Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009625.1 Hibiscus syriacus cultivar Beakdansim tig00117017_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6938204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 25
Found at i:5482100 original size:10 final size:10
Alignment explanation
Indices: 5482069--5482117 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
5482059 GTCGGGTCAG
* *
5482069 ACCGGTCCAG
1 ACCGGTTCAA
5482079 ACCGG-TCAA
1 ACCGGTTCAA
*
5482088 ACCGGTTCGA
1 ACCGGTTCAA
5482098 ACCGG-TCAA
1 ACCGGTTCAA
5482107 ACCGGTTCAA
1 ACCGGTTCAA
5482117 A
1 A
5482118 ACTAGTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 15 0.45
10 18 0.55
ACGTcount: A:0.29, C:0.33, G:0.24, T:0.14
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:5482113 original size:19 final size:20
Alignment explanation
Indices: 5482079--5482133 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
5482069 ACCGGTCCAG
*
5482079 ACCGGTCAAACCGGTTC-GA
1 ACCGGTCAAACCGGTTCAAA
5482098 ACCGGTCAAACCGGTTCAAA
1 ACCGGTCAAACCGGTTCAAA
**
5482118 ACTAGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
5482134 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (20 bp):
ACCGGTCAAACCGGTTCAAA
Found at i:5482127 original size:20 final size:19
Alignment explanation
Indices: 5482064--5482133 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
5482054 GACGGGTCGG
* * * *
5482064 GTCAGACCGGTCCAGACCG
1 GTCAAACCGGTTCAAACCA
* *
5482083 GTCAAACCGGTTCGAACCG
1 GTCAAACCGGTTCAAACCA
*
5482102 GTCAAACCGGTTCAAAACTA
1 GTCAAACCGGTTC-AAACCA
5482122 GTCAAACCGGTT
1 GTCAAACCGGTT
5482134 TTCCAGCAGC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 28 0.65
20 15 0.35
ACGTcount: A:0.29, C:0.30, G:0.24, T:0.17
Consensus pattern (19 bp):
GTCAAACCGGTTCAAACCA
Found at i:5485420 original size:31 final size:31
Alignment explanation
Indices: 5485361--5485420 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5485351 GTTATTGACA
* *
5485361 AATTTATTATAAATAAATAACGTTAGTGATC
1 AATTTATTATAAATAAATAACATCAGTGATC
* *
5485392 AATTTATTATAAATCAATAATATCAGTGA
1 AATTTATTATAAATAAATAACATCAGTGA
5485421 CAAATTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (31 bp):
AATTTATTATAAATAAATAACATCAGTGATC
Found at i:5487590 original size:26 final size:26
Alignment explanation
Indices: 5487559--5487650 Score: 184
Period size: 26 Copynumber: 3.5 Consensus size: 26
5487549 GCATGGTCTT
5487559 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
5487585 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
5487611 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
5487637 GTGCATCGATGCAT
1 GTGCATCGATGCAT
5487651 GGTATGTGCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 66 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (26 bp):
GTGCATCGATGCATCAAATGCACTGA
Found at i:5487733 original size:20 final size:20
Alignment explanation
Indices: 5487697--5487734 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5487687 TGAAAAAATA
**
5487697 ATTGGTGCATCGGTGCATAG
1 ATTGGTGCATCAATGCATAG
5487717 ATTGGTGCATCAATGCAT
1 ATTGGTGCATCAATGCAT
5487735 CACTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCAATGCATAG
Found at i:5496112 original size:45 final size:46
Alignment explanation
Indices: 5496023--5496113 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
5496013 TTGAAAAAGC
* *
5496023 CTGAGTGCATCGATGCATGGTCTTATGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATATGCATCGATGCATAAAATGCA
*
5496069 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATATGCATCGATGCATAAAATGCA
5496114 TTCGATGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.50
46 21 0.50
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATATGCATCGATGCATAAAATGCA
Found at i:5496158 original size:20 final size:20
Alignment explanation
Indices: 5496133--5496170 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5496123 TGAAAAAATA
5496133 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
5496153 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
5496171 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:5496733 original size:22 final size:19
Alignment explanation
Indices: 5496683--5496739 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 19
5496673 TCAATATCAG
5496683 TTTAATCATCTAATATATGA
1 TTTAATCAT-TAATATATGA
*
5496703 TTTAATCATTAATATTTAGAA
1 TTTAATCATTAATATAT-G-A
5496724 TTTAAATCATTAATAT
1 TTT-AATCATTAATAT
5496740 CAGTTCAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 7 0.21
20 10 0.30
21 4 0.12
22 12 0.36
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (19 bp):
TTTAATCATTAATATATGA
Found at i:5505982 original size:8 final size:8
Alignment explanation
Indices: 5505969--5506001 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
5505959 TATTCATTAT
5505969 TAAAATGA
1 TAAAATGA
5505977 TAAAATGA
1 TAAAATGA
*
5505985 TAAAATAA
1 TAAAATGA
5505993 TAAAATGA
1 TAAAATGA
5506001 T
1 T
5506002 CATTTGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (8 bp):
TAAAATGA
Found at i:5510147 original size:3 final size:3
Alignment explanation
Indices: 5510139--5510165 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5510129 CTAATTTCAA
5510139 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
5510166 GAAACAACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5518255 original size:21 final size:20
Alignment explanation
Indices: 5518209--5518266 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
5518199 TTTTGGTGCA
* *
5518209 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATTCCCCCTT
*
5518229 GAGGGAACCGATTCCCCTTT
1 GAGGGAACCGATTCCCCCTT
*
5518249 GAGGGGAACCAATTCCCC
1 GA-GGGAACCGATTCCCC
5518267 ACAGGGGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.22, C:0.33, G:0.26, T:0.19
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:5518390 original size:19 final size:19
Alignment explanation
Indices: 5518366--5518429 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
5518356 CTCTAAGCAT
5518366 TCAAATCTCCATTTTTGCC
1 TCAAATCTCCATTTTTGCC
* * ** *
5518385 TCAAATCACC-TCTAAGCAT
1 TCAAATCTCCATTTTTGC-C
5518404 TCAAATCTCCATTTTTGCC
1 TCAAATCTCCATTTTTGCC
5518423 TCAAATC
1 TCAAATC
5518430 AACGTTTTTA
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
18 4 0.12
19 25 0.76
20 4 0.12
ACGTcount: A:0.28, C:0.31, G:0.05, T:0.36
Consensus pattern (19 bp):
TCAAATCTCCATTTTTGCC
Found at i:5518403 original size:38 final size:38
Alignment explanation
Indices: 5518352--5518430 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
5518342 CCGCCGTTTC
5518352 TCACCTCTAAGCATTCAAATCTCCATTTTTGCCTCAAA
1 TCACCTCTAAGCATTCAAATCTCCATTTTTGCCTCAAA
5518390 TCACCTCTAAGCATTCAAATCTCCATTTTTGCCTCAAA
1 TCACCTCTAAGCATTCAAATCTCCATTTTTGCCTCAAA
5518428 TCA
1 TCA
5518431 ACGTTTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.29, C:0.32, G:0.05, T:0.34
Consensus pattern (38 bp):
TCACCTCTAAGCATTCAAATCTCCATTTTTGCCTCAAA
Found at i:5522738 original size:34 final size:35
Alignment explanation
Indices: 5522700--5522765 Score: 116
Period size: 34 Copynumber: 1.9 Consensus size: 35
5522690 CTAATATTTT
*
5522700 AATATAATTGAATACATTATT-ATAATATTAAAAA
1 AATATAATTGAATACATTATTAAAAATATTAAAAA
5522734 AATATAATTGAATACATTATTAAAAATATTAA
1 AATATAATTGAATACATTATTAAAAATATTAA
5522766 TATATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 21 0.70
35 9 0.30
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (35 bp):
AATATAATTGAATACATTATTAAAAATATTAAAAA
Found at i:5522802 original size:21 final size:21
Alignment explanation
Indices: 5522737--5522804 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
5522727 TTAAAAAAAT
*
5522737 ATAATTGAATACA-TTATTAAA
1 ATAATT-AATATATTTATTAAA
* **
5522758 A-ATATTAATATATATATTTTA
1 ATA-ATTAATATATTTATTAAA
*
5522779 ATAATTAATATTTTTATTAAA
1 ATAATTAATATATTTATTAAA
5522800 ATAAT
1 ATAAT
5522805 ATTAAAATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
20 6 0.17
21 29 0.81
22 1 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
ATAATTAATATATTTATTAAA
Found at i:5523072 original size:17 final size:17
Alignment explanation
Indices: 5523050--5523082 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5523040 CAAACAAACT
*
5523050 CTTAATTTCTGTTTTTA
1 CTTAATTTCTATTTTTA
5523067 CTTAATTTCTATTTTT
1 CTTAATTTCTATTTTT
5523083 GATAATCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (17 bp):
CTTAATTTCTATTTTTA
Found at i:5524668 original size:44 final size:44
Alignment explanation
Indices: 5524601--5524797 Score: 132
Period size: 44 Copynumber: 4.5 Consensus size: 44
5524591 TATCCAGCGT
** * * *
5524601 GAAGAACCACTTCATATGGCTTAAACTCGCAAAGGGGAGTCATTC
1 GAAGAA-CACTTCACCTGACTTAAACCCGCAAAGGGGAGTCATCC
* * *
5524646 GAAGAACACTTCACCTGACTTAAACCCACAAA--GAAGTCCTCC
1 GAAGAACACTTCACCTGACTTAAACCCGCAAAGGGGAGTCATCC
* * * * * * *
5524688 GAAAAACATTTCACC-CAGCTTAAACCCGCGAATGAGAGTCATCAA
1 GAAGAACACTTCACCTGA-CTTAAACCCGCAAAGGGGAGTCATC-C
* * ** *
5524733 AAAGAACATTTCATATGGCTTAAACCCGCAAAGGGGAGTCATCC
1 GAAGAACACTTCACCTGACTTAAACCCGCAAAGGGGAGTCATCC
* *
5524777 AAAGAATA-TTACACCTGACTT
1 GAAGAACACTT-CACCTGACTT
5524798 CACTCGCAAA
Statistics
Matches: 115, Mismatches: 31, Indels: 13
0.72 0.19 0.08
Matches are distributed among these distances:
41 1 0.01
42 32 0.28
43 2 0.02
44 41 0.36
45 39 0.34
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (44 bp):
GAAGAACACTTCACCTGACTTAAACCCGCAAAGGGGAGTCATCC
Found at i:5526796 original size:18 final size:17
Alignment explanation
Indices: 5526765--5526798 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5526755 GAATTTACGC
5526765 TTATTTTTTAAATATTA
1 TTATTTTTTAAATATTA
*
5526782 TTATTGTTTTTAATATT
1 TTATT-TTTTAAATATT
5526799 TTTAGGGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATTTTTTAAATATTA
Found at i:5528054 original size:6 final size:6
Alignment explanation
Indices: 5528043--5528068 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5528033 CGAAAATTCG
5528043 AAATTT AAATTT AAATTT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AA
5528069 CAGACCCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:5528256 original size:22 final size:22
Alignment explanation
Indices: 5528228--5528271 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5528218 GCAAAACACG
5528228 TAAAAATAATAAAAAAT-AATAA
1 TAAAAATAA-AAAAAATGAATAA
*
5528250 TAAAAATAAACAAAATGAATAA
1 TAAAAATAAAAAAAATGAATAA
5528272 AATGTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (22 bp):
TAAAAATAAAAAAAATGAATAA
Found at i:5528257 original size:19 final size:19
Alignment explanation
Indices: 5528235--5528273 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5528225 ACGTAAAAAT
5528235 AATAAAAAATAAT-AATAAA
1 AATAAAAAA-AATGAATAAA
*
5528254 AATAAACAAAATGAATAAA
1 AATAAAAAAAATGAATAAA
5528273 A
1 A
5528274 TGTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (19 bp):
AATAAAAAAAATGAATAAA
Found at i:5528426 original size:33 final size:34
Alignment explanation
Indices: 5528388--5528459 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
5528378 TAGTATTTAC
* *
5528388 TAAAACAAA-TAAAAATAAATATATAATACTAAG
1 TAAAACAAATTAAAAATAAAGATACAATACTAAG
*
5528421 TAAAACAAATTAAAAATAAAGATACAATATTAAG
1 TAAAACAAATTAAAAATAAAGATACAATACTAAG
*
5528455 AAAAA
1 TAAAA
5528460 ATAATAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 9 0.26
34 25 0.74
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22
Consensus pattern (34 bp):
TAAAACAAATTAAAAATAAAGATACAATACTAAG
Found at i:5528500 original size:23 final size:23
Alignment explanation
Indices: 5528474--5528538 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 23
5528464 TAGAAAAAAA
*
5528474 AAATAAAGTAAAATATAATATAT
1 AAATAAAGTAAAATATAATATAG
*
5528497 AAATAAA-TAAAA-ATAAAATAG
1 AAATAAAGTAAAATATAATATAG
*
5528518 AATATTAAG-AAAATAT-ATATA
1 AA-ATAAAGTAAAATATAATATA
5528539 AAAACGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 9 0.26
22 17 0.49
23 9 0.26
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (23 bp):
AAATAAAGTAAAATATAATATAG
Found at i:5528501 original size:39 final size:39
Alignment explanation
Indices: 5528432--5528516 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 39
5528422 AAAACAAATT
*
5528432 AAAAATAAAGATACAATATTAAGAAAAAATAATAGAAAAA
1 AAAAATAAAGATAAAATATTAAGAAAAAATAA-AGAAAAA
* * *
5528472 AAAAATAAAG-TAAAATA-TAATATATAAATAAATAAAAA
1 AAAAATAAAGATAAAATATTAAGA-AAAAATAAAGAAAAA
*
5528510 TAAAATA
1 AAAAATA
5528517 GAATATTAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
38 16 0.41
39 13 0.33
40 10 0.26
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (39 bp):
AAAAATAAAGATAAAATATTAAGAAAAAATAAAGAAAAA
Found at i:5528530 original size:16 final size:16
Alignment explanation
Indices: 5528511--5528564 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5528501 AAATAAAAAT
*
5528511 AAAATAGAATATTAAG
1 AAAATATAATATTAAG
**
5528527 AAAATATATATAAAAACG
1 AAAATATA-ATATTAA-G
*
5528545 TAAATATAATATTAAG
1 AAAATATAATATTAAG
5528561 AAAA
1 AAAA
5528565 AATATATACA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
16 11 0.38
17 10 0.34
18 8 0.28
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (16 bp):
AAAATATAATATTAAG
Found at i:5528531 original size:27 final size:27
Alignment explanation
Indices: 5528471--5528541 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
5528461 TAATAGAAAA
* *
5528471 AAAAAAT-AAAGTAAAATATAATATAT
1 AAAAAATAAAAATAAAATAGAATATAT
5528497 AAATAAATAAAAATAAAATAGAATAT-T
1 AAA-AAATAAAAATAAAATAGAATATAT
* *
5528524 AAGAAAATATATATAAAA
1 AA-AAAATAAAAATAAAA
5528542 ACGTAAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 3 0.08
27 19 0.50
28 16 0.42
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAAAATAAAAATAAAATAGAATATAT
Found at i:5528533 original size:39 final size:38
Alignment explanation
Indices: 5528431--5528536 Score: 98
Period size: 39 Copynumber: 2.8 Consensus size: 38
5528421 TAAAACAAAT
*
5528431 TAAAAATAAAGATACAATATTAAGAAAA-A-AT-AATAGA
1 TAAAAATAAA-ATA-AATATTAAGAAAATATATAAATAAA
* * *
5528468 -AAAAA-AAAATAAAGTA-AAATATAATATATAAATAAA
1 TAAAAATAAAATAAA-TATTAAGAAAATATATAAATAAA
5528504 TAAAAATAAAATAGAATATTAAGAAAATATATA
1 TAAAAATAAAATA-AATATTAAGAAAATATATA
5528537 TAAAAACGTA
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
33 7 0.13
34 6 0.11
35 5 0.09
36 10 0.19
37 5 0.09
38 8 0.15
39 13 0.24
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.24
Consensus pattern (38 bp):
TAAAAATAAAATAAATATTAAGAAAATATATAAATAAA
Found at i:5528632 original size:24 final size:24
Alignment explanation
Indices: 5528603--5528651 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5528593 TAATACATCT
* *
5528603 ATATATATTATATATAATGATATAAG
1 ATATATA-TA-ATAAAATAATATAAG
5528629 ATATATATAATAAAATAATATAA
1 ATATATATAATAAAATAATATAA
5528652 TATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 2 0.10
26 7 0.33
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
ATATATATAATAAAATAATATAAG
Found at i:5528646 original size:19 final size:19
Alignment explanation
Indices: 5528611--5528662 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5528601 CTATATATAT
* *
5528611 TATATATAATGATATAAGA
1 TATATATAATAAAATAAGA
*
5528630 TATATATAATAAAATAATA
1 TATATATAATAAAATAAGA
5528649 TA-ATATAAATAAAA
1 TATATAT-AATAAAA
5528663 AGAGGAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
TATATATAATAAAATAAGA
Found at i:5528651 original size:13 final size:14
Alignment explanation
Indices: 5528622--5528660 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
5528612 ATATATAATG
5528622 ATATAAGATATATATA
1 ATATAA-ATA-ATATA
5528638 ATA-AAATAATATA
1 ATATAAATAATATA
5528651 ATATAAATAA
1 ATATAAATAA
5528661 AAAGAGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 9 0.41
15 2 0.09
16 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATAAATAATATA
Found at i:5529988 original size:36 final size:36
Alignment explanation
Indices: 5529940--5530048 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 36
5529930 GGTTTTTTTT
*
5529940 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
**
5529976 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--AC
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* * * * *
5530010 TTCCAAAAGAAACTGTCTCAAGGGAGACGAGATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
5530046 TTT
1 TTT
5530049 AACGTAAAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
34 27 0.45
36 33 0.55
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:5530021 original size:34 final size:35
Alignment explanation
Indices: 5529948--5530037 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 35
5529938 TTTTTCAAGG
** * *
5529948 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAA
5529984 GAAACTGTCTCAAGAGAGACAAAA-ACTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
*
5530018 GAAACTGTCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
5530038 GAGATTTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 25 0.51
36 24 0.49
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:5530098 original size:30 final size:30
Alignment explanation
Indices: 5530062--5530120 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5530052 GTAAAACATA
*
5530062 TTCAAAGATTT-TGTTTCAA-AGGAAACTGTT
1 TTCAAAG-TTTATGCTTCAAGA-GAAACTGTT
5530092 TTCAAAGTTTATGCTTCAAGAGAAACTGT
1 TTCAAAGTTTATGCTTCAAGAGAAACTGT
5530121 CTCAAGGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 22 0.85
31 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (30 bp):
TTCAAAGTTTATGCTTCAAGAGAAACTGTT
Found at i:5530153 original size:36 final size:36
Alignment explanation
Indices: 5530106--5530275 Score: 124
Period size: 36 Copynumber: 4.9 Consensus size: 36
5530096 AAGTTTATGC
* *
5530106 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * * **
5530142 TTCAAGGGAAACTATCTCATGAGTGACAAAATTCAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
* * *
5530178 TTCAAGGGAAA-TGTTTTC-A-A-TG-----TTTATGT
1 TTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT-TGT
* *
5530207 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATATTGT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-TTGT
* *
5530244 TTCAAGGGAACCTATCTCAAGAGAGACAAAAT
1 TTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
5530276 GCATCTCAGG
Statistics
Matches: 100, Mismatches: 22, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
28 2 0.02
29 14 0.14
30 3 0.03
32 1 0.01
33 2 0.02
34 1 0.01
35 1 0.01
36 43 0.43
37 32 0.32
38 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:5530262 original size:37 final size:37
Alignment explanation
Indices: 5530204--5530275 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
5530194 TCAATGTTTA
* *
5530204 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATAT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATAT
* *
5530241 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
5530276 GCATCTCAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATAT
Found at i:5530274 original size:102 final size:101
Alignment explanation
Indices: 5530075--5530457 Score: 417
Period size: 102 Copynumber: 3.8 Consensus size: 101
5530065 AAAGATTTTG
* * *
5530075 TTTCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * *
5530140 GTTTCAAGGGAAACTATCTCATGAGTGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATGCA
5530177 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATATT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT-TT
*
5530242 GTTTCAAGGGAACCTATCTCAAGAGAGACAAAATGCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATGCA
* * * * *
5530279 TCTCAGGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* ** * * * * ***
5530344 GTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTG
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATGCA
* **** * * * * * *
5530381 TGTCAAGGGAAACAAATTCAAAGATTT-TGTTTCAAGAGAAACTATCTTAAGAGAGACATAATTC
1 TTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
5530445 ATTTCAAGGGAAA
65 GTTTCAAGGGAAA
5530458 TGTTTTCAAT
Statistics
Matches: 241, Mismatches: 37, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
101 59 0.24
102 178 0.74
103 4 0.02
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATGCA
Found at i:5530415 original size:167 final size:167
Alignment explanation
Indices: 5530240--5530712 Score: 811
Period size: 167 Copynumber: 2.8 Consensus size: 167
5530230 AGACAAAATA
* * * * *
5530240 TTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATGCATCTCAGGGGAAATGTTTTCAATGTTT
1 TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTT
5530305 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGA
66 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGA
*
5530370 GACGAAATTTGTGTCAAGGGAAACAAATTCAAAGATT
131 GACAAAATTTGTGTCAAGGGAAACAAATTCAAAGATT
* *
5530407 TTGTTTCAAGAGAAACTATCTTAAGAGAGACATAATTCATTTCAAGGGAAATGTTTTCAATGTTT
1 TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTT
*
5530472 ATGTTTCAAGTGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGA
66 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGA
* *
5530537 GACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATT
131 GACAAAATTTGTGTCAAGGGAAACAAATTCAAAGATT
*
5530574 TTGTTTCAAGAGAAACTATCTCAAAAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTT
1 TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTT
* * *
5530639 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGAAAATGTCTCAAGGGA
66 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGA
5530704 GACAAAATT
131 GACAAAATT
5530713 AATTTCAATG
Statistics
Matches: 288, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
167 288 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (167 bp):
TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTT
ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGA
GACAAAATTTGTGTCAAGGGAAACAAATTCAAAGATT
Found at i:5530523 original size:102 final size:102
Alignment explanation
Indices: 5530417--5530608 Score: 244
Period size: 102 Copynumber: 1.9 Consensus size: 102
5530407 TTGTTTCAAG
* * * * * *
5530417 AGAAACTATCTTAAGAGAGACATAATTCATTTCAAGGGAAA-TGTTTTCAATG-TTTATGTTTCA
1 AGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCA
* *
5530480 AGTGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
64 AGAGAAACTATCTCAAAAGAGACAAAACTTAGTTCCAAA
* * **
5530519 AGAAAATGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
1 AGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
5530584 AGAAACTATCTCAAAAGAGACAAAA
66 AGAAACTATCTCAAAAGAGACAAAA
5530609 TTCATTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
102 72 0.95
103 4 0.05
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (102 bp):
AGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
AGAAACTATCTCAAAAGAGACAAAACTTAGTTCCAAA
Found at i:5530623 original size:65 final size:65
Alignment explanation
Indices: 5530535--5530675 Score: 178
Period size: 65 Copynumber: 2.2 Consensus size: 65
5530525 TGTCTCAAGG
**
5530535 GAGACAAAATTTGTTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAA
1 GAGACAAAATTCATTTCAAGGGAAA-AGTATTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAA
5530598 AA
64 AA
* * * * **
5530600 GAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGG
1 GAGACAAAATTCATTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAAA
5530665 GAGACAAAATT
1 GAGACAAAATT
5530676 TAGTTCCAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
64 4 0.06
65 62 0.94
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (65 bp):
GAGACAAAATTCATTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAAA
Found at i:5531097 original size:106 final size:106
Alignment explanation
Indices: 5530905--5531223 Score: 397
Period size: 106 Copynumber: 3.0 Consensus size: 106
5530895 TGTATTGTTC
* * * * *** * **
5530905 CGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACA
* * * * *
5530970 GCCAGCCGCCCCTT-TTATGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCCGTCCCTTCGT-TGTGAAGTTGAACTTGTGTTGTCT
* * *
5531011 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACA
* *
5531076 ACCAGCCGTTCCTTCGTTGTGAAGTTGAACCTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
**
5531117 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACA
* * *
5531182 ACCAACCGTCCCTTCGTCGTGGAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
5531223 C
1 C
5531224 AAGTGGCACG
Statistics
Matches: 184, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
106 183 0.99
107 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:5531891 original size:32 final size:32
Alignment explanation
Indices: 5531805--5531892 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
5531795 TTTGCATCAG
* * *
5531805 GATGTTGAAT-TCCCAAAGATACCCCAATATTC
1 GATGTTGAATCT-ACAAAGATGCCCCAACATTC
* * *
5531837 GATGTTGAATCTAAAAAAATGCCCCAACATTT
1 GATGTTGAATCTACAAAGATGCCCCAACATTC
*
5531869 GATGTTGAATCTTCAAAGATGCCC
1 GATGTTGAATCTACAAAGATGCCC
5531893 TCATTGTTCC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
32 45 0.98
33 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (32 bp):
GATGTTGAATCTACAAAGATGCCCCAACATTC
Found at i:5532893 original size:69 final size:69
Alignment explanation
Indices: 5532778--5532915 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
5532768 TCTCTCTCTC
*
5532778 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCGAAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCAAAAATGATTGTGCTTGATCAATC
5532843 TCAT
66 TCAT
* *
5532847 TTGATGCTCTATGATCTTTGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCAAAAATGATTGTGCTTGATCAATC
5532912 TCAT
66 TCAT
5532916 AGTTTGAATC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAATGATTCAAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:5533016 original size:20 final size:20
Alignment explanation
Indices: 5532987--5533024 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5532977 TTTTTCTTCA
5532987 ATTTTCCTTTG-TTTTTTTT
1 ATTTTCCTTTGCTTTTTTTT
5533006 ATTTTCTCTTTGCTTTTTT
1 ATTTTC-CTTTGCTTTTTT
5533025 CTCCTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.76
Consensus pattern (20 bp):
ATTTTCCTTTGCTTTTTTTT
Found at i:5536139 original size:22 final size:23
Alignment explanation
Indices: 5536114--5536174 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 23
5536104 CAAACGTAAG
5536114 AATAATAAATAAAACA-AGAAAA
1 AATAATAAATAAAACACAGAAAA
*
5536136 AATAGA-AAATAACAAAACACATAAAA
1 AATA-ATAAAT---AAAACACAGAAAA
5536162 AATAAT-AATAAAA
1 AATAATAAATAAAA
5536175 ATAAACAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
22 12 0.38
23 1 0.03
25 10 0.31
26 9 0.28
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (23 bp):
AATAATAAATAAAACACAGAAAA
Found at i:5536171 original size:25 final size:24
Alignment explanation
Indices: 5536114--5536172 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
5536104 CAAACGTAAG
*
5536114 AATAATAAATAAAACAAGAAAAAAT
1 AATAAT-AACAAAACAAGAAAAAAT
* *
5536139 AGAAAATAACAAAACACATAAAAAAT
1 A-ATAATAACAAAACA-AGAAAAAAT
5536165 AATAATAA
1 AATAATAA
5536173 AAATAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (24 bp):
AATAATAACAAAACAAGAAAAAAT
Found at i:5536178 original size:19 final size:18
Alignment explanation
Indices: 5536132--5536191 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
5536122 ATAAAACAAG
* *
5536132 AAAAAATAGAAAATAACA
1 AAAAAATAAAAAATAATA
*
5536150 AAACACATAAAAAATAATA
1 AAA-AAATAAAAAATAATA
*
5536169 ATAAAAATAAACAATGAATA
1 A-AAAAATAAAAAAT-AATA
5536189 AAA
1 AAA
5536192 TGTTAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 3 0.09
19 24 0.71
20 7 0.21
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAAAATAAAAAATAATA
Found at i:5536457 original size:27 final size:27
Alignment explanation
Indices: 5536396--5536448 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
5536386 TAGAAAACAT
* *
5536396 AAAAAAAAATATAATATATAATAAATA
1 AAAAAAAAATAGAATATATAAGAAATA
5536423 AAAAAAAAATAGAATAT-TAAGAAATA
1 AAAAAAAAATAGAATATATAAGAAATA
5536449 TATATAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (27 bp):
AAAAAAAAATAGAATATATAAGAAATA
Found at i:5538993 original size:18 final size:18
Alignment explanation
Indices: 5538958--5539038 Score: 67
Period size: 18 Copynumber: 4.6 Consensus size: 18
5538948 TAGATGAATC
* *
5538958 AACATACTTAAATAAACT
1 AACATGCTTAAATGAACT
*
5538976 AACATGCTTTAATGAACT
1 AACATGCTTAAATGAACT
**
5538994 AA-ATGCTTAAATGATGT
1 AACATGCTTAAATGAACT
* *
5539011 -ACATGCTTTAGATGAAGT
1 AACATGC-TTAAATGAACT
*
5539029 AGCATGCTTA
1 AACATGCTTA
5539039 TTTACATGCA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
16 1 0.02
17 16 0.31
18 29 0.57
19 5 0.10
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (18 bp):
AACATGCTTAAATGAACT
Found at i:5539001 original size:17 final size:17
Alignment explanation
Indices: 5538972--5539026 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
5538962 TACTTAAATA
5538972 AACTAACATGCTTTAATG
1 AACTAA-ATGCTTTAATG
*
5538990 AACTAAATGCTTAAATG
1 AACTAAATGCTTTAATG
** *
5539007 ATGTACATGCTTTAGATG
1 AACTAAATGCTTTA-ATG
5539025 AA
1 AA
5539027 GTAGCATGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 20 0.67
18 10 0.33
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (17 bp):
AACTAAATGCTTTAATG
Found at i:5539573 original size:29 final size:29
Alignment explanation
Indices: 5539531--5539587 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
5539521 TCTGCTAAAG
*
5539531 TATAGCTCATTTCCCTCTCGTAGTTCAAC
1 TATAACTCATTTCCCTCTCGTAGTTCAAC
5539560 TATAACTCATTTCCCTCTCGTAGTTCAA
1 TATAACTCATTTCCCTCTCGTAGTTCAA
5539588 AACCAAGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.39
Consensus pattern (29 bp):
TATAACTCATTTCCCTCTCGTAGTTCAAC
Found at i:5541325 original size:11 final size:11
Alignment explanation
Indices: 5541293--5541325 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
5541283 TTCCATGTAC
*
5541293 TTTGTGAGCTA
1 TTTGTGAGCTG
5541304 TTTGTGAGCTG
1 TTTGTGAGCTG
5541315 TTTGTGAGCTG
1 TTTGTGAGCTG
5541326 CATATGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.12, C:0.09, G:0.33, T:0.45
Consensus pattern (11 bp):
TTTGTGAGCTG
Found at i:5542605 original size:187 final size:189
Alignment explanation
Indices: 5542290--5542665 Score: 738
Period size: 187 Copynumber: 2.0 Consensus size: 189
5542280 TTACGCCATG
5542290 CTTGTACACTATTTCGTATATGTAATTGATCTTGTTGTACTTCTTTAGGCGTCAAAGGCACCAAG
1 CTTGTACACTATTTCGTATATGTAATTGATCTTGTTGTACTTCTTTAGGCGTCAAAGGCACCAAG
5542355 GTTACCTTGCGTCCTTCATGCTTAAAGGTGTATTAATTGTGATAACAATCATGAATGGCCC-TTT
66 GTTACCTTGCGTCCTTCATGCTTAAAGGTGTATTAATTGTGATAACAATCATGAATGGCCCTTTT
5542419 GTCATACTTCCATGGTCTACCAAGTAGAATGT-GCTAGCATATATAGGGACAATGTCAC
131 GTCATACTTCCATGGTCTACCAAGTAGAATGTGGCTAGCATATATAGGGACAATGTCAC
5542477 CTTGTACACTATTTCGTATATGTAATTGATCTTGTTGTACTTCTTTAGGCGTCAAAGGCACCAAG
1 CTTGTACACTATTTCGTATATGTAATTGATCTTGTTGTACTTCTTTAGGCGTCAAAGGCACCAAG
5542542 GTTACCTTGCGTCCTTCATGCTTAAAGGTGTATTAATTGTGATAACAATCATGAATGGCCCTTTT
66 GTTACCTTGCGTCCTTCATGCTTAAAGGTGTATTAATTGTGATAACAATCATGAATGGCCCTTTT
5542607 GTCATACTTCCATGGTCTACCAAGTAGAATGTGGCTAGCATATATAGGGACAATGTCAC
131 GTCATACTTCCATGGTCTACCAAGTAGAATGTGGCTAGCATATATAGGGACAATGTCAC
5542666 AAAGCACCTC
Statistics
Matches: 187, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
187 126 0.67
188 35 0.19
189 26 0.14
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (189 bp):
CTTGTACACTATTTCGTATATGTAATTGATCTTGTTGTACTTCTTTAGGCGTCAAAGGCACCAAG
GTTACCTTGCGTCCTTCATGCTTAAAGGTGTATTAATTGTGATAACAATCATGAATGGCCCTTTT
GTCATACTTCCATGGTCTACCAAGTAGAATGTGGCTAGCATATATAGGGACAATGTCAC
Found at i:5544572 original size:22 final size:22
Alignment explanation
Indices: 5544533--5544582 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5544523 TTTTCTTACT
5544533 TTTTGAGTGCTTTCAATTTCGTC
1 TTTTGAGTGCTTTCAATTTC-TC
* *
5544556 TTTTGAGTTC-TTCAATTTCTT
1 TTTTGAGTGCTTTCAATTTCTC
5544577 TTTTGA
1 TTTTGA
5544583 TTTTCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.28
22 9 0.36
23 9 0.36
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.58
Consensus pattern (22 bp):
TTTTGAGTGCTTTCAATTTCTC
Found at i:5552472 original size:32 final size:32
Alignment explanation
Indices: 5552418--5552480 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
5552408 AAAAAATAAA
* * *
5552418 GTCGAGTGGAGGGTATATACTTTTTGGGTCGG
1 GTCGAGTGAAGGATATAAACTTTTTGGGTCGG
*
5552450 GTCGAGTGAAGGATTTAAACTTTTTGGGTCG
1 GTCGAGTGAAGGATATAAACTTTTTGGGTCG
5552481 AGTTGGGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.19, C:0.10, G:0.37, T:0.35
Consensus pattern (32 bp):
GTCGAGTGAAGGATATAAACTTTTTGGGTCGG
Found at i:5554492 original size:87 final size:87
Alignment explanation
Indices: 5554346--5554519 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
5554336 GACAAAAAAC
5554346 ATTTAAAGGCACACTTGAGCTTATATCGTCCAAATTTTATATAATTTCCAGTAGGTTTACAAGTC
1 ATTTAAAGGCACACTTGAGCTTATATCGTCCAAATTTTATATAATTTCCAGTAGGTTTACAAGTC
5554411 ATCATGCTTCATTGGTTACTGG
66 ATCATGCTTCATTGGTTACTGG
5554433 ATTTAAAGGCACACTTGAGCTTATATCGTCCAAATTTTATATAATTTCCAGTAGGTTTACAAGTC
1 ATTTAAAGGCACACTTGAGCTTATATCGTCCAAATTTTATATAATTTCCAGTAGGTTTACAAGTC
5554498 ATCATGCTTCATTGGTTACTGG
66 ATCATGCTTCATTGGTTACTGG
5554520 TTGGATGTCC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (87 bp):
ATTTAAAGGCACACTTGAGCTTATATCGTCCAAATTTTATATAATTTCCAGTAGGTTTACAAGTC
ATCATGCTTCATTGGTTACTGG
Found at i:5556068 original size:24 final size:24
Alignment explanation
Indices: 5556020--5556068 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
5556010 TGAGCAGCTC
*
5556020 AAAAATATAATATATTAAGATTTA
1 AAAAATATAATATATTAAAATTTA
5556044 AAAAATA-AAT-TATTAATAATATTA
1 AAAAATATAATATATTAA-AAT-TTA
5556068 A
1 A
5556069 CATTTATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
24 11 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
AAAAATATAATATATTAAAATTTA
Found at i:5556314 original size:25 final size:26
Alignment explanation
Indices: 5556266--5556314 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
5556256 AGCTCACGAG
* **
5556266 TTTTCGAGTCAAGCTCTATTTCAGAT
1 TTTTCGAGTCAAGCTCGAACTCAGAT
5556292 TTTTCGAGTCAAG-TCGAACTCAG
1 TTTTCGAGTCAAGCTCGAACTCAG
5556315 CAATACTCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (26 bp):
TTTTCGAGTCAAGCTCGAACTCAGAT
Found at i:5563823 original size:13 final size:13
Alignment explanation
Indices: 5563805--5563830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5563795 TGCACATAAC
5563805 AATGAACAACACA
1 AATGAACAACACA
5563818 AATGAACAACACA
1 AATGAACAACACA
5563831 CCCCCAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.23, G:0.08, T:0.08
Consensus pattern (13 bp):
AATGAACAACACA
Found at i:5565291 original size:20 final size:20
Alignment explanation
Indices: 5565266--5565325 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
5565256 TACTGGTCAC
5565266 ACAGTATCAGTACTATTCAT
1 ACAGTATCAGTACTATTCAT
* * * *
5565286 ATAGTATCGGCACTACTCAT
1 ACAGTATCAGTACTATTCAT
* *
5565306 ACAATA-CAATACTATTCAT
1 ACAGTATCAGTACTATTCAT
5565325 A
1 A
5565326 AAAAAAATTG
Statistics
Matches: 30, Mismatches: 10, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (20 bp):
ACAGTATCAGTACTATTCAT
Found at i:5566649 original size:19 final size:20
Alignment explanation
Indices: 5566625--5566664 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5566615 TGAGTTTATA
*
5566625 GTTG-TTTCTAGCCATTGGG
1 GTTGTTTTCGAGCCATTGGG
*
5566644 GTTGTTTTCGAGCCGTTGGG
1 GTTGTTTTCGAGCCATTGGG
5566664 G
1 G
5566665 ATTCATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.07, C:0.15, G:0.38, T:0.40
Consensus pattern (20 bp):
GTTGTTTTCGAGCCATTGGG
Found at i:5566808 original size:21 final size:21
Alignment explanation
Indices: 5566782--5566829 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
5566772 GATAGTGTCG
* *
5566782 ATACTACTGTTCACGGTATCA
1 ATACTACTGTTAACGATATCA
*
5566803 ATACTACTGTTAATGATATCA
1 ATACTACTGTTAACGATATCA
5566824 ATACTA
1 ATACTA
5566830 TTGTAGCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (21 bp):
ATACTACTGTTAACGATATCA
Found at i:5573528 original size:21 final size:21
Alignment explanation
Indices: 5573486--5573528 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5573476 AATTAATATT
* * *
5573486 ATTATTTTTTAAAAAATTAAA
1 ATTATTATTCAAAAAATAAAA
*
5573507 ATTATTATTCAAAAACTAAAA
1 ATTATTATTCAAAAAATAAAA
5573528 A
1 A
5573529 GTTAATAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATTATTCAAAAAATAAAA
Found at i:5573816 original size:26 final size:26
Alignment explanation
Indices: 5573782--5573831 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
5573772 ATTATTTAAA
* *
5573782 ACATTATT-AATTTTTTAAAAAAAAT
1 ACATTATTAAAATTATTAAAAAAAAT
5573807 ACATATATTAAAATTATTAAAAAAA
1 ACAT-TATTAAAATTATTAAAAAAA
5573832 TAGTATTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 4 0.19
27 13 0.62
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (26 bp):
ACATTATTAAAATTATTAAAAAAAAT
Found at i:5574710 original size:21 final size:20
Alignment explanation
Indices: 5574685--5574747 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
5574675 ATATCTTATA
5574685 GCACTAAGAATAAAATAATG
1 GCACTAAGAATAAAATAATG
*
5574705 GACACTAAAAATAAAATAATTG
1 G-CACTAAGAATAAAATAA-TG
**
5574727 GCACTAAGAATTTAATAATG
1 GCACTAAGAATAAAATAATG
5574747 G
1 G
5574748 GGGTCATGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.11
21 30 0.81
22 3 0.08
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (20 bp):
GCACTAAGAATAAAATAATG
Found at i:5577395 original size:18 final size:18
Alignment explanation
Indices: 5577372--5577420 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
5577362 AAGATGAGTT
*
5577372 CTAGACGTGGTCGTCGAA
1 CTAGACGTGGTCGTCAAA
5577390 CTAGACGTGGTCGTCAAA
1 CTAGACGTGGTCGTCAAA
*
5577408 CTAGTCGTGGTCG
1 CTAGACGTGGTCG
5577421 CGACAGAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.24
Consensus pattern (18 bp):
CTAGACGTGGTCGTCAAA
Found at i:5579069 original size:21 final size:21
Alignment explanation
Indices: 5579020--5579072 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5579010 ATATCTTATA
*
5579020 GCACTAAAAATAAAATAATGG
1 GCACTAAGAATAAAATAATGG
*
5579041 CCACTAAGAATAAAATAATGG
1 GCACTAAGAATAAAATAATGG
5579062 GCACTAAGAAT
1 GCACTAAGAAT
5579073 TTAATAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.53, C:0.13, G:0.15, T:0.19
Consensus pattern (21 bp):
GCACTAAGAATAAAATAATGG
Found at i:5580735 original size:23 final size:23
Alignment explanation
Indices: 5580674--5580735 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
5580664 CTCGTATAAA
* *
5580674 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
*
5580697 TGCACTGAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
5580720 TGCACCGAAGTGCCAT
1 TGCACCGAAGTGCCAT
5580736 ATAAAATGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:5582090 original size:20 final size:20
Alignment explanation
Indices: 5582065--5582113 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
5582055 TTTCCCTTGA
5582065 AGTGCATCGGTACATTCTAC
1 AGTGCATCGGTACATTCTAC
*
5582085 AGTGCATCGGTACATTCTAT
1 AGTGCATCGGTACATTCTAC
*
5582105 AGTGTATCG
1 AGTGCATCG
5582114 ATGCATCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGGTACATTCTAC
Found at i:5582967 original size:19 final size:19
Alignment explanation
Indices: 5582943--5582979 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5582933 ATATTACACC
*
5582943 CAAACTGTTTGACCCGACT
1 CAAACTATTTGACCCGACT
*
5582962 CAAACTATTTGACTCGAC
1 CAAACTATTTGACCCGAC
5582980 CTATTGACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.27
Consensus pattern (19 bp):
CAAACTATTTGACCCGACT
Found at i:5583337 original size:5 final size:5
Alignment explanation
Indices: 5583327--5583351 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5583317 GACTAATTAT
5583327 TGTTA TGTTA TGTTA TGTTA TGTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA
5583352 AAGGTACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TGTTA
Found at i:5585334 original size:19 final size:21
Alignment explanation
Indices: 5585289--5585336 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
5585279 TATTTAAAAA
*
5585289 TTTAAAAAAGCATAATTTATT
1 TTTAAAAAAACATAATTTATT
* *
5585310 TATAAAAAAAC-TGATTT-TT
1 TTTAAAAAAACATAATTTATT
5585329 TTTAAAAA
1 TTTAAAAA
5585337 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 9 0.39
20 5 0.22
21 9 0.39
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (21 bp):
TTTAAAAAAACATAATTTATT
Found at i:5585583 original size:27 final size:25
Alignment explanation
Indices: 5585544--5585598 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
5585534 AAGATTCCTA
5585544 TTTTACGACTCGAAGTTGACTTGAAAT
1 TTTTACGACTCG-AGTTGACTT-AAAT
* * *
5585571 TTTTTCGAGTCGAGTTGAGTTAAAT
1 TTTTACGACTCGAGTTGACTTAAAT
5585596 TTT
1 TTT
5585599 CGAGTTTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 8 0.32
27 10 0.40
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (25 bp):
TTTTACGACTCGAGTTGACTTAAAT
Found at i:5587015 original size:30 final size:31
Alignment explanation
Indices: 5586953--5587022 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
5586943 AGGTTTAAGG
* *
5586953 TTAGGGTTTAGGGTTTTTTACATTAAATTGGT
1 TTAGGG-TTAGGGTTTTTTACATAAAAATGGT
**
5586985 TTAGGGTTAGGG-TTTTTATGTAAAAATGGT
1 TTAGGGTTAGGGTTTTTTACATAAAAATGGT
*
5587015 TTAAGGTT
1 TTAGGGTT
5587023 TTTAAAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 21 0.64
31 6 0.18
32 6 0.18
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.47
Consensus pattern (31 bp):
TTAGGGTTAGGGTTTTTTACATAAAAATGGT
Found at i:5587246 original size:30 final size:32
Alignment explanation
Indices: 5587187--5587257 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
5587177 AAACAAGCTC
5587187 AAATCACAT-TAATTGAAAGTACAAGAAAATA
1 AAATCACATATAATTGAAAGTACAAGAAAATA
**
5587218 AAATCACATAT-ATTGAAA-TATTAGAAAATA
1 AAATCACATATAATTGAAAGTACAAGAAAATA
* *
5587248 CAATTACATA
1 AAATCACATA
5587258 AGTAGTGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.51
31 16 0.46
32 1 0.03
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (32 bp):
AAATCACATATAATTGAAAGTACAAGAAAATA
Found at i:5587596 original size:21 final size:21
Alignment explanation
Indices: 5587570--5587618 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
5587560 AAATGATAAT
5587570 GTGAGCAAGTTGCTATGACAC
1 GTGAGCAAGTTGCTATGACAC
*
5587591 GTGAGCAAGTTGCTATGACAT
1 GTGAGCAAGTTGCTATGACAC
5587612 GTGAGCA
1 GTGAGCA
5587619 TGGATACTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (21 bp):
GTGAGCAAGTTGCTATGACAC
Found at i:5589612 original size:102 final size:102
Alignment explanation
Indices: 5589421--5589671 Score: 283
Period size: 102 Copynumber: 2.5 Consensus size: 102
5589411 TTTGATGTTT
* * * * *
5589421 AGGTTAAACAAGTTTGCAGATGAATGTCTTCCACTTAAACTTGAAGGCATTGTGTTACATGGGTT
1 AGGTTAAACAAGTTAGCAGATGAATGTCTTCCACTGAAACTTGAAGGCATAGAGTTACATGGGTA
* * *
5589486 TTGAACAAACTGTTGTGTCTAAGGCATCTACATATTG
66 CTGAACAAACTGATGTGTCGAAGGCATCTACATATTG
* * * * * * *
5589523 AGGTTAAAAAAGTTGGTAGATGAATGCCTTCCTCTGGAACTTGAAGGCATAGAGTTATATGGGTA
1 AGGTTAAACAAGTTAGCAGATGAATGTCTTCCACTGAAACTTGAAGGCATAGAGTTACATGGGTA
* *
5589588 CTGAA-AAGATTGATGTGGT-GAAGGCATCTCCATATTG
66 CTGAACAA-ACTGATGT-GTCGAAGGCATCTACATATTG
* *
5589625 AGGTCAAACAAGTTAGCAGATGAATGTCTTCC-CATAAAACTTGAAGG
1 AGGTTAAACAAGTTAGCAGATGAATGTCTTCCAC-TGAAACTTGAAGG
5589672 GATGTTTCCA
Statistics
Matches: 123, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
101 3 0.02
102 118 0.96
103 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (102 bp):
AGGTTAAACAAGTTAGCAGATGAATGTCTTCCACTGAAACTTGAAGGCATAGAGTTACATGGGTA
CTGAACAAACTGATGTGTCGAAGGCATCTACATATTG
Found at i:5602880 original size:24 final size:24
Alignment explanation
Indices: 5602846--5602918 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
5602836 ATACATTACC
*
5602846 TGAATTTTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
** *
5602870 TGGGTTCTGTTCTGATATT-TGATC
1 TGAATTCTGTTCTGAT-TTCTGATA
* *
5602894 TGAATTCTGTTTTGACTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
5602918 T
1 T
5602919 CTCTGTTTAC
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
23 2 0.05
24 34 0.89
25 2 0.05
ACGTcount: A:0.18, C:0.11, G:0.19, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:5603089 original size:2 final size:2
Alignment explanation
Indices: 5603077--5603157 Score: 146
Period size: 2 Copynumber: 41.0 Consensus size: 2
5603067 CGGATAGGGG
*
5603077 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5603119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5603158 AATAAATCTG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 75 0.99
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5604600 original size:61 final size:61
Alignment explanation
Indices: 5604479--5604591 Score: 180
Period size: 57 Copynumber: 1.9 Consensus size: 61
5604469 TACTAAAGTT
*
5604479 TTGATTTGTTTTTATATATATATTTCAAGATAATGGGGAAGTGAATGATTGAGTACATTGA
1 TTGATTTGTTTTTATATATATATTTCAAGATAATGGGGAAGTGAATGATTGACTACATTGA
*
5604540 TTGATTTG-TTTT-TATATAT-TTT-AAGATAATGGGGGAGTGAATGATTGACTAC
1 TTGATTTGTTTTTATATATATATTTCAAGATAATGGGGAAGTGAATGATTGACTAC
5604592 GGGGATTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
57 28 0.56
58 3 0.06
59 7 0.14
60 4 0.08
61 8 0.16
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (61 bp):
TTGATTTGTTTTTATATATATATTTCAAGATAATGGGGAAGTGAATGATTGACTACATTGA
Found at i:5608060 original size:24 final size:24
Alignment explanation
Indices: 5608028--5608091 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
5608018 ATTTCCGATT
*
5608028 TGAATTCTGTTCTGATA-CATTACC
1 TGAATTCTGTTATGATATC-TTACC
*
5608052 TGAATTCTGTTATGATATCTTATC
1 TGAATTCTGTTATGATATCTTACC
*
5608076 TGAATTCTGTTTTGAT
1 TGAATTCTGTTATGAT
5608092 TTCTGATATC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTATGATATCTTACC
Found at i:5609565 original size:20 final size:20
Alignment explanation
Indices: 5609536--5609573 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5609526 TTTCAAAGGA
5609536 ATGCACCGATGCACCAATAC
1 ATGCACCGATGCACCAATAC
*
5609556 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
5609574 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATAC
Found at i:5609737 original size:64 final size:65
Alignment explanation
Indices: 5609584--5609745 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
5609574 GAATAAATTG
* * * * * * * *
5609584 AACATCAAATGCAGTTTATGCATCCATGCACTCTCCATGCATCGATGTACTCAGGTTTTAATGAA
1 AACATCGAATGCAATTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATAAA
* * *
5609649 AACATCGATTGCAATTTATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTTATTAAA
1 AACATCGAATGCAATTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATAAA
*
5609713 AACATCGAATGCATTTTATGCATCGATGCACAC
1 AACATCGAATGCAATTTATGCATCGATGCACAC
5609746 TTAGTGCACC
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCAATTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATAAA
Found at i:5609759 original size:64 final size:64
Alignment explanation
Indices: 5609584--5609761 Score: 196
Period size: 64 Copynumber: 2.8 Consensus size: 64
5609574 GAATAAATTG
* * * * * * *
5609584 AACATCAAATGCAGTTTATGCATCCATGCACTCTCCATGCATCGATGTACTCAGGTTTTAATGAA
1 AACATCGAATGCAATTTATGCATCGATGCACACT-CATGCATCGATGCACTCAGGTCTTAATAAA
* * * *
5609649 AACATCGATTGCAATTTATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTTATTAAA
1 AACATCGAATGCAATTTATGCATCGATGCACAC-TCATGCATCGATGCACTCAGGTCTTAATAAA
* * *
5609713 AACATCGAATGCATTTTATGCATCGATGCACACTTAGTGCACCGATGCA
1 AACATCGAATGCAATTTATGCATCGATGCACACTCA-TGCATCGATGCA
5609762 TTAAGTGTTC
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
63 1 0.01
64 48 0.51
65 46 0.48
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCAATTTATGCATCGATGCACACTCATGCATCGATGCACTCAGGTCTTAATAAA
Found at i:5614847 original size:23 final size:22
Alignment explanation
Indices: 5614766--5614846 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 22
5614756 ACACTTAATA
* *
5614766 GTGCATCGATGCATCCCTTTGTAT
1 GTGCATCGATGCAT-CC-ATGAAT
*
5614790 GTGCATCGATACAT-CATGAA-
1 GTGCATCGATGCATCCATGAAT
* *
5614810 GATGCACCAATGCACTCCATGAAT
1 G-TGCATCGATGCA-TCCATGAAT
5614834 GTGCATCGATGCA
1 GTGCATCGATGCA
5614847 CAAAGCTATG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 2 0.04
23 16 0.36
24 14 0.31
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCATGAAT
Found at i:5617500 original size:20 final size:20
Alignment explanation
Indices: 5617471--5617508 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5617461 TTTCAAAGGA
5617471 ATGCACCGATACACCAATCC
1 ATGCACCGATACACCAATCC
* *
5617491 ATGCATCGATGCACCAAT
1 ATGCACCGATACACCAAT
5617509 GAATAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.18
Consensus pattern (20 bp):
ATGCACCGATACACCAATCC
Found at i:5617610 original size:46 final size:45
Alignment explanation
Indices: 5617558--5617659 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 45
5617548 ACTCTCCATG
* * *
5617558 CATCGATGCACTCAGGTTTTATTGAAAACATCGATTGCATTTTATA
1 CATCGATGCACTCAGG-CTTATTAAAAACATCGAATGCATTTTATA
* * *
5617604 CATCGATGAACTTAGGCTTATTAAAAACATCGAATGCATTTTATG
1 CATCGATGCACTCAGGCTTATTAAAAACATCGAATGCATTTTATA
5617649 CATCGATGCAC
1 CATCGATGCAC
5617660 ACTTAGTGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 35 0.71
46 14 0.29
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (45 bp):
CATCGATGCACTCAGGCTTATTAAAAACATCGAATGCATTTTATA
Found at i:5618748 original size:2 final size:2
Alignment explanation
Indices: 5618741--5618803 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
5618731 GGTCTTCAAT
5618741 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5618783 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
5618804 TAAACACGTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5619605 original size:108 final size:108
Alignment explanation
Indices: 5619439--5619707 Score: 360
Period size: 108 Copynumber: 2.5 Consensus size: 108
5619429 GTGCTGATAT
* * * * * * * * *
5619439 GGTCATTCATAAGCTCATTATGAATTTCTTGGATTGCACACATATTGCCTATACGGTTGTTAATA
1 GGTCGTTCATAAACACATTATGAATTCCATGGGTTGCACACTTAGTGCCGATACGGTTGTTAATA
**
5619504 AACTTATTATGAATT-TCGTGGGTTGCACACTTAGTGTCAATAC
66 AACACATTATGAATTGT-GTGGGTTGCACACTTAGTGTCAATAC
* * * *
5619547 GGTCGTTCATAAATACATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATATGGTTGTTCATA
1 GGTCGTTCATAAACACATTATGAATTCCATGGGTTGCACACTTAGTGCCGATACGGTTGTTAATA
*
5619612 AACACATTATGAATTGTGTGGGTTGCACACTTAGTGTCGATAC
66 AACACATTATGAATTGTGTGGGTTGCACACTTAGTGTCAATAC
* *
5619655 GGTCGTTCATAAACACATTATGAATTCTATGGGTTGCACACTTAGTGTCGATA
1 GGTCGTTCATAAACACATTATGAATTCCATGGGTTGCACACTTAGTGCCGATA
5619708 GTACACATAT
Statistics
Matches: 141, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
108 140 0.99
109 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (108 bp):
GGTCGTTCATAAACACATTATGAATTCCATGGGTTGCACACTTAGTGCCGATACGGTTGTTAATA
AACACATTATGAATTGTGTGGGTTGCACACTTAGTGTCAATAC
Found at i:5619702 original size:54 final size:54
Alignment explanation
Indices: 5619434--5619707 Score: 327
Period size: 54 Copynumber: 5.1 Consensus size: 54
5619424 ATATAGTGCT
* * * * * * * *
5619434 GATATGGTCATTCATAAGCTCATTATGAATTTCT-TGGATTGCACACATATTGCC
1 GATACGGTCGTTCATAAACACATTATGAA-TTCTGTGGGTTGCACACTTAGTGTC
* * * **
5619488 TATACGGTTGTTAATAAACTTATTATGAATT-TCGTGGGTTGCACACTTAGTGTC
1 GATACGGTCGTTCATAAACACATTATGAATTCT-GTGGGTTGCACACTTAGTGTC
* * * *
5619542 AATACGGTCGTTCATAAATACATTATGAATTCCGTGGGTTGCACACTTAGTGCC
1 GATACGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTTAGTGTC
* * *
5619596 GATATGGTTGTTCATAAACACATTATGAATTGTGTGGGTTGCACACTTAGTGTC
1 GATACGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTTAGTGTC
*
5619650 GATACGGTCGTTCATAAACACATTATGAATTCTATGGGTTGCACACTTAGTGTC
1 GATACGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTTAGTGTC
5619704 GATA
1 GATA
5619708 GTACACATAT
Statistics
Matches: 187, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
52 1 0.01
53 2 0.01
54 184 0.98
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (54 bp):
GATACGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTTAGTGTC
Found at i:5626904 original size:48 final size:50
Alignment explanation
Indices: 5626843--5626946 Score: 167
Period size: 48 Copynumber: 2.1 Consensus size: 50
5626833 TGGTTGATTC
* *
5626843 TTTTAGTTTTTTCTTAATTATGGTTGAG-TTGTGTA-TTTTAATTACAAA
1 TTTTAGGTATTTCTTAATTATGGTTGAGATTGTGTATTTTTAATTACAAA
*
5626891 TTTTAGGTATTTCTTAATTGTGGTTGAGATTGTGTATTTTTAATTACAAA
1 TTTTAGGTATTTCTTAATTATGGTTGAGATTGTGTATTTTTAATTACAAA
5626941 TTTTAG
1 TTTTAG
5626947 AAGGTATTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
48 25 0.49
49 7 0.14
50 19 0.37
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.55
Consensus pattern (50 bp):
TTTTAGGTATTTCTTAATTATGGTTGAGATTGTGTATTTTTAATTACAAA
Found at i:5629094 original size:18 final size:18
Alignment explanation
Indices: 5629051--5629102 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 18
5629041 TTCGAACTCT
**
5629051 TGAAGATTTTGGCTTGGA
1 TGAAGATTTTGGCTCCGA
5629069 TGGAAGATTTTGGCTCCGA
1 T-GAAGATTTTGGCTCCGA
5629088 TGAAGATTTTGGCTC
1 TGAAGATTTTGGCTC
5629103 TTGAACCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.37
Consensus pattern (18 bp):
TGAAGATTTTGGCTCCGA
Found at i:5629202 original size:21 final size:21
Alignment explanation
Indices: 5629178--5629221 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5629168 GTTTTGCTGA
5629178 TTTATTCAAATTTTTCTTCTT
1 TTTATTCAAATTTTTCTTCTT
5629199 TTTATTCAAATTTTTCTTCTT
1 TTTATTCAAATTTTTCTTCTT
5629220 TT
1 TT
5629222 CAATTAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATTCAAATTTTTCTTCTT
Found at i:5629539 original size:20 final size:20
Alignment explanation
Indices: 5629514--5629553 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5629504 ATATAGTCCA
5629514 TTGTTGGCAAGGAATTTCAG
1 TTGTTGGCAAGGAATTTCAG
5629534 TTGTTGGCAAGGAATTTCAG
1 TTGTTGGCAAGGAATTTCAG
5629554 AGTTAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.30, T:0.35
Consensus pattern (20 bp):
TTGTTGGCAAGGAATTTCAG
Found at i:5635326 original size:37 final size:36
Alignment explanation
Indices: 5635254--5635327 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
5635244 ATTAGAAAAT
* *
5635254 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
* *
5635290 ATTTATATAATTTTTTTTGCAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTT-AAAAATTGAAAATCATAAA
5635327 A
1 A
5635328 AGGTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 8 0.25
37 14 0.44
38 10 0.31
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:5635628 original size:59 final size:59
Alignment explanation
Indices: 5635557--5635686 Score: 242
Period size: 59 Copynumber: 2.2 Consensus size: 59
5635547 GAAATGGAGG
*
5635557 TAATGACATTCCTGGTAATATACCCAAAAAATCCACTATTGGTAATGTAAGATTACCGC
1 TAATGACATTCCTGGTAATATACCCAAAAAATCAACTATTGGTAATGTAAGATTACCGC
5635616 TAATGACATTCCTGGTAATATACCCAAAAAATCAACTATTGGTAATGTAAGATTACCGC
1 TAATGACATTCCTGGTAATATACCCAAAAAATCAACTATTGGTAATGTAAGATTACCGC
*
5635675 GAATGACATTCC
1 TAATGACATTCC
5635687 CGGCCAACCA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 69 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (59 bp):
TAATGACATTCCTGGTAATATACCCAAAAAATCAACTATTGGTAATGTAAGATTACCGC
Found at i:5641352 original size:13 final size:13
Alignment explanation
Indices: 5641334--5641381 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
5641324 AATGATAAAT
5641334 AATAAAAAATTAC
1 AATAAAAAATTAC
5641347 AATAAAAAAGTT-C
1 AATAAAAAA-TTAC
* **
5641360 AATAAACAGCTAC
1 AATAAAAAATTAC
5641373 AATAAAAAA
1 AATAAAAAA
5641382 GTACTAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
12 1 0.04
13 25 0.89
14 2 0.07
ACGTcount: A:0.67, C:0.10, G:0.04, T:0.19
Consensus pattern (13 bp):
AATAAAAAATTAC
Found at i:5641363 original size:26 final size:26
Alignment explanation
Indices: 5641334--5641383 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5641324 AATGATAAAT
*
5641334 AATAAAAAATTACAATAAAAAAGTTC
1 AATAAAAAACTACAATAAAAAAGTTC
* *
5641360 AATAAACAGCTACAATAAAAAAGT
1 AATAAAAAACTACAATAAAAAAGT
5641384 ACTAAATACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.64, C:0.10, G:0.06, T:0.20
Consensus pattern (26 bp):
AATAAAAAACTACAATAAAAAAGTTC
Found at i:5643551 original size:17 final size:18
Alignment explanation
Indices: 5643531--5643568 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5643521 ACTCTATAAG
5643531 TAAAAT-ATTAAATAAAT
1 TAAAATGATTAAATAAAT
*
5643548 T-AAATGCTTAAATAAAT
1 TAAAATGATTAAATAAAT
5643565 TAAA
1 TAAA
5643569 TACAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 4 0.22
17 12 0.67
18 2 0.11
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
TAAAATGATTAAATAAAT
Found at i:5643647 original size:10 final size:10
Alignment explanation
Indices: 5643634--5643682 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
5643624 TTGAAAAAAT
5643634 TTGAGAGAAA
1 TTGAGAGAAA
*
5643644 TTGAGAGAAG
1 TTGAGAGAAA
*
5643654 TTGAGAGAAG
1 TTGAGAGAAA
*
5643664 TTGAGAGAGA
1 TTGAGAGAAA
5643674 TTGAGAGAA
1 TTGAGAGAA
5643683 TTTTGTGTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:5644344 original size:67 final size:67
Alignment explanation
Indices: 5644236--5644371 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
5644226 TAGATACTAA
5644236 AACTGAGTATTGTTTGTTTGATTGAGAACTTCGAAAATCTGCACCTGTCATCATAAAACTGCCTT
1 AACTGAGTATTGTTTGTTTGATTGAGAACTTCGAAAATCTGCACCTGTCATCATAAAACTGCCTT
5644301 TG
66 TG
5644303 AACTGAGTATTGTTTGTTTGATTGAGAACTTCGAAAATCTGCACCTGTCATCATAAAACTGCCTT
1 AACTGAGTATTGTTTGTTTGATTGAGAACTTCGAAAATCTGCACCTGTCATCATAAAACTGCCTT
5644368 TG
66 TG
5644370 AA
1 AA
5644372 TTGTGCATTG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (67 bp):
AACTGAGTATTGTTTGTTTGATTGAGAACTTCGAAAATCTGCACCTGTCATCATAAAACTGCCTT
TG
Found at i:5644805 original size:30 final size:32
Alignment explanation
Indices: 5644769--5644844 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
5644759 TAAAAAAACA
5644769 TAATATATGGTCA-TTTCG-TTTATATTCAAT
1 TAATATATGGTCACTTTCGTTTTATATTCAAT
* *
5644799 TAATATATGGTCACTTTCGTTTTCTATTTAAT
1 TAATATATGGTCACTTTCGTTTTATATTCAAT
* *
5644831 TAAGATATTGTCAC
1 TAATATATGGTCAC
5644845 CATGAGTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 13 0.32
31 5 0.12
32 22 0.55
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.49
Consensus pattern (32 bp):
TAATATATGGTCACTTTCGTTTTATATTCAAT
Found at i:5651207 original size:27 final size:26
Alignment explanation
Indices: 5651157--5651209 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
5651147 ATCTGACGCG
*
5651157 GTAGTTTTTAGAAGGTCCAATCAGCA
1 GTAGTTTTTAGAAGATCCAATCAGCA
* *
5651183 GTAGTTTTCTAGAAGATCTAGTCAGCA
1 GTAGTTTT-TAGAAGATCCAATCAGCA
5651210 CCTTCTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (26 bp):
GTAGTTTTTAGAAGATCCAATCAGCA
Found at i:5655532 original size:170 final size:165
Alignment explanation
Indices: 5655207--5655543 Score: 613
Period size: 170 Copynumber: 2.0 Consensus size: 165
5655197 GGCCGAGACG
5655207 TGATTTTGTGGAGGCTTACGATTCGAACCGATCTACATCACCGTTCATTTTGTCCTTGTTGTTTT
1 TGATTTTGTGGAGGCTTACGATTCGAACCGATCTACATCACCGTTCATTTTGTCCTTGTTGTTTT
5655272 TCAAGGAACCCATTGTAAGTATTCGCGCCCTTCCTCCCGATTTCGTTTTACGTACTTGGATCAAC
66 TCAAGGAACCCATTGTAAGTATTCGCGCCCTTCCTCCCGATTTCGTTTTACGTACTTGGATCAAC
5655337 TGGTGAGACCGTCGAGTTTTGTTTCTACTGCGCCA
131 TGGTGAGACCGTCGAGTTTTGTTTCTACTGCGCCA
5655372 TGATTTTGTGGAGGCTTACGATTCGAACCGATCTACATCACCAACGTTCATTGTTGTCCTTGTTG
1 TGATTTTGTGGAGGCTTACGATTCGAACCGATCTACATCA-C--CGTTCATT-TTGTCCTTGTTG
5655437 TTTTTCAAGGAACCCATTGTAAGTATTCGCGCCCCTTCCTCCCGATTTCGGTTTTACGTACTTGG
62 TTTTTCAAGGAACCCATTGTAAGTATTCGCG-CCCTTCCTCCCGATTTC-GTTTTACGTACTTGG
5655502 ATC-ACTGGTGAGACCGTCGAGTTTTGTTTCTACTGCGCCA
125 ATCAACTGGTGAGACCGTCGAGTTTTGTTTCTACTGCGCCA
5655542 TG
1 TG
5655544 GGGTGCACTG
Statistics
Matches: 166, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
165 40 0.24
166 1 0.01
168 8 0.05
169 43 0.26
170 56 0.34
171 18 0.11
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.36
Consensus pattern (165 bp):
TGATTTTGTGGAGGCTTACGATTCGAACCGATCTACATCACCGTTCATTTTGTCCTTGTTGTTTT
TCAAGGAACCCATTGTAAGTATTCGCGCCCTTCCTCCCGATTTCGTTTTACGTACTTGGATCAAC
TGGTGAGACCGTCGAGTTTTGTTTCTACTGCGCCA
Found at i:5661663 original size:153 final size:154
Alignment explanation
Indices: 5661385--5661682 Score: 375
Period size: 153 Copynumber: 1.9 Consensus size: 154
5661375 TTGATCTGCT
* * * *****
5661385 GAACTGCATAATACTCTTTTGGTTCAATGACTGATTGTTTAGAAGAAAACGATGTTTGTCTTCAT
1 GAACTGCATAATACTCTTTTGGTTCAATGACTAATTGCTTAAAAGAAAACGATGCCCACCTTCAT
** ** *
5661450 TAATTTTTCGATTGTTGAATTTCACATTTGAATTCAGAAGAATGTTTCTTCTACAGTTAAAACAT
66 TAATACTTCGATTGCAGAATTTCACATTTGAATTCAGAAGAATGTTTCTCCTACAGTTAAAACAT
*
5661515 CACTAAC-GAGTATTGACTTATGG
131 CACCAACTGAGTATTGACTTATGG
* *
5661538 GAACTGCATAATACTCTTTTGGTTCAATGCCTAATTGCTTAAAAGACAGA-GATGCCCACCTTCA
1 GAACTGCATAATACTCTTTTGGTTCAATGACTAATTGCTTAAAAGA-AAACGATGCCCACCTTCA
* * * * * *
5661602 TTTATACTTCGATTGCAGAATTTCACATTTGAGTTCGGACGAATGTTTCTCCTACGGTTAAAATA
65 TTAATACTTCGATTGCAGAATTTCACATTTGAATTCAGAAGAATGTTTCTCCTACAGTTAAAACA
5661667 TCACCAACTGAGTATT
130 TCACCAACTGAGTATT
5661683 TAATTATACG
Statistics
Matches: 121, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
153 112 0.93
154 9 0.07
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (154 bp):
GAACTGCATAATACTCTTTTGGTTCAATGACTAATTGCTTAAAAGAAAACGATGCCCACCTTCAT
TAATACTTCGATTGCAGAATTTCACATTTGAATTCAGAAGAATGTTTCTCCTACAGTTAAAACAT
CACCAACTGAGTATTGACTTATGG
Found at i:5664555 original size:13 final size:13
Alignment explanation
Indices: 5664518--5664568 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
5664508 AATGACGCTC
*
5664518 AATGCGCGTCATA
1 AATGAGCGTCATA
*
5664531 AATGAGCATCATA
1 AATGAGCGTCATA
* *
5664544 AATGTGTGTCATA
1 AATGAGCGTCATA
*
5664557 AATGCGCGTCAT
1 AATGAGCGTCAT
5664569 GGATTTGTGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (13 bp):
AATGAGCGTCATA
Found at i:5669659 original size:18 final size:18
Alignment explanation
Indices: 5669638--5669674 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5669628 TAGTCGGCCA
*
5669638 CTATTGGGTCGTCGTCCC
1 CTATTGGGCCGTCGTCCC
5669656 CTATTGGGCCGTCGTCCC
1 CTATTGGGCCGTCGTCCC
5669674 C
1 C
5669675 AGAGCAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.38, G:0.27, T:0.30
Consensus pattern (18 bp):
CTATTGGGCCGTCGTCCC
Found at i:5671629 original size:22 final size:22
Alignment explanation
Indices: 5671604--5671668 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
5671594 ACATTGATCA
5671604 TTGACCGATCTGACCGTTGACT
1 TTGACCGATCTGACCGTTGACT
5671626 TTGACCGATCTGACCGTTGACT
1 TTGACCGATCTGACCGTTGACT
* *
5671648 TTGACTGGTCTGACCGTTGAC
1 TTGACCGATCTGACCGTTGAC
5671669 CGTTGAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (22 bp):
TTGACCGATCTGACCGTTGACT
Found at i:5672584 original size:17 final size:17
Alignment explanation
Indices: 5672562--5672594 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5672552 ACCCGTATTT
*
5672562 TTTTTATATGCAAAATC
1 TTTTTATATGAAAAATC
5672579 TTTTTATATGAAAAAT
1 TTTTTATATGAAAAAT
5672595 AAAAAGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (17 bp):
TTTTTATATGAAAAATC
Found at i:5675936 original size:19 final size:19
Alignment explanation
Indices: 5675912--5675950 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5675902 TAAGATTTAT
5675912 TGATTGGAATTGGAATTAA
1 TGATTGGAATTGGAATTAA
5675931 TGATTGGAATTGGAATTAA
1 TGATTGGAATTGGAATTAA
5675950 T
1 T
5675951 CCTATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (19 bp):
TGATTGGAATTGGAATTAA
Found at i:5676234 original size:11 final size:11
Alignment explanation
Indices: 5676208--5676242 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
5676198 AATCTAAATA
5676208 ATATATTTATAT
1 ATATATTTA-AT
*
5676220 ATATATTGAAT
1 ATATATTTAAT
5676231 ATATATTTAAT
1 ATATATTTAAT
5676242 A
1 A
5676243 GATTCTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
ATATATTTAAT
Found at i:5676880 original size:23 final size:23
Alignment explanation
Indices: 5676853--5676899 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5676843 CATTTTTATT
5676853 AATTTAATGAATATTTAAAATTA
1 AATTTAATGAATATTTAAAATTA
5676876 AATTTAATGAATATTTAAAATTA
1 AATTTAATGAATATTTAAAATTA
5676899 A
1 A
5676900 TAAAAGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
AATTTAATGAATATTTAAAATTA
Found at i:5680332 original size:13 final size:13
Alignment explanation
Indices: 5680314--5680340 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5680304 TGATTCCTTA
5680314 TTTCTATCTCATT
1 TTTCTATCTCATT
5680327 TTTCTATCTCATT
1 TTTCTATCTCATT
5680340 T
1 T
5680341 ATCTCATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCTATCTCATT
Found at i:5680583 original size:12 final size:12
Alignment explanation
Indices: 5680568--5680611 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
5680558 TAGAATATTA
*
5680568 ATTCTATTATAT
1 ATTCTAATATAT
5680580 ATTCTAATATAT
1 ATTCTAATATAT
5680592 ATAT-TAATATAT
1 AT-TCTAATATAT
*
5680604 CTTCTAAT
1 ATTCTAAT
5680612 TTATTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 26 0.93
13 1 0.04
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTCTAATATAT
Found at i:5680642 original size:30 final size:32
Alignment explanation
Indices: 5680608--5680690 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 32
5680598 ATATATCTTC
*
5680608 TAATTTATTT-ATATT-TTATTTAGAA-TAATA
1 TAATTTATTTAATATTAATATTTA-AATTAATA
5680638 TAATTTATTTAATATTAATATTTAAATTAATA
1 TAATTTATTTAATATTAATATTTAAATTAATA
5680670 TTTAATATTAATTTAATATTA
1 --TAAT-TT-ATTTAATATTA
5680691 TTAATTACTA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
30 10 0.22
31 7 0.16
32 11 0.24
34 4 0.09
35 2 0.04
36 11 0.24
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (32 bp):
TAATTTATTTAATATTAATATTTAAATTAATA
Found at i:5680657 original size:6 final size:6
Alignment explanation
Indices: 5680646--5680690 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
5680636 TATAATTTAT
5680646 TTAATA TTAATA TTTAA-A TTAATA TTTAATA TTAAT- TTAATA TTA
1 TTAATA TTAATA -TTAATA TTAATA -TTAATA TTAATA TTAATA TTA
5680691 TTAATTACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 9 0.26
6 16 0.46
7 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAATA
Found at i:5680697 original size:18 final size:18
Alignment explanation
Indices: 5680638--5680697 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
5680628 TAGAATAATA
* *
5680638 TAATTTATTTAATATTAA
1 TAATTAATTTAATATTAT
* *
5680656 TATTTAAATTAATATT-T
1 TAATTAATTTAATATTAT
*
5680673 AATATTAATTTAATATTAT
1 TA-ATTAATTTAATATTAT
5680692 TAATTA
1 TAATTA
5680698 CTATTATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
17 1 0.03
18 29 0.91
19 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTTAATATTAT
Found at i:5680704 original size:13 final size:14
Alignment explanation
Indices: 5680633--5680729 Score: 54
Period size: 12 Copynumber: 7.7 Consensus size: 14
5680623 TTATTTAGAA
* *
5680633 TAATATAATTTATT
1 TAATATTATTAATT
*
5680647 TAATATTAAT-ATT
1 TAATATTATTAATT
*
5680660 TAA-ATTAAT-ATT
1 TAATATTATTAATT
5680672 T-A-A-TATTAATT
1 TAATATTATTAATT
5680683 TAATATTATTAA-T
1 TAATATTATTAATT
*
5680696 TACTATTATT--TT
1 TAATATTATTAATT
*
5680708 TTATATTATT--TT
1 TAATATTATTAATT
*
5680720 TTATATTATT
1 TAATATTATT
5680730 TTTTTTTATT
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.04
11 6 0.08
12 32 0.44
13 17 0.24
14 14 0.19
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (14 bp):
TAATATTATTAATT
Found at i:5680716 original size:12 final size:12
Alignment explanation
Indices: 5680685--5680758 Score: 80
Period size: 12 Copynumber: 6.1 Consensus size: 12
5680675 TATTAATTTA
**
5680685 ATATTATTAATT
1 ATATTATTTTTT
5680697 ACTATTATTTTTT
1 A-TATTATTTTTT
5680710 ATATTATTTTTT
1 ATATTATTTTTT
5680722 ATATTATTTTTT
1 ATATTATTTTTT
5680734 -T-TTATTATTTAT
1 ATATTATT-TTT-T
*
5680746 ATATTCTTTTTT
1 ATATTATTTTTT
5680758 A
1 A
5680759 CTTATTTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
10 5 0.09
11 4 0.07
12 27 0.50
13 14 0.26
14 4 0.07
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:5680729 original size:15 final size:14
Alignment explanation
Indices: 5680699--5680742 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
5680689 TATTAATTAC
5680699 TATTA-TTTTTTA-
1 TATTATTTTTTTAT
5680711 TATTATTTTTTATAT
1 TATTATTTTTT-TAT
5680726 TATT-TTTTTTTAT
1 TATTATTTTTTTAT
5680739 TATT
1 TATT
5680743 TATATATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.17
13 12 0.41
14 8 0.28
15 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTATTTTTTTAT
Done.