Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008737.1 Hibiscus syriacus cultivar Beakdansim tig00111812_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: 2791265
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 14
Found at i:1684184 original size:18 final size:19
Alignment explanation
Indices: 1684110--1684301 Score: 80
Period size: 18 Copynumber: 10.8 Consensus size: 19
1684100 ATATAATATA
**
1684110 TATATATATATAATATAAGTT
1 TATATATATAT-ATATAA-AC
* * *
1684131 TGTATATAAACTATATATA-
1 TATATATATA-TATATAAAC
1684150 TATATATATATATATAAAC
1 TATATATATATATATAAAC
*
1684169 TATATTTATAT-TATAAAC
1 TATATATATATATATAAAC
1684187 TATATA-AT-TAT-T--A-
1 TATATATATATATATAAAC
1684200 TA-AGT-TATATATATAAA-
1 TATA-TATATATATATAAAC
* *
1684217 T-TATGT-T-TATATGAAC
1 TATATATATATATATAAAC
* *
1684233 TATATATATAAACTATAAAA
1 TATATATATATA-TATAAAC
* *
1684253 AATATATA-ATTTATAAAC
1 TATATATATATATATAAAC
*
1684271 TATA-AT-T-TATATTAA-
1 TATATATATATATATAAAC
1684286 TATAGTATATATATAT
1 TATA-TATATATATAT
1684302 TATTCAAAGT
Statistics
Matches: 129, Mismatches: 21, Indels: 44
0.66 0.11 0.23
Matches are distributed among these distances:
12 1 0.01
13 5 0.04
14 4 0.03
15 12 0.09
16 11 0.09
17 15 0.12
18 30 0.23
19 25 0.19
20 12 0.09
21 13 0.10
22 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
TATATATATATATATAAAC
Found at i:1684392 original size:11 final size:11
Alignment explanation
Indices: 1684376--1684429 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
1684366 GATTTTATTT
1684376 GGGAATTTAGA
1 GGGAATTTAGA
1684387 GGGAATTT-GA
1 GGGAATTTAGA
1684397 --GAATTTAGA
1 GGGAATTTAGA
*
1684406 GAGAATTT-GA
1 GGGAATTTAGA
1684416 --GAATTTAGA
1 GGGAATTTAGA
1684425 GGGAA
1 GGGAA
1684430 ATTGAAAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
8 12 0.32
9 4 0.11
10 4 0.11
11 17 0.46
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.28
Consensus pattern (11 bp):
GGGAATTTAGA
Found at i:1684400 original size:19 final size:19
Alignment explanation
Indices: 1684372--1684478 Score: 108
Period size: 19 Copynumber: 5.6 Consensus size: 19
1684362 TTTTGATTTT
*
1684372 ATTTGGGAATTTAGAGGGA
1 ATTTGAGAATTTAGAGGGA
*
1684391 ATTTGAGAATTTAGAGAGA
1 ATTTGAGAATTTAGAGGGA
1684410 ATTTGAGAATTTAGAGGGA
1 ATTTGAGAATTTAGAGGGA
* * *
1684429 AATTGAAAAACTTAGAGGGA
1 ATTTG-AGAATTTAGAGGGA
* * *
1684449 A-TAGAAAATTTTGGAGGGA
1 ATTTGAGAA-TTTAGAGGGA
*
1684468 AATTGAGAATT
1 ATTTGAGAATT
1684479 GAGATTTTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
18 4 0.05
19 52 0.70
20 18 0.24
ACGTcount: A:0.41, C:0.01, G:0.29, T:0.29
Consensus pattern (19 bp):
ATTTGAGAATTTAGAGGGA
Found at i:1684459 original size:38 final size:39
Alignment explanation
Indices: 1684379--1684473 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 39
1684369 TTTATTTGGG
* * * * *
1684379 AATTTAGAGGGAATTTG-AGAATTTAGAGAGAATTTGAG
1 AATTTAGAGGGAAATTGAAAAACTTAGAGAGAATTAGAA
*
1684417 AATTTAGAGGGAAATTGAAAAACTTAGAGGGAA-TAGAA
1 AATTTAGAGGGAAATTGAAAAACTTAGAGAGAATTAGAA
*
1684455 AATTTTGGAGGGAAATTGA
1 AA-TTTAGAGGGAAATTGA
1684474 GAATTGAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.43, C:0.01, G:0.28, T:0.27
Consensus pattern (39 bp):
AATTTAGAGGGAAATTGAAAAACTTAGAGAGAATTAGAA
Found at i:1684672 original size:2 final size:2
Alignment explanation
Indices: 1684665--1684808 Score: 169
Period size: 2 Copynumber: 75.5 Consensus size: 2
1684655 TTTAGTTTTC
1684665 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
* * *
1684707 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TG TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1684748 TG TA TA TA TA -A TA TA TA TA TG TA T- TA TA TA -A T- TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1684785 TT TA TA T- TA -A TA TA GTA TA TA TA T
1 TA TA TA TA TA TA TA TA -TA TA TA TA T
1684809 GTATGTATAA
Statistics
Matches: 121, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
1 8 0.07
2 111 0.92
3 2 0.02
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1685538 original size:2 final size:2
Alignment explanation
Indices: 1685451--1685520 Score: 113
Period size: 2 Copynumber: 34.0 Consensus size: 2
1685441 ATAAACCAGG
*
1685451 TA TA GTA TA TA TA AA CTA 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
1685495 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
1685521 AAGTAAATTA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 61 0.95
3 3 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1685625 original size:14 final size:14
Alignment explanation
Indices: 1685608--1685655 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
1685598 CCCGAAATCA
1685608 TAAACCTTAAACCC
1 TAAACCTTAAACCC
* *
1685622 TAAACTTTAAACCA
1 TAAACCTTAAACCC
*
1685636 TAAACCATAAACCC
1 TAAACCTTAAACCC
1685650 TAAACC
1 TAAACC
1685656 CTAATATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:1685656 original size:7 final size:7
Alignment explanation
Indices: 1685608--1685659 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
1685598 CCCGAAATCA
*
1685608 TAAACCT
1 TAAACCC
1685615 TAAACCC
1 TAAACCC
**
1685622 TAAACTT
1 TAAACCC
*
1685629 TAAACCA
1 TAAACCC
*
1685636 TAAACCA
1 TAAACCC
1685643 TAAACCC
1 TAAACCC
1685650 TAAACCC
1 TAAACCC
1685657 TAA
1 TAA
1685660 TATAAATGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:1686049 original size:15 final size:15
Alignment explanation
Indices: 1686024--1686060 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
1686014 ATAAACCAGG
1686024 TATAGTATATATAAAC
1 TATA-TATATATAAAC
1686040 TATATATATATAAAC
1 TATATATATATAAAC
1686055 TATATA
1 TATATA
1686061 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:1686165 original size:21 final size:21
Alignment explanation
Indices: 1686141--1686180 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1686131 ATAAAAACCC
*
1686141 TAAATCATAAACCCTAAACTT
1 TAAACCATAAACCCTAAACTT
*
1686162 TAAACCATACACCCTAAAC
1 TAAACCATAAACCCTAAAC
1686181 CCTAATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCATAAACCCTAAACTT
Found at i:1686283 original size:18 final size:18
Alignment explanation
Indices: 1686256--1686291 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1686246 GGCTTATGTA
1686256 AACTAATGTAAATGGACT
1 AACTAATGTAAATGGACT
*
1686274 AACTATTGTAAATGGACT
1 AACTAATGTAAATGGACT
1686292 TATTTTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (18 bp):
AACTAATGTAAATGGACT
Found at i:1686497 original size:528 final size:528
Alignment explanation
Indices: 1685487--1687336 Score: 2440
Period size: 528 Copynumber: 3.5 Consensus size: 528
1685477 TATATATATA
*
1685487 TATA-TATATATATATATATATATATATA-TATATAAAGTAAATTACTTATATAGTTTATATAAA
1 TATAGTATATATATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATATAAA
*
1685550 CACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACCCGAAATCATAAACCT
66 CACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACCCTAAATC----A-C-
*
1685615 TAAACCCTAAACTTTAAACCATAAACCATAAACCCTAAACCCTAATATAAATGGACTAGCACTAA
125 TAAACCCTAAAC-TT------TAAACCATAAACCCTAAACCCTAATATAAATGGACTAACACTAA
*
1685680 TGCATATATATTTGTAATAAAAGAGTGG-CTTATGTATTGGGCTTATGTAAACTAATGTAAATGG
183 TGCATATATATTTGTAATAAAAGAGTGGACTTATGTATTGGGCCTATGTAAACTAATGTAAATGG
*
1685744 ACTAACTATTGCAAATGGACTTATTTTTTGGTTTTATTATTACTTATTCATAATAACAAAATAAA
248 ACTAACTATTGCAAATGGACTTATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAA
1685809 TGGGCTATTAATGTGAATT-ACCTAACATGCAACTAAAATATTAATTATGCAAATGAAATTAATA
313 TGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATATTAATTATGCAAATGAAATTAATA
* * *
1685873 TAACTTGTGCTACTATTTATGAACCATATAATATGCAATGTGACATACTAGTTATTTAACACCTA
378 TAACATGTACTACTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACCTA
1685938 ATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATAT
443 ATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATAT
*
1686003 AATATGTATGTATAAACCAGG
508 AATATGTATGTATAAACCATG
*
1686024 TATAGTATATATAAACTATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATATAA
1 TATAGTATATATATA-TATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATATAA
*
1686089 ACACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAAAAACCCTAAATCA-TAAAC
65 ACACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACCCTAAATCACTAAAC
* *
1686153 CCTAAACTTTAAACCATACACCCTAAACCCTAATATAAATGGACTAGCACTAATGCATATATATT
130 CCTAAACTTTAAACCATAAACCCTAAACCCTAATATAAATGGACTAACACTAATGCATATATATT
* *
1686218 TGTAATAAAAGAGTGGACTTATGTATTGGGCTTATGTAAACTAATGTAAATGGACTAACTATTGT
195 TGTAATAAAAGAGTGGACTTATGTATTGGGCCTATGTAAACTAATGTAAATGGACTAACTATTGC
1686283 AAATGGACTTATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGGCTATTAAT
260 AAATGGACTTATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGGCTATTAAT
* *
1686348 GTGAATTAACCTAACATGCAACTAAAATATTAATTATGCAAAGGAAATAAATATAACATGTACTA
325 GTGAATTAACCTAACATGCAACTAAAATATTAATTATGCAAATGAAATTAATATAACATGTACTA
* * * *
1686413 CTATTTATGAAACATATAATATGTAATGTGACATACTAATTATTTAACACATAATTAGTCATGTT
390 CTATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACCTAATTAATCATGTT
1686478 TTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAATATGTATGTA
455 TTATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAATATGTATGTA
1686543 TAAACCATG
520 TAAACCATG
* * * * * * ** *
1686552 TATAGTATATATATATAAAAAACTATATAAAGTA-ATAAAGTATA-TAGTTTTATAG-AAATCCT
1 TATAGTATATATATAT-ATATA-TATATAAACTATATAAAGTAAATTACTTATATAGTTTAT-AT
* * * *** * * * * *
1686614 AAAC-CTTAAAT-CCTAAACCCTAAACCTTAAA-TCATAAACCCTAAACTTTAAACCATAAACAC
63 AAACAC-T--ATGCATAAA--CTATA---TAAAGTAATAAAGTATATAGTTT--A-TAGAAACCC
*
1686676 TAAATACTAAACCATAAACCATAAACTTTAAACCATAAACACTAAACACTAAACCATAAACCCTA
117 TAAAT-C---A-C-TAAACCCTAAACTTTAAA-C-----CA-T-AA-AC----CC-TAAACCCTA
* * * * **
1686741 ATGTAAATAGACTAGCATTAATGCATATATATTTGTAATAAAAGAGTGGGTTTATGTATTGGGCC
162 ATATAAATGGACTAACACTAATGCATATATATTTGTAATAAAAGAGTGGACTTATGTATTGGGCC
* *
1686806 TATGTAAACTAATGTAAATGGACTAGCACTATTGCAAATGAACTTATTTTTTTGTTTTATTATTA
227 TATGTAAACTAATGTAAATGGACTA--ACTATTGCAAATGGACTTATTTTTTGGTTTTATTATTA
* *
1686871 CTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAATTAAAATAC
290 CTTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATAT
* *
1686936 TAATTATGCAAATGAAATTAATATGACATGTACTACTATTTACGAACCATATAATATGCAATGTG
355 TAATTATGCAAATGAAATTAATATAACATGTACTACTATTTATGAACCATATAATATGCAATGTG
* *
1687001 ACATACTAATTATTTAACACCCAATTAATCATG-TTT-TAT-A--TA-ATTT--AT-ATTTTAAT
420 ACATACTAATTATTTAACACCTAATTAATCATGTTTTATATAATTTACATTTAAATAATTTTATT
1687057 AATTTTATTAAATAATTTTATATAATATGTATGTATAAACCATG
485 AATTTTATTAAATAATTTTATATAATATGTATGTATAAACCATG
* * *
1687101 TATAG--TATA-GTATATATATA-A-AAACTATATAAAGTAAATTACTTATATTGTTTATAGAAA
1 TATAGTATATATATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATATAAA
* *
1687161 TACTATGCATAAACTATATAAAGTAATAAAATATATAGTTTATAGAAACCCTAAA-C-CTTAAAC
66 CACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACCCTAAATCAC-TAAAC
* ** * * *
1687224 CATAAACACTAAACAATAAACCATAAACCCTAATGTAAATGGACTAACACTAATGCATATATATT
130 CCTAAACTTTAAACCATAAACCCTAAACCCTAATATAAATGGACTAACACTAATGCATATATATT
*
1687289 TGTAATAAAAGAGTGGGCTTATGTATTGGGCCTATGTAAACTAATGTA
195 TGTAATAAAAGAGTGGACTTATGTATTGGGCCTATGTAAACTAATGTA
1687337 TTGCCAAAAT
Statistics
Matches: 1171, Mismatches: 94, Indels: 118
0.85 0.07 0.09
Matches are distributed among these distances:
515 86 0.07
516 1 0.00
520 2 0.00
521 2 0.00
522 1 0.00
523 1 0.00
526 74 0.06
527 134 0.11
528 218 0.19
529 29 0.02
530 4 0.00
532 14 0.01
533 16 0.01
534 2 0.00
535 11 0.01
536 12 0.01
537 5 0.00
538 13 0.01
539 26 0.02
540 90 0.08
541 4 0.00
542 24 0.02
543 16 0.01
544 14 0.01
545 6 0.01
546 3 0.00
547 4 0.00
548 2 0.00
549 57 0.05
550 3 0.00
551 2 0.00
552 4 0.00
553 2 0.00
555 3 0.00
556 96 0.08
557 3 0.00
558 187 0.16
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (528 bp):
TATAGTATATATATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATATAAA
CACTATGCATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACCCTAAATCACTAAACC
CTAAACTTTAAACCATAAACCCTAAACCCTAATATAAATGGACTAACACTAATGCATATATATTT
GTAATAAAAGAGTGGACTTATGTATTGGGCCTATGTAAACTAATGTAAATGGACTAACTATTGCA
AATGGACTTATTTTTTGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGGCTATTAATG
TGAATTAACCTAACATGCAACTAAAATATTAATTATGCAAATGAAATTAATATAACATGTACTAC
TATTTATGAACCATATAATATGCAATGTGACATACTAATTATTTAACACCTAATTAATCATGTTT
TATATAATTTACATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAATATGTATGTAT
AAACCATG
Found at i:1686637 original size:21 final size:21
Alignment explanation
Indices: 1686611--1686741 Score: 151
Period size: 21 Copynumber: 6.2 Consensus size: 21
1686601 TTATAGAAAT
1686611 CCTAAACCTTAAATCC-TAAAC
1 CCTAAACCTTAAA-CCATAAAC
*
1686632 CCTAAACCTTAAATCATAAAC
1 CCTAAACCTTAAACCATAAAC
*
1686653 CCTAAACTTTAAACCATAAAC
1 CCTAAACCTTAAACCATAAAC
* *
1686674 ACTAAATAC-TAAACCATAAAC
1 CCTAAA-CCTTAAACCATAAAC
* *
1686695 CATAAACTTTAAACCATAAAC
1 CCTAAACCTTAAACCATAAAC
*
1686716 ACTAAACAC-TAAACCATAAAC
1 CCTAAAC-CTTAAACCATAAAC
1686737 CCTAA
1 CCTAA
1686742 TGTAAATAGA
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.01
21 91 0.99
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.21
Consensus pattern (21 bp):
CCTAAACCTTAAACCATAAAC
Found at i:1686659 original size:7 final size:7
Alignment explanation
Indices: 1686611--1686741 Score: 91
Period size: 7 Copynumber: 18.7 Consensus size: 7
1686601 TTATAGAAAT
1686611 CCTAAAC
1 CCTAAAC
* *
1686618 CTTAAAT
1 CCTAAAC
1686625 CCTAAAC
1 CCTAAAC
1686632 CCTAAAC
1 CCTAAAC
* *
1686639 CTTAAAT
1 CCTAAAC
*
1686646 CATAAAC
1 CCTAAAC
1686653 CCTAAAC
1 CCTAAAC
**
1686660 TTTAAAC
1 CCTAAAC
*
1686667 CATAAAC
1 CCTAAAC
* *
1686674 ACTAAAT
1 CCTAAAC
*
1686681 ACTAAAC
1 CCTAAAC
*
1686688 CATAAAC
1 CCTAAAC
*
1686695 CATAAAC
1 CCTAAAC
**
1686702 TTTAAAC
1 CCTAAAC
*
1686709 CATAAAC
1 CCTAAAC
*
1686716 ACTAAAC
1 CCTAAAC
*
1686723 ACTAAAC
1 CCTAAAC
*
1686730 CATAAAC
1 CCTAAAC
1686737 CCTAA
1 CCTAA
1686742 TGTAAATAGA
Statistics
Matches: 96, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 96 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:1686673 original size:42 final size:41
Alignment explanation
Indices: 1686611--1686741 Score: 174
Period size: 42 Copynumber: 3.1 Consensus size: 41
1686601 TTATAGAAAT
* * *
1686611 CCTAAACCTTAAATCC-TAAACCCTAAACCTTAAATCATAAAC
1 CCTAAACTTTAAA-CCATAAACACTAAACC-TAAACCATAAAC
*
1686653 CCTAAACTTTAAACCATAAACACTAAATACTAAACCATAAAC
1 CCTAAACTTTAAACCATAAACACTAAA-CCTAAACCATAAAC
*
1686695 CATAAACTTTAAACCATAAACACTAAACACTAAACCATAAAC
1 CCTAAACTTTAAACCATAAACACTAAAC-CTAAACCATAAAC
1686737 CCTAA
1 CCTAA
1686742 TGTAAATAGA
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
41 2 0.03
42 76 0.96
43 1 0.01
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.21
Consensus pattern (41 bp):
CCTAAACTTTAAACCATAAACACTAAACCTAAACCATAAAC
Found at i:1687063 original size:16 final size:16
Alignment explanation
Indices: 1687034--1687065 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1687024 ATTAATCATG
1687034 TTTTATATAATTTATA
1 TTTTATATAATTTATA
1687050 TTTTA-ATAATTT-TA
1 TTTTATATAATTTATA
1687064 TT
1 TT
1687066 AAATAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 7 0.44
16 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATATAATTTATA
Found at i:1687216 original size:7 final size:7
Alignment explanation
Indices: 1687206--1687252 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
1687196 TAGTTTATAG
*
1687206 AAACCCT
1 AAACCAT
*
1687213 AAACCTT
1 AAACCAT
1687220 AAACCAT
1 AAACCAT
1687227 AAA-CACT
1 AAACCA-T
*
1687234 AAACAAT
1 AAACCAT
1687241 AAACCAT
1 AAACCAT
1687248 AAACC
1 AAACC
1687253 CTAATGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
6 2 0.06
7 31 0.91
8 1 0.03
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCAT
Found at i:1687235 original size:21 final size:21
Alignment explanation
Indices: 1687206--1687256 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1687196 TAGTTTATAG
**
1687206 AAACCCTAAACCTTAAACCAT
1 AAACCCTAAACAATAAACCAT
*
1687227 AAACACTAAACAATAAACCAT
1 AAACCCTAAACAATAAACCAT
1687248 AAACCCTAA
1 AAACCCTAA
1687257 TGTAAATGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (21 bp):
AAACCCTAAACAATAAACCAT
Found at i:1687442 original size:14 final size:14
Alignment explanation
Indices: 1687423--1687469 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1687413 ATTTTTTCTT
1687423 TATATAAATTAAAC
1 TATATAAATTAAAC
1687437 TATAT-AATT----
1 TATATAAATTAAAC
1687446 TATATAAATTAAAC
1 TATATAAATTAAAC
*
1687460 TATATTAATT
1 TATATAAATT
1687470 TTCATTGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:1687448 original size:23 final size:24
Alignment explanation
Indices: 1687421--1687470 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1687411 TAATTTTTTC
1687421 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
1687444 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1687468 TTT
1 TTT
1687471 TCATTGTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1687759 original size:16 final size:16
Alignment explanation
Indices: 1687738--1687792 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
1687728 CGGATCATTT
*
1687738 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
1687754 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
1687770 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
*
1687786 ATAGGTC
1 ACAGGTC
1687793 GGGTAATACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:1694374 original size:43 final size:42
Alignment explanation
Indices: 1694326--1694411 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 42
1694316 TTCAATGTCT
* *
1694326 AAAGTATCAA-TCTACAAATATACAAAACTAACATATTACAATC
1 AAAGTAACAATTC-ACAAATACACAAAACTAACATA-TACAATC
** *
1694369 AAAGTAACAATTCACAAATACATTAAAGTAACATATACAATC
1 AAAGTAACAATTCACAAATACACAAAACTAACATATACAATC
1694411 A
1 A
1694412 TTCTTTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 8 0.22
43 27 0.73
44 2 0.05
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.24
Consensus pattern (42 bp):
AAAGTAACAATTCACAAATACACAAAACTAACATATACAATC
Found at i:1704717 original size:359 final size:359
Alignment explanation
Indices: 1704059--1704774 Score: 1218
Period size: 359 Copynumber: 2.0 Consensus size: 359
1704049 AACGTTGCCG
* * * *
1704059 CTGGTAAAAATGTATTGACTAAATTAAGCAAAAGATTTTTTTTGAACAAGATAATCGTGGGAAGA
1 CTGGTAAAAACGTATTGACTAAATTAAGCAAAAGAATTTTTTTGAACAAGATAATCATGGAAAGA
*
1704124 ACAATTACATGAAGCAAAAAAAAGTTTATTTTGTGGACATAATGAATTCGAAGATAGAATTATCA
66 ACAATTACATGAAGCAAAAAAAAGTTTATTTCGTGGACATAATGAATTCGAAGATAGAATTATCA
*
1704189 TTAATGATCACGATCATGTTGTGCATGATATTGCTCGTGATGATATACTTGTGAGCAAATTTGAC
131 TTAATGATCACGATCATGTTGTGCATGATATTGCTCGTGATGATATACTTGTGAGCAAAGTTGAC
* *
1704254 CCTTATGATAACCATGTCGATGTGAATACTTAATTCAAGCTTAAAAAAAGCTTGGATTCTATCGG
196 CCTTATGATAACCATGTCGATGTAAAGACTTAATTCAAGCTTAAAAAAAGCTTGGATTCTATCGG
1704319 TGTCCATTACTAAAGATTACCCCTTTGAGGGGGTGTTGTGGAAGAGGTGGAGAACTTGTTTGTTG
261 TGTCCATTACTAAAGATTACCCCTTTGAGGGGGTGTTGTGGAAGAGGTGGAGAACTTGTTTGTTG
*
1704384 AAGTAAAGAATT-ATTTTTGTTGAGTTTGAGTGT
326 AAATAAAGAATTGATTTTTGTTGAGTTTGAGTGT
*
1704417 CTGGTAAAAACGTCTTGACTAAATTAAGCAAAAGAATTTTTTTGAACAAGATAATCATGGAAAGA
1 CTGGTAAAAACGTATTGACTAAATTAAGCAAAAGAATTTTTTTGAACAAGATAATCATGGAAAGA
* * * * *
1704482 ACGATTACATTAAGTAGAAAAGAGTTTAATTTCGTGGACATAATGAATTCGAAGATAGAATTATC
66 ACAATTACATGAAGCAAAAAAAAGTTT-ATTTCGTGGACATAATGAATTCGAAGATAGAATTATC
* * *
1704547 ATTAATGATCATGATCATGTTGTGCATGATATTTCTCGTGATGATATATTTGTGAGCAAAGTTGA
130 ATTAATGATCACGATCATGTTGTGCATGATATTGCTCGTGATGATATACTTGTGAGCAAAGTTGA
* *
1704612 TCCTTATGATAACCATGTCGATGTAAAGACTTAATTCAAGCTTAGAAAAAGCTTGGATTCTATCG
195 CCCTTATGATAACCATGTCGATGTAAAGACTTAATTCAAGCTTAAAAAAAGCTTGGATTCTATCG
1704677 GTGTCCATTACTAAAGATTACCCCTTTGAGGGGGTGTTGTGGAAGAGGTGGAGAACTTGTTTGTT
260 GTGTCCATTACTAAAGATTACCCCTTTGAGGGGGTGTTGTGGAAGAGGTGGAGAACTTGTTTGTT
* *
1704742 GAAATGAAGAATTGTTTTTTGTTGAGTTTGAGT
325 GAAATAAAGAATTGATTTTTGTTGAGTTTGAGT
1704775 CTCATCGAAT
Statistics
Matches: 334, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
358 82 0.25
359 234 0.70
360 18 0.05
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.34
Consensus pattern (359 bp):
CTGGTAAAAACGTATTGACTAAATTAAGCAAAAGAATTTTTTTGAACAAGATAATCATGGAAAGA
ACAATTACATGAAGCAAAAAAAAGTTTATTTCGTGGACATAATGAATTCGAAGATAGAATTATCA
TTAATGATCACGATCATGTTGTGCATGATATTGCTCGTGATGATATACTTGTGAGCAAAGTTGAC
CCTTATGATAACCATGTCGATGTAAAGACTTAATTCAAGCTTAAAAAAAGCTTGGATTCTATCGG
TGTCCATTACTAAAGATTACCCCTTTGAGGGGGTGTTGTGGAAGAGGTGGAGAACTTGTTTGTTG
AAATAAAGAATTGATTTTTGTTGAGTTTGAGTGT
Found at i:1712399 original size:6 final size:6
Alignment explanation
Indices: 1712391--1712424 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1712381 TCTCGGCTCG
* *
1712391 TGGTCG TGGTCA TGGTCG TGGTCA TGGTCA TGGT
1 TGGTCA TGGTCA TGGTCA TGGTCA TGGTCA TGGT
1712425 AATACGTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.09, C:0.15, G:0.41, T:0.35
Consensus pattern (6 bp):
TGGTCA
Found at i:1712408 original size:12 final size:12
Alignment explanation
Indices: 1712391--1712424 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1712381 TCTCGGCTCG
1712391 TGGTCGTGGTCA
1 TGGTCGTGGTCA
1712403 TGGTCGTGGTCA
1 TGGTCGTGGTCA
*
1712415 TGGTCATGGT
1 TGGTCGTGGT
1712425 AATACGTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.15, G:0.41, T:0.35
Consensus pattern (12 bp):
TGGTCGTGGTCA
Found at i:1712411 original size:18 final size:18
Alignment explanation
Indices: 1712388--1712424 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1712378 TCATCTCGGC
*
1712388 TCGTGGTCGTGGTCATGG
1 TCGTGGTCATGGTCATGG
1712406 TCGTGGTCATGGTCATGG
1 TCGTGGTCATGGTCATGG
1712424 T
1 T
1712425 AATACGTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.16, G:0.41, T:0.35
Consensus pattern (18 bp):
TCGTGGTCATGGTCATGG
Found at i:1712725 original size:22 final size:22
Alignment explanation
Indices: 1712700--1712754 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1712690 TTAGGAGTTA
* *
1712700 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1712722 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1712744 CGGGAGTTATA
1 CAGGAGTTATA
1712755 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1721242 original size:19 final size:19
Alignment explanation
Indices: 1721218--1721262 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1721208 TTATAGCTAC
1721218 TAATTTTCCCCTTTTATTT
1 TAATTTTCCCCTTTTATTT
**
1721237 TAATTTTTTCCTTTTATTT
1 TAATTTTCCCCTTTTATTT
1721256 TAATTTT
1 TAATTTT
1721263 TCAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (19 bp):
TAATTTTCCCCTTTTATTT
Found at i:1721263 original size:19 final size:19
Alignment explanation
Indices: 1721227--1721263 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1721217 CTAATTTTCC
1721227 CCTTTTATTTTAATTTTTT
1 CCTTTTATTTTAATTTTTT
1721246 CCTTTTATTTTAATTTTT
1 CCTTTTATTTTAATTTTT
1721264 CAATAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (19 bp):
CCTTTTATTTTAATTTTTT
Found at i:1723994 original size:45 final size:45
Alignment explanation
Indices: 1723936--1724028 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
1723926 GATAATACGC
* * *
1723936 TTGTTAAAAGTTCTATAGGGTCA-ATACATTCTGCTAGTAATGATG
1 TTGTTAAAAGTTCTA-AGGGTCATATACATCCTGCCAATAATGATG
* * *
1723981 TTGTTGAAGGTTCTAAGGTTCATATACATCCTGCCAATAATGATG
1 TTGTTAAAAGTTCTAAGGGTCATATACATCCTGCCAATAATGATG
1724026 TTG
1 TTG
1724029 CATCTAATGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 6 0.15
45 35 0.85
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (45 bp):
TTGTTAAAAGTTCTAAGGGTCATATACATCCTGCCAATAATGATG
Found at i:1729158 original size:21 final size:21
Alignment explanation
Indices: 1729128--1729190 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1729118 ACTACAAAAC
* * *
1729128 CTGCTAAAAATCCTATAGCCA
1 CTGCTGAAAATCCTACAACCA
1729149 CTGCTGAAAATCCTACAACCA
1 CTGCTGAAAATCCTACAACCA
*
1729170 CTGCTGAAATTCCTACAACCA
1 CTGCTGAAAATCCTACAACCA
1729191 TTGTAATTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.37, C:0.32, G:0.10, T:0.22
Consensus pattern (21 bp):
CTGCTGAAAATCCTACAACCA
Found at i:1742152 original size:12 final size:12
Alignment explanation
Indices: 1742135--1742231 Score: 72
Period size: 13 Copynumber: 7.8 Consensus size: 12
1742125 GACAAATCCA
1742135 TATTTATTTATT
1 TATTTATTTATT
*
1742147 TATTTATTTTCTT
1 TATTTA-TTTATT
* *
1742160 TATTCAATTATTT
1 TATTTATTTA-TT
* *
1742173 TCTTTCTTTATTT
1 TATTTATTTA-TT
1742186 TATTT-TTTATTT
1 TATTTATTTA-TT
*
1742198 TATTTATTCGA-T
1 TATTTATT-TATT
1742210 TATTTATTTATT
1 TATTTATTTATT
1742222 TATTTTATTT
1 TA-TTTATTT
1742232 GGTTTTAATT
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
11 1 0.01
12 32 0.47
13 34 0.50
14 1 0.01
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (12 bp):
TATTTATTTATT
Found at i:1742161 original size:21 final size:21
Alignment explanation
Indices: 1742135--1742231 Score: 85
Period size: 21 Copynumber: 4.6 Consensus size: 21
1742125 GACAAATCCA
1742135 TATTTATTTATTTATTTATTT
1 TATTTATTTATTTATTTATTT
* * *
1742156 TCTTTATTCAATTATTT-TCTT
1 TATTTATTTATTTATTTAT-TT
*
1742177 TCTTTATTTTATTT-TTTATTT
1 TATTTA-TTTATTTATTTATTT
*
1742198 TATTTATTCGA-TTATTTA-TT
1 TATTTATT-TATTTATTTATTT
1742218 TATTTATTTTATTT
1 TATTTA-TTTATTT
1742232 GGTTTTAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
20 14 0.23
21 41 0.67
22 6 0.10
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (21 bp):
TATTTATTTATTTATTTATTT
Found at i:1742229 original size:17 final size:17
Alignment explanation
Indices: 1742137--1742231 Score: 86
Period size: 17 Copynumber: 5.4 Consensus size: 17
1742127 CAAATCCATA
1742137 TTTATTTATTTATTTAT
1 TTTATTTATTTATTTAT
* * *
1742154 TTTCTTTATTCAATTAT
1 TTTATTTATTTATTTAT
* *
1742171 TTTCTTTCTTTATTT-T
1 TTTATTTATTTATTTAT
1742187 ATTT-TTTATTTTATTTAT
1 -TTTATTTA-TTTATTTAT
1742205 TCGATTATTTATTTATTTAT
1 T---TTATTTATTTATTTAT
1742225 TTTATTT
1 TTTATTT
1742232 GGTTTTAATT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
16 4 0.06
17 43 0.67
18 1 0.02
20 12 0.19
21 4 0.06
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (17 bp):
TTTATTTATTTATTTAT
Found at i:1742249 original size:4 final size:4
Alignment explanation
Indices: 1742135--1742231 Score: 72
Period size: 4 Copynumber: 23.2 Consensus size: 4
1742125 GACAAATCCA
* * * * *
1742135 TATT TATT TATT TATT TATTT TCTT TATT CAAT TATTT TCTT TCTT TATTT
1 TATT TATT TATT TATT TA-TT TATT TATT TATT TA-TT TATT TATT TA-TT
*
1742186 TATT T-TT TATTT TATT TATT CGA-T TATT TATT TATT TATTT TATT T
1 TATT TATT TA-TT TATT TATT -TATT TATT TATT TATT TA-TT TATT T
1742232 GGTTTTAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
3 4 0.05
4 53 0.71
5 18 0.24
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1746955 original size:201 final size:202
Alignment explanation
Indices: 1746679--1747108 Score: 517
Period size: 201 Copynumber: 2.1 Consensus size: 202
1746669 CTTTTTCATA
* * * * *
1746679 TTAACTTCCCGAAAATACGCTCCGAACATGTCTTTCAAGACATTTTAGCTTGTTCTTCATGCACA
1 TTAACTACCCGAAAATACGCCCCGAACATGTCTATCAAGACATTTTAGCTTCTTATTCATGCACA
* * * * *
1746744 AAACCAAGATTTGGAACCATTTTGAACACTATTTTTACCCCGCTTACAATGTCTCGTATGTGTCG
66 AAACCAAGATTTGGAACCAATTTGAACACGATTTTTAACCCGCTTACAATATCTAGTATGTGTCG
* * *
1746809 ATATTACCCTCAACTGAAAGATAAGTATCAATATTAAACCTATAATCTTATAAATTACGAAAAAA
131 ATATCAACCTCAACTGAAAGATAAGTATCAATACTAAACCTATAATCTTATAAATTACGAAAAAA
1746874 AATTAGG
196 AATTAGG
* *
1746881 TTAACTACCC-AAAATAC-CCCCGAACATGTCTATCAA-ACATTTTTTTATCTTCTTATTCTTGC
1 TTAACTACCCGAAAATACGCCCCGAACATGTCTATCAAGACA---TTTTAGCTTCTTATTCATGC
* * *
1746943 ACAAAA-CAAGATTTGGAACCAATTTGAACGCGATTTTTAACCTGCTTATAATATCTAGTATGTG
63 ACAAAACCAAGATTTGGAACCAATTTGAACACGATTTTTAACCCGCTTACAATATCTAGTATGTG
* * * * ** *
1747007 TTGATATCAACCTCAATTGAAAGATAATTTTCAATACTACGCCTTTAATCTTATAAATTACGAAA
128 TCGATATCAACCTCAACTGAAAGATAAGTATCAATACTAAACCTATAATCTTATAAATTACGAAA
* *
1747072 AAAATTTAGT
193 AAAAATTAGG
* * * * *
1747082 TTAATTGCACGAAAATACACCTCGAAC
1 TTAACTACCCGAAAATACGCCCCGAAC
1747109 GTGCCTCTAA
Statistics
Matches: 192, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
199 3 0.02
200 17 0.09
201 127 0.66
202 38 0.20
203 7 0.04
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (202 bp):
TTAACTACCCGAAAATACGCCCCGAACATGTCTATCAAGACATTTTAGCTTCTTATTCATGCACA
AAACCAAGATTTGGAACCAATTTGAACACGATTTTTAACCCGCTTACAATATCTAGTATGTGTCG
ATATCAACCTCAACTGAAAGATAAGTATCAATACTAAACCTATAATCTTATAAATTACGAAAAAA
AATTAGG
Found at i:1750014 original size:24 final size:24
Alignment explanation
Indices: 1749982--1750027 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1749972 GTTTTATTCA
1749982 TTTATTTTT-TAGTATTAGTTTATAT
1 TTTATTTTTGTA-TATTA-TTTATAT
1750007 TTTA-TTTTGTATATTATTTAT
1 TTTATTTTTGTATATTATTTAT
1750028 TTAATTAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.25
24 9 0.45
25 6 0.30
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (24 bp):
TTTATTTTTGTATATTATTTATAT
Found at i:1752676 original size:18 final size:18
Alignment explanation
Indices: 1752653--1752705 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
1752643 AAAAATTAGT
1752653 ATAATAAAATATAATAAA
1 ATAATAAAATATAATAAA
*
1752671 ATAATAAACTAT--T-AA
1 ATAATAAAATATAATAAA
*
1752686 ATAATTATAATATAATAAA
1 ATAA-TAAAATATAATAAA
1752705 A
1 A
1752706 AATTTAGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.21
16 7 0.25
18 12 0.43
19 3 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATAAAATATAATAAA
Found at i:1762157 original size:14 final size:15
Alignment explanation
Indices: 1762140--1762178 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
1762130 TATCTAGGAA
1762140 CATATATATTTT-TG
1 CATATATATTTTATG
1762154 CATATATATTTTATG
1 CATATATATTTTATG
*
1762169 TAT-TATATTT
1 CATATATATTT
1762179 GTACGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (15 bp):
CATATATATTTTATG
Found at i:1772826 original size:22 final size:22
Alignment explanation
Indices: 1772801--1772846 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1772791 ATTGAATAAG
**
1772801 ATATAACTTATAATTTAACCAA
1 ATATAACGGATAATTTAACCAA
* *
1772823 ATATTAGGGATAATTTAACCAA
1 ATATAACGGATAATTTAACCAA
1772845 AT
1 AT
1772847 GAACAATGTT
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:0.48, C:0.11, G:0.07, T:0.35
Consensus pattern (22 bp):
ATATAACGGATAATTTAACCAA
Found at i:1774578 original size:16 final size:15
Alignment explanation
Indices: 1774557--1774591 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1774547 AAAGGAAAAG
1774557 AAAATGAAAAAAATGA
1 AAAATGAAAAAAAT-A
*
1774573 AAAATGAATAAAATA
1 AAAATGAAAAAAATA
1774588 AAAA
1 AAAA
1774592 GAGGGTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (15 bp):
AAAATGAAAAAAATA
Found at i:1780898 original size:12 final size:12
Alignment explanation
Indices: 1780881--1780915 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1780871 GAAAGAGTTG
*
1780881 ATAAACGATCTC
1 ATAAACGAGCTC
1780893 ATAAACGAGCTC
1 ATAAACGAGCTC
*
1780905 ATAAACTAGCT
1 ATAAACGAGCT
1780916 TGTTCATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23
Consensus pattern (12 bp):
ATAAACGAGCTC
Found at i:1791555 original size:15 final size:16
Alignment explanation
Indices: 1791515--1791556 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1791505 AATTCATAGT
*
1791515 TATTTTAATTTAGTCAT
1 TATTTT-ATTTAGTCAC
*
1791532 TAATTTATTTA-TCAC
1 TATTTTATTTAGTCAC
1791547 TATTTTATTT
1 TATTTTATTT
1791557 TAATTTGGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 5 0.23
17 5 0.23
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (16 bp):
TATTTTATTTAGTCAC
Found at i:1793961 original size:19 final size:19
Alignment explanation
Indices: 1793933--1793970 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1793923 TGACATTAAA
*
1793933 TGCTTAATATCCTAATTGT
1 TGCTTAATATCCGAATTGT
*
1793952 TGCTTTATATCCGAATTGT
1 TGCTTAATATCCGAATTGT
1793971 CAATTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (19 bp):
TGCTTAATATCCGAATTGT
Found at i:1796729 original size:45 final size:45
Alignment explanation
Indices: 1796660--1796811 Score: 155
Period size: 45 Copynumber: 3.4 Consensus size: 45
1796650 TAATCCAATG
* * ** *
1796660 CTTTTGATTATTGAGTTATCAAAAGTAAAATCAAAGGATTAGTTC
1 CTTTCGATTATTGTGTTGCCAAAAGTAAAATCAAAAGATTAGTTC
** * *
1796705 CTTAGGATTATTGTGTTGCCAAAAGTAAAAT-AAATGATTATTTC
1 CTTTCGATTATTGTGTTGCCAAAAGTAAAATCAAAAGATTAGTTC
* * *
1796749 CTTTCGATT-TTTTGATTGCAAAAATTAAAATCAAAAGATTAGTTC
1 CTTTCGATTATTGTG-TTGCCAAAAGTAAAATCAAAAGATTAGTTC
* *
1796794 CTTTTGATTATTGGGTTG
1 CTTTCGATTATTGTGTTG
1796812 GTAAAATTAA
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
43 4 0.05
44 32 0.37
45 48 0.55
46 3 0.03
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (45 bp):
CTTTCGATTATTGTGTTGCCAAAAGTAAAATCAAAAGATTAGTTC
Found at i:1797036 original size:58 final size:58
Alignment explanation
Indices: 1796971--1797133 Score: 227
Period size: 59 Copynumber: 2.8 Consensus size: 58
1796961 AATCTTGCGT
* * *
1796971 TGATTCTAACTTTGTAAGGAAAATTAATTCTTGAACTTATTTCCTTGAGAATCTTTAA
1 TGATTCTAACTTTGTAAGGAAAATTAATTGTTGAAATTATTTCCTTGAGAATCTTAAA
* * * * *
1797029 TGATTCTAACTTTATAAAGAAAACTAGATTGATGAAATTATTTCCTTGTGAATCTTAAA
1 TGATTCTAACTTTGTAAGGAAAATTA-ATTGTTGAAATTATTTCCTTGAGAATCTTAAA
* *
1797088 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTT
1 TGATTCTAACTTTGTAAGGAAAATTAATTGTTGAAATTATTTCCTT
1797134 ACAAATCTTG
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
58 41 0.46
59 49 0.54
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGGAAAATTAATTGTTGAAATTATTTCCTTGAGAATCTTAAA
Found at i:1797287 original size:39 final size:39
Alignment explanation
Indices: 1797170--1797289 Score: 143
Period size: 39 Copynumber: 3.1 Consensus size: 39
1797160 TTATATAGTT
* *
1797170 CTATTTT-TAAAAGAAAATATAAATCGTTGGATTTATTTTA
1 CTATTTTGTAAAAG-AAA-ATAAATCGTTGAATTTATTTTC
* * * * *
1797210 TTGTTTTGTAAAAGGAAAGAAATGGTTGAATTTATTTTC
1 CTATTTTGTAAAAGAAAATAAATCGTTGAATTTATTTTC
*
1797249 CTATTTTGTAAAAGAAAATAAATTGTTGAATTTATTTTC
1 CTATTTTGTAAAAGAAAATAAATCGTTGAATTTATTTTC
1797288 CT
1 CT
1797290 GAAAATCTCA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
39 54 0.81
40 7 0.10
41 6 0.09
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (39 bp):
CTATTTTGTAAAAGAAAATAAATCGTTGAATTTATTTTC
Found at i:1797449 original size:97 final size:94
Alignment explanation
Indices: 1797216--1797582 Score: 376
Period size: 97 Copynumber: 3.8 Consensus size: 94
1797206 TTTATTGTTT
* * * * * * *
1797216 TGTAAAAGGAAAGAAATGGTTGAATTTATTTTCCTATTTTGTAAAAGAAAATAAATTGTTGAATT
1 TGTAAAAGAAAATAAATCGTTGAATTTATTTTCCTATTTTGAAAAAGGAAATAAATAG-TAAATT
*** *
1797281 TATTTTCCTGAAAATCTCACATGTTCTTATA
65 TATTTTCCT-AAAATCTTGTATGTTCTGATA
* * * * *
1797312 TGTAAAAGGAAATATATTGTAGAATTTATTTTCCTGTTTTGAAAAAGGAAATAAATAGATAAATT
1 TGTAAAAGAAAATAAATCGTTGAATTTATTTTCCTATTTTGAAAAAGGAAATAAATAG-TAAATT
*
1797377 TATTTTCCTAAGAATTTTGTATGATTCTGATA
65 TATTTTCCTAA-AATCTTGTATG-TTCTGATA
* * **
1797409 TGTAAAAGAAAATAAATCGTTGGATTTATTTTCTTATTTTGAAAAAATAAATAAATATGTAAATT
1 TGTAAAAGAAAATAAATCGTTGAATTTATTTTCCTATTTTGAAAAAGGAAATAAATA-GTAAATT
1797474 TATTTTCCTAATAATCTTGTATGTTTCTGATA
65 TATTTTCCTAA-AATCTTGTATG-TTCTGATA
* * * * **
1797506 TGTAAAATAAAATAAATCGTT-AGATTTATTTTCCTGTTTTAATAAAAAGGAAATAAATCATTGG
1 TGTAAAAGAAAATAAATCGTTGA-ATTTATTTTCCTATTTT--GAAAAAGGAAATAAAT-AGTAA
1797570 ATTTATTTTCCTA
62 ATTTATTTTCCTA
1797583 TTTTGTAAAA
Statistics
Matches: 227, Mismatches: 37, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
95 2 0.01
96 71 0.31
97 125 0.55
98 1 0.00
99 27 0.12
100 1 0.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (94 bp):
TGTAAAAGAAAATAAATCGTTGAATTTATTTTCCTATTTTGAAAAAGGAAATAAATAGTAAATTT
ATTTTCCTAAAATCTTGTATGTTCTGATA
Found at i:1803040 original size:26 final size:25
Alignment explanation
Indices: 1803011--1803094 Score: 64
Period size: 26 Copynumber: 3.3 Consensus size: 25
1803001 ATCATTCTAT
1803011 TTTATTTTAATTTAATTTAGTCACTG
1 TTTATTTT-ATTTAATTTAGTCACTG
* * * *
1803037 TTTATTTCTGATTT-AGTTA-CCATTAT
1 TTTATTT-T-ATTTAATTTAGTCACT-G
**
1803063 TTTATTTTATGCAATTTAGTCACTG
1 TTTATTTTATTTAATTTAGTCACTG
1803088 TTTATTT
1 TTTATTT
1803095 CTGATTTAGC
Statistics
Matches: 43, Mismatches: 11, Indels: 9
0.68 0.17 0.14
Matches are distributed among these distances:
24 2 0.05
25 15 0.35
26 21 0.49
27 5 0.12
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.58
Consensus pattern (25 bp):
TTTATTTTATTTAATTTAGTCACTG
Found at i:1803086 original size:51 final size:51
Alignment explanation
Indices: 1803008--1803133 Score: 198
Period size: 51 Copynumber: 2.5 Consensus size: 51
1802998 TTTATCATTC
** *
1803008 TATTTTATTTTAATTTAATTTAGTCACTGTTTATTTCTGATTTAGTTACCAT
1 TATTTTATTTT-ATGCAATTTAGTCACTGTTTATTTCTGATTTAGCTACCAT
**
1803060 TATTTTATTTTATGCAATTTAGTCACTGTTTATTTCTGATTTAGCTACTGT
1 TATTTTATTTTATGCAATTTAGTCACTGTTTATTTCTGATTTAGCTACCAT
1803111 TATTTTATTTTATGCAATTTAGT
1 TATTTTATTTTATGCAATTTAGT
1803134 TCTTTTATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
51 58 0.84
52 11 0.16
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (51 bp):
TATTTTATTTTATGCAATTTAGTCACTGTTTATTTCTGATTTAGCTACCAT
Found at i:1804543 original size:183 final size:183
Alignment explanation
Indices: 1804235--1804601 Score: 725
Period size: 183 Copynumber: 2.0 Consensus size: 183
1804225 CAGAGATAAA
1804235 TCTCTGAGAAAACGACTCACCGAATGTGAATTTGGAAAAATGAACTTTGGATTCGGACTCAAGAC
1 TCTCTGAGAAAACGACTCACCGAATGTGAATTTGGAAAAATGAACTTTGGATTCGGACTCAAGAC
*
1804300 GCCGAAAAACATAAAATATGATTTTTCCAAAAATTTAATTTTTTTGGTCAAAGTCAACTATCAAC
66 GCCGAAAAACATAAAATATGATTTTTCAAAAAATTTAATTTTTTTGGTCAAAGTCAACTATCAAC
1804365 GGGTCAGGTCAAAGTCAACGGGTCAGGTTGGATTGACAAGGTTCAGGTTGAGT
131 GGGTCAGGTCAAAGTCAACGGGTCAGGTTGGATTGACAAGGTTCAGGTTGAGT
1804418 TCTCTGAGAAAACGACTCACCGAATGTGAATTTGGAAAAATGAACTTTGGATTCGGACTCAAGAC
1 TCTCTGAGAAAACGACTCACCGAATGTGAATTTGGAAAAATGAACTTTGGATTCGGACTCAAGAC
1804483 GCCGAAAAACATAAAATATGATTTTTCAAAAAATTTAATTTTTTTGGTCAAAGTCAACTATCAAC
66 GCCGAAAAACATAAAATATGATTTTTCAAAAAATTTAATTTTTTTGGTCAAAGTCAACTATCAAC
1804548 GGGTCAGGTCAAAGTCAACGGGTCAGGTTGGATTGACAAGGTTCAGGTTGAGT
131 GGGTCAGGTCAAAGTCAACGGGTCAGGTTGGATTGACAAGGTTCAGGTTGAGT
1804601 T
1 T
1804602 GGGTCGGTAG
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 183 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (183 bp):
TCTCTGAGAAAACGACTCACCGAATGTGAATTTGGAAAAATGAACTTTGGATTCGGACTCAAGAC
GCCGAAAAACATAAAATATGATTTTTCAAAAAATTTAATTTTTTTGGTCAAAGTCAACTATCAAC
GGGTCAGGTCAAAGTCAACGGGTCAGGTTGGATTGACAAGGTTCAGGTTGAGT
Found at i:1806620 original size:64 final size:64
Alignment explanation
Indices: 1806547--1806668 Score: 208
Period size: 64 Copynumber: 1.9 Consensus size: 64
1806537 TGAGGGGAGT
*
1806547 ACTCTCAAGTCCATAAGGAGTTACCCAAACCACATAGCAGAGGTGCCACACTAAAGGAATTGGC
1 ACTCTCAAGTCCATAAGGACTTACCCAAACCACATAGCAGAGGTGCCACACTAAAGGAATTGGC
** *
1806611 ACTCTCAAGTCCATAAGGACTTACCCAAAGTATATAGCAGAGGTGCCACACTAAAGGA
1 ACTCTCAAGTCCATAAGGACTTACCCAAACCACATAGCAGAGGTGCCACACTAAAGGA
1806669 GTTCCTTAGG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (64 bp):
ACTCTCAAGTCCATAAGGACTTACCCAAACCACATAGCAGAGGTGCCACACTAAAGGAATTGGC
Found at i:1806828 original size:36 final size:35
Alignment explanation
Indices: 1806743--1806883 Score: 144
Period size: 35 Copynumber: 4.0 Consensus size: 35
1806733 CTTAGATCCG
** *
1806743 TAAGGAATTACCAGTTCAATCG-GTCTGAACCTATA
1 TAAGGAATTACCAGTTTGATCGAGT-TGAACCTGTA
*
1806778 TAAGGAATTACCAGTTTGATCGAGTTGAACCTGTCG
1 TAAGGAATTACCAGTTTGATCGAGTTGAACCTGT-A
** *
1806814 T-AGCGAATTACCAGTTCAATCG-GTCTGAACCTATA
1 TAAG-GAATTACCAGTTTGATCGAGT-TGAACCTGTA
* *
1806849 TAAGGAATAACCAGTTTGATCGAGCTGAACCTGTA
1 TAAGGAATTACCAGTTTGATCGAGTTGAACCTGTA
1806884 GAGACTTCAT
Statistics
Matches: 87, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
35 57 0.66
36 30 0.34
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (35 bp):
TAAGGAATTACCAGTTTGATCGAGTTGAACCTGTA
Found at i:1806863 original size:71 final size:71
Alignment explanation
Indices: 1806747--1806882 Score: 254
Period size: 71 Copynumber: 1.9 Consensus size: 71
1806737 GATCCGTAAG
* *
1806747 GAATTACCAGTTCAATCGGTCTGAACCTATATAAGGAATTACCAGTTTGATCGAGTTGAACCTGT
1 GAATTACCAGTTCAATCGGTCTGAACCTATATAAGGAATAACCAGTTTGATCGAGCTGAACCTGT
1806812 CGTAGC
66 CGTAGC
1806818 GAATTACCAGTTCAATCGGTCTGAACCTATATAAGGAATAACCAGTTTGATCGAGCTGAACCTGT
1 GAATTACCAGTTCAATCGGTCTGAACCTATATAAGGAATAACCAGTTTGATCGAGCTGAACCTGT
1806883 AGAGACTTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (71 bp):
GAATTACCAGTTCAATCGGTCTGAACCTATATAAGGAATAACCAGTTTGATCGAGCTGAACCTGT
CGTAGC
Found at i:1806880 original size:35 final size:35
Alignment explanation
Indices: 1806743--1806864 Score: 158
Period size: 35 Copynumber: 3.5 Consensus size: 35
1806733 CTTAGATCCG
1806743 TAAGGAATTACCAGTTCAATCGGTCTGAACCTATA
1 TAAGGAATTACCAGTTCAATCGGTCTGAACCTATA
** * *
1806778 TAAGGAATTACCAGTTTGATCGAGT-TGAACCTGTCG
1 TAAGGAATTACCAGTTCAATCG-GTCTGAACCTAT-A
1806814 T-AGCGAATTACCAGTTCAATCGGTCTGAACCTATA
1 TAAG-GAATTACCAGTTCAATCGGTCTGAACCTATA
*
1806849 TAAGGAATAACCAGTT
1 TAAGGAATTACCAGTT
1806865 TGATCGAGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
35 44 0.60
36 29 0.40
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (35 bp):
TAAGGAATTACCAGTTCAATCGGTCTGAACCTATA
Found at i:1812257 original size:23 final size:23
Alignment explanation
Indices: 1812227--1812273 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1812217 GGAAACCGTT
**
1812227 AGTTAACAAACGGTTAACGCTCC
1 AGTTAACAAACAATTAACGCTCC
1812250 AGTTAACAAACAATTAACGCTCC
1 AGTTAACAAACAATTAACGCTCC
1812273 A
1 A
1812274 AAATAAGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.26, G:0.13, T:0.21
Consensus pattern (23 bp):
AGTTAACAAACAATTAACGCTCC
Found at i:1829587 original size:20 final size:20
Alignment explanation
Indices: 1829562--1829641 Score: 133
Period size: 20 Copynumber: 4.0 Consensus size: 20
1829552 CTATATATAG
1829562 TAGTATCGATACCATAGGCA
1 TAGTATCGATACCATAGGCA
* *
1829582 TAGTATCGATATCATATGCA
1 TAGTATCGATACCATAGGCA
1829602 TAGTATCGATACCATAGGCA
1 TAGTATCGATACCATAGGCA
1829622 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCAT-AGGC
1829642 CCCAACAACT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
20 51 0.93
21 4 0.07
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (20 bp):
TAGTATCGATACCATAGGCA
Found at i:1834448 original size:21 final size:21
Alignment explanation
Indices: 1834422--1834462 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1834412 AATTTTCACT
1834422 GTGGTTTTGAAACCCCCTAAG
1 GTGGTTTTGAAACCCCCTAAG
1834443 GTGGTTTTGAAACCCCCTAA
1 GTGGTTTTGAAACCCCCTAA
1834463 AAATGACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (21 bp):
GTGGTTTTGAAACCCCCTAAG
Found at i:1835241 original size:21 final size:21
Alignment explanation
Indices: 1835217--1835281 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
1835207 ATCTAAATGC
1835217 ACTTTAGTTCAGTGCTAAGGA
1 ACTTTAGTTCAGTGCTAAGGA
* *
1835238 ACTTTAGTATATTAGTGCTAAGGT
1 ACTTTAG--T-TCAGTGCTAAGGA
*
1835262 ACTTT-CTTACAGTGCTAAGG
1 ACTTTAGTT-CAGTGCTAAGG
1835282 CACGTTAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.03
21 18 0.50
23 1 0.03
24 16 0.44
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (21 bp):
ACTTTAGTTCAGTGCTAAGGA
Found at i:1842822 original size:19 final size:19
Alignment explanation
Indices: 1842798--1842868 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
1842788 AATGCATTAT
1842798 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1842817 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1842836 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1842855 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1842869 TCAGGTTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:1842907 original size:65 final size:64
Alignment explanation
Indices: 1842836--1842978 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 64
1842826 TGCACATACC
1842836 ATGCATCGATGCACATACCATGCATCGATGCACTCAGG-TT-TTAATGAAAACATCGAATGCAAT
1 ATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTT--TG-AAACATCGAATGCAAT
1842899 TG
63 TG
* * * * *
1842901 ATGCATCGATACACATGCCATGCATCGATGCACTCGGGCTTGTTTGAAACATCGAATGCACTTT
1 ATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTTTGAAACATCGAATGCAATTG
*
1842965 ATGCATTGATGCAC
1 ATGCATCGATGCAC
1842979 TCTTAGTGCA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 28 0.41
65 37 0.54
66 2 0.03
67 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTTTGAAACATCGAATGCAATTG
Found at i:1851624 original size:19 final size:19
Alignment explanation
Indices: 1851600--1851651 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1851590 AATGCATTAT
1851600 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1851619 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1851638 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1851652 TCAGGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:1851699 original size:65 final size:64
Alignment explanation
Indices: 1851619--1851753 Score: 191
Period size: 65 Copynumber: 2.1 Consensus size: 64
1851609 TGCACATACC
* *
1851619 ATGCATCGATGCACATACCATGCATCGATGCACTCAGG-TTTTTATGAAAACATCGAATGCAATT
1 ATGCATCGATACACATACCATGCATCGATGCACTCAGGCTTATT-TG-AAACATCGAATGCAATT
1851683 G
64 G
* * * *
1851684 ATGCATCGATACACATGCCATGCATCGATGCACTCGGGCTTATTTGAAACATCGAATGCACTTT
1 ATGCATCGATACACATACCATGCATCGATGCACTCAGGCTTATTTGAAACATCGAATGCAATTG
1851748 ATGCAT
1 ATGCAT
1851754 TGATGCACTC
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 22 0.35
65 37 0.59
66 4 0.06
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (64 bp):
ATGCATCGATACACATACCATGCATCGATGCACTCAGGCTTATTTGAAACATCGAATGCAATTG
Found at i:1860427 original size:65 final size:63
Alignment explanation
Indices: 1860355--1860514 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 63
1860345 GAATAAATTG
*
1860355 AACATCGAATGCATTATATGCATCGATGCACATACCATGCATCGATGCACTCAGG-TTTTTATAA
1 AACATCGAATGCATT-TATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTT-T-A
1860419 A
63 A
* * * * *
1860420 AACATCGAATGCAATTGATGCATCGATACACATGCCATGCATCGATGCACTCGGGCTTGTTTGA
1 AACATCGAATGC-ATTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTTTAA
*
1860484 AACATCGAATGCACTTTATGCATTGATGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
1860515 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 27 0.33
65 48 0.58
66 7 0.08
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTTTAA
Found at i:1863467 original size:187 final size:191
Alignment explanation
Indices: 1863230--1863611 Score: 727
Period size: 187 Copynumber: 2.0 Consensus size: 191
1863220 GACATTGCAT
1863230 CTAATTGGATTATGCTTGTTGGTCATAGAATAGGAAACATTTACATGGTGCATTTAGATTCCATA
1 CTAATTGGATTATGCTTGTTGGTCATAGAATAGGAAACATTTACATGGTGCATTTAGATTCCATA
1863295 GATATGACTAATTTATGCCTAGTTGCTAAAGATGAGCATGATAGTTGGTTATGGCATA-AGA-GA
66 GATATGACTAATTTATGCCTAGTTGCTAAAGATGAGCATGATAGTTGGTTATGGCATAGAGACGA
1863358 AGATATGCTAGCATGAGTGTTTTGCAACGGCTAA-TCAAGGAGATTTAGTTCGAGGGTTGC
131 AGATATGCTAGCATGAGTGTTTTGCAACGGCTAATTCAAGGAGATTTAGTTCGAGGGTTGC
1863418 CTAA-TGGATTATGCTTGTTGGTCATAGAATAGGAAACATTTACATGGTGCATTTAGATTCCATA
1 CTAATTGGATTATGCTTGTTGGTCATAGAATAGGAAACATTTACATGGTGCATTTAGATTCCATA
*
1863482 GATATGACTAATTTATGCCTAGTTGCTAAAGATGAGCATGATAGTTGGTTATGGCATAGAGACTA
66 GATATGACTAATTTATGCCTAGTTGCTAAAGATGAGCATGATAGTTGGTTATGGCATAGAGACGA
1863547 AGATATGCTAGCATGAGTGTTTTGCAACGGCTAATTCAAGGAGATTTAGTTCGAGGGTTGC
131 AGATATGCTAGCATGAGTGTTTTGCAACGGCTAATTCAAGGAGATTTAGTTCGAGGGTTGC
1863608 CTAA
1 CTAA
1863612 ACTAAAATTT
Statistics
Matches: 190, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
187 118 0.62
188 7 0.04
189 35 0.18
190 30 0.16
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (191 bp):
CTAATTGGATTATGCTTGTTGGTCATAGAATAGGAAACATTTACATGGTGCATTTAGATTCCATA
GATATGACTAATTTATGCCTAGTTGCTAAAGATGAGCATGATAGTTGGTTATGGCATAGAGACGA
AGATATGCTAGCATGAGTGTTTTGCAACGGCTAATTCAAGGAGATTTAGTTCGAGGGTTGC
Found at i:1873056 original size:2 final size:2
Alignment explanation
Indices: 1873049--1873113 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1873039 TCAATCTACA
1873049 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
1873091 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1873114 ATTTTCAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1873291 original size:13 final size:13
Alignment explanation
Indices: 1873270--1873334 Score: 94
Period size: 13 Copynumber: 5.0 Consensus size: 13
1873260 AATGACGCTC
*
1873270 AATGTGCGTCATA
1 AATGCGCGTCATA
1873283 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
1873296 AATGTGAGTCATA
1 AATGCGCGTCATA
*
1873309 AATGCGTGTCATA
1 AATGCGCGTCATA
1873322 AATGCGCGTCATA
1 AATGCGCGTCATA
1873335 GATTTATGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:1877816 original size:77 final size:77
Alignment explanation
Indices: 1877725--1877934 Score: 321
Period size: 77 Copynumber: 2.7 Consensus size: 77
1877715 GAAAGAAAGG
*
1877725 AAGCATCGCACTTTCGATTCAAGTTGAACAAAAAGAGGCATAGCACTTTCGATTCCCGTCTAAAG
1 AAGCATCGCACTTTCGATTCAAGTAGAACAAAAAGAGGCATAGCACTTTCGATTCCCGTCTAAAG
1877790 TAGAATGGAAGA
66 TAGAATGGAAGA
* * * * *
1877802 AAGCATCGCACTTTCGATTCAAGTAGAGCGAAATGAGGCATAGAACTTTCGATTCTCGTCTAAAG
1 AAGCATCGCACTTTCGATTCAAGTAGAACAAAAAGAGGCATAGCACTTTCGATTCCCGTCTAAAG
*
1877867 TAGAATGGAAGG
66 TAGAATGGAAGA
* * *
1877879 AAGCATCACACTTTCGATTCAAGTAGAACGAAAAAGAGGCATAACACTTTTGATTC
1 AAGCATCGCACTTTCGATTCAAGTAGAAC-AAAAAGAGGCATAGCACTTTCGATTC
1877935 TCAATGATAG
Statistics
Matches: 118, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
77 97 0.82
78 21 0.18
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (77 bp):
AAGCATCGCACTTTCGATTCAAGTAGAACAAAAAGAGGCATAGCACTTTCGATTCCCGTCTAAAG
TAGAATGGAAGA
Found at i:1880070 original size:22 final size:22
Alignment explanation
Indices: 1880015--1880070 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1880005 ATTATCGTCT
1880015 TTTCCCCTTCCCCATTTCTCCCA
1 TTTCCCC-TCCCCATTTCTCCCA
* * *
1880038 TTTTCCTTCCCCTTTTCTCCC-
1 TTTCCCCTCCCCATTTCTCCCA
1880059 TTCTCCCCTCCC
1 TT-TCCCCTCCC
1880071 TTGCCATGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.07
22 20 0.74
23 5 0.19
ACGTcount: A:0.04, C:0.54, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTCCCCTCCCCATTTCTCCCA
Found at i:1881967 original size:21 final size:21
Alignment explanation
Indices: 1881921--1881999 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
1881911 TTTTTTGCTC
1881921 AAAGGATCT-ATCCCCTTG-CA
1 AAAGGAT-TGATCCCCTTGACA
* *
1881941 AAAGGATTGATCCCTTTGACC
1 AAAGGATTGATCCCCTTGACA
1881962 AAAGGATTGATCCCCTTGA-A
1 AAAGGATTGATCCCCTTGACA
*
1881982 AAAGGATCGAT-CCCTTGA
1 AAAGGATTGATCCCCTTGA
1882000 ATTCCAGTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.15
20 25 0.48
21 19 0.37
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (21 bp):
AAAGGATTGATCCCCTTGACA
Found at i:1881977 original size:41 final size:41
Alignment explanation
Indices: 1881920--1881997 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
1881910 ATTTTTTGCT
* *
1881920 CAAAGGATCTATCCCCTTGCAAAAGGATTGATCCCTTTGAC
1 CAAAGGATCTATCCCCTTGAAAAAGGATCGATCCCTTTGAC
1881961 CAAAGGAT-TGATCCCCTTGAAAAAGGATCGATCCCTT
1 CAAAGGATCT-ATCCCCTTGAAAAAGGATCGATCCCTT
1881998 GAATTCCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (41 bp):
CAAAGGATCTATCCCCTTGAAAAAGGATCGATCCCTTTGAC
Found at i:1889365 original size:83 final size:82
Alignment explanation
Indices: 1889273--1889657 Score: 394
Period size: 82 Copynumber: 4.7 Consensus size: 82
1889263 TATTGCACAA
* * * * * *
1889273 GTTTATAGCGGCGTTTTTACAAAAACGCCCCTATATATCTGGGCTATTGCGGCGTTTTATACATA
1 GTTTTTAGCGGCGTTTTCACAAAAACGCCACTATATAT-TCGGATATTGCGGCGTTTTTTACATA
* * *
1889338 AACGCCACTAAAGTATAT
65 AACACCACTAAAGTACAC
* * *
1889356 GTTTTTAGCGGCATTTTCACAAAAAGCGCCGCTATATATTCAGATATTGCGGCGTTTTTTACATA
1 GTTTTTAGCGGCGTTTTCACAAAAA-CGCCACTATATATTCGGATATTGCGGCGTTTTTTACATA
** * *
1889421 AATGCCACTAAATTACGC
65 AACACCACTAAAGTACAC
* * * * * * *
1889439 GTTTTTAGCGGCGTTTGCACAAAAACGCCATTATATATTTGGATATCGCGGCG-TTTGTCCAAAA
1 GTTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCGTTTTTTACATAA
**
1889503 ACACCACTAAAGTACGT
66 ACACCACTAAAGTACAC
** * **** * * *
1889520 GACTTTAGCGGCCTTTTTGTGAAAACGCCACGATATATTCGGATATTGTGGTGTTTTTTACATAA
1 GTTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCGTTTTTTACATAA
*
1889585 ATACCACTAAAGTACAC
66 ACACCACTAAAGTACAC
* * *
1889602 ATTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTTGGATATCGCGGCGTTT
1 GTTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCGTTT
1889658 GTAAAAAAAC
Statistics
Matches: 240, Mismatches: 60, Indels: 5
0.79 0.20 0.02
Matches are distributed among these distances:
81 60 0.25
82 88 0.37
83 80 0.33
84 12 0.05
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (82 bp):
GTTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTCGGATATTGCGGCGTTTTTTACATAA
ACACCACTAAAGTACAC
Found at i:1889367 original size:42 final size:39
Alignment explanation
Indices: 1889273--1889477 Score: 99
Period size: 42 Copynumber: 5.0 Consensus size: 39
1889263 TATTGCACAA
* * * *
1889273 GTTTATAGCGGCGTTTTTACAAAAACGCCCCTATATATCT
1 GTTTTTAGCGGCGTTTTTACATAAACGCCACTAAATAT-T
* *
1889313 GGGCTATT-GCGGCGTTTTATACATAAACGCCACTAAAGTATAT
1 --GTTTTTAGCGGCGTTTT-TACATAAACGCCACTAAA-TAT-T
* * * * *
1889356 GTTTTTAGCGGCATTTTCACAAAAAGCGCCGCTATATATT
1 GTTTTTAGCGGCGTTTTTACATAAA-CGCCACTAAATATT
* * * **
1889396 CAGATATT-GCGGCGTTTTTTACATAAATGCCACTAAATTACGC
1 --GTTTTTAGCGGCG-TTTTTACATAAACGCCACTAAA-TA-TT
** * * *
1889439 GTTTTTAGCGGCGTTTGCACAAAAACGCCATTATATATT
1 GTTTTTAGCGGCGTTTTTACATAAACGCCACTAAATATT
1889478 TGGATATCGC
Statistics
Matches: 119, Mismatches: 34, Indels: 23
0.68 0.19 0.13
Matches are distributed among these distances:
40 3 0.03
41 55 0.46
42 57 0.48
43 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (39 bp):
GTTTTTAGCGGCGTTTTTACATAAACGCCACTAAATATT
Found at i:1889710 original size:163 final size:164
Alignment explanation
Indices: 1889362--1889711 Score: 411
Period size: 163 Copynumber: 2.1 Consensus size: 164
1889352 ATATGTTTTT
* * * *
1889362 AGCGGCATTTTC-ACAAAAAGCGCCGCTATATATTCAGATATTGCGGCGTTTTTTACATAAATGC
1 AGCGGCATTTTCTATAAAAA-CGCCACGATATATTCAGATATTGCGGCGTTTTTTACATAAATAC
* * * *
1889426 CACTAAATTACGCGTTTTTAGCGGCGTTTGCACAAAAACGCCATTATATATTTGGATATCGCGGC
65 CACTAAAGTACACATTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATCGCGGC
** *** ** *
1889491 GTTTGTCCAAAAACACCACTAAAGTACGTGACTTT
130 GTTTGTAAAAAAACACCACTAAAGTACAAAAAATC
* * * * * *
1889526 AGCGGCCTTTT-TGTGAAAACGCCACGATATATTCGGATATTGTGGTGTTTTTTACATAAATACC
1 AGCGGCATTTTCTATAAAAACGCCACGATATATTCAGATATTGCGGCGTTTTTTACATAAATACC
*
1889590 ACTAAAGTACACATTTTTAGCGGCGTTTTCACAAAAACGCCACTATATATTTGGATATCGCGGCG
66 ACTAAAGTACACATTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATCGCGGCG
* * * *
1889655 TTTGTAAAAAAACGCCGCTACA-TATAAAAAATC
131 TTTGTAAAAAAACACCACTAAAGTACAAAAAATC
1889688 A-CTGGCATTTTCTATAAAAACGCC
1 AGC-GGCATTTTCTATAAAAACGCC
1889712 GCTAAATCTG
Statistics
Matches: 153, Mismatches: 30, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
161 1 0.01
162 12 0.08
163 126 0.82
164 14 0.09
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (164 bp):
AGCGGCATTTTCTATAAAAACGCCACGATATATTCAGATATTGCGGCGTTTTTTACATAAATACC
ACTAAAGTACACATTTTTAGCGGCGTTTGCACAAAAACGCCACTATATATTTGGATATCGCGGCG
TTTGTAAAAAAACACCACTAAAGTACAAAAAATC
Found at i:1897701 original size:36 final size:37
Alignment explanation
Indices: 1897619--1897711 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 37
1897609 TAGAAAGAAA
* ** *
1897619 TTTATCTCACTTGAGATTGTTTTTTCTTAAAACAAAC
1 TTTATCTCACTTGAGATAGTTTTCCCTCAAAACAAAC
*** *
1897656 TTCGCCTCACTTGAGA-AGTTTTCCCTCAAAACAAAT
1 TTTATCTCACTTGAGATAGTTTTCCCTCAAAACAAAC
1897692 TTTATCTCACTTGAGATAGT
1 TTTATCTCACTTGAGATAGT
1897712 CAATCTTTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
36 28 0.64
37 16 0.36
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTATCTCACTTGAGATAGTTTTCCCTCAAAACAAAC
Found at i:1901765 original size:3 final size:3
Alignment explanation
Indices: 1901757--1901788 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1901747 CATTCATTAA
1901757 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1901789 GATAAGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1903288 original size:46 final size:46
Alignment explanation
Indices: 1903229--1903530 Score: 482
Period size: 46 Copynumber: 6.6 Consensus size: 46
1903219 CACATTAACA
* * *
1903229 CATCCATTT-ATGCATTTTAATTATGGCATCCTTGCATG-TTGTAAAG
1 CATCC-TTTCATGCATTTTAATTATGGCATCCTTTCATGCCT-TAATG
*
1903275 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
1903321 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
*
1903367 CATCCTTTCATGCATTTTAATTATGGCACCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
*
1903413 CTTCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
*
1903459 CATCCTTTCATGGATTTTAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
* **
1903505 TATTATTTCATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
1903531 ATTTGATTTA
Statistics
Matches: 240, Mismatches: 14, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
45 3 0.01
46 236 0.98
47 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.44
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
Found at i:1903326 original size:20 final size:20
Alignment explanation
Indices: 1903301--1903470 Score: 133
Period size: 20 Copynumber: 7.6 Consensus size: 20
1903291 TTAATTATGA
1903301 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
1903321 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGC--CTT-A--AT-G
1903347 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
1903367 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGC--CTT-A--AT-G
*
1903393 CACCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
1903413 CTTCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGC--CTT-A--AT-G
1903439 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
1903459 CATCCTTTCATG
1 CATCCTTTCATG
1903471 GATTTTAATT
Statistics
Matches: 122, Mismatches: 10, Indels: 36
0.73 0.06 0.21
Matches are distributed among these distances:
20 52 0.43
21 6 0.05
22 6 0.05
23 6 0.05
24 6 0.05
25 6 0.05
26 40 0.33
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.43
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:1903984 original size:19 final size:19
Alignment explanation
Indices: 1903925--1903995 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 19
1903915 GGCTCCTCAT
**
1903925 TATCGATACCCCTACCATGG
1 TATCGATA-CCCTAATATGG
*
1903945 TATCAATACTACCATAATATGG
1 TATCGATAC--CC-TAATATGG
*
1903967 TATCGATACCCTATTATGG
1 TATCGATACCCTAATATGG
1903986 TATCGATACC
1 TATCGATACC
1903996 ATTTTTGCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 18 0.42
20 9 0.21
21 2 0.05
22 14 0.33
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (19 bp):
TATCGATACCCTAATATGG
Found at i:1904044 original size:20 final size:20
Alignment explanation
Indices: 1904019--1904070 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1904009 GTTTTGAAAT
*
1904019 GGTATCGATACATTCC-CTTC
1 GGTATCGATAC-TCCCTCTTC
*
1904039 GGTATCAATACTCCCTCTTC
1 GGTATCGATACTCCCTCTTC
1904059 GGTATCGATACT
1 GGTATCGATACT
1904071 GATTGAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (20 bp):
GGTATCGATACTCCCTCTTC
Found at i:1907481 original size:16 final size:16
Alignment explanation
Indices: 1907460--1907499 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1907450 AAACGTCGTC
1907460 TTACTTGATATAGTTT
1 TTACTTGATATAGTTT
1907476 TTACTTGATATAGTTT
1 TTACTTGATATAGTTT
*
1907492 TCACTTGA
1 TTACTTGA
1907500 AACAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (16 bp):
TTACTTGATATAGTTT
Found at i:1907604 original size:73 final size:74
Alignment explanation
Indices: 1907479--1907723 Score: 334
Period size: 73 Copynumber: 3.3 Consensus size: 74
1907469 ATAGTTTTTA
* * *
1907479 CTTGATATAGTTTTCACTTGAAACAAAATTTTATCTCACTCAAGATAATTTTTCTTAAAACAAAC
1 CTTGAGATAGTTTTCACTTGAAACAAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAC
*
1907544 TTTGTCTTG
66 TTTGTCTCG
*
1907553 CTTGAGATAGTTTTCACTCGAAACAAAA-TTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAC
1 CTTGAGATAGTTTTCACTTGAAACAAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAC
1907617 TTTGTCTCG
66 TTTGTCTCG
* * *
1907626 CTTGAGACAATTTTTACTTGAAACAAGAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAA
1 CTTGAGATAGTTTTCACTTGAAAC-A-AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAA
*
1907691 A-TTTCATCTCG
64 ACTTT-GTCTCG
* * *
1907702 CTTGAAAAAGTTTCCA-TTGAAA
1 CTTGAGATAGTTTTCACTTGAAA
1907724 AATAATATTT
Statistics
Matches: 152, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
73 62 0.41
74 27 0.18
75 12 0.08
76 51 0.34
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (74 bp):
CTTGAGATAGTTTTCACTTGAAACAAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAC
TTTGTCTCG
Found at i:1907640 original size:36 final size:36
Alignment explanation
Indices: 1907479--1907706 Score: 170
Period size: 36 Copynumber: 6.1 Consensus size: 36
1907469 ATAGTTTTTA
* * * * *
1907479 CTTGATATAGTTTTCACTTGAAACAAAATTTTATCTCA
1 CTTGAGATAGTTTT-TCTTAAAAC-AAACTTTATCTCG
** * * *
1907517 CTCAAGATAATTTTTCTTAAAACAAACTTTGTCTTG
1 CTTGAGATAGTTTTTCTTAAAACAAACTTTATCTCG
* ** * *
1907553 CTTGAGATAGTTTTCACTCGAAACAAAATTTATCTCA
1 CTTGAGATAGTTTT-TCTTAAAACAAACTTTATCTCG
* *
1907590 CTCGAGATAGTTTTTCTTAAAACAAACTTTGTCTCG
1 CTTGAGATAGTTTTTCTTAAAACAAACTTTATCTCG
* * * * *
1907626 CTTGAGACAATTTTTACTTGAAACAAGAAATTTTATCTCA
1 CTTGAGATAGTTTTT-CTT--AA-AACAAACTTTATCTCG
*
1907666 CTCGAGATAGTTTTTCTTAAAACAAA-TTTCATCTCG
1 CTTGAGATAGTTTTTCTTAAAACAAACTTT-ATCTCG
1907702 CTTGA
1 CTTGA
1907707 AAAAGTTTCC
Statistics
Matches: 144, Mismatches: 40, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
35 3 0.02
36 62 0.43
37 40 0.28
38 10 0.07
39 5 0.03
40 24 0.17
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (36 bp):
CTTGAGATAGTTTTTCTTAAAACAAACTTTATCTCG
Found at i:1907960 original size:105 final size:102
Alignment explanation
Indices: 1907634--1908012 Score: 455
Period size: 104 Copynumber: 3.7 Consensus size: 102
1907624 CGCTTGAGAC
1907634 AATT-TTT-ACTTGAAACAAGAAATTTTATCTCACTCGAGA-TAGTTTTTCTTAAAACAAATTTC
1 AATTGTTTCACTTGAAACAAGAAATTTTATCTCACTCGAGATTA-TTTTTCTTAAAACAAATTTC
* *
1907696 ATCTCGCTT-GAAAAAGTTTCCATTGAAAAATAATATTTGA
65 ATCTCG-TTGGAAAAA-TTTCC-TTGAAATATAAAATTTGA
* *
1907736 AATTGTTTTACTTAAAACAAGAAATTTTATCTCACTCGAGATTGA-TTTTCTTAAAACAAATTTC
1 AATTGTTTCACTTGAAACAAGAAATTTTATCTCACTCGAGATT-ATTTTTCTTAAAACAAATTTC
* * * *
1907800 ATCTCATTGGATAAAATTTCCTCGAAAATATAAATTTTGG
65 ATCTCGTTGGA-AAAATTTCCTTG-AAATATAAAATTTGA
*
1907840 AATTGTTTCACTTGAAACAAGAAATTTTATTTCACTCGAGATTATTTTTCTTAAAAACAAATTTC
1 AATTGTTTCACTTGAAACAAGAAATTTTATCTCACTCGAGATTATTTTTCTT-AAAACAAATTTC
* *
1907905 ATCTCGTTGGAGAAAATTATTCTTGAAATGTAAAATTTGA
65 ATCTCGTTGGA-AAAATT-TCCTTGAAATATAAAATTTGA
* * * * * * * *
1907945 AATTGTTTCAATTGAAACCAGAAA-TTTATCTTACTTGAGATTGTTTTTGTTAAAACAAACTTCG
1 AATTGTTTCACTTGAAACAAGAAATTTTATCTCACTCGAGATTATTTTTCTTAAAACAAATTTCA
1908009 TCTC
66 TCTC
1908013 ACTTGTGACA
Statistics
Matches: 241, Mismatches: 26, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
102 4 0.02
103 23 0.10
104 142 0.59
105 67 0.28
106 5 0.02
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (102 bp):
AATTGTTTCACTTGAAACAAGAAATTTTATCTCACTCGAGATTATTTTTCTTAAAACAAATTTCA
TCTCGTTGGAAAAATTTCCTTGAAATATAAAATTTGA
Found at i:1908000 original size:208 final size:206
Alignment explanation
Indices: 1907634--1908013 Score: 527
Period size: 208 Copynumber: 1.8 Consensus size: 206
1907624 CGCTTGAGAC
1907634 AATTTTTACTTGAAACAAGAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAATTTCATC
1 AATTTTTACTTGAAACAAGAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAATTTCATC
* * *
1907699 TCGCTTGAAAAAGTTTCCATTGAAAAATAATATTTGAAATTGTTTTACTTAAAACAAGAAATTTT
66 TCGCTTGAAAAAGTTTCCATTGAAAAATAAAATTTGAAATTGTTTCAATTAAAACAAGAAATTTT
*
1907764 ATCTCACTCGAGATTGATTTTCTTAAAACAAATTTCATCTCATTGGATAAAATTTCCTCGAAAAT
131 ATCTCACTCGAGATTGATTTTCTTAAAACAAACTTCATCTCATTGGATAAAATTTCCTCGAAAAT
1907829 ATAAATTTTGG
196 ATAAATTTTGG
*
1907840 AATTGTTTCACTTGAAACAAGAAATTTTATTTCACTCGAGATTA-TTTTTCTTAAAAACAAATTT
1 AATT-TTT-ACTTGAAACAAGAAATTTTATCTCACTCGAGA-TAGTTTTTCTT-AAAACAAATTT
* ** * *
1907904 CATCTCG-TTGGAGAAAA-TTATTC-TTGAAATGTAAAATTTGAAATTGTTTCAATTGAAACCAG
62 CATCTCGCTT-GA-AAAAGTT-TCCATTGAAAAATAAAATTTGAAATTGTTTCAATTAAAACAAG
* * * * *
1907966 AAA-TTTATCTTACTTGAGATTGTTTTTGTTAAAACAAACTTCGTCTCA
124 AAATTTTATCTCACTCGAGATTGATTTTCTTAAAACAAACTTCATCTCA
1908014 CTTGTGACAG
Statistics
Matches: 152, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
206 4 0.03
207 3 0.02
208 80 0.53
209 59 0.39
210 6 0.04
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (206 bp):
AATTTTTACTTGAAACAAGAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAATTTCATC
TCGCTTGAAAAAGTTTCCATTGAAAAATAAAATTTGAAATTGTTTCAATTAAAACAAGAAATTTT
ATCTCACTCGAGATTGATTTTCTTAAAACAAACTTCATCTCATTGGATAAAATTTCCTCGAAAAT
ATAAATTTTGG
Found at i:1913633 original size:44 final size:43
Alignment explanation
Indices: 1913495--1913687 Score: 159
Period size: 44 Copynumber: 4.6 Consensus size: 43
1913485 TGGTAACAAA
* * * *
1913495 AAACGTCGCAATAGG-TGAAGATATATAGCGGCGTTTTTGTAAT
1 AAACGCCGCAAAAGGTTG-AGATATATAACGGCGTTTTTGGAAT
* * * *
1913538 AAACGCCACAAAAGGTCGA-ATATAT-AGGGACGTTTGTAGG-AT
1 AAACGCCGCAAAAGGTTGAGATATATAACGG-CGTTT-TTGGAAT
*
1913580 AAACGCCGCAAAATGTTGAGATATATAACGGCGTTTTTGGATAT
1 AAACGCCGCAAAAGGTTGAGATATATAACGGCGTTTTTGGA-AT
* * *
1913624 AAACGCCGCAAAAGGTCT-AGATCTATAGCGGCG-TTTT-CAA-
1 AAACGCCGCAAAAGGT-TGAGATATATAACGGCGTTTTTGGAAT
* *
1913664 AAACGTCGCAACAGGTTGAGATAT
1 AAACGCCGCAAAAGGTTGAGATAT
1913688 TTAGAAGTTT
Statistics
Matches: 121, Mismatches: 20, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
39 1 0.01
40 19 0.16
41 3 0.02
42 33 0.27
43 30 0.25
44 34 0.28
45 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTTGAGATATATAACGGCGTTTTTGGAAT
Found at i:1913966 original size:21 final size:21
Alignment explanation
Indices: 1913942--1913985 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1913932 CATGACATCT
1913942 ATAACAA-CAA-ACTCAAATTCC
1 ATAACAATCAACA-TCAAA-TCC
1913963 ATAACAATCAACATCAAATCC
1 ATAACAATCAACATCAAATCC
1913984 AT
1 AT
1913986 TATAGTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 12 0.57
22 8 0.38
23 1 0.05
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.20
Consensus pattern (21 bp):
ATAACAATCAACATCAAATCC
Found at i:1919729 original size:20 final size:20
Alignment explanation
Indices: 1919704--1919744 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1919694 GAATCAATTA
*
1919704 AACAAATAGTAT-TATTCTTT
1 AACAAATACTATGTATT-TTT
1919724 AACAAATACTATGTATTTTT
1 AACAAATACTATGTATTTTT
1919744 A
1 A
1919745 GGGTTTTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
AACAAATACTATGTATTTTT
Found at i:1927517 original size:20 final size:20
Alignment explanation
Indices: 1927492--1927551 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
1927482 AGATTAGCAC
1927492 AGAACCGG-TAAAGAACCGGA
1 AGAACCGGCTAAA-AACCGGA
*
1927512 AGAACCGGCTAAAAACCGGGG
1 AGAACCGGCTAAAAACC-GGA
* *
1927533 TGAACCGGCTGAAAACCGG
1 AGAACCGGCTAAAAACCGG
1927552 CAAAACCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.38, C:0.23, G:0.32, T:0.07
Consensus pattern (20 bp):
AGAACCGGCTAAAAACCGGA
Found at i:1927827 original size:24 final size:24
Alignment explanation
Indices: 1927793--1927848 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1927783 TAGAAGTTCG
1927793 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
*
1927817 ATTGAATCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
1927841 ATTGAAGC
1 ATTGAAGC
1927849 GAAAGAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:1929950 original size:30 final size:30
Alignment explanation
Indices: 1929914--1929974 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1929904 CGGTGGTGCA
* *
1929914 GGTGGACTTGGTGGCGCTGCTGGGGGTCTC
1 GGTGGACTCGGAGGCGCTGCTGGGGGTCTC
* *
1929944 GGTGGACTCGGAGGTGGTGCTGGGGGTCTC
1 GGTGGACTCGGAGGCGCTGCTGGGGGTCTC
1929974 G
1 G
1929975 ATGGTGTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.05, C:0.18, G:0.52, T:0.25
Consensus pattern (30 bp):
GGTGGACTCGGAGGCGCTGCTGGGGGTCTC
Found at i:1932058 original size:42 final size:41
Alignment explanation
Indices: 1931966--1932060 Score: 100
Period size: 42 Copynumber: 2.3 Consensus size: 41
1931956 AATTGATACT
** * * *
1931966 TTAGCGGCGTTTGTAGTAAAAATGCTGCAATAGAGTTGAAA
1 TTAGCGGCGTTTGTACAAAAAACGCCGCAATAGAGTGGAAA
* * *
1932007 TATAACGGCGTTTTTACAAAAAACGCCGCAATAGGGTGGTAAA
1 T-TAGCGGCGTTTGTACAAAAAACGCCGCAATAGAGTGG-AAA
1932050 TTAGCGGCGTT
1 TTAGCGGCGTT
1932061 CCGCAATAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
41 1 0.02
42 38 0.88
43 4 0.09
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (41 bp):
TTAGCGGCGTTTGTACAAAAAACGCCGCAATAGAGTGGAAA
Found at i:1932196 original size:41 final size:41
Alignment explanation
Indices: 1932061--1932183 Score: 158
Period size: 42 Copynumber: 3.0 Consensus size: 41
1932051 TAGCGGCGTT
1932061 CCGCAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACG
1 CCGCAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACG
* * * * * **
1932102 CCGCAATAGAGTGGTAAA-TTAGCGGTGTTTGTGGTATAAACG
1 CCGCAATAGAGT-ATAAATTTTGCGGCGATTGAGCCA-AAACG
1932144 CCGCAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAAC
1 CCGCAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAAC
1932184 ACCTTAATAG
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
41 32 0.49
42 33 0.51
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (41 bp):
CCGCAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACG
Found at i:1932200 original size:83 final size:83
Alignment explanation
Indices: 1932061--1932214 Score: 263
Period size: 83 Copynumber: 1.9 Consensus size: 83
1932051 TAGCGGCGTT
* *
1932061 CCGCAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACGCCGCAATAGAGTGGTAAATTAGCG
1 CCGCAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACACCGCAATAGAGTGGTAAATTAACG
*
1932126 GTGTTTGTGGTATAAACG
66 GCGTTTGTGGTATAAACG
**
1932144 CCGCAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACACCTTAATAGAGTGGTAAATTAACG
1 CCGCAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACACCGCAATAGAGTGGTAAATTAACG
1932209 GCGTTT
66 GCGTTT
1932215 ATACCACAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 66 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (83 bp):
CCGCAATAGAGTATAAATTTTGCGGCGATTGAGCCAAAACACCGCAATAGAGTGGTAAATTAACG
GCGTTTGTGGTATAAACG
Found at i:1932211 original size:41 final size:41
Alignment explanation
Indices: 1932061--1932211 Score: 144
Period size: 41 Copynumber: 3.7 Consensus size: 41
1932051 TAGCGGCGTT
* *
1932061 CCGCAATAGAGT-ATAAATTTTGCGGCGATTGAGCCAAAACG
1 CCGCAATAGAGTGGTAAA-TTAGCGGCGATTGAGCCAAAACG
* * * **
1932102 CCGCAATAGAGTGGTAAATTAGCGGTGTTTGTGGTATAAACG
1 CCGCAATAGAGTGGTAAATTAGCGGCGATTGAGCCA-AAACG
* * *
1932144 CCGCAATAGAGT-ATAAATTTTGCGGCGATTGAGCCAAAACA
1 CCGCAATAGAGTGGTAAA-TTAGCGGCGATTGAGCCAAAACG
** *
1932185 CCTTAATAGAGTGGTAAATTAACGGCG
1 CCGCAATAGAGTGGTAAATTAGCGGCG
1932212 TTTATACCAC
Statistics
Matches: 86, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 49 0.57
42 37 0.43
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (41 bp):
CCGCAATAGAGTGGTAAATTAGCGGCGATTGAGCCAAAACG
Found at i:1932318 original size:41 final size:41
Alignment explanation
Indices: 1932263--1932456 Score: 277
Period size: 41 Copynumber: 4.8 Consensus size: 41
1932253 GTTTATTCCT
* *
1932263 CAAACGCCGTAATAGTGATAATCAATAGTGGCGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* *
1932304 CAAACGCCGCAATAGTGTTAATCAATAATGGTGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* *
1932345 AAAATGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* *
1932386 CAAACGTCGCAATAGTGTTAATCAATAGTGGTGTTTTTTA-A
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCG-TTTTTAGA
1932427 CAAACGCCAG-AATAGTG-TAATCAATAGTGG
1 CAAACGCC-GCAATAGTGTTAATCAATAGTGG
1932457 TATTTTTTTG
Statistics
Matches: 138, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
40 13 0.09
41 118 0.86
42 7 0.05
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (41 bp):
CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
Found at i:1932464 original size:41 final size:42
Alignment explanation
Indices: 1932263--1932488 Score: 259
Period size: 41 Copynumber: 5.5 Consensus size: 42
1932253 GTTTATTCCT
* * *
1932263 CAAACGCCGTAATAGTGATAATCAATAGTGG-CGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGTCTTTTTTAGA
* *
1932304 CAAACGCCGCAATAGTGTTAATCAATAATGGT-GTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGTCTTTTTTAGA
* * *
1932345 AAAATGCCGCAATAGTGTTAATCAATAGTGG-CGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGTCTTTTTTAGA
* *
1932386 CAAACGTCGCAATAGTGTTAATCAATAGTGGTGTTTTTTA-A
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGTCTTTTTTAGA
* *
1932427 CAAACGCCAG-AATAGTG-TAATCAATAGTGGTATTTTTTTGTA
1 CAAACGCC-GCAATAGTGTTAATCAATAGTGGTCTTTTTTAG-A
* *
1932469 TAAACGCCGCAA-AATGTTAA
1 CAAACGCCGCAATAGTGTTAA
1932489 ATATATAGTC
Statistics
Matches: 161, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
40 20 0.12
41 121 0.75
42 20 0.12
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (42 bp):
CAAACGCCGCAATAGTGTTAATCAATAGTGGTCTTTTTTAGA
Found at i:1932487 original size:123 final size:123
Alignment explanation
Indices: 1932263--1932488 Score: 298
Period size: 123 Copynumber: 1.8 Consensus size: 123
1932253 GTTTATTCCT
*
1932263 CAAACGCCGTAATAGTGATAATCAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTGTTAATCA
1 CAAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTGTTAATCA
* *
1932328 ATAATGGTGTTTTTAGAAAAATGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
66 ATAATGGTGTTTTTAGAAAAACGCCGCAATAATGTTAATCAATAGTGGCGTTTTTAGA
* * *
1932386 CAAACGTCGCAATAGTGTTAATCAATAGTGGTGTTTTTTA-ACAAACGCCAG-AATAGTG-TAAT
1 CAAACGCCGCAATAGTGATAATCAATAGTGGCG-TTTTTAGACAAACGCC-GCAATAGTGTTAAT
* * * *
1932448 CAATAGTGGTATTTTTTTGTATAAACGCCGCAA-AATGTTAA
64 CAATAATGGT-GTTTTTAG-AAAAACGCCGCAATAATGTTAA
1932489 ATATATAGTC
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
122 13 0.15
123 58 0.65
124 18 0.20
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (123 bp):
CAAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTGTTAATCA
ATAATGGTGTTTTTAGAAAAACGCCGCAATAATGTTAATCAATAGTGGCGTTTTTAGA
Found at i:1933543 original size:18 final size:18
Alignment explanation
Indices: 1933510--1933563 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
1933500 GTTCCTAACA
*
1933510 TTCTCTACCAGCGCAACC
1 TTCTCCACCAGCGCAACC
* * *
1933528 TTCTCCAGCAGTGCAAGC
1 TTCTCCACCAGCGCAACC
1933546 TTCTCCACCAGCGCAACC
1 TTCTCCACCAGCGCAACC
1933564 ACCACCAGCG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (18 bp):
TTCTCCACCAGCGCAACC
Found at i:1935296 original size:21 final size:21
Alignment explanation
Indices: 1935263--1935310 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
1935253 CAACCAGAGC
*
1935263 AGCAGCGGAAGCAGAGAAAGA
1 AGCAGCGGAAGCACAGAAAGA
** * *
1935284 AGCAGCGTCAGCACATAGAGA
1 AGCAGCGGAAGCACAGAAAGA
1935305 AGCAGC
1 AGCAGC
1935311 ATATCAACAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.21, G:0.33, T:0.04
Consensus pattern (21 bp):
AGCAGCGGAAGCACAGAAAGA
Found at i:1935756 original size:43 final size:43
Alignment explanation
Indices: 1935709--1935909 Score: 203
Period size: 43 Copynumber: 4.7 Consensus size: 43
1935699 AAATCTTTAC
* *
1935709 CGGCGTTT-TTAGCAAAAACGCCACAAAACATCAATACCTACTG
1 CGGCGTTTATGAG-AAAAACGCCGCAAAACATCAATACCTACTG
* * *
1935752 CGGCGTTTGTGAGAAAAACACCGCAAAACATCAAAACCTACTG
1 CGGCGTTTATGAGAAAAACGCCGCAAAACATCAATACCTACTG
* * * * *
1935795 CGGAGTTTATGTG-AAAACGCCGCAAAACAGCAACACCTACTA
1 CGGCGTTTATGAGAAAAACGCCGCAAAACATCAATACCTACTG
* * * *
1935837 CGGCGTTTATGAGAAAAATGCCTCTAAACATC-ATAACCTATTG
1 CGGCGTTTATGAGAAAAACGCCGCAAAACATCAAT-ACCTACTG
* *
1935880 CGGCGTTTATCTA-AAAAACGCCGCTAAACA
1 CGGCGTTTAT-GAGAAAAACGCCGCAAAACA
1935910 AACGCCGCTA
Statistics
Matches: 131, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
42 37 0.28
43 90 0.69
44 4 0.03
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (43 bp):
CGGCGTTTATGAGAAAAACGCCGCAAAACATCAATACCTACTG
Found at i:1935833 original size:85 final size:86
Alignment explanation
Indices: 1935722--1935909 Score: 234
Period size: 85 Copynumber: 2.2 Consensus size: 86
1935712 CGTTTTTAGC
* * * * *
1935722 AAAAACGCCACAAAACATCAATACCTACTGCGGCGTTTGTGAGAAAAACACCGCAAAACATCAAA
1 AAAAACGCCGCAAAACAGCAACACCTACTACGGCGTTTATGAGAAAAACACCGCAAAACATCAAA
*
1935787 ACCTACTGCGGAGTTTATGT-
66 ACCTACTGCGGAGTTTATCTA
* ** * * *
1935807 GAAAACGCCGCAAAACAGCAACACCTACTACGGCGTTTATGAGAAAAATGCCTCTAAACATCATA
1 AAAAACGCCGCAAAACAGCAACACCTACTACGGCGTTTATGAGAAAAACACCGCAAAACATCAAA
* *
1935872 ACCTATTGCGGCGTTTATCTA
66 ACCTACTGCGGAGTTTATCTA
*
1935893 AAAAACGCCGCTAAACA
1 AAAAACGCCGCAAAACA
1935910 AACGCCGCTA
Statistics
Matches: 86, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
85 71 0.83
86 15 0.17
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (86 bp):
AAAAACGCCGCAAAACAGCAACACCTACTACGGCGTTTATGAGAAAAACACCGCAAAACATCAAA
ACCTACTGCGGAGTTTATCTA
Found at i:1935914 original size:14 final size:13
Alignment explanation
Indices: 1935890--1935921 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
1935880 CGGCGTTTAT
1935890 CTAAAAAACGCCG
1 CTAAAAAACGCCG
1935903 CTAAACAAACGCCG
1 CTAAA-AAACGCCG
1935917 CTAAA
1 CTAAA
1935922 TATCAATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.47, C:0.31, G:0.12, T:0.09
Consensus pattern (13 bp):
CTAAAAAACGCCG
Found at i:1937262 original size:21 final size:21
Alignment explanation
Indices: 1937238--1937278 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1937228 TAATTAAATA
1937238 TTGAACCACAATTCCTTTAAT
1 TTGAACCACAATTCCTTTAAT
*
1937259 TTGAAGCACAATTCCTTTAA
1 TTGAACCACAATTCCTTTAA
1937279 CTCTAAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (21 bp):
TTGAACCACAATTCCTTTAAT
Found at i:1940076 original size:28 final size:28
Alignment explanation
Indices: 1940036--1940089 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1940026 TGGATACCAT
*
1940036 AGTGTGGAGAAGAAGAAGAAGAAAAAAC
1 AGTGTGGAGAAGAAGAAAAAGAAAAAAC
*
1940064 AGTGTGGGGAAGAAGAAAAAGAAAAA
1 AGTGTGGAGAAGAAGAAAAAGAAAAA
1940090 GAAGAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.33, T:0.07
Consensus pattern (28 bp):
AGTGTGGAGAAGAAGAAAAAGAAAAAAC
Found at i:1940092 original size:34 final size:34
Alignment explanation
Indices: 1940043--1940148 Score: 176
Period size: 34 Copynumber: 3.1 Consensus size: 34
1940033 CATAGTGTGG
* * * *
1940043 AGAAGAAGAAGAAGAAAAAACAGTGTGGGGAAGA
1 AGAAAAAGAAAAAGAAGAAACAATGTGGGGAAGA
1940077 AGAAAAAGAAAAAGAAGAAACAATGTGGGGAAGA
1 AGAAAAAGAAAAAGAAGAAACAATGTGGGGAAGA
1940111 AGAAAAAGAAAAAGAAGAAACAATGTGGGGAAGA
1 AGAAAAAGAAAAAGAAGAAACAATGTGGGGAAGA
1940145 AGAA
1 AGAA
1940149 GAAAAAGAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.60, C:0.03, G:0.31, T:0.06
Consensus pattern (34 bp):
AGAAAAAGAAAAAGAAGAAACAATGTGGGGAAGA
Found at i:1940112 original size:19 final size:19
Alignment explanation
Indices: 1940088--1940148 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
1940078 GAAAAAGAAA
1940088 AAGAAGAAACAATGTGGGG
1 AAGAAGAAACAATGTGGGG
***
1940107 AAGAAGAAA-AA---GAAA
1 AAGAAGAAACAATGTGGGG
1940122 AAGAAGAAACAATGTGGGG
1 AAGAAGAAACAATGTGGGG
1940141 AAGAAGAA
1 AAGAAGAA
1940149 GAAAAAGAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 10 0.31
16 2 0.06
18 2 0.06
19 18 0.56
ACGTcount: A:0.59, C:0.03, G:0.31, T:0.07
Consensus pattern (19 bp):
AAGAAGAAACAATGTGGGG
Found at i:1940204 original size:8 final size:8
Alignment explanation
Indices: 1940187--1940234 Score: 89
Period size: 8 Copynumber: 6.1 Consensus size: 8
1940177 TCCAATTTCA
1940187 TTTA-TAT
1 TTTATTAT
1940194 TTTATTAT
1 TTTATTAT
1940202 TTTATTAT
1 TTTATTAT
1940210 TTTATTAT
1 TTTATTAT
1940218 TTTATTAT
1 TTTATTAT
1940226 TTTATTAT
1 TTTATTAT
1940234 T
1 T
1940235 ATAATAAGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
7 4 0.10
8 36 0.90
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTATTAT
Found at i:1941439 original size:17 final size:18
Alignment explanation
Indices: 1941412--1941447 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1941402 ATATATATAT
1941412 ATTAGTTATTTTTATTTA
1 ATTAGTTATTTTTATTTA
1941430 ATTA-TTATTTTTATTTA
1 ATTAGTTATTTTTATTTA
1941447 A
1 A
1941448 GTACTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
ATTAGTTATTTTTATTTA
Found at i:1941623 original size:4 final size:4
Alignment explanation
Indices: 1941616--1941721 Score: 56
Period size: 4 Copynumber: 24.8 Consensus size: 4
1941606 TATATATATA
** * *
1941616 TTAT TTAT TTAT TTAT TTCC TTA- TTA- TTAT TATCAT TATAC CTACT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-T-AT T-TAT TTA-T
*
1941662 TTAT TTAT TTATT TTAT TTATT TTATT TCTAT TTAT TTAT TCTAT TTTT
1 TTAT TTAT TTA-T TTAT TTA-T TTA-T T-TAT TTAT TTAT T-TAT TTAT
1941711 ATTA- TTAT TTA
1 -TTAT TTAT TTA
1941722 ATACTATATT
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
3 9 0.11
4 44 0.53
5 23 0.28
6 7 0.08
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:1941679 original size:9 final size:9
Alignment explanation
Indices: 1941661--1941720 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
1941651 TTATACCTAC
1941661 TTTA-TTTA
1 TTTATTTTA
1941669 TTTATTTTA
1 TTTATTTTA
1941678 TTTATTTTA
1 TTTATTTTA
*
1941687 TTTCTATTTA
1 TTTAT-TTTA
*
1941697 TTTATTCTA
1 TTTATTTTA
1941706 TTT-TTATTA
1 TTTATT-TTA
1941715 -TTATTT
1 TTTATTT
1941721 AATACTATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 9 0.20
9 27 0.61
10 8 0.18
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1941682 original size:28 final size:28
Alignment explanation
Indices: 1941651--1941708 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
1941641 ATTATTATCA
*
1941651 TTATACCTACTT-TATTTATTTATTTTAT
1 TTAT-CCTACTTCTATTTATTTATTCTAT
** *
1941679 TTATTTTATTTCTATTTATTTATTCTAT
1 TTATCCTACTTCTATTTATTTATTCTAT
1941707 TT
1 TT
1941709 TTATTATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (28 bp):
TTATCCTACTTCTATTTATTTATTCTAT
Found at i:1941715 original size:28 final size:28
Alignment explanation
Indices: 1941663--1941716 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1941653 ATACCTACTT
*
1941663 TATTTATTTATTTTATTTATTTTATTTC
1 TATTTATTTATTCTATTTATTTTATTTC
1941691 TATTTATTTATTCTATTT-TTATTATT
1 TATTTATTTATTCTATTTATT-TTATT
1941717 ATTTAATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (28 bp):
TATTTATTTATTCTATTTATTTTATTTC
Found at i:1941945 original size:30 final size:29
Alignment explanation
Indices: 1941907--1941969 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
1941897 TATATATATG
*
1941907 TATTATTTCTTTACTA-TTATTTTTCCCTT
1 TATTATTTCCTTA-TATTTATTTTTCCCTT
**
1941936 TATTCATTTCCTTATATTTATTTTTTTCTT
1 TATT-ATTTCCTTATATTTATTTTTCCCTT
1941966 TATT
1 TATT
1941970 TTATTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.68
Consensus pattern (29 bp):
TATTATTTCCTTATATTTATTTTTCCCTT
Found at i:1941970 original size:26 final size:27
Alignment explanation
Indices: 1941938--1941997 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
1941928 TTTCCCTTTA
* *
1941938 TTCATTTCCTTATATTTATTTTTTTCT
1 TTCATTTCATTATATTTATTTTTTACT
* * *
1941965 TT-ATTTTATTTTATTTGTTTTTTACT
1 TTCATTTCATTATATTTATTTTTTACT
1941991 TTCATTT
1 TTCATTT
1941998 TTTTCTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (27 bp):
TTCATTTCATTATATTTATTTTTTACT
Found at i:1941974 original size:17 final size:18
Alignment explanation
Indices: 1941942--1941976 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1941932 CCTTTATTCA
1941942 TTTCCTTATATTTATTTT
1 TTTCCTTATATTTATTTT
*
1941960 TTTCTTTAT-TTTATTTT
1 TTTCCTTATATTTATTTT
1941977 ATTTGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCCTTATATTTATTTT
Found at i:1941978 original size:22 final size:22
Alignment explanation
Indices: 1941947--1941998 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1941937 ATTCATTTCC
*
1941947 TTATATTTATTTTTTTCTTTA-TT
1 TTAT-TTTATTTGTTT-TTTACTT
1941970 TTATTTTATTTGTTTTTTACTT
1 TTATTTTATTTGTTTTTTACTT
*
1941992 TCATTTT
1 TTATTTT
1941999 TTTCTTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 18 0.69
23 4 0.15
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (22 bp):
TTATTTTATTTGTTTTTTACTT
Found at i:1945998 original size:91 final size:93
Alignment explanation
Indices: 1945832--1946079 Score: 290
Period size: 91 Copynumber: 2.6 Consensus size: 93
1945822 ATTATAATAT
* *
1945832 TATACAATAAAGCTTGAGCTGTCCCTGTAGAGTAATTGGTTAAACGCCCCGGCTTTATGGAGAAG
1 TATACAATAAAGCTTGAGCTGTCCC--TAGAGTAATTGGTTAAACGCCCCGACTTTATGAAGAAG
*
1945897 ATTCAGCTAGCTTGATAAAGGTGATTATAA
64 ATTCAGCTAGCCTGATAAAGGTGATTATAA
* * *
1945927 TATACAATAAAGCTTGAGTTGTCCC-A-AGTAATTGGTTAAACGCCCCGACTTTATGAATAATAT
1 TATACAATAAAGCTTGAGCTGTCCCTAGAGTAATTGGTTAAACGCCCCGACTTTATGAAGAAGAT
1945990 TC-GTCTAGCCTGATAAAGGTGATTATAA
66 TCAG-CTAGCCTGATAAAGGTGATTATAA
* * *
1946018 TAT-CTATACAATGATATTGAGCTGTTCCTCTAGAGCAATTGGTTAAACGCCCC-AGCTTTATG
1 TATACAATA-AA-G--CTTGAGCTG-TCC-CTAGAGTAATTGGTTAAACGCCCCGA-CTTTATG
1946080 GATCCAGCTA
Statistics
Matches: 133, Mismatches: 10, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
90 5 0.04
91 63 0.47
92 2 0.02
94 7 0.05
95 27 0.20
96 1 0.01
97 2 0.02
98 26 0.20
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (93 bp):
TATACAATAAAGCTTGAGCTGTCCCTAGAGTAATTGGTTAAACGCCCCGACTTTATGAAGAAGAT
TCAGCTAGCCTGATAAAGGTGATTATAA
Found at i:1947591 original size:34 final size:30
Alignment explanation
Indices: 1947548--1947636 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 30
1947538 ATATTGGATT
1947548 TCAACTTCACGACGAAGGATATCCAATTCCATGC
1 TCAACTTCACGACGAAGGATATCC-A--CCAT-C
* * * *
1947582 TCAACTTCACAACGAATGGGTCATCCACGATT
1 TCAACTTCACGACGAA-GGAT-ATCCACCATC
1947614 TCAACTTCACGACGAAGGATATC
1 TCAACTTCACGACGAAGGATATC
1947637 ATGTTCACCA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
30 3 0.06
31 3 0.06
32 15 0.32
33 3 0.06
34 15 0.32
35 4 0.09
36 4 0.09
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.24
Consensus pattern (30 bp):
TCAACTTCACGACGAAGGATATCCACCATC
Found at i:1947626 original size:66 final size:65
Alignment explanation
Indices: 1947544--1947876 Score: 199
Period size: 66 Copynumber: 5.4 Consensus size: 65
1947534 CCTTATATTG
1947544 GATTTCAACTTCACGACGAAGGATATCCAATTCCATGCTCAACTTCACAACGAATGGGTCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATT-CATGCTCAACTTCACAACGAATGGGTCATCCA
1947609 C
65 C
* * ** * ***
1947610 GATTTCAACTTCACGACGAAGG--AT---A-TCATGTTC-AC--CAGTAAC--AT-CTTTATATT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCATGCTCAACTTCA-CAACGAATGGGTCATCCA
*
1947663 G
65 C
* * *
1947664 GATTTCAACTTCACAACGAAGGATATCCAATTTCATGCTCAACTTTACAACGAAGGGGTCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAA-TTCATGCTCAACTTCACAACGAATGGGTCATCCA
1947729 C
65 C
** *** * * * ** **
1947730 GATTTCAACTTCACGAAAAAGGATATCGTGTTCA--C-CAA--TAACATC--CTTAG--AT--TG
1 GATTTCAACTTCACGACGAAGGATATCCAATTCATGCTCAACTTCACAACGAATGGGTCATCCAC
* * *
1947784 GATTTCAACTTCACGACGAAGGATATCCAATTTCAAGCTCAACTTCACAATGAATGGGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAA-TTCATGCTCAACTTCACAACGAATGGGTCATCCA
1947849 C
65 C
* * *
1947850 GATTTTAACTTCACGATGAATGATATC
1 GATTTCAACTTCACGACGAAGGATATC
1947877 GTGTTCACCA
Statistics
Matches: 190, Mismatches: 51, Indels: 52
0.65 0.17 0.18
Matches are distributed among these distances:
54 49 0.26
55 6 0.03
56 6 0.03
57 4 0.02
58 6 0.03
59 7 0.04
60 10 0.05
61 8 0.04
62 7 0.04
63 4 0.02
64 5 0.03
65 5 0.03
66 73 0.38
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (65 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCATGCTCAACTTCACAACGAATGGGTCATCCAC
Done.