Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 105 of 131
Found at i:34795079 original size:1 final size:1
Alignment explanation
Indices: 34795073--34795107 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
34795063 AAGAATTTGC
**
34795073 AAAAAAAAAAATGAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
34795108 GAGGAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.00, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:34796303 original size:20 final size:21
Alignment explanation
Indices: 34796261--34796310 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
34796251 TCGGGCATGA
34796261 TATCGATACTGTTGTGAAAGG
1 TATCGATACTGTTGTGAAAGG
* *
34796282 TATCGATACT-TTGTTAAGGG
1 TATCGATACTGTTGTGAAAGG
34796302 TATCGATAC
1 TATCGATAC
34796311 ATTCGAGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (21 bp):
TATCGATACTGTTGTGAAAGG
Found at i:34802735 original size:27 final size:27
Alignment explanation
Indices: 34802697--34802751 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
34802687 TAATCCCCAG
34802697 ATATGACAAGCAGAGGAAGAAAAACTA
1 ATATGACAAGCAGAGGAAGAAAAACTA
34802724 ATATGACAAGCAGAGGAAGAAAAACTA
1 ATATGACAAGCAGAGGAAGAAAAACTA
34802751 A
1 A
34802752 CTCTAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.56, C:0.11, G:0.22, T:0.11
Consensus pattern (27 bp):
ATATGACAAGCAGAGGAAGAAAAACTA
Found at i:34811753 original size:37 final size:39
Alignment explanation
Indices: 34811663--34811759 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 39
34811653 ACACACCAAT
**
34811663 TTGGCACCTAGTGCCTCATCAGATAATTCGAAGCAGTAAA
1 TTGGCACCTAGTGCCTCATCAGATAAACCGAA-CAGTAAA
* * *
34811703 TTGACACCCAGTGCCTCATCAGTTAAACCG-A-AGTAAA
1 TTGGCACCTAGTGCCTCATCAGATAAACCGAACAGTAAA
34811740 TTGGCACCTAGTGCCTCATC
1 TTGGCACCTAGTGCCTCATC
34811760 GAATAAATCT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 24 0.48
39 1 0.02
40 25 0.50
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (39 bp):
TTGGCACCTAGTGCCTCATCAGATAAACCGAACAGTAAA
Found at i:34811799 original size:41 final size:37
Alignment explanation
Indices: 34811667--34811799 Score: 115
Period size: 37 Copynumber: 3.4 Consensus size: 37
34811657 ACCAATTTGG
* **
34811667 CACCTAGTGCCTCATCAGATAATTCGAAGCAGTAAATTGA
1 CACCCAGTGCCTCATCAGATAAACCG-A--AGTAAATTGA
* *
34811707 CACCCAGTGCCTCATCAGTTAAACCGAAGTAAATTGG
1 CACCCAGTGCCTCATCAGATAAACCGAAGTAAATTGA
* *
34811744 CACCTAGTGCCTCATC-GAATAAATCTGAAGTGATAGATTGA
1 CACCCAGTGCCTCATCAG-ATAAA-CCGAAGT-A-A-ATTGA
*
34811785 CACCCAGTGTCTCAT
1 CACCCAGTGCCTCAT
34811800 AAACTCAAAC
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
36 1 0.01
37 28 0.36
38 6 0.08
39 2 0.03
40 23 0.30
41 17 0.22
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (37 bp):
CACCCAGTGCCTCATCAGATAAACCGAAGTAAATTGA
Found at i:34812755 original size:16 final size:18
Alignment explanation
Indices: 34812712--34812756 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
34812702 CTTTTCTTTA
34812712 TTTTTCTTTCTGCTTCGT
1 TTTTTCTTTCTGCTTCGT
*
34812730 TTTGGT-TTTCT-CTTC-T
1 TTT-TTCTTTCTGCTTCGT
34812746 TTTTTCTTTCT
1 TTTTTCTTTCT
34812757 TTTTCTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 1 0.04
16 9 0.39
17 4 0.17
18 8 0.35
19 1 0.04
ACGTcount: A:0.00, C:0.20, G:0.09, T:0.71
Consensus pattern (18 bp):
TTTTTCTTTCTGCTTCGT
Found at i:34813288 original size:9 final size:9
Alignment explanation
Indices: 34813271--34813307 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
34813261 TGAGTTTTCG
34813271 AATTCGAAT
1 AATTCGAAT
*
34813280 AACTCGAAT
1 AATTCGAAT
34813289 AATTCGAAT
1 AATTCGAAT
34813298 AATTCGAAT
1 AATTCGAAT
34813307 A
1 A
34813308 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34814013 original size:5 final size:5
Alignment explanation
Indices: 34814003--34814033 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
34813993 CTCGAAAATT
34814003 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
34814034 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:34814316 original size:27 final size:25
Alignment explanation
Indices: 34814256--34814316 Score: 59
Period size: 27 Copynumber: 2.3 Consensus size: 25
34814246 AATATGATAA
* *
34814256 AATTAAAAATAAATAAAATCAAAAT
1 AATTAAAAATAAACAAAAACAAAAT
*
34814281 AATTGTAAAAATAAGCAAAAACAAAATTT
1 AA-T-TAAAAATAAACAAAAACAAAA--T
34814310 AATTAAA
1 AATTAAA
34814317 TAAACCCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 2 0.07
26 1 0.03
27 22 0.76
28 1 0.03
29 3 0.10
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (25 bp):
AATTAAAAATAAACAAAAACAAAAT
Found at i:34821678 original size:12 final size:12
Alignment explanation
Indices: 34821661--34821685 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34821651 AGTAATTTCG
34821661 GGTCGGTTAACC
1 GGTCGGTTAACC
34821673 GGTCGGTTAACC
1 GGTCGGTTAACC
34821685 G
1 G
34821686 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:34821894 original size:25 final size:26
Alignment explanation
Indices: 34821852--34821900 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
34821842 CAGTAAAATG
*
34821852 TTTTCTGAAAAATTATTTACTTTTAC
1 TTTTCTGAAAAATGATTTACTTTTAC
34821878 TTTTCTG-AAAATGATTTACTTTT
1 TTTTCTGAAAAATGATTTACTTTT
34821901 CTAGAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (26 bp):
TTTTCTGAAAAATGATTTACTTTTAC
Found at i:34822006 original size:18 final size:19
Alignment explanation
Indices: 34821979--34822028 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
34821969 AAAAAGCTGT
*
34821979 TTTTACATATATTAATAAA
1 TTTTATATATATTAATAAA
34821998 TTTATATATATATATTAATAAA
1 -TT-T-TATATATATTAATAAA
34822020 -TTTATATAT
1 TTTTATATAT
34822029 TAAACAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.26
19 1 0.04
20 3 0.11
21 1 0.04
22 15 0.56
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTATATATATTAATAAA
Found at i:34822012 original size:22 final size:22
Alignment explanation
Indices: 34821985--34822028 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
34821975 CTGTTTTTAC
34821985 ATATATTAATAAATTTATATAT
1 ATATATTAATAAATTTATATAT
34822007 ATATATTAATAAATTTATATAT
1 ATATATTAATAAATTTATATAT
34822029 TAAACAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATATTAATAAATTTATATAT
Found at i:34824724 original size:17 final size:17
Alignment explanation
Indices: 34824704--34824748 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
34824694 CAAGGATAGG
* *
34824704 GGGAGGGGAAGGGGAAA
1 GGGAAGGGAAAGGGAAA
34824721 GGGAAGGGAAAGGGAAA
1 GGGAAGGGAAAGGGAAA
34824738 GGGAAAGGGAA
1 GGG-AAGGGAA
34824749 GATCGGTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (17 bp):
GGGAAGGGAAAGGGAAA
Found at i:34824747 original size:6 final size:6
Alignment explanation
Indices: 34824709--34824748 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
34824699 ATAGGGGGAG
*
34824709 GGGAAG GGGAAA GGG-AA GGGAAA GGGAAA GGGAAA GGGAA
1 GGGAAA GGGAAA GGGAAA GGGAAA GGGAAA GGGAAA GGGAA
34824749 GATCGGTGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (6 bp):
GGGAAA
Found at i:34832695 original size:35 final size:35
Alignment explanation
Indices: 34832649--34832720 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
34832639 AACCACAATT
34832649 TTTGTTCCCAAATTAAATAATGATAATCACATTTC
1 TTTGTTCCCAAATTAAATAATGATAATCACATTTC
34832684 TTTGTTCCCAAATTAAATAATGATAATCACATTTC
1 TTTGTTCCCAAATTAAATAATGATAATCACATTTC
34832719 TT
1 TT
34832721 CTTCGAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (35 bp):
TTTGTTCCCAAATTAAATAATGATAATCACATTTC
Found at i:34834221 original size:12 final size:11
Alignment explanation
Indices: 34834190--34834223 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
34834180 AATAAAAAAA
34834190 TAAAATATATT
1 TAAAATATATT
34834201 T-AAATATATT
1 TAAAATATATT
34834211 TAAAATCATATT
1 TAAAAT-ATATT
34834223 T
1 T
34834224 TTTGTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 5 0.24
12 6 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAAATATATT
Found at i:34834760 original size:10 final size:10
Alignment explanation
Indices: 34834745--34834771 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
34834735 CAACTTAAAA
34834745 ACTTTCAGAT
1 ACTTTCAGAT
34834755 ACTTTCAGAT
1 ACTTTCAGAT
34834765 ACTTTCA
1 ACTTTCA
34834772 AAATTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (10 bp):
ACTTTCAGAT
Found at i:34843231 original size:27 final size:30
Alignment explanation
Indices: 34843201--34843256 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
34843191 ATTTTATGTT
34843201 TAGCAT-AT-ATT-AAAAATAATAAAATTA
1 TAGCATAATCATTCAAAAATAATAAAATTA
* *
34843228 TAGCTTAATCTTTCAAAAATAATAAAATT
1 TAGCATAATCATTCAAAAATAATAAAATT
34843257 TTGATTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 2 0.08
29 2 0.08
30 15 0.62
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.36
Consensus pattern (30 bp):
TAGCATAATCATTCAAAAATAATAAAATTA
Found at i:34843677 original size:18 final size:18
Alignment explanation
Indices: 34843654--34843692 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
34843644 CGAAAAATAT
34843654 TATTTTTGAATTTT-TTTA
1 TATTTTT-AATTTTCTTTA
34843672 TATTTTTAATTTTCTTTA
1 TATTTTTAATTTTCTTTA
34843690 TAT
1 TAT
34843693 ATTATTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TATTTTTAATTTTCTTTA
Found at i:34849109 original size:6 final size:6
Alignment explanation
Indices: 34849098--34849130 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
34849088 TTAATGATAT
34849098 AAAAGA AAAAG- AAAAG- AAAAGA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAG
34849131 CATAGTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:34849119 original size:16 final size:16
Alignment explanation
Indices: 34849098--34849128 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34849088 TTAATGATAT
34849098 AAAAGAAAAAGAAAAG
1 AAAAGAAAAAGAAAAG
34849114 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
34849129 AGCATAGTGT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAG
Found at i:34863653 original size:107 final size:107
Alignment explanation
Indices: 34863467--34863668 Score: 395
Period size: 107 Copynumber: 1.9 Consensus size: 107
34863457 GGCGTGTATC
34863467 AAGCCACTATCTTTAAGGTTATATTCGCCCCAACTTATCTTCAGTGTGCAAACGAGTTCCAAGCA
1 AAGCCACTATCTTTAAGGTTATATTCGCCCCAACTTATCTTCAGTGTGCAAACGAGTTCCAAGCA
34863532 AATTAACATCGAGGATACAATGAAGCCAATAAGGGCGTTTAA
66 AATTAACATCGAGGATACAATGAAGCCAATAAGGGCGTTTAA
34863574 AAGCCACTATCTTTAAGGTTATATTCGCCCCAACTTATCTTCAGTGTGCAAACGAGTTCCAAGCA
1 AAGCCACTATCTTTAAGGTTATATTCGCCCCAACTTATCTTCAGTGTGCAAACGAGTTCCAAGCA
*
34863639 AATTAACATCGAGGATTCAATGAAGCCAAT
66 AATTAACATCGAGGATACAATGAAGCCAAT
34863669 GACTATTTGC
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 94 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (107 bp):
AAGCCACTATCTTTAAGGTTATATTCGCCCCAACTTATCTTCAGTGTGCAAACGAGTTCCAAGCA
AATTAACATCGAGGATACAATGAAGCCAATAAGGGCGTTTAA
Found at i:34873875 original size:15 final size:15
Alignment explanation
Indices: 34873855--34873884 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34873845 TAAACAGACG
34873855 TGTGTTGCTCGCTCC
1 TGTGTTGCTCGCTCC
*
34873870 TGTGTTGCTTGCTCC
1 TGTGTTGCTCGCTCC
34873885 ACCATAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.30, G:0.27, T:0.43
Consensus pattern (15 bp):
TGTGTTGCTCGCTCC
Found at i:34874462 original size:90 final size:90
Alignment explanation
Indices: 34874303--34874471 Score: 234
Period size: 90 Copynumber: 1.9 Consensus size: 90
34874293 GAGTTTGTTA
** * * *
34874303 CTCTTAATGAGTTCATTGCTCAGAGTTTGGGTGGTCCTACTAAGACGGACTTGATGAATTCACCA
1 CTCTTAATGAGTTCACAGCTCAGAGTTTGGGTGGTCCTACTAAGACAGACTTGATAAACTCACCA
34874368 AATTTATAGGATGAACTACCAGAAG
66 AATTTATAGGATGAACTACCAGAAG
* *
34874393 CTCTTAATGAGTTCACAGC-CTAGAGTTTGGGTGGTCCTATTGAGACAGACTTGATAAAC-CTAC
1 CTCTTAATGAGTTCACAGCTC-AGAGTTTGGGTGGTCCTACTAAGACAGACTTGATAAACTC-AC
*
34874456 CGAATTTATAGGATGA
64 CAAATTTATAGGATGA
34874472 GCCACTAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
89 2 0.03
90 67 0.97
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (90 bp):
CTCTTAATGAGTTCACAGCTCAGAGTTTGGGTGGTCCTACTAAGACAGACTTGATAAACTCACCA
AATTTATAGGATGAACTACCAGAAG
Found at i:34885079 original size:92 final size:93
Alignment explanation
Indices: 34884910--34885158 Score: 264
Period size: 93 Copynumber: 2.7 Consensus size: 93
34884900 AAAAAAAAGT
* * *
34884910 AATTAAGCTCC-AACTTTTTTTTTTGCA-TTCAATT-GAGTACTTAAACTTTTAAAATGCATAAA
1 AATTAAGCTCCTGA-TTTTTTTTTTGCACTT-AATTAG-GTACTTGAACTTTCAAAATGCAT-AA
*
34884972 AAAAACCCTCAAAC-TTT-AAAAAAA-AAAGC
62 AAAAACCCTCAAACTTTTCAAAAAAATAAAAC
* *
34885001 AATTAAGC-CATTGCTTTTTTTTTTTTGCACTTAATTAGGTACTTGAACTTTCAAAATGCATAAA
1 AATTAAGCTC-CTG--ATTTTTTTTTTGCACTTAATTAGGTACTTGAACTTTCAAAATGCATAAA
* *
34885065 AAAAGCCTCAAACTTTTCAAAAAAATAAAAT
63 AAAACCCTCAAACTTTTCAAAAAAATAAAAC
* * * *
34885096 AATTAAGCTCCTGATTTTGTTTTT-CACTCAATTAGGTACTTGAACTGTC-AAATGCATCAAAAA
1 AATTAAGCTCCTGATTTTTTTTTTGCACTTAATTAGGTACTTGAACTTTCAAAATGCATAAAAAA
34885159 GGCTCTTTGG
Statistics
Matches: 134, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
90 1 0.01
91 21 0.16
92 38 0.28
93 50 0.37
94 10 0.07
95 13 0.10
96 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (93 bp):
AATTAAGCTCCTGATTTTTTTTTTGCACTTAATTAGGTACTTGAACTTTCAAAATGCATAAAAAA
ACCCTCAAACTTTTCAAAAAAATAAAAC
Found at i:34885300 original size:26 final size:25
Alignment explanation
Indices: 34885264--34885385 Score: 86
Period size: 26 Copynumber: 4.6 Consensus size: 25
34885254 CATGTGGCAA
34885264 AAAATTTATAAAAAATAAAATTAAAT
1 AAAA-TTATAAAAAATAAAATTAAAT
*
34885290 AAAAGTTATAAAAAATATTAAATTTTAAT
1 AAAA-TTATAAAAAATA--AAA-TTAAAT
* * *
34885319 AAAAATGTAAAATATAAAAATTAGAA-
1 AAAATTATAAAAAAT-AAAATTA-AAT
**
34885345 AAAA-TATAAAAATATAAAATTTTAT
1 AAAATTATAAAAA-ATAAAATTAAAT
*
34885370 AAAAATGATAAAAAAT
1 -AAAATTATAAAAAAT
34885386 TATAAAATGC
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
24 1 0.01
25 12 0.16
26 30 0.39
27 12 0.16
28 11 0.14
29 10 0.13
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.30
Consensus pattern (25 bp):
AAAATTATAAAAAATAAAATTAAAT
Found at i:34885338 original size:8 final size:8
Alignment explanation
Indices: 34885317--34885383 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
34885307 TTAAATTTTA
34885317 ATAAAAAT
1 ATAAAAAT
*
34885325 GT-AAAAT
1 ATAAAAAT
34885332 ATAAAAATT
1 ATAAAAA-T
*
34885341 AGAAAAAAT
1 A-TAAAAAT
34885350 ATAAAAAT
1 ATAAAAAT
*
34885358 ATAAAATTTT
1 ATAAAA--AT
34885368 ATAAAAAT
1 ATAAAAAT
34885376 GATAAAAA
1 -ATAAAAA
34885384 ATTATAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
7 6 0.13
8 18 0.38
9 11 0.23
10 12 0.26
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (8 bp):
ATAAAAAT
Found at i:34885399 original size:19 final size:19
Alignment explanation
Indices: 34885327--34885403 Score: 81
Period size: 18 Copynumber: 4.2 Consensus size: 19
34885317 ATAAAAATGT
* *
34885327 AAAA-TATAAAAATTAGAA
1 AAAATTATAAAAATGATAA
34885345 AAAA-TATAAAAAT-ATAA
1 AAAATTATAAAAATGATAA
**
34885362 AATTTTATAAAAATGATAA
1 AAAATTATAAAAATGATAA
34885381 AAAATTAT-AAAATGCATAA
1 AAAATTATAAAAATG-ATAA
34885400 AAAA
1 AAAA
34885404 ATGTCATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.10
18 28 0.55
19 18 0.35
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAATTATAAAAATGATAA
Found at i:34885402 original size:10 final size:9
Alignment explanation
Indices: 34885317--34885402 Score: 51
Period size: 10 Copynumber: 9.8 Consensus size: 9
34885307 TTAAATTTTA
34885317 ATAAAAATG
1 ATAAAAATG
34885326 -T-AAAAT-
1 ATAAAAATG
34885332 ATAAAAATTAG
1 ATAAAAA-T-G
34885343 A-AAAAAT-
1 ATAAAAATG
34885350 ATAAAAAT-
1 ATAAAAATG
* *
34885358 ATAAAATTTT
1 ATAAAA-ATG
34885368 ATAAAAATG
1 ATAAAAATG
*
34885377 ATAAAAAATT
1 AT-AAAAATG
34885387 AT-AAAATG
1 ATAAAAATG
34885395 CATAAAAA
1 -ATAAAAA
34885403 AATGTCATTT
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
7 7 0.11
8 22 0.36
9 8 0.13
10 23 0.38
11 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (9 bp):
ATAAAAATG
Found at i:34885605 original size:19 final size:19
Alignment explanation
Indices: 34885581--34885651 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
34885571 TACGATAATG
34885581 TTTATAATTTTTTACGAAT
1 TTTATAATTTTTTACGAAT
*
34885600 TTTAT-ATTTCTTTAC-ATTT
1 TTTATAATTT-TTTACGA-AT
* *
34885619 TTTATAATTTTCTTATG-AC
1 TTTATAATTTT-TTACGAAT
*
34885638 TTTATAATATTTTA
1 TTTATAATTTTTTA
34885652 AAAATTTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
18 8 0.19
19 27 0.64
20 7 0.17
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTATAATTTTTTACGAAT
Found at i:34886330 original size:12 final size:13
Alignment explanation
Indices: 34886313--34886355 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
34886303 TTTAATAAAT
*
34886313 TAAAAATAAATTC
1 TAAAACTAAATTC
*
34886326 TAAAACTAAA-AC
1 TAAAACTAAATTC
*
34886338 TAAAACTAAAGTC
1 TAAAACTAAATTC
34886351 TAAAA
1 TAAAA
34886356 ATAATTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.23
Consensus pattern (13 bp):
TAAAACTAAATTC
Found at i:34886399 original size:9 final size:9
Alignment explanation
Indices: 34886379--34886445 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
34886369 GTAGTGATTC
*
34886379 AATTTGGTT
1 AATTCGGTT
*
34886388 AATTCGGGT
1 AATTCGGTT
**
34886397 AATTTTGTT
1 AATTCGGTT
34886406 AATTCGGTT
1 AATTCGGTT
*
34886415 AATTCGGGT
1 AATTCGGTT
*
34886424 AATTAGGTT
1 AATTCGGTT
34886433 AATTCGGTT
1 AATTCGGTT
34886442 AATT
1 AATT
34886446 TTTAACCAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.46
Consensus pattern (9 bp):
AATTCGGTT
Found at i:34886414 original size:27 final size:27
Alignment explanation
Indices: 34886379--34886445 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
34886369 GTAGTGATTC
* **
34886379 AATTTGGTTAATTCGGGTAATTTTGTT
1 AATTCGGTTAATTCGGGTAATTAGGTT
34886406 AATTCGGTTAATTCGGGTAATTAGGTT
1 AATTCGGTTAATTCGGGTAATTAGGTT
34886433 AATTCGGTTAATT
1 AATTCGGTTAATT
34886446 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.46
Consensus pattern (27 bp):
AATTCGGTTAATTCGGGTAATTAGGTT
Found at i:34886861 original size:1 final size:1
Alignment explanation
Indices: 34886855--34886896 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
34886845 AGCAGCCTCT
* * *
34886855 CCCCCCCCCCCACCCCCCCCCCCCCCCTCCCCCCTCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
34886897 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.02, C:0.93, G:0.00, T:0.05
Consensus pattern (1 bp):
C
Found at i:34886876 original size:16 final size:16
Alignment explanation
Indices: 34886855--34886896 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
34886845 AGCAGCCTCT
34886855 CCCCCCCCCCCACCCC
1 CCCCCCCCCCCACCCC
*
34886871 CCCCCCCCCCCTCCCC
1 CCCCCCCCCCCACCCC
34886887 CCTCCCCCCC
1 CC-CCCCCCC
34886897 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.02, C:0.93, G:0.00, T:0.05
Consensus pattern (16 bp):
CCCCCCCCCCCACCCC
Found at i:34887047 original size:27 final size:27
Alignment explanation
Indices: 34886989--34887067 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
34886979 ACCAGCCGCT
* * *
34886989 TCTTCCTCTGAAGAAGATGAAGAGGTG
1 TCTTCATCTGAGGAAGAAGAAGAGGTG
* *
34887016 ACTTCTTCTGAGGAAGAAGAAGAAGG-G
1 TCTTCATCTGAGGAAGAAGAAG-AGGTG
* *
34887043 TCTTCAACTGAGGAAGAAGATGAGG
1 TCTTCATCTGAGGAAGAAGAAGAGG
34887068 AAGACCCCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 3 0.07
27 37 0.86
28 3 0.07
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.22
Consensus pattern (27 bp):
TCTTCATCTGAGGAAGAAGAAGAGGTG
Found at i:34890261 original size:22 final size:22
Alignment explanation
Indices: 34890209--34890261 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
34890199 TGCTGTTGTT
* * *
34890209 TTACTTTTTTGCTATTGTTTTG
1 TTACTATTTCGCTATTGTATTG
34890231 TTA-TCATTTCGCTATTGTATTG
1 TTACT-ATTTCGCTATTGTATTG
34890253 TTACTATTT
1 TTACTATTT
34890262 TGTTGTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 24 0.92
23 1 0.04
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.62
Consensus pattern (22 bp):
TTACTATTTCGCTATTGTATTG
Found at i:34891445 original size:2 final size:2
Alignment explanation
Indices: 34891438--34891462 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34891428 CATTTGTGTT
34891438 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
34891463 CGATAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34894477 original size:18 final size:18
Alignment explanation
Indices: 34894435--34894479 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
34894425 ACACTTACGA
*
34894435 TAAAAGTAAAAATTTATG
1 TAAAATTAAAAATTTATG
*
34894453 T-ATATTAAAAATTTATG
1 TAAAATTAAAAATTTATG
34894470 TAAAATTAAA
1 TAAAATTAAA
34894480 CATGAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (18 bp):
TAAAATTAAAAATTTATG
Found at i:34901002 original size:56 final size:56
Alignment explanation
Indices: 34900916--34901027 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
34900906 TGATGTAATG
* *
34900916 TTTGAATTGACATATGATAATGGAATGGGGAGAGTGGAGTGGAGAATGGGTAAAAT
1 TTTGAATTGACACACGATAATGGAATGGGGAGAGTGGAGTGGAGAATGGGTAAAAT
34900972 TTTGAATTGACACACGATAATGGAATGGGGAGAGTGGAGTGGAGAATGGGTAAAAT
1 TTTGAATTGACACACGATAATGGAATGGGGAGAGTGGAGTGGAGAATGGGTAAAAT
34901028 GAAATTTATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.36, C:0.04, G:0.36, T:0.25
Consensus pattern (56 bp):
TTTGAATTGACACACGATAATGGAATGGGGAGAGTGGAGTGGAGAATGGGTAAAAT
Found at i:34902706 original size:36 final size:36
Alignment explanation
Indices: 34902659--34902730 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
34902649 TGAGCGGTCC
*
34902659 GTTTAACTGTGTTTAGTGTAAAATAATATTAAATTT
1 GTTTAACTGTGTTTAGTATAAAATAATATTAAATTT
34902695 GTTTAACTGTGTTTAGTATAAAATAATATTAAATTT
1 GTTTAACTGTGTTTAGTATAAAATAATATTAAATTT
34902731 TATAGCGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (36 bp):
GTTTAACTGTGTTTAGTATAAAATAATATTAAATTT
Found at i:34903467 original size:19 final size:19
Alignment explanation
Indices: 34903445--34903483 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
34903435 TATAAAAAAT
34903445 AAAAATCAATAAAATTTTA
1 AAAAATCAATAAAATTTTA
** *
34903464 AAAAATTTATTAAATTTTA
1 AAAAATCAATAAAATTTTA
34903483 A
1 A
34903484 TATAAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATCAATAAAATTTTA
Found at i:34903507 original size:18 final size:18
Alignment explanation
Indices: 34903484--34903518 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34903474 TAAATTTTAA
34903484 TATAAAATATT-TAAAAAT
1 TATAAAA-ATTGTAAAAAT
34903502 TATAAAAATTGTAAAAA
1 TATAAAAATTGTAAAAA
34903519 AAAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TATAAAAATTGTAAAAAT
Found at i:34912124 original size:108 final size:107
Alignment explanation
Indices: 34911977--34912170 Score: 273
Period size: 109 Copynumber: 1.8 Consensus size: 107
34911967 ATATTTGGCA
*
34911977 ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTTCCAAACGCA
1 ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTTCCTCGAATTTCCAAAAGCA
* *
34912041 AAACATTGCCTTATTTTGAAATTTTTGAAAAGATATTTAACT
66 AAACATTGCCTCATTTAGAAATTTTTGAAAAGATATTTAACT
* * * * *
34912083 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACTTTAGGGCATGTTTTCTCGAATTTCCAAAAG
1 ATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACGTTTCCTCGAATTTCCAAAAG
* *
34912148 CTAAATATTGCCTCATTTAGAAA
64 CAAAACATTGCCTCATTTAGAAA
34912171 AATTTTCTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
106 14 0.19
108 25 0.33
109 36 0.48
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (107 bp):
ATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTTCCTCGAATTTCCAAAAGCA
AAACATTGCCTCATTTAGAAATTTTTGAAAAGATATTTAACT
Found at i:34912316 original size:4 final size:4
Alignment explanation
Indices: 34912307--34912394 Score: 65
Period size: 4 Copynumber: 21.8 Consensus size: 4
34912297 ATACAACAAC
* * ** * *
34912307 AAAT AAAT AAAT AAAT AAACT AAA- ACAT AAAA AAAT GGAC ATAT AAAT
1 AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT
34912355 AAAT AAAT AAAT GAACAT AAAGT -AA- AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT -AA-AT AAA-T AAAT AAAT AAAT AAAT AAA
34912395 ATAATAAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
3 4 0.06
4 51 0.77
5 9 0.14
6 2 0.03
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:34912418 original size:33 final size:33
Alignment explanation
Indices: 34912307--34912419 Score: 86
Period size: 33 Copynumber: 3.2 Consensus size: 33
34912297 ATACAACAAC
* *
34912307 AAATAAATAAATAAATAAACTAAAACATAAAAAAA
1 AAATAAATAAATAAATAAA-TGAAA-ATAAAATAA
* *
34912342 TGGACATATAAATAAATAAATAAATGAACATAAAGTAA
1 ---A-A-ATAAATAAATAAATAAATGAAAATAAAATAA
34912380 AAATAAATAAATAAA-ATAAT-AAAATAATAATAA
1 AAATAAATAAATAAATA-AATGAAAATAA-AATAA
*
34912413 CAATAAA
1 AAATAAA
34912420 GGAAAATAGA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
32 7 0.11
33 26 0.41
34 1 0.02
35 1 0.02
38 8 0.12
39 4 0.06
40 17 0.27
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (33 bp):
AAATAAATAAATAAATAAATGAAAATAAAATAA
Found at i:34914607 original size:46 final size:43
Alignment explanation
Indices: 34914506--34914883 Score: 259
Period size: 46 Copynumber: 8.7 Consensus size: 43
34914496 TTTTGACCCG
* * * *
34914506 CTCCACTGTAACTTCAGGGAGATAGGAT-TATGTCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCT-GGTCTTCGATCTA
* * * *
34914549 CTCCGCTGTAACCTCAGGGGGATAAGATCTGAAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTG---GTCTTCGATCTA
* * * * *
34914595 CTCTACTATAACCTCAGGGAGATAAGACCTGGT-GT-GATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGGTCTTCGATCTA
* * * *
34914636 CTCTACTGTAACTTCAGAGAGATAAGATCCT-GTCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGAT-CTGGTCTTCGATCTA
* *
34914679 CTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTG---GTCTTCGATCTA
* * * *
34914725 CTCCACTGTAACCTCAGGGAAATAAGACCT-GAC-GCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGGTCTTCGATCTA
* * * * ** *
34914766 CTCTACTGTAACTTCAGAGAGATAAGATCT-TTCATTTTAATCCA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGGTC--TTCGATCTA
* ** * *
34914810 CTCCACTGTAATCTCAGGGAGATAAGATTACT-AACTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGA-T-CTGGTCTTCGATCTA
* *
34914854 CTCCGCTGTAATCTCAGGGAGATAAGATCT
1 CTCCACTGTAACCTCAGGGAGATAAGATCT
34914884 AAAATTCTTC
Statistics
Matches: 264, Mismatches: 55, Indels: 33
0.75 0.16 0.09
Matches are distributed among these distances:
41 62 0.23
42 10 0.04
43 56 0.21
44 60 0.23
45 1 0.00
46 75 0.28
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
CTCCACTGTAACCTCAGGGAGATAAGATCTGGTCTTCGATCTA
Found at i:34914743 original size:130 final size:130
Alignment explanation
Indices: 34914505--34914794 Score: 454
Period size: 130 Copynumber: 2.2 Consensus size: 130
34914495 ATTTTGACCC
* * * * *
34914505 GCTCCACTGTAACTTCAGGGAGATAGGATTATGTCTTCGATCTGCTCCGCTGTAACCTCAGGGGG
1 GCTCTACTGTAACTTCAGAGAGATAAGATCATGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
* * * ** *
34914570 ATAAGATCTGAAATTCTTCGGTCTACTCTACTATAACCTCAGGGAGATAAGACCTGGTGTGATCT
66 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTATAACCTCAGGGAAATAAGACCTGACGCGATCT
*
34914635 GCTCTACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
1 GCTCTACTGTAACTTCAGAGAGATAAGATCATGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
*
34914700 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGACGCGATCT
66 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTATAACCTCAGGGAAATAAGACCTGACGCGATCT
*
34914765 ACTCTACTGTAACTTCAGAGAGATAAGATC
1 GCTCTACTGTAACTTCAGAGAGATAAGATC
34914795 TTTCATTTTA
Statistics
Matches: 146, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 146 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (130 bp):
GCTCTACTGTAACTTCAGAGAGATAAGATCATGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
ATAAGATCTGAAAGTCTTCGGTCTACTCCACTATAACCTCAGGGAAATAAGACCTGACGCGATCT
Found at i:34915037 original size:88 final size:89
Alignment explanation
Indices: 34914929--34915673 Score: 535
Period size: 87 Copynumber: 8.8 Consensus size: 89
34914919 GGTAAGGTTC
*
34914929 GTCTTCGACCTGCTTCGCTGTCAATGTAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCA-T-
1 GTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTG
34914992 C-ACAAATGAGGGAGGCAAGG-TTTGT
66 CAACAAATGA---AGGCAAGGCTTTGT
*
34915017 GTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCACTG
1 GTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTG
*
34915082 CAACCAATGAAGGCAAGGCTTTGT
66 CAACAAATGAAGGCAAGGCTTTGT
* * ** * * *
34915106 -T-TTCGATCTGCTTCGCTGTTAACACAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTG
1 GTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTG
**** *
34915168 ---C-AATGTTTTCAA---TCTGT
66 CAACAAATGAAGGCAAGGCTTTGT
* * * * * * * * *
34915185 -T-TT-G--CTGTTAACGCAG-GAAGGCAAGAT--------CTGCTATCTTCAACTAGCTCCACT
1 GTCTTCGACCTGCT-TCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACT
*
34915236 GCAACCAATGAAGGCAAGGCTTTGT
65 GCAACAAATGAAGGCAAGGCTTTGT
** * * * * * **
34915261 -T-TTCGATTTGCTTCGTTGTTAATGCAAGAAGGCAAGATATGCTATCTTTGACCAGCTCCACTG
1 GTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTG
*
34915324 CAACCAATGAAGGCAAGGCTTTGT
66 CAACAAATGAAGGCAAGGCTTTGT
* * * * * * * * * *
34915348 -T-TTCAATCTGTTTTGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTCAACTAGCTCCACTG
1 GTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTG
*
34915411 CAACCAATGAAGGCAAGGCTTTGT
66 CAACAAATGAAGGCAAGGCTTTGT
* * * * * * * * **
34915435 -T-TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCCAGATATGCTATCTTTGACCAGCTCCACTG
1 GTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTG
*
34915498 CAACCAATGAAGGCAAGGCTTTGT
66 CAACAAATGAAGGCAAGGCTTTGT
* * * * * *
34915522 -T-TTCGATCTGCTTCGTTGTTAATGCAGGAAGGCAAGATCTGAT-TCTTTAACCAGCTCCACTG
1 GTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTG
* *
34915584 CAACCAATGAAAGCAAGGCTTTGT
66 CAACAAATGAAGGCAAGGCTTTGT
* * * * * *
34915608 -T-TTCGATCTGCTTCGCTGTTAACGCAAGAAGGCAAAATCTGCT-TCTTTAACCAGCTCCACTG
1 GTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTG
34915670 CAAC
66 CAAC
34915674 CANNNNNNNN
Statistics
Matches: 558, Mismatches: 74, Indels: 52
0.82 0.11 0.08
Matches are distributed among these distances:
68 5 0.01
69 17 0.03
72 1 0.00
73 7 0.01
76 17 0.03
77 5 0.01
78 4 0.01
79 18 0.03
82 7 0.01
83 1 0.00
86 120 0.22
87 273 0.49
88 69 0.12
89 6 0.01
90 1 0.00
91 7 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (89 bp):
GTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTG
CAACAAATGAAGGCAAGGCTTTGT
Found at i:34915094 original size:44 final size:44
Alignment explanation
Indices: 34914958--34915098 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 44
34914948 GTCAATGTAA
* *
34914958 GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCA-T-C-ACAAAT
1 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCCACTGCAACCAAT
* * * * * * *
34914999 GAGGGAGGCAAGGT-TTGTGTCTTCGACCTGCTTCGCTGTCAATGCAA-
1 GA---AGGCAAGATCTTTTGTCTTCAACCAGCTCCACTG-CAA-CCAAT
34915046 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCCACTGCAACCAAT
1 GAAGGCAAGATCTTTTGTCTTCAACCAGCTCCACTGCAACCAAT
34915090 GAAGGCAAG
1 GAAGGCAAG
34915099 GCTTTGTTTT
Statistics
Matches: 74, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
41 2 0.03
43 18 0.24
44 29 0.39
45 19 0.26
46 1 0.01
47 3 0.04
48 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (44 bp):
GAAGGCAAGATCTTTTGTCTTCAACCAGCTCCACTGCAACCAAT
Found at i:34915212 original size:68 final size:69
Alignment explanation
Indices: 34915103--34915239 Score: 213
Period size: 68 Copynumber: 2.0 Consensus size: 69
34915093 GGCAAGGCTT
* *
34915103 TGTTTTCGATCTGCTTCGCTGTTAACACAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACT
1 TGTTTTCAATCTGCTTCGCTGTTAACACAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACT
34915167 GCAA
66 GCAA
* * * *
34915171 TGTTTTCAATCTGTTTTGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTCAACTAGCTCCACT
1 TGTTTTCAATCTGCTTCGCTGTTAACACAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACT
34915236 GCAA
66 GCAA
34915240 CCAATGAAGG
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
68 42 0.68
69 20 0.32
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (69 bp):
TGTTTTCAATCTGCTTCGCTGTTAACACAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACT
GCAA
Found at i:34915251 original size:44 final size:44
Alignment explanation
Indices: 34915201--34915427 Score: 130
Period size: 44 Copynumber: 5.2 Consensus size: 44
34915191 GTTAACGCAG
34915201 GAAGGCAAGATCTGCTATCTTCAACTAGCTCCACTGCAACCAAT
1 GAAGGCAAGATCTGCTATCTTCAACTAGCTCCACTGCAACCAAT
* * * * * * ** * *
34915245 GAAGGCAAGGCTTTG-T-T-TTCGATTTGCTTCGTTGTTAATGCAA-
1 GAAGGCAA-GATCTGCTATCTTCAACTAGCTCCACTG-CAA-CCAAT
* ** *
34915288 GAAGGCAAGATATGCTATCTTTGACCAGCTCCACTGCAACCAAT
1 GAAGGCAAGATCTGCTATCTTCAACTAGCTCCACTGCAACCAAT
* * * *** * *
34915332 GAAGGCAAGGCTTTG-T-T-TTCAATCT-GTTTTGCTGTTAACGC-AG
1 GAAGGCAA-GATCTGCTATCTTCAA-CTAGCTCCACTG-CAAC-CAAT
34915375 GAAGGCAAGATCTGCTATCTTCAACTAGCTCCACTGCAACCAAT
1 GAAGGCAAGATCTGCTATCTTCAACTAGCTCCACTGCAACCAAT
34915419 GAAGGCAAG
1 GAAGGCAAG
34915428 GCTTTGTTTT
Statistics
Matches: 127, Mismatches: 40, Indels: 32
0.64 0.20 0.16
Matches are distributed among these distances:
42 27 0.21
43 31 0.24
44 41 0.32
45 28 0.22
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (44 bp):
GAAGGCAAGATCTGCTATCTTCAACTAGCTCCACTGCAACCAAT
Found at i:34915318 original size:87 final size:87
Alignment explanation
Indices: 34915171--34915675 Score: 771
Period size: 87 Copynumber: 5.8 Consensus size: 87
34915161 TCCACTGCAA
* * * * *
34915171 TGTTTTCAATCTGTTTTGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTCAACTAGCTCCACT
1 TGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACT
34915236 GCAACCAATGAAGGCAAGGCTT
66 GCAACCAATGAAGGCAAGGCTT
* * * * * *
34915258 TGTTTTCGATTTGCTTCGTTGTTAATGCAAGAAGGCAAGATATGCTATCTTTGACCAGCTCCACT
1 TGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACT
34915323 GCAACCAATGAAGGCAAGGCTT
66 GCAACCAATGAAGGCAAGGCTT
* * * * *
34915345 TGTTTTCAATCTGTTTTGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTCAACTAGCTCCACT
1 TGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACT
34915410 GCAACCAATGAAGGCAAGGCTT
66 GCAACCAATGAAGGCAAGGCTT
* * *
34915432 TGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCCAGATATGCTATCTTTGACCAGCTCCACT
1 TGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACT
34915497 GCAACCAATGAAGGCAAGGCTT
66 GCAACCAATGAAGGCAAGGCTT
* * *
34915519 TGTTTTCGATCTGCTTCGTTGTTAATGCAGGAAGGCAAGATCTGAT-TCTTTAACCAGCTCCACT
1 TGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACT
*
34915583 GCAACCAATGAAAGCAAGGCTT
66 GCAACCAATGAAGGCAAGGCTT
* *
34915605 TGTTTTCGATCTGCTTCGCTGTTAACGCAAGAAGGCAAAATCTGCT-TCTTTAACCAGCTCCACT
1 TGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACT
34915669 GCAACCA
66 GCAACCA
34915676 NNNNNNNNNN
Statistics
Matches: 376, Mismatches: 42, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
86 104 0.28
87 272 0.72
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (87 bp):
TGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACT
GCAACCAATGAAGGCAAGGCTT
Found at i:34931098 original size:3 final size:3
Alignment explanation
Indices: 34931092--34931118 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34931082 ATTTGACATT
34931092 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
34931119 AAACCCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:34933974 original size:37 final size:40
Alignment explanation
Indices: 34933878--34933976 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
34933868 AACACACCAG
**
34933878 TTTGGCACCCAGTGCCTCATCAGATAATTTGAAATAATAA
1 TTTGGCACCCAGTGCCTCATCAGATAAACTGAAATAATAA
* * * *
34933918 TTTGGCACCCAGTGTCTCATCGGTTAAACTGAAGT-A-AA
1 TTTGGCACCCAGTGCCTCATCAGATAAACTGAAATAATAA
34933956 -TTGGCACCCAGTGCCTCATCA
1 TTTGGCACCCAGTGCCTCATCA
34933977 AATTAATCCA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 19 0.37
38 2 0.04
39 1 0.02
40 29 0.57
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (40 bp):
TTTGGCACCCAGTGCCTCATCAGATAAACTGAAATAATAA
Found at i:34934225 original size:24 final size:24
Alignment explanation
Indices: 34934180--34934226 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
34934170 TATATAAACC
34934180 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
34934204 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
34934227 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:34934764 original size:120 final size:121
Alignment explanation
Indices: 34934635--34934870 Score: 429
Period size: 120 Copynumber: 1.9 Consensus size: 121
34934625 AATTTAGTCC
34934635 TTATTACTCAAAATTTACAATTTATTCTACAATTCAATTCTTTTTCACTTTTAACTT-ATCTATC
1 TTATTACTCAAAATTTACAATTTATTCTACAATTCAATTCTTTTTCACTTTTAACTTAATCTATC
34934699 AATTTAATCCCTAATACTAAAATTATTCAACATAAACAGCACTTAAAATTTACAAT
66 AATTTAATCCCTAATACTAAAATTATTCAACATAAACAGCACTTAAAATTTACAAT
34934755 TTATTACTCAAAATTTACAATTTATTCTACAATTCAATTCTTTTTCACTTTTAACTTAAAAATCT
1 TTATTACTCAAAATTTACAATTTATTCTACAATTCAATTCTTTTTCACTTTTAACTT---AATCT
*
34934820 ATCAATTTAATCCCTAATACTAAAATTATTCAACATAAACATCACTTAAAA
63 ATCAATTTAATCCCTAATACTAAAATTATTCAACATAAACAGCACTTAAAA
34934871 ACTTAATAAT
Statistics
Matches: 111, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
120 57 0.51
124 54 0.49
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.41
Consensus pattern (121 bp):
TTATTACTCAAAATTTACAATTTATTCTACAATTCAATTCTTTTTCACTTTTAACTTAATCTATC
AATTTAATCCCTAATACTAAAATTATTCAACATAAACAGCACTTAAAATTTACAAT
Found at i:34935018 original size:4 final size:4
Alignment explanation
Indices: 34935009--34935078 Score: 95
Period size: 4 Copynumber: 17.0 Consensus size: 4
34934999 ACTTTTCTCC
*
34935009 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCCT TTCT TTCC
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT
* *
34935058 TTCT CTGT TTCGT TTCT TTCT
1 TTCT TTCT TTC-T TTCT TTCT
34935079 CTCCTTCTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
4 50 0.86
5 8 0.14
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:34956716 original size:9 final size:9
Alignment explanation
Indices: 34956702--34956733 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
34956692 TTAAAATACT
34956702 TTTTTTAAA
1 TTTTTTAAA
34956711 TTTTTTAAA
1 TTTTTTAAA
34956720 -TTTTTAAA
1 TTTTTTAAA
34956728 TTTTTT
1 TTTTTT
34956734 TAAAATACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:34956722 original size:41 final size:41
Alignment explanation
Indices: 34956669--34956748 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
34956659 AAATATTTTT
*
34956669 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAA
1 ATTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTTAA
* **
34956710 ATTTTTTAAATTTTTAAATTTTTTTAAAATACTTTTTTT
1 ATTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTT
34956749 CGGGCCAGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (41 bp):
ATTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTTAA
Found at i:34956723 original size:8 final size:8
Alignment explanation
Indices: 34956703--34956732 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
34956693 TAAAATACTT
34956703 TTTTTAAA
1 TTTTTAAA
34956711 TTTTTTAAA
1 -TTTTTAAA
34956720 TTTTTAAA
1 TTTTTAAA
34956728 TTTTT
1 TTTTT
34956733 TTAAAATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTTAAA
Found at i:34956745 original size:11 final size:11
Alignment explanation
Indices: 34956679--34956704 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
34956669 ATTTTTTTAA
34956679 TTTTAAAATAC
1 TTTTAAAATAC
34956690 TTTTAAAATAC
1 TTTTAAAATAC
34956701 TTTT
1 TTTT
34956705 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:34958575 original size:13 final size:13
Alignment explanation
Indices: 34958557--34958581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34958547 TTTTTCTAAA
34958557 AAATAATAATAAC
1 AAATAATAATAAC
34958570 AAATAATAATAA
1 AAATAATAATAA
34958582 AGGCAATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATAATAAC
Found at i:34959254 original size:51 final size:51
Alignment explanation
Indices: 34959194--34959290 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
34959184 AGTATTGAGA
** *
34959194 CATAAAATCTTCAATGACTAAAACAAATTAATAAGTAACTTAACCACTAGC
1 CATAAAATCTTCAAAAACTAAAACAAACTAATAAGTAACTTAACCACTAGC
* * *
34959245 CATAAAATCTTCAAAAATTAAAACAAACTACTAAGTATCTTAACCA
1 CATAAAATCTTCAAAAACTAAAACAAACTAATAAGTAACTTAACCA
34959291 AAGCAACAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.26
Consensus pattern (51 bp):
CATAAAATCTTCAAAAACTAAAACAAACTAATAAGTAACTTAACCACTAGC
Found at i:34960226 original size:17 final size:17
Alignment explanation
Indices: 34960204--34960238 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34960194 GTCGTACTCT
34960204 TAGTTGCTAAAATCTAA
1 TAGTTGCTAAAATCTAA
* *
34960221 TAGTTGTTAAAATTTAA
1 TAGTTGCTAAAATCTAA
34960238 T
1 T
34960239 TTGCCAGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (17 bp):
TAGTTGCTAAAATCTAA
Found at i:34964964 original size:24 final size:23
Alignment explanation
Indices: 34964932--34964980 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
34964922 TCATTAAACT
*
34964932 AATTTAAAT-TCAGAAATAAATATA
1 AATTCAAATATCA-AAATAAAT-TA
*
34964956 AATTCAAATATCAAAATGAATTA
1 AATTCAAATATCAAAATAAATTA
34964979 AA
1 AA
34964981 AATATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 4 0.18
24 15 0.68
25 3 0.14
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (23 bp):
AATTCAAATATCAAAATAAATTA
Found at i:34967962 original size:25 final size:27
Alignment explanation
Indices: 34967914--34967964 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
34967904 AGGCCAAGCC
* *
34967914 TAGCAGCCTCTTTTTTCTTTTTAACTT
1 TAGCAGCCTCTTATTTCTTCTTAACTT
34967941 TAGCAGCCT-TTATTTC-TCTTAACT
1 TAGCAGCCTCTTATTTCTTCTTAACT
34967965 GTAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 6 0.27
27 9 0.41
ACGTcount: A:0.18, C:0.24, G:0.08, T:0.51
Consensus pattern (27 bp):
TAGCAGCCTCTTATTTCTTCTTAACTT
Found at i:34970254 original size:13 final size:13
Alignment explanation
Indices: 34970236--34970261 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34970226 AATTGAAAAA
34970236 TAAATATTAAATT
1 TAAATATTAAATT
34970249 TAAATATTAAATT
1 TAAATATTAAATT
34970262 CAAGTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAATATTAAATT
Found at i:34992214 original size:151 final size:152
Alignment explanation
Indices: 34991928--34992231 Score: 592
Period size: 151 Copynumber: 2.0 Consensus size: 152
34991918 CAATGTCTTC
34991928 TTGTATTTCCGAATGGTTGTTCATAAATCCATTTTATTTAGAATCTTCTCCATCCATTAACCTTT
1 TTGTATTTCCGAATGGTTGTTCATAAATCCATTTTATTTAGAATCTTCTCCATCCATTAACCTTT
34991993 AAACAAAATGATAACACAATATTGCATAAAAATATACTCAAATAACGAAGATTTCAAAGTTACAT
66 AAACAAAATGATAACACAATATTGCATAAAAATATACTCAAATAACGAAGATTTCAAAGTTACAT
34992058 GAAAATATAAAAAAAAAATATA
131 GAAAATATAAAAAAAAAATATA
34992080 TTGTATTTCCG-ATGGTTGTTCATAAATCCATTTTATTTAGAATCTTCTCCATCCATTAACCTTT
1 TTGTATTTCCGAATGGTTGTTCATAAATCCATTTTATTTAGAATCTTCTCCATCCATTAACCTTT
*
34992144 AAACAAAATGATAACACAATATTGCATTAAAATATACTCAAATAACGAAGATTTCAAAGTTACAT
66 AAACAAAATGATAACACAATATTGCATAAAAATATACTCAAATAACGAAGATTTCAAAGTTACAT
34992209 GAAAATATAAAAAAAAAATATA
131 GAAAATATAAAAAAAAAATATA
34992231 T
1 T
34992232 ATATATATAT
Statistics
Matches: 151, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
151 140 0.93
152 11 0.07
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (152 bp):
TTGTATTTCCGAATGGTTGTTCATAAATCCATTTTATTTAGAATCTTCTCCATCCATTAACCTTT
AAACAAAATGATAACACAATATTGCATAAAAATATACTCAAATAACGAAGATTTCAAAGTTACAT
GAAAATATAAAAAAAAAATATA
Found at i:35013594 original size:18 final size:18
Alignment explanation
Indices: 35013554--35013596 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35013544 GTTAAAAGTG
35013554 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
35013572 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
35013590 TAATTAA
1 TAATTAA
35013597 AAACATATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:35014139 original size:4 final size:4
Alignment explanation
Indices: 35014130--35014155 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
35014120 GTGTTTGCAT
35014130 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
35014156 ATATGACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:35014793 original size:31 final size:31
Alignment explanation
Indices: 35014755--35014824 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
35014745 ATTTGACAAG
*
35014755 TACCAAATTAAGAAAAATAGTCAAGTTCAAA
1 TACCAAATTAAGAAAAATAGTCAAATTCAAA
* * *
35014786 TATCAAATTAAGAAAAATTGTCAAATTCAAT
1 TACCAAATTAAGAAAAATAGTCAAATTCAAA
35014817 TACCAAAT
1 TACCAAAT
35014825 ATTATATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (31 bp):
TACCAAATTAAGAAAAATAGTCAAATTCAAA
Found at i:35029210 original size:19 final size:19
Alignment explanation
Indices: 35029165--35029206 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
35029155 AATTACAAAA
35029165 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
35029184 AAAATTCAAAAT-A-TTTT
1 AAAATTCAAAATAATTTTT
35029201 AAAATT
1 AAAATT
35029207 TTCAGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.43
18 1 0.04
19 12 0.52
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:35032733 original size:12 final size:12
Alignment explanation
Indices: 35032718--35032742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35032708 TAAATATCTG
35032718 ATATTATATTAT
1 ATATTATATTAT
35032730 ATATTATATTAT
1 ATATTATATTAT
35032742 A
1 A
35032743 ACGTCTTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTATATTAT
Found at i:35033075 original size:17 final size:16
Alignment explanation
Indices: 35033030--35033082 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
35033020 GTTATGTATA
35033030 TTATACTAAATCAAAAT
1 TTATACTAAATC-AAAT
35033047 TTATA-T--ATCAAAT
1 TTATACTAAATCAAAT
35033060 TATATACTAAATCAAAGT
1 T-TATACTAAATCAAA-T
35033078 TTATA
1 TTATA
35033083 TATGAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 1 0.03
16 1 0.03
17 15 0.48
18 2 0.06
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (16 bp):
TTATACTAAATCAAAT
Found at i:35051709 original size:7 final size:7
Alignment explanation
Indices: 35051697--35051727 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
35051687 CCAAGTAAAA
35051697 TTTTATT
1 TTTTATT
35051704 TTTTATT
1 TTTTATT
35051711 TTTTATT
1 TTTTATT
35051718 TTTTATT
1 TTTTATT
35051725 TTT
1 TTT
35051728 AAATGATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:35057444 original size:118 final size:118
Alignment explanation
Indices: 35057233--35057449 Score: 267
Period size: 118 Copynumber: 1.8 Consensus size: 118
35057223 ACCGTATGTG
** ** * *
35057233 GTGACCTAAATTCCATAGGTCAAGGGTTTGAATTTTGCCAAGGGCAAGACGCTCACGTCGCCTCT
1 GTGACCTAAATTCCATAGGTCAAGGGTTCAAATCCTGCCAAGGACAAGACGCTCACGTCACCTCT
*
35057298 TCGTGAGTGCTTGTACATCCACCTATGGTCAAGGTGACCCCTTCGTGAATCGA
66 TCGTGAGTGCTCGTACATCCACCTATGGTCAAGGTGACCCCTTCGTGAATCGA
*
35057351 GTGACCTACATTCCATAGGTC-AGAGGTTCAAATCCTGCCAAGGACAAGACGCAT-ACGTCACCT
1 GTGACCTAAATTCCATAGGTCAAG-GGTTCAAATCCTGCCAAGGACAAGACGC-TCACGTCACCT
* * * * * * *
35057414 TTTGGTGGGTGGTCGTACGTCTACGTATGGTCAAGG
64 CTTCGTGAGTGCTCGTACATCCACCTATGGTCAAGG
35057450 CACCCGGCCT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
117 2 0.02
118 79 0.96
119 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (118 bp):
GTGACCTAAATTCCATAGGTCAAGGGTTCAAATCCTGCCAAGGACAAGACGCTCACGTCACCTCT
TCGTGAGTGCTCGTACATCCACCTATGGTCAAGGTGACCCCTTCGTGAATCGA
Found at i:35062855 original size:106 final size:106
Alignment explanation
Indices: 35062670--35062873 Score: 408
Period size: 106 Copynumber: 1.9 Consensus size: 106
35062660 CCCTGTATTC
35062670 TTTCCATTTATAATTTAGTCCTACTTTTTTATTTCAGAAATTTAGTCTCCTTACTTTTTCTTATT
1 TTTCCATTTATAATTTAGTCCTACTTTTTTATTTCAGAAATTTAGTCTCCTTACTTTTTCTTATT
35062735 AAATATTTAAAGATCAATGGATAACAAGGTTAAAATTTTCA
66 AAATATTTAAAGATCAATGGATAACAAGGTTAAAATTTTCA
35062776 TTTCCATTTATAATTTAGTCCTACTTTTTTATTTCAGAAATTTAGTCTCCTTACTTTTTCTTATT
1 TTTCCATTTATAATTTAGTCCTACTTTTTTATTTCAGAAATTTAGTCTCCTTACTTTTTCTTATT
35062841 AAATATTTAAAGATCAATGGATAACAAGGTTAA
66 AAATATTTAAAGATCAATGGATAACAAGGTTAA
35062874 TTTTTTTTTA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (106 bp):
TTTCCATTTATAATTTAGTCCTACTTTTTTATTTCAGAAATTTAGTCTCCTTACTTTTTCTTATT
AAATATTTAAAGATCAATGGATAACAAGGTTAAAATTTTCA
Found at i:35063532 original size:3 final size:3
Alignment explanation
Indices: 35063524--35063553 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
35063514 GAAAGAGAAA
35063524 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35063554 GAGAGAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35068231 original size:18 final size:18
Alignment explanation
Indices: 35068208--35068242 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35068198 AAACCTTAAC
35068208 ATATTTTAATCATAAAAG
1 ATATTTTAATCATAAAAG
* *
35068226 ATATTTTTATCTTAAAA
1 ATATTTTAATCATAAAA
35068243 TAATTACTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (18 bp):
ATATTTTAATCATAAAAG
Found at i:35073689 original size:20 final size:20
Alignment explanation
Indices: 35073664--35073704 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
35073654 AATTATAAAC
*
35073664 CTCAAAC-CTCGAATCCCAAA
1 CTCAAACTCT-GAAGCCCAAA
35073684 CTCAAACTCTGAAGCCCAAA
1 CTCAAACTCTGAAGCCCAAA
35073704 C
1 C
35073705 CTTGAACCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.39, C:0.39, G:0.07, T:0.15
Consensus pattern (20 bp):
CTCAAACTCTGAAGCCCAAA
Found at i:35073704 original size:34 final size:33
Alignment explanation
Indices: 35073666--35073729 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
35073656 TTATAAACCT
*
35073666 CAAACCTCGAATCCC-AAACTCAAACTCTGAAGCC
1 CAAACCTCGAA-CCCTAAACCCAAA-TCTGAAGCC
*
35073700 CAAACCTTGAACCCTAAACCCAAATCTGAA
1 CAAACCTCGAACCCTAAACCCAAATCTGAA
35073730 TCTTGTACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 9 0.33
34 18 0.67
ACGTcount: A:0.41, C:0.36, G:0.08, T:0.16
Consensus pattern (33 bp):
CAAACCTCGAACCCTAAACCCAAATCTGAAGCC
Found at i:35086124 original size:18 final size:18
Alignment explanation
Indices: 35086101--35086141 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35086091 TAAAAATTGG
*
35086101 AAAATCAT-TTTCATGATC
1 AAAATCATGTTT-ATCATC
35086119 AAAATCATGTTTATCATC
1 AAAATCATGTTTATCATC
35086137 AAAAT
1 AAAAT
35086142 TTTGTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (18 bp):
AAAATCATGTTTATCATC
Found at i:35088657 original size:24 final size:24
Alignment explanation
Indices: 35088630--35088685 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
35088620 GAACGAAGAG
*
35088630 GCCTGCGAATTGGAGAACGGCTCC
1 GCCTACGAATTGGAGAACGGCTCC
* *
35088654 GCCTACGAATTGGAGAAGGGCTAC
1 GCCTACGAATTGGAGAACGGCTCC
*
35088678 GTCTACGA
1 GCCTACGA
35088686 TTGAAGGGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.32, T:0.18
Consensus pattern (24 bp):
GCCTACGAATTGGAGAACGGCTCC
Found at i:35096168 original size:23 final size:23
Alignment explanation
Indices: 35096138--35096185 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
35096128 CAAAGTTTAT
35096138 TTATTTCTTATTTATTTAAAAAA
1 TTATTTCTTATTTATTTAAAAAA
35096161 TTATTTCTTATTTATTTAAAAAA
1 TTATTTCTTATTTATTTAAAAAA
35096184 TT
1 TT
35096186 CTTTGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTATTTCTTATTTATTTAAAAAA
Found at i:35099974 original size:20 final size:20
Alignment explanation
Indices: 35099946--35099983 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35099936 AATAAAAATG
*
35099946 GTGTTAAAATATATTTAACA
1 GTGTAAAAATATATTTAACA
*
35099966 GTGTAAAAATATGTTTAA
1 GTGTAAAAATATATTTAA
35099984 AATCTTAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (20 bp):
GTGTAAAAATATATTTAACA
Found at i:35103962 original size:27 final size:27
Alignment explanation
Indices: 35103918--35103971 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
35103908 AAAATATTAA
* * *
35103918 ATTATTTTTTCTTTTTTTGAATAAAAT
1 ATTATTTTTTCTTATTTTAAAAAAAAT
35103945 ATTATTATTTT-TTATTTTAAAAAAAAT
1 ATTATT-TTTTCTTATTTTAAAAAAAAT
35103972 TTTAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTATTTTTTCTTATTTTAAAAAAAAT
Found at i:35104835 original size:15 final size:16
Alignment explanation
Indices: 35104799--35104835 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
35104789 CTCATTTAAT
35104799 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
*
35104815 TTTTATATTATGTAA-
1 TTTTATATAATGTAAC
35104830 TTTTAT
1 TTTTAT
35104836 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:35104952 original size:27 final size:27
Alignment explanation
Indices: 35104922--35104978 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
35104912 CTCTCAACAT
*
35104922 GGCACCACTAATGGCACCTCTCAGATA
1 GGCACCACCAATGGCACCTCTCAGATA
* *
35104949 GGCACCACCATTGGCACCTCTGAGATA
1 GGCACCACCAATGGCACCTCTCAGATA
35104976 GGC
1 GGC
35104979 GTCAATACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.18
Consensus pattern (27 bp):
GGCACCACCAATGGCACCTCTCAGATA
Found at i:35113748 original size:41 final size:41
Alignment explanation
Indices: 35113651--35113761 Score: 149
Period size: 41 Copynumber: 2.8 Consensus size: 41
35113641 TAGATAATTT
* *
35113651 GAAGTAATAAATTGACACCCAGTGTCTTATCG-GTTAAACC
1 GAAGTAATAAATTGACACCCAGTGTCTCATCGAATTAAACC
* * *
35113691 GAAG---TAAATTGGCACCCAGTGCCTCATCGAATTAATCC
1 GAAGTAATAAATTGACACCCAGTGTCTCATCGAATTAAACC
35113729 GAAGTAATAAATTGACACCCAGTGTCTCATCGA
1 GAAGTAATAAATTGACACCCAGTGTCTCATCGA
35113762 CTCGAAGTCG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
37 22 0.37
38 10 0.17
40 4 0.07
41 24 0.40
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (41 bp):
GAAGTAATAAATTGACACCCAGTGTCTCATCGAATTAAACC
Found at i:35114644 original size:4 final size:4
Alignment explanation
Indices: 35114635--35114688 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
35114625 ACTATTCTCC
* * *
35114635 TTCT TTCT TTCT TTTT TTCTT TTCT TTCT TTCC TTCT TTGT TTCGT TTCT
1 TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TTCT TTCT TTCT TTC-T TTCT
35114685 TTCT
1 TTCT
35114689 CTCCTTCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.00, C:0.22, G:0.04, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:35114659 original size:21 final size:20
Alignment explanation
Indices: 35114635--35114688 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
35114625 ACTATTCTCC
* *
35114635 TTCTTTCTTTCTTTTTTTCTT
1 TTCTTTCTTTCTTTCTTT-GT
*
35114656 TTCTTTCTTTCCTTCTTTGT
1 TTCTTTCTTTCTTTCTTTGT
35114676 TTCGTTTCTTTCT
1 TTC-TTTCTTTCT
35114689 CTCCTTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.00, C:0.22, G:0.04, T:0.74
Consensus pattern (20 bp):
TTCTTTCTTTCTTTCTTTGT
Found at i:35114663 original size:25 final size:25
Alignment explanation
Indices: 35114635--35114695 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
35114625 ACTATTCTCC
* * *
35114635 TTCTTTCTTTCTTTTTTTCTTTTCT
1 TTCTTTCCTTCTTTGTTTCGTTTCT
35114660 TTCTTTCCTTCTTTGTTTCGTTTCT
1 TTCTTTCCTTCTTTGTTTCGTTTCT
*
35114685 TTCTCTCCTTC
1 TTCTTTCCTTC
35114696 ATTTTCCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.70
Consensus pattern (25 bp):
TTCTTTCCTTCTTTGTTTCGTTTCT
Found at i:35114671 original size:17 final size:17
Alignment explanation
Indices: 35114632--35114673 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
35114622 CTAACTATTC
35114632 TCCTTC-TTTCTTTCTT
1 TCCTTCTTTTCTTTCTT
**
35114648 TTTTTCTTTTCTTTCTT
1 TCCTTCTTTTCTTTCTT
35114665 TCCTTCTTT
1 TCCTTCTTT
35114674 GTTTCGTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
TCCTTCTTTTCTTTCTT
Found at i:35114795 original size:28 final size:31
Alignment explanation
Indices: 35114757--35114813 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
35114747 TACTTAACTT
35114757 TTAAGCTTT-AATATTT-TAATATATATATA
1 TTAAGCTTTAAATATTTATAATATATATATA
35114786 TTAA-CTTTAAATATTTATAATATATATA
1 TTAAGCTTTAAATATTTATAATATATATA
35114814 CACTTATGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 11 0.42
30 11 0.42
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (31 bp):
TTAAGCTTTAAATATTTATAATATATATATA
Found at i:35115407 original size:45 final size:45
Alignment explanation
Indices: 35115343--35115429 Score: 158
Period size: 45 Copynumber: 1.9 Consensus size: 45
35115333 TCACCTTATT
35115343 AAGGAAGATAAATCATACTTATCA-GATTCAATAGATGAGATAGAC
1 AAGGAAGATAAATCATACTTAT-AGGATTCAATAGATGAGATAGAC
35115388 AAGGAAGATAAATCATACTTATAGGATTCAATAGATGAGATA
1 AAGGAAGATAAATCATACTTATAGGATTCAATAGATGAGATA
35115430 AGTTATACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 1 0.02
45 40 0.98
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.25
Consensus pattern (45 bp):
AAGGAAGATAAATCATACTTATAGGATTCAATAGATGAGATAGAC
Found at i:35124393 original size:33 final size:32
Alignment explanation
Indices: 35124324--35124498 Score: 111
Period size: 27 Copynumber: 5.4 Consensus size: 32
35124314 TGTGAAAGGG
35124324 GGTTGCTAAGTGCTGATTCCCC---CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCATTC-ATTGGT
35124351 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCC-ATTCATTGGT
* *
35124384 GGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATT-C-CC-CAT-T--CAT-T---GGT
*
35124426 GGTTGCTAAGTGCTGATTCCCC---CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCATTCATTGGT
**
35124453 GGTTGCTGTGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCC-ATTCATTGGT
35124486 GGTTGCTAAGTGC
1 GGTTGCTAAGTGC
35124499 GGAATCCACC
Statistics
Matches: 116, Mismatches: 9, Indels: 40
0.70 0.05 0.24
Matches are distributed among these distances:
27 42 0.36
28 2 0.02
30 1 0.01
31 3 0.03
32 4 0.03
33 30 0.26
34 1 0.01
35 4 0.03
36 2 0.02
38 2 0.02
39 2 0.02
40 2 0.02
41 1 0.01
42 20 0.17
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.31
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCCATTCATTGGT
Found at i:35124480 original size:102 final size:103
Alignment explanation
Indices: 35124311--35124509 Score: 337
Period size: 102 Copynumber: 1.9 Consensus size: 103
35124301 ACCGTATTTT
* *
35124311 AAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCTAT
1 AAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAT
* *
35124376 TCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATCTG
66 TCATTGGTGGTTGCTAAGTGCGGAATCCACCGCATCTG
**
35124414 AAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTGTGTGCTGATTCCCCGAT
1 AAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAT
35124478 TCATTGGTGGTTGCTAAGTGCGGAATCCACCG
66 TCATTGGTGGTTGCTAAGTGCGGAATCCACCG
35124510 ATAACGGTTA
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
102 83 0.92
103 7 0.08
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (103 bp):
AAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAT
TCATTGGTGGTTGCTAAGTGCGGAATCCACCGCATCTG
Found at i:35126341 original size:15 final size:15
Alignment explanation
Indices: 35126321--35126351 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35126311 TTTAGTTACT
35126321 ACATCAATGTTTCAG
1 ACATCAATGTTTCAG
35126336 ACATCAATGTTTCAG
1 ACATCAATGTTTCAG
35126351 A
1 A
35126352 TTTTACTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (15 bp):
ACATCAATGTTTCAG
Found at i:35132430 original size:15 final size:16
Alignment explanation
Indices: 35132396--35132432 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
35132386 TCACGTACAA
35132396 TTCAATTTCTGTATAG
1 TTCAATTTCTGTATAG
35132412 TTCAATTTCAT-TA-AG
1 TTCAATTTC-TGTATAG
35132427 TTCAAT
1 TTCAAT
35132433 ACTAATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 11 0.55
17 1 0.05
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.49
Consensus pattern (16 bp):
TTCAATTTCTGTATAG
Found at i:35134084 original size:50 final size:50
Alignment explanation
Indices: 35133985--35134127 Score: 173
Period size: 50 Copynumber: 2.9 Consensus size: 50
35133975 NNNNNNCCGA
* * ** *
35133985 TACACGTAGTAGCCTGCACATAGTACTACATACGTGATGA-AACTATCCGG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCA-TATCCGG
* *
35134035 TACGCATAGTAGCCTGCACATAGTACTACACATGTGACCCATCAT-TCCGG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCATATCCGG
* *
35134085 TACACGTAGTACCCTGCACATAGTACTACACACGTGACCATCA
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCA
35134128 CTTTCACTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
49 6 0.08
50 71 0.89
51 2 0.03
52 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (50 bp):
TACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCATATCCGG
Found at i:35140258 original size:37 final size:32
Alignment explanation
Indices: 35140170--35140259 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 32
35140160 TATTTTTCGA
35140170 AATTTTTTTCTTTTTCTTTTAAACTTTGATATTT
1 AATTTTTTT-TTTTT-TTTTAAACTTTGATATTT
* *
35140204 GATTTTTTTTTGCTTTTTTAAACTTTGATCAATATAT
1 AATTTTTTTTT-TTTTTTTAAACTTTGAT--AT-T-T
35140241 AATTTTTTTTATTTTTTTT
1 AATTTTTTTT-TTTTTTTT
35140260 GGTTTGTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
33 16 0.35
34 10 0.22
35 2 0.04
36 1 0.02
37 16 0.35
38 1 0.02
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (32 bp):
AATTTTTTTTTTTTTTTTAAACTTTGATATTT
Found at i:35155355 original size:9 final size:9
Alignment explanation
Indices: 35155341--35155366 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35155331 TGAGGTAGAC
35155341 ATCATTATG
1 ATCATTATG
35155350 ATCATTATG
1 ATCATTATG
35155359 ATCATTAT
1 ATCATTAT
35155367 CACCTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (9 bp):
ATCATTATG
Found at i:35159792 original size:21 final size:22
Alignment explanation
Indices: 35159738--35159792 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
35159728 GAAAGGAGAA
*
35159738 GAGAAAAATAAAAGTGAAAAAG
1 GAGAAAAAGAAAAGTGAAAAAG
* *
35159760 AAGAAAATGAAAA-TGAAAAAG
1 GAGAAAAAGAAAAGTGAAAAAG
*
35159781 GAGAAAAGGAAA
1 GAGAAAAAGAAA
35159793 GCGAGAGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (22 bp):
GAGAAAAAGAAAAGTGAAAAAG
Found at i:35182890 original size:27 final size:27
Alignment explanation
Indices: 35182860--35183155 Score: 320
Period size: 27 Copynumber: 11.0 Consensus size: 27
35182850 TAAAACTATC
*
35182860 GAAATGCCCTCGAAGGGTAAAATTACT
1 GAAATACCCTCGAAGGGTAAAATTACT
* *
35182887 GAAATACCCTTGAAGGGTAAAATTACC
1 GAAATACCCTCGAAGGGTAAAATTACT
* *
35182914 AAAATACCCTCGAAGGGTAAAATTACC
1 GAAATACCCTCGAAGGGTAAAATTACT
* *
35182941 GAAATACCCTTGAAGGGTAAAATAACT
1 GAAATACCCTCGAAGGGTAAAATTACT
35182968 GAAATACCCTC-AATGGGT-AAATTA-T
1 GAAATACCCTCGAA-GGGTAAAATTACT
*
35182993 CGAAATACCCTCAAAGGGTAAAATTACT
1 -GAAATACCCTCGAAGGGTAAAATTACT
*
35183021 GAAATACCCTCGAAGGGTAAAA-CACT
1 GAAATACCCTCGAAGGGTAAAATTACT
*
35183047 GAAATATCCCT-AAAGGGTAAAATTA-T
1 GAAATA-CCCTCGAAGGGTAAAATTACT
*
35183073 CGAAATACTCCT-GAATGGTAAAATTACT
1 -GAAATAC-CCTCGAAGGGTAAAATTACT
* * * * *
35183101 AAAATACCTTCAAAGAGTAAAATTACC
1 GAAATACCCTCGAAGGGTAAAATTACT
* *
35183128 GAAATACCC-CTAAAGGGTAAAATGACT
1 GAAATACCCTC-GAAGGGTAAAATTACT
35183155 G
1 G
35183156 TTATACCCCT
Statistics
Matches: 229, Mismatches: 28, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
25 1 0.00
26 46 0.20
27 180 0.79
28 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (27 bp):
GAAATACCCTCGAAGGGTAAAATTACT
Found at i:35183011 original size:107 final size:108
Alignment explanation
Indices: 35182857--35183150 Score: 352
Period size: 107 Copynumber: 2.7 Consensus size: 108
35182847 GGATAAAACT
* ** *
35182857 ATCGAAATGCCCTCGAA-GGGTAAAATTACTGAAATACCCTTGAAGGGTAAAATTACCAAAATAC
1 ATCGAAATACCCTC-AATGGGTAAAATTACTGAAATACCCTCAAAGGGTAAAATTACCGAAATAC
* *
35182921 CCTCGAAGGGTAAAATTACCGAAATA-CCCTTGAAGGGTAAAATA
65 CCTCGAAGGGTAAAATCACCGAAATATCCC-TAAAGGGTAAAATA
*
35182965 A-CTGAAATACCCTCAATGGGT-AAATTA-TCGAAATACCCTCAAAGGGTAAAATTACTGAAATA
1 ATC-GAAATACCCTCAATGGGTAAAATTACT-GAAATACCCTCAAAGGGTAAAATTACCGAAATA
* *
35183027 CCCTCGAAGGGTAAAA-CACTGAAATATCCCTAAAGGGTAAAATT
64 CCCTCGAAGGGTAAAATCACCGAAATATCCCTAAAGGGTAAAATA
* * * *
35183071 ATCGAAATACTCCTGAAT-GGTAAAATTACTAAAATACCTTCAAAGAGTAAAATTACCGAAATAC
1 ATCGAAATAC-CCTCAATGGGTAAAATTACTGAAATACCCTCAAAGGGTAAAATTACCGAAATAC
*
35183135 CC-CTAAAGGGTAAAAT
65 CCTC-GAAGGGTAAAAT
35183151 GACTGTTATA
Statistics
Matches: 161, Mismatches: 15, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
106 33 0.20
107 112 0.70
108 16 0.10
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.22
Consensus pattern (108 bp):
ATCGAAATACCCTCAATGGGTAAAATTACTGAAATACCCTCAAAGGGTAAAATTACCGAAATACC
CTCGAAGGGTAAAATCACCGAAATATCCCTAAAGGGTAAAATA
Found at i:35183026 original size:80 final size:79
Alignment explanation
Indices: 35182860--35183150 Score: 354
Period size: 80 Copynumber: 3.6 Consensus size: 79
35182850 TAAAACTATC
* * *
35182860 GAAATGCCCTCGAAGGGTAAAATTACTGAAATACCCTTGAAGGGTAAAATTACCAAAATACCCTC
1 GAAATACCCTCGAAGGGTAAAATTACTGAAATACCC-T-AAGGGTAAAATTATCGAAATACCCTC
*
35182925 GAAGGGTAAAATTACC
64 GAAGGGTAAAATTACT
* *
35182941 GAAATACCCTTGAAGGGTAAAATAACTGAAATACCCTCAATGGGT-AAATTATCGAAATACCCTC
1 GAAATACCCTCGAAGGGTAAAATTACTGAAATACCCT-AA-GGGTAAAATTATCGAAATACCCTC
*
35183005 AAAGGGTAAAATTACT
64 GAAGGGTAAAATTACT
*
35183021 GAAATACCCTCGAAGGGTAAAA-CACTGAAATATCCCTAAAGGGTAAAATTATCGAAATACTCCT
1 GAAATACCCTCGAAGGGTAAAATTACTGAAATA-CCCT-AAGGGTAAAATTATCGAAATAC-CCT
*
35183085 -GAATGGTAAAATTACT
63 CGAAGGGTAAAATTACT
* * * * *
35183101 AAAATACCTTCAAAGAGTAAAATTACCGAAATACCCCTAAAGGGTAAAAT
1 GAAATACCCTCGAAGGGTAAAATTACTGAAATA-CCCT-AAGGGTAAAAT
35183151 GACTGTTATA
Statistics
Matches: 185, Mismatches: 20, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
79 13 0.07
80 108 0.58
81 64 0.35
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.22
Consensus pattern (79 bp):
GAAATACCCTCGAAGGGTAAAATTACTGAAATACCCTAAGGGTAAAATTATCGAAATACCCTCGA
AGGGTAAAATTACT
Found at i:35183318 original size:8 final size:8
Alignment explanation
Indices: 35183301--35183367 Score: 54
Period size: 7 Copynumber: 9.0 Consensus size: 8
35183291 ATTCTGATAT
35183301 AGGG-TTA
1 AGGGTTTA
35183308 AGGGTTTA
1 AGGGTTTA
35183316 A-GGTTT-
1 AGGGTTTA
*
35183322 AGGGTTTT
1 AGGGTTTA
35183330 AGGGTTT-
1 AGGGTTTA
* *
35183337 AGAGTTTT
1 AGGGTTTA
*
35183345 AGGGTTTT
1 AGGGTTTA
*
35183353 AGGGTTCA
1 AGGGTTTA
35183361 A-GGTTTA
1 AGGGTTTA
35183368 TGGCCCACAC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
6 1 0.02
7 25 0.49
8 25 0.49
ACGTcount: A:0.21, C:0.01, G:0.36, T:0.42
Consensus pattern (8 bp):
AGGGTTTA
Found at i:35183328 original size:7 final size:7
Alignment explanation
Indices: 35183300--35183358 Score: 64
Period size: 7 Copynumber: 8.0 Consensus size: 7
35183290 GATTCTGATA
35183300 TAGGGTT
1 TAGGGTT
*
35183307 AAGGGTT
1 TAGGGTT
*
35183314 TAAGGTT
1 TAGGGTT
35183321 TAGGGTTT
1 TAGGG-TT
35183329 TAGGGTT
1 TAGGGTT
*
35183336 TAGAGTTT
1 TAG-GGTT
35183344 TAGGGTTT
1 TAGGG-TT
35183352 TAGGGTT
1 TAGGGTT
35183359 CAAGGTTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 23 0.53
8 20 0.47
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (7 bp):
TAGGGTT
Found at i:35183335 original size:15 final size:15
Alignment explanation
Indices: 35183300--35183358 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
35183290 GATTCTGATA
*
35183300 TAGGGTTAAGGG-TT
1 TAGGGTTTAGGGTTT
*
35183314 TAAGGTTTAGGGTTT
1 TAGGGTTTAGGGTTT
*
35183329 TAGGGTTTAGAGTTT
1 TAGGGTTTAGGGTTT
35183344 TAGGGTTTTAGGGTT
1 TAGGG-TTTAGGGTT
35183359 CAAGGTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
14 10 0.26
15 20 0.53
16 8 0.21
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (15 bp):
TAGGGTTTAGGGTTT
Found at i:35183349 original size:23 final size:23
Alignment explanation
Indices: 35183308--35183367 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
35183298 TATAGGGTTA
35183308 AGGGTTT-AAGGTTTAGGGTTTT
1 AGGGTTTAAAGGTTTAGGGTTTT
* *
35183330 AGGGTTTAGAGTTTTAGGGTTTT
1 AGGGTTTAAAGGTTTAGGGTTTT
*
35183353 AGGG-TTCAAGGTTTA
1 AGGGTTTAAAGGTTTA
35183368 TGGCCCACAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.20, C:0.02, G:0.35, T:0.43
Consensus pattern (23 bp):
AGGGTTTAAAGGTTTAGGGTTTT
Found at i:35185409 original size:25 final size:25
Alignment explanation
Indices: 35185381--35185428 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
35185371 TTGTTGAGAG
*
35185381 AAGAATTTTCT-TTGAGGTTTTCTCC
1 AAGAATTCTCTCTTGA-GTTTTCTCC
35185406 AAGAATTCTCTCTTGAGTTTTCT
1 AAGAATTCTCTCTTGAGTTTTCT
35185429 TTAGAAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.48
Consensus pattern (25 bp):
AAGAATTCTCTCTTGAGTTTTCTCC
Found at i:35185725 original size:23 final size:23
Alignment explanation
Indices: 35185699--35185744 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
35185689 TAAATCTTTC
35185699 TCTTGTTGGCAGCAAGGAATCGG
1 TCTTGTTGGCAGCAAGGAATCGG
*
35185722 TCTTGTTGGTAGCAAGGAATCGG
1 TCTTGTTGGCAGCAAGGAATCGG
35185745 CCTTAAATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.35, T:0.28
Consensus pattern (23 bp):
TCTTGTTGGCAGCAAGGAATCGG
Found at i:35191931 original size:23 final size:23
Alignment explanation
Indices: 35191905--35191948 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
35191895 TAAATCTTTC
35191905 TCTTGTTGGCAGCAAGGAATCAG
1 TCTTGTTGGCAGCAAGGAATCAG
*
35191928 TCTTGTTGGTAGCAAGGAATC
1 TCTTGTTGGCAGCAAGGAATC
35191949 GGCCTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (23 bp):
TCTTGTTGGCAGCAAGGAATCAG
Found at i:35197992 original size:11 final size:12
Alignment explanation
Indices: 35197976--35198015 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
35197966 GTTGAACTGG
35197976 ATTTTTAAT-AT
1 ATTTTTAATGAT
35197987 ATTTTT-ATGA-
1 ATTTTTAATGAT
35197997 ATTTTTAATGAT
1 ATTTTTAATGAT
*
35198009 TTTTTTA
1 ATTTTTA
35198016 TTTAACACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 8 0.32
11 11 0.44
12 6 0.24
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (12 bp):
ATTTTTAATGAT
Found at i:35198002 original size:21 final size:22
Alignment explanation
Indices: 35197976--35198016 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35197966 GTTGAACTGG
35197976 ATTTTTAAT-ATATTTTTATGA
1 ATTTTTAATGATATTTTTATGA
*
35197997 ATTTTTAATGATTTTTTTAT
1 ATTTTTAATGATATTTTTAT
35198017 TTAACACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
ATTTTTAATGATATTTTTATGA
Found at i:35202765 original size:20 final size:20
Alignment explanation
Indices: 35202736--35202786 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
35202726 ACCTACAAAC
*
35202736 AAACACATTAAAAACACATT
1 AAACATATTAAAAACACATT
* **
35202756 AAACATATTAAACACATTTT
1 AAACATATTAAAAACACATT
35202776 AACACATATTA
1 AA-ACATATTA
35202787 GACTTAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (20 bp):
AAACATATTAAAAACACATT
Found at i:35202949 original size:19 final size:19
Alignment explanation
Indices: 35202922--35202960 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
35202912 TTATTCCAGC
*
35202922 AACTTAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
35202941 AACTCAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
35202960 A
1 A
35202961 GTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (19 bp):
AACTCAATTAACTAAGATG
Found at i:35205051 original size:14 final size:14
Alignment explanation
Indices: 35205024--35205065 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
35205014 TATCTAACTT
*
35205024 AAAAACTAAGAAATA
1 AAAAAATAA-AAATA
*
35205039 AATAAATAAAAATA
1 AAAAAATAAAAATA
35205053 AAAAAATAAAAAT
1 AAAAAATAAAAAT
35205066 CATTAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (14 bp):
AAAAAATAAAAATA
Done.