Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold253
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: 2064896
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 5 of 13
Found at i:551239 original size:33 final size:34
Alignment explanation
Indices: 551202--551336 Score: 100
Period size: 33 Copynumber: 3.9 Consensus size: 34
551192 TATAATATAA
551202 AAATA-ATTAAAATATAATATAATATAAATATTT
1 AAATATATTAAAATATAATATAATATAAATATTT
* * * *
551235 AAATATTTTAAATTTTAA-ATAATATTAAT-TATT
1 AAATATATTAAAATATAATATAATATAAATAT-TT
* *
551268 -AATATATAAAAAT-TTATATAAATATAAAATATTTT
1 AAATATATTAAAATATAATAT-AATAT-AAATA-TTT
* * *
551303 AAATTTAATTATAATATAATAAAATATATAATAT
1 AAATAT-ATTAAAATATAATATAATATA-AATAT
551337 AAACATAAAA
Statistics
Matches: 77, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
31 2 0.03
32 13 0.17
33 22 0.29
34 12 0.16
35 2 0.03
36 7 0.09
37 15 0.19
38 4 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AAATATATTAAAATATAATATAATATAAATATTT
Found at i:551302 original size:52 final size:51
Alignment explanation
Indices: 551244--551355 Score: 126
Period size: 50 Copynumber: 2.2 Consensus size: 51
551234 TAAATATTTT
* *
551244 AAATTTTAAATAATATTAATTATTAATAT-ATAAAA-AT-TTATATAAATATAA
1 AAATTTTAAA-AAT-TTAATTA-TAATATAATAAAATATATAATATAAACATAA
551295 AATATTTT--AAATTTAATTATAATATAATAAAATATATAATATAAACATAA
1 AA-ATTTTAAAAATTTAATTATAATATAATAAAATATATAATATAAACATAA
*
551345 AAATTATAAAA
1 AAATTTTAAAA
551356 TCTAATTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
47 6 0.12
48 13 0.25
49 9 0.17
50 15 0.29
51 4 0.08
52 5 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (51 bp):
AAATTTTAAAAATTTAATTATAATATAATAAAATATATAATATAAACATAA
Found at i:552334 original size:3 final size:3
Alignment explanation
Indices: 552326--552359 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
552316 CTCCTTTTAT
552326 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
552360 TAAAAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:554865 original size:17 final size:15
Alignment explanation
Indices: 554837--554879 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
554827 GAATTGAATC
554837 AATTTATTTTAAAAAT
1 AATTT-TTTTAAAAAT
*
554853 AAAATTTTTTTAATAAT
1 --AATTTTTTTAAAAAT
554870 AATTTTTTTA
1 AATTTTTTTA
554880 TTTATACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 10 0.42
17 9 0.38
18 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTTTTAAAAAT
Found at i:554867 original size:14 final size:15
Alignment explanation
Indices: 554850--554879 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
554840 TTATTTTAAA
554850 AATAA-AATTTTTTT
1 AATAATAATTTTTTT
554864 AATAATAATTTTTTT
1 AATAATAATTTTTTT
554879 A
1 A
554880 TTTATACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATAATAATTTTTTT
Found at i:555146 original size:6 final size:7
Alignment explanation
Indices: 555127--555279 Score: 76
Period size: 7 Copynumber: 22.4 Consensus size: 7
555117 CTATAATTTA
555127 ATAT-TT
1 ATATATT
555133 ATATATT
1 ATATATT
555140 ATA-ATT
1 ATATATT
555146 ATAT-TT
1 ATATATT
*
555152 AAAATATT
1 -ATATATT
555160 A-A-A-T
1 ATATATT
*
555164 ATATATA
1 ATATATT
*
555171 ATTTATT
1 ATATATT
555178 A-ATAATT
1 ATAT-ATT
555185 ACTATTATAT
1 A-TA-TAT-T
* *
555195 AAAAATT
1 ATATATT
*
555202 AAAATATT
1 ATA-TATT
555210 TATATATT
1 -ATATATT
555218 -TATATT
1 ATATATT
555224 ATATATT
1 ATATATT
555231 AT-TATT
1 ATATATT
555237 AT-TATT
1 ATATATT
* *
555243 TTATATC
1 ATATATT
*
555250 ATATTTT
1 ATATATT
*
555257 AAATATT
1 ATATATT
555264 ATATATT
1 ATATATT
555271 -TATATT
1 ATATATT
555277 ATA
1 ATA
555280 AATGATTAAG
Statistics
Matches: 113, Mismatches: 17, Indels: 33
0.69 0.10 0.20
Matches are distributed among these distances:
4 2 0.02
5 2 0.02
6 38 0.34
7 51 0.45
8 11 0.10
9 6 0.05
10 3 0.03
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (7 bp):
ATATATT
Found at i:555173 original size:49 final size:47
Alignment explanation
Indices: 555118--555243 Score: 122
Period size: 46 Copynumber: 2.7 Consensus size: 47
555108 TCCTTGGATC
555118 TATAATTTAATATTTATATATTATAATTATATTTAAAATATT-AAATATA
1 TATAATTT-ATATTTATATATTAT-ATTATATTTAAAA-ATTAAAATATA
* *
555167 TATAA-TT-TATTAATA-ATTACTATTATA--TAAAAATTAAAATATT
1 TATAATTTATATTTATATATTA-TATTATATTTAAAAATTAAAATATA
555210 TATATATTTATA-TTATATATTATTATTATTATTT
1 TATA-ATTTATATTTATATATTA-TATTA-TATTT
555244 TATATCATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
42 3 0.05
43 15 0.23
44 1 0.02
45 16 0.25
46 19 0.30
47 2 0.03
48 2 0.03
49 6 0.09
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (47 bp):
TATAATTTATATTTATATATTATATTATATTTAAAAATTAAAATATA
Found at i:555234 original size:43 final size:42
Alignment explanation
Indices: 555134--555235 Score: 104
Period size: 43 Copynumber: 2.4 Consensus size: 42
555124 TTAATATTTA
*
555134 TATATTATA-ATTA-TATTTAAAATATTAAATATATATAATT
1 TATATTATATATTATTATATAAAATATTAAATATATATAATT
* * *
555174 TAT-TAATAATTACTATTATATAAAA-ATTAAAATATTTATATATT
1 TATATTAT-A-TATTATTATATAAAATATT-AAATATATATA-ATT
555218 TATATTATATATTATTAT
1 TATATTATATATTATTAT
555236 TATTATTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
39 3 0.06
40 4 0.08
42 6 0.12
43 26 0.53
44 7 0.14
45 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (42 bp):
TATATTATATATTATTATATAAAATATTAAATATATATAATT
Found at i:555758 original size:29 final size:29
Alignment explanation
Indices: 555726--555805 Score: 85
Period size: 26 Copynumber: 2.9 Consensus size: 29
555716 TAATGTTTAT
*
555726 ATATCTTTATAATTAACTTTAAATAAAAA
1 ATATCTTTATAATTAAATTTAAATAAAAA
* * * *
555755 ATAT-TTT-TAA-CAAGTATAAATAATAA
1 ATATCTTTATAATTAAATTTAAATAAAAA
*
555781 TTATCTTTATAATTAAATTTAAATA
1 ATATCTTTATAATTAAATTTAAATA
555806 TTTTTATCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 15 0.38
27 6 0.15
28 6 0.15
29 13 0.32
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATCTTTATAATTAAATTTAAATAAAAA
Found at i:559398 original size:16 final size:16
Alignment explanation
Indices: 559377--559416 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
559367 TTTAAATTAT
559377 TTTTAAATTTTAATAA
1 TTTTAAATTTTAATAA
* *
559393 TTTT-AATTTTGATTA
1 TTTTAAATTTTAATAA
559408 TTTTAAATT
1 TTTTAAATT
559417 CAAATCATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTTAAATTTTAATAA
Found at i:560868 original size:99 final size:99
Alignment explanation
Indices: 560746--560947 Score: 350
Period size: 99 Copynumber: 2.0 Consensus size: 99
560736 AAAATTCACA
* * * *
560746 ATTTGCCTAGTCAGTCAACACATGTTCAGCCCTACAATTAACTGTGGAATCTTTTCTTTATGCCT
1 ATTTGCCTAGTCAATCAACACATGTTCAGCCCTACAATTAACAGTGGAATCCTTTCTTTATGCAT
560811 TTTGCATGTGCCTGATTCTGATTCAGGTTTATTT
66 TTTGCATGTGCCTGATTCTGATTCAGGTTTATTT
* *
560845 ATTTGCTTAGTCAATCAACACATGTTCGGCCCTACAATTAACAGTGGAATCCTTTCTTTATGCAT
1 ATTTGCCTAGTCAATCAACACATGTTCAGCCCTACAATTAACAGTGGAATCCTTTCTTTATGCAT
560910 TTTGCATGTGCCTGATTCTGATTCAGGTTTATTT
66 TTTGCATGTGCCTGATTCTGATTCAGGTTTATTT
560944 ATTT
1 ATTT
560948 ATTTATTTAT
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (99 bp):
ATTTGCCTAGTCAATCAACACATGTTCAGCCCTACAATTAACAGTGGAATCCTTTCTTTATGCAT
TTTGCATGTGCCTGATTCTGATTCAGGTTTATTT
Found at i:561070 original size:90 final size:89
Alignment explanation
Indices: 560939--561119 Score: 353
Period size: 90 Copynumber: 2.0 Consensus size: 89
560929 GATTCAGGTT
560939 TATTTATTTATTTATTTATTTTTTCCTATTGCAATTGAATTTGTTCATTTATTGTTAATGGTCAC
1 TATTTATTTATTTATTTATTTTTTCCTATTGCAATTGAATTTGTTCATTTATTGTTAATGGTCAC
561004 CTAATAAGATATTAACTCGATGAA
66 CTAATAAGATATTAACTCGATGAA
561028 TATTTATTTATTTATTTATTTTTTTCCTATTGCAATTGAATTTGTTCATTTATTGTTAATGGTCA
1 TATTTATTTATTTATTTA-TTTTTTCCTATTGCAATTGAATTTGTTCATTTATTGTTAATGGTCA
561093 CCTAATAAGATATTAACTCGATGAA
65 CCTAATAAGATATTAACTCGATGAA
561118 TA
1 TA
561120 ATTTCTTTCA
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 18 0.20
90 73 0.80
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (89 bp):
TATTTATTTATTTATTTATTTTTTCCTATTGCAATTGAATTTGTTCATTTATTGTTAATGGTCAC
CTAATAAGATATTAACTCGATGAA
Found at i:562058 original size:33 final size:33
Alignment explanation
Indices: 562019--562096 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 33
562009 TCATATTTAA
*
562019 AATAATTTATATTTATATAAATTTTAATA-AGTT
1 AATAATTTATATTTATATAAAATTTAATATA-TT
562052 AATAATTTATA-TTATATAAAATTTAATATATT
1 AATAATTTATATTTATATAAAATTTAATATATT
*
562084 CATATATTTATAT
1 AATA-ATTTATAT
562097 CATTTTCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 21 0.52
33 19 0.47
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (33 bp):
AATAATTTATATTTATATAAAATTTAATATATT
Found at i:563287 original size:24 final size:25
Alignment explanation
Indices: 563260--563314 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
563250 TCTGAGATTA
*
563260 AAATTATTATC-ACGTAAAAAT-TTT
1 AAATTATTATCGA-ATAAAAATATTT
563284 AAATTATTATCGAATAAAAATATTT
1 AAATTATTATCGAATAAAAATATTT
563309 AAATTA
1 AAATTA
563315 CTAAAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATTATTATCGAATAAAAATATTT
Found at i:564487 original size:22 final size:22
Alignment explanation
Indices: 564445--564487 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
564435 AAGATTAAAG
* *
564445 TAGATTTAAATTTTATTTTTTT
1 TAGATTTAAATTTAATATTTTT
564467 TAGATTTAAA-TTAAGTATTTT
1 TAGATTTAAATTTAA-TATTTT
564488 ATTATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (22 bp):
TAGATTTAAATTTAATATTTTT
Found at i:564882 original size:24 final size:24
Alignment explanation
Indices: 564852--564899 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
564842 GGGATTATAG
564852 AGTTAATGCA-TCATATCAAATAAT
1 AGTTAATGCATTCA-ATCAAATAAT
*
564876 AGTTAATGCATTGAATCAAATAAT
1 AGTTAATGCATTCAATCAAATAAT
564900 CATTGTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (24 bp):
AGTTAATGCATTCAATCAAATAAT
Found at i:565154 original size:16 final size:15
Alignment explanation
Indices: 565132--565179 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
565122 ATTTATATTA
565132 TATTTATATAAATTT
1 TATTTATATAAATTT
*
565147 TAATTTAT-TAATAATT
1 T-ATTTATATAA-ATTT
565163 TATATTATATAAATTT
1 TAT-TTATATAAATTT
565179 T
1 T
565180 TACATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 6 0.22
16 18 0.67
17 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTATATAAATTT
Found at i:565344 original size:20 final size:21
Alignment explanation
Indices: 565306--565344 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
565296 ATTATTATAA
*
565306 TATGTAAATTTTATATATTTT
1 TATGTAAATTTAATATATTTT
*
565327 TATG-AAATTTAATCTATT
1 TATGTAAATTTAATATATT
565345 AATATTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (21 bp):
TATGTAAATTTAATATATTTT
Found at i:566455 original size:18 final size:18
Alignment explanation
Indices: 566432--566484 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
566422 AAAGCTTTGG
* *
566432 AAAGAGATGATGAAGAAC
1 AAAGAGAAGAAGAAGAAC
566450 AAAGAGAAGAAGAAGAA-
1 AAAGAGAAGAAGAAGAAC
*
566467 GAAGAAGAAGAAGAAGAA
1 AAAG-AGAAGAAGAAGAA
566485 ACGACAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 3 0.10
18 28 0.90
ACGTcount: A:0.64, C:0.02, G:0.30, T:0.04
Consensus pattern (18 bp):
AAAGAGAAGAAGAAGAAC
Found at i:566501 original size:3 final size:3
Alignment explanation
Indices: 566454--566484 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
566444 AAGAACAAAG
566454 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
566485 ACGACAATGA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:568338 original size:21 final size:21
Alignment explanation
Indices: 568322--568379 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
568312 CCAAATTATT
568322 ATTTAATAATAAAAAATTTAA
1 ATTTAATAATAAAAAATTTAA
* *
568343 ATTTAATTATAAAAATATATAA
1 ATTTAATAATAAAAA-ATTTAA
568365 ATATTAAT-ATAAAAA
1 AT-TTAATAATAAAAA
568380 TAATTTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 14 0.42
22 14 0.42
23 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTTAATAATAAAAAATTTAA
Found at i:568365 original size:22 final size:22
Alignment explanation
Indices: 568322--568381 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
568312 CCAAATTATT
* *
568322 ATTTAATAATAAAAA-ATTTAA
1 ATTTAATTATAAAAATATATAA
568343 ATTTAATTATAAAAATATATAA
1 ATTTAATTATAAAAATATATAA
568365 ATATTAA-TATAAAAATA
1 AT-TTAATTATAAAAATA
568382 ATTTTATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 14 0.40
22 17 0.49
23 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTTAATTATAAAAATATATAA
Found at i:578334 original size:11 final size:11
Alignment explanation
Indices: 578318--578472 Score: 79
Period size: 11 Copynumber: 15.2 Consensus size: 11
578308 TTTAAATATG
578318 ATATAATATAA
1 ATATAATATAA
578329 ATATAATA-AA
1 ATATAATATAA
*
578339 AAATAAT-TAAA
1 ATATAATAT-AA
* * *
578350 AAATTATTTAA
1 ATATAATATAA
578361 ATATAA-A-AA
1 ATATAATATAA
*
578370 AT-TAA-ATTA
1 ATATAATATAA
*
578379 ATACAATAT-A
1 ATATAATATAA
578389 A-AT-ATATAA
1 ATATAATATAA
* *
578398 ATATATTAAAA
1 ATATAATATAA
*
578409 AT-TTATAT-A
1 ATATAATATAA
*
578418 ATATAAATTATTA
1 ATAT-AA-TATAA
578431 ATAT-AT-TAA
1 ATATAATATAA
*
578440 A-ATTATATAA
1 ATATAATATAA
578450 ATATAATATAA
1 ATATAATATAA
578461 ATAT-ATATAA
1 ATATAATATAA
578471 AT
1 AT
578473 TATTAAATTT
Statistics
Matches: 112, Mismatches: 16, Indels: 33
0.70 0.10 0.20
Matches are distributed among these distances:
8 10 0.09
9 18 0.16
10 31 0.28
11 44 0.39
12 4 0.04
13 5 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAATATAA
Found at i:578376 original size:14 final size:15
Alignment explanation
Indices: 578309--578471 Score: 53
Period size: 14 Copynumber: 10.9 Consensus size: 15
578299 TCTGATAATT
* *
578309 TTAAATATGATATAA
1 TTAAATATAATAAAA
578324 TATAAATATAATAAAA
1 T-TAAATATAATAAAA
* *
578340 -AATAAT-TAAAAAATTA
1 TTA-AATATAATAAA--A
578356 TTTAAATATAA-AAAA
1 -TTAAATATAATAAAA
*
578371 TTAAAT-TAATACAA
1 TTAAATATAATAAAA
578385 TATAAATAT-AT-AAA
1 T-TAAATATAATAAAA
*
578399 -T--ATATTA-AAAA
1 TTAAATATAATAAAA
*
578410 TT-TATATAATATAAA
1 TTAAATATAATA-AAA
*
578425 TTATTAATATATTAAAA
1 TTA--AATATAATAAAA
* *
578442 TTATATA-AATATAA
1 TTAAATATAATAAAA
578456 TATAAATATATATAAA
1 T-TAAATATA-ATAAA
578472 TTATTAAATT
Statistics
Matches: 111, Mismatches: 15, Indels: 42
0.66 0.09 0.25
Matches are distributed among these distances:
10 4 0.04
11 4 0.04
12 2 0.02
13 8 0.07
14 26 0.23
15 25 0.23
16 15 0.14
17 16 0.14
18 11 0.10
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38
Consensus pattern (15 bp):
TTAAATATAATAAAA
Found at i:578431 original size:57 final size:62
Alignment explanation
Indices: 578305--578457 Score: 156
Period size: 61 Copynumber: 2.5 Consensus size: 62
578295 TATATCTGAT
* * *
578305 AATT-TTAAATATGATATAATATAAATATAATAAAAAATAATTAAAAAATTATTTAAATATA
1 AATTATTAAATATAATACAATATAAATATAATAAAAAATAATTAAAAAATTATATAAATATA
** * *
578366 AAAAATTAAAT-TAATACAATATAAATAT-AT-AAATAT-ATTAAAAATTTATAT-AATATA
1 AATTATTAAATATAATACAATATAAATATAATAAAAAATAATTAAAAAATTATATAAATATA
* **
578423 AATTATTAATATATTAAAATTATATAAATATAATA
1 AATTATTAA-ATA-TAATACAATATAAATATAATA
578458 TAAATATATA
Statistics
Matches: 74, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
57 13 0.18
58 15 0.20
59 5 0.07
60 16 0.22
61 19 0.26
62 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (62 bp):
AATTATTAAATATAATACAATATAAATATAATAAAAAATAATTAAAAAATTATATAAATATA
Found at i:578453 original size:17 final size:17
Alignment explanation
Indices: 578400--578479 Score: 60
Period size: 17 Copynumber: 4.5 Consensus size: 17
578390 ATATATAAAT
578400 ATATTAAAAATT-TATATA
1 ATATT-AAAATTATATA-A
578418 ATA-T-AAATTAT-TAA
1 ATATTAAAATTATATAA
578432 TATATTAAAATTATATAA
1 -ATATTAAAATTATATAA
578450 ATATAATATAAATATATATAA
1 ATAT--TA-AAAT-TATATAA
578471 ATTATTAAA
1 A-TATTAAA
578480 TTTACGAGGT
Statistics
Matches: 52, Mismatches: 0, Indels: 19
0.73 0.00 0.27
Matches are distributed among these distances:
14 1 0.02
15 10 0.19
16 2 0.04
17 12 0.23
18 6 0.12
19 4 0.08
20 6 0.12
21 8 0.15
22 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTAAAATTATATAA
Found at i:578463 original size:71 final size:69
Alignment explanation
Indices: 578323--578467 Score: 177
Period size: 71 Copynumber: 2.1 Consensus size: 69
578313 ATATGATATA
*
578323 ATATAAATATAATAAAAAATAATTAAAAAATTATTTAAATATAAAAAATTAAATTAATACAATAT
1 ATATAAATATAATAAAAAATAATTAAAAAATTATTTAAATATAAAAAATTAAATAAATACAATAT
578388 AAAT
66 AAAT
* * * * * *
578392 ATATAAATATATTAAAAATTTATATAATATAAATTA-TT-AATATATTAAAATTATATAAATATA
1 ATATAAATATAATAAAAAATAAT-TAA-A-AAATTATTTAAATATA-AAAAATTAAATAAATACA
578455 ATATAAAT
62 ATATAAAT
578463 ATATA
1 ATATA
578468 TAAATTATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
69 20 0.31
70 9 0.14
71 30 0.46
72 6 0.09
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (69 bp):
ATATAAATATAATAAAAAATAATTAAAAAATTATTTAAATATAAAAAATTAAATAAATACAATAT
AAAT
Found at i:578467 original size:8 final size:8
Alignment explanation
Indices: 578384--578454 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 8
578374 AATTAATACA
578384 ATATAAAT
1 ATATAAAT
578392 ATATAAAT
1 ATATAAAT
*
578400 ATATTAAAA
1 ATA-TAAAT
* *
578409 ATTTATAT
1 ATATAAAT
578417 AATATAAAT
1 -ATATAAAT
*
578426 -TATTAAT
1 ATATAAAT
578433 ATATTAAAATT
1 ATA-T-AAA-T
578444 ATATAAAT
1 ATATAAAT
578452 ATA
1 ATA
578455 ATATAAATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
7 6 0.12
8 20 0.41
9 16 0.33
10 3 0.06
11 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAAAT
Found at i:578467 original size:21 final size:20
Alignment explanation
Indices: 578318--578472 Score: 100
Period size: 18 Copynumber: 8.1 Consensus size: 20
578308 TTTAAATATG
578318 ATATAATATAAA-TATAATAAA
1 ATATAATATAAATTAT-AT-AA
* * *
578339 AAATAATTAAAAAATTATTTAA
1 ATATAA-T-ATAAATTATATAA
* *
578361 ATATAA-A-AAATTAAATTA
1 ATATAATATAAATTATATAA
*
578379 ATACAATATAAA-TATATAA
1 ATATAATATAAATTATATAA
**
578398 ATAT-AT-TAAA--A-ATTT
1 ATATAATATAAATTATATAA
578413 ATATAATATAAATTAT-T-A
1 ATATAATATAAATTATATAA
*
578431 ATATATTA-AAATTATATAA
1 ATATAATATAAATTATATAA
578450 ATATAATATAAATATATATAA
1 ATATAATATAAAT-TATATAA
578471 AT
1 AT
578473 TATTAAATTT
Statistics
Matches: 104, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
15 6 0.06
16 3 0.03
17 15 0.14
18 23 0.22
19 20 0.19
20 7 0.07
21 14 0.13
22 8 0.08
23 5 0.05
24 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAATATAAATTATATAA
Found at i:578784 original size:20 final size:20
Alignment explanation
Indices: 578746--578784 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
578736 CCTTTCTCAC
**
578746 TCTTTCTTTTTTAGGTTTTA
1 TCTTTCTTTTTTACCTTTTA
578766 TCTTTCTTTTTTACCTTTT
1 TCTTTCTTTTTTACCTTTT
578785 TTTTTTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.15, G:0.05, T:0.72
Consensus pattern (20 bp):
TCTTTCTTTTTTACCTTTTA
Found at i:578935 original size:2 final size:2
Alignment explanation
Indices: 578928--578980 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
578918 ATATTTTAAA
* * * *
578928 AT AT AT AT A- AT AT AA AT -T AT AT AA AT AA AT TT 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
578968 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
578981 AAGATATTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:578948 original size:14 final size:15
Alignment explanation
Indices: 578887--578981 Score: 72
Period size: 14 Copynumber: 6.4 Consensus size: 15
578877 ATTAATTAAA
578887 ATATAATATAAAATAT
1 ATATAATAT-AAATAT
** *
578903 GATATAA-ATATGTAA
1 -ATATAATATAAATAT
**
578918 ATATTTTA-AAATAT
1 ATATAATATAAATAT
578932 ATATAATATAAAT-T
1 ATATAATATAAATAT
*
578946 ATATAA-ATAAATTT
1 ATATAATATAAATAT
*
578960 ATATATATATATATAT
1 ATATA-ATATAAATAT
578976 ATATAA
1 ATATAA
578982 AGATATTATA
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
13 6 0.10
14 26 0.43
15 10 0.16
16 13 0.21
17 6 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
ATATAATATAAATAT
Found at i:578987 original size:12 final size:11
Alignment explanation
Indices: 578883--578998 Score: 59
Period size: 10 Copynumber: 10.8 Consensus size: 11
578873 TATAATTAAT
578883 TAAAATATAATA
1 TAAAATAT-ATA
578895 TAAAATATGATA
1 TAAAATAT-ATA
*
578907 T--AA-ATATG
1 TAAAATATATA
*
578915 T-AAATAT-TT
1 TAAAATATATA
578924 TAAAATATATA
1 TAAAATATATA
* *
578935 TAATATAAATTA
1 TAAAATATA-TA
*
578947 TATAAATAAAT-
1 TA-AAATATATA
* *
578958 TTATATATATA
1 TAAAATATATA
*
578969 T-ATATATATA
1 TAAAATATATA
578979 TAAAGATAT-TA
1 TAAA-ATATATA
578990 TAAAATATA
1 TAAAATATA
578999 CAAACATAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
8 3 0.04
9 6 0.07
10 30 0.36
11 17 0.20
12 21 0.25
13 6 0.07
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
TAAAATATATA
Found at i:578987 original size:14 final size:13
Alignment explanation
Indices: 578883--578998 Score: 62
Period size: 14 Copynumber: 8.7 Consensus size: 13
578873 TATAATTAAT
578883 TAAAATATA-ATA
1 TAAAATATATATA
578895 TAAAATATGATATA
1 TAAAATAT-ATATA
* * *
578909 -AATATGTAAATATTT
1 TAA-A-ATATATA-TA
578924 TAAAATATATATAA
1 TAAAATATATAT-A
578938 TATAAAT-TATATA
1 TA-AAATATATATA
* *
578951 AATAAATTTATATA
1 TA-AAATATATATA
*
578965 T-ATATATATATA
1 TAAAATATATATA
*
578977 TATAAAGATAT-TA
1 TA-AAATATATATA
578990 TAAAATATA
1 TAAAATATA
578999 CAAACATAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
12 24 0.30
13 15 0.19
14 31 0.39
15 8 0.10
16 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
TAAAATATATATA
Found at i:579297 original size:15 final size:16
Alignment explanation
Indices: 579273--579309 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
579263 GTTTTTGAAG
*
579273 AAAAAA-TAAAGT-TA
1 AAAAAATTAAAATATA
579287 AAAAAATTAAAATATA
1 AAAAAATTAAAATATA
579303 AAAAAAT
1 AAAAAAT
579310 AATAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 6 0.30
15 5 0.25
16 9 0.45
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (16 bp):
AAAAAATTAAAATATA
Found at i:580369 original size:14 final size:16
Alignment explanation
Indices: 580340--580373 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
580330 ATAGCAGTTC
580340 TTTATTTCTCTTTATT
1 TTTATTTCTCTTTATT
580356 TTTATTT-T-TTTATT
1 TTTATTTCTCTTTATT
580370 TTTA
1 TTTA
580374 ATGTTCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 1 0.06
16 7 0.39
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTCTCTTTATT
Found at i:581857 original size:41 final size:45
Alignment explanation
Indices: 581759--581861 Score: 112
Period size: 43 Copynumber: 2.4 Consensus size: 45
581749 AGTAATTTTA
*
581759 TTTAAATTTAATTATAAAATATATTAATATTAATATAAAAATAAAT
1 TTTAAA-TTAATTATAATATATATTAATATTAATATAAAAATAAAT
* *
581805 TTTTAA-T-ATTATAATATATTTTAA-A-T-A-AT-AAAATAAAT
1 TTTAAATTAATTATAATATATATTAATATTAATATAAAAATAAAT
581843 TTTAAATTAAATTATAATA
1 TTTAAATT-AATTATAATA
581862 AATAAAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
38 14 0.28
39 3 0.06
40 1 0.02
41 10 0.20
42 1 0.02
43 15 0.30
44 1 0.02
46 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (45 bp):
TTTAAATTAATTATAATATATATTAATATTAATATAAAAATAAAT
Found at i:581864 original size:22 final size:21
Alignment explanation
Indices: 581759--581864 Score: 78
Period size: 19 Copynumber: 5.0 Consensus size: 21
581749 AGTAATTTTA
581759 TTTAAATTTAATTATAA-AATAT
1 TTTAAA-TTAATTATAATAA-AT
* *
581781 ATTAATATTAATATAAAAATAAAT
1 TTTAA-ATTAAT-T-ATAATAAAT
* *
581805 TTTTAA-T-ATTATAATATAT
1 TTTAAATTAATTATAATAAAT
*
581824 TTTAAA-TAA-TAAAATAAAT
1 TTTAAATTAATTATAATAAAT
581843 TTTAAATTAAATTATAATAAAT
1 TTTAAATT-AATTATAATAAAT
581865 AAAATATTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
19 27 0.41
20 3 0.05
21 4 0.06
22 19 0.29
23 3 0.05
24 8 0.12
25 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTAAATTAATTATAATAAAT
Found at i:582297 original size:16 final size:16
Alignment explanation
Indices: 582276--582341 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
582266 TATTTTAAAT
582276 TTTATAAAATAAATTA
1 TTTATAAAATAAATTA
* *
582292 TTTATATATTAAAATT-
1 TTTATAAAAT-AAATTA
*
582308 TATATAAAATAAA-TA
1 TTTATAAAATAAATTA
*
582323 TTATATTAAATATAATTA
1 TT-TATAAAATA-AATTA
582341 T
1 T
582342 AAAATAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
14 1 0.03
15 4 0.11
16 23 0.61
17 7 0.18
18 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTATAAAATAAATTA
Found at i:582310 original size:30 final size:27
Alignment explanation
Indices: 582255--582358 Score: 75
Period size: 29 Copynumber: 3.6 Consensus size: 27
582245 AAAATAATAT
* * * *
582255 AAATATATAAATATTTTAAATTTTATA
1 AAATAAATATATATATTAAAATTTATA
582282 AAATAAATTATTTATATATTAAAATTTATATA
1 AAATAAA-TA--TATATATTAAAA-TT-TATA
582314 AAATAAATAT-TATATTAAATATAATTATA
1 AAATAAATATATATATTAAA-AT--TTATA
*
582343 AAATAAAAATAATATA
1 AAATAAATAT-ATATA
582359 ATTGTAAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
27 6 0.10
28 12 0.19
29 15 0.24
30 10 0.16
31 8 0.13
32 11 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATAAATATATATATTAAAATTTATA
Found at i:582485 original size:14 final size:14
Alignment explanation
Indices: 582456--582534 Score: 57
Period size: 14 Copynumber: 6.1 Consensus size: 14
582446 AAAAATTTAA
582456 AATATTATATTATATT
1 AATATT-TA-TATATT
582472 AATATTTATATA-T
1 AATATTTATATATT
582485 --T-TTTATA-ATT
1 AATATTTATATATT
*
582495 AA-ATTTA-AT-TA
1 AATATTTATATATT
* *
582506 AATATTTTTATACT
1 AATATTTATATATT
582520 AATATTTATATATT
1 AATATTTATATATT
582534 A
1 A
582535 TTTTATTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
9 1 0.02
10 7 0.14
11 5 0.10
12 8 0.16
13 3 0.06
14 17 0.35
15 2 0.04
16 6 0.12
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTTATATATT
Found at i:582524 original size:48 final size:54
Alignment explanation
Indices: 582455--582558 Score: 148
Period size: 48 Copynumber: 2.0 Consensus size: 54
582445 TAAAAATTTA
*
582455 AAATATTATATTATATTAATATTTATATA-T-TTTTA-TAA-TTAAATTTAATT
1 AAATATTATATTATACTAATATTTATATATTATTTTATTAATTTAAATTTAATT
*
582505 AAATATT-T-TTATACTAATATTTATATATTATTTTATTAATTTAAATTTGATT
1 AAATATTATATTATACTAATATTTATATATTATTTTATTAATTTAAATTTAATT
582557 AA
1 AA
582559 TATAAATCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
48 18 0.38
49 2 0.04
50 12 0.25
51 3 0.06
52 13 0.27
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (54 bp):
AAATATTATATTATACTAATATTTATATATTATTTTATTAATTTAAATTTAATT
Found at i:582608 original size:26 final size:21
Alignment explanation
Indices: 582578--582655 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 21
582568 TAAAATTTTA
582578 TATTTAAATTTAACTTAATATAAAT
1 TATTTAAA--TAA-TTAA-ATAAAT
582603 TAATTTAAATAATTAAATAAAT
1 T-ATTTAAATAATTAAATAAAT
**
582625 TATTT-AATTTTTAAATAAATT
1 TATTTAAATAATTAAATAAA-T
*
582646 TATGTAAATA
1 TATTTAAATA
582656 TAATATTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 12 0.26
21 9 0.20
22 10 0.22
23 4 0.09
24 3 0.07
25 1 0.02
26 7 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
TATTTAAATAATTAAATAAAT
Found at i:582640 original size:20 final size:22
Alignment explanation
Indices: 582592--582655 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 22
582582 TAAATTTAAC
582592 TTAATATAAATTAATTTAAATAA
1 TTAA-ATAAATTAATTTAAATAA
**
582615 TTAAATAAATT-ATTT-AATTT
1 TTAAATAAATTAATTTAAATAA
* *
582635 TTAAATAAATTTATGTAAATA
1 TTAAATAAATTAATTTAAATA
582656 TAATATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 14 0.40
21 7 0.20
22 10 0.29
23 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAAATAAATTAATTTAAATAA
Found at i:583072 original size:38 final size:39
Alignment explanation
Indices: 583005--583101 Score: 101
Period size: 38 Copynumber: 2.5 Consensus size: 39
582995 GCATTCATAT
***
583005 TTAATGTATTAAAATTAATTTTTTTTTTATAAAAAATT-A
1 TTAAT-TATTAAAATTAATTTTAAATTTATAAAAAATTAA
* *
583044 -TAATTATTAAAATTTAATTTTAAATTTATTAAATATTAA
1 TTAATTATTAAAA-TTAATTTTAAATTTATAAAAAATTAA
583083 TTAATTA-TATAAATTAATT
1 TTAATTATTA-AAATTAATT
583102 GAATTAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
37 8 0.16
38 23 0.47
39 9 0.18
40 9 0.18
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (39 bp):
TTAATTATTAAAATTAATTTTAAATTTATAAAAAATTAA
Found at i:583096 original size:28 final size:28
Alignment explanation
Indices: 583053--583123 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
583043 ATAATTATTA
*
583053 AAATTTAATT-T-TAAATTTATTAAATAT
1 AAATTTAATTATATAAATTAATTAAAT-T
* *
583080 TAA-TTAATTATATAAATTAATTGAATT
1 AAATTTAATTATATAAATTAATTAAATT
583107 AAATTTAATTAATATAA
1 AAATTTAATT-ATATAA
583124 TTATAATTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 6 0.17
27 6 0.17
28 18 0.50
29 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
AAATTTAATTATATAAATTAATTAAATT
Found at i:583097 original size:13 final size:14
Alignment explanation
Indices: 583064--583123 Score: 61
Period size: 15 Copynumber: 4.2 Consensus size: 14
583054 AATTTAATTT
*
583064 TAAATTTATTAAATA
1 TAAATTAATT-AATA
*
583079 TTAATTAATT-ATA
1 TAAATTAATTAATA
583092 TAAATTAATTGAAT-
1 TAAATTAATT-AATA
583106 TAAATTTAATTAATA
1 TAAA-TTAATTAATA
583121 TAA
1 TAA
583124 TTATAATTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 12 0.32
14 7 0.18
15 19 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
TAAATTAATTAATA
Found at i:587029 original size:2 final size:2
Alignment explanation
Indices: 587022--587060 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
587012 AATAGTATTT
587022 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
587061 TATCTTGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:587932 original size:22 final size:22
Alignment explanation
Indices: 587907--587959 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
587897 AAATAAATTT
*
587907 AATTATTTTAAATATATAAAAA
1 AATTATTTTAAATACATAAAAA
** * *
587929 AATTAAATTAAATACATTAATA
1 AATTATTTTAAATACATAAAAA
587951 AATT-TTTTA
1 AATTATTTTA
587960 TTTCCTTTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTATTTTAAATACATAAAAA
Found at i:588591 original size:22 final size:22
Alignment explanation
Indices: 588563--588604 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
588553 TTAATTTATA
588563 TTAAATTGAATTTAA-ATAAAAT
1 TTAAATTGAA-TTAATATAAAAT
*
588585 TTAAATTTAATTAATATAAA
1 TTAAATTGAATTAATATAAA
588605 CATAAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAAATTGAATTAATATAAAAT
Found at i:588834 original size:73 final size:73
Alignment explanation
Indices: 588743--588885 Score: 259
Period size: 73 Copynumber: 2.0 Consensus size: 73
588733 CTAACAACTT
*
588743 ATTTAGGAGTTCCTAGTTATCATTGCTCCGCAGAGTTCAGTCAATTACCTGCAAGACAAGGAATA
1 ATTTAGGAGTTCCTAGTTATCATTGCTCAGCAGAGTTCAGTCAATTACCTGCAAGACAAGGAATA
588808 GTGAGAGA
66 GTGAGAGA
* *
588816 ATTTAGGAGTTCCTAGTTATCATTGTTCAGCAGAGTTCAGTCACTTACCTGCAAGACAAGGAATA
1 ATTTAGGAGTTCCTAGTTATCATTGCTCAGCAGAGTTCAGTCAATTACCTGCAAGACAAGGAATA
588881 GTGAG
66 GTGAG
588886 GGAGGTCGAA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (73 bp):
ATTTAGGAGTTCCTAGTTATCATTGCTCAGCAGAGTTCAGTCAATTACCTGCAAGACAAGGAATA
GTGAGAGA
Found at i:591633 original size:15 final size:15
Alignment explanation
Indices: 591593--591635 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
591583 GATCTATTAT
*
591593 ATTAAATTTAAAAAA
1 ATTAAATTTTAAAAA
591608 ATTATATATTTTAAAAA
1 ATTA-A-ATTTTAAAAA
591625 ATTAAATTTTA
1 ATTAAATTTTA
591636 TATGTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 10 0.40
16 2 0.08
17 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAAATTTTAAAAA
Found at i:592098 original size:16 final size:16
Alignment explanation
Indices: 592065--592098 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
592055 AATATAAATT
*
592065 AAACATAAATATTATA
1 AAACATAAAAATTATA
*
592081 AAACATAAAAATTTTA
1 AAACATAAAAATTATA
592097 AA
1 AA
592099 TATCGTAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AAACATAAAAATTATA
Found at i:594408 original size:2 final size:2
Alignment explanation
Indices: 594401--594432 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
594391 AAGTAGTTTA
594401 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
594433 TTACAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:598273 original size:2 final size:2
Alignment explanation
Indices: 598266--598293 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
598256 AAAAATTTAG
598266 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
598294 GATAATCATA
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:602278 original size:26 final size:25
Alignment explanation
Indices: 602249--602330 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 25
602239 TTTAAAAAAT
602249 TTAAATATTAAATAATTATTTTTATA
1 TTAAATATTAAATAA-TATTTTTATA
*
602275 TT-AATATT-TAT-ATATTTTTATAA
1 TTAAATATTAAATAATATTTTTAT-A
602298 TTAAAT-TTAAATAAATATTTTTATTA
1 TTAAATATTAAAT-AATATTTTTA-TA
*
602324 ATAAATA
1 TTAAATA
602331 ATAATTTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
22 9 0.20
23 6 0.13
24 7 0.15
25 6 0.13
26 17 0.37
27 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAAATATTAAATAATATTTTTATA
Found at i:602286 original size:12 final size:12
Alignment explanation
Indices: 602269--602326 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
602259 AATAATTATT
602269 TTTATATTAATA
1 TTTATATTAATA
*
602281 TTTATA-T-ATT
1 TTTATATTAATA
602291 TTTATAATTAA-A
1 TTTAT-ATTAATA
* *
602303 TTTAAATAAATA
1 TTTATATTAATA
*
602315 TTTTTATTAATA
1 TTTATATTAATA
602327 AATAATAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
10 7 0.20
11 6 0.17
12 21 0.60
13 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTATATTAATA
Found at i:602293 original size:22 final size:22
Alignment explanation
Indices: 602265--602306 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
602255 ATTAAATAAT
602265 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
602287 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
602307 AATAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:603111 original size:23 final size:24
Alignment explanation
Indices: 603064--603112 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
603054 CGATATGATC
603064 AAATATGATTAACACGATATATTT
1 AAATATGATTAACACGATATATTT
* *
603088 AAATATGATTAA-ATGATATTTTT
1 AAATATGATTAACACGATATATTT
603111 AA
1 AA
603113 TAAACATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (24 bp):
AAATATGATTAACACGATATATTT
Found at i:603481 original size:16 final size:16
Alignment explanation
Indices: 603460--603490 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
603450 TGAAACGTAT
603460 TATATTTATTTATTTA
1 TATATTTATTTATTTA
*
603476 TATATTTTTTTATTT
1 TATATTTATTTATTT
603491 TTTTAACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATATTTATTTATTTA
Found at i:603730 original size:2 final size:2
Alignment explanation
Indices: 603723--603755 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
603713 TCAAATAATT
603723 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
603756 CAAAGTATAA
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:603937 original size:2 final size:2
Alignment explanation
Indices: 603930--603955 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
603920 TAAGCCAATT
603930 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
603956 AGTATGAATG
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):
TA
Found at i:604329 original size:16 final size:15
Alignment explanation
Indices: 604308--604342 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
604298 ACTTTATATT
604308 TTAATACAAATTTTA
1 TTAATACAAATTTTA
*
604323 GTTAATACATATTTTA
1 -TTAATACAAATTTTA
604339 TTAA
1 TTAA
604343 CTTTATTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (15 bp):
TTAATACAAATTTTA
Found at i:604661 original size:20 final size:20
Alignment explanation
Indices: 604644--604726 Score: 63
Period size: 20 Copynumber: 4.3 Consensus size: 20
604634 ATATATAATT
*
604644 TATATTAATAAAATATAAAA
1 TATAATAATAAAATATAAAA
604664 TATAATAATAAAAT-T-AAA
1 TATAATAATAAAATATAAAA
604682 TA-AAT-ATAAATTATATAAACA
1 TATAATAATAAA--ATATAAA-A
*
604703 -ATTATAA-AAATATATAAAA
1 TATAATAATAAA-ATATAAAA
604722 T-TAAT
1 TATAAT
604727 TTAATTTTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
16 5 0.10
17 3 0.06
18 7 0.13
19 6 0.12
20 24 0.46
21 6 0.12
22 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (20 bp):
TATAATAATAAAATATAAAA
Found at i:604692 original size:15 final size:15
Alignment explanation
Indices: 604654--604700 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
604644 TATATTAATA
*
604654 AAATATAAAATATAAT
1 AAATATAAATTA-AAT
604670 -AATA-AAATTAAAT
1 AAATATAAATTAAAT
*
604683 AAATATAAATTATAT
1 AAATATAAATTAAAT
604698 AAA
1 AAA
604701 CAATTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 3 0.11
14 9 0.33
15 15 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATATAAATTAAAT
Found at i:604697 original size:49 final size:45
Alignment explanation
Indices: 604636--604725 Score: 110
Period size: 48 Copynumber: 1.9 Consensus size: 45
604626 AAAACTCGAT
*
604636 ATATAATTTATATTAATA-AAATATAAAATATAATAATAAAATTAAATAA
1 ATATAAATTATA-TAA-ACAAATATAAAA-AT-AT-ATAAAATTAAATAA
*
604685 ATATAAATTATATAAACAATTATAAAAATATATAAAATTAA
1 ATATAAATTATATAAACAAATATAAAAATATATAAAATTAA
604726 TTTAATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 10 0.26
46 2 0.05
47 3 0.08
48 12 0.32
49 11 0.29
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (45 bp):
ATATAAATTATATAAACAAATATAAAAATATATAAAATTAAATAA
Found at i:604713 original size:27 final size:28
Alignment explanation
Indices: 604647--604716 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
604637 TATAATTTAT
604647 ATTAATAAAATATAAAATATAATAATAAA
1 ATTAA-AAAATATAAAATATAATAATAAA
* *
604676 ATTAAATAAATATAAATTAT-ATAA-ACA
1 ATTAAA-AAATATAAAATATAATAATAAA
604703 ATTATAAAAATATA
1 ATTA-AAAAATATA
604717 TAAAATTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 13 0.35
28 7 0.19
29 17 0.46
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (28 bp):
ATTAAAAAATATAAAATATAATAATAAA
Found at i:604717 original size:29 final size:29
Alignment explanation
Indices: 604647--604720 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
604637 TATAATTTAT
604647 ATTAATAAAATATA-AAATATAATAATAAA
1 ATTAA-AAAATATATAAATATAATAATAAA
* *
604676 ATTAAATAA-ATATAAAT-TATATAA-ACA
1 ATTAAAAAATATATAAATATA-ATAATAAA
604703 ATTATAAAAATATATAAA
1 ATTA-AAAAATATATAAA
604721 ATTAATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 11 0.29
28 15 0.39
29 12 0.32
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (29 bp):
ATTAAAAAATATATAAATATAATAATAAA
Found at i:604756 original size:2 final size:2
Alignment explanation
Indices: 604749--604774 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
604739 CGATCTAAGT
604749 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
604775 AATGTCGGTT
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):
TA
Found at i:604901 original size:12 final size:12
Alignment explanation
Indices: 604884--604908 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
604874 TCTTGAATAA
604884 TGTTTATTTATT
1 TGTTTATTTATT
604896 TGTTTATTTATT
1 TGTTTATTTATT
604908 T
1 T
604909 TTCCTTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TGTTTATTTATT
Found at i:605820 original size:2 final size:2
Alignment explanation
Indices: 605815--605852 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
605805 TACTAACATA
605815 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
605853 GCCTTCACTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:606941 original size:19 final size:18
Alignment explanation
Indices: 606893--606944 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
606883 AATTTTATTA
*
606893 ATAA-TATATAAATAAAT
1 ATAATTATATATATAAAT
* *
606910 ATATTTTTAATATATAAAT
1 ATAATTAT-ATATATAAAT
606929 ATAAATTATATATATA
1 AT-AATTATATATATA
606945 TATTTATTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 2 0.07
19 18 0.67
20 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATTATATATATAAAT
Found at i:609836 original size:20 final size:20
Alignment explanation
Indices: 609802--609842 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
609792 AAAAGTCACA
* *
609802 TGATGTTATTATTTTTATAT
1 TGATGTTAATATTTTCATAT
*
609822 TGATGTTAATCTTTTCATAT
1 TGATGTTAATATTTTCATAT
609842 T
1 T
609843 TCATGATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (20 bp):
TGATGTTAATATTTTCATAT
Found at i:611861 original size:19 final size:19
Alignment explanation
Indices: 611839--611904 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
611829 TTTATTATAT
611839 TATTAAAATAATATTTTTA
1 TATTAAAATAATATTTTTA
*
611858 TATTATAATTAA-A--TTTA
1 TATTA-AAATAATATTTTTA
*
611875 -AATAAAA-AATATTTTTA
1 TATTAAAATAATATTTTTA
611892 TTATT-AAATAATA
1 -TATTAAAATAATA
611905 ATTTAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
14 2 0.06
15 3 0.08
16 3 0.08
17 8 0.22
18 3 0.08
19 12 0.33
20 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTAAAATAATATTTTTA
Found at i:611886 original size:34 final size:36
Alignment explanation
Indices: 611842--611912 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 36
611832 ATTATATTAT
*
611842 TAAAATAATATTTTTA-TATTATAATTA-AATTTAAA
1 TAAAATAATATTTTTATTATTA-AATAATAATTTAAA
611877 TAAAA-AATATTTTTATTATTAAATAATAATTTAAA
1 TAAAATAATATTTTTATTATTAAATAATAATTTAAA
611912 T
1 T
611913 TAATTTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
34 14 0.42
35 19 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (36 bp):
TAAAATAATATTTTTATTATTAAATAATAATTTAAA
Found at i:613858 original size:2 final size:2
Alignment explanation
Indices: 613851--613881 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
613841 ACATATAAGC
613851 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 T
613882 TCTCATTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:615858 original size:13 final size:13
Alignment explanation
Indices: 615840--615879 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
615830 CTCAATTACT
615840 ATTTAATTAATAA
1 ATTTAATTAATAA
615853 ATTTAAATT--TAA
1 ATTT-AATTAATAA
615865 ATTTAATTAATAA
1 ATTTAATTAATAA
615878 AT
1 AT
615880 ATATGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.17
12 7 0.29
13 9 0.38
14 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTAATTAATAA
Found at i:616169 original size:4 final size:4
Alignment explanation
Indices: 616160--616186 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
616150 AATGGACAAG
616160 GGGA GGGA GGGA GGGA GGGA GGGA GGG
1 GGGA GGGA GGGA GGGA GGGA GGGA GGG
616187 GTTGCTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.78, T:0.00
Consensus pattern (4 bp):
GGGA
Found at i:616685 original size:2 final size:2
Alignment explanation
Indices: 616680--616707 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
616670 TAGAAGTGTG
616680 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
616708 CACAACTCTA
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):
TA
Found at i:620408 original size:13 final size:13
Alignment explanation
Indices: 620390--620432 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
620380 AAAAATAAGA
620390 TTAATTTTTATAT
1 TTAATTTTTATAT
620403 TTAATTTTTA-AT
1 TTAATTTTTATAT
* *
620415 TTGATTATTTATTT
1 TTAATT-TTTATAT
620429 TTAA
1 TTAA
620433 ATTTAAGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 7 0.28
13 14 0.56
14 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TTAATTTTTATAT
Found at i:623173 original size:19 final size:19
Alignment explanation
Indices: 623151--623190 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
623141 CATATTTAAA
623151 TATATAATTTTATATTTAT
1 TATATAATTTTATATTTAT
* *
623170 TATATTATTTTTTATTTAT
1 TATATAATTTTATATTTAT
623189 TA
1 TA
623191 AATATCTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATATAATTTTATATTTAT
Found at i:623654 original size:47 final size:50
Alignment explanation
Indices: 623600--623699 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 50
623590 ATTAAAATTT
* *
623600 TTTAAATTTAAAT-TAAATTATTAT-TTAATA-ATAAAATATTATTT-TTA
1 TTTAAATTTAAATATAAATAATAATATTAATATA-AAAATATTATTTATTA
* *
623647 TTTAAATTTAATTATAAATAATAATATTAATATAAAAATATTTTTTATTA
1 TTTAAATTTAAATATAAATAATAATATTAATATAAAAATATTATTTATTA
623697 TTT
1 TTT
623700 TTATATTATC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
47 12 0.27
48 9 0.20
49 17 0.38
50 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (50 bp):
TTTAAATTTAAATATAAATAATAATATTAATATAAAAATATTATTTATTA
Found at i:623770 original size:36 final size:36
Alignment explanation
Indices: 623728--623798 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
623718 TAAATTAAAC
** *
623728 TTTTAAATTAATTTAACATGAATATAAATAAAAAAA
1 TTTTAAATTAACCTAACATAAATATAAATAAAAAAA
*
623764 TTTTAAATTAACCTAATATAAATATAAATAAAAAA
1 TTTTAAATTAACCTAACATAAATATAAATAAAAAA
623799 TTTCAAGCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (36 bp):
TTTTAAATTAACCTAACATAAATATAAATAAAAAAA
Found at i:624441 original size:17 final size:17
Alignment explanation
Indices: 624411--624458 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
624401 TTTTAAAATT
*
624411 TAAATAAAATAAATTAT-
1 TAAATAATA-AAATTATA
624428 TAACATAATAAAATTATA
1 TAA-ATAATAAAATTATA
*
624446 TAAATTATAAAAT
1 TAAATAATAAAAT
624459 ATGTTAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATAATAAAATTATA
Found at i:627917 original size:12 final size:11
Alignment explanation
Indices: 627900--627973 Score: 57
Period size: 11 Copynumber: 6.8 Consensus size: 11
627890 ATAGATTTCG
627900 TTAAAATTATAT
1 TTAAAATTA-AT
627912 TTAAAA-TAAT
1 TTAAAATTAAT
*
627922 TTAAAATTAAA
1 TTAAAATTAAT
* *
627933 ATAAATTTAAAT
1 TTAAAATT-AAT
627945 TTAAATATTAA-
1 TTAAA-ATTAAT
*
627956 --AAAATTAAC
1 TTAAAATTAAT
627965 TTAAAATTA
1 TTAAAATTA
627974 GTTTGCTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
8 5 0.10
9 3 0.06
10 8 0.16
11 18 0.36
12 14 0.28
13 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAAATTAAT
Found at i:627931 original size:16 final size:17
Alignment explanation
Indices: 627912--627949 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
627902 AAAATTATAT
627912 TTAAAAT-AATTTAAAA
1 TTAAAATAAATTTAAAA
*
627928 TTAAAATAAATTTAAAT
1 TTAAAATAAATTTAAAA
627945 TTAAA
1 TTAAA
627950 TATTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAATAAATTTAAAA
Found at i:627950 original size:16 final size:18
Alignment explanation
Indices: 627910--627952 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
627900 TTAAAATTAT
627910 ATTTAAA-ATAATTTAAA
1 ATTTAAATATAATTTAAA
*
627927 ATTAAAATA-AATTT-AA
1 ATTTAAATATAATTTAAA
627943 ATTTAAATAT
1 ATTTAAATAT
627953 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 10 0.45
17 11 0.50
18 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAAATATAATTTAAA
Found at i:628478 original size:19 final size:18
Alignment explanation
Indices: 628441--628514 Score: 51
Period size: 19 Copynumber: 4.0 Consensus size: 18
628431 TTGATAATTT
* *
628441 TAAATATAATATTATTATA
1 TAAAAATAATA-TAATATA
628460 TAAAAATAATATAAATATA
1 TAAAAATAATAT-AATATA
* * *
628479 TTATAATTATATAATAT-
1 TAAAAATAATATAATATA
* *
628496 TAAAATTTTATATAATATA
1 TAAAA-ATAATATAATATA
628515 AATCTTTAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
17 3 0.07
18 17 0.39
19 24 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAAATAATATAATATA
Found at i:628492 original size:24 final size:23
Alignment explanation
Indices: 628426--628495 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
628416 GTTCACACTG
*
628426 ATATATTGATAATTTTA-AATATA
1 ATATATT-ATAATTATATAATATA
* *
628449 ATATTATTAT-ATAAAAATAATATAA
1 ATA-TATTATAAT-TATATAATAT-A
628474 ATATATTATAATTATATAATAT
1 ATATATTATAATTATATAATAT
628496 TAAAATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
22 2 0.05
23 6 0.16
24 23 0.62
25 6 0.16
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (23 bp):
ATATATTATAATTATATAATATA
Found at i:628496 original size:16 final size:17
Alignment explanation
Indices: 628476--628513 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
628466 TAATATAAAT
*
628476 ATATTATAA-TTATATA
1 ATATTAAAATTTATATA
628492 ATATTAAAATTTTATATA
1 ATATTAAAA-TTTATATA
628510 ATAT
1 ATAT
628514 AAATCTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:628515 original size:31 final size:32
Alignment explanation
Indices: 628474--628544 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
628464 AATAATATAA
* *
628474 ATATATTATAATTATATAATAT-TAAAATTTT
1 ATATAATATAAATATATAATATATAAAATTTT
* * * *
628505 ATATAATATAAATCTTTAATATATCAATTTTT
1 ATATAATATAAATATATAATATATAAAATTTT
628537 ATATAATA
1 ATATAATA
628545 ATTTAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 18 0.55
32 15 0.45
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (32 bp):
ATATAATATAAATATATAATATATAAAATTTT
Found at i:629707 original size:21 final size:23
Alignment explanation
Indices: 629666--629718 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
629656 CTCCAAGGTA
629666 ATTTA-TTTTATTATTTCAAAAT
1 ATTTAGTTTTATTATTTCAAAAT
629688 -TTTAGTTTGTATTA-TT-AAAAT
1 ATTTAGTTT-TATTATTTCAAAAT
*
629709 AATTAGTTTT
1 ATTTAGTTTT
629719 TTTTAAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 10 0.37
22 12 0.44
23 5 0.19
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (23 bp):
ATTTAGTTTTATTATTTCAAAAT
Found at i:631374 original size:8 final size:8
Alignment explanation
Indices: 631345--631416 Score: 56
Period size: 8 Copynumber: 8.4 Consensus size: 8
631335 GACGTAATAT
*
631345 TTATTTGA
1 TTATTTTA
631353 TTCATTTT-
1 TT-ATTTTA
631361 TTATTTTA
1 TTATTTTA
631369 TTATTTTA
1 TTATTTTA
*
631377 TTATTTTT
1 TTATTTTA
631385 TTGAGTTTTTA
1 TT-A--TTTTA
*
631396 ATATTTTAA
1 TTATTTT-A
631405 TTATTTATA
1 TTATTT-TA
631414 TTA
1 TTA
631417 ATTAATATGA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
7 5 0.10
8 25 0.48
9 15 0.29
10 2 0.04
11 5 0.10
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.69
Consensus pattern (8 bp):
TTATTTTA
Found at i:631824 original size:23 final size:23
Alignment explanation
Indices: 631769--631825 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
631759 CAATCAAATT
631769 ATTTAATTTT-TAAATATATCTA
1 ATTTAATTTTATAAATATATCTA
631791 ATTT-ATATTTATAAACTATAT-TA
1 ATTTAAT-TTTATAAA-TATATCTA
631814 ATTTAATTTTAT
1 ATTTAATTTTAT
631826 CATTATTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 2 0.06
22 7 0.23
23 15 0.48
24 7 0.23
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAATTTTATAAATATATCTA
Found at i:634415 original size:25 final size:25
Alignment explanation
Indices: 634380--634449 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 25
634370 GTTTAAGCTG
*
634380 ATTTGAATTTATTTAATTTGATTG-AA
1 ATTT-AATTTATTTAATTT-AATGAAA
*
634406 ATTTAATTTAATTTGATTTAATGAAA
1 ATTTAATTT-ATTTAATTTAATGAAA
*
634432 ATGTTAA-TAATTTAATTT
1 AT-TTAATTTATTTAATTT
634450 TAAAATGTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 16 0.43
26 17 0.46
27 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.53
Consensus pattern (25 bp):
ATTTAATTTATTTAATTTAATGAAA
Found at i:634416 original size:21 final size:20
Alignment explanation
Indices: 634385--634423 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
634375 AGCTGATTTG
634385 AATTTATTTAATTTGATTGA
1 AATTTATTTAATTTGATTGA
634405 AATTTAATTTAATTTGATT
1 AATTT-ATTTAATTTGATT
634424 TAATGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
AATTTATTTAATTTGATTGA
Found at i:634424 original size:10 final size:10
Alignment explanation
Indices: 634378--634427 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
634368 CTGTTTAAGC
634378 TGATTTGAATT
1 TGATTT-AATT
634389 T-ATTTAATT
1 TGATTTAATT
*
634398 TGATTGAAATT
1 TGATT-TAATT
*
634409 TAATTTAATT
1 TGATTTAATT
634419 TGATTTAAT
1 TGATTTAAT
634428 GAAAATGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 5 0.15
10 19 0.58
11 9 0.27
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (10 bp):
TGATTTAATT
Found at i:635406 original size:2 final size:2
Alignment explanation
Indices: 635335--635388 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
635325 AGAAATTAAT
* * *
635335 TA TA TA TA TA TA TA TA TA TGA CA TA CA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
635378 TA TA TA TA TA T
1 TA TA TA TA TA T
635389 GTACAGATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 44 0.98
3 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:639021 original size:19 final size:20
Alignment explanation
Indices: 638997--639046 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
638987 ATAATTAATT
**
638997 TTAAATAAAAAT-ATTTTTA
1 TTAAATAAAAATAATTTAGA
639016 TTAAATAAATAATAATTTAGA
1 TTAAATAAA-AATAATTTAGA
639037 TTAAATAAAA
1 TTAAATAAAA
639047 TCAAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 4 0.15
21 14 0.52
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TTAAATAAAAATAATTTAGA
Found at i:642585 original size:20 final size:21
Alignment explanation
Indices: 642526--642585 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
642516 CGAAAATTTA
642526 TTTTAATTATTTATTTAATAAG
1 TTTTAATTATTT-TTTAATAAG
* * *
642548 TTTGAAGTTTAATTTTTAAT-AT
1 TTTTAA--TTATTTTTTAATAAG
642570 TTTTAATTATTTTTTA
1 TTTTAATTATTTTTTA
642586 TTTTAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 9 0.29
22 11 0.35
23 6 0.19
24 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTTAATTATTTTTTAATAAG
Found at i:643647 original size:19 final size:19
Alignment explanation
Indices: 643623--643668 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
643613 TAAGTATGAA
*
643623 AAAAATTTATTCAATAGAT
1 AAAAATTTATTCAACAGAT
*
643642 AAAAA-TTATTCAACATAT
1 AAAAATTTATTCAACAGAT
*
643660 TAAAATTTA
1 AAAAATTTA
643669 AAAATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAATTTATTCAACAGAT
Found at i:643946 original size:23 final size:24
Alignment explanation
Indices: 643895--643949 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
643885 TATAAATTAT
*
643895 AAAATTATATTTATGGATAAAAATT
1 AAAATTATATTTAT-GATAAAAATA
643920 AAAATTATATTTA--ATAAAAAATA
1 AAAATTATATTTATGAT-AAAAATA
643943 AAAATTA
1 AAAATTA
643950 ATAAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 13 0.46
25 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
AAAATTATATTTATGATAAAAATA
Found at i:644021 original size:13 final size:13
Alignment explanation
Indices: 644003--644030 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
643993 GTAAAATATT
644003 TTAATTTAATTAA
1 TTAATTTAATTAA
644016 TTAATTTAATTAA
1 TTAATTTAATTAA
644029 TT
1 TT
644031 TATTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:644759 original size:2 final size:2
Alignment explanation
Indices: 644754--644790 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
644744 TATATATATA
644754 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
644791 AGGATGACAG
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:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:646665 original size:2 final size:2
Alignment explanation
Indices: 646650--646686 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
646640 CATCATCGTG
*
646650 AT AT AT AC AT -T 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
646687 CTCAATCAAC
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:647245 original size:5 final size:5
Alignment explanation
Indices: 647237--647277 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
647227 TTATCTTCTC
647237 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
647278 CGGTTTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:648743 original size:23 final size:23
Alignment explanation
Indices: 648717--648762 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
648707 TAACAACCGC
* *
648717 ATCTGTATTATACCTCAGTTAGG
1 ATCTGGATTATAACTCAGTTAGG
648740 ATCTGGATTATAACTCAGTTAGG
1 ATCTGGATTATAACTCAGTTAGG
648763 GTCGAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (23 bp):
ATCTGGATTATAACTCAGTTAGG
Found at i:651838 original size:177 final size:177
Alignment explanation
Indices: 651535--651888 Score: 620
Period size: 177 Copynumber: 2.0 Consensus size: 177
651525 TTATCCAAAT
* * *
651535 TGAGATATCAGATGCCTTCAAAAGTTCAGAAAATGATCACCCAAAAATGGAGGTAAAATCCCATC
1 TGAGAAATCAGATGCCTTCAAAAGTTCAGAAAATGATCACCCAAAAATGGAAGAAAAATCCCATC
651600 AAAGAAACTCAGCTCTTGGTTCCCAATTTCCAGTTTTCTCAGTTTGAATACTCTCCCCTATTGCA
66 AAAGAAACTCAGCTCTTGGTTCCCAATTTCCAGTTTTCTCAGTTTGAATACTCTCCCCTATTGCA
* * *
651665 TACCATGTAG-TGTTAAACATTAAATCAGATTGTTTGAACTTTGAGGC
131 TAACATGTAGCT-TAAAACATCAAATCAGATTGTTTGAACTTTGAGGC
*
651712 TGAGAAATCAGATGCCTTCAAAAGTTCATAAAATGATCACCCAAAAATGGAAGAAAAATCCCATC
1 TGAGAAATCAGATGCCTTCAAAAGTTCAGAAAATGATCACCCAAAAATGGAAGAAAAATCCCATC
*
651777 AAAGAAACTCAGCTCTTGGTTCCCAATTTCCAGTTTTCTCAGTTTGAATACTCTGCCCTATTGCA
66 AAAGAAACTCAGCTCTTGGTTCCCAATTTCCAGTTTTCTCAGTTTGAATACTCTCCCCTATTGCA
651842 TAACATGTAGCTTAAAACATCAAATCAGATTGTTTGAACTTTGAGGC
131 TAACATGTAGCTTAAAACATCAAATCAGATTGTTTGAACTTTGAGGC
651889 ACCTTTCTGG
Statistics
Matches: 168, Mismatches: 8, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
177 167 0.99
178 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (177 bp):
TGAGAAATCAGATGCCTTCAAAAGTTCAGAAAATGATCACCCAAAAATGGAAGAAAAATCCCATC
AAAGAAACTCAGCTCTTGGTTCCCAATTTCCAGTTTTCTCAGTTTGAATACTCTCCCCTATTGCA
TAACATGTAGCTTAAAACATCAAATCAGATTGTTTGAACTTTGAGGC
Found at i:652200 original size:39 final size:35
Alignment explanation
Indices: 652157--652231 Score: 96
Period size: 39 Copynumber: 2.0 Consensus size: 35
652147 TCAAGATATC
652157 TTTTATATCGTAATCATATTTAATTTATTATATATACAT
1 TTTTATATCGTAATCATA-TTAATTT-TT-TAT-TACAT
* *
652196 TTTTATATCGTATTTATATTAATTTTTTATTACAT
1 TTTTATATCGTAATCATATTAATTTTTTATTACAT
652231 T
1 T
652232 ATGTTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 6 0.18
36 3 0.09
37 2 0.06
38 7 0.21
39 16 0.47
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.59
Consensus pattern (35 bp):
TTTTATATCGTAATCATATTAATTTTTTATTACAT
Found at i:653900 original size:32 final size:31
Alignment explanation
Indices: 653863--653953 Score: 76
Period size: 32 Copynumber: 2.9 Consensus size: 31
653853 TAATCAAATA
653863 TAATTA-AATCAATATTAATTAAAATTTATAAG
1 TAATTAGAAT-AATATTAATT-AAATTTATAAG
* * *
653895 TAATTATGTATAATATTTATTAAATTTATAAA
1 TAATTA-GAATAATATTAATTAAATTTATAAG
* * * * *
653927 TATTTATATTTATATTCATTAAATTTA
1 TAATTAGAATAATATTAATTAAATTTA
653954 CTATTAATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
31 16 0.33
32 21 0.44
33 9 0.19
34 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (31 bp):
TAATTAGAATAATATTAATTAAATTTATAAG
Found at i:653948 original size:31 final size:32
Alignment explanation
Indices: 653873--653953 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
653863 TAATTAAATC
* *
653873 AATATTAATTAAAATTTATAAGTAATTATGTAT
1 AATATTAATT-AAATTTATAAATAATTATATAT
* *
653906 AATATTTATTAAATTTATAAATATTTATAT-T
1 AATATTAATTAAATTTATAAATAATTATATAT
* *
653937 TATATTCATTAAATTTA
1 AATATTAATTAAATTTA
653954 CTATTAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 16 0.38
32 17 0.40
33 9 0.21
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (32 bp):
AATATTAATTAAATTTATAAATAATTATATAT
Found at i:654551 original size:21 final size:20
Alignment explanation
Indices: 654498--654548 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
654488 AATATATTCA
*
654498 TATAATCATATT-ATTTTTT
1 TATAATAATATTAATTTTTT
**
654517 TAT-ATTTTAATTAATTTTTT
1 TATAATAAT-ATTAATTTTTT
654537 TATAATAATATT
1 TATAATAATATT
654549 TAAAATTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 3 0.12
19 6 0.24
20 13 0.52
21 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TATAATAATATTAATTTTTT
Found at i:654643 original size:19 final size:18
Alignment explanation
Indices: 654619--654655 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
654609 ACCAATATAC
654619 AAAATAAATATAATATAAA
1 AAAATAAATATAA-ATAAA
654638 AAAATAAATATAAATAAA
1 AAAATAAATATAAATAAA
654656 CATCACAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATAAATATAAATAAA
Found at i:654649 original size:14 final size:16
Alignment explanation
Indices: 654619--654655 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
654609 ACCAATATAC
654619 AAAATAAATATAATAT
1 AAAATAAATATAATAT
654635 AAAA-AAATA-AATAT
1 AAAATAAATATAATAT
654649 -AAATAAA
1 AAAATAAA
654656 CATCACAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 8 0.40
15 5 0.25
16 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAAATATAATAT
Found at i:656480 original size:39 final size:39
Alignment explanation
Indices: 656407--656481 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
656397 GCTTAAGGAT
** *
656407 AATAATTTATTTTCAAGGACATGATCAAGCAATAAAATA
1 AATAATTTATTTTCAAAAACATGATCAAACAATAAAATA
*
656446 AATAATTTATTTTCAAAAACATGATCAAATAATAAA
1 AATAATTTATTTTCAAAAACATGATCAAACAATAAA
656482 TTGAGCATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (39 bp):
AATAATTTATTTTCAAAAACATGATCAAACAATAAAATA
Found at i:658493 original size:13 final size:13
Alignment explanation
Indices: 658475--658501 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
658465 CTACTTTCAA
658475 CTCTTGCAATTAT
1 CTCTTGCAATTAT
658488 CTCTTGCAATTAT
1 CTCTTGCAATTAT
658501 C
1 C
658502 ACACTAGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.44
Consensus pattern (13 bp):
CTCTTGCAATTAT
Found at i:660806 original size:20 final size:20
Alignment explanation
Indices: 660770--660829 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
660760 TAATACATTA
*
660770 TATATTTA-TTT-ATATAAT
1 TATATTTATTTTAAAATAAT
*
660788 TATATTTATTTTAAAATAAG
1 TATATTTATTTTAAAATAAT
660808 TAT-TATTACTTTTAAAAATAAT
1 TATAT-TTA-TTTT-AAAATAAT
660830 AACACATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.24
19 4 0.12
20 11 0.32
21 4 0.12
22 7 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TATATTTATTTTAAAATAAT
Found at i:668130 original size:37 final size:34
Alignment explanation
Indices: 668041--668130 Score: 99
Period size: 37 Copynumber: 2.5 Consensus size: 34
668031 AAATAAAATA
* *
668041 ATTTTAATTTAAAATTTAAATTTATATTATTATG
1 ATTTTAATTTAAATTTTAAATTCATATTATTATG
*
668075 ATTTTAATTAGATTAATTTTAAATTCATATTATTATG
1 ATTTTAATT---TAAATTTTAAATTCATATTATTATG
668112 AAGTTTTGAATTTAAATTT
1 -A-TTTT-AATTTAAATTT
668131 ATTTTGTCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
34 9 0.20
37 28 0.61
38 1 0.02
39 4 0.09
40 4 0.09
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (34 bp):
ATTTTAATTTAAATTTTAAATTCATATTATTATG
Found at i:668712 original size:15 final size:16
Alignment explanation
Indices: 668682--668714 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
668672 ACAAAATTAA
*
668682 TTTTTATATTATATAT
1 TTTTTATATTAAATAT
668698 TTTTTAT-TTAAATAT
1 TTTTTATATTAAATAT
668713 TT
1 TT
668715 AAAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATATTAAATAT
Found at i:668760 original size:17 final size:17
Alignment explanation
Indices: 668740--668773 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
668730 AAATAAATAT
*
668740 TTAAATTATTATTTTTA
1 TTAAATAATTATTTTTA
668757 TTAAATAATTATTTTTA
1 TTAAATAATTATTTTTA
668774 AGATATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAAATAATTATTTTTA
Done.