Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 29 of 32
Found at i:5265774 original size:16 final size:16
Alignment explanation
Indices: 5265744--5265860 Score: 87
Period size: 16 Copynumber: 7.3 Consensus size: 16
5265734 TTTTGGATCA
* *
5265744 ATTTGAATTAGTTTAT
1 ATTTAAATTATTTTAT
*
5265760 TTTTAAATTATTTTAT
1 ATTTAAATTATTTTAT
* * *
5265776 ATTT-AACTAATTTAA
1 ATTTAAATTATTTTAT
5265791 ATTTTAAATTATTTTAT
1 A-TTTAAATTATTTTAT
*
5265808 ATTTAAATTAAGTTTAAT
1 ATTTAAATT-A-TTTTAT
* * *
5265826 AGTTAAATTA-ATTAA
1 ATTTAAATTATTTTAT
*
5265841 ATTTAAA-TATTTTAG
1 ATTTAAATTATTTTAT
5265856 ATTTA
1 ATTTA
5265861 TATATTTAAT
Statistics
Matches: 78, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
14 2 0.03
15 25 0.32
16 27 0.35
17 11 0.14
18 13 0.17
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (16 bp):
ATTTAAATTATTTTAT
Found at i:5265859 original size:15 final size:15
Alignment explanation
Indices: 5265761--5265867 Score: 63
Period size: 15 Copynumber: 6.7 Consensus size: 15
5265751 TTAGTTTATT
*
5265761 TTTAAATTATTTTATA
1 TTTAAA-TATTTTAAA
* *
5265777 TTTAACTAATTTAAA
1 TTTAAATATTTTAAA
*
5265792 TTTTAAATTATTTTATA
1 -TTTAAA-TATTTTAAA
*
5265809 TTTAAATTAAGTTTAATA
1 TTTAAA-T-ATTTTAA-A
* *
5265827 GTTAAAT-TAATTAAA
1 TTTAAATAT-TTTAAA
*
5265842 TTTAAATATTTTAGA
1 TTTAAATATTTTAAA
*
5265857 TTTATATATTT
1 TTTAAATATTT
5265868 AATTCAATTA
Statistics
Matches: 70, Mismatches: 15, Indels: 13
0.71 0.15 0.13
Matches are distributed among these distances:
15 28 0.40
16 23 0.33
17 13 0.19
18 6 0.09
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTAAATATTTTAAA
Found at i:5265895 original size:28 final size:28
Alignment explanation
Indices: 5265810--5265896 Score: 77
Period size: 30 Copynumber: 3.0 Consensus size: 28
5265800 TATTTTATAT
*
5265810 TTAAATTAAGTTTAATAGTTAAA-TTAA
1 TTAAATTAAGTTTAATATTTAAATTTAA
* * *
5265837 TTAAATTTAAATATTTTAGATTTATATATTTAA
1 TTAAA-TT-AA-GTTTAATATTTA-A-ATTTAA
*
5265870 TTCAATTAAGTTTAATATTTAAATTTA
1 TTAAATTAAGTTTAATATTTAAATTTA
5265897 TTATTTTGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
27 5 0.11
28 7 0.15
29 3 0.07
30 17 0.37
31 3 0.07
32 3 0.07
33 8 0.17
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (28 bp):
TTAAATTAAGTTTAATATTTAAATTTAA
Found at i:5265976 original size:16 final size:16
Alignment explanation
Indices: 5265937--5265968 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5265927 TAAGTTAATT
*
5265937 ATTAAAATCATTTTAA
1 ATTAAAATAATTTTAA
5265953 ATTAAAATAATTTTAA
1 ATTAAAATAATTTTAA
5265969 GTTTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAAAATAATTTTAA
Found at i:5265993 original size:112 final size:114
Alignment explanation
Indices: 5265837--5266056 Score: 263
Period size: 112 Copynumber: 1.9 Consensus size: 114
5265827 GTTAAATTAA
* * * * * * *
5265837 TTAAATTTAAATATTTTAGATTTATATATTTAATTCAATTAAGTTTAATATTTAAATTTATTATT
1 TTAAATTAAAATATTTTAGATTTAAATATTTAACTCAATCAAGTTTAACACTTAAATTTATTAGT
* *
5265902 TTGAT-A-TTTTTAATTC-GAATCATTTT-AAGTTAATTATTAAAATCATT
66 TTAATAATTTTTTAATTCAAAAT-ATTTTGAA-TTAATTATTAAAATCATT
* *
5265949 TTAAATTAAAATAATTTTA-AGTTTAAAT-TTTTACTCAATCAAGTTTAACACTTAGATTTATTA
1 TTAAATTAAAAT-ATTTTAGA-TTTAAATATTTAACTCAATCAAGTTTAACACTTAAATTTATTA
5266012 GTTTAATAATTTTTTAATTCAAAATATTTTGAATTAATTATTAAA
64 GTTTAATAATTTTTTAATTCAAAATATTTTGAATTAATTATTAAA
5266057 GTAATTTCGA
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
112 46 0.51
113 13 0.14
114 27 0.30
115 5 0.05
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (114 bp):
TTAAATTAAAATATTTTAGATTTAAATATTTAACTCAATCAAGTTTAACACTTAAATTTATTAGT
TTAATAATTTTTTAATTCAAAATATTTTGAATTAATTATTAAAATCATT
Found at i:5266080 original size:114 final size:112
Alignment explanation
Indices: 5265815--5266089 Score: 256
Period size: 114 Copynumber: 2.4 Consensus size: 112
5265805 TATATTTAAA
* * * * * *
5265815 TTAAGTTTAA-TAGTTAAATTAA-TT-AAATTTAAAT-ATTTTAGATTTATATATTTAATTCAAT
1 TTAAG-TTAATTA-TTAAAATAATTTCAAATTAAAATAATTTTAAATTTAAAT-TTTTACTCAAT
* * * * * *
5265876 TAAGTTTAATATTTAAATTTATTATTTTGATATTTTTAATTCGAATCATT
63 CAAGTTTAACACTTAAATTTATTAGTTTAATATTTTTAATTCAAATCATT
* * *
5265926 TTAAGTTAATTATTAAAATCATTTTAAATTAAAATAATTTTAAGTTTAAATTTTTACTCAATCAA
1 TTAAGTTAATTATTAAAATAATTTCAAATTAAAATAATTTTAAATTTAAATTTTTACTCAATCAA
*
5265991 GTTTAACACTTAGATTTATTAGTTTAATAATTTTTTAATTCAAAAT-ATT
66 GTTTAACACTTAAATTTATTAGTTTAAT-A-TTTTTAATTC-AAATCATT
* * * * *
5266040 TTGAA-TTAATTATTAAAGTAATTTCGAGTTCAAATCATTTTAAATTTAAA
1 TT-AAGTTAATTATTAAAATAATTTCAAATTAAAATAATTTTAAATTTAAA
5266090 ATATTTTAAA
Statistics
Matches: 133, Mismatches: 23, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
110 11 0.08
111 9 0.07
112 43 0.32
113 13 0.10
114 52 0.39
115 5 0.04
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (112 bp):
TTAAGTTAATTATTAAAATAATTTCAAATTAAAATAATTTTAAATTTAAATTTTTACTCAATCAA
GTTTAACACTTAAATTTATTAGTTTAATATTTTTAATTCAAATCATT
Found at i:5266095 original size:16 final size:16
Alignment explanation
Indices: 5266071--5266134 Score: 67
Period size: 17 Copynumber: 3.9 Consensus size: 16
5266061 TTTCGAGTTC
5266071 AAATCATTTTAAATTTA
1 AAAT-ATTTTAAATTTA
5266088 AAATATTTTAAA-TTA
1 AAATATTTTAAATTTA
** * *
5266103 ATTTATTTTTAAGTTA
1 AAATATTTTAAATTTA
5266119 AAATTATTTTAAATTT
1 AAA-TATTTTAAATTT
5266135 TGATAATTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 12 0.32
16 12 0.32
17 14 0.37
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
AAATATTTTAAATTTA
Found at i:5266170 original size:22 final size:22
Alignment explanation
Indices: 5266130--5266186 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
5266120 AATTATTTTA
5266130 AATTTTGATAATTCTAAATTCATAT
1 AATTTT-A-AATTCTAAATTCAT-T
* *
5266155 ATTTTTAAATT-TAAATTGATT
1 AATTTTAAATTCTAAATTCATT
5266176 AATTTTAAATT
1 AATTTTAAATT
5266187 AATAATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.38
22 8 0.28
23 4 0.14
24 1 0.03
25 5 0.17
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (22 bp):
AATTTTAAATTCTAAATTCATT
Found at i:5266185 original size:37 final size:34
Alignment explanation
Indices: 5266134--5266205 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 34
5266124 ATTTTAAATT
*
5266134 TTGATAATTCTAAATTCATATATTTTTAAATTTAAA
1 TTGATAATTCTAAATTAATA-ATTTTTAAA-TTAAA
* *
5266170 TTGATTAATTTTAAATTAATAATTTTTTAATTAAA
1 TTGA-TAATTCTAAATTAATAATTTTTAAATTAAA
5266205 T
1 T
5266206 CAAATGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 6 0.19
36 12 0.38
37 14 0.44
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (34 bp):
TTGATAATTCTAAATTAATAATTTTTAAATTAAA
Found at i:5277650 original size:2 final size:2
Alignment explanation
Indices: 5277643--5277674 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5277633 GCTGCTCCTC
5277643 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5277675 ATCAGCAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5278873 original size:2 final size:2
Alignment explanation
Indices: 5278866--5278897 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5278856 AGGACACATA
5278866 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5278898 TTTATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5281585 original size:17 final size:16
Alignment explanation
Indices: 5281563--5281616 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
5281553 AGATTTAAAT
5281563 AAAAATATTAAATTTAA
1 AAAAATATT-AATTTAA
5281580 AAAAATA-T-ATTTAA
1 AAAAATATTAATTTAA
* *
5281594 AAAAAGTCTTATTTTAA
1 AAAAA-TATTAATTTAA
5281611 AAAAAT
1 AAAAAT
5281617 CTGAACCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 11 0.34
15 1 0.03
16 3 0.09
17 17 0.53
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAAATATTAATTTAA
Found at i:5281594 original size:29 final size:33
Alignment explanation
Indices: 5281526--5281596 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 33
5281516 AATCATCAAA
* *
5281526 ATTTAAAAATTCACTTAATATTTAAAAAGATTT
1 ATTTAAAAATTCACTTAATATTTAAAAAAATAT
**
5281559 AAATAAAAA-T-A-TTAA-ATTTAAAAAAATAT
1 ATTTAAAAATTCACTTAATATTTAAAAAAATAT
5281588 ATTTAAAAA
1 ATTTAAAAA
5281597 AAGTCTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 19 0.59
30 4 0.12
31 1 0.03
32 1 0.03
33 7 0.22
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (33 bp):
ATTTAAAAATTCACTTAATATTTAAAAAAATAT
Found at i:5283499 original size:3 final size:3
Alignment explanation
Indices: 5283493--5283521 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5283483 AAAGCTTGTC
5283493 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5283522 TTTCAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5290055 original size:19 final size:20
Alignment explanation
Indices: 5290033--5290082 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
5290023 ATTTTAATAG
5290033 AAAAATTATTAATTAAT-TT
1 AAAAATTATTAATTAATATT
*
5290052 -AAAATATAATAATTAATATT
1 AAAAAT-TATTAATTAATATT
*
5290072 ATAAATTATTA
1 AAAAATTATTA
5290083 GAAATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 5 0.20
19 10 0.40
20 6 0.24
21 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAATTATTAATTAATATT
Found at i:5294044 original size:2 final size:2
Alignment explanation
Indices: 5294039--5294066 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5294029 GTTACATATA
5294039 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5294067 AGAACACGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5295482 original size:5 final size:6
Alignment explanation
Indices: 5295461--5295511 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
5295451 AAAATTTTTT
*
5295461 ATTTAA ATTTAA ATTT-A ATTTAAA ATTTAA A-TTATT ATTTAA ATATTAA
1 ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTA-A ATTTAA AT-TTAA
5295510 AT
1 AT
5295512 AATCGAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 8 0.21
6 16 0.42
7 14 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:5295504 original size:18 final size:17
Alignment explanation
Indices: 5295457--5295511 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 17
5295447 TTTTAAAATT
5295457 TTTTATTTAAATTTAAA
1 TTTTATTTAAATTTAAA
*
5295474 TTTAATTTAAAATTTAAA
1 TTTTATTT-AAATTTAAA
5295492 TTATTATTTAAATATTAAA
1 TT-TTATTTAAAT-TTAAA
5295511 T
1 T
5295512 AATCGAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.21
18 15 0.45
19 11 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATTTAAATTTAAA
Found at i:5295614 original size:36 final size:36
Alignment explanation
Indices: 5295567--5295638 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
5295557 AACTACACCA
5295567 CCAACCTGTGTTTGCACGTAAAAGAATAAAGACCCT
1 CCAACCTGTGTTTGCACGTAAAAGAATAAAGACCCT
5295603 CCAACCTGTGTTTGCACGTAAAAGAATAAAGACCCT
1 CCAACCTGTGTTTGCACGTAAAAGAATAAAGACCCT
5295639 AAAATCTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (36 bp):
CCAACCTGTGTTTGCACGTAAAAGAATAAAGACCCT
Found at i:5301538 original size:2 final size:2
Alignment explanation
Indices: 5301533--5301568 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5301523 GTGTGTGTGT
*
5301533 GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5301569 TCATTGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5309266 original size:22 final size:22
Alignment explanation
Indices: 5309241--5309284 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
5309231 GTAGTTATTG
5309241 ATTATAATTTT-TTTTAAAAAAA
1 ATTA-AATTTTATTTTAAAAAAA
*
5309263 ATTAATTTTTAATTTTAAAAAA
1 ATTAAATTTT-ATTTTAAAAAA
5309285 TAATAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 4 0.21
23 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAAATTTTATTTTAAAAAAA
Found at i:5313316 original size:31 final size:32
Alignment explanation
Indices: 5313255--5313331 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 32
5313245 TTAGTGATAA
5313255 AATTAA-TAATATTATAATTTAATTTAAAATACT
1 AATTAATTAA-ATTAT-ATTTAATTTAAAATACT
*
5313288 AATTAATTAAATTAT-TTTAA-TTATAAATATT
1 AATTAATTAAATTATATTTAATTTA-AAATACT
* *
5313319 ATTTAATTTAATT
1 AATTAATTAAATT
5313332 TTAATTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
30 3 0.08
31 22 0.56
33 11 0.28
34 3 0.08
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
AATTAATTAAATTATATTTAATTTAAAATACT
Found at i:5313809 original size:27 final size:27
Alignment explanation
Indices: 5313745--5313818 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
5313735 TTTTTAATAA
5313745 AAATTATTTAATAAATTTAAAATTTAT
1 AAATTATTTAATAAATTTAAAATTTAT
* * * *
5313772 ATTATTTTTTAA-AAATTTTATATTTAAT
1 A-AATTATTTAATAAATTTAAAATTT-AT
*
5313800 AAATTATTTATATCAATTT
1 AAATTATTTA-ATAAATTT
5313819 TAAAGTAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
27 19 0.53
28 12 0.33
29 5 0.14
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (27 bp):
AAATTATTTAATAAATTTAAAATTTAT
Found at i:5321158 original size:888 final size:868
Alignment explanation
Indices: 5317779--5321254 Score: 5020
Period size: 867 Copynumber: 4.0 Consensus size: 868
5317769 GAATAACATT
* * * * * **
5317779 CTGGAGAATTCCCTTTTGGATGCTAATGCTGAACTTGGAGGATTGAGGGTAAAATTAAAGGGCTT
1 CTGGAGAATTCCCTTTTTGATGCAAATGCTGAACTTGAAGGATTGAGGGCAAAAGTAAAGATCTT
** * * * *
5317844 ACAAAATTCATGTCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAGAGAGAAGGTCTGA
66 GGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAGAGTGAAGTTTTGA
* * * *
5317909 TATCTGAGTTGGATGTCAGTCAGAAAAGGCTGGAAGATTTGGCAAAAAGATATCAGGGATTAGAA
131 TTTCTGAGTTGGATGTCAGTCAGAAAAGGCTGGCAGATTTGGAAAAAAGATATCAGGGATTGGAA
**
5317974 GAAAAATATGC-GGGCCTGGAGAAAGAGAGAGAATCAACACTTCGTGAAATAGAAGAGCTACAAA
196 GAAAAATAT-CTGGGCCTGGAGATGGAGAGAGAATCAACACTTC-TG---T------G------A
** * *
5318038 AGTCTCTAGATGCTGAAAAGCAAGAACATGCTAGTTTCGTGCAGTTGAATGAAACCCGAGTTACC
244 A----CTAGATGCTGAAAAGCAAGAACATGCTAGTTTTATGCAGTTGAATGAAACCCAAGTTACT
* * * *
5318103 GCTATGGAATCTCAGATCCATTTTCTACATGGGGAAAGT-TTTCGTAGAAAGAAAGAATATGAAG
305 GCTATGGAATCTCAGATCCATTTTCTACAAGGGGAAAGTCTGT-GCAGAAAGAAAAAATATGAAG
* * * * * *
5318167 AGGAACTAGACAATGTCATCAATACTCAA-GTAGAAATCTTCATCTTGCAGAAATGTGCACAAGA
369 AGGAAATGGACAAGGCCATCAATGCT-AAGGTAGAAACCTTCATCTTGCAGAAATGTGCACAAGA
* *
5318231 TCTGGAAGAGAACAATTTGTCCCTATTGCTTGAGTATAGGAAACTCTTGGCAA-CATCTGAATTA
433 TCTGGAAGAGAACAATTTATCCCTATTGCTTGAGTGTAGGAAACTCTTGG-AAGCATCTGAATTA
* * * *
5318295 TCTGAAAAACGTGTCTGCGAATTGGAGCTTGGAAATTCCAAAAAACAGATAGAGATAAATTCCTT
497 TCTGAAAAACTTATCTGCGAATTGGAGCTTGGAAATTCCAAAAAACAGATGGAGATAAAATCCTT
*
5318360 ATTTGATCAAATTACCATACTGAGGATGGGGCTATATCAGATGTTGAGGACTCTTGAGATTGATG
562 ATTTGATCAAAATACCATACTGAGGATGGGGCTATATCAGATGTTGAGGACTCTTGAGATTGATG
* * * * **
5318425 TTATCCATGGTTGTGATGATAAGATCAAACAAGACCAATCAGTTCTTGATAGTATATTTGGCAGA
627 CTATCCATGCTTATGATGATAAGATCAAACAAGACCAATCAGTTCTTGATTGTATATTCCGCAGA
*
5318490 CTCCAAAAGATGCAAAATTCACTTCTAAAGTCTTTGGATGAAAATCAGCAATTCGTAATTGAGAA
692 CTCCAAAAGATGCAAAATTCACTTCTAAAGTCTTTGGATGAAAATCAGCAATTCATAATTGAGAA
*
5318555 TTCAGTTCTCATCAGATTGCTTGGGCAACTGAAACTAGAGGCAGAAAATCTTGCTACGGAGAAGA
757 TTCAGTTCTCATCGGATTGCTTGGGCAACTGAAACTAGAGGCAGAAAATCTTGCTACGGAGAAGA
*
5318620 ATTCACTTCATCAAGAGTTGATGGTTCAGTCTGTGCGGTTTTCCGAG
822 ATTCACTTCATCAAGAGTTGAAGGTTCAGTCTGTGCGGTTTTCCGAG
*
5318667 CTGGAGAATGCCCTTTTTGATGCAAATGCTGAACTTGAAGGATTGAGGGCAAAAGTAAAGATCTT
1 CTGGAGAATTCCCTTTTTGATGCAAATGCTGAACTTGAAGGATTGAGGGCAAAAGTAAAGATCTT
5318732 GGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAGAGTGAAGTTTTGA
66 GGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAGAGTGAAGTTTTGA
*
5318797 TTTCTGAGTTGGATGTCAGTCAGAAAAGGTTGGCAGATTTGGAAAAAAGATATCAGGGATTGGAA
131 TTTCTGAGTTGGATGTCAGTCAGAAAAGGCTGGCAGATTTGGAAAAAAGATATCAGGGATTGGAA
*
5318862 GAAAAATATCTGGGCCTGGAGATGGAGAGGGAATCAACACTTC-GTGAACTAGATGCTGAAAAGC
196 GAAAAATATCTGGGCCTGGAGATGGAGAGAGAATCAACACTTCTGTGAACTAGATGCTGAAAAGC
* * * *
5318926 AAGAATATGCTAGTTTTATGCAGTTGCATGAATCCCAAGTTACTGCTATGGAATCTCAAATCCAT
261 AAGAACATGCTAGTTTTATGCAGTTGAATGAAACCCAAGTTACTGCTATGGAATCTCAGATCCAT
* * *
5318991 TTTCTACAAGGGGAAAGTCTGTGCATAAAGAAAAAATATGAGGAGGAAATGGACAAGGCCATGAA
326 TTTCTACAAGGGGAAAGTCTGTGCAGAAAGAAAAAATATGAAGAGGAAATGGACAAGGCCATCAA
* * *
5319056 TGCTCAGGTAGAAACCTTCATTTTGCAGAAATGTGCACAAGATCTGGAAGAGAACAATTTATGCC
391 TGCTAAGGTAGAAACCTTCATCTTGCAGAAATGTGCACAAGATCTGGAAGAGAACAATTTATCCC
* * * * *
5319121 TATTGCTTGTGTGTAGGAAACTCTTGGCAGCCTCTGAATTATCTGAAAAACATGTCTGCGAATTG
456 TATTGCTTGAGTGTAGGAAACTCTTGGAAGCATCTGAATTATCTGAAAAACTTATCTGCGAATTG
** * * * *
5319186 GAGCGCGGAAATTTCAAAAAACAGGTGGAGATAAAATCTTTATTTGATCAAAATACCATATTGAG
521 GAGCTTGGAAATTCCAAAAAACAGATGGAGATAAAATCCTTATTTGATCAAAATACCATACTGAG
* *
5319251 GATGGGGCTATATCAGATGTTGAAGACTCTTGAGATTGATGCTATCTATGCTTATGATGATAAGA
586 GATGGGGCTATATCAGATGTTGAGGACTCTTGAGATTGATGCTATCCATGCTTATGATGATAAGA
5319316 TCAAACAAGACCAATCAGTTCTTGATTGTATATTCCGCAGACTCCAAAAGATGCAAAATTCACTT
651 TCAAACAAGACCAATCAGTTCTTGATTGTATATTCCGCAGACTCCAAAAGATGCAAAATTCACTT
* * * *
5319381 CTAAAGTCTTCGGATGAAAATCAGCAATTTATAATTGAGAATTCAGTTCTTATTGGATTGCTTGG
716 CTAAAGTCTTTGGATGAAAATCAGCAATTCATAATTGAGAATTCAGTTCTCATCGGATTGCTTGG
**
5319446 GCAACTGAAACTAGAGGCAGAAAATCTTGCTATTGAGAAGAATTCACTTCATCAAGAGTTGAAGG
781 GCAACTGAAACTAGAGGCAGAAAATCTTGCTACGGAGAAGAATTCACTTCATCAAGAGTTGAAGG
*
5319511 TTCAGTCTGTGCGGTTTGCCGAG
846 TTCAGTCTGTGCGGTTTTCCGAG
* *
5319534 CTGGAGAATTCCCATTTTGATGCAAATGCTGAACTTGAAGGATTGAGGGAAAAAGTAAAGATCTT
1 CTGGAGAATTCCCTTTTTGATGCAAATGCTGAACTTGAAGGATTGAGGGCAAAAGTAAAGATCTT
*
5319599 GGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAGCACAGAGTGAAGTTTTGA
66 GGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAGAGTGAAGTTTTGA
*
5319664 TTTCTGAGTTGGATGTCAGTCAGAAAAGGCTGGCGGATTTGGAAAAAAGATATCAGGGATTGGAA
131 TTTCTGAGTTGGATGTCAGTCAGAAAAGGCTGGCAGATTTGGAAAAAAGATATCAGGGATTGGAA
5319729 GAAAAATATCTGGGCCTGGAGATGGAGAGAGAATCAACACTT-TGTGAACTAGATGCTGAAAAGC
196 GAAAAATATCTGGGCCTGGAGATGGAGAGAGAATCAACACTTCTGTGAACTAGATGCTGAAAAGC
* * *
5319793 AAGAACATGCCAGTTTTATGCAGTTGCATGAATCCCAAGTTACTGCTATGGAATCTCAGATCCAT
261 AAGAACATGCTAGTTTTATGCAGTTGAATGAAACCCAAGTTACTGCTATGGAATCTCAGATCCAT
* * * *
5319858 TTTCTACAAGGGCAAAGTCTGTGCATAAAGAAAAAATATGAGGAGGAAATGGACAAGGCCATGAA
326 TTTCTACAAGGGGAAAGTCTGTGCAGAAAGAAAAAATATGAAGAGGAAATGGACAAGGCCATCAA
* *
5319923 TGCTCAGGTAGAAACCTTCATCTTGCAGAAATGTGCACAAGATCTGGAAGAGAACAATTTATGCC
391 TGCTAAGGTAGAAACCTTCATCTTGCAGAAATGTGCACAAGATCTGGAAGAGAACAATTTATCCC
* * ** * *
5319988 TATCGCTTGTGTGTAGGAAACTCTTGGAAG-ACTCCAAATTATCTGAAAAACTAATCTCCGAATT
456 TATTGCTTGAGTGTAGGAAACTCTTGGAAGCA-TCTGAATTATCTGAAAAACTTATCTGCGAATT
* * *
5320052 GGAGCTTGGGAATTCCAAAAAACAGATGGAGATAAAATCTTTATTTGATCAAAATACCATATTGA
520 GGAGCTTGGAAATTCCAAAAAACAGATGGAGATAAAATCCTTATTTGATCAAAATACCATACTGA
* *
5320117 GGATGGGGCT-TGATGAGATGTTGAGGACTCTTGAGATTGATGCTATCTATGCTTATGATGATAA
585 GGATGGGGCTAT-ATCAGATGTTGAGGACTCTTGAGATTGATGCTATCCATGCTTATGATGATAA
* *
5320181 GATCAAACAAGACCAAGCAGCTCTTGATTGTATATTCCGCAGACTCCAAAAGATGCAAAATTCAC
649 GATCAAACAAGACCAATCAGTTCTTGATTGTATATTCCGCAGACTCCAAAAGATGCAAAATTCAC
5320246 TTCTAAAGTCTTTGGATGAAAATCAGCAATTCATAATTGAGAATTCAGTTCTCATCGGATTGCTT
714 TTCTAAAGTCTTTGGATGAAAATCAGCAATTCATAATTGAGAATTCAGTTCTCATCGGATTGCTT
*
5320311 GGGCAACTGAAACTAGAGGCAGAAAATCTTGCTACGGAAAAGAATTCACTTCATCAAGAGTTGAA
779 GGGCAACTGAAACTAGAGGCAGAAAATCTTGCTACGGAGAAGAATTCACTTCATCAAGAGTTGAA
5320376 GGTTCAGTCTGTGCGGTTTTCCGAG
844 GGTTCAGTCTGTGCGGTTTTCCGAG
* *
5320401 CTGGAGAATACCCTTTTTGATGCAAATGCTGAACTTGAAGGATTGAGGGCAAAAGTAGAGATCTT
1 CTGGAGAATTCCCTTTTTGATGCAAATGCTGAACTTGAAGGATTGAGGGCAAAAGTAAAGATCTT
* *
5320466 GGAAAATTCATGCCTGCTGCTAGATGATGAGAAGTCTGGCCTGATAACACAGAGTGAAGTTTTGA
66 GGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAGAGTGAAGTTTTGA
* *
5320531 TTTCTGATTTGGATGTCAGTCAGAAAAGGCTGGCGGATTTGGAAAAAAGATATCAGGGATTGGAA
131 TTTCTGAGTTGGATGTCAGTCAGAAAAGGCTGGCAGATTTGGAAAAAAGATATCAGGGATTGGAA
5320596 GAAAAATATCTGGGCCTGGAGATGGAGAGAGAATCAACACTTCGTGAAGTAGAAGAGCTACAAAA
196 GAAAAATATCTGGGCCTGGAGATGGAGAGAGAATCAACACTTC-T---GT------G-------A
* * * * *
5320661 GTTACTAGATGCTGAAAAGCAAGAACATGCTAGTTTTGTGAAGTTGAATGAAACCCGATTTACTT
244 ---ACTAGATGCTGAAAAGCAAGAACATGCTAGTTTTATGCAGTTGAATGAAACCCAAGTTACTG
* *
5320726 CTATGGAATC-CAAGATCCATTTTCTAAAAGGGGAAAGTCTGTGCAGAAAGAAAGAATATGAAGA
306 CTATGGAATCTC-AGATCCATTTTCTACAAGGGGAAAGTCTGTGCAGAAAGAAAAAATATGAAGA
* ** *
5320790 GGAATTGGACAAGGTAATCAATGCTAAGGTAGAAATCTTCATCTTGCAGAAATGTGCACAAGATC
370 GGAAATGGACAAGGCCATCAATGCTAAGGTAGAAACCTTCATCTTGCAGAAATGTGCACAAGATC
* *
5320855 TGGAAGAGAACAATTTATCCCTACTGCTCGAGTGTAGGAAACTCTTGGAAGCATC-GAAATTATC
435 TGGAAGAGAACAATTTATCCCTATTGCTTGAGTGTAGGAAACTCTTGGAAGCATCTG-AATTATC
* *
5320919 TGAACAACTTATCT-CTGAATTGGAGCTTGGAAACTCCAAAAAACAGATGGAGATAAAATCCTTA
499 TGAAAAACTTATCTGC-GAATTGGAGCTTGGAAATTCCAAAAAACAGATGGAGATAAAATCCTTA
* * *
5320983 TTTGATCAAATTACCATACTGCA-GA-GGAGGCTTTATCAGATGTTGGGGACTCTTGAGATTGAT
563 TTTGATCAAAATACCATACTG-AGGATGG-GGCTATATCAGATGTTGAGGACTCTTGAGATTGAT
* * * * *
5321046 GCTGTCCATAG-TTATGATGATATGATCAAACAAGACCAATCAGTTCTTGACTGCATATAT-GGC
626 GCTATCCAT-GCTTATGATGATAAGATCAAACAAGACCAATCAGTTCTTGATTGTATAT-TCCGC
* * *
5321109 AGACTTCAAAAGATGCAAAATTCGCTTCTAAAGTCTCTGGATGAAAATCAGCAATTCATAATTGA
689 AGACTCCAAAAGATGCAAAATTCACTTCTAAAGTCTTTGGATGAAAATCAGCAATTCATAATTGA
* * * * * *
5321174 GAATTCTGTTCTTATCGGATTGCTTAGGCAACTGAAACTAGAGGCGGAAAATCTTGCAACAGAGA
754 GAATTCAGTTCTCATCGGATTGCTTGGGCAACTGAAACTAGAGGCAGAAAATCTTGCTACGGAGA
* * *
5321239 ATAGTTCACTGCATCA
819 AGAATTCACTTCATCA
5321255 GATGCTCCGT
Statistics
Matches: 2371, Mismatches: 180, Indels: 74
0.90 0.07 0.03
Matches are distributed among these distances:
866 3 0.00
867 1614 0.68
868 2 0.00
869 1 0.00
871 2 0.00
872 2 0.00
877 1 0.00
878 1 0.00
883 1 0.00
885 1 0.00
886 1 0.00
887 5 0.00
888 732 0.31
889 5 0.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (868 bp):
CTGGAGAATTCCCTTTTTGATGCAAATGCTGAACTTGAAGGATTGAGGGCAAAAGTAAAGATCTT
GGAAAATTCATGCCTGCTGCTTGGTGATGAGAAGTCTGGCCTGATAACACAGAGTGAAGTTTTGA
TTTCTGAGTTGGATGTCAGTCAGAAAAGGCTGGCAGATTTGGAAAAAAGATATCAGGGATTGGAA
GAAAAATATCTGGGCCTGGAGATGGAGAGAGAATCAACACTTCTGTGAACTAGATGCTGAAAAGC
AAGAACATGCTAGTTTTATGCAGTTGAATGAAACCCAAGTTACTGCTATGGAATCTCAGATCCAT
TTTCTACAAGGGGAAAGTCTGTGCAGAAAGAAAAAATATGAAGAGGAAATGGACAAGGCCATCAA
TGCTAAGGTAGAAACCTTCATCTTGCAGAAATGTGCACAAGATCTGGAAGAGAACAATTTATCCC
TATTGCTTGAGTGTAGGAAACTCTTGGAAGCATCTGAATTATCTGAAAAACTTATCTGCGAATTG
GAGCTTGGAAATTCCAAAAAACAGATGGAGATAAAATCCTTATTTGATCAAAATACCATACTGAG
GATGGGGCTATATCAGATGTTGAGGACTCTTGAGATTGATGCTATCCATGCTTATGATGATAAGA
TCAAACAAGACCAATCAGTTCTTGATTGTATATTCCGCAGACTCCAAAAGATGCAAAATTCACTT
CTAAAGTCTTTGGATGAAAATCAGCAATTCATAATTGAGAATTCAGTTCTCATCGGATTGCTTGG
GCAACTGAAACTAGAGGCAGAAAATCTTGCTACGGAGAAGAATTCACTTCATCAAGAGTTGAAGG
TTCAGTCTGTGCGGTTTTCCGAG
Found at i:5321812 original size:231 final size:231
Alignment explanation
Indices: 5321397--5322324 Score: 1369
Period size: 231 Copynumber: 4.0 Consensus size: 231
5321387 TGATCGTCAA
* * *
5321397 AGTAAGGAGACTGAAAGC-TTTCGTCAGGCTAATCAGAAATTTGAGGCTGAGTTATCGAAATTGC
1 AGTATGGAGACTAAAAGCATTT-GTCAGGCTAATCAGAAATTTGAGGCTGAGTTATTGAAATTGC
* * * * *
5321461 ATGAAGAACTTCAACAAAGGAAACATAGAGAGGAGAGTTTGAGTGTTGAATTACAAAATGGAAGA
65 ATGAAGAAATTCAAGAAAGGAAACATAGGGAGGAGAGTTTGAGTGTTGAACTACAAAAGGGAAGA
*
5321526 AATGAGGTTGAACTTTGGGAGACTCAGGCTGCTGCATTGTTTGGTGAGTTACAGAGTTCTGCTGT
130 AATGAGGTTGAACTTTGGGAGACTCAGGCTGCTGCATTGTTTGGTGAGCTACAGAGTTCTGCTGT
* *
5321591 CCGTGAAACATTGCTTGAAGAGAAGGCTTATGAGCTC
195 CCGTGAAGCATTGCTTGAAGAGAAGGCTCATGAGCTC
* *
5321628 AGTATGGAGACTAAAAGCATTTGTCAGGCTAATCAGAAATTTGAGGCGGAGTTATTGAAATTGCG
1 AGTATGGAGACTAAAAGCATTTGTCAGGCTAATCAGAAATTTGAGGCTGAGTTATTGAAATTGCA
* * * *
5321693 TGAAGAAATTCAAGAAAGGAAACATAGGGAGGAGAGTTTGAGCGTTGAGCTAGAGAAGGGAAGAA
66 TGAAGAAATTCAAGAAAGGAAACATAGGGAGGAGAGTTTGAGTGTTGAACTACAAAAGGGAAGAA
* *
5321758 ATGATGTTGCACTTTGGGAGACTCAGGCTGCTGCATTGTTTGGTGAGCTACAGAGTTCTGCTGTC
131 ATGAGGTTGAACTTTGGGAGACTCAGGCTGCTGCATTGTTTGGTGAGCTACAGAGTTCTGCTGTC
* *
5321823 C-TAGAAGCGTTGCTTGTAGAGAAGGCTCATGAGCTC
196 CGT-GAAGCATTGCTTGAAGAGAAGGCTCATGAGCTC
* *
5321859 AGTATGGAGACTGAAAGCATTTGTCAGGCTAATCAGAAATTTGAGGCTGAGTTATTGATATTGCA
1 AGTATGGAGACTAAAAGCATTTGTCAGGCTAATCAGAAATTTGAGGCTGAGTTATTGAAATTGCA
* *
5321924 TGAAGAAATTCAAGAAAGGAAACATAGGGAGGAGAGTTTGAGTGTTGAGCTACGAAAGGGAAGAA
66 TGAAGAAATTCAAGAAAGGAAACATAGGGAGGAGAGTTTGAGTGTTGAACTACAAAAGGGAAGAA
** * *
5321989 ATGAGGTTGAAAGTTGGGAGACTCAAGCTGCTGCATTGTTTGGTGAGCTACAGAGTTCTGCTTTC
131 ATGAGGTTGAACTTTGGGAGACTCAGGCTGCTGCATTGTTTGGTGAGCTACAGAGTTCTGCTGTC
5322054 CGTGAAGCATTGCTTGAAGAGAAGGCTCATGAGCTC
196 CGTGAAGCATTGCTTGAAGAGAAGGCTCATGAGCTC
* * ** * *
5322090 AGTATGGAGACTGAAAA-TATTTGTGAGGCCCATC-GAAAATTTGAGGCTGAGTTATTGAGACTG
1 AGTATGGAGACT-AAAAGCATTTGTCAGGCTAATCAG-AAATTTGAGGCTGAGTTATTGAAATTG
* * * * * *
5322153 CATGAAGAACTTAAAGAGAGGAAACATAGGGAGGAGAATCTGAGTGTTGAACTACAAAAGGAAAG
64 CATGAAGAAATTCAAGAAAGGAAACATAGGGAGGAGAGTTTGAGTGTTGAACTACAAAAGGGAAG
* ** * *
5322218 AAATGAGGTTGAACTTTGGGAGACTCAGGCTACTGCATTGTTCAGTGAGCTACAGATTTCAGCTG
129 AAATGAGGTTGAACTTTGGGAGACTCAGGCTGCTGCATTGTTTGGTGAGCTACAGAGTTCTGCTG
*
5322283 TCCGTGAAGCATTGCTTGAAGAGAAAGCTCATGAGCTC
194 TCCGTGAAGCATTGCTTGAAGAGAAGGCTCATGAGCTC
5322321 AGTA
1 AGTA
5322325 CAGAATGTGA
Statistics
Matches: 630, Mismatches: 62, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
230 2 0.00
231 621 0.99
232 7 0.01
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (231 bp):
AGTATGGAGACTAAAAGCATTTGTCAGGCTAATCAGAAATTTGAGGCTGAGTTATTGAAATTGCA
TGAAGAAATTCAAGAAAGGAAACATAGGGAGGAGAGTTTGAGTGTTGAACTACAAAAGGGAAGAA
ATGAGGTTGAACTTTGGGAGACTCAGGCTGCTGCATTGTTTGGTGAGCTACAGAGTTCTGCTGTC
CGTGAAGCATTGCTTGAAGAGAAGGCTCATGAGCTC
Found at i:5325771 original size:2 final size:2
Alignment explanation
Indices: 5325755--5325797 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
5325745 TATATTAGAA
*
5325755 AT AT -T AT AG 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 AT AT AT AT
5325796 AT
1 AT
5325798 GCTGCAGTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5326889 original size:2 final size:2
Alignment explanation
Indices: 5326884--5326930 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
5326874 TCTCTCTCTC
* *
5326884 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5326926 TA TA T
1 TA TA T
5326931 GTAGATATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5332783 original size:2 final size:2
Alignment explanation
Indices: 5332776--5332810 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5332766 TGCATATTTA
*
5332776 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5332811 CACTTGCAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5345778 original size:20 final size:20
Alignment explanation
Indices: 5345753--5345800 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
5345743 GTGAAAAGTA
*
5345753 TAATTTATATTTATTTA-ATT
1 TAATTTATATAT-TTTATATT
*
5345773 TAATTTTTATATTTTATATT
1 TAATTTATATATTTTATATT
*
5345793 TTATTTAT
1 TAATTTAT
5345801 TTAAATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TAATTTATATATTTTATATT
Found at i:5348745 original size:19 final size:20
Alignment explanation
Indices: 5348702--5348768 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 20
5348692 CATTAATAAC
*
5348702 TTATA-TTATATATTTTTTA
1 TTATATTTATATATTTTATA
**
5348721 AAATATTTATATA-TTTATA
1 TTATATTTATATATTTTATA
5348740 TTATATTTA-ATATTTTATA
1 TTATATTTATATATTTTATA
5348759 TTATATTTAT
1 TTATATTTAT
5348769 GTAACTACGT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.08
19 30 0.75
20 7 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATATTTATATATTTTATA
Found at i:5353696 original size:16 final size:17
Alignment explanation
Indices: 5353675--5353729 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
5353665 AATAGTCTAT
5353675 AATTTAAATT-TTTTAA
1 AATTTAAATTATTTTAA
* ** *
5353691 AATTTATATTAAATT-G
1 AATTTAAATTATTTTAA
5353707 AATTTAAATTATTTTAA
1 AATTTAAATTATTTTAA
5353724 AATTTA
1 AATTTA
5353730 TTTTATTATT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTAAATTATTTTAA
Found at i:5353741 original size:12 final size:12
Alignment explanation
Indices: 5353685--5353734 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 12
5353675 AATTTAAATT
5353685 TTTTAAAATTTA
1 TTTTAAAATTTA
* *
5353697 TATT-AAATTGA
1 TTTTAAAATTTA
*
5353708 ATTT-AAA-TTA
1 TTTTAAAATTTA
5353718 TTTTAAAATTTA
1 TTTTAAAATTTA
5353730 TTTTA
1 TTTTA
5353735 TTATTTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
10 5 0.17
11 14 0.47
12 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTTTAAAATTTA
Found at i:5354618 original size:3 final size:3
Alignment explanation
Indices: 5354610--5354634 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5354600 ATGAGAGTTA
5354610 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
5354635 ATGTATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5354942 original size:23 final size:24
Alignment explanation
Indices: 5354911--5354956 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
5354901 TTTAAAAAAA
* *
5354911 TTTATTATTAAAATAATTTCAAAT
1 TTTATTATTAAAAAAAATTCAAAT
5354935 TTTA-TATTAAAAAAAATTCAAA
1 TTTATTATTAAAAAAAATTCAAA
5354957 CAAAACCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTATTATTAAAAAAAATTCAAAT
Found at i:5358284 original size:17 final size:18
Alignment explanation
Indices: 5358246--5358285 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5358236 AAAGAAGGAG
5358246 AAAACCAAAGAAGGGACA
1 AAAACCAAAGAAGGGACA
*
5358264 AAAACCAGAGAAGGGACA
1 AAAACCAAAGAAGGGACA
5358282 AAAA
1 AAAA
5358286 GGGAGGCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.15, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAACCAAAGAAGGGACA
Found at i:5359948 original size:23 final size:23
Alignment explanation
Indices: 5359876--5359987 Score: 56
Period size: 23 Copynumber: 5.0 Consensus size: 23
5359866 CATAATTTTT
* * *
5359876 ATTT-TTTATTATTGATAAATAT
1 ATTTATTTAATATTTATAAATAA
* *
5359898 A-TT-TTTAATAATATATAAAATTA
1 ATTTATTTAAT-ATTTAT-AAATAA
5359921 A-TTATTTAATATTTATAAATAA
1 ATTTATTTAATATTTATAAATAA
* * *
5359943 ATTTATCTAAT-TTAAATAATTAA
1 ATTTATTTAATATT-TATAAATAA
** *
5359966 ATTTAAATAA-ATTTATTAATAA
1 ATTTATTTAATATTTATAAATAA
5359988 TTAAATTAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
21 7 0.10
22 19 0.28
23 37 0.54
24 6 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTTATTTAATATTTATAAATAA
Found at i:5359978 original size:10 final size:10
Alignment explanation
Indices: 5359963--5360013 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
5359953 TTTAAATAAT
5359963 TAAATTTAAA
1 TAAATTTAAA
5359973 TAAATTTATTAA
1 TAAATTTA--AA
5359985 T-AA-TTAAA
1 TAAATTTAAA
5359993 TTAAATTTAAA
1 -TAAATTTAAA
*
5360004 TATATTTAAA
1 TAAATTTAAA
5360014 ATTTTTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 2 0.06
9 1 0.03
10 22 0.63
11 7 0.20
12 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:5359998 original size:31 final size:32
Alignment explanation
Indices: 5359936--5360011 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
5359926 TTAATATTTA
5359936 TAAATAAATTTATCTAATTTAAATAATTAAATT
1 TAAATAAATTTATCTAA-TTAAATAATTAAATT
*
5359969 TAAATAAATTTAT-TAA-TAATTAAATTAAATT
1 TAAATAAATTTATCTAATTAAAT-AATTAAATT
*
5360000 TAAATATATTTA
1 TAAATAAATTTA
5360012 AAATTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 4 0.10
31 20 0.50
32 3 0.08
33 13 0.32
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
TAAATAAATTTATCTAATTAAATAATTAAATT
Found at i:5360012 original size:21 final size:20
Alignment explanation
Indices: 5359965--5360013 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
5359955 TAAATAATTA
5359965 AATTTAAATAAATTTATTAAT
1 AATTTAAATAAATTTA-TAAT
5359986 AA-TTAAATTAAATTTA-AAT
1 AATTTAAA-TAAATTTATAAT
5360005 ATATTTAAA
1 A-ATTTAAA
5360014 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.16
20 6 0.24
21 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTAAATAAATTTATAAT
Found at i:5367118 original size:13 final size:13
Alignment explanation
Indices: 5367067--5367124 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
5367057 TTAATAATAA
*
5367067 AAATATTATTATTT
1 AAATATTAATA-TT
*
5367081 AAAT-TTAATAAT
1 AAATATTAATATT
*
5367093 AAA-AAT-ATA-T
1 AAATATTAATATT
5367103 AAATATTAATATT
1 AAATATTAATATT
5367116 AAATATTAA
1 AAATATTAA
5367125 ATAATAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 4 0.11
11 5 0.14
12 8 0.22
13 15 0.42
14 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATATTAATATT
Found at i:5367122 original size:7 final size:7
Alignment explanation
Indices: 5367095--5367127 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
5367085 TTAATAATAA
5367095 AAATATAT
1 AAATAT-T
5367103 AAATATT
1 AAATATT
5367110 -AATATT
1 AAATATT
5367116 AAATATT
1 AAATATT
5367123 AAATA
1 AAATA
5367128 ATAATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 12 0.50
8 6 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATATT
Found at i:5367139 original size:20 final size:22
Alignment explanation
Indices: 5367086--5367139 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 22
5367076 TATTTAAATT
5367086 TAATAATA--AAAATATATAAA
1 TAATAATATTAAAATATATAAA
*
5367106 TATTAATATT-AAATAT-TAAA
1 TAATAATATTAAAATATATAAA
5367126 TAATAAT-TTAAAAT
1 TAATAATATTAAAAT
5367140 TTCAGGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 21 0.72
21 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATAATATTAAAATATATAAA
Found at i:5367835 original size:14 final size:15
Alignment explanation
Indices: 5367816--5367854 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
5367806 ATAGATGGAT
*
5367816 AATTTAATTA-TTTA
1 AATTTAATAATTTTA
5367830 AATTTAATAATTTTA
1 AATTTAATAATTTTA
5367845 AATTTAATAA
1 AATTTAATAA
5367855 AGTAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTAATAATTTTA
Found at i:5367895 original size:23 final size:23
Alignment explanation
Indices: 5367843--5367914 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 23
5367833 TTAATAATTT
* *
5367843 TAAATTTAATA-AAGTAATATAATA
1 TAAATATAATATATGTAA-ATAA-A
* *
5367867 TAAATATTATATAT-TTAATAAA
1 TAAATATAATATATGTAAATAAA
5367889 TAGAATATAATATATGTAAATAAA
1 TA-AATATAATATATGTAAATAAA
5367913 TA
1 TA
5367915 TTATATTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 3 0.08
23 15 0.38
24 20 0.51
25 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
TAAATATAATATATGTAAATAAA
Found at i:5367976 original size:4 final size:4
Alignment explanation
Indices: 5367967--5367997 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
5367957 TCTAATACTT
5367967 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
5367998 GAGAAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:5368739 original size:21 final size:21
Alignment explanation
Indices: 5368710--5368749 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5368700 TTCATATTTA
5368710 ATTTGAGTTTAGTTTTGGGTTT
1 ATTTGAG-TTAGTTTTGGGTTT
*
5368732 ATTT-AGTTGGTTTTGGGT
1 ATTTGAGTTAGTTTTGGGT
5368750 GCTTCCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.12, C:0.00, G:0.30, T:0.57
Consensus pattern (21 bp):
ATTTGAGTTAGTTTTGGGTTT
Found at i:5376830 original size:18 final size:18
Alignment explanation
Indices: 5376807--5376848 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5376797 ATAAGTTTTA
* *
5376807 ATAAATTATTTATCAATT
1 ATAAATTATGTATAAATT
5376825 ATAAATTATGTATAAATT
1 ATAAATTATGTATAAATT
*
5376843 AAAAAT
1 ATAAAT
5376849 AAGATAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
ATAAATTATGTATAAATT
Found at i:5377099 original size:2 final size:2
Alignment explanation
Indices: 5377094--5377118 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5377084 ATATATATAT
5377094 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5377119 TCAAAGAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5377335 original size:22 final size:22
Alignment explanation
Indices: 5377292--5377342 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5377282 AAAGTTATAA
*
5377292 TTTTTAAAAATTATTAACTTAT
1 TTTTTAAAAATTACTAACTTAT
***
5377314 TTTTTAAAAATTACTCTTTTAT
1 TTTTTAAAAATTACTAACTTAT
5377336 TTTTTAA
1 TTTTTAA
5377343 GATTATCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTTAAAAATTACTAACTTAT
Found at i:5377338 original size:21 final size:22
Alignment explanation
Indices: 5377286--5377339 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
5377276 TTTAAAAAAG
*
5377286 TTATAATTTTTAAAAATTATTAAC
1 TTAT-ATTTTTAAAAATTACT-AC
5377310 TTAT-TTTTTAAAAATTACT-C
1 TTATATTTTTAAAAATTACTAC
*
5377330 TTTTATTTTT
1 TTATATTTTT
5377340 TAAGATTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 14 0.52
24 4 0.15
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATTTTTAAAAATTACTAC
Found at i:5381667 original size:16 final size:16
Alignment explanation
Indices: 5381640--5381673 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
5381630 TACACTTTTA
5381640 TAATTAATTAAT-ATT
1 TAATTAATTAATAATT
5381655 TAATTATATTAATAATT
1 TAATTA-ATTAATAATT
5381672 TA
1 TA
5381674 TAAAGTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATTAATTAATAATT
Found at i:5403766 original size:19 final size:18
Alignment explanation
Indices: 5403741--5403786 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
5403731 AAATATTGTT
5403741 AAATAAATTTAATTAAAA
1 AAATAAATTTAATTAAAA
5403759 ATAATAAA-TTAATTAAAA
1 A-AATAAATTTAATTAAAA
5403777 AAATGAAATT
1 AAAT-AAATT
5403787 GCTAACAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 15 0.60
19 7 0.28
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAATAAATTTAATTAAAA
Found at i:5407525 original size:25 final size:24
Alignment explanation
Indices: 5407496--5407567 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
5407486 AACACAGCTT
5407496 TTTTACTATT-TATAAAATATATTAA
1 TTTTA-TATTCTATAAAATATA-TAA
* *
5407521 TTTTATATTCTATATATTATATAA
1 TTTTATATTCTATAAAATATATAA
5407545 TTTT-TA-TCATATAAAAATATATA
1 TTTTATATTC-TAT-AAAATATATA
5407568 CAATATTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.05
23 5 0.12
24 19 0.47
25 14 0.35
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTATATTCTATAAAATATATAA
Found at i:5407633 original size:33 final size:32
Alignment explanation
Indices: 5407596--5407673 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
5407586 ATTAAAAAGT
**
5407596 AAATTAAATTATTTATTTTTTAAAATTTAATAA
1 AAATTAAATTATTTATAGTTTAAAATTT-ATAA
* *
5407629 AAATTAAATTA-ATATAGTTTAAAATTTTTAA
1 AAATTAAATTATTTATAGTTTAAAATTTATAA
*
5407660 AAATTATATT-TTTA
1 AAATTAAATTATTTA
5407674 AATAATAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
31 14 0.37
32 13 0.34
33 11 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (32 bp):
AAATTAAATTATTTATAGTTTAAAATTTATAA
Found at i:5407655 original size:32 final size:32
Alignment explanation
Indices: 5407596--5407665 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
5407586 ATTAAAAAGT
* **
5407596 AAATTAAATTATTTATTTTTTAAAATTTAATAA
1 AAATTAAATTATATATAGTTTAAAATTT-ATAA
*
5407629 AAATTAAATTA-ATATAGTTTAAAATTTTTAA
1 AAATTAAATTATATATAGTTTAAAATTTATAA
5407660 AAATTA
1 AAATTA
5407666 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 9 0.27
32 13 0.39
33 11 0.33
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (32 bp):
AAATTAAATTATATATAGTTTAAAATTTATAA
Found at i:5407672 original size:16 final size:15
Alignment explanation
Indices: 5407652--5407699 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
5407642 ATAGTTTAAA
5407652 ATTTTTAAAAATTAT
1 ATTTTTAAAAATTAT
*
5407667 ATTTTTAAATAA-TAA
1 ATTTTTAAA-AATTAT
5407682 ATTTATTAAAAAATTAT
1 ATTT-TT-AAAAATTAT
5407699 A
1 A
5407700 CAGATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 15 0.56
16 6 0.22
17 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTTTAAAAATTAT
Found at i:5420049 original size:15 final size:15
Alignment explanation
Indices: 5420029--5420059 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5420019 TCTCTGATCA
5420029 TAGAATGAACTTCTT
1 TAGAATGAACTTCTT
5420044 TAGAATGAACTTCTT
1 TAGAATGAACTTCTT
5420059 T
1 T
5420060 CAACTAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TAGAATGAACTTCTT
Found at i:5420578 original size:24 final size:24
Alignment explanation
Indices: 5420545--5420609 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
5420535 AATTAATATA
* *
5420545 ATATTATATATTTTAAATTTTAAT
1 ATATTTTATATTTTAAATTATAAT
*
5420569 ATATTTTATATTTTATATTATAAT
1 ATATTTTATATTTTAAATTATAAT
5420593 -TATATTTATATTATTAA
1 ATAT-TTTATATT-TTAA
5420610 TTTAAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.09
24 29 0.83
25 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATTTTATATTTTAAATTATAAT
Found at i:5420597 original size:18 final size:18
Alignment explanation
Indices: 5420574--5420611 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
5420564 TTAATATATT
5420574 TTATATTTTATATTA-TAA
1 TTATA-TTTATATTATTAA
5420592 TTATATTTATATTATTAA
1 TTATATTTATATTATTAA
5420610 TT
1 TT
5420612 TAAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATATTTATATTATTAA
Found at i:5422468 original size:28 final size:28
Alignment explanation
Indices: 5422428--5422482 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
5422418 TTTAATTTTA
5422428 ACAAGTACTAGCATCCATATTTTCCCTT
1 ACAAGTACTAGCATCCATATTTTCCCTT
5422456 ACAAGTACTAGCATCCATATTTTCCCT
1 ACAAGTACTAGCATCCATATTTTCCCT
5422483 CTTTTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.35
Consensus pattern (28 bp):
ACAAGTACTAGCATCCATATTTTCCCTT
Found at i:5423589 original size:46 final size:45
Alignment explanation
Indices: 5423524--5423623 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 45
5423514 TTTTTATATC
* * *
5423524 AATATAAATTTTTTAAAAAAATTATTAAATAATAAAAAATACTTTT
1 AATAAAAATTTTTTAAAAAAATTATCAAACAATAAAAAATA-TTTT
5423570 AATAAAAACTTTTTT-AAAAAATTATCAAACAATAAAAAATATTTT
1 AATAAAAA-TTTTTTAAAAAAATTATCAAACAATAAAAAATATTTT
5423615 -ATACAAAAT
1 AATA-AAAAT
5423624 CGTGCAAGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
44 4 0.08
45 8 0.16
46 31 0.63
47 6 0.12
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (45 bp):
AATAAAAATTTTTTAAAAAAATTATCAAACAATAAAAAATATTTT
Found at i:5430218 original size:15 final size:16
Alignment explanation
Indices: 5430198--5430239 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
5430188 TTGAATTTTT
5430198 TTTATTAATTT-TATA
1 TTTATTAATTTATATA
*
5430213 TTTATTATTTTTAATATA
1 TTTATTA-ATTT-ATATA
5430231 TTTATTAAT
1 TTTATTAAT
5430240 ATTTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 7 0.32
16 3 0.14
17 1 0.05
18 11 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTAATTTATATA
Found at i:5433723 original size:20 final size:22
Alignment explanation
Indices: 5433676--5433723 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
5433666 GTAATATAAT
5433676 ATATATATATATAAAGTAATTA
1 ATATATATATATAAAGTAATTA
* *
5433698 AAATATA-ATATAAA-TTATTA
1 ATATATATATATAAAGTAATTA
5433718 ATATAT
1 ATATAT
5433724 TAAAATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 10 0.43
21 7 0.30
22 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATATATATATAAAGTAATTA
Found at i:5433918 original size:24 final size:25
Alignment explanation
Indices: 5433884--5433939 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
5433874 TATTTAAGAG
*
5433884 ATAATATTATTT-AATTAAA-ATTAA
1 ATAATAATATTTAAATTAAATA-TAA
*
5433908 ATAATAATATTTAAATTTAATATAA
1 ATAATAATATTTAAATTAAATATAA
5433933 ATAATAA
1 ATAATAA
5433940 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 11 0.39
25 16 0.57
26 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATAATAATATTTAAATTAAATATAA
Found at i:5433938 original size:22 final size:20
Alignment explanation
Indices: 5433895--5433947 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
5433885 TAATATTATT
*
5433895 TAATTAAAATTAAATAATAA
1 TAATTAAATTTAAATAATAA
*
5433915 TATTTAAATTTAATATAAATAA
1 TAATTAAATTTAA-AT-AATAA
*
5433937 TAAATAAATTT
1 TAATTAAATTT
5433948 TAATTTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.41
21 2 0.07
22 14 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATTAAATTTAAATAATAA
Found at i:5433957 original size:22 final size:22
Alignment explanation
Indices: 5433909--5433958 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5433899 TAAAATTAAA
**
5433909 TAATAATATTTAAATTTAATAT
1 TAATAATAAATAAATTTAATAT
*
5433931 AAATAATAAATAAATTTTAAT-T
1 TAATAATAAATAAA-TTTAATAT
5433953 TAATAA
1 TAATAA
5433959 CTATTATGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATAATAAATAAATTTAATAT
Found at i:5434364 original size:2 final size:2
Alignment explanation
Indices: 5434359--5434384 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5434349 TTCAAATGTA
5434359 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
5434385 TGGCATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5451329 original size:3 final size:3
Alignment explanation
Indices: 5451321--5451355 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5451311 TACATATAAA
*
5451321 GAT GAT GAT GAC GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
5451356 AGAAGGGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:5451813 original size:3 final size:3
Alignment explanation
Indices: 5451805--5451832 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5451795 AGATCTGCTA
5451805 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5451833 GTCTAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5454083 original size:3 final size:3
Alignment explanation
Indices: 5454075--5454112 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5454065 TAAAAGTTTT
5454075 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5454113 TAAATAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5456629 original size:41 final size:41
Alignment explanation
Indices: 5456584--5456662 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 41
5456574 AGATAATATA
*
5456584 TTTAAATAT-AATTAATATAATATATTTA-ATATATATTTTAT
1 TTTAAATATAAATAAATATAATA-ATTTATAT-TATATTTTAT
* *
5456625 TTTAAATTTAAATAAATTTAATAATTTATATTATATTT
1 TTTAAATATAAATAAATATAATAATTTATATTATATTT
5456663 ATAATTATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 20 0.61
42 13 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (41 bp):
TTTAAATATAAATAAATATAATAATTTATATTATATTTTAT
Found at i:5456666 original size:18 final size:18
Alignment explanation
Indices: 5456590--5456668 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
5456580 TATATTTAAA
* *
5456590 TATAATTAATATAATATAT
1 TATAATTTATATTATAT-T
* *
5456609 T-TAATATATATTTTATT
1 TATAATTTATATTATATT
* *
5456626 T-TAAATTTA-AATAAATT
1 TAT-AATTTATATTATATT
5456643 TAATAATTTATATTATATT
1 T-ATAATTTATATTATATT
5456662 TATAATT
1 TATAATT
5456669 ATACAATAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
17 9 0.20
18 28 0.61
19 9 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATAATTTATATTATATT
Found at i:5457405 original size:35 final size:35
Alignment explanation
Indices: 5457351--5457419 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
5457341 AATATAATTT
*
5457351 TTTTAAAATTAATAAAAATAATTATTTTGTATTATA
1 TTTTAAAATTAATAAAAATAATTATTAT-TATTATA
* * *
5457387 TTTT-AAATTATTATAAATATTTATTATTATTAT
1 TTTTAAAATTAATAAAAATAATTATTATTATTAT
5457420 TATAATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 6 0.21
35 19 0.66
36 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (35 bp):
TTTTAAAATTAATAAAAATAATTATTATTATTATA
Found at i:5457415 original size:19 final size:19
Alignment explanation
Indices: 5457393--5457443 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5457383 TATATTTTAA
5457393 ATTATTATAAATATTTATT
1 ATTATTATAAATATTTATT
*
5457412 ATTATTAT-TATAATTTATT
1 ATTATTATAAAT-ATTTATT
5457431 A-TATTTATAAATA
1 ATTA-TTATAAATA
5457444 AAATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 4 0.15
19 21 0.78
20 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTATTATAAATATTTATT
Found at i:5463196 original size:3 final size:3
Alignment explanation
Indices: 5463188--5463221 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5463178 CTGCCTGCAA
5463188 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5463222 CGTAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5463327 original size:16 final size:16
Alignment explanation
Indices: 5463308--5463406 Score: 74
Period size: 16 Copynumber: 6.1 Consensus size: 16
5463298 ATATTTGATT
* *
5463308 TAAAATAATATTTTAA
1 TAAAATAATAATATAA
* * *
5463324 TAAAATAATTATTTTA
1 TAAAATAATAATATAA
*
5463340 TAAAAATAA-AATAAAA
1 T-AAAATAATAATATAA
*
5463356 TAAAATAAAAATATAA
1 TAAAATAATAATATAA
*
5463372 TAAAATAATTATAATAA
1 TAAAATAATAAT-ATAA
** *
5463389 TAATTTAATTATATAA
1 TAAAATAATAATATAA
5463405 TA
1 TA
5463407 TTATTAATAT
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
15 7 0.10
16 40 0.59
17 21 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAATAATAATATAA
Found at i:5463350 original size:5 final size:5
Alignment explanation
Indices: 5463342--5463379 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
5463332 TTATTTTATA
*
5463342 AAAAT AAAAT AAAAT AAAAT AAAAAT ATAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AA
5463380 TTATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:5463353 original size:11 final size:11
Alignment explanation
Indices: 5463339--5463376 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
5463329 TAATTATTTT
5463339 ATAAAAATAAA
1 ATAAAAATAAA
5463350 AT-AAAATAAA
1 ATAAAAATAAA
*
5463360 ATAAAAATATA
1 ATAAAAATAAA
5463371 ATAAAA
1 ATAAAA
5463377 TAATTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:5463365 original size:21 final size:21
Alignment explanation
Indices: 5463339--5463379 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5463329 TAATTATTTT
5463339 ATAAAAATAAAATAAAATAAA
1 ATAAAAATAAAATAAAATAAA
*
5463360 ATAAAAATATAATAAAATAA
1 ATAAAAATAAAATAAAATAA
5463380 TTATAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (21 bp):
ATAAAAATAAAATAAAATAAA
Found at i:5463385 original size:11 final size:11
Alignment explanation
Indices: 5463342--5463392 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 11
5463332 TTATTTTATA
5463342 AAAATAA-AAT
1 AAAATAATAAT
5463352 AAAATAA-AAT
1 AAAATAATAAT
5463362 AAAA-ATATAAT
1 AAAATA-ATAAT
*
5463373 AAAATAATTAT
1 AAAATAATAAT
5463384 AATAATAAT
1 AA-AATAAT
5463393 TTAATTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
9 1 0.03
10 15 0.42
11 13 0.36
12 7 0.19
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:5463413 original size:17 final size:16
Alignment explanation
Indices: 5463366--5463419 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
5463356 TAAAATAAAA
**
5463366 ATATAATAAAATAATT
1 ATATAATAATTTAATT
5463382 ATAATAATAATTTAATT
1 AT-ATAATAATTTAATT
*
5463399 ATATAATATTATTAA-T
1 ATATAATAAT-TTAATT
5463415 ATATA
1 ATATA
5463420 TTTAAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 15 0.45
17 18 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAATAATTTAATT
Found at i:5463570 original size:16 final size:17
Alignment explanation
Indices: 5463542--5463583 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
5463532 AAAATAGAAT
*
5463542 TAAAATAAATTATTTTA
1 TAAAATAAATTATTTAA
5463559 TAAAAT-AATTATTTAA
1 TAAAATAAATTATTTAA
*
5463575 TAAATTAAA
1 TAAAATAAA
5463584 CAACCGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATAAATTATTTAA
Found at i:5464246 original size:7 final size:7
Alignment explanation
Indices: 5464234--5464258 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5464224 AACAACTGGC
5464234 AAATGGA
1 AAATGGA
5464241 AAATGGA
1 AAATGGA
5464248 AAATGGA
1 AAATGGA
5464255 AAAT
1 AAAT
5464259 CAATTTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (7 bp):
AAATGGA
Found at i:5470285 original size:40 final size:40
Alignment explanation
Indices: 5470170--5470289 Score: 113
Period size: 40 Copynumber: 3.0 Consensus size: 40
5470160 TTTTTTAATA
* *
5470170 TTAATTAATTATTAATAAAATATTATTTTTAAATTAAA-TT
1 TTAATTAATTATTAATAATAT-TTAATTTTAAATTAAATTT
* * ***
5470210 TT-ATTAAATAATAA-AAT-TTTAATTCTTTCTTTTAAATTT
1 TTAATTAATTATTAATAATATTTAA-T-TTTAAATTAAATTT
*
5470249 TTAATTAATTATTAATATTATTTAATTTTAAATTAAATTT
1 TTAATTAATTATTAATAATATTTAATTTTAAATTAAATTT
5470289 T
1 T
5470290 ATTTAATAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
36 3 0.05
37 2 0.03
38 10 0.16
39 14 0.23
40 24 0.39
41 3 0.05
42 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (40 bp):
TTAATTAATTATTAATAATATTTAATTTTAAATTAAATTT
Found at i:5470294 original size:16 final size:17
Alignment explanation
Indices: 5470275--5470316 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5470265 ATTATTTAAT
5470275 TTTAAATTAAATTT-TA
1 TTTAAATTAAATTTATA
* *
5470291 TTTAATAATAATTTTATA
1 TTTAA-ATTAAATTTATA
5470309 TTTAAATT
1 TTTAAATT
5470317 TTTATAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 5 0.24
17 9 0.43
18 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTAAATTTATA
Found at i:5470296 original size:39 final size:38
Alignment explanation
Indices: 5470173--5470292 Score: 109
Period size: 39 Copynumber: 3.1 Consensus size: 38
5470163 TTTAATATTA
* *
5470173 ATTAATTATTAATAAAATATTATTTTTAAATTAAATTTT
1 ATTAATTATTAATAATAT-TTAATTTTAAATTAAATTTT
* * ***
5470212 ATTAAATAATAA-AAT-TTTAATTCTTTCTTTTAAATTTTT
1 ATTAATTATTAATAATATTTAA-T-TTTAAATTAAA-TTTT
*
5470251 AATTAATTATTAATATTATTTAATTTTAAATTAAATTTT
1 -ATTAATTATTAATAATATTTAATTTTAAATTAAATTTT
5470290 ATT
1 ATT
5470293 TAATAATAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
36 3 0.05
37 2 0.03
38 13 0.21
39 18 0.29
40 18 0.29
41 3 0.05
42 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (38 bp):
ATTAATTATTAATAATATTTAATTTTAAATTAAATTTT
Found at i:5470302 original size:28 final size:28
Alignment explanation
Indices: 5470271--5470349 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
5470261 TAATATTATT
* *
5470271 TAATTTTA-AATTAAATTTTATTTAATAA
1 TAATTTTATAATTAAATTTT-TATAAAAA
*
5470299 TAATTTTATATTTAAATTTTTATAAAAA
1 TAATTTTATAATTAAATTTTTATAAAAA
** * *
5470327 TAATTAAATAATAAAATATTTAT
1 TAATTTTATAATTAAATTTTTAT
5470350 TTTTTTTTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 32 0.76
29 10 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TAATTTTATAATTAAATTTTTATAAAAA
Found at i:5470721 original size:8 final size:8
Alignment explanation
Indices: 5470698--5470732 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
5470688 ATACTAAATT
5470698 AAATATAAA
1 AAAT-TAAA
5470707 AAA-TAAA
1 AAATTAAA
5470714 AAATTAAA
1 AAATTAAA
5470722 AAATTAAA
1 AAATTAAA
5470730 AAA
1 AAA
5470733 AATTAGAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.28
8 15 0.60
9 3 0.12
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAATTAAA
Found at i:5472666 original size:21 final size:22
Alignment explanation
Indices: 5472642--5472685 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
5472632 TCAATGTTTG
5472642 AAGTTCGATTTT-AATTTAATT
1 AAGTTCGATTTTAAATTTAATT
**
5472663 AAGTTTTATTTTAAAATTTAATT
1 AAGTTCGATTTT-AAATTTAATT
5472686 TTAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (22 bp):
AAGTTCGATTTTAAATTTAATT
Found at i:5472687 original size:18 final size:19
Alignment explanation
Indices: 5472650--5472697 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
5472640 TGAAGTTCGA
5472650 TTTTAATTT--AA-TTAAG
1 TTTTAATTTAAAATTTAAG
*
5472666 TTTTATTTTAAAATTTAA-
1 TTTTAATTTAAAATTTAAG
5472684 TTTTAATTTAAAAT
1 TTTTAATTTAAAAT
5472698 AAAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.30
18 15 0.56
19 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTAATTTAAAATTTAAG
Found at i:5476823 original size:15 final size:17
Alignment explanation
Indices: 5476790--5476830 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
5476780 ATTATTATCA
5476790 TATATTTTACACATATAT
1 TATA-TTTACACATATAT
5476808 TATATTTACA-AT-TAT
1 TATATTTACACATATAT
*
5476823 TTTATTTA
1 TATATTTA
5476831 ATAATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 10 0.45
16 2 0.09
17 6 0.27
18 4 0.18
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTTACACATATAT
Found at i:5476870 original size:23 final size:21
Alignment explanation
Indices: 5476809--5476870 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
5476799 CACATATATT
*
5476809 ATATTTACAATTATTTTATTTA
1 ATATTTA-AATTATTTAATTTA
* *
5476831 ATAATTTATATTTTTTAATTTTA
1 AT-ATTTAAATTATTTAA-TTTA
5476854 ATATGTTAAATTATTTA
1 ATAT-TTAAATTATTTA
5476871 TATCGTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATTTAAATTATTTAATTTA
Found at i:5477263 original size:17 final size:16
Alignment explanation
Indices: 5477235--5477272 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
5477225 GAATTTAATT
5477235 ATTTTAAAATTAAATTAA
1 ATTTTAAAATT-AA-TAA
5477253 ATTTT-AAATTAATAA
1 ATTTTAAAATTAATAA
5477268 ATTTT
1 ATTTT
5477273 TTAATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 2 0.10
17 5 0.25
18 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAAATTAATAA
Found at i:5480770 original size:2 final size:2
Alignment explanation
Indices: 5480757--5480786 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5480747 GCATACATAC
*
5480757 AT AT AC 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
5480787 TCTAAATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5484201 original size:2 final size:2
Alignment explanation
Indices: 5484194--5484223 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5484184 TGAAACACAA
5484194 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5484224 ATTGTTGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5494417 original size:26 final size:26
Alignment explanation
Indices: 5494386--5494437 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5494376 AATGACACTG
5494386 ATAATTT-TATCATATTTTTTGATATT
1 ATAATTTATATCATATTTTTT-ATATT
* *
5494412 ATAATTTATTTTATATTTTTTATATT
1 ATAATTTATATCATATTTTTTATATT
5494438 TTCATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
ATAATTTATATCATATTTTTTATATT
Found at i:5495056 original size:23 final size:23
Alignment explanation
Indices: 5495018--5495062 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
5495008 ATATAATTAT
5495018 TTTAAAATTTTAATATTTTATAAA
1 TTTAAAATTTTAATA-TTTATAAA
5495042 TTTAAAA-TTTAATATTTATAA
1 TTTAAAATTTTAATATTTATAA
5495063 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.33
23 7 0.33
24 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAAATTTTAATATTTATAAA
Found at i:5495233 original size:23 final size:24
Alignment explanation
Indices: 5495192--5495253 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
5495182 TTTTTAAAAT
*
5495192 ATTATTTAGTTATCAAT-AAATAA
1 ATTATTTATTTATCAATAAAATAA
* **
5495215 GTTATTTATTTATTGATAAAAATAA
1 ATTATTTATTTATCAAT-AAAATAA
5495240 ATTGATTTATTTAT
1 ATT-ATTTATTTAT
5495254 AAGGAATCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 13 0.42
25 8 0.26
26 10 0.32
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (24 bp):
ATTATTTATTTATCAATAAAATAA
Found at i:5496719 original size:19 final size:19
Alignment explanation
Indices: 5496676--5496731 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
5496666 ATGACTCAAG
5496676 ATTTCTTTAATTT-TTTAAA
1 ATTT-TTTAATTTATTTAAA
* *
5496695 AGTTTTTAATTTATTTATA
1 ATTTTTTAATTTATTTAAA
*
5496714 ATTTTTTTATTTAATTTA
1 ATTTTTTAATTT-ATTTA
5496732 CTTATTTGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 8 0.26
19 18 0.58
20 5 0.16
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTTTTAATTTATTTAAA
Found at i:5497383 original size:2 final size:2
Alignment explanation
Indices: 5497376--5497433 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
5497366 TACTTATAAC
5497376 AT AT AT AT 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 AT AT AT AT
5497418 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
5497434 GCACACACAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5498026 original size:5 final size:5
Alignment explanation
Indices: 5498018--5498046 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5498008 CTTTTTCTTT
5498018 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
5498047 TAATCGTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:5498617 original size:30 final size:32
Alignment explanation
Indices: 5498581--5498647 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
5498571 TATATTTAAA
5498581 ATAAAAT-TAAT-TATTAATATATAAAAAA-AT
1 ATAAAATATAATAT-TTAATATATAAAAAATAT
*
5498611 ATAAAATATAATATTTTATATATAAAAAATAT
1 ATAAAATATAATATTTAATATATAAAAAATAT
5498643 ATAAA
1 ATAAA
5498648 CACAAACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 7 0.21
31 18 0.55
32 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (32 bp):
ATAAAATATAATATTTAATATATAAAAAATAT
Found at i:5498701 original size:17 final size:19
Alignment explanation
Indices: 5498681--5498715 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5498671 TTTCTTTCTT
5498681 TCCTTT-TTT-ATTTTTTC
1 TCCTTTCTTTCATTTTTTC
5498698 TCCTTTCTTTCATTTTTT
1 TCCTTTCTTTCATTTTTT
5498716 TTTCAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (19 bp):
TCCTTTCTTTCATTTTTTC
Found at i:5498703 original size:22 final size:23
Alignment explanation
Indices: 5498661--5498704 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5498651 AAACATATAA
*
5498661 TTTTTTTCTTTTTCTTTCTTTCC
1 TTTTTTTCTTTTTCTTCCTTTCC
5498684 TTTTTTAT-TTTTTC-TCCTTTC
1 TTTTTT-TCTTTTTCTTCCTTTC
5498705 TTTCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 12 0.63
24 1 0.05
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTTCTTTTTCTTCCTTTCC
Found at i:5499821 original size:2 final size:2
Alignment explanation
Indices: 5499814--5499843 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5499804 ATTAAAGCTC
5499814 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
5499844 TAAATATTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5516011 original size:3 final size:3
Alignment explanation
Indices: 5516003--5516028 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5515993 CTCATTTGAT
5516003 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5516029 TTGTACTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5516516 original size:20 final size:21
Alignment explanation
Indices: 5516465--5516518 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
5516455 AAATTTATTT
*
5516465 TAATATTAATATATAAAATAATA
1 TAATATT-AT-TATAAAATAAAA
* *
5516488 TCATCTTATTAT-AAATAAAA
1 TAATATTATTATAAAATAAAA
5516508 TAATATTATTA
1 TAATATTATTA
5516519 ATTTATTTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 2 0.08
23 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATATTATTATAAAATAAAA
Found at i:5516524 original size:25 final size:25
Alignment explanation
Indices: 5516460--5516524 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
5516450 TTTTTAAATT
*
5516460 TATT-TTAATATTAATATATAAAATAA
1 TATTATTAAT-TT-ATAAATAAAATAA
* *
5516486 TATCATCTTA-TTATAAATAAAATAA
1 TATTAT-TAATTTATAAATAAAATAA
5516511 TATTATTAATTTAT
1 TATTATTAATTTAT
5516525 TTACATTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
24 2 0.06
25 21 0.68
26 5 0.16
27 1 0.03
28 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTATTAATTTATAAATAAAATAA
Found at i:5517135 original size:30 final size:29
Alignment explanation
Indices: 5517094--5517188 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 29
5517084 TTAAATATTA
*
5517094 ATTTATATATAAATTAAAAGTAAAAAATTT
1 ATTTA-ATATAAATTAAAAATAAAAAATTT
* * *
5517124 ATTTAAGTATAAGTTAAAAATTATAAATTT
1 ATTTAA-TATAAATTAAAAATAAAAAATTT
*
5517154 ATTTGAATGTAAATTAAAAATTAAAAAA-TT
1 ATTT-AATATAAATTAAAAA-TAAAAAATTT
5517184 ATTTA
1 ATTTA
5517189 TATGTAATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
29 2 0.04
30 45 0.83
31 7 0.13
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (29 bp):
ATTTAATATAAATTAAAAATAAAAAATTT
Found at i:5517194 original size:30 final size:29
Alignment explanation
Indices: 5517081--5517202 Score: 101
Period size: 30 Copynumber: 4.1 Consensus size: 29
5517071 TTTTTATATT
* *
5517081 AAATT-AAATATTAATTTATATATAAATT-A
1 AAATTAAAAAATT-ATTTA-ATGTAAATTAA
*
5517110 AAAGTAAAAAATTTATTTAA-GTATAAGTTAA
1 AAATTAAAAAA-TTATTTAATGTA-AA-TTAA
* *
5517141 AAATTATAAATTTATTTGAATGTAAATTAA
1 AAATTAAAAAATTATTT-AATGTAAATTAA
5517171 AAATTAAAAAATTATTTATATGT-AA-TAA
1 AAATTAAAAAATTATTTA-ATGTAAATTAA
5517199 AAAT
1 AAAT
5517203 ATCAAATTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
28 9 0.12
29 10 0.13
30 40 0.52
31 15 0.19
32 3 0.04
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (29 bp):
AAATTAAAAAATTATTTAATGTAAATTAA
Found at i:5521163 original size:9 final size:9
Alignment explanation
Indices: 5521151--5521176 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5521141 AAACTATCAA
5521151 GAGCAAGTC
1 GAGCAAGTC
5521160 GAGCAAGTC
1 GAGCAAGTC
5521169 GAGCAAGT
1 GAGCAAGT
5521177 GCAGTGACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.35, T:0.12
Consensus pattern (9 bp):
GAGCAAGTC
Found at i:5522583 original size:17 final size:17
Alignment explanation
Indices: 5522561--5522599 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5522551 ATTCAATTTT
*
5522561 TTAAAAAATATATTAAA
1 TTAAAAAATAAATTAAA
**
5522578 TTAAAATTTAAATTAAA
1 TTAAAAAATAAATTAAA
5522595 TTAAA
1 TTAAA
5522600 TTATTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAAATAAATTAAA
Found at i:5522927 original size:15 final size:13
Alignment explanation
Indices: 5522900--5522980 Score: 52
Period size: 13 Copynumber: 6.6 Consensus size: 13
5522890 TAATATTTAA
5522900 TATATTAATAATT
1 TATATTAATAATT
*
5522913 TATATTATATAAAT
1 TATATTA-ATAATT
5522927 T-TA--AATATATT
1 TATATTAATA-ATT
*
5522938 TTTATT-A-AATT
1 TATATTAATAATT
5522949 TATATTATATAA-T
1 TATATTA-ATAATT
*
5522962 TATA-TAATATTT
1 TATATTAATAATT
5522974 TAT-TTAA
1 TATATTAA
5522981 ATTTAATATT
Statistics
Matches: 54, Mismatches: 4, Indels: 21
0.68 0.05 0.27
Matches are distributed among these distances:
10 3 0.06
11 15 0.28
12 12 0.22
13 16 0.30
14 8 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATTAATAATT
Found at i:5522956 original size:36 final size:35
Alignment explanation
Indices: 5522909--5522992 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 35
5522899 ATATATTAAT
5522909 AATTTATATTATATAAATTTAAAT-ATATTTT-TATTA
1 AATTTATATTATAT-AA-TTAAATAATATTTTAT-TTA
*
5522945 AATTTATATTATATAATTATATAATATTTTATTTA
1 AATTTATATTATATAATTAAATAATATTTTATTTA
5522980 AATTTAATATTAT
1 AATTT-ATATTAT
5522993 CATATTACAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
34 5 0.11
35 17 0.39
36 22 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
AATTTATATTATATAATTAAATAATATTTTATTTA
Found at i:5522957 original size:22 final size:22
Alignment explanation
Indices: 5522917--5522973 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
5522907 ATAATTTATA
5522917 TTATATAAATTTAAATATATTT
1 TTATATAAATTTAAATATATTT
* **
5522939 TTAT-TAAATTTATATTATATAA
1 TTATATAAATTTA-AATATATTT
5522961 TTATATAATATTT
1 TTATATAA-ATTT
5522974 TATTTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 8 0.28
22 14 0.48
23 3 0.10
24 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATATAAATTTAAATATATTT
Found at i:5523009 original size:34 final size:32
Alignment explanation
Indices: 5522909--5523009 Score: 96
Period size: 36 Copynumber: 2.9 Consensus size: 32
5522899 ATATATTAAT
*
5522909 AATTTATATTATATAAATTTAAATATATTTTTATTA
1 AATTTATATTATAT-AA-TT--ACATATTTTTATTA
*
5522945 AATTTATATTATATAATTATATAATATTTTATTTA
1 AATTTATATTATATAATTACAT-AT-TTTTA-TTA
5522980 AATTTAATATTATCAT-ATTACATATTTTTA
1 AATTT-ATATTAT-ATAATTACATATTTTTA
5523010 AGAAAAGTTA
Statistics
Matches: 59, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
32 4 0.07
33 2 0.03
34 12 0.20
35 12 0.20
36 27 0.46
37 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
AATTTATATTATATAATTACATATTTTTATTA
Found at i:5523295 original size:15 final size:16
Alignment explanation
Indices: 5523268--5523297 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5523258 GTTAATAAAA
5523268 ATTTATCTTTTCAAAT
1 ATTTATCTTTTCAAAT
5523284 ATTTAT-TTTTCAAA
1 ATTTATCTTTTCAAA
5523298 GCCACGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTATCTTTTCAAAT
Found at i:5531400 original size:35 final size:38
Alignment explanation
Indices: 5531338--5531409 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 38
5531328 TGATTTTTAT
5531338 TTATTATTTTTAATATATTAAATAAAATATTATTATTA
1 TTATTATTTTTAATATATTAAATAAAATATTATTATTA
*
5531376 TTATTATTTTATAAT-T-TT-AA-AAAATATTTTTATT
1 TTATTATTTT-TAATATATTAAATAAAATATTATTATT
5531410 GAAAAGGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 13 0.41
36 2 0.06
37 2 0.06
38 11 0.34
39 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (38 bp):
TTATTATTTTTAATATATTAAATAAAATATTATTATTA
Found at i:5534422 original size:2 final size:2
Alignment explanation
Indices: 5534415--5534439 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5534405 AAAACATTTT
5534415 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
5534440 ATAACAAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5535588 original size:14 final size:14
Alignment explanation
Indices: 5535569--5535598 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5535559 TGAAACTCTG
5535569 AAATGACATGGACT
1 AAATGACATGGACT
5535583 AAATGACATGGACT
1 AAATGACATGGACT
5535597 AA
1 AA
5535599 GGCGTACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (14 bp):
AAATGACATGGACT
Done.