Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 72 of 132
Found at i:20879633 original size:13 final size:13
Alignment explanation
Indices: 20879615--20879649 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
20879605 TTCGAGCGCT
20879615 TGTGTGTGCAAGG
1 TGTGTGTGCAAGG
20879628 TGTGTGTGCAAGG
1 TGTGTGTGCAAGG
20879641 TGTGTGTGC
1 TGTGTGTGC
20879650 TTTAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.09, G:0.46, T:0.34
Consensus pattern (13 bp):
TGTGTGTGCAAGG
Found at i:20879845 original size:26 final size:24
Alignment explanation
Indices: 20879813--20879969 Score: 125
Period size: 26 Copynumber: 6.6 Consensus size: 24
20879803 AATTTGAACC
20879813 AAATATTTGAGTTGTTTTTAATAATT
1 AAATATTT-AGTT-TTTTTAATAATT
* *
20879839 AAATATTTA----ATTAAATAATT
1 AAATATTTAGTTTTTTTAATAATT
*
20879859 AAATATTTGGGTTATTTTTAATAATT
1 AAATATTT-AGTT-TTTTTAATAATT
20879885 AAATATTTAGGTTCTTTTTAATAATT
1 AAATATTTA-GTT-TTTTTAATAATT
* *
20879911 AAATATTTA----ATTAAATAATT
1 AAATATTTAGTTTTTTTAATAATT
20879931 AAATATTTGAGTTGTTTTTAATAATT
1 AAATATTT-AGTT-TTTTTAATAATT
*
20879957 AAATAATTA-TTTT
1 AAATATTTAGTTTT
20879970 GTAGAATCAA
Statistics
Matches: 106, Mismatches: 12, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
20 34 0.32
21 1 0.01
23 2 0.02
24 2 0.02
25 2 0.02
26 65 0.61
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.52
Consensus pattern (24 bp):
AAATATTTAGTTTTTTTAATAATT
Found at i:20879903 original size:72 final size:72
Alignment explanation
Indices: 20879813--20879961 Score: 255
Period size: 72 Copynumber: 2.1 Consensus size: 72
20879803 AATTTGAACC
* *
20879813 AAATATTTGAGTTGTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTGGGTTATTTTT
1 AAATATTTGAGTTCTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTGAGTTATTTTT
20879878 AATAATT
66 AATAATT
*
20879885 AAATATTT-AGGTTCTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTGAGTTGTTTT
1 AAATATTTGA-GTTCTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTGAGTTATTTT
20879949 TAATAATT
65 TAATAATT
20879957 AAATA
1 AAATA
20879962 ATTATTTTGT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
71 1 0.01
72 72 0.99
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (72 bp):
AAATATTTGAGTTCTTTTTAATAATTAAATATTTAATTAAATAATTAAATATTTGAGTTATTTTT
AATAATT
Found at i:20880554 original size:11 final size:11
Alignment explanation
Indices: 20880538--20880569 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
20880528 AAATACGTGA
20880538 GATTGAGCAAC
1 GATTGAGCAAC
20880549 GATTGAGCAAC
1 GATTGAGCAAC
20880560 GATTGAGCAA
1 GATTGAGCAA
20880570 AGTCTATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.19
Consensus pattern (11 bp):
GATTGAGCAAC
Found at i:20884714 original size:7 final size:7
Alignment explanation
Indices: 20884702--20884726 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20884692 AAAATAGTCA
20884702 AAAATTC
1 AAAATTC
20884709 AAAATTC
1 AAAATTC
20884716 AAAATTC
1 AAAATTC
20884723 AAAA
1 AAAA
20884727 CAATATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATTC
Found at i:20884755 original size:21 final size:21
Alignment explanation
Indices: 20884716--20884755 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20884706 TTCAAAATTC
*
20884716 AAAATTCAAAACAATATTATA
1 AAAATTCAAAACAAAATTATA
20884737 AAAAGTTCAAAA-AAAATTA
1 AAAA-TTCAAAACAAAATTA
20884756 GCATGGAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.65, C:0.07, G:0.03, T:0.25
Consensus pattern (21 bp):
AAAATTCAAAACAAAATTATA
Found at i:20885417 original size:41 final size:41
Alignment explanation
Indices: 20885372--20885769 Score: 425
Period size: 41 Copynumber: 9.8 Consensus size: 41
20885362 ATGTTTTTTC
* * *
20885372 CATAAACGCTGCTAATGCTCTTACCTTTTACGGTGTTTTCT
1 CATAAACGCCGCTAATGCTCTTACCTTTTACGGCGTTTTGT
* * * *
20885413 CATAAACGCCGCTAATGCTCATACCTTTTGCGGCATTTATGA
1 CATAAACGCCGCTAATGCTCTTACCTTTTACGGCGTTT-TGT
*
20885455 CA-AAATGCCGCTAATGCTCTTACCTTTTGA-GGCGTTTTGT
1 CATAAACGCCGCTAATGCTCTTACCTTTT-ACGGCGTTTTGT
* *
20885495 CATAAATGCCGCTAATGCTCTTACCTTTTGA-GGCATTTTGT
1 CATAAACGCCGCTAATGCTCTTACCTTTT-ACGGCGTTTTGT
**
20885536 CATAAACGCCGCT-ATGCTCTTACCTTTTGTGGCGTTTTGT
1 CATAAACGCCGCTAATGCTCTTACCTTTTACGGCGTTTTGT
* * * *
20885576 CATAAATGCCACTAATGCTCTTATCTTTTGCGGCGTTTTGT
1 CATAAACGCCGCTAATGCTCTTACCTTTTACGGCGTTTTGT
* * *
20885617 CATAAACGCCACTAATGCTCTTACCTTTTGCGGCGTTTTTTT
1 CATAAACGCCGCTAATGCTCTTACCTTTTACGGCG-TTTTGT
* * *
20885659 CATAAACGCTGCTATTGCT-TTACCTTTTACGGCGTTTATGA
1 CATAAACGCCGCTAATGCTCTTACCTTTTACGGCGTTT-TGT
* ** * * *
20885700 GA-AAACATCGCTATTGCT-TTACCTTTTGCGGCGTTTTTT
1 CATAAACGCCGCTAATGCTCTTACCTTTTACGGCGTTTTGT
* *
20885739 CATAAACGCCGCTAATGGT-TTACTTTTTACG
1 CATAAACGCCGCTAATGCTCTTACCTTTTACG
20885770 ACATTTTCGG
Statistics
Matches: 306, Mismatches: 43, Indels: 17
0.84 0.12 0.05
Matches are distributed among these distances:
39 2 0.01
40 94 0.31
41 186 0.61
42 24 0.08
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (41 bp):
CATAAACGCCGCTAATGCTCTTACCTTTTACGGCGTTTTGT
Found at i:20885593 original size:163 final size:164
Alignment explanation
Indices: 20885372--20885755 Score: 465
Period size: 163 Copynumber: 2.3 Consensus size: 164
20885362 ATGTTTTTTC
* * *
20885372 CATAAACGCTGCTAATGCTCTTACCTTTTACGGTGTTTTCTCATAAACGCCGCTAATGCTCATAC
1 CATAAACGCCGCT-ATGCTCTTACCTTTTGCGGCGTTTTCTCATAAACGCCGCTAATGCTCATAC
* *
20885437 CTTTTGCGGCATTTATGACA-AAATGCCGCTAATGCTCTTACCTTTTGAGGCG-TTTTGTCATAA
65 CTTTTGCGGCATTT-TGACATAAACGCCACTAATGCTCTTACCTTTTGAGGCGTTTTTGTCATAA
* *
20885500 ATGCCGCTAATGCTCTTACCTTTTGA-GGCATTT-TGT
129 ACGCCGCTAATGCT-TTACCTTTT-ACGGCATTTATGA
* * * * * *
20885536 CATAAACGCCGCTATGCTCTTACCTTTTGTGGCGTTTTGTCATAAATGCCACTAATGCTCTTATC
1 CATAAACGCCGCTATGCTCTTACCTTTTGCGGCGTTTTCTCATAAACGCCGCTAATGCTCATACC
* * * *
20885601 TTTTGCGGCGTTTTGTCATAAACGCCACTAATGCTCTTACCTTTTGCGGCGTTTTTTTCATAAAC
66 TTTTGCGGCATTTTGACATAAACGCCACTAATGCTCTTACCTTTTGAGGCGTTTTTGTCATAAAC
* * *
20885666 GCTGCTATTGCTTTACCTTTTACGGCGTTTATGA
131 GCCGCTAATGCTTTACCTTTTACGGCATTTATGA
* ** *
20885700 GA-AAACATCGCTATTGCT-TTACCTTTTGCGGCGTTTTTTCATAAACGCCGCTAATG
1 CATAAACGCCGCTA-TGCTCTTACCTTTTGCGGCGTTTTCTCATAAACGCCGCTAATG
20885756 GTTTACTTTT
Statistics
Matches: 188, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
162 5 0.03
163 143 0.76
164 40 0.21
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (164 bp):
CATAAACGCCGCTATGCTCTTACCTTTTGCGGCGTTTTCTCATAAACGCCGCTAATGCTCATACC
TTTTGCGGCATTTTGACATAAACGCCACTAATGCTCTTACCTTTTGAGGCGTTTTTGTCATAAAC
GCCGCTAATGCTTTACCTTTTACGGCATTTATGA
Found at i:20885605 original size:122 final size:122
Alignment explanation
Indices: 20885319--20885755 Score: 488
Period size: 122 Copynumber: 3.6 Consensus size: 122
20885309 AAATAAATTC
** * * * * ** * *
20885319 GCGGCGTTTATGGGAAAACGCCGCTATTGCT-TAACCTTTAGCGATGTTTTTTCCATAAACGCTG
1 GCGGCGTTTATGACAAAATGCCGCTAATGCTCTTACCTTTTGCGGCGTTTTGT-CATAAACGCCG
** *
20885383 CTAATGCTCTTACCTTTT-ACGGTGTTTTCTCATAAACGCCGCTAATGCTCATACCTTTT
65 CTAATGCTCTTACCTTTTGA-GGCATTTTCTCATAAACGCCGCT-ATGCTCTTACCTTTT
* * *
20885442 GCGGCATTTATGACAAAATGCCGCTAATGCTCTTACCTTTTGAGGCGTTTTGTCATAAATGCCGC
1 GCGGCGTTTATGACAAAATGCCGCTAATGCTCTTACCTTTTGCGGCGTTTTGTCATAAACGCCGC
*
20885507 TAATGCTCTTACCTTTTGAGGCATTTTGTCATAAACGCCGCTATGCTCTTACCTTTT
66 TAATGCTCTTACCTTTTGAGGCATTTTCTCATAAACGCCGCTATGCTCTTACCTTTT
* * * * *
20885564 GTGGCGTTT-TGTCATAAATGCCACTAATGCTCTTATCTTTTGCGGCGTTTTGTCATAAACGCCA
1 GCGGCGTTTATGACA-AAATGCCGCTAATGCTCTTACCTTTTGCGGCGTTTTGTCATAAACGCCG
* * * *
20885628 CTAATGCTCTTACCTTTTGCGGCGTTTTTTTCATAAACGCTGCTATTGCT-TTACCTTTT
65 CTAATGCTCTTACCTTTTGAGGC-ATTTTCTCATAAACGCCGCTA-TGCTCTTACCTTTT
* * *** * *
20885687 ACGGCGTTTATGAGAAAACATCGCTATTGCT-TTACCTTTTGCGGCGTTTTTTCATAAACGCCGC
1 GCGGCGTTTATGACAAAATGCCGCTAATGCTCTTACCTTTTGCGGCGTTTTGTCATAAACGCCGC
20885751 TAATG
66 TAATG
20885756 GTTTACTTTT
Statistics
Matches: 267, Mismatches: 41, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
121 4 0.01
122 122 0.46
123 118 0.44
124 23 0.09
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (122 bp):
GCGGCGTTTATGACAAAATGCCGCTAATGCTCTTACCTTTTGCGGCGTTTTGTCATAAACGCCGC
TAATGCTCTTACCTTTTGAGGCATTTTCTCATAAACGCCGCTATGCTCTTACCTTTT
Found at i:20890348 original size:23 final size:23
Alignment explanation
Indices: 20890318--20890374 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
20890308 TAAAAATATG
20890318 AAAAATAAAAAGATTAAATTTTT
1 AAAAATAAAAAGATTAAATTTTT
20890341 AAAAATAAAAAGATTAAATTTTT
1 AAAAATAAAAAGATTAAATTTTT
20890364 AAAAATAAAAA
1 AAAAATAAAAA
20890375 TACAAAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAAATAAAAAGATTAAATTTTT
Found at i:20926181 original size:14 final size:14
Alignment explanation
Indices: 20926158--20926195 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
20926148 TATTTTTGCA
20926158 TTTCCTTTTATCT-
1 TTTCCTTTTATCTG
*
20926171 TTTCACTTTTATTTG
1 TTTC-CTTTTATCTG
20926186 TTTCCTTTTA
1 TTTCCTTTTA
20926196 AATTCTATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 14 0.64
15 4 0.18
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTCCTTTTATCTG
Found at i:20931130 original size:33 final size:33
Alignment explanation
Indices: 20931084--20931149 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
20931074 ATCTTTATGC
*
20931084 CTTAAATTGAAAATGAT-TTTTA-TATAGGGGGAG
1 CTTAAATTCAAAATG-TCTTTTATTA-AGGGGGAG
20931117 CTTAAATTCAAAATGTCTTTTATTAAGGGGGAG
1 CTTAAATTCAAAATGTCTTTTATTAAGGGGGAG
20931150 TAATCTATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 1 0.03
33 27 0.90
34 2 0.07
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (33 bp):
CTTAAATTCAAAATGTCTTTTATTAAGGGGGAG
Found at i:20933100 original size:19 final size:19
Alignment explanation
Indices: 20933076--20933115 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
20933066 TGGATAAGAA
*
20933076 CAAAAATGTGTGAGCTATC
1 CAAAAAAGTGTGAGCTATC
*
20933095 CAAAAAAGTGTGAGTTATC
1 CAAAAAAGTGTGAGCTATC
20933114 CA
1 CA
20933116 GTCTGGTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (19 bp):
CAAAAAAGTGTGAGCTATC
Found at i:20949297 original size:17 final size:16
Alignment explanation
Indices: 20949270--20949311 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
20949260 GTCGTATAAA
20949270 AAAATAAAAGAGAAAAG
1 AAAA-AAAAGAGAAAAG
*
20949287 AAAGAAAAAGATAAAAG
1 AAA-AAAAAGAGAAAAG
20949304 AAAAAAAA
1 AAAAAAAA
20949312 TATATAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 17 0.74
18 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (16 bp):
AAAAAAAAGAGAAAAG
Found at i:20958682 original size:18 final size:18
Alignment explanation
Indices: 20958636--20958682 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
20958626 TCATGATCAA
*
20958636 ATGCAATCACATGCTCAG
1 ATGCAACCACATGCTCAG
*
20958654 ATGCAATCACATGCTC-G
1 ATGCAACCACATGCTCAG
*
20958671 TATGCAGCCACA
1 -ATGCAACCACA
20958683 GTAGACTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (18 bp):
ATGCAACCACATGCTCAG
Found at i:20968664 original size:21 final size:21
Alignment explanation
Indices: 20968621--20968664 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
20968611 CTCCAAAGAC
* * *
20968621 AAAAAGCGCAGGAAGGAGGAG
1 AAAAAGAGCAGGAAGAAGAAG
*
20968642 AAAAAGAGGAGGAAGAAGAAG
1 AAAAAGAGCAGGAAGAAGAAG
20968663 AA
1 AA
20968665 TCGTGTAGCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.39, T:0.00
Consensus pattern (21 bp):
AAAAAGAGCAGGAAGAAGAAG
Found at i:20977159 original size:20 final size:18
Alignment explanation
Indices: 20977131--20977178 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
20977121 CCACATCAGG
*
20977131 AAATAATTTTAAAATAATTA
1 AAATTATTTTAAAAT-A-TA
20977151 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
20977171 AAATTATT
1 AAATTATT
20977179 AAAATCATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 13 0.52
21 1 0.04
22 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:20977165 original size:22 final size:20
Alignment explanation
Indices: 20977137--20977178 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
20977127 CAGGAAATAA
20977137 TTTTAAAATAATTAAAATTATT
1 TTTTAAAAT-A-TAAAATTATT
20977159 TTTTAAAATATAAAATTATT
1 TTTTAAAATATAAAATTATT
20977179 AAAATCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 1 0.05
22 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTAAAATATAAAATTATT
Found at i:20978205 original size:6 final size:6
Alignment explanation
Indices: 20978191--20978229 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
20978181 AATTAAATAT
* *
20978191 AAGGAG AAGGGG AAGGGG AAGTGG AAGGGG CAAGGGG AA
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG AA
20978230 TAGAAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.38, C:0.03, G:0.56, T:0.03
Consensus pattern (6 bp):
AAGGGG
Found at i:20978316 original size:21 final size:20
Alignment explanation
Indices: 20978275--20978317 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
20978265 TAATTTTATA
**
20978275 TTTAAAAAATTTAAATTAAT
1 TTTAAAAAATTTAAAAAAAT
20978295 TTTAAAACAATTTAAAAAAAT
1 TTTAAAA-AATTTAAAAAAAT
20978316 TT
1 TT
20978318 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAAAAATTTAAAAAAAT
Found at i:20995040 original size:30 final size:29
Alignment explanation
Indices: 20995006--20995062 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
20994996 AACCGAATTT
*
20995006 AAAGAAAGAAAAATAATAAAAAATAAAAAC
1 AAAGAAACAAAAATAA-AAAAAATAAAAAC
* *
20995036 AAAGAACCAAAAATAAATAAAATAAAA
1 AAAGAAACAAAAATAAAAAAAATAAAA
20995063 TCATATCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (29 bp):
AAAGAAACAAAAATAAAAAAAATAAAAAC
Found at i:21012136 original size:17 final size:17
Alignment explanation
Indices: 21012094--21012130 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
21012084 ATGCATCTCA
* *
21012094 TTTAATTGTCATTGCAT
1 TTTAGTTGTCGTTGCAT
21012111 TTTAGTTGTCGTTGCAT
1 TTTAGTTGTCGTTGCAT
21012128 TTT
1 TTT
21012131 CTTTGTTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (17 bp):
TTTAGTTGTCGTTGCAT
Found at i:21017012 original size:13 final size:13
Alignment explanation
Indices: 21016994--21017018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21016984 TAAGTTAAAA
21016994 ATGCTAAAAATGC
1 ATGCTAAAAATGC
21017007 ATGCTAAAAATG
1 ATGCTAAAAATG
21017019 ATAAAATGGG
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:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:21018480 original size:26 final size:26
Alignment explanation
Indices: 21018451--21018591 Score: 171
Period size: 26 Copynumber: 5.4 Consensus size: 26
21018441 GGCTTCAAGT
*
21018451 CGATGAATATATAGCAGGCCTTGAGC
1 CGATGAATATATAGCAAGCCTTGAGC
21018477 CGATGAATATATAGCAAGCCTTGAGC
1 CGATGAATATATAGCAAGCCTTGAGC
21018503 C-AGTGAATATATAGCAAGCCTTG-GTC
1 CGA-TGAATATATAGCAAGCCTTGAG-C
* * * *
21018529 CGGTGAATA-ATTAGCAGGCCTTAAGT
1 CGATGAATATA-TAGCAAGCCTTGAGC
*
21018555 CGATGAATATATATCAAGCCTTGAGC
1 CGATGAATATATAGCAAGCCTTGAGC
*
21018581 CAATGAATATA
1 CGATGAATATA
21018592 CAGTAGGCTT
Statistics
Matches: 98, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
25 3 0.03
26 93 0.95
27 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (26 bp):
CGATGAATATATAGCAAGCCTTGAGC
Found at i:21047072 original size:19 final size:19
Alignment explanation
Indices: 21047045--21047082 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21047035 AATTACCCAA
*
21047045 AAATTAAAAGTCTT-AAAAT
1 AAATCAAAA-TCTTCAAAAT
21047064 AAATCAAAATCTTCAAAAT
1 AAATCAAAATCTTCAAAAT
21047083 TAAAGTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.29
Consensus pattern (19 bp):
AAATCAAAATCTTCAAAAT
Found at i:21066914 original size:14 final size:14
Alignment explanation
Indices: 21066892--21066935 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
21066882 CAGATCGAAA
21066892 GCAAAAATAAAAAT
1 GCAAAAATAAAAAT
*
21066906 GCAATAAT-AAAA-
1 GCAAAAATAAAAAT
*
21066918 GAAAAAATAAAAAT
1 GCAAAAATAAAAAT
21066932 GCAA
1 GCAA
21066936 TAATTCCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 6 0.25
13 8 0.33
14 10 0.42
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.14
Consensus pattern (14 bp):
GCAAAAATAAAAAT
Found at i:21066918 original size:26 final size:26
Alignment explanation
Indices: 21066889--21066939 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
21066879 GCACAGATCG
*
21066889 AAAGCAAAAATAAAAATGCAATAATA
1 AAAGAAAAAATAAAAATGCAATAATA
21066915 AAAGAAAAAATAAAAATGCAATAAT
1 AAAGAAAAAATAAAAATGCAATAAT
21066940 TCCTATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.16
Consensus pattern (26 bp):
AAAGAAAAAATAAAAATGCAATAATA
Found at i:21069906 original size:21 final size:22
Alignment explanation
Indices: 21069880--21069920 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
21069870 TATTTAGAAG
*
21069880 ATAAAAAC-TAAGTTAAAATCT
1 ATAAAAACATAAGTAAAAATCT
21069901 ATAAAAACATAAGTAAAAAT
1 ATAAAAACATAAGTAAAAAT
21069921 ACTTGATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.24
Consensus pattern (22 bp):
ATAAAAACATAAGTAAAAATCT
Found at i:21070585 original size:24 final size:24
Alignment explanation
Indices: 21070537--21070583 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
21070527 AAGAATTAAT
21070537 TTGTCAACGCAAATATAAAATAAA
1 TTGTCAACGCAAATATAAAATAAA
*
21070561 TTGTCAGA-GCAAAT-TAAGATAAA
1 TTGTCA-ACGCAAATATAAAATAAA
21070584 ATGAATGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.26
Consensus pattern (24 bp):
TTGTCAACGCAAATATAAAATAAA
Found at i:21103458 original size:3 final size:3
Alignment explanation
Indices: 21103450--21103509 Score: 72
Period size: 3 Copynumber: 20.0 Consensus size: 3
21103440 GTATTGAGGT
21103450 AGA AGA AGA AGAA AGA A-A AGA AGA AGA AGA AGA AGA AG- AGA AGGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA
21103495 AGA A-A GAGA AGA AGA
1 AGA AGA -AGA AGA AGA
21103510 TGTTGCCACG
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
2 5 0.10
3 39 0.76
4 7 0.14
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:21103482 original size:24 final size:25
Alignment explanation
Indices: 21103450--21103509 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
21103440 GTATTGAGGT
21103450 AGAAGAAGAAGAAAGA-AAAGAAGA
1 AGAAGAAGAAGAAAGAGAAAGAAGA
*
21103474 AGAAGAAGAAG-AAGAGAAGGAAGA
1 AGAAGAAGAAGAAAGAGAAAGAAGA
21103498 A-AGAGAAGAAGA
1 AGA-AGAAGAAGA
21103510 TGTTGCCACG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.16
24 27 0.84
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (25 bp):
AGAAGAAGAAGAAAGAGAAAGAAGA
Found at i:21108398 original size:22 final size:22
Alignment explanation
Indices: 21108359--21108403 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
21108349 TGCACCACCA
*
21108359 CCGTACCACAATCGCGCCATCG
1 CCGTACCACAATCACGCCATCG
** *
21108381 CCGTACCACTGTCACGCCGTCG
1 CCGTACCACAATCACGCCATCG
21108403 C
1 C
21108404 TGTCAATCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.16
Consensus pattern (22 bp):
CCGTACCACAATCACGCCATCG
Found at i:21109443 original size:45 final size:45
Alignment explanation
Indices: 21109353--21109446 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
21109343 GCATATCGAT
** * * *
21109353 ATAAGTGAGCTATTTTTGTCGAGCAACCTGGGGTAGCAATTTGAC
1 ATAAGTGAGCTATCGTTGTCGAGCAACCTGAGGCAGCAATATGAC
* *
21109398 ATAAGTGAGCTATCGTTGTCGGGCAA-CTCGAGGCAGTAATATGAC
1 ATAAGTGAGCTATCGTTGTCGAGCAACCT-GAGGCAGCAATATGAC
21109443 ATAA
1 ATAA
21109447 ATGGGCCAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (45 bp):
ATAAGTGAGCTATCGTTGTCGAGCAACCTGAGGCAGCAATATGAC
Found at i:21116990 original size:45 final size:45
Alignment explanation
Indices: 21116922--21117047 Score: 153
Period size: 45 Copynumber: 2.8 Consensus size: 45
21116912 TATAGATATG
* * * * *
21116922 AGTGAGCTATTGTTGCCGGGCAACCCGGGGTAGCAGTTTGACATA
1 AGTGAGCTATCGTTACCGGGCAACCTGGGGTAGCAATATGACATA
* * *
21116967 AGTGAGCTATCGTTACCGAGCAACTTAGGGTAGCAATATGACATA
1 AGTGAGCTATCGTTACCGGGCAACCTGGGGTAGCAATATGACATA
* * *
21117012 AGTGAGCCATCATTACCGGGCAACCTGGGGTGGCAA
1 AGTGAGCTATCGTTACCGGGCAACCTGGGGTAGCAA
21117048 GTCATTATTG
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (45 bp):
AGTGAGCTATCGTTACCGGGCAACCTGGGGTAGCAATATGACATA
Found at i:21124886 original size:24 final size:24
Alignment explanation
Indices: 21124854--21124903 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
21124844 ATTTGGTGTC
21124854 CTACAACGCAACAAGGTGGGAGTT
1 CTACAACGCAACAAGGTGGGAGTT
21124878 CTACAACGCAACAAGGTGGGAGTT
1 CTACAACGCAACAAGGTGGGAGTT
21124902 CT
1 CT
21124904 CACCAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (24 bp):
CTACAACGCAACAAGGTGGGAGTT
Found at i:21128237 original size:78 final size:77
Alignment explanation
Indices: 21128144--21128343 Score: 233
Period size: 78 Copynumber: 2.6 Consensus size: 77
21128134 TAGTAGGCCT
* * * ***
21128144 TGAGCCGGT-TATTATTTAGCAAGCTTTGAGCTGGTGTTTATTTAGTAGGCATTGAGTTGGTGTT
1 TGAGCCGGTGT-TTATTTAGCAAGCTTTGAGCCGATGTTTATTTAGCAGGCATTGAGCCAGTGTT
21128208 TATTTAACAAGCCA
65 TA-TTAACAAGCCA
** * *
21128222 TGAGGTGGTGTTTATTTAGC-AGACCTTGAGCCAATGTTTATTTAGCAGGCATTGAGCCAGTGTT
1 TGAGCCGGTGTTTATTTAGCAAG-CTTTGAGCCGATGTTTATTTAGCAGGCATTGAGCCAGTGTT
* **
21128286 TATTAGCAAGCTT
65 TATTAACAAGCCA
*
21128299 TGAGCCGGTGTTTATTTAGCAAGCTTTGAGCCGATGTGTATTTAG
1 TGAGCCGGTGTTTATTTAGCAAGCTTTGAGCCGATGTTTATTTAG
21128344 ACGATATTAT
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
77 47 0.47
78 53 0.52
79 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.38
Consensus pattern (77 bp):
TGAGCCGGTGTTTATTTAGCAAGCTTTGAGCCGATGTTTATTTAGCAGGCATTGAGCCAGTGTTT
ATTAACAAGCCA
Found at i:21128324 original size:26 final size:26
Alignment explanation
Indices: 21128116--21128343 Score: 194
Period size: 26 Copynumber: 8.8 Consensus size: 26
21128106 AATAGTAGAC
* * * *
21128116 CTTT-AGCAGGTGTTTAATTAGTAGG
1 CTTTGAGCCGGTGTTTATTTAGCAAG
*
21128141 CCTTGAGCCGGT-TATTATTTAGCAAG
1 CTTTGAGCCGGTGT-TTATTTAGCAAG
* * *
21128167 CTTTGAGCTGGTGTTTATTTAGTAGG
1 CTTTGAGCCGGTGTTTATTTAGCAAG
* ** *
21128193 CATTGAGTTGGTGTTTATTTAACAAG
1 CTTTGAGCCGGTGTTTATTTAGCAAG
** **
21128219 CCATGAGGTGGTGTTTATTTAGC-AG
1 CTTTGAGCCGGTGTTTATTTAGCAAG
* ** *
21128244 ACCTTGAGCCAATGTTTATTTAGCAGG
1 -CTTTGAGCCGGTGTTTATTTAGCAAG
* *
21128271 CATTGAGCCAGTGTTTA-TTAGCAAG
1 CTTTGAGCCGGTGTTTATTTAGCAAG
21128296 CTTTGAGCCGGTGTTTATTTAGCAAG
1 CTTTGAGCCGGTGTTTATTTAGCAAG
* *
21128322 CTTTGAGCCGATGTGTATTTAG
1 CTTTGAGCCGGTGTTTATTTAG
21128344 ACGATATTAT
Statistics
Matches: 166, Mismatches: 31, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
25 28 0.17
26 136 0.82
27 2 0.01
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.38
Consensus pattern (26 bp):
CTTTGAGCCGGTGTTTATTTAGCAAG
Found at i:21133532 original size:15 final size:15
Alignment explanation
Indices: 21133512--21133540 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21133502 AAGGGGCTAG
21133512 ATATTAATTGAAGAA
1 ATATTAATTGAAGAA
21133527 ATATTAATTGAAGA
1 ATATTAATTGAAGA
21133541 TATTATAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (15 bp):
ATATTAATTGAAGAA
Found at i:21133545 original size:13 final size:13
Alignment explanation
Indices: 21133510--21133545 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
21133500 AAAAGGGGCT
21133510 AGATATTAATTGA
1 AGATATTAATTGA
21133523 AGAAATATTAATTGA
1 AG--ATATTAATTGA
21133538 AGATATTA
1 AGATATTA
21133546 TAGACACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.38
15 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (13 bp):
AGATATTAATTGA
Found at i:21137586 original size:17 final size:17
Alignment explanation
Indices: 21137560--21137604 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
21137550 ATAGTATAAT
*
21137560 TGTCCCTGCATTATTAA
1 TGTCACTGCATTATTAA
* * *
21137577 TGTCATTGCATTTTTAT
1 TGTCACTGCATTATTAA
21137594 TGTCACTGCAT
1 TGTCACTGCAT
21137605 CTACATTATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (17 bp):
TGTCACTGCATTATTAA
Found at i:21138201 original size:18 final size:18
Alignment explanation
Indices: 21138170--21138218 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
21138160 TCAATCATTT
21138170 GAAAAA-GAA-AAAAATGA
1 GAAAAAGGAAGAAAAA-GA
21138187 GAAAAAGGAAGAAAAAGA
1 GAAAAAGGAAGAAAAAGA
* *
21138205 AAAAAAGAAAGAAA
1 GAAAAAGGAAGAAA
21138219 TTTTTGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 17 0.61
19 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
GAAAAAGGAAGAAAAAGA
Found at i:21143266 original size:21 final size:22
Alignment explanation
Indices: 21143240--21143281 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
21143230 AATCAAAAAG
21143240 AAAAGAAAAATGAGT-AGAAAC
1 AAAAGAAAAATGAGTAAGAAAC
**
21143261 AAAAGAATCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
21143282 ACATCTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.05, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAGAAAAATGAGTAAGAAAC
Found at i:21151378 original size:3 final size:3
Alignment explanation
Indices: 21151370--21151410 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
21151360 AGGGCAATTC
21151370 CTT CTT CTT CTT -TT CTCT CTT CTT C-T CTT GCTT CTT CTT CT
1 CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT -CTT CTT CTT CT
21151411 ACTGCAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.12
3 24 0.71
4 6 0.18
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:21151392 original size:15 final size:15
Alignment explanation
Indices: 21151370--21151410 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
21151360 AGGGCAATTC
*
21151370 CTTCTTCTTCT-TTT
1 CTTCTTCTTCTCTTG
21151384 CTCTCTTCTTCTCTTG
1 CT-TCTTCTTCTCTTG
21151400 CTTCTTCTTCT
1 CTTCTTCTTCT
21151411 ACTGCAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 2 0.08
15 18 0.75
16 4 0.17
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.63
Consensus pattern (15 bp):
CTTCTTCTTCTCTTG
Found at i:21167927 original size:3 final size:3
Alignment explanation
Indices: 21167919--21167980 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
21167909 AAAGGCCCAA
* * * *
21167919 ATT ATT ATT ATC ATT ACT ATT CTT ATT AATT GTT ATT ATT ATT AATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT -ATT
21167966 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
21167981 TCAGGGTTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:21167960 original size:16 final size:16
Alignment explanation
Indices: 21167919--21167978 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
21167909 AAAGGCCCAA
*
21167919 ATTATTATTA-TCATT
1 ATTATTATTATTAATT
* *
21167934 ACTATTCTTATTAATT
1 ATTATTATTATTAATT
*
21167950 GTTATTATTATTAATT
1 ATTATTATTATTAATT
21167966 ATTATTATTATTA
1 ATTATTATTATTA
21167979 TTTCAGGGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
15 8 0.22
16 29 0.78
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTATTATTATTAATT
Found at i:21168786 original size:22 final size:21
Alignment explanation
Indices: 21168755--21168799 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
21168745 TCATTAAAAA
* *
21168755 AGAAAAAAAAGTTTATATTTTT
1 AGAAAAAAAAATCTAT-TTTTT
*
21168777 AGAAATAAAAATCTATTTTTT
1 AGAAAAAAAAATCTATTTTTT
21168798 AG
1 AG
21168800 TTATTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (21 bp):
AGAAAAAAAAATCTATTTTTT
Found at i:21169033 original size:151 final size:150
Alignment explanation
Indices: 21168512--21169046 Score: 722
Period size: 150 Copynumber: 3.6 Consensus size: 150
21168502 GTTTTTTTAG
* * *
21168512 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATATTTTTTAACTATTTCAAAATAAAAGTTTAGATT
* *
21168577 TTTAAG-AAAGTAGTGATTTTCATTAAAAAGG-AAAAAGTTTATATTTTTAAAAATAAAAATTTG
66 TTTAAGTAAAGTAGTGATTTTCATTAAAAAGGAAAAAAGTTTATATTTTTAAAAATAAAAATCTA
* *
21168640 GTTTTTCGTTATTTTAAAGA
131 TTTTTTAGTTATTTTAAAGA
* * * *
21168660 AAATGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAATAAAAGTTTGGAGT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATATTTTTTAACTATTTCAAAATAAAAGTTTAGATT
* *
21168725 TTTAAGTAAAGTAGTGATTTTCATTAAAAAAGAAAAAAAAGTTTATATTTTTAGAAATAAAAATC
66 TTTAAGTAAAGTAGTGATTTTCATT-AAAAAG-GAAAAAAGTTTATATTTTTAAAAATAAAAATC
21168790 TATTTTTTAGTTATTTTAAAGA
129 TATTTTTTAGTTATTTTAAAGA
* * * *
21168812 AAAAGTTTATATTTTTAAATAAAG-TTTGAT-TTTTTCAACTATTTCGAAATAAAAGTTTAGATT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATATTTTTTAACTATTTCAAAATAAAAGTTTAGATT
* *
21168875 TTTAAGTAGAGTAGTGATTTTCATTAAAAAGGAAAGAAAGTTTAGATTTTTAAAAAATAAAAATC
66 TTTAAGTAAAGTAGTGATTTTCATTAAAAAGGAAA-AAAGTTTATATTTTT-AAAAATAAAAATC
* *
21168940 TATTTTTTAGTGATTTTAAACAA
129 TATTTTTTAGTTATTTTAAA-GA
* * * * * *
21168963 AAAAGTTTAAATTTTTTACCAAAG-TTT-AAATTTTTTAAATATTTTAAAATAAAAGTTTTGATT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATATTTTTTAACTATTTCAAAATAAAAGTTTAGATT
* *
21169026 TTGAAGTAAAATAGTGATTTT
66 TTTAAGTAAAGTAGTGATTTT
21169047 GTTTTAATTA
Statistics
Matches: 342, Mismatches: 37, Indels: 13
0.87 0.09 0.03
Matches are distributed among these distances:
148 69 0.20
149 38 0.11
150 91 0.27
151 76 0.22
152 68 0.20
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (150 bp):
AAAAGTTTAAATTTTTAAACAAAGTTTTGATATTTTTTAACTATTTCAAAATAAAAGTTTAGATT
TTTAAGTAAAGTAGTGATTTTCATTAAAAAGGAAAAAAGTTTATATTTTTAAAAATAAAAATCTA
TTTTTTAGTTATTTTAAAGA
Found at i:21170385 original size:161 final size:159
Alignment explanation
Indices: 21170091--21170396 Score: 490
Period size: 161 Copynumber: 1.9 Consensus size: 159
21170081 AAAATCATAA
21170091 TAATGAAAAAAAATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
1 TAATGAAAAAAAATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
* **
21170156 TTAGGCTTTTTTATGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTACTAGAATTA
66 TTAGGCTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAATATTTTACTAGAATTA
21170221 TTTAAGTAT-CTTTACAAGTAAATCGGAG
131 TTTAAGTATCCTTTACAAGTAAATCGGAG
* * *
21170249 TAATGATAAAATATCGAATAAGTTGTTGATGAATTTTAATATTTCTCTTAATTCATTAGTAATTT
1 TAATGAAAAAAAATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAA---
*
21170314 TTTTTAGG-TTTTGTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAATATTTTACTAGA
63 CTTTTAGGCTTTT-TTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAATATTTTACTAGA
*
21170378 ATTATTTAGGTATCCTTTA
127 ATTATTTAAGTATCCTTTA
21170397 GGGTTCTTAT
Statistics
Matches: 135, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
158 59 0.44
160 4 0.03
161 67 0.50
162 5 0.04
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (159 bp):
TAATGAAAAAAAATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
TTAGGCTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAATATTTTACTAGAATTA
TTTAAGTATCCTTTACAAGTAAATCGGAG
Found at i:21175414 original size:42 final size:42
Alignment explanation
Indices: 21174743--21175391 Score: 926
Period size: 42 Copynumber: 15.5 Consensus size: 42
21174733 AAGGAAAACA
* * * * *
21174743 TTCATTGCATTTAGAGGCCTAAGTGTGAAAGTCCATTTACAT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
21174785 TTCATCGCATTCAGAGGCGCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
21174827 TTCATTTCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
21174869 TTCATTGCATTTAGAGGCCCACGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
21174911 TTCATTACATTTAGAGGCCCAGGTATGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
21174953 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
21174995 TTCATTACATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
21175037 TTCATTGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * ** *
21175079 TTCATTGCATTTAGAGGCCTAGGTGAGGAGACCCATTAACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
21175121 TTCATTGCATTTAGAGGCCTAGGTGAGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
21175163 TGT-ATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 T-TCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
21175205 TTTATTGCATTTAGAAGACCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
21175247 TTCATTGCATTTAGACGCCGAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
21175289 TTCATTGCATTTAGAGGCTCAGGTGTGGAGGTTCAGTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
21175331 TTCATTTCATTTAGAGGCCCAGGTGTGGAGG-CTCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
*
21175373 TTCATTTCATTTAGAGGCC
1 TTCATTGCATTTAGAGGCC
21175392 TAGGCTTAAA
Statistics
Matches: 547, Mismatches: 55, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
41 2 0.00
42 543 0.99
43 2 0.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:21175868 original size:3 final size:3
Alignment explanation
Indices: 21175860--21175886 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21175850 AAAGGCCCAA
21175860 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
21175887 TTTAGGGTTT
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):
ATT
Found at i:21176576 original size:149 final size:150
Alignment explanation
Indices: 21176412--21176947 Score: 756
Period size: 149 Copynumber: 3.6 Consensus size: 150
21176402 TGTTTTTTAG
*
21176412 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAATAAAAGTTTAAATT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGA-TTTTTTTAACTATTTCAAAATAAAAGTTTAGATT
* * *
21176477 TTTGAG-AAAGTAGTTATTTTCATTAAAAAG-GAGAAAGTTTATATTTTTAAAAATAAAAATCTA
65 TTTAAGTAAAGTAGTGATTTTCATTAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATCTA
21176540 TTTTTTAGTTATTTTAAAGAA
130 TTTTTTAGTTATTTTAAAGAA
* * * *
21176561 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAATTTGGATTT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAATAAAAGTTTAGATTT
* * **
21176626 TTAAATAAAGTAGTGATTTTCATTAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATTTGG
66 TTAAGTAAAGTAGTGATTTTCATTAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATCTAT
21176691 TTTTTAGTTATTTTAAAG-A
131 TTTTTAGTTATTTTAAAGAA
** * * * * * *
21176710 AAATTTTTAAATTTTTAAATAAAATTTTTATTTTTTCAAGTATTTCGAAATAAAAGTTTAGATTT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAATAAAAGTTTAGATTT
* *
21176775 TTAAGTAGAGTAGTGATTTTCATTAAAAAATGAAAGAAAGTTTAGATTTTTTAAAAAATAAAAAT
66 TTAAGTAAAGTAGTGATTTTCATT-AAAAA-GAAAGAAAGTTTATA-TTTTT-AAAAATAAAAAT
*
21176840 CTATTTTTTAGTAATTTTAAAGAA
127 CTATTTTTTAGTTATTTTAAAGAA
* * *
21176864 AAAAGTTTAAATTTTTAAACAAAGTTTTGA-CTTTTTAAATATTTCAAAATAAAAGTTTTGATTT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAATAAAAGTTTAGATTT
*
21176928 TGAAGTAAAGTAGTGATTTT
66 TTAAGTAAAGTAGTGATTTT
21176948 GTTTTAATCA
Statistics
Matches: 341, Mismatches: 39, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
148 34 0.10
149 132 0.39
150 53 0.16
151 14 0.04
152 5 0.01
153 77 0.23
154 26 0.08
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (150 bp):
AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAATAAAAGTTTAGATTT
TTAAGTAAAGTAGTGATTTTCATTAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATCTAT
TTTTTAGTTATTTTAAAGAA
Found at i:21176745 original size:21 final size:21
Alignment explanation
Indices: 21176691--21176745 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
21176681 AAAAATTTGG
*
21176691 TTTTTAGTTATTTTAAAGAAAA
1 TTTTTA-TTTTTTTAAAGAAAA
** *
21176713 TTTTTAAATTTTTAAATAAAA
1 TTTTTATTTTTTTAAAGAAAA
21176734 TTTTTATTTTTT
1 TTTTTATTTTTT
21176746 CAAGTATTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTTTATTTTTTTAAAGAAAA
Found at i:21178041 original size:158 final size:159
Alignment explanation
Indices: 21177842--21178154 Score: 522
Period size: 159 Copynumber: 2.0 Consensus size: 159
21177832 AAATCTTTTA
* *
21177842 AAATCATAATAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTATTAATTCAT
1 AAATCAGAATAATGATAAAAGATCGAATAAGTTGTAAATGAATTTTAATATTTCTATTAATTCAT
**
21177907 TGGTAA-TTTTTAGGCTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTT
66 AAGTAATTTTTTAGG-TTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTT
21177971 ACTAGAATTATTTAAGTAT-CTTTACAAGT
130 ACTAGAATTATTTAAGTATCCTTTACAAGT
* *
21178000 AAATCAGAGTAATGATAAAAGATCGAATAAGTTGTAAATGAATTTTAATATTTCTCTTAATTCAT
1 AAATCAGAATAATGATAAAAGATCGAATAAGTTGTAAATGAATTTTAATATTTCTATTAATTCAT
*
21178065 AAGTAATTTTTTTAGGTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATGTATTTT
66 AAGTAA-TTTTTTAGGTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTT
*
21178130 ACTAGAATTATTTAGGTATCCTTTA
130 ACTAGAATTATTTAAGTATCCTTTA
21178155 GGGATATTAT
Statistics
Matches: 144, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
158 65 0.45
159 66 0.46
160 13 0.09
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (159 bp):
AAATCAGAATAATGATAAAAGATCGAATAAGTTGTAAATGAATTTTAATATTTCTATTAATTCAT
AAGTAATTTTTTAGGTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTA
CTAGAATTATTTAAGTATCCTTTACAAGT
Found at i:21180562 original size:19 final size:20
Alignment explanation
Indices: 21180516--21180564 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
21180506 ATTAGCATGA
21180516 GTTATATTAAGTATAAATAGG
1 GTTA-ATTAAGTATAAATAGG
*
21180537 TTTAATTAAG-ACTAAA-AGG
1 GTTAATTAAGTA-TAAATAGG
21180556 GTTAATTAA
1 GTTAATTAA
21180565 AGCGTAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.48
20 10 0.40
21 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (20 bp):
GTTAATTAAGTATAAATAGG
Found at i:21209612 original size:59 final size:59
Alignment explanation
Indices: 21209530--21209758 Score: 218
Period size: 59 Copynumber: 3.9 Consensus size: 59
21209520 TTTCATGGTA
* * *
21209530 AAAATGTAATTTT-AGAAAAGTTTGAAGGTTAAAATATAATTTTAGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGAG-AAAGTTTG-GGGTCAAAATATAATTTTAGAAAAGTTTAAGGGTT
* * * *
21209590 AAAATGTAATTTTGAG-AAGTTTGGGGCTCAAAATGTGATTTT-GAAAAAATTTAAGGGTA
1 AAAATGTAATTTTGAGAAAGTTTGGGG-TCAAAATATAATTTTAG-AAAAGTTTAAGGGTT
* * * * * *
21209649 AAAATATAATTTTG-GAAAGTTCAT-GGGTTAAAATGTAATTTTGGAAAAGTTCAAAGGTT
1 AAAATGTAATTTTGAGAAAGTT--TGGGGTCAAAATATAATTTTAGAAAAGTTTAAGGGTT
* *
21209708 AAAATGTAATTTTGGGAAAGTTTGGGGTCAAAAAATAATTTTA-AAAGAGTT
1 AAAATGTAATTTTGAGAAAGTTTGGGGTCAAAATATAATTTTAGAAA-AGTT
21209759 CGGGGGATCT
Statistics
Matches: 140, Mismatches: 19, Indels: 21
0.78 0.11 0.12
Matches are distributed among these distances:
58 8 0.06
59 105 0.75
60 24 0.17
61 3 0.02
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.35
Consensus pattern (59 bp):
AAAATGTAATTTTGAGAAAGTTTGGGGTCAAAATATAATTTTAGAAAAGTTTAAGGGTT
Found at i:21209622 original size:29 final size:29
Alignment explanation
Indices: 21209530--21209763 Score: 172
Period size: 30 Copynumber: 7.9 Consensus size: 29
21209520 TTTCATGGTA
*
21209530 AAAATGTAATTTTAGAAAAGTTTGAAGGTT
1 AAAATGTAATTTTAGAAAAGTTTG-GGGTT
*
21209560 AAAATATAATTTTAGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTAGAAAAGTTT-GGGGTT
* *
21209590 AAAATGTAATTTT-GAGAAGTTTGGGGCTC
1 AAAATGTAATTTTAGAAAAGTTTGGGG-TT
* * * *
21209619 AAAATGTGATTTT-GAAAAAATTTAAGGGTA
1 AAAATGTAATTTTAG-AAAAGTTT-GGGGTT
* *
21209649 AAAATATAATTTT-GGAAAGTTCAT-GGGTT
1 AAAATGTAATTTTAGAAAAGTT--TGGGGTT
* ***
21209678 AAAATGTAATTTTGGAAAAGTTCAAAGGTT
1 AAAATGTAATTTTAGAAAAGTT-TGGGGTT
* * *
21209708 AAAATGTAATTTTGGGAAAGTTTGGGGTC
1 AAAATGTAATTTTAGAAAAGTTTGGGGTT
** *
21209737 AAAAAATAATTTTA-AAAGAGTTCGGGG
1 AAAATGTAATTTTAGAAA-AGTTTGGGG
21209764 GATCTTTTAT
Statistics
Matches: 165, Mismatches: 30, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
28 6 0.04
29 65 0.39
30 89 0.54
31 5 0.03
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAAGTTTGGGGTT
Found at i:21209678 original size:118 final size:118
Alignment explanation
Indices: 21209526--21209740 Score: 301
Period size: 118 Copynumber: 1.8 Consensus size: 118
21209516 ACAATTTCAT
* * **
21209526 GGTAAAAATGTAATTTTAGAAAAGTTTGAAGGTTAAAATATAATTTTAGAAAAGTTTAGGGGTTA
1 GGTAAAAATATAATTTTAGAAAAGTTTG-AGGTTAAAATATAATTTTAGAAAAGTTCAAAGGTTA
21209591 AAATGTAATTTTGAG-AAGTTTGGGGCTCAAAATGTGATTTTGAAAAAATTTAAG
65 AAATGTAATTTTGAGAAAGTTTGGGG-TCAAAATGTGATTTTGAAAAAATTTAAG
* * *
21209645 GGTAAAAATATAATTTT-GGAAAGTTCATG-GGTTAAAATGTAATTTTGGAAAAGTTCAAAGGTT
1 GGTAAAAATATAATTTTAGAAAAGTT--TGAGGTTAAAATATAATTTTAGAAAAGTTCAAAGGTT
*
21209708 AAAATGTAATTTTGGGAAAGTTTGGGGTCAAAA
64 AAAATGTAATTTTGAGAAAGTTTGGGGTCAAAA
21209741 AATAATTTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
118 57 0.67
119 26 0.31
120 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.34
Consensus pattern (118 bp):
GGTAAAAATATAATTTTAGAAAAGTTTGAGGTTAAAATATAATTTTAGAAAAGTTCAAAGGTTAA
AATGTAATTTTGAGAAAGTTTGGGGTCAAAATGTGATTTTGAAAAAATTTAAG
Found at i:21212234 original size:12 final size:12
Alignment explanation
Indices: 21212217--21212260 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
21212207 AAGGATCAAG
21212217 AAGAAGAAGAAA
1 AAGAAGAAGAAA
*
21212229 AAGAAGAAGGAA
1 AAGAAGAAGAAA
* *
21212241 AGGAAGAAGAGA
1 AAGAAGAAGAAA
21212253 AAGAAGAA
1 AAGAAGAA
21212261 AAAGAACCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:21213348 original size:18 final size:19
Alignment explanation
Indices: 21213309--21213345 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21213299 CTTGAAAAAC
21213309 GAAAATGAAAAAAAAGAAA
1 GAAAATGAAAAAAAAGAAA
21213328 GAAAA-GAAAAAAGAAGAA
1 GAAAATGAAAAAA-AAGAA
21213346 GAATAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (19 bp):
GAAAATGAAAAAAAAGAAA
Found at i:21215271 original size:50 final size:51
Alignment explanation
Indices: 21215104--21215336 Score: 299
Period size: 51 Copynumber: 4.5 Consensus size: 51
21215094 TTCATTTAAT
* * * * * **
21215104 ACTCACGATGATA-TATAGTCATCGGACCTCTTATTCCATATAGGAATCCATAA
1 ACTCACGATGACACT-TAGTCATCGGACC-ATTAATCCATAAAGG-ATTCATTC
* * *
21215157 ACTCATGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
* *
21215208 ACTCACGATGACACTTAGTTATCGAACCATTAATCCAT-AAGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
* *
21215258 ATTCACGATGACACTTAGTCATTGGACCATTAATCCATAAAGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
21215309 ACTCACGATGACACTTAGTCATCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
21215337 CTTTCGTTTA
Statistics
Matches: 159, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
50 45 0.28
51 77 0.48
52 12 0.08
53 24 0.15
54 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.30
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
Found at i:21221543 original size:51 final size:52
Alignment explanation
Indices: 21221478--21221720 Score: 296
Period size: 51 Copynumber: 4.5 Consensus size: 52
21221468 GAATCCATAA
* * * *
21221478 ACTCACTACGACACTTAGTCATCGGACC-TTCAATCCATAAAGAATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCATTCAATCCATAAAGGATTCATTC
* *
21221529 ACTCACGATAACACTTAGTCATCGGACCATT-AATCCAT-ACGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCATTCAATCCATAAAGGATTCATTC
21221579 ACTCACGATGACACTTAGTCATCGGACCATTAATCCAACCATTAATCCATAAAGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCA-T--T-----C---AATCCATAAAGGATTCATTC
*
21221642 ACTCACGATGACACTTAGTCATCGGACC-TTTAATCCATAAAGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCATTCAATCCATAAAGGATTCATTC
21221693 ACTCACGATGACACTTAGTCATCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
21221721 CTTTCATTTA
Statistics
Matches: 169, Mismatches: 9, Indels: 28
0.82 0.04 0.14
Matches are distributed among these distances:
50 37 0.22
51 81 0.48
52 2 0.01
53 1 0.01
59 1 0.01
61 1 0.01
62 7 0.04
63 39 0.23
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (52 bp):
ACTCACGATGACACTTAGTCATCGGACCATTCAATCCATAAAGGATTCATTC
Found at i:21224048 original size:48 final size:48
Alignment explanation
Indices: 21223995--21224087 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
21223985 ATTGAGCTTC
** *
21223995 GCTTCATTGATTTGGTCTACTTCTCTATATCTCATC-AGGAAGATGACT
1 GCTTCATTGATTTAATCCACTTCTCTATATCTCATCGA-GAAGATGACT
21224043 GCTTCATTGATTTAATCCACTTCTCTATATCTCATCGAGAAGATG
1 GCTTCATTGATTTAATCCACTTCTCTATATCTCATCGAGAAGATG
21224088 GGGTTTGGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 40 0.98
49 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (48 bp):
GCTTCATTGATTTAATCCACTTCTCTATATCTCATCGAGAAGATGACT
Found at i:21224154 original size:124 final size:122
Alignment explanation
Indices: 21223925--21224211 Score: 412
Period size: 124 Copynumber: 2.3 Consensus size: 122
21223915 TCACCTCTTT
* * * **
21223925 ATTGCTTTAACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGA
1 ATTGATTTAATCCACTTCTCTGTATCTCATCA-GAAGATGGGGTTTGAAGTCTCACTCACATTGA
* * *
21223990 GCTTCGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACTGCTTC
65 GCTTCACTTCATTGAATTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTC
* *
21224048 ATTGATTTAATCCACTTCTCTATATCTCATCGAGAAGATGGGGTTTGGAAGTTTCACTCACATTG
1 ATTGATTTAATCCACTTCTCTGTATCTCATC-AGAAGATGGGGTTT-GAAGTCTCACTCACATTG
* * *
21224113 AGCTTCACTTCATTGAATTGGTCTACTTCTTTGTATTTCATCAGGAAGATGACCGCTTC
64 AGCTTCACTTCATTGAATTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTC
*
21224172 ATTGATTTAATCCACTTCTCTGTATCTTATCAAGAAGATG
1 ATTGATTTAATCCACTTCTCTGTATCTCATC-AGAAGATG
21224212 AATTTTGTCT
Statistics
Matches: 146, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
123 41 0.28
124 105 0.72
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (122 bp):
ATTGATTTAATCCACTTCTCTGTATCTCATCAGAAGATGGGGTTTGAAGTCTCACTCACATTGAG
CTTCACTTCATTGAATTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTC
Found at i:21224172 original size:48 final size:48
Alignment explanation
Indices: 21224120--21224212 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
21224110 TTGAGCTTCA
** * * *
21224120 CTTCATTGAATTGGTCTACTTCTTTGTAT-TTCATCAGGAAGATGACCG
1 CTTCATTGAATTAATCCACTTCTCTGTATCTT-ATCAAGAAGATGACCG
*
21224168 CTTCATTGATTTAATCCACTTCTCTGTATCTTATCAAGAAGATGA
1 CTTCATTGAATTAATCCACTTCTCTGTATCTTATCAAGAAGATGA
21224213 ATTTTGTCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 36 0.95
49 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (48 bp):
CTTCATTGAATTAATCCACTTCTCTGTATCTTATCAAGAAGATGACCG
Found at i:21224294 original size:85 final size:85
Alignment explanation
Indices: 21224133--21224296 Score: 220
Period size: 85 Copynumber: 1.9 Consensus size: 85
21224123 CATTGAATTG
* * * **
21224133 GTCTACTTCTTTGTATTTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATC
1 GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAACCCACTTCTCTACATC
*
21224198 TTATCAAGAAGATGAATTTT
66 TCATCAAGAAGATGAATTTT
* * * *
21224218 GTCTACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTGCTTTGACCCACTTCTCTACATC
1 GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAACCCACTTCTCTACATC
* *
21224283 TCATTAGGAAGATG
66 TCATCAAGAAGATG
21224297 GGGGTTTGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (85 bp):
GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAACCCACTTCTCTACATC
TCATCAAGAAGATGAATTTT
Found at i:21224369 original size:209 final size:208
Alignment explanation
Indices: 21224004--21224583 Score: 826
Period size: 209 Copynumber: 2.8 Consensus size: 208
21223994 CGCTTCATTG
* * * * *
21224004 ATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACTGCTTCATTGATTTAATCCACTTCTCT
1 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTTGACCCACTTCTCT
*
21224069 ATATCTCA-TCGAGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTCACTTCATTGAATTG
66 ATATCTCATTAG-GAAGATGGGGTTT-GAAGTTTCACTCACATTGAGCTTCACTTCATTGAATTG
* *
21224133 GTCTACTTCTTTGTATTTCATCAGGAAGATGACCGCTTCATTGA-TTTAATCCACTTCTCTGTAT
129 GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATT-ATTTTAATCCACTTCTCTGTAT
* *
21224197 CTTATCAAGAAGATGA
193 CTCATCAAGAAGACGA
*
21224213 ATTTTGTCTACTTCTCTGTATCTCATCAGGAAGATGACCT-CTTTATTGCTTTGACCCACTTCTC
1 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA-CTGCTTTATTGCTTTGACCCACTTCTC
* * * *
21224277 TACATCTCATTAGGAAGATGGGGGTTTGAAGTTTCGCTCATATTAAGCTTCACTTCATTGAATTG
65 TATATCTCATTAGGAAGAT-GGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGAATTG
21224342 GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTATTTTAATCCACTTCTCTGTATC
129 GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTATTTTAATCCACTTCTCTGTATC
* *
21224407 TCATCAGGAAGACGG
194 TCATCAAGAAGACGA
* * * * *
21224422 ATTTGGTCCACTTCTCTGTATCTCATCAAGAAGAT-AGTTGCTTTATTGCTTTGACCCATTTCTT
1 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA-CTGCTTTATTGCTTTGACCCACTTCTC
* * * * *
21224486 TGTATCTCATCAAGAAGATGAGGTTTGAAAGTTTCACTCACATTGAGTTTCACTTCATTGAATTG
65 TATATCTCATTAGGAAGATGGGGTTTG-AAGTTTCACTCACATTGAGCTTCACTTCATTGAATTG
21224551 GTCTACTTCTCTGTATCTCATCAGGAAGATGAC
129 GTCTACTTCTCTGTATCTCATCAGGAAGATGAC
21224584 GTTTTAAAGT
Statistics
Matches: 332, Mismatches: 33, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
208 10 0.03
209 311 0.94
210 11 0.03
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (208 bp):
ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTGCTTTATTGCTTTGACCCACTTCTCT
ATATCTCATTAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCACTTCATTGAATTGGT
CTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTATTTTAATCCACTTCTCTGTATCTC
ATCAAGAAGACGA
Found at i:21224490 original size:85 final size:85
Alignment explanation
Indices: 21224339--21224503 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 85
21224329 CTTCATTGAA
* * * *
21224339 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTATTTTAATCCACTTCTCTGT
1 TTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTACTTTAACCCACTTCTCTGT
*
21224404 ATCTCATCAGGAAGACGGAT
66 ATCTCATCAAGAAGACGGAT
** * * * * *
21224424 TTGGTCCACTTCTCTGTATCTCATCAAGAAGAT-AGTTGCTTTATTGCTTTGACCCATTTCTTTG
1 TTGGTCCACTTCTCTGTATCTCATCAAGAAGATGA-CCGCTTCATTACTTTAACCCACTTCTCTG
21224488 TATCTCATCAAGAAGA
65 TATCTCATCAAGAAGA
21224504 TGAGGTTTGA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
84 1 0.01
85 66 0.99
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (85 bp):
TTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTACTTTAACCCACTTCTCTGT
ATCTCATCAAGAAGACGGAT
Found at i:21225625 original size:41 final size:42
Alignment explanation
Indices: 21225575--21225694 Score: 138
Period size: 41 Copynumber: 2.9 Consensus size: 42
21225565 GTTTCAAGAT
* *
21225575 GCCCTTTACGAGTTTTCATCCTGATCCCTTTTTTT-TGAGAC
1 GCCCTTTACGGGTTTTCATCCTAATCCCTTTTTTTCTGAGAC
21225616 GCCCTTTACGGGTTTTCAT-CTCAATCCCCTTTTTTTTCTGAGAC
1 GCCCTTTACGGGTTTTCATCCT-AAT-CCC-TTTTTTTCTGAGAC
* * * *
21225660 GCCTTTTGCGGGTATTCATCTTAAT-CCTTTTTTTC
1 GCCCTTTACGGGTTTTCATCCTAATCCCTTTTTTTC
21225695 AGGCAAAACA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
40 2 0.03
41 28 0.41
42 5 0.07
43 7 0.10
44 25 0.37
45 1 0.01
ACGTcount: A:0.13, C:0.27, G:0.14, T:0.46
Consensus pattern (42 bp):
GCCCTTTACGGGTTTTCATCCTAATCCCTTTTTTTCTGAGAC
Found at i:21225672 original size:44 final size:41
Alignment explanation
Indices: 21225575--21225693 Score: 123
Period size: 44 Copynumber: 2.8 Consensus size: 41
21225565 GTTTCAAGAT
* * * *
21225575 GCCCTTTACGAGTTTTCATC-CTGATCCCTTTTTTTTGAGAC
1 GCCCTTTACGGGTATTCATCTC-AATCCTTTTTTTTTGAGAC
*
21225616 GCCCTTTACGGGTTTTCATCTCAATCCCCTTTTTTTTCTGAGAC
1 GCCCTTTACGGGTATTCATCTCAAT--CCTTTTTTTT-TGAGAC
* * *
21225660 GCCTTTTGCGGGTATTCATCTTAATCCTTTTTTT
1 GCCCTTTACGGGTATTCATCTCAATCCTTTTTTT
21225694 CAGGCAAAAC
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
41 21 0.31
42 10 0.15
43 9 0.13
44 27 0.40
ACGTcount: A:0.13, C:0.26, G:0.14, T:0.46
Consensus pattern (41 bp):
GCCCTTTACGGGTATTCATCTCAATCCTTTTTTTTTGAGAC
Found at i:21226962 original size:3 final size:3
Alignment explanation
Indices: 21226954--21226983 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21226944 TATCATCCCT
21226954 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
21226984 AATATCATAA
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:21236537 original size:30 final size:30
Alignment explanation
Indices: 21236503--21236694 Score: 210
Period size: 30 Copynumber: 6.4 Consensus size: 30
21236493 TTTCGGAGCA
*
21236503 AAAATGTAATTTTGGGAAAGTTT-GGGGGC
1 AAAATGTAATTTTGGGAAAGTTTAGGGGTC
* * * *
21236532 TAAAATATAATTTTAGAAAAGTTTAGGGGTT
1 -AAAATGTAATTTTGGGAAAGTTTAGGGGTC
* *
21236563 AAAATGTAATTTTAGGAAAGTTTAGGGGTA
1 AAAATGTAATTTTGGGAAAGTTTAGGGGTC
* *
21236593 AAAATATAATTTTGGGAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGGAAAGTTTAGGGGTC
* * *
21236623 AAAATGTAGTTTTGGAAAAG-TTCGGAGGTC
1 AAAATGTAATTTTGGGAAAGTTTAGG-GGTC
21236653 AAAATGTAATTTTTGGGAAAGTTT-GAGGGTC
1 AAAATGTAA-TTTTGGGAAAGTTTAG-GGGTC
*
21236684 AAAATGCAATT
1 AAAATGTAATT
21236695 CTGAAAGAGT
Statistics
Matches: 137, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.02
30 104 0.76
31 27 0.20
32 3 0.02
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (30 bp):
AAAATGTAATTTTGGGAAAGTTTAGGGGTC
Found at i:21236596 original size:90 final size:91
Alignment explanation
Indices: 21236502--21236694 Score: 232
Period size: 90 Copynumber: 2.1 Consensus size: 91
21236492 ATTTCGGAGC
* * *
21236502 AAAAATGTAATTTTGGGAAAGTTT-GGGGGCTAAAATATAATTTTAGAAAAGTTTAGG-GGTTAA
1 AAAAATGTAATTTTGGGAAAGTTTAAGGGTC-AAAATATAATTTTAGAAAAG-TTAGGAGGTCAA
21236565 AATGTAA-TTTTAGGAAAGTTT-AGGGGT
64 AATGTAATTTTTAGGAAAGTTTGA-GGGT
* * * * *
21236592 AAAAATATAATTTTGGGAAAGTTTAAGGGTCAAAATGTAGTTTTGGAAAAGTTCGGAGGTCAAAA
1 AAAAATGTAATTTTGGGAAAGTTTAAGGGTCAAAATATAATTTTAGAAAAGTTAGGAGGTCAAAA
*
21236657 TGTAATTTTTGGGAAAGTTTGAGGGT
66 TGTAATTTTTAGGAAAGTTTGAGGGT
* *
21236683 CAAAATGCAATT
1 AAAAATGTAATT
21236695 CTGAAAGAGT
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
89 4 0.05
90 52 0.60
91 30 0.34
92 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (91 bp):
AAAAATGTAATTTTGGGAAAGTTTAAGGGTCAAAATATAATTTTAGAAAAGTTAGGAGGTCAAAA
TGTAATTTTTAGGAAAGTTTGAGGGT
Found at i:21238622 original size:7 final size:7
Alignment explanation
Indices: 21238610--21238634 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21238600 TACCTCAGTG
21238610 CCCTTTC
1 CCCTTTC
21238617 CCCTTTC
1 CCCTTTC
21238624 CCCTTTC
1 CCCTTTC
21238631 CCCT
1 CCCT
21238635 CTTTCTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (7 bp):
CCCTTTC
Found at i:21239949 original size:19 final size:19
Alignment explanation
Indices: 21239917--21239961 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
21239907 AATAATTATA
*
21239917 AAAAATTATTAAAAATT-TCT
1 AAAAA-TATCAAAAATTCT-T
21239937 AAAAATATCAAAAATTCTT
1 AAAAATATCAAAAATTCTT
21239956 AAAAAT
1 AAAAAT
21239962 GTCTGAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATATCAAAAATTCTT
Found at i:21240021 original size:18 final size:20
Alignment explanation
Indices: 21239983--21240021 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
21239973 CATTATTTAT
21239983 TTTTTGAAATTATAAAATTA
1 TTTTTGAAATTATAAAATTA
*
21240003 TTTTT-AAATT-TATAATTA
1 TTTTTGAAATTATAAAATTA
21240021 T
1 T
21240022 ATAAACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 5 0.28
20 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTGAAATTATAAAATTA
Found at i:21245926 original size:57 final size:57
Alignment explanation
Indices: 21245851--21245975 Score: 223
Period size: 57 Copynumber: 2.2 Consensus size: 57
21245841 ACTCGAATCC
*
21245851 AAATTGCGTTTGGAATAATGAATATTTTTACTATCAAATTAACACACGAGGTTCCAT
1 AAATTCCGTTTGGAATAATGAATATTTTTACTATCAAATTAACACACGAGGTTCCAT
* *
21245908 GAATTCCGTTTGGAATAATGAATATTTTTACTATCAAATTAATACACGAGGTTCCAT
1 AAATTCCGTTTGGAATAATGAATATTTTTACTATCAAATTAACACACGAGGTTCCAT
21245965 AAATTCCGTTT
1 AAATTCCGTTT
21245976 TTCATAGGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (57 bp):
AAATTCCGTTTGGAATAATGAATATTTTTACTATCAAATTAACACACGAGGTTCCAT
Found at i:21251232 original size:1 final size:1
Alignment explanation
Indices: 21251226--21251250 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21251216 TAGGGTGTGA
21251226 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
21251251 AATAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:21256993 original size:18 final size:18
Alignment explanation
Indices: 21256972--21257017 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
21256962 GACCCGATCA
*
21256972 AATTAATTCGATTAATCG
1 AATTAATTCGATTAACCG
*
21256990 AATTCGA-TCGATTAACCG
1 AATT-AATTCGATTAACCG
21257008 AATTAATTCG
1 AATTAATTCG
21257018 GTTTTACTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
AATTAATTCGATTAACCG
Found at i:21257628 original size:26 final size:26
Alignment explanation
Indices: 21257599--21257653 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
21257589 TAAAACCATA
21257599 AAATGGGTTAAGTAAATCCGAATGTG
1 AAATGGGTTAAGTAAATCCGAATGTG
21257625 AAATGGGTTAAGTAAATCCGAATGTG
1 AAATGGGTTAAGTAAATCCGAATGTG
21257651 AAA
1 AAA
21257654 GAAGAAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.25
Consensus pattern (26 bp):
AAATGGGTTAAGTAAATCCGAATGTG
Found at i:21267757 original size:13 final size:13
Alignment explanation
Indices: 21267735--21267771 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
21267725 TTTCTTGGAC
21267735 AAAT-AATAAAAT
1 AAATAAATAAAAT
21267747 AAATAAATAAAAT
1 AAATAAATAAAAT
21267760 AGAA-AAATAAAA
1 A-AATAAATAAAA
21267772 ATAATTGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 17 0.74
14 2 0.09
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:21268979 original size:21 final size:21
Alignment explanation
Indices: 21268948--21269018 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
21268938 TAGATGACTT
*
21268948 AGTTTTCTTTTGAAAATCTAC
1 AGTTTGCTTTTGAAAATCTAC
* *
21268969 AGTTTGTTTTTGAAAATCTGC
1 AGTTTGCTTTTGAAAATCTAC
* *
21268990 AGTTTGCTTTTCAAAATCTAT
1 AGTTTGCTTTTGAAAATCTAC
*
21269011 AGATTGCT
1 AGTTTGCT
21269019 GCTGAAATTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (21 bp):
AGTTTGCTTTTGAAAATCTAC
Found at i:21270355 original size:15 final size:16
Alignment explanation
Indices: 21270325--21270357 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
21270315 TTTGGGGAAA
21270325 AATTAAAAGAAAATAG
1 AATTAAAAGAAAATAG
21270341 AATTAAAAG-AAATAG
1 AATTAAAAGAAAATAG
21270356 AA
1 AA
21270358 AATAGGAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (16 bp):
AATTAAAAGAAAATAG
Found at i:21276289 original size:36 final size:36
Alignment explanation
Indices: 21276242--21276342 Score: 166
Period size: 36 Copynumber: 2.8 Consensus size: 36
21276232 GGTAACAGGC
* *
21276242 ATGACCTTTGGGTCAACAAGGAGAAAAATGAGCATA
1 ATGACCTTTGGGTCAACAAGGAGTAAAACGAGCATA
21276278 ATGACCTTTGGGTCAACAAGGAGTAAAACGAGCATA
1 ATGACCTTTGGGTCAACAAGGAGTAAAACGAGCATA
* *
21276314 ATGACCTTTGGATCAACAGGGAGTAAAAC
1 ATGACCTTTGGGTCAACAAGGAGTAAAAC
21276343 AAATAACGAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.20
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAAGGAGTAAAACGAGCATA
Found at i:21277045 original size:116 final size:116
Alignment explanation
Indices: 21276841--21277081 Score: 369
Period size: 116 Copynumber: 2.1 Consensus size: 116
21276831 TGCTTGTACA
* *
21276841 GGTAGAAGTACAAGGTAGGAGAGAGGTTATTCTCTGACTTGAGTTGTTTTGGTAGTTGTATATCA
1 GGTAGAAGTACAAGGTAGGAGAGAGGTTATTCTCTGACTTGAGTTGATTCGGTAGTTGTATATCA
* * *
21276906 GGTATCGATAGTTCTGTACATTGAGGTATCGGTAGTTTAAATTCTTCTATC
66 GGTATCGATAGTTCTGTACATTGAGGTATCGATAGTTTAAATACTTCAATC
* * *
21276957 GGTAGAAGTACAGGGTAGGAGAGAGGTTGTTCTTTGACTTGAGTTGATTCGGTAGTTGTATAAT-
1 GGTAGAAGTACAAGGTAGGAGAGAGGTTATTCTCTGACTTGAGTTGATTCGGTAGTTGTAT-ATC
*
21277021 AGGTATC-AGTAGTTCTGTACATTGAGGTATCGATAGTTTAAATACTTGAATC
65 AGGTATCGA-TAGTTCTGTACATTGAGGTATCGATAGTTTAAATACTTCAATC
21277073 GGTAGAAGT
1 GGTAGAAGT
21277082 TATAGGATAG
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
115 1 0.01
116 111 0.97
117 2 0.02
ACGTcount: A:0.27, C:0.09, G:0.28, T:0.36
Consensus pattern (116 bp):
GGTAGAAGTACAAGGTAGGAGAGAGGTTATTCTCTGACTTGAGTTGATTCGGTAGTTGTATATCA
GGTATCGATAGTTCTGTACATTGAGGTATCGATAGTTTAAATACTTCAATC
Found at i:21280045 original size:14 final size:15
Alignment explanation
Indices: 21280016--21280052 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
21280006 ATAAATAAAC
21280016 AAGAAATAAGAAAAT
1 AAGAAATAAGAAAAT
*
21280031 AAGAAA-AATAAAAT
1 AAGAAATAAGAAAAT
21280045 AA-AAATAA
1 AAGAAATAA
21280053 AACCCATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 3 0.15
14 11 0.55
15 6 0.30
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (15 bp):
AAGAAATAAGAAAAT
Found at i:21291035 original size:22 final size:22
Alignment explanation
Indices: 21291010--21291054 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
21291000 GTGTGTAAAT
21291010 AATGTTTTAGACTT-GGGTTTTG
1 AATGTTTTA-ACTTAGGGTTTTG
*
21291032 AATGTTTTAACTTATGGTTTTG
1 AATGTTTTAACTTAGGGTTTTG
21291054 A
1 A
21291055 TATGATGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.51
Consensus pattern (22 bp):
AATGTTTTAACTTAGGGTTTTG
Found at i:21293791 original size:27 final size:26
Alignment explanation
Indices: 21293745--21293796 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
21293735 ACTCGACCTA
21293745 ACCCGACCCGTTGACTTTGACACATTG
1 ACCCGACCCGTTGACTTTGAC-CATTG
21293772 ACCCGACCCGTTGAGC-TTGACCATT
1 ACCCGACCCGTTGA-CTTTGACCATT
21293797 ACGCGTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.17
27 19 0.79
28 1 0.04
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (26 bp):
ACCCGACCCGTTGACTTTGACCATTG
Found at i:21310667 original size:18 final size:18
Alignment explanation
Indices: 21310640--21310682 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
21310630 GGTGGCATAG
*
21310640 GGTTGTTGTGGATATGTT
1 GGTTGCTGTGGATATGTT
21310658 GGTTGCTGTGGATATGTT
1 GGTTGCTGTGGATATGTT
21310676 GGTTGCT
1 GGTTGCT
21310683 TCGACAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.09, C:0.05, G:0.40, T:0.47
Consensus pattern (18 bp):
GGTTGCTGTGGATATGTT
Found at i:21315939 original size:24 final size:24
Alignment explanation
Indices: 21315911--21315986 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
21315901 GTATACTGGT
21315911 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
*
21315935 TAACCATTCTGGGCTTGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
*
21315959 TAACCATTCTGGGCTCGTAAGAGA
1 TAACCATTCTGGGCTCGTAAGAGC
21315983 TAAC
1 TAAC
21315987 AGTGCTTGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAGC
Found at i:21324270 original size:43 final size:43
Alignment explanation
Indices: 21324223--21324318 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
21324213 TGTCTCGGGT
* * *
21324223 TGAGCATGAGAATTTATATAAAAGGAAGACTTGTGACTCGGAA
1 TGAGCATGAGAATTTATATAAAAGGAAGACTCGTGAATCGAAA
21324266 TGAGCATGAGAATTTATATAAAAGGAAGACTCGTGAATCGAAA
1 TGAGCATGAGAATTTATATAAAAGGAAGACTCGTGAATCGAAA
21324309 TGAGCATGAG
1 TGAGCATGAG
21324319 CAAATGTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (43 bp):
TGAGCATGAGAATTTATATAAAAGGAAGACTCGTGAATCGAAA
Found at i:21324353 original size:41 final size:42
Alignment explanation
Indices: 21324205--21324401 Score: 130
Period size: 43 Copynumber: 4.7 Consensus size: 42
21324195 GTTTAAATGA
* * ** * * *
21324205 AAGACTCATGTCTCGGGTTGAGCATGAGAATTTATATAAAAGG
1 AAGACTCATGCCTTGGAATGAGCATGAGCA-TAATATTAAAGG
** * * * * *
21324248 AAGACTTGTGACTCGGAATGAGCATGAGAATTTATATAAAAGG
1 AAGACTCATGCCTTGGAATGAGCATGAGCA-TAATATTAAAGG
* ** * * *
21324291 AAGACTCGTGAATCGAAATGAGCATGAGCA-AATGTTAAAGG
1 AAGACTCATGCCTTGGAATGAGCATGAGCATAATATTAAAGG
* * *
21324332 AAGACTCATGTCTTAGG-ATGAGAATGAG-ATTATATTAAAGG
1 AAGACTCATGCCTT-GGAATGAGCATGAGCATAATATTAAAGG
*
21324373 AAGTCTCATGCCTTGGAATGAGCATGAGC
1 AAGACTCATGCCTTGGAATGAGCATGAGC
21324402 TTTTGTTCTA
Statistics
Matches: 127, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
40 3 0.02
41 59 0.46
42 1 0.01
43 64 0.50
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (42 bp):
AAGACTCATGCCTTGGAATGAGCATGAGCATAATATTAAAGG
Found at i:21329496 original size:21 final size:21
Alignment explanation
Indices: 21329449--21329501 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
21329439 GGAGTTTTTA
21329449 GTATCGGTAG-AAGTAAGCTT
1 GTATCGGTAGAAAGTAAGCTT
* *
21329469 GTTTCGGTAGAAGAGTCA-CTT
1 GTATCGGTAGAA-AGTAAGCTT
21329490 GTATCGGTAGAA
1 GTATCGGTAGAA
21329502 CTTTCACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 15 0.54
22 4 0.14
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAAGTAAGCTT
Found at i:21329508 original size:21 final size:21
Alignment explanation
Indices: 21329449--21329522 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
21329439 GGAGTTTTTA
*
21329449 GTATCGGTAG-A-AGTAAGCTT
1 GTATCGGTAGAACAGTCA-CTT
* *
21329469 GTTTCGGTAGAAGAGTCACTT
1 GTATCGGTAGAACAGTCACTT
**
21329490 GTATCGGTAGAACTTTCACTT
1 GTATCGGTAGAACAGTCACTT
* *
21329511 TTATTGGTAGAA
1 GTATCGGTAGAA
21329523 GTCTACACTA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
20 9 0.20
21 31 0.70
22 4 0.09
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAACAGTCACTT
Found at i:21331453 original size:21 final size:20
Alignment explanation
Indices: 21331423--21331467 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
21331413 TTATCTAAGT
**
21331423 TTTTAATTTATTTTTTTCAAA
1 TTTTAATTTAAATTTTT-AAA
*
21331444 TTTTAGTTTAAATTTTTAAA
1 TTTTAATTTAAATTTTTAAA
21331464 TTTT
1 TTTT
21331468 CTATAAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTAATTTAAATTTTTAAA
Found at i:21335859 original size:39 final size:38
Alignment explanation
Indices: 21335785--21335866 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 38
21335775 TAGGTTATAT
* * * *
21335785 ATTATTTTTCTAATACTATATATTATGATTTTTATTAA
1 ATTATTTTTCTAATAATATATATTAAGAATGTTATTAA
*
21335823 TTTATTTTTC-AATAATAATTATATTAAGAATGTTATTAA
1 ATTATTTTTCTAATAAT-A-TATATTAAGAATGTTATTAA
21335862 ATTAT
1 ATTAT
21335867 ATATTATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
37 5 0.14
38 10 0.28
39 21 0.58
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (38 bp):
ATTATTTTTCTAATAATATATATTAAGAATGTTATTAA
Found at i:21335949 original size:54 final size:56
Alignment explanation
Indices: 21335815--21335964 Score: 182
Period size: 54 Copynumber: 2.7 Consensus size: 56
21335805 TATTATGATT
* * *
21335815 TTTATTAATTTATTTTTCAATAATAATTATATTAAGAATGTTATTAAATTATATATTAT
1 TTTATTAAATTATATTT-AATAATAATTATATTAA-AATG-TATTAAATTATATATTAG
* *
21335874 TTTATTAAATTGTATTTAATAATAATTATATTAAATATG-ATTAAATTATTTATT-G
1 TTTATTAAATTATATTTAATAATAATTATATTAAA-ATGTATTAAATTATATATTAG
21335929 TTT-TTAAATTATATTTAATAATAATCT-TATTAAAAT
1 TTTATTAAATTATATTTAATAATAAT-TATATTAAAAT
21335965 TTAATAACAA
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
53 2 0.02
54 28 0.34
55 4 0.05
56 14 0.17
57 1 0.01
58 20 0.24
59 14 0.17
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (56 bp):
TTTATTAAATTATATTTAATAATAATTATATTAAAATGTATTAAATTATATATTAG
Found at i:21336158 original size:16 final size:16
Alignment explanation
Indices: 21336139--21336184 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
21336129 AGTACAACCT
21336139 TATTCCATTACAGCTC
1 TATTCCATTACAGCTC
** * *
21336155 TATTATATTATAGTTC
1 TATTCCATTACAGCTC
21336171 TATTCCATTACAGC
1 TATTCCATTACAGC
21336185 GAATCAAATG
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (16 bp):
TATTCCATTACAGCTC
Found at i:21340237 original size:25 final size:25
Alignment explanation
Indices: 21340184--21340248 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
21340174 TTACTAATAA
* * *
21340184 AAATACAAACATATTTAATTAAATAC
1 AAATACAAACATA-ATAAATAAAAAC
21340210 AAATACAAACATAATAAATAAAAAC
1 AAATACAAACATAATAAATAAAAAC
* *
21340235 AAACATAAACATAA
1 AAATACAAACATAA
21340249 ATTAAGTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 21 0.62
26 13 0.38
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (25 bp):
AAATACAAACATAATAAATAAAAAC
Found at i:21340238 original size:19 final size:21
Alignment explanation
Indices: 21340203--21340242 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
21340193 CATATTTAAT
21340203 TAAATACAAATACAAACATAA
1 TAAATACAAATACAAACATAA
21340224 TAAATA-AAA-ACAAACATAA
1 TAAATACAAATACAAACATAA
21340243 ACATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAATACAAATACAAACATAA
Found at i:21340651 original size:27 final size:27
Alignment explanation
Indices: 21340613--21340675 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
21340603 GGAAACTCCA
* * **
21340613 AATGATATCTGTTGCTTGGCCAGCTCG
1 AATGATATCTGTAGCCTAACCAGCTCG
21340640 AATGATATCTGTAGCCTAACCAGCTCG
1 AATGATATCTGTAGCCTAACCAGCTCG
*
21340667 GATGATATC
1 AATGATATC
21340676 CGTGACCTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (27 bp):
AATGATATCTGTAGCCTAACCAGCTCG
Found at i:21340690 original size:27 final size:27
Alignment explanation
Indices: 21340632--21340700 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
21340622 TGTTGCTTGG
* *
21340632 CCAGCTCGAATGATATCTGTAGCCTAA
1 CCAGCTCGGATGATATCCGTAGCCTAA
*
21340659 CCAGCTCGGATGATATCCGT-GACCTGA
1 CCAGCTCGGATGATATCCGTAG-CCTAA
*
21340686 TCAGCTCGGATGATA
1 CCAGCTCGGATGATA
21340701 AGACTCAAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (27 bp):
CCAGCTCGGATGATATCCGTAGCCTAA
Found at i:21347899 original size:12 final size:12
Alignment explanation
Indices: 21347878--21347912 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21347868 TTGTTTACAT
*
21347878 TTATACTTATAA
1 TTATATTTATAA
21347890 TTATATTTATAA
1 TTATATTTATAA
*
21347902 TTATGTTTATA
1 TTATATTTATA
21347913 GCCTCTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (12 bp):
TTATATTTATAA
Found at i:21347911 original size:18 final size:18
Alignment explanation
Indices: 21347869--21347912 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
21347859 TGTGATGAAT
* *
21347869 TGTTTACATTTATACTTA
1 TGTTTATATTTATAATTA
**
21347887 TAATTATATTTATAATTA
1 TGTTTATATTTATAATTA
21347905 TGTTTATA
1 TGTTTATA
21347913 GCCTCTTCAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
TGTTTATATTTATAATTA
Found at i:21358917 original size:36 final size:35
Alignment explanation
Indices: 21358858--21358925 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
21358848 ATTAAACATT
21358858 AAAATCTCAAAATAATTTAATAACACATTAATATGA
1 AAAATCTCAAAATAATTTAATAAC-CATTAATATGA
* *
21358894 AAAATCCTCAAAATAA-TTCATAACGATTAATA
1 AAAAT-CTCAAAATAATTTAATAACCATTAATA
21358926 AATGAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 7 0.24
36 12 0.41
37 10 0.34
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.29
Consensus pattern (35 bp):
AAAATCTCAAAATAATTTAATAACCATTAATATGA
Found at i:21360002 original size:19 final size:20
Alignment explanation
Indices: 21359969--21360017 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
21359959 GTTGGTCGAA
* *
21359969 AAAGTCAAAGGTTAAAG-TC
1 AAAGTCAACGATTAAAGATC
*
21359988 AAAGTCAACGATTAACGATC
1 AAAGTCAACGATTAAAGATC
*
21360008 AAAGTTAACG
1 AAAGTCAACG
21360018 GGTCGGGTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.20
Consensus pattern (20 bp):
AAAGTCAACGATTAAAGATC
Found at i:21363405 original size:46 final size:46
Alignment explanation
Indices: 21363336--21363456 Score: 122
Period size: 46 Copynumber: 2.6 Consensus size: 46
21363326 TCAAGTCAAG
* * * *
21363336 TTGTCTTCCACGATTTCAA-GGATTTGTTT-AGCTAAATTGTAGTCAT
1 TTGTCTTCCTCAATTT-AAGGGATTTGTTTGA-ATAAATTGTAGGCAT
* * *
21363382 TTGTCTTCCTCAATTTTAGGGATTTGTATGAATAAATTGTAGGCCT
1 TTGTCTTCCTCAATTTAAGGGATTTGTTTGAATAAATTGTAGGCAT
*
21363428 TTTTCTTCCAT-AATTTAAGGGATTTGTTT
1 TTGTCTTCC-TCAATTTAAGGGATTTGTTT
21363457 CTCTTTTATC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
45 1 0.02
46 59 0.95
47 2 0.03
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.46
Consensus pattern (46 bp):
TTGTCTTCCTCAATTTAAGGGATTTGTTTGAATAAATTGTAGGCAT
Found at i:21367124 original size:20 final size:20
Alignment explanation
Indices: 21367088--21367125 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21367078 ATGCTAACCT
*
21367088 TGATAAGTGTACTTTTTTCG
1 TGATAAGTGTAATTTTTTCG
21367108 TGATAAGT-TAATCTTTTT
1 TGATAAGTGTAAT-TTTTT
21367126 GGGTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (20 bp):
TGATAAGTGTAATTTTTTCG
Found at i:21368406 original size:32 final size:32
Alignment explanation
Indices: 21368359--21368426 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
21368349 TTTTAGAAAG
*
21368359 TATTATGAGGCAAGCTTGGAACTAAATTACTT
1 TATTATGAGGCAAGCTTGAAACTAAATTACTT
* *
21368391 TATTATGGGGTAAGCTTGAAACTAAATTACTT
1 TATTATGAGGCAAGCTTGAAACTAAATTACTT
21368423 TATT
1 TATT
21368427 CTACTACTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (32 bp):
TATTATGAGGCAAGCTTGAAACTAAATTACTT
Found at i:21369126 original size:46 final size:46
Alignment explanation
Indices: 21369057--21369173 Score: 146
Period size: 46 Copynumber: 2.5 Consensus size: 46
21369047 GCCAAGTTGC
* * *
21369057 CTTCCACAATTTCAAGCATTTGTTTAGCTAAA-TAGCAGTCATTTGT
1 CTTCCACAATTTCAGGGATTTGTTTAGCTAAATTA-CAGGCATTTGT
* * *
21369103 CTTCCACAATTTCAGGGACTTGTTTGGCTAAATTATAGGCATTTGT
1 CTTCCACAATTTCAGGGATTTGTTTAGCTAAATTACAGGCATTTGT
* *
21369149 CTTCCATAATTTTAGGGATTTGTTT
1 CTTCCACAATTTCAGGGATTTGTTT
21369174 CTCTTTTATT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 59 0.97
47 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (46 bp):
CTTCCACAATTTCAGGGATTTGTTTAGCTAAATTACAGGCATTTGT
Found at i:21371437 original size:25 final size:25
Alignment explanation
Indices: 21371409--21371457 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
21371399 CTGGTTAAAC
21371409 TCTGTCTGGGCTCGTAAGAGCTAAT
1 TCTGTCTGGGCTCGTAAGAGCTAAT
* *
21371434 TCTGTTTGGGCTCGTATGAGCTAA
1 TCTGTCTGGGCTCGTAAGAGCTAA
21371458 ATTTTGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (25 bp):
TCTGTCTGGGCTCGTAAGAGCTAAT
Found at i:21372511 original size:2 final size:2
Alignment explanation
Indices: 21372504--21372539 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
21372494 GGTGCTATAG
21372504 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
21372540 ATTTCAAGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:21373540 original size:19 final size:19
Alignment explanation
Indices: 21373516--21373557 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
21373506 CAAATCTTCA
*
21373516 AAACCCAACAAATAATTTT
1 AAACCCAACAAACAATTTT
*
21373535 AAACCCAAGAAACAATTTT
1 AAACCCAACAAACAATTTT
21373554 AAAC
1 AAAC
21373558 AAATTTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.21
Consensus pattern (19 bp):
AAACCCAACAAACAATTTT
Found at i:21375763 original size:31 final size:30
Alignment explanation
Indices: 21375698--21375769 Score: 72
Period size: 33 Copynumber: 2.3 Consensus size: 30
21375688 CCCCATTTAA
* *
21375698 TTTTTGTTTTTTATAATTTAGGCCTTATTG
1 TTTTTATTTTTTATAATTTAGCCCTTATTG
* * *
21375728 TTTTTATTTTTATTTAATTTAGTCCCTTTTTTT
1 TTTTTATTTTT-TATAATTTAG-CCC-TTATTG
21375761 TTTTTATTT
1 TTTTTATTT
21375770 GTATTCTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 10 0.29
31 9 0.26
32 2 0.06
33 13 0.38
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.71
Consensus pattern (30 bp):
TTTTTATTTTTTATAATTTAGCCCTTATTG
Found at i:21375832 original size:25 final size:25
Alignment explanation
Indices: 21375804--21375858 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
21375794 TTAATTTTCA
* *
21375804 TTTATTTA-TTGTTTTTTATATTGTT
1 TTTATTTATTTGTTTGTTAT-TTATT
21375829 TTTATTTATTTGTTTGTTATTTATT
1 TTTATTTATTTGTTTGTTATTTATT
21375854 TTTAT
1 TTTAT
21375859 GTCATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.76
Consensus pattern (25 bp):
TTTATTTATTTGTTTGTTATTTATT
Found at i:21375848 original size:15 final size:15
Alignment explanation
Indices: 21375803--21375854 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
21375793 TTTAATTTTC
*
21375803 ATTTATTT-ATTGTT
1 ATTTATTTGTTTGTT
*
21375817 TTTTATATTGTTT-TT
1 ATTTAT-TTGTTTGTT
21375832 ATTTATTTGTTTGTT
1 ATTTATTTGTTTGTT
21375847 ATTTATTT
1 ATTTATTT
21375855 TTATGTCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 11 0.34
15 19 0.59
16 2 0.06
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (15 bp):
ATTTATTTGTTTGTT
Found at i:21375865 original size:26 final size:26
Alignment explanation
Indices: 21375804--21375865 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
21375794 TTAATTTTCA
* * *
21375804 TTTATTTA-TTGTTTTTTATATTGTT
1 TTTATTCATTTGTTTGTTATATTATT
*
21375829 TTTATTTATTTGTTTGTTAT-TTATT
1 TTTATTCATTTGTTTGTTATATTATT
21375854 TTTATGTCATTT
1 TTTAT-TCATTT
21375866 TATATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 17 0.53
26 15 0.47
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.74
Consensus pattern (26 bp):
TTTATTCATTTGTTTGTTATATTATT
Found at i:21379870 original size:23 final size:23
Alignment explanation
Indices: 21379822--21379870 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
21379812 CAATTAGTGC
* *
21379822 TTAATTAACTTAACTAATCATTT
1 TTAATTAACTTAACTAAACATAT
*
21379845 TTAATTAACTTCA-TAAAACATAT
1 TTAATTAACTTAACT-AAACATAT
21379868 TTA
1 TTA
21379871 TTCATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAATTAACTTAACTAAACATAT
Found at i:21381380 original size:17 final size:17
Alignment explanation
Indices: 21381360--21381418 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
21381350 TCAACATGAT
21381360 TAAATAATTCAATAATA
1 TAAATAATTCAATAATA
*
21381377 TAAATAGTAT-AA-AATA
1 TAAATAAT-TCAATAATA
21381393 TGAAATTTAATTCAATAATA
1 T-AAA--TAATTCAATAATA
21381413 TAAATA
1 TAAATA
21381419 GTAGACATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 5 0.15
17 14 0.41
18 2 0.06
19 8 0.24
20 5 0.15
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAATAATTCAATAATA
Found at i:21383625 original size:21 final size:22
Alignment explanation
Indices: 21383587--21383627 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
21383577 AGAAAATAAT
*
21383587 TTAACTTAATTAAAATTTTTAA
1 TTAACTTAAATAAAATTTTTAA
*
21383609 TTAA-TTAAATAATATTTTT
1 TTAACTTAAATAAAATTTTT
21383628 TGGAATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAACTTAAATAAAATTTTTAA
Done.