Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1308201
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
File 4 of 11
Found at i:276422 original size:14 final size:14
Alignment explanation
Indices: 276411--276443 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
276401 CAAATAATTG
276411 AATATAATTAATAT
1 AATATAATTAATAT
*
276425 AATATATTTAATAT
1 AATATAATTAATAT
276439 -ATATA
1 AATATA
276444 TCATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATAATTAATAT
Found at i:276436 original size:18 final size:18
Alignment explanation
Indices: 276415--276462 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
276405 TAATTGAATA
276415 TAATTAATATAATATATT
1 TAATTAATATAATATATT
* *
276433 TAATATATATATCATATTTT
1 TAAT-TA-ATATAATATATT
*
276453 TATTTAATAT
1 TAATTAATAT
276463 TTAAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 8 0.32
19 4 0.16
20 13 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTAATATAATATATT
Found at i:276957 original size:19 final size:19
Alignment explanation
Indices: 276860--276957 Score: 55
Period size: 19 Copynumber: 5.1 Consensus size: 19
276850 TTTTTTTTTA
276860 ATATTTATATTTAATATAT
1 ATATTTATATTTAATATAT
* *
276879 A-A-TTAAATATTAATATAA
1 ATATTTATAT-TTAATATAT
*
276897 AAATTATAAATTATTTAA-A-AT
1 ATATT-T--A-TATTTAATATAT
*
276918 ATATTT-T-TTTAAATTAAAT
1 ATATTTATATTT-AA-TATAT
276937 ATATTTATATTTAATATAT
1 ATATTTATATTTAATATAT
276956 AT
1 AT
276958 TAATAATTAC
Statistics
Matches: 60, Mismatches: 6, Indels: 26
0.65 0.07 0.28
Matches are distributed among these distances:
15 3 0.05
16 3 0.05
17 5 0.08
18 11 0.18
19 16 0.27
20 5 0.08
21 9 0.15
22 1 0.02
23 5 0.08
24 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTATATTTAATATAT
Found at i:277313 original size:29 final size:29
Alignment explanation
Indices: 277274--277343 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
277264 AATTTCACTC
*
277274 AATAAACTTTTATACTTTTATTATAT-TA
1 AATAAATTTTTATACTTTTATTATATCTA
* *
277302 AA-ATAATTTTTTTAGTTTTATTATATCTA
1 AATA-AATTTTTATACTTTTATTATATCTA
277331 AATAAATTTTTAT
1 AATAAATTTTTAT
277344 TTTAAATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.03
28 21 0.60
29 12 0.34
30 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (29 bp):
AATAAATTTTTATACTTTTATTATATCTA
Found at i:277407 original size:30 final size:30
Alignment explanation
Indices: 277367--277521 Score: 113
Period size: 30 Copynumber: 5.2 Consensus size: 30
277357 TTAAATTATA
* *
277367 TTAAGTATTTATTTACGTATAAATTTAAAT
1 TTAAATATTTATTTAAGTATAAATTTAAAT
* * *
277397 TTAAATATTTATTTAAATATAAATTAAAAA
1 TTAAATATTTATTTAAGTATAAATTTAAAT
*
277427 ATAAA-ATTTTATTTAAGTATAAA-TTAAAT
1 TTAAATA-TTTATTTAAGTATAAATTTAAAT
* * **
277456 ATTACAA-ACTTATTTAAATAT-AATAAAAAT
1 -TTA-AATATTTATTTAAGTATAAATTTAAAT
* * *
277486 ATAAAAATTTATTTAAATA-AAATTATAAAAT
1 TTAAATATTTATTTAAGTATAAATT-T-AAAT
277517 TTAAA
1 TTAAA
277522 AACTTTCTTA
Statistics
Matches: 98, Mismatches: 19, Indels: 15
0.74 0.14 0.11
Matches are distributed among these distances:
28 2 0.02
29 24 0.24
30 61 0.62
31 11 0.11
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (30 bp):
TTAAATATTTATTTAAGTATAAATTTAAAT
Found at i:277447 original size:60 final size:58
Alignment explanation
Indices: 277373--277522 Score: 180
Period size: 60 Copynumber: 2.5 Consensus size: 58
277363 TATATTAAGT
* *
277373 ATTTATTTACGTATAAATTTAAATTTAAATATTTATTTAAATATAAATTAAAAA-ATAAAA
1 ATTTATTTAAGTATAAATTTAAATTTAAA-ACTTATTTAAATAT-AA-TAAAAATATAAAA
*
277433 TTTTATTTAAGTATAAA-TTAAATATTACAAACTTATTTAAATATAATAAAAATATAAAA
1 ATTTATTTAAGTATAAATTTAAAT-TTA-AAACTTATTTAAATATAATAAAAATATAAAA
*
277492 ATTTATTTAAATA-AAATTATAAAATTTAAAA
1 ATTTATTTAAGTATAAATT-T-AAATTTAAAA
277523 ACTTTCTTAT
Statistics
Matches: 79, Mismatches: 5, Indels: 13
0.81 0.05 0.13
Matches are distributed among these distances:
58 9 0.11
59 29 0.37
60 35 0.44
61 6 0.08
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (58 bp):
ATTTATTTAAGTATAAATTTAAATTTAAAACTTATTTAAATATAATAAAAATATAAAA
Found at i:277606 original size:3 final size:3
Alignment explanation
Indices: 277592--277632 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
277582 TAGGCCCTAA
*
277592 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
277633 AGAAAGAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:280723 original size:19 final size:19
Alignment explanation
Indices: 280699--280774 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 19
280689 ACTTTTTTAG
* *
280699 ATTATATCATATTTAAAAT
1 ATTATATAAAATTTAAAAT
280718 ATTATATAAAATTT--AAT
1 ATTATATAAAATTTAAAAT
280735 A-TATA-AATAATTT---AT
1 ATTATATAA-AATTTAAAAT
*
280750 ATTATATAAAATTT-TAAT
1 ATTATATAAAATTTAAAAT
280768 ATTATAT
1 ATTATAT
280775 GTTTATATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
15 5 0.10
16 18 0.36
17 6 0.12
18 9 0.18
19 12 0.24
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATATAAAATTTAAAAT
Found at i:280752 original size:32 final size:31
Alignment explanation
Indices: 280716--280785 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 31
280706 CATATTTAAA
280716 ATATTATATAAAA-TTTAATATATAAATAATTT
1 ATATTATATAAAATTTTAATAT-TAAAT-ATTT
* *
280748 ATATTATATAAAATTTTAATATTATATGTTT
1 ATATTATATAAAATTTTAATATTAAATATTT
280779 ATATTAT
1 ATATTAT
280786 TTTTTGTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 10 0.29
32 17 0.49
33 8 0.23
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
ATATTATATAAAATTTTAATATTAAATATTT
Found at i:280755 original size:18 final size:17
Alignment explanation
Indices: 280716--280774 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
280706 CATATTTAAA
280716 ATATTATAT-AAAATTT
1 ATATTATATAAAAATTT
280732 A-A-TATATAAATAATTT
1 ATATTATATAAA-AATTT
*
280748 ATATTATATAAAATTTT
1 ATATTATATAAAAATTT
280765 AATATTATAT
1 -ATATTATAT
280775 GTTTATATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 3 0.08
16 7 0.19
17 5 0.14
18 17 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTATATAAAAATTT
Found at i:280773 original size:16 final size:16
Alignment explanation
Indices: 280715--280773 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 16
280705 TCATATTTAA
280715 AATATTATATAAAATTT
1 AATATTATA-AAAATTT
280732 AATA-TATAAATAATTT
1 AATATTATAAA-AATTT
280748 -ATATTATATAAAATTTT
1 AATATTATA-AAAA-TTT
280765 AATATTATA
1 AATATTATA
280774 TGTTTATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.14
16 15 0.41
17 9 0.24
18 8 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATTATAAAAATTT
Found at i:281478 original size:32 final size:33
Alignment explanation
Indices: 281433--281500 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
281423 AGTGATATAA
* *
281433 ATTAATATTTTAAAATTTATAT-AATATAAATT
1 ATTAATATATTAAAATTTATATAAATATAAAAT
*
281465 ATTAATATATTAAAATTTTTATAAATATAAAAT
1 ATTAATATATTAAAATTTATATAAATATAAAAT
281498 ATT
1 ATT
281501 TTAAATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 20 0.62
33 12 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
ATTAATATATTAAAATTTATATAAATATAAAAT
Found at i:281492 original size:18 final size:18
Alignment explanation
Indices: 281442--281508 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 18
281432 AATTAATATT
*
281442 TTAAAATTTATAT-AATA
1 TTAAAATTTTTATAAATA
* *
281459 -T-AAATTATTA-ATATA
1 TTAAAATTTTTATAAATA
281474 TTAAAATTTTTATAAATA
1 TTAAAATTTTTATAAATA
*
281492 -TAAAATATTT-TAAATA
1 TTAAAATTTTTATAAATA
281508 T
1 T
281509 AATTATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
15 10 0.26
16 8 0.21
17 17 0.44
18 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAAATTTTTATAAATA
Found at i:281507 original size:16 final size:17
Alignment explanation
Indices: 281447--281510 Score: 69
Period size: 16 Copynumber: 3.8 Consensus size: 17
281437 ATATTTTAAA
*
281447 ATTTATATAATATAAATT
1 ATTTATA-AATATAAAAT
* *
281465 ATTAATATAT-TAAAAT
1 ATTTATAAATATAAAAT
*
281481 TTTTATAAATATAAAAT
1 ATTTATAAATATAAAAT
281498 ATTT-TAAATATAA
1 ATTTATAAATATAA
281511 TTATAATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 21 0.55
17 11 0.29
18 6 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTATAAATATAAAAT
Found at i:281534 original size:17 final size:16
Alignment explanation
Indices: 281443--281534 Score: 57
Period size: 16 Copynumber: 5.8 Consensus size: 16
281433 ATTAATATTT
281443 TAAAATT-T-ATATAA
1 TAAAATTATAATATAA
*
281457 TATAAATTATTAATATAT
1 TA-AAATTA-TAATATAA
* *
281475 TAAAATTTTTATA-AA
1 TAAAATTATAATATAA
* **
281490 TATAAAATATTTTA-AA
1 TA-AAATTATAATATAA
*
281506 TATAATTATAATATAA
1 TAAAATTATAATATAA
281522 TAAAATATATAAT
1 TAAAAT-TATAAT
281535 TATTATATAA
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
14 2 0.03
15 15 0.25
16 23 0.39
17 12 0.20
18 7 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATTATAATATAA
Found at i:284132 original size:16 final size:15
Alignment explanation
Indices: 284111--284169 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 15
284101 TTTTTAAATA
284111 TAAATATAATATATAT
1 TAAATATAAT-TATAT
284127 TAAATAT-ATTATAT
1 TAAATATAATTATAT
* * *
284141 TAATTATATTTAAAT
1 TAAATATAATTATAT
*
284156 T-TATATAA-TATAT
1 TAAATATAATTATAT
284169 T
1 T
284170 TATATTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
13 5 0.14
14 15 0.43
15 8 0.23
16 7 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TAAATATAATTATAT
Found at i:284141 original size:14 final size:14
Alignment explanation
Indices: 284111--284150 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
284101 TTTTTAAATA
284111 TAAATATAATATATAT
1 TAAATAT-AT-TATAT
284127 TAAATATATTATAT
1 TAAATATATTATAT
*
284141 TAATTATATT
1 TAAATATATT
284151 TAAATTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 2 0.09
16 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATATATTATAT
Found at i:284229 original size:38 final size:36
Alignment explanation
Indices: 284145--284229 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 36
284135 TTATATTAAT
*
284145 TATATTTAAATTTATATAATATATTTA-TATTTTTTA
1 TATATTTAAA-TTATATAATATATTTATTATTTTATA
*
284181 TATTTATTAAA-TATATAATATCATATTATTATTTTATA
1 TATAT-TTAAATTATATAATAT-AT-TTATTATTTTATA
284219 TCATATTTAAA
1 T-ATATTTAAA
284230 ATCATCTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
35 10 0.24
36 6 0.15
37 8 0.20
38 14 0.34
39 3 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (36 bp):
TATATTTAAATTATATAATATATTTATTATTTTATA
Found at i:284285 original size:26 final size:26
Alignment explanation
Indices: 284249--284301 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
284239 CGTGATTTTA
*
284249 CTAATTGTTCTTACTGATAGAGACTT
1 CTAATTGTTCTTACTGATAAAGACTT
*
284275 CTAATTGTTCTTACTGGTAAAGACTT
1 CTAATTGTTCTTACTGATAAAGACTT
284301 C
1 C
284302 CCACAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (26 bp):
CTAATTGTTCTTACTGATAAAGACTT
Found at i:284486 original size:12 final size:12
Alignment explanation
Indices: 284471--284511 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
284461 ATTACATAAA
284471 TTATATTATTTT
1 TTATATTATTTT
**
284483 TTATATTATAAT
1 TTATATTATTTT
*
284495 TTATTTTATTTT
1 TTATATTATTTT
284507 TTATA
1 TTATA
284512 ATTAAATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATATTATTTT
Found at i:284498 original size:24 final size:25
Alignment explanation
Indices: 284466--284519 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
284456 AAATAATTAC
*
284466 ATAAATTATATTATTTTTTAT-ATT
1 ATAATTTATATTATTTTTTATAATT
*
284490 ATAATTTATTTTATTTTTTATAATT
1 ATAATTTATATTATTTTTTATAATT
284515 A-AATT
1 ATAATT
284520 ATTATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATAATTTATATTATTTTTTATAATT
Found at i:284500 original size:19 final size:19
Alignment explanation
Indices: 284476--284514 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
284466 ATAAATTATA
284476 TTATTTT-TTATATTATAAT
1 TTATTTTATT-TATTATAAT
*
284495 TTATTTTATTTTTTATAAT
1 TTATTTTATTTATTATAAT
284514 T
1 T
284515 AAATTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTTATTTATTATAAT
Found at i:284535 original size:18 final size:18
Alignment explanation
Indices: 284500--284537 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
284490 ATAATTTATT
*
284500 TTATTTTTTATAATTAAA
1 TTATTATTTATAATTAAA
284518 TTATTATTT-TAATATAAA
1 TTATTATTTATAAT-TAAA
284536 TT
1 TT
284538 CAATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATTATTTATAATTAAA
Found at i:285463 original size:15 final size:16
Alignment explanation
Indices: 285445--285482 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
285435 ATTTAATTTT
*
285445 TTTAAA-AATTTTAAG
1 TTTAAATAATTTAAAG
*
285460 TTTAAATTATTTAAAG
1 TTTAAATAATTTAAAG
285476 TTTAAAT
1 TTTAAAT
285483 TTAAATAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
TTTAAATAATTTAAAG
Found at i:285463 original size:24 final size:24
Alignment explanation
Indices: 285429--285488 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
285419 GATTGAATTT
* *
285429 TTTTAAATTTAATTTTTTTAAAAA
1 TTTTAAATTTAAATTATTTAAAAA
*
285453 TTTTAAGTTTAAATTATTT--AAA
1 TTTTAAATTTAAATTATTTAAAAA
*
285475 GTTTAAATTTAAAT
1 TTTTAAATTTAAAT
285489 AAGTTTTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 15 0.48
24 16 0.52
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (24 bp):
TTTTAAATTTAAATTATTTAAAAA
Found at i:285476 original size:16 final size:16
Alignment explanation
Indices: 285452--285483 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
285442 TTTTTTAAAA
*
285452 ATTTTAAGTTTAAATT
1 ATTTAAAGTTTAAATT
285468 ATTTAAAGTTTAAATT
1 ATTTAAAGTTTAAATT
285484 TAAATAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
ATTTAAAGTTTAAATT
Found at i:287199 original size:10 final size:11
Alignment explanation
Indices: 287164--287212 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
287154 TCACTTTTAT
287164 ATTTTATAATAA
1 ATTTT-TAATAA
*
287176 ATTTTTAATTA
1 ATTTTTAATAA
287187 ATTTTT-ATAA
1 ATTTTTAATAA
287197 ATTTATTAATTAA
1 ATTT-TTAA-TAA
287210 ATT
1 ATT
287213 AATATTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 7 0.22
11 13 0.41
12 6 0.19
13 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAA
Found at i:291930 original size:2 final size:2
Alignment explanation
Indices: 291923--291953 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
291913 CTATATCAAA
*
291923 TC TC TC TC TC TC TC TC TC TC GC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
291954 TGGAGTCATT
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:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
TC
Found at i:294504 original size:2 final size:2
Alignment explanation
Indices: 294497--294525 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
294487 AAAATAAGTT
294497 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 T
294526 GGAGAGAGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:296298 original size:2 final size:2
Alignment explanation
Indices: 296291--296324 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
296281 ACAGGTAATC
*
296291 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
296325 GATTGGTTTG
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:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:299681 original size:15 final size:15
Alignment explanation
Indices: 299661--299714 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 15
299651 AAAGTATTAA
*
299661 ATATATGATATAAAT
1 ATATATAATATAAAT
**
299676 ATATATTTTA-AAAT
1 ATATATAATATAAAT
*
299690 TTATATAATATAAAT
1 ATATATAATATAAAT
299705 -TAT-TAATATA
1 ATATATAATATA
299715 TTAAAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 7 0.21
14 14 0.42
15 12 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATATATAATATAAAT
Found at i:299713 original size:18 final size:20
Alignment explanation
Indices: 299692--299735 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
299682 TTTAAAATTT
*
299692 ATATAATATAAATTAT-T-A
1 ATATAATAAAAATTATGTAA
*
299710 ATATATTAAAAATTATGTAA
1 ATATAATAAAAATTATGTAA
299730 ATATAA
1 ATATAA
299736 AATACTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 14 0.67
19 1 0.05
20 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATATAATAAAAATTATGTAA
Found at i:302641 original size:12 final size:12
Alignment explanation
Indices: 302621--302700 Score: 83
Period size: 12 Copynumber: 6.8 Consensus size: 12
302611 GTTTAACTCT
*
302621 TTATCACCACCA
1 TTATTACCACCA
302633 TTATTACCATCCA
1 TTATTACCA-CCA
* *
302646 -AATTACCACCC
1 TTATTACCACCA
*
302657 TTATTATCACCA
1 TTATTACCACCA
* *
302669 TCATTATCACCA
1 TTATTACCACCA
302681 -TATTACCACCA
1 TTATTACCACCA
302692 TTATTACCA
1 TTATTACCA
302701 TCCACATTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
11 11 0.20
12 42 0.75
13 3 0.05
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.33
Consensus pattern (12 bp):
TTATTACCACCA
Found at i:302730 original size:59 final size:59
Alignment explanation
Indices: 302626--302737 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
302616 ACTCTTTATC
**
302626 ACCACCATTATTACCATCCAAATTACCACCCTTATTATCACCATCATTATCACCATATT
1 ACCACCATTATTACCATCCAAATTACCACCCACATTATCACCATCATTATCACCATATT
* ** *
302685 ACCACCATTATTACCATCCACATTATGACCCACATT-TCCAGCATCATTATCAC
1 ACCACCATTATTACCATCCAAATTACCACCCACATTAT-CACCATCATTATCAC
302738 ATTCATTACC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 1 0.02
59 45 0.98
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.30
Consensus pattern (59 bp):
ACCACCATTATTACCATCCAAATTACCACCCACATTATCACCATCATTATCACCATATT
Found at i:303138 original size:13 final size:13
Alignment explanation
Indices: 303120--303146 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
303110 ATTTTGGAAC
303120 TGTGAATAAAGGT
1 TGTGAATAAAGGT
303133 TGTGAATAAAGGT
1 TGTGAATAAAGGT
303146 T
1 T
303147 CCTTATGATG
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:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (13 bp):
TGTGAATAAAGGT
Found at i:304808 original size:16 final size:16
Alignment explanation
Indices: 304786--304831 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 16
304776 GTATTTTTAA
304786 ATTTTTATAATTAAAT
1 ATTTTTATAATTAAAT
*
304802 -TTTTT-TAA-AAAAT
1 ATTTTTATAATTAAAT
*
304815 ATTTTTATTATTAAAT
1 ATTTTTATAATTAAAT
304831 A
1 A
304832 GTAATTTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
13 4 0.17
14 8 0.33
15 7 0.29
16 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTTATAATTAAAT
Found at i:307260 original size:13 final size:14
Alignment explanation
Indices: 307242--307274 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
307232 ATTAATTAAA
*
307242 TTAAATTTTAA-GT
1 TTAAATTTAAATGT
307255 TTAAATTTAAATGT
1 TTAAATTTAAATGT
307269 TTAAAT
1 TTAAAT
307275 GGCTACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TTAAATTTAAATGT
Found at i:307349 original size:2 final size:2
Alignment explanation
Indices: 307342--307373 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
307332 CTCTTCTTTC
307342 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
307374 TGAGTTTTAA
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:307649 original size:16 final size:18
Alignment explanation
Indices: 307628--307662 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
307618 TATATTATCT
307628 TAAATAATA-A-ATTTTA
1 TAAATAATATATATTTTA
307644 TAAATAATATATATTTTA
1 TAAATAATATATATTTTA
307662 T
1 T
307663 TTATTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATAATATATATTTTA
Found at i:307952 original size:32 final size:32
Alignment explanation
Indices: 307916--307997 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
307906 AAAAAAAATT
*
307916 AATAATTTAAATTTGATTAAT-TTAAAATTTAA
1 AATAATTTAAATTTGA-AAATATTAAAATTTAA
** *
307948 AATAATTTGTATTT-AAAATGATTCAAATTTAA
1 AATAATTTAAATTTGAAAAT-ATTAAAATTTAA
*
307980 AATGATTTAAATTTGAAA
1 AATAATTTAAATTTGAAA
307998 TGACTTAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 3 0.08
31 1 0.03
32 33 0.82
33 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (32 bp):
AATAATTTAAATTTGAAAATATTAAAATTTAA
Found at i:307977 original size:16 final size:16
Alignment explanation
Indices: 307958--308000 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
307948 AATAATTTGT
307958 ATTTAAAATGATTCAA
1 ATTTAAAATGATTCAA
*
307974 ATTTAAAATGATTTAA
1 ATTTAAAATGATTCAA
*
307990 ATTTGAAATGA
1 ATTTAAAATGA
308001 CTTAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (16 bp):
ATTTAAAATGATTCAA
Found at i:308005 original size:16 final size:15
Alignment explanation
Indices: 307958--308005 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 15
307948 AATAATTTGT
307958 ATTTAAAATGATTCAA
1 ATTTAAAATGATT-AA
307974 ATTTAAAATGATTTAA
1 ATTTAAAATGA-TTAA
*
307990 ATTTGAAATGACTTAA
1 ATTTAAAATGA-TTAA
308006 TAATTAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 27 0.93
17 2 0.07
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (15 bp):
ATTTAAAATGATTAA
Found at i:309369 original size:7 final size:7
Alignment explanation
Indices: 309359--309389 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
309349 AAAAAATAAA
309359 AAATTTT
1 AAATTTT
*
309366 AAATATT
1 AAATTTT
309373 AAATTTT
1 AAATTTT
309380 AAATTTT
1 AAATTTT
309387 AAA
1 AAA
309390 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
AAATTTT
Found at i:309452 original size:13 final size:14
Alignment explanation
Indices: 309434--309466 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
309424 ATTAATTAAA
*
309434 TTAAATTTTAA-GT
1 TTAAATTTAAATGT
309447 TTAAATTTAAATGT
1 TTAAATTTAAATGT
309461 TTAAAT
1 TTAAAT
309467 GGCTACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TTAAATTTAAATGT
Found at i:309616 original size:13 final size:13
Alignment explanation
Indices: 309598--309624 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
309588 ATTTATAATA
309598 ACACAAATAATTT
1 ACACAAATAATTT
309611 ACACAAATAATTT
1 ACACAAATAATTT
309624 A
1 A
309625 ATTGCATCGA
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:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
ACACAAATAATTT
Found at i:309830 original size:14 final size:13
Alignment explanation
Indices: 309808--309838 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
309798 CAACTTAAAT
*
309808 AATAAATTTTATA
1 AATAAAATTTATA
309821 AATAAAATTTATA
1 AATAAAATTTATA
309834 AATAA
1 AATAA
309839 TATATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATAAAATTTATA
Found at i:311480 original size:19 final size:19
Alignment explanation
Indices: 311456--311513 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
311446 TTAGTTTTAA
311456 ATATATTTAATTTATTTTT
1 ATATATTTAATTTATTTTT
* *
311475 ATATA-TGATTTTAATTTTTT
1 ATATATTTAATTT-A-TTTTT
311495 ATATAATTTATATTTATTT
1 ATAT-ATTTA-ATTTATTT
311514 AATTTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
18 5 0.17
19 6 0.20
20 9 0.30
21 4 0.13
22 3 0.10
23 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
ATATATTTAATTTATTTTT
Found at i:311492 original size:18 final size:18
Alignment explanation
Indices: 311457--311503 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
311447 TAGTTTTAAA
* *
311457 TATATTTAA-TTTATTTT
1 TATATATAATTTTAATTT
*
311474 TATATATGATTTTAATTT
1 TATATATAATTTTAATTT
*
311492 TTTATATAATTT
1 TATATATAATTT
311504 ATATTTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TATATATAATTTTAATTT
Found at i:311505 original size:29 final size:27
Alignment explanation
Indices: 311472--311525 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 27
311462 TTAATTTATT
311472 TTTATATATGATTTTAATTTTTTATATAA
1 TTTATAT-TGA-TTTAATTTTTTATATAA
*
311501 TTTATATTTATTTAATTTTTTATAT
1 TTTATATTGATTTAATTTTTTATAT
311526 TTTATGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 15 0.62
28 2 0.08
29 7 0.29
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTATATTGATTTAATTTTTTATATAA
Found at i:311509 original size:18 final size:18
Alignment explanation
Indices: 311463--311528 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
311453 TAAATATATT
*
311463 TAATTTAT-TTTTATATA
1 TAATTTATATTTTTTATA
*
311480 TGATTT-TAATTTTTTATA
1 TAATTTAT-ATTTTTTATA
311498 TAATTTATATTTATTTA-A
1 TAATTTATATTT-TTTATA
**
311516 TTTTTTATATTTT
1 TAATTTATATTTT
311529 ATGTTTTACA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
16 1 0.03
17 6 0.15
18 28 0.70
19 5 0.12
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TAATTTATATTTTTTATA
Found at i:311605 original size:17 final size:17
Alignment explanation
Indices: 311583--311635 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
311573 TGATATTTTT
311583 AATTAATATAAATATTA
1 AATTAATATAAATATTA
* *
311600 AATTAATTTAAAATTTTA
1 AATTAATAT-AAATATTA
**
311618 TGTATAATATAAATATTA
1 AAT-TAATATAAATATTA
311636 TTATATTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 8 0.29
18 15 0.54
19 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
AATTAATATAAATATTA
Found at i:311653 original size:16 final size:15
Alignment explanation
Indices: 311632--311680 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
311622 TAATATAAAT
311632 ATTATTATATTATTAA
1 ATTATTA-ATTATTAA
311648 ATTATTAATTTATTAA
1 ATTATTAA-TTATTAA
* *
311664 AATATTAATTATAAA
1 ATTATTAATTATTAA
311679 AT
1 AT
311681 AAAATATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATTAATTATTAA
Found at i:311661 original size:19 final size:18
Alignment explanation
Indices: 311581--311676 Score: 73
Period size: 17 Copynumber: 5.5 Consensus size: 18
311571 AGTGATATTT
311581 TTAATTA-A-TATAAATA
1 TTAATTATATTATAAATA
311597 TTAAATTA-ATT-TAAA-A
1 TT-AATTATATTATAAATA
* *
311613 TTTTATGTATAATATAAATA
1 -TTAAT-TATATTATAAATA
311633 TT-ATTATATTATTAAATTA
1 TTAATTATATTA-TAAA-TA
311652 TTAATT-TATTA-AAATA
1 TTAATTATATTATAAATA
311668 TTAATTATA
1 TTAATTATA
311677 AAATAAAATA
Statistics
Matches: 66, Mismatches: 3, Indels: 21
0.73 0.03 0.23
Matches are distributed among these distances:
16 13 0.20
17 25 0.38
18 9 0.14
19 15 0.23
20 4 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (18 bp):
TTAATTATATTATAAATA
Found at i:312127 original size:16 final size:18
Alignment explanation
Indices: 312093--312135 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
312083 ATTTAAAATT
*
312093 TAAATTT-TTTTAATTTA
1 TAAATTTATTTTAATATA
312110 T-AATTTATTTT-ATATA
1 TAAATTTATTTTAATATA
312126 TAAATTTATT
1 TAAATTTATT
312136 AAAAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TAAATTTATTTTAATATA
Found at i:312633 original size:27 final size:28
Alignment explanation
Indices: 312601--312671 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
312591 GCCACCCATT
*
312601 TGTTTGTAAAAAATGGTGGTTAT-TTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTG
*
312628 TGTTTGTCAAAAATGGTGGTTTTCTTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTG
* *
312656 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
312672 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (28 bp):
TGTTTGTCAAAAATGGTGGTTATCTTTG
Found at i:315274 original size:21 final size:22
Alignment explanation
Indices: 315245--315290 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
315235 TGTTCAGACA
* *
315245 AGTAGTACTCCACAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
315267 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
315288 AGT
1 AGT
315291 TTTAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:317228 original size:28 final size:27
Alignment explanation
Indices: 317173--317243 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
317163 GCCACCCATT
317173 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
317200 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
317228 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
317244 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:317345 original size:20 final size:20
Alignment explanation
Indices: 317320--317368 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
317310 AAATAGAGGC
317320 TCCCTCTTCCCTCTCAAGCA
1 TCCCTCTTCCCTCTCAAGCA
* ** *
317340 TCCCTCATCCCTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGCA
317360 TCCCTCTTC
1 TCCCTCTTC
317369 AATTCTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.49, G:0.04, T:0.37
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGCA
Found at i:317968 original size:34 final size:33
Alignment explanation
Indices: 317924--318005 Score: 87
Period size: 34 Copynumber: 2.5 Consensus size: 33
317914 TATTAATTTG
* *
317924 ATTTGAATTTAAAAAATTT-ATTTAATATATTAAA
1 ATTTAAATTTAAAAAATTTAATTTAAT-CA-TAAA
*
317958 ATTTAAATTTAATATAATTTAATTTAATCATAAA
1 ATTTAAATTTAA-AAAATTTAATTTAATCATAAA
*
317992 ATTTCAA-TTAAAAA
1 ATTTAAATTTAAAAA
318006 TCATTTAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
32 2 0.05
33 4 0.10
34 21 0.51
35 7 0.17
36 7 0.17
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (33 bp):
ATTTAAATTTAAAAAATTTAATTTAATCATAAA
Found at i:317978 original size:16 final size:16
Alignment explanation
Indices: 317957--317990 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
317947 AATATATTAA
317957 AATTTAAATTTAAT-AT
1 AATTT-AATTTAATCAT
317973 AATTTAATTTAATCAT
1 AATTTAATTTAATCAT
317989 AA
1 AA
317991 AATTTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAATTTAATCAT
Found at i:317984 original size:21 final size:21
Alignment explanation
Indices: 317936--317973 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
317926 TTGAATTTAA
317936 AAAATTT--ATTTAATATATT
1 AAAATTTAAATTTAATATATT
317955 AAAATTTAAATTTAATATA
1 AAAATTTAAATTTAATATA
317974 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATTTAAATTTAATATATT
Found at i:318493 original size:16 final size:16
Alignment explanation
Indices: 318432--318495 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
318422 ACTTGAAACG
*
318432 AATTTAAAATTT-TTAA
1 AATTT-AAATTTATTTA
*
318448 AATTTAAA-TTATTTT
1 AATTTAAATTTATTTA
**
318463 AATTTAAATAAATTTA
1 AATTTAAATTTATTTA
318479 AATTTAAATTTATTTA
1 AATTTAAATTTATTTA
318495 A
1 A
318496 TTCATCCATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 2 0.05
15 13 0.33
16 24 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTAAATTTATTTA
Found at i:318718 original size:8 final size:8
Alignment explanation
Indices: 318705--318800 Score: 53
Period size: 8 Copynumber: 12.5 Consensus size: 8
318695 TTAAAATATA
318705 ATATAAAT
1 ATATAAAT
318713 ATATAAAT
1 ATATAAAT
*
318721 ATTTTAAAAT
1 A-TAT-AAAT
*
318731 TTATAAA-
1 ATATAAAT
318738 ATATAAAT
1 ATATAAAT
*
318746 -TATTAAT
1 ATATAAAT
318753 ATATTAAA-
1 ATA-TAAAT
*
318761 A-A-ATAT
1 ATATAAAT
* *
318767 ATTTTAA-
1 ATATAAAT
*
318774 ATATAATT
1 ATATAAAT
318782 ATA-AAAT
1 ATATAAAT
318789 ATATAAAT
1 ATATAAAT
318797 ATAT
1 ATAT
318801 GTTGTTTTCG
Statistics
Matches: 64, Mismatches: 14, Indels: 20
0.65 0.14 0.20
Matches are distributed among these distances:
5 2 0.03
6 1 0.02
7 23 0.36
8 27 0.42
9 7 0.11
10 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAAAT
Found at i:318729 original size:38 final size:37
Alignment explanation
Indices: 318664--318798 Score: 93
Period size: 40 Copynumber: 3.5 Consensus size: 37
318654 AATAGTATTA
*
318664 AATATAATTATATAAAT-TTAACATAAAATAATTAAAATAT
1 AATATAAATATATAAATATT---ATAAAATAATT-AAATAT
* *
318704 AATATAAATATATAAATATTTTAAAAT--TT--ATAA
1 AATATAAATATATAAATATTATAAAATAATTAAATAT
*
318737 AATATAAAT-TATTAATATATTAAAAAATATATTTTAAATAT
1 AATATAAATATA-TAA-ATATTATAAAATA-A--TTAAATAT
318778 AATTATAAAATATATAAATAT
1 AA-TAT-AAATATATAAATAT
318799 ATGTTGTTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 24
0.72 0.06 0.23
Matches are distributed among these distances:
32 2 0.03
33 15 0.20
34 10 0.13
36 2 0.03
38 6 0.08
39 2 0.03
40 16 0.21
41 7 0.09
42 7 0.09
43 7 0.09
44 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (37 bp):
AATATAAATATATAAATATTATAAAATAATTAAATAT
Found at i:318744 original size:25 final size:26
Alignment explanation
Indices: 318695--318791 Score: 89
Period size: 24 Copynumber: 3.8 Consensus size: 26
318685 CATAAAATAA
318695 TTAAAATATAATATAAATATATAAATATT
1 TTAAAATAT--TATAAA-ATATAAATATT
*
318724 TTAAAAT-TTATAAAATATAAAT-TA
1 TTAAAATATTATAAAATATAAATATT
*
318748 TTAATATATTA-AAAA-AT--ATATT
1 TTAAAATATTATAAAATATAAATATT
318770 TTAAATATAATTATAAAATATA
1 TTAAA-AT-ATTATAAAATATA
318792 TAAATATATG
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
21 2 0.04
22 5 0.09
23 4 0.07
24 15 0.26
25 15 0.26
26 8 0.14
28 1 0.02
29 7 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TTAAAATATTATAAAATATAAATATT
Found at i:318775 original size:11 final size:11
Alignment explanation
Indices: 318689--318800 Score: 66
Period size: 9 Copynumber: 10.7 Consensus size: 11
318679 ATTTAACATA
318689 AAATA-ATTA-
1 AAATATATTAT
*
318698 AAATATAATAT
1 AAATATATTAT
318709 -AA-ATA-TAT
1 AAATATATTAT
318717 AAATAT-TT-T
1 AAATATATTAT
318726 AAA-AT-TTAT
1 AAATATATTAT
318735 AAAATATAAATTAT
1 -AAATAT--ATTAT
* *
318749 TAATATATTAAA
1 AAATATATT-AT
*
318761 AAATATATTTT
1 AAATATATTAT
318772 AAATATAATTAT
1 AAATAT-ATTAT
318784 AAA-ATA-TAT
1 AAATATATTAT
318793 AAATATAT
1 AAATATAT
318801 GTTGTTTTCG
Statistics
Matches: 81, Mismatches: 7, Indels: 28
0.70 0.06 0.24
Matches are distributed among these distances:
8 7 0.09
9 21 0.26
10 15 0.19
11 13 0.16
12 16 0.20
13 5 0.06
14 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAATATATTAT
Found at i:319669 original size:14 final size:12
Alignment explanation
Indices: 319634--319682 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
319624 AGAGATATTT
319634 TATATATTTAAA
1 TATATATTTAAA
*
319646 -AAAT-TTTAAAA
1 TATATATTT-AAA
319657 TATTATATTTAAA
1 TA-TATATTTAAA
319670 TATATA-TTAAA
1 TATATATTTAAA
319681 TA
1 TA
319683 AAAATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 3 0.10
11 13 0.42
12 5 0.16
13 7 0.23
14 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATATTTAAA
Found at i:320788 original size:20 final size:20
Alignment explanation
Indices: 320756--320794 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
320746 TATGCATATC
320756 ATATCATTAATTATATTTAA
1 ATATCATTAATTATATTTAA
320776 ATAT-ATTATATTATATTTA
1 ATATCATTA-ATTATATTTA
320795 TTATGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATCATTAATTATATTTAA
Found at i:321022 original size:2 final size:2
Alignment explanation
Indices: 321015--321043 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
321005 ATGATGCTAT
321015 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 T
321044 GAATAATTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:321092 original size:15 final size:14
Alignment explanation
Indices: 321060--321098 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
321050 TTATTTGATA
321060 ATAAAATAAAAATAT
1 ATAAAAT-AAAATAT
*
321075 ATATAAATAAAATTT
1 ATA-AAATAAAATAT
321090 ATAAAATAA
1 ATAAAATAA
321099 TACATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 12 0.55
16 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAAATAAAATAT
Found at i:322085 original size:15 final size:16
Alignment explanation
Indices: 322067--322097 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
322057 TTATTTTAAT
322067 AATTTATAT-TATATA
1 AATTTATATATATATA
322082 AATTTATATATATATA
1 AATTTATATATATATA
322098 TATATATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTATATATATATA
Found at i:322177 original size:17 final size:17
Alignment explanation
Indices: 322145--322178 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
322135 ATATTTTATT
322145 TATTTATTTAATAATTA
1 TATTTATTTAATAATTA
322162 TATTATATTTAA-AATTA
1 TATT-TATTTAATAATTA
322179 CTGTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTATTTAATAATTA
Found at i:322754 original size:52 final size:50
Alignment explanation
Indices: 322700--322797 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
322690 GTATTTTTAA
* *
322700 TTTTTTACAAATATATAATTTAAAAAGTTAAATATTTATAAATTACAATAAAT
1 TTTTTTACAAATATATAA-TTAAAAAG--AAATATTTAAAAATCACAATAAAT
* * *
322753 TTTTTTATAATTTTATAATTAAAAAGAAATATTTAAAAATCACAA
1 TTTTTTACAAATATATAATTAAAAAGAAATATTTAAAAATCACAA
322798 CTATGCATGC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
50 17 0.43
52 8 0.20
53 15 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (50 bp):
TTTTTTACAAATATATAATTAAAAAGAAATATTTAAAAATCACAATAAAT
Found at i:323503 original size:19 final size:19
Alignment explanation
Indices: 323479--323515 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
323469 GTAAAAATCG
323479 ATTAAATTT-GATTTAATTA
1 ATTAAATTTAG-TTTAATTA
323498 ATTAAATTTAGTTTAATT
1 ATTAAATTTAGTTTAATT
323516 GATTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
ATTAAATTTAGTTTAATTA
Found at i:323531 original size:14 final size:14
Alignment explanation
Indices: 323483--323536 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
323473 AAATCGATTA
323483 AATTTGATTTAATT
1 AATTTGATTTAATT
** *
323497 AATTAAATTTAGTTT
1 AATTTGATTTA-ATT
323512 AA-TTGATTTAATT
1 AATTTGATTTAATT
323525 AATTTGATTTAA
1 AATTTGATTTAA
323537 ATTTTAATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 4 0.12
14 24 0.75
15 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (14 bp):
AATTTGATTTAATT
Found at i:324762 original size:29 final size:29
Alignment explanation
Indices: 324701--324764 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
324691 TTGAGGGTTC
* * *
324701 AATTGAGTGAAAGTAAATATTTAAAGTTA
1 AATTGAATGAAAATAAATATTTAAACTTA
324730 AATTGAATGAAAATAAATATTTAAGACTT-
1 AATTGAATGAAAATAAATATTTAA-ACTTA
324759 AATTGA
1 AATTGA
324765 TAATGATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (29 bp):
AATTGAATGAAAATAAATATTTAAACTTA
Found at i:331015 original size:2 final size:2
Alignment explanation
Indices: 331008--331036 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
330998 GAACTCTTTA
331008 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
331037 AGAAAAGATG
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:331672 original size:17 final size:17
Alignment explanation
Indices: 331652--331693 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
331642 TTGTACTCAA
331652 TTAAGATTAAAA-TTAAT
1 TTAA-ATTAAAATTTAAT
*
331669 TTAATTTAAAATTTAAT
1 TTAAATTAAAATTTAAT
331686 TT-AATTAA
1 TTAAATTAA
331694 TTGATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
TTAAATTAAAATTTAAT
Found at i:331693 original size:16 final size:15
Alignment explanation
Indices: 331657--331693 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
331647 CTCAATTAAG
331657 ATTAAAATTAATTTA
1 ATTAAAATTAATTTA
331672 ATTTAAAATTTAATTTA
1 A-TTAAAA-TTAATTTA
331689 ATTAA
1 ATTAA
331694 TTGATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 10 0.50
17 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAAAATTAATTTA
Found at i:332266 original size:20 final size:20
Alignment explanation
Indices: 332238--332276 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
332228 TAATAAAAAA
*
332238 TTTTAAAAAATTCTTTTTAT
1 TTTTAAAAAATTATTTTTAT
*
332258 TTTTTAAAAATTATTTTTA
1 TTTTAAAAAATTATTTTTA
332277 ATGTGAGATG
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:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAAAAAATTATTTTTAT
Found at i:332388 original size:16 final size:17
Alignment explanation
Indices: 332349--332390 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
332339 TATTTTTATT
*
332349 AATTATTTATTATATAA
1 AATTATTTAATATATAA
332366 AATTTATTTAATAT-TAA
1 AA-TTATTTAATATATAA
332383 AATTATTT
1 AATTATTT
332391 TAAAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 7 0.30
18 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTATTTAATATATAA
Found at i:332392 original size:17 final size:18
Alignment explanation
Indices: 332349--332393 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
332339 TATTTTTATT
*
332349 AATTA-TTTATTATATAA
1 AATTATTTTAATATATAA
332366 AATT-TATTTAATAT-TAA
1 AATTAT-TTTAATATATAA
332383 AATTATTTTAA
1 AATTATTTTAA
332394 AAATATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTATTTTAATATATAA
Found at i:332754 original size:2 final size:2
Alignment explanation
Indices: 332747--332777 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
332737 CAAAGTTTGA
332747 AT AT AT AT 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
332778 GTATGTATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:335364 original size:3 final size:3
Alignment explanation
Indices: 335356--335389 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
335346 AAGGAAATGG
335356 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
335390 TTGTGTTTTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:335937 original size:14 final size:15
Alignment explanation
Indices: 335888--335944 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
335878 ATTAATTAGT
335888 TTTAATATTTATAA-TA
1 TTTAA-ATTTA-AATTA
*
335904 TTTTAATTTAAATTA
1 TTTAAATTTAAATTA
*
335919 TTTAAATTTAATTTA
1 TTTAAATTTAAATTA
*
335934 -TTAATTTTAAA
1 TTTAAATTTAAA
335945 ATTAAATCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 11 0.31
15 20 0.57
16 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATTTAAATTA
Found at i:336757 original size:36 final size:38
Alignment explanation
Indices: 336687--336760 Score: 107
Period size: 36 Copynumber: 2.0 Consensus size: 38
336677 CTTAAGTATG
* *
336687 AATTAAAAATTATTATATTTATTTTAATACATATTAAA
1 AATTAAAAAATATTATATTTATTTAAATACATATTAAA
*
336725 AATTAAAAAAT-TTAT-TTTATTTAAATATATATTAAA
1 AATTAAAAAATATTATATTTATTTAAATACATATTAAA
336761 TATTTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 19 0.58
37 4 0.12
38 10 0.30
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (38 bp):
AATTAAAAAATATTATATTTATTTAAATACATATTAAA
Found at i:336761 original size:11 final size:12
Alignment explanation
Indices: 336742--336776 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
336732 AAATTTATTT
336742 TATTTAAATATA
1 TATTTAAATATA
*
336754 TA-TTAAATATT
1 TATTTAAATATA
336765 TATTTAAATATA
1 TATTTAAATATA
336777 ATAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATTTAAATATA
Found at i:336771 original size:12 final size:12
Alignment explanation
Indices: 336740--336775 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
336730 AAAAATTTAT
336740 TTTATTTAAATA
1 TTTATTTAAATA
*
336752 TATA-TTAAATA
1 TTTATTTAAATA
336763 TTTATTTAAATA
1 TTTATTTAAATA
336775 T
1 T
336776 AATAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTATTTAAATA
Found at i:336786 original size:23 final size:23
Alignment explanation
Indices: 336740--336782 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
336730 AAAAATTTAT
*
336740 TTTATTTAAATATATATTAAATA
1 TTTATTTAAATATATATAAAATA
336763 TTTATTTAAATATA-ATAAAA
1 TTTATTTAAATATATATAAAA
336783 ATATAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATTTAAATATATATAAAATA
Found at i:336801 original size:17 final size:18
Alignment explanation
Indices: 336769--336807 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
336759 AATATTTATT
336769 TAAATATAATAAAAAT-A
1 TAAATATAATAAAAATAA
336786 TAAATATTAAT-AAAATAA
1 TAAATA-TAATAAAAATAA
336804 TAAA
1 TAAA
336808 ATTTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAATATAATAAAAATAA
Found at i:337016 original size:21 final size:22
Alignment explanation
Indices: 336989--337037 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
336979 TTATTTTTTT
*
336989 AATAAAAATTAT-AAT-TTAAA
1 AATAAAAAATATAAATATTAAA
337009 AATAAAAAATATAAATATTAAA
1 AATAAAAAATATAAATATTAAA
*
337031 ATTAAAA
1 AATAAAA
337038 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.44
21 3 0.12
22 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAAAAAATATAAATATTAAA
Found at i:337276 original size:13 final size:13
Alignment explanation
Indices: 337254--337283 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
337244 TGTTTGTTTG
337254 TTTT-TTTCTTTT
1 TTTTATTTCTTTT
337266 TTTTATTTCTTTT
1 TTTTATTTCTTTT
337279 TTTTA
1 TTTTA
337284 ATCATGGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTATTTCTTTT
Found at i:339790 original size:3 final size:3
Alignment explanation
Indices: 339782--339817 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
339772 CAAGGAACAA
339782 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
339818 GGTATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:340801 original size:16 final size:17
Alignment explanation
Indices: 340773--340807 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
340763 CAAAGTGCAC
*
340773 ATTTTACAATTTTTTTA
1 ATTTTACAATTTTTGTA
340790 ATTTTA-AATTTTTGTA
1 ATTTTACAATTTTTGTA
340806 AT
1 AT
340808 CTTATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTACAATTTTTGTA
Found at i:341388 original size:23 final size:20
Alignment explanation
Indices: 341338--341392 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 20
341328 TTTTAATTTT
341338 TTTTA-AATTTATTAAAAAA
1 TTTTATAATTTATTAAAAAA
341357 TTTAATATAATTATATTAAATAAA
1 TTT--TATAATT-TATTAAA-AAA
341381 TATTTAT-ATTTA
1 T-TTTATAATTTA
341393 ATATCCATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
19 3 0.10
21 4 0.13
22 7 0.23
23 10 0.33
24 4 0.13
25 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTATAATTTATTAAAAAA
Found at i:341747 original size:13 final size:13
Alignment explanation
Indices: 341731--341756 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
341721 GTGTTAAATA
341731 TATATTTATATTT
1 TATATTTATATTT
341744 TATATTTATATTT
1 TATATTTATATTT
341757 AAATCTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATATTTATATTT
Found at i:342284 original size:29 final size:30
Alignment explanation
Indices: 342244--342302 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
342234 TTTATATTGA
342244 TTTTATATTTAAAAATATA-TCAATTAGAT
1 TTTTATATTTAAAAATATATTCAATTAGAT
* * *
342273 TTTTA-ATCTTAACATTTTATTCAATTAGAT
1 TTTTATAT-TTAAAAATATATTCAATTAGAT
342303 CCTTCAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 2 0.08
29 13 0.52
30 10 0.40
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (30 bp):
TTTTATATTTAAAAATATATTCAATTAGAT
Found at i:343193 original size:23 final size:22
Alignment explanation
Indices: 343158--343201 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
343148 CTTTTTTAAA
343158 TTTTTTAAATTTATT-ATTTAT
1 TTTTTTAAATTTATTGATTTAT
343179 TTTTTTAAAATTTTATTGATTTA
1 TTTTTT-AAA-TTTATTGATTTA
343202 AGGATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 3 0.15
23 6 0.30
24 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTTAAATTTATTGATTTAT
Found at i:344715 original size:69 final size:69
Alignment explanation
Indices: 344634--344762 Score: 195
Period size: 69 Copynumber: 1.9 Consensus size: 69
344624 TATGACCATT
* ***
344634 AATTTATGCATTTTACAATAAATTTATAATAGATTCAAATCCATTATCTACAAAATTAATATGAA
1 AATTTATACATTTTACAATAAAAAGATAATAGATTCAAATCCATTATCTACAAAATTAATATGAA
344699 ATTG
66 ATTG
** *
344703 AATTTATACATTTTACAATAAAAAGATAATAGATTTGAATTCATTATCTACAAAATTAAT
1 AATTTATACATTTTACAATAAAAAGATAATAGATTCAAATCCATTATCTACAAAATTAAT
344763 GTAAATTTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (69 bp):
AATTTATACATTTTACAATAAAAAGATAATAGATTCAAATCCATTATCTACAAAATTAATATGAA
ATTG
Found at i:345378 original size:151 final size:150
Alignment explanation
Indices: 345178--345460 Score: 406
Period size: 151 Copynumber: 1.9 Consensus size: 150
345168 GCTATACAAG
* *
345178 TATTTATTTTATACAAATATATTTAAATTTTTTTAAAATTTTAATATATTTAAAA-GACCTTTAA
1 TATTTATTTGACACAAATATATTTAAATTTTTTTAAAATTTTAATATATTTAAAATG-CCTTTAA
* * *
345242 ATACTCATATCTTAATATTTATATTCGAATATACATCAAATACGAATATAAAATATAAATATTTA
65 AAACTCATATCTTAAAATTTATATTCGAATATACATCAAATACGAATATAAAATATAAATACTTA
345307 AAAAAAATCAAAATATATAGA
130 AAAAAAATCAAAATATATAGA
* ** *
345328 TATTTATTTGACATAAATATATTTATTTTTTTTTTAAGATTTTAATATATTTAAAATGCCTTTAA
1 TATTTATTTGACACAAATATATTTA-AATTTTTTTAAAATTTTAATATATTTAAAATGCCTTTAA
* * * * * *
345393 AAACTCATATTTTAAAATTTATATTCGAATATTCATCGAATATGAGTGTAAAATATAAATACTTA
65 AAACTCATATCTTAAAATTTATATTCGAATATACATCAAATACGAATATAAAATATAAATACTTA
345458 AAA
130 AAA
345461 GAACCAGCCA
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
150 22 0.19
151 93 0.80
152 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (150 bp):
TATTTATTTGACACAAATATATTTAAATTTTTTTAAAATTTTAATATATTTAAAATGCCTTTAAA
AACTCATATCTTAAAATTTATATTCGAATATACATCAAATACGAATATAAAATATAAATACTTAA
AAAAAATCAAAATATATAGA
Found at i:345668 original size:2 final size:2
Alignment explanation
Indices: 345661--345688 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
345651 ATATTACAAA
345661 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
345689 GTTTTTGCAG
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:351896 original size:19 final size:17
Alignment explanation
Indices: 351852--351899 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
351842 AAAATTAATT
351852 AAAATAAAA-AAGAAAA
1 AAAATAAAATAAGAAAA
*
351868 AATATGAAAATAAGGAAAA
1 AAAAT-AAAATAA-GAAAA
351887 ATAAATAAAATAA
1 A-AAATAAAATAA
351900 AAGTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 4 0.15
18 2 0.08
19 13 0.50
20 3 0.12
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (17 bp):
AAAATAAAATAAGAAAA
Found at i:352803 original size:13 final size:13
Alignment explanation
Indices: 352782--352935 Score: 60
Period size: 13 Copynumber: 11.9 Consensus size: 13
352772 ATTAATGTAT
352782 TTATATTATATTAA
1 TTATATTATA-TAA
352796 TT-TATTATATAA
1 TTATATTATATAA
352808 TTATATT-TA-AA
1 TTATATTATATAA
* *
352819 GTAT-TT-TATAT
1 TTATATTATATAA
* *
352830 TTATATAAATTTTAA
1 TTATAT-TA-TATAA
352845 -TATATTA-ATAA
1 TTATATTATATAA
352856 TTTATATTATATAAA
1 -TTATATTATAT-AA
* **
352871 TTTTAAAATATACA
1 TTATATTATATA-A
352885 -TATATTCATATAA
1 TTATATT-ATATAA
* *
352898 -TATTTTAATTATAT
1 TTATATT-A-TATAA
352912 TTATATTATAT--
1 TTATATTATATAA
352923 TTATATATATATA
1 TTATAT-TATATA
352936 TATATGTCTA
Statistics
Matches: 106, Mismatches: 18, Indels: 33
0.68 0.11 0.21
Matches are distributed among these distances:
10 4 0.04
11 18 0.17
12 13 0.12
13 33 0.31
14 28 0.26
15 10 0.09
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (13 bp):
TTATATTATATAA
Found at i:352823 original size:22 final size:21
Alignment explanation
Indices: 352773--352835 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
352763 CACTTGATAA
352773 TTAATGTATTTAT-ATTATA-
1 TTAATGTATTTATAATTATAT
*
352792 TTAATTTATTATATAATTATAT
1 TTAATGTATT-TATAATTATAT
* *
352814 TTAAAGTATTTTATATTTATAT
1 TTAATGTA-TTTATAATTATAT
352836 AAATTTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 9 0.25
20 3 0.08
21 6 0.17
22 16 0.44
23 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (21 bp):
TTAATGTATTTATAATTATAT
Found at i:352843 original size:27 final size:27
Alignment explanation
Indices: 352813--352922 Score: 82
Period size: 28 Copynumber: 3.9 Consensus size: 27
352803 TATAATTATA
352813 TTTAAAGTAT-TTTATATTTATATAAAT
1 TTTAAA-TATATTTATATTTATATAAAT
352840 TTT-AATATATTAATAATTTATATTATATAAAT
1 TTTAAATATATT--T-A--TAT-TTATATAAAT
** *
352872 TTTAAAATATACATATATTCATATAATAT
1 TTT-AAATATATTTATATTTATATAA-AT
*
352901 TTTAATTATATTTATA-TTATAT
1 TTTAAATATATTTATATTTATAT
352923 TTATATATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
25 3 0.05
26 4 0.06
27 8 0.12
28 18 0.27
29 9 0.14
31 4 0.06
32 14 0.21
34 6 0.09
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.54
Consensus pattern (27 bp):
TTTAAATATATTTATATTTATATAAAT
Found at i:352855 original size:18 final size:17
Alignment explanation
Indices: 352821--352875 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
352811 TATTTAAAGT
352821 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
352838 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
352855 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
352870 ATTTTA
1 ATTTTA
352876 AAATATACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 5 0.15
16 7 0.21
17 7 0.21
18 6 0.18
19 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:352857 original size:60 final size:64
Alignment explanation
Indices: 352782--352938 Score: 159
Period size: 62 Copynumber: 2.5 Consensus size: 64
352772 ATTAATGTAT
* ** *
352782 TTATATTATATTAATT-TATTATATAATTATATTTAAAGTAT-TTTATATTTATATAA-ATTTTA
1 TTATATTA-A-TAATTATATTATATAATTATATTTAAAATATACATATATTCATATAATATTTTA
352844 A
64 A
352845 -TATATTAATAATTTATATTATATAA--AT-TTTAAAATATACATATATTCATATAATATTTTAA
1 TTATATTAATAA-TTATATTATATAATTATATTTAAAATATACATATATTCATATAATATTTTAA
*
352906 TTATATTTAT-ATTATATTTATATATATATATAT
1 TTATATTAATAATTATA-TTATATA-AT-TATAT
352939 ATGTCTAATA
Statistics
Matches: 78, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
59 9 0.12
60 22 0.28
61 18 0.23
62 26 0.33
65 2 0.03
66 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (64 bp):
TTATATTAATAATTATATTATATAATTATATTTAAAATATACATATATTCATATAATATTTTAA
Found at i:352860 original size:33 final size:31
Alignment explanation
Indices: 352824--352929 Score: 107
Period size: 32 Copynumber: 3.4 Consensus size: 31
352814 TTAAAGTATT
352824 TTATATTTATATAAATTTTAATATATTAATAA
1 TTATATTTATATAAATTTTAATATATT-ATAA
352856 TT-TATATTATATAAATTTTAA-A-A-TATACA
1 TTATAT-TTATATAAATTTTAATATATTATA-A
*
352885 -TATATTCATATAATATTTTAATTATATT-TATA
1 TTATATTTATATAA-ATTTTAA-TATATTATA-A
352917 TTATATTTATATA
1 TTATATTTATATA
352930 TATATATATA
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
28 11 0.18
29 12 0.19
30 1 0.02
31 5 0.08
32 21 0.34
33 12 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
TTATATTTATATAAATTTTAATATATTATAA
Found at i:352881 original size:14 final size:14
Alignment explanation
Indices: 352831--352882 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
352821 ATTTTATATT
352831 TATATAAATTTTAA
1 TATATAAATTTTAA
*
352845 TATATTAATAATTTATAT
1 TATA-T-A-AATTT-TAA
352863 TATATAAATTTTAA
1 TATATAAATTTTAA
*
352877 AATATA
1 TATATA
352883 CATATATTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 11 0.35
15 6 0.19
16 2 0.06
17 6 0.19
18 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:358876 original size:2 final size:2
Alignment explanation
Indices: 358869--358895 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
358859 TGTTAATGTC
358869 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 A
358896 ACAGTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:359001 original size:26 final size:26
Alignment explanation
Indices: 358972--359022 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
358962 CAGTTTTCTA
358972 TTGTCATATA-TTACTTT-TTTATTTAG
1 TTGT-ATATATTTA-TTTATTTATTTAG
*
358998 TTGTATTTATTTATTTATTTATTTA
1 TTGTATATATTTATTTATTTATTTA
359023 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (26 bp):
TTGTATATATTTATTTATTTATTTAG
Found at i:359008 original size:4 final size:4
Alignment explanation
Indices: 358989--359023 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
358979 ATATTACTTT
358989 TTTA TTTA GTTGTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA -TT-TA TTTA TTTA TTTA TTTA TTTA T
359024 ATTAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 23 0.79
5 4 0.14
6 2 0.07
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:359671 original size:19 final size:17
Alignment explanation
Indices: 359628--359672 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
359618 GAAAAACATT
* *
359628 AAAATTTCATAATTAAA
1 AAAATTTTAAAATTAAA
359645 AAAATTTTAAAATTAAA
1 AAAATTTTAAAATTAAA
359662 ATATAATTTTA
1 A-A-AATTTTA
359673 TATTTTCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 16 0.67
18 1 0.04
19 7 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTTTAAAATTAAA
Found at i:360381 original size:15 final size:15
Alignment explanation
Indices: 360341--360385 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
360331 CAAATGATAA
360341 AAACTTAAAATAATTT
1 AAAC-TAAAATAATTT
* * *
360357 AAATTTAAATTATTT
1 AAACTAAAATAATTT
360372 AAACTAAAATAATT
1 AAACTAAAATAATT
360386 CGAGTATTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (15 bp):
AAACTAAAATAATTT
Found at i:360449 original size:16 final size:15
Alignment explanation
Indices: 360422--360477 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
360412 ATCTCAAATG
*
360422 ATTTAAATTTTAAATA
1 ATTTAAAATTTAAA-A
360438 ATTTAAAATTTAAAA
1 ATTTAAAATTTAAAA
360453 A--T-AAA-TTAAAA
1 ATTTAAAATTTAAAA
360464 ATTTTAAAATTTAA
1 A-TTTAAAATTTAA
360478 TTCGATTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
11 7 0.21
12 3 0.09
13 1 0.03
14 1 0.03
15 5 0.15
16 17 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTTAAAATTTAAAA
Found at i:360456 original size:18 final size:19
Alignment explanation
Indices: 360433--360473 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
360423 TTTAAATTTT
*
360433 AAAT-AATTTAAAATTTAA
1 AAATAAATTAAAAATTTAA
*
360451 AAATAAATTAAAAATTTTA
1 AAATAAATTAAAAATTTAA
360470 AAAT
1 AAAT
360474 TTAATTCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATAAATTAAAAATTTAA
Found at i:361414 original size:23 final size:23
Alignment explanation
Indices: 361388--361431 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
361378 AAATATTTTT
361388 TATTTTAAATTAAAAAATTATCA
1 TATTTTAAATTAAAAAATTATCA
** *
361411 TATTTTATTTTATAAAATTAT
1 TATTTTAAATTAAAAAATTAT
361432 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTTAAATTAAAAAATTATCA
Found at i:361707 original size:24 final size:23
Alignment explanation
Indices: 361679--361741 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
361669 TTATTTATTT
361679 TATATTTATAATTATAAT--AAA
1 TATATTTATAATTATAATAAAAA
361700 TATGA--TATAATTAATAATTAAAAA
1 TAT-ATTTATAATT-ATAA-TAAAAA
361724 TATATTTATAATTATAAT
1 TATATTTATAATTATAAT
361742 TTAAATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
20 7 0.20
21 7 0.20
22 2 0.06
23 2 0.06
24 10 0.29
25 7 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATATTTATAATTATAATAAAAA
Found at i:361730 original size:45 final size:44
Alignment explanation
Indices: 361679--361782 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 44
361669 TTATTTATTT
361679 TATATTTATAATTATAA-TAAATATGATATAATTAATAATTAAAAA
1 TATATTTATAATTATAATTAAAT-TGATAT-ATTAATAATTAAAAA
* *
361724 TATATTTATAATTATAATTTAAATTTATATTTTAATAATTAAAAA
1 TATATTTATAATTATAA-TTAAATTGATATATTAATAATTAAAAA
* **
361769 AATATACATAATTA
1 TATATTTATAATTA
361783 ATGTAACAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
45 42 0.81
46 5 0.10
47 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (44 bp):
TATATTTATAATTATAATTAAATTGATATATTAATAATTAAAAA
Found at i:361780 original size:21 final size:24
Alignment explanation
Indices: 361756--361808 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
361746 ATTTATATTT
*
361756 TAATAAT-TAA-AAAA-ATATACA
1 TAATAATGTAACAAAAGATATAAA
361777 TAATTAATGTAACAAAAGATATAAA
1 TAA-TAATGTAACAAAAGATATAAA
361802 TAATAAT
1 TAATAAT
361809 CTTACTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 3 0.11
22 4 0.15
23 3 0.11
24 8 0.30
25 9 0.33
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (24 bp):
TAATAATGTAACAAAAGATATAAA
Done.