Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007251.1 Hibiscus syriacus cultivar Beakdansim tig00019208_pilon, whole genome shotgun sequence
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: 47234
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:2499 original size:24 final size:24
Alignment explanation
Indices: 2472--2526 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2462 CCGATTTGAT
* * * *
2472 TTCTGTTCTGATTTTTGATCTGGA
1 TTCTGTTATGATATCTGATCTGAA
2496 TTCTGTTATGATATCTGATCTGAA
1 TTCTGTTATGATATCTGATCTGAA
*
2520 TTATGTT
1 TTCTGTT
2527 TTGTTTTCTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (24 bp):
TTCTGTTATGATATCTGATCTGAA
Found at i:2536 original size:24 final size:24
Alignment explanation
Indices: 2483--2538 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
2473 TCTGTTCTGA
* *
2483 TTTT-TGATCTGGATTCTGTTATG
1 TTTTCTGATCTGAATTATGTTATG
* * *
2506 ATATCTGATCTGAATTATGTTTTG
1 TTTTCTGATCTGAATTATGTTATG
2530 TTTTCTGAT
1 TTTTCTGAT
2539 ATCTTCGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (24 bp):
TTTTCTGATCTGAATTATGTTATG
Found at i:4789 original size:2 final size:2
Alignment explanation
Indices: 4778--4964 Score: 104
Period size: 2 Copynumber: 94.0 Consensus size: 2
4768 GTGAAACAAT
4778 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** * * *
4819 TA TA TA T- TA CG TA TA AA CTA TA TA -A TT TA TA TT TA TA T- TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
4859 TC TA TA CTA TC TA TA AA CTA TA TA TA T- TA TG TG TA AA CTA TA
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
4901 TA GTT TA T- TA -A TA TA -A CTA TA TA GTG TA TA TA TA AA GTA TA
1 TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA
*
4942 TA T- TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
4965 AATTATAGAG
Statistics
Matches: 140, Mismatches: 28, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
1 9 0.06
2 122 0.87
3 9 0.06
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4981 original size:37 final size:37
Alignment explanation
Indices: 4931--5003 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
4921 ATAGTGTATA
4931 TATAAAGTATATATTACATA-TATATATA-TATATAAAT
1 TATAAAGTATATATT-CATATTAT-TATACTATATAAAT
* * *
4968 TATAGAGTTTATATTTATATTATTATACTATATAAA
1 TATAAAGTATATATTCATATTATTATACTATATAAA
5004 CTGTATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 7 0.23
37 24 0.77
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (37 bp):
TATAAAGTATATATTCATATTATTATACTATATAAAT
Found at i:5023 original size:20 final size:20
Alignment explanation
Indices: 4998--5048 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
4988 TATTATACTA
* **
4998 TATAAACTGTATATATTATG
1 TATAAACTATATATACCATG
5018 TATAAACTATATATACCATG
1 TATAAACTATATATACCATG
5038 TATAAACTATA
1 TATAAACTATA
5049 GAGTTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (20 bp):
TATAAACTATATATACCATG
Found at i:5145 original size:21 final size:22
Alignment explanation
Indices: 5110--5153 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5100 TTATATAGTT
5110 TATACATAATTATATTTAAATA
1 TATACATAATTATATTTAAATA
* *
5132 TATACA-ACTTATATTTATATA
1 TATACATAATTATATTTAAATA
5153 T
1 T
5154 TATGTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (22 bp):
TATACATAATTATATTTAAATA
Found at i:5218 original size:27 final size:27
Alignment explanation
Indices: 5188--5264 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
5178 ACTATGTATA
*
5188 AATTATATAGT-TTATAATATAAACTAT
1 AATTATATA-TATAATAATATAAACTAT
*
5215 AATTATATATATAATAATATAAAGTAT
1 AATTATATATATAATAATATAAACTAT
* *
5242 AAGTATATATATAAAAAGTATAA
1 AATTATATATATAATAA-TATAA
5265 TTATAAAGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.02
27 38 0.86
28 5 0.11
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (27 bp):
AATTATATATATAATAATATAAACTAT
Found at i:5248 original size:21 final size:22
Alignment explanation
Indices: 5224--5270 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
5214 TAATTATATA
*
5224 TATAATA-ATATAAAGTATAAG
1 TATAATATATAAAAAGTATAAG
*
5245 TAT-ATATATAAAAAGTATAAT
1 TATAATATATAAAAAGTATAAG
5266 TATAA
1 TATAA
5271 AGACTAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 3 0.14
21 18 0.82
22 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (22 bp):
TATAATATATAAAAAGTATAAG
Found at i:5299 original size:6 final size:7
Alignment explanation
Indices: 5232--5319 Score: 53
Period size: 8 Copynumber: 12.4 Consensus size: 7
5222 TATATAATAA
5232 TATAAAG
1 TATAAAG
5239 TAT-AAG
1 TATAAAG
5245 TATATATA-
1 TATA-A-AG
*
5253 TAAAAAG
1 TATAAAG
*
5260 TAT-AAT
1 TATAAAG
5266 TATAAAG
1 TATAAAG
5273 -ACTAAAG
1 TA-TAAAG
5280 TATATAAG
1 TATA-AAG
5288 TATATAAG
1 TATA-AAG
5296 TATATACA-
1 TATA-A-AG
5304 TATAAAG
1 TATAAAG
5311 TAT-AAG
1 TATAAAG
5317 TAT
1 TAT
5320 GTAATATCTA
Statistics
Matches: 67, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
6 20 0.30
7 19 0.28
8 26 0.39
9 2 0.03
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.34
Consensus pattern (7 bp):
TATAAAG
Found at i:5301 original size:10 final size:8
Alignment explanation
Indices: 5277--5669 Score: 78
Period size: 8 Copynumber: 52.9 Consensus size: 8
5267 ATAAAGACTA
5277 AAGTATAT
1 AAGTATAT
5285 AAGTATAT
1 AAGTATAT
5293 AAGTATAT
1 AAGTATAT
5301 ACA-TATA-
1 A-AGTATAT
5308 AAG--TAT
1 AAGTATAT
*
5314 AAGTATGT
1 AAGTATAT
*
5322 AA-TATCT
1 AAGTATAT
5329 AAAGT-T-T
1 -AAGTATAT
*
5336 TAGTATA-
1 AAGTATAT
5343 AA-TATAT
1 AAGTATAT
*
5350 -ACTATAT
1 AAGTATAT
5357 AA-TATA-
1 AAGTATAT
5363 AAG--TAT
1 AAGTATAT
5369 AAGTATAT
1 AAGTATAT
*
5377 TA-TATAT
1 AAGTATAT
5384 -A-TATAT
1 AAGTATAT
5390 AA-T-TAT
1 AAGTATAT
*
5396 AA-AACTA-
1 AAGTA-TAT
5403 AAGTATAT
1 AAGTATAT
5411 AAGCATATAAT
1 AAG--TAT-AT
5422 AAGTATAT
1 AAGTATAT
5430 -AGTAT-T
1 AAGTATAT
5436 AA--ATAT
1 AAGTATAT
5442 -AGTATAT
1 AAGTATAT
5449 AA--AGTAT
1 AAGTA-TAT
*
5456 AATTATA-
1 AAGTATAT
5463 AAG-ACTA-
1 AAGTA-TAT
5470 AAGTATAT
1 AAGTATAT
5478 AAGTATAT
1 AAGTATAT
*
5486 ATA-AAGTAT
1 A-AGTA-TAT
*
5495 AGGTATAT
1 AAGTATAT
*
5503 AAATATAT
1 AAGTATAT
*
5511 -A-TACAT
1 AAGTATAT
*
5517 AA-AATAT
1 AAGTATAT
*
5524 AAGTATGT
1 AAGTATAT
* *
5532 ATGTAAAT
1 AAGTATAT
5540 -A-TATAT
1 AAGTATAT
*
5546 AAACTGTAAAGT
1 -AA--GTATA-T
5558 AAAGTATATT
1 -AAGTATA-T
5568 ATA-TATAT
1 A-AGTATAT
5576 ATA-TATAT
1 A-AGTATAT
5584 ATA-TATAT
1 A-AGTATAT
5592 AAG--TAT
1 AAGTATAT
*
5598 AATTATA-
1 AAGTATAT
5605 AAG-ACTA-
1 AAGTA-TAT
*
5612 AAGTATAC
1 AAGTATAT
5620 AAGTATAT
1 AAGTATAT
5628 AA-TATA-
1 AAGTATAT
5634 AAGTA-AT
1 AAGTATAT
5641 AAGTATAT
1 AAGTATAT
5649 AAAGTATAT
1 -AAGTATAT
5658 -A-TATA-
1 AAGTATAT
5663 AAGTATA
1 AAGTATA
5670 AGTGTATATA
Statistics
Matches: 297, Mismatches: 29, Indels: 119
0.67 0.07 0.27
Matches are distributed among these distances:
5 7 0.02
6 54 0.18
7 85 0.29
8 105 0.35
9 25 0.08
10 9 0.03
11 8 0.03
12 4 0.01
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.37
Consensus pattern (8 bp):
AAGTATAT
Found at i:5356 original size:72 final size:70
Alignment explanation
Indices: 5207--5369 Score: 163
Period size: 72 Copynumber: 2.3 Consensus size: 70
5197 GTTTATAATA
* * *
5207 TAAACTATA-ATTATATA-TATAATA-ATATAAAGTATAAGTATATATATAAAAAGTATAATTAT
1 TAAACTATATAATATAAAGTAT-ATACATATAAAGTATAAGTATATATATAAAAAGTATAAGTAT
5269 AAAGAC
65 AAAGAC
* * ** * *
5275 TAAAGTATATAAGTATATAAGTATATACATATAAAGTATAAGTATGTAATATCTAAAGTTTTAGT
1 TAAACTATATAA-TATA-AAGTATATACATATAAAGTATAAGTATAT-ATATAAAAAGTATAAGT
*
5340 ATAAATA-
63 ATAAAGAC
*
5347 TATACTATATAATATAAAGTATA
1 TAAACTATATAATATAAAGTATA
5370 AGTATATTAT
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
68 8 0.10
69 1 0.01
70 11 0.14
71 8 0.10
72 31 0.40
73 18 0.23
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (70 bp):
TAAACTATATAATATAAAGTATATACATATAAAGTATAAGTATATATATAAAAAGTATAAGTATA
AAGAC
Found at i:5357 original size:7 final size:7
Alignment explanation
Indices: 5339--5838 Score: 73
Period size: 7 Copynumber: 69.9 Consensus size: 7
5329 AAAGTTTTAG
5339 TATA-AA
1 TATATAA
*
5345 TATATAC
1 TATATAA
5352 TATATAA
1 TATATAA
5359 TATA-AA
1 TATATAA
*
5365 GTATA-AG
1 -TATATAA
*
5372 TATATTA
1 TATATAA
5379 TATAT-A
1 TATATAA
5385 TATATAA
1 TATATAA
5392 T-TATAA
1 TATATAA
*
5398 AACTA-AA
1 TA-TATAA
5405 GTATATAA
1 -TATATAA
*
5413 GCATATAA
1 -TATATAA
5421 TA-AGTATA
1 TATA-TA-A
5429 TAGTATTAA
1 TA-TA-TAA
*
5438 -ATATAG
1 TATATAA
5444 TATATAA
1 TATATAA
5451 -AGTATAA
1 TA-TATAA
5458 T-TATAA
1 TATATAA
*
5464 -AGACTAAA
1 TATA-T-AA
5472 GTATATAA
1 -TATATAA
5480 GTATATATA
1 -TATATA-A
* *
5489 AAGTATAGG
1 TA-TATA-A
5498 TATATAA
1 TATATAA
5505 -ATATATA
1 TATATA-A
*
5512 TACATAA
1 TATATAA
*
5519 AATATAA
1 TATATAA
*
5526 GTATGT-A
1 -TATATAA
*
5533 TGTA-AA
1 TATATAA
5539 TATATATA
1 TATATA-A
* *
5547 AACTGTAA
1 TA-TATAA
5555 -AGTA-AA
1 TA-TATAA
*
5561 GTATATTA
1 -TATATAA
5569 TATAT-A
1 TATATAA
5575 TATAT-A
1 TATATAA
5581 TATAT-A
1 TATATAA
5587 TATATAA
1 TATATAA
*
5594 -GTATAA
1 TATATAA
5600 T-TATAA
1 TATATAA
*
5606 -AGACTAAA
1 TATA-T-AA
*
5614 GTATACAA
1 -TATATAA
5622 GTATATAA
1 -TATATAA
5630 TATA-AA
1 TATATAA
5636 GTA-ATAA
1 -TATATAA
5643 GTATATAA
1 -TATATAA
5651 -AGTAT-A
1 TA-TATAA
5657 TATATAA
1 TATATAA
5664 -AGTATAA
1 TA-TATAA
*
5671 GTGTAT-A
1 -TATATAA
5678 TATATAA
1 TATATAA
* **
5685 -AAAGTTT
1 TATA-TAA
5692 TAGTATAA
1 TA-TATAA
5700 -AGTATATA
1 TA-TATA-A
*
5708 TACATAA
1 TATATAA
5715 TA-ATAA
1 TATATAA
5721 -AGTATAA
1 TA-TATAA
5728 GTATATTATA
1 -TATA-TA-A
5738 TATATAA
1 TATATAA
5745 -AGTATATA
1 TA-TATA-A
5753 TATATAA
1 TATATAA
*
5760 TATAAAA
1 TATATAA
5767 TATA-AA
1 TATATAA
5773 TATATAAAA
1 TATAT--AA
5782 TATATATA
1 TATATA-A
5790 TATATAA
1 TATATAA
5797 TATA-AA
1 TATATAA
5803 GTATA-AA
1 -TATATAA
5810 TATTATATA
1 TA-TATA-A
*
5819 TATATAC
1 TATATAA
* *
5826 TTTATAT
1 TATATAA
5833 TATATA
1 TATATA
5839 CTTATATCTT
Statistics
Matches: 372, Mismatches: 51, Indels: 141
0.66 0.09 0.25
Matches are distributed among these distances:
5 1 0.00
6 103 0.28
7 140 0.38
8 89 0.24
9 31 0.08
10 8 0.02
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (7 bp):
TATATAA
Found at i:5443 original size:12 final size:13
Alignment explanation
Indices: 5426--5513 Score: 60
Period size: 12 Copynumber: 6.8 Consensus size: 13
5416 TATAATAAGT
5426 ATATAGTAT-TAA
1 ATATAGTATATAA
5438 ATATAGTATATAA
1 ATATAGTATATAA
*
5451 AGTATAAT-TATAAA
1 A-TATAGTATAT-AA
*
5465 GACTAAAGTATATAA
1 -A-TATAGTATATAA
*
5480 GTATA-TATA-AA
1 ATATAGTATATAA
*
5491 GTATAGGTATATAA
1 ATATA-GTATATAA
5505 ATATA-TATA
1 ATATAGTATA
5514 CATAAAATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
11 7 0.11
12 17 0.28
13 14 0.23
14 13 0.21
15 7 0.11
16 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.36
Consensus pattern (13 bp):
ATATAGTATATAA
Found at i:5478 original size:29 final size:29
Alignment explanation
Indices: 5442--5679 Score: 105
Period size: 29 Copynumber: 8.3 Consensus size: 29
5432 TATTAAATAT
5442 AGTATATAAAGTATAAT-TATAAAGACTAA
1 AGTATATAAAGTATAATATATAAAGA-TAA
5471 AGTATAT-AAG--T-ATATATAAAG-TATA
1 AGTATATAAAGTATAATATATAAAGATA-A
* *
5496 GGTATATAAA-TATATATACATAAA-ATATA
1 AGTATATAAAGTATA-ATATATAAAGATA-A
* * *
5525 AGTATGT-ATGTAAATATATATAAACTG-TAA
1 AGTATATAAAGTATA-ATATATAAA--GATAA
* * * * * *
5555 AGTAAAGTATATTAT-ATATATATATATAT
1 AGTATA-TAAAGTATAATATATAAAGATAA
5584 A-TATATATAAGTATAAT-TATAAAGACTAA
1 AGTATATA-AAGTATAATATATAAAGA-TAA
*
5613 AGTATA-CAAGTAT-ATAATATAAAG-TAATA
1 AGTATATAAAGTATAAT-ATATAAAGAT-A-A
5642 AGTATATAAAGTAT-ATATATAAAGTATAA
1 AGTATATAAAGTATAATATATAAAG-ATAA
*
5671 GTGTATATA
1 -AGTATATA
5680 TATAAAAAGT
Statistics
Matches: 157, Mismatches: 25, Indels: 53
0.67 0.11 0.23
Matches are distributed among these distances:
24 2 0.01
25 9 0.06
26 10 0.06
27 6 0.04
28 24 0.15
29 67 0.43
30 33 0.21
31 4 0.03
32 2 0.01
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (29 bp):
AGTATATAAAGTATAATATATAAAGATAA
Found at i:5574 original size:2 final size:2
Alignment explanation
Indices: 5562--5592 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5552 TAAAGTAAAG
5562 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5593 AGTATAATTA
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):
TA
Found at i:5708 original size:30 final size:29
Alignment explanation
Indices: 5661--5747 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 29
5651 AGTATATATA
*
5661 TAAAGTATAAGTGTATATATATAAAAAGT
1 TAAAGTATAAGTATATATATATAAAAAGT
** * *
5690 TTTAGTATAAAGTATATATACATAATAA--
1 TAAAGTAT-AAGTATATATATATAAAAAGT
*
5718 TAAAGTATAAGTATATTATATATATAAAGT
1 TAAAGTATAAGTATA-TATATATAAAAAGT
5748 ATATATATAT
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
27 7 0.16
28 15 0.34
29 6 0.14
30 16 0.36
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (29 bp):
TAAAGTATAAGTATATATATATAAAAAGT
Found at i:5708 original size:142 final size:138
Alignment explanation
Indices: 5425--5687 Score: 340
Period size: 142 Copynumber: 1.9 Consensus size: 138
5415 ATATAATAAG
*
5425 TATATAGTATTAAATATAGTATATAAAGTATAATTATAAAGACTAAAGTATATAAGTATATATAA
1 TATATAGTATTAAATATAGTATATAAAGTATAATTATAAAGACTAAAGTATACAAGTATATATAA
* *
5490 AGTATAGGTATATAAATATATATACATAAAATATAAGTATGTATGTAAATATATATAAACTGTAA
66 AGTATAAGTATATAAATATATATA-ATAAAATATAAG-ATGTA-GT-AATATATAAAAACTGTAA
5555 AGTAAAGTATAT
127 AGTAAAGTATAT
*
5567 TATATA-TATATATATATA-TATATATAAGTATAATTATAAAGACTAAAGTATACAAGTATATAA
1 TATATAGTAT-TAAATATAGTATATA-AAGTATAATTATAAAGACTAAAGTATACAAG--TAT-A
*
5630 TATAAAGTAATAAGTATATAAAGTATATAT-ATAAAGTATAAG-TGTA-T-ATATATAAAAA
61 TATAAAGT-ATAAGTATATAAA-TATATATAATAAAATATAAGATGTAGTAATATATAAAAA
5688 GTTTTAGTAT
Statistics
Matches: 109, Mismatches: 5, Indels: 17
0.83 0.04 0.13
Matches are distributed among these distances:
139 10 0.09
141 10 0.09
142 43 0.39
143 4 0.04
144 3 0.03
145 20 0.18
146 12 0.11
147 7 0.06
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (138 bp):
TATATAGTATTAAATATAGTATATAAAGTATAATTATAAAGACTAAAGTATACAAGTATATATAA
AGTATAAGTATATAAATATATATAATAAAATATAAGATGTAGTAATATATAAAAACTGTAAAGTA
AAGTATAT
Found at i:5741 original size:2 final size:2
Alignment explanation
Indices: 5729--5838 Score: 81
Period size: 2 Copynumber: 57.0 Consensus size: 2
5719 AAAGTATAAG
* *
5729 TA TA T- TA TA TA TA TA AA GTA TA TA TA TA TA -A TA TA -A AA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
5769 TA AA TA TA TA -A AA TA TA TA TA TA TA TA -A TA TA AA GTA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
*
5810 TA T- TA TA TA TA TA TA CTT TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
5839 CTTATATCTT
Statistics
Matches: 86, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
1 7 0.08
2 76 0.88
3 3 0.03
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5776 original size:37 final size:38
Alignment explanation
Indices: 5735--5838 Score: 133
Period size: 37 Copynumber: 2.8 Consensus size: 38
5725 TAAGTATATT
*
5735 ATATATATAAA-GTATATATATATAATATAAAATATAA
1 ATATATATAAATATATATATATATAATATAAAATATAA
*
5772 ATATATA-AAATATATATATATATAATATAAAGTATAA
1 ATATATATAAATATATATATATATAATATAAAATATAA
* * *
5809 ATAT-TATATATATATACTTTATATTATATA
1 ATATATATAAATATATA-TATATATAATATA
5839 CTTATATCTT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
36 5 0.08
37 43 0.73
38 11 0.19
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (38 bp):
ATATATATAAATATATATATATATAATATAAAATATAA
Found at i:5784 original size:29 final size:31
Alignment explanation
Indices: 5750--5824 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
5740 TATAAAGTAT
5750 ATATATATAATATAAAATATAAA-TATATAA-A
1 ATATATAT-ATATAAAATATAAAGTATA-AATA
*
5781 ATATATATATATATAATATAAAGTATAAATA
1 ATATATATATATAAAATATAAAGTATAAATA
*
5812 TTATATATATATA
1 ATATATATATATA
5825 CTTTATATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 15 0.38
31 25 0.62
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
ATATATATATATAAAATATAAAGTATAAATA
Found at i:5830 original size:15 final size:15
Alignment explanation
Indices: 5812--5885 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
5802 AGTATAAATA
5812 TTATATATATATACT
1 TTATATATATATACT
5827 TTATAT-TATATAC-
1 TTATATATATATACT
* *
5840 TTATATCTTTAGT-CT
1 TTATATATATA-TACT
5855 TTATA-AT-TATACT
1 TTATATATATATACT
5868 CTCTATATATATATACT
1 -T-TATATATATATACT
5885 T
1 T
5886 ATACTTTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
12 1 0.02
13 10 0.20
14 13 0.27
15 16 0.33
16 3 0.06
17 6 0.12
ACGTcount: A:0.34, C:0.11, G:0.01, T:0.54
Consensus pattern (15 bp):
TTATATATATATACT
Found at i:5836 original size:29 final size:29
Alignment explanation
Indices: 5779--5911 Score: 73
Period size: 29 Copynumber: 4.6 Consensus size: 29
5769 TAAATATATA
* * * *
5779 AAATA-TATATATATATAATATAAAGTAT
1 AAATATTATATATATATACTTTATATTAT
5807 AAATATTATATATATATACTTTATATTAT
1 AAATATTATATATATATACTTTATATTAT
* *
5836 --ATACTTATATCTTTAGT-CTTTATAATTAT
1 AAATA-TTATATATATA-TACTTTAT-ATTAT
* *
5865 -ACTCTCTATATATATATAC-TTATACTT-T
1 AAATAT-TATATATATATACTTTATA-TTAT
* *
5893 ATATTATTATATATGTATA
1 A-AATATTATATATATATA
5912 TATTGTAACA
Statistics
Matches: 82, Mismatches: 13, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
27 3 0.04
28 22 0.27
29 44 0.54
30 13 0.16
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (29 bp):
AAATATTATATATATATACTTTATATTAT
Found at i:12501 original size:4 final size:4
Alignment explanation
Indices: 12492--12522 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
12482 ACTGTTCAAC
12492 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
12523 ACATGCATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:13538 original size:12 final size:12
Alignment explanation
Indices: 13518--13587 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
13508 GATACATTAC
*
13518 CTGAATTCTGTT
1 CTGATTTCTGTT
*
13530 CTGATTTCTGAT
1 CTGATTTCTGTT
13542 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* * *
13554 ATGATATCTGAT
1 CTGATTTCTGTT
*
13566 CTGAATTCTGTT
1 CTGATTTCTGTT
*
13578 TTGATTTCTG
1 CTGATTTCTG
13588 ATATCTCCAT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:13586 original size:48 final size:48
Alignment explanation
Indices: 13481--13589 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
13471 AAATCTTTTA
* * *
13481 TCTGATTTCCGA-CTTGAATTCTGTTATGATACATTACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTATGATACATGACCTGAATTCTGT
*
13529 TCTGATTTCTGATCTGGATTCTGTTATGATATC-TGATCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTATGATA-CATGACCTGAATTCTGT
*
13577 TTTGATTTCTGAT
1 TCTGATTTCTGAT
13590 ATCTCCATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 52 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTATGATACATGACCTGAATTCTGT
Found at i:13587 original size:24 final size:24
Alignment explanation
Indices: 13495--13589 Score: 111
Period size: 24 Copynumber: 4.0 Consensus size: 24
13485 ATTTCCGACT
* * *
13495 TGAATTCTGTTATGA-TACATTACC
1 TGAATTCTGTTATGATTTC-TGATC
*
13519 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTATGATTTCTGATC
* *
13543 TGGATTCTGTTATGATATCTGATC
1 TGAATTCTGTTATGATTTCTGATC
*
13567 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTATGATTTCTGAT
13590 ATCTCCATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 58 0.97
25 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATC
Found at i:14360 original size:2 final size:2
Alignment explanation
Indices: 14353--14433 Score: 51
Period size: 2 Copynumber: 40.0 Consensus size: 2
14343 ACTAAAACTT
* * *
14353 TA TA TA TA TA TA TA TA TA TA TA CA CTT TA TA GTT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* * *
14397 GA TA CT- TA TA TA CTT TA TA T- TA T- TA TA TA TG TA TA TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
14434 CACTTAATAT
Statistics
Matches: 60, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
1 3 0.05
2 54 0.90
3 3 0.05
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14395 original size:24 final size:25
Alignment explanation
Indices: 14355--14484 Score: 78
Period size: 25 Copynumber: 5.2 Consensus size: 25
14345 TAAAACTTTA
*
14355 TATATA-TATATATATATATACACT
1 TATATACTTTATATATATATACACT
* * *
14379 T-TATAGTTTATATATATAGATACT
1 TATATACTTTATATATATATACACT
*
14403 TATATACTTTATAT-TATTATATA-T
1 TATATACTTTATATATA-TATACACT
* *
14427 GTATATACACTTA-ATATTTAATA-A-T
1 -TATATAC-TTTATATATAT-ATACACT
14452 TATATACTTTATATTATTATATACA-T
1 TATATACTTTATA-TA-TATATACACT
14478 GTATATA
1 -TATATA
14485 TATAAACACA
Statistics
Matches: 85, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
23 7 0.08
24 28 0.33
25 33 0.39
26 11 0.13
27 6 0.07
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (25 bp):
TATATACTTTATATATATATACACT
Found at i:14424 original size:17 final size:17
Alignment explanation
Indices: 14402--14475 Score: 75
Period size: 17 Copynumber: 4.5 Consensus size: 17
14392 ATATAGATAC
14402 TTATATACTTTATATTA
1 TTATATACTTTATATTA
* *
14419 TTATATA-TGTATATACA
1 TTATATACTTTATAT-TA
*
14436 CTTA-ATA-TTTA-ATAA
1 -TTATATACTTTATATTA
14451 TTATATACTTTATATTA
1 TTATATACTTTATATTA
14468 TTATATAC
1 TTATATAC
14476 ATGTATATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
14 3 0.06
15 4 0.09
16 12 0.26
17 25 0.53
18 3 0.06
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (17 bp):
TTATATACTTTATATTA
Found at i:14432 original size:59 final size:59
Alignment explanation
Indices: 14349--14628 Score: 189
Period size: 59 Copynumber: 4.6 Consensus size: 59
14339 TTATACTAAA
14349 ACTTTATA-TATATATATATATATATACACTTTATAGTTTATATATATAGATACTTATAT
1 ACTTTATATTAT-TATATATATATATACACTTTATAGTTTATATATATAGATACTTATAT
* * *
14408 ACTTTATATTATTATATATGTATATACACTTAATA-TTTA-ATA-ATTATATACTT-TAT
1 ACTTTATATTATTATATATATATATACACTTTATAGTTTATATATA-TAGATACTTATAT
* * * * *
14464 ATTATTATATACATGTATATATATAAACACACAATTTATAGTTTATACTTTAT-G-TACTTATAT
1 ACT-TTATAT-TAT-TATATATATATATACAC--TTTATAGTTTATA-TATATAGATACTTATAT
* * ** * * *
14527 ACTTTATATT-GTATACTTATATATTTTATTCTTTATAGTTATACTTTATACATATATAATATAC
1 ACTTTATATTATTATA--TATATA-TATACACTTTATAGTT-TA---TATATATAGATACT-TA-
14591 TTAT
57 -TAT
* *
14595 ACTTTATATTATTATATATGTATATATACTTTAT
1 ACTTTATATTATTATATATATATATACACTTTAT
14629 GCTAAAACTT
Statistics
Matches: 169, Mismatches: 27, Indels: 43
0.71 0.11 0.18
Matches are distributed among these distances:
56 6 0.04
57 17 0.10
58 6 0.04
59 47 0.28
60 12 0.07
61 13 0.08
62 17 0.10
63 9 0.05
64 4 0.02
65 4 0.02
66 12 0.07
67 5 0.03
68 13 0.08
69 4 0.02
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (59 bp):
ACTTTATATTATTATATATATATATACACTTTATAGTTTATATATATAGATACTTATAT
Found at i:14510 original size:7 final size:7
Alignment explanation
Indices: 14498--14602 Score: 67
Period size: 7 Copynumber: 14.9 Consensus size: 7
14488 AAACACACAA
*
14498 TTTATAG
1 TTTATAC
14505 TTTATAC
1 TTTATAC
14512 TTTATGTAC
1 TTTA--TAC
14521 TTATATAC
1 TT-TATAC
14529 TTTATA-
1 TTTATAC
14535 TTGTATAC
1 TT-TATAC
*
14543 TTATATAT
1 TT-TATAC
*
14551 TTTATTC
1 TTTATAC
14558 TTTATA-
1 TTTATAC
*
14564 GTTATAC
1 TTTATAC
14571 TTTATAC
1 TTTATAC
*
14578 -ATATA-
1 TTTATAC
*
14583 TAATATAC
1 T-TTATAC
14591 -TTATAC
1 TTTATAC
14597 TTTATA
1 TTTATA
14603 TTATTATATA
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
6 16 0.21
7 42 0.54
8 13 0.17
9 5 0.06
10 2 0.03
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.55
Consensus pattern (7 bp):
TTTATAC
Found at i:14573 original size:13 final size:13
Alignment explanation
Indices: 14524--14606 Score: 62
Period size: 13 Copynumber: 6.2 Consensus size: 13
14514 TATGTACTTA
*
14524 TATACTTTATATT
1 TATACTTTATACT
*
14537 GTATACTTATATATTT
1 -TATACTT-TATA-CT
* *
14553 TATTCTTTATAGT
1 TATACTTTATACT
*
14566 TATACTTTATACA
1 TATACTTTATACT
*
14579 TATA-TAATATACT
1 TATACT-TTATACT
14592 TATACTTTATA-T
1 TATACTTTATACT
14604 TAT
1 TAT
14607 TATATATGTA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
12 5 0.09
13 28 0.49
14 12 0.21
15 10 0.18
16 2 0.04
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.55
Consensus pattern (13 bp):
TATACTTTATACT
Found at i:14609 original size:15 final size:15
Alignment explanation
Indices: 14506--14610 Score: 50
Period size: 15 Copynumber: 7.3 Consensus size: 15
14496 AATTTATAGT
14506 TTATACTTTATGTACTTA
1 TTATACTTTA--TA-TTA
14524 -TATACTTTATATT-
1 TTATACTTTATATTA
*
14537 GTATACTTATATATT-
1 TTATACTT-TATATTA
* *
14552 TTATTCTTTATA--G
1 TTATACTTTATATTA
*
14565 TTATACTTTATA-CA
1 TTATACTTTATATTA
*
14579 -TATA--TAATA-TA
1 TTATACTTTATATTA
14590 CTTATACTTTATATTA
1 -TTATACTTTATATTA
14606 TTATA
1 TTATA
14611 TATGTATATA
Statistics
Matches: 71, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
11 5 0.07
13 19 0.27
14 13 0.18
15 23 0.32
16 2 0.03
17 9 0.13
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATACTTTATATTA
Found at i:14610 original size:26 final size:26
Alignment explanation
Indices: 14560--14628 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
14550 TTTTATTCTT
14560 TATAGTTATACTTTATACATATATA-A
1 TATA-TTATACTTTATACATATATATA
*
14586 TATACTTATACTTTATA-TTATTATATA
1 TATA-TTATACTTTATACATA-TATATA
*
14613 TGTATATATACTTTAT
1 TATAT-TATACTTTAT
14629 GCTAAAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.05
26 21 0.57
27 14 0.38
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (26 bp):
TATATTATACTTTATACATATATATA
Found at i:14665 original size:14 final size:14
Alignment explanation
Indices: 14648--14675 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14638 TTATATTTAT
14648 AAGTATATAATATA
1 AAGTATATAATATA
14662 AAGTATATAATATA
1 AAGTATATAATATA
14676 TATAAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTATATAATATA
Found at i:14692 original size:22 final size:23
Alignment explanation
Indices: 14667--14819 Score: 75
Period size: 23 Copynumber: 6.5 Consensus size: 23
14657 ATATAAAGTA
*
14667 TATAATATATATAAAGTTT-TAG
1 TATAATATATATAAACTTTATAG
*
14689 TATAA-AGTATATATACTTTATAG
1 TATAATA-TATATAAACTTTATAG
* * *
14712 TAT-ATATATATATA-TATATACT
1 TATAATATATATAAACTTTATA-G
*
14734 TATAATATACT-TATACTTTATAG
1 TATAATATA-TATAAACTTTATAG
* *
14757 TTATATATATATATTTATACTTTATAC
1 -TATA-ATATATA--TAAACTTTATAG
* * *
14784 TTTAA-AGTATATATACCTTATAG
1 TATAATA-TATATAAACTTTATAG
*
14807 TTTATATATATAT
1 TATA-ATATATAT
14820 TATATATACT
Statistics
Matches: 106, Mismatches: 10, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
21 6 0.06
22 27 0.25
23 30 0.28
24 18 0.17
25 11 0.10
26 3 0.03
27 11 0.10
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (23 bp):
TATAATATATATAAACTTTATAG
Found at i:14703 original size:2 final size:2
Alignment explanation
Indices: 14696--14775 Score: 51
Period size: 2 Copynumber: 39.0 Consensus size: 2
14686 TAGTATAAAG
*
14696 TA TA TA TA CTT TA TA GTA TA TA TA TA TA TA TA TA TA CT- TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
14738 -A TA TA CT- TA TA CTT TA TA GT- TA TA TA TA TA TA TT TA TA
1 TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
14776 CTTTATACTT
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
1 4 0.06
2 51 0.82
3 7 0.11
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14736 original size:27 final size:27
Alignment explanation
Indices: 14696--14827 Score: 88
Period size: 25 Copynumber: 5.1 Consensus size: 27
14686 TAGTATAAAG
14696 TATATATACTTTATAGTATATATATATA
1 TATATATACTTTATA-TATATATATATA
14724 TATATATAC-TTATA-ATATACT-TATA
1 TATATATACTTTATATATATA-TATATA
* *
14749 CT-T-TATA-GTTATATATATATATTTA
1 -TATATATACTTTATATATATATATATA
* *
14774 TACTTTATACTTTA-A-A-GTATATATA
1 TA-TATATACTTTATATATATATATATA
** *
14799 CCT-TATAGTTTATATATATAT-TATA
1 TATATATACTTTATATATATATATATA
14824 TATA
1 TATA
14828 CTTTATAGTT
Statistics
Matches: 81, Mismatches: 10, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
23 8 0.10
24 13 0.16
25 31 0.38
26 7 0.09
27 10 0.12
28 12 0.15
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (27 bp):
TATATATACTTTATATATATATATATA
Found at i:14762 original size:34 final size:35
Alignment explanation
Indices: 14724--14805 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 35
14714 TATATATATA
*
14724 TATATATACTTATA-ATATAC-TTATACTTTATAG
1 TATATATACTTATATATATACTTTATACTTTAAAG
*
14757 T-TATATA-TATATATTTATACTTTATACTTTAAAG
1 TATATATACT-TATATATATACTTTATACTTTAAAG
14791 TATATATACCTTATA
1 TATATATA-CTTATA
14806 GTTTATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
31 1 0.02
32 10 0.24
33 6 0.15
34 13 0.32
35 6 0.15
36 4 0.10
37 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (35 bp):
TATATATACTTATATATATACTTTATACTTTAAAG
Found at i:14785 original size:40 final size:44
Alignment explanation
Indices: 14700--14782 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
14690 ATAAAGTATA
14700 TATACTTTATAGTATATATATATATATATATACTTATAATATACT
1 TATACTTTATAGTATATATATATATATATATACTTAT-ATATACT
*
14745 TATACTTTATAGT-TATATATATATATTTATACTT-TATA
1 TATACTTTATAGTATATATATATATATATATACTTATATA
14783 CTTTAAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 3 0.08
43 1 0.03
44 20 0.54
45 13 0.35
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (44 bp):
TATACTTTATAGTATATATATATATATATATACTTATATATACT
Found at i:14850 original size:27 final size:27
Alignment explanation
Indices: 14700--14878 Score: 133
Period size: 27 Copynumber: 6.6 Consensus size: 27
14690 ATAAAGTATA
*
14700 TATACTTTATAGTATATA-TATATATA-TA
1 TATACTTTATA-TATATACT-T-TATACTT
14728 TATAC-TTATA-ATATACTT-ATACTT
1 TATACTTTATATATATACTTTATACTT
*
14752 TATAGTTATATATATATA-TTTATACTT
1 TATACTT-TATATATATACTTTATACTT
* *
14779 TATACTTTAAAGTATATATACCTTATAGTT
1 TATACTTT--A-TATATATACTTTATACTT
*
14809 TATA-TATATATTATATATACTTTATAGTT
1 TATACT-T-TA-TATATATACTTTATACTT
*
14838 TACACTTTATATATATACTTT-TAC-T
1 TATACTTTATATATATACTTTATACTT
* *
14863 TATATTTTTTATATAT
1 TATACTTTATATATAT
14879 GTATATTTAA
Statistics
Matches: 126, Mismatches: 12, Indels: 29
0.75 0.07 0.17
Matches are distributed among these distances:
23 3 0.02
24 5 0.04
25 21 0.17
26 10 0.08
27 34 0.27
28 8 0.06
29 31 0.25
30 13 0.10
31 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (27 bp):
TATACTTTATATATATACTTTATACTT
Found at i:14875 original size:25 final size:27
Alignment explanation
Indices: 14819--14878 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
14809 TATATATATA
*
14819 TTATATATACTTTATAGTTTACACTTT
1 TTATATATACTTTATAGCTTACACTTT
* * *
14846 ATATATATACTTT-TA-CTTATATTTT
1 TTATATATACTTTATAGCTTACACTTT
14871 TTATATAT
1 TTATATAT
14879 GTATATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 14 0.50
26 2 0.07
27 12 0.43
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (27 bp):
TTATATATACTTTATAGCTTACACTTT
Found at i:15330 original size:6 final size:6
Alignment explanation
Indices: 15319--16011 Score: 339
Period size: 6 Copynumber: 115.3 Consensus size: 6
15309 TTTGGTACTT
* * * *
15319 TATATA TATATA TATATA AACTATA AAGTATA -AGTATA TGTATA TGTATA
1 TATATA TATATA TATATA TA-TATA TA-TATA TA-TATA TATATA TATATA
* * * * * * * *
15369 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15417 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA T-TATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15464 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15512 TATATG TATATG TATATG TATATG TATATG TATATG T-TATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15559 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15607 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15655 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15703 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15751 TATATG TATATG TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15799 TATGTA TATGTA TATGTA TATGTA TGTATA TGTATA TGTATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15847 TATATG TATATG TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15895 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
15943 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* *
15991 TATGTA TATGTA TATAGTA TA
1 TATATA TATATA TATA-TA TA
16012 ATGTACATTA
Statistics
Matches: 669, Mismatches: 13, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
5 9 0.01
6 646 0.97
7 14 0.02
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.49
Consensus pattern (6 bp):
TATATA
Found at i:15367 original size:18 final size:18
Alignment explanation
Indices: 15346--16016 Score: 1231
Period size: 18 Copynumber: 37.8 Consensus size: 18
15336 AAACTATAAA
*
15346 GTATAAGTATATGTATAT
1 GTATATGTATATGTATAT
15364 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15382 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15400 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15418 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15436 GTATATGTATATGTATA-
1 GTATATGTATATGTATAT
15453 -T-TATGTATATGTATAT
1 GTATATGTATATGTATAT
15469 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15487 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15505 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15523 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15541 GTATATGT-TATGTATAT
1 GTATATGTATATGTATAT
15558 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15576 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15594 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15612 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15630 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15648 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15666 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15684 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15702 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15720 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15738 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15756 GTATATG--TATGTATAT
1 GTATATGTATATGTATAT
15772 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15790 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15808 GTATATGTATATG--TAT
1 GTATATGTATATGTATAT
15824 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15842 GTATA--TATATGTATAT
1 GTATATGTATATGTATAT
15858 G--TATGTATATGTATAT
1 GTATATGTATATGTATAT
15874 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15892 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15910 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15928 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15946 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15964 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
15982 GTATATGTATATGTATAT
1 GTATATGTATATGTATAT
16000 GTATATAGTATAATGTA
1 GTATAT-GTAT-ATGTA
16017 CATTATATAT
Statistics
Matches: 638, Mismatches: 1, Indels: 26
0.96 0.00 0.04
Matches are distributed among these distances:
14 2 0.00
15 14 0.02
16 57 0.09
17 18 0.03
18 538 0.84
19 4 0.01
20 5 0.01
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.50
Consensus pattern (18 bp):
GTATATGTATATGTATAT
Found at i:16397 original size:24 final size:25
Alignment explanation
Indices: 16350--16402 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
16340 CAATTTAGTC
*
16350 CATTTTATATTAATATCAGCTTCA-
1 CATTTTATATTAATATCAACTTCAT
*
16374 CATTTTATAATTAAT-TCAATTTCAT
1 CATTTTAT-ATTAATATCAACTTCAT
16399 CATT
1 CATT
16403 CATCAATGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.49
Consensus pattern (25 bp):
CATTTTATATTAATATCAACTTCAT
Found at i:16521 original size:2 final size:2
Alignment explanation
Indices: 16502--16556 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
16492 TAAGTATAAG
* * *
16502 TA TA TA TG TA TA TG TA TA TA TA TA TA TA TA TA TA AA GTA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
*
16544 AA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA
16557 AAGTATTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.93
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:16555 original size:29 final size:30
Alignment explanation
Indices: 16516--16674 Score: 87
Period size: 30 Copynumber: 5.1 Consensus size: 30
16506 TATGTATATG
*
16516 TATATATATATATA-TATATAAAGTATAAAA
1 TATATATATATAAAGTAT-TAAAGTATAAAA
*
16546 TATATA-ATATAAAGTATTAAAGTATATAA
1 TATATATATATAAAGTATTAAAGTATAAAA
* * *
16575 TATAAAGTA-ATAAAGTGTTTGGATATATGTATTAAAG
1 TATATA-TATATAAAGT-ATT--A-A-A-GTA-TAAAA
* * *
16612 CATATAAATAT-AAGTATTAAA-TATAAAG
1 TATATATATATAAAGTATTAAAGTATAAAA
* *
16640 TATATA-AGTATATAAGTACTAAAGTATATAA
1 TATATATA-TATA-AAGTATTAAAGTATAAAA
16671 TATA
1 TATA
16675 AAGTATTGAA
Statistics
Matches: 100, Mismatches: 14, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
27 1 0.01
28 13 0.13
29 24 0.24
30 25 0.25
31 13 0.13
32 1 0.01
33 2 0.02
34 1 0.01
35 3 0.03
36 8 0.08
37 9 0.09
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.37
Consensus pattern (30 bp):
TATATATATATAAAGTATTAAAGTATAAAA
Found at i:16568 original size:8 final size:7
Alignment explanation
Indices: 16532--16680 Score: 78
Period size: 8 Copynumber: 20.4 Consensus size: 7
16522 TATATATATA
16532 TATAAAG
1 TATAAAG
*
16539 TATAAAA
1 TATAAAG
16546 TATATAA-
1 TATA-AAG
16553 TATAAAG
1 TATAAAG
16560 TATTAAAG
1 TA-TAAAG
16568 TATATAA-
1 TATA-AAG
16575 TATAAAG
1 TATAAAG
16582 TAATAAAG
1 T-ATAAAG
* **
16590 TGT-TTG
1 TATAAAG
* *
16596 GATATATG
1 TATA-AAG
16604 TATTAAAG
1 TA-TAAAG
16612 CATATAAA-
1 --TATAAAG
16620 TAT-AAG
1 TATAAAG
16626 TATTAAA-
1 TA-TAAAG
16633 TATAAAG
1 TATAAAG
16640 TATATAAG
1 TATA-AAG
16648 TATATAAG
1 TATA-AAG
16656 TACTAAAG
1 TA-TAAAG
16664 TATATAA-
1 TATA-AAG
16671 TATAAAG
1 TATAAAG
16678 TAT
1 TAT
16681 TGAACAATAT
Statistics
Matches: 114, Mismatches: 9, Indels: 38
0.71 0.06 0.24
Matches are distributed among these distances:
5 2 0.02
6 17 0.15
7 40 0.35
8 45 0.39
9 8 0.07
10 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.36
Consensus pattern (7 bp):
TATAAAG
Found at i:16589 original size:22 final size:22
Alignment explanation
Indices: 16524--16590 Score: 100
Period size: 22 Copynumber: 3.0 Consensus size: 22
16514 TGTATATATA
*
16524 TATATATATATAAAGT-ATAAAA
1 TATATA-ATATAAAGTAATAAAG
*
16546 TATATAATATAAAGTATTAAAG
1 TATATAATATAAAGTAATAAAG
16568 TATATAATATAAAGTAATAAAG
1 TATATAATATAAAGTAATAAAG
16590 T
1 T
16591 GTTTGGATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.22
22 32 0.78
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
TATATAATATAAAGTAATAAAG
Found at i:16644 original size:22 final size:22
Alignment explanation
Indices: 16619--16752 Score: 80
Period size: 22 Copynumber: 5.8 Consensus size: 22
16609 AAGCATATAA
16619 ATATAAGTATTAAATATAAAGT
1 ATATAAGTATTAAATATAAAGT
*
16641 ATATAAGTATATAAGTACTAAAGT
1 ATATAAGTAT-TAAATA-TAAAGT
*
16665 ATATAA-TA-TAAAGTATTGAACAATAT
1 ATATAAGTATTAAA-TA-T--A-AA-GT
* *
16691 AATATAATTATTAAATATAAAAT
1 -ATATAAGTATTAAATATAAAGT
16714 AT-TAAAGTATATAAATAT-AAGT
1 ATAT-AAGTAT-TAAATATAAAGT
* *
16736 AT-TAAATATAAAATATA
1 ATATAAGTATTAAATATA
16753 TTAATTATCA
Statistics
Matches: 91, Mismatches: 8, Indels: 27
0.72 0.06 0.21
Matches are distributed among these distances:
20 6 0.07
21 9 0.10
22 26 0.29
23 16 0.18
24 15 0.16
25 3 0.03
26 1 0.01
27 7 0.08
28 4 0.04
29 4 0.04
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (22 bp):
ATATAAGTATTAAATATAAAGT
Found at i:16739 original size:36 final size:36
Alignment explanation
Indices: 16604--16751 Score: 167
Period size: 36 Copynumber: 4.1 Consensus size: 36
16594 TGGATATATG
* *
16604 TATTAAAGCATATAAATATAAGTATTAAATATAAAG
1 TATTAAAGTATATAAATATAAGTATTAAATATAAAA
* *
16640 TA-TATAAGTATATAAGTACTAAAGTA-TATAATATAAAG
1 TATTA-AAGTATATAAATA-T-AAGTATTA-AATATAAAA
* ** *
16678 TATTGAACAATAT-AATATAATTATTAAATATAAAA
1 TATTAAAGTATATAAATATAAGTATTAAATATAAAA
16713 TATTAAAGTATATAAATATAAGTATTAAATATAAAA
1 TATTAAAGTATATAAATATAAGTATTAAATATAAAA
16749 TAT
1 TAT
16752 ATTAATTATC
Statistics
Matches: 93, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
35 24 0.26
36 40 0.43
37 6 0.06
38 22 0.24
39 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (36 bp):
TATTAAAGTATATAAATATAAGTATTAAATATAAAA
Found at i:16753 original size:22 final size:22
Alignment explanation
Indices: 16529--16733 Score: 84
Period size: 22 Copynumber: 9.0 Consensus size: 22
16519 ATATATATAT
* *
16529 ATATATAAAGTATAAAATATATA
1 ATATAT-AAGTATTAAATATAAA
*
16552 ATATA-AAGTATTAAAGTATATA
1 ATATATAAGTATTAAA-TATAAA
* * ***
16574 ATATA-AAGTAATAAAGTGTTTGG
1 ATATATAAGTATTAAA-T-ATAAA
* *
16597 ATATAT--GTATTAAAGCATATA
1 ATATATAAGTATTAAA-TATAAA
16618 A-ATATAAGTATTAAATATAAA
1 ATATATAAGTATTAAATATAAA
* *
16639 GTATATAAGTATATAAGTACTAAA
1 ATATATAAGTAT-TAAATA-TAAA
*
16663 GTATATAA-TA-TAAAGTATTGAACAA
1 ATATATAAGTATTAAA-TA-T--A-AA
*
16688 TATAATATAATTATTAAATATAAA
1 -AT-ATATAAGTATTAAATATAAA
16712 ATAT-TAAAGTATATAAATATAA
1 ATATAT-AAGTAT-TAAATATAA
16734 GTATTAAATA
Statistics
Matches: 144, Mismatches: 20, Indels: 36
0.72 0.10 0.18
Matches are distributed among these distances:
20 4 0.03
21 19 0.13
22 58 0.40
23 29 0.20
24 15 0.10
25 3 0.02
26 1 0.01
27 7 0.05
28 4 0.03
29 4 0.03
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (22 bp):
ATATATAAGTATTAAATATAAA
Found at i:16766 original size:73 final size:73
Alignment explanation
Indices: 16613--16751 Score: 187
Period size: 73 Copynumber: 1.9 Consensus size: 73
16603 GTATTAAAGC
* * * *
16613 ATATAAATATAAGTATTAAATATAAAGTATATAAGTATATAAGTACTAAAGTATATAATATAAAG
1 ATAT-AATATAATTATTAAATATAAAATATATAAGTATATAAATACTAAAGTATATAATATAAAA
16678 TATTGAACA
65 TATTGAACA
16687 ATATAATATAATTATTAAATATAAAATAT-TAAAGTATATAAATA-T-AAGTAT-TAAATATAAA
1 ATATAATATAATTATTAAATATAAAATATAT-AAGTATATAAATACTAAAGTATAT-AATATAAA
16748 ATAT
64 ATAT
16752 ATTAATTATC
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
70 1 0.02
71 17 0.29
72 2 0.03
73 35 0.59
74 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.36
Consensus pattern (73 bp):
ATATAATATAATTATTAAATATAAAATATATAAGTATATAAATACTAAAGTATATAATATAAAAT
ATTGAACA
Found at i:16797 original size:39 final size:39
Alignment explanation
Indices: 16753--16850 Score: 196
Period size: 39 Copynumber: 2.5 Consensus size: 39
16743 ATAAAATATA
16753 TTAATTATCATAATTAATATACTGAGTATATTTATTAAT
1 TTAATTATCATAATTAATATACTGAGTATATTTATTAAT
16792 TTAATTATCATAATTAATATACTGAGTATATTTATTAAT
1 TTAATTATCATAATTAATATACTGAGTATATTTATTAAT
16831 TTAATTATCATAATTAATAT
1 TTAATTATCATAATTAATAT
16851 TTAATTATAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (39 bp):
TTAATTATCATAATTAATATACTGAGTATATTTATTAAT
Found at i:16809 original size:18 final size:18
Alignment explanation
Indices: 16786--16858 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
16776 GAGTATATTT
16786 ATTAATTTAATTATCATA
1 ATTAATTTAATTATCATA
* * *
16804 ATTAATATACTGAGTAT-ATTT
1 ATTAAT-T--TAATTATCA-TA
16825 ATTAATTTAATTATCATA
1 ATTAATTTAATTATCATA
16843 ATTAATATTTAATTAT
1 ATT-A-ATTTAATTAT
16859 AACATTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
18 15 0.36
19 3 0.07
20 12 0.29
21 12 0.29
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTAATTTAATTATCATA
Found at i:16867 original size:20 final size:20
Alignment explanation
Indices: 16829--16867 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16819 ATATTTATTA
* *
16829 ATTTAATTATCATAATTAAT
1 ATTTAATTATAACAATTAAT
*
16849 ATTTAATTATAACATTTAA
1 ATTTAATTATAACAATTAA
16868 AAATTAATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAATTATAACAATTAAT
Found at i:19456 original size:36 final size:36
Alignment explanation
Indices: 19410--19682 Score: 420
Period size: 36 Copynumber: 7.6 Consensus size: 36
19400 ATGAATCGCC
19410 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
* * * *
19446 TCATTTCGTTCGACTTGAATCGGAAGTGTCTATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
*
19482 TCCTTCCGTTCGTCTTGAATCGGAAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGG-AAGTGCCGATGCT
*
19519 TCCTTCCGTTCGACTTGAATCGAAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
* *
19555 TCCTTCCGTTCGACTTGAATCGAAAATGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
* * *
19591 TTCTTCCGTTCAACTTGAATCGGAAGTGCCGTTGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
* *
19627 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGTTGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
19663 TCCTTCCGTTCGACTTGAAT
1 TCCTTCCGTTCGACTTGAAT
19683 TGTAACAACC
Statistics
Matches: 216, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
36 184 0.85
37 32 0.15
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
Found at i:20438 original size:19 final size:21
Alignment explanation
Indices: 20414--20462 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
20404 GAACGCTGGA
20414 AACCGGTTTTGA-CCGG-TTT
1 AACCGGTTTTGACCCGGTTTT
20433 AACCGGTTTTGACCCGGTTTT
1 AACCGGTTTTGACCCGGTTTT
*
20454 GACCGGTTT
1 AACCGGTTT
20463 ACCCGTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 12 0.44
20 4 0.15
21 11 0.41
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.37
Consensus pattern (21 bp):
AACCGGTTTTGACCCGGTTTT
Found at i:20451 original size:11 final size:10
Alignment explanation
Indices: 20415--20462 Score: 71
Period size: 10 Copynumber: 4.8 Consensus size: 10
20405 AACGCTGGAA
20415 ACCGGTTTTG
1 ACCGGTTTTG
*
20425 ACCGG-TTTA
1 ACCGGTTTTG
20434 ACCGGTTTTG
1 ACCGGTTTTG
20444 ACCCGGTTTTG
1 A-CCGGTTTTG
20455 ACCGGTTT
1 ACCGGTTT
20463 ACCCGTTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 8 0.24
10 16 0.47
11 10 0.29
ACGTcount: A:0.12, C:0.23, G:0.27, T:0.38
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:20504 original size:18 final size:18
Alignment explanation
Indices: 20483--20517 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
20473 CCGACCCGTT
20483 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
20501 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
20518 GTTGACCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:20517 original size:13 final size:13
Alignment explanation
Indices: 20463--20506 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
20453 TGACCGGTTT
*
20463 ACCCGTTTACCCG
1 ACCCGTTGACCCG
20476 ACCCGTTGACCCG
1 ACCCGTTGACCCG
20489 ACCCGTTGACCCG
1 ACCCGTTGACCCG
20502 ACCCG
1 ACCCG
20507 ACCCGTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.16, C:0.48, G:0.20, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:20586 original size:29 final size:29
Alignment explanation
Indices: 20526--20591 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
20516 CCGTTGACCA
* *** *
20526 GTGCTATTATGGGAATTAATTCGGTTTTG
1 GTGCTATTATGAGAATTAATTCGAAATGG
20555 GTGCTATTATGAGAATTAATTCGAAATGG
1 GTGCTATTATGAGAATTAATTCGAAATGG
20584 GTGCTATT
1 GTGCTATT
20592 TTGGTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (29 bp):
GTGCTATTATGAGAATTAATTCGAAATGG
Found at i:20600 original size:29 final size:28
Alignment explanation
Indices: 20526--20600 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
20516 CCGTTGACCA
*** *
20526 GTGCTATTATGGGAATTAATTCGGTTTTG
1 GTGCTATTAT-GGAATTAATTCGAAATGG
20555 GTGCTATTATGAGAATTAATTCGAAATGG
1 GTGCTATTATG-GAATTAATTCGAAATGG
*
20584 GTGCTATTTTGGTAATT
1 GTGCTATTATGG-AATT
20601 TTTTTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 37 0.95
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (28 bp):
GTGCTATTATGGAATTAATTCGAAATGG
Found at i:21349 original size:24 final size:24
Alignment explanation
Indices: 21317--21385 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
21307 ATAGTTTATC
*
21317 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * * *
21341 TGATATTTGATCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
21365 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
21386 TTTTGTACTT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:27630 original size:10 final size:10
Alignment explanation
Indices: 27615--27658 Score: 65
Period size: 9 Copynumber: 4.6 Consensus size: 10
27605 AACGCTGGAA
27615 ACCGGTTTTG
1 ACCGGTTTTG
*
27625 ACCGG-TTTA
1 ACCGGTTTTG
27634 ACCGGTTTTG
1 ACCGGTTTTG
27644 ACCGG-TTTG
1 ACCGGTTTTG
27653 ACCGGT
1 ACCGGT
27659 CACGACCCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 17 0.57
10 13 0.43
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.34
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:27638 original size:19 final size:19
Alignment explanation
Indices: 27614--27658 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
27604 GAACGCTGGA
27614 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
27633 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
*
27652 GACCGGT
1 AACCGGT
27659 CACGACCCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:27665 original size:19 final size:19
Alignment explanation
Indices: 27624--27671 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
27614 AACCGGTTTT
***
27624 GACCGGTTTAACCGGTTTT
1 GACCGGTTTAACCGGTCAC
*
27643 GACCGGTTTGACCGGTCAC
1 GACCGGTTTAACCGGTCAC
*
27662 GACCCGTTTA
1 GACCGGTTTA
27672 CCCGTTTACC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (19 bp):
GACCGGTTTAACCGGTCAC
Found at i:27712 original size:13 final size:13
Alignment explanation
Indices: 27671--27701 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
27661 CGACCCGTTT
*
27671 ACCCGTTTACCCG
1 ACCCGTTGACCCG
27684 ACCCGTTGACCCG
1 ACCCGTTGACCCG
27697 ACCCG
1 ACCCG
27702 ACCCGTTGAC
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:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:27774 original size:29 final size:29
Alignment explanation
Indices: 27714--27777 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
27704 CCGTTGACCA
* *** *
27714 GTGCTATTATGGGAATTAATTCGGTTTTG
1 GTGCTATTATGAGAATTAATTCGAAATGG
27743 GTGCTATTATGAGAATTAATTCGAAATGG
1 GTGCTATTATGAGAATTAATTCGAAATGG
27772 GTGCTA
1 GTGCTA
27778 ATTTGGTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.39
Consensus pattern (29 bp):
GTGCTATTATGAGAATTAATTCGAAATGG
Found at i:28544 original size:24 final size:24
Alignment explanation
Indices: 28512--28580 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
28502 AATAGTTATC
*
28512 TGATTTTTGACCTGGATTCTGATA
1 TGATATTTGACCTGGATTCTGATA
* * * *
28536 TGATATTTGATCTGAATTTTTATA
1 TGATATTTGACCTGGATTCTGATA
* * *
28560 TGATACTTGACATGGACTCTG
1 TGATATTTGACCTGGATTCTG
28581 TTTTGTACTT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATTTGACCTGGATTCTGATA
Found at i:29116 original size:1 final size:1
Alignment explanation
Indices: 29110--29135 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
29100 TATAAGTTGT
29110 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
29136 CCTCTGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30931 original size:30 final size:30
Alignment explanation
Indices: 30863--30931 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
30853 TGGGTTGGGT
* *
30863 TGGGTTTAATCTCATATGGATTGCTCGAAC
1 TGGGTTGAATCTCATATGAATTGCTCGAAC
* * *
30893 TCGATTGAATCTCATATGAATTGCTGGAA-
1 TGGGTTGAATCTCATATGAATTGCTCGAAC
30922 TGGGGTTGAA
1 T-GGGTTGAA
30932 CCTCTTGTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (30 bp):
TGGGTTGAATCTCATATGAATTGCTCGAAC
Found at i:31789 original size:19 final size:19
Alignment explanation
Indices: 31765--31802 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31755 TTGCATTATA
31765 TATATATATATATATGGAG
1 TATATATATATATATGGAG
31784 TATATATATATATATGGAG
1 TATATATATATATATGGAG
31803 AGAGAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TATATATATATATATGGAG
Found at i:32066 original size:32 final size:32
Alignment explanation
Indices: 32029--32134 Score: 104
Period size: 32 Copynumber: 3.3 Consensus size: 32
32019 TATCACATTA
*
32029 ATGATGTAATATGTGTCAAATCACCTAAAACG
1 ATGATGTAATATGTGTCAAATCACCCAAAACG
* * * *
32061 ATGATGTAATATGTATGATATCACCCAAAATG
1 ATGATGTAATATGTGTCAAATCACCCAAAACG
* * * ** *
32093 ATGATGTGATATATGTCACATCAATCAAAATG
1 ATGATGTAATATGTGTCAAATCACCCAAAACG
*
32125 ATGATATAAT
1 ATGATGTAAT
32135 TTATGTCATG
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (32 bp):
ATGATGTAATATGTGTCAAATCACCCAAAACG
Found at i:32740 original size:204 final size:201
Alignment explanation
Indices: 32375--32974 Score: 701
Period size: 205 Copynumber: 3.0 Consensus size: 201
32365 GGGAGTAGGG
* * * * * *
32375 GAGAAAG-AA-AGAGATAATCCGATTACACATAATGTAAAACTAAAAGTTTTAAATATGATTGTT
1 GAGAAAGAAAGAGAGATGATCCAATAACACTTAGTGTAAAACTAAAA-TTTTACATATGATTGTT
* * * * * *
32438 GGATGAGGGAAATCAAATAATGAGATTAAT--CTTTTATTTTTTCAGTAAATATCTTCACATGAT
65 -GATGA-GGAAATCAAAGATTGAGATTAATCCCTTATATTTTTTCAGTGAATATCTTTACATGGT
* * * *
32501 ATTATTTTTCTTTGTCCTCCATTTTTTATAATTGAAAGCAACCT-AGTTAAAACGTTAGACATTT
128 AATATTTCTCTTTGCCCTCCATTTTTTAAAATTGAAAGCAACCTAAGTTAAAACGTTAGACATTT
*
32565 TTTTAGAGA
193 TTTTAGAAA
* * * *
32574 GAGAAAGAAATAGAGTAATGATCTAATTAC-GTCTAGTGTAAAACTAACAATTTTACATATGATT
1 GAGAAAGAAAGAGAG--ATGATCCAATAACACT-TAGTGTAAAACTAA-AATTTTACATATGATT
*
32638 GATTGATGAGGAAATCTAAGATTGAGATTAATCCCTTATATTTTTTCAGTGAATATCTTTACATG
62 G-TTGATGAGGAAATCAAAGATTGAGATTAATCCCTTATATTTTTTCAGTGAATATCTTTACATG
* * * * * * *
32703 GTAATGTTTCTCTTTACCCTCTATTTTTCAGAATTGAAAGCAACCTAAGTTAGAATGTTAGACAT
126 GTAATATTTCTCTTTGCCCTCCATTTTTTAAAATTGAAAGCAACCTAAGTTAAAACGTTAGACA-
32768 TTTTTTTAGAAA
190 TTTTTTTAGAAA
** * * *
32780 GAGAGGGGAAGAGAGATTATCCAATAACACTTAGTATAAAACTAATAATTTTACATATGATTGTT
1 GAGAAAGAAAGAGAGATGATCCAATAACACTTAGTGTAAAACTAA-AATTTTACATATGATTGTT
* * * *
32845 GAATGAAAGAAATCAAAGATTGAGATTAATCCCTTATTTTTTTTTAGTGAATATCTTTGCATGGT
65 G-ATG-AGGAAATCAAAGATTGAGATTAATCCCTTATATTTTTTCAGTGAATATCTTTACATGGT
32910 AATATTTCTCTTTGCCCTCCATTTTTTAAAATTGAAAGCAACCTAAGTTAAAACGTTAGAC-TTT
128 AATATTTCTCTTTGCCCTCCATTTTTTAAAATTGAAAGCAACCTAAGTTAAAACGTTAGACATTT
32974 T
193 T
32975 GAAGGATCGA
Statistics
Matches: 340, Mismatches: 47, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
199 7 0.02
200 2 0.01
201 4 0.01
202 20 0.06
203 49 0.14
204 112 0.33
205 124 0.36
206 22 0.06
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (201 bp):
GAGAAAGAAAGAGAGATGATCCAATAACACTTAGTGTAAAACTAAAATTTTACATATGATTGTTG
ATGAGGAAATCAAAGATTGAGATTAATCCCTTATATTTTTTCAGTGAATATCTTTACATGGTAAT
ATTTCTCTTTGCCCTCCATTTTTTAAAATTGAAAGCAACCTAAGTTAAAACGTTAGACATTTTTT
TAGAAA
Found at i:33961 original size:26 final size:26
Alignment explanation
Indices: 33910--33962 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
33900 CTATTATACC
33910 CTATATTGGTTTGATATACTTATCAT
1 CTATATTGGTTTGATATACTTATCAT
33936 CTATATTGGTTTGATATACTTATCAT
1 CTATATTGGTTTGATATACTTATCAT
33962 C
1 C
33963 ATTTTTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.49
Consensus pattern (26 bp):
CTATATTGGTTTGATATACTTATCAT
Found at i:34090 original size:20 final size:21
Alignment explanation
Indices: 34065--34104 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
34055 AAATCTAAGG
34065 TAAATTA-CATGTTTAGTACC
1 TAAATTATCATGTTTAGTACC
*
34085 TAAATTATCATTTTTAGTAC
1 TAAATTATCATGTTTAGTAC
34105 GTTTCAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAATTATCATGTTTAGTACC
Found at i:39999 original size:30 final size:30
Alignment explanation
Indices: 39920--40005 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 30
39910 AAATTGATTG
* * *
39920 GACCTCGATTCGAGTTTGGGATTTTGATTT
1 GACCTCGTTTCGAGTTTGGGATTTTGACTA
** *
39950 GACAC-AATTT-GAATTTGGGATTTTGACTA
1 GAC-CTCGTTTCGAGTTTGGGATTTTGACTA
39979 GACCTCGTTTCGAGTTTGGGATTTTGA
1 GACCTCGTTTCGAGTTTGGGATTTTGA
40006 GTGGACCTGG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
28 1 0.02
29 22 0.50
30 20 0.45
31 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.41
Consensus pattern (30 bp):
GACCTCGTTTCGAGTTTGGGATTTTGACTA
Found at i:40013 original size:30 final size:30
Alignment explanation
Indices: 39913--40042 Score: 122
Period size: 30 Copynumber: 4.4 Consensus size: 30
39903 CTTTGAGAAA
*
39913 TTGATTGGACCTCGATTCGAGTTTGGGATT
1 TTGATTGGACCTCGTTTCGAGTTTGGGATT
* ** *
39943 TTGATTTGACAC-AATTT-GAATTTGGGATT
1 TTGATTGGAC-CTCGTTTCGAGTTTGGGATT
* *
39972 TTGACTAGACCTCGTTTCGAGTTTGGGATT
1 TTGATTGGACCTCGTTTCGAGTTTGGGATT
* * * *
40002 TTGAGTGGACCTGGGTTTGGA-TTTGGGATA
1 TTGATTGGACCT-CGTTTCGAGTTTGGGATT
40032 TTGATTGGACC
1 TTGATTGGACC
40043 ATAGTTCGAC
Statistics
Matches: 80, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.01
29 22 0.28
30 50 0.62
31 7 0.09
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.40
Consensus pattern (30 bp):
TTGATTGGACCTCGTTTCGAGTTTGGGATT
Found at i:41597 original size:2 final size:2
Alignment explanation
Indices: 41592--41664 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
41582 TATCATTAAC
41592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41634 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41665 ATAATAGATC
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:42974 original size:29 final size:29
Alignment explanation
Indices: 42929--43236 Score: 244
Period size: 30 Copynumber: 10.4 Consensus size: 29
42919 CTTTGAGAAA
*
42929 TTGACTGGACCTCGATTCGAGTTTGGGA-T
1 TTGACTGGA-CTAGATTCGAGTTTGGGATT
* *
42958 TTGACGGGACTTGGATTCGAGTTTGGGATT
1 TTGACTGGAC-TAGATTCGAGTTTGGGATT
* * * *
42988 TTGATTCGACCACAGTTCGAGTTTGGGATT
1 TTGACTGGACTAGA-TTCGAGTTTGGGATT
*
43018 TTGACTGGACATCGATTCGAGTTTGGGATT
1 TTGACTGGAC-TAGATTCGAGTTTGGGATT
* * * * *
43048 TTGATTCGACCACAGTTCGAATTTGGGATT
1 TTGACTGGACTAGA-TTCGAGTTTGGGATT
*
43078 TTGACTGGACCTCGATTCGAGTTTGGGATT
1 TTGACTGGA-CTAGATTCGAGTTTGGGATT
* * * * *
43108 TTGATTCGACCACAGTTCGAATTTGGGATT
1 TTGACTGGACTAGA-TTCGAGTTTGGGATT
*
43138 TTGACTGGACCTCA-ATACGAGTTTGGGATT
1 TTGACTGGA-CT-AGATTCGAGTTTGGGATT
* * * * **
43168 TTGATTCGACCACAGTTCGAACTTGGGATT
1 TTGACTGGACTAGA-TTCGAGTTTGGGATT
* *
43198 TTGACTGGAC-CGTTTCGAGTTTGGGATT
1 TTGACTGGACTAGATTCGAGTTTGGGATT
*
43226 TTGAGTGGACT
1 TTGACTGGACT
43237 GGGTTTGGCT
Statistics
Matches: 217, Mismatches: 50, Indels: 24
0.75 0.17 0.08
Matches are distributed among these distances:
28 24 0.11
29 30 0.14
30 157 0.72
31 5 0.02
32 1 0.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.36
Consensus pattern (29 bp):
TTGACTGGACTAGATTCGAGTTTGGGATT
Found at i:43007 original size:30 final size:30
Alignment explanation
Indices: 42973--43229 Score: 292
Period size: 30 Copynumber: 8.6 Consensus size: 30
42963 GGGACTTGGA
*
42973 TTCGAGTTTGGGATTTTGATTCGACCACAG
1 TTCGAGTTTGGGATTTTGACTCGACCACAG
*
43003 TTCGAGTTTGGGATTTTGACTGGA-CATC-G
1 TTCGAGTTTGGGATTTTGACTCGACCA-CAG
*
43032 ATTCGAGTTTGGGATTTTGATTCGACCACAG
1 -TTCGAGTTTGGGATTTTGACTCGACCACAG
* * *
43063 TTCGAATTTGGGATTTTGACTGGACCTC-G
1 TTCGAGTTTGGGATTTTGACTCGACCACAG
*
43092 ATTCGAGTTTGGGATTTTGATTCGACCACAG
1 -TTCGAGTTTGGGATTTTGACTCGACCACAG
* * * *
43123 TTCGAATTTGGGATTTTGACTGGACCTCAA
1 TTCGAGTTTGGGATTTTGACTCGACCACAG
* *
43153 TACGAGTTTGGGATTTTGATTCGACCACAG
1 TTCGAGTTTGGGATTTTGACTCGACCACAG
** *
43183 TTCGAACTTGGGATTTTGACTGGA-C-C-G
1 TTCGAGTTTGGGATTTTGACTCGACCACAG
43210 TTTCGAGTTTGGGATTTTGA
1 -TTCGAGTTTGGGATTTTGA
43230 GTGGACTGGG
Statistics
Matches: 190, Mismatches: 30, Indels: 16
0.81 0.13 0.07
Matches are distributed among these distances:
27 1 0.01
28 18 0.09
29 5 0.03
30 162 0.85
31 4 0.02
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (30 bp):
TTCGAGTTTGGGATTTTGACTCGACCACAG
Found at i:43040 original size:60 final size:60
Alignment explanation
Indices: 42944--43229 Score: 461
Period size: 60 Copynumber: 4.8 Consensus size: 60
42934 TGGACCTCGA
* * * *
42944 TTCGAGTTTGGGA-TTTGACGGGACTTGGATTCGAGTTTGGGATTTTGATTCGACCACAG
1 TTCGAATTTGGGATTTTGACTGGACCTCGATTCGAGTTTGGGATTTTGATTCGACCACAG
* *
43003 TTCGAGTTTGGGATTTTGACTGGACATCGATTCGAGTTTGGGATTTTGATTCGACCACAG
1 TTCGAATTTGGGATTTTGACTGGACCTCGATTCGAGTTTGGGATTTTGATTCGACCACAG
43063 TTCGAATTTGGGATTTTGACTGGACCTCGATTCGAGTTTGGGATTTTGATTCGACCACAG
1 TTCGAATTTGGGATTTTGACTGGACCTCGATTCGAGTTTGGGATTTTGATTCGACCACAG
* *
43123 TTCGAATTTGGGATTTTGACTGGACCTCAATACGAGTTTGGGATTTTGATTCGACCACAG
1 TTCGAATTTGGGATTTTGACTGGACCTCGATTCGAGTTTGGGATTTTGATTCGACCACAG
* *
43183 TTCGAACTTGGGATTTTGACTGGA-C-CGTTTCGAGTTTGGGATTTTGA
1 TTCGAATTTGGGATTTTGACTGGACCTCGATTCGAGTTTGGGATTTTGA
43230 GTGGACTGGG
Statistics
Matches: 215, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
58 19 0.09
59 14 0.07
60 182 0.85
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.37
Consensus pattern (60 bp):
TTCGAATTTGGGATTTTGACTGGACCTCGATTCGAGTTTGGGATTTTGATTCGACCACAG
Found at i:43831 original size:16 final size:16
Alignment explanation
Indices: 43810--43848 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
43800 ATATATAAAT
43810 TAACCGGGTACTCGGG
1 TAACCGGGTACTCGGG
43826 TAACCGGGTACTCGGG
1 TAACCGGGTACTCGGG
43842 TAACCGG
1 TAACCGG
43849 ATACCCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.36, T:0.18
Consensus pattern (16 bp):
TAACCGGGTACTCGGG
Found at i:44717 original size:27 final size:26
Alignment explanation
Indices: 44683--44747 Score: 121
Period size: 27 Copynumber: 2.5 Consensus size: 26
44673 GTAATTCCAA
44683 GGTTTTCCCTTCTCGTCCGTGTTGAT
1 GGTTTTCCCTTCTCGTCCGTGTTGAT
44709 GGTTTTTCCCTTCTCGTCCGTGTTGAT
1 GG-TTTTCCCTTCTCGTCCGTGTTGAT
44736 GGTTTTCCCTTC
1 GGTTTTCCCTTC
44748 CATTAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 12 0.32
27 26 0.68
ACGTcount: A:0.03, C:0.28, G:0.22, T:0.48
Consensus pattern (26 bp):
GGTTTTCCCTTCTCGTCCGTGTTGAT
Found at i:46012 original size:32 final size:32
Alignment explanation
Indices: 45976--46039 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
45966 TCGAATTACA
*
45976 TAGTCCAACATCCAAACATTA-TTAAAAAATGT
1 TAGTCCAACATCC-AACATAATTTAAAAAATGT
*
46008 TAGTCCAACATCCAATATAATTTAAAAAATGT
1 TAGTCCAACATCCAACATAATTTAAAAAATGT
46040 CATGTTAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.17
32 24 0.83
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (32 bp):
TAGTCCAACATCCAACATAATTTAAAAAATGT
Found at i:46212 original size:68 final size:68
Alignment explanation
Indices: 46125--46324 Score: 296
Period size: 68 Copynumber: 3.0 Consensus size: 68
46115 AAAAAAAAAA
*
46125 CGAGTGACCAAAACATAAATTAAATTATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAT
1 CGAGTGACCAAAACATAAATTAGATTATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAT
46190 AAT
66 AAT
* * *
46193 CGGGTGACCAAAACATAAATTAGATAATATATAAGTGATCAAATAGGTAGTTTACCCTAAATAAT
1 CGAGTGACCAAAACATAAATTAGATTATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAT
46258 AAT
66 AAT
* * * **
46261 CGAGTGGCCAAAATATAAATTAGA-TA-ATATAAGTAACCAAATAAATAGTTTACCCTAAAATAA
1 CGAGTGACCAAAACATAAATTAGATTATATATAAGTGACCAAATAGGTAGTTTACCCT-AAATAA
46324 T
65 T
46325 CCCTAATCGG
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
66 26 0.22
67 8 0.07
68 85 0.71
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (68 bp):
CGAGTGACCAAAACATAAATTAGATTATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAT
AAT
Done.