Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 35 of 144
Found at i:8979732 original size:6 final size:6
Alignment explanation
Indices: 8979681--8979737 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
8979671 AAACTTTTCT
* * *
8979681 TTTAAG TTTAAA TTTAAA -TTAAG TTTAAA TTT-AA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
8979727 TTTAAA ATTAA
1 TTTAAA TTTAA
8979738 TTAAAAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
5 9 0.20
6 35 0.80
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:8979739 original size:17 final size:17
Alignment explanation
Indices: 8979682--8979737 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 17
8979672 AACTTTTCTT
8979682 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
*
8979699 TTAAGTTTAAATTTAAT
1 TTAAGTTTAAATTTAAA
8979716 TTGAA-TTTAAATTTAAAA
1 TT-AAGTTTAAATTT-AAA
8979734 TTAA
1 TTAA
8979738 TTAAAAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 29 0.83
18 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:8980609 original size:30 final size:29
Alignment explanation
Indices: 8980392--8980609 Score: 210
Period size: 30 Copynumber: 7.4 Consensus size: 29
8980382 AACTATCTAT
* * *
8980392 AAATTATATTTTGACCCTCAAACTTCTCCA
1 AAATTACATTTTGACCCTAAAACTTC-CAA
*
8980422 AAATTACATATTTGACCCTAAAACTTCTAA
1 AAATTACAT-TTTGACCCTAAAACTTCCAA
* * * * *
8980452 AAATTAAATTTTAAACCTTAAACTTTCAA
1 AAATTACATTTTGACCCTAAAACTTCCAA
*
8980481 AAATTACATTTTTACCCCCT-AAACTTCCAA
1 AAATTACATTTTGA--CCCTAAAACTTCCAA
*
8980511 AAATTACATTTTTAACTCC-AAAACTTCCAA
1 AAATTACA-TTTTGAC-CCTAAAACTTCCAA
***
8980541 AAATTACATTTT--CCCCCGAACTTCCAA
1 AAATTACATTTTGACCCTAAAACTTCCAA
*
8980568 AAATTCCATTTTGACCCTAAAACTTCCAA
1 AAATTACATTTTGACCCTAAAACTTCCAA
8980597 AAATTACCATTTT
1 AAATTA-CATTTT
8980610 ACCTCGGATG
Statistics
Matches: 156, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.01
27 21 0.13
29 49 0.31
30 60 0.38
31 24 0.15
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.34
Consensus pattern (29 bp):
AAATTACATTTTGACCCTAAAACTTCCAA
Found at i:8980624 original size:57 final size:57
Alignment explanation
Indices: 8980471--8980630 Score: 182
Period size: 57 Copynumber: 2.8 Consensus size: 57
8980461 TTTAAACCTT
* * *
8980471 AAACTTTCAAAAATTACATTTTTACCCCCTAAACTTCCAAAAATTACATTTTTAACTCCA
1 AAACTTCCAAAAATTACA-TTTTA-CCCC-GAACTTCCAAAAATTCCATTTTTAACTCCA
* *
8980531 AAACTTCCAAAAATTACATTTTCCCCCGAACTTCCAAAAATTCCA-TTTTGAC-CCTA
1 AAACTTCCAAAAATTACATTTTACCCCGAACTTCCAAAAATTCCATTTTTAACTCC-A
* *
8980587 AAACTTCCAAAAATTACCATTTTACCTCGGA-TGTCCAAAAATTC
1 AAACTTCCAAAAATTA-CATTTTACCCCGAACT-TCCAAAAATTC
8980631 TGTTTTTCAT
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
55 2 0.02
56 24 0.27
57 38 0.43
58 4 0.04
59 4 0.04
60 17 0.19
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (57 bp):
AAACTTCCAAAAATTACATTTTACCCCGAACTTCCAAAAATTCCATTTTTAACTCCA
Found at i:8980686 original size:58 final size:59
Alignment explanation
Indices: 8980475--8980729 Score: 169
Period size: 58 Copynumber: 4.4 Consensus size: 59
8980465 AACCTTAAAC
* **
8980475 TTTCAAAAATTA-CATTTTTACCCCCTAAACT-TCCAAAAAT-TACATTTTTAACTCC-AAAAC
1 TTTCAAAAATTACCA-TTTTACCCCC-AGA-TGTCCAAAAATGT-CATTTTTAAC-CCTAAATT
* * **
8980535 TTCCAAAAATTA-CATTTT-CCCCC-GAACT-TCCAAAAAT-TCCA-TTTTGACCCTAAAAC
1 TTTCAAAAATTACCATTTTACCCCCAG-A-TGTCCAAAAATGT-CATTTTTAACCCTAAATT
* * * * * * *
8980591 TTCCAAAAATTACCATTTTA-CCTCGGATGTCCAAAAAT-TCTGTTTTTCATCCT-GATT
1 TTTCAAAAATTACCATTTTACCCCCAGATGTCCAAAAATGTC-ATTTTTAACCCTAAATT
* *
8980648 TTTCTAAAAATTACCGTTTTACCCCCAGATGT-CTAAAATGTCATTTTTAACCCTAAATT
1 TTTC-AAAAATTACCATTTTACCCCCAGATGTCCAAAAATGTCATTTTTAACCCTAAATT
*
8980707 TTTCCAAAATTACCATTTTACCC
1 TTTCAAAAATTACCATTTTACCC
8980730 TCGGGTATCC
Statistics
Matches: 161, Mismatches: 22, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
55 2 0.01
56 25 0.16
57 39 0.24
58 61 0.38
59 21 0.13
60 13 0.08
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.36
Consensus pattern (59 bp):
TTTCAAAAATTACCATTTTACCCCCAGATGTCCAAAAATGTCATTTTTAACCCTAAATT
Found at i:8986221 original size:43 final size:42
Alignment explanation
Indices: 8986163--8986260 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 42
8986153 AATAAATATA
*
8986163 AAAAGAAGAGAAAGAAAAAAGAAAAGAA-AAA-AAAAAAGAAGAAG
1 AAAA-AAGAAAAAG-AAAAAGAAAA-AAGAAAGAAAAAAGAAG-AG
*
8986207 AAAAAAGAAAAAGAAAAAGAAAAAAGAAAGGAAAAAGAAGAG
1 AAAAAAGAAAAAGAAAAAGAAAAAAGAAAGAAAAAAGAAGAG
8986249 AGAAAAAGAAAA
1 A-AAAAAGAAAA
8986261 GGAGAGGTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
41 2 0.04
42 16 0.33
43 27 0.55
44 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (42 bp):
AAAAAAGAAAAAGAAAAAGAAAAAAGAAAGAAAAAAGAAGAG
Found at i:8986225 original size:37 final size:37
Alignment explanation
Indices: 8986162--8986260 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 37
8986152 AAATAAATAT
8986162 AAAAAGAAG-AG-AAAGA-AAAAAG-AAAAGAAAAAA
1 AAAAAGAAGAAGAAAAGAGAAAAAGAAAAAGAAAAAA
*
8986195 AAAAAGAAGAAGAAAAAAGAAAAAGAAAAAGAAAAAA
1 AAAAAGAAGAAGAAAAGAGAAAAAGAAAAAGAAAAAA
* * * *
8986232 GAAAGGAAAAAGAAGAGAGAAAAAGAAAA
1 AAAAAGAAGAAGAAAAGAGAAAAAGAAAA
8986261 GGAGAGGTCG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
33 9 0.16
34 2 0.04
35 4 0.07
36 6 0.11
37 35 0.62
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (37 bp):
AAAAAGAAGAAGAAAAGAGAAAAAGAAAAAGAAAAAA
Found at i:8986243 original size:7 final size:6
Alignment explanation
Indices: 8986168--8986260 Score: 91
Period size: 6 Copynumber: 15.2 Consensus size: 6
8986158 ATATAAAAAG
* * *
8986168 AAGAGA AAGAAA AA-AGAA AAGAAA AAAAAA AAGAAG AAGAAAA AAGAAA
1 AAGAAA AAGAAA AAGA-AA AAGAAA AAGAAA AAGAAA AAG-AAA AAGAAA
* *
8986217 AAGAAA AAGAAA AA-AGAA AGGAAA AAGAAGA GAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGA-AA AAGAAA AAGAA-A AAGAAA AAGAAA A
8986261 GGAGAGGTCG
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
5 2 0.03
6 58 0.81
7 12 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:8987540 original size:51 final size:51
Alignment explanation
Indices: 8987443--8987806 Score: 396
Period size: 51 Copynumber: 7.2 Consensus size: 51
8987433 CAGGTTTTAC
* * * * *
8987443 AGGGAAGGATCTAAG-CCACGACAGCGGATCTAGTACCACAAAGATACAGA
1 AGGGAAAGATCTAAGACCACAACGGCAGATCCAGTACCACAAAGATACAGA
* * * *
8987493 AGGGAAAGATCTAAGACCGCAATGGTAGATCCAATACCACAAAGATACAGA
1 AGGGAAAGATCTAAGACCACAACGGCAGATCCAGTACCACAAAGATACAGA
* * * *
8987544 GGGGAAAGATCTAAGACCGCAAAGGCAGATCTAGTACCACAAAGATACAGA
1 AGGGAAAGATCTAAGACCACAACGGCAGATCCAGTACCACAAAGATACAGA
* * * * * *
8987595 AGGGAAAGATATAAGACCACAATGGCGGAACCAGTACCACGAAG--ACATA
1 AGGGAAAGATCTAAGACCACAACGGCAGATCCAGTACCACAAAGATACAGA
* * * * *
8987644 AGGGAAAGATCTAAGACCACGACGGTAGATTCAGTACCACAAATATACAAA
1 AGGGAAAGATCTAAGACCACAACGGCAGATCCAGTACCACAAAGATACAGA
* * * * *
8987695 AGAGAAAGATCTAAGACTACAACGGCGGATCCAATACCACGAAG--ACAGA
1 AGGGAAAGATCTAAGACCACAACGGCAGATCCAGTACCACAAAGATACAGA
* * * *
8987744 AGGGAAAGACCAAAGATCGCAACGGCAGATCCAGTACCACAAAGATACAGA
1 AGGGAAAGATCTAAGACCACAACGGCAGATCCAGTACCACAAAGATACAGA
8987795 AGGGAAAGATCT
1 AGGGAAAGATCT
8987807 CTAGTACCAC
Statistics
Matches: 255, Mismatches: 54, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
49 78 0.31
50 14 0.05
51 163 0.64
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (51 bp):
AGGGAAAGATCTAAGACCACAACGGCAGATCCAGTACCACAAAGATACAGA
Found at i:8987586 original size:20 final size:20
Alignment explanation
Indices: 8987550--8987587 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8987540 CAGAGGGGAA
*
8987550 AGATCTAAGACCGCAAAGGC
1 AGATCTAAGACCACAAAGGC
8987570 AGATCT-AGTACCACAAAG
1 AGATCTAAG-ACCACAAAG
8987588 ATACAGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.13
Consensus pattern (20 bp):
AGATCTAAGACCACAAAGGC
Found at i:8987710 original size:100 final size:100
Alignment explanation
Indices: 8987443--8987806 Score: 444
Period size: 100 Copynumber: 3.6 Consensus size: 100
8987433 CAGGTTTTAC
* * * *
8987443 AGGGAAGGATCTAAG-CCACGACAGCGGATCTAGTACCACAAAGATACAGAAGGGAAAGATCTAA
1 AGGGAAAGATCTAAGACCACAACGGCAGATCTAGTACCACAAAGATACAGAAGGGAAAGATCTAA
* ** *
8987507 GACCGCAATGGTAGATCCAATACCACAAAGATACAGA
66 GACCACAATGGCGGATCCAATACCACGAAG--ACAGA
* * * *
8987544 GGGGAAAGATCTAAGACCGCAAAGGCAGATCTAGTACCACAAAGATACAGAAGGGAAAGATATAA
1 AGGGAAAGATCTAAGACCACAACGGCAGATCTAGTACCACAAAGATACAGAAGGGAAAGATCTAA
* * *
8987609 GACCACAATGGCGGAACCAGTACCACGAAGACATA
66 GACCACAATGGCGGATCCAATACCACGAAGACAGA
* * * * *
8987644 AGGGAAAGATCTAAGACCACGACGGTAGAT-TCAGTACCACAAATATACAAAAGAGAAAGATCTA
1 AGGGAAAGATCTAAGACCACAACGGCAGATCT-AGTACCACAAAGATACAGAAGGGAAAGATCTA
* *
8987708 AGACTACAACGGCGGATCCAATACCACGAAGACAGA
65 AGACCACAATGGCGGATCCAATACCACGAAGACAGA
* * * * *
8987744 AGGGAAAGACCAAAGATCGCAACGGCAGATCCAGTACCACAAAGATACAGAAGGGAAAGATCT
1 AGGGAAAGATCTAAGACCACAACGGCAGATCTAGTACCACAAAGATACAGAAGGGAAAGATCT
8987807 CTAGTACCAC
Statistics
Matches: 221, Mismatches: 39, Indels: 7
0.83 0.15 0.03
Matches are distributed among these distances:
99 1 0.00
100 140 0.63
101 13 0.06
102 67 0.30
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (100 bp):
AGGGAAAGATCTAAGACCACAACGGCAGATCTAGTACCACAAAGATACAGAAGGGAAAGATCTAA
GACCACAATGGCGGATCCAATACCACGAAGACAGA
Found at i:8987798 original size:151 final size:152
Alignment explanation
Indices: 8987469--8987806 Score: 405
Period size: 151 Copynumber: 2.2 Consensus size: 152
8987459 CACGACAGCG
* * *
8987469 GATCTAGTACCACAAAGATACAGAAGGGAAAGATCTAAGACCGCAATGGTAGATCCAATACCACA
1 GATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAGACCACAACGGTAGATCCAATACCACA
* * * * * *
8987534 AAGATACAGAGGGGAAAGATCTAAGACCGCAAAGGCAGATCTAGTACCACAAAGATACAGAAGGG
66 AAGATACAAAAGAGAAAGATCTAAGACCACAAAGGCAGATCCAATACCACAAAGA-ACAGAAGGG
* * *
8987599 AAAGATATAAGACCACAATGGCG
130 AAAGACATAAGACCACAACGGCA
* * * * * *
8987622 GAACCAGTACCACGAAG--ACATAAGGGAAAGATCTAAGACCACGACGGTAGATTCAGTACCACA
1 GATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAGACCACAACGGTAGATCCAATACCACA
* * * * *
8987685 AATATACAAAAGAGAAAGATCTAAGACTACAACGGCGGATCCAATACCACGAAG-ACAGAAGGGA
66 AAGATACAAAAGAGAAAGATCTAAGACCACAAAGGCAGATCCAATACCACAAAGAACAGAAGGGA
* *
8987749 AAGACCA-AAGATCGCAACGGCA
131 AAGA-CATAAGACCACAACGGCA
8987771 GATCCAGTACCACAAAGATACAGAAGGGAAAGATCT
1 GATCCAGTACCACAAAGATACAGAAGGGAAAGATCT
8987807 CTAGTACCAC
Statistics
Matches: 154, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
149 40 0.26
150 1 0.01
151 99 0.64
153 14 0.09
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (152 bp):
GATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAGACCACAACGGTAGATCCAATACCACA
AAGATACAAAAGAGAAAGATCTAAGACCACAAAGGCAGATCCAATACCACAAAGAACAGAAGGGA
AAGACATAAGACCACAACGGCA
Found at i:8987910 original size:49 final size:49
Alignment explanation
Indices: 8987831--8988119 Score: 260
Period size: 49 Copynumber: 5.9 Consensus size: 49
8987821 AAAACAAGAC
** * * * * * *
8987831 GGGAAAGATCTAAGGCTACAACGACGGATCCAGTACCGCAAAGATACAAA
1 GGGAAAGATCTAA-GCCGCAACGGCAGATCCAGTACCACGAAGACATAAA
* * * * * * * *
8987881 GGGTAAGGTTTAAGTCGCAACGGCAGATCCAGTACCGCAAAGATACAAA
1 GGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCACGAAGACATAAA
* * * * * * * * *
8987930 GGGTAAGGTTTAAGTCGTAATGGC-GAATCTTA-TACCTCGAAGACATGAA
1 GGGAAAGATCTAAGCCGCAACGGCAG-ATC-CAGTACCACGAAGACATAAA
* * *
8987979 GGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCACGAAGACATGAA
1 GGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCACGAAGACATAAA
*
8988028 GGGAAAGATCTAAGCCGCGACGGCAGATCCAGTACCACGAAGACATGAAA
1 GGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCACGAAGACAT-AAA
8988078 -GGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCACGAAGA
1 GGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCACGAAGA
8988120 TTTGAAGGGA
Statistics
Matches: 206, Mismatches: 28, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
48 2 0.01
49 190 0.92
50 14 0.07
ACGTcount: A:0.37, C:0.21, G:0.27, T:0.15
Consensus pattern (49 bp):
GGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCACGAAGACATAAA
Found at i:8988131 original size:49 final size:49
Alignment explanation
Indices: 8987962--8988132 Score: 279
Period size: 49 Copynumber: 3.5 Consensus size: 49
8987952 GCGAATCTTA
* * *
8987962 TACCTCGAAGACATGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAG
1 TACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAG
*
8988011 TACCACGAAGACATGAAGGGAAAGATCTAAGCCGCGACGGCAGATCCAG
1 TACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAG
*
8988060 TACCACGAAGACATGAAAGGAAAGATCTAAGCCGCAACGGCAGATCCAG
1 TACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAG
**
8988109 TACCACGAAGATTTGAAGGGAAAG
1 TACCACGAAGACATGAAGGGAAAG
8988133 GTTTAAGTCA
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 113 1.00
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.12
Consensus pattern (49 bp):
TACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCAGATCCAG
Found at i:8988161 original size:98 final size:98
Alignment explanation
Indices: 8987891--8988161 Score: 312
Period size: 98 Copynumber: 2.8 Consensus size: 98
8987881 GGGTAAGGTT
* * * ** * *
8987891 TAAGTCGCAACGGCAGATCCAGTACCGCAAAGATACAAAGGGTAAGGTTTAAGTCGTAATGGCGA
1 TAAGCCGCAACGGCAGATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGCGA
* * *
8987956 ATCTTA-TACCTCGAAGACATGAAGGGAAAGATC
66 A-CCTAGTACCACGAAGACATGAAAGGAAAGATC
* * * * * * * *
8987989 TAAGCCGCAATGGCGGATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCCGCGACGGCAG
1 TAAGCCGCAACGGCAGATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGC-G
*
8988054 ATCC-AGTACCACGAAGACATGAAAGGAAAGATC
65 AACCTAGTACCACGAAGACATGAAAGGAAAGATC
* *
8988087 TAAGCCGCAACGGCAGATCCAGTACCACGAAGATTTGAAGGGAAAGGTTTAAGTCACAATGGCGA
1 TAAGCCGCAACGGCAGATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGCGA
*
8988152 ACCTGGTACC
66 ACCTAGTACC
8988162 TTAGAAACAT
Statistics
Matches: 139, Mismatches: 31, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
97 5 0.04
98 132 0.95
99 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.27, T:0.16
Consensus pattern (98 bp):
TAAGCCGCAACGGCAGATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGCGA
ACCTAGTACCACGAAGACATGAAAGGAAAGATC
Found at i:8988890 original size:207 final size:207
Alignment explanation
Indices: 8988526--8989173 Score: 1010
Period size: 207 Copynumber: 3.1 Consensus size: 207
8988516 AGTGAGGTGG
*
8988526 TCATCTTCCTGATGAGATACTGAGAAGAGGACCAAATCAAACCCACGCTCGATATGAGCATGTCT
1 TCATCTTCCTGATGAGATACTGAGAAGAGGACCAAATCAAACCCACGCTCGATATGAGCAAGTCT
** *
8988591 TCGAACCCCCAATTTCCTGATGAGATACTAAGAAGCAGGTCAAAGTAATAAAATGGTTAGCTTCC
66 TCGAACCCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCC
8988656 TGATGAGATACTAAGAAGTGGACCAAATCCGTCTTCCTGATGAAATACAAAGAAGCGGATTGAAA
131 TGATGAGATACTAAGAAGTGGACCAAATCCGTCTTCCTGATGAAATACAAAGAAGCGGATTGAAA
*
8988721 CAAGCGATGCAA
196 CAAGCGATGCGA
* *
8988733 TAATCTTCTTGATGAGATACTGAGAAGAGGACCAAATCAAACCCACGCTCGATATGAGCAAGTCT
1 TCATCTTCCTGATGAGATACTGAGAAGAGGACCAAATCAAACCCACGCTCGATATGAGCAAGTCT
* *
8988798 TCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTCGCTTCC
66 TCGAACCCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCC
* *
8988863 TGATGAGATACTAAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAA
131 TGATGAGATACTAAGAAGTGGACCAAATCCGTCTTCCTGATGAAATACAAAGAAGCGGATTGAAA
*
8988928 CAAACGATGCGA
196 CAAGCGATGCGA
* *
8988940 TCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATATGAGCAAGTCT
1 TCATCTTCCTGATGAGATACTGAGAAGAGGACCAAATCAAACCCACGCTCGATATGAGCAAGTCT
* * * *
8989005 TCGAACCCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAGTGGTTAGTTTTC
66 TCGAACCCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCC
* ** * * * **
8989070 AGATGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAA-AAGTGGATCAAA
131 TGATGAGATACTAAGAAGTGGACCAAATCCGTCTTCCTGATGAAATACA-AAGAAGCGGATTGAA
* * *
8989134 ACAAGTGAGGCGG
195 ACAAGCGATGCGA
*
8989147 TCATCTTCCTGATGAGATACAGAGAAG
1 TCATCTTCCTGATGAGATACTGAGAAG
8989174 TATACCAACT
Statistics
Matches: 404, Mismatches: 36, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
207 403 1.00
208 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (207 bp):
TCATCTTCCTGATGAGATACTGAGAAGAGGACCAAATCAAACCCACGCTCGATATGAGCAAGTCT
TCGAACCCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCC
TGATGAGATACTAAGAAGTGGACCAAATCCGTCTTCCTGATGAAATACAAAGAAGCGGATTGAAA
CAAGCGATGCGA
Found at i:8989600 original size:17 final size:17
Alignment explanation
Indices: 8989578--8989628 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
8989568 AACTTTTCTT
8989578 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
*
8989595 TTAAGTTTAAATTTAAT
1 TTAAGTTTAAATTTAAA
8989612 TTGAA-TTTAAATTTAAA
1 TT-AAGTTTAAATTTAAA
8989629 ATTAGTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 29 0.94
18 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:8989603 original size:11 final size:11
Alignment explanation
Indices: 8989584--8989628 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
8989574 TCTTTTAAGT
8989584 TTAAATTTAAA
1 TTAAATTTAAA
*
8989595 TTAAGTTTAAA
1 TTAAATTTAAA
* *
8989606 TTTAATTTGAAT
1 TTAAATTT-AAA
8989618 TTAAATTTAAA
1 TTAAATTTAAA
8989629 ATTAGTTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:8989626 original size:6 final size:6
Alignment explanation
Indices: 8989545--8989628 Score: 66
Period size: 6 Copynumber: 14.3 Consensus size: 6
8989535 TTCATGATTG
* * * ** *
8989545 AATTTT AATTT- AGTTTA AATTTA AACTTTT CTTTTA AGTTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AA-TTTA AATTTA AATTTA AATTTA
* *
8989593 AA-TTA AGTTTA AATTT- AATTTG AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
8989629 ATTAGTTAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
5 13 0.21
6 46 0.74
7 3 0.05
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:8990359 original size:28 final size:29
Alignment explanation
Indices: 8990287--8990538 Score: 213
Period size: 30 Copynumber: 8.5 Consensus size: 29
8990277 TCAACTGTCC
* * *
8990287 AAAAATTATATTTTGACCCTCAAAA-TTTT
1 AAAAATTACATTTTAACCC-CAAAACTTCT
* *
8990316 CCAAAATTACATATTTAACCCAAAAACTTCT
1 -AAAAATTACAT-TTTAACCCCAAAACTTCT
** *
8990347 AAATGTTACATTTTTAACCCTAAAACTTCT
1 AAAAATTACA-TTTTAACCCCAAAACTTCT
* *
8990377 AAAAATTACATTTTTACCCCTAAACTT-T
1 AAAAATTACATTTTAACCCCAAAACTTCT
* *
8990405 AAAAATTACATTTTTACCCCCAAACTTCT
1 AAAAATTACATTTTAACCCCAAAACTTCT
* * *
8990434 AAAAATTACATTTTAACCTCGAATCTT-T
1 AAAAATTACATTTTAACCCCAAAACTTCT
* * *
8990462 CAAAAATTACATTTTTACCGCCTAAACTTCC
1 -AAAAATTACATTTTAACC-CCAAAACTTCT
* * * *
8990493 AAAAATTATATTTTTGACCCTAAAACTTCC
1 AAAAATTACA-TTTTAACCCCAAAACTTCT
8990523 AAAAATTACCATTTTA
1 AAAAATTA-CATTTTA
8990539 CCCTTAAATC
Statistics
Matches: 183, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
28 28 0.15
29 55 0.30
30 81 0.44
31 19 0.10
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCCAAAACTTCT
Found at i:8990401 original size:29 final size:29
Alignment explanation
Indices: 8990318--8990574 Score: 240
Period size: 30 Copynumber: 8.8 Consensus size: 29
8990308 AAAATTTTCC
* **
8990318 AAAATTACATATTTAACCCAAAAACTTCTA
1 AAAATTACAT-TTTTACCCCTAAACTTCTA
** *
8990348 AATGTTACATTTTTAACCCTAAAACTTCTA
1 AAAATTACATTTTTACCCCT-AAACTTCTA
8990378 AAAATTACATTTTTACCCCTAAACTT-TA
1 AAAATTACATTTTTACCCCTAAACTTCTA
*
8990406 AAAATTACATTTTTACCCCCAAACTTCTA
1 AAAATTACATTTTTACCCCTAAACTTCTA
* * * *
8990435 AAAATTACATTTTAACCTCGAATCTT-TCA
1 AAAATTACATTTTTACCCCTAAACTTCT-A
*
8990464 AAAATTACATTTTTACCGCCTAAACTTCCA
1 AAAATTACATTTTTACC-CCTAAACTTCTA
* *
8990494 AAAATTATATTTTTGA-CCCTAAAACTTCCA
1 AAAATTACATTTTT-ACCCCT-AAACTTCTA
*
8990524 AAAATTACCA-TTTTACCCTTAAA-TCTCT-
1 AAAATTA-CATTTTTACCCCTAAACT-TCTA
*
8990552 AAAATGT-CATTTTTAACCCTAAA
1 AAAAT-TACATTTTTACCCCTAAA
8990575 TTTTTCCAAA
Statistics
Matches: 190, Mismatches: 25, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
27 2 0.01
28 45 0.24
29 63 0.33
30 78 0.41
31 2 0.01
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCTAAACTTCTA
Found at i:8990610 original size:27 final size:28
Alignment explanation
Indices: 8990579--8990668 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
8990569 CCTAAATTTT
8990579 TCCAAAATTACCATTTT-CCCTCGAGAG
1 TCCAAAATTACCATTTTGCCCTCGAGAG
* * *
8990606 TCCAAAATTGCCATTTTGCCCCCAAGAG
1 TCCAAAATTACCATTTTGCCCTCGAGAG
*
8990634 TTCAAAATTACCATTTTGCCCTCGAGTA-
1 TCCAAAATTACCATTTTGCCCTCGAG-AG
8990662 TCCAAAA
1 TCCAAAA
8990669 AGTCTCGTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 16 0.30
28 36 0.68
29 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGCCCTCGAGAG
Found at i:8993880 original size:43 final size:43
Alignment explanation
Indices: 8993813--8993963 Score: 214
Period size: 43 Copynumber: 3.5 Consensus size: 43
8993803 AAGATTATAT
*
8993813 TTCGGTATATCCGATGATGCACTATGTGTGCCAGTGTAGTTAC
1 TTCGGTATATCCGATGATGCACTATGTGTGCCAGTATAGTTAC
* * * * *
8993856 TTCGATATATCCGATGATGTACTATTTGTGTCGGTATAGTTAC
1 TTCGGTATATCCGATGATGCACTATGTGTGCCAGTATAGTTAC
* *
8993899 TTCTGTATATTCGATGATGCACTATGTGTGCCAGTATAGTT-C
1 TTCGGTATATCCGATGATGCACTATGTGTGCCAGTATAGTTAC
*
8993941 TTCGGTATATCCGGTGATGCACT
1 TTCGGTATATCCGATGATGCACT
8993964 GTGTATGCTA
Statistics
Matches: 92, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 21 0.23
43 71 0.77
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TTCGGTATATCCGATGATGCACTATGTGTGCCAGTATAGTTAC
Found at i:8994543 original size:75 final size:75
Alignment explanation
Indices: 8994460--8994610 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 75
8994450 ATATTAATAA
* *
8994460 AATAATAATTAAAATTAAAGCATATCATTAAAACTAAAATTTGTTTAGTGAAAAGAGAGAATAAC
1 AATAATAATTAAAATTAAAGCATATCATTAAAACTAAAATTGGTTTAGTGAAAAGAGAGAAGAAC
*
8994525 ATTTTCTTTC
66 ATATTCTTTC
*
8994535 AATAATAATTAAAATTAAAGCATATCATTAAAGCTAAAATTGGTTTAGTGAAAAGAGAGAAGAAC
1 AATAATAATTAAAATTAAAGCATATCATTAAAACTAAAATTGGTTTAGTGAAAAGAGAGAAGAAC
8994600 ATATTCTTTC
66 ATATTCTTTC
8994610 A
1 A
8994611 TTTCTTCATG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.32
Consensus pattern (75 bp):
AATAATAATTAAAATTAAAGCATATCATTAAAACTAAAATTGGTTTAGTGAAAAGAGAGAAGAAC
ATATTCTTTC
Found at i:8996777 original size:20 final size:19
Alignment explanation
Indices: 8996730--8996777 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
8996720 TTTTTTCAAT
*
8996730 TCTGGTGGCTTGTCCACAA
1 TCTGGTAGCTTGTCCACAA
* *
8996749 CTCTAGTAGCTTGTCTACAA
1 -TCTGGTAGCTTGTCCACAA
8996769 TACTGGTAG
1 T-CTGGTAG
8996778 TCTGAGATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (19 bp):
TCTGGTAGCTTGTCCACAA
Found at i:9000732 original size:111 final size:111
Alignment explanation
Indices: 9000538--9000759 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
9000528 AACAAAACCT
9000538 AATATGATTATAACATTAAAACTTAAGAAATAAGCTAATGTTCTTTAGCTTTCTTCTTCACAAAA
1 AATATGATTATAACATTAAAACTTAAGAAATAAGCTAATGTTCTTTAGCTTTCTTCTTCACAAAA
9000603 CTGAAACCACCATAGCTAGGGCTTGGAGAGCTTCGGTCAAGTTTGG
66 CTGAAACCACCATAGCTAGGGCTTGGAGAGCTTCGGTCAAGTTTGG
9000649 AATATGATTATAACATTAAAACTTAAGAAATAAGCTAATGTTCTTTAGCTTTCTTCTTCACAAAA
1 AATATGATTATAACATTAAAACTTAAGAAATAAGCTAATGTTCTTTAGCTTTCTTCTTCACAAAA
9000714 CTGAAACCACCATAGCTAGGGCTTGGAGAGCTTCGGTCAAGTTTGG
66 CTGAAACCACCATAGCTAGGGCTTGGAGAGCTTCGGTCAAGTTTGG
9000760 CTCACCGGTT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (111 bp):
AATATGATTATAACATTAAAACTTAAGAAATAAGCTAATGTTCTTTAGCTTTCTTCTTCACAAAA
CTGAAACCACCATAGCTAGGGCTTGGAGAGCTTCGGTCAAGTTTGG
Found at i:9004545 original size:26 final size:26
Alignment explanation
Indices: 9004509--9004575 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
9004499 TCTGAAGAAT
* * *
9004509 TACTATACTGGTTCGTAAGAGTAATA
1 TACTGTACTGGCTCGTAAAAGTAATA
*
9004535 TACTGTACTGGCTCGTAAAAGTGATA
1 TACTGTACTGGCTCGTAAAAGTAATA
* *
9004561 TATTGAACTGGCTCG
1 TACTGTACTGGCTCG
9004576 GGAGAGTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (26 bp):
TACTGTACTGGCTCGTAAAAGTAATA
Found at i:9004583 original size:26 final size:26
Alignment explanation
Indices: 9004515--9004584 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 26
9004505 GAATTACTAT
* * * *
9004515 ACTGGTTCGTAAGAGTAATATACTGT
1 ACTGGCTCGGAAGAGTGATATACTGA
* * *
9004541 ACTGGCTCGTAAAAGTGATATATTGA
1 ACTGGCTCGGAAGAGTGATATACTGA
*
9004567 ACTGGCTCGGGAGAGTGA
1 ACTGGCTCGGAAGAGTGA
9004585 ATGTAACACC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.29
Consensus pattern (26 bp):
ACTGGCTCGGAAGAGTGATATACTGA
Found at i:9005600 original size:23 final size:22
Alignment explanation
Indices: 9005574--9005720 Score: 154
Period size: 23 Copynumber: 6.3 Consensus size: 22
9005564 TAGGCACCAA
* *
9005574 AGAGCACACACAGTGCTAAACAA
1 AGAGCACACA-AGTGCTAATCAG
* *
9005597 AGAGTACACGAAGTACTAATCAG
1 AGAGCACAC-AAGTGCTAATCAG
9005620 AGAGCACACGAAGTGCTAATCAG
1 AGAGCACAC-AAGTGCTAATCAG
9005643 AGAGCACACATAGTGCTAATAACAG
1 AGAGCACACA-AGTGCTAAT--CAG
9005668 AGAGCACACACAGTGCTAATCAG
1 AGAGCACACA-AGTGCTAATCAG
9005691 AGAGCACGA-AATGTGCTAAAT-AG
1 AGAGCAC-ACAA-GTGCT-AATCAG
9005714 AGAGCAC
1 AGAGCAC
9005721 CGAGGTCCTA
Statistics
Matches: 110, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.02
23 81 0.74
24 5 0.05
25 22 0.20
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.14
Consensus pattern (22 bp):
AGAGCACACAAGTGCTAATCAG
Found at i:9005716 original size:71 final size:68
Alignment explanation
Indices: 9005534--9005720 Score: 175
Period size: 71 Copynumber: 2.6 Consensus size: 68
9005524 CAGAGAGTAT
** * *
9005534 CGAAGTACTAAAT-AGAGAGCACGTAAGTGCTAGGCACCAAAGAGCACACACAGTGCTAAACAAA
1 CGAAGTACT-AATCAGAGAGCACACAAGTGCTA---ATCAGAGAGCACACACAGTGCTAAACAAA
*
9005598 GAGTACA
62 GAGCACA
* *
9005605 CGAAGTACTAATCAGAGAGCACACGAAGTGCTAATCAGAGAGCACACATAGTGCTAATAACAGAG
1 CGAAGTACTAATCAGAGAGCACAC-AAGTGCTAATCAGAGAGCACACACAGTGCT-A-AACAAAG
9005670 AGCACA
63 AGCACA
*
9005676 C-ACAGTGCTAATCAGAGAGCACGA-AATGTGCTAAAT-AGAGAGCAC
1 CGA-AGTACTAATCAGAGAGCAC-ACAA-GTGCT-AATCAGAGAGCAC
9005721 CGAGGTCCTA
Statistics
Matches: 100, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
69 19 0.19
70 7 0.07
71 62 0.62
72 12 0.12
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (68 bp):
CGAAGTACTAATCAGAGAGCACACAAGTGCTAATCAGAGAGCACACACAGTGCTAAACAAAGAGC
ACA
Found at i:9012290 original size:23 final size:23
Alignment explanation
Indices: 9012264--9012414 Score: 153
Period size: 23 Copynumber: 6.5 Consensus size: 23
9012254 AGTGCTGGGC
*
9012264 AACAGAGAGCACACACAGTGCCA
1 AACAGAGAGCACACACAGTGCTA
* * *
9012287 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
9012310 ATCAGAGAGCGCACGA-AGTGCTA
1 AACAGAGAGCACAC-ACAGTGCTA
*
9012333 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
9012357 TAACAGAGAGCACACATAGTGCTA
1 -AACAGAGAGCACACACAGTGCTA
* *
9012381 ATCAGAGAGCACGAAACA-TGCTA
1 AACAGAGAGCAC-ACACAGTGCTA
*
9012404 AATAGAGAGCA
1 AACAGAGAGCA
9012415 TTGATGTGCT
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
22 1 0.01
23 80 0.75
24 6 0.06
25 20 0.19
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:9012403 original size:48 final size:46
Alignment explanation
Indices: 9012264--9012404 Score: 144
Period size: 48 Copynumber: 3.0 Consensus size: 46
9012254 AGTGCTGGGC
* * * *
9012264 AACAGAGAGCACACACAGTGCCAAACAGAGAGTACACAA-A-G-TACT
1 AACAGAGAGCACACA-AGTGCTAATCAGAGAGCACA-AACATGCTAAT
* *
9012309 AATCAGAGAGCGCACGAAGTGCTAATCAGAGAGCACACACAGTGCTAAT
1 AA-CAGAGAGCACAC-AAGTGCTAATCAGAGAGCACAAACA-TGCTAAT
9012358 AACAGAGAGCACACATAGTGCTAATCAGAGAGCACGAAACATGCTAA
1 AACAGAGAGCACACA-AGTGCTAATCAGAGAGCAC-AAACATGCTAA
9012405 ATAGAGAGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
45 3 0.04
46 29 0.36
47 2 0.03
48 37 0.46
49 9 0.11
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (46 bp):
AACAGAGAGCACACAAGTGCTAATCAGAGAGCACAAACATGCTAAT
Found at i:9012403 original size:71 final size:69
Alignment explanation
Indices: 9012266--9012414 Score: 187
Period size: 71 Copynumber: 2.1 Consensus size: 69
9012256 TGCTGGGCAA
* * *
9012266 CAGAGAGCACACACAGTGCCAAACAGAGAGTACACAAAGTACTAATCAGAGAGCGCACGAAGTGC
1 CAGAGAGCACACACAGTGCAAAACAGAGAGCACACAAAGTACTAATCAGAGA-CGCACGAAATGC
9012331 T-AAT
65 TAAAT
* *
9012335 CAGAGAGCACACACAGTGCTAATAACAGAGAGCACACATAGTGCTAATCAGAGA-GCACGAAACA
1 CAGAGAGCACACACAGTGC-AA-AACAGAGAGCACACAAAGTACTAATCAGAGACGCACG-AA-A
9012399 TGCTAAAT
62 TGCTAAAT
9012407 -AGAGAGCA
1 CAGAGAGCA
9012415 TTGATGTGCT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
69 24 0.34
70 3 0.04
71 40 0.57
72 3 0.04
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (69 bp):
CAGAGAGCACACACAGTGCAAAACAGAGAGCACACAAAGTACTAATCAGAGACGCACGAAATGCT
AAAT
Found at i:9012768 original size:7 final size:7
Alignment explanation
Indices: 9012756--9012789 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
9012746 TTGCTCTTCT
9012756 CTTTTCC
1 CTTTTCC
9012763 CTTTTCC
1 CTTTTCC
9012770 CTTTTCC
1 CTTTTCC
9012777 CTTTTCC
1 CTTTTCC
9012784 CTTTTC
1 CTTTTC
9012790 TTCAATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
CTTTTCC
Found at i:9013434 original size:26 final size:26
Alignment explanation
Indices: 9013405--9013481 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 26
9013395 TACTGTATTG
9013405 GCTCGTAAGAGCGATATACTGAACTA
1 GCTCGTAAGAGCGATATACTGAACTA
* * *
9013431 GCTCGTGAGAGCGCAT-TACTGTACTG
1 GCTCGTAAGAGCG-ATATACTGAACTA
* *
9013457 GCTCGTAAGAGCAATATATTGAACT
1 GCTCGTAAGAGCGATATACTGAACT
9013482 GATTGATTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 2 0.05
26 38 0.90
27 2 0.05
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (26 bp):
GCTCGTAAGAGCGATATACTGAACTA
Found at i:9019879 original size:21 final size:24
Alignment explanation
Indices: 9019833--9019885 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
9019823 TTAAAAATGG
9019833 TAATAATAATAAGTGCTTTAATAA
1 TAATAATAATAAGTGCTTTAATAA
*
9019857 TAATAATAATAATTG-TTTAAATAA
1 TAATAATAATAAGTGCTTT-AATAA
9019881 TAATA
1 TAATA
9019886 TTTATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.40
Consensus pattern (24 bp):
TAATAATAATAAGTGCTTTAATAA
Found at i:9033507 original size:31 final size:31
Alignment explanation
Indices: 9033469--9033530 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
9033459 TTACTTTGGC
9033469 AGGTTGAATCTTAGCGATGGAATAATATAAT
1 AGGTTGAATCTTAGCGATGGAATAATATAAT
9033500 AGGTTGAATCTTAGCGATGGAATAATATAAT
1 AGGTTGAATCTTAGCGATGGAATAATATAAT
9033531 TAAGTCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (31 bp):
AGGTTGAATCTTAGCGATGGAATAATATAAT
Found at i:9037846 original size:13 final size:15
Alignment explanation
Indices: 9037828--9037866 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
9037818 GAAGATGGAT
9037828 AAATAAA-AAAA-AG
1 AAATAAATAAAATAG
9037841 AAATAAATAAAATAG
1 AAATAAATAAAATAG
9037856 AATATAAATAA
1 AA-ATAAATAA
9037867 GATAAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 4 0.17
15 4 0.17
16 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (15 bp):
AAATAAATAAAATAG
Found at i:9039172 original size:21 final size:21
Alignment explanation
Indices: 9039133--9039172 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9039123 TTTTAAAAAA
*
9039133 AATATAAATGATATAGAATAT
1 AATATAAATGAAATAGAATAT
*
9039154 AATATAAATGAAATGGAAT
1 AATATAAATGAAATAGAAT
9039173 TGCTGATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
AATATAAATGAAATAGAATAT
Found at i:9039222 original size:23 final size:21
Alignment explanation
Indices: 9039180--9039220 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9039170 AATTGCTGAT
*
9039180 AAAAGTTCTATATATCTATAG
1 AAAAGTTCGATATATCTATAG
*
9039201 AAAAGTTGGATATATCTATA
1 AAAAGTTCGATATATCTATA
9039221 TAATTAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAAGTTCGATATATCTATAG
Found at i:9041043 original size:19 final size:19
Alignment explanation
Indices: 9041016--9041055 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
9041006 TCTTTTTTTT
*
9041016 ATTATACTTTTCT-ATTCTA
1 ATTAAACTTTT-TGATTCTA
9041035 ATTAAACTTTTTGATTCTA
1 ATTAAACTTTTTGATTCTA
9041054 AT
1 AT
9041056 AAAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTAAACTTTTTGATTCTA
Found at i:9042435 original size:30 final size:30
Alignment explanation
Indices: 9042401--9042606 Score: 256
Period size: 30 Copynumber: 6.9 Consensus size: 30
9042391 CCCTAGACTG
9042401 TCTAAAAATTACATTTTAACCCTAAAACTT
1 TCTAAAAATTACATTTTAACCCTAAAACTT
* * *
9042431 TCTAAAAAATATATTTTGACCCCT-AAACTT
1 TCTAAAAATTACATTTT-AACCCTAAAACTT
* * *
9042461 T-TCCAAATTTATATTTTAACCCTAAAACTT
1 TCT-AAAAATTACATTTTAACCCTAAAACTT
* *
9042491 TTTGAAAATTACATTTTAACCCTAAAACTT
1 TCTAAAAATTACATTTTAACCCTAAAACTT
* * *
9042521 TTTCCAAAATTGCATTTTAACCCTAAAACTT
1 TCT-AAAAATTACATTTTAACCCTAAAACTT
*
9042552 TCTAAAAATTACATTTTAACCCTAAAACTA
1 TCTAAAAATTACATTTTAACCCTAAAACTT
9042582 TCT-AAAATTACATTTTAACCCTAAA
1 TCTAAAAATTACATTTTAACCCTAAA
9042607 TTTTCCAAAA
Statistics
Matches: 155, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
29 28 0.18
30 94 0.61
31 33 0.21
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (30 bp):
TCTAAAAATTACATTTTAACCCTAAAACTT
Found at i:9042551 original size:61 final size:60
Alignment explanation
Indices: 9042405--9042606 Score: 282
Period size: 61 Copynumber: 3.4 Consensus size: 60
9042395 AGACTGTCTA
* * *
9042405 AAAATTACATTTTAACCCTAAAACTTTCTAAAAAATATATTTTGACCCCT-AAACTTTTCC
1 AAAATTACATTTTAACCCTAAAACTTTCTAAAAATTACATTTT-AACCCTAAAACTTTTCC
* * * *
9042465 AAATTTATATTTTAACCCTAAAACTTTTTGAAAATTACATTTTAACCCTAAAACTTTTTCC
1 AAAATTACATTTTAACCCTAAAACTTTCTAAAAATTACATTTTAACCCTAAAAC-TTTTCC
* * *
9042526 AAAATTGCATTTTAACCCTAAAACTTTCTAAAAATTACATTTTAACCCTAAAAC-TATCT
1 AAAATTACATTTTAACCCTAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCC
9042585 AAAATTACATTTTAACCCTAAA
1 AAAATTACATTTTAACCCTAAA
9042607 TTTTCCAAAA
Statistics
Matches: 125, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
59 29 0.23
60 41 0.33
61 55 0.44
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (60 bp):
AAAATTACATTTTAACCCTAAAACTTTCTAAAAATTACATTTTAACCCTAAAACTTTTCC
Found at i:9042626 original size:29 final size:28
Alignment explanation
Indices: 9042405--9042793 Score: 167
Period size: 30 Copynumber: 13.2 Consensus size: 28
9042395 AGACTGTCTA
* * *
9042405 AAAATTACATTTTAACCCTAAAACTTTCTA
1 AAAATTCCATTTTAACCCT-AAATTTTC-C
* ** *
9042435 AAAAATATATTTTGACCCCTAAACTTTTCC
1 AAAATTCCATTTT-AACCCTAAA-TTTTCC
* ** **
9042465 AAATTTATATTTTAACCCTAAAACTTTTTG
1 AAAATTCCATTTTAACCCT-AAA-TTTTCC
*
9042495 AAAATTACATTTTAACCCTAAAACTTTTTCC
1 AAAATTCCATTTTAACCCT-AAA--TTTTCC
* * *
9042526 AAAATTGCATTTTAACCCTAAAACTTTCTA
1 AAAATTCCATTTTAACCCT-AAATTTTC-C
* * * *
9042556 AAAATTACATTTTAACCCTAAAACTATCT
1 AAAATTCCATTTTAACCCT-AAATTTTCC
*
9042585 AAAATTACATTTTAACCCTAAATTTTCC
1 AAAATTCCATTTTAACCCTAAATTTTCC
**
9042613 AAAATTCCATTTTTTAACCC-CGATTTTACC
1 AAAATTCCA--TTTTAACCCTAAATTTT-CC
* * * *
9042643 AAAATTACCATTTTACCCCTGAACTTTCT
1 AAAATT-CCATTTTAACCCTAAATTTTCC
* * **
9042672 AAAATTCTATTTTTAA-CTTCGATTTTACC
1 AAAATTCCA-TTTTAACCCTAAATTTT-CC
* * *
9042701 AAAATTACCACTTT-ACCCTTAAACTTTCT
1 AAAATT-CCATTTTAACCC-TAAATTTTCC
* * *
9042730 AAAATTTCATTTTTGACCCT-GATTTTGCC
1 AAAATTCCA-TTTTAACCCTAAATTTT-CC
* *
9042759 AAAAATTACCATTTT-ACCCTCGAACTTTCC
1 -AAAATT-CCATTTTAACCCT-AAATTTTCC
9042789 AAAAT
1 AAAAT
9042794 CTCGTTTTTA
Statistics
Matches: 283, Mismatches: 54, Indels: 45
0.74 0.14 0.12
Matches are distributed among these distances:
28 29 0.10
29 86 0.30
30 124 0.44
31 44 0.16
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCTAAATTTTCC
Found at i:9042695 original size:58 final size:58
Alignment explanation
Indices: 9042585--9042836 Score: 255
Period size: 58 Copynumber: 4.3 Consensus size: 58
9042575 AAAACTATCT
* *
9042585 AAAATTA-CATTTTAACCCTAAATTTTCCAAAATTC-CATTTTTTAACCCCGATTTTACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTCA-TTTTTAA-CCCGATTTTACC
* * *
9042643 AAAATTACCATTTTACCCCTGAACTTTCTAAAATTCT-ATTTTTAACTTCGATTTTACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTCATTTTTAAC-CCGATTTTACC
* * * * *
9042701 AAAATTACCACTTTACCCTTAAACTTTCTAAAATT-TCATTTTTGACCCTGATTTTGCC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTCATTTTTAACCC-GATTTTACC
* * * * *
9042759 AAAAATTACCATTTTA-CCCTCGAACTTTCCAAAA-TCTCGTTTTTATCCCAATTTCGACC
1 -AAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCTCATTTTTAACCCGATTT-TACC
*
9042818 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
9042837 CGGGTATCCA
Statistics
Matches: 162, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
57 3 0.02
58 94 0.58
59 65 0.40
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTCATTTTTAACCCGATTTTACC
Found at i:9042819 original size:117 final size:117
Alignment explanation
Indices: 9042585--9042827 Score: 282
Period size: 117 Copynumber: 2.1 Consensus size: 117
9042575 AAAACTATCT
* *
9042585 AAAATTA-CATTTTAACCCTAAATTTTCCAAAATTCCATTTTTTAACCCCGATTTTACCAAAATT
1 AAAATTACCACTTTAACCCTAAACTTTCCAAAATTCCATTTTTTAACCCCGATTTTACCAAAATT
* * * *
9042649 ACCATTTTACCCCTGAACTTTCTAAAATTCTATTTTTAACTTCGATTTTACC
66 ACCATTTTACCCCTGAACTTTCCAAAATTCTATTTTTAACTCCAATTTGACC
* * * * *
9042701 AAAATTACCACTTT-ACCCTTAAACTTTCTAAAATTTCA-TTTTTGACCCTGATTTTGCCAAAAA
1 AAAATTACCACTTTAACCC-TAAACTTTCCAAAATTCCATTTTTTAACCCCGATTTTACC-AAAA
* *
9042764 TTACCATTTTA-CCCTCGAACTTTCCAAAA-TCTCGTTTTTATC-CCAATTTCGACC
64 TTACCATTTTACCCCT-GAACTTTCCAAAATTCT-ATTTTTAACTCCAATTT-GACC
9042818 AAAATTACCA
1 AAAATTACCA
9042828 TTTTGCCCCC
Statistics
Matches: 108, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
116 40 0.37
117 68 0.63
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (117 bp):
AAAATTACCACTTTAACCCTAAACTTTCCAAAATTCCATTTTTTAACCCCGATTTTACCAAAATT
ACCATTTTACCCCTGAACTTTCCAAAATTCTATTTTTAACTCCAATTTGACC
Found at i:9053949 original size:92 final size:92
Alignment explanation
Indices: 9053792--9054553 Score: 1328
Period size: 92 Copynumber: 8.3 Consensus size: 92
9053782 TGAAGATTTG
9053792 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
1 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
* *
9053857 GTTGGATAGCAAATCTTTATCTCTCTA
66 GTTGGATAACGAATCTTTATCTCTCTA
*
9053884 AAGTTATAGTTAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
1 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
* *
9053949 GTTGGATAACGAACCTTTATCTCTCTG
66 GTTGGATAACGAATCTTTATCTCTCTA
9053976 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
1 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
*** *
9054041 GTTGGATAGTTAATCTTTATCTCTCTG
66 GTTGGATAACGAATCTTTATCTCTCTA
9054068 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
1 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
9054133 GTTGGATAACGAATCTTTATCTCTCTA
66 GTTGGATAACGAATCTTTATCTCTCTA
* *
9054160 AAGTTATAATAAGAGCAAGATGAAGCTTCAAACGTTAATTCTTATCCTCTTGAAGTTATAGTAAA
1 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
*
9054225 GTTGGATAACGAATCTTTATCTCTCTG
66 GTTGGATAACGAATCTTTATCTCTCTA
9054252 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
1 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
*
9054317 GTTGGATAGCGAATCTTTATCTCTCTA
66 GTTGGATAACGAATCTTTATCTCTCTA
*
9054344 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTTTTGAAGTTATAGTAAA
1 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
*
9054409 GTTGGATAACGAATCTTTATCTCTCTG
66 GTTGGATAACGAATCTTTATCTCTCTA
*
9054436 AAGTTATAGTAAGAGCAAGACGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
1 AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
*
9054501 GTTGGATAAC-AAACATTTATCTCTCTA
66 GTTGGATAACGAATC-TTTATCTCTCTA
* * *
9054528 AAGTTGTAGTAAGAGTAAGATAAAGC
1 AAGTTATAGTAAGAGCAAGATGAAGC
9054554 CTCGACATCA
Statistics
Matches: 637, Mismatches: 32, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
91 3 0.00
92 634 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (92 bp):
AAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAA
GTTGGATAACGAATCTTTATCTCTCTA
Found at i:9055693 original size:18 final size:21
Alignment explanation
Indices: 9055649--9055699 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
9055639 AAAAACGGTT
9055649 ATAATAATAATAAGTGCTTTA
1 ATAATAATAATAAGTGCTTTA
*
9055670 ATAATAATAATAATTG-TTTAA
1 ATAATAATAATAAGTGCTTT-A
9055691 ATAATAATA
1 ATAATAATA
9055700 TTTATTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (21 bp):
ATAATAATAATAAGTGCTTTA
Found at i:9056792 original size:30 final size:30
Alignment explanation
Indices: 9056756--9056976 Score: 216
Period size: 30 Copynumber: 7.5 Consensus size: 30
9056746 TGGACTGTCC
*
9056756 AAAAATTACACTTTAACCCCAAAACTTTCT
1 AAAAATTACATTTTAACCCCAAAACTTTCT
* *
9056786 AAAAATTATATTTTAACCCCTAAACTTT-T
1 AAAAATTACATTTTAACCCCAAAACTTTCT
* * * *
9056815 CCAAAATTATATTTTAACCCAAAAAGTTTCT
1 -AAAAATTACATTTTAACCCCAAAACTTTCT
* *
9056846 AAAAATTACATTTTAACCCTAAAACTTTTT
1 AAAAATTACATTTTAACCCCAAAACTTTCT
* * *
9056876 GAAAGTTACATTTTAACCCTAAAACTTTCT
1 AAAAATTACATTTTAACCCCAAAACTTTCT
* * * * *
9056906 AAAAAATATATTTTGACCCTAAAA-TTTTT
1 AAAAATTACATTTTAACCCCAAAACTTTCT
* * *
9056935 TAAAATTACATTTTAA-CCCTAAATTTTC-
1 AAAAATTACATTTTAACCCCAAAACTTTCT
*
9056963 AAAAATTCCATTTT
1 AAAAATTACATTTT
9056977 TTAACCTCGA
Statistics
Matches: 158, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
28 17 0.11
29 20 0.13
30 120 0.76
31 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCCAAAACTTTCT
Found at i:9056847 original size:60 final size:58
Alignment explanation
Indices: 9056757--9057035 Score: 260
Period size: 60 Copynumber: 4.7 Consensus size: 58
9056747 GGACTGTCCA
* *
9056757 AAAATTACACTTTAACCCCAAAACTTTCTAAAAATTATATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAA-CCCAAAACTTTCTAAAAATTATATTTTAA-CCCTAAACTTTTTC
* * * *
9056817 AAAATTATATTTTAACCCAAAAAGTTTCTAAAAATTACATTTTAACCCTAAAACTTTTTG
1 AAAATTACATTTTAACCC-AAAACTTTCTAAAAATTATATTTTAACCCT-AAACTTTTTC
* * * * *
9056877 AAAGTTACATTTTAACCCTAAAACTTTCTAAAAAATATATTTTGACCCTAAAATTTTTT
1 AAAATTACATTTTAACCC-AAAACTTTCTAAAAATTATATTTTAACCCTAAACTTTTTC
* * * ** **
9056936 AAAATTACATTTTAACCCTAAATTTTC-AAAAATTCCATTTTTTAA-CCTCGA-TTTCACC
1 AAAATTACATTTTAACCCAAAACTTTCTAAAAATT--ATATTTTAACCCTAAACTTT-TTC
* * *
9056994 AAAATTACCATTTTAGCCCTAAACTTTCT-AAAATTCTATTTT
1 AAAATTA-CATTTTAACCCAAAACTTTCTAAAAATTATATTTT
9057036 TAAACCCGAT
Statistics
Matches: 182, Mismatches: 30, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
57 14 0.08
58 18 0.10
59 63 0.35
60 87 0.48
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.39
Consensus pattern (58 bp):
AAAATTACATTTTAACCCAAAACTTTCTAAAAATTATATTTTAACCCTAAACTTTTTC
Found at i:9056916 original size:90 final size:89
Alignment explanation
Indices: 9056756--9056976 Score: 261
Period size: 90 Copynumber: 2.5 Consensus size: 89
9056746 TGGACTGTCC
* * * *
9056756 AAAAATTACACTTTAACCCCAAAACTTTCTAAAAATTATATTTTAACCCCTAAACTTTTCCAAAA
1 AAAAATTACATTTTAACCCTAAAACTTTCTAAAAATTACATTTTAACCCCTAAACTTTTCAAAAA
*
9056821 TTATATTTTAACCCAAAAAGTTTCT
66 ATATATTTTAACCCAAAAA-TTTCT
* * *
9056846 AAAAATTACATTTTAACCCTAAAACTTTTTGAAAGTTACATTTTAA-CCCTAAAAC-TTTCTAAA
1 AAAAATTACATTTTAACCCTAAAACTTTCTAAAAATTACATTTTAACCCCT-AAACTTTTC-AAA
* * *
9056909 AAATATATTTTGACCCTAAAATTTTT
64 AAATATATTTTAACCCAAAAATTTCT
* * *
9056935 TAAAATTACATTTTAACCCT-AAATTTTC-AAAAATTCCATTTT
1 AAAAATTACATTTTAACCCTAAAACTTTCTAAAAATTACATTTT
9056977 TTAACCTCGA
Statistics
Matches: 112, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
87 11 0.10
88 6 0.05
89 31 0.28
90 64 0.57
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (89 bp):
AAAAATTACATTTTAACCCTAAAACTTTCTAAAAATTACATTTTAACCCCTAAACTTTTCAAAAA
ATATATTTTAACCCAAAAATTTCT
Found at i:9056981 original size:30 final size:28
Alignment explanation
Indices: 9056755--9057028 Score: 183
Period size: 30 Copynumber: 9.3 Consensus size: 28
9056745 ATGGACTGTC
* * *
9056755 CAAAAATTACACTTTAACCCCAAAACTTT
1 CAAAAATTACATTTTAA-CCCTAAATTTT
*
9056784 CTAAAAATTATATTTTAACCCCTAAACTTTT
1 C-AAAAATTACATTTTAA-CCCTAAA-TTTT
* * * *
9056815 CCAAAATTATATTTTAACCCAAAAAGTTT
1 CAAAAATTACATTTTAACCC-TAAATTTT
9056844 CTAAAAATTACATTTTAACCCTAAAACTTTT
1 C-AAAAATTACATTTTAACCCT-AAA-TTTT
** * *
9056875 TGAAAGTTACATTTTAACCCTAAAACTTT
1 CAAAAATTACATTTTAACCCT-AAATTTT
* * *
9056904 CTAAAAAATATATTTTGACCCTAAAATTTT
1 C-AAAAATTACATTTTAACCCT-AAATTTT
**
9056934 TTAAAATTACATTTTAACCCTAAATTTT
1 CAAAAATTACATTTTAACCCTAAATTTT
* **
9056962 CAAAAATTCCATTTTTTAA-CCTCGA-TTT
1 CAAAAATTACA--TTTTAACCCTAAATTTT
* *
9056990 CACCAAAATTACCATTTTAGCCCTAAACTTT
1 CA--AAAATTA-CATTTTAACCCTAAATTTT
*
9057021 CTAAAATT
1 CAAAAATT
9057029 CTATTTTTAA
Statistics
Matches: 194, Mismatches: 37, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
28 20 0.10
29 42 0.22
30 119 0.61
31 13 0.07
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (28 bp):
CAAAAATTACATTTTAACCCTAAATTTT
Found at i:9057046 original size:58 final size:56
Alignment explanation
Indices: 9056936--9057240 Score: 306
Period size: 58 Copynumber: 5.2 Consensus size: 56
9056926 AAAATTTTTT
* * *
9056936 AAAATTA-CATTTTAACCCTAAATTTTCAAAAATTCCATTTTTTAACCTCGATTTCACC
1 AAAATTACCATTTT-ACCCTGAACTTTCCAAAATTCCA-TTTTTAACC-CGATTTCACC
* * *
9056994 AAAATTACCATTTTAGCCCTAAACTTTCTAAAATTCTATTTTTAAACCCGATTTCACC
1 AAAATTACCATTTTA-CCCTGAACTTTCCAAAATTCCATTTTT-AACCCGATTTCACC
* * * *
9057052 AAAATTACCATTTTACCTCCGAACTTTCTAAAATTCCATTTTTAACTTCTATTTCACC
1 AAAATTACCATTTTACC-CTGAACTTTCCAAAATTCCATTTTTAAC-CCGATTTCACC
* * * * *
9057110 AAAATTACCACTTTACCCTCGTACTTTCCAAAATTCCATTTTTGACCTCGATTTTATCA
1 AAAATTACCATTTTACCCT-GAACTTTCCAAAATTCCATTTTTAACC-CGATTTCA-CC
* ** * * *
9057169 AAAATTACCATTCTACCCTCGAACTTTCCAAAAACCCATTTTTATCCCAATTTGAACC
1 AAAATTACCATTTTACCCT-GAACTTTCCAAAATTCCATTTTTAACCCGATTT-CACC
9057227 AAAATTACCATTTT
1 AAAATTACCATTTT
9057241 GCCCCTGGGT
Statistics
Matches: 210, Mismatches: 28, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
57 6 0.03
58 133 0.63
59 71 0.34
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (56 bp):
AAAATTACCATTTTACCCTGAACTTTCCAAAATTCCATTTTTAACCCGATTTCACC
Found at i:9057066 original size:29 final size:29
Alignment explanation
Indices: 9056964--9057065 Score: 77
Period size: 29 Copynumber: 3.4 Consensus size: 29
9056954 TAAATTTTCA
*
9056964 AAAATTCCATTTTTTAACCTCGATTTCACC
1 AAAATTCCATTTTTAAACC-CGATTTCACC
* * *
9056994 AAAATTACCA-TTTT-AGCCCTAAACTTT--CT
1 AAAATT-CCATTTTTAAACCC--GA-TTTCACC
*
9057023 AAAATTCTATTTTTAAACCCGATTTCACC
1 AAAATTCCATTTTTAAACCCGATTTCACC
9057052 AAAATTACCATTTT
1 AAAATT-CCATTTT
9057066 ACCTCCGAAC
Statistics
Matches: 55, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
27 3 0.05
28 4 0.07
29 21 0.38
30 21 0.38
31 6 0.11
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATTCCATTTTTAAACCCGATTTCACC
Found at i:9057073 original size:29 final size:28
Alignment explanation
Indices: 9057041--9057185 Score: 77
Period size: 29 Copynumber: 5.0 Consensus size: 28
9057031 ATTTTTAAAC
9057041 CCGATTTCACCAAAATTACCATTTTACCT
1 CCGATTT-ACCAAAATTACCATTTTACCT
* *
9057070 CCGAACTTT-CTAAAATT-CCATTTTTAACT
1 CCG-A-TTTACCAAAATTACCA-TTTTACCT
* * *
9057099 TCTATTTCACCAAAATTACCACTTTACC-
1 CCGATTT-ACCAAAATTACCATTTTACCT
9057127 CTCGTACTTT-CCAAAATT-CCATTTTTGACCT
1 C-CG-A-TTTACCAAAATTACCA-TTTT-ACCT
* *
9057158 -CGATTTTATCAAAAATTACCATTCTACC
1 CCGA-TTTA-CCAAAATTACCATTTTACC
9057186 CTCGAACTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 30
0.67 0.10 0.23
Matches are distributed among these distances:
27 3 0.03
28 11 0.12
29 47 0.53
30 18 0.20
31 9 0.10
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.38
Consensus pattern (28 bp):
CCGATTTACCAAAATTACCATTTTACCT
Found at i:9057201 original size:30 final size:29
Alignment explanation
Indices: 9057110--9057202 Score: 77
Period size: 30 Copynumber: 3.1 Consensus size: 29
9057100 CTATTTCACC
9057110 AAAATTACCACTTTACCCTCGTACTTTCC-
1 AAAATTACCACTTTACCCTCG-ACTTTCCA
* * *
9057139 AAAATT-CCATTTTTGA-CCTCGATTTTATCA
1 AAAATTACCA-CTTT-ACCCTCGACTTT-CCA
9057169 AAAATTACCA-TTCTACCCTCGAACTTTCCA
1 AAAATTACCACTT-TACCCTCG-ACTTTCCA
9057199 AAAA
1 AAAA
9057203 CCCATTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
28 7 0.14
29 18 0.35
30 19 0.37
31 7 0.14
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATTACCACTTTACCCTCGACTTTCCA
Found at i:9062829 original size:34 final size:34
Alignment explanation
Indices: 9062752--9062829 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
9062742 TTATCTGGTA
* * *
9062752 TGTTAGATGGTTTGGCTCATAGAAGCATTTGGTG
1 TGTTAGATGGATTGGCTCATAGAAGCATCTAGTG
* *
9062786 TGCTGGATGGATTGGCTCATATG-AGCATCTAGTG
1 TGTTAGATGGATTGGCTCATA-GAAGCATCTAGTG
9062820 TGTTAGATGG
1 TGTTAGATGG
9062830 TTAACCGTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 35 0.97
35 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.33, T:0.36
Consensus pattern (34 bp):
TGTTAGATGGATTGGCTCATAGAAGCATCTAGTG
Found at i:9063505 original size:13 final size:13
Alignment explanation
Indices: 9063487--9063511 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9063477 TGTCATGGAT
9063487 GACACATGGGTTA
1 GACACATGGGTTA
9063500 GACACATGGGTT
1 GACACATGGGTT
9063512 GAGTATTTTG
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:0.28, C:0.16, G:0.32, T:0.24
Consensus pattern (13 bp):
GACACATGGGTTA
Found at i:9065931 original size:16 final size:16
Alignment explanation
Indices: 9065910--9065962 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
9065900 TAAAAATGTG
9065910 TAAAATTATAAAATAT
1 TAAAATTATAAAATAT
* *
9065926 TAAAATAATATAATA-
1 TAAAATTATAAAATAT
* *
9065941 TAAATATTTTAAAAAAT
1 TAAA-ATTATAAAATAT
9065958 TAAAA
1 TAAAA
9065963 AATAATATAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 4 0.14
16 21 0.72
17 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAATTATAAAATAT
Found at i:9075904 original size:18 final size:18
Alignment explanation
Indices: 9075881--9075925 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
9075871 CGTAAGGGAT
*
9075881 TTACAAGATCTTCTAAGA
1 TTACAAAATCTTCTAAGA
*
9075899 TTACAAAATCTTCTAATA
1 TTACAAAATCTTCTAAGA
9075917 TTACAAAAT
1 TTACAAAAT
9075926 ATTCACCCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (18 bp):
TTACAAAATCTTCTAAGA
Found at i:9077604 original size:14 final size:14
Alignment explanation
Indices: 9077587--9077618 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
9077577 AAATATTACA
*
9077587 AAATTAATAAAAAT
1 AAATCAATAAAAAT
9077601 AAATCAATAAAAAT
1 AAATCAATAAAAAT
9077615 AAAT
1 AAAT
9077619 AAATGGTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATCAATAAAAAT
Found at i:9086429 original size:15 final size:16
Alignment explanation
Indices: 9086409--9086439 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9086399 TATAATAAGC
9086409 ATATTTA-AAAAATAA
1 ATATTTATAAAAATAA
9086424 ATATTTATAAAAATAA
1 ATATTTATAAAAATAA
9086440 TTTTGATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATTTATAAAAATAA
Found at i:9087246 original size:19 final size:19
Alignment explanation
Indices: 9087203--9087246 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 19
9087193 TAATTGATTG
*
9087203 CTAATGAAGATTTGTCCTA
1 CTAATGAAGATTTATCCTA
9087222 --AA-GAAGATTTATCCTA
1 CTAATGAAGATTTATCCTA
9087238 CTAATGAAG
1 CTAATGAAG
9087247 TCGAATATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
16 13 0.62
17 2 0.10
18 2 0.10
19 4 0.19
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
CTAATGAAGATTTATCCTA
Found at i:9087664 original size:6 final size:6
Alignment explanation
Indices: 9087653--9087678 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
9087643 CAAAAAGGAA
9087653 GAAGAT GAAGAT GAAGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GA
9087679 GAGGTGTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GAAGAT
Found at i:9088278 original size:12 final size:12
Alignment explanation
Indices: 9088246--9088279 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9088236 GACAGTGACA
*
9088246 GGAGTGGGAGTG
1 GGAGTGGGGGTG
9088258 GGAGTGGGGGTG
1 GGAGTGGGGGTG
*
9088270 GGGGTGGGGG
1 GGAGTGGGGG
9088280 AGAGGGACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.00, G:0.76, T:0.15
Consensus pattern (12 bp):
GGAGTGGGGGTG
Found at i:9088335 original size:30 final size:28
Alignment explanation
Indices: 9088264--9088337 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 28
9088254 AGTGGGAGTG
* *
9088264 GGGGTGGGGGTGGGGGAGAGGGACGTAC
1 GGGGTGGGGGAGGGGGAGAGGGACGAAC
*
9088292 GGTGGTGGAGGGAGGGGGAGAGGGAGAGGAAC
1 GG-GGTGG-GGGAGGGGGAGA-GG-GACGAAC
9088324 GGGGTGGGGGAGGG
1 GGGGTGGGGGAGGG
9088338 TTTTTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 2 0.05
29 5 0.13
30 18 0.46
31 7 0.18
32 7 0.18
ACGTcount: A:0.18, C:0.04, G:0.70, T:0.08
Consensus pattern (28 bp):
GGGGTGGGGGAGGGGGAGAGGGACGAAC
Found at i:9088386 original size:21 final size:21
Alignment explanation
Indices: 9088362--9088401 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9088352 TGAATATTAA
9088362 TATTAATATAAAATTTAAATT
1 TATTAATATAAAATTTAAATT
* * *
9088383 TATTATTATATATTTTAAA
1 TATTAATATAAAATTTAAA
9088402 AAGATTTACG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTAATATAAAATTTAAATT
Found at i:9088419 original size:2 final size:2
Alignment explanation
Indices: 9088412--9088448 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9088402 AAGATTTACG
9088412 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
9088449 TTAAATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9089570 original size:18 final size:18
Alignment explanation
Indices: 9089549--9089599 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
9089539 TTTAAATTTC
9089549 TTTTAGTTTTTCTAGTTT
1 TTTTAGTTTTTCTAGTTT
* *
9089567 TTTTAGTTTCTCTTTATTTT
1 TTTTAGTTT-T-TCTAGTTT
9089587 TTTTA-TTTTTCTA
1 TTTTAGTTTTTCTA
9089600 CTATATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.11
18 10 0.36
19 4 0.14
20 11 0.39
ACGTcount: A:0.12, C:0.08, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTAGTTTTTCTAGTTT
Found at i:9089582 original size:29 final size:28
Alignment explanation
Indices: 9089535--9089596 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
9089525 TGATGTTTAT
9089535 TTTTTTTAAATTTCTTTTAGTTTTTCTA
1 TTTTTTTAAATTTCTTTTAGTTTTTCTA
* * *
9089563 GTTTTTTT-AGTTTCTCTTTATTTTTTTTA
1 -TTTTTTTAAATTTCT-TTTAGTTTTTCTA
9089592 TTTTT
1 TTTTT
9089597 CTACTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.13, C:0.06, G:0.05, T:0.76
Consensus pattern (28 bp):
TTTTTTTAAATTTCTTTTAGTTTTTCTA
Found at i:9089591 original size:9 final size:9
Alignment explanation
Indices: 9089530--9089596 Score: 53
Period size: 9 Copynumber: 7.0 Consensus size: 9
9089520 TGGTCTGATG
9089530 TTTATTTTT
1 TTTATTTTT
*
9089539 TTTAAATTTCT
1 TTT--ATTTTT
*
9089550 TTTAGTTTT
1 TTTATTTTT
* *
9089559 TCTAGTTTT
1 TTTATTTTT
*
9089568 TTTAGTTTCTC
1 TTTA-TTT-TT
9089579 TTTATTTTT
1 TTTATTTTT
9089588 TTTATTTTT
1 TTTATTTTT
9089597 CTACTATATT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
9 28 0.61
10 5 0.11
11 13 0.28
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.76
Consensus pattern (9 bp):
TTTATTTTT
Found at i:9089597 original size:21 final size:21
Alignment explanation
Indices: 9089564--9089608 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
9089554 GTTTTTCTAG
*
9089564 TTTTTTTAGTTTCT-CTTTAT
1 TTTTTTTAGTTTCTACTATAT
*
9089584 TTTTTTTATTTTTCTACTATAT
1 TTTTTTTA-GTTTCTACTATAT
9089606 TTT
1 TTT
9089609 AATTTCGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 5 0.24
22 8 0.38
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTTAGTTTCTACTATAT
Found at i:9090221 original size:15 final size:15
Alignment explanation
Indices: 9090201--9090230 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9090191 GTTTAGTTAG
9090201 TTTTTTAATTTATTT
1 TTTTTTAATTTATTT
*
9090216 TTTTTTATTTTATTT
1 TTTTTTAATTTATTT
9090231 AATTTTTCAC
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTAATTTATTT
Found at i:9090551 original size:92 final size:92
Alignment explanation
Indices: 9090353--9090621 Score: 314
Period size: 92 Copynumber: 2.9 Consensus size: 92
9090343 GCTAGGTACC
* * *
9090353 ATAATAAAACACATATTGATACTTCATGTACCACATTGGATATTTTCAAAGTATAAGTA-TCATA
1 ATAATAAAACACATATTGATAGTTCAAGTACCACATTGGATATTTTCAAAG-ATAAGTACTCACA
** *
9090417 TTGGACATTTTATGAAAGTACATGTACT
65 TTGGACATTTTATGAAAGTACAAATACG
*
9090445 ATAATAAAACACATATTGATAGTCCAAGTACCACATTGGATATTTTCAAAGA-AAGGTACTC-CA
1 ATAATAAAACACATATTGATAGTTCAAGTACCACATTGGATATTTTCAAAGATAA-GTACTCACA
*
9090508 TTGGATATTTTATGAAAGTACAAATACG
65 TTGGACATTTTATGAAAGTACAAATACG
* * * * * **
9090536 ATAATAAAAATACATATGGATAGTTCAGGTATCACACTGGGCATTTTCAAA-ATATATGTAC-CA
1 ATAAT-AAAACACATATTGATAGTTCAAGTACCACATTGGATATTTTCAAAGATA-A-GTACTCA
9090599 CATTGGGACATTTTATGAAAGTA
63 CATT-GGACATTTTATGAAAGTA
9090622 TAAGTACCAA
Statistics
Matches: 152, Mismatches: 18, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
90 2 0.01
91 35 0.23
92 89 0.59
93 9 0.06
94 17 0.11
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (92 bp):
ATAATAAAACACATATTGATAGTTCAAGTACCACATTGGATATTTTCAAAGATAAGTACTCACAT
TGGACATTTTATGAAAGTACAAATACG
Found at i:9091209 original size:22 final size:22
Alignment explanation
Indices: 9091179--9091223 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
9091169 AGTTTCAATG
* *
9091179 TTCAGTTTGGTACTTGA-GTTTT
1 TTCAATTTGATACTT-ATGTTTT
9091201 TTCAATTTGATACTTATGTTTT
1 TTCAATTTGATACTTATGTTTT
9091223 T
1 T
9091224 ATTTGTCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.58
Consensus pattern (22 bp):
TTCAATTTGATACTTATGTTTT
Found at i:9094046 original size:28 final size:28
Alignment explanation
Indices: 9094015--9094075 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
9094005 AAAACGGGAC
9094015 TTTTGGA-TACCCGGGGGC-AAAATGGTAA
1 TTTTGGACT-CCCGGGGGCAAAAAT-GTAA
* *
9094043 TTTTTGACTCTCGGGGGCAAAAATGTAA
1 TTTTGGACTCCCGGGGGCAAAAATGTAA
9094071 TTTTG
1 TTTTG
9094076 AGAAAATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
TTTTGGACTCCCGGGGGCAAAAATGTAA
Found at i:9094181 original size:29 final size:28
Alignment explanation
Indices: 9094149--9094372 Score: 134
Period size: 29 Copynumber: 7.6 Consensus size: 28
9094139 AAACCGAGGT
*
9094149 TAAAAGTGGGATTTTGGAAAGCTCGGGGG
1 TAAAA-TGGAATTTTGGAAAGCTCGGGGG
* * * *
9094178 TAAAACGGTAATTTTTGGTGAA-CTCGTGGT
1 TAAAATGG-AA-TTTTGG-AAAGCTCGGGGG
* *
9094208 TAAAAATGAAATTTTGGAAAGTTCGGGGG
1 T-AAAATGGAATTTTGGAAAGCTCGGGGG
* *
9094237 TAAAATGGTAATTTTAGGTGAAA--TCGAGGT
1 TAAAATGG-AATTTT--G-GAAAGCTCGGGGG
*
9094267 TAAAATGGAATTTTGGAAAGTTCGGGGG
1 TAAAATGGAATTTTGGAAAGCTCGGGGG
*
9094295 TAAAATGGTAATTTTCGGTGAAA--TCGGGGT
1 TAAAATGG-AATTTT--G-GAAAGCTCGGGGG
* ** *
9094325 TAAAAATGGAATTTTGGAAAGTTTAGGGA
1 T-AAAATGGAATTTTGGAAAGCTCGGGGG
9094354 TAAAATGGTAATTTCTGGA
1 TAAAATGG-AATTT-TGGA
9094373 CAGTTCAGGG
Statistics
Matches: 155, Mismatches: 20, Indels: 39
0.72 0.09 0.18
Matches are distributed among these distances:
26 4 0.03
27 5 0.03
28 31 0.20
29 46 0.30
30 45 0.29
31 16 0.10
32 8 0.05
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.31
Consensus pattern (28 bp):
TAAAATGGAATTTTGGAAAGCTCGGGGG
Found at i:9094212 original size:30 final size:30
Alignment explanation
Indices: 9094126--9094339 Score: 126
Period size: 30 Copynumber: 7.3 Consensus size: 30
9094116 GGGTAAAACA
*
9094126 GTAATTTTTGGTGAAAC-CGAGGTTAAAAGTG
1 GTAATTTTTGGTG-AACTCGGGGTTAAAA-TG
* * * *
9094157 G-GA-TTTTGG-AAAGCTCGGGGGTAAAACG
1 GTAATTTTTGGTGAA-CTCGGGGTTAAAATG
*
9094185 GTAATTTTTGGTGAACTCGTGGTTAAAAAT-
1 GTAATTTTTGGTGAACTCGGGGTT-AAAATG
* * * *
9094215 G-AAATTTTGG-AAAGTTCGGGGGTAAAATG
1 GTAATTTTTGGTGAA-CTCGGGGTTAAAATG
* * *
9094244 GTAATTTTAGGTGAAATCGAGGTTAAAATG
1 GTAATTTTTGGTGAACTCGGGGTTAAAATG
* * *
9094274 G-AA-TTTTGG-AAAGTTCGGGGGTAAAATG
1 GTAATTTTTGGTGAA-CTCGGGGTTAAAATG
* *
9094302 GTAATTTTCGGTGAAATCGGGGTTAAAAATG
1 GTAATTTTTGGTGAACTCGGGGTT-AAAATG
9094333 G-AATTTT
1 GTAATTTT
9094340 GGAAAGTTTA
Statistics
Matches: 138, Mismatches: 30, Indels: 31
0.69 0.15 0.16
Matches are distributed among these distances:
27 4 0.03
28 28 0.20
29 35 0.25
30 53 0.38
31 18 0.13
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (30 bp):
GTAATTTTTGGTGAACTCGGGGTTAAAATG
Found at i:9094300 original size:58 final size:59
Alignment explanation
Indices: 9094087--9094367 Score: 361
Period size: 59 Copynumber: 4.8 Consensus size: 59
9094077 GAAAATTTGG
** ** *
9094087 GGTTAAAAAT-GAGATTTT-GAAAGGTTTAGGGGTAAAACAGTAATTTTTGGTGAAACCGA
1 GGTTAAAAATGGA-ATTTTGGAAA-GTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGA
* * * * * *
9094146 GGTTAAAAGTGGGATTTTGGAAAGCTCGGGGGTAAAACGGTAATTTTTGGTGAACTCGT
1 GGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGA
* *
9094205 GGTTAAAAATGAAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTAGGTGAAATCGA
1 GGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGA
* *
9094264 GGTT-AAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTCGGTGAAATCGG
1 GGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGA
** *
9094322 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGATAAAATGGTAATTT
1 GGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTT
9094368 CTGGACAGTT
Statistics
Matches: 196, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
58 55 0.28
59 136 0.69
60 5 0.03
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (59 bp):
GGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGA
Found at i:9094338 original size:117 final size:118
Alignment explanation
Indices: 9094085--9094367 Score: 401
Period size: 117 Copynumber: 2.4 Consensus size: 118
9094075 GAGAAAATTT
** *
9094085 GGGGTTAAAAAT-GAGATTTT-GAAAGGTTTAGGGGTAAAACAGTAATTTTTGGTGAAACCGAGG
1 GGGGTTAAAAATGGA-ATTTTGGAAA-GTTTAGGGGTAAAATGGTAATTTTAGGTGAAACCGAGG
* * *
9094148 TTAAAAGTGGGATTTTGGAAAGCTCGGGGGTAAAACGGTAATTTTTGGTGAACTC
64 TTAAAAGTGGAATTTTGGAAAGCTCGGGGGTAAAACGGTAATTTTCGGTGAAATC
* * ** *
9094203 GTGGTTAAAAATGAAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTAGGTGAAATCGAGGTT
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTAGGTGAAACCGAGGTT
* *
9094268 AAAA-TGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTCGGTGAAATC
66 AAAAGTGGAATTTTGGAAAGCTCGGGGGTAAAACGGTAATTTTCGGTGAAATC
*
9094320 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGATAAAATGGTAATTT
1 GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTT
9094368 CTGGACAGTT
Statistics
Matches: 145, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
117 86 0.59
118 54 0.37
119 5 0.03
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (118 bp):
GGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTAGGTGAAACCGAGGTT
AAAAGTGGAATTTTGGAAAGCTCGGGGGTAAAACGGTAATTTTCGGTGAAATC
Found at i:9096417 original size:17 final size:17
Alignment explanation
Indices: 9096382--9096417 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9096372 CCAAACAAGT
*
9096382 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
*
9096399 TTTAAATTTAAAATGAA
1 TTTAAATTTAAAATAAA
9096416 TT
1 TT
9096418 AAAAATCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:9097184 original size:91 final size:91
Alignment explanation
Indices: 9097065--9097233 Score: 259
Period size: 91 Copynumber: 1.9 Consensus size: 91
9097055 TGGTGTCGAA
* * *
9097065 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGATTTGCTATCCAACTTT-ATTATAAC
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTGATT-CAAC
9097129 TTCAAGAGGATAGGGATTGACTTTGAT
65 TTCAAGAGGATAGGGATTGACTTTGAT
* * * *
9097156 GCTTCATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGCTATCCAACTTTGCTTCAATT
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTGATTCAACT
9097221 TCAAGAGGATAGG
66 TCAAGAGGATAGG
9097234 AAATGATCTT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
91 68 0.97
92 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (91 bp):
GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTGATTCAACT
TCAAGAGGATAGGGATTGACTTTGAT
Found at i:9097294 original size:76 final size:76
Alignment explanation
Indices: 9097161--9097763 Score: 1008
Period size: 76 Copynumber: 7.9 Consensus size: 76
9097151 TTGATGCTTC
* * *
9097161 ATCTAGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGCTATCCAACTTTGCTTCAATTTCAAG
1 ATCTTGCTCTTACTTCAATTTC--AGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAG
9097226 AGGATAGGAAATG
64 AGGATAGGAAATG
* *
9097239 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAG
9097304 GATAGGAAATG
66 GATAGGAAATG
* *
9097315 ATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAG
9097380 GATAGGAAATG
66 GATAGGAAATG
* * *
9097391 ATCTTGCTCTTACTTCAATTTTAGAGATGAAGACTTGTTATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAG
9097456 GATAGGAAATG
66 GATAGGAAATG
* *
9097467 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAG
9097532 GATAGGAAATG
66 GATAGGAAATG
* * *
9097543 ATCTTACTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAG
9097608 GATAGGAAATG
66 GATAGGAAATG
* *
9097619 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAG
9097684 GATAGGAAATG
66 GATAGGAAATG
* * *
9097695 ATCTTACTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAG
9097760 GATA
66 GATA
9097764 AAACTTAACA
Statistics
Matches: 503, Mismatches: 22, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
76 482 0.96
78 21 0.04
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (76 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAG
GATAGGAAATG
Found at i:9098041 original size:50 final size:51
Alignment explanation
Indices: 9097980--9098108 Score: 145
Period size: 51 Copynumber: 2.5 Consensus size: 51
9097970 GTGATATTGA
* * * *
9097980 ATCTGCCGTTGCGGGCTTAGATCTTTCCCGTC-GTGTCTTCGTGGTACTAGG
1 ATCTACCGTTGCGGTCTTAGATCTTTCCCGTCTGTATCTTCGTGGCACT-GG
* * *
9098031 -TCTACCGTTGCGATCTTAGATCTTTCCCTTCTGTATCTTTGTGGCACTGG
1 ATCTACCGTTGCGGTCTTAGATCTTTCCCGTCTGTATCTTCGTGGCACTGG
* * *
9098081 ATCTGCTGTTGCAGTCTTAGATCTTTCC
1 ATCTACCGTTGCGGTCTTAGATCTTTCC
9098109 GGTCCATGCT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
50 29 0.45
51 36 0.55
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (51 bp):
ATCTACCGTTGCGGTCTTAGATCTTTCCCGTCTGTATCTTCGTGGCACTGG
Found at i:9098103 original size:51 final size:50
Alignment explanation
Indices: 9097937--9098285 Score: 212
Period size: 50 Copynumber: 7.0 Consensus size: 50
9097927 TCATGTATCA
* * * * *
9097937 CCGTTGCGACTTAGACCTTTCCCTT-T-TGTCTTTGTGATATTGAATCTG
1 CCGTTGCGTCTTAGATCTTTCCCTTCTGTGTCTTTGTGGTACTGGATCTG
* * * *
9097985 CCGTTGCGGGCTTAGATCTTTCCCGTC-GTGTCTTCGTGGTACTAGG-TCTA
1 CCGTTGC-GTCTTAGATCTTTCCCTTCTGTGTCTTTGTGGTACT-GGATCTG
* *
9098035 CCGTTGCGATCTTAGATCTTTCCCTTCTGTATCTTTGTGGCACTGGATCTG
1 CCGTTGCG-TCTTAGATCTTTCCCTTCTGTGTCTTTGTGGTACTGGATCTG
* ** ** * * *
9098086 CTGTTGCAGTCTTAGATCTTTCCGGTCCATG-CTTTTGAGGTACACGG-TCCG
1 CCGTTGC-GTCTTAGATCTTTCCCTTCTGTGTC-TTTGTGGTAC-TGGATCTG
* * * * * * * **
9098137 CAGTTGCGACTTAGACCTTTCCCTTTTCTATTTTTACGGTACTGGATCTG
1 CCGTTGCGTCTTAGATCTTTCCCTTCTGTGTCTTTGTGGTACTGGATCTG
** *
9098187 -CGATTGCGGTCTTAGATCTTTCCCTTCCATG-CTTTTGAGGTACAT-GATCTG
1 CCG-TTGC-GTCTTAGATCTTTCCCTTCTGTGTC-TTTGTGGTAC-TGGATCTG
* * * * * *
9098238 CCGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTAGATC
1 CCGTTGCGTCTTAGATCTTTCCCTTCTGTGTCTTTGTGGTACTGGATC
9098286 CACCATTGTG
Statistics
Matches: 227, Mismatches: 55, Indels: 36
0.71 0.17 0.11
Matches are distributed among these distances:
48 7 0.03
49 20 0.09
50 102 0.45
51 92 0.41
52 6 0.03
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.40
Consensus pattern (50 bp):
CCGTTGCGTCTTAGATCTTTCCCTTCTGTGTCTTTGTGGTACTGGATCTG
Found at i:9098150 original size:101 final size:100
Alignment explanation
Indices: 9097939--9098355 Score: 407
Period size: 101 Copynumber: 4.2 Consensus size: 100
9097929 ATGTATCACC
* * * * * *
9097939 GTTGCGACTTAGACCTTTCCCTTTTG--TCTTTGTGATATTGAATCTGCCGTTGCGGGCTTAGAT
1 GTTGCGACTTAGACCTTTCCCTTTTGTATTTTTGCGGTACTGGATCTG-CGTTGCGGTCTTAGAT
* * * * *
9098002 CTTTCCCGT-CGTG-TCTTCGTGGTACTA-GGTCTACC
65 CTTTCCCGTCCATGCT-TTTGAGGTAC-ACGGTCTGCA
* * * * * *
9098037 GTTGCGATCTTAGATCTTTCCCTTCTGTATCTTTGTGGCACTGGATCTGCTGTTGCAGTCTTAGA
1 GTTGCGA-CTTAGACCTTTCCCTTTTGTATTTTTGCGGTACTGGATCTGC-GTTGCGGTCTTAGA
* *
9098102 TCTTTCCGGTCCATGCTTTTGAGGTACACGGTCCGCA
64 TCTTTCCCGTCCATGCTTTTGAGGTACACGGTCTGCA
* *
9098139 GTTGCGACTTAGACCTTTCCCTTTTCTATTTTTACGGTACTGGATCTGCGATTGCGGTCTTAGAT
1 GTTGCGACTTAGACCTTTCCCTTTTGTATTTTTGCGGTACTGGATCTGCG-TTGCGGTCTTAGAT
* * * *
9098204 CTTTCCCTTCCATGCTTTTGAGGTACATGATCTGCC
65 CTTTCCCGTCCATGCTTTTGAGGTACACGGTCTGCA
* * ** * * *
9098240 GTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTGCGGTACTAGATCCACCATTGTGGTTTTAGAT
1 GTTGCGACTTAGACCTTTCCCTTTTGTATTTTTGCGGTACTGGAT-CTGCGTTGCGGTCTTAGAT
*
9098305 CTTTCCCGT-CATGCTTCTGAGGTACACGGTCTGCCA
65 CTTTCCCGTCCATGCTTTTGAGGTACACGGTCTG-CA
*
9098341 -TTGTGACTTAGACCT
1 GTTGCGACTTAGACCT
9098356 CTCCTTGTTG
Statistics
Matches: 265, Mismatches: 44, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
98 7 0.03
99 17 0.06
100 37 0.14
101 178 0.67
102 25 0.09
103 1 0.00
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.39
Consensus pattern (100 bp):
GTTGCGACTTAGACCTTTCCCTTTTGTATTTTTGCGGTACTGGATCTGCGTTGCGGTCTTAGATC
TTTCCCGTCCATGCTTTTGAGGTACACGGTCTGCA
Found at i:9110329 original size:30 final size:30
Alignment explanation
Indices: 9110293--9110573 Score: 76
Period size: 29 Copynumber: 9.5 Consensus size: 30
9110283 ACTCTCGGGG
9110293 AAAAATGTAATTTTGGGAAAATTCAGGGTT
1 AAAAATGTAATTTTGGGAAAATTCAGGGTT
* * *
9110323 AAAAATG-AGATTTT--GAAAGGTTTAGGGGT
1 AAAAATGTA-ATTTTGGGAAA-ATTCAGGGTT
*
9110352 -AAAATAGTAATTTTTGGTG-AAA--CCGAGGTT
1 AAAAAT-GTAA-TTTTGG-GAAAATTCAG-GGTT
* ** * ** * *
9110382 AAAAGTGGGATTTT-GGCAAGCTCGGGGGT
1 AAAAATGTAATTTTGGGAAAATTCAGGGTT
** * ** * *
9110411 AAAACGGTAATTTTTGGTGAACTCGGGGTT
1 AAAAATGTAATTTTGGGAAAATTCAGGGTT
* * *
9110441 AAAAATGGAATTTT-GGAAAGTTCAGGGGT
1 AAAAATGTAATTTTGGGAAAATTCAGGGTT
*
9110470 -AAAATGGTAATTTTAGGTAAAA-TC-GAGGTT
1 AAAAAT-GTAATTTT-GGGAAAATTCAG-GGTT
* *
9110500 AAAAATGGAATTTT--GAAAAGTTCAGGGGT
1 AAAAATGTAATTTTGGGAAAA-TTCAGGGTT
*
9110529 -AAAATGGTAATTTTGATG-AAA-TC-GAGGTT
1 AAAAAT-GTAATTTTG-GGAAAATTCAG-GGTT
*
9110558 AAAAATGGAATTTTGG
1 AAAAATGTAATTTTGG
9110574 AAAGTTTGGG
Statistics
Matches: 182, Mismatches: 41, Indels: 58
0.65 0.15 0.21
Matches are distributed among these distances:
27 5 0.03
28 23 0.13
29 70 0.38
30 64 0.35
31 16 0.09
32 3 0.02
33 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (30 bp):
AAAAATGTAATTTTGGGAAAATTCAGGGTT
Found at i:9110423 original size:29 final size:29
Alignment explanation
Indices: 9110391--9110600 Score: 146
Period size: 29 Copynumber: 7.2 Consensus size: 29
9110381 TAAAAGTGGG
* *
9110391 ATTTTGGCAAGCTCGGGGGTAAAACGGTA
1 ATTTTGGAAAGCTCGGGGGTAAAATGGTA
* *
9110420 ATTTTTGGTGAA-CTCGGGGTTAAAAATGG-A
1 A-TTTTGG-AAAGCTCGGGGGT-AAAATGGTA
* *
9110450 ATTTTGGAAAGTTCAGGGGTAAAATGGTA
1 ATTTTGGAAAGCTCGGGGGTAAAATGGTA
* * *
9110479 ATTTTAGGTAAA-ATCGAGGTTAAAAATGG-A
1 ATTTT-GG-AAAGCTCGGGGGT-AAAATGGTA
* * *
9110509 ATTTTGAAAAGTTCAGGGGTAAAATGGTA
1 ATTTTGGAAAGCTCGGGGGTAAAATGGTA
* *
9110538 ATTTTGATGAAA--TCGAGGTTAAAAATGG-A
1 ATTTTG--GAAAGCTCGGGGGT-AAAATGGTA
* *
9110567 ATTTTGGAAAGTTTGGGGGTAAAATGGTA
1 ATTTTGGAAAGCTCGGGGGTAAAATGGTA
9110596 ATTTT
1 ATTTT
9110601 TGGACAGTTC
Statistics
Matches: 142, Mismatches: 23, Indels: 32
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.03
28 26 0.18
29 55 0.39
30 36 0.25
31 21 0.15
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.32
Consensus pattern (29 bp):
ATTTTGGAAAGCTCGGGGGTAAAATGGTA
Found at i:9110578 original size:58 final size:58
Alignment explanation
Indices: 9110289--9110600 Score: 364
Period size: 59 Copynumber: 5.3 Consensus size: 58
9110279 TTTGACTCTC
* *
9110289 GGGGAAAAAT-GTAATTTTGG-GAAAATTC-AGGGTTAAAAAT-GAGATTTT-GAAAGGTTTA
1 GGGGTAAAATGGTAATTTTGGTG-AAA-TCGA-GGTTAAAAATGGA-ATTTTGGAAA-GTTCA
* * * * * * *
9110347 GGGGTAAAATAGTAATTTTTGGTGAAACCGAGGTTAAAAGTGGGATTTTGGCAAGCTCG
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCA
* * *
9110406 GGGGTAAAACGGTAATTTTTGGTGAACTCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCA
* *
9110465 GGGGTAAAATGGTAATTTTAGGTAAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTCA
1 GGGGTAAAATGGTAATTTT-GGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCA
* **
9110524 GGGGTAAAATGGTAATTTTGATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCA
9110582 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
9110601 TGGACAGTTC
Statistics
Matches: 219, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
58 66 0.30
59 138 0.63
60 14 0.06
61 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCA
Found at i:9112646 original size:17 final size:17
Alignment explanation
Indices: 9112611--9112646 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9112601 CCAAACAAGT
*
9112611 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
*
9112628 TTTAAATTTAAAATGAA
1 TTTAAATTTAAAATAAA
9112645 TT
1 TT
9112647 AAAAATCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:9112948 original size:16 final size:16
Alignment explanation
Indices: 9112872--9112960 Score: 63
Period size: 18 Copynumber: 5.1 Consensus size: 16
9112862 TAAAAAATAC
9112872 ATAAAAATATTT-AAAA
1 ATAAAAA-ATTTAAAAA
**
9112888 ATGAAAAAAATACAAAAA
1 AT--AAAAAATTTAAAAA
9112906 AGTACAAAAATAATTAAAAA
1 A-TA-AAAAAT--TTAAAAA
* *
9112926 TTAAAAAATTTTAAGAA
1 ATAAAAAA-TTTAAAAA
9112943 ATAAAAAATTTAAAAA
1 ATAAAAAATTTAAAAA
9112959 AT
1 AT
9112961 TTAAAAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
16 11 0.19
17 16 0.28
18 21 0.37
19 4 0.07
20 5 0.09
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (16 bp):
ATAAAAAATTTAAAAA
Found at i:9112958 original size:9 final size:9
Alignment explanation
Indices: 9112921--9112967 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
9112911 AAAAATAATT
9112921 AAAAA-TTA
1 AAAAATTTA
9112929 AAAAATTTTA
1 AAAAA-TTTA
*
9112939 AGAAA--TA
1 AAAAATTTA
9112946 AAAAATTTA
1 AAAAATTTA
9112955 AAAAATTTA
1 AAAAATTTA
9112964 AAAA
1 AAAA
9112968 TATTATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 6 0.18
8 5 0.15
9 15 0.45
10 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAAATTTA
Found at i:9112981 original size:18 final size:17
Alignment explanation
Indices: 9112921--9112992 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 17
9112911 AAAAATAATT
*
9112921 AAAAATTAAAAAATTTTA
1 AAAAATTTAAAAA-TTTA
* *
9112939 AGAAA-TAAAAAATTTA
1 AAAAATTTAAAAATTTA
9112955 AAAAATTTAAAAATATTA
1 AAAAATTTAAAAAT-TTA
* * * *
9112973 TAAATTTTAATATTTTA
1 AAAAATTTAAAAATTTA
9112990 AAA
1 AAA
9112993 TTTTATAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
16 8 0.18
17 19 0.43
18 17 0.39
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (17 bp):
AAAAATTTAAAAATTTA
Found at i:9113161 original size:18 final size:20
Alignment explanation
Indices: 9113122--9113161 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
9113112 CTTTTTTCAA
9113122 ATTATTTAAATAATATTATTT
1 ATTATTTAAAT-ATATTATTT
9113143 ATTATTTAAAT-TATT-TTT
1 ATTATTTAAATATATTATTT
9113161 A
1 A
9113162 AAAAAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
21 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATTTAAATATATTATTT
Found at i:9113195 original size:19 final size:18
Alignment explanation
Indices: 9113172--9113215 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
9113162 AAAAAATAGA
* *
9113172 AATTTTTTTTATTTTTAT
1 AATTTTTTGTAATTTTAT
*
9113190 ATATTTATTGTAATTTTAT
1 A-ATTTTTTGTAATTTTAT
9113209 AATTTTT
1 AATTTTT
9113216 CTACATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
AATTTTTTGTAATTTTAT
Found at i:9113223 original size:18 final size:19
Alignment explanation
Indices: 9113184--9113225 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
9113174 TTTTTTTTAT
*
9113184 TTTTATATATTTATTGTAA
1 TTTTATATATTTATTCTAA
9113203 TTTTATA-ATTT-TTCTACA
1 TTTTATATATTTATTCTA-A
9113221 TTTTA
1 TTTTA
9113226 ATAAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTATATATTTATTCTAA
Found at i:9114349 original size:96 final size:96
Alignment explanation
Indices: 9114172--9114356 Score: 212
Period size: 96 Copynumber: 1.9 Consensus size: 96
9114162 GAAAAGGATG
* ** *
9114172 TTCGATTATCTCGATTTAAAGAAAGGTTGCACCTAGTGAGTTAAGGCGCAAATATTTAGAATCGG
1 TTCGATTATCTCGATTCAAAGAAAAATTGCACCTAGTGAGTTAAGGCACAAATATTTAGAATCGG
* **
9114237 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AAATAAAAAAACATTGCCTCGATTAAGGGTA
* * * * *
9114268 TTCGATTATTTCGATTCGAAGAAAAATTGCAGCTAGTGAGTTAAGGTACAAA-ATTTTGAAACTC
1 TTCGATTATCTCGATTCAAAGAAAAATTGCACCTAGTGAGTTAAGGCACAAATATTTAG-AA-TC
* *
9114332 -GAAATAAAAAAATATTGCCTTGATT
64 GGAAATAAAAAAACATTGCCTCGATT
9114357 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
95 5 0.07
96 66 0.90
97 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTCAAAGAAAAATTGCACCTAGTGAGTTAAGGCACAAATATTTAGAATCGG
AAATAAAAAAACATTGCCTCGATTAAGGGTA
Found at i:9114763 original size:59 final size:58
Alignment explanation
Indices: 9114699--9114820 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 58
9114689 AATCAAGATA
* * * *
9114699 AAAAATGGAACTTTTAGATATTCGGGGGTAAAAACATAATTTTTGGAAAGTTTTAGGGTT
1 AAAATTGGAACTTTTAGAAATTCGAGGGT-AAAACATAATTTTTGG-AAGTTTTAGGGTC
* * * **
9114759 AAAATTGGAATTTTTGGAAATTTGAGGGTAAAATGTAATTTTTGGAAGTTTTAGGGTC
1 AAAATTGGAACTTTTAGAAATTCGAGGGTAAAACATAATTTTTGGAAGTTTTAGGGTC
9114817 AAAA
1 AAAA
9114821 ACGTAATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 16 0.30
59 14 0.26
60 23 0.43
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (58 bp):
AAAATTGGAACTTTTAGAAATTCGAGGGTAAAACATAATTTTTGGAAGTTTTAGGGTC
Found at i:9114828 original size:89 final size:89
Alignment explanation
Indices: 9114724--9114928 Score: 267
Period size: 89 Copynumber: 2.3 Consensus size: 89
9114714 AGATATTCGG
* * *
9114724 GGGT-AAAAACATAATTTTTGGAAAGTTTTAGGGTTAAAATTGGAATTTTTGGAAATTT-GAGGG
1 GGGTCAAAAACATAATTTTTGGAAAGTTTTAGGGGTAAAAATGGAATTTTGGGAAATTTCGA-GG
9114787 T-AAAATGTAATTTTTGGAAGTTTTA
65 TAAAAATGTAATTTTTGGAAG-TTTA
* * *
9114812 GGGTCAAAAACGTAATTTTTGG-AAG-TTTAGGGGTAAAAATGTAATTTTGGGAATTTTCGAGGT
1 GGGTCAAAAACATAATTTTTGGAAAGTTTTAGGGGTAAAAATGGAATTTTGGGAAATTTCGAGGT
9114875 CAAAAATGTAATTTTTGGAAGTTTA
66 -AAAAATGTAATTTTTGGAAGTTTA
* *
9114900 GAGGTCAAAAATATAATTTTTGGACAGTT
1 G-GGTCAAAAACATAATTTTTGGAAAGTT
9114929 CAAGGACCTC
Statistics
Matches: 101, Mismatches: 9, Indels: 11
0.83 0.07 0.09
Matches are distributed among these distances:
87 30 0.30
88 14 0.14
89 54 0.53
90 2 0.02
91 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (89 bp):
GGGTCAAAAACATAATTTTTGGAAAGTTTTAGGGGTAAAAATGGAATTTTGGGAAATTTCGAGGT
AAAAATGTAATTTTTGGAAGTTTA
Found at i:9114829 original size:30 final size:29
Alignment explanation
Indices: 9114724--9114928 Score: 211
Period size: 30 Copynumber: 6.9 Consensus size: 29
9114714 AGATATTCGG
**
9114724 GGGTAAAAACATAATTTTTGGAAAGTTTTA
1 GGGTAAAAATGTAATTTTTGG-AAGTTTTA
* * * *
9114754 GGGTTAAAATTGGAATTTTTGGAAATTTGA
1 GGG-TAAAAATGTAATTTTTGGAAGTTTTA
9114784 GGGT-AAAATGTAATTTTTGGAAGTTTTA
1 GGGTAAAAATGTAATTTTTGGAAGTTTTA
*
9114812 GGGTCAAAAACGTAATTTTTGGAAG-TTTA
1 GGGT-AAAAATGTAATTTTTGGAAGTTTTA
* *
9114841 GGGGTAAAAATGTAATTTTGGGAA-TTTTC
1 -GGGTAAAAATGTAATTTTTGGAAGTTTTA
9114870 GAGGTCAAAAATGTAATTTTTGGAAG-TTTA
1 G-GGT-AAAAATGTAATTTTTGGAAGTTTTA
*
9114900 GAGGTCAAAAATATAATTTTTGGACAGTT
1 G-GGT-AAAAATGTAATTTTTGGA-AGTT
9114929 CAAGGACCTC
Statistics
Matches: 148, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
28 25 0.17
29 28 0.19
30 78 0.53
31 16 0.11
32 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTTA
Found at i:9114853 original size:59 final size:59
Alignment explanation
Indices: 9114723--9114928 Score: 247
Period size: 59 Copynumber: 3.5 Consensus size: 59
9114713 TAGATATTCG
* * * * *
9114723 GGGGTAAAAACATAATTTTTGGAAAGTTTTAGGGTTAAAATTGGAATTTTTGGAAATTT-
1 GGGGTAAAAATATAATTTTTGG-AAGTTTTAGGGTCAAAAATGTAATTTTTGGAAGTTTA
* *
9114782 GAGGGT-AAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAACGTAATTTTTGGAAGTTTA
1 G-GGGTAAAAATATAATTTTTGGAAGTTTTAGGGTCAAAAATGTAATTTTTGGAAGTTTA
* * *
9114841 GGGGTAAAAATGTAATTTTGGGAA-TTTTCGAGGTCAAAAATGTAATTTTTGGAAGTTTA
1 GGGGTAAAAATATAATTTTTGGAAGTTTTAG-GGTCAAAAATGTAATTTTTGGAAGTTTA
*
9114900 GAGGTCAAAAATATAATTTTTGGACAGTT
1 GGGGT-AAAAATATAATTTTTGGA-AGTT
9114929 CAAGGACCTC
Statistics
Matches: 127, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
58 40 0.31
59 64 0.50
60 20 0.16
61 1 0.01
62 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (59 bp):
GGGGTAAAAATATAATTTTTGGAAGTTTTAGGGTCAAAAATGTAATTTTTGGAAGTTTA
Found at i:9116029 original size:17 final size:16
Alignment explanation
Indices: 9116007--9116044 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9115997 ATTTTTATTA
9116007 ATTATTTAATAAATACT
1 ATTATTTAATAAA-ACT
*
9116024 ATTA-TTAATAAAATT
1 ATTATTTAATAAAACT
9116039 ATTATT
1 ATTATT
9116045 ATTATTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 9 0.47
17 4 0.21
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATTTAATAAAACT
Found at i:9116047 original size:21 final size:21
Alignment explanation
Indices: 9116023--9116062 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9116013 TAATAAATAC
9116023 TATTATTAATAAAATTATTAT
1 TATTATTAATAAAATTATTAT
* *
9116044 TATTATTAATGAGATTATT
1 TATTATTAATAAAATTATT
9116063 TAATACGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TATTATTAATAAAATTATTAT
Found at i:9116838 original size:6 final size:6
Alignment explanation
Indices: 9116829--9116938 Score: 92
Period size: 6 Copynumber: 19.0 Consensus size: 6
9116819 TCATAATAGT
* *
9116829 TTTAAA TTTAAA TATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTTAGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTA-AA
*
9116878 --TAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAAA -GTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
9116921 TCTTAAA -ATAAA TTTAAA
1 T-TTAAA TTTAAA TTTAAA
9116939 ATGGGTTGAG
Statistics
Matches: 85, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
4 4 0.05
5 20 0.24
6 51 0.60
7 8 0.09
8 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:9116862 original size:29 final size:29
Alignment explanation
Indices: 9116830--9116938 Score: 95
Period size: 29 Copynumber: 3.8 Consensus size: 29
9116820 CATAATAGTT
9116830 TTAAAT-TTAAATATAAATTTAAACTTAAA
1 TTAAATCTTAAATATAAATTTAAA-TTAAA
*
9116859 TTAAAT-TTAAATTTTAGAA--TAAATTTAAA
1 TTAAATCTTAAA-TATA-AATTTAAA-TTAAA
* * *
9116888 TT-TATCTTAAATTTAAATTTAAAGTAAA
1 TTAAATCTTAAATATAAATTTAAATTAAA
*
9116916 TTTAATCTTAAA-ATAAATTTAAA
1 TTAAATCTTAAATATAAATTTAAA
9116939 ATGGGTTGAG
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
27 2 0.03
28 22 0.32
29 39 0.57
30 3 0.04
31 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (29 bp):
TTAAATCTTAAATATAAATTTAAATTAAA
Found at i:9116865 original size:17 final size:17
Alignment explanation
Indices: 9116829--9116938 Score: 125
Period size: 17 Copynumber: 6.4 Consensus size: 17
9116819 TCATAATAGT
9116829 TTTAAATTTAAATATAAA
1 TTTAAATTTAAAT-TAAA
*
9116847 TTTAAACTTAAATTAAA
1 TTTAAATTTAAATTAAA
9116864 TTTAAATTTTAGAA-TAAA
1 TTTAAA-TTTA-AATTAAA
**
9116882 TTTAAATTTATCTTAAA
1 TTTAAATTTAAATTAAA
*
9116899 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAATTAAA
*
9116916 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAATTAAA
9116933 TTTAAA
1 TTTAAA
9116939 ATGGGTTGAG
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
16 3 0.04
17 47 0.59
18 27 0.34
19 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:9117321 original size:18 final size:16
Alignment explanation
Indices: 9117298--9117332 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
9117288 TAATTAATTT
9117298 TAATTAAATTATTTAAAA
1 TAATT-AATT-TTTAAAA
9117316 TAATTAATTTTTAAAA
1 TAATTAATTTTTAAAA
9117332 T
1 T
9117333 TATAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTAATTTTTAAAA
Found at i:9117521 original size:28 final size:29
Alignment explanation
Indices: 9117457--9117522 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
9117447 GGATTTTGGA
*
9117457 TTTGGGGTTCAAGGTTTATAGCTTTGAGG
1 TTTGGGGTTCAAGGTTTATAGCTTTAAGG
* * *
9117486 ATTAGGGTTCAA-GTTTA-AGGTTTAAGGG
1 TTTGGGGTTCAAGGTTTATAGCTTTAA-GG
9117514 TTTGGGGTT
1 TTTGGGGTT
9117523 ATAGGGTACA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 6 0.20
28 14 0.47
29 10 0.33
ACGTcount: A:0.20, C:0.05, G:0.35, T:0.41
Consensus pattern (29 bp):
TTTGGGGTTCAAGGTTTATAGCTTTAAGG
Found at i:9118033 original size:2 final size:2
Alignment explanation
Indices: 9118026--9118059 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9118016 ACAAATTCAG
9118026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9118060 TGTTCACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9128750 original size:198 final size:199
Alignment explanation
Indices: 9128247--9129019 Score: 1147
Period size: 201 Copynumber: 3.8 Consensus size: 199
9128237 ATGACTTATT
* *
9128247 ACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCTAGAGAAGTGAATTAGAACAAGTGA
1 ACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCTAGAGAAGCGAATTAAAACAAGTGA
* *
9128312 GGCGGTCATCTTCTTGATGAGATA-AAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAATC
66 GGCGATCATCTTCCTGATGAGATACAA-AGAAGAATACCAACTCAACGCTCAACGCGAGCAAATC
* *
9128376 TTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCGGGTCGAAGCAATAAAATGGTTAGCTTCC
130 TTCGAA-CCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCATTAAAA-GGTTAGCTTCC
*
9128441 TAATGAG
193 TGATGAG
* * * *
9128448 ACACGGAGAAGTGGACCAAATTCCTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAAGCGA
1 ACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCTAGAGAAGCGAATTAAAACAAGTGA
* * * *
9128513 GGTGGTCATCTTCTTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACGCGAGCAAATCT
66 GGCGATCATCTTCCTGATGAGATACAAAGAAGAATACCAACTCAACGCTCAACGCGAGCAAATCT
* * * *
9128578 TCGAACCCATCTTCCTGATGAGGCACTGAGAAGTAGGTTGAAGCATTAAAAGGTTAGCTTCCTGA
131 TCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCATTAAAAGGTTAGCTTCCTGA
9128643 TGAG
196 TGAG
9128647 ACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATC-AGAGAAGCGAATTAAAACAAGTGA
1 ACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCTAGAGAAGCGAATTAAAACAAGTGA
9128711 GGCGATCATCTTCCTGATGAGATACAAAGAAGAATACCAACTCAACGCTCAACGCGAGCAAATCT
66 GGCGATCATCTTCCTGATGAGATACAAAGAAGAATACCAACTCAACGCTCAACGCGAGCAAATCT
* *
9128776 TCGAACCTAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATTAAATGGTTAGCTTCCTG
131 TCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGC-ATTAAAAGGTTAGCTTCCTG
9128841 ATGAG
195 ATGAG
* * * * *
9128846 ATACAGAGAAGTGGACCAAATTCATATTCCTGAGGAGATCTAGAGAAGCGAATTAAAACAATTAA
1 ACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCTAGAGAAGCGAATTAAAACAAGTGA
* * * * *
9128911 GGC-AGTCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCAACGCTCAATGCGAGC
66 GGCGA-TCATCTTCCTGATGAGATACAAAGAAGAATACC-AA-C---TCAACGCTCAACGCGAGC
*
9128975 AAATCTTTGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTC
125 AAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTC
9129020 AAAGTCAACG
Statistics
Matches: 523, Mismatches: 40, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
198 123 0.24
199 117 0.22
200 95 0.18
201 127 0.24
202 2 0.00
205 59 0.11
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (199 bp):
ACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCTAGAGAAGCGAATTAAAACAAGTGA
GGCGATCATCTTCCTGATGAGATACAAAGAAGAATACCAACTCAACGCTCAACGCGAGCAAATCT
TCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCATTAAAAGGTTAGCTTCCTGA
TGAG
Found at i:9129385 original size:17 final size:17
Alignment explanation
Indices: 9129363--9129436 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
9129353 CAATGGGATA
*
9129363 TAAATTTATTTTTAAAT
1 TAAATTTATTTTAAAAT
* *
9129380 TAAATTTATTTTGAATT
1 TAAATTTATTTTAAAAT
**
9129397 TAAATTTA-CATAAAATT
1 TAAATTTATTTTAAAA-T
*
9129414 TAAATTTATTTAAAAAT
1 TAAATTTATTTTAAAAT
9129431 TAAATT
1 TAAATT
9129437 AATGTCCAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
16 3 0.07
17 39 0.85
18 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
TAAATTTATTTTAAAAT
Found at i:9131538 original size:30 final size:30
Alignment explanation
Indices: 9131405--9131557 Score: 134
Period size: 29 Copynumber: 5.1 Consensus size: 30
9131395 AAAAATTGTA
* * *
9131405 TTTTGACCCCCGAACTTCTCCAAAATTACATT
1 TTTTGACCCCCAAACTTC-CAAAAATTCCA-T
* * * *
9131437 TTTTAACCTCGC-AACTTCCAAGAATTACAT
1 TTTTGACC-CCCAAACTTCCAAAAATTCCAT
***
9131467 TTTTG-CCTTGAAACTTCCAAAAATTCCAT
1 TTTTGACCCCCAAACTTCCAAAAATTCCAT
9131496 TTTTGA-CCCCAAACTTCCAAAAATTCCAT
1 TTTTGACCCCCAAACTTCCAAAAATTCCAT
**
9131525 TTTTGACCCCCAAAC-TCCTGAAATTACCAT
1 TTTTGACCCCCAAACTTCCAAAAATT-CCAT
9131555 TTT
1 TTT
9131558 GCCCTCGGAC
Statistics
Matches: 101, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
29 57 0.56
30 20 0.20
31 9 0.09
32 13 0.13
33 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.35
Consensus pattern (30 bp):
TTTTGACCCCCAAACTTCCAAAAATTCCAT
Found at i:9135934 original size:21 final size:21
Alignment explanation
Indices: 9135910--9135953 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9135900 CAATTCCTAC
9135910 AAAGCAATG-CAATAATATAAG
1 AAAGCAATGTCAAT-ATATAAG
* *
9135931 AAAGCTATGTCTATATATAAG
1 AAAGCAATGTCAATATATAAG
9135952 AA
1 AA
9135954 GGGAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (21 bp):
AAAGCAATGTCAATATATAAG
Found at i:9138750 original size:21 final size:21
Alignment explanation
Indices: 9138725--9138768 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9138715 AAATTCCTAT
9138725 AAAGTAATGTA-ATAATATAAG
1 AAAGTAATGTATAT-ATATAAG
* *
9138746 AAAGTTATGTCTATATATAAG
1 AAAGTAATGTATATATATAAG
9138767 AA
1 AA
9138769 GGGAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (21 bp):
AAAGTAATGTATATATATAAG
Found at i:9142466 original size:23 final size:22
Alignment explanation
Indices: 9142436--9142500 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 22
9142426 CATTAAATAT
9142436 CTTAAAAG-AATAGGTGATTTATG
1 CTTAAAAGTAAT--GTGATTTATG
9142459 CTTAAAAGTTAATGTGATTTATG
1 CTTAAAAG-TAATGTGATTTATG
* *
9142482 CTCAAATGATAATGTGATT
1 CTTAAAAG-TAATGTGATT
9142501 AATGTGTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 34 0.92
25 3 0.08
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.38
Consensus pattern (22 bp):
CTTAAAAGTAATGTGATTTATG
Found at i:9143855 original size:22 final size:22
Alignment explanation
Indices: 9143827--9143870 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9143817 TATTGATAAA
9143827 TTGTTGAGACCAAATGTGGAGC
1 TTGTTGAGACCAAATGTGGAGC
*
9143849 TTGTTGAGACCAAATGTTGAGC
1 TTGTTGAGACCAAATGTGGAGC
9143871 AATTATGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (22 bp):
TTGTTGAGACCAAATGTGGAGC
Found at i:9144576 original size:16 final size:17
Alignment explanation
Indices: 9144549--9144581 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
9144539 TTGATACGCA
*
9144549 AACAACTTTAGATGGTT
1 AACAACTTTAGAAGGTT
9144566 AACAA-TTTAGAAGGTT
1 AACAACTTTAGAAGGTT
9144582 TCTAACCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (17 bp):
AACAACTTTAGAAGGTT
Found at i:9144951 original size:37 final size:37
Alignment explanation
Indices: 9144882--9144962 Score: 128
Period size: 37 Copynumber: 2.1 Consensus size: 37
9144872 ATAAGACTTC
9144882 TAAAAACCCAAATAAAAGAAATTCATTATTTTAAATTAA
1 TAAAAACCCAAATAAAAG--ATTCATTATTTTAAATTAA
9144921 TAAAAACCCAAAATAAAAG-TTCATTATTTTAAATTAA
1 TAAAAACCC-AAATAAAAGATTCATTATTTTAAATTAA
9144958 TAAAA
1 TAAAA
9144963 CAAAATAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
37 23 0.56
39 9 0.22
40 9 0.22
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (37 bp):
TAAAAACCCAAATAAAAGATTCATTATTTTAAATTAA
Found at i:9147902 original size:18 final size:19
Alignment explanation
Indices: 9147868--9147916 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
9147858 TAAAAAATAA
9147868 AATC-ATATATTTATTTAACT
1 AATCTATATA-TT-TTTAACT
*
9147888 AGT-TATATATTTTTAACT
1 AATCTATATATTTTTAACT
9147906 AATCTATATAT
1 AATCTATATAT
9147917 GTATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 9 0.36
19 9 0.36
20 7 0.28
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (19 bp):
AATCTATATATTTTTAACT
Found at i:9147977 original size:21 final size:22
Alignment explanation
Indices: 9147922--9147993 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 22
9147912 TATATGTATT
9147922 TAAAATA-AATATTTTTTAATA
1 TAAAATATAATATTTTTTAATA
*
9147943 TTAAATATACATATTTTTTAA-A
1 TAAAATATA-ATATTTTTTAATA
* *
9147965 TAAAATATTATATTAATTTAATA
1 TAAAATATAATATT-TTTTAATA
9147988 TAAAAT
1 TAAAAT
9147994 TCTATACATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.26
22 14 0.33
23 18 0.42
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAATATAATATTTTTTAATA
Done.