Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold300
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: 551762
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 31891 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:292 original size:43 final size:42
Alignment explanation
Indices: 214--352 Score: 215
Period size: 42 Copynumber: 3.3 Consensus size: 42
204 NNNNNNNNNN
* * *
214 TCTTAAGCGGTGCTTAGAAAAAAACGCCTCTAAAGACCGTGT
1 TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCGTGT
256 TCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGACCGTGT
1 TCTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGACCGTGT
* * *
299 TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGG
1 TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCGTGT
341 TCTTTAGCGGCG
1 TCTTTAGCGGCG
353 TTTTTTTTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
42 49 0.54
43 41 0.46
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (42 bp):
TCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCGTGT
Found at i:10398 original size:20 final size:20
Alignment explanation
Indices: 10371--10414 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
10361 TTTTTAATGG
10371 TTTTTAAAAT-TTTATAA-TA
1 TTTTTAAAATGTTT-TAACTA
10390 TTTTCTAAAATGTTTTAACTA
1 TTTT-TAAAATGTTTTAACTA
10411 TTTT
1 TTTT
10415 GGTCGTCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 9 0.41
21 9 0.41
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTTAAAATGTTTTAACTA
Found at i:15673 original size:20 final size:20
Alignment explanation
Indices: 15650--15699 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
15640 TTTATAATTT
* *
15650 ATATCTATATATCTATATAC
1 ATATCTATATATATATACAC
* *
15670 ATATTTATACATATATACAC
1 ATATCTATATATATATACAC
*
15690 ATACCTATAT
1 ATATCTATAT
15700 GTTTTATATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATCTATATATATATACAC
Found at i:16028 original size:39 final size:33
Alignment explanation
Indices: 15951--16015 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
15941 TTGCTCATCT
15951 TTATTTTTATGAAATGCTTTAGTTCTTTTTACA
1 TTATTTTTATGAAATGCTTTAGTTCTTTTTACA
15984 TTATTTTTATGAAATGCTTTAGTTCTTTTTAC
1 TTATTTTTATGAAATGCTTTAGTTCTTTTTAC
16016 TTACTCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58
Consensus pattern (33 bp):
TTATTTTTATGAAATGCTTTAGTTCTTTTTACA
Found at i:20555 original size:16 final size:17
Alignment explanation
Indices: 20534--20566 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20524 ACAAACAAAC
20534 GAAAAG-AGAAAGAAAA
1 GAAAAGAAGAAAGAAAA
*
20550 GAAAAGAAGAATGAAAA
1 GAAAAGAAGAAAGAAAA
20567 AAGAAAAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (17 bp):
GAAAAGAAGAAAGAAAA
Found at i:21111 original size:97 final size:97
Alignment explanation
Indices: 21004--21193 Score: 244
Period size: 97 Copynumber: 2.0 Consensus size: 97
20994 TTCATTTTGA
* **
21004 ATCTTAGCAAAATTCGCTGT-TC-TGCTTAATTTATTTGTTTAGAGCTCTGCTCTCAATAAAATT
1 ATCTTAGCAAAATTCG-T-TATCTTGATTAATTTATTCATTTAGAGCTCTGCTCTCAATAAAATT
21067 TCATCTT-TCCCACTA-TGATAATCTTTTTCATCTT
64 TCATCTTAT-CCA-TATTGATAATCTTTTTCATCTT
* * * * *
21101 ATCTTAGCAAAATTTGTTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTTAATAAAATTTC
1 ATCTTAGCAAAATTCGTTATCTTGATTAATTTATTCATTTAGAGCTCTGCTCTCAATAAAATTTC
21166 ATCTTATCCATATTGATAATCTTTTTCA
66 ATCTTATCCATATTGATAATCTTTTTCA
21194 AGCATTTTAC
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
95 1 0.01
96 5 0.06
97 74 0.91
98 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (97 bp):
ATCTTAGCAAAATTCGTTATCTTGATTAATTTATTCATTTAGAGCTCTGCTCTCAATAAAATTTC
ATCTTATCCATATTGATAATCTTTTTCATCTT
Found at i:22134 original size:46 final size:46
Alignment explanation
Indices: 22081--22614 Score: 771
Period size: 46 Copynumber: 11.7 Consensus size: 46
22071 AGTGGACTAG
*
22081 AGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGAAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
22127 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
22173 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* *
22219 AGATAGCAGATCTTGTTTTCCTGTATTTGGCAGC-AGAGTAGATCAT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGT
* * *
22265 AGATAGCAGATCTTGTCTTCTTATATTTGGCAGCGGAA-TAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGC-GAAGTAGATCGT
*
22311 AGATAGCAGATCTTGCCTTCCTGTATTTGGCAGCG-A--AG--CGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
*
22352 AGATAGCAGATCTTGTCTTTCTGTATTTGGCAGCGAAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* * * * *
22398 AGATAACAGATCTTGTCTTCCTGTATTTGGTAGAGGAGTAGATCAT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* *
22444 AGATAGCAGATCTTGTCTTCTTGTATTTGGCAGC-AGAGTAGATCGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGT
* * *
22490 AGATAGCAGATATTGTCTTCCTGTATTTGGCAGCGAAGTAGATTGA
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
* **
22536 AGATAACAGATCTTGTCTTCCTGTATTTGGCA-ATAGAGTAGATCGT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGA-AGTAGATCGT
*
22582 AGATAGTAGATCTTGTCTTCCTGTATTTGGCAG
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAG
22615 TGGAGTAGGT
Statistics
Matches: 438, Mismatches: 38, Indels: 23
0.88 0.08 0.05
Matches are distributed among these distances:
41 35 0.08
42 1 0.00
43 2 0.00
44 3 0.01
45 3 0.01
46 391 0.89
47 2 0.00
48 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.34
Consensus pattern (46 bp):
AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGT
Found at i:26154 original size:16 final size:16
Alignment explanation
Indices: 26133--26164 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
26123 CATGTGACCG
26133 TAATCCTTCCTCGTGC
1 TAATCCTTCCTCGTGC
26149 TAATCCTTCCTCGTGC
1 TAATCCTTCCTCGTGC
26165 GTAACCGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.38, G:0.12, T:0.38
Consensus pattern (16 bp):
TAATCCTTCCTCGTGC
Found at i:29646 original size:22 final size:21
Alignment explanation
Indices: 29608--29648 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29598 AGATTATTAT
**
29608 CTCTTTTTCTTCTTTTGTTGA
1 CTCTTTTTCTTAGTTTGTTGA
29629 CTCTTTTTCATTAGTTTGTT
1 CTCTTTTTC-TTAGTTTGTT
29649 ATTTCTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.07, C:0.17, G:0.10, T:0.66
Consensus pattern (21 bp):
CTCTTTTTCTTAGTTTGTTGA
Found at i:30049 original size:28 final size:28
Alignment explanation
Indices: 29985--30049 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 28
29975 TTTTATACTG
29985 TTTAATATAACTTTAATAGTTTTTAATTT
1 TTTAA-ATAACTTTAATAGTTTTTAATTT
* * *
30014 TTAAAAATAA-TTTTATATTTTTTGAATTT
1 TT-TAAATAACTTTAATAGTTTTT-AATTT
30043 TTTAAAT
1 TTTAAAT
30050 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
28 15 0.50
29 13 0.43
30 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTAAATAACTTTAATAGTTTTTAATTT
Found at i:38063 original size:140 final size:141
Alignment explanation
Indices: 37893--38173 Score: 555
Period size: 140 Copynumber: 2.0 Consensus size: 141
37883 TTTATATTTC
37893 ACTTTAATATTTAACAATAATAAGTTAATTAATATAATATTAAATTTAAATAAAATGGTTATTTT
1 ACTTTAATATTTAACAATAATAAGTTAATTAATATAATATTAAATTTAAATAAAATGGTTATTTT
37958 ATAAAATAATTGTTTTTTCATTTATGATATATGGACTTTTATTTCTCAAGTTTTTATAAAATAAG
66 ATAAAATAATTGTTTTTTCATTTATGATATATGGACTTTTATTTCTCAAGTTTTTATAAAATAAG
38023 GCTGTTAGGGT
131 GCTGTTAGGGT
38034 ACTTTAATA-TTAACAATAATAAGTTAATTAATATAATATTAAATTTAAATAAAATGGTTATTTT
1 ACTTTAATATTTAACAATAATAAGTTAATTAATATAATATTAAATTTAAATAAAATGGTTATTTT
38098 ATAAAATAATTGTTTTTTCATTTATGATATATGGACTTTTATTTCTCAAGTTTTTATAAAATAAG
66 ATAAAATAATTGTTTTTTCATTTATGATATATGGACTTTTATTTCTCAAGTTTTTATAAAATAAG
38163 GCTGTTAGGGT
131 GCTGTTAGGGT
38174 TGTTGCGTAT
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
140 131 0.94
141 9 0.06
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (141 bp):
ACTTTAATATTTAACAATAATAAGTTAATTAATATAATATTAAATTTAAATAAAATGGTTATTTT
ATAAAATAATTGTTTTTTCATTTATGATATATGGACTTTTATTTCTCAAGTTTTTATAAAATAAG
GCTGTTAGGGT
Found at i:47053 original size:21 final size:22
Alignment explanation
Indices: 47020--47067 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
47010 GTAGTTATGA
* *
47020 CACATGCCCATGTG-AAGGAGG
1 CACACGCCCATGTGAAAAGAGG
*
47041 CACACGCCTATGTGAAAAGAGG
1 CACACGCCCATGTGAAAAGAGG
47063 CACAC
1 CACAC
47068 ACACGACCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.12
Consensus pattern (22 bp):
CACACGCCCATGTGAAAAGAGG
Found at i:47700 original size:16 final size:17
Alignment explanation
Indices: 47663--47702 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
47653 TCCCCAACAA
47663 AAACAAAAAAAAATTTGG
1 AAACAAAAAAAAA-TTGG
47681 -AACAAAAAAAAA-TGG
1 AAACAAAAAAAAATTGG
47696 AAACAAA
1 AAACAAA
47703 TCTAACGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 3 0.14
16 6 0.29
17 12 0.57
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.10
Consensus pattern (17 bp):
AAACAAAAAAAAATTGG
Found at i:48563 original size:33 final size:33
Alignment explanation
Indices: 48498--48576 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 33
48488 TTTTAATATT
* * *
48498 TAATTAATTTTAAATATTATATTTTTAATTGAAA
1 TAATTAATGTAAAATAATATATTTTTAATTG-AA
*
48532 TAATTAATGTAAAATAATAT-TTTTTATTTGAA
1 TAATTAATGTAAAATAATATATTTTTAATTGAA
*
48564 TTATTGAATGTAA
1 TAATT-AATGTAA
48577 TTAAAATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 6 0.15
33 16 0.41
34 17 0.44
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (33 bp):
TAATTAATGTAAAATAATATATTTTTAATTGAA
Found at i:52961 original size:45 final size:44
Alignment explanation
Indices: 52892--53023 Score: 187
Period size: 45 Copynumber: 3.0 Consensus size: 44
52882 CTTGGTATGC
52892 TTTACAAACGAGGTTGAGATTTTGTTACATATTTTGTTTATTTTT
1 TTTA-AAACGAGGTTGAGATTTTGTTACATATTTTGTTTATTTTT
52937 TTTAAAAACGAGGTTGAGATTTTGTTACATATTTTGTTT-TTTTT
1 TTT-AAAACGAGGTTGAGATTTTGTTACATATTTTGTTTATTTTT
* * * * *
52981 TTT-AAATGAGATTGAAATTTTGTTACATATCTTATTTATTTTT
1 TTTAAAACGAGGTTGAGATTTTGTTACATATTTTGTTTATTTTT
53024 CAAAAAATTC
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
42 29 0.36
43 5 0.06
44 8 0.10
45 37 0.46
46 1 0.01
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.55
Consensus pattern (44 bp):
TTTAAAACGAGGTTGAGATTTTGTTACATATTTTGTTTATTTTT
Found at i:53626 original size:53 final size:53
Alignment explanation
Indices: 53568--53671 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
53558 ATAACAAAAA
53568 TAATAAATAAAAAATTTACATATAATTTGGAATTTCTAATTGTACTTAGAATT
1 TAATAAATAAAAAATTTACATATAATTTGGAATTTCTAATTGTACTTAGAATT
53621 TAATAAATAAAAAATTTACATATAATTTGGAATTTCTAATTGTACTTAGAA
1 TAATAAATAAAAAATTTACATATAATTTGGAATTTCTAATTGTACTTAGAA
53672 GTATAACGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (53 bp):
TAATAAATAAAAAATTTACATATAATTTGGAATTTCTAATTGTACTTAGAATT
Found at i:53987 original size:44 final size:44
Alignment explanation
Indices: 53924--54007 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
53914 TACCCAATTG
53924 CATCTGAACTTCAAACGGGTTTGGCCTTAACCATGTTAATATTA
1 CATCTGAACTTCAAACGGGTTTGGCCTTAACCATGTTAATATTA
53968 CATCTGAACTTCAAACGGGTTTGGCCTTAACCATGTTAAT
1 CATCTGAACTTCAAACGGGTTTGGCCTTAACCATGTTAAT
54008 GGTCCCAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (44 bp):
CATCTGAACTTCAAACGGGTTTGGCCTTAACCATGTTAATATTA
Found at i:54301 original size:68 final size:68
Alignment explanation
Indices: 54227--54360 Score: 268
Period size: 68 Copynumber: 2.0 Consensus size: 68
54217 AAAAATTAAT
54227 ACACACTCACTTTCCAAAAAAGATTAATACACCAAGGACTACACTTAGATTTATTAGATTTGTTG
1 ACACACTCACTTTCCAAAAAAGATTAATACACCAAGGACTACACTTAGATTTATTAGATTTGTTG
54292 CAC
66 CAC
54295 ACACACTCACTTTCCAAAAAAGATTAATACACCAAGGACTACACTTAGATTTATTAGATTTGTTG
1 ACACACTCACTTTCCAAAAAAGATTAATACACCAAGGACTACACTTAGATTTATTAGATTTGTTG
54360 C
66 C
54361 TAAAATATCG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (68 bp):
ACACACTCACTTTCCAAAAAAGATTAATACACCAAGGACTACACTTAGATTTATTAGATTTGTTG
CAC
Found at i:54546 original size:14 final size:14
Alignment explanation
Indices: 54527--54576 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
54517 CTCCTTTTCC
54527 ATTTATTCTATTCT
1 ATTTATTCTATTCT
54541 ATTTATAT-TATTCT
1 ATTTAT-TCTATTCT
*
54555 AATTATTCTAATTCT
1 ATTTATTCT-ATTCT
*
54570 ATGTATT
1 ATTTATT
54577 TCTTTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 11 0.37
ACGTcount: A:0.28, C:0.10, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTATTCTATTCT
Found at i:55111 original size:396 final size:391
Alignment explanation
Indices: 54355--55143 Score: 1338
Period size: 396 Copynumber: 2.0 Consensus size: 391
54345 TTATTAGATT
*
54355 TGTTGCTAAAATATCGGTATTAACCCCGAAACTCTCGGCGGATGGCCAGTGACCCAAGGAAACGA
1 TGTTGCTAAAATATCGGTATTAACCCCGAAACTCTCGGCAGATGGCCAGTGACCCAAGGAAACGA
*
54420 AAGAATCGGTTACATTTTTCATATGATCTCCTATTTTATTTTAGATAGACTAAAAAAAAAGAACT
66 AAGAATCGATTACATTTTTCATATGATCTCCTATTTTATTTTAGATAGACTAAAAAAAAAGAACT
*
54485 CGGTTCTTTCTTTTTGTATTATATCGCTTTGACTCCTTTTCCATTTATTCTATTCTATTTATATT
131 CAGTTCTTTCTTTTTGTATTATATCGCTTTGACTCCTTTTCCATTTATTCTATTCTATTTATATT
*
54550 ATTCTAATTATTCTAATTCTATGTATTTCTTTTTTTGTTTTAATAAATTATTAAATTTATTATAA
196 ATTCTAATTATTCTAATTCTATGTATTTCTTTATTTGTTTTAATAAATTATTAAATTTATTATAA
*
54615 AATTATTCATTATTATGATTATGAATTTTCATTTACCTATGTATAAACGGAGTCAAAAATAGATT
261 AATTATTCATTATTATGATTATGAATTTTCATTTACCTATGTATAAACGGAGTAAAAAATAGATT
54680 CTATTTATCTAGTTAGCTAGAAATGTATTTTTTTTTTTTCAATTGAAAATTCCCAATAATAATAA
326 CTATTTATCTAGTTAGCTAGAAATGTA----TTTTTTTT-AATTGAAAATTCCCAATAATAATAA
54745 TTCTTA
386 TTCTTA
54751 TGTTGCT-AAA-ATCGGTATTAACCCCGAAACTCTCGGCAGATGGCCAGTGACCCAAGGAAACGA
1 TGTTGCTAAAATATCGGTATTAACCCCGAAACTCTCGGCAGATGGCCAGTGACCCAAGGAAACGA
* *
54814 AAGAATCGATTACATTTTTCATATGATCTCCTATTTTATTTTAGATAGACT-AACAAAAAGAATT
66 AAGAATCGATTACATTTTTCATATGATCTCCTATTTTATTTTAGATAGACTAAAAAAAAAGAACT
54878 CAGTT-TTT-TTTTTGTATTATATCGCTTTGACTCCTTTTCCATTTATTCTATTCTATCATATTT
131 CAGTTCTTTCTTTTTGTATTATATCGCTTTGACTCCTTTTCCATTTATTCTA---T-TC-TATTT
*
54941 ATATTATTCTAATTATTCTAATTCTATTTATTTCTTTATTTGTTTTAATAAATTATTAAATTTAT
191 ATATTATTCTAATTATTCTAATTCTATGTATTTCTTTATTTGTTTTAATAAATTATTAAATTTAT
*
55006 TATAAAATTATTCATTATTATGATTATGAATTTTCATTTACCTATGTCTAAACGGAGTTAAAAAA
256 TATAAAATTATTCATTATTATGATTATGAATTTTCATTTACCTATGTATAAACGGAG-T-AAAAA
*
55071 ATATATTCTATTTATCTAGTTAGCTAGAAATGTA-TTTTTTTAATTGAAAATTCCCAATAATAAT
319 ATAGATTCTATTTATCTAGTTAGCTAGAAATGTATTTTTTTTAATTGAAAATTCCCAATAATAAT
55135 AATTCTTA
384 AATTCTTA
55143 T
1 T
55144 TAGAATTAGG
Statistics
Matches: 376, Mismatches: 10, Indels: 18
0.93 0.02 0.04
Matches are distributed among these distances:
391 42 0.11
392 35 0.09
393 22 0.06
394 103 0.27
395 5 0.01
396 131 0.35
397 1 0.00
398 37 0.10
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (391 bp):
TGTTGCTAAAATATCGGTATTAACCCCGAAACTCTCGGCAGATGGCCAGTGACCCAAGGAAACGA
AAGAATCGATTACATTTTTCATATGATCTCCTATTTTATTTTAGATAGACTAAAAAAAAAGAACT
CAGTTCTTTCTTTTTGTATTATATCGCTTTGACTCCTTTTCCATTTATTCTATTCTATTTATATT
ATTCTAATTATTCTAATTCTATGTATTTCTTTATTTGTTTTAATAAATTATTAAATTTATTATAA
AATTATTCATTATTATGATTATGAATTTTCATTTACCTATGTATAAACGGAGTAAAAAATAGATT
CTATTTATCTAGTTAGCTAGAAATGTATTTTTTTTAATTGAAAATTCCCAATAATAATAATTCTT
A
Found at i:59912 original size:52 final size:53
Alignment explanation
Indices: 59833--59938 Score: 205
Period size: 52 Copynumber: 2.0 Consensus size: 53
59823 TCCACGGTCT
59833 TCAGACTATATCGTAGAATCCATTTCACAGCTTGCCAATGTCCTTTTCCAAGA
1 TCAGACTATATCGTAGAATCCATTTCACAGCTTGCCAATGTCCTTTTCCAAGA
59886 TCAGACTATA-CGTAGAATCCATTTCACAGCTTGCCAATGTCCTTTTCCAAGA
1 TCAGACTATATCGTAGAATCCATTTCACAGCTTGCCAATGTCCTTTTCCAAGA
59938 T
1 T
59939 TATGCATATA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 43 0.81
53 10 0.19
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (53 bp):
TCAGACTATATCGTAGAATCCATTTCACAGCTTGCCAATGTCCTTTTCCAAGA
Found at i:66062 original size:14 final size:14
Alignment explanation
Indices: 66043--66092 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
66033 CTCCTTTTCC
66043 ATTTATTCTATTCT
1 ATTTATTCTATTCT
66057 ATTTATAT-TATTCT
1 ATTTAT-TCTATTCT
*
66071 AATTATTCTAATTCT
1 ATTTATTCT-ATTCT
*
66086 ATGTATT
1 ATTTATT
66093 TCTTTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 11 0.37
ACGTcount: A:0.28, C:0.10, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTATTCTATTCT
Found at i:71703 original size:20 final size:18
Alignment explanation
Indices: 71679--71726 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
71669 ATCTTTTTAT
71679 AATTTTTATTTACTTTTTTG
1 AATTTTTATTT--TTTTTTG
*
71699 GATTTATCTATTTTTTTTTG
1 AATTT-T-TATTTTTTTTTG
71719 AATTTTTA
1 AATTTTTA
71727 GAATTTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
18 2 0.08
19 1 0.04
20 15 0.62
21 1 0.04
22 5 0.21
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (18 bp):
AATTTTTATTTTTTTTTG
Found at i:78043 original size:2 final size:2
Alignment explanation
Indices: 78036--78065 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
78026 ATTTGAAACA
78036 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
78066 GAAAACTATA
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:84292 original size:15 final size:15
Alignment explanation
Indices: 84274--84313 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
84264 GAAATTCAAC
84274 TATATTTCAAATATATA
1 TATATTT-AAA-ATATA
*
84291 TATATATAAAATATA
1 TATATTTAAAATATA
84306 TATATTTA
1 TATATTTA
84314 GGACTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 3 0.14
17 6 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATTTAAAATATA
Found at i:84882 original size:11 final size:11
Alignment explanation
Indices: 84866--84908 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
84856 ATATAATATT
*
84866 ATATGTACGTA
1 ATATGTATGTA
*
84877 ATATGTATATA
1 ATATGTATGTA
84888 TTATATGTATGTA
1 --ATATGTATGTA
84901 ATATGTAT
1 ATATGTAT
84909 TATACATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (11 bp):
ATATGTATGTA
Found at i:84893 original size:24 final size:24
Alignment explanation
Indices: 84861--84908 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
84851 ACTGCATATA
84861 ATATTATATGTACGTAATATGTAT
1 ATATTATATGTACGTAATATGTAT
*
84885 ATATTATATGTATGTAATATGTAT
1 ATATTATATGTACGTAATATGTAT
84909 TATACATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (24 bp):
ATATTATATGTACGTAATATGTAT
Found at i:84911 original size:20 final size:21
Alignment explanation
Indices: 84856--84912 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 21
84846 ATGTAACTGC
*
84856 ATATAATATTATATGTACGTA
1 ATATGATATTATATGTACGTA
*
84877 ATATGTATATATTATATGTATGTA
1 ATATG---ATATTATATGTACGTA
84901 ATATG-TATTATA
1 ATATGATATTATA
84913 CATTATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 7 0.23
21 4 0.13
24 20 0.65
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (21 bp):
ATATGATATTATATGTACGTA
Found at i:85011 original size:24 final size:26
Alignment explanation
Indices: 84983--85042 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
84973 CATGTAACTG
84983 ATATTTATAT-TACGTAATATGTA-T
1 ATATTTATATGTACGTAATATGTATT
*
85007 ATA-TTATATGTATGTAATATGTATT
1 ATATTTATATGTACGTAATATGTATT
85032 ATATATTATAT
1 ATAT-TTATAT
85043 AACCCCACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 6 0.19
24 15 0.48
25 4 0.13
27 6 0.19
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (26 bp):
ATATTTATATGTACGTAATATGTATT
Found at i:85037 original size:11 final size:12
Alignment explanation
Indices: 84999--85043 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
84989 ATATTACGTA
84999 ATATGTATATATT
1 ATATGTATATA-T
*
85012 ATATGTATGTA-
1 ATATGTATATAT
85023 ATATGTAT-TAT
1 ATATGTATATAT
85034 ATAT-TATATA
1 ATATGTATATA
85044 ACCCCACATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
13 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:85078 original size:122 final size:123
Alignment explanation
Indices: 84864--85094 Score: 446
Period size: 122 Copynumber: 1.9 Consensus size: 123
84854 GCATATAATA
84864 TTATATGTACGTAATATGTATATATTATATGTATGTAATATGTATTATACATTATATAACCCCAC
1 TTATATGTACGTAATATGTATATATTATATGTATGTAATATGTATTATACATTATATAACCCCAC
84929 ATATATGTGTATATATATACACACATATAGCATTTTGTCTCTCACATGTAACTGATAT
66 ATATATGTGTATATATATACACACATATAGCATTTTGTCTCTCACATGTAACTGATAT
*
84987 TTATAT-TACGTAATATGTATATATTATATGTATGTAATATGTATTATATATTATATAACCCCAC
1 TTATATGTACGTAATATGTATATATTATATGTATGTAATATGTATTATACATTATATAACCCCAC
85051 ATATATGTGTATATATATACACACATATAGCATTTTGTCTCTCA
66 ATATATGTGTATATATATACACACATATAGCATTTTGTCTCTCA
85095 TTGCACATCG
Statistics
Matches: 107, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
122 101 0.94
123 6 0.06
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (123 bp):
TTATATGTACGTAATATGTATATATTATATGTATGTAATATGTATTATACATTATATAACCCCAC
ATATATGTGTATATATATACACACATATAGCATTTTGTCTCTCACATGTAACTGATAT
Found at i:91745 original size:34 final size:34
Alignment explanation
Indices: 91702--91767 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
91692 TTATTACTAT
*
91702 AAAACCATTTTTGAACCTAATTTTTTTCAACAAG
1 AAAACCATTTTCGAACCTAATTTTTTTCAACAAG
*
91736 AAAATCATTTTCGAACCTAATTTTTTTCAACA
1 AAAACCATTTTCGAACCTAATTTTTTTCAACA
91768 GTTAGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (34 bp):
AAAACCATTTTCGAACCTAATTTTTTTCAACAAG
Found at i:92575 original size:21 final size:23
Alignment explanation
Indices: 92550--92598 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
92540 TTCAACTATT
92550 TAATTAT-AACAAATT-AATTAA
1 TAATTATAAACAAATTAAATTAA
*
92571 TAATT-TAAATAAATTAAATTAA
1 TAATTATAAACAAATTAAATTAA
*
92593 TCATTA
1 TAATTA
92599 AGTTATCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATTATAAACAAATTAAATTAA
Found at i:94662 original size:15 final size:15
Alignment explanation
Indices: 94642--94719 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
94632 TTTATGGAAA
*
94642 ATCAAAGATATGGGT
1 ATCAAAGATATGGAT
* * *
94657 ATCAAATA-ATAGAA
1 ATCAAAGATATGGAT
94671 AGTCAAAGATATGGAT
1 A-TCAAAGATATGGAT
* *
94687 ATCAAATAT-TGGAA
1 ATCAAAGATATGGAT
*
94701 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGAT
94717 ATC
1 ATC
94720 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGAT
Found at i:94679 original size:30 final size:30
Alignment explanation
Indices: 94638--94719 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
94628 CATATTTATG
*
94638 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* * *
94668 GAAAGTCAAAGATATGGATATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
94698 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
94720 GAGATATTGG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:100462 original size:23 final size:23
Alignment explanation
Indices: 100420--100480 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
100410 ATAATATACG
* *
100420 ATAAATTT-AAACAATATTAATA
1 ATAAATTTAAAATAATATTAAGA
* *
100442 ATGAATTTAAAATAATATTAAGC
1 ATAAATTTAAAATAATATTAAGA
100465 ATAAATATTAAAATAA
1 ATAAAT-TTAAAATAA
100481 GGTTAGATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 7 0.22
23 16 0.50
24 9 0.28
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (23 bp):
ATAAATTTAAAATAATATTAAGA
Found at i:109285 original size:17 final size:17
Alignment explanation
Indices: 109265--109300 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
109255 ACTATTATTT
* *
109265 TATAATTTTAATTAGTA
1 TATAATTCTAATGAGTA
109282 TATAATTCTAATGAGTA
1 TATAATTCTAATGAGTA
109299 TA
1 TA
109301 ATATATTATT
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:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (17 bp):
TATAATTCTAATGAGTA
Found at i:118064 original size:34 final size:32
Alignment explanation
Indices: 117974--118067 Score: 93
Period size: 37 Copynumber: 2.8 Consensus size: 32
117964 AAAATAAAGG
* *
117974 AAAAAAATGCATATG-TATATATTTACAAAAT
1 AAAAAAATGTATATGTTATATATTTACAACAT
*
118005 AGAAAAAAAAATGTATAAGTCTATATATTTACAACAT
1 ----AAAAAAATGTATATGT-TATATATTTACAACAT
118042 AAAAGAAATGTATATG-TATATATTTA
1 AAAA-AAATGTATATGTTATATATTTA
118068 TAAAACATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
32 10 0.19
33 4 0.08
34 10 0.19
35 13 0.25
37 15 0.29
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (32 bp):
AAAAAAATGTATATGTTATATATTTACAACAT
Found at i:118075 original size:34 final size:33
Alignment explanation
Indices: 117974--118079 Score: 106
Period size: 34 Copynumber: 3.1 Consensus size: 33
117964 AAAATAAAGG
* * * *
117974 AAAAAAATGCATATGTATATATTTACAAAATAGAA
1 AAAAAAATGTATATGTATATATTTA-TAAA-ACAT
* * *
118009 AAAAAAATGTATAAGTCTATATATT-TACAACAT
1 AAAAAAATGTATATGTATATAT-TTATAAAACAT
118042 AAAAGAAATGTATATGTATATATTTATAAAACAT
1 AAAA-AAATGTATATGTATATATTTATAAAACAT
118076 AAAA
1 AAAA
118080 TATATAAAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
33 8 0.14
34 29 0.50
35 19 0.33
36 2 0.03
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (33 bp):
AAAAAAATGTATATGTATATATTTATAAAACAT
Found at i:120097 original size:44 final size:43
Alignment explanation
Indices: 120049--120714 Score: 420
Period size: 44 Copynumber: 15.0 Consensus size: 43
120039 GGACCTACTA
*
120049 TCTTTGATCTCCTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-TT
* * *** *
120093 TCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTT
1 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGTT
*
120137 TCGTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-TT
* * * *
120181 TCTTTGATCTGCTTCGCAACCAGT--ATGGAAGACAATATCTGTT
1 TCTTTGATCTACTTCAC-GCCAGTACAT-GAAGACAAGATCTGTT
*
120224 GACTTTGATCTACTTCACGCC-GATACATGAAGACAAGATCTGCTT
1 -TCTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTG-TT
* * *** *
120269 TCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTT
1 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGTT
* * * * *
120313 GACTTTGATCTACTTCACG-CTGATACATGAAGATAATATCTACTT
1 -TCTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCT-GTT
* ** * * * *
120358 TCTTTCGATCTGCTT--CGCCACCAATATGGAAAGGCGAGATCTGTA
1 TCTTT-GATCTACTTCACGCCA-GTACAT-G-AAGACAAGATCTGTT
* * *
120403 TATTCGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTAT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGT-T
* * * * * * * *
120447 TCCTTCGCTCTGCTTCGCCACCAGTATAGGAATG-CGAGATCTGTT
1 T-CTTTGATCTACTTC-ACGCCAGTACATGAA-GACAAGATCTGTT
*
120492 ATCTTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGCTTTT
1 -TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG---TT
* * * * *
120539 TCCTTCGATCTACTT--CGCCACTAGTATGGGAATG-CGAGATCTGTA
1 T-CTTTGATCTACTTCACGCCAGTA-CAT--GAA-GACAAGATCTGTT
* *
120584 TATTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTAT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGT-T
* * ** * *
120628 TCCTTCGATCTGCTT--CGCCACCAGCATGGGAAGGCGAGATCTGTT
1 T-CTTTGATCTACTTCACGCCAGTA-CAT--GAAGACAAGATCTGTT
*
120673 ATCTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCTG
1 -TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG
120715 CTTTTTCCTT
Statistics
Matches: 474, Mismatches: 102, Indels: 92
0.71 0.15 0.14
Matches are distributed among these distances:
42 2 0.00
43 62 0.13
44 181 0.38
45 135 0.28
46 61 0.13
47 21 0.04
48 11 0.02
49 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTT
Found at i:120342 original size:89 final size:89
Alignment explanation
Indices: 120050--120763 Score: 849
Period size: 89 Copynumber: 8.0 Consensus size: 89
120040 GACCTACTAT
* * * * *
120050 CTTTGATCTCCTTCACGCCAGTACATGAAGACAAGATCTGCTTT-CTTTGATCTACTCCACCACC
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCCTTCGATCTGCTTCGCCACC
* * *
120114 AGTATGGGGAGACAAGATCTGTTT
66 AGTATGGGAAGACGAGATCTGTTA
* * *
120138 CGTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-CTTTGATCTGCTTCGCAACC
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCCTTCGATCTGCTTCGCCACC
* *
120202 AGTAT-GGAAGACAATATCTGTTGA
66 AGTATGGGAAGACGAGATCTGTT-A
* * * *
120226 CTTTGATCTACTTCACGCC-GATACATGAAGACAAGATCTGCTTT-CTTTGATCTACTCCACCAC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTTTCCTTCGATCTGCTTCGCCAC
* *
120289 CAGTATGGGGAGACAAGATCTGTTGA
65 CAGTATGGGAAGACGAGATCTGTT-A
* * * * *
120315 CTTTGATCTACTTCACG-CTGATACATGAAGATAATATCTACTTTCTTTCGATCTGCTTCGCCAC
1 CTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTTTCCTTCGATCTGCTTCGCCAC
* * *
120379 CAATATGGAAAGGCGAGATCTGTATA
65 CAGTATGGGAAGACGAGATCTGT-TA
* * *
120405 -TTCGATCTACTTCACGCTAGTACATGAAGACAAGATCTG-TATTCCTTCGCTCTGCTTCGCCAC
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TTCCTTCGATCTGCTTCGCCAC
*
120468 CAGTATAGGAATG-CGAGATCTGTTA
65 CAGTATGGGAA-GACGAGATCTGTTA
* *
120493 TCTTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGCTTTTTCCTTCGATCTACTTCGCC
1 -CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC--TTTCCTTCGATCTGCTTCGCC
*
120558 ACTAGTATGGGAATG-CGAGATCTGTATA
63 ACCAGTATGGGAA-GACGAGATCTGT-TA
*
120586 -TTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-TATTCCTTCGATCTGCTTCGCCAC
1 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TTCCTTCGATCTGCTTCGCCAC
* *
120649 CAGCATGGGAAGGCGAGATCTGTTA
65 CAGTATGGGAAGACGAGATCTGTTA
*
120674 TCTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCC
1 -CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC--TTTCCTTCGATCTGCTTCGCC
*
120739 ACCAGTATGGGAAGGCGAGATCTGT
63 ACCAGTATGGGAAGACGAGATCTGT
120764 ATATTCGATC
Statistics
Matches: 549, Mismatches: 55, Indels: 40
0.85 0.09 0.06
Matches are distributed among these distances:
87 16 0.03
88 133 0.24
89 165 0.30
90 108 0.20
91 38 0.07
92 85 0.15
93 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (89 bp):
CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCCTTCGATCTGCTTCGCCACC
AGTATGGGAAGACGAGATCTGTTA
Found at i:120598 original size:181 final size:178
Alignment explanation
Indices: 120054--120779 Score: 914
Period size: 181 Copynumber: 4.1 Consensus size: 178
120044 TACTATCTTT
* *
120054 GATCTCCTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTAT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTAT
* *
120119 GGGGAGACAAGATCTGTT-TCGTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTT-
66 GGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTC
* * * * * *
120182 CTTTGATCTGCTTCGCAACCAGTAT-GGAAGACAATATCTGT-TGACTTT
131 CTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTAT-A-TTC
*
120230 GATCTACTTCACGCC-GATACATGAAGACAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTA
1 GATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTA
* * * * *
120294 TGGGGAGACAAGATCTGTTGA-CTTTGATCTACTTCACG-CTGATACATGAAGATAATATCTACT
65 TGGGAAGACAAGATCTGTT-ATCTTTGATCTACTTCACGCCAG-TACATGAAGACAAGATCTGCT
* * *
120357 TTCTTTCGATCTGCTTCGCCACCAATATGGAAAGGCGAGATCTGTATATTC
128 TTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATATTC
* * * * *
120408 GATCTACTTCACGCTAGTACATGAAGACAAGATCTG-TATTCCTTCGCTCTGCTTCGCCACCAGT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TT-CTTCGATCTACTCCACCACCAGT
* * *
120472 ATAGGAATG-CGAGATCTGTTATCTTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGCT
64 ATGGGAA-GACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC-
* * *
120536 TTTTCCTTCGATCTACTTCGCCACTAGTATGGGAATGCGAGATCTGTATATTC
127 -TTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATATTC
* * * *
120589 GATCTACTTCACGCCAGTACATGAAGACAAGATCTG-TATTCCTTCGATCTGCTTCGCCACCAGC
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCT-TT-CTTCGATCTACTCCACCACCAGT
* * *
120653 ATGGGAAGGCGAGATCTGTTATCTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT
64 ATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGC--
120718 TTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATATTC
127 TTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATATTC
*
120770 GATCCACTTC
1 GATCTACTTC
120780 GCTACCAATA
Statistics
Matches: 489, Mismatches: 45, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
175 1 0.00
176 82 0.17
177 37 0.08
178 59 0.12
179 80 0.16
180 5 0.01
181 225 0.46
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (178 bp):
GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTAT
GGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTC
CTTCGATCTGCTTCGCCACCAGTATGGGAAGGCGAGATCTGTATATTC
Found at i:125975 original size:19 final size:20
Alignment explanation
Indices: 125951--125990 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
125941 AGAGGTGTCT
* *
125951 AATGCATATG-ATGTAATGA
1 AATGCAAATGCATATAATGA
125970 AATGCAAATGCATATAATGA
1 AATGCAAATGCATATAATGA
125990 A
1 A
125991 TGCCTAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (20 bp):
AATGCAAATGCATATAATGA
Found at i:127800 original size:34 final size:34
Alignment explanation
Indices: 127736--127825 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 34
127726 AATGCATATG
* *
127736 TATATATTTACAAAATAGAAAAAAAATGTATAAGTC
1 TATATATTTACAACAT--AAAAAAAATGTATAAGTA
* * *
127772 TATATATTTACAACATAAAAGAACTGTATATGTA
1 TATATATTTACAACATAAAAAAAATGTATAAGTA
*
127806 TATAT-TTATAAAACATAAAA
1 TATATATT-TACAACATAAAA
127826 TATATAAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
33 2 0.04
34 30 0.64
36 15 0.32
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (34 bp):
TATATATTTACAACATAAAAAAAATGTATAAGTA
Found at i:131917 original size:16 final size:16
Alignment explanation
Indices: 131880--131935 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
131870 TTAAATTCTA
* *
131880 AAAGATAAATACAATT
1 AAAGATAAAAATAATT
131896 -AA-ATAAAAATAATT
1 AAAGATAAAAATAATT
** *
131910 AAAGATAAGGATAAAT
1 AAAGATAAAAATAATT
131926 AAAGATAAAA
1 AAAGATAAAA
131936 GCTAAAATTA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
14 10 0.32
15 4 0.13
16 17 0.55
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAGATAAAAATAATT
Found at i:139581 original size:26 final size:26
Alignment explanation
Indices: 139547--139601 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
139537 TAATTATATT
*
139547 ATTATGTTTTATAATAAGTTGTGCGA
1 ATTATGTTTTATAATAAGTTGTGCAA
139573 ATTATGTTTTATAATAAGTTGTGCAA
1 ATTATGTTTTATAATAAGTTGTGCAA
139599 ATT
1 ATT
139602 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (26 bp):
ATTATGTTTTATAATAAGTTGTGCAA
Found at i:141402 original size:3 final size:3
Alignment explanation
Indices: 141394--141427 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
141384 AAGAAAATTT
141394 GAA GAA GAA GAA GAA GAA GAA GAA GAA GGAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA
141428 CCTTCATCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:149947 original size:28 final size:29
Alignment explanation
Indices: 149887--149947 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
149877 AAAAGCCCTT
*
149887 TTTTTTCAATATTTACCGAAATGGGCCGG
1 TTTTTTCAATATTTACCGAAATGGGCCGA
* *
149916 TTTTTT-AATTATTTACCGGAATGGTCC-A
1 TTTTTTCAA-TATTTACCGAAATGGGCCGA
149944 TTTT
1 TTTT
149948 CAGCGAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46
Consensus pattern (29 bp):
TTTTTTCAATATTTACCGAAATGGGCCGA
Found at i:152357 original size:37 final size:37
Alignment explanation
Indices: 152286--152366 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 37
152276 AGTACAGTGC
* *
152286 ATATTATTTTTTTAAAATTATAAATAATTATATATTT
1 ATATTATTTTTTTAAAATTAGAAATAATTATATATAT
* *
152323 ATATTATTTTAATTTAATATTGGAAA-AATT-TATATAT
1 ATATTATTTT--TTTAAAATTAGAAATAATTATATATAT
152360 AT-TTATT
1 ATATTATT
152367 AATATATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
36 5 0.13
37 18 0.47
38 4 0.11
39 11 0.29
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (37 bp):
ATATTATTTTTTTAAAATTAGAAATAATTATATATAT
Found at i:155010 original size:36 final size:36
Alignment explanation
Indices: 154963--155031 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
154953 GTTTTGCAGG
154963 GTTCTACTGTTACTGGTGATATAGCTGTGTCATTGT
1 GTTCTACTGTTACTGGTGATATAGCTGTGTCATTGT
*
154999 GTTCTACTGTTACTGGTGATGTAGCTGTGTCAT
1 GTTCTACTGTTACTGGTGATATAGCTGTGTCAT
155032 CCTCTTCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.43
Consensus pattern (36 bp):
GTTCTACTGTTACTGGTGATATAGCTGTGTCATTGT
Found at i:158299 original size:16 final size:18
Alignment explanation
Indices: 158273--158306 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
158263 CCAAATTATT
158273 CTTTCAAAATAT-TTTAA
1 CTTTCAAAATATATTTAA
158290 CTTT-AAAATATATTTAA
1 CTTTCAAAATATATTTAA
158307 TTATTTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (18 bp):
CTTTCAAAATATATTTAA
Found at i:163170 original size:32 final size:32
Alignment explanation
Indices: 163134--163197 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
163124 TTCAAGCAAC
* * *
163134 ATTAATTGAATAGTTACGTTTATTTAAAAGAT
1 ATTAATTAAATAATTACATTTATTTAAAAGAT
* *
163166 ATTAATTAAATAATTATATTTATTTTAAAGAT
1 ATTAATTAAATAATTACATTTATTTAAAAGAT
163198 GTGGTTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (32 bp):
ATTAATTAAATAATTACATTTATTTAAAAGAT
Found at i:164463 original size:29 final size:29
Alignment explanation
Indices: 164406--164464 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
164396 TCATGGAAGA
* * **
164406 GGTGAAGAACTTGTTCGTTGAGAGTTCGT
1 GGTGAAAAACTTGTTCATTGAGAACTCGT
*
164435 GGTGAAAAACTTGTTTATTGAGAACTCGT
1 GGTGAAAAACTTGTTCATTGAGAACTCGT
164464 G
1 G
164465 TCAAGGTAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.31, T:0.34
Consensus pattern (29 bp):
GGTGAAAAACTTGTTCATTGAGAACTCGT
Found at i:164606 original size:44 final size:45
Alignment explanation
Indices: 164556--164666 Score: 127
Period size: 49 Copynumber: 2.4 Consensus size: 45
164546 TCCGTATAGA
*
164556 ACTACACT-TCTTTTATTTTGATT-AGAATAAGATTTTTCAACCTT
1 ACTACACTATCTTTTATTTTGATTGA-AATAAGATGTTTCAACCTT
* *
164600 ACTACACTTCATCTATTTGATATTGATTGAAATAAGATGTTTCAACTTT
1 ACTACAC-T-ATCT-TTT-ATTTTGATTGAAATAAGATGTTTCAACCTT
*
164649 ACTACACTACCTTTTATT
1 ACTACACTATCTTTTATT
164667 AGAATATGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
44 7 0.12
45 3 0.05
46 3 0.05
47 6 0.11
48 4 0.07
49 32 0.57
50 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (45 bp):
ACTACACTATCTTTTATTTTGATTGAAATAAGATGTTTCAACCTT
Found at i:170099 original size:3 final size:3
Alignment explanation
Indices: 170091--170115 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
170081 TAGTGACAAA
170091 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
170116 GAGTTGGTGA
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:174417 original size:24 final size:27
Alignment explanation
Indices: 174364--174447 Score: 67
Period size: 26 Copynumber: 3.4 Consensus size: 27
174354 TATTTAATGA
** *
174364 TTTTATATATTTTTTAT-TTATTAATA-
1 TTTTATATATAGTTTATATTA-TAGTAT
*
174390 TTTTATATATAG-TTATCTTA-AG-AT
1 TTTTATATATAGTTTATATTATAGTAT
174414 TTTT-T-TA-AGTTTATATTATAGTAT
1 TTTTATATATAGTTTATATTATAGTAT
174438 TTTTATATAT
1 TTTTATATAT
174448 TACTATAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
21 2 0.04
22 9 0.20
23 4 0.09
24 11 0.24
25 5 0.11
26 15 0.33
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (27 bp):
TTTTATATATAGTTTATATTATAGTAT
Found at i:179880 original size:245 final size:245
Alignment explanation
Indices: 179450--179904 Score: 743
Period size: 245 Copynumber: 1.9 Consensus size: 245
179440 TGCCCACATG
*
179450 GGAGATATTAACTTCTTGTATGAGTTGATTCTGAATGATCCATATGTTTTACAGCGTATTGATGA
1 GGAGATATTAACTTCTTGTATGAGTTAATTCTGAATGATCCATATGTTTTACAGCGTATTGATGA
* *
179515 TGTGCCTTTTTTTAATACTCAATTGCAAGTAGCAACCTCTGTTGGGCATATTGAATTTATGATGG
66 TGTGCCTTTTTTTAATACTCAATTGCAAGTAGCAACCTCTGCTGGGAATATTGAATTTATGATGG
179580 AGATGATCAAATTAAAGCCAACGTTTGCAAGAAAGCTAAACCAAGCAGGGTTTAGCCCCATGCAC
131 AGATGATCAAATTAAAGCCAACGTTTGCAAGAAAGCTAAACCAAGCAGGGTTTAGCCCCATGCAC
*
179645 TTGGCTCTGCAAAATCACAGAACTCGAGGATTATAGAGGCTGCACAAACA
196 TTAGCTCTGCAAAATCACAGAACTCGAGGATTATAGAGGCTGCACAAACA
179695 GGAGATATTAA-TCTCTTGTATGAGTTAATTGC-GAATGATCCATATGTTTTACAGCGTATTGAT
1 GGAGATATTAACT-TCTTGTATGAGTTAATT-CTGAATGATCCATATGTTTTACAGCGTATTGAT
* * * * *
179758 GATGTGCCTTTTTTTCATACTCCATTGCATGTAGCAGCCTCTGCTGGGAATATTGAGTTTATGAT
64 GATGTGCCTTTTTTTAATACTCAATTGCAAGTAGCAACCTCTGCTGGGAATATTGAATTTATGAT
* * ** * *
179823 GGAGATTATCAAATTAAAGCCATCGTTTGCAAGAAAGCTAAACCAAGGTGGGTTTAGCCCCCTTC
129 GGAGATGATCAAATTAAAGCCAACGTTTGCAAGAAAGCTAAACCAAGCAGGGTTTAGCCCCATGC
179888 ACTTAGCTCTGCAAAAT
194 ACTTAGCTCTGCAAAAT
179905 GACAAAATTC
Statistics
Matches: 193, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
244 1 0.01
245 191 0.99
246 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (245 bp):
GGAGATATTAACTTCTTGTATGAGTTAATTCTGAATGATCCATATGTTTTACAGCGTATTGATGA
TGTGCCTTTTTTTAATACTCAATTGCAAGTAGCAACCTCTGCTGGGAATATTGAATTTATGATGG
AGATGATCAAATTAAAGCCAACGTTTGCAAGAAAGCTAAACCAAGCAGGGTTTAGCCCCATGCAC
TTAGCTCTGCAAAATCACAGAACTCGAGGATTATAGAGGCTGCACAAACA
Found at i:181909 original size:5 final size:5
Alignment explanation
Indices: 181899--181955 Score: 114
Period size: 5 Copynumber: 11.4 Consensus size: 5
181889 CATGCATTAA
181899 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
181949 ATATT AT
1 ATATT AT
181956 CTTAAACAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 52 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:190456 original size:75 final size:76
Alignment explanation
Indices: 190359--190511 Score: 299
Period size: 75 Copynumber: 2.0 Consensus size: 76
190349 TAAGATTTTG
190359 TAATATATTGTTTAATAATTTTAATAAGGAACAAATCTTAAAATTACATAAAATTTTAGTTTAAT
1 TAATATATTGTTTAATAATTTTAATAAGGAACAAATCTTAAAATTACATAAAATTTTAGTTTAAT
190424 GTGCAATGTAT
66 GTGCAATGTAT
190435 TAATATATTG-TTAATAATTTTAATAAGGAACAAATCTTAAAATTACATAAAATTTTAGTTTAAT
1 TAATATATTGTTTAATAATTTTAATAAGGAACAAATCTTAAAATTACATAAAATTTTAGTTTAAT
190499 GTGCAATGTAT
66 GTGCAATGTAT
190510 TA
1 TA
190512 TATCTGAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 67 0.87
76 10 0.13
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (76 bp):
TAATATATTGTTTAATAATTTTAATAAGGAACAAATCTTAAAATTACATAAAATTTTAGTTTAAT
GTGCAATGTAT
Found at i:190489 original size:35 final size:35
Alignment explanation
Indices: 190375--190491 Score: 101
Period size: 35 Copynumber: 3.2 Consensus size: 35
190365 ATTGTTTAAT
190375 AATTTTAATAAGGAACAAATCTTAAAATTACATAA
1 AATTTTAATAAGGAACAAATCTTAAAATTACATAA
* * ** * * **
190410 AATTTTAGTTTAATGTGCAATGTATTAATATATT-GTTAA
1 AATTTTA--ATAAGGAACAA-ATCTTAA-A-ATTACATAA
190449 TAATTTTAATAAGGAACAAATCTTAAAATTACATAA
1 -AATTTTAATAAGGAACAAATCTTAAAATTACATAA
190485 AATTTTA
1 AATTTTA
190492 GTTTAATGTG
Statistics
Matches: 59, Mismatches: 16, Indels: 14
0.66 0.18 0.16
Matches are distributed among these distances:
35 17 0.29
36 4 0.07
37 12 0.20
38 12 0.20
39 4 0.07
40 10 0.17
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (35 bp):
AATTTTAATAAGGAACAAATCTTAAAATTACATAA
Found at i:191618 original size:20 final size:20
Alignment explanation
Indices: 191593--191634 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
191583 ATATTTTAAA
191593 TTTTAAAAATGATTATGAAT
1 TTTTAAAAATGATTATGAAT
* * *
191613 TTTTAAAATTTATTTTGAAT
1 TTTTAAAAATGATTATGAAT
191633 TT
1 TT
191635 CTTTTTTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTAAAAATGATTATGAAT
Found at i:192448 original size:30 final size:30
Alignment explanation
Indices: 192412--192470 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
192402 AATAATCTAT
* *
192412 ATTTTTATAATTTTTAAAAAGATTAAATTA
1 ATTTTTATAATTTTCAAAAAGATAAAATTA
* *
192442 ATTTTTATCATTTTCAATAAGATAAAATT
1 ATTTTTATAATTTTCAAAAAGATAAAATT
192471 TTAAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (30 bp):
ATTTTTATAATTTTCAAAAAGATAAAATTA
Found at i:196562 original size:114 final size:112
Alignment explanation
Indices: 196369--196575 Score: 270
Period size: 114 Copynumber: 1.8 Consensus size: 112
196359 TTATTTTTAC
* *
196369 TTTTTTTTCTTAAAAATATATTAAACCTATTGACACAAAGAGAGATGACAGCCAAGCACCGCACC
1 TTTTTTTTCTTAAAAATATATTAAACCTATTGACACAAAGAGAGATGACAGCCAAACACCCCACC
* *** *
196434 CCGGTTATTTAGCCTAACATACTCCTAATTTATTATATTTATATATG
66 CCGATTACCCAGCCTAACACACTCCTAATTTATTATATTTATATATG
* * * * * *
196481 TTTTTTTCCTCTTAAGAATATATTGAACCTTTTGACGCGAATAGAGATGACAGCCAAACACCCCA
1 TTTTTTT--TCTTAAAAATATATTAAACCTATTGACACAAAGAGAGATGACAGCCAAACACCCCA
*
196546 CCCCGATTACCCAGCCTAACACATTCCTAA
64 CCCCGATTACCCAGCCTAACACACTCCTAA
196576 AAATATTTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
112 7 0.09
114 72 0.91
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.31
Consensus pattern (112 bp):
TTTTTTTTCTTAAAAATATATTAAACCTATTGACACAAAGAGAGATGACAGCCAAACACCCCACC
CCGATTACCCAGCCTAACACACTCCTAATTTATTATATTTATATATG
Found at i:200826 original size:6 final size:6
Alignment explanation
Indices: 200815--200883 Score: 77
Period size: 6 Copynumber: 11.0 Consensus size: 6
200805 ATCTTCTTCA
* *
200815 TATTTT TATTTT TATTTTT TATATT TATGTT TATTTT TATTTT TAGTTGTT
1 TATTTT TATTTT TA-TTTT TATTTT TATTTT TATTTT TATTTT TA-TT-TT
200866 T-TGTTT TATTTT TATTTT
1 TAT-TTT TATTTT TATTTT
200884 CTTGTACTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
6 42 0.76
7 10 0.18
8 3 0.05
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:200851 original size:25 final size:27
Alignment explanation
Indices: 200818--200883 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 27
200808 TTCTTCATAT
200818 TTTTATTTTTATTTTTTA-TAT-TTATG
1 TTTTATTTTTATTTTTTAGT-TGTTATG
*
200844 -TTTATTTTTA-TTTTTAGTTGTTTTG
1 TTTTATTTTTATTTTTTAGTTGTTATG
200869 TTTTATTTTTATTTT
1 TTTTATTTTTATTTT
200884 CTTGTACTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
24 7 0.20
25 15 0.43
26 10 0.29
27 3 0.09
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (27 bp):
TTTTATTTTTATTTTTTAGTTGTTATG
Found at i:200853 original size:31 final size:32
Alignment explanation
Indices: 200815--200883 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
200805 ATCTTCTTCA
200815 TATTTTTATTTTTA-TT-TTTTATATTTATGTT
1 TATTTTTATTTTTAGTTGTTTTAT-TTTATGTT
* *
200846 TATTTTTATTTTTAGTTGTTTTGTTTTATTTT
1 TATTTTTATTTTTAGTTGTTTTATTTTATGTT
200878 TATTTT
1 TATTTT
200884 CTTGTACTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 14 0.41
32 15 0.44
33 5 0.15
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (32 bp):
TATTTTTATTTTTAGTTGTTTTATTTTATGTT
Found at i:203889 original size:20 final size:20
Alignment explanation
Indices: 203864--203901 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
203854 TTGTAATTAA
203864 ATATTATT-TAATTATAATGT
1 ATATTATTAT-ATTATAATGT
203884 ATATTATTATATTATAAT
1 ATATTATTATATTATAAT
203902 ATTGTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATATTATTATATTATAATGT
Found at i:203948 original size:20 final size:18
Alignment explanation
Indices: 203912--203948 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
203902 ATTGTAATTT
203912 ATATTAATTATAAATAAG
1 ATATTAATTATAAATAAG
203930 ATATTATATTATGAAATAA
1 ATATTA-ATTAT-AAATAA
203949 ATCAAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATATTAATTATAAATAAG
Found at i:205661 original size:31 final size:31
Alignment explanation
Indices: 205626--205684 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
205616 TACAAAAATA
*
205626 AAAATTTAAATTTTGACCCCTAAA-TTTTCCT
1 AAAA-TTAAATTTTAACCCCTAAACTTTTCCT
* *
205657 AAAATTATATTTTAAGCCCTAAACTTTT
1 AAAATTAAATTTTAACCCCTAAACTTTT
205685 TTAAATTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.42
Consensus pattern (31 bp):
AAAATTAAATTTTAACCCCTAAACTTTTCCT
Found at i:205758 original size:30 final size:29
Alignment explanation
Indices: 205635--205751 Score: 105
Period size: 29 Copynumber: 4.0 Consensus size: 29
205625 AAAAATTTAA
* * * *
205635 ATTTTGACCCCTAAATTTTCCTAAAATTAT
1 ATTTTGACCCTTAAATTTT-TTGAAATTAC
*
205665 ATTTTAAGCCC-TAAACTTTTTT-AAATTAC
1 ATTTTGA-CCCTTAAA-TTTTTTGAAATTAC
**
205694 ATTTTGACCCATT-AACCTTTTGAAATTAC
1 ATTTTGACCC-TTAAATTTTTTGAAATTAC
205723 ATTTTGACCCTTAAATTTTCTTGAAATTA
1 ATTTTGACCCTTAAATTTT-TTGAAATTA
205752 TGTTTTGGCC
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
28 9 0.12
29 35 0.49
30 21 0.29
31 7 0.10
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.44
Consensus pattern (29 bp):
ATTTTGACCCTTAAATTTTTTGAAATTAC
Found at i:206122 original size:4 final size:4
Alignment explanation
Indices: 206101--206169 Score: 71
Period size: 4 Copynumber: 18.5 Consensus size: 4
206091 GATCCGAGAG
206101 AAGA AGAGA AA-A AA-A AAGA AAGA AAGA AAGA AAG- AAG- AAGA AAGA
1 AAGA A-AGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
206146 AA-A AAGA AA-A AGAGA AA-A AAGA AA
1 AAGA AAGA AAGA A-AGA AAGA AAGA AA
206170 AAGAAAAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
3 20 0.34
4 32 0.55
5 6 0.10
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:206132 original size:22 final size:21
Alignment explanation
Indices: 206107--206177 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 21
206097 AGAGAAGAAG
206107 AGAAAAAAAAAGAAAGAAAGAA
1 AGAAAAAAAAAGAAAGAAA-AA
* *
206129 AGAAAGAAGAAGAAAGAAAAA
1 AGAAAAAAAAAGAAAGAAAAA
206150 AGAAAAAGAGAAA-AAAG-AAAA
1 AGAAAAA-A-AAAGAAAGAAAAA
206171 AGAAAAA
1 AGAAAAA
206178 TAATAAAGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
21 19 0.44
22 22 0.51
23 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAAGAAAGAAAAA
Found at i:206177 original size:7 final size:7
Alignment explanation
Indices: 206107--206177 Score: 83
Period size: 7 Copynumber: 10.0 Consensus size: 7
206097 AGAGAAGAAG
206107 AGAAAAA
1 AGAAAAA
206114 A-AAAGAA
1 AGAAA-AA
206121 AGAAAGAA
1 AGAAA-AA
*
206129 AGAAAGA
1 AGAAAAA
*
206136 AGAAGAA
1 AGAAAAA
206143 AGAAAAA
1 AGAAAAA
206150 AGAAAAA
1 AGAAAAA
206157 GAGAAAAA
1 -AGAAAAA
206165 AG-AAAA
1 AGAAAAA
206171 AGAAAAA
1 AGAAAAA
206178 TAATAAAGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
6 9 0.16
7 29 0.52
8 18 0.32
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:206308 original size:21 final size:21
Alignment explanation
Indices: 206283--206332 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
206273 AAGCAGCCCA
206283 AAAAAAAGAAAAAAACAG-AGC
1 AAAAAAAGAAAAAAA-AGCAGC
* *
206304 AAAAAAAGAGAAAGAAGCAGC
1 AAAAAAAGAAAAAAAAGCAGC
206325 AAAAAAAG
1 AAAAAAAG
206333 GGGCAGGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.74, C:0.08, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAGCAGC
Found at i:206502 original size:11 final size:11
Alignment explanation
Indices: 206462--206518 Score: 64
Period size: 10 Copynumber: 5.2 Consensus size: 11
206452 CCAGTCCAGC
*
206462 AAAAAAA-AAA
1 AAAAAAAGAAG
206472 AAAAAAGAGAAAG
1 AAAAAA-AG-AAG
*
206485 GAAAAAAGAAG
1 AAAAAAAGAAG
206496 AAAAAAAGAAG
1 AAAAAAAGAAG
206507 -AAAAAAGAAG
1 AAAAAAAGAAG
206517 AA
1 AA
206519 GGAAAAAGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 16 0.40
11 15 0.38
12 2 0.05
13 7 0.17
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:207050 original size:18 final size:18
Alignment explanation
Indices: 207027--207085 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
207017 AAAAATCGGG
207027 TTTCAAAAATTTTCGTCT
1 TTTCAAAAATTTTCGTCT
207045 TTTCAAAAAAATTTTC-TCGT
1 TTTC--AAAAATTTTCGTC-T
*
207065 GTTTC-AAAATTTTCGTGT
1 -TTTCAAAAATTTTCGTCT
207083 TTT
1 TTT
207086 TTAAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
17 3 0.09
18 14 0.40
19 3 0.09
20 11 0.31
21 4 0.11
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTCT
Found at i:207056 original size:20 final size:21
Alignment explanation
Indices: 207031--207073 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
207021 ATCGGGTTTC
207031 AAAAATTTTCGTC-T-TTTCAA
1 AAAAATTTTC-TCGTGTTTCAA
207051 AAAAATTTTCTCGTGTTTCAA
1 AAAAATTTTCTCGTGTTTCAA
207072 AA
1 AA
207074 TTTTCGTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.10
20 11 0.52
21 8 0.38
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAAATTTTCTCGTGTTTCAA
Found at i:207111 original size:37 final size:35
Alignment explanation
Indices: 207026--207147 Score: 111
Period size: 37 Copynumber: 3.3 Consensus size: 35
207016 AAAAAATCGG
* * *
207026 GTTTCAAAAATTTTCGTCTTTTCAAAAAAATTTTCTCGT
1 GTTTC-AAAATTTTCGTTTTTTTAAAAAAA-ATTCT--T
207065 GTTTCAAAATTTTCGTGTTTTTTAAAAAAAATTCTT
1 GTTTCAAAATTTTCGT-TTTTTTAAAAAAAATTCTT
* *
207101 GTTTCTAAAATTCTT-GTATTTTTTTAAAAAAATTCGT
1 GTTTC-AAAATT-TTCGT-TTTTTTAAAAAAAATTCTT
207138 GTTTTCAAAA
1 G-TTTCAAAA
207148 AAAGAAAAAG
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
36 6 0.08
37 30 0.41
38 21 0.29
39 16 0.22
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (35 bp):
GTTTCAAAATTTTCGTTTTTTTAAAAAAAATTCTT
Found at i:209303 original size:16 final size:15
Alignment explanation
Indices: 209270--209299 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
209260 AAAATAAAAG
209270 AATATATGAATTTTT
1 AATATATGAATTTTT
209285 AATATATGAATTTTT
1 AATATATGAATTTTT
209300 TAATCCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
AATATATGAATTTTT
Found at i:209828 original size:27 final size:25
Alignment explanation
Indices: 209803--209852 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
209793 GAACCTTAGC
* *
209803 GCGCTCTCTGATTATTAGCACGTTA
1 GCGCTATCTGATTATTAGAACGTTA
*
209828 GTGCTATCTGATTATTAGAACGTTA
1 GCGCTATCTGATTATTAGAACGTTA
209853 TTGCTCTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (25 bp):
GCGCTATCTGATTATTAGAACGTTA
Found at i:209837 original size:25 final size:25
Alignment explanation
Indices: 209809--209863 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
209799 TAGCGCGCTC
*
209809 TCTGATTATTAGCACGTTAGTGCTA
1 TCTGATTATTAGAACGTTAGTGCTA
* *
209834 TCTGATTATTAGAACGTTATTGCTC
1 TCTGATTATTAGAACGTTAGTGCTA
209859 TCTGA
1 TCTGA
209864 ATAGCACATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (25 bp):
TCTGATTATTAGAACGTTAGTGCTA
Found at i:214804 original size:24 final size:24
Alignment explanation
Indices: 214772--214817 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
214762 ACTGCATATA
214772 ATATTATATGTACGTAATATGTAT
1 ATATTATATGTACGTAATATGTAT
**
214796 ATATTATATGTGTGTAATATGT
1 ATATTATATGTACGTAATATGT
214818 GTTATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (24 bp):
ATATTATATGTACGTAATATGTAT
Found at i:218168 original size:31 final size:31
Alignment explanation
Indices: 218130--218199 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
218120 ATAGATTTAA
218130 AAAGGAAAGAAAAAATAACTTTCATCATTAT
1 AAAGGAAAGAAAAAATAACTTTCATCATTAT
218161 AAAGGAAAGAAAAAATAACTTTCATCATTAT
1 AAAGGAAAGAAAAAATAACTTTCATCATTAT
218192 AAAGGAAA
1 AAAGGAAA
218200 AGTGAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.23
Consensus pattern (31 bp):
AAAGGAAAGAAAAAATAACTTTCATCATTAT
Found at i:219176 original size:11 final size:11
Alignment explanation
Indices: 219160--219202 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
219150 ATATAATATT
*
219160 ATATGTACGTA
1 ATATGTATGTA
*
219171 ATATGTATATA
1 ATATGTATGTA
219182 TTATATGTATGTA
1 --ATATGTATGTA
219195 ATATGTAT
1 ATATGTAT
219203 TATACATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (11 bp):
ATATGTATGTA
Found at i:219187 original size:24 final size:24
Alignment explanation
Indices: 219155--219202 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
219145 ACTGCATATA
219155 ATATTATATGTACGTAATATGTAT
1 ATATTATATGTACGTAATATGTAT
*
219179 ATATTATATGTATGTAATATGTAT
1 ATATTATATGTACGTAATATGTAT
219203 TATACATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (24 bp):
ATATTATATGTACGTAATATGTAT
Found at i:219205 original size:20 final size:21
Alignment explanation
Indices: 219150--219206 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 21
219140 ATGTAACTGC
*
219150 ATATAATATTATATGTACGTA
1 ATATGATATTATATGTACGTA
*
219171 ATATGTATATATTATATGTATGTA
1 ATATG---ATATTATATGTACGTA
219195 ATATG-TATTATA
1 ATATGATATTATA
219207 CATTATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 7 0.23
21 4 0.13
24 20 0.65
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (21 bp):
ATATGATATTATATGTACGTA
Found at i:220589 original size:77 final size:76
Alignment explanation
Indices: 220453--220610 Score: 289
Period size: 77 Copynumber: 2.1 Consensus size: 76
220443 AATTAAAGAC
* *
220453 TGGTATGGTCCGTCAATTACGGTCGACAAGGAAACAATATTATAAAGTAAGAAAAGGCAGGCAAT
1 TGGTGTGGCCCGTCAATTACGGTCGACAAGGAAACAATATTATAAAGTAAGAAAAGGCAGGCAAT
220518 TATGTTTGGTAG
66 TAT-TTTGGTAG
220530 TGGTGTGGCCCGTCAATTACGGTCGACAAGGAAACAATATTATAAAGTAAGAAAAGGCAGGCAAT
1 TGGTGTGGCCCGTCAATTACGGTCGACAAGGAAACAATATTATAAAGTAAGAAAAGGCAGGCAAT
220595 TATTTTGGTAG
66 TATTTTGGTAG
220606 TGGTG
1 TGGTG
220611 AAGGTTAAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
76 13 0.16
77 66 0.84
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (76 bp):
TGGTGTGGCCCGTCAATTACGGTCGACAAGGAAACAATATTATAAAGTAAGAAAAGGCAGGCAAT
TATTTTGGTAG
Found at i:225545 original size:21 final size:23
Alignment explanation
Indices: 225520--225568 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
225510 TTCAACTATT
225520 TAATTAT-AACAAATT-AATTAA
1 TAATTATAAACAAATTAAATTAA
*
225541 TAATT-TAAATAAATTAAATTAA
1 TAATTATAAACAAATTAAATTAA
*
225563 TCATTA
1 TAATTA
225569 AGTTATCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATTATAAACAAATTAAATTAA
Found at i:227026 original size:15 final size:15
Alignment explanation
Indices: 227006--227037 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
226996 ATGTATAAAA
227006 AAAATGGAAGAATTT
1 AAAATGGAAGAATTT
227021 AAAATGGAAGAATTT
1 AAAATGGAAGAATTT
227036 AA
1 AA
227038 TTCAATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (15 bp):
AAAATGGAAGAATTT
Found at i:229367 original size:6 final size:6
Alignment explanation
Indices: 229356--229391 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
229346 GGGAAGTTAC
229356 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
229392 TATAAGTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:230920 original size:99 final size:99
Alignment explanation
Indices: 230736--230930 Score: 230
Period size: 99 Copynumber: 2.0 Consensus size: 99
230726 ATGCTCCTAC
* * *
230736 AAGATGGAGTTTATACAACTCAACCAGTTTACCCAGAGTGCAGGGTTAACCCAATTGAAACAAAT
1 AAGATGGAGTTTATACAACTAAACCAGTTTACCCAGAGTGCAGGGTTAACCCAATTCAAAAAAAT
* *
230801 CAATTTAACAGACATATTGGAAGTAGCCTCCCAG
66 CAACTCAACAGACATATTGGAAGTAGCCTCCCAG
* *** * * *
230835 AAGATGGAGTTTATACAGCTAAACCAGTTTACTTGGAGTGTAGGGTTAACTCACTTCAAAAAAAT
1 AAGATGGAGTTTATACAACTAAACCAGTTTACCCAGAGTGCAGGGTTAACCCAATTCAAAAAAAT
** * *
230900 -ACACTCAATGGTCATGTTGGAAGTAGCCTCC
66 CA-ACTCAACAGACATATTGGAAGTAGCCTCC
230931 AAGATGAGCT
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
98 1 0.01
99 78 0.99
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (99 bp):
AAGATGGAGTTTATACAACTAAACCAGTTTACCCAGAGTGCAGGGTTAACCCAATTCAAAAAAAT
CAACTCAACAGACATATTGGAAGTAGCCTCCCAG
Found at i:233170 original size:30 final size:30
Alignment explanation
Indices: 233134--233192 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
233124 CATCAATCAT
*
233134 AGAGAGAACCATCCACATTGCCAATGCCAC
1 AGAGAGAACCATCCACAATGCCAATGCCAC
* *
233164 AGAGAGATCCATCCACAATGTCAATGCCA
1 AGAGAGAACCATCCACAATGCCAATGCCA
233193 ACGCCAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.15
Consensus pattern (30 bp):
AGAGAGAACCATCCACAATGCCAATGCCAC
Found at i:238109 original size:20 final size:21
Alignment explanation
Indices: 238066--238122 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
238056 ATATATGAAC
*
238066 ATTTTGGAATTTTTGAAAAAT
1 ATTTTGGAATTTTTTAAAAAT
**
238087 ATTTT-GAATTTTTTAAATTT
1 ATTTTGGAATTTTTTAAAAAT
238107 ATTTTGGAATTGTTTT
1 ATTTTGGAATT-TTTT
238123 GTATTTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.55
21 10 0.32
22 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (21 bp):
ATTTTGGAATTTTTTAAAAAT
Found at i:241035 original size:15 final size:14
Alignment explanation
Indices: 241005--241038 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
240995 AGGCGCCATG
*
241005 AGTAAATAATTAAT
1 AGTAAATAAGTAAT
241019 AGTAAAGTAAGTAAT
1 AGTAAA-TAAGTAAT
241034 AGTAA
1 AGTAA
241039 TAAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (14 bp):
AGTAAATAAGTAAT
Found at i:242803 original size:44 final size:43
Alignment explanation
Indices: 242746--243078 Score: 264
Period size: 44 Copynumber: 7.7 Consensus size: 43
242736 GTTTCTTTTG
* * *
242746 TCTGCTCCGCTACTGCTTAGGGAGATAAGACTTACAATCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TTGCCATCTTCGA
* * * **** **
242790 CCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATTGCCATCTTCGA
* * * *
242833 TCTGCTTCACTACTGTTTAGGAAGATAAGATTTGCCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TTGCCATCTTCGA
* * * *
242877 TCTGCTCCACTACTGCTTAAGGAGATAGGATCTACCATCTTTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGAT-TGCCATCTTCGA
* * * * ** **
242921 -CTTGTTCCTCTACTGCTTAGGGAGATAGGACTCGTGA-CTTAAA
1 TC-TGCTCCACTACTGCTTAGGGAGATAAGA-TTGCCATCTTCGA
* * *
242964 TCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATT-GCCATCTTCGA
*
243008 TCTGCTCCACTACTGCTTAGGGAGATAAGATTTG--A--TGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TTGCCATCTTCGA
*
243048 TCTACTCCACTACTGCTTAGGGAGATAAGAT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGAT
243079 CTACAATCTT
Statistics
Matches: 226, Mismatches: 55, Indels: 21
0.75 0.18 0.07
Matches are distributed among these distances:
39 1 0.00
40 33 0.15
42 1 0.00
43 60 0.27
44 128 0.57
45 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (43 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATTGCCATCTTCGA
Found at i:242984 original size:131 final size:131
Alignment explanation
Indices: 242746--243074 Score: 461
Period size: 131 Copynumber: 2.5 Consensus size: 131
242736 GTTTCTTTTG
*
242746 TCTGCTCCGCTACTGCTTAGGGAGATAAGACTTACAATCTTCGACCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTACAATCTTCGACCTGCTCCACTACTGCTTAGG
* * * *
242811 GAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGTTTAGGAAGATAAGATTTGCCGTCTTCG
66 GAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCG
242876 A
131 A
* * * * * * *
242877 TCTGCTCCACTACTGCTTAAGGAGATAGGA-TCTACCATCTTTGACTTGTTCCTCTACTGCTTAG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACT-TACAATCTTCGACCTGCTCCACTACTGCTTAG
242941 GGAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTC
65 GGAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTC
243006 GA
130 GA
** * * *
243008 TCTGCTCCACTACTGCTTAGGGAGATAAGA-TT-TGA--TGCGATCTACTCCACTACTGCTTAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTACAATCTTCGACCTGCTCCACTACTGCTTAGG
243069 GAGATA
66 GAGATA
243075 AGATCTACAA
Statistics
Matches: 174, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
127 25 0.14
129 1 0.01
130 2 0.01
131 146 0.84
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (131 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTACAATCTTCGACCTGCTCCACTACTGCTTAGG
GAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCG
A
Found at i:243100 original size:84 final size:87
Alignment explanation
Indices: 242747--243102 Score: 254
Period size: 87 Copynumber: 4.1 Consensus size: 87
242737 TTTCTTTTGT
* **** * *
242747 CTGCTCCGCTACTGCTTAGGGAGATAAGACTTACAATCTTCGACCTGCTCCACTACTGCTTAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGACTCGTGA-CTGCGATCTGCTCCACTACTGCTTAGGG
* ***** ** *
242812 AGATAGGA-CTGGTGGCTTAAAT
65 AGATAAGATCTACCATCTTCGAC
* * * * * * * * *
242834 CTGCTTCACTACTGTTTAGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAAGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGACTCG-TGACTGCGATCTGCTCCACTACTGCTTAGGG
* *
242899 AGATAGGATCTACCATCTTTGAC
65 AGATAAGATCTACCATCTTCGAC
* * * * *** * *
242922 TTGTTCCTCTACTGCTTAGGGAGATAGGACTCGTGACTTAAATCTGCTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAAGACTCGTGACTGCGATCTGCTCCACTACTGCTTAGGGA
* * *
242987 GATAAGAT-TCGCCGTCTTCGAT
66 GATAAGATCT-ACCATCTTCGAC
* *
243009 CTGCTCCACTACTGCTTAGGGAGATAAGA-T-TTGA-TGCGATCTACTCCACTACTGCTTAGGGA
1 CTGCTCCACTACTGCTTAGGGAGATAAGACTCGTGACTGCGATCTGCTCCACTACTGCTTAGGGA
* *
243071 GATAAGATCTACAATCTTCAAC
66 GATAAGATCTACCATCTTCGAC
*
243093 CTACTCCACT
1 CTGCTCCACT
243103 GCTNNNNNNN
Statistics
Matches: 209, Mismatches: 56, Indels: 11
0.76 0.20 0.04
Matches are distributed among these distances:
84 46 0.22
85 4 0.02
86 2 0.01
87 126 0.60
88 31 0.15
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (87 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGACTCGTGACTGCGATCTGCTCCACTACTGCTTAGGGA
GATAAGATCTACCATCTTCGAC
Found at i:243518 original size:87 final size:87
Alignment explanation
Indices: 243427--243588 Score: 200
Period size: 87 Copynumber: 1.9 Consensus size: 87
243417 GCCGTTTTCG
* * * *
243427 ATCTGCTCCACTACTGCTTAAGGAGATAGGATCTAATATCATT-GACCTGCTCCGCTACTGCTTA
1 ATCTGCTCCACTACTGCTTAAGAAGATAAGATCTAACATC-TTCGACCTGCTCCACTACTGCTTA
243491 GGGAGATAGGACTGGTGGCTTAA
65 GGGAGATAGGACTGGTGGCTTAA
* * * * ** * *
243514 ATCTGCTTCGCTACTGTTTAAGAAGATAAGATTTGCCATCTTCGATCTGCTCCATTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAAGAAGATAAGATCTAACATCTTCGACCTGCTCCACTACTGCTTAG
243579 GGAGATAGGA
66 GGAGATAGGA
243589 TCTACCATCT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
86 2 0.03
87 60 0.97
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (87 bp):
ATCTGCTCCACTACTGCTTAAGAAGATAAGATCTAACATCTTCGACCTGCTCCACTACTGCTTAG
GGAGATAGGACTGGTGGCTTAA
Found at i:243576 original size:131 final size:131
Alignment explanation
Indices: 243342--243733 Score: 586
Period size: 131 Copynumber: 3.0 Consensus size: 131
243332 NNNNNNNNNN
*
243342 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGTCTTAAATCTACTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
* * * * *
243407 GATGAGATTCGCCGTTTTCGATCTGCTCCACTACTGCTTAAGGAGATAGGATCTAATATCATTGA
66 GATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGA
243472 C
131 C
* * * * *
243473 CTGCTCCGCTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCGCTACTGTTTAAGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
* * * *
243538 GATAAGATTTGCCATCTTCGATCTGCTCCATTACTGCTTAGGGAGATAGGATCTACCATCTTTGA
66 GATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGA
243603 C
131 C
* * * * *
243604 TTGTTCCTCTACTGCTTAGGGAGATAGGACTCGTGGCTTAAATATACTTCACTACTGCTTAGGAA
1 CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
* *
243669 GATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGA
66 GATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGA
243734 TCTATTCTCT
Statistics
Matches: 231, Mismatches: 30, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
131 231 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (131 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAA
GATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGA
C
Found at i:243585 original size:44 final size:44
Alignment explanation
Indices: 243342--243720 Score: 221
Period size: 44 Copynumber: 8.7 Consensus size: 44
243332 NNNNNNNNNN
* ** **
243342 CTGCTCCACTACTGCTTAGGGAGATAGGA-CTGGTGTCTTAAAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGATTTGCCGTCTTCGAT
* * * * *
243385 CTACTTCACTACTGCTTAGGAAGAT-GAGATTCGCCGTTTTCGAT
1 CTGCTCCACTACTGCTTAGGGAGATAG-GATTTGCCGTCTTCGAT
* * **** *
243429 CTGCTCCACTACTGCTTAAGGAGATAGGATCTAATATCATT-GAC
1 CTGCTCCACTACTGCTTAGGGAGATAGGATTTGCCGTC-TTCGAT
* * ** * **
243473 CTGCTCCGCTACTGCTTAGGGAGATAGGA-CTGGTGGCTTAAAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGATTTGCCGTCTTCGAT
* * * * * * *
243516 CTGCTTCGCTACTGTTTAAGAAGATAAGATTTGCCATCTTCGAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGATTTGCCGTCTTCGAT
* * * * *
243560 CTGCTCCATTACTGCTTAGGGAGATAGGATCTACCATCTTTGA-
1 CTGCTCCACTACTGCTTAGGGAGATAGGATTTGCCGTCTTCGAT
* * * * * * **
243603 CTTGTTCCTCTACTGCTTAGGGAGATAGGACTCG-TGGCTTAAAT
1 C-TGCTCCACTACTGCTTAGGGAGATAGGATTTGCCGTCTTCGAT
* * * * * ** *
243647 ATACTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCAAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGATTTGCCGTCTTCGAT
243691 CTGCTCCACTACTGCTTAGGGAGATAGGAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGAT
243721 CTAACATCTT
Statistics
Matches: 246, Mismatches: 81, Indels: 17
0.72 0.24 0.05
Matches are distributed among these distances:
42 3 0.01
43 82 0.33
44 158 0.64
45 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (44 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGATTTGCCGTCTTCGAT
Found at i:245841 original size:6 final size:6
Alignment explanation
Indices: 245830--245864 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
245820 TGGCCTCTCC
245830 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
245865 ATCCTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:245960 original size:7 final size:7
Alignment explanation
Indices: 245950--245988 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
245940 TTGATTTTGA
245950 TTTTTCT
1 TTTTTCT
245957 TTTTTCT
1 TTTTTCT
245964 TTTTTCT
1 TTTTTCT
245971 TTTTGT-T
1 TTTT-TCT
*
245978 TTTTTAT
1 TTTTTCT
245985 TTTT
1 TTTT
245989 ATTTTTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 1 0.03
7 28 0.93
8 1 0.03
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.87
Consensus pattern (7 bp):
TTTTTCT
Found at i:245967 original size:14 final size:14
Alignment explanation
Indices: 245950--245995 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
245940 TTGATTTTGA
245950 TTTTTCTTTTT-TCT
1 TTTTTCTTTTTGT-T
245964 TTTTTCTTTTTGTT
1 TTTTTCTTTTTGTT
* *
245978 TTTTTATTTTTATT
1 TTTTTCTTTTTGTT
245992 TTTT
1 TTTT
245996 GATTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 28 0.97
15 1 0.03
ACGTcount: A:0.04, C:0.07, G:0.02, T:0.87
Consensus pattern (14 bp):
TTTTTCTTTTTGTT
Found at i:246000 original size:14 final size:13
Alignment explanation
Indices: 245943--246002 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
245933 TTTGATCTTG
*
245943 ATTTTGATTTTTCT
1 ATTTTTATTTTT-T
*
245957 -TTTTTCTTTTTT
1 ATTTTTATTTTTT
* *
245969 CTTTTTGTTTTTTT
1 ATTTTT-ATTTTTT
245983 ATTTTTATTTTTT
1 ATTTTTATTTTTT
245996 GATTTTT
1 -ATTTTT
246003 TTCATTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 20 0.53
14 17 0.45
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:252676 original size:44 final size:43
Alignment explanation
Indices: 252531--252687 Score: 145
Period size: 44 Copynumber: 3.6 Consensus size: 43
252521 TGGATGCGAT
* * * *
252531 CTGCTCTACTATTGCTTAGAGAGATAAGATATACAATCTTCAAC
1 CTGCTCCACTACTGCTTAGGGAGATAAGAT-TACAATCTTCGAC
* * * * **** * *
252575 CTACTCCACTGCTGCTCAGGGAGATAGGATTGGTTTCTTTTG-T
1 CTGCTCCACTACTGCTTAGGGAGATAAGATTACAATC-TTCGAC
*
252618 CTGCTCCGCTACTGCTTAGGGAGATAAGACTTACAATCTTCGAC
1 CTGCTCCACTACTGCTTAGGGAGATAAGA-TTACAATCTTCGAC
252662 CTGCTCCACTACTGCTTAGGGAGATA
1 CTGCTCCACTACTGCTTAGGGAGATA
252688 GGACTGGTGG
Statistics
Matches: 84, Mismatches: 26, Indels: 6
0.72 0.22 0.05
Matches are distributed among these distances:
43 30 0.36
44 54 0.64
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (43 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATTACAATCTTCGAC
Found at i:252708 original size:87 final size:87
Alignment explanation
Indices: 252529--252718 Score: 229
Period size: 87 Copynumber: 2.2 Consensus size: 87
252519 ACTGGATGCG
* * *
252529 ATCTGCTCTACTATTGCTTAGAGAGATAAGATATACAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGAGAGATAAGATATACAATCTTCAACCTACTCCACTACTGCTCAG
* ** **
252594 GGAGATAGGATTGGTTTCTTTT
66 GGAGATAGGACTGGTGGCTTAA
* * * * * *
252616 GTCTGCTCCGCTACTGCTTAGGGAGATAAGACT-TACAATCTTCGACCTGCTCCACTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGAGAGATAAGA-TATACAATCTTCAACCTACTCCACTACTGCTCA
252680 GGGAGATAGGACTGGTGGCTTAA
65 GGGAGATAGGACTGGTGGCTTAA
*
252703 ATCTGCTTCACTACTG
1 ATCTGCTCCACTACTG
252719 NNNNNNNNNN
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
87 84 0.99
88 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (87 bp):
ATCTGCTCCACTACTGCTTAGAGAGATAAGATATACAATCTTCAACCTACTCCACTACTGCTCAG
GGAGATAGGACTGGTGGCTTAA
Found at i:253299 original size:44 final size:44
Alignment explanation
Indices: 253236--254182 Score: 1885
Period size: 44 Copynumber: 21.5 Consensus size: 44
253226 CTTCGATCTG
253236 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253280 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253324 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253368 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253412 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253456 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253500 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253544 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253588 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253632 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253676 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253720 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253764 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253808 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253852 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253896 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253940 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
253984 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
254028 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
254072 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
*
254116 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTG
1 CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
254160 CTCCACTACTGCTTAGGGAGATA
1 CTCCACTACTGCTTAGGGAGATA
254183 AGACTGGTGG
Statistics
Matches: 902, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 902 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAGGATCTAACATCTTTGACCTA
Found at i:255704 original size:15 final size:14
Alignment explanation
Indices: 255674--255707 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
255664 AGGCGCCATG
*
255674 AGTAAATAATTAAT
1 AGTAAATAAGTAAT
255688 AGTAAAGTAAGTAAT
1 AGTAAA-TAAGTAAT
255703 AGTAA
1 AGTAA
255708 TAAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (14 bp):
AGTAAATAAGTAAT
Found at i:255717 original size:15 final size:15
Alignment explanation
Indices: 255678--255748 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
255668 GCCATGAGTA
255678 AATAATTAATAGTAA-
1 AATAA-TAATAGTAAT
*
255693 AGTAAGTAATAGTAAT
1 AATAA-TAATAGTAAT
*
255709 AA-ATATAATACTAAT
1 AATA-ATAATAGTAAT
*
255724 AATAATAATAGTAGT
1 AATAATAATAGTAAT
*
255739 AGTAATAATA
1 AATAATAATA
255749 TAGTAAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
15 43 0.93
16 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.10, T:0.32
Consensus pattern (15 bp):
AATAATAATAGTAAT
Found at i:260940 original size:20 final size:20
Alignment explanation
Indices: 260915--260952 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
260905 AAATTTTGAG
260915 ATTTTTGAAATATATTTTTA
1 ATTTTTGAAATATATTTTTA
*
260935 ATTTTTGAAATTTATTTT
1 ATTTTTGAAATATATTTT
260953 GAACTCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTTTTGAAATATATTTTTA
Found at i:267997 original size:103 final size:104
Alignment explanation
Indices: 267837--268024 Score: 290
Period size: 103 Copynumber: 1.8 Consensus size: 104
267827 TTTAAGAATG
* * *
267837 TGTTGGGCTAAGTAACCAGGATGGGGTGTTTGGTTATCATCTTTCTTTGCGTCAAAAGGTTCAAT
1 TGTTGGGCTAAGTAACCAGGATGGGGTGCTTGGTTATCATCTCTCTTCGCGTCAAAAGGTTCAAT
267902 ATATTATTAAGAAAAGAAAACATATATAAATTAGAAGTA
66 ATATTATTAAGAAAAGAAAACATATATAAATTAGAAGTA
* * *
267941 TGTTGGGCTGAGTAACCAGGGT-GGGTGCTTGGTTGTCATCTCTCTTCGCG-CGAAAAGGTTCAA
1 TGTTGGGCTAAGTAACCAGGATGGGGTGCTTGGTTATCATCTCTCTTCGCGTC-AAAAGGTTCAA
*
268004 TATATTCTTAAGAAAAGAAAA
65 TATATTATTAAGAAAAGAAAA
268025 AAAAAGAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
102 1 0.01
103 55 0.72
104 20 0.26
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (104 bp):
TGTTGGGCTAAGTAACCAGGATGGGGTGCTTGGTTATCATCTCTCTTCGCGTCAAAAGGTTCAAT
ATATTATTAAGAAAAGAAAACATATATAAATTAGAAGTA
Found at i:268061 original size:26 final size:25
Alignment explanation
Indices: 268013--268063 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
268003 ATATATTCTT
268013 AAGAAAAGAAAAAAAAAGAAAAAAG
1 AAGAAAAGAAAAAAAAAGAAAAAAG
* *
268038 AAGAAGAAGGAAAAACAAGTAAAAAA
1 AAGAA-AAGAAAAAAAAAG-AAAAAA
268064 TAATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 11 0.50
27 6 0.27
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (25 bp):
AAGAAAAGAAAAAAAAAGAAAAAAG
Found at i:273213 original size:12 final size:12
Alignment explanation
Indices: 273196--273220 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
273186 TGATATTAAG
273196 AACTATCATATA
1 AACTATCATATA
273208 AACTATCATATA
1 AACTATCATATA
273220 A
1 A
273221 TTACACTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
AACTATCATATA
Found at i:276453 original size:15 final size:16
Alignment explanation
Indices: 276433--276466 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
276423 TCAATTTTTT
276433 TTCTTTCTT-TCTTTC
1 TTCTTTCTTATCTTTC
*
276448 TTCTTTCTTATGTTTC
1 TTCTTTCTTATCTTTC
276464 TTC
1 TTC
276467 CGCCATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.03, C:0.24, G:0.03, T:0.71
Consensus pattern (16 bp):
TTCTTTCTTATCTTTC
Found at i:296005 original size:31 final size:30
Alignment explanation
Indices: 295950--296025 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
295940 ACGTGAAAGG
* **
295950 CTTAATTGATTTATT-ATTATTTTAGGAGGT
1 CTTAATTGATTT-TTAAGTATTTTAGGAGAA
295980 CTTAATTGACTTTTTAAGTATTTTAGGAGAA
1 CTTAATTGA-TTTTTAAGTATTTTAGGAGAA
296011 CTTAATTGATTTTTA
1 CTTAATTGATTTTTA
296026 GGGACTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
30 17 0.41
31 24 0.59
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
CTTAATTGATTTTTAAGTATTTTAGGAGAA
Found at i:297000 original size:36 final size:36
Alignment explanation
Indices: 296960--297043 Score: 159
Period size: 36 Copynumber: 2.3 Consensus size: 36
296950 ATTTTGTCCA
296960 GGCCCGGCCCGAAAAAAATTTCTTAGGCCCGAGCCC
1 GGCCCGGCCCGAAAAAAATTTCTTAGGCCCGAGCCC
*
296996 GGCCCGGCCCGGAAAAAATTTCTTAGGCCCGAGCCC
1 GGCCCGGCCCGAAAAAAATTTCTTAGGCCCGAGCCC
297032 GGCCCGGCCCGA
1 GGCCCGGCCCGA
297044 TCCGTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.21, C:0.38, G:0.29, T:0.12
Consensus pattern (36 bp):
GGCCCGGCCCGAAAAAAATTTCTTAGGCCCGAGCCC
Found at i:297967 original size:28 final size:27
Alignment explanation
Indices: 297936--298005 Score: 63
Period size: 29 Copynumber: 2.4 Consensus size: 27
297926 ATCAATAAAA
297936 TTTTATAACATTTA-GCAATATTT-ATAAT
1 TTTTATAA-ATTTATG--ATATTTAATAAT
*
297964 TTTTTTAAAATTTTATGATATTTAATAAT
1 TTTTAT-AAA-TTTATGATATTTAATAAT
297993 TTTCTATAAATTT
1 TTT-TATAAATTT
298006 TATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
28 15 0.43
29 17 0.49
30 3 0.09
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (27 bp):
TTTTATAAATTTATGATATTTAATAAT
Found at i:298006 original size:29 final size:30
Alignment explanation
Indices: 297952--298026 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
297942 AACATTTAGC
*
297952 AATATTT-ATAATTTT-TTTAAAATTTTAT
1 AATATTTAATAATTTTCTATAAAATTTTAT
*
297980 GATATTTAATAATTTTCTAT-AAATTTTAT
1 AATATTTAATAATTTTCTATAAAATTTTAT
298009 AATAAATTTAAT-ATTTTC
1 AAT--ATTTAATAATTTTC
298027 AATTTAGTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.15
29 19 0.47
30 8 0.20
31 7 0.17
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (30 bp):
AATATTTAATAATTTTCTATAAAATTTTAT
Found at i:298153 original size:30 final size:30
Alignment explanation
Indices: 298119--298197 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
298109 CATATAATCC
298119 TTAAAAATCAATTAAGCTCTCCTAAAATAA
1 TTAAAAATCAATTAAGCTCTCCTAAAATAA
*
298149 TTAAAAATCAATTAAGCCCTCCTAAAATAA
1 TTAAAAATCAATTAAGCTCTCCTAAAATAA
*
298179 --AGAAAATTAATTAAGCTCT
1 TTA-AAAATCAATTAAGCTCT
298198 TCACATCAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.02
29 15 0.33
30 29 0.64
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.29
Consensus pattern (30 bp):
TTAAAAATCAATTAAGCTCTCCTAAAATAA
Found at i:306630 original size:99 final size:100
Alignment explanation
Indices: 306502--306703 Score: 397
Period size: 99 Copynumber: 2.0 Consensus size: 100
306492 TCTAATAAAA
306502 AATTTCAATTTTTACATAGAATTATTTTAAGAAAACACTCGCTCTTAATATTGTTTATATTAATA
1 AATTTCAATTTTTACATAGAATTATTTTAAGAAAACACTCGCTCTTAATATTGTTTATATTAATA
306567 AAAAATTAGAATATTTTTAAATTAAATAAAAGGTT
66 AAAAATTAGAATATTTTTAAATTAAATAAAAGGTT
306602 AATTTCAATTTTT-CATAGAATTATTTTAAGAAAACACTCGCTCTTAATATTGTTTATATTAATA
1 AATTTCAATTTTTACATAGAATTATTTTAAGAAAACACTCGCTCTTAATATTGTTTATATTAATA
306666 AAAAATTAGAATATTTTTAAATTAAATAAAAGGTT
66 AAAAATTAGAATATTTTTAAATTAAATAAAAGGTT
306701 AAT
1 AAT
306704 ATGTAATTTG
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 89 0.87
100 13 0.13
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (100 bp):
AATTTCAATTTTTACATAGAATTATTTTAAGAAAACACTCGCTCTTAATATTGTTTATATTAATA
AAAAATTAGAATATTTTTAAATTAAATAAAAGGTT
Done.