Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold6
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: 1308201
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
File 3 of 11
Found at i:187647 original size:30 final size:27
Alignment explanation
Indices: 187525--187670 Score: 92
Period size: 26 Copynumber: 5.5 Consensus size: 27
187515 ATAAAATTTA
* *
187525 ATAT-AATAAAAAAAT-TAAAAATATG
1 ATATAAATATAAAAATATATAAATATG
* * *
187550 ATATAAATATACATATATTTAAA-AT-
1 ATATAAATATAAAAATATATAAATATG
* * *
187575 TTATATAATAT--TAATATATCAAAT-TT
1 ATATA-AATATAAAAATATAT-AAATATG
* *
187601 ATTTAAATAT-AAAATATTTAAATATG
1 ATATAAATATAAAAATATATAAATATG
*
187627 ATTATAATATGATAAAAATATATGAATATG
1 A-TATAA-AT-ATAAAAATATATAAATATG
187657 ATATAAATATAAAA
1 ATATAAATATAAAA
187671 TCTTTTAATT
Statistics
Matches: 92, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
24 5 0.05
25 21 0.23
26 26 0.28
27 14 0.15
28 4 0.04
29 7 0.08
30 15 0.16
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (27 bp):
ATATAAATATAAAAATATATAAATATG
Found at i:187665 original size:11 final size:11
Alignment explanation
Indices: 187607--187666 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
187597 ATTTATTTAA
187607 ATATAAA-AT-
1 ATATAAATATG
*
187616 ATTTAAATATG
1 ATATAAATATG
187627 AT-TATAATATG
1 ATATA-AATATG
187638 ATA-AAA-AT-
1 ATATAAATATG
*
187646 ATATGAATATG
1 ATATAAATATG
187657 ATATAAATAT
1 ATATAAATAT
187667 AAAATCTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
8 3 0.07
9 10 0.24
10 8 0.20
11 20 0.49
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (11 bp):
ATATAAATATG
Found at i:187707 original size:15 final size:14
Alignment explanation
Indices: 187675--187718 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
187665 ATAAAATCTT
*
187675 TTAATTATTTATAAA
1 TTAA-TATTTATATA
187690 TTAATATTTAATATA
1 TTAATATTT-ATATA
*
187705 TTAAAATTTATATA
1 TTAATATTTATATA
187719 AATATACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAATATTTATATA
Found at i:187764 original size:17 final size:17
Alignment explanation
Indices: 187709--187764 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
187699 AATATATTAA
187709 AATTTATATAAATATACAAT
1 AATTTA-ATAAA-ATA-AAT
* *
187729 ATTTTAAATAAAAT-TAT
1 AATTT-AATAAAATAAAT
187746 AATTTAATAAAATAAAT
1 AATTTAATAAAATAAAT
187763 AA
1 AA
187765 AGTGTAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 8 0.27
17 10 0.33
19 2 0.07
20 9 0.30
21 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTTAATAAAATAAAT
Found at i:188042 original size:16 final size:16
Alignment explanation
Indices: 188023--188068 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
188013 TATTAATTAT
188023 TTATTATATTTAATAA
1 TTATTATATTTAATAA
*
188039 TTATTAAATATTAA-AA
1 TTATTATAT-TTAATAA
*
188055 TTA-TGTATTTAATA
1 TTATTATATTTAATA
188069 TTTAATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 4 0.16
15 4 0.16
16 13 0.52
17 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TTATTATATTTAATAA
Found at i:188078 original size:20 final size:18
Alignment explanation
Indices: 188015--188075 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 18
188005 TATATTTTTA
188015 TTAATTATTTATT--ATAT
1 TTAATTA-TTATTAAATAT
*
188032 TTAATAATTATTAAATAT
1 TTAATTATTATTAAATAT
* *
188050 TAAAATTATGTATTTAATAT
1 T-TAATTAT-TATTAAATAT
188070 TTAATT
1 TTAATT
188076 TATTTTTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 5 0.14
17 6 0.17
18 5 0.14
19 9 0.26
20 10 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTAATTATTATTAAATAT
Found at i:188870 original size:30 final size:30
Alignment explanation
Indices: 188836--188893 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
188826 ATTTTTATAT
188836 TAATATTTATTT-ATAATTAAATATAAATAA
1 TAATATTT-TTTAATAATTAAATATAAATAA
* *
188866 TAATATTTTTTAATTATTAAATTTAAAT
1 TAATATTTTTTAATAATTAAATATAAAT
188894 TTAAATCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TAATATTTTTTAATAATTAAATATAAATAA
Found at i:189352 original size:3 final size:3
Alignment explanation
Indices: 189344--189384 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
189334 ACTTAACACC
189344 TTA 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 TTA TT
189385 TGATTAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:189743 original size:21 final size:22
Alignment explanation
Indices: 189692--189747 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
189682 AGTACATTCG
*
189692 AATTAATTTTTAAATATATCTTT
1 AATTAA-TTTTAAATAAATCTTT
189715 --TTATATTTTAAATAAAT-TTT
1 AATTA-ATTTTAAATAAATCTTT
189735 AATTAA-TTTAAAT
1 AATTAATTTTAAAT
189748 TATTATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
20 10 0.34
21 15 0.52
22 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AATTAATTTTAAATAAATCTTT
Found at i:191289 original size:17 final size:17
Alignment explanation
Indices: 191267--191299 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
191257 ACCAAGCAAT
*
191267 TTTTAATCATGATTTAG
1 TTTTAATCATAATTTAG
191284 TTTTAATCATAATTTA
1 TTTTAATCATAATTTA
191300 ATATTCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTTAATCATAATTTAG
Found at i:192352 original size:16 final size:16
Alignment explanation
Indices: 192333--192399 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
192323 TTTTTATATT
192333 TTAATATTAATTTAAA
1 TTAATATTAATTTAAA
*
192349 TTAATATT-TTATTAAA
1 TTAATATTAAT-TTAAA
* *
192365 TAAAATATTTAA-TAAAA
1 T-TAATA-TTAATTTAAA
192382 TTAAT-TTAATTT-AA
1 TTAATATTAATTTAAA
192396 TTAA
1 TTAA
192400 AAATAATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
14 10 0.25
15 2 0.05
16 17 0.43
17 9 0.22
18 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAATATTAATTTAAA
Found at i:192410 original size:53 final size:55
Alignment explanation
Indices: 192276--192410 Score: 136
Period size: 53 Copynumber: 2.4 Consensus size: 55
192266 AATAATATTA
192276 AATTTAATTAAAAGTATAA-ATTATTATTAATAAAATATTAAAAAATATTTTTATATTTT
1 AATTTAATTAAAA--ATAATATT-TTATTAATAAAATATTAAAAAATA--TTTATATTTT
* * *
192335 AATATTAATTTAAATTAATATTTTATTAAATAAAATATTTAATAAA-A-TTA-A-TTT
1 AAT-TTAATTAAAAATAATATTTTATT-AATAAAATA-TTAAAAAATATTTATATTTT
192389 AATTTAATTAAAAATAATATTT
1 AATTTAATTAAAAATAATATTT
192411 AAAATTTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
53 17 0.25
54 6 0.09
55 1 0.01
56 3 0.04
58 8 0.12
59 16 0.24
60 16 0.24
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (55 bp):
AATTTAATTAAAAATAATATTTTATTAATAAAATATTAAAAAATATTTATATTTT
Found at i:192906 original size:21 final size:21
Alignment explanation
Indices: 192882--192923 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
192872 ATATTTTATA
192882 ATTAAATTTAAATAAAAATAT
1 ATTAAATTTAAATAAAAATAT
* *
192903 ATTAATTTTAATTAAAAATAT
1 ATTAAATTTAAATAAAAATAT
192924 TATTCTAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAAATTTAAATAAAAATAT
Found at i:192919 original size:20 final size:19
Alignment explanation
Indices: 192886--192925 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
192876 TTTATAATTA
192886 AATTTAAATAAAAATATATT
1 AATTTAAATAAAAA-ATATT
* *
192906 AATTTTAATTAAAAATATT
1 AATTTAAATAAAAAATATT
192925 A
1 A
192926 TTCTAAGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTAAATAAAAAATATT
Found at i:193794 original size:16 final size:15
Alignment explanation
Indices: 193769--193802 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
193759 CTTACGTTTC
*
193769 TAAATTTATATTATTT
1 TAAATATATATT-TTT
193785 TAAATATATATTTTT
1 TAAATATATATTTTT
193800 TAA
1 TAA
193803 TATTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATATATATTTTT
Found at i:194736 original size:29 final size:29
Alignment explanation
Indices: 194704--194822 Score: 97
Period size: 29 Copynumber: 4.1 Consensus size: 29
194694 AGATATAAAG
194704 ATAATATTAAAAAATAATTAAAATATTAT
1 ATAATATTAAAAAATAATTAAAATATTAT
*
194733 ATAATATAAAAATAAT-ATTAAAAT-TTAT
1 ATAATATTAAAA-AATAATTAAAATATTAT
* * * *
194761 AAAAATATATTAAATATAATTATAATA-TAT
1 -ATAATAT-TAAAAAATAATTAAAATATTAT
194791 A-AA-ATTACAAAAATAA-TAAATATATATAT
1 ATAATATTA-AAAAATAATTAAA-ATAT-TAT
194820 ATA
1 ATA
194823 TCTAAATTAT
Statistics
Matches: 71, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
26 4 0.06
27 12 0.17
28 6 0.08
29 32 0.45
30 17 0.24
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (29 bp):
ATAATATTAAAAAATAATTAAAATATTAT
Found at i:194756 original size:38 final size:37
Alignment explanation
Indices: 194696--194814 Score: 100
Period size: 38 Copynumber: 3.1 Consensus size: 37
194686 AAATAGTAAG
* *
194696 ATATAAAGATAATATTAAAAAATAATTAAAATAT-TATATA
1 ATATAAAAATAATATT--AAAATAATAAAAATATAT-TA-A
*
194736 ATATAAAAATAATATTAAAATTTATAAAAATATATTAA
1 ATATAAAAATAATATTAAAA-TAATAAAAATATATTAA
** * *
194774 ATATAATTATAATATATAAAATTACAAAAATA-A-TAA
1 ATATAAAAATAATAT-TAAAATAATAAAAATATATTAA
194810 ATATA
1 ATATA
194815 TATATATATC
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
36 8 0.11
37 1 0.01
38 28 0.40
39 17 0.24
40 16 0.23
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (37 bp):
ATATAAAAATAATATTAAAATAATAAAAATATATTAA
Found at i:194816 original size:38 final size:38
Alignment explanation
Indices: 194723--194816 Score: 102
Period size: 38 Copynumber: 2.4 Consensus size: 38
194713 AAAAATAATT
* ** *
194723 AAAATATTATATAATATAAAAATAATATTAAAATTTATA
1 AAAATA-TATAAAATATAATTATAATATTAAAATTTACA
*
194762 AAAATATATTAAATATAATTATAATATATAAAA-TTACA
1 AAAATATATAAAATATAATTATAATAT-TAAAATTTACA
194800 AAAATA-ATAAATATATA
1 AAAATATATAAA-ATATA
194817 TATATATCTA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
37 4 0.09
38 32 0.68
39 11 0.23
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (38 bp):
AAAATATATAAAATATAATTATAATATTAAAATTTACA
Found at i:195075 original size:19 final size:20
Alignment explanation
Indices: 195027--195075 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
195017 TCATATTTAT
* *
195027 TTAATTTGATTAAAATTATTA
1 TTAATTT-AATAAAAATATTA
195048 TTAATTTAATAAAAATATT-
1 TTAATTTAATAAAAATATTA
*
195067 TTTATTTAA
1 TTAATTTAA
195076 ATTTAATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.32
20 10 0.40
21 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTAATTTAATAAAAATATTA
Found at i:195405 original size:18 final size:18
Alignment explanation
Indices: 195374--195437 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
195364 AATAATAAAT
*
195374 AAATATATTATTTAATTAA
1 AAAT-TATTTTTTAATTAA
195393 AAATTATTTTTT-ATATAA
1 AAATTATTTTTTAAT-TAA
* *
195411 AAATTATAGTTTTAAATAAA
1 AAATTAT--TTTTTAATTAA
195431 AAATTAT
1 AAATTAT
195438 AAATTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.05
18 17 0.45
19 4 0.11
20 13 0.34
21 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
AAATTATTTTTTAATTAA
Found at i:195432 original size:20 final size:19
Alignment explanation
Indices: 195384--195438 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
195374 AAATATATTA
* *
195384 TTTAATTAAAAATTAT-TT
1 TTTAAATAAAAATTATAGT
*
195402 TTTATATAAAAATTATAGT
1 TTTAAATAAAAATTATAGT
195421 TTTAAATAAAAAATTATA
1 TTTAAAT-AAAAATTATA
195439 AATTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 14 0.45
19 7 0.23
20 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTAAATAAAAATTATAGT
Found at i:195454 original size:14 final size:15
Alignment explanation
Indices: 195430--195459 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
195420 TTTTAAATAA
195430 AAAATTATAAATTTT
1 AAAATTATAAATTTT
195445 AAAATT-TAAATTTT
1 AAAATTATAAATTTT
195459 A
1 A
195460 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATTATAAATTTT
Found at i:195714 original size:23 final size:23
Alignment explanation
Indices: 195684--195738 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
195674 TATGTATTAC
*
195684 TATTTAAATAATAAATATATATT
1 TATTTAAATAATAAATAAATATT
195707 TATTTAAATAATAAATAAATATT
1 TATTTAAATAATAAATAAATATT
195730 TATTTAAAT
1 TATTTAAAT
195739 TTAATTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTTAAATAATAAATAAATATT
Found at i:195726 original size:34 final size:34
Alignment explanation
Indices: 195688--195771 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
195678 TATTACTATT
*
195688 TAAATAATAAATATATATTT-ATT-TAAATAATAAA
1 TAAAT-ATAAATATAAATTTAATTATAAA-AATAAA
** *
195722 TAAATATTTATTTAAATTTAATTATAAAAATAAA
1 TAAATATAAATATAAATTTAATTATAAAAATAAA
195756 TAAATATAAATATAAA
1 TAAATATAAATATAAA
195772 AATAAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
33 10 0.24
34 27 0.66
35 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
TAAATATAAATATAAATTTAATTATAAAAATAAA
Found at i:195769 original size:22 final size:22
Alignment explanation
Indices: 195734--195778 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
195724 AATATTTATT
* *
195734 TAAATTTAATTATAAAAATAAA
1 TAAATATAAATATAAAAATAAA
195756 TAAATATAAATATAAAAATAAA
1 TAAATATAAATATAAAAATAAA
195778 T
1 T
195779 TTTAATATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATATAAATATAAAAATAAA
Found at i:196469 original size:21 final size:22
Alignment explanation
Indices: 196440--196480 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
196430 ATAAATTTAA
196440 AATATTAAATAAGTAATTAATT
1 AATATTAAATAAGTAATTAATT
* *
196462 AATA-TAAATATGTATTTAA
1 AATATTAAATAAGTAATTAA
196481 CTTATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (22 bp):
AATATTAAATAAGTAATTAATT
Found at i:196607 original size:21 final size:22
Alignment explanation
Indices: 196583--196630 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
196573 TTTTTACCAA
*
196583 TTTAATA-TAATT-TATATCATT
1 TTTAATACTAATTAAATAT-ATT
196604 TTTAA-ACTAATTAAATATATT
1 TTTAATACTAATTAAATATATT
196625 TTTAAT
1 TTTAAT
196631 GATTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAATACTAATTAAATATATT
Found at i:196754 original size:12 final size:12
Alignment explanation
Indices: 196737--196763 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
196727 TAAAAATATT
196737 AAATTTAAATAA
1 AAATTTAAATAA
196749 AAATTTAAATAA
1 AAATTTAAATAA
196761 AAA
1 AAA
196764 ATAAAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATTTAAATAA
Found at i:196756 original size:18 final size:19
Alignment explanation
Indices: 196722--196758 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
196712 TTACAAAAGA
*
196722 TTAAGTAAAAATATTAAAT
1 TTAAATAAAAATATTAAAT
196741 TTAAATAAAAAT-TTAAAT
1 TTAAATAAAAATATTAAAT
196759 AAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TTAAATAAAAATATTAAAT
Found at i:197873 original size:23 final size:23
Alignment explanation
Indices: 197829--197873 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
197819 GCTATGGATA
* *
197829 TTTTTTATAAAAAATTATATTAT
1 TTTTTTATAAAAAATAAAATTAT
* *
197852 TTTTTTATGATAAATAAAATTA
1 TTTTTTATAAAAAATAAAATTA
197874 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTTTTATAAAAAATAAAATTAT
Found at i:197979 original size:13 final size:14
Alignment explanation
Indices: 197956--197984 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
197946 AATATTAAAT
197956 ATAATAAATATTTA
1 ATAATAAATATTTA
197970 ATAA-AAATATTTA
1 ATAATAAATATTTA
197983 AT
1 AT
197985 TATTTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAAATATTTA
Found at i:198006 original size:11 final size:12
Alignment explanation
Indices: 197957--198008 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 12
197947 ATATTAAATA
197957 TAATA-AATATT
1 TAATATAATATT
*
197968 TAATAAAAATATT
1 TAAT-ATAATATT
197981 TAAT-T-AT-TT
1 TAATATAATATT
197990 TAATATAAT-TT
1 TAATATAATATT
198001 TAATATAA
1 TAATATAA
198009 ATTAAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
9 6 0.17
10 3 0.08
11 16 0.44
12 1 0.03
13 10 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATATAATATT
Found at i:198312 original size:33 final size:31
Alignment explanation
Indices: 198275--198335 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
198265 TTTAGTAATT
198275 TTAAATATAATTATA-AAATATATAATATAAAAA
1 TTAAA-AT-ATTATATAAA-ATATAATATAAAAA
198308 TTAAAATATTATATAAAATATAATATAA
1 TTAAAATATTATATAAAATATAATATAA
198336 TATATCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 17 0.63
32 5 0.19
33 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
TTAAAATATTATATAAAATATAATATAAAAA
Found at i:198340 original size:12 final size:12
Alignment explanation
Indices: 198277--198340 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 12
198267 TAGTAATTTT
198277 AAATATAATTATA
1 AAATATAA-TATA
198290 AAATAT-ATAATA
1 AAATATAAT-ATA
*
198302 TAA-A-AAT-TA
1 AAATATAATATA
*
198311 AAATATTATATA
1 AAATATAATATA
198323 AAATATAATATA
1 AAATATAATATA
*
198335 ATATAT
1 AAATAT
198341 CAAAGTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
9 4 0.10
10 1 0.02
11 6 0.15
12 24 0.59
13 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATAATATA
Found at i:200693 original size:2 final size:2
Alignment explanation
Indices: 200686--200716 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
200676 TTATCATCTT
200686 AG AG AG 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 AG AG AG A
200717 ACAAACCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:204151 original size:27 final size:27
Alignment explanation
Indices: 204100--204154 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
204090 AAATTATAGT
204100 ATTATAAATATATAAAATATAAAATAA
1 ATTATAAATATATAAAATATAAAATAA
204127 ATTA-AAATATGATACAAATAT-AAATAA
1 ATTATAAATAT-ATA-AAATATAAAATAA
204154 A
1 A
204155 AAATAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 6 0.23
27 14 0.54
28 6 0.23
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
ATTATAAATATATAAAATATAAAATAA
Found at i:204534 original size:22 final size:21
Alignment explanation
Indices: 204494--204550 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
204484 TGCAACTTAA
204494 ATATAT-AAATACAT-CTAAAT
1 ATATATAAAATA-ATACTAAAT
204514 ATATATAAAATAATACTTAAAT
1 ATATATAAAATAATAC-TAAAT
204536 -TATATCAAAATAATA
1 ATATAT-AAAATAATA
204551 AGAATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.24
21 11 0.33
22 14 0.42
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
ATATATAAAATAATACTAAAT
Found at i:205893 original size:39 final size:38
Alignment explanation
Indices: 205835--205917 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 38
205825 ATTTAAGTTC
** * *
205835 AATTTAAATAAATTTATAAATTTATTTTAATATTAATAA
1 AATTTAAATAAATAAATAAATTTATATAAATA-TAATAA
* *
205874 AATTTAAATATATAAATAAATTTATATAAATATAATTA
1 AATTTAAATAAATAAATAAATTTATATAAATATAATAA
205912 AATTTA
1 AATTTA
205918 TTTTATTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
38 11 0.29
39 27 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (38 bp):
AATTTAAATAAATAAATAAATTTATATAAATATAATAA
Found at i:205899 original size:14 final size:15
Alignment explanation
Indices: 205882--205910 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
205872 AAAATTTAAA
205882 TATATAAATA-AATT
1 TATATAAATATAATT
205896 TATATAAATATAATT
1 TATATAAATATAATT
205911 AAATTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATAAATATAATT
Found at i:205908 original size:20 final size:20
Alignment explanation
Indices: 205850--205918 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
205840 AAATAAATTT
* * *
205850 ATAAATTTATTTTAATATTA
1 ATAAATTTATATAAATATAA
*
205870 ATAAAATTTA-A-ATATATAA
1 AT-AAATTTATATAAATATAA
205889 ATAAATTTATATAAATATAA
1 ATAAATTTATATAAATATAA
*
205909 TTAAATTTAT
1 ATAAATTTAT
205919 TTTATTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 7 0.17
19 8 0.20
20 18 0.45
21 7 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAATTTATATAAATATAA
Found at i:208929 original size:21 final size:19
Alignment explanation
Indices: 208894--208940 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
208884 TTAAAGTAAT
*
208894 AAATAAT-ATTTATTATATA
1 AAATAATAACTTATTAT-TA
208913 AATATAATAACTTATTATTA
1 AA-ATAATAACTTATTATTA
208933 AAATAATA
1 AAATAATA
208941 GTATAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 8 0.32
20 9 0.36
21 8 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATAACTTATTATTA
Found at i:216065 original size:16 final size:17
Alignment explanation
Indices: 216044--216079 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
216034 TATTTTATAA
*
216044 TTATATTTA-AAATATT
1 TTATATTTATAAAAATT
216060 TTATATTTATAAAAATT
1 TTATATTTATAAAAATT
216077 TTA
1 TTA
216080 ATATATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATAAAAATT
Found at i:216090 original size:27 final size:29
Alignment explanation
Indices: 216031--216090 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 29
216021 GGACCCCTTT
** *
216031 TTATATTTTATAATTATATTTAAAATATT
1 TTATATTTTATAAAAATATTTAAAATATG
*
216060 TTATA-TTTATAAAAAT-TTTAATATATG
1 TTATATTTTATAAAAATATTTAAAATATG
216087 TTAT
1 TTAT
216091 GTAAATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 13 0.48
28 9 0.33
29 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (29 bp):
TTATATTTTATAAAAATATTTAAAATATG
Found at i:216096 original size:21 final size:19
Alignment explanation
Indices: 216072--216126 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
216062 ATATTTATAA
216072 AAATTTTAATATATGTTATGT
1 AAATTTTAATATAT-TT-TGT
216093 AAA-TTTATATATATTTTGT
1 AAATTTTA-ATATATTTTGT
*
216112 ATATTTT--TATATTTT
1 AAATTTTAATATATTTT
216127 AATGTCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 8 0.26
19 5 0.16
20 9 0.29
21 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
AAATTTTAATATATTTTGT
Found at i:216104 original size:19 final size:19
Alignment explanation
Indices: 216080--216123 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
216070 AAAAATTTTA
*
216080 ATATATGTTATGTAAATTT
1 ATATATATTATGTAAATTT
* *
216099 ATATATATTTTGTATATTT
1 ATATATATTATGTAAATTT
*
216118 TTATAT
1 ATATAT
216124 TTTAATGTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
ATATATATTATGTAAATTT
Found at i:218608 original size:21 final size:21
Alignment explanation
Indices: 218578--218626 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
218568 GGAGTTTCAC
**
218578 TTCTCCTTTTTTTTTTTTTTT
1 TTCTCCTTTTCCTTTTTTTTT
*
218599 TTCTCTTTTTCCTTTTTTTTT
1 TTCTCCTTTTCCTTTTTTTTT
218620 TTCTCCT
1 TTCTCCT
218627 CTTGATATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TTCTCCTTTTCCTTTTTTTTT
Found at i:219186 original size:14 final size:14
Alignment explanation
Indices: 219167--219209 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
219157 TAACTTGTCG
219167 TAATAATATTTATT
1 TAATAATATTTATT
* *
219181 TAATAATATTAATA
1 TAATAATATTTATT
219195 TAA-AATATTTATT
1 TAATAATATTTATT
219208 TA
1 TA
219210 TTTTACAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATAATATTTATT
Found at i:219869 original size:14 final size:14
Alignment explanation
Indices: 219852--219878 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
219842 TTAATTTTTT
219852 TTATTATTTAAATA
1 TTATTATTTAAATA
219866 TTATTATTTAAAT
1 TTATTATTTAAAT
219879 TCACATACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTATTTAAATA
Found at i:228137 original size:23 final size:21
Alignment explanation
Indices: 228095--228173 Score: 52
Period size: 21 Copynumber: 3.6 Consensus size: 21
228085 AAAATATTAT
**
228095 TTTTATATTAATATTTATAAA
1 TTTTATATTAATATAAATAAA
228116 TTTTATAATTAAATATAAATAAAA
1 TTTTAT-ATT-AATATAAAT-AAA
* *
228140 TATTTTTATT-ATTTAAATAATA
1 T-TTTATATTAATATAAATAA-A
* *
228162 ATTTAAATTAAT
1 TTTTATATTAAT
228174 TTAATTTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
21 14 0.31
22 13 0.29
23 7 0.16
24 7 0.16
25 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTATATTAATATAAATAAA
Found at i:228180 original size:15 final size:16
Alignment explanation
Indices: 228160--228192 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
228150 ATTTAAATAA
228160 TAATTTAAATTAA-TT
1 TAATTTAAATTAAGTT
*
228175 TAATTTAATTTAAGTT
1 TAATTTAAATTAAGTT
228191 TA
1 TA
228193 TAAATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TAATTTAAATTAAGTT
Found at i:228579 original size:18 final size:18
Alignment explanation
Indices: 228548--228582 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
228538 TTAAATTTGT
228548 TAAATTTTATATTTTATG
1 TAAATTTTATATTTTATG
228566 TAAATATTTA-ATTTTAT
1 TAAAT-TTTATATTTTAT
228583 CAGAATCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TAAATTTTATATTTTATG
Found at i:230843 original size:14 final size:14
Alignment explanation
Indices: 230824--230863 Score: 50
Period size: 12 Copynumber: 3.1 Consensus size: 14
230814 TGATTATATA
230824 AAAATAATATAAAT
1 AAAATAATATAAAT
230838 AAAAT-AT-TAAA-
1 AAAATAATATAAAT
*
230849 AATATAATATAAAT
1 AAAATAATATAAAT
230863 A
1 A
230864 TATCTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
11 4 0.18
12 6 0.27
13 6 0.27
14 6 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATAATATAAAT
Found at i:230862 original size:11 final size:11
Alignment explanation
Indices: 230819--230979 Score: 57
Period size: 11 Copynumber: 14.7 Consensus size: 11
230809 ATATATGATT
*
230819 ATATAAAAATA
1 ATATAAATATA
*
230830 ATATAAATAAA
1 ATATAAATATA
230841 ATATTAAAAATATA
1 ATA-T--AAATATA
230855 ATATAAATAT-
1 ATATAAATATA
* *
230865 ATCT-AATAAA
1 ATATAAATATA
* * *
230875 ATTTATAT-TT
1 ATATAAATATA
*
230885 ATATAATATTTA
1 ATATAA-ATATA
* * *
230897 TTATTAATATG
1 ATATAAATATA
*
230908 TTA-AAAT-TA
1 ATATAAATATA
**
230917 ATATAGTTATA
1 ATATAAATATA
* * *
230928 AAAT-ATTTTA
1 ATATAAATATA
230938 ATATAAATATA
1 ATATAAATATA
*
230949 ATAT-AATAAAA
1 ATATAAAT-ATA
230960 TATATAAATATA
1 -ATATAAATATA
230972 ATATAAAT
1 ATATAAAT
230980 TATTAAATTA
Statistics
Matches: 108, Mismatches: 29, Indels: 26
0.66 0.18 0.16
Matches are distributed among these distances:
9 7 0.06
10 25 0.23
11 51 0.47
12 12 0.11
13 4 0.04
14 9 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
ATATAAATATA
Found at i:230932 original size:27 final size:29
Alignment explanation
Indices: 230902--230962 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 29
230892 ATTTATTATT
* *
230902 AATATGTTAAAATTAATATAGT-T-ATAA
1 AATATGTTAAAATAAATATAATATAATAA
* *
230929 AATATTTTAATATAAATATAATATAATAA
1 AATATGTTAAAATAAATATAATATAATAA
230958 AATAT
1 AATAT
230963 ATAAATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 18 0.64
28 1 0.04
29 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
AATATGTTAAAATAAATATAATATAATAA
Found at i:230953 original size:5 final size:5
Alignment explanation
Indices: 230936--230977 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
230926 TAAAATATTT
*
230936 TAATA TAAATA TAATA TAATA AAATA T-ATA -AATA TAATA TAA
1 TAATA T-AATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
230978 ATTATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 6 0.19
5 21 0.66
6 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
TAATA
Found at i:231072 original size:30 final size:29
Alignment explanation
Indices: 231038--231167 Score: 121
Period size: 28 Copynumber: 4.5 Consensus size: 29
231028 TTTTGAGTTG
231038 ATAATATTATATATATAAAATAATTA-AAAT
1 ATAATATTA-ATATATAAAAT-ATTATAAAT
*
231068 ATAATA-TAATAT-TTAAAT-TTATATAAT
1 ATAATATTAATATATAAAATATTATA-AAT
*
231095 A-AATAATTAATATATTAAAATTTATATAAAT
1 ATAAT-ATTAATATA-TAAAATAT-TATAAAT
231126 AT-ATA-TAATATAATAAAATATTATAAAT
1 ATAATATTAATAT-ATAAAATATTATAAAT
*
231154 ATAATATAAATATA
1 ATAATATTAATATA
231168 ATATTAATAT
Statistics
Matches: 84, Mismatches: 4, Indels: 25
0.74 0.04 0.22
Matches are distributed among these distances:
25 3 0.04
26 4 0.05
27 10 0.12
28 19 0.23
29 19 0.23
30 18 0.21
31 7 0.08
32 4 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAATATTAATATATAAAATATTATAAAT
Found at i:231093 original size:17 final size:17
Alignment explanation
Indices: 231071--231123 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
231061 TTAAAATATA
231071 ATATAATATTTAAATTT
1 ATATAATATTTAAATTT
**
231088 ATATAATAAAT-AA-TT
1 ATATAATATTTAAATTT
*
231103 A-AT-ATATTAAAATTT
1 ATATAATATTTAAATTT
231118 ATATAA
1 ATATAA
231124 ATATATATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
13 3 0.11
14 4 0.15
15 6 0.22
16 4 0.15
17 10 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAATATTTAAATTT
Found at i:231099 original size:40 final size:40
Alignment explanation
Indices: 231044--231210 Score: 117
Period size: 40 Copynumber: 4.0 Consensus size: 40
231034 GTTGATAATA
*
231044 TTATATATATAAAATAATTAAAATATAATATAATATTTAAAT
1 TTATATA-AT-AAATAATTAAAATATAATATAATATATAAAT
* * *
231086 TTATATAATAAATAATTAATATATTAAAAT-TTATATAAAT
1 TTATATAATAAATAATTAAAATA-TAATATAATATATAAAT
*
231126 ATATATAATATAATAAAATATTATAAATATAATATAA-ATATAATAT
1 TTATATAATA-AAT---A-ATTA-AAATATAATATAATATATAA-AT
* * * * *
231172 TAATATTA-AAATTATT-ACATATACTATTAATATATAAAT
1 TTATATAATAAATAATTAAAATATAATA-TAATATATAAAT
231211 GATTAAATTT
Statistics
Matches: 100, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
38 8 0.08
39 5 0.05
40 39 0.39
41 10 0.10
42 7 0.07
44 4 0.04
45 16 0.16
46 11 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (40 bp):
TTATATAATAAATAATTAAAATATAATATAATATATAAAT
Found at i:231134 original size:29 final size:30
Alignment explanation
Indices: 231038--231167 Score: 130
Period size: 29 Copynumber: 4.4 Consensus size: 30
231028 TTTTGAGTTG
* *
231038 ATAATATTATATATATAAAA-TAAT-TAAAAT
1 ATAATATAATATAT-TAAAATTTATAT-AAAT
*
231068 ATAATATAATAT-TT-AAATTTATATAATAA
1 ATAATATAATATATTAAAATTTATATAA-AT
231097 ATAAT-TAATATATTAAAATTTATATAAAT
1 ATAATATAATATATTAAAATTTATATAAAT
* *
231126 AT-ATATAATATAATAAAATAT-TATAAAT
1 ATAATATAATATATTAAAATTTATATAAAT
231154 ATAATATAAATATA
1 ATAATAT-AATATA
231168 ATATTAATAT
Statistics
Matches: 86, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
27 3 0.03
28 23 0.27
29 31 0.36
30 29 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
ATAATATAATATATTAAAATTTATATAAAT
Found at i:231168 original size:30 final size:29
Alignment explanation
Indices: 231038--231183 Score: 126
Period size: 30 Copynumber: 5.0 Consensus size: 29
231028 TTTTGAGTTG
*
231038 ATAATATTATATATATAAAATAATTA-AAAT
1 ATAATATAATATA-ATAAAAT-ATTATAAAT
*
231068 ATAATATAATAT--TTAAAT-TTATATAAT
1 ATAATATAATATAATAAAATATTATA-AAT
* *
231095 A-AATAATTAATATATTAAAATTTATATAAAT
1 ATAAT-A-TAATATAATAAAATAT-TATAAAT
231126 AT-ATATAATATAATAAAATATTATAAAT
1 ATAATATAATATAATAAAATATTATAAAT
*
231154 ATAATATAAATATAATATTAATATTA-AAAT
1 ATAATAT-AATATAATA-AAATATTATAAAT
231184 TATTACATAT
Statistics
Matches: 98, Mismatches: 6, Indels: 24
0.77 0.05 0.19
Matches are distributed among these distances:
25 3 0.03
26 4 0.04
27 10 0.10
28 15 0.15
29 18 0.18
30 30 0.31
31 14 0.14
32 4 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAATATAATATAATAAAATATTATAAAT
Found at i:231182 original size:39 final size:36
Alignment explanation
Indices: 231088--231188 Score: 107
Period size: 39 Copynumber: 2.7 Consensus size: 36
231078 ATTTAAATTT
* *
231088 ATATAATA-AATAATTAATATATTAAAATTTATATAA
1 ATATAATATAAT-ATTAAAATATTAAAATTAATATAA
231124 ATAT-ATATAATATAATAAAATATTATAAATATAATATAA
1 ATATAATATAATAT--TAAAATATTA-AAAT-TAATATAA
231163 ATATAATATTAATATTAAAATTATTA
1 ATATAATA-TAATATTAAAA-TATTA
231189 CATATACTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
35 5 0.09
36 7 0.13
37 9 0.16
38 4 0.07
39 16 0.29
40 8 0.15
41 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (36 bp):
ATATAATATAATATTAAAATATTAAAATTAATATAA
Found at i:231205 original size:38 final size:35
Alignment explanation
Indices: 231040--231176 Score: 117
Period size: 35 Copynumber: 4.0 Consensus size: 35
231030 TTGAGTTGAT
* * * * *
231040 AATATTATATATATAAAATAATTAAAATATAATAT
1 AATATTATAAATATAATATAAATATAATATAATAA
* *
231075 AATATT-TAAATTTATATAATAAATAATTAATATATTAA
1 AATATTATAAATATA-AT-ATAAAT-A-TAATATAATAA
231113 AAT-TTAT--ATA-AATAT--ATATAATATAATAA
1 AATATTATAAATATAATATAAATATAATATAATAA
231142 AATATTATAAATATAATATAAATATAATATTAATA
1 AATATTATAAATATAATATAAATATAATA-TAATA
231177 TTAAAATTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
29 13 0.16
30 5 0.06
31 2 0.02
32 3 0.04
33 7 0.09
34 8 0.10
35 16 0.20
36 12 0.15
37 3 0.04
38 12 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
AATATTATAAATATAATATAAATATAATATAATAA
Found at i:231210 original size:27 final size:27
Alignment explanation
Indices: 231163--231215 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
231153 TATAATATAA
*
231163 ATATAATATTAATATTAAAATTATTAC
1 ATATAATATTAATATTAAAATGATTAC
*
231190 ATATACTATTAATA-TATAAATGATTA
1 ATATAATATTAATATTA-AAATGATTA
231216 AATTTAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
ATATAATATTAATATTAAAATGATTAC
Found at i:231387 original size:20 final size:20
Alignment explanation
Indices: 231336--231389 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
231326 TTTAAATAAT
*
231336 TTTATTTTTT-AAA-AATTA
1 TTTATTTTTTAAAATAACTA
* * *
231354 TTTATATATAAAAATAACTA
1 TTTATTTTTTAAAATAACTA
231374 TTTATTTTTTAAAATA
1 TTTATTTTTTAAAATA
231390 TTTTTTTGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 7 0.26
19 3 0.11
20 17 0.63
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTATTTTTTAAAATAACTA
Found at i:238126 original size:16 final size:16
Alignment explanation
Indices: 238110--238167 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
238100 GTATCGAATT
* *
238110 TAAAATAATTTATATT
1 TAAAATAATTTAAATA
*
238126 TAAAATAATTAAAATA
1 TAAAATAATTTAAATA
*
238142 TAAAATAATGTAAATA
1 TAAAATAATTTAAATA
238158 TAAAATAATT
1 TAAAATAATT
238168 ATTTTTTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAAATAATTTAAATA
Found at i:238211 original size:17 final size:17
Alignment explanation
Indices: 238191--238225 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
238181 TTTAAATATT
*
238191 AAATTTGATTAATTTAA
1 AAATTTGATAAATTTAA
*
238208 AAATTTTATAAATTTAA
1 AAATTTGATAAATTTAA
238225 A
1 A
238226 TAAATTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AAATTTGATAAATTTAA
Found at i:238236 original size:9 final size:9
Alignment explanation
Indices: 238190--238236 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
238180 ATTTAAATAT
*
238190 TAAATTTGA
1 TAAATTTAA
*
238199 TTAATTTAA
1 TAAATTTAA
*
238208 -AAATTTTA
1 TAAATTTAA
238216 TAAATTTAAA
1 TAAATTT-AA
238226 TAAATTTAA
1 TAAATTTAA
238235 TA
1 TA
238237 TTTTATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
8 6 0.19
9 17 0.55
10 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (9 bp):
TAAATTTAA
Found at i:238257 original size:14 final size:15
Alignment explanation
Indices: 238230--238258 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
238220 TTTAAATAAA
238230 TTTAATATTTTATTT
1 TTTAATATTTTATTT
238245 TTTAATA-TTTATTT
1 TTTAATATTTTATTT
238259 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTAATATTTTATTT
Found at i:238283 original size:22 final size:21
Alignment explanation
Indices: 238258--238312 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
238248 AATATTTATT
238258 TAATTATATATATATATAAACA
1 TAATTATATATATATATAAA-A
* *
238280 TAA-TATTTTAAATATATAAAA
1 TAATTA-TATATATATATAAAA
*
238301 AAATTA-ATATAT
1 TAATTATATATAT
238313 TTGCATAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
20 4 0.15
21 5 0.19
22 17 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATTATATATATATATAAAA
Found at i:238648 original size:20 final size:22
Alignment explanation
Indices: 238623--238681 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
238613 ATAATTTAAA
238623 TTAATTAAATAAT-TATT-TAT
1 TTAATTAAATAATATATTATAT
* *
238643 TTAATTAATTAATATTTTATAT
1 TTAATTAAATAATATATTATAT
238665 TTAATTATAA-AATATAT
1 TTAATTA-AATAATATAT
238682 AAATATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.38
21 3 0.09
22 16 0.50
23 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAATTAAATAATATATTATAT
Found at i:238681 original size:24 final size:24
Alignment explanation
Indices: 238606--238681 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 24
238596 ATGAGATAAA
*
238606 ATATTTTATAATTTAAATTAATTAAAT
1 ATATTTTAT-ATTT-AATT-ATAAAAT
**
238633 A-ATTATT-TATTTAATTA-ATTA-
1 ATATT-TTATATTTAATTATAAAAT
238654 ATATTTTATATTTAATTATAAAAT
1 ATATTTTATATTTAATTATAAAAT
238678 ATAT
1 ATAT
238682 AAATATTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 13
0.68 0.09 0.23
Matches are distributed among these distances:
21 3 0.08
22 14 0.36
23 3 0.08
24 8 0.21
25 4 0.10
26 4 0.10
27 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATTTTATATTTAATTATAAAAT
Found at i:238732 original size:17 final size:16
Alignment explanation
Indices: 238712--238750 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
238702 TTTATTATTT
238712 TTAAATTATAATTTAAA
1 TTAAATTA-AATTTAAA
*
238729 TTAAATTAAATTTTAA
1 TTAAATTAAATTTAAA
238745 -TAAATT
1 TTAAATT
238751 TTAAATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 7 0.33
17 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATTAAATTTAAA
Found at i:238987 original size:17 final size:16
Alignment explanation
Indices: 238949--238991 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
238939 TCGATCTCTT
*
238949 TAAATATTTATAATAA
1 TAAATATTAATAATAA
*
238965 TAAAATATTAATAAATCA
1 T-AAATATTAAT-AATAA
238983 TAAATATTA
1 TAAATATTA
238992 CATAGAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 17 0.74
18 5 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATATTAATAATAA
Found at i:239595 original size:34 final size:34
Alignment explanation
Indices: 239557--239633 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 34
239547 ATATATAATA
* *
239557 AATAATAAAATA-TTATTAAATTTATATTTATGTT
1 AATAAT-AAATACATATTAAAATTATATTTATGTT
239591 AATAATAAATACATATTAAAATTATATTTATGTT
1 AATAATAAATACATATTAAAATTATATTTATGTT
239625 AA-AA-AAATA
1 AATAATAAATA
239634 AATTAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 5 0.12
33 7 0.17
34 28 0.70
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (34 bp):
AATAATAAATACATATTAAAATTATATTTATGTT
Found at i:239626 original size:17 final size:17
Alignment explanation
Indices: 239572--239628 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
239562 TAAAATATTA
*
239572 TTAAATTTATATTTATG
1 TTAAAATTATATTTATG
* ** *
239589 TTAATAA-TAAATACATA
1 TTAA-AATTATATTTATG
239606 TTAAAATTATATTTATG
1 TTAAAATTATATTTATG
239623 TTAAAA
1 TTAAAA
239629 AAATAAATTA
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
16 2 0.07
17 26 0.90
18 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
TTAAAATTATATTTATG
Found at i:240869 original size:29 final size:30
Alignment explanation
Indices: 240837--240908 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
240827 TATCTACGTC
240837 ATATTTATATATTTTAT-TATATTTTAATT-
1 ATATTTATATATTTTATATAT-TTTTAATTA
* *
240866 ATATTTA-AAATATTTATATATTTTTTATTA
1 ATATTTATATAT-TTTATATATTTTTAATTA
*
240896 ATTTTTATATATT
1 ATATTTATATATT
240909 AATAATTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
28 3 0.09
29 19 0.54
30 10 0.29
31 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
ATATTTATATATTTTATATATTTTTAATTA
Found at i:240979 original size:3 final size:3
Alignment explanation
Indices: 240971--241008 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
240961 ATTAAATCCC
240971 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
241009 AGTTTCATTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:241314 original size:14 final size:14
Alignment explanation
Indices: 241297--241343 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
241287 ATATGAATAT
*
241297 AATATTATTTTTAA
1 AATATTATATTTAA
*
241311 AATATTATAATTAA
1 AATATTATATTTAA
*
241325 AA-ATAATATTTAA
1 AATATTATATTTAA
241338 AATATT
1 AATATT
241344 TTAGTAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTATATTTAA
Found at i:241357 original size:24 final size:23
Alignment explanation
Indices: 241325--241393 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
241315 TTATAATTAA
241325 AAATAATATTTAAAATATTTTAGT
1 AAATAATATTTAAAATATTTTA-T
* * * *
241349 AAATTATATTAAAAAGATATTAT
1 AAATAATATTTAAAATATTTTAT
*
241372 ATATAATATTTAATAATATTTT
1 AAATAATATTTAA-AATATTTT
241394 TTTTAAATAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 11 0.31
24 24 0.69
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (23 bp):
AAATAATATTTAAAATATTTTAT
Found at i:241650 original size:20 final size:21
Alignment explanation
Indices: 241611--241654 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
241601 GTCTAGCGAG
241611 CCACGTGGGCTTACGTTAGAAA
1 CCACGTGGGC-TACGTTAGAAA
*
241633 CCACGTGGGC-AGGTTAGAAA
1 CCACGTGGGCTACGTTAGAAA
241653 CC
1 CC
241655 CTTTCTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
22 10 0.48
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (21 bp):
CCACGTGGGCTACGTTAGAAA
Found at i:242629 original size:23 final size:23
Alignment explanation
Indices: 242603--242647 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
242593 AGTTTTACTT
*
242603 TGTCTTTCTTGTTGCTCTTTCAA
1 TGTCTTTCTTGTTGCTCCTTCAA
*
242626 TGTCTTTTTTGTTGCTCCTTCA
1 TGTCTTTCTTGTTGCTCCTTCA
242648 TTGTAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.07, C:0.22, G:0.13, T:0.58
Consensus pattern (23 bp):
TGTCTTTCTTGTTGCTCCTTCAA
Found at i:246749 original size:25 final size:25
Alignment explanation
Indices: 246721--246781 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
246711 TTTAATATAT
*
246721 TATTTTAAATTTATTAAAT-TTTAAA
1 TATTTTAAATTTA-TAAATATATAAA
* *
246746 TATTTTTAATTTATATATATATAAA
1 TATTTTAAATTTATAAATATATAAA
246771 TATTTTTAAAT
1 TA-TTTTAAAT
246782 ATGAACTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.13
25 19 0.63
26 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTTTAAATTTATAAATATATAAA
Found at i:247533 original size:7 final size:7
Alignment explanation
Indices: 247521--247550 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
247511 GATTTTATAT
247521 TAATCTA
1 TAATCTA
247528 TAATCTA
1 TAATCTA
247535 TAATCTA
1 TAATCTA
*
247542 TAATATA
1 TAATCTA
247549 TA
1 TA
247551 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATCTA
Found at i:247540 original size:14 final size:14
Alignment explanation
Indices: 247516--247565 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
247506 ATATAGATTT
247516 TATATTAATCTATAA
1 TATA-TAATCTATAA
*
247531 TCTATAATCTATAA
1 TATATAATCTATAA
*
247545 TATAT-ATATATATA
1 TATATAATCTATA-A
247559 TATATAA
1 TATATAA
247566 ATGCCAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 6 0.20
14 20 0.67
15 4 0.13
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (14 bp):
TATATAATCTATAA
Found at i:248097 original size:4 final size:4
Alignment explanation
Indices: 248088--248127 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
248078 TTGACAAAAG
* * *
248088 ATAA ATAA ATAA ATAA ATAA ATAG TTAA ATGA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
248128 TTACTTGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:248528 original size:21 final size:21
Alignment explanation
Indices: 248491--248530 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
248481 ATGTTCAAAG
248491 ACAAAAAAATAAAATAAAATA
1 ACAAAAAAATAAAATAAAATA
*
248512 ACAAATAAAA-AACATAAAA
1 ACAAA-AAAATAAAATAAAA
248531 CATTTGCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (21 bp):
ACAAAAAAATAAAATAAAATA
Found at i:248677 original size:21 final size:21
Alignment explanation
Indices: 248625--248690 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
248615 TATATGAATT
*
248625 TATTATGTTAATA-ATTTATGA
1 TATTATTTTAATATATTTAT-A
248646 TATATAAATTTTAATATATTTATA
1 TAT-T--ATTTTAATATATTTATA
*
248670 TATTATTTTATTATA-TTATA
1 TATTATTTTAATATATTTATA
248690 T
1 T
248691 TTTAATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 6 0.15
21 13 0.33
22 1 0.03
23 1 0.03
24 12 0.31
25 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
TATTATTTTAATATATTTATA
Found at i:248681 original size:16 final size:15
Alignment explanation
Indices: 248576--248705 Score: 56
Period size: 16 Copynumber: 8.7 Consensus size: 15
248566 ATTGTGTTTG
248576 TATATTTT-TATATAT
1 TATATTTTAT-TATAT
*
248591 TATAGTTATATT-TAT
1 TATA-TTTTATTATAT
*
248606 TATATATT-TTATAT
1 TATATTTTATTATAT
* *
248620 GA-A-TTTATTATGT
1 TATATTTTATTATAT
* *
248633 TAATAATTTATGATAT
1 T-ATATTTTATTATAT
* *
248649 ATAAATTTTAATATATT
1 -TATATTTTATTATA-T
* *
248666 TATATATTATTTTAT
1 TATATTTTATTATAT
* *
248681 TATATTATATTTTAAT
1 TATATTTTATTAT-AT
248697 TAT-TTTTAT
1 TATATTTTAT
248706 ATTTAATAAT
Statistics
Matches: 85, Mismatches: 20, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
12 2 0.02
13 8 0.09
14 7 0.08
15 29 0.34
16 36 0.42
17 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TATATTTTATTATAT
Found at i:248701 original size:35 final size:37
Alignment explanation
Indices: 248639--248708 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
248629 ATGTTAATAA
248639 TTTATGATATATAAATTTTAATATATTTATATATTAT
1 TTTATGATATATAAATTTTAATATATTTATATATTAT
* * *
248676 TTTATTATAT-TATATTTTAAT-TATTTTTATATT
1 TTTATGATATATAAATTTTAATATATTTATATATT
248709 TAATAATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 11 0.37
36 10 0.33
37 9 0.30
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (37 bp):
TTTATGATATATAAATTTTAATATATTTATATATTAT
Found at i:248703 original size:10 final size:11
Alignment explanation
Indices: 248653--248708 Score: 53
Period size: 10 Copynumber: 5.0 Consensus size: 11
248643 TGATATATAA
*
248653 ATTTTAATA-T
1 ATTTTTATATT
*
248663 ATTTATATATT
1 ATTTTTATATT
248674 ATTTTATTATATT
1 A-TTT-TTATATT
248687 ATATTTTA-ATT
1 AT-TTTTATATT
248698 ATTTTTATATT
1 ATTTTTATATT
248709 TAATAATCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 12 0.32
11 10 0.26
12 7 0.18
13 9 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTTTTATATT
Found at i:248966 original size:19 final size:21
Alignment explanation
Indices: 248944--248996 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
248934 ATAAATAAAT
248944 ATAAATTAATTAATT-T-TTA
1 ATAAATTAATTAATTCTATTA
*
248963 ATAAATTAATCAATTCTATTA
1 ATAAATTAATTAATTCTATTA
248984 A-AAATTATATTAA
1 ATAAATTA-ATTAA
248997 CTCAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 14 0.48
20 7 0.24
21 8 0.28
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAATTAATTAATTCTATTA
Found at i:251371 original size:19 final size:19
Alignment explanation
Indices: 251349--251392 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
251339 GATATTTATA
*
251349 TTATTTATTTTAATTTTTT
1 TTATTTATTTTAATTATTT
**
251368 TTATAAATTTTAATTATTT
1 TTATTTATTTTAATTATTT
251387 TTATTT
1 TTATTT
251393 TTTAAATTCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTTATTTTAATTATTT
Found at i:251552 original size:16 final size:16
Alignment explanation
Indices: 251533--251583 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
251523 TTAAATGTTT
251533 AATTTAATATGATATA
1 AATTTAATATGATATA
* *
251549 AATTTAA-ATGTTTTTA
1 AATTTAATATG-ATATA
*
251565 AATTT-ATATAATATA
1 AATTTAATATGATATA
251580 AATT
1 AATT
251584 ATTAATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (16 bp):
AATTTAATATGATATA
Found at i:251555 original size:29 final size:30
Alignment explanation
Indices: 251523--251614 Score: 89
Period size: 32 Copynumber: 3.0 Consensus size: 30
251513 TAAATTTTTA
*
251523 TTAAATG-TTT-AATTTAATATGATATAAAT
1 TTAAATGTTTTAAATTT-ATATAATATAAAT
251552 TTAAATGTTTTTAAATTTATATAATATAAAT
1 TTAAATG-TTTTAAATTTATATAATATAAAT
* * *
251583 TATTAATATATTAAAATTTATATAAATATAAA
1 T-TAAATGT-TTTAAATTTATAT-AATATAAA
251615 ATATTTTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
29 7 0.13
31 17 0.32
32 21 0.40
33 8 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
TTAAATGTTTTAAATTTATATAATATAAAT
Found at i:251591 original size:13 final size:15
Alignment explanation
Indices: 251563--251614 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
251553 TAAATGTTTT
251563 TAAATTTATATAATA
1 TAAATTTATATAATA
*
251578 TAAATTATTAATATATTA
1 TAAA-T-TT-ATATAATA
251596 -AAATTTATATAAATA
1 TAAATTTATAT-AATA
251611 TAAA
1 TAAA
251615 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 5 0.17
17 5 0.17
18 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTTATATAATA
Found at i:251600 original size:32 final size:32
Alignment explanation
Indices: 251533--251619 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
251523 TTAAATGTTT
* * * * *
251533 AATTTAATATGATATAAATT-TAAATGTTTTTA
1 AATTT-ATATAATATAAATTATTAATATATTAA
251565 AATTTATATAATATAAATTATTAATATATTAA
1 AATTTATATAATATAAATTATTAATATATTAA
*
251597 AATTTATATAAATATAAAATATT
1 AATTTATAT-AATATAAATTATT
251620 TTAAAGTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 13 0.28
32 22 0.47
33 12 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
AATTTATATAATATAAATTATTAATATATTAA
Found at i:251614 original size:17 final size:17
Alignment explanation
Indices: 251564--251616 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
251554 AAATGTTTTT
251564 AAATTTATAT-AATAT-
1 AAATTTATATAAATATA
251579 AAA-TTAT-TAATATATTA
1 AAATTTATATAA-ATA-TA
251596 AAATTTATATAAATATA
1 AAATTTATATAAATATA
251613 AAAT
1 AAAT
251617 ATTTTAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 6 0.19
16 1 0.03
17 9 0.28
18 7 0.22
19 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:252788 original size:26 final size:25
Alignment explanation
Indices: 252748--252806 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
252738 TGTAATTAAA
* *
252748 TTAAATTAAATTTAATAATAAAAAAT
1 TTAAATTTAACTTAA-AATAAAAAAT
** *
252774 TTAAATTTAACTTAAAATTTATAAT
1 TTAAATTTAACTTAAAATAAAAAAT
252799 TTAAATTT
1 TTAAATTT
252807 GATTTGTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAAATTTAACTTAAAATAAAAAAT
Found at i:254081 original size:3 final size:3
Alignment explanation
Indices: 254075--254104 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
254065 AATAATAATA
254075 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
254105 TAAACTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:255148 original size:13 final size:13
Alignment explanation
Indices: 255110--255148 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
255100 TTTATAAAAG
255110 TAAATAAAATTTTT
1 TAAAT-AAATTTTT
*
255124 TAATATATATTTTT
1 TAA-ATAAATTTTT
255138 TAAATAAATTT
1 TAAATAAATTT
255149 AAAATTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 7 0.32
14 13 0.59
15 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAATAAATTTTT
Found at i:255244 original size:21 final size:22
Alignment explanation
Indices: 255220--255286 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 22
255210 TTTTTTAAAA
*
255220 TAAATAGTTAGT-ATTAATTTT
1 TAAATAGTTAATGATTAATTTT
*
255241 TAAA-A-TTAAATGAGTAATTTT
1 TAAATAGTT-AATGATTAATTTT
255262 TAAAT-G-TAATTGATTAATTTT
1 TAAATAGTTAA-TGATTAATTTT
255283 TAAA
1 TAAA
255287 AAAATATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
19 2 0.05
20 5 0.13
21 31 0.82
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (22 bp):
TAAATAGTTAATGATTAATTTT
Found at i:256783 original size:25 final size:26
Alignment explanation
Indices: 256755--256816 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
256745 TTATACAATT
* *
256755 ATAATATAATTATGATATG-TATAAA
1 ATAATAAAAATATGATATGATATAAA
256780 ATAATAAAAATATGATATGATAT-AA
1 ATAATAAAAATATGATATGATATAAA
256805 A-AATAAAAATAT
1 ATAATAAAAATAT
256817 TTAAAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 11 0.32
25 20 0.59
26 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (26 bp):
ATAATAAAAATATGATATGATATAAA
Found at i:256847 original size:31 final size:33
Alignment explanation
Indices: 256812--256875 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
256802 TAAAAATAAA
256812 AATAT-TTAAAAATTT-TAT-AACATAAAATATT
1 AATATATT-AAAATTTATATAAACATAAAATATT
*
256843 AATATATTAAAATTTATATAAATATAAAATATT
1 AATATATTAAAATTTATATAAACATAAAATATT
256876 TTAAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 12 0.41
32 5 0.17
33 12 0.41
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATATTAAAATTTATATAAACATAAAATATT
Found at i:256873 original size:27 final size:28
Alignment explanation
Indices: 256843--256935 Score: 88
Period size: 27 Copynumber: 3.4 Consensus size: 28
256833 ATAAAATATT
*
256843 AATATATTAAAAT-TTATATAAATATAA
1 AATATATTAAAATATTATATATATATAA
*
256870 AATATTTTAAATATAATTATA-ATATAATAA
1 AATATATTAAA-AT-ATTATATATAT-ATAA
*
256900 AATATA-T-AAATATAATATATATATCAA
1 AATATATTAAAATATTATATATATAT-AA
256927 AAT-TATTAA
1 AATATATTAA
256936 TTTAATAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
26 9 0.17
27 22 0.41
28 5 0.09
29 4 0.07
30 14 0.26
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
AATATATTAAAATATTATATATATATAA
Found at i:256882 original size:16 final size:16
Alignment explanation
Indices: 256818--256885 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
256808 TAAAAATATT
*
256818 TAAAA-ATTTTATAACA
1 TAAAATATTTTA-AATA
256834 TAAAATA--TTAATATA
1 TAAAATATTTTAA-ATA
256849 TTAAAAT-TTATATAAATA
1 -TAAAATATT-T-TAAATA
256867 TAAAATATTTTAAATA
1 TAAAATATTTTAAATA
256883 TAA
1 TAA
256886 TTATAATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
14 1 0.02
15 5 0.12
16 20 0.47
17 8 0.19
18 6 0.14
19 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATATTTTAAATA
Found at i:262326 original size:28 final size:27
Alignment explanation
Indices: 262260--262362 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 27
262250 AAAAGCCACC
*
262260 CTTTGTATTTGTCAAAAATGGTGGTTA
1 CTTTGTATTTGTCAAAAATGGTGGTCA
262287 CTTTGTATTTGTCAAAAATGGTGGATCA
1 CTTTGTATTTGTCAAAAATGGTGG-TCA
* * * *
262315 TTTTTTGTTTGTCAAAAATTGTGG---
1 CTTTGTATTTGTCAAAAATGGTGGTCA
*
262339 C-TTGTTATTTGTCAAAATTGGTGG
1 CTTTG-TATTTGTCAAAAATGGTGG
262363 CTAATTTTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.03
24 16 0.25
27 24 0.38
28 22 0.34
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.46
Consensus pattern (27 bp):
CTTTGTATTTGTCAAAAATGGTGGTCA
Found at i:265099 original size:28 final size:27
Alignment explanation
Indices: 265033--265106 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
265023 AAAAGCCACC
*
265033 CTTTGTGTTTGTCAAAAATGATAGTTA
1 CTTTGTGTTTGTCAAAAATGATAGATA
* * *
265060 CTTTGTATTTGTCAAAAATGATGGATC
1 CTTTGTGTTTGTCAAAAATGATAGATA
*
265087 CTTTTTTGTTTGTCAAAAAT
1 C-TTTGTGTTTGTCAAAAAT
265107 TGTGCTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 24 0.60
28 16 0.40
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.46
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGATAGATA
Found at i:266674 original size:17 final size:18
Alignment explanation
Indices: 266634--266675 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
266624 GTCATTGATA
*
266634 TAAAATATTTTTTAATAT
1 TAAAATATTTTTTAATAG
*
266652 TTAAAT-TTTTTTAATAG
1 TAAAATATTTTTTAATAG
266669 TAAAATA
1 TAAAATA
266676 AATTTCTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAAAATATTTTTTAATAG
Found at i:271123 original size:21 final size:23
Alignment explanation
Indices: 271081--271128 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
271071 AAAAATATAA
*
271081 AAAAAATATATATAAAATATTTT
1 AAAAAATATAAATAAAATATTTT
*
271104 AAAAAATA-AAATAATA-ATTTT
1 AAAAAATATAAATAAAATATTTT
271125 AAAA
1 AAAA
271129 GGAGGACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 6 0.26
23 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAAATATAAATAAAATATTTT
Found at i:272137 original size:21 final size:20
Alignment explanation
Indices: 272113--272168 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
272103 ATATTTTTAT
* *
272113 TTAAATTTAATTATAAAAATA
1 TTAAAATTAA-TATAAAAAAA
272134 TTAAAATTAATATAAAAAAA
1 TTAAAATTAATATAAAAAAA
272154 TTAATAAATTAATAT
1 TT-A-AAATTAATAT
272169 TTTTTAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 11 0.35
21 10 0.32
22 10 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAAAATTAATATAAAAAAA
Found at i:272167 original size:22 final size:21
Alignment explanation
Indices: 272114--272168 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
272104 TATTTTTATT
*
272114 TAAATTTAATTATAAAAATATTA
1 TAAA-TTAA-TATAAAAAAATTA
272137 -AAATTAATATAAAAAAATTAA
1 TAAATTAATATAAAAAAATT-A
272158 TAAATTAATAT
1 TAAATTAATAT
272169 TTTTTAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 11 0.38
21 5 0.17
22 13 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTAATATAAAAAAATTA
Found at i:272769 original size:33 final size:33
Alignment explanation
Indices: 272732--272803 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
272722 ATATATTACG
272732 ATATAAA-TATCTAAATATT-TTAAAATTTAAATA
1 ATATAAATTAT-TAAAT-TTATTAAAATTTAAATA
* *
272765 ATATAAATTATTTAATTTATTAAAATTTATATA
1 ATATAAATTATTAAATTTATTAAAATTTAAATA
272798 A-ATAAA
1 ATATAAA
272804 AAATATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 7 0.20
33 25 0.71
34 3 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (33 bp):
ATATAAATTATTAAATTTATTAAAATTTAAATA
Found at i:272771 original size:16 final size:16
Alignment explanation
Indices: 272732--272804 Score: 51
Period size: 16 Copynumber: 4.5 Consensus size: 16
272722 ATATATTACG
*
272732 ATATAAATATCTAAATA
1 ATATAAA-ATTTAAATA
* *
272749 TTTTAAAATTTAAATA
1 ATATAAAATTTAAATA
* *
272765 ATATAAATTATTTAATTT
1 ATATAAA--ATTTAAATA
*
272783 AT-TAAAATTTATATA
1 ATATAAAATTTAAATA
272798 A-ATAAAA
1 ATATAAAA
272805 AATATTTTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
15 12 0.28
16 13 0.30
17 9 0.21
18 9 0.21
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAAAATTTAAATA
Found at i:273225 original size:23 final size:23
Alignment explanation
Indices: 273199--273247 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
273189 TTATATACCA
273199 AAACTATTATCATATATAAAAAT
1 AAACTATTATCATATATAAAAAT
273222 AAACTATTATCATATATAAAAAT
1 AAACTATTATCATATATAAAAAT
273245 AAA
1 AAA
273248 AACTACGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (23 bp):
AAACTATTATCATATATAAAAAT
Found at i:275157 original size:73 final size:72
Alignment explanation
Indices: 275020--275489 Score: 416
Period size: 73 Copynumber: 6.5 Consensus size: 72
275010 GGTGGTAATT
* * * * *
275020 TAAATAATACTCTAAAAATTTAAACTCATATAATTA-ATTTAAAAAATAAATTTAAATTTCTACA
1 TAAATTATACTATAAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAAA-TTCTACA
275084 AATAAAAA
65 AATAAAAA
* * * * *
275092 TAAACTATACTATAAAAAATATAAACTCATATAATCATGTCTAAAAAACACATTTAAATTTTACA
1 TAAATTATACTAT-AAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAAATTCTACA
275157 AATAAAAA
65 AATAAAAA
* ** * * *
275165 TAAATTATA-TCATAAAAAATATAAACTTGTACAATCATATCTAATAAACAAATTTAAGCTTCTA
1 TAAATTATACT-AT-AAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAA-ATTCTA
* *
275229 AAAATAAAGA
63 CAAATAAAAA
* * * * * *
275239 TAAATAATACTCT-AAAATTTAAACTCATATAATCATACCCAAAAAACAAATTTAAGCTTCAACA
1 TAAATTATACTATAAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAA-ATTCTACA
275303 AAT-AAAA
65 AATAAAAA
* * * * * *
275310 TAAATAATACTTTAAAAATTTAAACTCATATAATTAAAT-AAAAAAATAAATTTAAACTTCT--A
1 TAAATTATACTATAAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAAA-TTCTACA
* *
275372 TATATAAA
65 AATAAAAA
* * * *
275380 TAAATTATACTTTCAAATATTTAAACTCATATAATTATA-CTTAAAAAACACATTTAAACTTCTA
1 TAAATTATACTAT-AAAAATTTAAACTCATATAATCATATC-TAAAAAACAAATTTAAA-TTCTA
* *
275444 TAAATCAAAA
63 CAAATAAAAA
** * *
275454 TAAATTATACCCTAAAAATTTAAATTCACATAATCA
1 TAAATTATACTATAAAAATTTAAACTCATATAATCA
275490 AATAAAAATA
Statistics
Matches: 327, Mismatches: 58, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
69 3 0.01
70 15 0.05
71 55 0.17
72 97 0.30
73 102 0.31
74 54 0.17
75 1 0.00
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (72 bp):
TAAATTATACTATAAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAAATTCTACAA
ATAAAAA
Found at i:275275 original size:72 final size:72
Alignment explanation
Indices: 275020--275489 Score: 436
Period size: 72 Copynumber: 6.5 Consensus size: 72
275010 GGTGGTAATT
* * * * *
275020 TAAATAATACTCTAAAAATTTAAACTCATATAATTA-ATTTAAAAAATAAATTTAAATTTCTACA
1 TAAATAATACTCTAAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAAACTTCTAAA
275084 AATAAAAA
66 AAT-AAAA
* * * * *
275092 TAAACT-ATACTATAAAAAATATAAACTCATATAATCATGTCTAAAAAACACATTTAAA-TTTTA
1 TAAA-TAATACTCT-AAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAAACTTCTA
*
275155 CAAATAAAAA
64 AAAAT-AAAA
* * ** * * *
275165 TAAATTATA-TCATAAAAAATATAAACTTGTACAATCATATCTAATAAACAAATTTAAGCTTCTA
1 TAAATAATACTC-T-AAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAAACTTCTA
275229 AAAATAAAGA
64 AAAATAAA-A
* * *
275239 TAAATAATACTCT-AAAATTTAAACTCATATAATCATACCCAAAAAACAAATTTAAGCTTC-AAC
1 TAAATAATACTCTAAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAAACTTCTAA-
275302 AAATAAAA
65 AAATAAAA
* * * * * *
275310 TAAATAATACTTTAAAAATTTAAACTCATATAATTAAAT-AAAAAAATAAATTTAAACTTCTATA
1 TAAATAATACTCTAAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAAACTTCTAAA
*
275374 TAT-AAA
66 AATAAAA
* * * * *
275380 TAAATTATACTTTCAAATATTTAAACTCATATAATTATA-CTTAAAAAACACATTTAAACTTCTA
1 TAAATAATACTCT-AAAAATTTAAACTCATATAATCATATC-TAAAAAACAAATTTAAACTTCTA
*
275444 TAAATCAAAA
64 AAAAT-AAAA
* * * *
275454 TAAATTATACCCTAAAAATTTAAATTCACATAATCA
1 TAAATAATACTCTAAAAATTTAAACTCATATAATCA
275490 AATAAAAATA
Statistics
Matches: 334, Mismatches: 48, Indels: 31
0.81 0.12 0.08
Matches are distributed among these distances:
70 15 0.04
71 59 0.18
72 106 0.32
73 104 0.31
74 48 0.14
75 2 0.01
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (72 bp):
TAAATAATACTCTAAAAATTTAAACTCATATAATCATATCTAAAAAACAAATTTAAACTTCTAAA
AATAAAA
Found at i:275531 original size:44 final size:44
Alignment explanation
Indices: 275445--275533 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
275435 AAACTTCTAT
* *
275445 AAATCAAAATAAATTATACCCTAAAAATTTAAATTCACATAATC
1 AAATAAAAATAAATTATACCCTAAAAATTTAAACTCACATAATC
* * * * **
275489 AAATAAAAATACATTGTACCTTTAAAATTTAAACTCGTATAATC
1 AAATAAAAATAAATTATACCCTAAAAATTTAAACTCACATAATC
275533 A
1 A
275534 TTTCTTGCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (44 bp):
AAATAAAAATAAATTATACCCTAAAAATTTAAACTCACATAATC
Found at i:275947 original size:19 final size:17
Alignment explanation
Indices: 275901--275946 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 17
275891 TTTACCTTTA
275901 TTATTAAAATTTTTATT
1 TTATTAAAATTTTTATT
275918 TTAATTTAAAATTTTTTATT
1 TT-A-TTAAAA-TTTTTATT
275938 TTATTAAAA
1 TTATTAAAA
275947 AATTAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 2 0.08
18 7 0.27
19 7 0.27
20 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTAAAATTTTTATT
Found at i:275950 original size:20 final size:20
Alignment explanation
Indices: 275906--275947 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
275896 CTTTATTATT
*
275906 AAAA-TTTTTATTTTAATTT
1 AAAATTTTTTATTTTAATTA
275925 AAAATTTTTTATTTT-ATTA
1 AAAATTTTTTATTTTAATTA
275944 AAAA
1 AAAA
275948 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAAATTTTTTATTTTAATTA
Found at i:276227 original size:3 final size:3
Alignment explanation
Indices: 276219--276249 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
276209 GAAAATTAAA
276219 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
276250 AATAAACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Done.