Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 43
Found at i:1412649 original size:375 final size:376
Alignment explanation
Indices: 1411942--1412696 Score: 1246
Period size: 375 Copynumber: 2.0 Consensus size: 376
1411932 CCGTCCGACC
* *
1411942 TCCGATCGATGAGCTGAAACCACCATCGTGTTCATTGTCAACCGAGGAACAAAACCCCTTAAACC
1 TCCGATCGATGAGCCGAAACCACCATCGTGTTCATTGTCAACCGAGGAACAAAACCCCTCAAACC
* * *
1412007 TTTCGTCGTGAATCATCTCCGTTCGTCGCTAATTTCAGTCGGAAGTATCGTCGGTAATAACTCGG
66 TTTCGTCGTGAATCATCTCCGTTCGTCGCTAATTTCAGTCAGAAATATCGTCGGTAATAACTCAG
* *
1412072 TTTTAGTTGGTTTTTCATCGATTCACGACGATCGGGTCATCCGTTTACGACACCTCCCGCACCAT
131 TTTTAGTTGGTTTTTCATCGATTCACGACGATCAGGTCATCCGTTTACGACACATCCCGCACCAT
* * ** *
1412137 CGTGTTCGTTGTATCGTTCCGAGTTTGCCGGTGTCATCCTTGGTCTCCGTTAACGGCGGCGCGTG
196 CGTGTTCGTTGCATCGTTCCAAGTTCACCGGTGTCATCCTTGGTCTCCGTCAACGGCGGCGCGTG
* *
1412202 AGGAGGTGAAGCGGTCAAAGTTTCTGATTTGTTGAAATCGAGCTCTCCGCCGTTCAAAATTGTGA
261 AGGAGGTGAAGCGGTCAAAGTTTCCGATTTGTTGAAATCGAGCTCTCCGCCGTTCAAAATTATGA
1412267 ACCGAGCTTTGTAAGTATCTTGAAATCGCTCAAAATAATTTTTAAG-AATTT
326 ACCGAGCTTTGTAAGTATCTTGAAATCGCTCAAAATAA-TTTTAAGAAATTT
* *
1412318 TCCGATTGATGAGCCGAAACCACCATCGTGTTCGTTGTCAACCGAGGAACAAAACCCCTCAAACC
1 TCCGATCGATGAGCCGAAACCACCATCGTGTTCATTGTCAACCGAGGAACAAAACCCCTCAAACC
* *
1412383 TTTCGTCGTGAATCATCTCTGTTCGTCGTTAATTTCAGTCAGAAATATCGTCGGTAATAACTCAG
66 TTTCGTCGTGAATCATCTCCGTTCGTCGCTAATTTCAGTCAGAAATATCGTCGGTAATAACTCAG
1412448 TTTTAGTTGGTTTTTCATCGATTCAC-ACGATCAGGTCATCCGTTTACGACACATCCCGCACCAT
131 TTTTAGTTGGTTTTTCATCGATTCACGACGATCAGGTCATCCGTTTACGACACATCCCGCACCAT
* * *
1412512 CGTGTTCGTTGCATCGTTCCAAGTTCACCGGTGTCATCCTTGGTCTCCGTCGACGGTGGCGGGTG
196 CGTGTTCGTTGCATCGTTCCAAGTTCACCGGTGTCATCCTTGGTCTCCGTCAACGGCGGCGCGTG
* *
1412577 AGGAGGTTAAGCGGTCAAAGTTTCCGA-TTGTTTGAAATCGAGCTCTCCGCCTTTCAAAATTATG
261 AGGAGGTGAAGCGGTCAAAGTTTCCGATTTG-TTGAAATCGAGCTCTCCGCCGTTCAAAATTATG
* *
1412641 AACCGAGCTTTGTTAGTATCTTGAAATCGCTGAAAATAATTTTAAGAAATTT
325 AACCGAGCTTTGTAAGTATCTTGAAATCGCTCAAAATAATTTTAAGAAATTT
1412693 TCCG
1 TCCG
1412697 TGATTTTTAG
Statistics
Matches: 352, Mismatches: 25, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
374 10 0.03
375 195 0.55
376 147 0.42
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (376 bp):
TCCGATCGATGAGCCGAAACCACCATCGTGTTCATTGTCAACCGAGGAACAAAACCCCTCAAACC
TTTCGTCGTGAATCATCTCCGTTCGTCGCTAATTTCAGTCAGAAATATCGTCGGTAATAACTCAG
TTTTAGTTGGTTTTTCATCGATTCACGACGATCAGGTCATCCGTTTACGACACATCCCGCACCAT
CGTGTTCGTTGCATCGTTCCAAGTTCACCGGTGTCATCCTTGGTCTCCGTCAACGGCGGCGCGTG
AGGAGGTGAAGCGGTCAAAGTTTCCGATTTGTTGAAATCGAGCTCTCCGCCGTTCAAAATTATGA
ACCGAGCTTTGTAAGTATCTTGAAATCGCTCAAAATAATTTTAAGAAATTT
Found at i:1412831 original size:18 final size:18
Alignment explanation
Indices: 1412808--1412848 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1412798 ACCAGTCATA
1412808 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
1412826 ACCCGACCTGTTGACCCG
1 ACCCGACCCGTTGACCCG
1412844 ACCCG
1 ACCCG
1412849 TTGATCGCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:1413693 original size:17 final size:18
Alignment explanation
Indices: 1413671--1413710 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1413661 TTTTACAGAC
1413671 ATATTGATCTG-ATAAAA
1 ATATTGATCTGCATAAAA
* *
1413688 ATATTGATGTGCATAAGA
1 ATATTGATCTGCATAAAA
1413706 ATATT
1 ATATT
1413711 AGTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (18 bp):
ATATTGATCTGCATAAAA
Found at i:1415270 original size:12 final size:12
Alignment explanation
Indices: 1415255--1415293 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1415245 GATACGTTAC
1415255 CTGAATTCTGTT
1 CTGAATTCTGTT
*
1415267 CTG-ATTCTGAT
1 CTGAATTCTGTT
*
1415278 CTGGATTCTGTT
1 CTGAATTCTGTT
1415290 CTGA
1 CTGA
1415294 TATCTTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1415275 original size:11 final size:11
Alignment explanation
Indices: 1415259--1415294 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1415249 CGTTACCTGA
1415259 ATTCTGTTCTG
1 ATTCTGTTCTG
*
1415270 ATTCTGATCTGG
1 ATTCTGTTCT-G
1415282 ATTCTGTTCTG
1 ATTCTGTTCTG
1415293 AT
1 AT
1415295 ATCTTATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.14, C:0.17, G:0.19, T:0.50
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:1415288 original size:23 final size:24
Alignment explanation
Indices: 1415256--1415325 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 24
1415246 ATACGTTACC
*
1415256 TGAATTCTGTTCTGAT-TCTGATC
1 TGAATTCTGTTCTGATATCTGATA
* *
1415279 TGGATTCTGTTCTGATATCTTATA
1 TGAATTCTGTTCTGATATCTGATA
*
1415303 TGAATTCTG-T-TGATTTCTGATA
1 TGAATTCTGTTCTGATATCTGATA
1415325 T
1 T
1415326 CTCCGTTTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 11 0.28
23 16 0.40
24 13 0.32
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATA
Found at i:1418101 original size:10 final size:10
Alignment explanation
Indices: 1418086--1418126 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1418076 CCGATTTTCA
1418086 ACCGGTTCTG
1 ACCGGTTCTG
1418096 ACCGGTTC-G
1 ACCGGTTCTG
1418105 AACCGGTT-TG
1 -ACCGGTTCTG
1418115 ACCGG-TCTG
1 ACCGGTTCTG
1418124 ACC
1 ACC
1418127 CGATCCGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 1 0.04
9 11 0.39
10 16 0.57
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.24
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:1418140 original size:14 final size:14
Alignment explanation
Indices: 1418121--1418163 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1418111 TTTGACCGGT
*
1418121 CTGACCCGATCCGA
1 CTGACCCGACCCGA
1418135 CTGACCCGACCCGA
1 CTGACCCGACCCGA
* **
1418149 CCGAATCGACCCGA
1 CTGACCCGACCCGA
1418163 C
1 C
1418164 CGTTGACCGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.23, C:0.47, G:0.21, T:0.09
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:1418147 original size:19 final size:19
Alignment explanation
Indices: 1418123--1418164 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1418113 TGACCGGTCT
*
1418123 GACCCGATCCGACT-GACCC
1 GACCCGA-CCGAATCGACCC
1418142 GACCCGACCGAATCGACCC
1 GACCCGACCGAATCGACCC
1418161 GACC
1 GACC
1418165 GTTGACCGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.24, C:0.48, G:0.21, T:0.07
Consensus pattern (19 bp):
GACCCGACCGAATCGACCC
Found at i:1425322 original size:17 final size:17
Alignment explanation
Indices: 1425289--1425337 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
1425279 ACCGGTCTGT
1425289 CCCGACCCGA-C--TGA
1 CCCGACCCGACCGTTGA
1425303 CCCGACCCGACCGTTGA
1 CCCGACCCGACCGTTGA
1425320 CCCGACCCGACCGTTGA
1 CCCGACCCGACCGTTGA
1425337 C
1 C
1425338 TGTGACCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
17 21 0.66
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.10
Consensus pattern (17 bp):
CCCGACCCGACCGTTGA
Found at i:1431932 original size:21 final size:21
Alignment explanation
Indices: 1431903--1431955 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1431893 ATTCTGACTA
1431903 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1431924 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1431945 TCGCAATGCGA
1 TCGCATTGCGA
1431956 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1431970 original size:20 final size:20
Alignment explanation
Indices: 1431945--1432070 Score: 168
Period size: 20 Copynumber: 6.3 Consensus size: 20
1431935 TTTTCCTAAT
*
1431945 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
1431965 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
1431985 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
*
1432005 TCGCAATGCGAATTA-GAAAAA
1 TCGCAATGCG-ATTACG-TAAA
*
1432026 TTGCAATGCGATTACGT-AA
1 TCGCAATGCGATTACGTAAA
*
1432045 TCGCATTGCGATTTACGT-AA
1 TCGCAATGCGA-TTACGTAAA
1432065 TCGCAA
1 TCGCAA
1432071 CGAGATTCTG
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
19 11 0.12
20 67 0.71
21 17 0.18
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:1431975 original size:41 final size:41
Alignment explanation
Indices: 1431930--1432070 Score: 155
Period size: 40 Copynumber: 3.5 Consensus size: 41
1431920 AAATTCGCGT
* * *
1431930 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTACATAATTCGCAATGCGATTACGTAAATCGCAA
* *
1431971 TGCGA-TTACGTAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATTTACATAATTCGCAATGCGATTACGTAAATCGCAA
* * * *
1432011 TGCGAATTAGAAAAATT-GCAATGCGATTACGT-AATCGCAT
1 TGCGATTTA-CATAATTCGCAATGCGATTACGTAAATCGCAA
*
1432051 TGCGATTTACGTAA-TCGCAA
1 TGCGATTTACATAATTCGCAA
1432071 CGAGATTCTG
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 6 0.07
40 51 0.61
41 23 0.27
42 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCGATTTACATAATTCGCAATGCGATTACGTAAATCGCAA
Found at i:1432017 original size:60 final size:60
Alignment explanation
Indices: 1431930--1432070 Score: 180
Period size: 60 Copynumber: 2.3 Consensus size: 60
1431920 AAATTCGCGT
* * *
1431930 TGCGATTTTCCTAATTCGCAATGCGAA-TACG-TAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATTTACGTAA-TCGCAATGCGAATTA-GAAAAATCGCAATGCGATTACGT-AATCGCAA
* *
1431991 TGCGA-TTACGTAAATCGCAATGCGAATTAGAAAAATTGCAATGCGATTACGTAATCGCAT
1 TGCGATTTACGT-AATCGCAATGCGAATTAGAAAAATCGCAATGCGATTACGTAATCGCAA
1432051 TGCGATTTACGTAATCGCAA
1 TGCGATTTACGTAATCGCAA
1432071 CGAGATTCTG
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
60 37 0.52
61 34 0.48
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (60 bp):
TGCGATTTACGTAATCGCAATGCGAATTAGAAAAATCGCAATGCGATTACGTAATCGCAA
Found at i:1432077 original size:20 final size:20
Alignment explanation
Indices: 1432037--1432077 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1432027 TGCAATGCGA
** *
1432037 TTACGTAATCGCATTGCGAT
1 TTACGTAATCGCAACGAGAT
1432057 TTACGTAATCGCAACGAGAT
1 TTACGTAATCGCAACGAGAT
1432077 T
1 T
1432078 CTGACTATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (20 bp):
TTACGTAATCGCAACGAGAT
Found at i:1432976 original size:23 final size:23
Alignment explanation
Indices: 1432927--1432978 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1432917 GTATTCGAAA
*
1432927 TTTGATCTTGGTCATACCCGGAC
1 TTTGATCTTGGTCATACCCAGAC
* *
1432950 TTTGATCTTGGTCATACTCAGAT
1 TTTGATCTTGGTCATACCCAGAC
1432973 TTTGAT
1 TTTGAT
1432979 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (23 bp):
TTTGATCTTGGTCATACCCAGAC
Found at i:1435477 original size:20 final size:20
Alignment explanation
Indices: 1435410--1435502 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
1435400 GGCATTCATT
1435410 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
**
1435430 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-CA-CGGAAA
* *
1435451 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACACGGAAA
*
1435471 TGACTATCGCAATAC-GAAA
1 TGACTATCGCAACACGGAAA
**
1435490 TGAAAATCGCAAC
1 TGACTATCGCAAC
1435503 GAGAGAATCG
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 15 0.27
20 26 0.46
21 14 0.25
22 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:1435556 original size:32 final size:33
Alignment explanation
Indices: 1435476--1435601 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
1435466 GGAAATGACT
*
1435476 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1435509 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1435542 ATCGC-ATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1435574 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1435602 CGAATTTAGT
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 31 0.35
33 58 0.65
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1435589 original size:65 final size:66
Alignment explanation
Indices: 1435476--1435601 Score: 218
Period size: 65 Copynumber: 1.9 Consensus size: 66
1435466 GGAAATGACT
*
1435476 ATCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGAGAG
1435541 A
66 A
* *
1435542 ATCGC-ATGCGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACG
1435602 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
65 52 0.91
66 5 0.09
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (66 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGAGAG
A
Found at i:1435636 original size:19 final size:19
Alignment explanation
Indices: 1435601--1435677 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
1435591 AAATCGCAAC
*
1435601 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1435620 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1435639 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
1435653 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
1435672 ACGATT
1 GCGATT
1435678 CTCTCGTTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.24
16 1 0.02
17 1 0.02
18 1 0.02
19 35 0.70
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1435658 original size:33 final size:33
Alignment explanation
Indices: 1435616--1435698 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
1435606 TTTAGTTTCG
* * *
1435616 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCGTTACGATTCTCT
1435649 CGTTGCGATTTTCATTTCGCGTTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTACGATTCTCT
1435682 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
1435699 TGCATTGCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 45 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTACGATTCTCT
Found at i:1435828 original size:13 final size:14
Alignment explanation
Indices: 1435812--1435847 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1435802 CATCAATTAA
1435812 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
1435825 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1435839 ACAAATCAA
1 ACAAATCAA
1435848 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1437761 original size:39 final size:39
Alignment explanation
Indices: 1437703--1437798 Score: 138
Period size: 39 Copynumber: 2.5 Consensus size: 39
1437693 TCTGGAACTC
* * ** *
1437703 AAATCGCAACGTGAAAATGACTATCGCAACGCGAAATGA
1 AAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACGA
*
1437742 AAATCGTAACGAGAGAATGAAAATCGCAACGCGAAACGA
1 AAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACGA
1437781 AAATCGCAACGAGAGAAT
1 AAATCGCAACGAGAGAAT
1437799 CGCAACACGA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (39 bp):
AAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACGA
Found at i:1437762 original size:20 final size:20
Alignment explanation
Indices: 1437703--1437798 Score: 106
Period size: 19 Copynumber: 4.9 Consensus size: 20
1437693 TCTGGAACTC
* *
1437703 AAATCGCAACGTGAAAATGA
1 AAATCGCAACGAGAGAATGA
** *
1437723 CTATCGCAACGCGA-AATGA
1 AAATCGCAACGAGAGAATGA
*
1437742 AAATCGTAACGAGAGAATGA
1 AAATCGCAACGAGAGAATGA
* *
1437762 AAATCGCAACGCGA-AACGA
1 AAATCGCAACGAGAGAATGA
1437781 AAATCGCAACGAGAGAAT
1 AAATCGCAACGAGAGAAT
1437799 CGCAACACGA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
19 32 0.52
20 30 0.48
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (20 bp):
AAATCGCAACGAGAGAATGA
Found at i:1437839 original size:20 final size:20
Alignment explanation
Indices: 1437814--1437851 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1437804 CACGATTATA
1437814 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
*
1437834 GTTTCGCGTTGTGATTTT
1 GTTTCGCGTTGCGATTTT
1437852 GTCGTTGCGA
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:0.05, C:0.13, G:0.29, T:0.53
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTG
Found at i:1437863 original size:14 final size:14
Alignment explanation
Indices: 1437853--1437919 Score: 116
Period size: 14 Copynumber: 4.8 Consensus size: 14
1437843 TGTGATTTTG
*
1437853 TCGTTGCGATTCTG
1 TCGTTGCGATTCTA
1437867 TCGTTGCGATTCTA
1 TCGTTGCGATTCTA
1437881 TCGTTGCGATTCTA
1 TCGTTGCGATTCTA
*
1437895 TCGTTGTGATTCTA
1 TCGTTGCGATTCTA
1437909 TCGTTGCGATT
1 TCGTTGCGATT
1437920 TTCGTTTCGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 50 1.00
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (14 bp):
TCGTTGCGATTCTA
Found at i:1438169 original size:94 final size:94
Alignment explanation
Indices: 1438057--1438621 Score: 921
Period size: 94 Copynumber: 6.1 Consensus size: 94
1438047 ATGGATTGAA
* *
1438057 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1438121 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
1438150 TTACTTTCAACCAAAAGACAAAACAAAGACAAATATTAATTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1438215 TTAGCAGAATTAGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1438244 TTACTTTCAACCAAAAGACAAAACAAAGACAACTACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1438309 TTAGCAGAATTGGCAGCAACCGAAAAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1438338 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
1438402 TTTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1438432 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1438497 TTAGCAGAATTGGCAGCAACCCGAATAAAT
66 TTAGCAGAATTGGCAGCAA-CCGAACAAAT
* *
1438527 TTAC-TTCAACCAAAAGACAAAAACAAAGAC-AATATTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGAC-AAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1438586 TTTAGCAGTATTGGCAGCAAACCGAATAAAT
65 TTTAGCAGAATTGGCAGC-AACCGAACAAAT
1438617 TTACT
1 TTACT
1438622 AAGCAATCTA
Statistics
Matches: 448, Mismatches: 17, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
90 39 0.09
91 2 0.00
93 23 0.05
94 341 0.76
95 43 0.10
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1440305 original size:20 final size:20
Alignment explanation
Indices: 1440280--1440375 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
1440270 TTTTGGTTGA
1440280 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
1440300 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
1440319 AAATGACTATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
1440338 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
1440353 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1440373 AAT
1 AAT
1440376 CGCAATGCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 8 0.13
16 4 0.06
17 2 0.03
18 1 0.02
19 14 0.23
20 33 0.53
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1440346 original size:14 final size:14
Alignment explanation
Indices: 1440327--1440380 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1440317 GGAAATGACT
1440327 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1440341 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1440360 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1440374 ATCGCAA
1 ATCGCAA
1440381 TGCAAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1440364 original size:19 final size:19
Alignment explanation
Indices: 1440278--1440418 Score: 122
Period size: 19 Copynumber: 7.8 Consensus size: 19
1440268 TCTTTTGGTT
*
1440278 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
1440297 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1440317 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1440335 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1440351 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
1440368 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAACGC
* *
1440384 AAAATGAACATCGCAACGC
1 GAAATGAAAATCGCAACGC
1440403 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1440419 TGCAATTTTG
Statistics
Matches: 97, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
14 19 0.20
15 2 0.02
16 3 0.03
17 3 0.03
18 3 0.03
19 37 0.38
20 28 0.29
21 2 0.02
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1440364 original size:33 final size:33
Alignment explanation
Indices: 1440278--1440401 Score: 140
Period size: 33 Copynumber: 3.5 Consensus size: 33
1440268 TCTTTTGGTT
1440278 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
**
1440317 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1440351 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1440384 AAAATGAACATCGCAACG
1 GAAATGAAAATCGCAACG
1440402 CGAAATGAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
33 46 0.60
34 11 0.14
36 1 0.01
37 1 0.01
38 3 0.04
40 15 0.19
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1441026 original size:20 final size:20
Alignment explanation
Indices: 1441003--1441096 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
1440993 CGATAGTCAG
1441003 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1441023 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
1441043 AATTCGCATTACGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* * *
1441064 AATCGCGTTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
1441084 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1441097 ATTATGAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 44 0.72
21 17 0.28
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1441058 original size:41 final size:40
Alignment explanation
Indices: 1441003--1441092 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
1440993 CGATAGTCAG
* * *
1441003 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTACGATTTACGTAATCGCATTGCGATTTACCT
* * *
1441043 AATTCGCATTACGATTTACGTAATCGCGTTGTGATTTACGT
1 -ATTCGCATTACGATTTACGTAATCGCATTGCGATTTACCT
1441084 ATTCGCATT
1 ATTCGCATT
1441093 GCGAATTATG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 9 0.21
41 34 0.79
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (40 bp):
ATTCGCATTACGATTTACGTAATCGCATTGCGATTTACCT
Found at i:1441117 original size:21 final size:21
Alignment explanation
Indices: 1441093--1441179 Score: 97
Period size: 21 Copynumber: 4.2 Consensus size: 21
1441083 TATTCGCATT
1441093 GCGAATTATGAAAATCGCAAC
1 GCGAATTATGAAAATCGCAAC
* * *
1441114 GCGAA-TACGTAAATCGCAAT
1 GCGAATTATGAAAATCGCAAC
*
1441134 GCGAATTAGGAAAATCGCAAC
1 GCGAATTATGAAAATCGCAAC
* *
1441155 GCGAATT-TGGGAAATCGCAAT
1 GCGAATTAT-GAAAATCGCAAC
1441176 GCGA
1 GCGA
1441180 TAGTCAGAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.31
21 38 0.69
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
GCGAATTATGAAAATCGCAAC
Found at i:1441192 original size:41 final size:41
Alignment explanation
Indices: 1441086--1441179 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
1441076 ATTTACGTAT
* *
1441086 TCGCATTGCGAATTATG-AAAATCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATTA-GCAAAATCGCAACGCGAATACGGAAA
* **
1441127 TCGCAATGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGCAAAATCGCAACGCGAA-TACGGAAA
1441169 TCGCAATGCGA
1 TCGCAATGCGA
1441180 TAGTCAGAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
40 1 0.02
41 30 0.64
42 16 0.34
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTAGCAAAATCGCAACGCGAATACGGAAA
Found at i:1442651 original size:12 final size:13
Alignment explanation
Indices: 1442627--1442660 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1442617 TTATTTTGGA
1442627 AAATTTGAATTTT
1 AAATTTGAATTTT
*
1442640 TAATTT-AATTTT
1 AAATTTGAATTTT
1442652 AAATTTGAA
1 AAATTTGAA
1442661 GTATGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
AAATTTGAATTTT
Found at i:1445999 original size:231 final size:232
Alignment explanation
Indices: 1445596--1446054 Score: 523
Period size: 231 Copynumber: 2.0 Consensus size: 232
1445586 TAAGTTTACT
* *
1445596 GACGACATTGTTCCTTCGTGTTGAGGAAGTCTAGTCATATTGCAAAGATTGTGCATCTGAAGACA
1 GACGACATTGTTCCTTCGTGTTGAGGAAGTCTAGTCATATTGCAAAGATTGTACATCGGAAGACA
* * * * * *
1445661 ACATTTTTCCTTCACGTTGAGGAAATCTGATTGCCTATAGATAATTTGACTTTGGAAATTATATT
66 ACATTGTTCCTTCACGTTGAAGAAATCTGATTACCTAGAGATAATTTGACTTTGGAAATGACATT
* * * * * * * * *
1445726 GTCCCTTCGTGTTGAAGATATTTGGTCGCTTCAGAGTGATTTGCTTGATATTAAATCTGATGATG
131 GTCCCTACATGCTAAAGAGATCTGATCGCTTCAGAGTGATTTGCTCGATATCAAATCTGATGATG
**
1445791 ACATTGTTCATTTGCG-TTGAGGAGGTCTAGTCTATA
196 ACATTGTTCATTCACGTTTGAGGAGGTCTAGTCTATA
* * * * * *
1445827 GACGACATTGTTCCTTCGTGTTGAGTACA-TCTAGTCATATTTGGATA-ATTGTACCTGGGGAGA
1 GACGACATTGTTCCTTCGTGTTGAGGA-AGTCTAGTCATA-TTGCAAAGATTGTACATCGGAAGA
* * * * *
1445890 CAACATTGTTCTTTCACGTT-AAGAAAGTCTTATTATCTAGAGATAATTTGATTTTGTAAATGAC
64 CAACATTGTTCCTTCACGTTGAAGAAA-TCTGATTACCTAGAGATAATTTGACTTTGGAAATGAC
** * * *
1445954 ATT-TCCCCTACATGCTAAAGAGATCTGATCGCTTTTGGGTGATTTGCTCGATGTCAAATTTGAT
128 ATTGT-CCCTACATGCTAAAGAGATCTGATCGCTTCAGAGTGATTTGCTCGATATCAAATCTGAT
*
1446018 GATGACATTGTTCATTCACGTTTGAGGAGGTTTAGTC
192 GATGACATTGTTCATTCACGTTTGAGGAGGTCTAGTC
1446055 ATAATTAAAA
Statistics
Matches: 187, Mismatches: 36, Indels: 9
0.81 0.16 0.04
Matches are distributed among these distances:
230 6 0.03
231 160 0.86
232 21 0.11
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (232 bp):
GACGACATTGTTCCTTCGTGTTGAGGAAGTCTAGTCATATTGCAAAGATTGTACATCGGAAGACA
ACATTGTTCCTTCACGTTGAAGAAATCTGATTACCTAGAGATAATTTGACTTTGGAAATGACATT
GTCCCTACATGCTAAAGAGATCTGATCGCTTCAGAGTGATTTGCTCGATATCAAATCTGATGATG
ACATTGTTCATTCACGTTTGAGGAGGTCTAGTCTATA
Found at i:1446343 original size:30 final size:30
Alignment explanation
Indices: 1446309--1446388 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
1446299 AGTTCATATG
1446309 CTATTTAACATTGATGGCCAACT-CCTTCTA
1 CTATTTAACATTGATGGCCAACTCCCTT-TA
* * * *
1446339 CTATTTATCCTTGGTGTCCAACTCCCTTTA
1 CTATTTAACATTGATGGCCAACTCCCTTTA
1446369 CTATTTAACATT-AGTGGCCA
1 CTATTTAACATTGA-TGGCCA
1446389 GATCCCTAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 36 0.90
31 4 0.10
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (30 bp):
CTATTTAACATTGATGGCCAACTCCCTTTA
Found at i:1446395 original size:30 final size:28
Alignment explanation
Indices: 1446309--1446403 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 28
1446299 AGTTCATATG
1446309 CTATTTAACATTGATGGCCAA-CTCCTTCTA
1 CTATTTAACATTG-TGGCCAATC-CCTT-TA
* * *
1446339 CTATTTATCCTTGGTGTCCAACTCCCTTTA
1 CTATTTAACATT-GTGGCCAA-TCCCTTTA
*
1446369 CTATTTAACATTAGTGGCCAGATCCC-TAA
1 CTATTTAACATT-GTGGCCA-ATCCCTTTA
1446398 CTATTT
1 CTATTT
1446404 GGTACTTAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
29 8 0.15
30 38 0.72
31 6 0.11
32 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (28 bp):
CTATTTAACATTGTGGCCAATCCCTTTA
Found at i:1446779 original size:13 final size:13
Alignment explanation
Indices: 1446739--1446805 Score: 54
Period size: 13 Copynumber: 5.3 Consensus size: 13
1446729 TTTCAAAAGG
*
1446739 TGAAAATGTTTAA
1 TGAAAATGTTTGA
1446752 TGAATAA-GTTT--
1 TGAA-AATGTTTGA
1446763 TGAAAATGTTTGA
1 TGAAAATGTTTGA
1446776 TGAAAGAAT-TTTGA
1 TG-AA-AATGTTTGA
*
1446790 -AAAAATGTTTGA
1 TGAAAATGTTTGA
1446802 TGAA
1 TGAA
1446806 GTTTTGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
10 2 0.05
11 11 0.25
12 7 0.16
13 12 0.27
14 9 0.20
15 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.37
Consensus pattern (13 bp):
TGAAAATGTTTGA
Found at i:1446814 original size:23 final size:24
Alignment explanation
Indices: 1446741--1446816 Score: 86
Period size: 24 Copynumber: 3.1 Consensus size: 24
1446731 TCAAAAGGTG
*
1446741 AAAATGTTTAATGAATAAGTTTTG--
1 AAAATGTTTGATG-A-AAGTTTTGAA
1446765 AAAATGTTTGATGAAAGAATTTTGAA
1 AAAATGTTTGATGAAAG--TTTTGAA
1446791 AAAATGTTTGATG-AAGTTTTGAA
1 AAAATGTTTGATGAAAGTTTTGAA
1446814 AAA
1 AAA
1446817 TAGTGCCCCT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
22 3 0.06
23 11 0.23
24 17 0.36
25 3 0.06
26 13 0.28
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (24 bp):
AAAATGTTTGATGAAAGTTTTGAA
Found at i:1452868 original size:20 final size:20
Alignment explanation
Indices: 1452843--1452883 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1452833 AAAACTATGT
1452843 TGTTTTGGATGGATTATATA
1 TGTTTTGGATGGATTATATA
1452863 TGTTTTGGATGGATTATATA
1 TGTTTTGGATGGATTATATA
1452883 T
1 T
1452884 ATATATACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (20 bp):
TGTTTTGGATGGATTATATA
Found at i:1456168 original size:2 final size:2
Alignment explanation
Indices: 1456161--1456197 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1456151 ATCCAACCTA
1456161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1456198 TTCATCCGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1463049 original size:12 final size:12
Alignment explanation
Indices: 1463032--1463060 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1463022 TTGCACTGAT
1463032 ACGGATACGGGG
1 ACGGATACGGGG
1463044 ACGGATACGGGG
1 ACGGATACGGGG
1463056 ACGGA
1 ACGGA
1463061 AAATGATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.48, T:0.07
Consensus pattern (12 bp):
ACGGATACGGGG
Found at i:1467631 original size:26 final size:26
Alignment explanation
Indices: 1467602--1467691 Score: 94
Period size: 26 Copynumber: 3.4 Consensus size: 26
1467592 TGAATGAATT
1467602 TTTAAAATGATCAAATTCCCCTAAAC
1 TTTAAAATGATCAAATTCCCCTAAAC
*
1467628 TTTAAAATAACTC-AATTACCCCTAAAC
1 TTTAAAATGA-TCAAATT-CCCCTAAAC
* * * *
1467655 TTTAAAATGACCAAAAT-ACCTCAAGC
1 TTTAAAATGATCAAATTCCCCT-AAAC
1467681 TTTAAAATGAT
1 TTTAAAATGAT
1467692 AAAAATACCC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.06
26 27 0.51
27 23 0.43
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.30
Consensus pattern (26 bp):
TTTAAAATGATCAAATTCCCCTAAAC
Found at i:1467674 original size:27 final size:26
Alignment explanation
Indices: 1467602--1467690 Score: 99
Period size: 27 Copynumber: 3.4 Consensus size: 26
1467592 TGAATGAATT
* *
1467602 TTTAAAATGATCAAATTCCCCTAAAC
1 TTTAAAATGACCAAATACCCCTAAAC
* *
1467628 TTTAAAATAACTCAATTACCCCTAAAC
1 TTTAAAATGAC-CAAATACCCCTAAAC
* *
1467655 TTTAAAATGACCAAAATACCTC-AAGC
1 TTTAAAATGACC-AAATACCCCTAAAC
1467681 TTTAAAATGA
1 TTTAAAATGA
1467691 TAAAAATACC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 23 0.43
27 30 0.57
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.29
Consensus pattern (26 bp):
TTTAAAATGACCAAATACCCCTAAAC
Found at i:1467711 original size:27 final size:26
Alignment explanation
Indices: 1467654--1467732 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 26
1467644 TACCCCTAAA
*
1467654 CTTTAAAATGACCAAAATACCTCAAG
1 CTTTAAAATGACAAAAATACCTCAAG
* *
1467680 CTTTAAAATGATAAAAATACCCTCGAG
1 CTTTAAAATGACAAAAATA-CCTCAAG
* * **
1467707 TTTTAGAATGACCTAAATACCCTCAA
1 CTTTAAAATGACAAAAATA-CCTCAA
1467733 AACTAAGATT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 17 0.40
27 26 0.60
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.27
Consensus pattern (26 bp):
CTTTAAAATGACAAAAATACCTCAAG
Found at i:1472264 original size:19 final size:19
Alignment explanation
Indices: 1472240--1472278 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1472230 TCGAATGCAT
1472240 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1472259 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1472278 T
1 T
1472279 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1472403 original size:64 final size:65
Alignment explanation
Indices: 1472229--1472388 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 65
1472219 TTAATTGAAT
* * * *
1472229 ATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAAC
1 ATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAAAAC
* ** **
1472294 ATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-AAA
1 ATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCAAAA
1472357 C
65 C
1472358 ATCGAATGCATTTCATGCATCGATGCACACT
1 ATCGAATGCATTTCATGCATCGATGCACACT
1472389 TGGTGCACCG
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.44
65 46 0.56
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (65 bp):
ATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAAAAC
Found at i:1473756 original size:19 final size:20
Alignment explanation
Indices: 1473732--1473779 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1473722 AATGATTTTC
* *
1473732 TTTTGAAAGCAAAAATG-GA
1 TTTTGAAAACAAAAATGAAA
*
1473751 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1473771 TTTTGAAAA
1 TTTTGAAAA
1473780 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1473822 original size:23 final size:22
Alignment explanation
Indices: 1473787--1473830 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1473777 AAAAGGATTT
1473787 AGAGCTTTCAAAAATGAAAATTG
1 AGAGCTTTCAAAAA-GAAAATTG
* *
1473810 AGAGTTTTGAAAAAGAAAATT
1 AGAGCTTTCAAAAAGAAAATT
1473831 TTGATTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (22 bp):
AGAGCTTTCAAAAAGAAAATTG
Found at i:1475065 original size:34 final size:30
Alignment explanation
Indices: 1475027--1475095 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1475017 TTGATATAAC
1475027 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1475061 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1475090 AATTTA
1 AATTTA
1475096 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1475106 original size:29 final size:30
Alignment explanation
Indices: 1475036--1475095 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1475026 CAATTTAAGG
1475036 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1475067 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1475096 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1475201 original size:21 final size:21
Alignment explanation
Indices: 1475175--1475275 Score: 109
Period size: 21 Copynumber: 4.8 Consensus size: 21
1475165 AGGGTGTCAA
1475175 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
1475196 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCATCCCTGC
1475217 AGTGCATCCATGCAT--CTGCAC
1 AGTGCATCCATGCATCCCTG--C
* * *
1475238 TAATGCATCGATGCAT-CATGC
1 -AGTGCATCCATGCATCCCTGC
*
1475259 AATGCATCCATGCATCC
1 AGTGCATCCATGCATCC
1475276 AAACATCGAA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.04
20 14 0.20
21 37 0.54
22 13 0.19
23 2 0.03
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:1475264 original size:20 final size:20
Alignment explanation
Indices: 1475239--1475341 Score: 67
Period size: 20 Copynumber: 5.4 Consensus size: 20
1475229 CATCTGCACT
1475239 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATCATGC
*
1475259 AATGCATCCATGCATC---C
1 AATGCATCGATGCATCATGC
* *
1475276 AA-ACATCGAATGCA--AT-T
1 AATGCATCG-ATGCATCATGC
* *
1475293 AGTGCATCGATGCATCCTTGC
1 AATGCATCGATGCAT-CATGC
* *
1475314 CATGCATCGATGCATCCTGC
1 AATGCATCGATGCATCATGC
*
1475334 CATGCATC
1 AATGCATC
1475342 CTGCCATGCA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
16 4 0.06
17 14 0.22
18 5 0.08
20 28 0.44
21 13 0.20
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (20 bp):
AATGCATCGATGCATCATGC
Found at i:1475321 original size:21 final size:20
Alignment explanation
Indices: 1475295--1475341 Score: 85
Period size: 21 Copynumber: 2.3 Consensus size: 20
1475285 ATGCAATTAG
1475295 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCC-TGCCA
1475316 TGCATCGATGCATCCTGCCA
1 TGCATCGATGCATCCTGCCA
1475336 TGCATC
1 TGCATC
1475342 CTGCCATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.19, C:0.34, G:0.19, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCATCCTGCCA
Found at i:1475340 original size:12 final size:12
Alignment explanation
Indices: 1475302--1475353 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
1475292 TAGTGCATCG
1475302 ATGCATCCTTGCC
1 ATGCATCC-TGCC
1475315 ATGCAT-C-G--
1 ATGCATCCTGCC
1475323 ATGCATCCTGCC
1 ATGCATCCTGCC
1475335 ATGCATCCTGCC
1 ATGCATCCTGCC
1475347 ATGCATC
1 ATGCATC
1475354 AAGGCTGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 6 0.17
9 1 0.03
10 2 0.06
12 20 0.57
13 6 0.17
ACGTcount: A:0.19, C:0.37, G:0.17, T:0.27
Consensus pattern (12 bp):
ATGCATCCTGCC
Found at i:1476643 original size:19 final size:19
Alignment explanation
Indices: 1476619--1476670 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1476609 TTGGACTCTT
1476619 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
1476638 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
*
1476657 AGTGCATCGATGCA
1 AGTGCATCGGTGCA
1476671 TAAAATGCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:1476761 original size:46 final size:45
Alignment explanation
Indices: 1476699--1476786 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 45
1476689 TTGAAAAAGC
* *
1476699 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
*
1476745 CTGAGTGCATGGATGCATGGTATGTGCATCGATGCATAAAAT
1 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAAT
1476787 TCATTCGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 19 0.49
46 20 0.51
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (45 bp):
CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCA
Found at i:1476834 original size:20 final size:20
Alignment explanation
Indices: 1476809--1476846 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1476799 TGAAAAATTA
*
1476809 ATTGGTGCATCGATGCATGG
1 ATTGGTACATCGATGCATGG
*
1476829 ATTGGTACATCGGTGCAT
1 ATTGGTACATCGATGCAT
1476847 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:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGGTACATCGATGCATGG
Found at i:1483509 original size:22 final size:21
Alignment explanation
Indices: 1483467--1483506 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1483457 GAGTTTATTT
*
1483467 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1483488 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1483507 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1485466 original size:45 final size:46
Alignment explanation
Indices: 1485378--1485467 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 46
1485368 TTGAAAAAGC
* * *
1485378 CTGAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCAACGATGCATGGTCATGTGCATCGATGCATAAAATGCA
1485424 CTGAGTGCAACGATGCATGGT-ATGTGCATCGATGCATAAAATGC
1 CTGAGTGCAACGATGCATGGTCATGTGCATCGATGCATAAAATGC
1485468 CTTCGATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (46 bp):
CTGAGTGCAACGATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:1485513 original size:20 final size:20
Alignment explanation
Indices: 1485488--1485525 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1485478 TGAAAAATTA
1485488 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
1485508 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
1485526 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:1489089 original size:178 final size:178
Alignment explanation
Indices: 1488790--1489123 Score: 488
Period size: 178 Copynumber: 1.9 Consensus size: 178
1488780 CTGATTCTAC
* * * *
1488790 TTGATAAAGGATCGTCCACACTCCTCCAACAATGAAGAAGGATGTAATGCCTTGATTGTTTCCCA
1 TTGATAAAGGACCGTCCACACTCCTCCAACAATGAAGAAGAATGGAATACCTTGATTGTTTCCCA
* * * * **
1488855 ATCTAGGATAAACAATAAGTTTTGTTCCCACTTTGAAAACTTGGGTTGTAAATAAGAAAAATTTA
66 ATCTAGGACAAACAATAAGTGTTATTCCCACTTTGAAAACTTGGGATACAAATAAGAAAAATTTA
* *
1488920 AGTTAGAATGATGTAATTATAAGTAAATGCATTCTGATGGATAAGGTT
131 AGTTAGAATGATGTAATAACAAGTAAATGCATTCTGATGGATAAGGTT
** * * *
1488968 TTGATAAAGGACCGTCCACACTCCTCCAAGGATGAAGAAGAATGGGATACCTTTATTGTTTCCCG
1 TTGATAAAGGACCGTCCACACTCCTCCAACAATGAAGAAGAATGGAATACCTTGATTGTTTCCCA
* * *
1489033 ATCTAGGACGAACAATAAGTGTTATTCCCACTTTGAAAGCTTGGGATACAAATAAGAAAAGTTTA
66 ATCTAGGACAAACAATAAGTGTTATTCCCACTTTGAAAACTTGGGATACAAATAAGAAAAATTTA
1489098 AGTTAGAATGATGTAATAACAAGTAA
131 AGTTAGAATGATGTAATAACAAGTAA
1489124 TAAAAGAAAT
Statistics
Matches: 136, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
178 136 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (178 bp):
TTGATAAAGGACCGTCCACACTCCTCCAACAATGAAGAAGAATGGAATACCTTGATTGTTTCCCA
ATCTAGGACAAACAATAAGTGTTATTCCCACTTTGAAAACTTGGGATACAAATAAGAAAAATTTA
AGTTAGAATGATGTAATAACAAGTAAATGCATTCTGATGGATAAGGTT
Found at i:1489627 original size:18 final size:20
Alignment explanation
Indices: 1489604--1489654 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1489594 TGGAAGCCTT
*
1489604 TGAAAATATATG-ATTTAA-
1 TGAAAATACATGCATTTAAG
*
1489622 TGAAAATACATGCCTTTAAG
1 TGAAAATACATGCATTTAAG
1489642 TGAAAATACATGC
1 TGAAAATACATGC
1489655 TCTTGGACGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.38
19 5 0.17
20 13 0.45
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (20 bp):
TGAAAATACATGCATTTAAG
Found at i:1491390 original size:13 final size:13
Alignment explanation
Indices: 1491372--1491402 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1491362 TTGATTCGTT
1491372 GAGCCGAGTCATC
1 GAGCCGAGTCATC
1491385 GAGCCGAGTCATC
1 GAGCCGAGTCATC
1491398 GAGCC
1 GAGCC
1491403 TAGCTGAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.32, G:0.32, T:0.13
Consensus pattern (13 bp):
GAGCCGAGTCATC
Found at i:1492893 original size:21 final size:21
Alignment explanation
Indices: 1492867--1492914 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1492857 ACGGCTAGGG
* * *
1492867 AACACCCTGGTGCTGCTGGAT
1 AACACCCCGGTGCGGCTGGAC
1492888 AACACCCCGGTGCGGCTGGAC
1 AACACCCCGGTGCGGCTGGAC
1492909 AACACC
1 AACACC
1492915 GTGGGATGCC
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:0.23, C:0.35, G:0.27, T:0.15
Consensus pattern (21 bp):
AACACCCCGGTGCGGCTGGAC
Found at i:1494586 original size:18 final size:18
Alignment explanation
Indices: 1494563--1494613 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 18
1494553 ATTTTTTAGC
1494563 ATCGATACTATTCATGGT
1 ATCGATACTATTCATGGT
1494581 ATCGATACTATTGTTCATGGT
1 ATCGATACTA---TTCATGGT
*
1494602 ATTGATACTATT
1 ATCGATACTATT
1494614 GTTCATACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 12 0.41
21 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (18 bp):
ATCGATACTATTCATGGT
Found at i:1494599 original size:21 final size:21
Alignment explanation
Indices: 1494573--1494619 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1494563 ATCGATACTA
1494573 TTCATGGTATCGATACTATTG
1 TTCATGGTATCGATACTATTG
*
1494594 TTCATGGTATTGATACTATTG
1 TTCATGGTATCGATACTATTG
1494615 TTCAT
1 TTCAT
1494620 ACAATACAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCATGGTATCGATACTATTG
Found at i:1494634 original size:22 final size:21
Alignment explanation
Indices: 1494606--1494654 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
1494596 CATGGTATTG
1494606 ATACTATTGTTCATACAATACA
1 ATACTATT-TTCATACAATACA
1494628 ATACTA--TTCATACAATACA
1 ATACTATTTTCATACAATACA
*
1494647 ATAATATT
1 ATACTATT
1494655 CATAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 18 0.75
22 6 0.25
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.37
Consensus pattern (21 bp):
ATACTATTTTCATACAATACA
Found at i:1494639 original size:19 final size:19
Alignment explanation
Indices: 1494615--1494658 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1494605 GATACTATTG
*
1494615 TTCATACAATACAATACTA
1 TTCATACAATACAATAATA
1494634 TTCATACAATACAATAATA
1 TTCATACAATACAATAATA
1494653 TTCATA
1 TTCATA
1494659 AAAAAATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (19 bp):
TTCATACAATACAATAATA
Found at i:1496001 original size:19 final size:20
Alignment explanation
Indices: 1495965--1496012 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1495955 TGTAAATCCT
*
1495965 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTGG
*
1495985 TTTTCAAAA-TCCATTTTTG
1 TTTTCAAAATTCCATTTTGG
*
1496004 CTTTCAAAA
1 TTTTCAAAA
1496013 GAAAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGG
Found at i:1497627 original size:134 final size:132
Alignment explanation
Indices: 1497445--1497684 Score: 299
Period size: 134 Copynumber: 1.8 Consensus size: 132
1497435 AGGCTTTCAA
*
1497445 TTTGAATCTGGCAAAACAGACTTCGAATCAGGCTCAGGACGTCG-AAAAACATAAAATATAACTT
1 TTTGAATCTGGCAAAACAGACTTCGAATCAGGCTCAGGACATCGAAAAAAC-T-AAA-ATAACTT
* *
1497509 TTTGAAAAAATTGACTTTTTGTTCAAAGTCAA-AGTCAACGGGTTTGACTGATAATTTCGAGGCT
63 TTCG-AAAAATTGACTTTTTGGTCAAAGTCAACAGTCAACGGGTTTGACTGATAATTTCGAGGCT
1497573 TTCGGG
127 TTCGGG
* * * * *
1497579 TTTGAATTTGGCAAAACGGACTTCAGATTC-GGACTCAGGATATC-AAAAAACTAAAATGACTTT
1 TTTGAATCTGGCAAAACAGACTTC-GAATCAGG-CTCAGGACATCGAAAAAACTAAAATAACTTT
* * *
1497642 TCGAAAAATTTACTTTTTGGTCAAAGTTAACGGTCAACGGGTT
64 TCGAAAAATTGACTTTTTGGTCAAAGTCAACAGTCAACGGGTT
1497685 GGGTCAACGG
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
131 24 0.26
132 20 0.22
133 3 0.03
134 25 0.27
135 19 0.21
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (132 bp):
TTTGAATCTGGCAAAACAGACTTCGAATCAGGCTCAGGACATCGAAAAAACTAAAATAACTTTTC
GAAAAATTGACTTTTTGGTCAAAGTCAACAGTCAACGGGTTTGACTGATAATTTCGAGGCTTTCG
GG
Found at i:1497689 original size:13 final size:13
Alignment explanation
Indices: 1497673--1497702 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1497663 CAAAGTTAAC
*
1497673 GGTCAACGGGTTG
1 GGTCAACGGGTCG
1497686 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1497699 GGTC
1 GGTC
1497703 GGGTCAGACC
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:0.13, C:0.20, G:0.47, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1497717 original size:20 final size:18
Alignment explanation
Indices: 1497679--1497730 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 18
1497669 TAACGGTCAA
*
1497679 CGGGTTGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1497697 CGGGTCGGGTCAGACCGGGT
1 CGGGTCGGGTCA-A-CGGGT
1497717 CGGGTCGGGTCAAC
1 CGGGTCGGGTCAAC
1497731 CCAGGTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 12 0.39
19 2 0.06
20 17 0.55
ACGTcount: A:0.12, C:0.23, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1497737 original size:20 final size:20
Alignment explanation
Indices: 1497694--1497737 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1497684 TGGGTCAACG
*
1497694 GGTCGGGTCGGGTCAGACCG
1 GGTCGGGTCGGGTCAGACCA
1497714 GGTCGGGTCGGGTCA-ACCCA
1 GGTCGGGTCGGGTCAGA-CCA
1497734 GGTC
1 GGTC
1497738 AAACTGCCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.11, C:0.27, G:0.45, T:0.16
Consensus pattern (20 bp):
GGTCGGGTCGGGTCAGACCA
Found at i:1499507 original size:21 final size:21
Alignment explanation
Indices: 1499481--1499534 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1499471 GGGCTTGATA
*
1499481 GTATCGATACTACTGTTCATG
1 GTATCGATACTACTATTCATG
1499502 GTATCGATACTACTATTCATG
1 GTATCGATACTACTATTCATG
*
1499523 GTATCGGTACTA
1 GTATCGATACTA
1499535 TTGTAGCAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (21 bp):
GTATCGATACTACTATTCATG
Found at i:1499649 original size:20 final size:19
Alignment explanation
Indices: 1499626--1499672 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1499616 ACAGTATCGG
1499626 TACTATTAATACAATATCAA
1 TACTATTAATACAATA-CAA
* * *
1499646 TACTATTCATACAGTACAG
1 TACTATTAATACAATACAA
1499665 TACTATTA
1 TACTATTA
1499673 TAATTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (19 bp):
TACTATTAATACAATACAA
Found at i:1502445 original size:3 final size:3
Alignment explanation
Indices: 1502437--1502475 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1502427 ATAAAGAGTT
1502437 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1502476 GAGTTTATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1503644 original size:18 final size:18
Alignment explanation
Indices: 1503619--1503659 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1503609 GTTTTCTGGA
* *
1503619 ATTTTTTTTTCTTTTTCTC
1 ATTTTTTTTACCTTTT-TC
1503638 ATTTTTTTTACCTTTTTC
1 ATTTTTTTTACCTTTTTC
1503656 ATTT
1 ATTT
1503660 ATTTGTTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTTTTTACCTTTTTC
Found at i:1504899 original size:51 final size:51
Alignment explanation
Indices: 1504816--1504930 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
1504806 GTAACTACTG
* * * * *
1504816 AATAAAATAATAATAAATTAAATATAATATTTTGATTCTATCA-TAATTTCAT
1 AATAAAATAATAATAAACTAAAAATAACATTTTAACTCTAT-ATTAA-TTCAT
*
1504868 -ATAAAATAATAATAAACTAAAAATAACATTTTAACTCTATATTAATTCTT
1 AATAAAATAATAATAAACTAAAAATAACATTTTAACTCTATATTAATTCAT
1504918 AATAAAATAATAA
1 AATAAAATAATAA
1504931 ATTTAATCCT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
50 5 0.09
51 50 0.91
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAAATAACATTTTAACTCTATATTAATTCAT
Found at i:1507876 original size:20 final size:20
Alignment explanation
Indices: 1507827--1507876 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1507817 TGATTTTAAT
** *
1507827 TTTTTTTAAAAAAATTTTTA
1 TTTTTTTAAAAAAACCTTGA
* *
1507847 TATTTATAAAAAAACCTTGA
1 TTTTTTTAAAAAAACCTTGA
1507867 TTTTTTTAAA
1 TTTTTTTAAA
1507877 TTATAGAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTTTTTAAAAAAACCTTGA
Found at i:1519499 original size:16 final size:16
Alignment explanation
Indices: 1519478--1519519 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1519468 CATGCATGCA
1519478 GAATCATTTTTCAAAT
1 GAATCATTTTTCAAAT
1519494 GAATCATTTTTCAAAT
1 GAATCATTTTTCAAAT
*
1519510 AAATCATTTT
1 GAATCATTTT
1519520 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (16 bp):
GAATCATTTTTCAAAT
Found at i:1519543 original size:24 final size:25
Alignment explanation
Indices: 1519516--1519564 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
1519506 AAATAAATCA
1519516 TTTTAAAATT-TTAATTAAAAATAT
1 TTTTAAAATTATTAATTAAAAATAT
* *
1519540 TTTTAATATTCATTATTTAAAAATA
1 TTTTAAAATT-ATTAATTAAAAATA
1519565 AAAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
26 12 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTTAAAATTATTAATTAAAAATAT
Found at i:1522967 original size:22 final size:24
Alignment explanation
Indices: 1522914--1522981 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 24
1522904 TAAAAAATAC
1522914 TAAGTTAATAGTAAAATATATTTAA
1 TAAGTTAATA-TAAAATATATTTAA
*
1522939 TAAGTTAATATAAAA-ATATTT-T
1 TAAGTTAATATAAAATATATTTAA
*
1522961 TAAGTTAATATATATATATAT
1 TAAGTTAATATA-AAATATAT
1522982 ATATAATTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 12 0.31
23 8 0.21
24 9 0.23
25 10 0.26
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (24 bp):
TAAGTTAATATAAAATATATTTAA
Found at i:1524219 original size:31 final size:31
Alignment explanation
Indices: 1524149--1524219 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1524139 TTATATAAAA
** *
1524149 AATATCTTAATTAAATAAAAATGAAAGTGAC
1 AATATCTTAATTAAATAAAAACAAAAGTCAC
* *
1524180 CATATCTTAATTAAATAAAAACAAAAGTCAT
1 AATATCTTAATTAAATAAAAACAAAAGTCAC
*
1524211 AATTTCTTA
1 AATATCTTA
1524220 TGTTTTTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (31 bp):
AATATCTTAATTAAATAAAAACAAAAGTCAC
Found at i:1524334 original size:20 final size:20
Alignment explanation
Indices: 1524309--1524346 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1524299 TTTGGTTCAC
*
1524309 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
1524329 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
1524347 GGAATAGGAT
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:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:1524349 original size:18 final size:19
Alignment explanation
Indices: 1524309--1524352 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1524299 TTTGGTTCAC
*
1524309 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
1524329 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
1524347 GGAATA
1 GGAATA
1524353 GGATTACTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:1524682 original size:3 final size:3
Alignment explanation
Indices: 1524674--1524745 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
1524664 TTTTTTCATT
* * * * *
1524674 TTA TTA TTA TTA TAA TTA TTT TTA TAA ATA TTA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1524722 TTA TTA TAA ATA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
1524746 AAAGCCAAAT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1524710 original size:30 final size:30
Alignment explanation
Indices: 1524674--1524745 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
1524664 TTTTTTCATT
*
1524674 TTATTATTATTATAATTATTTTTATAAATA
1 TTATTATTATTATAATTATTATTATAAATA
* *
1524704 TTATTATTGTTATTATTATTATTATAAATA
1 TTATTATTATTATAATTATTATTATAAATA
*
1524734 ATATTATTATTA
1 TTATTATTATTA
1524746 AAAGCCAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TTATTATTATTATAATTATTATTATAAATA
Found at i:1524811 original size:20 final size:21
Alignment explanation
Indices: 1524784--1524844 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
1524774 AATTACAAAT
1524784 GAGGCCCAGATCTAGAACCCG
1 GAGGCCCAGATCTAGAACCCG
* * *
1524805 G-GGCCCAGATCCAAAACCTG
1 GAGGCCCAGATCTAGAACCCG
*
1524825 GAGGCCCATATCTAG-ACCCG
1 GAGGCCCAGATCTAGAACCCG
1524845 ACCCAACACA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.28, C:0.34, G:0.26, T:0.11
Consensus pattern (21 bp):
GAGGCCCAGATCTAGAACCCG
Found at i:1527425 original size:7 final size:7
Alignment explanation
Indices: 1527413--1527438 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1527403 ACTGTAATTA
1527413 TTATTCT
1 TTATTCT
1527420 TTATTCT
1 TTATTCT
1527427 TTATTCT
1 TTATTCT
1527434 TTATT
1 TTATT
1527439 TTCATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTCT
Found at i:1527458 original size:2 final size:2
Alignment explanation
Indices: 1527451--1527482 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1527441 CATTTTAATC
1527451 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
1527483 TGATTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1527734 original size:2 final size:2
Alignment explanation
Indices: 1527727--1527754 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1527717 ATAAATATCT
1527727 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
1527755 AAATTAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1528318 original size:26 final size:26
Alignment explanation
Indices: 1528266--1528334 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
1528256 TTTTCAAAAT
*
1528266 TTTATATATACTTATTATTTTCCTAATA
1 TTTATATATA-TTATT-TTTTACTAATA
* *
1528294 TTTATATATATTATTTTTTATTAATG
1 TTTATATATATTATTTTTTACTAATA
*
1528320 TTT-T-TATTTTATTTT
1 TTTATATATATTATTTT
1528335 CAAGTATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 10 0.27
25 1 0.03
26 11 0.30
27 5 0.14
28 10 0.27
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (26 bp):
TTTATATATATTATTTTTTACTAATA
Found at i:1529772 original size:7 final size:7
Alignment explanation
Indices: 1529753--1529800 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
1529743 TTTTCATACA
1529753 TGCA-TT
1 TGCATTT
1529759 TGCATTT
1 TGCATTT
*
1529766 TGTATTT
1 TGCATTT
1529773 TGCATTT
1 TGCATTT
1529780 TGCATCTT
1 TGCAT-TT
*
1529788 TACATTT
1 TGCATTT
1529795 T-CATTT
1 TGCATTT
1529801 ATATTTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 9 0.24
7 22 0.59
8 6 0.16
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.58
Consensus pattern (7 bp):
TGCATTT
Found at i:1529930 original size:14 final size:14
Alignment explanation
Indices: 1529866--1529942 Score: 50
Period size: 14 Copynumber: 5.5 Consensus size: 14
1529856 CATATTTACA
1529866 TTTGCATTTTGCATTT
1 TTTGCATTTT-CA-TT
* *
1529882 TTTTCATTTTCGTT
1 TTTGCATTTTCATT
* *
1529896 TTT--ATTTTTATA
1 TTTGCATTTTCATT
**
1529908 TTTATATTTTCATT
1 TTTGCATTTTCATT
* *
1529922 TTTGCATTTGCATA
1 TTTGCATTTTCATT
1529936 TTTGCAT
1 TTTGCAT
1529943 AATTACATTT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
12 9 0.19
14 29 0.60
15 1 0.02
16 9 0.19
ACGTcount: A:0.17, C:0.10, G:0.08, T:0.65
Consensus pattern (14 bp):
TTTGCATTTTCATT
Found at i:1532645 original size:7 final size:7
Alignment explanation
Indices: 1532633--1532685 Score: 79
Period size: 7 Copynumber: 7.1 Consensus size: 7
1532623 CTTAAAGAAG
1532633 AGGAAAA
1 AGGAAAA
1532640 AGGAAAAA
1 AGG-AAAA
1532648 AGGAAAA
1 AGGAAAA
1532655 AGGAAAAA
1 AGG-AAAA
1532663 AGGAAAAA
1 AGG-AAAA
1532671 AGGAAAA
1 AGGAAAA
1532678 AGGAAAA
1 AGGAAAA
1532685 A
1 A
1532686 AAAAGAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
7 22 0.50
8 22 0.50
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (7 bp):
AGGAAAA
Found at i:1532649 original size:8 final size:8
Alignment explanation
Indices: 1532636--1532718 Score: 93
Period size: 8 Copynumber: 10.6 Consensus size: 8
1532626 AAAGAAGAGG
1532636 AAAAAGGA
1 AAAAAGGA
1532644 AAAAAGG-
1 AAAAAGGA
1532651 AAAAAGGA
1 AAAAAGGA
1532659 AAAAAGGA
1 AAAAAGGA
1532667 AAAAAGG-
1 AAAAAGGA
1532674 AAAAAGGAAA
1 AAAAAGG--A
*
1532684 AAAAAAGA
1 AAAAAGGA
1532692 AAAAA--A
1 AAAAAGGA
*
1532698 ATAAAGGA
1 AAAAAGGA
*
1532706 AAAAAAGA
1 AAAAAGGA
1532714 AAAAA
1 AAAAA
1532719 TTGAATCAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
6 5 0.08
7 14 0.22
8 40 0.62
10 6 0.09
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (8 bp):
AAAAAGGA
Found at i:1532653 original size:15 final size:15
Alignment explanation
Indices: 1532633--1532717 Score: 91
Period size: 15 Copynumber: 5.5 Consensus size: 15
1532623 CTTAAAGAAG
1532633 AGGAAAAAGGAAAAA
1 AGGAAAAAGGAAAAA
1532648 AGGAAAAAGGAAAAA
1 AGGAAAAAGGAAAAA
1532663 AGGAAAAAAGG-AAAA
1 AGG-AAAAAGGAAAAA
**
1532678 AGGAAAAAAAAAGAAA
1 AGGAAAAAGGAA-AAA
**
1532694 AAAAATAAAGGAAAAA
1 AGGAA-AAAGGAAAAA
*
1532710 AAGAAAAA
1 AGGAAAAA
1532718 ATTGAATCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
14 5 0.08
15 29 0.49
16 20 0.34
17 5 0.08
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (15 bp):
AGGAAAAAGGAAAAA
Found at i:1532666 original size:23 final size:23
Alignment explanation
Indices: 1532636--1532718 Score: 107
Period size: 23 Copynumber: 3.6 Consensus size: 23
1532626 AAAGAAGAGG
*
1532636 AAAAAGGAAAAAAGGAAAAAGGA
1 AAAAAAGAAAAAAGGAAAAAGGA
*
1532659 AAAAAGGAAAAAAGGAAAAAGGAAA
1 AAAAAAGAAAAAAGGAAAAAGG--A
1532684 AAAAAAGAAAAAA--AATAAAGGA
1 AAAAAAGAAAAAAGGAA-AAAGGA
1532706 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
1532719 TTGAATCAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
22 14 0.25
23 24 0.43
24 5 0.09
25 13 0.23
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (23 bp):
AAAAAAGAAAAAAGGAAAAAGGA
Found at i:1533214 original size:32 final size:32
Alignment explanation
Indices: 1533173--1533234 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1533163 TCTGGAATTA
* *
1533173 AGAAGTATCTCTACGAGATGAGCATAACAACT
1 AGAAGTATCTCTACCAGATAAGCATAACAACT
1533205 AGAAGTATCTCTACCAGATAAGCATAACAA
1 AGAAGTATCTCTACCAGATAAGCATAACAA
1533235 TCACTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (32 bp):
AGAAGTATCTCTACCAGATAAGCATAACAACT
Found at i:1536930 original size:21 final size:21
Alignment explanation
Indices: 1536891--1536932 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1536881 ATTCAAAGAG
1536891 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATT-CCCTGCTACA
1536913 GGGAACCGATAT-CCTGCTAC
1 GGGAACCGAT-TCCCTGCTAC
1536933 GGTACTGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 10 0.53
23 1 0.05
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (21 bp):
GGGAACCGATTCCCTGCTACA
Found at i:1537665 original size:24 final size:24
Alignment explanation
Indices: 1537638--1537729 Score: 84
Period size: 24 Copynumber: 3.9 Consensus size: 24
1537628 CACCACAGCT
*
1537638 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
1537662 CGTAGAAATTGTC-CCGAAG-GAACG
1 CGTAGAAATTG-CACCGAAGTG-CCA
*
1537686 CGTAGAAA-TGCATCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
1537709 CATAG-AATTGCACCGTAGTGC
1 CGTAGAAATTGCACCGAAGTGC
1537730 TATATAAGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
22 3 0.06
23 24 0.44
24 26 0.48
25 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:1541595 original size:2 final size:2
Alignment explanation
Indices: 1541588--1541637 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1541578 ACTATCCATA
1541588 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
1541630 AT AT AT AT
1 AT AT AT AT
1541638 TCTTTCCAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1544141 original size:24 final size:24
Alignment explanation
Indices: 1544114--1544202 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 24
1544104 CAGCTCGTAT
1544114 AAATTGCACCGAAGTGCCAGGTAG
1 AAATTGCACCGAAGTGCCAGGTAG
1544138 AAATTGTC-CCGAAG-GACC-GAGTAG
1 AAATTG-CACCGAAGTG-CCAG-GTAG
**
1544162 AAA-TGCACCGAAGTGCCACATAG
1 AAATTGCACCGAAGTGCCAGGTAG
*
1544185 -AATTGCACCGTAGTGCCA
1 AAATTGCACCGAAGTGCCA
1544203 TATAAGATTG
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
22 3 0.05
23 29 0.53
24 22 0.40
25 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.17
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCCAGGTAG
Found at i:1545216 original size:21 final size:21
Alignment explanation
Indices: 1545190--1545230 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1545180 TTTTTTCTTT
1545190 AGGGGGGAATC-GATACCCCCC
1 AGGGGGGAATCTG-TACCCCCC
1545211 AGGGGGGAATCTGTACCCCC
1 AGGGGGGAATCTGTACCCCC
1545231 TGCACAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.22, C:0.32, G:0.34, T:0.12
Consensus pattern (21 bp):
AGGGGGGAATCTGTACCCCCC
Found at i:1546778 original size:22 final size:22
Alignment explanation
Indices: 1546741--1546818 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
1546731 TACATCTAAT
1546741 TCTTC-AATATGATAGATTCTC
1 TCTTCAAATATGATAGATTCTC
*
1546762 TCTTCAAATATGGTAGATTCTC
1 TCTTCAAATATGATAGATTCTC
*
1546784 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAATATGATAGATTCTC
* *
1546806 TTTTCAAAGATGA
1 TCTTCAAATATGA
1546819 AAGCCTTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 5 0.10
22 47 0.90
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.40
Consensus pattern (22 bp):
TCTTCAAATATGATAGATTCTC
Found at i:1547630 original size:44 final size:45
Alignment explanation
Indices: 1547471--1547777 Score: 388
Period size: 45 Copynumber: 6.8 Consensus size: 45
1547461 CTATTTCCCA
* *
1547471 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAGCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1547515 CATCTGT-AGCCCTTTAGTGCATGATG-TTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1547558 CATCCTGTAAGCCCTTCAGTGCACGATGTTTTCAAAGCCTTC-GGT
1 CAT-CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
1547603 CATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1547648 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAAAAACATTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC---AAAACCTTCGGGT
* * * * *
1547696 TATCCGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGT
* * *
1547743 CATCCGTAAGACCTTCAGTGCAAGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1547778 TGAGATTTTA
Statistics
Matches: 233, Mismatches: 21, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
42 4 0.02
43 31 0.13
44 46 0.20
45 56 0.24
46 20 0.09
47 37 0.16
48 39 0.17
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1547668 original size:89 final size:89
Alignment explanation
Indices: 1547471--1547777 Score: 393
Period size: 88 Copynumber: 3.4 Consensus size: 89
1547461 CTATTTCCCA
* * *
1547471 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCTTTGGGTCATCTGT-AGCCCTTTAGTGC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCATTCGGTCATCTGTAAGCCCTTCAGTGC
1547535 ATGATG-TTTCAAAACCTTCGGGT
66 ATGATGTTTTCAAAACCTTCGGGT
* * *
1547558 CATCCTGTAAGCCCTTCAGTGCACGATGTTTTCAAAGCCTTCGGTCATCTGTAAGCCCTTCAATG
1 CAT-CTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCATTCGGTCATCTGTAAGCCCTTCAGTG
1547623 CATGATGTTTTCAAAACCTTCGGGT
65 CATGATGTTTTCAAAACCTTCGGGT
* * * * *
1547648 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAAAAACATTCGGGTTATCCGTAAGACCTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC---AAAGCATTC-GGTCATCTGTAAGCCCTTCA
* *
1547713 GTGCAGGATGTTTTCAAAAAGCCTTCAGGT
62 GTGCATGATGTTTTC-AAAA-CCTTCGGGT
* * *
1547743 CATCCGTAAGACCTTCAGTGCAAGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1547778 TGAGATTTTA
Statistics
Matches: 192, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
87 3 0.02
88 45 0.23
89 44 0.23
90 20 0.10
92 10 0.05
93 30 0.16
94 4 0.02
95 36 0.19
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (89 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCATTCGGTCATCTGTAAGCCCTTCAGTGC
ATGATGTTTTCAAAACCTTCGGGT
Found at i:1548016 original size:3 final size:3
Alignment explanation
Indices: 1548008--1548078 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
1547998 TTTTTTCATT
* * *
1548008 TTA TTA TTA -TA TAA TTA TT- TT- TTAA ATA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* *
1548051 TTA TTA TTA -TA TAA ATA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1548079 CAAGCCAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 10 0.19
3 43 0.80
4 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1548142 original size:21 final size:21
Alignment explanation
Indices: 1548116--1548177 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1548106 AATTACAAAT
*
1548116 GAGGCCTAGATCTAGAACCCG
1 GAGGCCCAGATCTAGAACCCG
* * *
1548137 GAGGCCCAGATCCAAAACCCA
1 GAGGCCCAGATCTAGAACCCG
*
1548158 GAGGCCCATATCTAG-ACCCG
1 GAGGCCCAGATCTAGAACCCG
1548178 ACCCAACACC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.31, C:0.34, G:0.24, T:0.11
Consensus pattern (21 bp):
GAGGCCCAGATCTAGAACCCG
Found at i:1549239 original size:13 final size:13
Alignment explanation
Indices: 1549223--1549260 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1549213 GTTTCAATAT
1549223 TTTTAATTTATTA
1 TTTTAATTTATTA
1549236 TTTTAA-TTATTA
1 TTTTAATTTATTA
*
1549248 TCTTTATTTTATT
1 T-TTTAATTTATT
1549261 TTTATTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 10 0.45
14 5 0.23
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTAATTTATTA
Found at i:1552487 original size:28 final size:29
Alignment explanation
Indices: 1552429--1552646 Score: 186
Period size: 29 Copynumber: 7.6 Consensus size: 29
1552419 TACATTCGAA
1552429 AATTCCCAAAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* *
1552458 AATTCCCATAATGTCA-TTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
1552486 AATT-CCAAAATTGTCACC-TTTTCAAAAT
1 AATTCCCAAAA-TGTCACCTTTTTCAAAAT
1552514 AATTCCCAAAATGTCACCTTTTTCACACAAT
1 AATTCCCAAAATGTCACCTTTTTCA-A-AAT
* * * *
1552545 --TTCTCATAATTTCACTTTTTTCACAAA-
1 AATTCCCAAAATGTCACCTTTTTCA-AAAT
* * *
1552572 ATTTCCCAGAATGTCACCATTTTT-AACAAA
1 AATTCCCAAAATGTCACC-TTTTTCAA-AAT
* *
1552602 AATTCCCAGAATGTCA--TATTTTCACTAA-
1 AATTCCCAAAATGTCACCT-TTTTCA-AAAT
*
1552630 AATTCCCATAATGTCAC
1 AATTCCCAAAATGTCAC
1552647 TAAGTCGGGT
Statistics
Matches: 159, Mismatches: 15, Indels: 30
0.78 0.07 0.15
Matches are distributed among these distances:
27 6 0.04
28 63 0.40
29 66 0.42
30 21 0.13
31 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:1552681 original size:17 final size:18
Alignment explanation
Indices: 1552649--1552695 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
1552639 AATGTCACTA
1552649 AGTCGGGTCGGGTCAACG
1 AGTCGGGTCGGGTCAACG
*
1552667 AGTCGGTTC-GGTCAACG
1 AGTCGGGTCGGGTCAACG
* *
1552684 GGTCAGGTCGGG
1 AGTCGGGTCGGG
1552696 CCAGACCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19
Consensus pattern (18 bp):
AGTCGGGTCGGGTCAACG
Found at i:1560042 original size:29 final size:29
Alignment explanation
Indices: 1559973--1560132 Score: 157
Period size: 29 Copynumber: 5.5 Consensus size: 29
1559963 AGATTGCCAA
* * *
1559973 AATGTCACCTTTTTCAAAATAATTACCAG
1 AATGTCACTTTTTTTAAAATAATTCCCAG
*
1560002 AATGTCA--TTTTTTAAAATAATTTCCA-
1 AATGTCACTTTTTTTAAAATAATTCCCAG
* *
1560028 AATTGTCACTTTTTTCAGAATAATTCCCAG
1 AA-TGTCACTTTTTTTAAAATAATTCCCAG
** * *
1560058 AATGTCACCTTTTTCAAAAAAAAATTCCCGG
1 AATGTCA-CTTTTT-TTAAAATAATTCCCAG
*
1560089 AATGTCACTTTTTTTACAAA-AATTCTCAG
1 AATGTCACTTTTTTTA-AAATAATTCCCAG
1560118 AATGTCACTTTTTTT
1 AATGTCACTTTTTTT
1560133 TAACAAAAAT
Statistics
Matches: 110, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
26 2 0.02
27 22 0.20
29 51 0.46
30 17 0.15
31 18 0.16
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.40
Consensus pattern (29 bp):
AATGTCACTTTTTTTAAAATAATTCCCAG
Found at i:1560144 original size:60 final size:60
Alignment explanation
Indices: 1559973--1560131 Score: 159
Period size: 60 Copynumber: 2.7 Consensus size: 60
1559963 AGATTGCCAA
* * * * * *
1559973 AATGTCACCTTTTTCA-AAATAATTACCAGAATGTCA--TTTTT--TAAAATAATTTCC-A
1 AATGTCACTTTTTTCACAAA-AATTCCCAGAATGTCACCTTTTTCAAAAAAAAATTCCCGG
* *
1560028 AATTGTCACTTTTTTCAGAATAATTCCCAGAATGTCACCTTTTTCAAAAAAAAATTCCCGG
1 AA-TGTCACTTTTTTCACAAAAATTCCCAGAATGTCACCTTTTTCAAAAAAAAATTCCCGG
* * *
1560089 AATGTCACTTTTTTTACAAAAATTCTCAGAATGTCACTTTTTT
1 AATGTCACTTTTTTCACAAAAATTCCCAGAATGTCACCTTTTT
1560132 TTAACAAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
55 2 0.02
56 28 0.33
57 2 0.02
58 5 0.06
60 46 0.54
61 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.40
Consensus pattern (60 bp):
AATGTCACTTTTTTCACAAAAATTCCCAGAATGTCACCTTTTTCAAAAAAAAATTCCCGG
Found at i:1560163 original size:30 final size:30
Alignment explanation
Indices: 1560099--1560172 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
1560089 AATGTCACTT
* * **
1560099 TTTTTACAAAAATTCTCAGAATGTCACTTT
1 TTTTTACAAAAATTCTCAAAATATCACTAA
1560129 TTTTTAACAAAAATTCTCAAAATATCA-TAA
1 TTTTT-ACAAAAATTCTCAAAATATCACTAA
1560159 TTTTTACTAAAAAT
1 TTTTTAC-AAAAAT
1560173 CCCATTATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 2 0.05
30 17 0.45
31 19 0.50
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.42
Consensus pattern (30 bp):
TTTTTACAAAAATTCTCAAAATATCACTAA
Found at i:1566168 original size:36 final size:35
Alignment explanation
Indices: 1566100--1566172 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 35
1566090 TTCATTAAAC
*
1566100 ATTTTATATTTTAATTTTGTAAAAAAATTATATAA
1 ATTTTATATTTAAATTTTGTAAAAAAATTATATAA
1566135 ATTTTATAAATTTAAATTTT-TAAAGAAAA-TATATAA
1 ATTTTAT--ATTTAAATTTTGTAAA-AAAATTATATAA
1566171 AT
1 AT
1566173 ATTTTCAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
35 7 0.21
36 13 0.38
37 14 0.41
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (35 bp):
ATTTTATATTTAAATTTTGTAAAAAAATTATATAA
Found at i:1567209 original size:10 final size:10
Alignment explanation
Indices: 1567191--1567272 Score: 65
Period size: 11 Copynumber: 7.4 Consensus size: 10
1567181 AGATCCAATC
*
1567191 AGAACAAAAA
1 AGAAAAAAAA
1567201 AGAAAAAAAA
1 AGAAAAAAAA
1567211 AGAAAAAAACAA
1 AG-AAAAAA-AA
1567223 AGAAAATAAAA
1 AGAAAA-AAAA
1567234 AGAGAAACAAAA
1 AGA-AAA-AAAA
*
1567246 ACAAAGGAAAAA
1 AGAAA--AAAAA
*
1567258 ATGAAGAAAAA
1 A-GAAAAAAAA
1567269 AGAA
1 AGAA
1567273 GAGACGCATA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
10 14 0.23
11 23 0.38
12 20 0.33
13 3 0.05
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.02
Consensus pattern (10 bp):
AGAAAAAAAA
Done.