Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 57 of 198
Found at i:17440597 original size:11 final size:10
Alignment explanation
Indices: 17440568--17440615 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
17440558 GAATATGTCA
* *
17440568 AAAATAAATC
1 AAAATTAATT
17440578 AAAATTAATT
1 AAAATTAATT
17440588 AAAATGTAATAT
1 AAAAT-TAAT-T
17440600 AAAATTAATT
1 AAAATTAATT
17440610 AAAATT
1 AAAATT
17440616 CAACATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 20 0.59
11 8 0.24
12 6 0.18
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAATTAATT
Found at i:17445722 original size:16 final size:16
Alignment explanation
Indices: 17445701--17445731 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17445691 ATTTAATTTA
17445701 AATTAATTAATTTTCC
1 AATTAATTAATTTTCC
17445717 AATTAATTAATTTTC
1 AATTAATTAATTTTC
17445732 TCAACCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTAATTAATTTTCC
Found at i:17446632 original size:36 final size:36
Alignment explanation
Indices: 17446585--17446656 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
17446575 TCACAAGTGA
17446585 ATAAATTCATAAATAGATTCATGATTTATTCTACTT
1 ATAAATTCATAAATAGATTCATGATTTATTCTACTT
17446621 ATAAATTCATAAATAGATTCATGATTTATTCTACTT
1 ATAAATTCATAAATAGATTCATGATTTATTCTACTT
17446657 GGGTCCTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (36 bp):
ATAAATTCATAAATAGATTCATGATTTATTCTACTT
Found at i:17455264 original size:15 final size:15
Alignment explanation
Indices: 17455244--17455277 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17455234 GTTTAACTAC
17455244 AGTTTCACAATCTAT
1 AGTTTCACAATCTAT
**
17455259 AGTTTCACGGTCTAT
1 AGTTTCACAATCTAT
17455274 AGTT
1 AGTT
17455278 CCAGTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (15 bp):
AGTTTCACAATCTAT
Found at i:17457358 original size:51 final size:51
Alignment explanation
Indices: 17457282--17457387 Score: 194
Period size: 51 Copynumber: 2.1 Consensus size: 51
17457272 GTTTTTAAGT
17457282 TTTTAAGTGCACTTAATCACAGGAATCAAGAGTGTTAGTAGAATTATCTGA
1 TTTTAAGTGCACTTAATCACAGGAATCAAGAGTGTTAGTAGAATTATCTGA
* *
17457333 TTTTAAGTGCACTTAATCATAGGAATCAAGAGTGTTAGTAGAATTATTTGA
1 TTTTAAGTGCACTTAATCACAGGAATCAAGAGTGTTAGTAGAATTATCTGA
17457384 TTTT
1 TTTT
17457388 TCCACTAATC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (51 bp):
TTTTAAGTGCACTTAATCACAGGAATCAAGAGTGTTAGTAGAATTATCTGA
Found at i:17470655 original size:27 final size:26
Alignment explanation
Indices: 17470625--17470682 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
17470615 TAACGGAATC
*
17470625 TTAAACACGGGATAGTTTGACGAGACT
1 TTAAACACGGGATA-TCTGACGAGACT
*
17470652 TTAAACATGGGATATCTGACGAGACT
1 TTAAACACGGGATATCTGACGAGACT
17470678 TTAAA
1 TTAAA
17470683 AAATGATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (26 bp):
TTAAACACGGGATATCTGACGAGACT
Found at i:17470678 original size:26 final size:27
Alignment explanation
Indices: 17470608--17470682 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
17470598 TGGCATCAAA
* *
17470608 GATAGTCTAACG-GAATCTTAAACACGG
1 GATAGTCTGACGAGACT-TTAAACACGG
* *
17470635 GATAGTTTGACGAGACTTTAAACATGG
1 GATAGTCTGACGAGACTTTAAACACGG
17470662 GATA-TCTGACGAGACTTTAAA
1 GATAGTCTGACGAGACTTTAAA
17470683 AAATGATAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 16 0.38
27 23 0.55
28 3 0.07
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (27 bp):
GATAGTCTGACGAGACTTTAAACACGG
Found at i:17473165 original size:15 final size:15
Alignment explanation
Indices: 17473145--17473192 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
17473135 TCTTAACAGA
17473145 ACAAACAGTAGTAAT
1 ACAAACAGTAGTAAT
*
17473160 ACAAACA-TTG-AA-
1 ACAAACAGTAGTAAT
*
17473172 A-TAACAGTAGTAAT
1 ACAAACAGTAGTAAT
17473186 ACAAACA
1 ACAAACA
17473193 TTGAAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
11 4 0.16
12 3 0.12
13 4 0.16
14 3 0.12
15 11 0.44
ACGTcount: A:0.56, C:0.15, G:0.10, T:0.19
Consensus pattern (15 bp):
ACAAACAGTAGTAAT
Found at i:17473177 original size:26 final size:26
Alignment explanation
Indices: 17473148--17473201 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
17473138 TAACAGAACA
17473148 AACAGTAGTAATACAAACATTGAAAT
1 AACAGTAGTAATACAAACATTGAAAT
17473174 AACAGTAGTAATACAAACATTGAAAT
1 AACAGTAGTAATACAAACATTGAAAT
17473200 AA
1 AA
17473202 TCACTGTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (26 bp):
AACAGTAGTAATACAAACATTGAAAT
Found at i:17473685 original size:37 final size:36
Alignment explanation
Indices: 17473638--17473727 Score: 92
Period size: 37 Copynumber: 2.5 Consensus size: 36
17473628 ATAACAATGT
* *
17473638 CAATACAGTGGCATGCTAAACATGCATTCAGTAAAA
1 CAATACAGTGGCATGCTAAACATACATTCAATAAAA
* ***
17473674 CAATATCAGTGGTATGCTTTGCATACATTCAATAAAA
1 CAATA-CAGTGGCATGCTAAACATACATTCAATAAAA
*
17473711 -AATAACGGTGGCATGCT
1 CAAT-ACAGTGGCATGCT
17473728 TACATGTAGG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
36 18 0.41
37 26 0.59
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (36 bp):
CAATACAGTGGCATGCTAAACATACATTCAATAAAA
Found at i:17475966 original size:39 final size:38
Alignment explanation
Indices: 17475883--17475968 Score: 120
Period size: 38 Copynumber: 2.2 Consensus size: 38
17475873 TGTCCCCAAA
* *
17475883 TTGGAGTGTTTGGATGGACGAGTTATGAGAACTCAATT
1 TTGGAGTGTTTAGATGGACGAGTTAGGAGAACTCAATT
*
17475921 TTGGAGTGTTTATATGGACGAGTTCCAGGA-AACTCAATT
1 TTGGAGTGTTTAGATGGACGAGTT--AGGAGAACTCAATT
17475960 TTGGAGTGT
1 TTGGAGTGT
17475969 AGCGGTGATG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 22 0.51
39 18 0.42
40 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.35
Consensus pattern (38 bp):
TTGGAGTGTTTAGATGGACGAGTTAGGAGAACTCAATT
Found at i:17484453 original size:18 final size:18
Alignment explanation
Indices: 17484430--17484482 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
17484420 GATTTTGTAT
17484430 TTTTATAATTTTATATTG
1 TTTTATAATTTTATATTG
* *
17484448 TTTTATACTTTTTGTAATTG
1 TTTTATA-ATTTTAT-ATTG
17484468 -TTT-TAATTTTATATT
1 TTTTATAATTTTATATT
17484483 TTTATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 3 0.10
17 5 0.17
18 9 0.31
19 8 0.28
20 4 0.14
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.68
Consensus pattern (18 bp):
TTTTATAATTTTATATTG
Found at i:17484733 original size:2 final size:2
Alignment explanation
Indices: 17484728--17484756 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17484718 GACGTGTGTG
17484728 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17484757 CGTTCCTNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17499966 original size:26 final size:26
Alignment explanation
Indices: 17499891--17499973 Score: 107
Period size: 26 Copynumber: 3.2 Consensus size: 26
17499881 CATATCGAAT
17499891 AGCTC-CGAAGAGCCATTAATCGGGA
1 AGCTCACGAAGAGCCATTAATCGGGA
* * *
17499916 AGCTCACAAAGATCCTTTAATCGGGA
1 AGCTCACGAAGAGCCATTAATCGGGA
17499942 AGCTCACGAAGAGCCATATAA-CGGGA
1 AGCTCACGAAGAGCCAT-TAATCGGGA
*
17499968 CGCTCA
1 AGCTCA
17499974 TAAGTGCGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
25 5 0.10
26 41 0.84
27 3 0.06
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.17
Consensus pattern (26 bp):
AGCTCACGAAGAGCCATTAATCGGGA
Found at i:17509129 original size:25 final size:26
Alignment explanation
Indices: 17509100--17509174 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
17509090 AGCGAGCCGT
*
17509100 ATCGGGTAGCTC-CGGAGAGCCATTA
1 ATCGGGTAGCTCACGAAGAGCCATTA
* * *
17509125 ATCGGGAAGCTCACAAAGAGCCTTTA
1 ATCGGGTAGCTCACGAAGAGCCATTA
**
17509151 ATCAAGTAGCTCACGAAGAGCCAT
1 ATCGGGTAGCTCACGAAGAGCCAT
17509175 ATAACGGTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 11 0.28
26 29 0.73
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (26 bp):
ATCGGGTAGCTCACGAAGAGCCATTA
Found at i:17509263 original size:24 final size:25
Alignment explanation
Indices: 17509247--17509293 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
17509237 GGATGCTCCG
17509247 AAGAACTAT-TAACGGGAAGCTCGC
1 AAGAACTATATAACGGGAAGCTCGC
*
17509271 AAGAACTATATAAGGGGAA-CTCG
1 AAGAACTATATAACGGGAAGCTCG
17509294 AGAGAGCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (25 bp):
AAGAACTATATAACGGGAAGCTCGC
Found at i:17522419 original size:19 final size:19
Alignment explanation
Indices: 17522395--17522433 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
17522385 GATGATGAGA
17522395 TTGAGTACATGTCACATGT
1 TTGAGTACATGTCACATGT
17522414 TTGAGTACATGTCACATGT
1 TTGAGTACATGTCACATGT
17522433 T
1 T
17522434 CCATACTCTA
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (19 bp):
TTGAGTACATGTCACATGT
Found at i:17523069 original size:5 final size:5
Alignment explanation
Indices: 17523059--17523089 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
17523049 TGAGCATTCG
17523059 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
17523090 AATTTTCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:17523879 original size:30 final size:31
Alignment explanation
Indices: 17523840--17523899 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
17523830 GGAGGTGAAA
*
17523840 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
17523871 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
17523900 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:17524127 original size:9 final size:9
Alignment explanation
Indices: 17524113--17524149 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
17524103 TATAGTTTGA
17524113 TATTCGAAT
1 TATTCGAAT
17524122 TATTCGAAT
1 TATTCGAAT
*
17524131 TATTCGAGT
1 TATTCGAAT
17524140 TATTCGAAT
1 TATTCGAAT
17524149 T
1 T
17524150 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17524218 original size:9 final size:9
Alignment explanation
Indices: 17524201--17524249 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
17524191 TCGAGTTGAT
17524201 TCGAATAAC
1 TCGAATAAC
*
17524210 TCGATTAAC
1 TCGAATAAC
17524219 TCGAATAAC
1 TCGAATAAC
*
17524228 TCGATTAAC
1 TCGAATAAC
*
17524237 TTGAATAAC
1 TCGAATAAC
17524246 TCGA
1 TCGA
17524250 TTCGTTTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (9 bp):
TCGAATAAC
Found at i:17524224 original size:18 final size:18
Alignment explanation
Indices: 17524201--17524251 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
17524191 TCGAGTTGAT
17524201 TCGAATAACTCGATTAAC
1 TCGAATAACTCGATTAAC
17524219 TCGAATAACTCGATTAAC
1 TCGAATAACTCGATTAAC
*
17524237 TTGAATAACTCGATT
1 TCGAATAACTCGATT
17524252 CGTTTAACTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (18 bp):
TCGAATAACTCGATTAAC
Found at i:17525504 original size:17 final size:18
Alignment explanation
Indices: 17525474--17525507 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17525464 AGATGTTTTG
*
17525474 ATAATTTCACATTTAAAA
1 ATAATTTCAAATTTAAAA
17525492 ATAA-TTCAAATTTAAA
1 ATAATTTCAAATTTAAA
17525508 TTGTATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATTTCAAATTTAAAA
Found at i:17528077 original size:19 final size:19
Alignment explanation
Indices: 17528048--17528120 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
17528038 AATCTTCAAG
*
17528048 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
17528067 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
17528086 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
17528105 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
17528121 AGATATAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:17528609 original size:6 final size:6
Alignment explanation
Indices: 17528599--17528645 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
17528589 TCTTGTATCA
*
17528599 TTATTA TTATTT ATTATTT TTATTT TTATTT TTATTT TTATTT TTAT
1 TTATTT TTATTT -TTATTT TTATTT TTATTT TTATTT TTATTT TTAT
17528646 ATTCATGCGC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:17533798 original size:14 final size:15
Alignment explanation
Indices: 17533772--17533804 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
17533762 CCCCAAGCTG
17533772 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
17533787 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
17533801 GGAA
1 GGAA
17533805 AAGTGTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:17535255 original size:45 final size:45
Alignment explanation
Indices: 17535201--17535343 Score: 121
Period size: 45 Copynumber: 3.2 Consensus size: 45
17535191 CCTGGGTTGT
* * *
17535201 AGCGGAGCAGGTTAAAAATAGCAGATCTTACCTTCCTGTACCGAC
1 AGCGAAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGAC
* ** * * * * ****
17535246 AGCGAAGCAGATCGAAGACA-CTAG-CCTTGCCTCCCTGGGTTG-C
1 AGCGAAGCAGGTTAAAAATAGC-AGATCTTGCCTTCCTGCACCGAC
*
17535289 AGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGAC
1 AGCGAAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGAC
17535334 AGCGAAGCAG
1 AGCGAAGCAG
17535344 ATCGAAGACA
Statistics
Matches: 68, Mismatches: 26, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
43 17 0.25
44 25 0.37
45 26 0.38
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.19
Consensus pattern (45 bp):
AGCGAAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGAC
Found at i:17535283 original size:88 final size:88
Alignment explanation
Indices: 17535134--17535419 Score: 475
Period size: 88 Copynumber: 3.2 Consensus size: 88
17535124 GTGAAGATAA
* * * *
17535134 CAGATGTTGCCTTCCTGCACCGGCAGCGAAGCAGATCGAAGACACCAACCTTGCTTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
17535199 GTAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
17535222 CAGATCTTACCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
17535287 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
17535310 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
17535375 GCAGCGGAGCAGGTTAAAAATTA-
66 GCAGCGGAGCAGGTTAAAAA-TAG
*
17535398 CAGATCTCGCCTTCCTGCACCG
1 CAGATCTTGCCTTCCTGCACCG
17535420 GCACCGACAG
Statistics
Matches: 185, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
88 183 0.99
89 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.25, T:0.20
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:17535298 original size:43 final size:42
Alignment explanation
Indices: 17535245--17535386 Score: 122
Period size: 43 Copynumber: 3.3 Consensus size: 42
17535235 CCTGTACCGA
17535245 CAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTTG
1 CAGCGAAGCAGATCGAAGACAC-AGCCTTGCCTCCCTGGGTTG
* * ** * * * * ****
17535288 CAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCG
1 CAGCGAAGCAGATCGAAGACA-CAG-CCTTGCCTCCCTGGGTTG
17535332 ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTG
1 -CAGCGAAGCAGATCGAAGACA-CAGCCTTGCCTCCCTGGGTTG
*
17535376 CAGCGGAGCAG
1 CAGCGAAGCAG
17535387 GTTAAAAATT
Statistics
Matches: 70, Mismatches: 26, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
43 27 0.39
44 25 0.36
45 18 0.26
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (42 bp):
CAGCGAAGCAGATCGAAGACACAGCCTTGCCTCCCTGGGTTG
Found at i:17535363 original size:44 final size:43
Alignment explanation
Indices: 17535140--17535370 Score: 122
Period size: 44 Copynumber: 5.3 Consensus size: 43
17535130 ATAACAGATG
*
17535140 TTGCCTTCCTGCACCGGCAGCGAAGCAGATCGAAGACACCAACC
1 TTGCCTTCCTGCACC-GCAGCGAAGCAGATCGAAGACACCAGCC
**** * * * ** * * * *
17535184 TTG-CTTCCCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAGATC
1 TTGCCTT-CCTGCACCGCAGCGAAGCAGATCGAAGACACCAG-CC
* * *
17535228 TTACCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACTAGCC
1 TTGCCTTCCTGCACCG-CAGCGAAGCAGATCGAAGACACCAGCC
* **** * * ** * * * *
17535272 TTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATC
1 TTGCCTTCCTGCACCGCAGCGAAGCAGATCGAAGACACCAG-CC
17535316 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
1 TTGCCTTCCTGCACCG-CAGCGAAGCAGATCGAAGACACCAGCC
*
17535360 TTGCCTCCCTG
1 TTGCCTTCCTG
17535371 GGTTGCAGCG
Statistics
Matches: 123, Mismatches: 58, Indels: 12
0.64 0.30 0.06
Matches are distributed among these distances:
43 37 0.30
44 49 0.40
45 37 0.30
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.20
Consensus pattern (43 bp):
TTGCCTTCCTGCACCGCAGCGAAGCAGATCGAAGACACCAGCC
Found at i:17535505 original size:44 final size:44
Alignment explanation
Indices: 17535453--17535574 Score: 167
Period size: 44 Copynumber: 2.8 Consensus size: 44
17535443 TGACCCCAAC
**
17535453 CCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGT-AAGT
1 CCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTGAA-T
* *
17535497 CTTATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTGAAT
*
17535541 CCTATCTCCCT-GAGCAACAGTGGAGTAGGTTGAA
1 CCTATCTCCCTGGA-CAACAGTGGAATAGGTTGAA
17535575 AATAACAGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 1 0.01
44 66 0.96
45 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:17536170 original size:88 final size:90
Alignment explanation
Indices: 17536068--17536238 Score: 247
Period size: 88 Copynumber: 1.9 Consensus size: 90
17536058 TCACATCTAG
* * * **
17536068 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACT-AAGTAAGCAAG-CTTATCCTCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACTCAAGAAAGCAAGTCTTATCCCCCTGAAATTAC
*
17536131 AGTGAGGCAGACTGAATATGGCGAA
66 AGTGAGGCAGACTAAATATGGCGAA
* *
17536156 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCAAGTCTTATCCCCCTGAAATTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAACAGACTCAAGAAAGCAAGTCTTATCCCCCTGAAATTAC
*
17536221 AGTGGGGCAGACTAAATA
66 AGTGAGGCAGACTAAATA
17536239 AACAAATCCC
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 32 0.44
89 9 0.12
90 31 0.43
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (90 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAACAGACTCAAGAAAGCAAGTCTTATCCCCCTGAAATTAC
AGTGAGGCAGACTAAATATGGCGAA
Found at i:17536172 original size:45 final size:43
Alignment explanation
Indices: 17535938--17536271 Score: 175
Period size: 44 Copynumber: 7.7 Consensus size: 43
17535928 GAAGATGGCG
* * * * *
17535938 AATCTTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAGCCAA-T
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGC
* * ** * *
17535982 AATCCTATCTCCCTGAAGTCGCAGTGGAGTGGATTAA--AATC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
* * * * *
17536023 ATAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCA--CATC
1 --A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
* *
17536065 TAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTAAGTAAGC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
* * *
17536109 AAGCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAA-TATGGC
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGC
* *
17536153 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGC
* * * * * *
17536198 AAGTCTTATCCCCCTGAAATTACAGTGGGGCAGACTAAATAAAC
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
** * *
17536242 AAATCCCATCTCCCTAAAGTTGTAGTGGAG
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAG
17536272 TGGATTAGAA
Statistics
Matches: 224, Mismatches: 48, Indels: 36
0.73 0.16 0.12
Matches are distributed among these distances:
40 23 0.10
41 8 0.04
42 10 0.04
43 36 0.16
44 81 0.36
45 62 0.28
46 4 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
Found at i:17538314 original size:14 final size:14
Alignment explanation
Indices: 17538303--17538329 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17538293 TATTAATTGT
17538303 AACAATGAAATTTA
1 AACAATGAAATTTA
17538317 AACAATGAAATTT
1 AACAATGAAATTT
17538330 TATTAACTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (14 bp):
AACAATGAAATTTA
Found at i:17538449 original size:13 final size:13
Alignment explanation
Indices: 17538431--17538462 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
17538421 TAATTGTAAC
17538431 ACCCGTAACCTAT
1 ACCCGTAACCTAT
17538444 ACCCGTAACCTAT
1 ACCCGTAACCTAT
17538457 ACCCGT
1 ACCCGT
17538463 CGCTGGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.28, C:0.41, G:0.09, T:0.22
Consensus pattern (13 bp):
ACCCGTAACCTAT
Found at i:17543615 original size:8 final size:8
Alignment explanation
Indices: 17543602--17543629 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
17543592 TTTCATACTT
17543602 TTATTTTA
1 TTATTTTA
17543610 TTATTTTA
1 TTATTTTA
17543618 TTATTTTA
1 TTATTTTA
17543626 TTAT
1 TTAT
17543630 CAATTTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTTTA
Found at i:17548998 original size:107 final size:106
Alignment explanation
Indices: 17548860--17549054 Score: 245
Period size: 107 Copynumber: 1.8 Consensus size: 106
17548850 TGAGATATCC
* * *
17548860 CTTCAAATTCTCAATACTTGTTCTTGATGTC-TAATGACATC-CTTTCAAAGTC-TCAAGACAAG
1 CTTCAAAGTCTCAAGACTCGTTCTTGATGTCTTAA-GACATCTC-TTCAAAGTCTTCAA-ACAAG
17548922 TTGTCTTCTAAC-TATTATAATTTTCAACGATGTCTCAAAACATCA
63 TTGTCTTCTAACAT-TTAT-ATTTTCAACGATGTCTCAAAACATCA
* * * **
17548967 CTTCAAAGTCTTAAGACTCGTTCTTGATGTCTTGAGACATCTCTTCAAAGTCTTGAAACATTTTG
1 CTTCAAAGTCTCAAGACTCGTTCTTGATGTCTTAAGACATCTCTTCAAAGTCTTCAAACAAGTTG
17549032 TCTTCTAACATTTATATTTTCAA
66 TCTTCTAACATTTATATTTTCAA
17549055 TGATCTCTTG
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
106 8 0.11
107 61 0.80
108 7 0.09
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (106 bp):
CTTCAAAGTCTCAAGACTCGTTCTTGATGTCTTAAGACATCTCTTCAAAGTCTTCAAACAAGTTG
TCTTCTAACATTTATATTTTCAACGATGTCTCAAAACATCA
Found at i:17549019 original size:21 final size:21
Alignment explanation
Indices: 17548961--17549027 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
17548951 ATGTCTCAAA
* *
17548961 ACATCACTTCAAAGTCTTAAG
1 ACATCTCTTCAAAGTCTTGAG
* *
17548982 AC-TCGTTCTT-GATGTCTTGAG
1 ACATC--TCTTCAAAGTCTTGAG
*
17549003 ACATCTCTTCAAAGTCTTGAA
1 ACATCTCTTCAAAGTCTTGAG
17549024 ACAT
1 ACAT
17549028 TTTGTCTTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
20 6 0.17
21 24 0.69
22 5 0.14
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.34
Consensus pattern (21 bp):
ACATCTCTTCAAAGTCTTGAG
Found at i:17564321 original size:21 final size:21
Alignment explanation
Indices: 17564295--17564357 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
17564285 TTGGTATTTG
17564295 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
17564316 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
17564337 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
17564358 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:17566168 original size:13 final size:13
Alignment explanation
Indices: 17566150--17566192 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
17566140 TATAAACTCT
*
17566150 TTTTCAACTTATG
1 TTTTCAAGTTATG
*
17566163 TTTTCAAGTCATG
1 TTTTCAAGTTATG
*
17566176 TTTTCAAGTTATA
1 TTTTCAAGTTATG
17566189 TTTT
1 TTTT
17566193 ATATGTGCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (13 bp):
TTTTCAAGTTATG
Found at i:17567486 original size:25 final size:25
Alignment explanation
Indices: 17567457--17567505 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
17567447 TTGTGCGAAC
17567457 TCATGCTTTA-TGTTGTTATGCAAAG
1 TCATGCTTTACT-TTGTTATGCAAAG
17567482 TCATGCTTTACTTTGTTATGCAAA
1 TCATGCTTTACTTTGTTATGCAAA
17567506 CCTTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.45
Consensus pattern (25 bp):
TCATGCTTTACTTTGTTATGCAAAG
Found at i:17569500 original size:6 final size:6
Alignment explanation
Indices: 17569483--17569511 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
17569473 TTAAGATAAG
17569483 TATTAA -ATTAA TATTAA TATTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA
17569512 AACTATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TATTAA
Found at i:17569501 original size:65 final size:69
Alignment explanation
Indices: 17569374--17569505 Score: 175
Period size: 65 Copynumber: 2.0 Consensus size: 69
17569364 TGATTAAACT
* *
17569374 TAATCACTTTAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATATAATAATTATCAAGATAAATATTAAATTAAATTTAATATT
17569439 AAGA
66 AAGA
* * *
17569443 TAATCGCTTTAATATTAAA-TAA-ATAA-AATT-TTAAGATAAGTATTAAATT-AATATTAATAT
1 TAATCACTTTAATATTAAATTAATATAATAATTATCAAGATAAATATTAAATTAAAT-TTAATAT
17569503 TAA
65 TAA
17569506 TATTAAAACT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
64 3 0.05
65 26 0.46
66 3 0.05
67 4 0.07
68 3 0.05
69 18 0.32
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (69 bp):
TAATCACTTTAATATTAAATTAATATAATAATTATCAAGATAAATATTAAATTAAATTTAATATT
AAGA
Found at i:17574338 original size:147 final size:147
Alignment explanation
Indices: 17574071--17574366 Score: 511
Period size: 147 Copynumber: 2.0 Consensus size: 147
17574061 ATCAAAACAC
* * *
17574071 ACACGACACTTTTCTCCATACAGATAGTGTCTCCAAATCTTCCATGCTAATACTACGCAGCCAGT
1 ACACGACACTTTTCTCCATACAGATAGTGTATCCAAATCTTCAATGCCAATACTACGCAGCCAGT
* * *
17574136 TCCAAATCATGGGTTGGATAGTTCCTCTCATGTGGTTTCAGTTAGCACGATGCATAAGTTATAAC
66 TCCAAATCATGGGATCGATAGTTCCTCTCATGTGGTTTCAGTTAGCACGATGCATAAGCTATAAC
*
17574201 CTTGCCCTTCTGCATAA
131 CTTACCCTTCTGCATAA
*
17574218 ACACGACACTTTTCTCTATACAGATAGTGTATCCAAATCTTCAATGCCAATACTACGCAGCCAGT
1 ACACGACACTTTTCTCCATACAGATAGTGTATCCAAATCTTCAATGCCAATACTACGCAGCCAGT
*
17574283 TCCAAATCATGGGATCGATAGTTCCTCTCATGTGGTTTGAGTTAGCACGATGCATAAGCTATAAC
66 TCCAAATCATGGGATCGATAGTTCCTCTCATGTGGTTTCAGTTAGCACGATGCATAAGCTATAAC
17574348 CTTACCCTTCTGCATAA
131 CTTACCCTTCTGCATAA
17574365 AC
1 AC
17574367 CCACATCCAA
Statistics
Matches: 140, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
147 140 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (147 bp):
ACACGACACTTTTCTCCATACAGATAGTGTATCCAAATCTTCAATGCCAATACTACGCAGCCAGT
TCCAAATCATGGGATCGATAGTTCCTCTCATGTGGTTTCAGTTAGCACGATGCATAAGCTATAAC
CTTACCCTTCTGCATAA
Found at i:17588182 original size:31 final size:31
Alignment explanation
Indices: 17588147--17588239 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
17588137 AGGCAAATTA
*
17588147 CAAGAGTAATTGAATCCTAATAAAATTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
*
17588178 CAAGAGCAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
17588209 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
17588240 AAAATTATCT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:17593960 original size:26 final size:25
Alignment explanation
Indices: 17593920--17593997 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
17593910 GTAGGCAACT
17593920 TTTTTTTTGCGCTTTTTGCTTTTTC
1 TTTTTTTTGCGCTTTTTGCTTTTTC
* *
17593945 TTTTTTTTGCATCTTTTTGCTTCTTC
1 TTTTTTTTGC-GCTTTTTGCTTTTTC
*
17593971 -TTTTTTTACGCTTTTTGCTTTTT-
1 TTTTTTTTGCGCTTTTTGCTTTTTC
17593994 TTTT
1 TTTT
17593998 AAAGAATAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.33
25 18 0.39
26 13 0.28
ACGTcount: A:0.03, C:0.15, G:0.09, T:0.73
Consensus pattern (25 bp):
TTTTTTTTGCGCTTTTTGCTTTTTC
Found at i:17594204 original size:3 final size:3
Alignment explanation
Indices: 17594196--17594233 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
17594186 AAATTAGTTA
*
17594196 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17594234 AAGGATAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:17594568 original size:31 final size:31
Alignment explanation
Indices: 17594533--17594625 Score: 186
Period size: 31 Copynumber: 3.0 Consensus size: 31
17594523 AGGAAAATTA
17594533 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
17594564 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
17594595 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
17594626 AAAATTATCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:17599677 original size:12 final size:12
Alignment explanation
Indices: 17599660--17599684 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17599650 CCCTAATCCC
17599660 TCAATTTTTCCT
1 TCAATTTTTCCT
17599672 TCAATTTTTCCT
1 TCAATTTTTCCT
17599684 T
1 T
17599685 GCTTCTTGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCAATTTTTCCT
Found at i:17606443 original size:20 final size:20
Alignment explanation
Indices: 17606418--17606523 Score: 97
Period size: 20 Copynumber: 5.3 Consensus size: 20
17606408 TATTGGATTT
17606418 CAGGGGTACCAAAGTACAAA
1 CAGGGGTACCAAAGTACAAA
* ** *
17606438 CAGGGGCACGTATGTACAAA
1 CAGGGGTACCAAAGTACAAA
*
17606458 TAGGGGTACCAAAGTACAAA
1 CAGGGGTACCAAAGTACAAA
* * *
17606478 CAGGGGTA-TATATGTTCAAA
1 CAGGGGTACCA-AAGTACAAA
* * *
17606498 CAAGGGTATCGAAGTACAAA
1 CAGGGGTACCAAAGTACAAA
17606518 CAGGGG
1 CAGGGG
17606524 CACGTATGTA
Statistics
Matches: 65, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
19 1 0.02
20 64 0.98
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (20 bp):
CAGGGGTACCAAAGTACAAA
Found at i:17606463 original size:40 final size:40
Alignment explanation
Indices: 17606418--17606544 Score: 173
Period size: 40 Copynumber: 3.2 Consensus size: 40
17606408 TATTGGATTT
17606418 CAGGGGTACCAAAGTACAAACAGGGGCACGTATGTACAAA
1 CAGGGGTACCAAAGTACAAACAGGGGCACGTATGTACAAA
* * ** *
17606458 TAGGGGTACCAAAGTACAAACAGGGGTATATATGTTCAAA
1 CAGGGGTACCAAAGTACAAACAGGGGCACGTATGTACAAA
* * *
17606498 CAAGGGTATCGAAGTACAAACAGGGGCACGTATGTACAAA
1 CAGGGGTACCAAAGTACAAACAGGGGCACGTATGTACAAA
*
17606538 CAAGGGT
1 CAGGGGT
17606545 TCAATAATTA
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.17
Consensus pattern (40 bp):
CAGGGGTACCAAAGTACAAACAGGGGCACGTATGTACAAA
Found at i:17606534 original size:20 final size:20
Alignment explanation
Indices: 17606431--17606544 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
17606421 GGGTACCAAA
*
17606431 GTACAAACAGGGGCACGTAT
1 GTACAAACAGGGGTACGTAT
* ** *
17606451 GTACAAATAGGGGTACCAAA
1 GTACAAACAGGGGTACGTAT
**
17606471 GTACAAACAGGGGTATATAT
1 GTACAAACAGGGGTACGTAT
* * *
17606491 GTTCAAACAAGGGTATCG-AA
1 GTACAAACAGGGGTA-CGTAT
*
17606511 GTACAAACAGGGGCACGTAT
1 GTACAAACAGGGGTACGTAT
*
17606531 GTACAAACAAGGGT
1 GTACAAACAGGGGT
17606545 TCAATAATTA
Statistics
Matches: 71, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
19 2 0.03
20 69 0.97
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (20 bp):
GTACAAACAGGGGTACGTAT
Found at i:17606606 original size:32 final size:32
Alignment explanation
Indices: 17606570--17606638 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
17606560 TGACCTTTAA
17606570 AAACACTATGAACTTACCTAATATTCAACTCT
1 AAACACTATGAACTTACCTAATATTCAACTCT
17606602 AAACACTATGAACTTACCTAATATTCAACTCT
1 AAACACTATGAACTTACCTAATATTCAACTCT
17606634 AAACA
1 AAACA
17606639 ACACGTAGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.29
Consensus pattern (32 bp):
AAACACTATGAACTTACCTAATATTCAACTCT
Found at i:17610308 original size:29 final size:29
Alignment explanation
Indices: 17610275--17610332 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
17610265 ATAATCTATA
*
17610275 CATAGTTTCATTGACTCATCTTTCTTTTT
1 CATAGTTTCATTGACCCATCTTTCTTTTT
17610304 CATAGTTTCATTGACCCATCTTTCTTTTT
1 CATAGTTTCATTGACCCATCTTTCTTTTT
17610333 TATGAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.17, C:0.22, G:0.07, T:0.53
Consensus pattern (29 bp):
CATAGTTTCATTGACCCATCTTTCTTTTT
Found at i:17611169 original size:20 final size:20
Alignment explanation
Indices: 17611144--17611182 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17611134 ATCGACCTAC
*
17611144 AAACAGGGGTACTAAAGTAG
1 AAACAGGGGTACCAAAGTAG
17611164 AAACAGGGGTACCAAAGTA
1 AAACAGGGGTACCAAAGTA
17611183 CAAGCATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.13, G:0.28, T:0.13
Consensus pattern (20 bp):
AAACAGGGGTACCAAAGTAG
Found at i:17615906 original size:3 final size:3
Alignment explanation
Indices: 17615898--17615970 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
17615888 GGCATCTCCA
17615898 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
17615946 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
17615971 CTCTCCACNN
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:17616869 original size:38 final size:38
Alignment explanation
Indices: 17616809--17616885 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
17616799 TCAATGCATA
* *
17616809 TGCTCTGTTTTGTCATAAATTCTCACCATTGATGTTAG
1 TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
17616847 TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
1 TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
17616885 T
1 T
17616886 ATTAACATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (38 bp):
TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
Found at i:17618978 original size:9 final size:9
Alignment explanation
Indices: 17618964--17618988 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17618954 ATCATATAAG
17618964 ATTATTATC
1 ATTATTATC
17618973 ATTATTATC
1 ATTATTATC
17618982 ATTATTA
1 ATTATTA
17618989 GGTAGCGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATTATC
Found at i:17630797 original size:34 final size:34
Alignment explanation
Indices: 17630754--17630821 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
17630744 AAAAAGAAAA
17630754 ATAAAAACAGCCAACACTAAATTAAGTGAGAATT
1 ATAAAAACAGCCAACACTAAATTAAGTGAGAATT
17630788 ATAAAAACAGCCAACACTAAATTAAGTGAGAATT
1 ATAAAAACAGCCAACACTAAATTAAGTGAGAATT
17630822 GCACCAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.21
Consensus pattern (34 bp):
ATAAAAACAGCCAACACTAAATTAAGTGAGAATT
Found at i:17633423 original size:35 final size:35
Alignment explanation
Indices: 17633340--17633501 Score: 182
Period size: 35 Copynumber: 4.6 Consensus size: 35
17633330 GTACATTGTC
* * * * * *
17633340 AGTCCAACCAAAACACAACAGATGCTCATAGGAACC
1 AGTCCAACCGAAACACACCA-ATACTCATAAGATCT
* * * *
17633376 AATCCAAACGAAACATACCAATACTCATAAGATCC
1 AGTCCAACCGAAACACACCAATACTCATAAGATCT
* * *
17633411 AGTTCAACCGAAACACACCAATGCTCATAAGAGCT
1 AGTCCAACCGAAACACACCAATACTCATAAGATCT
17633446 AGTCCAACCGAAACACACCAATACTCATAAGAGT-T
1 AGTCCAACCGAAACACACCAATACTCATAAGA-TCT
17633481 AGTCCAACCGAAACACACCAA
1 AGTCCAACCGAAACACACCAA
17633502 ACAGAGAGTA
Statistics
Matches: 107, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
35 92 0.86
36 15 0.14
ACGTcount: A:0.44, C:0.30, G:0.11, T:0.14
Consensus pattern (35 bp):
AGTCCAACCGAAACACACCAATACTCATAAGATCT
Found at i:17633437 original size:70 final size:70
Alignment explanation
Indices: 17633337--17633501 Score: 215
Period size: 70 Copynumber: 2.3 Consensus size: 70
17633327 AAAGTACATT
* * * *
17633337 GTCAGTCCAACCAAAACACAACAGATGCTCATAGGAACCAATCCAAACGAAACATACCAATACTC
1 GTCAGTCCAACCGAAACACACCA-ATGCTCATAAGAACCAATCCAAACGAAACACACCAATACTC
17633402 ATAAGA
65 ATAAGA
* * * * *
17633408 -TCCAGTTCAACCGAAACACACCAATGCTCATAAGAGCTAGTCCAACCGAAACACACCAATACTC
1 GT-CAGTCCAACCGAAACACACCAATGCTCATAAGAACCAATCCAAACGAAACACACCAATACTC
17633472 ATAAGA
65 ATAAGA
*
17633478 GTTAGTCCAACCGAAACACACCAA
1 GTCAGTCCAACCGAAACACACCAA
17633502 ACAGAGAGTA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
70 62 0.77
71 19 0.23
ACGTcount: A:0.44, C:0.30, G:0.12, T:0.15
Consensus pattern (70 bp):
GTCAGTCCAACCGAAACACACCAATGCTCATAAGAACCAATCCAAACGAAACACACCAATACTCA
TAAGA
Found at i:17636972 original size:20 final size:20
Alignment explanation
Indices: 17636949--17636997 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
17636939 TTCCTTCGTT
17636949 TTTTTATTTCAATCTTTCTA
1 TTTTTATTTCAATCTTTCTA
** * *
17636969 TTTTTATTTTTATTTTTTTA
1 TTTTTATTTCAATCTTTCTA
17636989 TTTTTATTT
1 TTTTTATTT
17636998 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTATTTCAATCTTTCTA
Found at i:17636978 original size:6 final size:6
Alignment explanation
Indices: 17636967--17637013 Score: 58
Period size: 6 Copynumber: 7.2 Consensus size: 6
17636957 TCAATCTTTC
17636967 TATTTT TATTTT TATTTTTT TATTTT TATTTTT TATTTTT TATTTT T
1 TATTTT TATTTT TA--TTTT TATTTT TA-TTTT TA-TTTT TATTTT T
17637014 GTATACGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 19 0.50
7 13 0.34
8 6 0.16
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TATTTT
Found at i:17636985 original size:7 final size:7
Alignment explanation
Indices: 17636969--17637013 Score: 67
Period size: 7 Copynumber: 6.6 Consensus size: 7
17636959 AATCTTTCTA
17636969 TTTTTA-
1 TTTTTAT
17636975 TTTTTAT
1 TTTTTAT
17636982 TTTTT-T
1 TTTTTAT
17636988 ATTTTTAT
1 -TTTTTAT
17636996 TTTTTAT
1 TTTTTAT
17637003 TTTTTAT
1 TTTTTAT
17637010 TTTT
1 TTTT
17637014 GTATACGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 7 0.19
7 28 0.78
8 1 0.03
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:17636986 original size:14 final size:14
Alignment explanation
Indices: 17636969--17637013 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
17636959 AATCTTTCTA
17636969 TTTTTATTTTTATT
1 TTTTTATTTTTATT
17636983 TTTTTATTTTTA-T
1 TTTTTATTTTTATT
17636996 TTTTTATTTTTTATT
1 TTTTTA-TTTTTATT
17637011 TTT
1 TTT
17637014 GTATACGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.24
14 18 0.62
15 4 0.14
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:17636998 original size:20 final size:20
Alignment explanation
Indices: 17636967--17637013 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
17636957 TCAATCTTTC
17636967 TATTTTTA-TTTTTATTTTTT
1 TATTTTTATTTTTTA-TTTTT
17636987 TATTTTTATTTTTTATTTTT
1 TATTTTTATTTTTTATTTTT
17637007 TATTTTT
1 TATTTTT
17637014 GTATACGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (20 bp):
TATTTTTATTTTTTATTTTT
Found at i:17637965 original size:26 final size:26
Alignment explanation
Indices: 17637918--17637967 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
17637908 ACACGCATAC
*
17637918 TTTTATAATATATATACGTACATATT
1 TTTTATAATATATATACATACATATT
* *
17637944 TTTTATAATTTATATATATACATA
1 TTTTATAATATATATACATACATA
17637968 CTTATATATA
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:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTTATAATATATATACATACATATT
Found at i:17638521 original size:71 final size:72
Alignment explanation
Indices: 17638402--17638543 Score: 223
Period size: 71 Copynumber: 2.0 Consensus size: 72
17638392 TCTTTTCAAA
*
17638402 CTCAAATTTCAAACGATCTAGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGAGCATGAT-CC
1 CTCAAATTTCAAACGATCTAGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGAGCATGATCCC
17638466 TTTTTTC
66 TTTTTTC
* * * * *
17638473 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCTTAACTTACTGGGCATGATCCC
1 CTCAAATTTCAAACGATCTAGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGAGCATGATCCC
17638538 TTTTTT
66 TTTTTT
17638544 AAATCCGAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
71 56 0.88
72 8 0.12
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (72 bp):
CTCAAATTTCAAACGATCTAGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGAGCATGATCCC
TTTTTTC
Found at i:17641777 original size:47 final size:46
Alignment explanation
Indices: 17641644--17641779 Score: 134
Period size: 47 Copynumber: 2.9 Consensus size: 46
17641634 AAGAGAAAGG
* * *
17641644 GACCAAAGTGAAAACCCGCAAAGGGGTGTTTTGAGTCCT---AAAAAA
1 GACCAAGGTGAAAACCCGCAAA-GGGCGCTTTGAGT-CTAAAAAAAAA
** * * *
17641689 GATTAAGGTGAAAACCCGCAAAGGACGCCTTAAGTTCTAAAAAAAAA
1 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAG-TCTAAAAAAAAA
*
17641736 GACCAAGGTGAAAACCCACAAAGGGCGCTTTGAGTCGTAAAAAA
1 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTC-TAAAAAA
17641780 TAATAAAAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
44 9 0.12
45 20 0.28
46 2 0.03
47 41 0.57
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (46 bp):
GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCTAAAAAAAAA
Found at i:17641934 original size:42 final size:42
Alignment explanation
Indices: 17641868--17641986 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
17641858 AAAAGGGCGT
* * * * *
17641868 CTCAAATGTT-GATCAGAATGGGGCATGATGTTATCAGAGTAG
1 CTCAAAT-TTCGATCAAAATAGGGCATGATGTGATCAGAGCAA
* *
17641910 CTCAAATTTCGATTAAAATAGGGCATGATGTGATCATAGCAA
1 CTCAAATTTCGATCAAAATAGGGCATGATGTGATCAGAGCAA
* * * *
17641952 CTCAAATTTTGATCAGATTAGGGCATGTTGTGATC
1 CTCAAATTTCGATCAAAATAGGGCATGATGTGATC
17641987 TTGCTATACC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.03
42 62 0.97
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (42 bp):
CTCAAATTTCGATCAAAATAGGGCATGATGTGATCAGAGCAA
Found at i:17642788 original size:24 final size:24
Alignment explanation
Indices: 17642753--17642810 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
17642743 ATGTCCCAAA
*
17642753 ATTACAGCGGATTGAACATTGAAG
1 ATTACAGTGGATTGAACATTGAAG
* *
17642777 ATTACAGTGGATTGAACTTTGAAT
1 ATTACAGTGGATTGAACATTGAAG
17642801 ATTACAGTGG
1 ATTACAGTGG
17642811 GGAGAATCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (24 bp):
ATTACAGTGGATTGAACATTGAAG
Found at i:17643460 original size:123 final size:123
Alignment explanation
Indices: 17643187--17643744 Score: 428
Period size: 123 Copynumber: 4.4 Consensus size: 123
17643177 TTTCTTGGCA
* * * ** * * *
17643187 TTGTAGTGGAACAGATTAAAGCTAAAAGCAGCGAATCTTATTTCCCTAGCGTCACAGTAGATTAA
1 TTGTAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGCAGTGGAATAG
* * * * * *
17643252 AGTTGAAG-TGGAGTAGATTAAAGCTGGCGTT-AAGACTG-AGAGCAGCGAATCTTATTTCCTTG
66 A-TTAAAGCT-GA--AG-TT-GAGC-GG-ATTAAAG-CTGAAG-GCAGCGGATCTTATCTCTTTG
*
17643314 ACG
121 ATG
* * * *
17643317 TTGTAGCT-GAACAAATTAAAGCTAAAGGTAGCGAATATTATTTCCCTACCGTTGCAGTGGAATA
1 TTGTAG-TGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGCAGTGGAATA
*
17643381 GATTAAAGCTGAAGTTGAGCGGATTAAAGCAGAAGGCAGCGGATCTTATCTCTTTGATG
65 GATTAAAGCTGAAGTTGAGCGGATTAAAGCTGAAGGCAGCGGATCTTATCTCTTTGATG
* * * *
17643440 TTGTGGTGGAATAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAATAG
1 TTGTAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGCAGTGGAATAG
* * *
17643505 ATTAAAGCTGAAGGCAGCTAATCTTATCTCCCTGGCATT-AAGACTG-AGAGCAGCGAATCTTAT
66 ATTAAAGCTG-A---AG----T-TGA----GC-GG-ATTAAAG-CTGAAG-GCAGCGGATCTTAT
* ** *
17643568 TTCCCTGACG
114 CTCTTTGATG
* * *
17643578 TTGCAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCTCTAGCGTTGTAGTGGAATAG
1 TTGTAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGCAGTGGAATAG
* * * * *
17643643 GTTAAAGCTGAAGTGGAGCGAATTAAAGCTGAAGGCAGCGGATCCTATCTCTTTGGT-
66 ATTAAAGCTGAAGTTGAGCGGATTAAAGCTGAAGGCAGCGGATCTTATCTCTTTGATG
* * *
17643700 TTCATAGTGGAACAAATTAAAGTTAAAGGTAGCGAATCTTGTTTC
1 TT-GTAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTC
17643745 TTTGGCGTTG
Statistics
Matches: 346, Mismatches: 57, Indels: 57
0.75 0.12 0.12
Matches are distributed among these distances:
122 3 0.01
123 149 0.43
124 14 0.04
125 4 0.01
126 2 0.01
127 4 0.01
129 8 0.02
130 56 0.16
131 2 0.01
132 2 0.01
134 2 0.01
136 1 0.00
137 8 0.02
138 91 0.26
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (123 bp):
TTGTAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGCAGTGGAATAG
ATTAAAGCTGAAGTTGAGCGGATTAAAGCTGAAGGCAGCGGATCTTATCTCTTTGATG
Found at i:17643502 original size:51 final size:51
Alignment explanation
Indices: 17643447--17643543 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
17643437 ATGTTGTGGT
* * *
17643447 GGAATAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGC
1 GGAATAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGCATTGCAGC
* * *
17643498 GGAATAGATTAAAGCTGAAGGCAGCTAATCTTATCTCCCTGGCATT
1 GGAATAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGCATT
17643544 AAGACTGAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (51 bp):
GGAATAGATTAAAGCTAAAGGCAGCGAATCTTATCTCCCTAGCATTGCAGC
Found at i:17643631 original size:51 final size:52
Alignment explanation
Indices: 17643556--17643665 Score: 134
Period size: 51 Copynumber: 2.1 Consensus size: 52
17643546 GACTGAGAGC
*
17643556 AGCGAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTAAAG-GT
1 AGCGAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTAAAGTGG
* * * * * *
17643607 AGCGAATCTTGTTTCTCT-AGCGTTGTAGTGGAATAGGTTAAAGCTGAAGTGG
1 AGCGAATCTTATTTCCCTGA-CGTTGCAGTGGAACAGATTAAAGCTAAAGTGG
17643659 AGCGAAT
1 AGCGAAT
17643666 TAAAGCTGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 1 0.02
51 41 0.82
52 8 0.16
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (52 bp):
AGCGAATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTAAAGTGG
Found at i:17643639 original size:261 final size:261
Alignment explanation
Indices: 17643275--17643795 Score: 733
Period size: 261 Copynumber: 2.0 Consensus size: 261
17643265 TAGATTAAAG
* * *
17643275 CTGGCGTTAAGACTGAGAGCAGCGAATCTTATTTCCTTGACGTTGTAGCTGAACAAATTAAAGCT
1 CTGGCATTAAGACTGAGAGCAGCGAATCTTATTTCCCTGACGTTGCAGCTGAACAAATTAAAGCT
* *
17643340 AAAGGTAGCGAATATTATTTCCCTACCGTTGCAGTGGAATAGATTAAAGCTGAAGTTGAGCGGAT
66 AAAGGTAGCGAATATTATTTCCCTACCGTTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGAAT
* * * * *
17643405 TAAAGCAGAAGGCAGCGGATCTTATCTCTTTGATGTT-GTGGTGGAATAGATTAAAGCTAAAGGT
131 TAAAGCAGAAGGCAGCGGATCCTATCTCTTTGAT-TTCATAGTGGAACAAATTAAAGCTAAAGGT
* * *
17643469 AGCGAATCTTGTTTCCCTAGCATTGCAGCGGAA-TAGATTAAAGCTGAAGGCAGCTAATCTTATC
195 AGCGAATCTTGTTTCCCTAGCATTGCAGC-GAAGCAGATTAAAGCTGAAGGCAACGAATCTTATC
17643533 TCC
259 TCC
*
17643536 CTGGCATTAAGACTGAGAGCAGCGAATCTTATTTCCCTGACGTTGCAG-TGGAACAGATTAAAGC
1 CTGGCATTAAGACTGAGAGCAGCGAATCTTATTTCCCTGACGTTGCAGCT-GAACAAATTAAAGC
* * * * * *
17643600 TAAAGGTAGCGAATCTTGTTTCTCTAGCGTTGTAGTGGAATAGGTTAAAGCTGAAGTGGAGCGAA
65 TAAAGGTAGCGAATATTATTTCCCTACCGTTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGAA
* * *
17643665 TTAAAGCTGAAGGCAGCGGATCCTATCTCTTTGGTTTCATAGTGGAACAAATTAAAGTTAAAGGT
130 TTAAAGCAGAAGGCAGCGGATCCTATCTCTTTGATTTCATAGTGGAACAAATTAAAGCTAAAGGT
** * * * *
17643730 AGCGAATCTTGTTTCTTTGGCGTTGCAGCTAAGCAGTTTAAAGCTGAAGGCAACGAATCTTATCT
195 AGCGAATCTTGTTTCCCTAGCATTGCAGCGAAGCAGATTAAAGCTGAAGGCAACGAATCTTATCT
17643795 C
260 C
17643796 TTTGGTGTTA
Statistics
Matches: 228, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
260 5 0.02
261 223 0.98
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (261 bp):
CTGGCATTAAGACTGAGAGCAGCGAATCTTATTTCCCTGACGTTGCAGCTGAACAAATTAAAGCT
AAAGGTAGCGAATATTATTTCCCTACCGTTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGAAT
TAAAGCAGAAGGCAGCGGATCCTATCTCTTTGATTTCATAGTGGAACAAATTAAAGCTAAAGGTA
GCGAATCTTGTTTCCCTAGCATTGCAGCGAAGCAGATTAAAGCTGAAGGCAACGAATCTTATCTC
C
Found at i:17644119 original size:132 final size:131
Alignment explanation
Indices: 17643857--17644125 Score: 305
Period size: 132 Copynumber: 2.0 Consensus size: 131
17643847 AGACAGACTA
* * *
17643857 AAGATGACGAATCTTATCTTCCCAAGGTAGTTGGGAAGCAGATTTAAGCCACCAGTCCTATCTCT
1 AAGACGACGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
*** * * *
17643922 CTGAGCAGCAGTGGAGTAGGTTGAAGATTACAGATCCTGTCTCCTTAAGCAGTAGTGGAGCAGAT
66 CTGAGCAGCAGTGGAGTAAACTGAAGATTACAGATCCTGTCTCCTTAAG-AGCAGCGAAGCAGAT
17643987 CG
130 CG
* *
17643989 TAGACGACGAATCTTA-CTTTCCCAATGTAGTAGGGAAGCAGATTTAAGCCACCAG-CCTTATCT
1 AAGACGACGAATCTTATC-TTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCC-TATCT
* * *
17644052 CCCTGAGCAGTAGTGGAGTAAACTGAAGA-TAGCAGA-CTTGTCTTCCTGTATTG-GCAGCGAAG
64 CCCTGAGCAGCAGTGGAGTAAACTGAAGATTA-CAGATCCTGTC-TCCT-TA-AGAGCAGCGAAG
*
17644114 TAGATCG
125 CAGATCG
17644121 AAGAC
1 AAGAC
17644126 ACCAGCCTTA
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
131 10 0.09
132 102 0.89
133 2 0.02
134 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (131 bp):
AAGACGACGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCC
CTGAGCAGCAGTGGAGTAAACTGAAGATTACAGATCCTGTCTCCTTAAGAGCAGCGAAGCAGATC
G
Found at i:17644221 original size:88 final size:88
Alignment explanation
Indices: 17644038--17644686 Score: 696
Period size: 88 Copynumber: 7.4 Consensus size: 88
17644028 AGATTTAAGC
* **
17644038 CACCAGCCTTATCTCCCTGAGCAGTAGTGGAGTAAACTGAAGATAGCAGA-CTTGTCTTCCTGTA
1 CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTGGACTGAAGATAGCAGATCTTGTCTTCCTGTA
17644102 TTGGCAGCGAAGTAGATCGAAGA
66 TTGGCAGCGAAGTAGATCGAAGA
* * *
17644125 CACCAGCCTTATCTCCCTGAGCAGTAGTGGAGTGGACTGAAGATAACATATCTTGTCTTCCTGTA
1 CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTGGACTGAAGATAGCAGATCTTGTCTTCCTGTA
*
17644190 TTGGCAGCAAAGTAGATCGAAGA
66 TTGGCAGCGAAGTAGATCGAAGA
* ** * * ** * * * *
17644213 CACTAGCCTTATCTCCCTGAGTTTGCAGCGGGGCAGACTAAAGATAACAGATTTTGTTTTCCTGT
1 CACCAGCCTTATCTCCCTGAG-CAGCAGTGGAGTGGACTGAAGATAGCAGATCTTGTCTTCCTGT
17644278 ATTGGCAGCGAAGTAGATCGAAGA
65 ATTGGCAGCGAAGTAGATCGAAGA
** * *** ** * **
17644302 CACCAGCCTTGCCTCCCTAAATTTGCAACGGGGCAGACTGAAGATAGCAGATCTTGTCTTCCTGT
1 CACCAGCCTTATCTCCCT-GAGCAGCAGTGGAGTGGACTGAAGATAGCAGATCTTGTCTTCCTGT
*
17644367 -TTGGCAGTGAAGTAGATCGAAGA
65 ATTGGCAGCGAAGTAGATCGAAGA
* * * * *
17644390 TACCAGCCTTATCTCCCTGAGCAGCAGTGAAGTAGG-TTGAAGATAACAAATCTTGTCTTCCTGT
1 CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGT-GGACTGAAGATAGCAGATCTTGTCTTCCTGT
*
17644454 ATTGGCAGCGAAGTAGATCGAATA
65 ATTGGCAGCGAAGTAGATCGAAGA
* * * *
17644478 TACCAGCCTTATCTCTCTGAGTAGCAGTGGAGTAGG-TTGAAGATAGCAGATCTTGTCTTCCTGT
1 CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGT-GGACTGAAGATAGCAGATCTTGTCTTCCTGT
17644542 ATTGGCAGCGAAGTAGATCGAAGA
65 ATTGGCAGCGAAGTAGATCGAAGA
* *** * * * * *
17644566 TACCAATTTTATCTCCCCGAGCAGCAGTGGAGTAGG-TTGAAAATAGCAGATTTTGTCTTCCTAT
1 CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGT-GGACTGAAGATAGCAGATCTTGTCTTCCTGT
* * * *
17644630 ACTGACAGTGAAGTAGATCGAATA
65 ATTGGCAGCGAAGTAGATCGAAGA
* ** *
17644654 AACCAATCTTATCTCTCTGAAGCAGCAGTGGAG
1 CACCAGCCTTATCTCCCTG-AGCAGCAGTGGAG
17644687 CAGATTAAAG
Statistics
Matches: 486, Mismatches: 70, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
87 77 0.16
88 287 0.59
89 121 0.25
90 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (88 bp):
CACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTGGACTGAAGATAGCAGATCTTGTCTTCCTGTA
TTGGCAGCGAAGTAGATCGAAGA
Found at i:17644419 original size:43 final size:43
Alignment explanation
Indices: 17644370--17644600 Score: 174
Period size: 43 Copynumber: 5.3 Consensus size: 43
17644360 TTCCTGTTTG
* *
17644370 GCAGTGAAGTAGATCGAAGATACCAGCCTTATCTCCCTGAGCA
1 GCAGTGAAGTAGATCGAAGATACCAGTCTTATCTCCCTGAGTA
* * * * * * * *
17644413 GCAGTGAAGTAGGTTGAAGATAACAAATCTTGTCTTCCTGTATTG
1 GCAGTGAAGTAGATCGAAGAT-ACCAGTCTTATCTCCCTG-AGTA
* * * *
17644458 GCAGCGAAGTAGATCGAATATACCAGCCTTATCTCTCTGAGTA
1 GCAGTGAAGTAGATCGAAGATACCAGTCTTATCTCCCTGAGTA
* * * * * * * *
17644501 GCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTG
1 GCAGTGAAGTAGATCGAAGATACCAG-TCTTATCTCCCTG-AGTA
* * * * *
17644546 GCAGCGAAGTAGATCGAAGATACCAATTTTATCTCCCCGAGCA
1 GCAGTGAAGTAGATCGAAGATACCAGTCTTATCTCCCTGAGTA
*
17644589 GCAGTGGAGTAG
1 GCAGTGAAGTAG
17644601 GTTGAAAATA
Statistics
Matches: 135, Mismatches: 49, Indels: 8
0.70 0.26 0.04
Matches are distributed among these distances:
43 52 0.39
44 43 0.32
45 40 0.30
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (43 bp):
GCAGTGAAGTAGATCGAAGATACCAGTCTTATCTCCCTGAGTA
Found at i:17644645 original size:45 final size:44
Alignment explanation
Indices: 17644501--17644645 Score: 114
Period size: 45 Copynumber: 3.3 Consensus size: 44
17644491 TCTCTGAGTA
* * * *
17644501 GCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATT
1 GCAGTGAAGTAGGTTGAAGATAGCAGATTTTGTCTTCCTATACT
* * * * * * * * *
17644545 GGCAGCGAAGTAGATCGAAGATACCA-ATTTTATCTCCCCGA-GCA
1 -GCAGTGAAGTAGGTTGAAGATAGCAGATTTTGTCT-TCCTATACT
* *
17644589 GCAGTGGAGTAGGTTGAAAATAGCAGATTTTGTCTTCCTATACT
1 GCAGTGAAGTAGGTTGAAGATAGCAGATTTTGTCTTCCTATACT
17644633 GACAGTGAAGTAG
1 G-CAGTGAAGTAG
17644646 ATCGAATAAA
Statistics
Matches: 71, Mismatches: 25, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 22 0.31
44 17 0.24
45 32 0.45
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (44 bp):
GCAGTGAAGTAGGTTGAAGATAGCAGATTTTGTCTTCCTATACT
Found at i:17644680 original size:265 final size:265
Alignment explanation
Indices: 17644038--17644683 Score: 769
Period size: 265 Copynumber: 2.4 Consensus size: 265
17644028 AGATTTAAGC
* * * *
17644038 CACCAGCCTTATCTCCCTGAGCAGTAGTGGAGTAAACTGAAGATAGCAGA-CTTGTCTTCCTGTA
1 CACCAACCTTATCTCCCAGAGCAGCAGTGGAGTAGACTGAAGATAGCAGATCTTGTCTTCCTGTA
* * * *
17644102 TTGGCAGCGAAGTAGATCGAAGACACCAGCCTTATCTCCCTGAGCAGTAGTGGAGTGGACTGAAG
66 TTGGCAGTGAAGTAGATCGAAGAAACCAGCCTTATCTCCCTGAGCAGCAGTGAAGTGGACTGAAG
* *
17644167 ATAACATATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGAAGACACTAGCCTTATCTCCCTG
131 ATAACAAATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGAAGACACCAGCCTTATCTCCCTG
* * * *
17644232 AGTTTGCAGCGGGGCAGACTAAAGATAACAGATTTTGTTTTCCTGTATTGGCAGCGAAGTAGATC
196 AGTTAGCAGCGGAGCAGACTAAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
17644297 GAAGA
261 GAAGA
* ** * *** ** * *
17644302 CACCAGCCTTGCCTCCCTAAATTTGCAACGGGGCAGACTGAAGATAGCAGATCTTGTCTTCCTGT
1 CACCAACCTTATCTCCC-AGAGCAGCAGTGGAGTAGACTGAAGATAGCAGATCTTGTCTTCCTGT
* *
17644367 -TTGGCAGTGAAGTAGATCGAAGATACCAGCCTTATCTCCCTGAGCAGCAGTGAAGTAGG-TTGA
65 ATTGGCAGTGAAGTAGATCGAAGAAACCAGCCTTATCTCCCTGAGCAGCAGTGAAGT-GGACTGA
* * * *
17644430 AGATAACAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAATATACCAGCCTTATCTCTC
129 AGATAACAAATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGAAGACACCAGCCTTATCTCCC
* * ** * *
17644495 TGAG-TAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGA
194 TGAGTTAGCAGCGGAGCAGACTAAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGA
17644559 TCGAAGA
259 TCGAAGA
* ** * ** * * *
17644566 TACCAATTTTATCTCCCCGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATTTTGTCTTCCTATA
1 CACCAACCTTATCTCCCAGAGCAGCAGTGGAGTAGACTGAAGATAGCAGATCTTGTCTTCCTGTA
* * * ** *
17644631 CTGACAGTGAAGTAGATCGAATAAACCAATCTTATCTCTCTGAAGCAGCAGTG
66 TTGGCAGTGAAGTAGATCGAAGAAACCAGCCTTATCTCCCTG-AGCAGCAGTG
17644684 GAGCAGATTA
Statistics
Matches: 316, Mismatches: 61, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
263 33 0.10
264 118 0.37
265 150 0.47
266 15 0.05
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (265 bp):
CACCAACCTTATCTCCCAGAGCAGCAGTGGAGTAGACTGAAGATAGCAGATCTTGTCTTCCTGTA
TTGGCAGTGAAGTAGATCGAAGAAACCAGCCTTATCTCCCTGAGCAGCAGTGAAGTGGACTGAAG
ATAACAAATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATCGAAGACACCAGCCTTATCTCCCTG
AGTTAGCAGCGGAGCAGACTAAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
GAAGA
Found at i:17645057 original size:44 final size:44
Alignment explanation
Indices: 17644920--17645171 Score: 169
Period size: 44 Copynumber: 5.8 Consensus size: 44
17644910 CAGATAATAT
* * *
17644920 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGTC-GGTT---TA-A
1 CAAACCTTATCTCCCTGAAGTTGCAGTAGAG-CAGATTGAAGATA
* * * * * * *
17644960 CCAATCTTATCTCCCTAAACTTGCAGT-GGGACAGGTTGAAGATG
1 CAAACCTTATCTCCCTGAAGTTGCAGTAGAG-CAGATTGAAGATA
** *
17645004 CAAGTCTTATC-CCCTGAAGTTGCAGTAGAGCAGACTGAAGATAA
1 CAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGAT-A
* * * * *
17645048 CAAACCTTATCTCCCTAAACTTGCAGTGGGGCAGGTTGAAGATA
1 CAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATA
*** * *
17645092 CAAGTTTTATCTCCCTGAAGTTGCAGTAGAGAAGATTGAAGCTA
1 CAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATA
* * * *
17645136 CTAATCC-TATCTCCATAAAGTTGCAGTGGAGCAGAT
1 C-AAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
17645172 AAAAACGATG
Statistics
Matches: 162, Mismatches: 41, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
39 3 0.02
40 27 0.17
43 24 0.15
44 81 0.50
45 27 0.17
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
CAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGATA
Found at i:17645070 original size:88 final size:89
Alignment explanation
Indices: 17644965--17645164 Score: 289
Period size: 88 Copynumber: 2.3 Consensus size: 89
17644955 TTTAACCAAT
*
17644965 CTTATCTCCCTAAACTTGCAGTGGGACAGGTTGAAGATGCAAGTCTTATC-CCCTGAAGTTGCAG
1 CTTATCTCCCTAAACTTGCAGTGGGACAGGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
*
17645029 TAGAGCAGACTGAAGATAAC-AAAC
66 TAGAGAAGACTGAAGAT-ACTAAAC
* *
17645053 CTTATCTCCCTAAACTTGCAGTGGGGCAGGTTGAAGATACAAGTTTTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTAAACTTGCAGTGGGACAGGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
* * *
17645118 TAGAGAAGATTGAAGCTACTAATC
66 TAGAGAAGACTGAAGATACTAAAC
* *
17645142 C-TATCTCCATAAAGTTGCAGTGG
1 CTTATCTCCCTAAACTTGCAGTGG
17645165 AGCAGATAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
88 69 0.68
89 32 0.32
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (89 bp):
CTTATCTCCCTAAACTTGCAGTGGGACAGGTTGAAGATACAAGTCTTATCTCCCTGAAGTTGCAG
TAGAGAAGACTGAAGATACTAAAC
Found at i:17646042 original size:6 final size:6
Alignment explanation
Indices: 17646019--17646057 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
17646009 TCAATCTTTC
*
17646019 TATTTC TATTTT TATTTT TATTTTT TATTTTT TATTTT T
1 TATTTT TATTTT TATTTT TA-TTTT TA-TTTT TATTTT T
17646058 GTATACGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 18 0.58
7 13 0.42
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:17646043 original size:7 final size:7
Alignment explanation
Indices: 17646027--17646057 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
17646017 TCTATTTCTA
17646027 TTTTTA-
1 TTTTTAT
17646033 TTTTTAT
1 TTTTTAT
17646040 TTTTTAT
1 TTTTTAT
17646047 TTTTTAT
1 TTTTTAT
17646054 TTTT
1 TTTT
17646058 GTATACGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:17647012 original size:28 final size:26
Alignment explanation
Indices: 17646963--17647014 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
17646953 ACACGCATAC
*
17646963 TTTTATAATATATATACGTACATATT
1 TTTTATAATATATATACATACATATT
*
17646989 TTTTATAATTTATATATATATACATA
1 TTTTATAA--TATATATACATACATA
17647015 CTTATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
28 14 0.64
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTTATAATATATATACATACATATT
Found at i:17647575 original size:70 final size:72
Alignment explanation
Indices: 17647447--17647584 Score: 226
Period size: 71 Copynumber: 1.9 Consensus size: 72
17647437 TTTCAAACTC
* * * *
17647447 AAGTTTTAAACGATCTCGGGAATTAATAAGATATCGTGTCCTAACTTACTGGGCATGAT-CCTTT
1 AAGTTTTAAACGATCTAGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCCTTT
17647511 TTTCCTT
66 TTTCCTT
17647518 AAGTTTTAAACGATCTAGGGAATTAAGAAAAGA-CGTGTCCTAACTTACTGGGCATGATCCCTTT
1 AAGTTTTAAACGATCTAGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCCTTT
17647582 TTT
66 TTT
17647585 AAATCCGAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 25 0.40
71 37 0.60
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (72 bp):
AAGTTTTAAACGATCTAGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCCTTT
TTTCCTT
Found at i:17648756 original size:13 final size:13
Alignment explanation
Indices: 17648738--17648763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17648728 GGCTTCCCCT
17648738 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
17648751 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
17648764 AGTTTAGCTG
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:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (13 bp):
TTCCTTCTGTTTC
Found at i:17648782 original size:39 final size:39
Alignment explanation
Indices: 17648738--17648813 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
17648728 GGCTTCCCCT
17648738 TTCCTTCTGTTTCTTCCTTCTGTTTCAGTTTAGCTGCCG
1 TTCCTTCTGTTTCTTCCTTCTGTTTCAGTTTAGCTGCCG
17648777 TTCCTTCTGTTTCTTCCTTCTGTTTCAGTTTAGCTGC
1 TTCCTTCTGTTTCTTCCTTCTGTTTCAGTTTAGCTGC
17648814 TTCACAACCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.05, C:0.28, G:0.14, T:0.53
Consensus pattern (39 bp):
TTCCTTCTGTTTCTTCCTTCTGTTTCAGTTTAGCTGCCG
Found at i:17648795 original size:13 final size:13
Alignment explanation
Indices: 17648777--17648802 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17648767 TTAGCTGCCG
17648777 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
17648790 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
17648803 AGTTTAGCTG
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:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (13 bp):
TTCCTTCTGTTTC
Found at i:17654610 original size:18 final size:18
Alignment explanation
Indices: 17654582--17654630 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
17654572 AATTATAAGA
17654582 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
17654599 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
17654615 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
17654631 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:17654616 original size:16 final size:16
Alignment explanation
Indices: 17654582--17654636 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
17654572 AATTATAAGA
17654582 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
17654599 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
17654615 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
17654629 ATGTTTAA
1 AT-TTTAA
17654637 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:17654728 original size:156 final size:157
Alignment explanation
Indices: 17654424--17654729 Score: 560
Period size: 156 Copynumber: 2.0 Consensus size: 157
17654414 NNNATATTAT
*
17654424 AATTTTAGTAAATTCATATATTTTAATTAAAATATATTTAGTAATAATTATGTTTAAATATGATT
1 AATTTTAGTAAATTCATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATT
*
17654489 AAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACATTAACAATAATCATTTA
66 AAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTA
*
17654554 CCAAAACAATTTTCTGCTAATTATAAG
131 CCAAAACAATTTTATGCTAATTATAAG
* *
17654581 AATTTTATTAAATT-ATATATTTTAATTAAAATATATTTAATTATAATTATGTTTAAATATGATT
1 AATTTTAGTAAATTCATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATT
17654645 AAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTA
66 AAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTA
17654710 CCAAAACAATTTTATGCTAA
131 CCAAAACAATTTTATGCTAA
17654730 GGGTATTCTA
Statistics
Matches: 144, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
156 131 0.91
157 13 0.09
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (157 bp):
AATTTTAGTAAATTCATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATT
AAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTA
CCAAAACAATTTTATGCTAATTATAAG
Found at i:17654846 original size:44 final size:45
Alignment explanation
Indices: 17654781--17654871 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
17654771 ACCTCTATTC
* * *
17654781 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
17654825 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
17654870 CA
1 CA
17654872 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:17654886 original size:17 final size:16
Alignment explanation
Indices: 17654852--17654904 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
17654842 GATTAGCTAT
17654852 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17654868 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
17654885 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
17654901 TACA
1 TACA
17654905 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:17661151 original size:26 final size:25
Alignment explanation
Indices: 17661077--17661151 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 25
17661067 TTAAACATAA
*
17661077 AATTAAATTAAAAAATAATTATTGGT
1 AATTAAATTAAATAATAATTATT-GT
*
17661103 AATATATAATTAAATACAAAATTATT-T
1 AAT-TA-AATTAAATA-ATAATTATTGT
17661130 AAGTTAAATTAAATGAATAATT
1 AA-TTAAATTAAAT-AATAATT
17661152 TTTTTAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
26 16 0.39
27 8 0.20
28 9 0.22
29 8 0.20
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (25 bp):
AATTAAATTAAATAATAATTATTGT
Found at i:17662375 original size:20 final size:20
Alignment explanation
Indices: 17662338--17662387 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
17662328 GGCACTTTCA
*
17662338 TATCGATACTTAACAAAATT
1 TATCGATACTAAACAAAATT
* * **
17662358 TATCGCTACTAAAGAAAAAA
1 TATCGATACTAAACAAAATT
17662378 TATCGATACT
1 TATCGATACT
17662388 TATCTATAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (20 bp):
TATCGATACTAAACAAAATT
Found at i:17664144 original size:17 final size:19
Alignment explanation
Indices: 17664124--17664158 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
17664114 TTAAAATAGT
17664124 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
17664141 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
17664159 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:17664249 original size:19 final size:20
Alignment explanation
Indices: 17664217--17664265 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
17664207 CAAAATAGTG
*
17664217 AAAAAAATAACAAGAAA-A-T
1 AAAAAAA-AGCAAGAAACAGT
17664236 AATAAAAAAGCAAGAAACAGT
1 AA-AAAAAAGCAAGAAACAGT
17664257 AAAAAAAAG
1 AAAAAAAAG
17664266 TAGTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.38
20 13 0.50
21 3 0.12
ACGTcount: A:0.76, C:0.06, G:0.10, T:0.08
Consensus pattern (20 bp):
AAAAAAAAGCAAGAAACAGT
Found at i:17664726 original size:51 final size:52
Alignment explanation
Indices: 17664666--17664771 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 52
17664656 ATAATAAATT
** * * * *
17664666 TAACCCTCAATTTTTACATATTATAT-CAATTTAGTCATAATTTTAAAA-AAA
1 TAACCCTCAAAATTTACAAATGAT-TCCAATTTAATCATAATTCTAAAATAAA
* *
17664717 TAACTCTCAAAATTTACAAATGATTCCAATTTAATCCTAATTCTAAAATAAA
1 TAACCCTCAAAATTTACAAATGATTCCAATTTAATCATAATTCTAAAATAAA
17664769 TAA
1 TAA
17664772 AAAATACATA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
50 1 0.02
51 38 0.84
52 6 0.13
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (52 bp):
TAACCCTCAAAATTTACAAATGATTCCAATTTAATCATAATTCTAAAATAAA
Found at i:17664840 original size:20 final size:23
Alignment explanation
Indices: 17664789--17664847 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 23
17664779 ATAAATATTT
17664789 TTAAATA-TATAATAAATTTAATA
1 TTAAATATTA-AATAAATTTAATA
17664812 TTAAATATTAAATAAA-TT-ATA
1 TTAAATATTAAATAAATTTAATA
17664833 TT-AATATTAAATAAA
1 TTAAATATTAAATAAA
17664848 ATAACCCCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.37
21 5 0.14
22 2 0.06
23 13 0.37
24 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAAATATTAAATAAATTTAATA
Found at i:17665501 original size:19 final size:20
Alignment explanation
Indices: 17665454--17665504 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
17665444 TGGGAGATCT
*
17665454 TTTATTTTATTTAATATTAA
1 TTTATTATATTTAATATTAA
*
17665474 TTAATTATATTT-AT-TTAA
1 TTTATTATATTTAATATTAA
17665492 TATTATTATATTT
1 T-TTATTATATTT
17665505 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.19
19 12 0.44
20 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTATTATATTTAATATTAA
Found at i:17672776 original size:20 final size:20
Alignment explanation
Indices: 17672717--17672778 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 20
17672707 GGTTAAGAAA
17672717 TTTGATATTT-GATT-TAAAT
1 TTTGATATTTAG-TTATAAAT
** * *
17672736 TTCAATACTTA-TTAGAAAT
1 TTTGATATTTAGTTATAAAT
17672755 TTTGATATTTAGTTATAAAT
1 TTTGATATTTAGTTATAAAT
17672775 TTTG
1 TTTG
17672779 GTACTATCAA
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
18 2 0.06
19 19 0.59
20 11 0.34
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTGATATTTAGTTATAAAT
Found at i:17673467 original size:19 final size:19
Alignment explanation
Indices: 17673439--17673476 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
17673429 ATTTATTTAT
17673439 TAAAATAATATTTTTATAAA
1 TAAAATAATATTTTT-TAAA
17673459 TAAAA-AATATTTTTTAAA
1 TAAAATAATATTTTTTAAA
17673477 AAACCTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 9 0.50
20 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAATAATATTTTTTAAA
Found at i:17674109 original size:15 final size:16
Alignment explanation
Indices: 17674091--17674120 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17674081 ACATTTAAAT
17674091 AATTTTTT-ATTTTTC
1 AATTTTTTAATTTTTC
17674106 AATTTTTTAATTTTT
1 AATTTTTTAATTTTT
17674121 AAGAATTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
AATTTTTTAATTTTTC
Found at i:17674513 original size:19 final size:19
Alignment explanation
Indices: 17674466--17674522 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
17674456 ATATGATGCG
*
17674466 ATACCAATATTTTTAAAGCA-
1 ATACCAATATTTAT-AA-CAT
17674486 ATACCAATATTTATAACAT
1 ATACCAATATTTATAACAT
* *
17674505 ATACTAATATTTCTAACA
1 ATACCAATATTTATAACA
17674523 AGAATACCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 2 0.06
19 18 0.55
20 13 0.39
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.37
Consensus pattern (19 bp):
ATACCAATATTTATAACAT
Found at i:17674640 original size:18 final size:19
Alignment explanation
Indices: 17674619--17674658 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
17674609 CAAAAATTGT
17674619 TAAT-GATAACAAAATTTC
1 TAATAGATAACAAAATTTC
* *
17674637 TAATAGATTACAATATTTC
1 TAATAGATAACAAAATTTC
17674656 TAA
1 TAA
17674659 CGCGATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (19 bp):
TAATAGATAACAAAATTTC
Found at i:17678930 original size:26 final size:26
Alignment explanation
Indices: 17678894--17678945 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17678884 GAATGCTAAG
17678894 CTCAGAAATGAAATTACCACATTTCA
1 CTCAGAAATGAAATTACCACATTTCA
17678920 CTCAGAAATGAAATTACCACATTTCA
1 CTCAGAAATGAAATTACCACATTTCA
17678946 GCAATTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (26 bp):
CTCAGAAATGAAATTACCACATTTCA
Found at i:17681932 original size:9 final size:9
Alignment explanation
Indices: 17681918--17681943 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
17681908 ATTAAAGATT
17681918 TCTCCAAAA
1 TCTCCAAAA
17681927 TCTCCAAAA
1 TCTCCAAAA
17681936 TCTCCAAA
1 TCTCCAAA
17681944 TCACCCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (9 bp):
TCTCCAAAA
Found at i:17685674 original size:42 final size:42
Alignment explanation
Indices: 17685627--17685725 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
17685617 CATGGCATAG
* *
17685627 CACACGGACGTGTGGAGCTATTTCGAGAGTTACACGGCCTGA
1 CACACGGACGTGTGAAGCTATTTCAAGAGTTACACGGCCTGA
* * *
17685669 CACACGGGCGTGTGAAGCTATTTCAAGAGTTACACGGCTTGG
1 CACACGGACGTGTGAAGCTATTTCAAGAGTTACACGGCCTGA
17685711 CACACAGGA-GTGTGA
1 CACAC-GGACGTGTGA
17685726 CTTGGCTGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 48 0.96
43 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.21
Consensus pattern (42 bp):
CACACGGACGTGTGAAGCTATTTCAAGAGTTACACGGCCTGA
Found at i:17687754 original size:17 final size:17
Alignment explanation
Indices: 17687718--17687760 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
17687708 TATAACTAAG
*
17687718 ATAAATAAAATAGAATA
1 ATAAATAAAATAGAAGA
**
17687735 ATAAATAAAATATTAGA
1 ATAAATAAAATAGAAGA
17687752 AT-AATAAAA
1 ATAAATAAAA
17687761 AAAGATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAAATAAAATAGAAGA
Found at i:17688009 original size:20 final size:20
Alignment explanation
Indices: 17687981--17688034 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
17687971 TTAAAAAGAA
*
17687981 AACTCAAAGAGAATTTTATT
1 AACTCAAAGTGAATTTTATT
*
17688001 AACTTAAAGTGAATTTTATT
1 AACTCAAAGTGAATTTTATT
17688021 AACTCAAAGTGAAT
1 AACTCAAAGTGAAT
17688035 AATGAATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (20 bp):
AACTCAAAGTGAATTTTATT
Found at i:17699903 original size:26 final size:27
Alignment explanation
Indices: 17699869--17699920 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
17699859 TCATGAATTA
*
17699869 TATTACAA-TATTTATTTTATTTTATTC
1 TATTACAATTA-TAATTTTATTTTATTC
17699896 TATT-CAATTATAATTTTATTTTATT
1 TATTACAATTATAATTTTATTTTATT
17699921 TCATTTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTACAATTATAATTTTATTTTATTC
Found at i:17710024 original size:23 final size:23
Alignment explanation
Indices: 17709998--17710049 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
17709988 TGATTTTTAA
* *
17709998 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAATAATAAT
*
17710021 ATTTATAATTATTTAATAATAAT
1 ATTTAGAATTATTTAATAATAAT
17710044 ATTTAG
1 ATTTAG
17710050 GGAAAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (23 bp):
ATTTAGAATTATTTAATAATAAT
Found at i:17713811 original size:44 final size:44
Alignment explanation
Indices: 17713761--17713848 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
17713751 CAATAATGTA
17713761 AGAATTCCAAGTGAACATAATGGAAGAATTAATTCTTGAGAAAC
1 AGAATTCCAAGTGAACATAATGGAAGAATTAATTCTTGAGAAAC
17713805 AGAATTCCAAGTGAACATAATGGAAGAATTAATTCTTGAGAAAC
1 AGAATTCCAAGTGAACATAATGGAAGAATTAATTCTTGAGAAAC
17713849 CAAATGAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.25
Consensus pattern (44 bp):
AGAATTCCAAGTGAACATAATGGAAGAATTAATTCTTGAGAAAC
Found at i:17715399 original size:23 final size:23
Alignment explanation
Indices: 17715380--17715424 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17715370 TAAATTTAAT
* *
17715380 ATTATTTAGTGATAATATTTAGA
1 ATTATTTAATAATAATATTTAGA
17715403 ATTATTTAATAATAATATTTAG
1 ATTATTTAATAATAATATTTAG
17715425 GAAAAATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (23 bp):
ATTATTTAATAATAATATTTAGA
Found at i:17738761 original size:25 final size:26
Alignment explanation
Indices: 17738679--17738819 Score: 116
Period size: 25 Copynumber: 5.7 Consensus size: 26
17738669 GGATATATAA
17738679 CGGGAAGCTCAT-AAGAGCCA-TAAT
1 CGGGAAGCTCATGAAGAGCCATTAAT
* * * * *
17738703 CGGGAAGCTCATG-CGAACGAATGA-
1 CGGGAAGCTCATGAAGAGCCATTAAT
*
17738727 CGGGTAGCTC-TGAAGAGCCATTAAT
1 CGGGAAGCTCATGAAGAGCCATTAAT
* *
17738752 CGGGAAGCTC-CGGAGAGCCATTAAT
1 CGGGAAGCTCATGAAGAGCCATTAAT
* ** *
17738777 CAGGAAGCTCACAAAGAGCCTTTAAT
1 CGGGAAGCTCATGAAGAGCCATTAAT
*
17738803 CGGGATGCTCAT-AAGAG
1 CGGGAAGCTCATGAAGAG
17738820 TTGCGGTGTG
Statistics
Matches: 92, Mismatches: 20, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
23 2 0.02
24 31 0.34
25 38 0.41
26 21 0.23
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (26 bp):
CGGGAAGCTCATGAAGAGCCATTAAT
Found at i:17746653 original size:26 final size:25
Alignment explanation
Indices: 17746543--17746655 Score: 85
Period size: 25 Copynumber: 4.6 Consensus size: 25
17746533 GATAGCTCTT
*
17746543 AAGAGCCATTAATC-GAGAAGCTCCG
1 AAGAGCCATTAATCAG-GAAGCTCCA
* * *
17746568 AATAGCCA-TATATCGGGAAG-TTC-
1 AAGAGCCATTA-ATCAGGAAGCTCCA
17746591 AAGCTAGCCA-T-ATCAGGAAGCTCCA
1 AAG--AGCCATTAATCAGGAAGCTCCA
*
17746616 GAGAGCCATTAATCAGGAAGCTCACA
1 AAGAGCCATTAATCAGGAAGCTC-CA
*
17746642 AAGAGCCTTTAATC
1 AAGAGCCATTAATC
17746656 GAGATGCTCA
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
23 15 0.21
24 7 0.10
25 34 0.48
26 15 0.21
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (25 bp):
AAGAGCCATTAATCAGGAAGCTCCA
Found at i:17749455 original size:27 final size:28
Alignment explanation
Indices: 17749378--17749455 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
17749368 ATTGAGCTAG
* * * *
17749378 ATCAAGTATAACACGTATAAAACGTTGA
1 ATCAAATATAACACGCATAAAGCATTGA
* *
17749406 ATCAAATATAACACACATGAAGCATTGA
1 ATCAAATATAACACGCATAAAGCATTGA
*
17749434 ATC-AATGTAACACGCATAAAGC
1 ATCAAATATAACACGCATAAAGC
17749456 GCAGGATCTC
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 16 0.39
28 25 0.61
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (28 bp):
ATCAAATATAACACGCATAAAGCATTGA
Found at i:17752662 original size:42 final size:42
Alignment explanation
Indices: 17752591--17752687 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
17752581 GTGTCACAAG
** *
17752591 CCGTGT-GCCAGGCCATGTAAGTCTCTAACTT-GTGACACACGA
1 CCGTGTCG-CAGGCCATGTAACACTCTAACTTAAT-ACACACGA
17752633 CCGTGTCGCAGGCCATGTAACACAT-TAACTTAATACACACGA
1 CCGTGTCGCAGGCCATGTAACAC-TCTAACTTAATACACACGA
**
17752675 CTATGTCGCAGGC
1 CCGTGTCGCAGGC
17752688 TGTGTGTGGC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
42 44 0.94
43 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (42 bp):
CCGTGTCGCAGGCCATGTAACACTCTAACTTAATACACACGA
Found at i:17753660 original size:37 final size:37
Alignment explanation
Indices: 17753589--17753744 Score: 197
Period size: 37 Copynumber: 4.2 Consensus size: 37
17753579 AGTACACAAG
* * * *
17753589 TAATCCAACCGA-AACATGTCAATCGCTTATAAGAGC
1 TAATCCACCCGATAACACGCCAATCGCTCATAAGAGC
* *
17753625 TAATCCACCCGATAACACGCCAATTGCTAATAAGAGC
1 TAATCCACCCGATAACACGCCAATCGCTCATAAGAGC
* *
17753662 TAATCCACTCGATAACACACCAATCGCTCATAAGAGC
1 TAATCCACCCGATAACACGCCAATCGCTCATAAGAGC
* **
17753699 TAATCAACTTGATAACACGCCAATCGCTCATAAGAGC
1 TAATCCACCCGATAACACGCCAATCGCTCATAAGAGC
*
17753736 CAATCCACC
1 TAATCCACC
17753745 TAAAAACACA
Statistics
Matches: 104, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 11 0.11
37 93 0.89
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (37 bp):
TAATCCACCCGATAACACGCCAATCGCTCATAAGAGC
Done.