Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 108 of 168
Found at i:31845694 original size:34 final size:34
Alignment explanation
Indices: 31845634--31845699 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
31845624 TCCTATAAAT
* *
31845634 AATCCTTATTATAATAAAGTCCAATTAGCATAGA
1 AATCCTTATTATAAAAAAATCCAATTAGCATAGA
*
31845668 AATCCTTA-TACTAAAAAAATCTAATTAGCATA
1 AATCCTTATTA-TAAAAAAATCCAATTAGCATA
31845700 AATTGTAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (34 bp):
AATCCTTATTATAAAAAAATCCAATTAGCATAGA
Found at i:31847156 original size:14 final size:14
Alignment explanation
Indices: 31847137--31847189 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 14
31847127 AGACATTTTA
*
31847137 TTTTTCAAAAGCGC
1 TTTTTCAAAAGCAC
*
31847151 TTTTTCATAA-CAC
1 TTTTTCAAAAGCAC
* *
31847164 TTTTTTAAAAACAC
1 TTTTTCAAAAGCAC
31847178 -TTTTCAAAAGCA
1 TTTTTCAAAAGCA
31847190 ATGCTAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
13 20 0.62
14 12 0.38
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.40
Consensus pattern (14 bp):
TTTTTCAAAAGCAC
Found at i:31848306 original size:63 final size:64
Alignment explanation
Indices: 31848189--31848311 Score: 167
Period size: 63 Copynumber: 1.9 Consensus size: 64
31848179 GCTGTGTGTT
* *
31848189 AGGCTGTGTAACTCACTATTTTGGAATTAGAGTCACACAGGCTAGAAACACAGG-CATGTGTCC
1 AGGCCGTGTAACTCACTATTTTGGAATTAGAGTCACACAGGCCAGAAACACAGGCCATGTGTCC
* ** ** *
31848252 AGGCCGTGTGACTCACTATTTTGGAATTAGAGTCACATGGGCCAGCCACCCAGGCCATGT
1 AGGCCGTGTAACTCACTATTTTGGAATTAGAGTCACACAGGCCAGAAACACAGGCCATGT
31848312 CAATCCACAC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
63 46 0.90
64 5 0.10
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (64 bp):
AGGCCGTGTAACTCACTATTTTGGAATTAGAGTCACACAGGCCAGAAACACAGGCCATGTGTCC
Found at i:31848685 original size:76 final size:76
Alignment explanation
Indices: 31848556--31848704 Score: 271
Period size: 76 Copynumber: 2.0 Consensus size: 76
31848546 TAAGGTATGT
*
31848556 TGTTGACACTATTTTTTGATAAAACGGGGTCAACTTGGGTTTTGAAAAATGAAAACGAAAGTGGG
1 TGTTGACACCATTTTTTGATAAAACGGGGTCAACTTGGGTTTTGAAAAATGAAAACGAAAGTGGG
31848621 AGTCGCCAAGC
66 AGTCGCCAAGC
* *
31848632 TGTTGACACCATTTTTTGATAAAACGGGGTCGACTTGGGTTTTGAAAATTGAAAACGAAAGTGGG
1 TGTTGACACCATTTTTTGATAAAACGGGGTCAACTTGGGTTTTGAAAAATGAAAACGAAAGTGGG
31848697 AGTCGCCA
66 AGTCGCCA
31848705 CCAATCCTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (76 bp):
TGTTGACACCATTTTTTGATAAAACGGGGTCAACTTGGGTTTTGAAAAATGAAAACGAAAGTGGG
AGTCGCCAAGC
Found at i:31849146 original size:109 final size:109
Alignment explanation
Indices: 31848973--31849318 Score: 507
Period size: 116 Copynumber: 3.1 Consensus size: 109
31848963 TGGATTAAGA
* *
31848973 TTTAAGAGGATATTTGGCTATTTGGTCGAACGAG--AAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCAAGCACATTAGGGCACGT
* *
31849036 TTTCTCGAATTTCCAAACGTAAAACATTGCCTTATTGTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
* *
31849080 TTTAAAAGGATATTTGACTATTTGGTCGAACGAGAAAAATCGAAACCTAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCAAGCACATTAGGGCACGT
31849145 TTTCTCGAATTTCCAAACGCAAAACGCAAAACATTGCCTTATTTTGAAATT
66 TTTCTCGAATTT-----C-C-AAACGCAAAACATTGCCTTATTTTGAAATT
* * *
31849196 TTTAAAACGATATTTGGCTATTTGGTCGAATGAGAAAAATCGAAACCAAGCATATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCAAGCACATTAGGGCACGT
* * *
31849261 TTTCTCGAATTTTCAAACGCAAAATATTGCCTTATTTTAAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
31849305 TTTAAAAGGATATT
1 TTTAAAAGGATATT
31849319 AGTATGCATA
Statistics
Matches: 216, Mismatches: 14, Indels: 16
0.88 0.06 0.07
Matches are distributed among these distances:
107 32 0.15
109 81 0.38
110 1 0.00
114 1 0.00
115 1 0.00
116 100 0.46
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (109 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCAAGCACATTAGGGCACGT
TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
Found at i:31849733 original size:2 final size:2
Alignment explanation
Indices: 31849728--31849752 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31849718 TAAAAGTATG
31849728 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
31849753 GAAAATAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31856184 original size:76 final size:76
Alignment explanation
Indices: 31856093--31856254 Score: 315
Period size: 76 Copynumber: 2.1 Consensus size: 76
31856083 CTTCCCCAGT
31856093 GGAGTCGCCAAGCTGTTGACACCATTTTTTGATAAAACGGGGTCGACTTGGGTTTTGAAAAATGA
1 GGAGTCGCCAAGCTGTTGACACCATTTTTTGATAAAACGGGGTCGACTTGGGTTTTGAAAAATGA
31856158 AAACGAAAGTG
66 AAACGAAAGTG
31856169 GGAGTCGCCAAGCTGTTGACACCATTTTTTGATAAAACGGGGTCGACTTGGGTTTTGAAAAATGA
1 GGAGTCGCCAAGCTGTTGACACCATTTTTTGATAAAACGGGGTCGACTTGGGTTTTGAAAAATGA
31856234 AAACGAAAGTG
66 AAACGAAAGTG
*
31856245 GAAGTCGCCA
1 GGAGTCGCCA
31856255 CTAATCCTTT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 85 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.25
Consensus pattern (76 bp):
GGAGTCGCCAAGCTGTTGACACCATTTTTTGATAAAACGGGGTCGACTTGGGTTTTGAAAAATGA
AAACGAAAGTG
Found at i:31856712 original size:109 final size:109
Alignment explanation
Indices: 31856523--31856861 Score: 601
Period size: 109 Copynumber: 3.1 Consensus size: 109
31856513 TGGATTAAGA
* *
31856523 TTTAAGAGGATATTTAGCTATTTGGTCGAACGAG--AAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
31856586 TTTCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAACT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
31856630 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
31856695 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
* *
31856739 TTTAAAAGGATATTTGGTTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACAT
1 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
31856804 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
66 TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
*
31856848 TTTAAAGGGATATT
1 TTTAAAAGGATATT
31856862 AGTATGCGTA
Statistics
Matches: 223, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
107 32 0.14
109 191 0.86
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (109 bp):
TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATT
Found at i:31857470 original size:8 final size:7
Alignment explanation
Indices: 31857459--31857505 Score: 50
Period size: 6 Copynumber: 7.3 Consensus size: 7
31857449 TTTAAAAACT
31857459 ATAAATGA
1 ATAAAT-A
31857467 ATAAATA
1 ATAAATA
31857474 AT-AATA
1 ATAAATA
31857480 AT-AATA
1 ATAAATA
31857486 AT-AATA
1 ATAAATA
31857492 AT-AATA
1 ATAAATA
31857498 AT-AATA
1 ATAAATA
31857504 AT
1 AT
31857506 GGTATAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 30 0.77
7 3 0.08
8 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (7 bp):
ATAAATA
Found at i:31857478 original size:3 final size:3
Alignment explanation
Indices: 31857470--31857505 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
31857460 TAAATGAATA
31857470 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31857506 GGTATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31859483 original size:26 final size:26
Alignment explanation
Indices: 31859451--31859510 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
31859441 TCTTCTATTT
31859451 TGTTATACGATCGTTATGAAAATCTA
1 TGTTATACGATCGTTATGAAAATCTA
*
31859477 TGTTATACGATCGTTATGAAAATCTC
1 TGTTATACGATCGTTATGAAAATCTA
*
31859503 TGTGATAC
1 TGTTATAC
31859511 TCTGATTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (26 bp):
TGTTATACGATCGTTATGAAAATCTA
Found at i:31862952 original size:32 final size:32
Alignment explanation
Indices: 31862892--31862952 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
31862882 TTTTTTAATA
* *
31862892 TTTATATTATATATTAGTATAAATATAAATTT
1 TTTATATTATAAATTAGTATAAACATAAATTT
*
31862924 TTTATGTTATAAATTA-TATAATACATAAA
1 TTTATATTATAAATTAGTATAA-ACATAAA
31862953 AATAACATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (32 bp):
TTTATATTATAAATTAGTATAAACATAAATTT
Found at i:31874650 original size:21 final size:22
Alignment explanation
Indices: 31874615--31874667 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
31874605 TCAAATAAAA
* *
31874615 TAATAATATTTATATTTATTAT
1 TAATAATATTAATATATATTAT
*
31874637 TAAT-ATATTAATATATATTTT
1 TAATAATATTAATATATATTAT
31874658 TCAATAATAT
1 T-AATAATAT
31874668 ATTAAGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 15 0.58
22 7 0.27
23 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAATATTAATATATATTAT
Found at i:31874804 original size:13 final size:15
Alignment explanation
Indices: 31874770--31874806 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
31874760 TGTATATTTA
*
31874770 ATAATATTGAATATT
1 ATAATATTTAATATT
31874785 ATAATATTTAAT-TT
1 ATAATATTTAATATT
31874799 -TAATATTT
1 ATAATATTT
31874807 TAACATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.38
14 2 0.10
15 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
ATAATATTTAATATT
Found at i:31874805 original size:21 final size:19
Alignment explanation
Indices: 31874779--31874822 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
31874769 AATAATATTG
*
31874779 AATATTATAATATTTAATTTT
1 AATATTATAACATTT--TTTT
*
31874800 AATATTTTAACATTTTTTT
1 AATATTATAACATTTTTTT
31874819 AATA
1 AATA
31874823 AAATATCTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
21 13 0.62
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTATAACATTTTTTT
Found at i:31876710 original size:114 final size:114
Alignment explanation
Indices: 31876578--31876950 Score: 457
Period size: 114 Copynumber: 3.3 Consensus size: 114
31876568 CGTTTTTAAA
* *
31876578 AAAACGCCGTAAAAGAACA-TCATTAGTGGCGTTTATTTGTAAGCGCCGCAAAATACCTTAACCA
1 AAAACGCCGCAAAAGAACAGT-ATTAGTGGCGTTTATTTATAAGCGCCGCAAAATACCTTAACCA
* * *
31876642 AAACGCAGCGTTTCGTTTTGAGGTATATTAGAATTCGTGGCGTTTACGAT
65 AAACGCAACGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGAT
* ** * *
31876692 AAAACGCCGCAAAAGAACAGTATTAGCGGCGTATTA-CAAAAAGCGCCGC-AAATATCTTAACCA
1 AAAACGCCGCAAAAGAACAGTATTAGTGGCGT-TTATTTATAAGCGCCGCAAAATACCTTAACCA
* * * ** * *** *
31876755 AAACGCACCGTTTGGTCTTGAGGTAGATTAGTGTTTGTGGCGTTTTTAAA
65 AAACGCAACGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGAT
* * *
31876805 AAAACGCCGTAAAAGAACA-TCGTTAGTGGCGTTTATTTTTAAGCGCCGCAAAATACCTTAACCA
1 AAAACGCCGCAAAAGAACAGT-ATTAGTGGCGTTTATTTATAAGCGCCGCAAAATACCTTAACCA
*
31876869 AAACGCAACGTTTGGTTTTGAGGTATATTAAAATTAGTGGCGTTTACGAT
65 AAACGCAACGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGAT
* *
31876919 AAAACGCCACTAAAGAACAGTATTAGTGGCGT
1 AAAACGCCGCAAAAGAACAGTATTAGTGGCGT
31876951 ATTACAAAAA
Statistics
Matches: 212, Mismatches: 41, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
112 4 0.02
113 88 0.42
114 115 0.54
115 5 0.02
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (114 bp):
AAAACGCCGCAAAAGAACAGTATTAGTGGCGTTTATTTATAAGCGCCGCAAAATACCTTAACCAA
AACGCAACGTTTGGTTTTGAGGTATATTAGAATTAGTGGCGTTTACGAT
Found at i:31876809 original size:113 final size:114
Alignment explanation
Indices: 31876562--31877041 Score: 456
Period size: 113 Copynumber: 4.2 Consensus size: 114
31876552 CCCGAACAAC
* ****
31876562 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGCAAAAGAACATCATTAGTGGCGTTTATCAAAAAGCGCCGC
* * *
31876627 AAAATACCTTAACCAAAACGCAGCGTTTCGTTTTGAGGTATATTAGAAT
66 AAAATACCTTAACCAAAACGCACCGTTTGGTTTTGAGGTAGATTAGAAT
* *** * *
31876676 TCGTGGCGTTTACGATAAAACGCCGCAAAAGAACAGT-ATTAGCGGCGTATTA-CAAAAAGCGCC
1 TAGTGGCGTTTTTAAAAAAACGCCGCAAAAGAACA-TCATTAGTGGCGT-TTATCAAAAAGCGCC
* * **
31876739 GC-AAATATCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAGTGT
64 GCAAAATACCTTAACCAAAACGCACCGTTTGGTTTTGAGGTAGATTAGAAT
* * * ****
31876789 TTGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATCGTTAGTGGCGTTTATTTTTAAGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGCAAAAGAACATCATTAGTGGCGTTTATCAAAAAGCGCCGC
* * *
31876854 AAAATACCTTAACCAAAACGCAACGTTTGGTTTTGAGGTATATTAAAAT
66 AAAATACCTTAACCAAAACGCACCGTTTGGTTTTGAGGTAGATTAGAAT
*** * * *
31876903 TAGTGGCGTTTACGATAAAACGCCACTAAAGAACAGT-ATTAGTGGCGTATTA-CAAAAAGCGCC
1 TAGTGGCGTTTTTAAAAAAACGCCGCAAAAGAACA-TCATTAGTGGCGT-TTATCAAAAAGCGCC
* ** * * **
31876966 AC-AAATATCGGT-ACTAAAACGCACCGTTTGGTGTTGAGG-AGGATTAGTGT
64 GCAAAATA-CCTTAACCAAAACGCACCGTTTGGTTTTGAGGTA-GATTAGAAT
*
31877016 TAGTGGCGCTTATT-AAAAAACGCCGC
1 TAGTGGCG-TTTTTAAAAAAACGCCGC
31877042 CAAATATCGG
Statistics
Matches: 291, Mismatches: 65, Indels: 21
0.77 0.17 0.06
Matches are distributed among these distances:
112 5 0.02
113 140 0.48
114 138 0.47
115 8 0.03
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (114 bp):
TAGTGGCGTTTTTAAAAAAACGCCGCAAAAGAACATCATTAGTGGCGTTTATCAAAAAGCGCCGC
AAAATACCTTAACCAAAACGCACCGTTTGGTTTTGAGGTAGATTAGAAT
Found at i:31876959 original size:227 final size:227
Alignment explanation
Indices: 31876562--31877040 Score: 775
Period size: 227 Copynumber: 2.1 Consensus size: 227
31876552 CCCGAACAAC
31876562 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
* * *
31876627 AAAATACCTTAACCAAAACGCAGCGTTTCGTTTTGAGGTATATTAGAATTCGTGGCGTTTACGAT
66 AAAATACCTTAACCAAAACGCAACGTTTCGTTTTGAGGTATATTAAAATTAGTGGCGTTTACGAT
* * *
31876692 AAAACGCCGCAAAAGAACAGTATTAGCGGCGTATTACAAAAAGCGCCGCAAATATC-TTAACCAA
131 AAAACGCCACAAAAGAACAGTATTAGCGGCGTATTACAAAAAGCGCCACAAATATCGGT-ACCAA
31876756 AACGCACCGTTTGGTCTTGAGGTA-GATTAGTGT
195 AACGCACCGTTTGGTCTTGAGG-AGGATTAGTGT
* * *
31876789 TTGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATCGTTAGTGGCGTTTATTTTTAAGCGCCGC
1 TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
*
31876854 AAAATACCTTAACCAAAACGCAACGTTTGGTTTTGAGGTATATTAAAATTAGTGGCGTTTACGAT
66 AAAATACCTTAACCAAAACGCAACGTTTCGTTTTGAGGTATATTAAAATTAGTGGCGTTTACGAT
* * *
31876919 AAAACGCCACTAAAGAACAGTATTAGTGGCGTATTACAAAAAGCGCCACAAATATCGGTACTAAA
131 AAAACGCCACAAAAGAACAGTATTAGCGGCGTATTACAAAAAGCGCCACAAATATCGGTACCAAA
*
31876984 ACGCACCGTTTGGTGTTGAGGAGGATTAGTGT
196 ACGCACCGTTTGGTCTTGAGGAGGATTAGTGT
*
31877016 TAGTGGCGCTTATT-AAAAAACGCCG
1 TAGTGGCG-TTTTTAAAAAAACGCCG
31877041 CCAAATATCG
Statistics
Matches: 233, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
226 1 0.00
227 227 0.97
228 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (227 bp):
TAGTGGCGTTTTTAAAAAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
AAAATACCTTAACCAAAACGCAACGTTTCGTTTTGAGGTATATTAAAATTAGTGGCGTTTACGAT
AAAACGCCACAAAAGAACAGTATTAGCGGCGTATTACAAAAAGCGCCACAAATATCGGTACCAAA
ACGCACCGTTTGGTCTTGAGGAGGATTAGTGT
Found at i:31879715 original size:23 final size:23
Alignment explanation
Indices: 31879671--31879716 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31879661 GCCCGATTCT
*
31879671 TCGTATTTATAAATTGGGTTTTG
1 TCGTATTTATAAATTGGATTTTG
* * *
31879694 TCGTATTTTTAATTTTGATTTTG
1 TCGTATTTATAAATTGGATTTTG
31879717 CTTTCTTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.04, G:0.17, T:0.59
Consensus pattern (23 bp):
TCGTATTTATAAATTGGATTTTG
Found at i:31879903 original size:44 final size:45
Alignment explanation
Indices: 31879826--31879919 Score: 172
Period size: 44 Copynumber: 2.1 Consensus size: 45
31879816 GCTTCTATTA
31879826 TTGTTCATTACTGTTTTTTTTGAATGGTTTAGGGTGTTAGGAACT
1 TTGTTCATTACTGTTTTTTTTGAATGGTTTAGGGTGTTAGGAACT
31879871 TTGTTCATTACTG-TTTTTTTGAATGGTTTAGGGTGTTAGGAACT
1 TTGTTCATTACTGTTTTTTTTGAATGGTTTAGGGTGTTAGGAACT
*
31879915 GTGTT
1 TTGTT
31879920 TAACTATTGT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 35 0.73
45 13 0.27
ACGTcount: A:0.17, C:0.06, G:0.26, T:0.51
Consensus pattern (45 bp):
TTGTTCATTACTGTTTTTTTTGAATGGTTTAGGGTGTTAGGAACT
Found at i:31879933 original size:44 final size:44
Alignment explanation
Indices: 31879834--31879935 Score: 150
Period size: 44 Copynumber: 2.3 Consensus size: 44
31879824 TATTGTTCAT
* * *
31879834 TACTGTTTTTTTTGAATGGTTTAGGGTGTTAGGAACTTTGTTCAT
1 TACTG-TTTTTTTGAATGGTTTAGGGTGTTAGGAACTGTGTTAAC
31879879 TACTGTTTTTTTGAATGGTTTAGGGTGTTAGGAACTGTGTTTAAC
1 TACTGTTTTTTTGAATGGTTTAGGGTGTTAGGAACTGTG-TTAAC
*
31879924 TATTGTTTTTTT
1 TACTGTTTTTTT
31879936 TCTCCAGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 33 0.63
45 19 0.37
ACGTcount: A:0.18, C:0.06, G:0.24, T:0.53
Consensus pattern (44 bp):
TACTGTTTTTTTGAATGGTTTAGGGTGTTAGGAACTGTGTTAAC
Found at i:31880254 original size:219 final size:218
Alignment explanation
Indices: 31879871--31880271 Score: 628
Period size: 219 Copynumber: 1.8 Consensus size: 218
31879861 GTTAGGAACT
* *
31879871 TTGTTCATTACTGTTTTTTTGAATGGTTTAGGGTGTTAGGAACTGTGTTTAACTATTGTTTTTTT
1 TTGTTCATTACTGTTTTTTTG-ATGGTTTAAGGTGTTAGGAACTGTGTTTAACTATTGTTTTTCT
* * * * *
31879936 TCTCCAGTTTTTGGTCAATCCATTTCATTGCTTTCATTTCATTTTTCTTCATCGTTCTTAAGGTA
65 TCTCCAGATTTTGGTCAATCCATTTCATTGCTTTCATTTCAGTATTCGTCATCGTTCTGAAGGTA
* *
31880001 CAGAACACATGCTTTGTTACTGTTGATTTGTTGAACTCATTTTGTACTGTTTGACACGGTTATTT
130 CAGAACACATGCTTTGTTACTGTTGATGTGTTGAACTCATTTGGTACTGTTTGACACGGTTATTT
31880066 TCAGTCAATTTGGTACTGCTTCTA
195 TCAGTCAATTTGGTACTGCTTCTA
**
31880090 TTGTTCATTACTGTTTTTGTCTG-TGGTTTAATTTGTTAGGAACTGAT-TTTAACT-TGTGTTTT
1 TTGTTCATTACTGTTTTT-T-TGATGGTTTAAGGTGTTAGGAACTG-TGTTTAACTAT-TGTTTT
31880152 TCTTCTCCAGATTTTGGTCAATCCATTTCATTGCTTTCATTTCAGTATTCGTCATCGTTCTGAAG
62 TCTTCTCCAGATTTTGGTCAATCCATTTCATTGCTTTCATTTCAGTATTCGTCATCGTTCTGAAG
*
31880217 GTACAGAACACATGCTTTGTTACTGTTTATGTGTTGAACTCATTTGGTACTGTTT
127 GTACAGAACACATGCTTTGTTACTGTTGATGTGTTGAACTCATTTGGTACTGTTT
31880272 TCAAAGTATG
Statistics
Matches: 166, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
218 1 0.01
219 161 0.97
220 2 0.01
221 2 0.01
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.49
Consensus pattern (218 bp):
TTGTTCATTACTGTTTTTTTGATGGTTTAAGGTGTTAGGAACTGTGTTTAACTATTGTTTTTCTT
CTCCAGATTTTGGTCAATCCATTTCATTGCTTTCATTTCAGTATTCGTCATCGTTCTGAAGGTAC
AGAACACATGCTTTGTTACTGTTGATGTGTTGAACTCATTTGGTACTGTTTGACACGGTTATTTT
CAGTCAATTTGGTACTGCTTCTA
Found at i:31881166 original size:17 final size:17
Alignment explanation
Indices: 31881144--31881193 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
31881134 TTAATATCTA
31881144 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
31881161 TATAAGTTTTCT-AA--
1 TATAAGTTTTCTAAATT
31881175 -ATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
31881191 TAT
1 TAT
31881194 TTGTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.38
14 2 0.07
16 2 0.07
17 14 0.48
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:31881180 original size:13 final size:13
Alignment explanation
Indices: 31881162--31881189 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31881152 TTCTAAATTT
31881162 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
31881175 ATAAGTTTTCTAA
1 ATAAGTTTTCTAA
31881188 AT
1 AT
31881190 TTATTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
ATAAGTTTTCTAA
Found at i:31881220 original size:15 final size:15
Alignment explanation
Indices: 31881185--31881223 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
31881175 ATAAGTTTTC
*
31881185 TAAATTTATTTGTAT
1 TAAATTTATTAGTAT
31881200 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
31881216 TAAATTTA
1 TAAATTTA
31881224 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:31881266 original size:62 final size:61
Alignment explanation
Indices: 31881155--31881303 Score: 165
Period size: 62 Copynumber: 2.4 Consensus size: 61
31881145 ATAAGTTTTC
* *** * * *
31881155 TAAATTTATAAGTTTTCTAAATAAGTTTTCTAAATTTATTTGTATTAAAATTTAT-TAGTAT
1 TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATATATGT-GTAT
** *
31881216 TAAATTTACTTCGTTTTCTAAATAAGTGTTCTAAATTTGGGAGAAATAAAATATATGTGTAT
1 TAAATTTA-TAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATATATGTGTAT
* *
31881278 TAAGTTTATAAGTTTTCTACATAAGT
1 TAAATTTATAAGTTTTCTAAATAAGT
31881304 TACATAATAC
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
61 23 0.32
62 48 0.67
63 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATATATGTGTAT
Found at i:31881454 original size:9 final size:9
Alignment explanation
Indices: 31881440--31881785 Score: 257
Period size: 9 Copynumber: 39.8 Consensus size: 9
31881430 TATGTTATAA
*
31881440 TACATAACC
1 TACATAACT
*
31881449 TACATAAAT
1 TACATAACT
31881458 TA-AGTAACT
1 TACA-TAACT
31881467 TACATAACT
1 TACATAACT
*
31881476 TACATAAAT
1 TACATAACT
31881485 TA-AGTAACT
1 TACA-TAACT
31881494 TACATAACT
1 TACATAACT
*
31881503 TACATAAACC
1 TACAT-AACT
*
31881513 TGCAT-ACAT
1 TACATAAC-T
*
31881522 TAAATAACT
1 TACATAACT
31881531 TACATAACT
1 TACATAACT
*
31881540 TACATAACC
1 TACATAACT
*
31881549 TACATAAAT
1 TACATAACT
31881558 TA-AGTAACT
1 TACA-TAACT
31881567 TACATAACT
1 TACATAACT
* *
31881576 TGCATAAAT
1 TACATAACT
*
31881585 TAAATAACT
1 TACATAACT
31881594 TACATAACT
1 TACATAACT
*
31881603 TACATAACC
1 TACATAACT
*
31881612 TACATAAAT
1 TACATAACT
31881621 TA-AGTAACT
1 TACA-TAACT
*
31881630 TACACAACT
1 TACATAACT
*
31881639 TACATTA--
1 TACATAACT
31881646 TACATAACCT
1 TACATAA-CT
*
31881656 T-CTTAACT
1 TACATAACT
*
31881664 TACATTA-T
1 TACATAACT
*
31881672 T-CACAACT
1 TACATAACT
*
31881680 CACATAA-T
1 TACATAACT
31881688 TA-AT-A-T
1 TACATAACT
*
31881694 TAACACAACT
1 T-ACATAACT
31881704 TACATAA--
1 TACATAACT
*
31881711 TACATTACT
1 TACATAACT
31881720 TACATAACT
1 TACATAACT
*
31881729 TACATTACT
1 TACATAACT
31881738 TACAGT-ACT
1 TACA-TAACT
31881747 TACATAA--
1 TACATAACT
31881754 TACATAA--
1 TACATAACT
31881761 TACATAACT
1 TACATAACT
*
31881770 TACATTACT
1 TACATAACT
31881779 TACATAA
1 TACATAA
31881786 TACATAAAAA
Statistics
Matches: 266, Mismatches: 44, Indels: 54
0.73 0.12 0.15
Matches are distributed among these distances:
6 3 0.01
7 32 0.12
8 16 0.06
9 198 0.74
10 17 0.06
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (9 bp):
TACATAACT
Found at i:31881771 original size:32 final size:33
Alignment explanation
Indices: 31881720--31881792 Score: 112
Period size: 32 Copynumber: 2.2 Consensus size: 33
31881710 ATACATTACT
*
31881720 TACATAACTTACATTACTTACAGTACTTACATAA
1 TACATAAC-TACATAACTTACAGTACTTACATAA
*
31881754 TACATAA-TACATAACTTACATTACTTACATAA
1 TACATAACTACATAACTTACAGTACTTACATAA
31881786 TACATAA
1 TACATAA
31881793 AAATGTATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 30 0.81
34 7 0.19
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.34
Consensus pattern (33 bp):
TACATAACTACATAACTTACAGTACTTACATAA
Found at i:31887327 original size:21 final size:21
Alignment explanation
Indices: 31887301--31887371 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
31887291 CTACAACTTA
* *
31887301 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
31887322 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
31887343 AAGCGGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
31887364 AAGCAGAG
1 AAGCAGAG
31887372 CAGAGCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.31, C:0.18, G:0.48, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:31887732 original size:42 final size:41
Alignment explanation
Indices: 31887651--31887890 Score: 336
Period size: 42 Copynumber: 5.7 Consensus size: 41
31887641 AAAAAAAAGT
* *
31887651 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAGAC
1 GCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAG-AAAAA-AC
* *
31887694 GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
1 GCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAG-AAAAAAC
*
31887736 GCCGCTAAAGAACTTGTTCTTTAGAGGCGCTTAGAAAAAAAC
1 GCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAG-AAAAAAC
*
31887778 GCCGCTAAAGAACATGTTTTTTAGAGGCGCTTAGAAACAAAC
1 GCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAGAAA-AAAC
* *
31887820 GCCGCCAAAGAACTTGTTCTTTAGAGGCGCTTAGGAAAAAAC
1 GCCGCTAAAGAACATGTTCTTTAGAGGCGCTTA-GAAAAAAC
* *
31887862 GCCGCTAAAGAACATGGTCTTTAGCGGCG
1 GCCGCTAAAGAACATGTTCTTTAGAGGCG
31887891 TTTTTGTTTG
Statistics
Matches: 183, Mismatches: 12, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
41 3 0.02
42 136 0.74
43 44 0.24
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (41 bp):
GCCGCTAAAGAACATGTTCTTTAGAGGCGCTTAGAAAAAAC
Found at i:31887801 original size:84 final size:84
Alignment explanation
Indices: 31887642--31887890 Score: 381
Period size: 84 Copynumber: 2.9 Consensus size: 84
31887632 CGAAAAAATA
* * * * *
31887642 AAAAAAAGTGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAGACGCCGCTAAAGACC
1 AAAAAAA-CGCCGCTAAAGAACTTGTTCTTTAGAGGCGCTTAGAAAAAA-ACGCCGCTAAAGAAC
31887707 ATGTTCTTTAGCGGCGCTTAG
64 ATGTTCTTTAGCGGCGCTTAG
31887728 AAAAAAACGCCGCTAAAGAACTTGTTCTTTAGAGGCGCTTAGAAAAAAACGCCGCTAAAGAACAT
1 AAAAAAACGCCGCTAAAGAACTTGTTCTTTAGAGGCGCTTAGAAAAAAACGCCGCTAAAGAACAT
* *
31887793 GTTTTTTAGAGGCGCTTAG
66 GTTCTTTAGCGGCGCTTAG
* * *
31887812 AAACAAACGCCGCCAAAGAACTTGTTCTTTAGAGGCGCTTAGGAAAAAACGCCGCTAAAGAACAT
1 AAAAAAACGCCGCTAAAGAACTTGTTCTTTAGAGGCGCTTAGAAAAAAACGCCGCTAAAGAACAT
*
31887877 GGTCTTTAGCGGCG
66 GTTCTTTAGCGGCG
31887891 TTTTTGTTTG
Statistics
Matches: 150, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
84 106 0.71
85 37 0.25
86 7 0.05
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.22
Consensus pattern (84 bp):
AAAAAAACGCCGCTAAAGAACTTGTTCTTTAGAGGCGCTTAGAAAAAAACGCCGCTAAAGAACAT
GTTCTTTAGCGGCGCTTAG
Found at i:31889532 original size:35 final size:35
Alignment explanation
Indices: 31889481--31889594 Score: 185
Period size: 35 Copynumber: 3.2 Consensus size: 35
31889471 ACTCTCTGTT
31889481 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* *
31889516 TTGGTGTGTTTTGGAGGGATTAGCTCTTACGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
31889551 TTGGTGTGTTTCGGAGGGATT-GCCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAG-CTCTTATGAGCA
31889586 TCTGGTGTG
1 T-TGGTGTG
31889595 CTTTGGTTGG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
34 1 0.01
35 65 0.89
36 7 0.10
ACGTcount: A:0.15, C:0.12, G:0.35, T:0.38
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
Found at i:31897230 original size:29 final size:28
Alignment explanation
Indices: 31897198--31897284 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
31897188 TCATAAGAAC
31897198 ATTTTATGAAATTATATTTAATAATAATT
1 ATTTTAT-AAATTATATTTAATAATAATT
* * *
31897227 A-TTT-TAAATTGTATTAAATCAT-A-T
1 ATTTTATAAATTATATTTAATAATAATT
* *
31897251 ATTTTAATTAAAATATATTTAATATTAATT
1 ATTTT-A-TAAATTATATTTAATAATAATT
31897281 ATTT
1 ATTT
31897285 CAAATTTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 14 0.32
27 1 0.02
28 16 0.36
29 2 0.05
30 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTTATAAATTATATTTAATAATAATT
Found at i:31897460 original size:67 final size:65
Alignment explanation
Indices: 31897385--31897597 Score: 150
Period size: 67 Copynumber: 3.2 Consensus size: 65
31897375 ATTATAATGT
31897385 ATTT-AATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTA
1 ATTTAAATAATAATTATGTTTAAATAT-ATTAAA-TATTTATTATTGATATTAATAATCTTATTA
31897449 AA
64 AA
** *** * * * *
31897451 ATTTAAATAACAATAACAAAT-TTTTGCTA-ATTATAAGAATT-TTATT-AAATT-ATATATTTT
1 ATTTAAAT---AATAA-TTATGTTTAAATATATTA-AATATTTATTATTGATATTAATA-ATCTT
31897511 AATTAAAA
60 -ATT-AAA
* * *
31897519 TATATTTAATAATAATTATGTTTAAATATAATTAAAATATTTATTACTGATAATAATAATCTTAT
1 -AT-TTAAATAATAATTATGTTTAAATAT-ATT-AAATATTTATTATTGATATTAATAATCTTAT
31897584 TAAA
62 TAAA
31897588 ATTTAAATAA
1 ATTTAAATAA
31897598 CATTAACAAT
Statistics
Matches: 107, Mismatches: 22, Indels: 35
0.65 0.13 0.21
Matches are distributed among these distances:
65 3 0.03
66 14 0.13
67 28 0.26
68 12 0.11
69 15 0.14
70 23 0.21
71 9 0.08
72 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (65 bp):
ATTTAAATAATAATTATGTTTAAATATATTAAATATTTATTATTGATATTAATAATCTTATTAAA
Found at i:31897495 original size:137 final size:138
Alignment explanation
Indices: 31897341--31897606 Score: 426
Period size: 137 Copynumber: 1.9 Consensus size: 138
31897331 TAAGAATATG
* *
31897341 AATTATTAAGAATTTTATTAAATTATATACCAAAATTATAATGTATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
* * * *
31897406 AATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAAA
66 AATATAATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
31897471 TTTTTGCT
131 TTTTTGCT
****
31897479 AATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
*
31897543 AATATAATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACATTAACAA
66 AATATAATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
31897607 TAATCATTTA
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
137 112 0.96
138 5 0.04
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (138 bp):
AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAATTATGTTTA
AATATAATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAAA
TTTTTGCT
Found at i:31897517 original size:18 final size:17
Alignment explanation
Indices: 31897489--31897523 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
31897479 AATTATAAGA
*
31897489 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
31897506 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
31897524 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:31897588 original size:70 final size:68
Alignment explanation
Indices: 31897375--31897589 Score: 172
Period size: 70 Copynumber: 3.1 Consensus size: 68
31897365 ATATACCAAA
* * * *
31897375 ATTATAATGTATTTAATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTAATA
1 ATTAAAATATATTTAATAATAATTATGTTTAAATAT-ATTAAAATATTTATTA-TGATAATAATA
31897440 ATCTT
64 ATCTT
* ** * ** * * * *
31897445 ATTAAAATTTAAATAACAATAACAAATTTTTGCTAAT-TA-TAAGAAT-TTTATTA-AATTAT-A
1 ATTAAAATATATTTAATAATAA-TTATGTTT--AAATATATTAA-AATATTTATTATGATAATAA
*
31897505 T-ATTTT
62 TAATCTT
31897511 AATTAAAATATATTTAATAATAATTATGTTTAAATATAATTAAAATATTTATTACTGATAATAAT
1 -ATTAAAATATATTTAATAATAATTATGTTTAAATAT-ATTAAAATATTTATTA-TGATAATAAT
31897576 AATCTT
63 AATCTT
31897582 ATTAAAAT
1 ATTAAAAT
31897590 TTAAATAACA
Statistics
Matches: 107, Mismatches: 25, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
64 3 0.03
65 1 0.01
66 13 0.12
67 30 0.28
68 3 0.03
69 4 0.04
70 37 0.35
71 12 0.11
72 1 0.01
73 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (68 bp):
ATTAAAATATATTTAATAATAATTATGTTTAAATATATTAAAATATTTATTATGATAATAATAAT
CTT
Found at i:31897639 original size:137 final size:138
Alignment explanation
Indices: 31897374--31897692 Score: 350
Period size: 137 Copynumber: 2.3 Consensus size: 138
31897364 TATATACCAA
* * * * * *
31897374 AATTATAATGTATTTAATAATAATTATGTTTAAATATGATTAAATTATTTATTATTGATATTAAT
1 AATTAAAATATATTTAATAATAATTATGTTTAAATATAATTAAAATATTTATTACTGATAATAAT
* * *
31897439 AATCTTATTAAAATTTAAATAACAATAACAAATTTTTGCTAATTATAAGAATTTTATTAAATTAT
66 AATCTTATTAAAATTTAAATAACAATAACAAATATTTACTAA-TATAACAATTTTATTAAATTAT
*
31897504 -A-TATTTT
130 AAGAATTTT
31897511 AATTAAAATATATTTAATAATAATTATGTTTAAATATAATTAAAATATTTATTACTGATAATAAT
1 AATTAAAATATATTTAATAATAATTATGTTTAAATATAATTAAAATATTTATTACTGATAATAAT
* * *
31897576 AATCTTATTAAAATTTAAATAACATTAACAATAATCATTTAC-CA-A-AACAATTTTCTGCT-AA
66 AATCTTATTAAAATTTAAATAACAATAAC-A-AAT-ATTTACTAATATAACAATTTTAT--TAAA
31897637 TTATAAGAATTTT
126 TTATAAGAATTTT
* *
31897650 -ATTAAATTATATATTTTAATTAA-AA-TATATTTAATTATAATTA
1 AATTAAA--ATATA-TTTAA-TAATAATTATGTTTAAATATAATTA
31897693 TGTTTAAATA
Statistics
Matches: 156, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
136 9 0.06
137 94 0.60
138 9 0.06
139 9 0.06
140 25 0.16
141 7 0.04
142 3 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (138 bp):
AATTAAAATATATTTAATAATAATTATGTTTAAATATAATTAAAATATTTATTACTGATAATAAT
AATCTTATTAAAATTTAAATAACAATAACAAATATTTACTAATATAACAATTTTATTAAATTATA
AGAATTTT
Found at i:31897643 original size:156 final size:155
Alignment explanation
Indices: 31897469--31897792 Score: 594
Period size: 156 Copynumber: 2.1 Consensus size: 155
31897459 AACAATAACA
31897469 AATTTTTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAA
1 AATTTTTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAA
31897534 TTATGTTTAAATATAATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAAC
66 TTATGTTTAAATATAATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAAC
*
31897599 ATTAACAATAATCATTTACCAAAAC
131 AATAACAATAATCATTTACCAAAAC
*
31897624 AATTTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATA
1 AATTTT-TGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATA
*
31897689 ATTATGTTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAA
65 ATTATGTTTAAATATAATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAA
*
31897754 CAATAACAATAATTATTTACCAAAAC
130 CAATAACAATAATCATTTACCAAAAC
31897780 AATTTTATGCTAA
1 AATTTT-TGCTAA
31897793 GAGTATTCTA
Statistics
Matches: 163, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
155 6 0.04
156 157 0.96
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (155 bp):
AATTTTTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAA
TTATGTTTAAATATAATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAAC
AATAACAATAATCATTTACCAAAAC
Found at i:31897673 original size:18 final size:18
Alignment explanation
Indices: 31897645--31897693 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
31897635 AATTATAAGA
31897645 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
31897662 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
31897678 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
31897694 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:31897679 original size:16 final size:16
Alignment explanation
Indices: 31897645--31897699 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
31897635 AATTATAAGA
31897645 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
31897662 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
31897678 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
31897692 ATGTTTAA
1 AT-TTTAA
31897700 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:31897909 original size:44 final size:45
Alignment explanation
Indices: 31897844--31897934 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
31897834 ACCTCTATTC
* * *
31897844 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
31897888 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
31897933 CA
1 CA
31897935 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:31897936 original size:16 final size:16
Alignment explanation
Indices: 31897915--31897983 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
31897905 GATTAGCTAT
31897915 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31897931 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
31897948 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
31897964 TATACCTCTAATCCAA
1 TACACCTCTAATCCAA
31897980 TACA
1 TACA
31897984 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:31897957 original size:33 final size:32
Alignment explanation
Indices: 31897915--31897983 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
31897905 GATTAGCTAT
31897915 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
31897948 TACACCTCTAATCCAATATACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
31897980 TACA
1 TACA
31897984 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:31900270 original size:18 final size:18
Alignment explanation
Indices: 31900247--31900289 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
31900237 GAATAGGTTT
31900247 TTAATTAAACAATTTT-AA
1 TTAATTAAA-AATTTTAAA
31900265 TTAATTAAAAATTTTAAA
1 TTAATTAAAAATTTTAAA
31900283 TTAATTA
1 TTAATTA
31900290 CACCTTGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAA
Found at i:31903591 original size:21 final size:21
Alignment explanation
Indices: 31903565--31903606 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
31903555 GTAATTCATG
* *
31903565 CTTTTTTTTTTAATTTTTAAA
1 CTTTTTTTTATAAATTTTAAA
31903586 CTTTTTTTTATAAATTTTAAA
1 CTTTTTTTTATAAATTTTAAA
31903607 TTATTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTTTTTTTATAAATTTTAAA
Found at i:31906225 original size:116 final size:115
Alignment explanation
Indices: 31906082--31906418 Score: 554
Period size: 116 Copynumber: 2.9 Consensus size: 115
31906072 ATATTTATTT
* * * *
31906082 TTTTCACTTATATTATGAGTATGGTAAATTCTAATATTATAAAATTATAAAATTATTTAAAATAT
1 TTTTCACCTACATTGTGGGTATGGTAAATTCTAATATTATAAAATTAT-AAATTATTTAAAATAT
31906147 CATTATTTTATATGTGAAATATTTCAATTAATTATTTAAAATATCATTATA
65 CATTATTTTATATGTGAAATATTTCAATTAATTATTTAAAATATCATTATA
31906198 TTTTCACCTACATTGTGGGTATGGTAAATTCTAATATTATAAAATTATATAATTATTTAAAATAT
1 TTTTCACCTACATTGTGGGTATGGTAAATTCTAATATTATAAAATTATA-AATTATTTAAAATAT
31906263 CATTATTTTATATGTGAAATATTTCAATTAATTATTTAAAATATCATTATA
65 CATTATTTTATATGTGAAATATTTCAATTAATTATTTAAAATATCATTATA
*
31906314 TTTTCACCTACATTGTGGGTATGGTAAATTCTAATATTATAAAA--AT-AATTATTTCAAATATC
1 TTTTCACCTACATTGTGGGTATGGTAAATTCTAATATTATAAAATTATAAATTATTTAAAATATC
* * *
31906376 ATTATTTTTATATGTGAAATATTTGAAATAATTATTTGAAATA
66 ATTA-TTTTATATGTGAAATATTTCAATTAATTATTTAAAATA
31906419 CACATACAAA
Statistics
Matches: 211, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
112 19 0.09
113 35 0.17
114 2 0.01
115 1 0.00
116 154 0.73
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.46
Consensus pattern (115 bp):
TTTTCACCTACATTGTGGGTATGGTAAATTCTAATATTATAAAATTATAAATTATTTAAAATATC
ATTATTTTATATGTGAAATATTTCAATTAATTATTTAAAATATCATTATA
Found at i:31908088 original size:12 final size:13
Alignment explanation
Indices: 31908065--31908124 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 13
31908055 ATTTAGCCAT
*
31908065 TTTTAT-TTTTTA
1 TTTTATATTTATA
31908077 TTTTAATATTTATA
1 TTTT-ATATTTATA
31908091 -TTTATATTTATA
1 TTTTATATTTATA
*
31908103 TTTTTTATTTA-A
1 TTTTATATTTATA
31908115 TTTTTATATT
1 -TTTTATATT
31908125 CTAATTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 14 0.34
13 22 0.54
14 5 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATATTTATA
Found at i:31908134 original size:26 final size:25
Alignment explanation
Indices: 31908066--31908134 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
31908056 TTTAGCCATT
* *
31908066 TTTAT-TTTTTATTTTAATATTTATA
1 TTTATATTTATATTTT-TTATTTATA
*
31908091 TTTATATTTATATTTTTTATTTAATT
1 TTTATATTTATATTTTTTATTT-ATA
31908117 TTTATATTCTA-ATTTTTT
1 TTTATATT-TATATTTTTT
31908135 CGTTTGTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 10 0.26
26 26 0.68
27 2 0.05
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTATATTTATATTTTTTATTTATA
Found at i:31910716 original size:13 final size:13
Alignment explanation
Indices: 31910694--31910723 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31910684 TTTCAAAAGA
*
31910694 AGAAAGAAAATAG
1 AGAAAAAAAATAG
31910707 AGAAAAAAAATAG
1 AGAAAAAAAATAG
31910720 AGAA
1 AGAA
31910724 CGTGCCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (13 bp):
AGAAAAAAAATAG
Found at i:31910751 original size:18 final size:18
Alignment explanation
Indices: 31910730--31910765 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31910720 AGAACGTGCC
31910730 AAAAGAAAAGAAAATAAA
1 AAAAGAAAAGAAAATAAA
* *
31910748 AAAATAAAATAAAATAAA
1 AAAAGAAAAGAAAATAAA
31910766 TATTAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (18 bp):
AAAAGAAAAGAAAATAAA
Found at i:31916889 original size:17 final size:17
Alignment explanation
Indices: 31916869--31916902 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31916859 AAATCTAAAT
*
31916869 AATAATTTTGATTATTA
1 AATAATTTTAATTATTA
*
31916886 AATATTTTTAATTATTA
1 AATAATTTTAATTATTA
31916903 TTTAAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
AATAATTTTAATTATTA
Found at i:31918116 original size:35 final size:37
Alignment explanation
Indices: 31918076--31918147 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
31918066 TACGTATGAT
31918076 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTCCCTGATCAGATAAGTGTAGC
* *
31918111 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTCCCTGATCAGATAAGTGTAGC
31918148 TAAAGCTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 10 0.30
36 3 0.09
37 20 0.61
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTTCCCTGATCAGATAAGTGTAGC
Found at i:31918163 original size:46 final size:46
Alignment explanation
Indices: 31918111--31918523 Score: 493
Period size: 46 Copynumber: 8.6 Consensus size: 46
31918101 TAAGTGTAGC
* **
31918111 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
**
31918157 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
*
31918203 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
*
31918249 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
31918301 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
31918353 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
31918399 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
* * ** *
31918445 TACTTATCACTTCCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC-T-----TTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
*
31918497 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCTCTTGATCAGA
31918524 AGTACTCAAA
Statistics
Matches: 339, Mismatches: 15, Indels: 26
0.89 0.04 0.07
Matches are distributed among these distances:
46 202 0.60
47 1 0.00
49 1 0.00
50 1 0.00
51 4 0.01
52 130 0.38
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:31918206 original size:39 final size:41
Alignment explanation
Indices: 31918077--31918239 Score: 158
Period size: 46 Copynumber: 3.9 Consensus size: 41
31918067 ACGTATGATC
* *
31918077 ACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC----C
1 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAG
*
31918112 ACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAG
1 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAG
31918153 CTATCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAG
1 -----ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAG
*
31918199 CTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 -----ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
31918240 CGAAGCTATC
Statistics
Matches: 112, Mismatches: 5, Indels: 11
0.88 0.04 0.09
Matches are distributed among these distances:
35 9 0.08
36 4 0.04
37 19 0.17
46 80 0.71
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (41 bp):
ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAG
Found at i:31918309 original size:98 final size:92
Alignment explanation
Indices: 31918253--31918523 Score: 346
Period size: 98 Copynumber: 2.8 Consensus size: 92
31918243 AGCTATCACT
* *
31918253 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCA
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCAC--T---
* *
31918317 CTTGTCACTTGATCAGATAAGTGTAGCTGAAGC
61 -TTGTCACTTGATCAGATAAGTATAGCCGAAGC
* *
31918350 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTC
31918415 ACTTGATCAGATAAGTATAGCCGAAGC
66 ACTTGATCAGATAAGTATAGCCGAAGC
* * *
31918442 TATTACTTATCACTTCCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TATCACTTATCAC-T-----TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCAC
31918507 TTTGTCACTTGATCAGA
60 TTTGTCACTTGATCAGA
31918524 AGTACTCAAA
Statistics
Matches: 158, Mismatches: 9, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
92 42 0.27
93 1 0.01
96 1 0.01
97 12 0.08
98 102 0.65
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (92 bp):
TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTC
ACTTGATCAGATAAGTATAGCCGAAGC
Found at i:31918465 original size:196 final size:196
Alignment explanation
Indices: 31918128--31918509 Score: 656
Period size: 196 Copynumber: 1.9 Consensus size: 196
31918118 CACTTTGTTT
* *
31918128 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
31918193 CTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCA
66 CCAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCA
** * *
31918258 CTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTGTC
131 CTTCCCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTACCACTTATCACTTTCCACTTGTC
31918323 A
196 A
*
31918324 CTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
31918389 CCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCA
66 CCAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCA
*
31918454 CTTCCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
131 CTTCCCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTACCACTTATCACTTT
31918510 GTCACTTGAT
Statistics
Matches: 174, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
196 174 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (196 bp):
CTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
CCAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCA
CTTCCCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTACCACTTATCACTTTCCACTTGTC
A
Found at i:31921413 original size:3 final size:3
Alignment explanation
Indices: 31921405--31921459 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
31921395 GCTTTTGTTA
31921405 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31921453 ATT ATT A
1 ATT ATT A
31921460 CAACTTTAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:31926598 original size:20 final size:20
Alignment explanation
Indices: 31926527--31926604 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
31926517 GAAATTTAAG
31926527 ATTTAGGGTTTAAGG-TTTA
1 ATTTAGGGTTTAAGGTTTTA
* ** *
31926546 ATTTTAGAGTTTGGGGTTTGTG
1 A-TTTAGGGTTTAAGGTTT-TA
*
31926568 A-TTATGGGTTTAGGGTTTTA
1 ATTTA-GGGTTTAAGGTTTTA
31926588 ATTTAGGGTTTAAGGTT
1 ATTTAGGGTTTAAGGTT
31926605 ATAGGTTCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
19 1 0.02
20 27 0.59
21 16 0.35
22 2 0.04
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.49
Consensus pattern (20 bp):
ATTTAGGGTTTAAGGTTTTA
Found at i:31926660 original size:21 final size:21
Alignment explanation
Indices: 31926601--31926661 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
31926591 TAGGGTTTAA
*
31926601 GGTTAT-AGGTTCAAGGTTCTG
1 GGTTATGA-GTTCAAGGTTCGG
* * *
31926622 GTTTAGGA-TACAATGGTTCGG
1 GGTTATGAGTTCAA-GGTTCGG
31926643 GGTTATGAGTTCAAGGTTC
1 GGTTATGAGTTCAAGGTTC
31926662 ATTAGAGGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 4 0.13
21 21 0.70
22 5 0.17
ACGTcount: A:0.21, C:0.10, G:0.33, T:0.36
Consensus pattern (21 bp):
GGTTATGAGTTCAAGGTTCGG
Found at i:31928239 original size:34 final size:34
Alignment explanation
Indices: 31928200--31928266 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
31928190 TGGAGTTTGG
31928200 GGTTTGCGATTATAGA-TTTAGAGTTTTGATTTAA
1 GGTTTGCGATTATAGATTTTAG-GTTTTGATTTAA
* * *
31928234 GGTTTGGGGTTATAGATTTTAGGTTTTGGTTTA
1 GGTTTGCGATTATAGATTTTAGGTTTTGATTTA
31928267 GGATTCAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 24 0.83
35 5 0.17
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.49
Consensus pattern (34 bp):
GGTTTGCGATTATAGATTTTAGGTTTTGATTTAA
Found at i:31928334 original size:7 final size:7
Alignment explanation
Indices: 31928298--31928331 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
31928288 TAGGTTACGT
31928298 GTTCAAG
1 GTTCAAG
31928305 GTTCAAG
1 GTTCAAG
31928312 GTTCAAG
1 GTTCAAG
*
31928319 ATTCAAGG
1 GTTCAA-G
31928327 GTTCA
1 GTTCA
31928332 GGGGTTATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (7 bp):
GTTCAAG
Found at i:31939070 original size:5 final size:5
Alignment explanation
Indices: 31939050--31939086 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
31939040 AATGCCTTTT
31939050 TTTCA TTT-A TTTTCA TTTCA TTTCA TTTCA TTTCA TT
1 TTTCA TTTCA -TTTCA TTTCA TTTCA TTTCA TTTCA TT
31939087 ACATGCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 1 0.03
5 28 0.93
6 1 0.03
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (5 bp):
TTTCA
Found at i:31947201 original size:44 final size:43
Alignment explanation
Indices: 31947151--31947308 Score: 185
Period size: 44 Copynumber: 3.6 Consensus size: 43
31947141 TACCATAGGG
*
31947151 AATCTTATCTCTCTGAAGTTGCAGTGAAGCAAGATGAAGCTACA
1 AATCTTATCTC-CTGAAGTTGCAGTGGAGCAAGATGAAGCTACA
*
31947195 AATCTTATCTCCTTGAAGTTGCAGTGGAG-AGGATGAAGCTACA
1 AATCTTATCTCC-TGAAGTTGCAGTGGAGCAAGATGAAGCTACA
* *
31947238 AATCTTATCTCCCTAAAGTTGTAGTGGAGC-AGATTGAAGCTACA
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAAGA-TGAAGCTACA
* * * *
31947282 AATCCTATACCCCTAAAGTTACAGTGG
1 AATCTTAT-CTCCTGAAGTTGCAGTGG
31947309 GTTGGATTGA
Statistics
Matches: 100, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
43 40 0.40
44 59 0.59
45 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACA
Found at i:31947244 original size:43 final size:43
Alignment explanation
Indices: 31947151--31947285 Score: 184
Period size: 43 Copynumber: 3.1 Consensus size: 43
31947141 TACCATAGGG
*
31947151 AATCTTATCT-CTCTGAAGTTGCAGTGAAGCAAGATGAAGCTACA
1 AATCTTATCTCCT-TGAAGTTGCAGTGGAGC-AGATGAAGCTACA
31947195 AATCTTATCTCCTTGAAGTTGCAGTGGAG-AGGATGAAGCTACA
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCA-GATGAAGCTACA
* * *
31947238 AATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACA
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGA-TGAAGCTACA
31947282 AATC
1 AATC
31947286 CTATACCCCT
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
42 1 0.01
43 40 0.48
44 40 0.48
45 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATGAAGCTACA
Found at i:31947486 original size:94 final size:94
Alignment explanation
Indices: 31947097--31947473 Score: 364
Period size: 94 Copynumber: 4.1 Consensus size: 94
31947087 CATGAAACAA
* * * * *
31947097 TACAAATTCTATACCCCTAAAGTTGTAGTAGGTCAGATTGAAGT-TACCATAGGGAATCTTATCT
1 TACAAATCCTATACCCCTGAAGTTGCAGTAGGTCGGATTGAA-TCTACCATAGCGAATCTTATCT
*
31947161 CTCTGAAGTTGCAGTGAAGCAAGA-TGAAGC
65 CACTGAAGTTGCAGTGAAGC-AGATTGAAGC
* * ** *
31947191 TACAAATCTTAT-CTCCTTGAAGTTGCAGT-GGAGAGGA-TGAAGCTA-C--A---AATCTTATC
1 TACAAATCCTATAC-CCCTGAAGTTGCAGTAGG-TCGGATTGAATCTACCATAGCGAATCTTATC
* * * *
31947247 TCCCTAAAGTTGTAGTGGAGCAGATTGAAGC
64 TCACTGAAGTTGCAGTGAAGCAGATTGAAGC
* * * * * *
31947278 TACAAATCCTATACCCCTAAAGTTACAGTGGGTTGGATTGATTCTACTATAGCGAATCTTATCTC
1 TACAAATCCTATACCCCTGAAGTTGCAGTAGGTCGGATTGAATCTACCATAGCGAATCTTATCTC
* *
31947343 ACTGAAGTTTCTA-TGGAGCAGATTGAAGC
66 ACTGAAGTTGC-AGTGAAGCAGATTGAAGC
* * *
31947372 TACAAATCCCATACCCCTGAATTTGCAGTAGGTCGGATTGAATCTACCATAGCGAATCTTATCTT
1 TACAAATCCTATACCCCTGAAGTTGCAGTAGGTCGGATTGAATCTACCATAGCGAATCTTATCTC
* * *
31947437 ACTGAAGTTGCAGTTAAACAGATTAAAGC
66 ACTGAAGTTGCAGTGAAGCAGATTGAAGC
31947466 TACAAATC
1 TACAAATC
31947474 TTATTTCACT
Statistics
Matches: 228, Mismatches: 40, Indels: 30
0.77 0.13 0.10
Matches are distributed among these distances:
86 3 0.01
87 58 0.25
88 9 0.04
90 1 0.00
91 1 0.00
92 1 0.00
93 10 0.04
94 144 0.63
95 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (94 bp):
TACAAATCCTATACCCCTGAAGTTGCAGTAGGTCGGATTGAATCTACCATAGCGAATCTTATCTC
ACTGAAGTTGCAGTGAAGCAGATTGAAGC
Found at i:31947489 original size:44 final size:44
Alignment explanation
Indices: 31947426--31947517 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
31947416 TACCATAGCG
*
31947426 AATCTTATCTTACTGAAGTTGCAGT-TAAACAGATTAAAGCTACA
1 AATCTTATCTTACTGAAGTTACAGTGT-AACAGATTAAAGCTACA
* * *
31947470 AATCTTAT-TTCACTGAAGTTATAGTGTAGCAGATTGAAGCTACA
1 AATCTTATCTT-ACTGAAGTTACAGTGTAACAGATTAAAGCTACA
31947514 AATC
1 AATC
31947518 CTATACCCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 2 0.05
44 39 0.93
45 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (44 bp):
AATCTTATCTTACTGAAGTTACAGTGTAACAGATTAAAGCTACA
Found at i:31947598 original size:138 final size:138
Alignment explanation
Indices: 31947332--31947615 Score: 351
Period size: 138 Copynumber: 2.1 Consensus size: 138
31947322 TACTATAGCG
* * *
31947332 AATCTTATCTCACTGAAGTTTCTATGGAGCAGATTGAAGCTACAAATCCCATACCCCTGAATTTG
1 AATCTTATCTCACTGAAGTTTATATGGAGCAGATTGAAGCTACAAATCCCATACCCCTGAAGTGG
* * *
31947397 CAGTAGGTCGGATTGAATCTACCATAGCGAATCTTATCTTACTGAAGTTGCAGTTAAACAGATT-
66 CAGTAGGTCGGATTGAATCAACCATAGCGAATCTTATCTTACTGAAATTGCAGTGAAACAGATTG
31947461 AAAGCTACA
131 AAA-CTACA
* * * *
31947470 AATCTTATTTCACTGAAG-TTATAGTGTAGCAGATTGAAGCTACAAATCCTATACCCTTGAAGTG
1 AATCTTATCTCACTGAAGTTTATA-TGGAGCAGATTGAAGCTACAAATCCCATACCCCTGAAGTG
* * * * * *
31947534 GCAGT-GGATCGGATTGAATCAACCATAGTGACTCTTATC-TCCTTGAAATTGTAGTGGAATAGA
65 GCAGTAGG-TCGGATTGAATCAACCATAGCGAATCTTATCTTAC-TGAAATTGCAGTGAAACAGA
*
31947597 TTGAAACTATA
128 TTGAAACTACA
31947608 AATCTTAT
1 AATCTTAT
31947616 ACCTCTAAAG
Statistics
Matches: 125, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
137 8 0.06
138 114 0.91
139 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (138 bp):
AATCTTATCTCACTGAAGTTTATATGGAGCAGATTGAAGCTACAAATCCCATACCCCTGAAGTGG
CAGTAGGTCGGATTGAATCAACCATAGCGAATCTTATCTTACTGAAATTGCAGTGAAACAGATTG
AAACTACA
Found at i:31947600 original size:232 final size:232
Alignment explanation
Indices: 31947230--31947667 Score: 538
Period size: 232 Copynumber: 1.9 Consensus size: 232
31947220 GGAGAGGATG
* *
31947230 AAGCTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCCTATACCCC
1 AAGCTACAAATCTTATCTCACTAAAGTTATAGTGGAGCAGATTGAAGCTACAAATCCTATACCCC
* * * * * * *
31947295 TAAAGTTACAGTGGGTTGGATTGATTCTACTATAGCGAATCTTATCTCACTGAAGTTTCTATGGA
66 TAAAGTGACAGTGGATCGGATTGAATCAACCATAGCGAATCTTATCTCACTGAAGATTCTATGGA
* * * * * *
31947360 GCAGATTGAAGCTACAAATCCCATACCCCTGAATTTGCAGTAGGTCGGATTGAATCTACCATAGC
131 ACAGATTGAAACTACAAATCCCATACCCCTAAAGTTGCAATAGGTCAGATTGAATCTACCATAGC
31947425 GAATCTTATCTTACTGAAGTTGCAGTTAAACAGATTA
196 GAATCTTATCTTACTGAAGTTGCAGTTAAACAGATTA
* * * *
31947462 AAGCTACAAATCTTATTTCACTGAAGTTATAGTGTAGCAGATTGAAGCTACAAATCCTATACCCT
1 AAGCTACAAATCTTATCTCACTAAAGTTATAGTGGAGCAGATTGAAGCTACAAATCCTATACCCC
* * * * *
31947527 TGAAGTGGCAGTGGATCGGATTGAATCAACCATAGTGACTCTTATCTC-CTTGAA-ATTGTAGTG
66 TAAAGTGACAGTGGATCGGATTGAATCAACCATAGCGAATCTTATCTCAC-TGAAGATTCTA-TG
* * ** * * * * *
31947590 GAATAGATTGAAACTATAAATCTTATACCTCTAAAGTTGCAATGGGTTAGATTGATTCTACTATA
129 GAACAGATTGAAACTACAAATCCCATACCCCTAAAGTTGCAATAGGTCAGATTGAATCTACCATA
*
31947655 GTGAATCTTATCT
194 GCGAATCTTATCT
31947668 CCCTTGTAAC
Statistics
Matches: 170, Mismatches: 34, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
231 5 0.03
232 165 0.97
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (232 bp):
AAGCTACAAATCTTATCTCACTAAAGTTATAGTGGAGCAGATTGAAGCTACAAATCCTATACCCC
TAAAGTGACAGTGGATCGGATTGAATCAACCATAGCGAATCTTATCTCACTGAAGATTCTATGGA
ACAGATTGAAACTACAAATCCCATACCCCTAAAGTTGCAATAGGTCAGATTGAATCTACCATAGC
GAATCTTATCTTACTGAAGTTGCAGTTAAACAGATTA
Found at i:31949000 original size:24 final size:23
Alignment explanation
Indices: 31948972--31949040 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 23
31948962 TTGTTATTTG
31948972 GTAAAGGATGAATTGACAGAAAAT
1 GTAAAGGATGAATTGAC-GAAAAT
* *
31948996 GTAAAGGCTGAATTGGCGGAAAAT
1 GTAAAGGATGAATTGAC-GAAAAT
*
31949020 GTAAATGATG-ATTGACGAAAA
1 GTAAAGGATGAATTGACGAAAA
31949041 ATTACCTAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.13
23 5 0.13
24 29 0.74
ACGTcount: A:0.45, C:0.06, G:0.28, T:0.22
Consensus pattern (23 bp):
GTAAAGGATGAATTGACGAAAAT
Found at i:31951338 original size:7 final size:7
Alignment explanation
Indices: 31951326--31951364 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
31951316 TTTTTTACCG
31951326 AAAAATT
1 AAAAATT
31951333 AAAAATT
1 AAAAATT
31951340 AAAAATT
1 AAAAATT
31951347 AAAAATT
1 AAAAATT
31951354 AAAAATT
1 AAAAATT
31951361 AAAA
1 AAAA
31951365 TATCTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:31951517 original size:23 final size:23
Alignment explanation
Indices: 31951487--31951540 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
31951477 GGCTGAGGGA
31951487 TTTTTTTTGTATTTTCCCTTCCT
1 TTTTTTTTGTATTTTCCCTTCCT
*
31951510 TTTTTTTTGTATTTTCCTTTCCT
1 TTTTTTTTGTATTTTCCCTTCCT
31951533 TTTTTTTT
1 TTTTTTTT
31951541 TTTGAGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTTTTTGTATTTTCCCTTCCT
Found at i:31958135 original size:38 final size:38
Alignment explanation
Indices: 31958069--31958186 Score: 121
Period size: 38 Copynumber: 3.1 Consensus size: 38
31958059 ATTGTAAATA
* * *
31958069 TTGTCAGATTCACTAGCCAGTGTTGGGCACACATACAT
1 TTGTCAGATTCACCAACCAGTGCTGGGCACACATACAT
* * *
31958107 TTGTCAGATTCACCAACTAGTGCAGGGCACACATATAT
1 TTGTCAGATTCACCAACCAGTGCTGGGCACACATACAT
* ** * *
31958145 TCGTTGGATAT-ACCAACCAATGCTGGGCACACATACAA
1 TTGTCAGAT-TCACCAACCAGTGCTGGGCACACATACAT
31958183 TTGT
1 TTGT
31958187 TGGTTTTACC
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
38 63 0.98
39 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (38 bp):
TTGTCAGATTCACCAACCAGTGCTGGGCACACATACAT
Found at i:31960559 original size:16 final size:17
Alignment explanation
Indices: 31960538--31960570 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31960528 AACCTTTGTA
31960538 ATCATC-CATAATTCAT
1 ATCATCACATAATTCAT
*
31960554 ATCATCACATATTTCAT
1 ATCATCACATAATTCAT
31960571 TTACTTGTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.39
Consensus pattern (17 bp):
ATCATCACATAATTCAT
Found at i:31962764 original size:36 final size:36
Alignment explanation
Indices: 31962722--31962792 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
31962712 GATTATGTAA
*
31962722 TCTTAGAGTTTTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
31962758 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTAT
31962793 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:31967876 original size:36 final size:36
Alignment explanation
Indices: 31967834--31967904 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
31967824 GATTATGTAA
*
31967834 TCTTAGAGTTTTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
31967870 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTAT
31967905 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:31974690 original size:29 final size:31
Alignment explanation
Indices: 31974632--31974709 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
31974622 TTAGTTTAAT
* *
31974632 ATGCAATTTTATATA-TGAACTTTGATTTTG
1 ATGCAATTTTATAAATTAAACTTTGATTTTG
*
31974662 -TGCAATTTTATAAATTAAATTTTGA-TTTG
1 ATGCAATTTTATAAATTAAACTTTGATTTTG
* *
31974691 ATCCAATTTTCACAAATTA
1 ATGCAATTTT-ATAAATTA
31974710 TTAACACAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 17 0.43
30 16 0.40
31 7 0.17
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (31 bp):
ATGCAATTTTATAAATTAAACTTTGATTTTG
Found at i:31979149 original size:21 final size:21
Alignment explanation
Indices: 31979125--31979171 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
31979115 AAGAAGGAAT
31979125 GAAATACATCAAATAAAAATA
1 GAAATACATCAAATAAAAATA
** *
31979146 GAAATACATGTATTAAAAATA
1 GAAATACATCAAATAAAAATA
31979167 -AAATA
1 GAAATA
31979172 AAAGTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.23
Consensus pattern (21 bp):
GAAATACATCAAATAAAAATA
Found at i:31979178 original size:20 final size:20
Alignment explanation
Indices: 31979137--31979182 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
31979127 AATACATCAA
* *
31979137 ATAAAAATAGAAATACATGT
1 ATAAAAATAGAAATAAAAGT
31979157 ATTAAAAATA-AAATAAAAGT
1 A-TAAAAATAGAAATAAAAGT
31979177 ATAAAA
1 ATAAAA
31979183 GTATGCATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 10 0.43
21 8 0.35
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (20 bp):
ATAAAAATAGAAATAAAAGT
Found at i:31979523 original size:2 final size:2
Alignment explanation
Indices: 31979460--31979505 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
31979450 AAAGCTTAGA
31979460 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
31979502 AT AT
1 AT AT
31979506 TAAAACATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31990374 original size:30 final size:30
Alignment explanation
Indices: 31990338--31990399 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
31990328 TTTCCACTCA
*
31990338 GGTTGGGCATACGCCTGTGTGAGCCACACG
1 GGTTGGGCATACGCCCGTGTGAGCCACACG
*
31990368 GGTTGGGCATATGCCCGTGTGAGCCACACG
1 GGTTGGGCATACGCCCGTGTGAGCCACACG
31990398 GG
1 GG
31990400 CTAGCCACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.16, C:0.26, G:0.39, T:0.19
Consensus pattern (30 bp):
GGTTGGGCATACGCCCGTGTGAGCCACACG
Found at i:31994086 original size:63 final size:63
Alignment explanation
Indices: 31993904--31994087 Score: 201
Period size: 63 Copynumber: 2.9 Consensus size: 63
31993894 GTGTGAGGTT
* * * * * * *
31993904 TCACAGGGGCGTGTGAGAAGCGAAGGAAAACACACACGACCAAGCCAC-CAGACGTGTGGGATC
1 TCACATGGGCGTGAGAGAAGTGAAGGAAAACACACACGGCC-TGACACACGGACGTGTGGGATC
* * * * * *
31993967 TCATATGGGCGTGGGAGAAGTGAAAG-AAACACACACGGCCTAACCACAGGGGCGTGTGGGATC
1 TCACATGGGCGTGAGAGAAGTGAAGGAAAACACACACGGCCTGA-CACACGGACGTGTGGGATC
* *
31994030 TCACATGGACGTGAGAGAAGTGAAGGAAAACACACACGGCCTGACACACGGCCGTGTG
1 TCACATGGGCGTGAGAGAAGTGAAGGAAAACACACACGGCCTGACACACGGACGTGTG
31994088 AGCCACATGG
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
62 16 0.16
63 67 0.68
64 16 0.16
ACGTcount: A:0.32, C:0.23, G:0.33, T:0.12
Consensus pattern (63 bp):
TCACATGGGCGTGAGAGAAGTGAAGGAAAACACACACGGCCTGACACACGGACGTGTGGGATC
Found at i:31994350 original size:12 final size:12
Alignment explanation
Indices: 31994332--31994374 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
31994322 TCTGCTATTT
31994332 CTATTATTTTTA
1 CTATTATTTTTA
*
31994344 GTATTATTTTTTA
1 CTATTA-TTTTTA
*
31994357 CTATTATTCTTA
1 CTATTATTTTTA
*
31994369 CAATTA
1 CTATTA
31994375 CCTTTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.60
Consensus pattern (12 bp):
CTATTATTTTTA
Found at i:31994356 original size:13 final size:13
Alignment explanation
Indices: 31994332--31994364 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
31994322 TCTGCTATTT
31994332 CTATTA-TTTTTA
1 CTATTATTTTTTA
*
31994344 GTATTATTTTTTA
1 CTATTATTTTTTA
31994357 CTATTATT
1 CTATTATT
31994365 CTTACAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (13 bp):
CTATTATTTTTTA
Found at i:31994418 original size:6 final size:6
Alignment explanation
Indices: 31994403--31994466 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
31994393 TCATTGAGTT
* * * *
31994403 TTTTTC -TTTTC TTTTTC TTTTTC GTTTTC GTTTTC GTTTTAC -TTTTG
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC
* *
31994450 TTTTTG TTTTTG TTTTT
1 TTTTTC TTTTTC TTTTT
31994467 AGTTGCTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
5 8 0.16
6 38 0.76
7 4 0.08
ACGTcount: A:0.02, C:0.11, G:0.09, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:31994430 original size:18 final size:17
Alignment explanation
Indices: 31994403--31994465 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 17
31994393 TCATTGAGTT
31994403 TTTTTCTTTTCTTTTTC
1 TTTTTCTTTTCTTTTTC
*
31994420 TTTTTCGTTTTCGTTTTC
1 TTTTTC-TTTTCTTTTTC
* * *
31994438 GTTTTACTTTTGTTTTTG
1 -TTTTTCTTTTCTTTTTC
*
31994456 TTTTTGTTTT
1 TTTTTCTTTT
31994466 TAGTTGCTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 14 0.38
18 18 0.49
19 5 0.14
ACGTcount: A:0.02, C:0.11, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTTC
Found at i:32011453 original size:14 final size:14
Alignment explanation
Indices: 32011434--32011461 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
32011424 TTGTTTGGTG
32011434 GAAAATATTTTCCA
1 GAAAATATTTTCCA
32011448 GAAAATATTTTCCA
1 GAAAATATTTTCCA
32011462 CCTTTTCCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
GAAAATATTTTCCA
Found at i:32014181 original size:14 final size:14
Alignment explanation
Indices: 32014158--32014197 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
32014148 ACAGAAAAGT
*
32014158 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
32014172 AAATCATTTTACGG
1 AAAACATTTTACAG
32014186 AAAACATTTTAC
1 AAAACATTTTAC
32014198 TGGCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:32014189 original size:34 final size:35
Alignment explanation
Indices: 32014123--32014189 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
32014113 CAAACACCAG
* *
32014123 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
32014158 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
32014190 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:32027862 original size:56 final size:56
Alignment explanation
Indices: 32027800--32027934 Score: 252
Period size: 56 Copynumber: 2.4 Consensus size: 56
32027790 AATGATAGTA
*
32027800 TTATATAGTTATGTTTATACATAAGTATGTAACTTTGCATGTGTATGGAATGAATT
1 TTATATAATTATGTTTATACATAAGTATGTAACTTTGCATGTGTATGGAATGAATT
*
32027856 TTATATAATTATGTTTATACATAAGTATGTAACTTTGTATGTGTATGGAATGAATT
1 TTATATAATTATGTTTATACATAAGTATGTAACTTTGCATGTGTATGGAATGAATT
32027912 TTATATAATTATGTTTATACATA
1 TTATATAATTATGTTTATACATA
32027935 TGATACACTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 77 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (56 bp):
TTATATAATTATGTTTATACATAAGTATGTAACTTTGCATGTGTATGGAATGAATT
Found at i:32027924 original size:28 final size:28
Alignment explanation
Indices: 32027838--32027925 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 28
32027828 GTAACTTTGC
32027838 ATGTGTATGGAATGAATTTTATATAATT
1 ATGTGTATGGAATGAATTTTATATAATT
* * *
32027866 ATGTTTAT--ACAT-AAGTATGTA-ACT-TTGT
1 ATGTGTATGGA-ATGAA-T-TTTATA-TAAT-T
32027894 ATGTGTATGGAATGAATTTTATATAATT
1 ATGTGTATGGAATGAATTTTATATAATT
32027922 ATGT
1 ATGT
32027926 TTATACATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 20
0.63 0.09 0.29
Matches are distributed among these distances:
26 3 0.07
27 5 0.11
28 28 0.64
29 5 0.11
30 3 0.07
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (28 bp):
ATGTGTATGGAATGAATTTTATATAATT
Found at i:32030590 original size:54 final size:54
Alignment explanation
Indices: 32030502--32030617 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
32030492 CTACTTACTC
* * *
32030502 TTTTCAAATGAAAAATAATAAAACAAATAGTTATTTTAATAA-CCATAATATGATG
1 TTTT-AAATGAAAAATAATAAAACAAACAATTATTTTAA-AATCCATAATATGATA
* * * *
32030557 TTTTAAATGAAAAATAGTGAAAGAAACAATTATTTTAAAATCCATAATGTGATA
1 TTTTAAATGAAAAATAATAAAACAAACAATTATTTTAAAATCCATAATATGATA
32030611 TTTTAAA
1 TTTTAAA
32030618 AATAAGTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 2 0.04
54 47 0.89
55 4 0.08
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (54 bp):
TTTTAAATGAAAAATAATAAAACAAACAATTATTTTAAAATCCATAATATGATA
Found at i:32031979 original size:18 final size:18
Alignment explanation
Indices: 32031941--32031979 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
32031931 TCTGCTCCCA
* *
32031941 TTTTGCACTTTTTTGTGT
1 TTTTCCACTTTTTTGTAT
*
32031959 TTTTCCACTTTTTTTTAT
1 TTTTCCACTTTTTTGTAT
32031977 TTT
1 TTT
32031980 CTTTCTTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.72
Consensus pattern (18 bp):
TTTTCCACTTTTTTGTAT
Found at i:32035826 original size:15 final size:15
Alignment explanation
Indices: 32035808--32035837 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
32035798 TATATTAATT
32035808 ATTATTATAATTATA
1 ATTATTATAATTATA
32035823 ATTATTATAATTATA
1 ATTATTATAATTATA
32035838 TATTTACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTATTATAATTATA
Found at i:32035829 original size:9 final size:9
Alignment explanation
Indices: 32035803--32035836 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
32035793 ATTAGTATAT
32035803 TAATTATTA
1 TAATTATTA
* *
32035812 TTATAATTA
1 TAATTATTA
32035821 TAATTATTA
1 TAATTATTA
32035830 TAATTAT
1 TAATTAT
32035837 ATATTTACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAATTATTA
Found at i:32035939 original size:16 final size:18
Alignment explanation
Indices: 32035910--32035942 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
32035900 ACTAAAAATA
32035910 TTAAAGAAATTAAATTTG
1 TTAAAGAAATTAAATTTG
32035928 TTAAA-AAA-TAAATTT
1 TTAAAGAAATTAAATTT
32035943 TATAAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (18 bp):
TTAAAGAAATTAAATTTG
Found at i:32057628 original size:4 final size:4
Alignment explanation
Indices: 32057619--32057643 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
32057609 ATTAAAACAA
32057619 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
32057644 CACAGAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:32065704 original size:3 final size:3
Alignment explanation
Indices: 32065696--32065736 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
32065686 AGCAAATTTC
32065696 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
32065737 TCGGTCATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:32066576 original size:12 final size:10
Alignment explanation
Indices: 32066547--32066581 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
32066537 CAGTACACTT
32066547 AAACAAACCC
1 AAACAAACCC
32066557 AAACAAACCC
1 AAACAAACCC
32066567 AATTACAAACCC
1 AA--ACAAACCC
32066579 AAA
1 AAA
32066582 TCAGATGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.60, C:0.34, G:0.00, T:0.06
Consensus pattern (10 bp):
AAACAAACCC
Found at i:32067777 original size:2 final size:2
Alignment explanation
Indices: 32067770--32067805 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32067760 ATACATACGC
32067770 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
32067806 TTCTTATAGT
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:32068078 original size:18 final size:19
Alignment explanation
Indices: 32068035--32068078 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
32068025 TACATAAATT
*
32068035 TTATTTTATTTTTATTTTGA
1 TTATTTTA-TTTTATTTTCA
*
32068055 TAATTTTA-TTTATTTTCA
1 TTATTTTATTTTATTTTCA
32068073 TTATTT
1 TTATTT
32068079 GTTGTTATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 14 0.67
20 7 0.33
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTATTTTATTTTATTTTCA
Found at i:32068254 original size:21 final size:21
Alignment explanation
Indices: 32068228--32068267 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
32068218 TGTATTATGT
32068228 TTATTTACATTAT-CATATTTA
1 TTATTT-CATTATGCATATTTA
32068249 TTATTTCATTATGCATATT
1 TTATTTCATTATGCATATT
32068268 AACATCGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (21 bp):
TTATTTCATTATGCATATTTA
Found at i:32068490 original size:109 final size:109
Alignment explanation
Indices: 32068294--32068721 Score: 658
Period size: 109 Copynumber: 3.9 Consensus size: 109
32068284 AAAGAAAACT
* * * * *
32068294 TTTCTAAATAAGGCAATATTTAGCATTTGGAAATTCGAGGAAACGTGCCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* *
32068359 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTCTAAAAA
66 CGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAA
*
32068403 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
*
32068468 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAA
* * *
32068512 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCATAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* *
32068577 CGATTTTTCTCGTTTAACCAAATGGCTTAATATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAA
* * * * *
32068621 TTTTAAAATAAGACAATGTTTTGTATTTGGAAATTTGAGAAAACATACCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* * *
32068686 CGATTTTTCTCGTTTAACCAAATTGCCAAATATCCT
66 CGATTTTTCTCGTTCAACCAAATGGCTAAATATCCT
32068722 CTTGAATTTT
Statistics
Matches: 298, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 298 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
CGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTTAAAAA
Found at i:32069717 original size:6 final size:6
Alignment explanation
Indices: 32069706--32069736 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
32069696 TCCATGCATT
32069706 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC T
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC T
32069737 TTCTTTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTTTC
Found at i:32073115 original size:19 final size:19
Alignment explanation
Indices: 32073069--32073108 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
32073059 ATTTATGTTT
* *
32073069 TTTTAATATAATATAATTA
1 TTTTAATATAATAAAATAA
32073088 TTTTAATATAATAAAATAA
1 TTTTAATATAATAAAATAA
32073107 TT
1 TT
32073109 ATTATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTAATATAATAAAATAA
Found at i:32076105 original size:13 final size:12
Alignment explanation
Indices: 32076084--32076133 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
32076074 TTAACAATGT
*
32076084 TTTTAAAAAGTG
1 TTTTGAAAAGTG
32076096 CTTTTGAAAAGTG
1 -TTTTGAAAAGTG
*
32076109 TTGTGAAAAAGTG
1 TTTTG-AAAAGTG
32076122 TTTTTGAAAAGT
1 -TTTTGAAAAGT
32076134 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 4 0.12
13 24 0.75
14 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.40
Consensus pattern (12 bp):
TTTTGAAAAGTG
Found at i:32081277 original size:25 final size:25
Alignment explanation
Indices: 32081243--32081290 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
32081233 CCTCATACAT
32081243 ATTTCAATACAAATAAGATGCTGTA
1 ATTTCAATACAAATAAGATGCTGTA
*
32081268 ATTTCAATACAAATACGATGCTG
1 ATTTCAATACAAATAAGATGCTG
32081291 ACAGTTTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (25 bp):
ATTTCAATACAAATAAGATGCTGTA
Found at i:32085519 original size:51 final size:51
Alignment explanation
Indices: 32085464--32085564 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
32085454 GATGAAGAAA
* *
32085464 AAGAAAAGAAAGAGGCAAAGGGTGATGATGGATCTTTAGTGATTAATGCAG
1 AAGAAAAGAAAGAAGCAAAGGGTGATGATGGATCTTTAGTGATGAATGCAG
32085515 AAGAAAAGAAAGAAGCAAAGGGTGATGATGGATCTTTAGTGATGAATGCA
1 AAGAAAAGAAAGAAGCAAAGGGTGATGATGGATCTTTAGTGATGAATGCA
32085565 TCCATTGTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.43, C:0.06, G:0.31, T:0.21
Consensus pattern (51 bp):
AAGAAAAGAAAGAAGCAAAGGGTGATGATGGATCTTTAGTGATGAATGCAG
Found at i:32086621 original size:15 final size:16
Alignment explanation
Indices: 32086595--32086627 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
32086585 GTTAAAAGTT
32086595 TTTTGAATTTGGGTTA
1 TTTTGAATTTGGGTTA
*
32086611 TTTTG-ATTTGGTTTA
1 TTTTGAATTTGGGTTA
32086626 TT
1 TT
32086628 ATAAGAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.64
Consensus pattern (16 bp):
TTTTGAATTTGGGTTA
Found at i:32094470 original size:195 final size:195
Alignment explanation
Indices: 32094137--32094600 Score: 732
Period size: 195 Copynumber: 2.4 Consensus size: 195
32094127 AACATTATAG
32094137 TTTTGATATTAAATTAGGAATTTTGATATCCATAGAAATTTTGGTATGACTTTAAAAATTTTGGT
1 TTTTGATATTAAATTAGGAATTTTGATATCCATAGAAATTTTGGTATGACTTTAAAAA-TTTGGT
* * * **
32094202 TCAAGCTATTGGTGAGACCACGAGCTAGAAAAGAGAATTTTAATATACCAAACTATCTAATGGTT
65 TCAAGCTATTGGTGAGACCACAAGCTACAAAAAAGAATTTTAATATACCAAAAAATCTAATGGTT
* * * *
32094267 TCATTAAAAGTAGTAGTATAGCGTTAGAAATTTTGATAGAAGCTCTTACGGGCGAGAAAGGGAAA
130 TCATTAAAAATAGTAGTATAGCGTTAGAAATTTTGATACAAACTCGTACGGGCGAGAAAGGGAAA
32094332 A
195 A
*
32094333 TTTTGATCTTAAATTAGGAATTTTGATATCCATAGAAATTTTGGTATGACTTTAAAAATTTGGTT
1 TTTTGATATTAAATTAGGAATTTTGATATCCATAGAAATTTTGGTATGACTTTAAAAATTTGGTT
*
32094398 CAAGCTATTGGTGAGACTACAAGCTACAAAAAAGAATTTTAATATACCAAAAAATCTAATGGTTT
66 CAAGCTATTGGTGAGACCACAAGCTACAAAAAAGAATTTTAATATACCAAAAAATCTAATGGTTT
* * *
32094463 CATTAAAAATATTAGTATAGCGTTAGAAATTTTGATACAAACTCGTACGGGTGAGAAAGGGGAAA
131 CATTAAAAATAGTAGTATAGCGTTAGAAATTTTGATACAAACTCGTACGGGCGAGAAAGGGAAAA
* * *
32094528 TTTTGATATTTAAA-TAGGAATTTTAATATCCATAAAAAATTTGGTATGACTTTAAAAATTTGGG
1 TTTTGATA-TTAAATTAGGAATTTTGATATCCATAGAAATTTTGGTATGACTTTAAAAATTT-GG
*
32094592 TTGAAGCTA
64 TTCAAGCTA
32094601 AAAGAGAAAT
Statistics
Matches: 247, Mismatches: 19, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
195 175 0.71
196 72 0.29
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (195 bp):
TTTTGATATTAAATTAGGAATTTTGATATCCATAGAAATTTTGGTATGACTTTAAAAATTTGGTT
CAAGCTATTGGTGAGACCACAAGCTACAAAAAAGAATTTTAATATACCAAAAAATCTAATGGTTT
CATTAAAAATAGTAGTATAGCGTTAGAAATTTTGATACAAACTCGTACGGGCGAGAAAGGGAAAA
Found at i:32096269 original size:19 final size:19
Alignment explanation
Indices: 32096231--32096282 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
32096221 ATTTATTATT
***
32096231 TGTTTTATAATATTTTAAA
1 TGTTTTATAATATACCAAA
32096250 TGTTTTATAATATACCAAA
1 TGTTTTATAATATACCAAA
*
32096269 TAATTTTA-AATATA
1 T-GTTTTATAATATA
32096283 ATTTTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (19 bp):
TGTTTTATAATATACCAAA
Found at i:32096325 original size:21 final size:22
Alignment explanation
Indices: 32096301--32096346 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
32096291 AAAACGTTTG
* *
32096301 AATAAAAAAT-ATTATAAAATA
1 AATAAAAAATAATTAAAAAACA
*
32096322 AATAATAAATAATTAAAAAACA
1 AATAAAAAATAATTAAAAAACA
32096344 AAT
1 AAT
32096347 TTAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AATAAAAAATAATTAAAAAACA
Found at i:32096393 original size:81 final size:80
Alignment explanation
Indices: 32096306--32096548 Score: 374
Period size: 81 Copynumber: 3.1 Consensus size: 80
32096296 GTTTGAATAA
32096306 AAAATATTATAAAATAAATAATAAATAATTAAAAAACAAATTTAAAAAAAACGTTTGAATAAAAA
1 AAAATATTATAAAATAAATAATAAATAATTAAAAAACAAATTT-AAAAAAACGTTTGAATAAAAA
32096371 ATATTATAAAACATTT
65 ATATTATAAAACATTT
32096387 AAAATATTATAAAATAAATAATAAATAATTAAAAAACAAATTTTAAAAAAACGTTTGAATAAAAA
1 AAAATATTATAAAATAAATAATAAATAATTAAAAAACAAA-TTTAAAAAAACGTTTGAATAAAAA
32096452 ATATTATAAAACATTT
65 ATATTATAAAACATTT
* ** *
32096468 AAAATATTAT-AAA-AACTAATAAAT-ATT-TTAAA-AAA--TAAAAAAATGTTTGAATAAACAA
1 AAAATATTATAAAATAAATAATAAATAATTAAAAAACAAATTTAAAAAAACGTTTGAATAAA-AA
32096526 ATATTATAAAACATTT
65 ATATTATAAAACATTT
32096542 AAAATAT
1 AAAATAT
32096549 GCATTTACAA
Statistics
Matches: 156, Mismatches: 4, Indels: 11
0.91 0.02 0.06
Matches are distributed among these distances:
73 19 0.12
74 25 0.16
76 3 0.02
77 3 0.02
78 3 0.02
79 10 0.06
80 3 0.02
81 87 0.56
82 3 0.02
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (80 bp):
AAAATATTATAAAATAAATAATAAATAATTAAAAAACAAATTTAAAAAAACGTTTGAATAAAAAA
TATTATAAAACATTT
Found at i:32096399 original size:10 final size:10
Alignment explanation
Indices: 32096368--32096402 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
32096358 GTTTGAATAA
32096368 AAAATATTAT
1 AAAATATTAT
*
32096378 AAAACATT-T
1 AAAATATTAT
32096387 AAAATATTAT
1 AAAATATTAT
32096397 AAAATA
1 AAAATA
32096403 AATAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATATTAT
Found at i:32096480 original size:10 final size:10
Alignment explanation
Indices: 32096449--32096481 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
32096439 GTTTGAATAA
32096449 AAAATATTAT
1 AAAATATTAT
*
32096459 AAAACATT-T
1 AAAATATTAT
32096468 AAAATATTAT
1 AAAATATTAT
32096478 AAAA
1 AAAA
32096482 ACTAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATATTAT
Found at i:32096491 original size:19 final size:18
Alignment explanation
Indices: 32096448--32096508 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
32096438 CGTTTGAATA
*
32096448 AAAAATATTATAAAACATT
1 AAAAATATTATAAAA-ACT
*
32096467 TAAAATATTATAAAAACT
1 AAAAATATTATAAAAACT
* *
32096485 AATAAATATTTTAAAAAAT
1 AA-AAATATTATAAAAACT
32096504 AAAAA
1 AAAAA
32096509 AATGTTTGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 6 0.17
19 30 0.83
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATATTATAAAAACT
Found at i:32096579 original size:73 final size:68
Alignment explanation
Indices: 32096407--32096579 Score: 166
Period size: 73 Copynumber: 2.4 Consensus size: 68
32096397 AAAATAAATA
* **
32096407 ATAAATAATTAAAAAACAAATTTTAAAAAAACGTTTGAATAAAAAATATTATAAAACATTTAAAA
1 ATAAA-AATTATAAAACAAATAATAAAAAAACGTTTGAATAAAAAATATTATAAAACATTTAAAA
32096472 TATT
65 TATT
* * * *
32096476 ATAAAAACTAATAAATATTTTAAAAAATAAAAAAATGTTTGAATAAACAAATATTATAAAACATT
1 ATAAAAA-TTATAAA-A---CAAATAATAAAAAAACGTTTGAATAAA-AAATATTATAAAACATT
32096541 TAAAATATGCAT
60 TAAAATAT---T
* *
32096553 TTACAATATTATAAAACAAATAATAAA
1 ATA-AAAATTATAAAACAAATAATAAA
32096580 TAATTTTTAA
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
68 2 0.02
69 10 0.12
70 1 0.01
73 31 0.38
74 25 0.30
76 1 0.01
77 9 0.11
78 3 0.04
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (68 bp):
ATAAAAATTATAAAACAAATAATAAAAAAACGTTTGAATAAAAAATATTATAAAACATTTAAAAT
ATT
Found at i:32096644 original size:28 final size:28
Alignment explanation
Indices: 32096587--32096646 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
32096577 AAATAATTTT
** *
32096587 TAAAAAAAATTCAAAAAAAAATTTTGAA
1 TAAAAAAAATTCAAAAAAAAATAATAAA
*
32096615 TAAAAAAAATT-ATAAAACAAATAATAAA
1 TAAAAAAAATTCA-AAAAAAAATAATAAA
32096643 TAAA
1 TAAA
32096647 CCAGAAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (28 bp):
TAAAAAAAATTCAAAAAAAAATAATAAA
Found at i:32100393 original size:32 final size:31
Alignment explanation
Indices: 32100347--32100406 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
32100337 CTCTCCATTG
32100347 ATTCAATAATATAAT-TAAAATATTTTAATTT
1 ATTCAATAATATAATAT-AAATATTTTAATTT
* *
32100378 ATTCAAATATTATAATATAAATTTTTTAA
1 ATTC-AATAATATAATATAAATATTTTAA
32100407 ATAATAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 4 0.16
32 20 0.80
33 1 0.04
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (31 bp):
ATTCAATAATATAATATAAATATTTTAATTT
Found at i:32101862 original size:18 final size:18
Alignment explanation
Indices: 32101848--32101911 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
32101838 TACTTTTATT
32101848 TAATTTT-T-AATTTTTA
1 TAATTTTATAAATTTTTA
32101864 TAATTTTATAAATTTTTAA
1 TAATTTTATAAATTTTT-A
* **
32101883 AAATAATATAAATTTTTTTA
1 TAATTTTATAAA--TTTTTA
32101903 TAATTTTAT
1 TAATTTTAT
32101912 TTATGATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.19
17 1 0.03
18 7 0.19
19 10 0.27
20 7 0.19
21 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAATTTTATAAATTTTTA
Done.