Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009630.1 Hibiscus syriacus cultivar Beakdansim tig00117026_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: 1249403
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:555199 original size:5 final size:4
Alignment explanation
Indices: 555180--555218 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
555170 TTTTTTTTCT
* *
555180 TACA TACA TACA TAACA TAAA TACA TACA TGCA TACA TA
1 TACA TACA TACA T-ACA TACA TACA TACA TACA TACA TA
555219 TATCATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:555333 original size:124 final size:124
Alignment explanation
Indices: 555023--555333 Score: 421
Period size: 124 Copynumber: 2.5 Consensus size: 124
555013 CATAATTTTT
* *
555023 TACGTTATCAAGCCAAGGCAAGTTTCTTTTTCTTTACATACATGCATGCAT-ACATACATGCATG
1 TACGTTATCAAGCCAAGGCAAGTTTCTTTTTC-TTACATACATGCATACATAACATACATACATG
* * ** *
555087 CATACATATGTCATTGTTGGAAGGCTATGCTTGTTTTTGACAGTTTTATTCATACTTCTT
65 CATACATATATCATTGTTGGAAGGATATGCTTGTTTTTGACAGCCTTATTCATACTTCTC
* * * * *
555147 TACGTTATCAAACTAAGGAAAGTTTTTTTTTCTTACATACATACATAACATAA-ATACATACATG
1 TACGTTATCAAGCCAAGGCAAGTTTCTTTTTCTTACATACATGCAT-ACATAACATACATACATG
* *
555211 CATACATATATCATT-TTAGGAAGGATATGCTTGTTTTTGGCAGCCTTCTTCATACTTCTC
65 CATACATATATCATTGTT-GGAAGGATATGCTTGTTTTTGACAGCCTTATTCATACTTCTC
* * *
555271 TATGTTATCAAGCCAAGGCAAGTTTCTTTTTCTTACATACATGCATACGTAACATACGTACAT
1 TACGTTATCAAGCCAAGGCAAGTTTCTTTTTCTTACATACATGCATACATAACATACATACAT
555334 ATATGCATTC
Statistics
Matches: 161, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
123 20 0.12
124 140 0.87
125 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (124 bp):
TACGTTATCAAGCCAAGGCAAGTTTCTTTTTCTTACATACATGCATACATAACATACATACATGC
ATACATATATCATTGTTGGAAGGATATGCTTGTTTTTGACAGCCTTATTCATACTTCTC
Found at i:561684 original size:84 final size:84
Alignment explanation
Indices: 561541--561708 Score: 264
Period size: 84 Copynumber: 2.0 Consensus size: 84
561531 TGAACCTCAC
561541 ATATCTCAGGATATCCAGCACCAAGATTACCAACATGTTAACCAGCGCATGCCAATTAAACCTCA
1 ATATCTCAGGATATCCAGCACCAAGATTACCAACATGTTAACCAGCGCATGCCAATTAAACCTCA
*
561606 GCCTATGGAAGTGAAGACT
66 GCCTATGGAAGTCAAGACT
* * * * * *
561625 ATATCTCAGGATATCCAGTACCAAGATTATCAACATGTTAGCCAGTGTATGCCAGTTAAACCTCA
1 ATATCTCAGGATATCCAGCACCAAGATTACCAACATGTTAACCAGCGCATGCCAATTAAACCTCA
*
561690 TCCTATGGAAGTCAAGACT
66 GCCTATGGAAGTCAAGACT
561709 GAAGTCCCCA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (84 bp):
ATATCTCAGGATATCCAGCACCAAGATTACCAACATGTTAACCAGCGCATGCCAATTAAACCTCA
GCCTATGGAAGTCAAGACT
Found at i:563227 original size:2 final size:2
Alignment explanation
Indices: 563216--563249 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
563206 TCTCTCTCTC
*
563216 TA TA TC 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
563250 GTGTAACACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:568726 original size:13 final size:13
Alignment explanation
Indices: 568708--568738 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
568698 TGATCCCTTA
568708 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
568721 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
*
568734 CTCTT
1 TTCTT
568739 AATCCAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
TTCTTCTTCTTCT
Found at i:573675 original size:12 final size:12
Alignment explanation
Indices: 573658--573690 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
573648 GCTCGAATAT
573658 GCATCACGGCAA
1 GCATCACGGCAA
573670 GCATCACGGCAA
1 GCATCACGGCAA
*
573682 GCTTCACGG
1 GCATCACGG
573691 TTATGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.12
Consensus pattern (12 bp):
GCATCACGGCAA
Found at i:580193 original size:2 final size:2
Alignment explanation
Indices: 580139--580174 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
580129 TATTATCTTA
580139 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
580175 TAATATGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:585467 original size:53 final size:55
Alignment explanation
Indices: 585302--586047 Score: 1061
Period size: 55 Copynumber: 13.8 Consensus size: 55
585292 TGAGTTCGCT
* * * **
585302 CCCTATTTCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAACAATCGCGTCTGCC
* *
585357 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
585412 CCCTGTTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
585465 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * * * *
585520 CCCTATATGTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
585573 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
585628 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
585681 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * * * *
585736 CCCTATATGTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGTGTCTG-C
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
585788 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * * *
585843 CCCTATTTCTTTAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTCCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
585896 CCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
585951 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
586004 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAA
586048 ATGGGTTCGC
Statistics
Matches: 613, Mismatches: 64, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
52 25 0.04
53 258 0.42
54 31 0.05
55 299 0.49
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
Found at i:585470 original size:108 final size:108
Alignment explanation
Indices: 585350--586045 Score: 1250
Period size: 108 Copynumber: 6.5 Consensus size: 108
585340 CAACAAACTT
585350 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
*
585415 TGTTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGC
66 TATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGC
* *
585458 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
* * *
585523 TATATGTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGT
66 TATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGC
585566 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
585631 TATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGC
66 TATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGC
* *
585674 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
* * *
585739 TATATGTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGT
66 TATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGC
585782 GTCTG-CCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
*
585846 TATTTCTTTAGAGAGTATAAGACCCACAATCTTCATCAATCGC
66 TATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGC
* *
585889 GTCTCCCCCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
585954 TATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGC
66 TATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGC
*
585997 GTCTGTCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
586046 AAATGGGTTC
Statistics
Matches: 559, Mismatches: 28, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
107 100 0.18
108 459 0.82
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (108 bp):
GTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCC
TATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGC
Found at i:586121 original size:108 final size:107
Alignment explanation
Indices: 585357--586151 Score: 976
Period size: 108 Copynumber: 7.4 Consensus size: 107
585347 CTTGTCTGCC
* * *
585357 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTGTTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAATGCGTCTGCCCCCTATTTCT
* *
585422 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCG-TCTGCC
66 T-AGAGAGTATAAGACCCACAATCTTCATCAATCGGGTTC-GCT
* *
585465 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGCGTCTGCCCCCTATATG
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAAT-GCGTCTGCCCCCTATTTC
* *
585529 TTCAGAGAGTATAAGACCCACAATCTTCATCAATCGTG-TCTGCC
65 TT-AGAGAGTATAAGACCCACAATCTTCATCAATCGGGTTC-GCT
* *
585573 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAATGCGTCTGCCCCCTATTTCT
* *
585638 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCG-TCTGCC
66 T-AGAGAGTATAAGACCCACAATCTTCATCAATCGGGTTC-GCT
* *
585681 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGCGTCTGCCCCCTATATG
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAAT-GCGTCTGCCCCCTATTTC
*
585745 TTCAGAGAGTATAAGACCCACAATCTTCATCAATCGTG-TCTGC-
65 TT-AGAGAGTATAAGACCCACAATCTTCATCAATCGGGTTC-GCT
* *
585788 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAATGCGTCTGCCCCCTATTTC-
* *
585853 TTAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTC-CC
65 TTAGAGAGTATAAGACCCACAATCTTCATCAATCGGGT-TCGCT
* * *
585896 CCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAATGCGTCTGCCCCCTATTTCT
*
585961 TCAGAGAGTATAAGACCCACAATCTTCATCAATCGCG-TCTG-T
66 T-AGAGAGTATAAGACCCACAATCTTCATCAATCGGGTTC-GCT
* *
586003 CCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAATGGGT-TCGCTCCCTATTT
1 -CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAATGCGTCT-GCCCCCTATTT
* * * *
586067 CTCTAGGGAGTAT-AGAACTCGA-ACATC-TCTTCAAACGGGTTCGCT
64 CT-TAGAGAGTATAAG-AC-CCACA-ATCTTCATCAATCGGGTTCGCT
* * *
586112 CCTTCTTTCTTTA-AGGAGTAT-AGAACTCGAAC-ATCTTCAA
1 CCCTATTTCTTCAGA-GAGTATAAG-ACTCGAACAATCTTCAA
586152 ACGGGTTCGC
Statistics
Matches: 634, Mismatches: 32, Indels: 43
0.89 0.05 0.06
Matches are distributed among these distances:
106 2 0.00
107 113 0.18
108 506 0.80
109 13 0.02
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (107 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAATGCGTCTGCCCCCTATTTCT
TAGAGAGTATAAGACCCACAATCTTCATCAATCGGGTTCGCT
Found at i:586170 original size:51 final size:51
Alignment explanation
Indices: 586019--586562 Score: 646
Period size: 51 Copynumber: 10.5 Consensus size: 51
586009 TTTCTTCAGA
* * * * *
586019 GAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCTCCCTATTTCTCTAGG
1 GAGTATAGA-ACTCGAAC-ATCTT---CAAACGGGTTCGCTCCTTCTTTCTTTAAG
586074 GAGTATAGAACTCGAACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACA--TCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
586127 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
586178 GAGTATAGAACTCGAACATCTTC-AACTGGGTTCGCTCCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTCAAAC-GGGTTCGCT-CCTTCTTTCTTTAAG
* * * *
586230 GGGTATAGAACTTGAACATCTTC-AACTGGGTTCGCTCCCTT-TTTCTTCAGG
1 GAGTATAGAACTCGAACATCTTCAAAC-GGGTTCGCT-CCTTCTTTCTTTAAG
* * * ** * * *
586281 GAGTATATAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCTTCTCTCTCTAAA
1 GAGTATAGAACTC--GAA-CATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
*
586335 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCATTAAG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* * * * * * *
586386 GAGTATGGAACTCGGATATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* **
586437 GAGTATGGAACTATAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* *
586488 GAGTATGGAACTCGAACATCTTCGAACGGGTTCGCTCCTTCTTTCTTTAAG
1 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* *
586539 GAGTATAGAACTCGCATATCTTCA
1 GAGTATAGAACTCGAACATCTTCA
586563 TTTGCTTCAC
Statistics
Matches: 427, Mismatches: 52, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
50 3 0.01
51 265 0.62
52 56 0.13
53 48 0.11
54 33 0.08
55 17 0.04
56 5 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (51 bp):
GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
Found at i:586341 original size:208 final size:206
Alignment explanation
Indices: 586045--586562 Score: 687
Period size: 208 Copynumber: 2.5 Consensus size: 206
586035 CAATCTTCAA
* *
586045 CAAA-TGGGTTCGCTCCCTATTTC-TCTAGGGAGTATAGAACTCGAACATCTCTTCAAACGGGTT
1 CAAACTGGGTTCGCTCCCTTTTTCTTC-AGGGAGTATAGAACTC-AAAATCTCTTCAAACGGGTT
*
586108 CGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCT
64 CGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCA
*
586173 TTAAGGAGTATAGAACTCGAACATCTTCA-ACTGGGTTCGCTCCCTTCTTTCTTTAAGGG-GTAT
129 TTAAGGAGTATAGAACTCGAACATCTTCACAC-GGGTTCGCTCCC-TCTTTCTCT-AGGGAGTAT
586236 AGAACT-TGAACATCTT
191 AGAACTAT-AACATCTT
* **
586252 C-AACTGGGTTCGCTCCCTTTTTCTTCAGGGAGTATATAACTCAAAAATCTTCTTCTTACGGGTT
1 CAAACTGGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTC-AAAATC-TCTTCAAACGGGTT
* * *
586316 CGCTCCTTCTCTCTCTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCA
64 CGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCA
* * * *
586381 TTAAGGAGTATGGAACTCGGATATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
129 TTAAGGAGTATAGAACTCGAACATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGA
586446 ACTATAACATCTT
194 ACTATAACATCTT
* * * * *
586459 CAAAC-GGGTTCGCT-CCTTCTTTCTTTAAGGAGTATGGAACTC-GAA-CATCTTCGAACGGGTT
1 CAAACTGGGTTCGCTCCCTT-TTTCTTCAGGGAGTATAGAACTCAAAATC-TCTTCAAACGGGTT
* *
586520 CGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTTCA
64 CGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCA
586563 TTTGCTTCAC
Statistics
Matches: 275, Mismatches: 28, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
204 51 0.19
205 2 0.01
206 10 0.04
207 93 0.34
208 117 0.43
209 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (206 bp):
CAAACTGGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCAAAATCTCTTCAAACGGGTTCG
CTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCATT
AAGGAGTATAGAACTCGAACATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
TATAACATCTT
Found at i:586992 original size:36 final size:36
Alignment explanation
Indices: 586932--587197 Score: 311
Period size: 36 Copynumber: 7.4 Consensus size: 36
586922 ACTCTTCTGA
* * **
586932 GAAGGCTTAAAATGGATCTGCTTCACTACTT-TTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * * *
586969 GAAGACTTAAGATGGTTTACTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
587005 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
587041 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
587077 GAAGGCTTCAGATGGTTAGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
587113 GAAGGCTTAGGATGGTTTGCTTCACTATTCTCCAGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
587149 GAAGGCTTCAGATGGTTTGCTTCACT-TCTCTTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTAT-TCTCCGGT
*
587185 GTAGGCTTAAGAT
1 GAAGGCTTAAGAT
587198 TAACTTTGCT
Statistics
Matches: 199, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
35 2 0.01
36 184 0.92
37 13 0.07
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:596057 original size:2 final size:2
Alignment explanation
Indices: 596050--596116 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
596040 CGATGATGTA
596050 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
596092 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
596117 ATTTATCTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:597053 original size:20 final size:21
Alignment explanation
Indices: 597007--597053 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
596997 ACCATTTTTT
* *
597007 TTTTGAAAAACAATTATGTAT
1 TTTTAAAAAACAATTATGTAC
*
597028 TATTTAAAAAACGATTATG-AC
1 T-TTTAAAAAACAATTATGTAC
597049 TTTTA
1 TTTTA
597054 TTTGGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 3 0.14
22 15 0.68
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (21 bp):
TTTTAAAAAACAATTATGTAC
Found at i:600571 original size:37 final size:37
Alignment explanation
Indices: 600514--600615 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 37
600504 CTTTTTCGTC
*
600514 CTACTAGGATTCAAACTCCTAAAAATA-AGATAGAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGA-ATAGAATT
* * *
600551 TTGCTAAGATTCAAACTCCTAAAAATAGAATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGAATAGAATT
* * *
600588 CTACTATGATTTAAACTCCTAAAGATAG
1 CTACTAAGATTCAAACTCCTAAAAATAG
600616 TATCCACAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
37 54 0.98
38 1 0.02
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGAATAGAATT
Found at i:603110 original size:3 final size:3
Alignment explanation
Indices: 603096--603144 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
603086 AATGTAAATG
* *
603096 TAA TAT TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TGA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
603142 TAA
1 TAA
603145 ATTAAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 3 0.08
3 37 0.93
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:603122 original size:17 final size:18
Alignment explanation
Indices: 603096--603144 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
603086 AATGTAAATG
*
603096 TAATATTAATAATAAT-A
1 TAATAATAATAATAATAA
603113 TAATAATAATAATAATAA
1 TAATAATAATAATAATAA
*
603131 TGA-AATAATAATAA
1 TAATAATAATAATAA
603145 ATTAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 26 0.90
18 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TAATAATAATAATAATAA
Found at i:603125 original size:20 final size:20
Alignment explanation
Indices: 603096--603144 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
603086 AATGTAAATG
*
603096 TAATATTAATAATAAT-ATAA
1 TAATAATAATAATAATGA-AA
603116 TAATAATAATAATAATGAAA
1 TAATAATAATAATAATGAAA
603136 TAATAATAA
1 TAATAATAA
603145 ATTAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
TAATAATAATAATAATGAAA
Found at i:611273 original size:15 final size:15
Alignment explanation
Indices: 611255--611294 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
611245 TATTTTAAAT
611255 TTAAAATATAAAAAA
1 TTAAAATATAAAAAA
*
611270 TTAAAATAATAAATAA
1 TTAAAAT-ATAAAAAA
611286 -TAAAATATA
1 TTAAAATATA
611295 TATTATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 3 0.13
15 13 0.57
16 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAAATATAAAAAA
Found at i:611919 original size:23 final size:23
Alignment explanation
Indices: 611881--611925 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
611871 ATAAAAAAAT
611881 AATAATATATATTTTTAGTTTTTG
1 AATAATATATATTTTTA-TTTTTG
*
611905 AATAATTTA-ATTTTTATTTTT
1 AATAATATATATTTTTATTTTT
611926 ATTCATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
AATAATATATATTTTTATTTTTG
Found at i:612881 original size:3 final size:3
Alignment explanation
Indices: 612873--612904 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
612863 TACATTACTC
612873 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
612905 TGTTTACGTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:614145 original size:2 final size:2
Alignment explanation
Indices: 614140--614174 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
614130 TTTGTTCTAA
614140 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
614175 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:614179 original size:2 final size:2
Alignment explanation
Indices: 614174--614205 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
614164 ATATATATAT
614174 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
614206 GGGGGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:619178 original size:30 final size:31
Alignment explanation
Indices: 619093--619197 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 31
619083 TTATAACTAG
*
619093 TTATTAAAATTT-TCAAACTGCTATAAAATAA
1 TTATT-AAATTTATCAAACTGTTATAAAATAA
* * ** *
619124 TTATTAATTTTTTTGAATTGTTATAAAAT-A
1 TTATTAAATTTATCAAACTGTTATAAAATAA
* *
619154 TTATTAAATTTATCAAACTATTAT-AAATCA
1 TTATTAAATTTATCAAACTGTTATAAAATAA
*
619184 TTCCTTAAATTTAT
1 TT-ATTAAATTTAT
619198 TAATTTTTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
29 4 0.07
30 27 0.46
31 28 0.47
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.48
Consensus pattern (31 bp):
TTATTAAATTTATCAAACTGTTATAAAATAA
Found at i:626816 original size:22 final size:21
Alignment explanation
Indices: 626774--626813 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
626764 GAGTTTATTT
*
626774 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
626795 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
626814 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:628849 original size:23 final size:23
Alignment explanation
Indices: 628809--628866 Score: 100
Period size: 22 Copynumber: 2.6 Consensus size: 23
628799 AAACCATTCA
628809 GGGGGAAATCGGTACCCCCTT-G
1 GGGGGAAATCGGTACCCCCTTGG
628831 GGGGGAAATCGGTACCCCCTTGG
1 GGGGGAAATCGGTACCCCCTTGG
*
628854 GGGGGGAATCGGT
1 GGGGGAAATCGGT
628867 TCCCTCTGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.17, C:0.22, G:0.43, T:0.17
Consensus pattern (23 bp):
GGGGGAAATCGGTACCCCCTTGG
Found at i:629220 original size:22 final size:22
Alignment explanation
Indices: 629158--629232 Score: 107
Period size: 22 Copynumber: 3.4 Consensus size: 22
629148 AAAAATTATG
* * *
629158 TAATTAATATTT-TATTTTAAA
1 TAATTTATATTTAAATTTTAAT
629179 TAATTTATATTTAAAATTTTAAT
1 TAATTTATATTT-AAATTTTAAT
629202 TAATTTATATTTAAATTTTAAT
1 TAATTTATATTTAAATTTTAAT
629224 TAATTTATA
1 TAATTTATA
629233 ATTATACGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
21 11 0.22
22 19 0.39
23 19 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TAATTTATATTTAAATTTTAAT
Found at i:629226 original size:11 final size:12
Alignment explanation
Indices: 629180--629236 Score: 59
Period size: 11 Copynumber: 5.0 Consensus size: 12
629170 TATTTTAAAT
*
629180 AATTTATATTTAA
1 AATTTATAATT-A
629193 AATTT-TAATT-
1 AATTTATAATTA
*
629203 AATTTATATTTA
1 AATTTATAATTA
629215 AATTT-TAATT-
1 AATTTATAATTA
629225 AATTTATAATTA
1 AATTTATAATTA
629237 TACGTTGAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 10 0.27
11 13 0.35
12 9 0.24
13 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATTTATAATTA
Found at i:629306 original size:26 final size:26
Alignment explanation
Indices: 629277--629328 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
629267 TATAAATTAA
*
629277 ATTAATGATGCTCAACAATATTCATC
1 ATTAATGATGCTCAACAATACTCATC
* * *
629303 ATTAGTGATTCTCAACTATACTCATC
1 ATTAATGATGCTCAACAATACTCATC
629329 CAACGTGGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (26 bp):
ATTAATGATGCTCAACAATACTCATC
Found at i:629852 original size:61 final size:59
Alignment explanation
Indices: 629755--629903 Score: 217
Period size: 61 Copynumber: 2.4 Consensus size: 59
629745 CAAAAACTCG
* *
629755 AAATAAAAATTTGAAGCTCGACTCGAAAACTTGTGAGTTTAAAATTTTCAAGGTCGACTAT
1 AAATAAAAA-TTGAAGCTCGACTTG-AAACTTGTGAGCTTAAAATTTTCAAGGTCGACTAT
* *
629816 AAATCAAAAATTGAAGTTCGACTTGAAAGTTGGTGAGCTTAAAATTTTCAAGGTCGACTAT
1 AAAT-AAAAATTGAAGCTCGACTTGAAACTT-GTGAGCTTAAAATTTTCAAGGTCGACTAT
629877 AAATAAAAAATTGAAGCTCGACTTGAA
1 AAAT-AAAAATTGAAGCTCGACTTGAA
629904 CTTAAACCTT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
60 5 0.06
61 70 0.88
62 5 0.06
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (59 bp):
AAATAAAAATTGAAGCTCGACTTGAAACTTGTGAGCTTAAAATTTTCAAGGTCGACTAT
Found at i:630374 original size:2 final size:2
Alignment explanation
Indices: 630367--630406 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
630357 AGTATTAAAT
630367 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
630407 TGAATAGGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:630389 original size:19 final size:19
Alignment explanation
Indices: 630365--630404 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
630355 ATAGTATTAA
630365 ATTATATATATATATATAT
1 ATTATATATATATATATAT
630384 ATTATATATATATATATAT
1 ATTATATATATATATATAT
630403 AT
1 AT
630405 ATTGAATAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTATATATATATATATAT
Found at i:631193 original size:35 final size:36
Alignment explanation
Indices: 631146--631242 Score: 126
Period size: 36 Copynumber: 2.7 Consensus size: 36
631136 AACACATTTA
* *
631146 TCAATTACATTCTAAAGCC-CAAATTTC-AAAATACT
1 TCAATTATATTCTAAA-CCTCAAATTCCAAAAATACT
631181 TCAATTATATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTATATTCTAAACCTCAAATTCCAAAAATACT
* **
631217 TCAATTATATACCCAACCTCAAATTC
1 TCAATTATATTCTAAACCTCAAATTC
631243 ATAATCCATT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
34 2 0.04
35 22 0.40
36 31 0.56
ACGTcount: A:0.42, C:0.25, G:0.01, T:0.32
Consensus pattern (36 bp):
TCAATTATATTCTAAACCTCAAATTCCAAAAATACT
Found at i:631994 original size:148 final size:148
Alignment explanation
Indices: 631726--632018 Score: 514
Period size: 148 Copynumber: 2.0 Consensus size: 148
631716 AAACTATTTA
* * * *
631726 AATTAGAATAAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
1 AATTAGAATAAAATAATAGTATAATATGATAAATATTTATAATTAAATTTAAACAAAAACTCGAA
*
631791 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTAAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTCGAGTAAACT
631856 ATTTTATAAACTGAACTG
131 ATTTTATAAACTGAACTG
*
631874 AATTAGAATCAAATAATAGTATAATATGATAAATATTTATAATTAAATTTAAACAAAAACTCGAA
1 AATTAGAATAAAATAATAGTATAATATGATAAATATTTATAATTAAATTTAAACAAAAACTCGAA
* *
631939 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTCGAGTCAATT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTCGAGTAAACT
632004 ATTTTATAAACTGAA
131 ATTTTATAAACTGAA
632019 TTGAGTATTT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
148 137 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.35
Consensus pattern (148 bp):
AATTAGAATAAAATAATAGTATAATATGATAAATATTTATAATTAAATTTAAACAAAAACTCGAA
AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCAAAAAAAATTCGAGTAAACT
ATTTTATAAACTGAACTG
Found at i:632235 original size:35 final size:35
Alignment explanation
Indices: 632196--632275 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
632186 GGGGTTGGGC
*
632196 ATGTAATTGAAGTATTTTGGAATTTGA-GGTTTAAA
1 ATGTAATTGAAATATTTTGG-ATTTGAGGGTTTAAA
* *
632231 ATGTAATTGAAATATTTTGGATTTTAGGGTTTAGA
1 ATGTAATTGAAATATTTTGGATTTGAGGGTTTAAA
632266 ATGTAATTGA
1 ATGTAATTGA
632276 TGACTATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 5 0.12
35 36 0.88
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.44
Consensus pattern (35 bp):
ATGTAATTGAAATATTTTGGATTTGAGGGTTTAAA
Found at i:639205 original size:18 final size:17
Alignment explanation
Indices: 639182--639241 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
639172 AACCTGTTTG
639182 TTTTAGGTTGCAACCATA
1 TTTTAGGTTG-AACCATA
*
639200 TTTTAGGTTGAAAC-T-
1 TTTTAGGTTGAACCATA
639215 TGTTTA-G-TGAAACCATA
1 T-TTTAGGTTG-AACCATA
639232 TTTTAGGTTG
1 TTTTAGGTTG
639242 GAACTTGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 2 0.06
15 5 0.15
16 10 0.29
17 5 0.15
18 12 0.35
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (17 bp):
TTTTAGGTTGAACCATA
Found at i:639270 original size:31 final size:32
Alignment explanation
Indices: 639193--639275 Score: 132
Period size: 32 Copynumber: 2.6 Consensus size: 32
639183 TTTAGGTTGC
639193 AACCATATTTTAGGTTGAAACTTGTTTAGTGA
1 AACCATATTTTAGGTTGAAACTTGTTTAGTGA
* *
639225 AACCATATTTTAGGTTGGAACTTGTTTAGTGT
1 AACCATATTTTAGGTTGAAACTTGTTTAGTGA
*
639257 AA-CATATTCTAGGTTGAAA
1 AACCATATTTTAGGTTGAAA
639276 AATCAAACCT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 15 0.32
32 32 0.68
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (32 bp):
AACCATATTTTAGGTTGAAACTTGTTTAGTGA
Found at i:639640 original size:79 final size:79
Alignment explanation
Indices: 639509--639796 Score: 380
Period size: 79 Copynumber: 3.6 Consensus size: 79
639499 TTTAAATAAA
** * * *
639509 GTGGTGATGTATTGTACATGATACACACCCAACTATAGCAATATGATGTATCGTACGAGCTACAT
1 GTGGTGATGTATTGTACGGGATACACACCCAACTATAGCAAGATGATGTATCGTACGAGGTACAC
*
639574 AACTAAATATGAAG
66 ATCTAAATATGAAG
* * *
639588 GTGGTGATGTATTGTATGGGATACACACCCATA-TATAGCAAGATGATGTATCGTACGGGGTATA
1 GTGGTGATGTATTGTACGGGATACACACCCA-ACTATAGCAAGATGATGTATCGTACGAGGTACA
*
639652 CATCTAAATATGAAT
65 CATCTAAATATGAAG
* * * ** *
639667 ATGGTGATGTATTGTACGGGATACACATCCAACTACAATAAGATGATGTATCATACGAGGTACAC
1 GTGGTGATGTATTGTACGGGATACACACCCAACTATAGCAAGATGATGTATCGTACGAGGTACAC
639732 ATCTAAATATGAAG
66 ATCTAAATATGAAG
* * *
639746 GTGGTGATGTATTGTATGTGATACACACCCAACTACAAGCAAGATGATGTA
1 GTGGTGATGTATTGTACGGGATACACACCCAACTA-TAGCAAGATGATGTA
639797 CCATCTATAT
Statistics
Matches: 179, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
78 1 0.01
79 165 0.92
80 13 0.07
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (79 bp):
GTGGTGATGTATTGTACGGGATACACACCCAACTATAGCAAGATGATGTATCGTACGAGGTACAC
ATCTAAATATGAAG
Found at i:639677 original size:40 final size:40
Alignment explanation
Indices: 639552--639757 Score: 148
Period size: 40 Copynumber: 5.2 Consensus size: 40
639542 TATAGCAATA
* * * * **
639552 TGATGTATCGTACGAGCTACATAACTAAATATGAAGGTGG
1 TGATGTATCGTACGGGGTACACATCTAAATATGAATATGG
* * * * * * * *
639592 TGATGTATTGTATGGGATACACACCCATATATAGCA-A-GA
1 TGATGTATCGTACGGGGTACACATCTAAATAT-GAATATGG
*
639631 TGATGTATCGTACGGGGTATACATCTAAATATGAATATGG
1 TGATGTATCGTACGGGGTACACATCTAAATATGAATATGG
* * * * * * *
639671 TGATGTATTGTACGGGATACACATCCAACTA-CAATAAGA
1 TGATGTATCGTACGGGGTACACATCTAAATATGAATATGG
* * **
639710 TGATGTATCATACGAGGTACACATCTAAATATGAAGGTGG
1 TGATGTATCGTACGGGGTACACATCTAAATATGAATATGG
639750 TGATGTAT
1 TGATGTAT
639758 TGTATGTGAT
Statistics
Matches: 123, Mismatches: 39, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
38 2 0.02
39 57 0.46
40 62 0.50
41 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (40 bp):
TGATGTATCGTACGGGGTACACATCTAAATATGAATATGG
Found at i:639731 original size:39 final size:39
Alignment explanation
Indices: 639592--639741 Score: 115
Period size: 39 Copynumber: 3.8 Consensus size: 39
639582 ATGAAGGTGG
* * * * **
639592 TGATGTATTGTATGGGATACACACCCATATAT-AGCAAGA
1 TGATGTATCGTACGGG-TACACATCCAAATATCAATAAGA
* * * * *
639631 TGATGTATCGTACGGGGTATACATCTAAATATGAATATGG
1 TGATGTATCGTAC-GGGTACACATCCAAATATCAATAAGA
* *
639671 TGATGTATTGTACGGGATACACATCCAACTA-CAATAAGA
1 TGATGTATCGTACGGG-TACACATCCAAATATCAATAAGA
* *
639710 TGATGTATCATACGAGGTACACATCTAAATAT
1 TGATGTATCGTACG-GGTACACATCCAAATAT
639742 GAAGGTGGTG
Statistics
Matches: 85, Mismatches: 21, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
39 54 0.64
40 31 0.36
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (39 bp):
TGATGTATCGTACGGGTACACATCCAAATATCAATAAGA
Found at i:639878 original size:40 final size:40
Alignment explanation
Indices: 639817--640109 Score: 137
Period size: 40 Copynumber: 7.4 Consensus size: 40
639807 ACGAAATTGG
* * *
639817 TGATGTATTGTAAGGGATACACACCCAACTACAAGCAAGA
1 TGATGTATCGTACGGGGTACACACCCAACTACAAGCAAGA
* * * * * ** *
639857 TGATGTATCCTACGGGGTACACATCTAAATATGAAG-GTGG
1 TGATGTATCGTACGGGGTACACACCCAACTA-CAAGCAAGA
* * * *
639897 TGATGTATTGTACGGGATACACGCCCAACTATAA-CAAGA
1 TGATGTATCGTACGGGGTACACACCCAACTACAAGCAAGA
* * * * * ** *
639936 TGATGTATCGTATGGGGTACACATCTAAATATGAAG-GTGG
1 TGATGTATCGTACGGGGTACACACCCAACTA-CAAGCAAGA
* * *** *
639976 TAATGTATTGTATATGATACACACCCAACTACAAGC-AGA
1 TGATGTATCGTACGGGGTACACACCCAACTACAAGCAAGA
* ** * * * * ** *
640015 TTATGTATCGTACATGGTACACATCTAAATATAAAG-GTGG
1 TGATGTATCGTACGGGGTACACACCCAACTA-CAAGCAAGA
* * * *
640055 TGATGTATTGTACGAGATACACACCCAAATACAAGCAAGA
1 TGATGTATCGTACGGGGTACACACCCAACTACAAGCAAGA
640095 TGATGTATCGTACGG
1 TGATGTATCGTACGG
640110 AGTATACATC
Statistics
Matches: 178, Mismatches: 67, Indels: 16
0.68 0.26 0.06
Matches are distributed among these distances:
39 58 0.33
40 117 0.66
41 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (40 bp):
TGATGTATCGTACGGGGTACACACCCAACTACAAGCAAGA
Found at i:639966 original size:79 final size:80
Alignment explanation
Indices: 639814--640193 Score: 514
Period size: 79 Copynumber: 4.8 Consensus size: 80
639804 TATACGAAAT
* * *
639814 TGGTGATGTATTGTAAGGGATACACACCCAACTACAAGCAAGATGATGTATCCTACGGGGTACAC
1 TGGTGATGTATTGTACGAGATACACACCCAACTACAAGCAAGATGATGTATCGTACGGGGTACAC
639879 ATCTAAATATGAAGG
66 ATCTAAATATGAAGG
* * * *
639894 TGGTGATGTATTGTACGGGATACACGCCCAACTATAA-CAAGATGATGTATCGTATGGGGTACAC
1 TGGTGATGTATTGTACGAGATACACACCCAACTACAAGCAAGATGATGTATCGTACGGGGTACAC
639958 ATCTAAATATGAAGG
66 ATCTAAATATGAAGG
* * * **
639973 TGGTAATGTATTGTA-TATGATACACACCCAACTACAAGC-AGATTATGTATCGTACATGGTACA
1 TGGTGATGTATTGTACGA-GATACACACCCAACTACAAGCAAGATGATGTATCGTACGGGGTACA
*
640036 CATCTAAATATAAAGG
65 CATCTAAATATGAAGG
* * *
640052 TGGTGATGTATTGTACGAGATACACACCCAAATACAAGCAAGATGATGTATCGTACGGAGTATAC
1 TGGTGATGTATTGTACGAGATACACACCCAACTACAAGCAAGATGATGTATCGTACGGGGTACAC
*
640117 ATCTAAATATGAAAG
66 ATCTAAATATGAAGG
* * * * * * *
640132 TGGTGATGTATTGTACAAGATATACACTCAATTATAAGCAAGGTGATGTATCGTACGAGGTA
1 TGGTGATGTATTGTACGAGATACACACCCAACTACAAGCAAGATGATGTATCGTACGGGGTA
640194 ACACCAAAAT
Statistics
Matches: 263, Mismatches: 33, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
79 140 0.53
80 123 0.47
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (80 bp):
TGGTGATGTATTGTACGAGATACACACCCAACTACAAGCAAGATGATGTATCGTACGGGGTACAC
ATCTAAATATGAAGG
Found at i:640156 original size:40 final size:39
Alignment explanation
Indices: 639874--640187 Score: 109
Period size: 40 Copynumber: 7.9 Consensus size: 39
639864 TCCTACGGGG
* * **
639874 TACACATCTAAATATGAAGGTGGTGATGTATTGTACGGGA
1 TACACATCTAAATAT-AAAGTGGTGATGTATCGTACAAGA
** * * * * *** *
639914 TACACGCCCAACTATAACA-AGATGATGTATCGTATGGGG
1 TACACATCTAAATATAA-AGTGGTGATGTATCGTACAAGA
* * * * *
639953 TACACATCTAAATATGAAGGTGGTAATGTATTGTATATGA
1 TACACATCTAAATAT-AAAGTGGTGATGTATCGTACAAGA
* * * * * * * * *
639993 TACACACCCAACTA-CAAGCAGATTATGTATCGTACATGG
1 TACACATCTAAATATAAAG-TGGTGATGTATCGTACAAGA
* *
640032 TACACATCTAAATATAAAGGTGGTGATGTATTGTACGAGA
1 TACACATCTAAATATAAA-GTGGTGATGTATCGTACAAGA
* * * * * *
640072 TACACACCCAAATA-CAAGCAAGATGATGTATCGTAC-GGA
1 TACACATCTAAATATAAAG--TGGTGATGTATCGTACAAGA
* *
640111 GTATACATCTAAATATGAAAGTGGTGATGTATTGTACAAGA
1 -TACACATCTAAATAT-AAAGTGGTGATGTATCGTACAAGA
* * *
640152 TATACA-CTCAAT-TATAAGCAAGGTGATGTATCGTAC
1 TACACATCTAAATATA-AAG--TGGTGATGTATCGTAC
640188 GAGGTAACAC
Statistics
Matches: 197, Mismatches: 62, Indels: 30
0.68 0.21 0.10
Matches are distributed among these distances:
37 1 0.01
38 7 0.04
39 62 0.31
40 121 0.61
41 3 0.02
42 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (39 bp):
TACACATCTAAATATAAAGTGGTGATGTATCGTACAAGA
Found at i:642764 original size:199 final size:200
Alignment explanation
Indices: 642278--642774 Score: 795
Period size: 199 Copynumber: 2.5 Consensus size: 200
642268 GACCAAAAAC
* ** *
642278 TCAATCTATAAAGTTGAGTGATCAAATTGAAAAGTTTGAAAGTATAGTGAGTAAAATAAGAATCA
1 TCAATCCATAAAACTGAGTGATAAAATTGAAAAGTTTGAAAGTATAGTGAGTAAAATAAGAATCA
*
642343 TACAAAAGTTCTGTTATCAAATTTGTAATTTACCCTTATTATTGTTATGTGGAAATTTGATGTGT
66 TACGAAAGTTCTGTTATCAAATTTGTAATTTACCCTTATTATTGTTATGTGGAAATTTGATGTGT
642408 CATGTTTAATATTAAAATATTCCACGTCAACGAGCTGTTAGTGATATAACGGTGGAGTGACAAAA
131 CATGTTTAATATTAAAATATTCCACGTCAACGAGCTGTTAGTGATATAACGGTGGAGTGACAAAA
642473 AAAGT
196 AAAGT
642478 TCAATCCATAAAACTGAGTGATAAAATTGAAAAGTTTGAAAGTATAGTGAGTAAAATAAGAATCA
1 TCAATCCATAAAACTGAGTGATAAAATTGAAAAGTTTGAAAGTATAGTGAGTAAAATAAGAATCA
642543 TACGAAAGTT-TGTTATCAAATTTGTAATTTACCCTTATTATTGTTATGTGGAAATTTGATGTGT
66 TACGAAAGTTCTGTTATCAAATTTGTAATTTACCCTTATTATTGTTATGTGGAAATTTGATGTGT
* *
642607 CATGTTTAATATTAAAATATTCCATGTCAGCGAGCTGTTAGTGATATAACGGTGGAGTGACAAAA
131 CATGTTTAATATTAAAATATTCCACGTCAACGAGCTGTTAGTGATATAACGGTGGAGTGACAAAA
642672 AAAGT
196 AAAGT
* * * *
642677 TCAATCCA-AAAACTGAGTGAGAAAATTGAAAATTTTGAAAGTA-CGAT-ACGTAAAATAGGAAT
1 TCAATCCATAAAACTGAGTGATAAAATTGAAAAGTTTGAAAGTATAG-TGA-GTAAAATAAGAAT
* * ** * *
642739 CGTATGAAAGTTCAATTACCAAATTTATAATTTACC
64 CATACGAAAGTTCTGTTATCAAATTTGTAATTTACC
642775 ATAAATGTTT
Statistics
Matches: 277, Mismatches: 17, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
197 2 0.01
198 56 0.20
199 149 0.54
200 70 0.25
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (200 bp):
TCAATCCATAAAACTGAGTGATAAAATTGAAAAGTTTGAAAGTATAGTGAGTAAAATAAGAATCA
TACGAAAGTTCTGTTATCAAATTTGTAATTTACCCTTATTATTGTTATGTGGAAATTTGATGTGT
CATGTTTAATATTAAAATATTCCACGTCAACGAGCTGTTAGTGATATAACGGTGGAGTGACAAAA
AAAGT
Found at i:649139 original size:24 final size:25
Alignment explanation
Indices: 649111--649230 Score: 96
Period size: 24 Copynumber: 5.0 Consensus size: 25
649101 TAAGAAAAGA
*
649111 ATTAAAAT-TAAAAAGTTATTTAAAT
1 ATTAAAATATAAAAA-TTATTAAAAT
649136 -TTAAAATATAAAAATTATTAAAAT
1 ATTAAAATATAAAAATTATTAAAAT
*
649160 ATT-AAATATAAAAGA-TACT-AAAT
1 ATTAAAATATAAAA-ATTATTAAAAT
*
649183 A-TAAAA-A-ATAAATTATTAAAA-
1 ATTAAAATATAAAAATTATTAAAAT
*
649204 ATAAAAATACTAAAAATATTATTAAAA
1 ATTAAAATA-T-AAAA-ATTATTAAAA
649231 CTTTTATAGT
Statistics
Matches: 77, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
20 1 0.01
21 7 0.09
22 9 0.12
23 9 0.12
24 29 0.38
25 9 0.12
26 3 0.04
27 10 0.13
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
ATTAAAATATAAAAATTATTAAAAT
Found at i:649166 original size:7 final size:8
Alignment explanation
Indices: 649127--649224 Score: 55
Period size: 7 Copynumber: 12.6 Consensus size: 8
649117 ATTAAAAAGT
*
649127 TATTTAAA
1 TATTAAAA
649135 T-TTAAAA
1 TATTAAAA
*
649142 TATAAAAA
1 TATTAAAA
649150 TTATTAAAA
1 -TATTAAAA
649159 TATT-AAA
1 TATTAAAA
*
649166 TATAAAAGA
1 TATTAAA-A
*
649175 TACT-AAA
1 TATTAAAA
649182 TA-TAAAA
1 TATTAAAA
* *
649189 -AATAAAT
1 TATTAAAA
649196 TATTAAAA
1 TATTAAAA
*
649204 -ATAAAAA
1 TATTAAAA
*
649211 TACTAAAAA
1 TA-TTAAAA
649220 TATTA
1 TATTA
649225 TTAAAACTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
6 2 0.03
7 28 0.40
8 22 0.31
9 18 0.26
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (8 bp):
TATTAAAA
Found at i:649211 original size:16 final size:15
Alignment explanation
Indices: 649138--649222 Score: 68
Period size: 15 Copynumber: 5.5 Consensus size: 15
649128 ATTTAAATTT
*
649138 AAAATATAAAAATTA
1 AAAATATAAATATTA
649153 TTAAAATATTAAATA-TA
1 --AAAATA-TAAATATTA
649170 AAAGATACTAAATA-TA
1 AAA-ATA-TAAATATTA
649186 AAAA-ATAAATTATTA
1 AAAATATAAA-TATTA
* *
649201 AAAATAAAAATACTA
1 AAAATATAAATATTA
649216 AAAATAT
1 AAAATAT
649223 TATTAAAACT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
13 4 0.07
14 3 0.05
15 20 0.34
16 18 0.31
17 8 0.14
18 5 0.09
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (15 bp):
AAAATATAAATATTA
Found at i:653847 original size:31 final size:31
Alignment explanation
Indices: 653806--653876 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
653796 AAAACATAAC
*
653806 ATATGATCACTTTCGTTTTTATTTAATTAAG
1 ATATGGTCACTTTCGTTTTTATTTAATTAAG
653837 ATATGGTCACTTTCGTTTTTATTTAATTAAG
1 ATATGGTCACTTTCGTTTTTATTTAATTAAG
*
653868 ATGTGGTCA
1 ATATGGTCA
653877 TCCCGAGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (31 bp):
ATATGGTCACTTTCGTTTTTATTTAATTAAG
Found at i:654799 original size:20 final size:19
Alignment explanation
Indices: 654755--654801 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
654745 TAAATTAGAA
654755 TTAAATAATTTTATAATAT
1 TTAAATAATTTTATAATAT
*
654774 TATAAATATTTATTATTAA-AT
1 T-TAAATAATT-TTA-TAATAT
654795 TTAAATA
1 TTAAATA
654802 GAAACTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 14 0.58
21 6 0.25
22 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATAATTTTATAATAT
Found at i:655375 original size:31 final size:31
Alignment explanation
Indices: 655330--655405 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
655320 GTAACTCGAG
*
655330 GTGAGCATATCTTAATTAAATAAAAACAAAA
1 GTGATCATATCTTAATTAAATAAAAACAAAA
*
655361 GTGATCGTATCTTAATTAAATAAAAACAAAA
1 GTGATCATATCTTAATTAAATAAAAACAAAA
655392 GTGATCATATCTTA
1 GTGATCATATCTTA
655406 TGTTTTTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (31 bp):
GTGATCATATCTTAATTAAATAAAAACAAAA
Found at i:663738 original size:42 final size:41
Alignment explanation
Indices: 663666--663773 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
663656 ACAATTTAAG
* * **
663666 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAATAAGCCTTTAGAGCAAAATGAT-AAA
* ** *
663708 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAAATGATAAG
1 TCCTTCGGGCCATCAATAAGCCTTTAGAGCAAAATGATAAA
*
663749 TCCTTCGGGCCATCCATAAGACCTT
1 TCCTTCGGGCCATCAATAAG-CCTT
663774 CGGGTAGGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 19 0.35
42 35 0.65
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (41 bp):
TCCTTCGGGCCATCAATAAGCCTTTAGAGCAAAATGATAAA
Found at i:664007 original size:42 final size:42
Alignment explanation
Indices: 663876--663996 Score: 163
Period size: 42 Copynumber: 2.9 Consensus size: 42
663866 TTTCGCACTT
* * * *
663876 AGTAAGTCTTTCGAGTATAATGCTTAAGTCCTTCGGGCCATC
1 AGTAAGTTTTTCGAGCATGATGATTAAGTCCTTCGGGCCATC
* *
663918 AGTAA-TTCTTTCGAGCATGACGATGAAGTCCTTCGGGCCATC
1 AGTAAGTT-TTTCGAGCATGATGATTAAGTCCTTCGGGCCATC
*
663960 AGTAAGTTTTTCGAGCATGATGATTAAATCCTTCGGG
1 AGTAAGTTTTTCGAGCATGATGATTAAGTCCTTCGGG
663997 TAATTTGTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 65 0.96
43 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (42 bp):
AGTAAGTTTTTCGAGCATGATGATTAAGTCCTTCGGGCCATC
Found at i:664104 original size:42 final size:40
Alignment explanation
Indices: 664041--664126 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 40
664031 AAATCCATCA
* *
664041 GTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCGAGCAAGATGAT-AAATCATTCGGG-CATTT
*
664083 GTAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCATTT
1 GTAAGTCTTTCGAGCAAGATGATAAATCATTCGGGCATTT
664123 -TAAG
1 GTAAG
664127 CCTTCTCGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
39 4 0.10
40 5 0.12
41 10 0.24
42 22 0.54
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (40 bp):
GTAAGTCTTTCGAGCAAGATGATAAATCATTCGGGCATTT
Found at i:664557 original size:53 final size:53
Alignment explanation
Indices: 664494--664747 Score: 386
Period size: 53 Copynumber: 4.8 Consensus size: 53
664484 ATCACACCAA
*
664494 AAGATTGTTCGAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
*
664547 AAGATTGTTCGAGTTTTACT-CCTGAAGCAA-AGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* *
664598 AAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGTGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * *
664651 AAGATTATTCGAGTTCTACCCCCTAAAGAAAGAGGGAGCGAACCCGTAAGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
664704 AAGATTATTCGAGTTCTACTACCTGAAGCAATAGGGAGCGAACC
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACC
664748 GTTTTCGAGT
Statistics
Matches: 182, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
51 40 0.22
52 18 0.10
53 124 0.68
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:666529 original size:6 final size:7
Alignment explanation
Indices: 666509--666534 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
666499 TTAATATGCA
666509 TAATTTT
1 TAATTTT
666516 TAATTTT
1 TAATTTT
666523 TAATTTT
1 TAATTTT
666530 TAATT
1 TAATT
666535 AAATATACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TAATTTT
Found at i:670697 original size:40 final size:41
Alignment explanation
Indices: 670653--670753 Score: 116
Period size: 41 Copynumber: 2.5 Consensus size: 41
670643 AAATACTGAC
*
670653 CCAACTCCTTATGTGATGGAT-AACCTATGGT-GACGTTGAT
1 CCAACTCCTTATGTGATGGATGAACC-AAGGTCGACGTTGAT
* * * ** *
670693 CCAACTCTTTATGTGATTGATGAGCCAAGGTCGGTGTTGTT
1 CCAACTCCTTATGTGATGGATGAACCAAGGTCGACGTTGAT
670734 CCAACTCCTTATGTGATGGA
1 CCAACTCCTTATGTGATGGA
670754 ATCAAGAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
40 23 0.46
41 27 0.54
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (41 bp):
CCAACTCCTTATGTGATGGATGAACCAAGGTCGACGTTGAT
Found at i:671825 original size:33 final size:35
Alignment explanation
Indices: 671788--671865 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 35
671778 TTGAACCCTC
671788 CTTTTCATTTTCACTTTTTTTC-CTTA-TTTTTTT
1 CTTTTCATTTTCACTTTTTTTCTCTTAGTTTTTTT
* ** *
671821 CTTTTTCA-TCTCTTTTTTTTTCTTTTAGTTTTTTT
1 C-TTTTCATTTTCACTTTTTTTCTCTTAGTTTTTTT
671856 -TTTTCATTTT
1 CTTTTCATTTT
671866 TTCTAAGCGT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
33 18 0.50
34 11 0.31
35 7 0.19
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (35 bp):
CTTTTCATTTTCACTTTTTTTCTCTTAGTTTTTTT
Found at i:674947 original size:14 final size:14
Alignment explanation
Indices: 674925--674957 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
674915 GTGAACTATG
*
674925 TGTGTATGTGTATA
1 TGTGAATGTGTATA
674939 TGTGAATGTGTATA
1 TGTGAATGTGTATA
674953 TGTGA
1 TGTGA
674958 TACAAGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.45
Consensus pattern (14 bp):
TGTGAATGTGTATA
Found at i:675484 original size:21 final size:20
Alignment explanation
Indices: 675447--675485 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
675437 TATTGTTTGA
*
675447 TTAAATGAATCATATATGGT
1 TTAAATGAATAATATATGGT
675467 TTAAATGAATGAATATATG
1 TTAAATGAAT-AATATATG
675486 AGTATATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (20 bp):
TTAAATGAATAATATATGGT
Found at i:677055 original size:14 final size:14
Alignment explanation
Indices: 677036--677066 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
677026 TCGATAATAT
677036 GTTCATTTATGGTC
1 GTTCATTTATGGTC
*
677050 GTTCATTTATGTTC
1 GTTCATTTATGGTC
677064 GTT
1 GTT
677067 TACTTTCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (14 bp):
GTTCATTTATGGTC
Found at i:677061 original size:24 final size:24
Alignment explanation
Indices: 677033--677086 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
677023 CGTTCGATAA
677033 TATGTTCATTTA-TGGTCGTTCATT
1 TATGTTCATTTACT-GTCGTTCATT
* * *
677057 TATGTTCGTTTACTTTCGTTCGTT
1 TATGTTCATTTACTGTCGTTCATT
677081 TATGTT
1 TATGTT
677087 TAGCTCAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (24 bp):
TATGTTCATTTACTGTCGTTCATT
Found at i:677322 original size:10 final size:10
Alignment explanation
Indices: 677300--677347 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
677290 TTTTGTTTTA
*
677300 TTCATTTATG
1 TTCATTTACG
*
677310 TTCGTTTACG
1 TTCATTTACG
*
677320 TTCATTTATG
1 TTCATTTACG
677330 TTCATTTACG
1 TTCATTTACG
*
677340 TCCATTTA
1 TTCATTTA
677348 TTGTGTTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (10 bp):
TTCATTTACG
Found at i:677325 original size:20 final size:20
Alignment explanation
Indices: 677300--677348 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
677290 TTTTGTTTTA
*
677300 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCATTTACG
677320 TTCATTTATGTTCATTTACG
1 TTCATTTATGTTCATTTACG
*
677340 TCCATTTAT
1 TTCATTTAT
677349 TGTGTTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.55
Consensus pattern (20 bp):
TTCATTTATGTTCATTTACG
Found at i:677364 original size:33 final size:33
Alignment explanation
Indices: 677324--677393 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
677314 TTTACGTTCA
*
677324 TTTATGTTCATTTACGTCCATTTA-TTGTGTTTG
1 TTTATGTTCA-TTACGTCCATTCATTTGTGTTTG
* *
677357 TTTATGTTCATTACGTTCGTTCATTTGTGTTTG
1 TTTATGTTCATTACGTCCATTCATTTGTGTTTG
677390 TTTA
1 TTTA
677394 CATCCGTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 10 0.30
33 23 0.70
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (33 bp):
TTTATGTTCATTACGTCCATTCATTTGTGTTTG
Found at i:680965 original size:26 final size:26
Alignment explanation
Indices: 680931--680988 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
680921 TGTATTTATA
*
680931 ATTTGATGAATGGTAGAAATATAAAT
1 ATTTAATGAATGGTAGAAATATAAAT
*
680957 ATTTAATGAATGGTATAAATATAAAT
1 ATTTAATGAATGGTAGAAATATAAAT
680983 ATTTAA
1 ATTTAA
680989 AGGTTAACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (26 bp):
ATTTAATGAATGGTAGAAATATAAAT
Found at i:681098 original size:14 final size:15
Alignment explanation
Indices: 681051--681100 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
681041 AATTGATTTT
**
681051 TTAAAATAAAATATT
1 TTAAAATAAAATACA
*
681066 TTAAATTAAAATACA
1 TTAAAATAAAATACA
681081 --AAAATAAAATA-A
1 TTAAAATAAAATACA
681093 TTAAAATA
1 TTAAAATA
681101 TTTTTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 1 0.03
13 10 0.34
14 6 0.21
15 12 0.41
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAAATAAAATACA
Found at i:694832 original size:13 final size:13
Alignment explanation
Indices: 694811--694844 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
694801 GGGCATCTTA
694811 ATTTATAATAGAG
1 ATTTATAATAGAG
*
694824 ATTTCTAATAGAG
1 ATTTATAATAGAG
694837 ATGTTATA
1 AT-TTATA
694845 TAATTAGGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (13 bp):
ATTTATAATAGAG
Found at i:699792 original size:16 final size:16
Alignment explanation
Indices: 699773--699824 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
699763 ATAACTGATA
699773 AAAATTAAACTTTGTC
1 AAAATTAAACTTTGTC
* ** *
699789 AAAACT-AGTTTTGATA
1 AAAATTAAACTTTG-TC
699805 AAAATTAAACTTTGTC
1 AAAATTAAACTTTGTC
699821 AAAA
1 AAAA
699825 CTAGTGATCA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 5 0.19
16 16 0.62
17 5 0.19
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.35
Consensus pattern (16 bp):
AAAATTAAACTTTGTC
Found at i:699804 original size:32 final size:32
Alignment explanation
Indices: 699768--699829 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
699758 AAAACATAAC
699768 TGATAAAAATTAAACTTTGTCAAAACTAGTTT
1 TGATAAAAATTAAACTTTGTCAAAACTAGTTT
699800 TGATAAAAATTAAACTTTGTCAAAACTAGT
1 TGATAAAAATTAAACTTTGTCAAAACTAGT
699830 GATCAAAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (32 bp):
TGATAAAAATTAAACTTTGTCAAAACTAGTTT
Found at i:699843 original size:29 final size:30
Alignment explanation
Indices: 699768--699843 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 30
699758 AAAACATAAC
**
699768 TGATAAAAATTAAACTTTGTCAAAACTAGTTT
1 TGATAAAAACGAAACTTTGTCAAAACTAG--T
**
699800 TGATAAAAATTAAACTTTGTCAAAACTAG-
1 TGATAAAAACGAAACTTTGTCAAAACTAGT
*
699829 TGATCAAAACGAAAC
1 TGATAAAAACGAAAC
699844 AAATCAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
29 12 0.29
32 29 0.71
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (30 bp):
TGATAAAAACGAAACTTTGTCAAAACTAGT
Found at i:702317 original size:20 final size:20
Alignment explanation
Indices: 702292--702332 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
702282 AGTATTTATT
702292 TTTTAAATATATCTT-TTTTA
1 TTTTAAA-ATATCTTATTTTA
*
702312 TTTTAAAATATTTTATTTTA
1 TTTTAAAATATCTTATTTTA
702332 T
1 T
702333 ATTAGTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTAAAATATCTTATTTTA
Found at i:702717 original size:30 final size:30
Alignment explanation
Indices: 702683--702779 Score: 115
Period size: 30 Copynumber: 3.3 Consensus size: 30
702673 ACCATCCTAA
* * *
702683 TTTCATATTAGTTCTTAAACTACATCAGAT
1 TTTCATATTAGTACTTAAACTATATCCGAT
*
702713 TTTCATATTAGTACTTATACTATATCCGA-
1 TTTCATATTAGTACTTAAACTATATCCGAT
* * *
702742 TTTCGTATTAGTGCTTGAACTATATCCGAT
1 TTTCATATTAGTACTTAAACTATATCCGAT
*
702772 TTCCATAT
1 TTTCATAT
702780 GGCATGTGTG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 25 0.45
30 31 0.55
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (30 bp):
TTTCATATTAGTACTTAAACTATATCCGAT
Found at i:702763 original size:29 final size:28
Alignment explanation
Indices: 702682--702779 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 28
702672 AACCATCCTA
* * *
702682 ATTTCATATTAGTTCTTAAACTACATCAG
1 ATTTCATATTAGTACTT-AACTATATCCG
702711 ATTTTCATATTAGTACTTATACTATATCCG
1 A-TTTCATATTAGTACTTA-ACTATATCCG
* *
702741 ATTTCGTATTAGTGCTTGAACTATATCCG
1 ATTTCATATTAGTACTT-AACTATATCCG
702770 ATTTCCATAT
1 ATTT-CATAT
702780 GGCATGTGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
29 30 0.51
30 29 0.49
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (28 bp):
ATTTCATATTAGTACTTAACTATATCCG
Found at i:705803 original size:2 final size:2
Alignment explanation
Indices: 705796--705821 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
705786 AGATATTACA
705796 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
705822 TCAAAGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:706239 original size:14 final size:14
Alignment explanation
Indices: 706220--706274 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
706210 CGTTCGTGAA
706220 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
706234 CGTTCGGTT-TGTT
1 CGTTCGGTTATGTT
706247 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
706257 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
706271 CGTT
1 CGTT
706275 TATGTTCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.06
10 6 0.17
11 1 0.03
12 1 0.03
13 6 0.17
14 20 0.56
ACGTcount: A:0.07, C:0.15, G:0.25, T:0.53
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:706253 original size:23 final size:24
Alignment explanation
Indices: 706221--706293 Score: 105
Period size: 23 Copynumber: 3.1 Consensus size: 24
706211 GTTCGTGAAC
* *
706221 GTTCGGTTATGTTCGTTCGGTT-T
1 GTTCGTTTATGTTCGTTCGATTAT
706244 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
706268 GTTCGTTTATGTTCATTC-ATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
706291 GTT
1 GTT
706294 TAACCCATCT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 28 0.61
24 18 0.39
ACGTcount: A:0.11, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:707026 original size:10 final size:10
Alignment explanation
Indices: 707011--707085 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
707001 GGGTCTCCAA
707011 CGTTTATGTT
1 CGTTTATGTT
707021 CGTTTATGTT
1 CGTTTATGTT
707031 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
707042 ATGTTCGTGTT
1 -CGTTTATGTT
707053 CGTTTATGTT
1 CGTTTATGTT
707063 CG----TGTT
1 CGTTTATGTT
707069 CGTTTATGTT
1 CGTTTATGTT
707079 CGTTTAT
1 CGTTTAT
707086 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:707042 original size:16 final size:16
Alignment explanation
Indices: 707017--707081 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
707007 CCAACGTTTA
707017 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
707033 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
707049 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
707065 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
707081 T
1 T
707082 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:707168 original size:15 final size:16
Alignment explanation
Indices: 707148--707179 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
707138 AAAAAAATTT
707148 TGTTCGTTTA-GTTCG
1 TGTTCGTTTATGTTCG
707163 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
707179 T
1 T
707180 CTATTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:707425 original size:102 final size:102
Alignment explanation
Indices: 707249--707454 Score: 394
Period size: 102 Copynumber: 2.0 Consensus size: 102
707239 CAGGCCTATC
* *
707249 AATGGTTAAACGAATTGTTGTTGTTTTTGAGGTCACGAGTTCAAGTACTAGCGATTGCAGTAGGG
1 AATGGTTAAACGAATTGTTGTTGTTTTTGAGGTCACGAGTTCAAGTACCAGCGATTGCAGTAGGA
707314 TGATTAAGATTTTATTATCAAATGGTTGAGAGTATTT
66 TGATTAAGATTTTATTATCAAATGGTTGAGAGTATTT
707351 AATGGTTAAACGAATTGTTGTTGTTTTTGAGGTCACGAGTTCAAGTACCAGCGATTGCAGTAGGA
1 AATGGTTAAACGAATTGTTGTTGTTTTTGAGGTCACGAGTTCAAGTACCAGCGATTGCAGTAGGA
707416 TGATTAAGATTTTATTATCAAATGGTTGAGAGTATTT
66 TGATTAAGATTTTATTATCAAATGGTTGAGAGTATTT
707453 AA
1 AA
707455 AACATATGCT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.37
Consensus pattern (102 bp):
AATGGTTAAACGAATTGTTGTTGTTTTTGAGGTCACGAGTTCAAGTACCAGCGATTGCAGTAGGA
TGATTAAGATTTTATTATCAAATGGTTGAGAGTATTT
Found at i:708770 original size:35 final size:36
Alignment explanation
Indices: 708652--708793 Score: 223
Period size: 36 Copynumber: 4.0 Consensus size: 36
708642 AAATATGAAC
*
708652 ACTTGAATCGAAAGTGTCGATGCCTCATTCCGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
* * *
708688 ATTTGAATCGAAAGTGCCGATGCTTCTTTCCGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
708724 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTC-
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
* *
708759 ACTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTC
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTC
708794 TTCTTGTTCA
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 33 0.34
36 64 0.66
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (36 bp):
ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
Found at i:714150 original size:3 final size:3
Alignment explanation
Indices: 714142--714235 Score: 170
Period size: 3 Copynumber: 31.3 Consensus size: 3
714132 CATGAAATTG
* *
714142 ATA ATA ATA ATA ATA ATA ATA AGA ATA ATA ATA ATA ATA ATA AGA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
714190 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
714236 AAGGAGTCCA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:714313 original size:4 final size:4
Alignment explanation
Indices: 714304--714342 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
714294 TGCTATTCTC
714304 ATTA ATTA ATTA ATTA ATTA ATTA ATT- ATTA ATATA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT-TA ATT
714343 TCTACTTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
4 26 0.79
5 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
ATTA
Found at i:715483 original size:3 final size:3
Alignment explanation
Indices: 715475--715501 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
715465 TTTTTGGAAC
715475 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
715502 CTTAATATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:719043 original size:2 final size:2
Alignment explanation
Indices: 719036--719067 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
719026 CTTTTACCCT
719036 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
719068 ACTAGAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:721017 original size:23 final size:23
Alignment explanation
Indices: 720991--721034 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
720981 CTGTCATAAC
*
720991 TATTCTTTTAAAAAATAATTAAA
1 TATTATTTTAAAAAATAATTAAA
721014 TATTATTTTAAAAAATAATTA
1 TATTATTTTAAAAAATAATTA
721035 TGATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATTTTAAAAAATAATTAAA
Found at i:741684 original size:10 final size:10
Alignment explanation
Indices: 741669--741693 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
741659 GAAGAACTTC
741669 CTTCCTTCAG
1 CTTCCTTCAG
741679 CTTCCTTCAG
1 CTTCCTTCAG
741689 CTTCC
1 CTTCC
741694 CTTTGGAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.44, G:0.08, T:0.40
Consensus pattern (10 bp):
CTTCCTTCAG
Found at i:742477 original size:4 final size:4
Alignment explanation
Indices: 742468--742497 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
742458 ACACACAGAT
742468 ATGG ATGG ATGG ATGG ATGG ATGG ATGG AT
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG AT
742498 ATGAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.47, T:0.27
Consensus pattern (4 bp):
ATGG
Found at i:759146 original size:14 final size:14
Alignment explanation
Indices: 759126--759167 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
759116 TTTAAATGAT
759126 AAACGAACACAAAC
1 AAACGAACACAAAC
* *
759140 GAACGAACATAAAC
1 AAACGAACACAAAC
*
759154 AAAC-AATACAAAC
1 AAACGAACACAAAC
759167 A
1 A
759168 CAAAAAAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.64, C:0.24, G:0.07, T:0.05
Consensus pattern (14 bp):
AAACGAACACAAAC
Found at i:761468 original size:12 final size:12
Alignment explanation
Indices: 761445--761478 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
761435 CCAAACCCTA
761445 TAAGAGAAAAAAT
1 TAAGA-AAAAAAT
761458 TAAGAAAAAAAT
1 TAAGAAAAAAAT
761470 TAAGAAAAA
1 TAAGAAAAA
761479 GATGCATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (12 bp):
TAAGAAAAAAAT
Found at i:762123 original size:13 final size:13
Alignment explanation
Indices: 762105--762129 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
762095 TCATATGGTG
762105 TCTTTTTTTTCTT
1 TCTTTTTTTTCTT
762118 TCTTTTTTTTCT
1 TCTTTTTTTTCT
762130 GAGGACCTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TCTTTTTTTTCTT
Found at i:763000 original size:72 final size:72
Alignment explanation
Indices: 762917--763061 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
762907 AACAATAAAC
762917 CAAAATTTAATTTTGGTTTATTCCACCAAAAATAATTTAGTTAGAAACTAGTAAAAAATTTGTTA
1 CAAAATTTAATTTTGGTTTATTCCACCAAAAATAATTTAGTTAGAAACTAGTAAAAAATTTGTTA
762982 CTTTCAA
66 CTTTCAA
*
762989 CAAAATTTAATTTTGGTTTATTCCACCAAAAATAATTTAGTTAGAAACTAGTAACAAATTTGTTA
1 CAAAATTTAATTTTGGTTTATTCCACCAAAAATAATTTAGTTAGAAACTAGTAAAAAATTTGTTA
763054 CTTTCAA
66 CTTTCAA
763061 C
1 C
763062 GATTTCTATT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (72 bp):
CAAAATTTAATTTTGGTTTATTCCACCAAAAATAATTTAGTTAGAAACTAGTAAAAAATTTGTTA
CTTTCAA
Found at i:772290 original size:139 final size:139
Alignment explanation
Indices: 772115--772395 Score: 517
Period size: 139 Copynumber: 2.0 Consensus size: 139
772105 CCGGCTGAAA
*
772115 GATATGCATTACCTCATACATGCTAAAATCATATAGAATATTATAGAACAAAATTAACTTTAACT
1 GATATGCATTACCTCATACATGCTAAAATCATATAGAATATTACAGAACAAAATTAACTTTAACT
* *
772180 CCTACAGCTTTTTTTATTGTCTTTGAGAAAACCCTGTAAGGAGATCAAGAACAAAAAGGTGGAAG
66 CCTACAGCTTTTTTTATTGCCTTTGAGAAAACCATGTAAGGAGATCAAGAACAAAAAGGTGGAAG
772245 TGACCCTAT
131 TGACCCTAT
*
772254 GATATGCATTTCCTCATACATGCTAAAATCATATAGAATATTACAGAACAAAATTAACTTTAACT
1 GATATGCATTACCTCATACATGCTAAAATCATATAGAATATTACAGAACAAAATTAACTTTAACT
*
772319 CCTACAGCTTTTTTTATTGCCTTTGAGAAAACCATGTAAGGAGATCAAGAACAAAAAGGTGGAAT
66 CCTACAGCTTTTTTTATTGCCTTTGAGAAAACCATGTAAGGAGATCAAGAACAAAAAGGTGGAAG
772384 TGACCCTAT
131 TGACCCTAT
772393 GAT
1 GAT
772396 GATAGTGACC
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 137 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (139 bp):
GATATGCATTACCTCATACATGCTAAAATCATATAGAATATTACAGAACAAAATTAACTTTAACT
CCTACAGCTTTTTTTATTGCCTTTGAGAAAACCATGTAAGGAGATCAAGAACAAAAAGGTGGAAG
TGACCCTAT
Found at i:772853 original size:30 final size:30
Alignment explanation
Indices: 772817--772875 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
772807 GAGGTATGAT
772817 ACATGACACACAACCCTTTGCAACCCTTTA
1 ACATGACACACAACCCTTTGCAACCCTTTA
* *
772847 ACATGACACACAACCCTTTGTAACTCTTT
1 ACATGACACACAACCCTTTGCAACCCTTT
772876 TAAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.34, G:0.07, T:0.27
Consensus pattern (30 bp):
ACATGACACACAACCCTTTGCAACCCTTTA
Found at i:781635 original size:29 final size:29
Alignment explanation
Indices: 781592--781674 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
781582 CTCACCTAAC
781592 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
781622 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
781651 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
781675 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:786397 original size:29 final size:29
Alignment explanation
Indices: 786354--786436 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
786344 CTCACCTAAC
786354 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
786384 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
786413 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
786437 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:787286 original size:13 final size:13
Alignment explanation
Indices: 787268--787303 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
787258 GAATTCCTTT
787268 TAACTAACAATAA
1 TAACTAACAATAA
787281 TAACTAACAATAA
1 TAACTAACAATAA
787294 TAACTAACAA
1 TAACTAACAA
787304 ACTCATATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.61, C:0.17, G:0.00, T:0.22
Consensus pattern (13 bp):
TAACTAACAATAA
Found at i:788218 original size:10 final size:10
Alignment explanation
Indices: 788203--788274 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
788193 TTTAATAAAT
788203 AACGAACATA
1 AACGAACATA
788213 AACGAAC---
1 AACGAACATA
788220 -ACGAACATA
1 AACGAACATA
**
788229 AACGAACACG
1 AACGAACATA
*
788239 AAC-ATAAATGA
1 AACGA-ACAT-A
788250 ACACGAACATA
1 A-ACGAACATA
788261 AACGAACATA
1 AACGAACATA
788271 AACG
1 AACG
788275 TTGGAGACCC
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 32 0.67
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (10 bp):
AACGAACATA
Found at i:788225 original size:16 final size:16
Alignment explanation
Indices: 788204--788268 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
788194 TTAATAAATA
788204 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
788220 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
788236 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
788252 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
788268 A
1 A
788269 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:789038 original size:14 final size:14
Alignment explanation
Indices: 789021--789076 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
789011 AATGAACATA
789021 AACGAACATAATCG
1 AACGAACATAATCG
789035 AACGAACAT-A---
1 AACGAACATAATCG
* *
789045 AACAAACATAACCG
1 AACGAACATAATCG
789059 AACGAACATAATCG
1 AACGAACATAATCG
789073 AACG
1 AACG
789077 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:789041 original size:24 final size:24
Alignment explanation
Indices: 789001--789075 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
788991 GATTGAGTTA
*
789001 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
789025 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
789049 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
789073 AAC
1 AAC
789076 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:792151 original size:68 final size:68
Alignment explanation
Indices: 792018--792175 Score: 244
Period size: 68 Copynumber: 2.2 Consensus size: 68
792008 TTTAAGGTTT
*
792018 GAGATCCCTGTGCATTAAATCATGAAGGGGTTTTTAATGAAACCTTCAATTCTTATAAAAAAAAA
1 GAGATCCCTGTGCATTAAATCATGAAGGGGTTTTTAATGAAACCTTAAATTCTTATAAAAAAAAA
792083 AAA
66 AAA
* *
792086 GAGATCCCTGTGCATTAAATCATGAAGGGTTTTTTTAATGAAATCTTAAATTCTTATATATAAAA
1 GAGATCCCTGTGCATTAAATCATGAAGGG-GTTTTTAATGAAACCTTAAATTC-T-TATA-AAAA
792151 AAAAGAAA
62 AAAA-AAA
792159 GAGATCCCTGTGCATTA
1 GAGATCCCTGTGCATTA
792176 TACCATTTGC
Statistics
Matches: 82, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
68 29 0.35
69 20 0.24
70 1 0.01
71 4 0.05
72 8 0.10
73 20 0.24
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (68 bp):
GAGATCCCTGTGCATTAAATCATGAAGGGGTTTTTAATGAAACCTTAAATTCTTATAAAAAAAAA
AAA
Found at i:793333 original size:14 final size:13
Alignment explanation
Indices: 793305--793340 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
793295 TATTTTTTGT
793305 GTTTGTGTTGTTC
1 GTTTGTGTTGTTC
*
793318 GTTTATGTTCGTTC
1 GTTTGTGTT-GTTC
793332 GTTTGTGTT
1 GTTTGTGTT
793341 TGTTTACGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.03, C:0.08, G:0.28, T:0.61
Consensus pattern (13 bp):
GTTTGTGTTGTTC
Found at i:793357 original size:34 final size:33
Alignment explanation
Indices: 793300--793364 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
793290 AAGTTTATTT
*
793300 TTTGTGTTTGTGTTGTTCGTTTATGTTCGTTCG
1 TTTGTGTTTGTGTTGTTCGTTTATATTCGTTCG
793333 TTTGTGTTTGT-TTACGTTCGTTTATATTCGTT
1 TTTGTGTTTGTGTT--GTTCGTTTATATTCGTT
793365 TATCATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 2 0.07
33 11 0.38
34 16 0.55
ACGTcount: A:0.06, C:0.09, G:0.23, T:0.62
Consensus pattern (33 bp):
TTTGTGTTTGTGTTGTTCGTTTATATTCGTTCG
Found at i:793365 original size:20 final size:20
Alignment explanation
Indices: 793327--793366 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
793317 CGTTTATGTT
* * *
793327 CGTTCGTTTGTGTTTGTTTA
1 CGTTCGTTTATATTCGTTTA
793347 CGTTCGTTTATATTCGTTTA
1 CGTTCGTTTATATTCGTTTA
793367 TCATTTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.57
Consensus pattern (20 bp):
CGTTCGTTTATATTCGTTTA
Found at i:793409 original size:31 final size:31
Alignment explanation
Indices: 793374--793455 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
793364 TTATCATTTA
* *
793374 AATGAACGAATATGAACAAGCTATATTCCTT
1 AATGAACGAACATGAACAAACTATATTCCTT
*
793405 AATGAACGAACATGAACAAACTATATTTCTT
1 AATGAACGAACATGAACAAACTATATTCCTT
*
793436 AATGAACGAACATAAACAAA
1 AATGAACGAACATGAACAAA
793456 AAAAATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (31 bp):
AATGAACGAACATGAACAAACTATATTCCTT
Found at i:794487 original size:76 final size:71
Alignment explanation
Indices: 794362--794591 Score: 223
Period size: 76 Copynumber: 3.1 Consensus size: 71
794352 TAAACTCAAG
* * ** *
794362 TTTAAGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAATTTAAATAGGTTTTAGTGTT
1 TTTAAGATATTATTTTAAATA-T-TATTTT-T-TAAGTATTTTAGTTTAAATAGGTTTTAGTGTT
794427 TTAATTAAGT
62 TTAATTAAGT
* * * *
794437 TTTAAGATATTATTTTTATATTTTATTTTTGTTTTAAGTATTTTAGTTTAAATAGGTTTAAGTAT
1 TTTAAGATATTA-TTTTA-A--ATATTATT-TTTTAAGTATTTTAGTTTAAATAGGTTTTAGTGT
* *
794502 TTTAATTAGGA
61 TTTAATTAAGT
*
794513 TTT-AGAATATTATTTTAAATATTATTTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTT
1 TTTAAG-ATATTATTTTAAATATTATTTTTTAAGTATTTTAGTTTAAATAGGTTTT-AGTGTTTT
794576 AATT-AGT
64 AATTAAGT
794583 ATTTAAGAT
1 -TTTAAGAT
794592 GTTTTTAGGA
Statistics
Matches: 128, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
70 5 0.04
71 38 0.30
72 8 0.06
74 1 0.01
75 18 0.14
76 49 0.38
77 5 0.04
78 3 0.02
79 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (71 bp):
TTTAAGATATTATTTTAAATATTATTTTTTAAGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAA
TTAAGT
Found at i:794576 original size:71 final size:75
Alignment explanation
Indices: 794398--794591 Score: 238
Period size: 71 Copynumber: 2.6 Consensus size: 75
794388 TTTTATCTTT
* * * *
794398 GTATTTTAATTTAAATAGGTTTT-AGTGTTTTAATTAAGTTTTAAGATATTATTTTTATATTTTA
1 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTAAGATATTATTTTTATA-TATA
*
794462 TTTTTGTTTTAA
64 TTATTGTTTTAA
* *
794474 GTATTTTAGTTTAAATAGGTTTAAGTATTTTAATTAGGATTT-AGAATATTA-TTTTA-A-ATAT
1 GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAG-ATATTATTTTTATATATAT
*
794535 TATT-TTTTAG
65 TATTGTTTTAA
*
794545 GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGTATTTAAGAT
1 GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAGAT
794592 GTTTTTAGGA
Statistics
Matches: 104, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
71 46 0.44
72 8 0.08
74 1 0.01
75 11 0.11
76 38 0.37
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (75 bp):
GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAGATATTATTTTTATATATATT
ATTGTTTTAA
Found at i:794582 original size:19 final size:21
Alignment explanation
Indices: 794554--794596 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
794544 GGTATTTTAG
794554 TTTAAATAGT-TTTAAG-TGT
1 TTTAAATAGTATTTAAGATGT
*
794573 TTTAATTAGTATTTAAGATGT
1 TTTAAATAGTATTTAAGATGT
794594 TTT
1 TTT
794597 TAGGAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 6 0.29
21 6 0.29
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (21 bp):
TTTAAATAGTATTTAAGATGT
Found at i:799174 original size:40 final size:39
Alignment explanation
Indices: 799104--799192 Score: 124
Period size: 40 Copynumber: 2.3 Consensus size: 39
799094 TATTTTAGGG
* * *
799104 ACCAAAGATGAAATTCCCATGTGCACAAGTTGGCCACCT
1 ACCAAAGATGAAATTCCAATGTGCACAAGTTAGCCACCA
* *
799143 ACCAAAGATGAATTTTCCAATGTGTACAAGTTAGCCACCA
1 ACCAAAGATGAA-ATTCCAATGTGCACAAGTTAGCCACCA
799183 ACCAAAGATG
1 ACCAAAGATG
799193 TCGACTATGC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 12 0.27
40 32 0.73
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (39 bp):
ACCAAAGATGAAATTCCAATGTGCACAAGTTAGCCACCA
Found at i:802951 original size:2 final size:2
Alignment explanation
Indices: 802944--802969 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
802934 TAATAATTTC
802944 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
802970 CATTAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:810482 original size:21 final size:21
Alignment explanation
Indices: 810458--810497 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
810448 TTGTTTGATG
810458 AAGA-AGAGGAAGAAGAAGACA
1 AAGATAGA-GAAGAAGAAGACA
810479 AAGATAGAGAAGAAGAAGA
1 AAGATAGAGAAGAAGAAGA
810498 AGGTGATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.62, C:0.03, G:0.33, T:0.03
Consensus pattern (21 bp):
AAGATAGAGAAGAAGAAGACA
Found at i:818160 original size:23 final size:23
Alignment explanation
Indices: 818134--818224 Score: 137
Period size: 23 Copynumber: 4.0 Consensus size: 23
818124 GACATTATAT
818134 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* * *
818157 GGCACTTCGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
818180 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* *
818203 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCATTTCTACG
818225 AGCTGTGGTG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:819357 original size:18 final size:17
Alignment explanation
Indices: 819314--819364 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
819304 TATGGAATTG
* *
819314 GATTCCAATTCCTGACC
1 GATTCCAATTCCTCACA
*
819331 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-TCACA
819349 GATTCCAATTCTCTCA
1 GATTCCAATTC-CTCA
819365 AAAACATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 11 0.39
18 16 0.57
19 1 0.04
ACGTcount: A:0.25, C:0.31, G:0.08, T:0.35
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:823005 original size:18 final size:18
Alignment explanation
Indices: 822978--823030 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 18
822968 GCTATGATTG
* *
822978 ATACATACATATATATAT
1 ATACACACATATATACAT
*
822996 ATACACACATGTATAC--
1 ATACACACATATATACAT
*
823012 ATACACACATGTATACAT
1 ATACACACATATATACAT
823030 A
1 A
823031 CACATGCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 16 0.53
18 14 0.47
ACGTcount: A:0.47, C:0.19, G:0.04, T:0.30
Consensus pattern (18 bp):
ATACACACATATATACAT
Found at i:823015 original size:16 final size:16
Alignment explanation
Indices: 822991--823034 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
822981 CATACATATA
*
822991 TATATATACACACATG
1 TATACATACACACATG
823007 TATACATACACACATG
1 TATACATACACACATG
823023 TATACATACACA
1 TATACATACACA
823035 TGCATAACGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.27
Consensus pattern (16 bp):
TATACATACACACATG
Found at i:826238 original size:15 final size:15
Alignment explanation
Indices: 826202--826239 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
826192 ATGACGATTT
826202 CATAAAATTTTAAGA
1 CATAAAATTTTAAGA
*
826217 TATAAAATTTTAAGGA
1 CATAAAATTTTAA-GA
826233 CA-AAAAT
1 CATAAAAT
826240 AGATTGTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (15 bp):
CATAAAATTTTAAGA
Found at i:837514 original size:22 final size:22
Alignment explanation
Indices: 837486--837536 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
837476 TATAACTAAT
837486 AATTTATTTA-AATAAAATATCA
1 AATTTATTTACAATAAAAT-TCA
*
837508 AATTTATTTATCAATAAAATTTA
1 AATTTATTTA-CAATAAAATTCA
837531 AATTTA
1 AATTTA
837537 AACCGAATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 10 0.38
23 8 0.31
24 8 0.31
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTATTTACAATAAAATTCA
Found at i:845136 original size:25 final size:23
Alignment explanation
Indices: 845094--845142 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 23
845084 ATTTTCGAAT
845094 ATTTTAGTTTTTTTTTAAATAAA
1 ATTTTAGTTTTTTTTTAAATAAA
845117 ATTTTGAGTCTTTTTTTTAAATAAA
1 ATTTT-AGT-TTTTTTTTAAATAAA
845142 A
1 A
845143 ATTACCAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.21
24 3 0.12
25 16 0.67
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (23 bp):
ATTTTAGTTTTTTTTTAAATAAA
Done.