Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009120.1 Hibiscus syriacus cultivar Beakdansim tig00112609_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: 584398
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:212713 original size:14 final size:14
Alignment explanation
Indices: 212696--212728 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
212686 ATTTCTATGT
*
212696 AGGGAATTATTTGC
1 AGGGAATTATTTAC
212710 AGGGAATTATTTAC
1 AGGGAATTATTTAC
212724 AGGGA
1 AGGGA
212729 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:216622 original size:64 final size:64
Alignment explanation
Indices: 216543--216682 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 64
216533 CGGATCTTGG
* *
216543 CAGGTCGGGTAAAATCGGGTACAGGTAAACTT-AGGTTGATTTAACAT-CAGATCCAAATCGGGT
1 CAGGTCGGGTCAAATC-AGTACAGGTAAACTTCAGGTTGATTTAAC-TCCAGATCCAAATCGGGT
216606 T
64 T
* * * * ** * *
216607 CAGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGGTTGATTTGACTCCAGATCCATATCGGGTT
1 CAGGTCGGGTCAAATCAGTACAGGTAAACTTCAGGTTGATTTAACTCCAGATCCAAATCGGGTT
216671 CAGGTCGGGTCA
1 CAGGTCGGGTCA
216683 TTTTCAGTTC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 10 0.16
64 53 0.84
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (64 bp):
CAGGTCGGGTCAAATCAGTACAGGTAAACTTCAGGTTGATTTAACTCCAGATCCAAATCGGGTT
Found at i:217375 original size:15 final size:15
Alignment explanation
Indices: 217355--217477 Score: 58
Period size: 15 Copynumber: 7.8 Consensus size: 15
217345 AATTGAAAAA
217355 AATATATATATATAT
1 AATATATATATATAT
*
217370 AATATAAAATTATATAT
1 AATAT-ATA-TATATAT
*
217387 AAACTATATTTATATTAT
1 -AA-TATATATATA-TAT
*
217405 AAAATATATAATTATTAT
1 AATATATAT-A-TA-TAT
217423 AA-ACTATATATATA-
1 AATA-TATATATATAT
* *
217437 AAT-TATATTTATGT
1 AATATATATATATAT
217451 AA-ACTATATATATA-
1 AATA-TATATATATAT
*
217465 AACTATGTATATA
1 AA-TATATATATA
217478 AAATTATAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
13 8 0.10
14 6 0.07
15 22 0.26
16 10 0.12
17 16 0.19
18 19 0.23
19 3 0.04
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:217414 original size:20 final size:20
Alignment explanation
Indices: 217351--217522 Score: 87
Period size: 18 Copynumber: 9.0 Consensus size: 20
217341 TAAAAATTGA
*
217351 AAAAAATATATATATA-TAT
1 AAAATATATATATATATTAT
* *
217370 AATATA-AAAT-TATA-TAT
1 AAAATATATATATATATTAT
*
217387 AAACTATAT-T-TATATTAT
1 AAAATATATATATATATTAT
217405 AAAATATATA-AT-TATTAT
1 AAAATATATATATATATTAT
* *
217423 AAACTATATATATAAATTAT
1 AAAATATATATATATATTAT
** * *
217443 -ATTTATGTAAACTATATATAT
1 AAAATATATATA-TATAT-TAT
* * *
217464 AAACTATGTATATAAAATTAT
1 AAAATATATATAT-ATATTAT
*
217485 AAACTATATA-AT-TATTAT
1 AAAATATATATATATATTAT
** *
217503 AAGCTATATATATAAATTAT
1 AAAATATATATATATATTAT
217523 GTTTATGTGA
Statistics
Matches: 119, Mismatches: 22, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
17 16 0.13
18 44 0.37
19 16 0.13
20 16 0.13
21 16 0.13
22 11 0.09
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAATATATATATATATTAT
Found at i:217438 original size:13 final size:13
Alignment explanation
Indices: 217356--217577 Score: 133
Period size: 13 Copynumber: 17.2 Consensus size: 13
217346 ATTGAAAAAA
*
217356 ATATATATATA-T
1 ATATATATAAACT
*
217368 ATA-ATATAAAAT
1 ATATATATAAACT
217380 -TATATATAAACT
1 ATATATATAAACT
* *
217392 ATAT-T-TATATT
1 ATATATATAAACT
*
217403 ATAAAATATATAA-T
1 AT-ATATATA-AACT
217417 -TAT-TATAAACT
1 ATATATATAAACT
*
217428 ATATATATAAATT
1 ATATATATAAACT
*
217441 ATATTTATGTAAACT
1 ATA--TATATAAACT
217456 ATATATATAAACT
1 ATATATATAAACT
* *
217469 ATGTATATAAAATT
1 ATATATAT-AAACT
*
217483 ATAAACTATATAA-T
1 ATATA-TATA-AACT
*
217497 -TAT-TATAAGCT
1 ATATATATAAACT
*
217508 ATATATATAAATT
1 ATATATATAAACT
* * *
217521 ATGTTTATGTGAACT
1 A--TATATATAAACT
217536 ATATATATAAACT
1 ATATATATAAACT
*
217549 ATGTATATAAACT
1 ATATATATAAACT
*
217562 ATATGTATAAACT
1 ATATATATAAACT
217575 ATA
1 ATA
217578 AAAAGTACAT
Statistics
Matches: 161, Mismatches: 29, Indels: 39
0.70 0.13 0.17
Matches are distributed among these distances:
10 3 0.02
11 24 0.15
12 21 0.13
13 75 0.47
14 12 0.07
15 26 0.16
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:217461 original size:28 final size:28
Alignment explanation
Indices: 217397--217577 Score: 128
Period size: 28 Copynumber: 6.6 Consensus size: 28
217387 AAACTATATT
*
217397 TATAT-TATAAAATATATAATTATTATAAAC
1 TATATATAT-AAAT-TATATTTA-TATAAAC
*
217427 TATATATATAAATTATATTTATGTAAAC
1 TATATATATAAATTATATTTATATAAAC
* *
217455 TATATATATAAA--CTATGTATATAAA-
1 TATATATATAAATTATATTTATATAAAC
* * *
217480 -AT-TATA-AACTATATAATTATTATAAGC
1 TATATATATAAAT-TATATTTA-TATAAAC
* * *
217507 TATATATATAAATTATGTTTATGTGAAC
1 TATATATATAAATTATATTTATATAAAC
* *
217535 TATATATATAAA--CTATGTATATAAAC
1 TATATATATAAATTATATTTATATAAAC
* *
217561 TATATGTATAAACTATA
1 TATATATATAAATTATA
217578 AAAAGTACAT
Statistics
Matches: 117, Mismatches: 23, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
22 2 0.02
23 4 0.03
24 2 0.02
25 4 0.03
26 35 0.30
28 38 0.32
29 17 0.15
30 12 0.10
31 3 0.03
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (28 bp):
TATATATATAAATTATATTTATATAAAC
Found at i:217504 original size:80 final size:80
Alignment explanation
Indices: 217380--217559 Score: 285
Period size: 80 Copynumber: 2.3 Consensus size: 80
217370 AATATAAAAT
* *
217380 TATATATAAACTA--TAT-TTATATTATAAAATATATAATTATTATAAACTATATATATAAATTA
1 TATATATAAACTATGTATATAAAATTATAAAATATATAATTATTATAAACTATATATATAAATTA
217442 TATTTATGTAAACTA
66 TATTTATGTAAACTA
* *
217457 TATATATAAACTATGTATATAAAATTATAAACTATATAATTATTATAAGCTATATATATAAATTA
1 TATATATAAACTATGTATATAAAATTATAAAATATATAATTATTATAAACTATATATATAAATTA
* *
217522 TGTTTATGTGAACTA
66 TATTTATGTAAACTA
217537 TATATATAAACTATGTATATAAA
1 TATATATAAACTATGTATATAAA
217560 CTATATGTAT
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
77 13 0.14
79 3 0.03
80 78 0.83
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (80 bp):
TATATATAAACTATGTATATAAAATTATAAAATATATAATTATTATAAACTATATATATAAATTA
TATTTATGTAAACTA
Found at i:217608 original size:80 final size:79
Alignment explanation
Indices: 217433--217672 Score: 203
Period size: 80 Copynumber: 3.1 Consensus size: 79
217423 AAACTATATA
* ** *
217433 TATAAATTATATTTATGTAAACTATATATATAAACTATGTATATAAAATTATAAACTATATAATT
1 TATAAATTATATTTATGTAAACTATATATATAAACTATGTATAT-AAACTAT-ATGTATA-AACT
* * *
217498 ATTATAAG--CTATA-TA
63 ATAAAAAGTAC-ATAGTT
* *
217513 TATAAATTATGTTTATGTGAACTATATATATAAACTATGTATATAAACTATATGTATAAACTATA
1 TATAAATTATATTTATGTAAACTATATATATAAACTATGTATATAAACTATATGTATAAACTATA
217578 AAAAGTACATAGTT
66 AAAAGTACATAGTT
* * * *
217592 TATAAAATATTATTTATATTAA-TATAGTATAT---GTA--TATATAAACTATATATGTATAAAC
1 TATAAATTA-TATTTATGTAAACTATA-TATATAAACTATGTATATAAAC--TATATGTATAAAC
*
217651 TATATAAAA-TATATAGTT
62 TATA-AAAAGTACATAGTT
217669 TATA
1 TATA
217673 TGTTATAATT
Statistics
Matches: 137, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
75 9 0.07
77 40 0.29
78 12 0.09
79 20 0.15
80 56 0.41
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (79 bp):
TATAAATTATATTTATGTAAACTATATATATAAACTATGTATATAAACTATATGTATAAACTATA
AAAAGTACATAGTT
Found at i:217651 original size:77 final size:75
Alignment explanation
Indices: 217552--217700 Score: 201
Period size: 77 Copynumber: 2.0 Consensus size: 75
217542 ATAAACTATG
* *
217552 TATATAAACTATATGTATAAACTATA-AAAAGTACATAGTTTATAAAATATTATTTATATTAATA
1 TATATAAACTATATGTATAAACTATATAAAA-TACATAGTTTATAAAATATAATTTATAATAATA
217616 TAGTATATGTA
65 TAGTATATGTA
* ***
217627 TATATAAACTATATATGTATAAACTATATAAAATATATAGTTTATATGTTATAATTTATAATAAT
1 TATATAAAC--TATATGTATAAACTATATAAAATACATAGTTTATAAAATATAATTTATAATAAT
*
217692 ATATTATAT
64 ATAGTATAT
217701 ATACGAATGT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
75 9 0.14
77 51 0.80
78 4 0.06
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (75 bp):
TATATAAACTATATGTATAAACTATATAAAATACATAGTTTATAAAATATAATTTATAATAATAT
AGTATATGTA
Found at i:218042 original size:2 final size:2
Alignment explanation
Indices: 218031--218107 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
218021 ATAAACTATG
218031 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
218072 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
218108 CAAAGTAAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 73 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:218221 original size:21 final size:21
Alignment explanation
Indices: 218209--218250 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
218199 AACTTCAAAT
218209 CCTAAAACATAAACCTTAAAC
1 CCTAAAACATAAACCTTAAAC
** *
218230 CCTAAAATTTAAACCCTAAAC
1 CCTAAAACATAAACCTTAAAC
218251 ATGTATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (21 bp):
CCTAAAACATAAACCTTAAAC
Found at i:218323 original size:14 final size:14
Alignment explanation
Indices: 218304--218336 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
218294 TAAAAGGGAT
218304 ATTTATGGTTTAGG
1 ATTTATGGTTTAGG
218318 ATTTATGGTTTAGG
1 ATTTATGGTTTAGG
218332 ATTTA
1 ATTTA
218337 AGAATCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (14 bp):
ATTTATGGTTTAGG
Found at i:218414 original size:6 final size:6
Alignment explanation
Indices: 218403--218437 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
218393 ATTTAGGGTG
*
218403 TATATT TATATT TATATT TATGTT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATATT TATAT
218438 AAACTGCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:218470 original size:20 final size:20
Alignment explanation
Indices: 218445--218484 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
218435 TATAAACTGC
218445 ATACTATAATTTATAT-CTAT
1 ATACTAT-ATTTATATACTAT
218465 ATACTATATTTATATACTAT
1 ATACTATATTTATATACTAT
218485 TTATATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
ATACTATATTTATATACTAT
Found at i:218510 original size:32 final size:33
Alignment explanation
Indices: 218469--218550 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 33
218459 ATCTATATAC
* *
218469 TATATTTATATACTATTTATAT-AAATATAGTT
1 TATATTTATATACTATATATATGAAATATAGAT
*
218501 TATATTTATATACTATATATATGAACTATAGAT
1 TATATTTATATACTATATATATGAAATATAGAT
*
218534 TATA--TATAAACTATATA
1 TATATTTATATACTATATA
218551 GTTTATATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
31 12 0.27
32 21 0.47
33 12 0.27
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (33 bp):
TATATTTATATACTATATATATGAAATATAGAT
Found at i:218518 original size:13 final size:13
Alignment explanation
Indices: 218456--218505 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
218446 TACTATAATT
*
218456 TATATCTATATAC
1 TATATTTATATAC
218469 TATATTTATATAC
1 TATATTTATATAC
*
218482 --TATTTATATAAA
1 TATATTTATAT-AC
218494 TATAGTTTATAT
1 TATA-TTTATAT
218506 TTATATACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
11 9 0.29
12 1 0.03
13 12 0.39
14 2 0.06
15 7 0.23
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:218537 original size:18 final size:18
Alignment explanation
Indices: 218516--218594 Score: 88
Period size: 18 Copynumber: 4.3 Consensus size: 18
218506 TTATATACTA
* *
218516 TATATATGAACTATAGAT
1 TATATATAAACTATAGTT
218534 TATATATAAACTATATAGTT
1 TATATATAAAC--TATAGTT
218554 TATATACT-AACTATAGTT
1 TATATA-TAAACTATAGTT
*
218572 TACATATAAACTATAGTT
1 TATATATAAACTATAGTT
*
218590 GATAT
1 TATAT
218595 TTACATATGA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.02
18 35 0.67
20 15 0.29
21 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (18 bp):
TATATATAAACTATAGTT
Found at i:218550 original size:38 final size:38
Alignment explanation
Indices: 218507--218586 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
218497 AGTTTATATT
*
218507 TATATACTATATATA-TGAACTATAGATTATATATAAAC
1 TATATACTATATATACT-AACTATAGATTACATATAAAC
* * *
218545 TATATAGTTTATATACTAACTATAGTTTACATATAAAC
1 TATATACTATATATACTAACTATAGATTACATATAAAC
218583 TATA
1 TATA
218587 GTTGATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 36 0.97
39 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (38 bp):
TATATACTATATATACTAACTATAGATTACATATAAAC
Found at i:218617 original size:18 final size:18
Alignment explanation
Indices: 218594--218628 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
218584 ATAGTTGATA
*
218594 TTTACATATGAATTATAG
1 TTTACATATGAACTATAG
218612 TTTACATATGAACTATA
1 TTTACATATGAACTATA
218629 TATATAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (18 bp):
TTTACATATGAACTATAG
Found at i:218644 original size:33 final size:33
Alignment explanation
Indices: 218607--218734 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
218597 ACATATGAAT
*
218607 TATAGTTTACATATGAACTATATATATAAACTA
1 TATAGTTTACATATGACCTATATATATAAACTA
218640 TATAGTTTACATATGACCTATATATATAAACTA
1 TATAGTTTACATATGACCTATATATATAAACTA
** * *
218673 TATAGTTTACATATGAGTTGATATTTATATACTA
1 TATAGTTTACATATGACCT-ATATATATAAACTA
*
218707 TATGGTTTACATATGACCTATATATATA
1 TATAGTTTACATATGACCTATATATATA
218735 CTATAGTCTA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
33 57 0.67
34 28 0.33
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (33 bp):
TATAGTTTACATATGACCTATATATATAAACTA
Found at i:218719 original size:67 final size:66
Alignment explanation
Indices: 218607--218734 Score: 202
Period size: 67 Copynumber: 1.9 Consensus size: 66
218597 ACATATGAAT
218607 TATAGTTTACATATGAACTATATATATAAACTATATAGTTTACATATGACCTATATATATAAACT
1 TATAGTTTACATATGAACTATATATATAAACTATATAGTTTACATATGACCTATATATATAAACT
218672 A
66 A
** * * *
218673 TATAGTTTACATATGAGTTGATATTTATATACTATATGGTTTACATATGACCTATATATATA
1 TATAGTTTACATATGAACT-ATATATATAAACTATATAGTTTACATATGACCTATATATATA
218735 CTATAGTCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
66 17 0.30
67 39 0.70
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (66 bp):
TATAGTTTACATATGAACTATATATATAAACTATATAGTTTACATATGACCTATATATATAAACT
A
Found at i:218732 original size:2 final size:2
Alignment explanation
Indices: 218725--218790 Score: 53
Period size: 2 Copynumber: 31.0 Consensus size: 2
218715 ACATATGACC
* *
218725 TA TA TA TA TA CTA TA GTC TA TA TT TA TA TA CTA TA TA T- TA TA
1 TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
218767 TA TA TA AA CTA TA TA TA CTA TA TA
1 TA TA TA TA -TA TA TA TA -TA TA TA
218791 GTTTAGTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
1 1 0.02
2 43 0.83
3 8 0.15
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:218739 original size:9 final size:9
Alignment explanation
Indices: 218727--218790 Score: 51
Period size: 9 Copynumber: 6.7 Consensus size: 9
218717 ATATGACCTA
218727 TATATATAC
1 TATATATAC
218736 TATAGTCTATA-
1 TATA---TATAC
*
218747 TTTATATAC
1 TATATATAC
218756 TATATATTA-
1 TATATA-TAC
218765 TATATATAAAC
1 TATATAT--AC
218776 TATATATAC
1 TATATATAC
218785 TATATA
1 TATATA
218791 GTTTAGTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
8 5 0.11
9 23 0.51
10 3 0.07
11 10 0.22
12 4 0.09
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.47
Consensus pattern (9 bp):
TATATATAC
Found at i:218779 original size:51 final size:52
Alignment explanation
Indices: 218658--218859 Score: 165
Period size: 51 Copynumber: 3.9 Consensus size: 52
218648 ACATATGACC
* *
218658 TATATATATAAACTATATAGTTTACATATGAGTTGATATTTATATACTATATGGT
1 TATATATATAAACTATATA-TATAC-TAT-AGTTGATATTTATATACTATATGAT
* * *
218713 T-TACATATGACCTATATATATACTATAGTCT-ATATTTATATACTATAT-AT
1 TATATATATAAACTATATATATACTATAGT-TGATATTTATATACTATATGAT
* *
218763 TATATATATAAACTATATATACTA-TATAGTT--TA-GT-T-TAC-ATATGAAC
1 TATATATATAAACTATATATA-TACTATAGTTGATATTTATATACTATATG-AT
218810 TATATATA-AAACCATATAAACTATATACTATAGTTGATATTTATATACTA
1 TATATATATAAA-C-TAT--A-TATATACTATAGTTGATATTTATATACTA
218860 AATAAAATAA
Statistics
Matches: 119, Mismatches: 11, Indels: 32
0.73 0.07 0.20
Matches are distributed among these distances:
45 4 0.03
46 6 0.05
47 11 0.09
48 4 0.03
49 2 0.02
50 6 0.05
51 53 0.45
52 6 0.05
53 6 0.05
54 15 0.13
55 2 0.02
56 3 0.03
57 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (52 bp):
TATATATATAAACTATATATATACTATAGTTGATATTTATATACTATATGAT
Found at i:218788 original size:20 final size:19
Alignment explanation
Indices: 218725--218923 Score: 92
Period size: 20 Copynumber: 10.3 Consensus size: 19
218715 ACATATGACC
*
218725 TATATATATACTATAGTCTA
1 TATATATATACTATA-TATA
*
218745 TATTTATATACTATATATTA
1 TATATATATACTATATA-TA
*
218765 TATATATAAACTATATATA
1 TATATATATACTATATATA
* * * *
218784 CTATATAGTTTAGTTTACATA
1 -TATATA-TATACTATATATA
* *
218805 TGA-ACTATATA-TAAAACCATA
1 T-ATA-TATATACT-ATA-TATA
*
218826 TAAACTATATACTATAGT-TGA
1 TATA-TATATACTATA-TAT-A
* *
218847 TATTTATATACTAAATA-A
1 TATATATATACTATATATA
* *
218865 AATAAATTATACTATAT-TA
1 TATATA-TATACTATATATA
218884 TATATA-A-ACTATATA-A
1 TATATATATACTATATATA
*
218900 TATATATAAACTATATAT-
1 TATATATATACTATATATA
218918 TATATA
1 TATATA
218924 GTTCATTAGT
Statistics
Matches: 138, Mismatches: 24, Indels: 36
0.70 0.12 0.18
Matches are distributed among these distances:
16 14 0.10
17 2 0.01
18 18 0.13
19 19 0.14
20 55 0.40
21 29 0.21
22 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.43
Consensus pattern (19 bp):
TATATATATACTATATATA
Found at i:218903 original size:18 final size:18
Alignment explanation
Indices: 218877--218923 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
218867 TAAATTATAC
218877 TATATTATATATAAACTA
1 TATATTATATATAAACTA
*
218895 TATAATATATATAAACTA
1 TATATTATATATAAACTA
218913 TATATTATATA
1 TATATTATATA
218924 GTTCATTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
TATATTATATATAAACTA
Found at i:219052 original size:13 final size:14
Alignment explanation
Indices: 219029--219060 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
219019 AACCTAAACC
219029 TAAACCTCAAACTT
1 TAAACCTCAAACTT
219043 TAAACC-CAAACTT
1 TAAACCTCAAACTT
219056 TAAAC
1 TAAAC
219061 TCTAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCTCAAACTT
Found at i:219060 original size:20 final size:20
Alignment explanation
Indices: 219013--219066 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
219003 ATTTAAACAG
*
219013 AACC-CAAAC-CTAAACCTA
1 AACCTCAAACTCTAAACCCA
*
219031 AACCTCAAACTTTAAACCCA
1 AACCTCAAACTCTAAACCCA
* *
219051 AACTTTAAACTCTAAA
1 AACCTCAAACTCTAAA
219067 TTATGTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 20 0.69
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCTCAAACTCTAAACCCA
Found at i:219198 original size:20 final size:19
Alignment explanation
Indices: 219175--219215 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
219165 GATTAAAGAC
219175 TTTCAGTTAAAAATAAAATT
1 TTTCA-TTAAAAATAAAATT
* *
219195 TTTCATTAGAAGTAAAATT
1 TTTCATTAAAAATAAAATT
219214 TT
1 TT
219216 CGCTCTCCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (19 bp):
TTTCATTAAAAATAAAATT
Found at i:220677 original size:13 final size:13
Alignment explanation
Indices: 220659--220688 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
220649 CCCTAAAATA
*
220659 ATTCGAATTGGAG
1 ATTCGAATAGGAG
220672 ATTCGAATAGGAG
1 ATTCGAATAGGAG
220685 ATTC
1 ATTC
220689 TGTCTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (13 bp):
ATTCGAATAGGAG
Found at i:221749 original size:10 final size:10
Alignment explanation
Indices: 221734--221808 Score: 60
Period size: 10 Copynumber: 7.1 Consensus size: 10
221724 CTTCTATTGC
221734 TGCTTGTTGT
1 TGCTTGTTGT
*
221744 TGCTTGCTGT
1 TGCTTGTTGT
*
221754 TGCCTGTTGT
1 TGCTTGTTGT
*
221764 TGCTTGCTGTT
1 TGCTTGTTG-T
* *
221775 TCCTGTTGCCTGT
1 TGC--TTG-TTGT
*
221788 TGCTTGTTGG
1 TGCTTGTTGT
221798 TGCTTGTTGT
1 TGCTTGTTGT
221808 T
1 T
221809 TGTTGCCTGT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 36 0.71
11 6 0.12
13 6 0.12
14 3 0.06
ACGTcount: A:0.00, C:0.17, G:0.29, T:0.53
Consensus pattern (10 bp):
TGCTTGTTGT
Found at i:221763 original size:20 final size:20
Alignment explanation
Indices: 221738--221826 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
221728 TATTGCTGCT
221738 TGTTGTTGCTTGCTGTTGCC
1 TGTTGTTGCTTGCTGTTGCC
*
221758 TGTTGTTGCTTGCTGTTTCC
1 TGTTGTTGCTTGCTGTTGCC
* *
221778 TGTTGCCTG-TTGCTTGTTG-G
1 TGTTG-TTGCTTGC-TGTTGCC
221798 TGCTTGTTG-TT--TGTTGCC
1 TG-TTGTTGCTTGCTGTTGCC
221816 TGTTGTTGCTT
1 TGTTGTTGCTT
221827 TGTATTTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.19
18 4 0.07
20 34 0.59
21 9 0.16
ACGTcount: A:0.00, C:0.17, G:0.29, T:0.54
Consensus pattern (20 bp):
TGTTGTTGCTTGCTGTTGCC
Found at i:221805 original size:24 final size:24
Alignment explanation
Indices: 221778--221826 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
221768 TGCTGTTTCC
*
221778 TGTTGCCTGTTGCTTGTTGGTGCT
1 TGTTGCCTGTTGCCTGTTGGTGCT
** *
221802 TGTTGTTTGTTGCCTGTTGTTGCT
1 TGTTGCCTGTTGCCTGTTGGTGCT
221826 T
1 T
221827 TGTATTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.31, T:0.55
Consensus pattern (24 bp):
TGTTGCCTGTTGCCTGTTGGTGCT
Found at i:222455 original size:13 final size:13
Alignment explanation
Indices: 222437--222461 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
222427 TAATTTACAT
222437 TTAAATAATTTTA
1 TTAAATAATTTTA
222450 TTAAATAATTTT
1 TTAAATAATTTT
222462 TATATAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:222674 original size:16 final size:16
Alignment explanation
Indices: 222653--222696 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
222643 TTTACATGTT
222653 AGGTTAAAAACAAATC
1 AGGTTAAAAACAAATC
**
222669 AGGTTAAAAACATGTC
1 AGGTTAAAAACAAATC
*
222685 AGGTTGAAAACA
1 AGGTTAAAAACA
222697 GGTCGGGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.20
Consensus pattern (16 bp):
AGGTTAAAAACAAATC
Found at i:227978 original size:27 final size:27
Alignment explanation
Indices: 227928--227985 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
227918 AGGGGTGCAC
227928 AAAAAATTCGAATATCCGATTTTGTGGA
1 AAAAAATTCGAATATCCGATTTTG-GGA
*
227956 AAAAATATTCGAA-ATCGGA-TTTGGGA
1 AAAAA-ATTCGAATATCCGATTTTGGGA
227982 AAAA
1 AAAA
227986 CTGGTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.25
27 4 0.14
28 10 0.36
29 7 0.25
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (27 bp):
AAAAAATTCGAATATCCGATTTTGGGA
Found at i:230403 original size:21 final size:21
Alignment explanation
Indices: 230379--230418 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
230369 TTTATTTTAT
230379 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
230400 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
230419 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:230466 original size:33 final size:33
Alignment explanation
Indices: 230413--230511 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
230403 TTTGTTTCAA
230413 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
230445 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
230478 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
230511 T
1 T
230512 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:230773 original size:21 final size:21
Alignment explanation
Indices: 230747--230803 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
230737 TGGAGCGTGG
*
230747 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
230768 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
230789 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
230804 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:236052 original size:20 final size:20
Alignment explanation
Indices: 236007--236052 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
235997 TCATGTAATA
*
236007 TTATAAATGATAATAATTTT
1 TTATAAATGATAAAAATTTT
*
236027 TAATAAAT-ATAAAAATTATT
1 TTATAAATGATAAAAATT-TT
236047 TTATAA
1 TTATAA
236053 TAATATGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TTATAAATGATAAAAATTTT
Found at i:236075 original size:31 final size:31
Alignment explanation
Indices: 236027--236098 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
236017 TAATAATTTT
*
236027 TAATAAATATAAAAATTATTTTATAATAATA
1 TAATAAATTTAAAAATTATTTTATAATAATA
* * * *
236058 TGATAAATTTAATAATTATTTTATAATGATT
1 TAATAAATTTAAAAATTATTTTATAATAATA
236089 TAATAAATTT
1 TAATAAATTT
236099 TATTGACCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (31 bp):
TAATAAATTTAAAAATTATTTTATAATAATA
Found at i:237066 original size:2 final size:2
Alignment explanation
Indices: 237061--237289 Score: 97
Period size: 2 Copynumber: 121.0 Consensus size: 2
237051 AGTAGTGTGT
237061 TA TA TA T- TA TA GTA T- TA TGA TA T- TA TA T- TA TA TA TA GTA
1 TA TA TA TA TA TA -TA TA TA T-A TA TA TA TA TA TA TA TA TA -TA
* * *
237100 TA TA -A TA TGG TA T- TA TA T- TA TT TA T- TA TA TA GTA TT TA T-
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
237139 TA T- TA TA TA TA TA TA TA TA TA -A TA T- TA TA CA -A TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
237177 CA CA -A TA TA TG TCA TA TA TA T- TA TA T- TA TA TG TA TG TT TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
237217 TA T- TA TA TA GTA T- TA TA TA TA T- TA TA T- TA TA TA -A TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
237255 TA TT TA TA T- TA TA TA GTA TA TT TG TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
237290 GTGTTATATT
Statistics
Matches: 174, Mismatches: 22, Indels: 62
0.67 0.09 0.24
Matches are distributed among these distances:
1 22 0.13
2 136 0.78
3 16 0.09
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (2 bp):
TA
Found at i:237088 original size:5 final size:5
Alignment explanation
Indices: 237063--237268 Score: 108
Period size: 5 Copynumber: 41.0 Consensus size: 5
237053 TAGTGTGTTA
* * * * **
237063 TATAT TATAG TATTAT GATAT TATAT TATA- TATAG TATAT AATAT GGTAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
237113 TATAT TAT-T TAT-T ATATAG TAT-T TATTAT TATAT ATATAT ATATAT
1 TATAT TATAT TATAT -TATAT TATAT TA-TAT TATAT -TATAT -TATAT
* * * * * *
237159 AATAT TATAC AATAT T-TA- CACAA TATAT GTCATA- TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT -T-ATAT TATAT TATAT TATAT
* *
237208 GTATGTT TATAT TATA- TAGTAT TATA- TATAT TATAT TATAT AATA-
1 -TAT-AT TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT
237253 TATATT TATAT TATAT
1 TATA-T TATAT TATAT
237269 AGTATATTTG
Statistics
Matches: 155, Mismatches: 27, Indels: 38
0.70 0.12 0.17
Matches are distributed among these distances:
4 26 0.17
5 95 0.61
6 30 0.19
7 4 0.03
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (5 bp):
TATAT
Found at i:237113 original size:29 final size:29
Alignment explanation
Indices: 237061--237303 Score: 137
Period size: 27 Copynumber: 8.9 Consensus size: 29
237051 AGTAGTGTGT
*
237061 TATATATTATAGTATTATGATATTATATTA
1 TATATATTATA-TAATATGATATTATATTA
* *
237091 TATATAGTATATAATATGGTATTATATTA
1 TATATATTATATAATATGATATTATATTA
* *
237120 T-T-TATTATATAGTAT-TTA-T-TATTA
1 TATATATTATATAATATGATATTATATTA
* *
237144 TATATA-TATAT-ATATAATATTATA-CA
1 TATATATTATATAATATGATATTATATTA
* * * *
237170 -ATAT-TTACACAATAT-ATGTCATA-TA
1 TATATATTATATAATATGATATTATATTA
*
237195 TATTATATTATAT-GTATG-T-TTATATTA
1 TA-TATATTATATAATATGATATTATATTA
* *
237222 TATAGTATTATAT-ATATTATATTATATAA
1 TATA-TATTATATAATATGATATTATATTA
* *
237251 TATATATT-TATATTAT-ATAGTATATT-
1 TATATATTATATAATATGATATTATATTA
* * * * *
237277 TGTATAGTATATAGTGTTATATTATAT
1 TATATATTATATAATATGATATTATAT
237304 GTAACATATA
Statistics
Matches: 166, Mismatches: 29, Indels: 38
0.71 0.12 0.16
Matches are distributed among these distances:
24 9 0.05
25 23 0.14
26 23 0.14
27 52 0.31
28 21 0.13
29 28 0.17
30 10 0.06
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (29 bp):
TATATATTATATAATATGATATTATATTA
Found at i:237167 original size:39 final size:38
Alignment explanation
Indices: 237063--237325 Score: 175
Period size: 39 Copynumber: 6.8 Consensus size: 38
237053 TAGTGTGTTA
* *
237063 TATATTATAGTAT-TAT-GATATTATATTATAT-ATA-G
1 TATATTATA-TATATATATATATTATATTATATAATATT
* * *
237098 TATATAATATGGTAT-TATATTATT-TATTATATAGTATT
1 TATATTATAT-ATATATATA-TATTATATTATATAATATT
* *
237136 TATTATTATATATATATATATATAATATTATACAATATT
1 TA-TATTATATATATATATATATTATATTATATAATATT
* ** * * *
237175 TACACAATATATGTCATATATATTATATTATATGTATGTT
1 TATATTATATATAT-ATATATATTATATTATAT-AATATT
*
237215 TATATTATATAGTATTATATATATTATATTATATAATATA
1 TATATTATATA-TA-TATATATATTATATTATATAATATT
* * * *
237255 TAT-TTATATTATATAGTATATTTGTATAGTATATAGT-GT
1 TATATTATA-TATATA-TATATAT-TATATTATATAATATT
* *
237294 TATATTATATGTA-ACATATAGTTATATTATAT
1 TATATTATATATATATATATA-TTATATTATAT
237326 TTATAGTGTT
Statistics
Matches: 176, Mismatches: 34, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
34 1 0.01
35 10 0.06
36 10 0.06
37 19 0.11
38 20 0.11
39 60 0.34
40 36 0.20
41 19 0.11
42 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (38 bp):
TATATTATATATATATATATATTATATTATATAATATT
Found at i:237201 original size:7 final size:7
Alignment explanation
Indices: 237191--237303 Score: 72
Period size: 7 Copynumber: 15.7 Consensus size: 7
237181 ATATATGTCA
237191 TATATAT
1 TATATAT
237198 TATAT-T
1 TATATAT
*
237204 ATATGTAT
1 -TATATAT
*
237212 GTTTATAT
1 -TATATAT
*
237220 TATATAG
1 TATATAT
237227 TATTATAT
1 TA-TATAT
237235 ATATTATAT
1 -TA-TATAT
*
237244 TATATAA
1 TATATAT
237251 TATATAT
1 TATATAT
237258 T-TATAT
1 TATATAT
*
237264 TATATAG
1 TATATAT
237271 TATAT-T
1 TATATAT
* *
237277 TGTATAG
1 TATATAT
237284 TATATAGT
1 TATATA-T
237292 GT-TATAT
1 -TATATAT
237299 TATAT
1 TATAT
237304 GTAACATATA
Statistics
Matches: 82, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
6 12 0.15
7 45 0.55
8 16 0.20
9 9 0.11
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (7 bp):
TATATAT
Found at i:237274 original size:27 final size:26
Alignment explanation
Indices: 237061--237330 Score: 123
Period size: 25 Copynumber: 10.2 Consensus size: 26
237051 AGTAGTGTGT
*
237061 TATATATTATAGTAT-TATGATATTATA
1 TATATATAATA-TATATAT-ATATTATA
* *
237088 TTATATATAGTATATAATATGGTATTATA
1 -TATATATAATATAT-ATAT-ATATTATA
* * *
237117 T-TATTTATTATATAGTATTTATTAT-
1 TATATATAATATATA-TATATATTATA
237142 TATATAT-ATATATATATAATATTATA
1 TATATATAATATATATAT-ATATTATA
* * * *
237168 CA-ATAT-TTACACA-ATATATGTCATA
1 TATATATAATATATATATATAT-T-ATA
* * *
237193 TATATTATATTATATGTATGT-TTATA
1 TATA-TATAATATATATATATATTATA
*
237219 T-TATATAGTAT-TATATATATTATA
1 TATATATAATATATATATATATTATA
*
237243 T-TATATAATATATATTTATATTATA
1 TATATATAATATATATATATATTATA
** *
237268 TAGTATATTTGTATAGTATATAGTGTTATA
1 TA-TATA-TAATATA-TATATA-TATTATA
* *
237298 TTATATGTAACATATAGT-TATATTATA
1 -TATATATAATATATA-TATATATTATA
*
237325 TTTATA
1 TATATA
237331 GTGTTATCAA
Statistics
Matches: 187, Mismatches: 34, Indels: 44
0.71 0.13 0.17
Matches are distributed among these distances:
23 9 0.05
24 28 0.15
25 40 0.21
26 21 0.11
27 30 0.16
28 24 0.13
29 24 0.13
30 9 0.05
31 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (26 bp):
TATATATAATATATATATATATTATA
Found at i:237302 original size:20 final size:20
Alignment explanation
Indices: 237234--237337 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
237224 TAGTATTATA
* * *
237234 TATATTATATTATATAAT-A
1 TATATTATAGTATATAGTGT
* *
237253 TATATTTATATTATATAGT-A
1 TATA-TTATAGTATATAGTGT
*
237273 TATTTGTATAGTATATAGTGT
1 TATAT-TATAGTATATAGTGT
*
237294 TATATTATATGTAACATA-TAGT
1 TATATTATA-GT-ATATAGT-GT
*
237316 TATATTATA-TTTATAGTGT
1 TATATTATAGTATATAGTGT
237335 TAT
1 TAT
237338 CAATATTATT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
19 13 0.19
20 35 0.50
21 7 0.10
22 15 0.21
ACGTcount: A:0.38, C:0.01, G:0.09, T:0.53
Consensus pattern (20 bp):
TATATTATAGTATATAGTGT
Found at i:241476 original size:24 final size:24
Alignment explanation
Indices: 241358--241473 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
241348 TTCGATTTGA
241358 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
* * *
241382 ATCCTGATCTGATA-TCTGACATAG
1 ATTCTGATATGATACT-TGACATGG
*
241406 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* * *
241430 ATTCTAATCTGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
241454 AGTT-TGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
241474 CTGATTTATG
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
23 1 0.01
24 73 0.95
25 3 0.04
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:251659 original size:24 final size:24
Alignment explanation
Indices: 251632--251747 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
251622 TTCGATTTGA
* *
251632 ATTCTGATCTGATGCTTGGCATGG
1 ATTCTGATCTGATACTTGACATGG
* *
251656 ATTCTGATATGATA-TATGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
251680 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
251704 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
*
251728 AGTT-TGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
251748 CTGATTTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.01
24 76 0.95
25 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:263398 original size:28 final size:28
Alignment explanation
Indices: 263365--263448 Score: 107
Period size: 29 Copynumber: 3.0 Consensus size: 28
263355 ATAATAATTA
263365 ACTTGATTTTATAATAATTTATGTATAT
1 ACTTGATTTTATAATAATTTATGTATAT
* * * *
263393 ATTTGATTTTATAGTAATTAACT-TAATTT
1 ACTTGATTTTATAATAATTTA-TGT-ATAT
263422 ACTTGATTTTATAATAATTTATGTATA
1 ACTTGATTTTATAATAATTTATGTATA
263449 ATAATTAACT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 22 0.49
29 23 0.51
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (28 bp):
ACTTGATTTTATAATAATTTATGTATAT
Found at i:263433 original size:29 final size:29
Alignment explanation
Indices: 263359--263474 Score: 101
Period size: 29 Copynumber: 3.9 Consensus size: 29
263349 TTTTTTATAA
* *
263359 TAATTAACTTGATTTTATAATAATTTATG
1 TAATTTACTTGATTTTATAATAATTAATG
* * *
263388 T-ATATATTTGATTTTATAGTAATTAACT-
1 TAATTTACTTGATTTTATAATAATTAA-TG
*
263416 TAATTTACTTGATTTTATAATAATTTATG
1 TAATTTACTTGATTTTATAATAATTAATG
*
263445 TATAATAATTAACTTTATTTTATAATAATT
1 --TAAT--TT-ACTTGATTTTATAATAATT
263475 TATGCATTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
28 22 0.32
29 23 0.33
31 4 0.06
33 2 0.03
34 18 0.26
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (29 bp):
TAATTTACTTGATTTTATAATAATTAATG
Found at i:263439 original size:20 final size:20
Alignment explanation
Indices: 263416--263476 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
263406 GTAATTAACT
263416 TAATTTACTTGATTTTATAA
1 TAATTTACTTGATTTTATAA
263436 TAATTTA--TG----TATAA
1 TAATTTACTTGATTTTATAA
* *
263450 TAATTAACTTTATTTTATAA
1 TAATTTACTTGATTTTATAA
263470 TAATTTA
1 TAATTTA
263477 TGCATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
14 11 0.34
16 1 0.03
18 2 0.06
20 18 0.56
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
TAATTTACTTGATTTTATAA
Found at i:263593 original size:31 final size:30
Alignment explanation
Indices: 263556--263652 Score: 92
Period size: 29 Copynumber: 3.2 Consensus size: 30
263546 TATGAAATAA
*
263556 ATTTTATTATTAAAATAACAATAAAATATAT
1 ATTTTATTATT-ATATAACAATAAAATATAT
* * **
263587 ATTTTATTTTTATTTATTAA-AAAATATAT
1 ATTTTATTATTATATAACAATAAAATATAT
*
263616 AATTTT-TTATTATCTAAC-ATAAAAATATAT
1 -ATTTTATTATTATATAACAAT-AAAATATAT
263646 ATTTTAT
1 ATTTTAT
263653 CTCATCTTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
28 1 0.02
29 22 0.42
30 20 0.38
31 10 0.19
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTTTATTATTATATAACAATAAAATATAT
Found at i:263610 original size:29 final size:30
Alignment explanation
Indices: 263517--263652 Score: 97
Period size: 30 Copynumber: 4.6 Consensus size: 30
263507 TTTAAAGTTG
*
263517 AAAAA-ATATATTTTATTTTTATCTTAA-ATT
1 AAAAATATATATTTTATTATTATC-TAACA-T
* **
263547 ATGAAATA-A-ATTTTATTATTAAAATAACA-
1 A-AAAATATATATTTTATTATT-ATCTAACAT
* * **
263576 ATAAAATATATATTTTATTTTTATTTATTA-
1 A-AAAATATATATTTTATTATTATCTAACAT
263606 AAAAATATATAATTTT-TTATTATCTAACAT
1 AAAAATATAT-ATTTTATTATTATCTAACAT
263636 AAAAATATATATTTTAT
1 AAAAATATATATTTTAT
263653 CTCATCTTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
29 30 0.36
30 36 0.43
31 16 0.19
32 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (30 bp):
AAAAATATATATTTTATTATTATCTAACAT
Found at i:263620 original size:61 final size:58
Alignment explanation
Indices: 263517--263652 Score: 145
Period size: 59 Copynumber: 2.3 Consensus size: 58
263507 TTTAAAGTTG
**
263517 AAAAA-ATATATTTTATTTTTATCTTAAATTATGAAATAAATTTTATTATTAAAATAACA-
1 AAAAATATATATTTTATTTTTATCTT-AATTAAAAAATAAATTTT-TTATT-AAATAACAT
**
263576 ATAAAATATATATTTTATTTTTAT-TT-ATTAAAAAATATATAATTTTTTATTATCTAACAT
1 A-AAAATATATATTTTATTTTTATCTTAATT-AAAAA-ATA-AATTTTTTATTAAATAACAT
263636 AAAAATATATATTTTAT
1 AAAAATATATATTTTAT
263653 CTCATCTTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
58 3 0.04
59 26 0.39
60 15 0.22
61 23 0.34
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (58 bp):
AAAAATATATATTTTATTTTTATCTTAATTAAAAAATAAATTTTTTATTAAATAACAT
Found at i:264839 original size:35 final size:36
Alignment explanation
Indices: 264793--264863 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
264783 TATGTGCAGG
264793 GGGAACAGATT-CCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
264828 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
264864 CTAAATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 11 0.31
36 24 0.69
ACGTcount: A:0.17, C:0.30, G:0.34, T:0.20
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
Found at i:266251 original size:30 final size:30
Alignment explanation
Indices: 266215--266279 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
266205 CCCGCAGGAC
*
266215 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
266245 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
266275 CTATC
1 CTATC
266280 TATAGGTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:266393 original size:32 final size:32
Alignment explanation
Indices: 266292--266397 Score: 112
Period size: 31 Copynumber: 3.4 Consensus size: 32
266282 TAGGTTCCAA
* * *
266292 AGAACCTAGGTGA-ACTGTCCATATGTTCCTT
1 AGAACATAGGTAATACTGTCCATATGTTCCGT
*
266323 AGAACATAGG-CATACTGTCCATATG-TCTCG-
1 AGAACATAGGTAATACTGTCCATATGTTC-CGT
* *
266353 AAAGACATAGGTAATTCTGTCCATATGTTCCGT
1 AGA-ACATAGGTAATACTGTCCATATGTTCCGT
266386 AGAACATAGGTA
1 AGAACATAGGTA
266398 CCCTTGACTC
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
30 5 0.08
31 29 0.47
32 24 0.39
33 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (32 bp):
AGAACATAGGTAATACTGTCCATATGTTCCGT
Found at i:267970 original size:15 final size:15
Alignment explanation
Indices: 267952--267984 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
267942 CGAGGGTATT
*
267952 GTAGTCCTTCGGGTC
1 GTAGTCCTTCGGGAC
267967 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
267982 GTA
1 GTA
267985 ATGGTCCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.30
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:270036 original size:2 final size:2
Alignment explanation
Indices: 270029--270053 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
270019 GTTGAGTAAG
270029 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 A
270054 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:273408 original size:20 final size:20
Alignment explanation
Indices: 273385--273447 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
273375 GGGGGAACAT
273385 ATTCCCCCTGGGGGGTATCG
1 ATTCCCCCTGGGGGGTATCG
*
273405 ATT-CCCC----GGG-AACAG
1 ATTCCCCCTGGGGGGTATC-G
273420 ATTCCCCCTGGGGGGTATCG
1 ATTCCCCCTGGGGGGTATCG
273440 ATTCCCCC
1 ATTCCCCC
273448 CTAAATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
14 2 0.06
15 7 0.21
16 4 0.12
19 4 0.12
20 15 0.44
21 2 0.06
ACGTcount: A:0.14, C:0.35, G:0.29, T:0.22
Consensus pattern (20 bp):
ATTCCCCCTGGGGGGTATCG
Found at i:273424 original size:35 final size:35
Alignment explanation
Indices: 273377--273446 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
273367 TATGTGCAGG
*
273377 GGGAACATATTCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
273412 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
273447 CCTAAATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.31, G:0.30, T:0.21
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
Found at i:273879 original size:22 final size:20
Alignment explanation
Indices: 273854--273895 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
273844 CTAATGTGAA
273854 ATGAAATAAGCTATATGAATAT
1 ATGAAATAA-C-ATATGAATAT
*
273876 ATGAAATGACATATGAATAT
1 ATGAAATAACATATGAATAT
273896 GCAATATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGAAATAACATATGAATAT
Found at i:274072 original size:15 final size:15
Alignment explanation
Indices: 274054--274086 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
274044 CGAGGGTATT
*
274054 GTAGTCCTTTGGGAC
1 GTAGTCCTTCGGGAC
274069 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
274084 GTA
1 GTA
274087 ATGGTCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:275512 original size:21 final size:20
Alignment explanation
Indices: 275474--275512 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
275464 TAATAGATGG
*
275474 TTGTTTTTGTATGCTGTTAC
1 TTGTTTTTGTATGATGTTAC
*
275494 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TGTATGATGTT
275513 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.10, C:0.05, G:0.21, T:0.64
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAC
Found at i:277002 original size:38 final size:37
Alignment explanation
Indices: 276954--277045 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 37
276944 ATTTATACCA
276954 TTTATTAAATAATAA-ATTAATCAT-AAACTAATAATAT
1 TTTATTAAATAATAATATTAATC-TCAAA-TAATAATAT
**
276991 TTT-TCTCAAATAATAATATTTTTCTCAAATAATAATAT
1 TTTAT-T-AAATAATAATATTAATCTCAAATAATAATAT
277029 TTTATTAAATAATAATA
1 TTTATTAAATAATAATA
277046 ACACTATCGC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
36 1 0.02
37 15 0.31
38 23 0.48
39 9 0.19
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.45
Consensus pattern (37 bp):
TTTATTAAATAATAATATTAATCTCAAATAATAATAT
Found at i:277031 original size:18 final size:19
Alignment explanation
Indices: 276982--277045 Score: 105
Period size: 19 Copynumber: 3.4 Consensus size: 19
276972 AATCATAAAC
276982 TAATAATATTTTTCTCAAA
1 TAATAATATTTTTCTCAAA
277001 TAATAATATTTTTCTCAAA
1 TAATAATATTTTTCTCAAA
277020 TAATAATATTTTAT-T-AAA
1 TAATAATATTTT-TCTCAAA
277038 TAATAATA
1 TAATAATA
277046 ACACTATCGC
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.25
19 32 0.73
20 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATAATATTTTTCTCAAA
Found at i:277720 original size:21 final size:21
Alignment explanation
Indices: 277696--277740 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
277686 TCTTCTCGTC
277696 TTCT-TTCTTCCTCTT-TTCTCT
1 TTCTCTTC-TCCTCTTCTT-TCT
277717 TTCTCTTCTCCTCTTCTTTCT
1 TTCTCTTCTCCTCTTCTTTCT
277738 TTC
1 TTC
277741 ACTCCCAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (21 bp):
TTCTCTTCTCCTCTTCTTTCT
Found at i:278249 original size:147 final size:149
Alignment explanation
Indices: 277995--278325 Score: 479
Period size: 147 Copynumber: 2.2 Consensus size: 149
277985 GGGAAGATAA
* * * *
277995 ATGGAAAGCCATGCATCTTCGAGGGGTTTTCCTTGGGTGTGCTCAGTGCATGCATGCAAGAGAAA
1 ATGGAATGCCATGCGTCTTCGAGGGGTTTTCCTTGAGTGTGCTCAGTACATGCATGCAAGAGAAA
* * * *
278060 TGGGAGGTGTTTTCATTGGGTGTTCATGCAAATTGGGTGGGAAGATCCAATCACGTTGAATGCAG
66 TGGGAGGGGTTTTCATTGGGTGTTCATGCAAATGGGGTGGGAAGAGCCAATAACGTTGAATGCAG
* *
278125 AGAGGGGGTGAGAAGACGT
131 AGAAGGGGTGAGAAGACGC
* * *
278144 ATGGAATGCCATGCGTCTTCGAGGGGTTTTCCTTGAGTGT-C-GA-TACATGCATGTAGAGAGGA
1 ATGGAATGCCATGCGTCTTCGAGGGGTTTTCCTTGAGTGTGCTCAGTACATGCATGCA-AGAGAA
* * *
278206 ATGGGAGGGGTTTTCGTTGGTTGTTCATGCAAATGGGGTGGGAAGAGCCAATAACGTTGCATGCA
65 ATGGGAGGGGTTTTCATTGGGTGTTCATGCAAATGGGGTGGGAAGAGCCAATAACGTTGAATGCA
*
278271 GAGAAGGGGTGGGAAGACGC
130 GAGAAGGGGTGAGAAGACGC
278291 ATGGAATGCCATGCGTCTTCGAGGGGTTTTCCTTG
1 ATGGAATGCCATGCGTCTTCGAGGGGTTTTCCTTG
278326 GACGCTTGGA
Statistics
Matches: 164, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
146 10 0.06
147 116 0.71
148 1 0.01
149 37 0.23
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.27
Consensus pattern (149 bp):
ATGGAATGCCATGCGTCTTCGAGGGGTTTTCCTTGAGTGTGCTCAGTACATGCATGCAAGAGAAA
TGGGAGGGGTTTTCATTGGGTGTTCATGCAAATGGGGTGGGAAGAGCCAATAACGTTGAATGCAG
AGAAGGGGTGAGAAGACGC
Found at i:279324 original size:17 final size:17
Alignment explanation
Indices: 279302--279334 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
279292 AGCTTATTTA
*
279302 TTTATTTTAAATATAAG
1 TTTATTTAAAATATAAG
279319 TTTATTTAAAATATAA
1 TTTATTTAAAATATAA
279335 TAAATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTATTTAAAATATAAG
Found at i:283854 original size:27 final size:27
Alignment explanation
Indices: 283816--283878 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
283806 AAGATCAACT
283816 AGCAGATATTTTTACAAAGCCATTGAG
1 AGCAGATATTTTTACAAAGCCATTGAG
283843 AGCAGATATTTTTACAAAGCCATTGAG
1 AGCAGATATTTTTACAAAGCCATTGAG
283870 AGCAGATAT
1 AGCAGATAT
283879 ATTCAACCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (27 bp):
AGCAGATATTTTTACAAAGCCATTGAG
Found at i:285624 original size:18 final size:18
Alignment explanation
Indices: 285601--285640 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
285591 ATATTAATTT
285601 GGGCTTCTTAGTTTGTTA
1 GGGCTTCTTAGTTTGTTA
285619 GGGCTTCTTAGTTTGTTA
1 GGGCTTCTTAGTTTGTTA
285637 GGGC
1 GGGC
285641 CCACATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.12, G:0.33, T:0.45
Consensus pattern (18 bp):
GGGCTTCTTAGTTTGTTA
Found at i:286124 original size:25 final size:26
Alignment explanation
Indices: 286096--286150 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
286086 CTAATTATTG
286096 TAATTATATT-TAAATATTT-ATAAAA
1 TAATTATATTAT-AATATTTGATAAAA
286121 TAATTATATTATAATATTTGATAAAA
1 TAATTATATTATAATATTTGATAAAA
286147 -AATT
1 TAATT
286151 TCAACCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
TAATTATATTATAATATTTGATAAAA
Found at i:289706 original size:3 final size:3
Alignment explanation
Indices: 289698--289731 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
289688 TGTAATTATA
289698 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
289732 AATGAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:290234 original size:45 final size:45
Alignment explanation
Indices: 290178--290275 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
290168 CCCGAAAGCT
* * * ** *
290178 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGA
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGA
*
290223 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGA
290268 TTTTGAAA
1 TTTTGAAA
290276 TCAAAAAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGA
Found at i:290320 original size:210 final size:205
Alignment explanation
Indices: 289934--290324 Score: 570
Period size: 210 Copynumber: 1.9 Consensus size: 205
289924 TTATAGATGG
* * *
289934 CCCGGAGGCTTTAAATATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATTCTGCACTGTAGGTCT
1 CCCGAAGGCTTTAAACATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATCCTGCACTGTAGGTCT
* * * * * * * *
289999 TATGGATGGCCCTGAGGTCTTATCATCTTGCACTGCAGGTCTTACAGATGACCCGGAGGATTTAA
66 TATGGATGACCCTGAGATCTTAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGGATTTAA
* *
290064 GATCAAGAAACCTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCATGTACTGAAGGGC
131 GATCAAAAAAACTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCATGTACTGAAGGGC
290129 TTACAAATGA
196 TTACAAATGA
290139 CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATCCTGCACTGTAGGT
1 CCCGAAGGCTTT--AAACATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATCCTGCACTGTAGGT
*
290204 CTTATGGATGACCC-GAAGATTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGG
64 CTTATGGATGACCCTG-AGATCTT---AACATCATGCACTGAAGGGCTTACAGATGACCAGAAGG
*
290268 TTTTGAA-ATCAAAAAAACTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATC
125 ATTT-AAGATCAAAAAAACTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATC
290325 CTGCACTGTA
Statistics
Matches: 164, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
205 11 0.07
206 1 0.01
207 67 0.41
210 83 0.51
211 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (205 bp):
CCCGAAGGCTTTAAACATCAAAAAGCTCCCGAAAGCTTTTTGAAAACATCCTGCACTGTAGGTCT
TATGGATGACCCTGAGATCTTAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGGATTTAA
GATCAAAAAAACTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCATGTACTGAAGGGC
TTACAAATGA
Found at i:290382 original size:22 final size:23
Alignment explanation
Indices: 290321--290383 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
290311 CATTTGAAAA
*
290321 CATCCTGCACTGTAGGTCTTATG
1 CATCTTGCACTGTAGGTCTTATG
* * *
290344 GA--TGGCTCTG-AGGTCTTAT-
1 CATCTTGCACTGTAGGTCTTATG
290363 CATCTTGCACTGTAGGTCTTA
1 CATCTTGCACTGTAGGTCTTA
290384 CATATGACCC
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 9 0.30
21 11 0.37
22 8 0.27
23 1 0.03
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (23 bp):
CATCTTGCACTGTAGGTCTTATG
Found at i:290541 original size:45 final size:45
Alignment explanation
Indices: 290430--290715 Score: 500
Period size: 45 Copynumber: 6.3 Consensus size: 45
290420 GAAGGCTTTT
290430 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
290475 CATTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 --TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
290522 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
290567 TTTTGAAAACATCATGTACTGAAGGTCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
290612 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
290657 TTTTGAAAACATCATGCACTGAAGGGCTTAAAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
290702 CTTTGAAAATATCA
1 TTTTGAAAACATCA
290716 AAAAGCTTCC
Statistics
Matches: 230, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 185 0.80
47 45 0.20
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:290750 original size:76 final size:76
Alignment explanation
Indices: 290650--291095 Score: 657
Period size: 76 Copynumber: 5.9 Consensus size: 76
290640 TACAGATGAC
*
290650 CCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTAAAGATGACCCGAAGGCTTTGAAAATA
1 CCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATA
290713 TCAAAAAGCTT
66 TCAAAAAGCTT
* * * *
290724 CCGAAGGCTTTATGAAAACATCATGCATTGAAGGGCTTATAGATGACCCGAAGGCTTTAAAAATA
1 CCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATA
290789 TCAAAAAGC-T
66 TCAAAAAGCTT
* * *
290799 CCAAAAGGATTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGCTTTGAAAAT
1 CC-GAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
290864 ATCAAAAAGC-T
65 ATCAAAAAGCTT
*
290875 CCAGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAT
1 CC-GAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
*
290940 ATCAAAAAGCTC
65 ATCAAAAAGCTT
* *
290952 CCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAATA
1 CCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATA
*
291017 TCAAAAAGCTC
66 TCAAAAAGCTT
* * * * ** * *
291028 CCGAAGGCTTTTTGAAAATATCCTGCACTGTAGGCCTTATGGATGACCCGAAGGTTTTGAAAACA
1 CCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATA
291093 TCA
66 TCA
291096 TGCACTGTAT
Statistics
Matches: 345, Mismatches: 23, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
74 7 0.02
75 3 0.01
76 333 0.97
77 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (76 bp):
CCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATA
TCAAAAAGCTT
Found at i:291827 original size:22 final size:22
Alignment explanation
Indices: 291772--291828 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
291762 AATAAAACTT
*
291772 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
291794 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
291816 TCATCTTTGAAGA
1 TCATCTTTGAAGA
291829 ATGTAGATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:292356 original size:2 final size:2
Alignment explanation
Indices: 292349--292415 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
292339 TTATTTATTA
292349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
292391 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 A
292416 CAATTACATC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:293711 original size:27 final size:28
Alignment explanation
Indices: 293680--293732 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
293670 TTGGCAATTT
*
293680 AATATTATTGCTTTTA-AAT-TTATTTTA
1 AATATTATT-CATTTATAATATTATTTTA
293707 AATATTATTCATTTATAATATTATTT
1 AATATTATTCATTTATAATATTATTT
293733 ATTATTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 12 0.52
28 6 0.26
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (28 bp):
AATATTATTCATTTATAATATTATTTTA
Found at i:293758 original size:23 final size:23
Alignment explanation
Indices: 293709--293755 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
293699 TTATTTTAAA
293709 TATTATTCATTTATAATATTATT
1 TATTATTCATTTATAATATTATT
* *
293732 TATTATTACTTTTATATTATTATT
1 TATTATT-CATTTATAATATTATT
293756 ATTTCATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTATTCATTTATAATATTATT
Found at i:293782 original size:2 final size:2
Alignment explanation
Indices: 293775--293822 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
293765 TAGTCACATA
* *
293775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
293817 GT AT AT
1 AT AT AT
293823 TTATTTTCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:301390 original size:114 final size:114
Alignment explanation
Indices: 301190--301409 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
301180 CATGTTCTCG
* *
301190 TAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
301255 GGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCA
*
301304 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * * *
301369 GGTAGGAACCTCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAA
301410 CTGCATGATC
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCA
Found at i:302365 original size:34 final size:34
Alignment explanation
Indices: 302322--302386 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
302312 TTCAACCAGA
302322 AATATAATATTGGGGCATT-TTGAAGGCTCACAC
1 AATATAATATTGGGGCATTCTTGAAGGCTCACAC
* *
302355 AATATGAATATTTGGGCATTCTTGGAGGCTCA
1 AATAT-AATATTGGGGCATTCTTGAAGGCTCA
302387 TCTCAACAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.18
34 13 0.46
35 10 0.36
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (34 bp):
AATATAATATTGGGGCATTCTTGAAGGCTCACAC
Found at i:302655 original size:76 final size:74
Alignment explanation
Indices: 302507--302677 Score: 189
Period size: 76 Copynumber: 2.3 Consensus size: 74
302497 AATAAGAAGC
* *
302507 AAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTATCCTGAATAT
1 AAATG-TGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACAT
*
302572 TTATATCAGCA
65 TCATATCAG-A
* ** * ** *
302583 AAATGATGGGGCATGCTGAAAGCTTTTTTCAATCAGAATGAAGAATGTTGATGTATTTTGAACGT
1 AAATG-TGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACAT
* *
302648 TCGTATCAGT
65 TCATATCAGA
*
302658 AATTGTCGGGGCATGCTGAA
1 AAATGT-GGGGCATGCTGAA
302678 GGCCCACATC
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
74 1 0.01
75 17 0.21
76 62 0.77
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (74 bp):
AAATGTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAACATT
CATATCAGA
Found at i:304037 original size:22 final size:22
Alignment explanation
Indices: 304011--304090 Score: 124
Period size: 22 Copynumber: 3.6 Consensus size: 22
304001 TACATCTACA
304011 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
304033 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* * *
304055 CTTTTTAAAGATGATAGATTAT
1 CTCTTCAAAGATGATAGATTCT
*
304077 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
304091 AAGCTTTATT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:305089 original size:73 final size:73
Alignment explanation
Indices: 304967--305467 Score: 939
Period size: 73 Copynumber: 6.8 Consensus size: 73
304957 GTTTTCAAAT
*
304967 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTATCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
305032 CTCGAAAC
66 CTCGAAAC
305040 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
305105 CTCGAAAC
66 CTCGAAAC
305113 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
305178 CTCGAAAC
66 CTCGAAAC
* *
305186 AGAACTTTATCTCACTTGATATTTTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
305251 CTCGAAAC
66 CTCGAAAC
305259 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
305324 CTCGAAAC
66 CTCGAAAC
305332 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
*
305397 CTTGAAAC
66 CTCGAAAC
* *
305405 AAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTGAGACAGTT
1 AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGACAGTT
305468 ATTTCGAGTT
Statistics
Matches: 419, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
73 397 0.95
74 22 0.05
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (73 bp):
AGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCA
CTCGAAAC
Found at i:305826 original size:17 final size:19
Alignment explanation
Indices: 305800--305879 Score: 93
Period size: 16 Copynumber: 4.5 Consensus size: 19
305790 TAATAATAAT
305800 TATA-ATTATTATTA-ATA
1 TATATATTATTATTATATA
305817 TA-ATATTATTATTATATA
1 TATATATTATTATTATATA
305835 TATATA-TA-TA-TATATA
1 TATATATTATTATTATATA
305851 TATATA-TATATATATATATA
1 TATATATTAT-TAT-TATATA
305871 TATATATTA
1 TATATATTA
305880 CAAATTACAT
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
16 15 0.27
17 14 0.25
18 9 0.16
19 3 0.05
20 12 0.22
21 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATATTATTATTATATA
Found at i:305829 original size:20 final size:21
Alignment explanation
Indices: 305789--305870 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 21
305779 TAATTTTTTC
305789 ATAATAATAATTATAATTATTAT
1 ATAAT-ATAA-TATAATTATTAT
*
305812 -TAATATAATATTATTATTAT
1 ATAATATAATATAATTATTAT
305832 AT-ATATATATATATATATATATAT
1 ATAATATA-ATATA-AT-TAT-TAT
305856 ATATATATATATATA
1 ATA-ATATA-ATATA
305871 TATATATTAC
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
20 16 0.32
21 9 0.18
22 6 0.12
23 3 0.06
24 5 0.10
26 11 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATATAATATAATTATTAT
Found at i:305836 original size:2 final size:2
Alignment explanation
Indices: 305814--305877 Score: 100
Period size: 2 Copynumber: 34.0 Consensus size: 2
305804 ATTATTATTA
305814 AT AT A- AT AT -T AT -T AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
305852 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
305878 TACAAATTAC
Statistics
Matches: 58, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
1 4 0.07
2 54 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:307215 original size:17 final size:17
Alignment explanation
Indices: 307195--307228 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
307185 TATTATTTTG
307195 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
307212 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
307229 GTCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:307245 original size:2 final size:2
Alignment explanation
Indices: 307238--307263 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
307228 AGTCACATAA
307238 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
307264 TAAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:307371 original size:22 final size:22
Alignment explanation
Indices: 307346--307391 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
307336 GATATTTTAA
307346 ATAATTAAATATTATAAAAATT
1 ATAATTAAATATTATAAAAATT
* * **
307368 ATAATTTAATTTTATTTAAATT
1 ATAATTAAATATTATAAAAATT
307390 AT
1 AT
307392 TATATTTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATTAAATATTATAAAAATT
Found at i:311022 original size:121 final size:121
Alignment explanation
Indices: 310808--311051 Score: 409
Period size: 121 Copynumber: 2.0 Consensus size: 121
310798 GACATTAGCC
* *
310808 TTCATTGGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGATTTGACAATCACAATAGAGC
1 TTCATTAGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGAATTGACAATCACAATAGAGC
310873 AAACACCAAGCTGACAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTT
66 AAACACCAAGCTGACAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTT
* * *
310929 TTCATTAGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGAATTGACAATCACAGTGGAGT
1 TTCATTAGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGAATTGACAATCACAATAGAGC
* *
310994 AAATACCGAA-CTGCCAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTT
66 AAACACC-AAGCTGACAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTT
311050 TT
1 TT
311052 TCTTTTTCTT
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
121 113 0.98
122 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (121 bp):
TTCATTAGACTAATTAAAGGGTTCAACTCATCACAATGTCTTTGAATTGACAATCACAATAGAGC
AAACACCAAGCTGACAAATACCCGATCAAGGTCATGCTTTGAATATATGACTTTTT
Found at i:313080 original size:7 final size:8
Alignment explanation
Indices: 313055--313082 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
313045 AATGCGATGT
313055 AAATGCAA
1 AAATGCAA
313063 AAATGCAA
1 AAATGCAA
313071 AAATGCAA
1 AAATGCAA
313079 AAAT
1 AAAT
313083 AAGAATGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.14
Consensus pattern (8 bp):
AAATGCAA
Found at i:313091 original size:14 final size:15
Alignment explanation
Indices: 313055--313093 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
313045 AATGCGATGT
313055 AAATGCAAAAATGCAA
1 AAATGCAAAAAT-CAA
313071 AAATGCAAAAAT-AA
1 AAATGCAAAAATCAA
*
313085 GAATGCAAA
1 AAATGCAAA
313094 CTGTGCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
16 12 0.55
ACGTcount: A:0.64, C:0.10, G:0.13, T:0.13
Consensus pattern (15 bp):
AAATGCAAAAATCAA
Found at i:313127 original size:13 final size:13
Alignment explanation
Indices: 313109--313147 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
313099 CAATGCAAAG
313109 ATGAAAATATAAA
1 ATGAAAATATAAA
*
313122 ATGAAAATGT-AA
1 ATGAAAATATAAA
313134 ATGAAAATATAAA
1 ATGAAAATATAAA
313147 A
1 A
313148 ATGCAAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (13 bp):
ATGAAAATATAAA
Found at i:313137 original size:12 final size:12
Alignment explanation
Indices: 313109--313146 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
313099 CAATGCAAAG
313109 ATGAAAATATAAA
1 ATGAAAATAT-AA
*
313122 ATGAAAATGTAA
1 ATGAAAATATAA
313134 ATGAAAATATAA
1 ATGAAAATATAA
313146 A
1 A
313147 AATGCAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.24
Consensus pattern (12 bp):
ATGAAAATATAA
Found at i:313137 original size:25 final size:26
Alignment explanation
Indices: 313100--313161 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
313090 CAAACTGTGC
313100 AATGCAAAGATGAAAATAT-AAAATGAA
1 AATGC-AA-ATGAAAATATAAAAATGAA
* *
313127 AATGTAAATGAAAATATAAAAATGCA
1 AATGCAAATGAAAATATAAAAATGAA
313153 AATGCAAAT
1 AATGCAAAT
313162 ATAAAAAGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.32
26 17 0.55
27 4 0.13
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (26 bp):
AATGCAAATGAAAATATAAAAATGAA
Found at i:313173 original size:21 final size:20
Alignment explanation
Indices: 313125--313176 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
313115 ATATAAAATG
*
313125 AAAATGTAAATGAAAATATA
1 AAAATGCAAATGAAAATATA
*
313145 AAAATGCAAATGCAAATATA
1 AAAATGCAAATGAAAATATA
313165 AAAAGTGCAAAT
1 AAAA-TGCAAAT
313177 ATAATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (20 bp):
AAAATGCAAATGAAAATATA
Found at i:316396 original size:2 final size:2
Alignment explanation
Indices: 316389--316419 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
316379 ATACTTATTA
316389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
316420 AATAAGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:316430 original size:81 final size:80
Alignment explanation
Indices: 316337--316509 Score: 294
Period size: 81 Copynumber: 2.2 Consensus size: 80
316327 TTAAAAATAA
* *
316337 ATAAATATTATTATTTAATTAATTGGTGAAATTAATTAAATAATACTTATTAATATATATATATA
1 ATAAATAGTATTATTTAATTAATTGGTGAAACTAATTAAATAATACTTATTAATATATATATATA
316402 TATATATATATATAT
66 TATATATATATATAT
*
316417 ATAAATAAGTATTATTTAATTAATTGGTGGAACTAATTAAATAATACTTATTAATATATATATAT
1 ATAAAT-AGTATTATTTAATTAATTGGTGAAACTAATTAAATAATACTTATTAATATATATATAT
316482 ATATATATATATATAT
65 ATATATATATATATAT
*
316498 ATATATA-TATTA
1 ATAAATAGTATTA
316510 ATATGACTAG
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
79 5 0.06
80 7 0.08
81 76 0.86
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (80 bp):
ATAAATAGTATTATTTAATTAATTGGTGAAACTAATTAAATAATACTTATTAATATATATATATA
TATATATATATATAT
Found at i:316477 original size:2 final size:2
Alignment explanation
Indices: 316470--316507 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
316460 ATACTTATTA
316470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
316508 TAATATGACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:317821 original size:3 final size:3
Alignment explanation
Indices: 317813--317850 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
317803 TGTAATTATA
* *
317813 AAT AAT AAT AAT AAT ATT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
317851 AATGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:317831 original size:21 final size:21
Alignment explanation
Indices: 317807--317849 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
317797 TGGGCTTGTA
317807 ATTATAAATAATAATAATAAT
1 ATTATAAATAATAATAATAAT
*
317828 ATTATTAATAATAATAATAAT
1 ATTATAAATAATAATAATAAT
317849 A
1 A
317850 AAATGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATAAATAATAATAATAAT
Found at i:321152 original size:18 final size:18
Alignment explanation
Indices: 321126--321166 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
321116 ATGAAATCTG
* *
321126 ATTAAATTAAAGATAATT
1 ATTATATTAAAAATAATT
*
321144 ATTATATTAAAAATTATT
1 ATTATATTAAAAATAATT
321162 ATTAT
1 ATTAT
321167 TTTGAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTATATTAAAAATAATT
Found at i:325610 original size:17 final size:16
Alignment explanation
Indices: 325588--325620 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
325578 TGTGATCGTA
325588 AATTTTTTTTATATTTT
1 AATTTTTTTTAT-TTTT
325605 AATTTTTTTTATTTTT
1 AATTTTTTTTATTTTT
325621 CATAAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
AATTTTTTTTATTTTT
Found at i:327107 original size:33 final size:33
Alignment explanation
Indices: 327070--327134 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
327060 AAAAGGATTG
*
327070 TATTA-ATTTCTTAATATTAATATAAAAAATATT
1 TATTATATTTCTT-ATAGTAATATAAAAAATATT
* * *
327103 TATTATATTTGTTATAGTATTATAAATAATAT
1 TATTATATTTCTTATAGTAATATAAAAAATAT
327135 AATAAATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 21 0.78
34 6 0.22
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (33 bp):
TATTATATTTCTTATAGTAATATAAAAAATATT
Found at i:328561 original size:3 final size:3
Alignment explanation
Indices: 328553--328588 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
328543 TATAGACAAG
328553 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
328589 ATTATAATAA
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:330066 original size:18 final size:19
Alignment explanation
Indices: 330043--330079 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
330033 CCAGTAATCC
330043 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
330061 TATTCCTACTGGTAATCTT
1 TATTCC-ACTGGTAATCTT
330080 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:330085 original size:20 final size:20
Alignment explanation
Indices: 330049--330086 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
330039 ATCCTATTCC
**
330049 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTACATTCCTA
330069 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
330087 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:332468 original size:81 final size:81
Alignment explanation
Indices: 332314--332468 Score: 183
Period size: 81 Copynumber: 1.9 Consensus size: 81
332304 ATATATATAT
* *
332314 ATTCACCTTGAGTTTTAGGTCACCAGACACTAACCTTTCTAATATGACTTTAGTTTATCTATCTA
1 ATTCACCTTGAGTTTTAGGTCACCAGACACTAACCTTTCCAATATGACTTTAGCTTATCTATCTA
*
332379 TGGTAAAGTACACAAG
66 TGGAAAAGTACACAAG
* * * *
332395 ATTCACCTTGA-TGTTTAGGTCACCCGACACTCATGCTTTTCCAATATGAGTTT-GCTT-T-TAT
1 ATTCACCTTGAGT-TTTAGGTCACCAGACACT-A-ACCTTTCCAATATGACTTTAGCTTATCTAT
332456 CTATGAGAAAAGT
63 CTATG-GAAAAGT
332469 TTGACTTAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
80 9 0.14
81 35 0.56
82 4 0.06
83 15 0.24
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (81 bp):
ATTCACCTTGAGTTTTAGGTCACCAGACACTAACCTTTCCAATATGACTTTAGCTTATCTATCTA
TGGAAAAGTACACAAG
Found at i:337539 original size:26 final size:26
Alignment explanation
Indices: 337506--337566 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
337496 AATTTTGTTA
337506 AAAT-AAAA-CTGGAATGAGAAAACTG
1 AAATGAAAATCTGG-ATGAGAAAACTG
* * *
337531 AAATGAAAATTTTGATGCGAAAACTG
1 AAATGAAAATCTGGATGAGAAAACTG
337557 AAATGAAAAT
1 AAATGAAAAT
337567 TTTGATTCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.13
26 25 0.81
27 2 0.06
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.21
Consensus pattern (26 bp):
AAATGAAAATCTGGATGAGAAAACTG
Found at i:337567 original size:26 final size:26
Alignment explanation
Indices: 337523--337572 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
337513 ACTGGAATGA
337523 GAAAACTGAAATGAAAATTTTGATGC
1 GAAAACTGAAATGAAAATTTTGATGC
337549 GAAAACTGAAATGAAAATTTTGAT
1 GAAAACTGAAATGAAAATTTTGAT
337573 TCAGAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (26 bp):
GAAAACTGAAATGAAAATTTTGATGC
Found at i:339788 original size:2 final size:2
Alignment explanation
Indices: 339781--339811 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
339771 TTTTATTAAA
339781 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
339812 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:344444 original size:20 final size:20
Alignment explanation
Indices: 344416--344453 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
344406 TTATACATTT
344416 AAAACATAAATAAAACAATC
1 AAAACATAAATAAAACAATC
*
344436 AAAAGATAAATAAAACAA
1 AAAACATAAATAAAACAA
344454 ACTCATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.11, G:0.03, T:0.13
Consensus pattern (20 bp):
AAAACATAAATAAAACAATC
Found at i:345741 original size:29 final size:29
Alignment explanation
Indices: 345677--345734 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
345667 CAATAGACTG
345677 AAATAAATACAACATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
*
345706 AAATAAATACAAGATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
345735 GATTAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.17
Consensus pattern (29 bp):
AAATAAATACAACATACAAATTAGAAACC
Done.