAAAATCAAATTGA
Found at i:46132428 original size:36 final size:36
Alignment explanation
Indices: 46132353--46132428 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
46132343 CACTCTCAAA
* **
46132353 CTCCTTAATTTTCTCCTAAAATCTCTCCCCTTATAC
1 CTCCTTAATTTTCTCCTAAAATCTATCCCCAAATAC
* *
46132389 CTCCTTAATTTTCTCCATCAAATC-ATCCCCAAATCC
1 CTCCTTAATTTTCTCC-TAAAATCTATCCCCAAATAC
46132425 CTCC
1 CTCC
46132429 ATGACCAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 28 0.82
37 6 0.18
ACGTcount: A:0.24, C:0.39, G:0.00, T:0.37
Consensus pattern (36 bp):
CTCCTTAATTTTCTCCTAAAATCTATCCCCAAATAC
Found at i:46134320 original size:20 final size:20
Alignment explanation
Indices: 46134297--46134336 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
46134287 TGTGCCTTTA
*
46134297 TTTGTACTTTGGTGCCCCTG
1 TTTGTACTTCGGTGCCCCTG
46134317 TTTGTACTTCGGTGCCCCTG
1 TTTGTACTTCGGTGCCCCTG
46134337 AATAGCACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.28, G:0.25, T:0.42
Consensus pattern (20 bp):
TTTGTACTTCGGTGCCCCTG
Found at i:46136359 original size:18 final size:19
Alignment explanation
Indices: 46136332--46136367 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
46136322 CAATATAGTG
*
46136332 TCATTGATTTC-ACTTAAA
1 TCATTCATTTCAACTTAAA
46136350 TCATTCATTTCAACTTAA
1 TCATTCATTTCAACTTAA
46136368 GCAAACAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.44
Consensus pattern (19 bp):
TCATTCATTTCAACTTAAA
Found at i:46141236 original size:21 final size:22
Alignment explanation
Indices: 46141190--46141236 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
46141180 CAGACAGAAA
* *
46141190 ACCAGCCCAAACCAACCAATAG
1 ACCAGCCCAAACCAACCAACAC
*
46141212 ACCA-CCCATACCAACCAACAC
1 ACCAGCCCAAACCAACCAACAC
46141233 ACCA
1 ACCA
46141237 TGTGGGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.45, C:0.47, G:0.04, T:0.04
Consensus pattern (22 bp):
ACCAGCCCAAACCAACCAACAC
Found at i:46141660 original size:27 final size:27
Alignment explanation
Indices: 46141618--46141742 Score: 103
Period size: 27 Copynumber: 4.6 Consensus size: 27
46141608 TTTACCCTAG
**
46141618 GGGTATTTTGGTCATTTTACACTTTGA
1 GGGTATTTCAGTCATTTTACACTTTGA
* * * *
46141645 GGATATTTCAGACATTTTACCCTTCG-
1 GGGTATTTCAGTCATTTTACACTTTGA
* *
46141671 GGGTTACTTT-GGTCATTTTA-ACCTTTGG
1 GGG-TA-TTTCAGTCATTTTACA-CTTTGA
*
46141699 GGGTATTTCAGTCATTTTACCCTTTGA
1 GGGTATTTCAGTCATTTTACACTTTGA
**
46141726 GGGTATTTTGGTCATTT
1 GGGTATTTCAGTCATTT
46141743 AACGACCCTT
Statistics
Matches: 76, Mismatches: 16, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
26 5 0.07
27 65 0.86
28 6 0.08
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.46
Consensus pattern (27 bp):
GGGTATTTCAGTCATTTTACACTTTGA
Found at i:46141687 original size:54 final size:53
Alignment explanation
Indices: 46141606--46141742 Score: 179
Period size: 54 Copynumber: 2.6 Consensus size: 53
46141596 TAAAACGGTA
46141606 ATTTTACCC-TAGGGGTATTTTGGTCATTTT-ACACTTTGAGGATATTTCAGAC
1 ATTTTACCCTTAGGGGTATTTTGGTCATTTTAAC-CTTTGAGGATATTTCAGAC
* * * * *
46141658 ATTTTACCCTTCGGGGTTACTTTGGTCATTTTAACCTTTGGGGGTATTTCAGTC
1 ATTTTACCCTTAGGGG-TATTTTGGTCATTTTAACCTTTGAGGATATTTCAGAC
*
46141712 ATTTTACCCTTTGAGGGTATTTTGGTCATTT
1 ATTTTACCCTTAG-GGGTATTTTGGTCATTT
46141743 AACGACCCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
52 9 0.12
53 5 0.07
54 55 0.74
55 5 0.07
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.45
Consensus pattern (53 bp):
ATTTTACCCTTAGGGGTATTTTGGTCATTTTAACCTTTGAGGATATTTCAGAC
Found at i:46148127 original size:284 final size:284
Alignment explanation
Indices: 46147617--46148162 Score: 792
Period size: 284 Copynumber: 1.9 Consensus size: 284
46147607 TGAGCCATCC
*
46147617 CAGCCAAGAATAAATTTTAACCCTAATTATTAATTAAGTCAACAATAACCTTTAATTAAGTATTT
1 CAGCCAAGAATAAATTTTAACCCTAATTATTAACTAAGTCAACAATAACCTTTAATTAAGTATTT
* * * *
46147682 ACTACCCTTAGCTAAGAATACCCTCTTGGTTTCATCTTCACTAAGAATTACCATCTAAGATGCCC
66 ACTACCCTTAGCTAAGAATACCCTCTAGGTTTCATCTTCACCAAGAATTACAACCTAAGATGCCC
* * * * ** *
46147747 TTTCAGTCTCATCTAGGCATACGGATACTCTATTGGTCCCATGACTTGGTACGAGTTCTACTGAA
131 TCTCAGTCTCAGCTAGGCAAACGGATACTCTATTAGTCCCACCACTTGGTACGAGTTCTACTCAA
* * * * *
46147812 CAAGATACCCTCTCGGTCTCACTTGTCTAGATCTTCTACTAGGGTGTCATTTCCCTT-TATATTA
196 CAAGACACCCTCTAGGTCTCACCTATCTAGATCTTCTACTAGGGTGTCACTT-CCTTGTATATTA
46147876 AGTCAAGAATCAATTTTAGCCCTCT
260 AGTCAAGAATCAATTTTAGCCCTCT
* * * *
46147901 CAGCCAAGAATCAATTTTAGCCCTAATTATTAACTAAGTCAACAATGACCTTTGATTAAGTATTT
1 CAGCCAAGAATAAATTTTAACCCTAATTATTAACTAAGTCAACAATAACCTTTAATTAAGTATTT
* * * *
46147966 ACTACCCTTAGTTTAGAATACCCTCTAGGTTTCATCTTCACCGATAATTACAACCTAAGATGCCC
66 ACTACCCTTAGCTAAGAATACCCTCTAGGTTTCATCTTCACCAAGAATTACAACCTAAGATGCCC
* * *
46148031 TCTCGGTCTCAGCTAGGCAAAC-GAGTACTCTCTTAGTCCCACCACTTGGTACGAGTTCTATTCA
131 TCTCAGTCTCAGCTAGGCAAACGGA-TACTCTATTAGTCCCACCACTTGGTACGAGTTCTACTCA
46148095 A-AATGACACCCTCTAGGTCTCACCTATCTAGATCTTCTACTAGGGTGTCACTTCCTTGTATATT
195 ACAA-GACACCCTCTAGGTCTCACCTATCTAGATCTTCTACTAGGGTGTCACTTCCTTGTATATT
46148159 AAGT
259 AAGT
46148163 ATTCTCGAAT
Statistics
Matches: 231, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
283 8 0.03
284 223 0.97
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (284 bp):
CAGCCAAGAATAAATTTTAACCCTAATTATTAACTAAGTCAACAATAACCTTTAATTAAGTATTT
ACTACCCTTAGCTAAGAATACCCTCTAGGTTTCATCTTCACCAAGAATTACAACCTAAGATGCCC
TCTCAGTCTCAGCTAGGCAAACGGATACTCTATTAGTCCCACCACTTGGTACGAGTTCTACTCAA
CAAGACACCCTCTAGGTCTCACCTATCTAGATCTTCTACTAGGGTGTCACTTCCTTGTATATTAA
GTCAAGAATCAATTTTAGCCCTCT
Found at i:46160719 original size:41 final size:41
Alignment explanation
Indices: 46160673--46160775 Score: 116
Period size: 49 Copynumber: 2.3 Consensus size: 41
46160663 TAAGCATGTA
* *
46160673 TTGGTTGATTAATTAATTAGTTAGAGGACGAGAGGTTATAG
1 TTGGTTAATTAATTAATTAGTTAGAGGACGAGAGGTAATAG
46160714 TTGGTTAATTAATAGCTAAGTTAATTAGTTAGAGGACGAGAGGTAATAG
1 TTGG----TTAAT---TAA-TTAATTAGTTAGAGGACGAGAGGTAATAG
46160763 TTGGTTAATTAAT
1 TTGGTTAATTAAT
46160776 AGCTAACTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
41 5 0.10
42 3 0.06
45 9 0.17
48 3 0.06
49 32 0.62
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (41 bp):
TTGGTTAATTAATTAATTAGTTAGAGGACGAGAGGTAATAG
Found at i:46160741 original size:49 final size:49
Alignment explanation
Indices: 46160685--46160781 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
46160675 GGTTGATTAA
*
46160685 TTAATTAGTTAGAGGACGAGAGGTTATAGTTGGTTAATTAATAGCTAAG
1 TTAATTAGTTAGAGGACGAGAGGTAATAGTTGGTTAATTAATAGCTAAG
46160734 TTAATTAGTTAGAGGACGAGAGGTAATAGTTGGTTAATTAATAGCTAA
1 TTAATTAGTTAGAGGACGAGAGGTAATAGTTGGTTAATTAATAGCTAA
46160782 CTCAATAAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (49 bp):
TTAATTAGTTAGAGGACGAGAGGTAATAGTTGGTTAATTAATAGCTAAG
Found at i:46169499 original size:25 final size:26
Alignment explanation
Indices: 46169468--46169561 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 26
46169458 CGAATACTCC
46169468 ACAGCTCGTA-AGAGCATACTGATTT
1 ACAGCTCGTAGAGAGCATACTGATTT
* ** * *
46169493 ATAGCTCGT-GATTGCATATTGATCT
1 ACAGCTCGTAGAGAGCATACTGATTT
* *
46169518 ACAGCTCG-AGTGAGCATACTGATTC
1 ACAGCTCGTAGAGAGCATACTGATTT
*
46169543 ACAGCTCGTATA-AGCATAC
1 ACAGCTCGTAGAGAGCATAC
46169562 ATGTACACGA
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
25 51 0.98
26 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (26 bp):
ACAGCTCGTAGAGAGCATACTGATTT
Found at i:46169721 original size:17 final size:17
Alignment explanation
Indices: 46169699--46169736 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
46169689 AATATATGAA
46169699 CTTACTAAGCTTAAATG
1 CTTACTAAGCTTAAATG
46169716 CTTACTAAGCTTAAATG
1 CTTACTAAGCTTAAATG
46169733 CTTA
1 CTTA
46169737 AATGTTGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (17 bp):
CTTACTAAGCTTAAATG
Found at i:46171327 original size:27 final size:27
Alignment explanation
Indices: 46171255--46171367 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 27
46171245 GGTATAATAG
* * *
46171255 TCATCTTACCCTACGA-GGTGTTTC-A
1 TCATTTTACCCTTCGAGGGTATTTCGA
* * *
46171280 GTCATTTTATCCTTCGGGGGTATTTTGA
1 -TCATTTTACCCTTCGAGGGTATTTCGA
* *
46171308 TCATTTTACCCATCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
46171335 TCATTTTACCCTTCGAGCGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
46171362 TCATTT
1 TCATTT
46171368 GCCCACGAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
26 12 0.17
27 58 0.82
28 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCGA
Found at i:46174164 original size:102 final size:104
Alignment explanation
Indices: 46174006--46174203 Score: 328
Period size: 102 Copynumber: 1.9 Consensus size: 104
46173996 AATGATTCGA
* *
46174006 GGAATCAGCACTTAGCAACCCCTTTTCACATTAGAAAATACGGTTGAATCAGCACTTAGCAACCA
1 GGAATCAGCACTTAGCAACCCCTCTTCACATTAGAAAATACGGTGGAATCAGCACTTAGCAACCA
** *
46174071 CCAATGAATTGGGGAATTAGCACTTAGCAACCCCTTGGG
66 CCAATGAATCAGGGAATCAGCACTTAGCAACCCCTTGGG
*
46174110 GGAATCAGCACTTAGCAACCCC-CTTCACATT-TAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGAATCAGCACTTAGCAACCCCTCTTCACATTAGAAAATACGGTGGAATCAGCACTTAGCAACCA
46174173 CCAATGAATCAGGGAATCAGCACTTAGCAAC
66 CCAATGAATCAGGGAATCAGCACTTAGCAAC
46174204 TATATTCAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 58 0.66
103 8 0.09
104 22 0.25
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (104 bp):
GGAATCAGCACTTAGCAACCCCTCTTCACATTAGAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAATCAGGGAATCAGCACTTAGCAACCCCTTGGG
Found at i:46174560 original size:30 final size:30
Alignment explanation
Indices: 46174526--46174583 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
46174516 AAATAGTCCT
*
46174526 CCCAAATTTTTGAAAATTTACAATTTTGCC
1 CCCAAACTTTTGAAAATTTACAATTTTGCC
* * *
46174556 CCCAAACTTTTGCATATTTACACTTTTG
1 CCCAAACTTTTGAAAATTTACAATTTTG
46174584 TCCCTAAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.41
Consensus pattern (30 bp):
CCCAAACTTTTGAAAATTTACAATTTTGCC
Found at i:46181336 original size:38 final size:38
Alignment explanation
Indices: 46181285--46181357 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
46181275 TGGTGGAGGA
* *
46181285 GTGTTGGAGTGATTTTAGGAGGAAAATATGAGATTGGC
1 GTGTTGGACTGATTTTAGGAGGAAAACATGAGATTGGC
*
46181323 GTGTTGGACTGATTTTAGGAGGAAAACATGGGATT
1 GTGTTGGACTGATTTTAGGAGGAAAACATGAGATT
46181358 ATGGAGTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.32
Consensus pattern (38 bp):
GTGTTGGACTGATTTTAGGAGGAAAACATGAGATTGGC
Found at i:46186000 original size:18 final size:19
Alignment explanation
Indices: 46185972--46186007 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
46185962 TTTATGCTAA
46185972 CTTTATATTTTTATTATTT
1 CTTTATATTTTTATTATTT
46185991 CTTT-TATTTTTATTATT
1 CTTTATATTTTTATTATT
46186008 ATTAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (19 bp):
CTTTATATTTTTATTATTT
Found at i:46211875 original size:46 final size:46
Alignment explanation
Indices: 46211822--46211919 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 46
46211812 TGGGCTGTTC
* * * *
46211822 TGGGCCTC-ATTGGGCCGAAATGGGCTGTGTGGGCCCAGTGGGCTTG
1 TGGGCCTCAATT-GGCCGAAATGGGCTGTATGGGCCCAATAGGCTTA
* *
46211868 TGGGCCTCAATTGGTCGAAATGGGCTGTATGGTCCCAATAGGCTTA
1 TGGGCCTCAATTGGCCGAAATGGGCTGTATGGGCCCAATAGGCTTA
46211914 TGGGCC
1 TGGGCC
46211920 CATACGGGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 42 0.93
47 3 0.07
ACGTcount: A:0.15, C:0.21, G:0.38, T:0.26
Consensus pattern (46 bp):
TGGGCCTCAATTGGCCGAAATGGGCTGTATGGGCCCAATAGGCTTA
Found at i:46212152 original size:27 final size:27
Alignment explanation
Indices: 46212077--46212136 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
46212067 TAATAAGTAT
* *
46212077 CGTAATACCCCTGTAGGGTAAAATGAC
1 CGTAATACCCTTGTAGGGTAAAAGGAC
46212104 CGTAATACCCTTGTAGGGTAAAAGGAC
1 CGTAATACCCTTGTAGGGTAAAAGGAC
46212131 CGTAAT
1 CGTAAT
46212137 GCCTTTGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (27 bp):
CGTAATACCCTTGTAGGGTAAAAGGAC
Found at i:46212248 original size:24 final size:24
Alignment explanation
Indices: 46212221--46212266 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
46212211 GAATTTTTTG
* *
46212221 TGATATAAATGATTGATTTGTCCT
1 TGATACAAATGACTGATTTGTCCT
* *
46212245 TGATGCAAATGACTGCTTTGTC
1 TGATACAAATGACTGATTTGTC
46212267 TGTGTTTGGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (24 bp):
TGATACAAATGACTGATTTGTCCT
Found at i:46212499 original size:32 final size:33
Alignment explanation
Indices: 46212458--46212627 Score: 192
Period size: 32 Copynumber: 5.4 Consensus size: 33
46212448 GCTGCGATGC
*
46212458 TACTGATGGCTTTGTGCT-GATCATGTTACCGT
1 TACTGATGGCTTTGTGCTCGATCATATTACCGT
*
46212490 TACTGATGGCTTGGTG-TCGATCATATTACCGT
1 TACTGATGGCTTTGTGCTCGATCATATTACCGT
*
46212522 TACT-ATGGCTTTGTGC-CAATCATATTACCGT
1 TACTGATGGCTTTGTGCTCGATCATATTACCGT
* * * *
46212553 TACTGATGGCTGTGTG-TCGATCATATCACTGC
1 TACTGATGGCTTTGTGCTCGATCATATTACCGT
* * *
46212585 TACTGATGGCTTTGTGC-CAATCACATTACTG-
1 TACTGATGGCTTTGTGCTCGATCATATTACCGT
*
46212616 TACTTATGGCTT
1 TACTGATGGCTT
46212628 GCAGCCATTC
Statistics
Matches: 119, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
31 40 0.34
32 79 0.66
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (33 bp):
TACTGATGGCTTTGTGCTCGATCATATTACCGT
Found at i:46212562 original size:63 final size:65
Alignment explanation
Indices: 46212456--46212628 Score: 237
Period size: 63 Copynumber: 2.7 Consensus size: 65
46212446 TTGCTGCGAT
** * *
46212456 GCTACTGATGGCTTTGTGCTGATCATGTTACCGTTACTGATGGCTTG-GTGTCGATCATATTACC
1 GCTACTGATGGCTTTGTGCCAATCATATTACCGTTACTGATGGCTTGTGTGTCGATCATATCACC
* *
46212520 GTTACT-ATGGCTTTGTGCCAATCATATTACCGTTACTGATGGC-TGTGTGTCGATCATATCACT
1 GCTACTGATGGCTTTGTGCCAATCATATTACCGTTACTGATGGCTTGTGTGTCGATCATATCACC
* * *
46212583 GCTACTGATGGCTTTGTGCCAATCACATTACTG-TACTTATGGCTTG
1 GCTACTGATGGCTTTGTGCCAATCATATTACCGTTACTGATGGCTTG
46212629 CAGCCATTCT
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
62 2 0.02
63 63 0.66
64 31 0.32
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (65 bp):
GCTACTGATGGCTTTGTGCCAATCATATTACCGTTACTGATGGCTTGTGTGTCGATCATATCACC
Found at i:46212644 original size:22 final size:22
Alignment explanation
Indices: 46212619--46212683 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
46212609 ATTACTGTAC
**
46212619 TTATGGCTTGCAGCCATTCTGT
1 TTATGGCTTATAGCCATTCTGT
* * * *
46212641 TTATAGCTTATAGCTATCCTAT
1 TTATGGCTTATAGCCATTCTGT
*
46212663 TTATGGCTTTTAGCCATTCTG
1 TTATGGCTTATAGCCATTCTG
46212684 ACTACCGGCA
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (22 bp):
TTATGGCTTATAGCCATTCTGT
Found at i:46212878 original size:28 final size:28
Alignment explanation
Indices: 46212838--46212938 Score: 103
Period size: 28 Copynumber: 3.4 Consensus size: 28
46212828 CCTGCACCAT
*
46212838 ACTGTTACTGTATCGGGCTTAGGCCCAC
1 ACTGTTTCTGTATCGGGCTTAGGCCCAC
* *
46212866 ACTGTTTCTGTATTGGGCTAAGGCCCAC
1 ACTGTTTCTGTATCGGGCTTAGGCCCAC
* *
46212894 ACTGTACTGTTACTTTTATCGGGCATAGGCCCAC
1 ACTG---T-TT-C-TGTATCGGGCTTAGGCCCAC
46212928 ACTGTTTCTGT
1 ACTGTTTCTGT
46212939 TTCTATATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
28 31 0.53
29 1 0.02
30 2 0.03
31 2 0.03
32 2 0.03
33 1 0.02
34 20 0.34
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.34
Consensus pattern (28 bp):
ACTGTTTCTGTATCGGGCTTAGGCCCAC
Found at i:46220653 original size:14 final size:14
Alignment explanation
Indices: 46220634--46220662 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46220624 AGGGACGTGT
46220634 TAGGTTTGAAACAA
1 TAGGTTTGAAACAA
46220648 TAGGTTTGAAACAA
1 TAGGTTTGAAACAA
46220662 T
1 T
46220663 TTAATCACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (14 bp):
TAGGTTTGAAACAA
Found at i:46223508 original size:27 final size:27
Alignment explanation
Indices: 46223470--46223850 Score: 449
Period size: 27 Copynumber: 14.1 Consensus size: 27
46223460 TTCCCATGTA
*
46223470 ATTTTACCCTATGGGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
46223497 ATTTTACCCTATGAGGGTATTTCTGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * * *
46223524 GTTTTACTCTATGGAGGTATTTCTGTT
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * *
46223551 ATTCTACCTTATGGTGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * **
46223578 ATTCTACCCTATTGGGGTATTTTAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
46223605 ATTTTACCATATGGGGGTCTTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
46223632 ATTTTACCCTATGAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
46223659 ATTTTACCTTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* **
46223686 ATTCTACCCTATAAGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
46223713 ATTCTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
46223740 ATTTTATCCTACGGGGGTATTTCAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
46223767 ATTTTACCCTAT-AGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
46223793 ATTTTACCCTATAGGGGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* *
46223820 ATTTTACCCTATGGGGGTATATCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
46223847 ATTT
1 ATTT
46223851 ATCGACCTCT
Statistics
Matches: 301, Mismatches: 52, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
26 23 0.08
27 278 0.92
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:46224533 original size:12 final size:12
Alignment explanation
Indices: 46224516--46224557 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
46224506 ATCCCAATAT
46224516 TCTCTCCTAAAA
1 TCTCTCCTAAAA
46224528 TCTCTCC-AAATA
1 TCTCTCCTAAA-A
* *
46224540 TCCCTCCTCAAA
1 TCTCTCCTAAAA
46224552 TCTCTC
1 TCTCTC
46224558 TATGACTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 3 0.12
12 20 0.80
13 2 0.08
ACGTcount: A:0.26, C:0.40, G:0.00, T:0.33
Consensus pattern (12 bp):
TCTCTCCTAAAA
Found at i:46243776 original size:27 final size:27
Alignment explanation
Indices: 46243738--46244147 Score: 433
Period size: 27 Copynumber: 15.1 Consensus size: 27
46243728 GGTCGATATC
***
46243738 TGACCGAAATACCTTTATAGGGTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAA
*
46243765 TGACCGAAATACCCCCAAAGGGTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAA
* *
46243792 TGATCAAAATACCCCCATAGGGTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAA
* *
46243819 TGACCGAAATACCCTCATAGGGTAGAA
1 TGACCGAAATACCCCCATAGGGTAAAA
* *
46243846 TGACCAAAATACCCCCATAGTGTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAA
* *
46243873 TGACCGAAATACCCCCATAGGATAGAA
1 TGACCGAAATACCCCCATAGGGTAAAA
**
46243900 TGATTGAAATACCCCCATAGGGTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAA
* * * * *
46243927 TGACTGAAATACTCCTATAAGATAAAA
1 TGACCGAAATACCCCCATAGGGTAAAA
* *
46243954 TGATCGAAATACCCCCATAGGTTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAA
* * * * *
46243981 TGACTGAAATATCCTCATAAGGTAGAA
1 TGACCGAAATACCCCCATAGGGTAAAA
* * *
46244008 TAACCGAAATACCCCCCATAAGGTAGAA
1 TGACCGAAATA-CCCCCATAGGGTAAAA
* * * *
46244036 TGACCAAAATAACCCTATAGGCTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAA
* * * * * *
46244063 TGAGCAAAACATCCCCACAGGGTAGAA
1 TGACCGAAATACCCCCATAGGGTAAAA
*
46244090 TGACTGAAATACCCCCATAGGGTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAA
* *
46244117 TGACCGAAATACCCCTATAAGGTAAAA
1 TGACCGAAATACCCCCATAGGGTAAAA
46244144 TGAC
1 TGAC
46244148 TGTTATATCC
Statistics
Matches: 313, Mismatches: 69, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
27 290 0.93
28 23 0.07
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
TGACCGAAATACCCCCATAGGGTAAAA
Found at i:46246693 original size:40 final size:40
Alignment explanation
Indices: 46246648--46246794 Score: 141
Period size: 40 Copynumber: 3.7 Consensus size: 40
46246638 AGAGCATTCT
* * * *
46246648 TTTCAGTAGATTCAGTAGTTATGGATCGAAAGAGCATATG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCGCATACG
* * * * * *
46246688 TTTCAGAAAATTTAGTAGGTGTGGCTCAAAATCGCATACG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCGCATACG
* ** * *
46246728 TTTCAGTAGATTTAGTAAATATGGCTCGAAGGCGCATGCG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCGCATACG
* *
46246768 TTTTAGTAGATTCAGAAGGTATGGCTC
1 TTTCAGTAGATTCAGTAGGTATGGCTC
46246795 TTCTGAGCAC
Statistics
Matches: 83, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 83 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (40 bp):
TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCGCATACG
Found at i:46248664 original size:40 final size:40
Alignment explanation
Indices: 46248613--46248775 Score: 191
Period size: 40 Copynumber: 4.1 Consensus size: 40
46248603 ATTTCTTTTA
* * *
46248613 CTCGATAGAGCATTCTTTTCAGTAGATTCAGTAGGTATGG
1 CTCGAAAGAGCATACGTTTCAGTAGATTCAGTAGGTATGG
* * *
46248653 CTTGAAAGAGCATACGTTTCAGTAAATTCAGTAGGTGTGG
1 CTCGAAAGAGCATACGTTTCAGTAGATTCAGTAGGTATGG
* * * * *
46248693 CTCAAAAGCGCATACGTTTCAGTAGATTTAGTAAGTATTG
1 CTCGAAAGAGCATACGTTTCAGTAGATTCAGTAGGTATGG
* * * *
46248733 CTCGAAGGCGCATGCGTTTTAGTAGATTCAGTAGGTATGG
1 CTCGAAAGAGCATACGTTTCAGTAGATTCAGTAGGTATGG
46248773 CTC
1 CTC
46248776 TTCTGAGTAC
Statistics
Matches: 102, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (40 bp):
CTCGAAAGAGCATACGTTTCAGTAGATTCAGTAGGTATGG
Found at i:46251449 original size:20 final size:22
Alignment explanation
Indices: 46251426--46251473 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
46251416 CGAATTTGCC
46251426 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
46251446 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
46251468 AAAAAT
1 AAAAAT
46251474 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:46254285 original size:16 final size:17
Alignment explanation
Indices: 46254266--46254315 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 17
46254256 TTACTTTCTC
46254266 AAAAATTTGAAATATTA
1 AAAAATTTGAAATATTA
46254283 AAAATTTATTTGAAATATT-
1 AAAA---ATTTGAAATATTA
46254302 AAAAATTTGAAATA
1 AAAAATTTGAAATA
46254316 CTTTCTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.33
17 4 0.13
19 4 0.13
20 12 0.40
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
AAAAATTTGAAATATTA
Found at i:46254295 original size:20 final size:20
Alignment explanation
Indices: 46254270--46254309 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
46254260 TTTCTCAAAA
46254270 ATTTGAAATATTAAAAATTT
1 ATTTGAAATATTAAAAATTT
46254290 ATTTGAAATATTAAAAATTT
1 ATTTGAAATATTAAAAATTT
46254310 GAAATACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTGAAATATTAAAAATTT
Found at i:46260514 original size:15 final size:15
Alignment explanation
Indices: 46260496--46260532 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
46260486 TGGTGGTAGA
*
46260496 GGTGCTGGTCGGCGT
1 GGTGCTGGTCAGCGT
*
46260511 GGTGCTGGTCAGTGT
1 GGTGCTGGTCAGCGT
46260526 GGTGCTG
1 GGTGCTG
46260533 CTCAATGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.03, C:0.16, G:0.51, T:0.30
Consensus pattern (15 bp):
GGTGCTGGTCAGCGT
Found at i:46260541 original size:15 final size:15
Alignment explanation
Indices: 46260509--46260543 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
46260499 GCTGGTCGGC
* *
46260509 GTGGTGCTGGTCAGT
1 GTGGTGCTGCTCAAT
46260524 GTGGTGCTGCTCAAT
1 GTGGTGCTGCTCAAT
46260539 GTGGT
1 GTGGT
46260544 CCAACCAAAG
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:0.09, C:0.14, G:0.43, T:0.34
Consensus pattern (15 bp):
GTGGTGCTGCTCAAT
Found at i:46261949 original size:107 final size:108
Alignment explanation
Indices: 46261792--46262066 Score: 383
Period size: 110 Copynumber: 2.5 Consensus size: 108
46261782 ATCGAAACTT
* * ***
46261792 AGCATATTAGGGCACG-TTCCTCGAATTTCCAAACGCAAAATATAATCTTACTTTGAAATTTTAA
1 AGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAA
* *
46261856 AAGGTTATTTGGCTATTTGGTCGAATG-AAAAAATCGAAACCC
66 AAGGATATTTGGCTATTTGGTCGAATGAAAAAAATAGAAACCC
* *
46261898 ATCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTTTAA
1 AGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAA
* * *
46261963 TAGGATATTTTGCTGTTTGGTCGAATGAAAAAAAAATAGAAACCC
66 AAGGATATTTGGCTATTTGGTCGAATG--AAAAAAATAGAAACCC
* * *
46262008 AGCAGATTAGGGCGCATTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
1 AGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
46262067 CATTTTCCTT
Statistics
Matches: 148, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
106 14 0.09
107 66 0.45
110 68 0.46
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (108 bp):
AGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAA
AAGGATATTTGGCTATTTGGTCGAATGAAAAAAATAGAAACCC
Found at i:46262045 original size:110 final size:107
Alignment explanation
Indices: 46261752--46262066 Score: 373
Period size: 110 Copynumber: 2.9 Consensus size: 107
46261742 GAGATTTATG
* ** * * * ** * * *
46261752 AGGATATTTAGCTATTTGGTTAAACG-AGAAATCGAAACTTAGCATATTAGGGCAC-GTTCCTCG
1 AGGATATTTGGCTATTTGGTCGAATGAAAAAATAGAAACCCAGCACATTAGGGCACATTTTCTCG
***
46261815 AATTTCCAAACGCAAAATATAATCTTACTTTGAAATTTTAAA
66 AATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
* * * *
46261857 AGGTTATTTGGCTATTTGGTCGAATGAAAAAATCGAAACCCATCACATTAGGGCACGTTTTCTCG
1 AGGATATTTGGCTATTTGGTCGAATGAAAAAATAGAAACCCAGCACATTAGGGCACATTTTCTCG
* *
46261922 AATTTCCAAACGCAAAACATTGCCTTACTTTGAAATTTTAAT
66 AATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
* * * *
46261964 AGGATATTTTGCTGTTTGGTCGAATGAAAAAAAAATAGAAACCCAGCAGATTAGGGCGCATTTTC
1 AGGATATTTGGCTATTTGGTCGAATG---AAAAAATAGAAACCCAGCACATTAGGGCACATTTTC
46262029 TCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
63 TCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAA
46262067 CATTTTCCTT
Statistics
Matches: 179, Mismatches: 26, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
105 21 0.12
106 24 0.13
107 66 0.37
110 68 0.38
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (107 bp):
AGGATATTTGGCTATTTGGTCGAATGAAAAAATAGAAACCCAGCACATTAGGGCACATTTTCTCG
AATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
Found at i:46262712 original size:3 final size:3
Alignment explanation
Indices: 46262692--46262831 Score: 111
Period size: 3 Copynumber: 47.0 Consensus size: 3
46262682 AAATGGAAAT
* * * * * *
46262692 ATA ATG ATA ATA ACA ATA ATA TTA ACA ATA ATA CTA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
** * * * *
46262740 AGG ATA ATA ATA ATA ATA TTA ATA ATA CTT ATA ATA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * ** * *
46262788 A-A CTA ATT AGC TTA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46262832 GGACTAAATT
Statistics
Matches: 101, Mismatches: 35, Indels: 2
0.73 0.25 0.01
Matches are distributed among these distances:
2 1 0.01
3 100 0.99
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46263760 original size:20 final size:20
Alignment explanation
Indices: 46263735--46263774 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
46263725 GATGGGCGGT
46263735 GACGTGACCATGGCAGTGGC
1 GACGTGACCATGGCAGTGGC
*
46263755 GACGTGACCGTGGCAGTGGC
1 GACGTGACCATGGCAGTGGC
46263775 AGGGCTAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.25, G:0.42, T:0.15
Consensus pattern (20 bp):
GACGTGACCATGGCAGTGGC
Found at i:46264407 original size:44 final size:44
Alignment explanation
Indices: 46264359--46264462 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 44
46264349 CGGCCTACTG
* * * *
46264359 CAACTTCAGAGG-TATAGGATTTATCATTTTAATCTGCTCCACTA
1 CAACTTCAG-GGAGATAGGATTAATCACTTCAATCTGCTCCACTA
* * *
46264403 CAACTTCAGGGAGATAGGATTAATTACTTCAATCTGCTCCAGTG
1 CAACTTCAGGGAGATAGGATTAATCACTTCAATCTGCTCCACTA
46264447 CAACTTCAGGGAGATA
1 CAACTTCAGGGAGATA
46264463 AGACTGGATG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
43 2 0.04
44 50 0.96
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (44 bp):
CAACTTCAGGGAGATAGGATTAATCACTTCAATCTGCTCCACTA
Found at i:46264491 original size:41 final size:41
Alignment explanation
Indices: 46264434--46264635 Score: 154
Period size: 41 Copynumber: 4.8 Consensus size: 41
46264424 AATTACTTCA
* *
46264434 ATCTGCTCCAGTGCAACTTCAGGGAGATAAGACTGGATGCG
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGACTGGATGCG
* * * * ***
46264475 ATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGA-C--TGGATGCG
* * * * * * *
46264519 ATCCGGTCCACTACAACTTCAGGGAGATAGGATTGGTTTATTCTG
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGACTGG---ATGC-G
* *
46264564 -TCTTCTCTAATGCAACTTCAGGGAGATAAGACTGGATGCG
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGACTGGATGCG
* *
46264604 ATCTACTCTACTGCAACTTCAGAGAGATAAGA
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGA
46264636 TCTATGGTTT
Statistics
Matches: 121, Mismatches: 32, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
40 1 0.01
41 62 0.51
42 1 0.01
44 57 0.47
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (41 bp):
ATCTGCTCTACTGCAACTTCAGGGAGATAAGACTGGATGCG
Found at i:46264587 original size:129 final size:129
Alignment explanation
Indices: 46264353--46264725 Score: 489
Period size: 129 Copynumber: 2.9 Consensus size: 129
46264343 TTAATCCGGC
* * ** *
46264353 CTACTGCAACTTCAGAG-GTATAGGATTTATCATTTTAATCTGCTCCACTACAACTTCAGGGAGA
1 CTACTGCAACTTCAGAGAG-ATAAGATCTATGGTTTTAATCCGCTCCACTACAACTTCAGGGAGA
** * * *
46264417 TAGGATT-AATTACTTCAATCTGCTCCAGTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGC
65 TAGGATTGGTTTA-TTCTATCTGCTCCAATGCAACTTCAGGGAGATAAGACTGGATGCGATCTAC
46264481 T
129 T
* * * *
46264482 CTATTGCAACTTTAGAGAGATAAGATCTGTGGTTTTAATCCGGTCCACTACAACTTCAGGGAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTACAACTTCAGGGAGAT
* * *
46264547 AGGATTGGTTTATTCTGTCTTCTCTAATGCAACTTCAGGGAGATAAGACTGGATGCGATCTACT
66 AGGATTGGTTTATTCTATCTGCTCCAATGCAACTTCAGGGAGATAAGACTGGATGCGATCTACT
* *
46264611 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGCGAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTACAACTTCAGGGAGAT
* * * * * *
46264676 AGGATTGGTTTCTTCTATCTGCTCCACTACAAGTTTAGAGAGATAAGACT
66 AGGATTGGTTTATTCTATCTGCTCCAATGCAACTTCAGGGAGATAAGACT
46264726 TGTATCTTCA
Statistics
Matches: 210, Mismatches: 32, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
129 206 0.98
130 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (129 bp):
CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTACAACTTCAGGGAGAT
AGGATTGGTTTATTCTATCTGCTCCAATGCAACTTCAGGGAGATAAGACTGGATGCGATCTACT
Found at i:46264666 original size:44 final size:43
Alignment explanation
Indices: 46264385--46264766 Score: 207
Period size: 44 Copynumber: 8.8 Consensus size: 43
46264375 GGATTTATCA
* * **
46264385 TTTTAATCTGCTCCACTACAACTTCAGGGAGATAGGA--TTAA
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTTGG
*
46264426 TTACTTCAATCTGCTCCAGTGCAACTTCAGGGAGATAAGA-C-TGG
1 TT--TT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTTGG
* *** * * * *
46264470 ATGCGATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-TGG
* * * *
46264514 TTTTAATCCGGTCCACTACAACTTCAGGGAGATAGGA--TTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTTGG
* *
46264555 -TTTATTCTGTCTTCTCTAATGCAACTTCAGGGAGATAAGA-C-TGG
1 TTTTAATCTG-C-TC-C-ACTGCAACTTCAGGGAGATAAGATCTTGG
* *** * * *
46264599 ATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-TGG
* * *
46264643 TTTTAATCCGCTCCACTGCAACTTCAGCGAGATAGGA--TTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTTGG
* * * * *
46264684 TTTCTTCTATCTGCTCCACTACAAGTTTAGAGAGATAAGA-CTT-G
1 -TT-TT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTTGG
*
46264728 TATCTTCAATCTGCCCCACTGCAACTTCAAGGG-GATAAG
1 T-T-TT-AATCTGCTCCACTGCAACTTC-AGGGAGATAAG
46264767 GTTTGATATG
Statistics
Matches: 258, Mismatches: 61, Indels: 41
0.72 0.17 0.11
Matches are distributed among these distances:
40 7 0.03
41 57 0.22
42 8 0.03
43 8 0.03
44 169 0.66
45 9 0.03
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTTGG
Found at i:46265008 original size:45 final size:45
Alignment explanation
Indices: 46264783--46265007 Score: 333
Period size: 45 Copynumber: 5.0 Consensus size: 45
46264773 TATGATATTT
* * * *
46264783 GATCTACTTCGCTGCCAATACAGGAAAACAAGACCTACTAGCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
46264828 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * *
46264873 GATCTGCTTCACTACCAATACAAGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
*
46264918 GATCTGCTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * *
46264963 AATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
46265008 ACTGATTTGT
Statistics
Matches: 164, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 164 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (45 bp):
GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
Found at i:46276815 original size:106 final size:106
Alignment explanation
Indices: 46276653--46277056 Score: 528
Period size: 108 Copynumber: 3.8 Consensus size: 106
46276643 GAGATTTATG
* * * * * *
46276653 AGGATATTTAGCTATTTGGTTAAACAAGAAATCGAAACTCAGCACATTATGGCACG-TTCCTCGA
1 AGGATATTTAGCTATTTGGTCAAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAA
* *
46276717 ATTTCCAAACGCAAAATATAGTCTTACTTTCAAATTTTAAA
66 ATTTCCAAACGCAAAATATAGCCTTACTTTGAAATTTTAAA
* * *
46276758 AGGTTATTTGGCTATTTGGTCAAACGAAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCTCA
1 AGGATATTTAGCTATTTGGTCAAAC-AAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCA
* *
46276823 AATTTCCAAACACAAAATATTA-CCTTACTTTGAAAATTTAAA
65 AATTTCCAAACGCAAAATA-TAGCCTTACTTTGAAATTTTAAA
*
46276865 AGGATATTTAGCTATTTGGTCGAATGA-AAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCT
1 AGGATATTTAGCTATTTGGTC-AA--ACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCT
* * * *
46276929 CAAATTTCCAAACGCAAAACATTGCCTTACTTTGGAATTTTAAT
63 CAAATTTCCAAACGCAAAATATAGCCTTACTTTGAAATTTTAAA
* * * *
46276973 AGGATATTTTGCTATTTGGACGAAA-AAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCA
1 AGGATATTTAGCTATTTGGTC-AAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCA
46277037 AATTTCCAAACGCAAAATAT
65 AATTTCCAAACGCAAAATAT
46277057 TGACTTCGTT
Statistics
Matches: 265, Mismatches: 27, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
105 22 0.08
106 83 0.31
107 60 0.23
108 99 0.37
110 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (106 bp):
AGGATATTTAGCTATTTGGTCAAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAA
ATTTCCAAACGCAAAATATAGCCTTACTTTGAAATTTTAAA
Found at i:46277023 original size:214 final size:211
Alignment explanation
Indices: 46276653--46277075 Score: 566
Period size: 214 Copynumber: 2.0 Consensus size: 211
46276643 GAGATTTATG
* * * * *
46276653 AGGATATTTAGCTATTTGGTTAAACAAGAAATCGAAACTCAGCACATTATGGCACGTTCCTCGAA
1 AGGATATTTAGCTATTTGGTGAAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTCCTCAAA
* * * *
46276718 TTTCCAAACGCAAAATATAGTCTTACTTTCAAATTTTAAAAGGTTATTTGGCTATTTGGTCAAAC
66 TTTCCAAACGCAAAACATAGCCTTACTTTCAAATTTTAAAAGGATATTTGGCTATTTGGACAAAC
* * *
46276783 GAAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCTCAAATTTCCAAACACAAAATATT-ACC
131 -AAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCAAATTTCCAAACACAAAATATTGA-C
46276847 TTAC-TTTGAAAATTTAAA
194 TT-CGTTTGAAAATTTAAA
* *
46276865 AGGATATTTAGCTATTTGGTCGAATGA-AAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCT
1 AGGATATTTAGCTATTTGGT-GAA--ACAAAAAATCGAAACCCAGCACATTAGGGCACG-TTCCT
* ** * *
46276929 CAAATTTCCAAACGCAAAACATTGCCTTACTTTGGAATTTTAATAGGATATTTTGCTATTTGGAC
62 CAAATTTCCAAACGCAAAACATAGCCTTACTTTCAAATTTTAAAAGGATATTTGGCTATTTGGAC
*
46276994 GAAA-AAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCAAATTTCCAAACGCAAAATATT
127 -AAACAAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCAAATTTCCAAACACAAAATATT
46277058 GACTTCGTTTGAAAATTT
191 GACTTCGTTTGAAAATTT
46277076 TTCCTTTTTG
Statistics
Matches: 184, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
212 20 0.11
213 3 0.02
214 97 0.53
215 61 0.33
216 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (211 bp):
AGGATATTTAGCTATTTGGTGAAACAAAAAATCGAAACCCAGCACATTAGGGCACGTTCCTCAAA
TTTCCAAACGCAAAACATAGCCTTACTTTCAAATTTTAAAAGGATATTTGGCTATTTGGACAAAC
AAAAAATCGAAACCCAACACATTAGGGCACATTTTCTCAAATTTCCAAACACAAAATATTGACTT
CGTTTGAAAATTTAAA
Found at i:46277122 original size:21 final size:20
Alignment explanation
Indices: 46277098--46277142 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
46277088 GCATGGTGTT
46277098 AATATGCATAAT-GGAATAATA
1 AATATG-ATAATAGGAATAA-A
*
46277119 AATATGATAATATGAATAAA
1 AATATGATAATAGGAATAAA
46277139 AATA
1 AATA
46277143 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (20 bp):
AATATGATAATAGGAATAAA
Found at i:46277278 original size:19 final size:19
Alignment explanation
Indices: 46277251--46277291 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
46277241 ATGAATAAAT
46277251 AAATAAATGA-ACATAAAGTA
1 AAATAAATGACA-ATAAAG-A
46277271 AAAT-AATGACAATAAAGA
1 AAATAAATGACAATAAAGA
46277289 AAA
1 AAA
46277292 CAGATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (19 bp):
AAATAAATGACAATAAAGA
Found at i:46277721 original size:3 final size:3
Alignment explanation
Indices: 46277688--46277827 Score: 59
Period size: 3 Copynumber: 47.0 Consensus size: 3
46277678 AAATGGAAAT
* * * * * *
46277688 ATA ATG ATA ATTA ACA ATA ATA TTA ACA ATA ATA CTA CTA ATA ATA
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* ** * * * * * *
46277734 GTA AGG ATA ATA ATA ATG ATA ATA TTA ATA ATA CTT CTA ATA ATA ATC
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * ** * *
46277782 GT- ATA ATA A-A CTA ATT AGC TTA ATA ATA ATA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46277828 GGACTAAATA
Statistics
Matches: 96, Mismatches: 38, Indels: 6
0.69 0.27 0.04
Matches are distributed among these distances:
2 2 0.02
3 91 0.95
4 3 0.03
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:46281329 original size:49 final size:50
Alignment explanation
Indices: 46281275--46281373 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
46281265 GCTGATAACG
* *
46281275 TATTATAAAATAAA-AAGAGATGGA-AGAATAAAGAACTAAGAAAATATGA
1 TATTATAAAATAAAGAA-AGATGGAGAGAATAAAAAACAAAGAAAATATGA
46281324 TATTATAAAATAAAGAAAGATGGAGAGAATAAAAAACAAAGAAAATATGA
1 TATTATAAAATAAAGAAAGATGGAGAGAATAAAAAACAAAGAAAATATGA
46281374 AAGCAATAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
49 21 0.46
50 25 0.54
ACGTcount: A:0.63, C:0.02, G:0.16, T:0.19
Consensus pattern (50 bp):
TATTATAAAATAAAGAAAGATGGAGAGAATAAAAAACAAAGAAAATATGA
Found at i:46282979 original size:22 final size:22
Alignment explanation
Indices: 46282919--46282976 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
46282909 AGTCTTCAAG
46282919 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
46282938 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
46282960 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
46282977 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:46285659 original size:19 final size:19
Alignment explanation
Indices: 46285635--46285679 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
46285625 TCTTTCTTTT
*
46285635 TGCATT-CATTCCATGCATC
1 TGCATTACATTCCAT-CATA
*
46285654 TGCATTACATTGCATCATA
1 TGCATTACATTCCATCATA
46285673 TGCATTA
1 TGCATTA
46285680 GACTTTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (19 bp):
TGCATTACATTCCATCATA
Found at i:46294011 original size:45 final size:45
Alignment explanation
Indices: 46293952--46294151 Score: 231
Period size: 45 Copynumber: 4.4 Consensus size: 45
46293942 AGATCTTGTA
* * *
46293952 TATTGGCAGTGAAGTAGATCAAAGATAGTAAATCCTGTCTTCCTG
1 TATTGGCAGCGAAGTAGATCAAAGATAGCAAATCTTGTCTTCCTG
* *
46293997 TATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTG
1 TATTGGCAGCGAAGTAGATCAAAGATAGCAAATCTTGTCTTCCTG
* * * * ** *
46294042 TATTGGCAACAAAGTAGATCGAAGTTAGCGGATCTTGTCTTCCTA
1 TATTGGCAGCGAAGTAGATCAAAGATAGCAAATCTTGTCTTCCTG
** *
46294087 TATTAACAGCGAAGTAGATCAAAGATAGTAGAA-CTTGTCTTCCTG
1 TATTGGCAGCGAAGTAGATCAAAGATAGCA-AATCTTGTCTTCCTG
* *
46294132 TACTGGCAGCAAAGTAGATC
1 TATTGGCAGCGAAGTAGATC
46294152 GATGTCACCA
Statistics
Matches: 130, Mismatches: 24, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
45 129 0.99
46 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (45 bp):
TATTGGCAGCGAAGTAGATCAAAGATAGCAAATCTTGTCTTCCTG
Found at i:46294083 original size:90 final size:90
Alignment explanation
Indices: 46293987--46294153 Score: 262
Period size: 90 Copynumber: 1.9 Consensus size: 90
46293977 TAGTAAATCC
* ** * * *
46293987 TGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAAC
1 TGTCTTCCTATATTAACAGCGAAGTAGATCAAAGATAGCAGAACTTGTCTTCCTGTACTGGCAAC
46294052 AAAGTAGATCGAAGTTAGCGGATCT
66 AAAGTAGATCGAAGTTAGCGGATCT
* *
46294077 TGTCTTCCTATATTAACAGCGAAGTAGATCAAAGATAGTAGAACTTGTCTTCCTGTACTGGCAGC
1 TGTCTTCCTATATTAACAGCGAAGTAGATCAAAGATAGCAGAACTTGTCTTCCTGTACTGGCAAC
46294142 AAAGTAGATCGA
66 AAAGTAGATCGA
46294154 TGTCACCAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 69 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (90 bp):
TGTCTTCCTATATTAACAGCGAAGTAGATCAAAGATAGCAGAACTTGTCTTCCTGTACTGGCAAC
AAAGTAGATCGAAGTTAGCGGATCT
Found at i:46298888 original size:73 final size:71
Alignment explanation
Indices: 46298769--46298924 Score: 204
Period size: 73 Copynumber: 2.2 Consensus size: 71
46298759 GATGTTTTCC
* ** * *
46298769 AGAAAGCGCCGCAAAAACCTAAGCCCAATTACGCCGTTTTCAGAGCTTTCAGAGATTTAGCGGCG
1 AGAAAGCGCCACAAAAACCTAAGCCCAACGACGCCGTTTTCAGAGCTTTCAGAGATTTAGAGGCA
46298834 TTTTTA
66 TTTTTA
* * * *
46298840 AGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCTTTCGGGGATTTAGAGG
1 AGAAAGCGCCAC--AAAAACCTAAGCCCAACGACGCCGTTTTCAGAGCTTTCAGAGATTTAGAGG
46298905 CATTTTTA
64 CATTTTTA
*
46298913 AGAGAGCGCCAC
1 AGAAAGCGCCAC
46298925 TAATGCTCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
71 11 0.15
73 62 0.85
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (71 bp):
AGAAAGCGCCACAAAAACCTAAGCCCAACGACGCCGTTTTCAGAGCTTTCAGAGATTTAGAGGCA
TTTTTA
Found at i:46299136 original size:192 final size:186
Alignment explanation
Indices: 46298769--46299227 Score: 611
Period size: 192 Copynumber: 2.4 Consensus size: 186
46298759 GATGTTTTCC
** *
46298769 AGAAAGCGCCGC--AAAAACCTAAGCCCAATTACGCCGTTTTCAGAGCTTTCAGAGATTTAGCGG
1 AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAGAGATTTAGCGG
* *
46298832 CGTTTTTAAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCTGTTTTCTGAGCTTTCGGGGA
66 CATTTTTAAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCAGTTTTCTGAGCTTTCGGGGA
*
46298897 TTTAGAGGCATTTTTAAGAGAGCGCCACTAATGCTCAAGGCTTTAGCGGCGTTTTT
131 TTTAGAGGCATTTTTAAGAAAGCGCCACTAATGCTCAAGGCTTTAGCGGCGTTTTT
* * *
46298953 GAGAAAGCGCCGCAAAAAAACCTAGGCCCAACGACGCCGTTTTCTGAGCTATGCTCAGGGCTTTT
1 -AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT-T--TCAGAG--ATT
* * *
46299018 TAGCGGCATTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCGACGACGCAGTTTTCTGAGCTTT
60 TAGCGGCATTTTTAAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCAGTTTTCTGAGCTTT
* * * *
46299083 -GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTTAGCGGCGTTTTT
125 CGGGGATTTAGAGGCATTTTTAAGAAAGCGCCACTAATGCTCAAGGC-TTTAGCGGCGTTTTT
* * * * * *
46299145 ATGAAAGCGCCGCAAAAAAACCTAAGCCCGACGATGCCATTTTTTGAGCTTT-GGGGATTTAGCG
1 A-GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAGAGATTTAGCG
*
46299209 GCGTTTTTAAGAAAGCGCC
65 GCATTTTTAAGAAAGCGCC
46299228 GCTAATGCTC
Statistics
Matches: 240, Mismatches: 25, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
185 12 0.05
186 24 0.10
187 31 0.13
188 4 0.02
189 1 0.00
190 5 0.02
191 43 0.18
192 120 0.50
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (186 bp):
AGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCAGAGATTTAGCGG
CATTTTTAAGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCAGTTTTCTGAGCTTTCGGGGA
TTTAGAGGCATTTTTAAGAAAGCGCCACTAATGCTCAAGGCTTTAGCGGCGTTTTT
Found at i:46299204 original size:114 final size:115
Alignment explanation
Indices: 46299003--46299469 Score: 658
Period size: 114 Copynumber: 4.1 Consensus size: 115
46298993 TTTCTGAGCT
* *
46299003 ATGCTCAGGGCTTTTTAGCGGCATTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCGACGACG-
1 ATGCTCAGGGCTTTTTAGCGACATTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGC
46299067 CAGTTTTCTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
66 CA-TTTTCTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
* * * *
46299118 ATGCTCAGGGC-TTTTAGCGGCGTTTTT-ATGAAAGCGCCGCAAAAAAACCTAAGCCCGACGATG
1 ATGCTCAGGGCTTTTTAGCGACATTTTTGA-GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACG
*
46299181 CCATTTTTTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
65 CCATTTTCTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
* * *
46299232 ATGCTCAGGGC-TTTTAGCGACGTTTTTGTGAAAGCGCCGC-AAAAAACCTTAAGTCCAACGACG
1 ATGCTCAGGGCTTTTTAGCGACATTTTTGAGAAAGCGCCGCAAAAAAACC-TAAGCCCAACGACG
* * ** * *
46299295 CCGTTTTCTGAGCTTTGGTGATTTAGCCACGTTTTTAAGAAAACGCCTCTA
65 CCATTTTCTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
*
46299346 ATGCTCAAGGCTTTTTAGCGACATTTTTGAGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACG
1 ATGCTCAGGGCTTTTTAGCGACATTTTTGAGAAAGCGCCGC-AAAAAAACCTAAGCCCAACGACG
* * *
46299411 CCGGTTTT-TGAGCTTTTGGGGATTTAGCGGTGTTTTTATGAAAGCGCCGCTA
65 CC-ATTTTCTGAGC-TTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
46299463 ATGCTCA
1 ATGCTCA
46299470 AATAGTTATA
Statistics
Matches: 317, Mismatches: 26, Indels: 16
0.88 0.07 0.04
Matches are distributed among these distances:
113 9 0.03
114 197 0.62
115 40 0.13
116 20 0.06
117 51 0.16
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (115 bp):
ATGCTCAGGGCTTTTTAGCGACATTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGC
CATTTTCTGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTA
Found at i:46299698 original size:7 final size:7
Alignment explanation
Indices: 46299686--46299923 Score: 94
Period size: 7 Copynumber: 33.4 Consensus size: 7
46299676 GGTTAGGAGC
46299686 TTAGGGT
1 TTAGGGT
*
46299693 TTAGGGG
1 TTAGGGT
*
46299700 TTATGGGC
1 TTA-GGGT
46299708 TTAGGGT
1 TTAGGGT
*
46299715 CTATGGG-
1 TTA-GGGT
*
46299722 TTAGTGGC
1 TTAG-GGT
*
46299730 TTATGGT
1 TTAGGGT
46299737 TTAGGGT
1 TTAGGGT
*
46299744 TTA--AT
1 TTAGGGT
* *
46299749 TAAGAGT
1 TTAGGGT
* *
46299756 TTATGAT
1 TTAGGGT
46299763 TTAGGGGT
1 TTA-GGGT
46299771 TTAGGGGT
1 TTA-GGGT
46299779 TTAGGGGT
1 TTA-GGGT
* *
46299787 TTATGCT
1 TTAGGGT
46299794 TTAGAGGT
1 TTAG-GGT
* *
46299802 TTAAGTT
1 TTAGGGT
*
46299809 TTAAGGT
1 TTAGGGT
46299816 TTAGGGT
1 TTAGGGT
*
46299823 TTATGGT
1 TTAGGGT
46299830 TTAGGGT
1 TTAGGGT
46299837 TTAGGGGT
1 TTA-GGGT
46299845 TTA-GG-
1 TTAGGGT
* *
46299850 TTATCGGC
1 TTA-GGGT
46299858 TTAGGGT
1 TTAGGGT
*
46299865 CTAAGGG-
1 -TTAGGGT
*
46299872 TTATTGGT
1 TTA-GGGT
* *
46299880 TTACGAT
1 TTAGGGT
*
46299887 TTAGTGT
1 TTAGGGT
*
46299894 TTATGGT
1 TTAGGGT
46299901 TTAGGGT
1 TTAGGGT
*
46299908 GTA-GGT
1 TTAGGGT
*
46299914 TTATGGT
1 TTAGGGT
46299921 TTA
1 TTA
46299924 AAGTATACAG
Statistics
Matches: 173, Mismatches: 42, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
5 6 0.03
6 10 0.06
7 101 0.58
8 56 0.32
ACGTcount: A:0.18, C:0.03, G:0.35, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:46299701 original size:22 final size:21
Alignment explanation
Indices: 46299676--46299742 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 21
46299666 AGTGTGTAAA
46299676 GGTTAGGAGCTTAGGGTTTAGG
1 GGTTAGG-GCTTAGGGTTTAGG
* *
46299698 GGTTATGGGCTTAGGGTCTATG
1 GGTTA-GGGCTTAGGGTTTAGG
*
46299720 GGTTAGTGGCTTATGGTTTAGG
1 GGTTAG-GGCTTAGGGTTTAGG
46299742 G
1 G
46299743 TTTAATTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.92
23 2 0.05
ACGTcount: A:0.15, C:0.06, G:0.43, T:0.36
Consensus pattern (21 bp):
GGTTAGGGCTTAGGGTTTAGG
Found at i:46299802 original size:15 final size:15
Alignment explanation
Indices: 46299730--46299818 Score: 53
Period size: 15 Copynumber: 6.2 Consensus size: 15
46299720 GGTTAGTGGC
*
46299730 TTATGGTTTAG-GGT
1 TTATGATTTAGAGGT
*
46299744 TTA--ATTAAGA-GT
1 TTATGATTTAGAGGT
*
46299756 TTATGATTTAGGGGT
1 TTATGATTTAGAGGT
* * *
46299771 TTAGGGGTTTAGGGGT
1 TTA-TGATTTAGAGGT
*
46299787 TTATGCTTTAGAGGT
1 TTATGATTTAGAGGT
* *
46299802 TTAAGTTTTA-AGGT
1 TTATGATTTAGAGGT
46299816 TTA
1 TTA
46299819 GGGTTTATGG
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
12 9 0.15
14 15 0.25
15 22 0.37
16 13 0.22
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.46
Consensus pattern (15 bp):
TTATGATTTAGAGGT
Found at i:46299903 original size:14 final size:14
Alignment explanation
Indices: 46299799--46300014 Score: 68
Period size: 14 Copynumber: 15.5 Consensus size: 14
46299789 ATGCTTTAGA
*
46299799 GGTTTAAGT-TTTAA
1 GGTTT-AGTGTTTAT
*
46299813 GGTTTAGGGTTTAT
1 GGTTTAGTGTTTAT
* *
46299827 GGTTTAGGGTTTAGG
1 GGTTTAGTGTTTA-T
46299842 GGTTTAG-G-TTAT
1 GGTTTAGTGTTTAT
* * * *
46299854 CGGCTTAGGGTCTAA
1 -GGTTTAGTGTTTAT
* * *
46299869 GGGTTATTGGTTTAC
1 GGTTTAGT-GTTTAT
*
46299884 GATTTAGTGTTTAT
1 GGTTTAGTGTTTAT
* *
46299898 GGTTTAGGGTGTA-
1 GGTTTAGTGTTTAT
*
46299911 GGTTTA-TGGTTTAA
1 GGTTTAGT-GTTTAT
* * **
46299925 AGTATACAGTTTAT
1 GGTTTAGTGTTTAT
*
46299939 GATTTAGTGTTTAT
1 GGTTTAGTGTTTAT
* *
46299953 GGTTTAGCGTGTA-
1 GGTTTAGTGTTTAT
* * *
46299966 GGCTGT-GGGTTTGT
1 GG-TTTAGTGTTTAT
*
46299980 GGTTTAGTTTTTAT
1 GGTTTAGTGTTTAT
* * *
46299994 TGTTTATTGTTTAG
1 GGTTTAGTGTTTAT
46300008 GGTTTAG
1 GGTTTAG
46300015 CTAGTAGCTT
Statistics
Matches: 143, Mismatches: 47, Indels: 24
0.67 0.22 0.11
Matches are distributed among these distances:
13 29 0.20
14 96 0.67
15 18 0.13
ACGTcount: A:0.18, C:0.03, G:0.31, T:0.48
Consensus pattern (14 bp):
GGTTTAGTGTTTAT
Found at i:46300080 original size:103 final size:102
Alignment explanation
Indices: 46300002--46300209 Score: 335
Period size: 103 Copynumber: 2.0 Consensus size: 102
46299992 ATTGTTTATT
* * *
46300002 GTTTAGGGTTTAGCTAGTAGCTTAGAGTTTAGGGATTAATATGGGCATAGGGTATATGGGTTAAG
1 GTTTAGGGTTTAGCTAATAGCTTAGAGTTTAGGGATTAATACGGGAATAGGGTATATGGGTTAAG
*
46300067 AGGGCATATGGTTTAGGGTTTAAATTTTATATTTTAGG
66 AGAGCATATGGTTT-GGGTTTAAATTTTATATTTTAGG
* *
46300105 GTTTAGGGTTTAGGTAATAGCTTAGAGTTTTGGGATTAATACGGGAATAGGGTATATGGGTTAAG
1 GTTTAGGGTTTAGCTAATAGCTTAGAGTTTAGGGATTAATACGGGAATAGGGTATATGGGTTAAG
* *
46300170 AGAGCATATGGTTAGGGTTTAAAATTTATATTTTAGG
66 AGAGCATATGGTTTGGGTTTAAATTTTATATTTTAGG
46300207 GTT
1 GTT
46300210 AGGATTATGG
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
102 25 0.26
103 72 0.74
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.38
Consensus pattern (102 bp):
GTTTAGGGTTTAGCTAATAGCTTAGAGTTTAGGGATTAATACGGGAATAGGGTATATGGGTTAAG
AGAGCATATGGTTTGGGTTTAAATTTTATATTTTAGG
Found at i:46300089 original size:24 final size:24
Alignment explanation
Indices: 46300028--46300086 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
46300018 GTAGCTTAGA
*
46300028 GTTTAGGGATTAATATGGGCATAGG
1 GTTTAGGG-TTAAGATGGGCATAGG
* *
46300053 GTATATGGGTTAAGA-GGGCATATG
1 GTTTA-GGGTTAAGATGGGCATAGG
46300077 GTTTAGGGTT
1 GTTTAGGGTT
46300087 TAAATTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 5 0.17
24 12 0.41
25 9 0.31
26 3 0.10
ACGTcount: A:0.25, C:0.03, G:0.37, T:0.34
Consensus pattern (24 bp):
GTTTAGGGTTAAGATGGGCATAGG
Found at i:46302252 original size:9 final size:9
Alignment explanation
Indices: 46302238--46302519 Score: 241
Period size: 9 Copynumber: 32.3 Consensus size: 9
46302228 TAATTATGTA
46302238 TACATAACT
1 TACATAACT
46302247 TACATAACT
1 TACATAACT
* *
46302256 TAAATATCT
1 TACATAACT
* *
46302265 TAGACAACT
1 TACATAACT
*
46302274 TACATAACC
1 TACATAACT
46302283 TACATAA--
1 TACATAACT
46302290 TACATTTAACT
1 TACA--TAACT
*
46302301 TAAATAACT
1 TACATAACT
46302310 TACATAA--
1 TACATAACT
*
46302317 TACAAAACT
1 TACATAACT
46302326 TACATAACT
1 TACATAACT
* *
46302335 TAAATATCT
1 TACATAACT
*
46302344 TACACAACT
1 TACATAACT
*
46302353 TACATAACC
1 TACATAACT
46302362 TACATAA--
1 TACATAACT
46302369 TACATTTAACT
1 TACA--TAACT
46302380 TACATAACT
1 TACATAACT
46302389 TACATAACT
1 TACATAACT
46302398 TAC--AACT
1 TACATAACT
*
46302405 TACATAACA
1 TACATAACT
*
46302414 TACATTACT
1 TACATAACT
**
46302423 TTGATAACT
1 TACATAACT
46302432 TACATAACT
1 TACATAACT
46302441 TACATAA--
1 TACATAACT
*
46302448 TACACAACT
1 TACATAACT
*
46302457 TACATAGCT
1 TACATAACT
*
46302466 TACTTAA--
1 TACATAACT
46302473 TACATAACT
1 TACATAACT
46302482 TACATAA--
1 TACATAACT
*
46302489 TACATACACA
1 TACATA-ACT
46302499 TACATAACT
1 TACATAACT
*
46302508 TACATAATT
1 TACATAACT
46302517 TAC
1 TAC
46302520 TTAATACATA
Statistics
Matches: 219, Mismatches: 35, Indels: 38
0.75 0.12 0.13
Matches are distributed among these distances:
7 39 0.18
8 1 0.00
9 166 0.76
10 6 0.03
11 7 0.03
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.33
Consensus pattern (9 bp):
TACATAACT
Found at i:46302329 original size:79 final size:79
Alignment explanation
Indices: 46302237--46302488 Score: 343
Period size: 79 Copynumber: 3.2 Consensus size: 79
46302227 TTAATTATGT
46302237 ATACATAACTTACATAACTTAAATATCTTAGACAACTTACATAACCTACATAATACATTTAACTT
1 ATACATAACTTACATAACTTAAATATCTTAGACAACTTACATAACCTACATAATACATTTAACTT
*
46302302 AAATAACTTACATA
66 ACATAACTTACATA
* *
46302316 ATACAAAACTTACATAACTTAAATATCTTACACAACTTACATAACCTACATAATACATTTAACTT
1 ATACATAACTTACATAACTTAAATATCTTAGACAACTTACATAACCTACATAATACATTTAACTT
46302381 ACATAACTTACATA
66 ACATAACTTACATA
* * * * * *
46302395 ACTTAC--AACTTACATAACATACAT-TACTTTGATAACTTACATAACTTACATAATACA--CAA
1 A--TACATAACTTACATAACTTAAATAT-CTTAGACAACTTACATAACCTACATAATACATTTAA
* *
46302455 CTTACATAGCTTACTTA
63 CTTACATAACTTACATA
46302472 ATACATAACTTACATAA
1 ATACATAACTTACATAA
46302489 TACATACACA
Statistics
Matches: 156, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
75 3 0.02
77 29 0.19
78 1 0.01
79 120 0.77
81 3 0.02
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.33
Consensus pattern (79 bp):
ATACATAACTTACATAACTTAAATATCTTAGACAACTTACATAACCTACATAATACATTTAACTT
ACATAACTTACATA
Found at i:46302330 original size:52 final size:50
Alignment explanation
Indices: 46302237--46302530 Score: 243
Period size: 52 Copynumber: 5.7 Consensus size: 50
46302227 TTAATTATGT
* * * * * *
46302237 ATACATAACTTACATAACTTAAATATCTTAGACAACTTACATAACCTACATA
1 ATACACAACTTACATAACTTACATA--ATACATAACTTACATAACTTACATA
* * * *
46302289 ATACATTTAACTTAAATAACTTACATAATACAAAACTTACATAACTTAAATA
1 ATACA--CAACTTACATAACTTACATAATACATAACTTACATAACTTACATA
* *
46302341 TCTTACACAACTTACATAACCTACATAATACATTTAACTTACATAACTTACATA
1 --ATACACAACTTACATAACTTACATAATACA--TAACTTACATAACTTACATA
* * * **
46302395 ACT-TACAACTTACATAACATACATTACTTTGATAACTTACATAACTTACATA
1 A-TACACAACTTACATAACTTACA-TA-ATACATAACTTACATAACTTACATA
* *
46302447 ATACACAACTTACATAGCTTACTTAATACATAACTTACATAA--TACATACA
1 ATACACAACTTACATAACTTACATAATACATAACTTACATAACTTACAT--A
* * *
46302497 CATACATAACTTACATAATTTACTTAATACATAA
1 -ATACACAACTTACATAACTTACATAATACATAA
46302531 ATATATATCA
Statistics
Matches: 200, Mismatches: 29, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
48 5 0.03
50 15 0.08
51 33 0.17
52 102 0.51
53 3 0.01
54 42 0.21
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (50 bp):
ATACACAACTTACATAACTTACATAATACATAACTTACATAACTTACATA
Found at i:46308048 original size:21 final size:21
Alignment explanation
Indices: 46308024--46308092 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
46308014 CTACAACTTA
*
46308024 AAGCAGAGG-TGGCAACGAGGG
1 AAGCAGAGGCT-GCAACGAGAG
*
46308045 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAACGAGAG
* * *
46308066 AAGCAAAGGCTGCAGCGCGAG
1 AAGCAGAGGCTGCAACGAGAG
46308087 AAGCAG
1 AAGCAG
46308093 CGAGAGAAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAACGAGAG
Found at i:46308597 original size:42 final size:41
Alignment explanation
Indices: 46308476--46308788 Score: 385
Period size: 42 Copynumber: 7.4 Consensus size: 41
46308466 AATTCCAAAA
* * *
46308476 TTAGTGGCGTTTTTTATAAAAGCGCCGCTAAAGAACATTA-CTT
1 TTAGCGGCGTTTTTT-T-TAAGCGCCGCTAAAGAACATGATC-T
* **
46308519 TTAGCGGCGTTTGTGATGAAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTT-T-TTTTAAGCGCCGCTAAAGAACATGATCT
*
46308562 TTAGCGGCGTTTCTATTTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTT-TTTTTAAGCGCCGCTAAAGAACATGATCT
* *
46308604 TTAGCGACGTCTTTTTTTAAGCGCCGCTAAAGAACATAATCT
1 TTAGCGGCGT-TTTTTTTAAGCGCCGCTAAAGAACATGATCT
* *
46308646 TTAGCGGCATTTTTTTCTAAGTGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTT-TAAGCGCCGCTAAAGAACATGATCT
*
46308688 TAAGCGGCGTCTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCG--TTTTTTTTAAGCGCCGCTAAAGAACATGATCT
* *
46308731 TTAGCGGTGTTTTTTATTAAGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCGTTTTTT-TTAAGCGCCGCTAAAGAACATGATCT
*
46308773 TTAGTGGCGTTTTTTT
1 TTAGCGGCGTTTTTTT
46308789 CTGTAAATGC
Statistics
Matches: 240, Mismatches: 22, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
41 13 0.05
42 138 0.57
43 79 0.33
44 9 0.04
45 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (41 bp):
TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
Found at i:46308737 original size:85 final size:84
Alignment explanation
Indices: 46308476--46308788 Score: 391
Period size: 85 Copynumber: 3.7 Consensus size: 84
46308466 AATTCCAAAA
* * * ** **
46308476 TTAGTGGCGTTTTTTATAAAAGCGCCGCTAAAGAACATTA-CTTTTAGCGGCGT-TTGTGATGAA
1 TTAGCGGCGTTTTTT-T-TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTCTT-TTTTTTA
46308539 AGCGCCGCTAAAGAACATGATCT
62 AGCGCCGCTAAAGAACATGATCT
* *
46308562 TTAGCGGCGTTTCTATTTAAGCGCCGCTAAAGAACATGATCTTTAGCGACGTC-TTTTTTTAAGC
1 TTAGCGGCGTTT-TTTTTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTTAAGC
*
46308626 GCCGCTAAAGAACATAATCT
65 GCCGCTAAAGAACATGATCT
* * *
46308646 TTAGCGGCATTTTTTTCTAAGTGCCGCTAAAGAACATGATCTTAAGCGGCGTCTTTTTTTTAAGC
1 TTAGCGGCGTTTTTTT-TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTTAAGC
46308711 GCCGCTAAAGAACATGATCT
65 GCCGCTAAAGAACATGATCT
* * *
46308731 TTAGCGGTGTTTTTTATTAAGCGCCGCTAAAGAACATGACCTTTAGTGGCGT-TTTTTT
1 TTAGCGGCGTTTTTT-TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTT
46308789 CTGTAAATGC
Statistics
Matches: 199, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
83 3 0.02
84 75 0.38
85 105 0.53
86 14 0.07
87 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (84 bp):
TTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTTAAGCG
CCGCTAAAGAACATGATCT
Done.