Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 4 of 20
Found at i:493001 original size:10 final size:10
Alignment explanation
Indices: 492986--493016 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
492976 TTTCAAGTGA
492986 ACATATATAT
1 ACATATATAT
492996 ACATATATAT
1 ACATATATAT
*
493006 ATATATATAT
1 ACATATATAT
493016 A
1 A
493017 ATCACCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (10 bp):
ACATATATAT
Found at i:493081 original size:27 final size:27
Alignment explanation
Indices: 493043--493096 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
493033 TCCAGTGTTC
493043 TGTTAATTAATTAGCTTGTGGGAATTA
1 TGTTAATTAATTAGCTTGTGGGAATTA
493070 TGTTAATTAATTAGCTTGTGGGAATTA
1 TGTTAATTAATTAGCTTGTGGGAATTA
493097 ATCTCTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (27 bp):
TGTTAATTAATTAGCTTGTGGGAATTA
Found at i:496345 original size:2 final size:2
Alignment explanation
Indices: 496338--496366 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
496328 AATCGACAAC
496338 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
496367 AGCACCCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:498869 original size:39 final size:38
Alignment explanation
Indices: 498815--498890 Score: 134
Period size: 39 Copynumber: 2.0 Consensus size: 38
498805 TACCACTCCA
498815 GCATTGTATCATGAAAGGGAGGTAAATTATTAGGTTATT
1 GCATTGTATCATGAAAGGGAGGTAAATTATTA-GTTATT
*
498854 GCATTGTATCTTGAAAGGGAGGTAAATTATTAGTTAT
1 GCATTGTATCATGAAAGGGAGGTAAATTATTAGTTAT
498891 CGTATCACCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 5 0.14
39 31 0.86
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (38 bp):
GCATTGTATCATGAAAGGGAGGTAAATTATTAGTTATT
Found at i:504779 original size:2 final size:2
Alignment explanation
Indices: 504772--504800 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
504762 TCCATTTGAG
504772 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
504801 TTTCGTCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:507268 original size:5 final size:5
Alignment explanation
Indices: 507249--507443 Score: 52
Period size: 5 Copynumber: 38.6 Consensus size: 5
507239 AAATATGATT
*
507249 ATATG ATATA TATATA ATATA A-A-A A-ATA AT-TAA GATATA ATATAAA
1 ATATA ATATA -ATATA ATATA ATATA ATATA ATAT-A -ATATA ATAT--A
* * * *
507295 ATATA ATATA ATA-A AAATA ATATTA ATATA ACATAA ATATA TTAAA ATATTAA
1 ATATA ATATA ATATA ATATA ATA-TA ATATA ATAT-A ATATA ATATA ATA-T-A
* * * * * * * *
507348 ATTTT ATATA ATATA A-ATT GT-TA ATGT- ATAAA ATTTT ATATA A-AT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * *
507393 ATATA ATATT TTA-A ATACAA ATATA ATATA ATAAATA ATATGA ATATA
1 ATATA ATATA ATATA ATA-TA ATATA ATATA AT--ATA ATAT-A ATATA
507441 ATA
1 ATA
507444 AAAAATATAA
Statistics
Matches: 138, Mismatches: 29, Indels: 46
0.65 0.14 0.22
Matches are distributed among these distances:
3 4 0.03
4 19 0.14
5 74 0.54
6 27 0.20
7 14 0.10
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:507364 original size:33 final size:33
Alignment explanation
Indices: 507288--507407 Score: 102
Period size: 32 Copynumber: 3.6 Consensus size: 33
507278 TTAAGATATA
* * * *
507288 ATATAAAATATAATATAATAAAA-ATAATA-TTA
1 ATATAATATA-AATATATTAAAATATAAAATTTT
* *
507320 ATATAACATAAATATATTAAAATATTAAATTTT
1 ATATAATATAAATATATTAAAATATAAAATTTT
* **
507353 ATATAATATAAAT-TGTTAATGTATAAAATTTT
1 ATATAATATAAATATATTAAAATATAAAATTTT
*
507385 ATATAAATATATAATATTTTAAA
1 ATAT-AATATA-AATATATTAAA
507408 TACAAATATA
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
31 11 0.15
32 32 0.45
33 20 0.28
34 3 0.04
35 5 0.07
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (33 bp):
ATATAATATAAATATATTAAAATATAAAATTTT
Found at i:507419 original size:20 final size:20
Alignment explanation
Indices: 507374--507421 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
507364 ATTGTTAATG
* *
507374 TATAAAATTTTATATAAATA
1 TATAATATTTTAAATAAATA
507394 TATAATATTTTAAATACAA-A
1 TATAATATTTTAAATA-AATA
507414 TATAATAT
1 TATAATAT
507422 AATAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAATATTTTAAATAAATA
Found at i:507440 original size:18 final size:17
Alignment explanation
Indices: 507411--507453 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 17
507401 TTTTAAATAC
507411 AAATATAATATAATAAA
1 AAATATAATATAATAAA
*
507428 TAATATGAATATAATAAA
1 AAATAT-AATATAATAAA
507446 AAATATAA
1 AAATATAA
507454 ATTGATAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AAATATAATATAATAAA
Found at i:509137 original size:14 final size:14
Alignment explanation
Indices: 509114--509147 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
509104 TATATTTTTT
*
509114 TATTATATTTAAAA
1 TATTAAATTTAAAA
509128 TATTAAATTTAAAA
1 TATTAAATTTAAAA
509142 TATTAA
1 TATTAA
509148 TAATTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTAAATTTAAAA
Found at i:509196 original size:24 final size:24
Alignment explanation
Indices: 509145--509234 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 24
509135 TTTAAAATAT
* * *
509145 TAATA-ATTTATATTATATAAATTT
1 TAATATATTTATA-TATTTATATTA
509169 TAATATATTTATATATTTATATTA
1 TAATATATTTATATATTTATATTA
509193 TAATATATTT-T-TATTT-T-TTA
1 TAATATATTTATATATTTATATTA
*
509213 T--TATATTTATATAATTATATTA
1 TAATATATTTATATATTTATATTA
509235 AATTTTTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
18 7 0.12
19 1 0.02
20 8 0.14
21 2 0.04
22 8 0.14
23 1 0.02
24 23 0.40
25 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATATATTTATATATTTATATTA
Found at i:509199 original size:18 final size:18
Alignment explanation
Indices: 509150--509224 Score: 54
Period size: 18 Copynumber: 4.4 Consensus size: 18
509140 AATATTAATA
509150 ATTTATATTAT-ATA-A-
1 ATTTATATTATAATATAT
* *
509165 ATTT-TAATATATTTATAT
1 ATTTATATTATA-ATATAT
509183 ATTTATATTATAATATAT
1 ATTTATATTATAATATAT
* * *
509201 TTTTAT-TTTTTAT-TAT
1 ATTTATATTATAATATAT
509217 ATTTATAT
1 ATTTATAT
509225 AATTATATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
14 5 0.11
15 4 0.09
16 10 0.22
17 7 0.15
18 14 0.30
19 6 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTATATTATAATATAT
Found at i:509786 original size:16 final size:16
Alignment explanation
Indices: 509761--509801 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
509751 AAAATCCAAG
*
509761 ATATACATACATACAT
1 ATATATATACATACAT
* *
509777 ATATGTATACATATAT
1 ATATATATACATACAT
509793 ATATATATA
1 ATATATATA
509802 TAGTCTGGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (16 bp):
ATATATATACATACAT
Found at i:510026 original size:27 final size:26
Alignment explanation
Indices: 509969--510104 Score: 77
Period size: 27 Copynumber: 5.2 Consensus size: 26
509959 AATTTAAAAA
*
509969 ATAATATA-AAATATGATAAAAATAAT
1 ATAATATATAAATAT-TTAAAAATAAT
*
509995 ATAATATATAAATATTTAAAAATTTAT
1 ATAATATATAAATATTTAAAAA-TAAT
* ** *
510022 TTAATAT-T-AATA-TTAAATTTTAT
1 ATAATATATAAATATTTAAAAATAAT
* *
510045 ATAA-ATAAAAAATATATTAAATATAATT
1 ATAATAT-ATAAATAT-TTAAAAATAA-T
*
510073 ATAATATAATAAA-ATATACAAATATAAT
1 ATAATAT-ATAAATATTTA-AAA-ATAAT
510101 ATAA
1 ATAA
510105 AAACAATCAC
Statistics
Matches: 87, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
22 2 0.02
23 7 0.08
24 5 0.06
25 8 0.09
26 15 0.17
27 25 0.29
28 14 0.16
29 11 0.13
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (26 bp):
ATAATATATAAATATTTAAAAATAAT
Found at i:510099 original size:15 final size:15
Alignment explanation
Indices: 510042--510099 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
510032 TATTAAATTT
*
510042 TATATAAATAAAAAA
1 TATATAAATATAAAA
510057 TATATTAAATAT--AA
1 TATA-TAAATATAAAA
510071 T-TATAATATAATAAAA
1 TATATAA-AT-ATAAAA
*
510087 TATACAAATATAA
1 TATATAAATATAA
510100 TATAAAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
12 3 0.09
13 4 0.11
14 5 0.14
15 8 0.23
16 11 0.31
17 4 0.11
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
TATATAAATATAAAA
Found at i:510310 original size:8 final size:8
Alignment explanation
Indices: 510299--510343 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
510289 ATTTTTAATA
510299 AAATATAT
1 AAATATAT
510307 AAATATTAAT
1 AAATA-T-AT
510317 AAAT-T-T
1 AAATATAT
510323 AAATATA-
1 AAATATAT
510330 AAATATAT
1 AAATATAT
510338 AAATAT
1 AAATAT
510344 TAATATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
6 5 0.16
7 8 0.25
8 12 0.38
9 1 0.03
10 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AAATATAT
Found at i:510341 original size:21 final size:24
Alignment explanation
Indices: 510299--510351 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 24
510289 ATTTTTAATA
510299 AAATATATAAATATTAATAAAT-TT
1 AAATATA-AAATATTAATAAATATT
510323 AAATATAAAATA-T-ATAAATATT
1 AAATATAAAATATTAATAAATATT
510345 -AATATAA
1 AAATATAA
510352 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 13 0.46
22 3 0.11
23 5 0.18
24 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATATAAAATATTAATAAATATT
Found at i:510989 original size:22 final size:22
Alignment explanation
Indices: 510946--510989 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
510936 TAAAAAAATA
* *
510946 TAATTTAAATTTCTTAATTTTT
1 TAATTTAAATTTCTAAAATTTT
*
510968 TAATTTAAATTT-TAAAAATTT
1 TAATTTAAATTTCTAAAATTTT
510989 T
1 T
510990 GATAACATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TAATTTAAATTTCTAAAATTTT
Found at i:521629 original size:16 final size:17
Alignment explanation
Indices: 521599--521631 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
521589 AATAAATATT
521599 AAATAAAAATGTTTAAA
1 AAATAAAAATGTTTAAA
521616 AAATAAAAAT-TTTAAA
1 AAATAAAAATGTTTAAA
521632 TAATGTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAATAAAAATGTTTAAA
Found at i:523221 original size:22 final size:22
Alignment explanation
Indices: 523191--523242 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
523181 ATTAATTCAT
* *
523191 TAATTATAAAATATTTTA-TAAA
1 TAATAATAAAAT-TTATATTAAA
523213 TAATAATAAAATTTATATTAAA
1 TAATAATAAAATTTATATTAAA
523235 TAATAATA
1 TAATAATA
523243 GATAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAATAAAATTTATATTAAA
Found at i:531817 original size:14 final size:14
Alignment explanation
Indices: 531795--531836 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
531785 ATATGATTAC
*
531795 ATTACATAAAAAAT
1 ATTAAATAAAAAAT
*
531809 ATTAAATAAATAAT
1 ATTAAATAAAAAAT
*
531823 -TAAAATAAAAAAT
1 ATTAAATAAAAAAT
531836 A
1 A
531837 ATATAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (14 bp):
ATTAAATAAAAAAT
Found at i:531837 original size:16 final size:18
Alignment explanation
Indices: 531811--531844 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
531801 TAAAAAATAT
531811 TAAATAAATAAT-TAAAA
1 TAAATAAATAATATAAAA
531828 TAAA-AAATAATATAAAA
1 TAAATAAATAATATAAAA
531845 ATTATTTAAA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATAAATAATATAAAA
Found at i:531846 original size:27 final size:27
Alignment explanation
Indices: 531800--531856 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
531790 ATTACATTAC
*
531800 ATAAAAAATATTAAATAAATAATTAAA
1 ATAAAAAATAATAAATAAATAATTAAA
* *
531827 ATAAAAAATAATATAA-AAATTATTTAA
1 ATAAAAAATAATA-AATAAATAATTAAA
531854 ATA
1 ATA
531857 TATGACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
ATAAAAAATAATAAATAAATAATTAAA
Found at i:532514 original size:5 final size:5
Alignment explanation
Indices: 532504--532544 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
532494 ATTTATAAGT
*
532504 TTATA TTATA TT-TA -TATA TTTTA TTATA TTATAA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TT
532545 TAAGATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
3 1 0.03
4 4 0.13
5 21 0.68
6 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:532680 original size:12 final size:14
Alignment explanation
Indices: 532620--532673 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
532610 ATTTATTTTT
532620 ATTATATTATATAATA
1 ATTATATT-TAT-ATA
532636 ATTAT-TTTATACGT-
1 ATTATATTTATA--TA
532650 ATTATATTTATATA
1 ATTATATTTATATA
532664 ATTATATTTA
1 ATTATATTTA
532674 AAATTATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.06
14 18 0.53
15 9 0.26
16 5 0.15
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTATATTTATATA
Found at i:535800 original size:27 final size:26
Alignment explanation
Indices: 535761--535824 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 26
535751 TGTAAACTTT
535761 AAAAAATTATAATT-ATTTATGTTTTAA
1 AAAAAATTATAATTAATTT-T-TTTTAA
535788 AAATAAATT-TAATTAAATTTTTTTTAA
1 AAA-AAATTATAATT-AATTTTTTTTAA
535815 AAAAAATTAT
1 AAAAAATTAT
535825 TTTTTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
26 5 0.15
27 18 0.55
28 6 0.18
29 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
AAAAAATTATAATTAATTTTTTTTAA
Found at i:536838 original size:14 final size:15
Alignment explanation
Indices: 536821--536849 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
536811 TTTATATTAA
536821 AAATTAAAAT-AATT
1 AAATTAAAATCAATT
536835 AAATTAAAATCAATT
1 AAATTAAAATCAATT
536850 TGTTTGATTT
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:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTAAAATCAATT
Found at i:537244 original size:32 final size:33
Alignment explanation
Indices: 537208--537269 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
537198 AATATAATAT
537208 ATAAG-TTATTAAATAAATTAAAAT-TTATTAAA
1 ATAAGATT-TTAAATAAATTAAAATATTATTAAA
* *
537240 ATAAGATTTTAATTAAATTTAAATATTATT
1 ATAAGATTTTAAATAAATTAAAATATTATT
537270 TTATATCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (33 bp):
ATAAGATTTTAAATAAATTAAAATATTATTAAA
Found at i:537270 original size:22 final size:22
Alignment explanation
Indices: 537245--537291 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
537235 TTAAAATAAG
*
537245 ATTTTA-ATTAAATTTAAATATT
1 ATTTTATATCAAATTTAAA-ATT
*
537267 ATTTTATATCATATTTAAAATT
1 ATTTTATATCAAATTTAAAATT
537289 ATT
1 ATT
537292 AAATTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTATATCAAATTTAAAATT
Found at i:541802 original size:3 final size:3
Alignment explanation
Indices: 541796--541825 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
541786 CAGTGTCCCT
*
541796 CAC CAC CAC CAC CAC CAC CAC TAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
541826 TAACAACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.63, G:0.00, T:0.03
Consensus pattern (3 bp):
CAC
Found at i:543219 original size:11 final size:13
Alignment explanation
Indices: 543185--543228 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
543175 TAATTATAAA
543185 AATATATAAATATT
1 AATATA-AAATATT
543199 AATATAAAATATT
1 AATATAAAATATT
*
543212 -AT-TAAAATTTT
1 AATATAAAATATT
543223 AATATA
1 AATATA
543229 TTTGAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 8 0.30
12 4 0.15
13 9 0.33
14 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATATAAAATATT
Found at i:543887 original size:13 final size:13
Alignment explanation
Indices: 543869--543902 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
543859 TTTTATCACA
*
543869 TTATAATTATATT
1 TTATAATTAAATT
543882 TTATAATTAAATT
1 TTATAATTAAATT
*
543895 TTAAAATT
1 TTATAATT
543903 TTAATCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATAATTAAATT
Found at i:544460 original size:15 final size:15
Alignment explanation
Indices: 544440--544476 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
544430 TATAAAGTAT
544440 ATAAATATTAATAAA
1 ATAAATATTAATAAA
* *
544455 ATAAATTTTAATAAG
1 ATAAATATTAATAAA
544470 ATAAATA
1 ATAAATA
544477 ATATATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
ATAAATATTAATAAA
Found at i:544476 original size:24 final size:23
Alignment explanation
Indices: 544440--544518 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 23
544430 TATAAAGTAT
*
544440 ATAAATATTAATAAAATAAATTTTA
1 ATAAATA--AATAAAATAAATTTAA
544465 ATAAGATAAATAATATATTAAATTTAA
1 ATAA-ATAAATAA-A-A-TAAATTTAA
* *
544492 ATTAATAAATTAAATTAAATTTAA
1 ATAAATAAA-TAAAATAAATTTAA
544516 ATA
1 ATA
544519 TAAACTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
24 16 0.36
25 5 0.11
26 10 0.22
27 14 0.31
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (23 bp):
ATAAATAAATAAAATAAATTTAA
Found at i:544506 original size:31 final size:31
Alignment explanation
Indices: 544462--544527 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 31
544452 AAAATAAATT
*
544462 TTAATAAGATAAA-TAATATATTAAATTTAAA-
1 TTAATAAGATAAATTAA-AT-TTAAATATAAAC
544493 TTAATAA-ATTAAATTAAATTTAAATATAAAC
1 TTAATAAGA-TAAATTAAATTTAAATATAAAC
544524 TTAA
1 TTAA
544528 AATTTTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
30 11 0.35
31 17 0.55
32 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (31 bp):
TTAATAAGATAAATTAAATTTAAATATAAAC
Found at i:544515 original size:19 final size:19
Alignment explanation
Indices: 544471--544512 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
544461 TTTAATAAGA
*
544471 TAAA-TAATATATTAAATT
1 TAAATTAATAAATTAAATT
544489 TAAATTAATAAATTAAA-T
1 TAAATTAATAAATTAAATT
544507 TAAATT
1 TAAATT
544513 TAAATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATTAATAAATTAAATT
Found at i:544527 original size:18 final size:17
Alignment explanation
Indices: 544471--544538 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 17
544461 TTTAATAAGA
* *
544471 TAAATAATATATTAAATT
1 TAAATTATAAATTAAA-T
544489 TAAATTAATAAATTAAAT
1 TAAATT-ATAAATTAAAT
544507 TAAATT-TAAATATAAACT
1 TAAATTATAAAT-TAAA-T
*
544525 TAAAATTTTAAATT
1 T-AAATTATAAATT
544539 TTTTTAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
16 5 0.12
17 4 0.09
18 14 0.33
19 15 0.35
20 5 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTATAAATTAAAT
Found at i:544912 original size:19 final size:19
Alignment explanation
Indices: 544890--544946 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
544880 TTTATATTTT
544890 TAATTTAAATATATAAATA
1 TAATTTAAATATATAAATA
*
544909 TAATATAAAT-TATTAAATA
1 TAATTTAAATATA-TAAATA
*
544928 T-A-TTAAA-ATTTAAATA
1 TAATTTAAATATATAAATA
544944 TAA
1 TAA
544947 ATATAACACA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 7 0.22
17 6 0.19
18 3 0.09
19 16 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTTAAATATATAAATA
Found at i:544982 original size:19 final size:19
Alignment explanation
Indices: 544958--544994 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
544948 TATAACACAT
*
544958 ATATTAAATTTATTATATA
1 ATATTAAATTAATTATATA
*
544977 ATATTATATTAATTATAT
1 ATATTAAATTAATTATAT
544995 TATTTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTAAATTAATTATATA
Found at i:544985 original size:5 final size:5
Alignment explanation
Indices: 544957--545001 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
544947 ATATAACACA
* *
544957 TATAT TAAAT T-TAT TATAT AATAT TATAT TA-AT TATAT TAT-T TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
545002 TAAATATGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
4 11 0.32
5 23 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:547249 original size:2 final size:2
Alignment explanation
Indices: 547242--547278 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
547232 AAAATAGTCA
547242 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
547279 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:547283 original size:2 final size:2
Alignment explanation
Indices: 547278--547310 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
547268 TCTCTCTCTC
547278 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
547311 CAAAGAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:547564 original size:18 final size:18
Alignment explanation
Indices: 547538--547582 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
547528 TGGTTCGGTC
* *
547538 AGTTTTTTTAATTTTTTT
1 AGTTATTTTAACTTTTTT
**
547556 AGTTATTTTTGCTTTTTT
1 AGTTATTTTAACTTTTTT
547574 AGTTATTTT
1 AGTTATTTT
547583 TGCATTTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (18 bp):
AGTTATTTTAACTTTTTT
Found at i:547583 original size:18 final size:18
Alignment explanation
Indices: 547550--547585 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
547540 TTTTTTTAAT
547550 TTTTTTAGTTATTTTTGC
1 TTTTTTAGTTATTTTTGC
547568 TTTTTTAGTTATTTTTGC
1 TTTTTTAGTTATTTTTGC
547586 ATTTCATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.06, G:0.11, T:0.72
Consensus pattern (18 bp):
TTTTTTAGTTATTTTTGC
Found at i:547873 original size:19 final size:19
Alignment explanation
Indices: 547845--547899 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
547835 TATAACTTAT
547845 AAGCACTAAACATAATTAA
1 AAGCACTAAACATAATTAA
* *
547864 AAGCATTAAATATAATTACA
1 AAGCACTAAACATAATTA-A
*
547884 AA-CAC-AAGCATAATTA
1 AAGCACTAAACATAATTA
547900 TAATTATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 9 0.30
19 18 0.60
20 3 0.10
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (19 bp):
AAGCACTAAACATAATTAA
Found at i:557109 original size:2 final size:2
Alignment explanation
Indices: 557102--557137 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
557092 TCTGTGAAGA
557102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
557138 CTTCTAAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:557312 original size:2 final size:2
Alignment explanation
Indices: 557305--557332 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
557295 GAGACGGCCA
557305 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
557333 TTGTATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:557957 original size:24 final size:24
Alignment explanation
Indices: 557930--557979 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
557920 TATACTAAAT
557930 AAATATAATATAAAAAATTAAT-TA
1 AAATATAATATAAAAAA-TAATATA
*
557954 AAATATAATATGAAAAATAATATA
1 AAATATAATATAAAAAATAATATA
557978 AA
1 AA
557980 TACGAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATATAATATAAAAAATAATATA
Found at i:557973 original size:12 final size:11
Alignment explanation
Indices: 557928--557979 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
557918 ATTATACTAA
*
557928 ATAAATATAAT
1 ATAAAAATAAT
557939 ATAAAAAATTAAT
1 AT-AAAAA-TAAT
557952 -TAAAATATAAT
1 ATAAAA-ATAAT
557963 ATGAAAAATAAT
1 AT-AAAAATAAT
557975 ATAAA
1 ATAAA
557980 TACGAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
11 13 0.37
12 14 0.40
13 8 0.23
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:558839 original size:32 final size:32
Alignment explanation
Indices: 558764--558839 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 32
558754 TAAATTATTA
558764 TTAAA-AATATTAAAATATTAAAAAAAATATTTT
1 TTAAATAA-ATTAAAATA-TAAAAAAAATATTTT
* *
558797 TATAATTAAATTAAAATA-AAAAATTAATATTTT
1 T-TAAATAAATTAAAATATAAAAA-AAATATTTT
558830 TTAAATAAAT
1 TTAAATAAAT
558840 AATAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
32 13 0.35
33 10 0.27
34 12 0.32
35 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TTAAATAAATTAAAATATAAAAAAAATATTTT
Found at i:558869 original size:15 final size:17
Alignment explanation
Indices: 558829--558871 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
558819 ATTAATATTT
558829 TTTAAAT-AAATAATAA
1 TTTAAATCAAATAATAA
558845 TTTAAATCAAATAA-AA
1 TTTAAATCAAATAATAA
*
558861 -TTAATTCAAAT
1 TTTAAATCAAAT
558872 CATTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 10 0.40
16 9 0.36
17 6 0.24
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
TTTAAATCAAATAATAA
Found at i:558871 original size:20 final size:21
Alignment explanation
Indices: 558832--558873 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
558822 AATATTTTTT
*
558832 AAATAAATAATAATTTAAATC
1 AAATAAATAATAATTCAAATC
*
558853 AAATAAA-ATTAATTCAAATC
1 AAATAAATAATAATTCAAATC
558873 A
1 A
558874 TTTAAATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAATAATAATTCAAATC
Found at i:560734 original size:2 final size:2
Alignment explanation
Indices: 560727--560760 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
560717 GTATTTGGCT
560727 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
560761 CACCTTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:561237 original size:51 final size:51
Alignment explanation
Indices: 561161--561262 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
561151 ACCCAACAAC
*
561161 CTTGAAATTTTGAAGCATGGCCCTTGCACTGCTCCTAGAGGTGTTGATGGT
1 CTTGAAATTTTGAAGCATGGCCCTTGCACTGCTCCCAGAGGTGTTGATGGT
* * *
561212 CTTGAACTTTTGAAGCATGGCCCTTGCATTGCTCCCAGAGGTGTTTATGGT
1 CTTGAAATTTTGAAGCATGGCCCTTGCACTGCTCCCAGAGGTGTTGATGGT
561263 AGGTCGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (51 bp):
CTTGAAATTTTGAAGCATGGCCCTTGCACTGCTCCCAGAGGTGTTGATGGT
Found at i:561832 original size:24 final size:23
Alignment explanation
Indices: 561805--561877 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 23
561795 AATTTAATAT
561805 AATAACTATGATATGATATATTTA
1 AATAA-TATGATATGATATATTTA
* * *
561829 AATAAAAATAATATGATAT-TTTT
1 AAT-AATATGATATGATATATTTA
*
561852 AAT-ATATGATTATGTTTATATTTA
1 AATAATATGA-TATG-ATATATTTA
561876 AA
1 AA
561878 ATTTTAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 4 0.11
22 4 0.11
23 9 0.24
24 19 0.50
25 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (23 bp):
AATAATATGATATGATATATTTA
Found at i:561909 original size:19 final size:17
Alignment explanation
Indices: 561867--561910 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
561857 ATGATTATGT
561867 TTATATTTAAAATTTTA
1 TTATATTTAAAATTTTA
* *
561884 ATATATTTAATTATTTATA
1 TTATATTTAA-AATTT-TA
561903 TTATATTT
1 TTATATTT
561911 TTATTTACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 9 0.41
18 4 0.18
19 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTAAAATTTTA
Found at i:563185 original size:3 final size:3
Alignment explanation
Indices: 563179--563220 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
563169 AGAAGAAAAG
563179 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
563221 GAGTTAGTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:564002 original size:19 final size:19
Alignment explanation
Indices: 563978--564056 Score: 72
Period size: 19 Copynumber: 4.1 Consensus size: 19
563968 CTGATTTTAT
563978 TTAAAATAATATTTTTAAA
1 TTAAAATAATATTTTTAAA
*
563997 TTAAAATAATATATTTT-AT
1 TTAAAATAATAT-TTTTAAA
* * * *
564016 TTAAATTTA-ATTATAAAA
1 TTAAAATAATATTTTTAAA
564034 TATATAAATAATATTTTTAAA
1 T-TA-AAATAATATTTTTAAA
564055 TT
1 TT
564057 TTTTAAAAAG
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
17 2 0.04
18 4 0.09
19 22 0.49
20 9 0.20
21 8 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAATAATATTTTTAAA
Found at i:564055 original size:21 final size:20
Alignment explanation
Indices: 563981--564056 Score: 63
Period size: 21 Copynumber: 3.9 Consensus size: 20
563971 ATTTTATTTA
563981 AAATAATATTTTTAAATTA-
1 AAATAATATTTTTAAATTAT
564000 AAATAATATATTTT--ATT-T
1 AAATAATAT-TTTTAAATTAT
* * *
564018 AAAT-TTAATTATAAAATATAT
1 AAATAAT-ATTTTTAAAT-TAT
564039 AAATAATATTTTTAAATT
1 AAATAATATTTTTAAATT
564057 TTTTAAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 15
0.67 0.09 0.23
Matches are distributed among these distances:
17 3 0.07
18 9 0.21
19 11 0.26
20 6 0.14
21 13 0.30
22 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAATATTTTTAAATTAT
Found at i:564509 original size:20 final size:21
Alignment explanation
Indices: 564486--564524 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
564476 AAAATTATTA
564486 TTTAATT-AATAAAAAATATC
1 TTTAATTAAATAAAAAATATC
* *
564506 TTTATTTAAATAAATAATA
1 TTTAATTAAATAAAAAATA
564525 AAATAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAATTAAATAAAAAATATC
Found at i:565023 original size:2 final size:2
Alignment explanation
Indices: 565012--565051 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
565002 CGCAATCCTT
565012 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
565052 AAGGTTGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:565251 original size:29 final size:31
Alignment explanation
Indices: 565185--565253 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
565175 ATTTTTATTT
* **
565185 TATTTTAAATTTAATAATATTAGAACAATTGT
1 TATTTT-AATATAATAATATTAGAACAATTAA
*
565217 TATTTTAATATAATAATATT-TAA-AATTAA
1 TATTTTAATATAATAATATTAGAACAATTAA
565246 TATTTTAA
1 TATTTTAA
565254 AAAATTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 12 0.36
30 2 0.06
31 13 0.39
32 6 0.18
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (31 bp):
TATTTTAATATAATAATATTAGAACAATTAA
Found at i:565298 original size:20 final size:18
Alignment explanation
Indices: 565265--565302 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
565255 AAATTATTAA
565265 AAATAATTTTTTATTTTT
1 AAATAATTTTTTATTTTT
565283 AAATATATTTTCTTATTTTT
1 AAATA-ATTTT-TTATTTTT
565303 TATAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
AAATAATTTTTTATTTTT
Found at i:569257 original size:11 final size:11
Alignment explanation
Indices: 569229--569261 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
569219 GTAATGATAA
*
569229 ATTTGATTTTT
1 ATTTGATTTTG
569240 A-TTGATTTTG
1 ATTTGATTTTG
569250 ATTTGATTTTG
1 ATTTGATTTTG
569261 A
1 A
569262 CATGGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (11 bp):
ATTTGATTTTG
Found at i:570479 original size:13 final size:13
Alignment explanation
Indices: 570455--570492 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
570445 AATTAAAAAT
570455 TATTTATAAATTAA
1 TATTTAT-AATTAA
570469 TATTTATAATTAA
1 TATTTATAATTAA
570482 -ATTTAATAATT
1 TATTT-ATAATT
570493 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 12 0.52
14 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTTATAATTAA
Found at i:578162 original size:17 final size:19
Alignment explanation
Indices: 578128--578162 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
578118 ACATCTTTAA
578128 TTAGAGATAAATAAGAAAG
1 TTAGAGATAAATAAGAAAG
578147 TTAGAGA-AAA-AAGAAA
1 TTAGAGATAAATAAGAAA
578163 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (19 bp):
TTAGAGATAAATAAGAAAG
Found at i:579181 original size:13 final size:15
Alignment explanation
Indices: 579154--579185 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
579144 AATATAAATT
579154 TTTTCAAAAATATAA
1 TTTTCAAAAATATAA
579169 TTTT-AAAAA-ATAA
1 TTTTCAAAAATATAA
579182 TTTT
1 TTTT
579186 TATCGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTTCAAAAATATAA
Found at i:580877 original size:2 final size:2
Alignment explanation
Indices: 580870--580910 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
580860 AAAATTTATG
580870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
580911 CATGGTCCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:582441 original size:2 final size:2
Alignment explanation
Indices: 582434--582475 Score: 66
Period size: 2 Copynumber: 20.0 Consensus size: 2
582424 AATCTCCTCC
582434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT
582476 TACTATATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 34 0.89
3 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:583393 original size:2 final size:2
Alignment explanation
Indices: 583386--583415 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
583376 GTAGGATTAA
583386 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
583416 CATTTCATTC
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:584182 original size:25 final size:25
Alignment explanation
Indices: 584154--584205 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
584144 TTTTTTCATA
*
584154 TTTTCAAAATCAAATTATTTTGATT
1 TTTTCAAAATAAAATTATTTTGATT
****
584179 TTTTTTTCATAAAATTATTTTGATT
1 TTTTCAAAATAAAATTATTTTGATT
584204 TT
1 TT
584206 GGATACAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTTCAAAATAAAATTATTTTGATT
Found at i:584643 original size:2 final size:2
Alignment explanation
Indices: 584638--584673 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
584628 ATTTTTTCTT
584638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
584674 AATTATAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:585762 original size:2 final size:2
Alignment explanation
Indices: 585755--585794 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
585745 CACTTGGGGC
585755 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
585795 TATCATGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:591612 original size:22 final size:20
Alignment explanation
Indices: 591584--591629 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
591574 ATTAATATAA
591584 AAATAAT-ATTTTAATATATTTT
1 AAATAATGA-TTTAA-AT-TTTT
591606 AAATAATGATTTAAATTTTT
1 AAATAATGATTTAAATTTTT
591626 AAAT
1 AAAT
591630 TGATCTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 12 0.52
23 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AAATAATGATTTAAATTTTT
Found at i:591638 original size:18 final size:19
Alignment explanation
Indices: 591602--591639 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
591592 TTTTAATATA
*
591602 TTTTAAATAATGATTTAAAT
1 TTTTAAAT-ATGATCTAAAT
591622 TTTTAAAT-TGATCTAAAT
1 TTTTAAATATGATCTAAAT
591640 CTAACTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTTAAATATGATCTAAAT
Found at i:591831 original size:34 final size:34
Alignment explanation
Indices: 591765--591949 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
591755 AATACTTTAA
* *
591765 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
591798 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
591832 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
591866 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
591900 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
591934 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
591950 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:592310 original size:19 final size:19
Alignment explanation
Indices: 592254--592316 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
592244 TGGTTGTCGA
**
592254 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
592273 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
592292 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
592311 GTTACT
1 GGTACT
592317 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:596448 original size:34 final size:34
Alignment explanation
Indices: 596382--596566 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
596372 AAGTGGGAGA
* *
596382 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
596415 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
596449 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
596483 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
596517 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
596551 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
596567 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:597823 original size:22 final size:22
Alignment explanation
Indices: 597798--597840 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
597788 TTTTCATAGA
597798 GATAAAATACAATATCAATCAT
1 GATAAAATACAATATCAATCAT
*
597820 GATAAAATACAATATCCATCA
1 GATAAAATACAATATCAATCA
597841 CCCTTATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (22 bp):
GATAAAATACAATATCAATCAT
Found at i:598803 original size:2 final size:2
Alignment explanation
Indices: 598796--598837 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
598786 TTGTTTGAAA
598796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
598838 GGCAAAAGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:599007 original size:2 final size:2
Alignment explanation
Indices: 599000--599030 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
598990 AGTTAATAGT
*
599000 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
599031 TTGTTCTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:599425 original size:18 final size:18
Alignment explanation
Indices: 599402--599439 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
599392 TTCAATCAGA
599402 CACGTATAATATACATAT
1 CACGTATAATATACATAT
599420 CACGTATAATATACATAT
1 CACGTATAATATACATAT
599438 CA
1 CA
599440 AGCTGATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (18 bp):
CACGTATAATATACATAT
Found at i:600651 original size:2 final size:2
Alignment explanation
Indices: 600644--600680 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
600634 TACATTGAGA
*
600644 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
600681 TTTATGCAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:600925 original size:14 final size:14
Alignment explanation
Indices: 600906--600934 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
600896 TGAATTTAAT
600906 TTAAAATATAAAAA
1 TTAAAATATAAAAA
600920 TTAAAATATAAAAA
1 TTAAAATATAAAAA
600934 T
1 T
600935 ATTTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:602728 original size:17 final size:17
Alignment explanation
Indices: 602708--602740 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
602698 TATTTCCCTC
602708 TCTTTTCTTTT-TCTTTT
1 TCTTTT-TTTTCTCTTTT
602725 TCTTTTTTTTCTCTTT
1 TCTTTTTTTTCTCTTT
602741 GTCCTGAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TCTTTTTTTTCTCTTTT
Found at i:603474 original size:24 final size:26
Alignment explanation
Indices: 603410--603475 Score: 86
Period size: 24 Copynumber: 2.7 Consensus size: 26
603400 ATAATCTATA
*
603410 TAAATAAAATATAAA--ATATAATAAT
1 TAAAT-AAATATAAATTATATAAAAAT
603435 TAAATAAATATAAATTATATAAAAAT
1 TAAATAAATATAAATTATATAAAAAT
603461 TAAA-AAA-ATAAATTA
1 TAAATAAATATAAATTA
603476 ATTTTACAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
24 17 0.45
25 8 0.21
26 13 0.34
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
TAAATAAATATAAATTATATAAAAAT
Found at i:606086 original size:3 final size:3
Alignment explanation
Indices: 606078--606113 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
606068 CATGACATGT
* *
606078 TAA TAA TAA CAA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
606114 AATCTACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:606095 original size:12 final size:12
Alignment explanation
Indices: 606078--606110 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
606068 CATGACATGT
606078 TAATAATAACAA
1 TAATAATAACAA
606090 TAATAATAACAA
1 TAATAATAACAA
606102 TAATAATAA
1 TAATAATAA
606111 TAAAATCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (12 bp):
TAATAATAACAA
Found at i:606834 original size:20 final size:20
Alignment explanation
Indices: 606811--606848 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
606801 TTTTTTTGTT
606811 TTTTCCCCCTACTTTTTAAC
1 TTTTCCCCCTACTTTTTAAC
**
606831 TTTTCCTTCTACTTTTTA
1 TTTTCCCCCTACTTTTTA
606849 TGCTTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTCCCCCTACTTTTTAAC
Found at i:608181 original size:60 final size:61
Alignment explanation
Indices: 608107--608268 Score: 166
Period size: 60 Copynumber: 2.6 Consensus size: 61
608097 TCGAAATATT
* *** *
608107 TTTAAGTAGTTTTTTTATTTTATTATTTATAAATTTAGTGTTATTA-TTGTAATATTTTTTTG
1 TTTATGTA-TTTTTTTATTTTATTATTTATAAATTTAGTACCATTACTT-TAATATATTTTTG
*** * *
608169 TTTATGTATTTTTTT-TAAAATTATTTATGAATTTAGTACCGTTACTTTAATATATTTTTG
1 TTTATGTATTTTTTTATTTTATTATTTATAAATTTAGTACCATTACTTTAATATATTTTTG
608229 TTTATGTATTTTTTTAAATTTTAATTTATTTATAAATTTA
1 TTTATGTATTTTTTT--ATTTT-A-TTATTTATAAATTTA
608269 TTAATTATTC
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
60 48 0.60
61 9 0.11
62 7 0.09
63 1 0.01
64 1 0.01
65 14 0.17
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.62
Consensus pattern (61 bp):
TTTATGTATTTTTTTATTTTATTATTTATAAATTTAGTACCATTACTTTAATATATTTTTG
Found at i:609074 original size:26 final size:25
Alignment explanation
Indices: 609016--609074 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
609006 ATAATCTATC
609016 ATTTAAAAAATTATTTTTATATTAA
1 ATTTAAAAAATTATTTTTATATTAA
* *
609041 GTAATAAAAAATTATTTTTATAATTAA
1 AT-TTAAAAAATTATTTTTAT-ATTAA
609068 ATTTAAA
1 ATTTAAA
609075 TAAAAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.04
26 21 0.75
27 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
ATTTAAAAAATTATTTTTATATTAA
Found at i:609228 original size:14 final size:15
Alignment explanation
Indices: 609209--609241 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
609199 TTGATAATTT
609209 TAAATATAAT-TATA
1 TAAATATAATATATA
609223 TAAATATAATATATA
1 TAAATATAATATATA
609238 TAAA
1 TAAA
609242 ATTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATATAATATATA
Found at i:609313 original size:33 final size:33
Alignment explanation
Indices: 609274--609338 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
609264 CGACATGAAT
* * *
609274 ATATATTTAAAATTTATGT-AATATAAATTATTA
1 ATATA-TTAAAATTAATATAAATATAAAATATTA
609307 ATATATTAAAATTAATATAAATATAAAATATT
1 ATATATTAAAATTAATATAAATATAAAATATT
609339 TTAAATATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (33 bp):
ATATATTAAAATTAATATAAATATAAAATATTA
Found at i:609336 original size:27 final size:28
Alignment explanation
Indices: 609292--609368 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 28
609282 AAAATTTATG
*
609292 TAATATAAAT-TATTAATATATTAAA-AT
1 TAATATAAATATA-AAATATATTAAATAT
*
609319 TAATATAAATATAAAATATTTTAAATAT
1 TAATATAAATATAAAATATATTAAATAT
* *
609347 GATTATAATATAATAAAATATA
1 TAATATAA-AT-ATAAAATATA
609369 CAATTATGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 20 0.49
28 10 0.24
29 2 0.05
30 9 0.22
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
TAATATAAATATAAAATATATTAAATAT
Found at i:609939 original size:13 final size:14
Alignment explanation
Indices: 609903--609929 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
609893 CGTGATATTA
609903 AAATATTTAAATTT
1 AAATATTTAAATTT
609917 AAATATTTAAATT
1 AAATATTTAAATT
609930 AATTTTTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATTTAAATTT
Found at i:612339 original size:26 final size:26
Alignment explanation
Indices: 612324--612372 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
612314 TCATAATTTT
612324 AATTTTATATTAATATTAAAATAATA
1 AATTTTATATTAATATTAAAATAATA
*
612350 AATTTTATATTAAT-TTAATATAA
1 AATTTTATATTAATATTAAAATAA
612373 CTTACACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AATTTTATATTAATATTAAAATAATA
Found at i:614582 original size:17 final size:17
Alignment explanation
Indices: 614509--614583 Score: 55
Period size: 17 Copynumber: 4.2 Consensus size: 17
614499 TAAATTATTA
*
614509 TTAAGTTATATTCTAAT
1 TTAAGTTATATTATAAT
*
614526 TTAAGTGTATATTAAATACT
1 TTAAGT-TATATT--ATAAT
* *
614546 TTAAAATTAT-TTTTAAT
1 TT-AAGTTATATTATAAT
614563 TTAA-TTATATTATAACT
1 TTAAGTTATATTATAA-T
614580 TTAA
1 TTAA
614584 AATTAATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
15 4 0.09
16 7 0.15
17 16 0.35
18 6 0.13
19 2 0.04
20 8 0.17
21 3 0.07
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (17 bp):
TTAAGTTATATTATAAT
Found at i:617808 original size:66 final size:66
Alignment explanation
Indices: 617732--617863 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 66
617722 GAATCACTTA
*
617732 AACTCAATATACTGATATAATCATTGAATTTAAATCTTGACTTCTCAAAGCATGATACATATTTA
1 AACTCAATATACTGATATAATCATTGAATTCAAATCTTGACTTCTCAAAGCATGATACATATTTA
617797 T
66 T
* * *
617798 AACTCAATATATTGATATAATCATTGAATTCAAATCTTGACTTTTTAAAGCATGATACATATTTA
1 AACTCAATATACTGATATAATCATTGAATTCAAATCTTGACTTCTCAAAGCATGATACATATTTA
617863 T
66 T
617864 GACAATGCAC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (66 bp):
AACTCAATATACTGATATAATCATTGAATTCAAATCTTGACTTCTCAAAGCATGATACATATTTA
T
Found at i:617968 original size:18 final size:18
Alignment explanation
Indices: 617935--617980 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
617925 TTTAAATTTT
**
617935 ATATAAATAATTAATTAA
1 ATATAAATAAAAAATTAA
*
617953 ATATAAATAAAAAATTCA
1 ATATAAATAAAAAATTAA
617971 A-A-AAATAAAA
1 ATATAAATAAAA
617981 GTGAAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 8 0.32
17 1 0.04
18 16 0.64
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
ATATAAATAAAAAATTAA
Found at i:619277 original size:66 final size:67
Alignment explanation
Indices: 619171--619300 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 67
619161 TCACTTAAAT
619171 TCAATATATTGATATAATCATTGAATTCAAATCTTGACTTTTC-AAAGCATGATACATATTTATA
1 TCAATATATTGATATAATCATTGAATTCAAATCTTGACTTTTCTAAAGCATGATACATATTTATA
619235 AC
66 AC
* *
619237 TCAATATATTGATATAATTATTGCATTCAAATCTTGACTTTTCTAAAGCATGATACATATTTAT
1 TCAATATATTGATATAATCATTGAATTCAAATCTTGACTTTTCTAAAGCATGATACATATTTAT
619301 GACAATGCAC
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
66 41 0.67
67 20 0.33
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (67 bp):
TCAATATATTGATATAATCATTGAATTCAAATCTTGACTTTTCTAAAGCATGATACATATTTATA
AC
Found at i:620256 original size:24 final size:24
Alignment explanation
Indices: 620229--620276 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
620219 AAATCAAATA
*
620229 ATATATAAGCCAAAAATGTAATGT
1 ATATATAAGCAAAAAATGTAATGT
620253 ATATATAAGCAAAAAATGTAATGT
1 ATATATAAGCAAAAAATGTAATGT
620277 TAAAGATAGA
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:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (24 bp):
ATATATAAGCAAAAAATGTAATGT
Found at i:620381 original size:17 final size:16
Alignment explanation
Indices: 620356--620395 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
620346 TATAAAAAAA
620356 TTAATTTTATTATATAAT
1 TTAA-TTTATTAT-TAAT
*
620374 TTAATTTATTATTTAT
1 TTAATTTATTATTAAT
620390 TTAATT
1 TTAATT
620396 ATATAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 8 0.38
18 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATTTATTATTAAT
Found at i:620566 original size:2 final size:2
Alignment explanation
Indices: 620559--620592 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
620549 AAAACGCAAC
*
620559 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
620593 TCAACAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:624634 original size:13 final size:13
Alignment explanation
Indices: 624616--624646 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
624606 AATACCCCTT
624616 GCAATAATTGTTG
1 GCAATAATTGTTG
624629 GCAATAATTGTTG
1 GCAATAATTGTTG
624642 GCAAT
1 GCAAT
624647 TATAGCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (13 bp):
GCAATAATTGTTG
Found at i:631423 original size:23 final size:23
Alignment explanation
Indices: 631397--631448 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
631387 AATAATATTT
631397 TTATTTTAAAT-TTAATAATAAAA
1 TTATTTTAAATATTAAT-ATAAAA
* *
631420 TTA-TATAACTATTAATATAAAA
1 TTATTTTAAATATTAATATAAAA
*
631442 ATATTTT
1 TTATTTT
631449 TTAATATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTATTTTAAATATTAATATAAAA
Found at i:632633 original size:21 final size:20
Alignment explanation
Indices: 632606--632657 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
632596 TGAAATATTT
632606 AAAAATTATTAATATTTTAA
1 AAAAATTATTAATATTTTAA
* *
632626 ATAAAATT-TCAGT-TTATTAA
1 A-AAAATTATTAATATT-TTAA
632646 AAAAATTATTAA
1 AAAAATTATTAA
632658 ATATGTTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
19 8 0.32
20 11 0.44
21 6 0.24
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAAATTATTAATATTTTAA
Found at i:640070 original size:14 final size:14
Alignment explanation
Indices: 640051--640079 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
640041 ACCTGCACAA
640051 GCATTTTCATCTGT
1 GCATTTTCATCTGT
640065 GCATTTTCATCTGT
1 GCATTTTCATCTGT
640079 G
1 G
640080 AAATTGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (14 bp):
GCATTTTCATCTGT
Found at i:643007 original size:2 final size:2
Alignment explanation
Indices: 642994--643027 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
642984 TATAGCTAGC
*
642994 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
643028 GGAAAGAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:645454 original size:29 final size:29
Alignment explanation
Indices: 645421--645479 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
645411 GGAATACTGA
645421 CTCAGTCCAATCCTTAATAGCATCTCTGG
1 CTCAGTCCAATCCTTAATAGCATCTCTGG
645450 CTCAGTCCAATCCTTAATAGCATCTCTGG
1 CTCAGTCCAATCCTTAATAGCATCTCTGG
645479 C
1 C
645480 GCGTTGAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.31
Consensus pattern (29 bp):
CTCAGTCCAATCCTTAATAGCATCTCTGG
Found at i:650929 original size:2 final size:2
Alignment explanation
Indices: 650922--650947 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
650912 TTTGCAATAA
650922 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
650948 GTTAAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:651604 original size:43 final size:43
Alignment explanation
Indices: 651547--651644 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 43
651537 CTCTTTTATT
*
651547 TTTTTAATTCTTTATAATTTATAAAACG-ACTT-TATTTATTTTAG
1 TTTTTAATT-TTTAT-ATTTA-AAAACGAACTTCTATTTATTTTAA
* * *
651591 TTTTAAATTTTTATTTTTAAAAATGTAACTTCTATTTATTTTAA
1 TTTTTAATTTTTATATTTAAAAACG-AACTTCTATTTATTTTAA
651635 TTTTTAATTT
1 TTTTTAATTT
651645 ATACTTTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
41 5 0.11
42 4 0.09
43 9 0.20
44 28 0.61
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (43 bp):
TTTTTAATTTTTATATTTAAAAACGAACTTCTATTTATTTTAA
Found at i:651657 original size:44 final size:43
Alignment explanation
Indices: 651575--651657 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 43
651565 TTATAAAACG
* * * *
651575 ACTTTATTTATTTTAGTTTTAAATTTTTATTTTTAAAAATGTA
1 ACTTTATTTATTTTAATTTTAAATTTATACTTTGAAAAATGTA
*
651618 ACTTCTATTTATTTTAATTTTTAATTTATACTTTGAAAAA
1 ACTT-TATTTATTTTAATTTTAAATTTATACTTTGAAAAA
651658 ATGTTGAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 4 0.12
44 30 0.88
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.58
Consensus pattern (43 bp):
ACTTTATTTATTTTAATTTTAAATTTATACTTTGAAAAATGTA
Found at i:653878 original size:19 final size:19
Alignment explanation
Indices: 653856--653898 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
653846 TATCATTTTT
*
653856 TTAAAAAAATT-TAAATACA
1 TTAAAAAAATTAAAAATA-A
653875 TTAAAAAAATTAAAAATAA
1 TTAAAAAAATTAAAAATAA
653894 TTAAA
1 TTAAA
653899 TATATTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TTAAAAAAATTAAAAATAA
Found at i:653896 original size:10 final size:9
Alignment explanation
Indices: 653856--653898 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
653846 TATCATTTTT
653856 TTAAAAAAA
1 TTAAAAAAA
* *
653865 TTTAAATACA
1 -TTAAAAAAA
653875 TTAAAAAAA
1 TTAAAAAAA
653884 TTAAAAATAA
1 TTAAAAA-AA
653894 TTAAA
1 TTAAA
653899 TATATTTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 14 0.50
10 14 0.50
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:655235 original size:16 final size:15
Alignment explanation
Indices: 655210--655262 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
655200 TTTTAAGTTA
655210 ATTTTGAGTTTGAATT
1 ATTTT-AGTTTGAATT
*
655226 ATTTTAAGTTTGGATT
1 ATTTT-AGTTTGAATT
*
655242 ATTTTAGATTTAAATT
1 ATTTTAG-TTTGAATT
655258 ATTTT
1 ATTTT
655263 GCGTTCGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 2 0.06
16 30 0.94
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.58
Consensus pattern (15 bp):
ATTTTAGTTTGAATT
Found at i:656322 original size:16 final size:16
Alignment explanation
Indices: 656301--656345 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
656291 AATTATTCCG
*
656301 ATCATTTCGAGTTCAA
1 ATCATTTCGAATTCAA
*
656317 ATCATTTCGAATTCAT
1 ATCATTTCGAATTCAA
* *
656333 GTCATTTTGAATT
1 ATCATTTCGAATT
656346 TGAGTCATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (16 bp):
ATCATTTCGAATTCAA
Found at i:656352 original size:16 final size:17
Alignment explanation
Indices: 656334--656394 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 17
656324 CGAATTCATG
656334 TCATTTTGAATTTGAG-
1 TCATTTTGAATTTGAGA
*
656350 TCA-TTTCAGATTT-AGA
1 TCATTTTGA-ATTTGAGA
656366 TCATTTTGAATTTG-GA
1 TCATTTTGAATTTGAGA
*
656382 TCATTTCGAATTT
1 TCATTTTGAATTT
656395 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 6 0.16
16 28 0.74
17 4 0.11
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (17 bp):
TCATTTTGAATTTGAGA
Found at i:656395 original size:32 final size:31
Alignment explanation
Indices: 656317--656395 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 31
656307 TCGAGTTCAA
*
656317 ATCATTTCGAATTCATGTCATTTTGAATTTG
1 ATCATTTCGAATTTATGTCATTTTGAATTTG
656348 AGTCATTTC-AGATTTA-GATCATTTTGAATTTGG
1 A-TCATTTCGA-ATTTATG-TCATTTTGAATTT-G
656381 ATCATTTCGAATTTA
1 ATCATTTCGAATTTA
656396 AATTTTTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
31 3 0.07
32 36 0.86
33 3 0.07
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (31 bp):
ATCATTTCGAATTTATGTCATTTTGAATTTG
Found at i:656405 original size:32 final size:32
Alignment explanation
Indices: 656334--656430 Score: 90
Period size: 32 Copynumber: 3.0 Consensus size: 32
656324 CGAATTCATG
*
656334 TCATTTTGAATTTGAGTCATTTCAGATTTAGA
1 TCATTTTGAATTTGAGTCATTTCAGATTTAAA
656366 TCATTTTGAATTTG-GATCATTTC-GAATTTAAA
1 TCATTTTGAATTTGAG-TCATTTCAG-ATTTAAA
** * * * * *
656398 TTTTTTTGAGTTTAAATCAATTCAGATTCAAA
1 TCATTTTGAATTTGAGTCATTTCAGATTTAAA
656430 T
1 T
656431 TATTAATTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
31 2 0.04
32 50 0.94
33 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (32 bp):
TCATTTTGAATTTGAGTCATTTCAGATTTAAA
Found at i:658935 original size:21 final size:21
Alignment explanation
Indices: 658909--658957 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
658899 TGATATATTA
* * *
658909 ATATATTGAATGTATTTAAAT
1 ATATATTCAATATAATTAAAT
*
658930 ATATATTCAATATAATTAATT
1 ATATATTCAATATAATTAAAT
658951 ATATATT
1 ATATATT
658958 AAATTTTTAT
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:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (21 bp):
ATATATTCAATATAATTAAAT
Done.