Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 90 of 130
Found at i:17630304 original size:5 final size:5
Alignment explanation
Indices: 17630294--17630319 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17630284 AATAATGTGG
17630294 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
17630320 ATGGAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:17631159 original size:9 final size:9
Alignment explanation
Indices: 17631135--17631178 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
17631125 ATCATGTGTG
*
17631135 AAAAAAGGA
1 AAAAAAGAA
*
17631144 AAGAAAGAA
1 AAAAAAGAA
17631153 AAAAAAGAAGA
1 AAAAAAG-A-A
17631164 AAAAAAGAA
1 AAAAAAGAA
17631173 AAAAAA
1 AAAAAA
17631179 TAACAATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 20 0.67
10 2 0.07
11 8 0.27
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:17631195 original size:3 final size:3
Alignment explanation
Indices: 17631177--17631223 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
17631167 AAAGAAAAAA
* * *
17631177 AAT AAC AAT AAC AAT AAT AAT GAT AAT AAT AAT -AT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17631223 A
1 A
17631224 GAACAGAAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:17631264 original size:3 final size:3
Alignment explanation
Indices: 17631258--17631293 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
17631248 AAAAATAGTG
17631258 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
17631294 GTAAAATCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17631689 original size:119 final size:119
Alignment explanation
Indices: 17631534--17632217 Score: 766
Period size: 119 Copynumber: 5.8 Consensus size: 119
17631524 CAAGACAAAG
* * * * * * *
17631534 CGACTAGGATCGAGTCTAGGTCGAA-AATAAACGATCGAGATGGAACCATGAATCATTAGAGATG
1 CGACCAGGATCGAGTCAAGGTC-AAGAATAAATGATCGAGATGAAACCACGAATCATAAGAAATG
* ** *
17631598 ATTTGGATTGAGTTAAGATCAAGTGATCGGGACAAAACTACAAGTCAAAACAAAA
65 ATCTGGATTGAGCCAAGATCAAGTGATCGGGACAAAACTACAAGTCAAAATAAAA
* * * *
17631653 CGACTAGGATCGAGTCAAGGTTAAGAATAAATGATCGAGACGAAACCACGGATCATAAGAAATGA
1 CGACCAGGATCGAGTCAAGGTCAAGAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGA
* * *
17631718 TCTGGATTGAGCCAAGATCGAGTGACCGGGACAAAATCATA-AA-TCAAAATAAAG
66 TCTGGATTGAGCCAAGATCAAGTGATCGGGACAAAA-C-TACAAGTCAAAATAAAA
* * * *
17631772 TGACCAGGA-CTGAGTCAAGGTCAAAAATAAATAATCAAGATGAAACCACGAATCATAAGAAATG
1 CGACCAGGATC-GAGTCAAGGTCAAGAATAAATGATCGAGATGAAACCACGAATCATAAGAAATG
* * *
17631836 ATCTGGATTGAGCCAAGATCAAGTGATCGGTACAAAACTATAAGTTAAAATAAAA
65 ATCTGGATTGAGCCAAGATCAAGTGATCGGGACAAAACTACAAGTCAAAATAAAA
* ** ** * * * * *
17631891 TGACCAAAATCGAGTCAAGGTTGAGAATAAAAGATCGGGATAAAATCACGAATCATAAAAAATGA
1 CGACCAGGATCGAGTCAAGGTCAAGAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGA
* * * * * * *
17631956 TCTGGATTGAGCTAAGATCGAGTGCT-GAGATAAAACCACAAGTCAAAATAAAT
66 TCTGGATTGAGCCAAGATCAAGTGATCGGGACAAAACTACAAGTCAAAATAAAA
* * * * * *
17632009 CAATCAGGATCGAGTCAAGGTAAAAAATAAATGATCGGGATGAAACCACTAATCATAAGAAATGA
1 CGACCAGGATCGAGTCAAGGTCAAGAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGA
* * * * * *
17632074 TCTAGATTGAGCCAAGATCAAGTGACCGAGATAAAACCATAAGTCAAAATAAAA
66 TCTGGATTGAGCCAAGATCAAGTGATCGGGACAAAACTACAAGTCAAAATAAAA
* * * * *
17632128 CGACCAAGATCGAGTCAAGGTCGAGAATAAATGATTGGGATGAAACCACGAATCATAAGAAATTA
1 CGACCAGGATCGAGTCAAGGTCAAGAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGA
17632193 TCTGGATTGAGCCAAGATCAAGTGA
66 TCTGGATTGAGCCAAGATCAAGTGA
17632218 GTGAAATAAT
Statistics
Matches: 476, Mismatches: 81, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
117 2 0.00
118 99 0.21
119 369 0.78
120 4 0.01
121 2 0.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (119 bp):
CGACCAGGATCGAGTCAAGGTCAAGAATAAATGATCGAGATGAAACCACGAATCATAAGAAATGA
TCTGGATTGAGCCAAGATCAAGTGATCGGGACAAAACTACAAGTCAAAATAAAA
Found at i:17632125 original size:237 final size:237
Alignment explanation
Indices: 17631539--17632217 Score: 862
Period size: 237 Copynumber: 2.9 Consensus size: 237
17631529 CAAAGCGACT
* * * * * * *
17631539 AGGATCGAGTCTAGGTCGAAAATAAACGATCGAGATGGAACCA-TGAATCATTAGAGATGATTTG
1 AGGATCGAGTCAAGGTCAAAAATAAATGATCGAGATGAAACCACT-AATCATAAGAAATGATCTG
** * * * *
17631603 GATTGAGTTAAGATCAAGTGATCGGGACAAAACTACAAGTCAAAACAAAACGACTAGGATCGAGT
65 GATTGAGCCAAGATCAAGTGATC-GGACAAAACTATAAGTCAAAATAAAACGACCAAGATCGAGT
* * * *
17631668 CAAGGTTAAGAATAAATGATCGAGACGAAACCACGGATCATAAGAAATGATCTGGATTGAGCCAA
129 CAAGGTTGAGAATAAATGATCGGGATGAAACCACGAATCATAAGAAATGATCTGGATTGAGCCAA
* * * *
17631733 GATCGAGTGACCGGGACAAAATCATAAATCAAAATAAAGTGACC
194 GATCGAGTGACCGAGACAAAACCACAAATCAAAATAAAGTAACC
* * *
17631777 AGGA-CTGAGTCAAGGTCAAAAATAAATAATCAAGATGAAACCACGAATCATAAGAAATGATCTG
1 AGGATC-GAGTCAAGGTCAAAAATAAATGATCGAGATGAAACCACTAATCATAAGAAATGATCTG
* * *
17631841 GATTGAGCCAAGATCAAGTGATCGGTACAAAACTATAAGTTAAAATAAAATGACCAAAATCGAGT
65 GATTGAGCCAAGATCAAGTGATCGG-ACAAAACTATAAGTCAAAATAAAACGACCAAGATCGAGT
* * * * *
17631906 CAAGGTTGAGAATAAAAGATCGGGATAAAATCACGAATCATAAAAAATGATCTGGATTGAGCTAA
129 CAAGGTTGAGAATAAATGATCGGGATGAAACCACGAATCATAAGAAATGATCTGGATTGAGCCAA
* * * *
17631971 GATCGAGTG-CTGAGATAAAACCACAAGTCAAAATAAA-TCAATC
194 GATCGAGTGACCGAGACAAAACCACAAATCAAAATAAAGT-AACC
* * *
17632014 AGGATCGAGTCAAGGTAAAAAATAAATGATCGGGATGAAACCACTAATCATAAGAAATGATCTAG
1 AGGATCGAGTCAAGGTCAAAAATAAATGATCGAGATGAAACCACTAATCATAAGAAATGATCTGG
* * *
17632079 ATTGAGCCAAGATCAAGTGACCGAGATAAAACCATAAGTCAAAATAAAACGACCAAGATCGAGTC
66 ATTGAGCCAAGATCAAGTGATCG-GACAAAACTATAAGTCAAAATAAAACGACCAAGATCGAGTC
* * *
17632144 AAGGTCGAGAATAAATGATTGGGATGAAACCACGAATCATAAGAAATTATCTGGATTGAGCCAAG
130 AAGGTTGAGAATAAATGATCGGGATGAAACCACGAATCATAAGAAATGATCTGGATTGAGCCAAG
*
17632209 ATCAAGTGA
195 ATCGAGTGA
17632218 GTGAAATAAT
Statistics
Matches: 377, Mismatches: 57, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
236 1 0.00
237 205 0.54
238 171 0.45
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (237 bp):
AGGATCGAGTCAAGGTCAAAAATAAATGATCGAGATGAAACCACTAATCATAAGAAATGATCTGG
ATTGAGCCAAGATCAAGTGATCGGACAAAACTATAAGTCAAAATAAAACGACCAAGATCGAGTCA
AGGTTGAGAATAAATGATCGGGATGAAACCACGAATCATAAGAAATGATCTGGATTGAGCCAAGA
TCGAGTGACCGAGACAAAACCACAAATCAAAATAAAGTAACC
Found at i:17632470 original size:34 final size:34
Alignment explanation
Indices: 17632432--17632523 Score: 121
Period size: 34 Copynumber: 2.7 Consensus size: 34
17632422 TGCATTTTTG
* * *
17632432 GCAAAGAAACCATCTTTCATCGGCTTGAATACAT
1 GCAAAGAAACCATTTTTCATCGACTTGAAGACAT
* * *
17632466 GCAAAGAAACCATTTTTCATCAACTTGGAGGCAT
1 GCAAAGAAACCATTTTTCATCGACTTGAAGACAT
*
17632500 GCAAAGAAATCATTTTTCATCGAC
1 GCAAAGAAACCATTTTTCATCGAC
17632524 CTAAGGGCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (34 bp):
GCAAAGAAACCATTTTTCATCGACTTGAAGACAT
Found at i:17632533 original size:34 final size:34
Alignment explanation
Indices: 17632463--17632534 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
17632453 GGCTTGAATA
**
17632463 CATGCAAAGAAACCATTTTTCATCAACTTGGAGG
1 CATGCAAAGAAACCATTTTTCATCAACTAAGAGG
* *
17632497 CATGCAAAGAAATCATTTTTCATCGACCTAAG-GG
1 CATGCAAAGAAACCATTTTTCATC-AACTAAGAGG
17632531 CATG
1 CATG
17632535 TTTTTAGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 29 0.88
35 4 0.12
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (34 bp):
CATGCAAAGAAACCATTTTTCATCAACTAAGAGG
Found at i:17643294 original size:5 final size:5
Alignment explanation
Indices: 17643284--17643336 Score: 61
Period size: 5 Copynumber: 9.8 Consensus size: 5
17643274 AATAATATGG
*
17643284 ATAAA ATAAA ATAAA ATAAA ATAAA ATAGAA ATCTGAAA ATAAA AAAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA-AA A--T-AAA ATAAA ATAAA
17643333 ATAA
1 ATAA
17643337 GGAAAACTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 33 0.79
6 4 0.10
8 4 0.10
9 1 0.02
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:17644200 original size:3 final size:3
Alignment explanation
Indices: 17644181--17644474 Score: 112
Period size: 3 Copynumber: 102.3 Consensus size: 3
17644171 AAAGAAAGAA
17644181 AAT AAT AA- AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
17644226 AAT AAT GAT GAT GAT AAT AAT -AT AAT -AT AAT -AG AAC AAA AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
17644270 AGT CAA- AA- AAG AA- AAT AGT AAT AAT AAT GAT GAT GAT GAT GAT
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
17644313 GAT GAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT GAT GAT GAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * * *
17644361 GAT GAT GAT AAT AAT -AT AAT -AT AAT -AG AAC AAA AAG AA- AGT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * * * * *
17644405 AAA AAT AGT AAT AAT AAT GAT GAT GAT GAT GAT GAT GAT GAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17644453 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
17644475 GGAAAATCTA
Statistics
Matches: 250, Mismatches: 28, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
2 24 0.10
3 225 0.90
4 1 0.00
ACGTcount: A:0.58, C:0.01, G:0.12, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:17644538 original size:32 final size:32
Alignment explanation
Indices: 17644497--17644567 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
17644487 CAGACCTAAA
* *
17644497 TGGGTCAGAATGAAAATGGAC-CTAGTTGAGCT
1 TGGGCCAGAATGAAAATGGACTCTA-TTAAGCT
*
17644529 TGGGCCAGAATGAAAATGGACTTTATTAAGCT
1 TGGGCCAGAATGAAAATGGACTCTATTAAGCT
17644561 TGGGCCA
1 TGGGCCA
17644568 AAATAGGCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (32 bp):
TGGGCCAGAATGAAAATGGACTCTATTAAGCT
Found at i:17655151 original size:11 final size:10
Alignment explanation
Indices: 17655124--17655149 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
17655114 ATCTTGAACC
17655124 TTTTTTAATT
1 TTTTTTAATT
17655134 TTTTTTAATT
1 TTTTTTAATT
17655144 TTTTTT
1 TTTTTT
17655150 TAGGTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:17656686 original size:55 final size:55
Alignment explanation
Indices: 17656626--17656763 Score: 213
Period size: 55 Copynumber: 2.5 Consensus size: 55
17656616 AATAAAATAT
*
17656626 TAAAAAAATTAAAATATATAAGTCTATATTGATAATCTCTAACAATCAGTATAGG
1 TAAAAAAATTAAAAAATATAAGTCTATATTGATAATCTCTAACAATCAGTATAGG
* * * **
17656681 TAAAAAAATTAAAACATATAATTCTATATTGATAATCTCTAACCATTGGTATAGG
1 TAAAAAAATTAAAAAATATAAGTCTATATTGATAATCTCTAACAATCAGTATAGG
*
17656736 TAAGAAAATTAAAAAATATAAGTCTATA
1 TAAAAAAATTAAAAAATATAAGTCTATA
17656764 CTGACGAATG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 75 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (55 bp):
TAAAAAAATTAAAAAATATAAGTCTATATTGATAATCTCTAACAATCAGTATAGG
Found at i:17656785 original size:55 final size:55
Alignment explanation
Indices: 17656626--17656871 Score: 182
Period size: 55 Copynumber: 4.6 Consensus size: 55
17656616 AATAAAATAT
* * * * * **
17656626 TAAAAAAATTAAAATATATAAGTCTATATTGATAATCTCTAACAATCAGTATAGG
1 TAAAAAAATTAAAAAATATAAGTCTATACTGAGAATCGCTAACCATTGGTATAGG
* * * * *
17656681 TAAAAAAATTAAAACATATAATTCTATATTGATAATCTCTAACCATTGGTATAGG
1 TAAAAAAATTAAAAAATATAAGTCTATACTGAGAATCGCTAACCATTGGTATAGG
* *** *
17656736 TAAGAAAATTAAAAAATATAAGTCTATACTGACGAAT-GCTAAGTGTTGGTATAAG
1 TAAAAAAATTAAAAAATATAAGTCTATACTGA-GAATCGCTAACCATTGGTATAGG
* * * ** * *
17656791 T----AAA--AAAAATTACAAGTCTATACTGATAGGCGTTAACCATTGGTATAAG
1 TAAAAAAATTAAAAAATATAAGTCTATACTGAGAATCGCTAACCATTGGTATAGG
* * * *
17656840 TAAGAAAATTAAAATATATAAATATATACTGA
1 TAAAAAAATTAAAAAATATAAGTCTATACTGA
17656872 CAGGCTTTAA
Statistics
Matches: 154, Mismatches: 29, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
48 1 0.01
49 35 0.23
51 3 0.02
53 3 0.02
55 109 0.71
56 3 0.02
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (55 bp):
TAAAAAAATTAAAAAATATAAGTCTATACTGAGAATCGCTAACCATTGGTATAGG
Found at i:17656834 original size:49 final size:49
Alignment explanation
Indices: 17656781--17656921 Score: 156
Period size: 55 Copynumber: 2.8 Consensus size: 49
17656771 ATGCTAAGTG
*
17656781 TTGGTATAAGTAAAAAAAATTACAAGTCTATACTGATAGGCGTTAACCA
1 TTGGTATAAGTAAAAAAAATTATAAGTCTATACTGATAGGCGTTAACCA
* * * * *
17656830 TTGGTATAAGTAAGAAAATTAAAATATATAAATATATACTGACAGGCTTTAAGCA
1 TTGGTATAAGT---AAAA--AAAAT-TATAAGTCTATACTGATAGGCGTTAACCA
**
17656885 TTACTATAAGTAAAAAAAATTATAAGTCTATACTGAT
1 TTGGTATAAGTAAAAAAAATTATAAGTCTATACTGAT
17656922 GAGCATTAAC
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
49 25 0.33
50 5 0.07
52 8 0.11
54 5 0.07
55 32 0.43
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.31
Consensus pattern (49 bp):
TTGGTATAAGTAAAAAAAATTATAAGTCTATACTGATAGGCGTTAACCA
Found at i:17656845 original size:104 final size:103
Alignment explanation
Indices: 17656720--17656980 Score: 319
Period size: 104 Copynumber: 2.5 Consensus size: 103
17656710 TGATAATCTC
* ** *
17656720 TAACCATTGGTATAGGTAAGAAAATTAAAAAATATAAGTCTATACTGACGAATGC-TAAGTGTTG
1 TAACCATTGGTATAGGTAAGAAAATTAAAAAATATAAGTCTATACTGAC--AGGCTTAAGCATTA
* *
17656784 GTATAAGTAAAAAAAATTACAAGTCTATACTGAT-AGGCGT
64 CTATAAGTAAAAAAAATTACAAGTCTATACTGATGA-GCAT
* * * *
17656824 TAACCATTGGTATAAGTAAGAAAATTAAAATATATAAATATATACTGACAGGCTTTAAGCATTAC
1 TAACCATTGGTATAGGTAAGAAAATTAAAAAATATAAGTCTATACTGACAGGC-TTAAGCATTAC
*
17656889 TATAAGTAAAAAAAATTATAAGTCTATACTGATGAGCAT
65 TATAAGTAAAAAAAATTACAAGTCTATACTGATGAGCAT
* * * * *
17656928 TAACTATCGGTATAGGCAAGAAAAATTAAAACATACAAGTCTATACTGACAGG
1 TAACCATTGGTATAGGTAAG-AAAATTAAAAAATATAAGTCTATACTGACAGG
17656981 TTTTAACTGT
Statistics
Matches: 134, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
102 3 0.02
104 102 0.76
105 29 0.22
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (103 bp):
TAACCATTGGTATAGGTAAGAAAATTAAAAAATATAAGTCTATACTGACAGGCTTAAGCATTACT
ATAAGTAAAAAAAATTACAAGTCTATACTGATGAGCAT
Found at i:17662960 original size:26 final size:27
Alignment explanation
Indices: 17662928--17662985 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
17662918 ATATAAATCT
17662928 TAACATATT-ATATATATTGTTCTCTG
1 TAACATATTAATATATATTGTTCTCTG
*
17662954 TAACATATTAAATATATATTGTTCTTTG
1 TAACATATT-AATATATATTGTTCTCTG
17662982 TAAC
1 TAAC
17662986 TTTTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 9 0.31
28 20 0.69
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (27 bp):
TAACATATTAATATATATTGTTCTCTG
Found at i:17667388 original size:19 final size:19
Alignment explanation
Indices: 17667366--17667403 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17667356 TTATGTATCC
* *
17667366 ATGTATATCAGTGTTATTA
1 ATGTAAATCAATGTTATTA
17667385 ATGTAAATCAATGTTATTA
1 ATGTAAATCAATGTTATTA
17667404 GTGTTTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (19 bp):
ATGTAAATCAATGTTATTA
Found at i:17669963 original size:16 final size:16
Alignment explanation
Indices: 17669926--17669963 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17669916 TAGAGGAGAG
* *
17669926 AAAAAA-AAGGAATAA
1 AAAAAATAAGAAAGAA
17669941 AAAAAATAAGAAAGAA
1 AAAAAATAAGAAAGAA
17669957 AAAAAAT
1 AAAAAAT
17669964 CATTGCTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.08
Consensus pattern (16 bp):
AAAAAATAAGAAAGAA
Found at i:17670015 original size:9 final size:9
Alignment explanation
Indices: 17670001--17670027 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
17669991 TTACTTGTTA
17670001 TCTTGCATT
1 TCTTGCATT
17670010 TCTTGCATT
1 TCTTGCATT
17670019 TCTTGCATT
1 TCTTGCATT
17670028 CTCATTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.11, T:0.56
Consensus pattern (9 bp):
TCTTGCATT
Found at i:17670935 original size:17 final size:18
Alignment explanation
Indices: 17670913--17670950 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17670903 TCACATGCAT
17670913 AATTCCC-TCAAAACCCA
1 AATTCCCGTCAAAACCCA
* *
17670930 AATTCCCGTGAAATCCCA
1 AATTCCCGTCAAAACCCA
17670948 AAT
1 AAT
17670951 GTGAAAACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.39, C:0.34, G:0.05, T:0.21
Consensus pattern (18 bp):
AATTCCCGTCAAAACCCA
Found at i:17671026 original size:14 final size:14
Alignment explanation
Indices: 17671009--17671046 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
17670999 TTTAAATTTG
*
17671009 AAACCCTAAATCGT
1 AAACCCTAAATCCT
*
17671023 AAACCTTAAATCCT
1 AAACCCTAAATCCT
17671037 AAACCCTAAA
1 AAACCCTAAA
17671047 CCACCTTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.29, G:0.03, T:0.21
Consensus pattern (14 bp):
AAACCCTAAATCCT
Found at i:17676385 original size:48 final size:48
Alignment explanation
Indices: 17676314--17676408 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
17676304 GCAATGCCAA
* * **
17676314 ATTTTACCAATTACAATATTAATCGCTTTTACTCTGTGTTCACAAAGG
1 ATTTTACCAATTACAAAATTAATCACTTTTACTCAATGTTCACAAAGG
*
17676362 ATTTTACCAATTACAAAATTAATCATTTTTACTCAATGTTCACAAAG
1 ATTTTACCAATTACAAAATTAATCACTTTTACTCAATGTTCACAAAG
17676409 ATATATCCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (48 bp):
ATTTTACCAATTACAAAATTAATCACTTTTACTCAATGTTCACAAAGG
Found at i:17679077 original size:7 final size:7
Alignment explanation
Indices: 17679067--17679118 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
17679057 CCTTTTTATG
17679067 TTTTGGT
1 TTTTGGT
17679074 TTTTGGT
1 TTTTGGT
17679081 TTTTGGT
1 TTTTGGT
17679088 TTTTGGT
1 TTTTGGT
*
17679095 TTTCGGT
1 TTTTGGT
*
17679102 TTTCGGT
1 TTTTGGT
*
17679109 TTTTGAT
1 TTTTGGT
17679116 TTT
1 TTT
17679119 GTCTTTCTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.02, C:0.04, G:0.25, T:0.69
Consensus pattern (7 bp):
TTTTGGT
Found at i:17696915 original size:20 final size:20
Alignment explanation
Indices: 17696878--17696915 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17696868 TGTCAAATCA
*
17696878 TGATCTTAAAATTGAATTAT
1 TGATCTTAAAATTCAATTAT
*
17696898 TGATCTTAACATTCAATT
1 TGATCTTAAAATTCAATT
17696916 TTAATAAAAT
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:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (20 bp):
TGATCTTAAAATTCAATTAT
Found at i:17698426 original size:52 final size:52
Alignment explanation
Indices: 17698358--17698460 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
17698348 GGACAAAATA
* * *
17698358 ACTTATAGAAGAAGAATTCTAAAAGAAAAGAGATTCTTAATAGGTAAGTTTG
1 ACTTACAGAAAAAGAATTCTAAAAGAAAAGAGATTCTTAATAGATAAGTTTG
* *
17698410 ACTTACAGAAAAAGAATTCTAAGATAAAAGAGATTCTTAATAGATAAGTTT
1 ACTTACAGAAAAAGAATTCTAAAAGAAAAGAGATTCTTAATAGATAAGTTT
17698461 TTATCCTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.29
Consensus pattern (52 bp):
ACTTACAGAAAAAGAATTCTAAAAGAAAAGAGATTCTTAATAGATAAGTTTG
Found at i:17704007 original size:2 final size:2
Alignment explanation
Indices: 17704000--17704033 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17703990 TGCAACAATT
17704000 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17704034 ATTAATTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17707370 original size:38 final size:38
Alignment explanation
Indices: 17707319--17707396 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
17707309 TTGTACTAGC
* *
17707319 TATGTTTTTGTGTTTTGTAGTATGTAATGGAGCTTTCT
1 TATGTTTTTGTGTTTTGTAGCATGTAATGGAACTTTCT
17707357 TATGTTTTTGTGTTTTGTAGCATGTAATGGAACTTTCT
1 TATGTTTTTGTGTTTTGTAGCATGTAATGGAACTTTCT
17707395 TA
1 TA
17707397 CAACAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.18, C:0.06, G:0.22, T:0.54
Consensus pattern (38 bp):
TATGTTTTTGTGTTTTGTAGCATGTAATGGAACTTTCT
Found at i:17718370 original size:8 final size:9
Alignment explanation
Indices: 17718341--17718370 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
17718331 ATTTTTTATT
17718341 AAAAATTTA
1 AAAAATTTA
17718350 AAAAATTTA
1 AAAAATTTA
*
17718359 AAAAATATA
1 AAAAATTTA
17718368 AAA
1 AAA
17718371 GATAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATTTA
Found at i:17726334 original size:62 final size:58
Alignment explanation
Indices: 17726152--17726446 Score: 285
Period size: 59 Copynumber: 5.0 Consensus size: 58
17726142 TTATATAAAG
* ** **
17726152 AAAATTGATACTTTTAACTTTTTTTCAAAAAATATTTTTAAAAAATTTTATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTAAAATTTTATTTTCAAGA
* * * *
17726211 AAAATTGATACTTTCAACTCTTCCTTAAAAATATTTTTCTTCAAATTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTT-TTAAAATTTTATTTTCAAGA
* * *
17726270 AAAATT-AGTACTTCCAACTTTTTCTCAAGAAATGTTTATTTTGAAAATTTTTATTTTCAAGA
1 AAAATTGA-TACTTTCAACTTTTCCTCAA-AAATATTT-TTTT-AAAA-TTTTATTTTCAAGA
* * * * *
17726332 AAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTT-TATTTTTATGTTCAAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAATTTTATTTTC-AAGA
* * *
17726390 AAAA-TGATACATTCAAC-TTTCCTTAAAAAATATTTTTTT-AAATTTTCATTTTAAAGA
1 AAAATTGATACTTTCAACTTTTCC-TCAAAAATATTTTTTTAAAATTTT-ATTTTCAAGA
17726447 GATTATTGAA
Statistics
Matches: 195, Mismatches: 31, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
56 5 0.03
57 44 0.23
58 25 0.13
59 59 0.30
60 13 0.07
61 12 0.06
62 36 0.18
63 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.47
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAATTTTATTTTCAAGA
Found at i:17726441 original size:121 final size:121
Alignment explanation
Indices: 17726140--17726446 Score: 316
Period size: 121 Copynumber: 2.6 Consensus size: 121
17726130 AAACTCGTGC
* * ** ** * *
17726140 TTTTATAT-AAAGAAAATTGA-TACTTTTAACTTTTTTTCAAAAAATA--T-TTTTAAAAAATTT
1 TTTTATTTCAAAGAAAAATGAGTACTTCCAACTTTTCCTCAAAAAATATTTATTTTGAAAATTTT
17726200 TATTTTCAAGAAAAATTGATACTTTCAACTCTTCCTTAAAAATATTTTTCTTCAAA
66 TATTTTCAAGAAAAATTGATACTTTCAACTCTTCCTTAAAAATATTTTTCTTCAAA
** * * * *
17726256 TTTTATTTTTAAGAAAAATTAGTACTTCCAACTTTTTCTCAAGAAATGTTTATTTTGAAAATTTT
1 TTTTATTTCAAAGAAAAATGAGTACTTCCAACTTTTCCTCAAAAAATATTTATTTTGAAAATTTT
* * *
17726321 TATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTT-TT-TAT
66 TATTTTCAAGAAAAATTGATACTTTCAACTCTTCCTTAAAAATATTTTTCTTCAAA
* *
17726375 TTTTATGTTCAAAGGAAAATGA-TACATT-CAAC-TTTCCTTAAAAAATATTT-TTTT--AAATT
1 TTTTAT-TTCAAAGAAAAATGAGTAC-TTCCAACTTTTCCTCAAAAAATATTTATTTTGAAAATT
* *
17726434 TTCATTTTAAAGA
64 TTTATTTTCAAGA
17726447 GATTATTGAA
Statistics
Matches: 160, Mismatches: 24, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
115 16 0.10
116 7 0.04
117 13 0.08
118 35 0.22
119 14 0.09
120 16 0.10
121 59 0.37
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (121 bp):
TTTTATTTCAAAGAAAAATGAGTACTTCCAACTTTTCCTCAAAAAATATTTATTTTGAAAATTTT
TATTTTCAAGAAAAATTGATACTTTCAACTCTTCCTTAAAAATATTTTTCTTCAAA
Found at i:17727369 original size:6 final size:6
Alignment explanation
Indices: 17727358--17727386 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17727348 GACCAAAAAT
17727358 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
17727387 TTATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:17730219 original size:2 final size:2
Alignment explanation
Indices: 17730210--17730245 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
17730200 TCTCTCTCTC
17730210 TA TA -A TA 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 TA TA TA TA T
17730246 TCTGAAAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17732759 original size:3 final size:3
Alignment explanation
Indices: 17732751--17732794 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
17732741 AGTATTAGAT
17732751 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17732795 GTGTATTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17740898 original size:14 final size:13
Alignment explanation
Indices: 17740855--17740904 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
17740845 TTATAAATTT
17740855 AATAATTA-ATGT-
1 AATAATTACAT-TA
17740867 AATAATTACATTA
1 AATAATTACATTA
*
17740880 AATAATTAGATTCA
1 AATAATTACATT-A
*
17740894 AATAATAACAT
1 AATAATTACAT
17740905 ATGACACATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 9 0.28
13 13 0.41
14 10 0.31
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (13 bp):
AATAATTACATTA
Found at i:17741787 original size:20 final size:20
Alignment explanation
Indices: 17741758--17741808 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
17741748 TTGTATATTC
* *
17741758 ATATAATTTTATATAAATAT
1 ATATAATTTTAAATAAAAAT
*
17741778 ATATATTTTTAAATAAAAAT
1 ATATAATTTTAAATAAAAAT
17741798 AT-TAATTTTAA
1 ATATAATTTTAA
17741809 TTAATCTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATAATTTTAAATAAAAAT
Found at i:17742104 original size:38 final size:37
Alignment explanation
Indices: 17742062--17742139 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
17742052 TTAAATTAAA
* *
17742062 ATAAAATATATGTATTT-GATAATTTAAGATAAATAATT
1 ATAAAAT-TATATATTTAAATAATTTAA-ATAAATAATT
*
17742100 AT-AAATTATATATTTAAAATAATTTTAATAAATAATT
1 ATAAAATTATATATTT-AAATAATTTAAATAAATAATT
17742137 ATA
1 ATA
17742140 GATAAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
36 8 0.24
37 16 0.47
38 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (37 bp):
ATAAAATTATATATTTAAATAATTTAAATAAATAATT
Found at i:17745450 original size:20 final size:21
Alignment explanation
Indices: 17745414--17745465 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
17745404 CTCGAAATTA
17745414 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
17745436 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
17745457 AT-AAATATT
1 ATAAAATATT
17745466 TAAAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:17745456 original size:21 final size:22
Alignment explanation
Indices: 17745414--17745465 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
17745404 CTCGAAATTA
17745414 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
17745436 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
17745457 AT-AAATATT
1 ATAAAATATT
17745466 TAAAAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:17745467 original size:14 final size:14
Alignment explanation
Indices: 17745450--17745501 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
17745440 AATATTATTT
17745450 TTTAAATATAAATA
1 TTTAAATATAAATA
*
17745464 TTTAAAAATATAATTA
1 TTT--AAATATAAATA
* *
17745480 TATAAATATATATA
1 TTTAAATATAAATA
*
17745494 ATTAAATA
1 TTTAAATA
17745502 ATTAATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 18 0.60
16 12 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAAATATAAATA
Found at i:17745473 original size:30 final size:30
Alignment explanation
Indices: 17745438--17745509 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
17745428 TTTAAAATAT
* * * *
17745438 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATAATTATATAAATATAAATAATTA
*
17745468 AAAATATAATTATATAAATATATATAATTA
1 AAAATATAATTATATAAATATAAATAATTA
17745498 AATAAT-TAATTA
1 AA-AATATAATTA
17745510 AAAAATAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 33 0.92
31 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATATAATTATATAAATATAAATAATTA
Found at i:17745474 original size:16 final size:16
Alignment explanation
Indices: 17745453--17745491 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17745443 ATTATTTTTT
*
17745453 AAATATAAATATTTAA
1 AAATATAAATATATAA
*
17745469 AAATATAATTATATAA
1 AAATATAAATATATAA
*
17745485 ATATATA
1 AAATATA
17745492 TAATTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATAAATATATAA
Found at i:17750147 original size:19 final size:19
Alignment explanation
Indices: 17750123--17750190 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
17750113 AGTTTATGTC
17750123 AAATAATAATTTTATTAAT
1 AAATAATAATTTTATTAAT
* *
17750142 AAATAATTAAGTTATCTTATAT
1 AAATAA-TAA-TTTTATTA-AT
*
17750164 CAAATAATAATTTTATTAGT
1 -AAATAATAATTTTATTAAT
17750184 AAATAAT
1 AAATAAT
17750191 TAAAATTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
19 13 0.32
20 4 0.10
21 12 0.30
22 5 0.12
23 6 0.15
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
AAATAATAATTTTATTAAT
Found at i:17750179 original size:23 final size:22
Alignment explanation
Indices: 17750115--17750180 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
17750105 ATTAAATTAG
*
17750115 TTTATGTCAAATAATAATTTTA
1 TTTATATCAAATAATAATTTTA
*
17750137 -TTA-AT-AAATAATTAA-GTTA
1 TTTATATCAAATAA-TAATTTTA
17750156 TCTTATATCAAATAATAATTTTA
1 T-TTATATCAAATAATAATTTTA
17750179 TT
1 TT
17750181 AGTAAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
19 9 0.26
20 4 0.11
21 6 0.17
22 6 0.17
23 10 0.29
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (22 bp):
TTTATATCAAATAATAATTTTA
Found at i:17755487 original size:18 final size:18
Alignment explanation
Indices: 17755460--17755494 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17755450 GAATTACTAA
17755460 AGGAAAATGTTAGTCAAT
1 AGGAAAATGTTAGTCAAT
*
17755478 AGGAACATGTTAGTCAA
1 AGGAAAATGTTAGTCAA
17755495 CCATGCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.26
Consensus pattern (18 bp):
AGGAAAATGTTAGTCAAT
Found at i:17757857 original size:11 final size:11
Alignment explanation
Indices: 17757841--17757865 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17757831 TAAAAGTAAC
17757841 TTTTTATTTTA
1 TTTTTATTTTA
17757852 TTTTTATTTTA
1 TTTTTATTTTA
17757863 TTT
1 TTT
17757866 CTTTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:17757971 original size:20 final size:20
Alignment explanation
Indices: 17757934--17757972 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17757924 TAAATAATAA
* *
17757934 ATAATAAAAACTCAAAATTC
1 ATAAAAAAAACACAAAATTC
*
17757954 ATAAAAAAAACACCAAATT
1 ATAAAAAAAACACAAAATT
17757973 ACAAACTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (20 bp):
ATAAAAAAAACACAAAATTC
Found at i:17768352 original size:19 final size:18
Alignment explanation
Indices: 17768319--17768361 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
17768309 TGAACAAGTG
*
17768319 AAAAAACAAAGATGA-AA
1 AAAAAACAAAAATGAGAA
17768336 AATAAAACAAAAAATGAGAA
1 AA-AAAAC-AAAAATGAGAA
17768356 AAAAAA
1 AAAAAA
17768362 AAGGAACGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 5 0.23
19 11 0.50
20 4 0.18
ACGTcount: A:0.79, C:0.05, G:0.09, T:0.07
Consensus pattern (18 bp):
AAAAAACAAAAATGAGAA
Found at i:17770172 original size:16 final size:16
Alignment explanation
Indices: 17770151--17770181 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17770141 TTAGGATTTT
17770151 GATTTTAGAGTTTGGA
1 GATTTTAGAGTTTGGA
*
17770167 GATTTTAGGGTTTGG
1 GATTTTAGAGTTTGG
17770182 GTTTTGTGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (16 bp):
GATTTTAGAGTTTGGA
Found at i:17770236 original size:16 final size:15
Alignment explanation
Indices: 17770212--17770350 Score: 118
Period size: 16 Copynumber: 8.9 Consensus size: 15
17770202 GATTTAAGGG
* *
17770212 TTTGCATTTTAGAAAT
1 TTTGAATTTTAG-GAT
17770228 TTTGAATTTTAGGA-
1 TTTGAATTTTAGGAT
*
17770242 TTTGGATTTTAGGGAT
1 TTTGAATTTTA-GGAT
* *
17770258 TTCGGATTTTAGGGAT
1 TTTGAATTTTA-GGAT
* *
17770274 TTTAGATTTTTAGAGGT
1 TTT-GAATTTTAG-GAT
*
17770291 TTCGAATTTTAGGAT
1 TTTGAATTTTAGGAT
*
17770306 TTTGAATTTAAGGAT
1 TTTGAATTTTAGGAT
17770321 TTTGAATTTTAGGGGAT
1 TTTGAATTTTA--GGAT
*
17770338 TTTGGATTTTAGG
1 TTTGAATTTTAGG
17770351 GGTTTTAGAA
Statistics
Matches: 102, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
14 10 0.10
15 31 0.30
16 37 0.36
17 24 0.24
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (15 bp):
TTTGAATTTTAGGAT
Found at i:17770286 original size:17 final size:15
Alignment explanation
Indices: 17770198--17770356 Score: 112
Period size: 16 Copynumber: 10.3 Consensus size: 15
17770188 TGGTTTGGGG
*
17770198 TTTTGATTTAAGGG-
1 TTTTGATTTTAGGGA
**
17770212 -TTTGCATTTTAGAAA
1 TTTTG-ATTTTAGGGA
17770227 TTTTGAATTTTA-GGA
1 TTTTG-ATTTTAGGGA
*
17770242 TTTGGATTTTAGGGA
1 TTTTGATTTTAGGGA
*
17770257 TTTCGGATTTTAGGGA
1 TTT-TGATTTTAGGGA
17770273 TTTTAGATTTTTAGAGG-
1 TTTT-GA-TTTTAG-GGA
*
17770290 TTTCGAATTTTA-GGA
1 TTTTG-ATTTTAGGGA
* *
17770305 TTTTGAATTTAAGGA
1 TTTTGATTTTAGGGA
17770320 TTTTGAATTTTAGGGGA
1 TTTTG-ATTTTA-GGGA
*
17770337 TTTTGGATTTTAGGGG
1 TTTT-GATTTTAGGGA
17770353 TTTT
1 TTTT
17770357 AGAAACCTAA
Statistics
Matches: 117, Mismatches: 14, Indels: 26
0.75 0.09 0.17
Matches are distributed among these distances:
13 4 0.03
14 19 0.16
15 23 0.20
16 45 0.38
17 23 0.20
18 3 0.03
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.50
Consensus pattern (15 bp):
TTTTGATTTTAGGGA
Found at i:17770299 original size:63 final size:63
Alignment explanation
Indices: 17770217--17770355 Score: 172
Period size: 63 Copynumber: 2.2 Consensus size: 63
17770207 AAGGGTTTGC
** * * * *
17770217 ATTTTAGAAATTTTGAATTTTAGGATTTGGATTTTAGGGATTTCGGATTTTA-GGGATTTTAG
1 ATTTTAGAGGTTTCGAATTTTAGGATTTGGAATTTAAGGATTTCGAATTTTAGGGGATTTTAG
* * *
17770279 ATTTTTAGAGGTTTCGAATTTTAGGATTTTGAATTTAAGGATTTTGAATTTTAGGGGATTTTGG
1 A-TTTTAGAGGTTTCGAATTTTAGGATTTGGAATTTAAGGATTTCGAATTTTAGGGGATTTTAG
*
17770343 ATTTTAGGGGTTT
1 ATTTTAGAGGTTT
17770356 TAGAAACCTA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
62 1 0.02
63 54 0.83
64 10 0.15
ACGTcount: A:0.24, C:0.01, G:0.25, T:0.49
Consensus pattern (63 bp):
ATTTTAGAGGTTTCGAATTTTAGGATTTGGAATTTAAGGATTTCGAATTTTAGGGGATTTTAG
Found at i:17771896 original size:22 final size:21
Alignment explanation
Indices: 17771850--17771897 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
17771840 ATTTGCTTTC
* *
17771850 TTTA-TTTTTAATAATTAATA
1 TTTATTTTTTAAAAAATAATA
*
17771870 ATTATTTTTTAAAAAATATATA
1 TTTATTTTTTAAAAAATA-ATA
17771892 TTTATT
1 TTTATT
17771898 ATTATTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 11 0.50
22 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTATTTTTTAAAAAATAATA
Found at i:17773532 original size:12 final size:12
Alignment explanation
Indices: 17773515--17773539 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17773505 TTCTTTAACC
17773515 CCTTTTTTTTTT
1 CCTTTTTTTTTT
17773527 CCTTTTTTTTTT
1 CCTTTTTTTTTT
17773539 C
1 C
17773540 TTCTCCCAAG
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
CCTTTTTTTTTT
Found at i:17775409 original size:16 final size:15
Alignment explanation
Indices: 17775390--17775442 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
17775380 GATTTTAGAT
17775390 TTTTGAGGGTTTTGGA
1 TTTT-AGGGTTTTGGA
*
17775406 TTTTAGGAGTTTCGGA
1 TTTTAGG-GTTTTGGA
17775422 TTTTATGGGATTTTGGA
1 TTTTA-GGG-TTTTGGA
17775439 TTTT
1 TTTT
17775443 TTGGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 3 0.09
16 17 0.53
17 12 0.38
ACGTcount: A:0.15, C:0.02, G:0.30, T:0.53
Consensus pattern (15 bp):
TTTTAGGGTTTTGGA
Found at i:17775441 original size:17 final size:17
Alignment explanation
Indices: 17775380--17775452 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
17775370 GAATTTTAAA
*
17775380 GATTTTAGATTTT-TGAG
1 GATTTTGGATTTTATG-G
*
17775397 GGTTTTGGATTTTA--G
1 GATTTTGGATTTTATGG
*
17775412 GAGTTTCGGATTTTATGG
1 GA-TTTTGGATTTTATGG
*
17775430 GATTTTGGATTTTTTGG
1 GATTTTGGATTTTATGG
*
17775447 GGTTTT
1 GATTTT
17775453 AAAAACTTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
15 2 0.04
16 11 0.24
17 29 0.64
18 3 0.07
ACGTcount: A:0.15, C:0.01, G:0.30, T:0.53
Consensus pattern (17 bp):
GATTTTGGATTTTATGG
Found at i:17775869 original size:11 final size:11
Alignment explanation
Indices: 17775855--17775890 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
17775845 TTAAAATAAC
17775855 AAAATTAAAAA
1 AAAATTAAAAA
17775866 AAAATT---AA
1 AAAATTAAAAA
17775874 AAAATTAAAAA
1 AAAATTAAAAA
17775885 AAAATT
1 AAAATT
17775891 TTTTACCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.36
11 14 0.64
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAATTAAAAA
Found at i:17775869 original size:19 final size:18
Alignment explanation
Indices: 17775847--17775889 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
17775837 AAATATACTT
17775847 AAAATAACAAAATTAAAAA
1 AAAATAA-AAAATTAAAAA
17775866 AAAATTAAAAAATTAAAAA
1 AAAA-TAAAAAATTAAAAA
17775885 AAAAT
1 AAAAT
17775890 TTTTTACCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.04
19 19 0.83
20 3 0.13
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAATAAAAAATTAAAAA
Found at i:17776966 original size:32 final size:31
Alignment explanation
Indices: 17776916--17776986 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 31
17776906 TGTTTACTTT
*
17776916 TTTTATTTTTTTTTTATTAATAATTATT-TTA
1 TTTTATTTTTTTTTTATTAA-AAATATTATTA
17776947 TTTTATTTTATTTTTTATTAAAAATATTATTA
1 TTTTATTTT-TTTTTTATTAAAAATATTATTA
17776979 TTATTATT
1 TT-TTATT
17776987 AAAATTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 15 0.42
32 16 0.44
33 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (31 bp):
TTTTATTTTTTTTTTATTAAAAATATTATTA
Found at i:17777245 original size:21 final size:21
Alignment explanation
Indices: 17777216--17777278 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
17777206 AGGAATCATG
*
17777216 CCCGGAGGTCTTACAGAATTA
1 CCCGAAGGTCTTACAGAATTA
* *
17777237 CCCGAAGGTCTTAGA-AATCATG
1 CCCGAAGGTCTTACAGAAT--TA
*
17777259 TCCGAAGGTCTTACAGAATT
1 CCCGAAGGTCTTACAGAATT
17777279 GATTGAGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 3 0.09
21 14 0.41
22 14 0.41
23 3 0.09
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (21 bp):
CCCGAAGGTCTTACAGAATTA
Found at i:17777433 original size:43 final size:44
Alignment explanation
Indices: 17777345--17777438 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 44
17777335 ATTGAAATTA
* * * * *
17777345 TGTCCGGAGGTCTTACAGAATCATGCCCGGTGATTTTTCAGAAT
1 TGTCTGGAGGTCTTACAGAATCATGCCCGGAGATCTTACAAAAT
* *
17777389 TGTCTGGAGGTCTTAGA-AATCATGCCCGGAGGTCTTACAAAAT
1 TGTCTGGAGGTCTTACAGAATCATGCCCGGAGATCTTACAAAAT
*
17777432 TGACTGG
1 TGTCTGG
17777439 GATAACACCG
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 27 0.64
44 15 0.36
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (44 bp):
TGTCTGGAGGTCTTACAGAATCATGCCCGGAGATCTTACAAAAT
Found at i:17777523 original size:22 final size:22
Alignment explanation
Indices: 17777493--17777545 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
17777483 CCGTGAATCA
* *
17777493 AAATTATGCTCGGAGGTCTTAG
1 AAATCATGCTCAGAGGTCTTAG
17777515 AAATCATGCTCAGAGGTCTTAG
1 AAATCATGCTCAGAGGTCTTAG
17777537 AAATCATGC
1 AAATCATGC
17777546 CTGAAAGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (22 bp):
AAATCATGCTCAGAGGTCTTAG
Found at i:17777556 original size:154 final size:152
Alignment explanation
Indices: 17777121--17777557 Score: 477
Period size: 154 Copynumber: 2.8 Consensus size: 152
17777111 TTGAAAACAT
* * * * *
17777121 AAAA-TGATTGGGATGACACCGTAACTCGAAAA-ATAATGAATCGATCGAGATAACATCGCGAAT
1 AAAATTGATTGGGATAACACCGTAAGTC-AAAAGATAAAGAATCGATCGAGATAACACCGTGAAT
* * * * * * *
17777184 CAAAATTATGCCCGGAAGTCATAGGAATCATGCCCGGAGGTCTTACAGAATTACCCGAAGGTCTT
65 CAAAATTATGCTCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTAGA-AATTGCCTGAAGGTCTT
*
17777249 AGAAATCATGTCCGAAGGTCTTAC
129 AGAAATCATGCCCGAAGGTCTTAC
* * * * * *
17777273 AGAATTGATTGAGATAAAATCGTAAGTCGAAAGATAAAGAATCGATCGAGATAACACCGTGAATT
1 AAAATTGATTGGGATAACACCGTAAGTCAAAAGATAAAGAATCGATCGAGATAACACCGTGAATC
* * * * * * *
17777338 GAAATTATG-TCCGGAGGTCTTACAGAATCATGCCCGGTGATTTTTCAG-AATTGTCTGGAGGTC
66 AAAATTATGCT-CGGAGGTCTTAGA-AATCATGCCCGGAG-GTCTT-AGAAATTGCCTGAAGGTC
*
17777401 TTAGAAATCATGCCCGGAGGTCTTAC
127 TTAGAAATCATGCCCGAAGGTCTTAC
* * *
17777427 AAAATTGACTGGGATAACACCGCAAGTCAAAAGATAAAGAATCGATTGAGATAACACCGTGAATC
1 AAAATTGATTGGGATAACACCGTAAGTCAAAAGATAAAGAATCGATCGAGATAACACCGTGAATC
* * *
17777492 AAAATTATGCTCGGAGGTCTTAGAAATCATGCTCAGAGGTCTTAGAAATCATGCCTGAAAGTCTT
66 AAAATTATGCTCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTAGAAAT--TGCCTGAAGGTCTT
17777557 A
129 A
17777558 CAGAATTGAC
Statistics
Matches: 229, Mismatches: 46, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
151 2 0.01
152 12 0.05
153 74 0.32
154 136 0.59
155 4 0.02
156 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (152 bp):
AAAATTGATTGGGATAACACCGTAAGTCAAAAGATAAAGAATCGATCGAGATAACACCGTGAATC
AAAATTATGCTCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTAGAAATTGCCTGAAGGTCTTAG
AAATCATGCCCGAAGGTCTTAC
Found at i:17777726 original size:131 final size:129
Alignment explanation
Indices: 17777398--17777780 Score: 464
Period size: 131 Copynumber: 2.9 Consensus size: 129
17777388 TTGTCTGGAG
*
17777398 GTCTTAGAAATCATGCCCGGAGGTCTTACAAAATTGACTGGGATAACACCGCAAGTCAAAAGATA
1 GTCTTAGAAATCAT-CCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTC-AAAGATA
* * * * *
17777463 AAGAATCGATTGAGATAACACCGTGAATCAAAATTATGCTCGGAGGTCTTAGAAATCATGCTCAG
64 AAGAATCGATCGAGATAACACCGCGAATCAAAATTATGCCCGGAGGTCTTACAAAT-ATACTCAG
*
17777528 AG
128 AA
* * * * *
17777530 GTCTTAGAAATCATGCCTGAAAGTCTTACAGAATTGACTGAGATAACACCGCAAGTCAAAAATAA
1 GTCTTAGAAATCAT-CCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTCAAAGATAA
* *
17777595 AGAATCGATCGAGACAATACCGCGAATCAAAATTATGCCCGGAGGTCTTACAGAAT-TACTC-GA
65 AGAATCGATCGAGATAACACCGCGAATCAAAATTATGCCCGGAGGTCTTACA-AATATACTCAG-
17777658 AA
128 AA
* * * *
17777660 GTCTTAGAAATCATATCCGGAGGTCTTATAGAATTGATTGGGATAACACCGTAAGTCGAAAGATA
1 GTCTTAGAAATCAT-CCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTC-AAAGATA
* * * * * *
17777725 AAAAATCGATCGGGATAACACCGCGAATCGAAATTATGCCCGAAAGTCTTATAAAT
64 AAGAATCGATCGAGATAACACCGCGAATCAAAATTATGCCCGGAGGTCTTACAAAT
17777781 CTCAAAATCT
Statistics
Matches: 216, Mismatches: 32, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
129 1 0.00
130 56 0.26
131 104 0.48
132 55 0.25
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (129 bp):
GTCTTAGAAATCATCCCGGAGGTCTTACAGAATTGACTGGGATAACACCGCAAGTCAAAGATAAA
GAATCGATCGAGATAACACCGCGAATCAAAATTATGCCCGGAGGTCTTACAAATATACTCAGAA
Found at i:17777997 original size:40 final size:41
Alignment explanation
Indices: 17777913--17778001 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 41
17777903 AGGTTCCCTC
**
17777913 TAAACAGAAGCTTTGAAATCTTGATTGAAATTGATTCCTAT
1 TAAACAGAAGCTTTGAAATCTTGATTGAAAACGATTCCTAT
* * * *
17777954 TAAACAG-GGCTTTGAAATCTTGATTGAAAACGGTTCTTCT
1 TAAACAGAAGCTTTGAAATCTTGATTGAAAACGATTCCTAT
17777994 TAAACAGA
1 TAAACAGA
17778002 GACTTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 34 0.83
41 7 0.17
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (41 bp):
TAAACAGAAGCTTTGAAATCTTGATTGAAAACGATTCCTAT
Found at i:17778418 original size:28 final size:28
Alignment explanation
Indices: 17778365--17778418 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
17778355 CTTGCCCCAC
*
17778365 TTTTTTTTGAAAAATTTTTGTTTTTATT
1 TTTTTTTTGAAAAATTTTTGTGTTTATT
17778393 TTTTTTTTGAAAAAATTTTT-TGTTTA
1 TTTTTTTTG-AAAAATTTTTGTGTTTA
17778419 AATTTTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (28 bp):
TTTTTTTTGAAAAATTTTTGTGTTTATT
Found at i:17778424 original size:30 final size:28
Alignment explanation
Indices: 17778365--17778424 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
17778355 CTTGCCCCAC
**
17778365 TTTTTTTTGAAAAATTTTTGTTTTTATT
1 TTTTTTTTGAAAAATTTTTGTTTAAATT
17778393 TTTTTTTTGAAAAAATTTTTTGTTTAAATT
1 TTTTTTTTG-AAAAA-TTTTTGTTTAAATT
17778423 TT
1 TT
17778425 CATTGTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 9 0.32
29 5 0.18
30 14 0.50
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (28 bp):
TTTTTTTTGAAAAATTTTTGTTTAAATT
Found at i:17785506 original size:23 final size:23
Alignment explanation
Indices: 17785479--17785526 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 23
17785469 AAGATTTAAC
17785479 ACAATAATCTTTAAAATGAAATA
1 ACAATAATCTTTAAAATGAAATA
17785502 AC---AATCTTTAAAATGAAATA
1 ACAATAATCTTTAAAATGAAATA
17785522 ACAAT
1 ACAAT
17785527 CTTTATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 20 0.91
23 2 0.09
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.29
Consensus pattern (23 bp):
ACAATAATCTTTAAAATGAAATA
Found at i:17785539 original size:24 final size:20
Alignment explanation
Indices: 17785484--17785531 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
17785474 TTAACACAAT
17785484 AATCTTTAAAATGAAATAAC
1 AATCTTTAAAATGAAATAAC
17785504 AATCTTTAAAATGAAATAAC
1 AATCTTTAAAATGAAATAAC
17785524 AATCTTTA
1 AATCTTTA
17785532 TTGAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (20 bp):
AATCTTTAAAATGAAATAAC
Found at i:17785670 original size:14 final size:15
Alignment explanation
Indices: 17785651--17785679 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17785641 GTATTATTCT
17785651 TTTTATTAT-AAATA
1 TTTTATTATCAAATA
17785665 TTTTATTATCAAATA
1 TTTTATTATCAAATA
17785680 GAGAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTATTATCAAATA
Found at i:17786159 original size:14 final size:15
Alignment explanation
Indices: 17786137--17786170 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
17786127 AGTTTAGAGA
*
17786137 TTTTAGGGTTT-GGG
1 TTTTGGGGTTTGGGG
17786151 TTTTGGGGTTTGGGG
1 TTTTGGGGTTTGGGG
17786166 TTTTG
1 TTTTG
17786171 ATTTAAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.03, C:0.00, G:0.44, T:0.53
Consensus pattern (15 bp):
TTTTGGGGTTTGGGG
Found at i:17786205 original size:16 final size:16
Alignment explanation
Indices: 17786180--17786255 Score: 64
Period size: 17 Copynumber: 4.6 Consensus size: 16
17786170 GATTTAAGAG
17786180 TTTGGATTTTAAGGAT
1 TTTGGATTTTAAGGAT
* * *
17786196 TTTAGATTTTTGAGGGT
1 TTTGGA-TTTTAAGGAT
17786213 TTTGGATTTT-AGGAGT
1 TTTGGATTTTAAGGA-T
* * *
17786229 TTCGAATTTTATGAGAT
1 TTTGGATTTTAAG-GAT
17786246 TTTGGATTTT
1 TTTGGATTTT
17786256 TTGGGGTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
15 3 0.07
16 18 0.39
17 23 0.50
18 2 0.04
ACGTcount: A:0.21, C:0.01, G:0.25, T:0.53
Consensus pattern (16 bp):
TTTGGATTTTAAGGAT
Found at i:17786218 original size:33 final size:33
Alignment explanation
Indices: 17786180--17786255 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
17786170 GATTTAAGAG
* *
17786180 TTTGGATTTTAAGGATTTTAG-ATTTT-TGAGGGT
1 TTTGGATTTT-AGGAGTTTAGAATTTTATGA-GAT
*
17786213 TTTGGATTTTAGGAGTTTCGAATTTTATGAGAT
1 TTTGGATTTTAGGAGTTTAGAATTTTATGAGAT
17786246 TTTGGATTTT
1 TTTGGATTTT
17786256 TTGGGGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 8 0.21
33 27 0.71
34 3 0.08
ACGTcount: A:0.21, C:0.01, G:0.25, T:0.53
Consensus pattern (33 bp):
TTTGGATTTTAGGAGTTTAGAATTTTATGAGAT
Found at i:17789401 original size:25 final size:24
Alignment explanation
Indices: 17789358--17789406 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
17789348 TTGTCAAATG
*
17789358 ATTAAAATATAACTTTAAAATAAAA
1 ATTAAAATATAACTGT-AAATAAAA
17789383 ATTAAAATAT-ACATGTAAATAAAA
1 ATTAAAATATAAC-TGTAAATAAAA
17789407 TAAATAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (24 bp):
ATTAAAATATAACTGTAAATAAAA
Found at i:17789419 original size:12 final size:12
Alignment explanation
Indices: 17789404--17789438 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
17789394 CATGTAAATA
*
17789404 AAATAAATAAAC
1 AAATTAATAAAC
*
17789416 AAATTAATAAGC
1 AAATTAATAAAC
17789428 AAATTAATAAA
1 AAATTAATAAA
17789439 TAACAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (12 bp):
AAATTAATAAAC
Found at i:17790395 original size:50 final size:50
Alignment explanation
Indices: 17790335--17790435 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
17790325 ATTGGGTAAA
17790335 ATATTGTTGATTTTAACGTGTACGCTACAAATTCTTTGAAAAAATTAGAG
1 ATATTGTTGATTTTAACGTGTACGCTACAAATTCTTTGAAAAAATTAGAG
17790385 ATATTGTTGATTTTAACGTGTACGCTACAAATTCTTTGAAAAAATTAGAG
1 ATATTGTTGATTTTAACGTGTACGCTACAAATTCTTTGAAAAAATTAGAG
17790435 A
1 A
17790436 AATTTGAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (50 bp):
ATATTGTTGATTTTAACGTGTACGCTACAAATTCTTTGAAAAAATTAGAG
Found at i:17794592 original size:12 final size:12
Alignment explanation
Indices: 17794575--17794599 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17794565 AACCAAATCC
17794575 TTTTTTCTTTTT
1 TTTTTTCTTTTT
17794587 TTTTTTCTTTTT
1 TTTTTTCTTTTT
17794599 T
1 T
17794600 AATTTTTAAT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:17800104 original size:12 final size:12
Alignment explanation
Indices: 17800087--17800113 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17800077 TAATATTTTG
17800087 GAAGGAAACAGT
1 GAAGGAAACAGT
17800099 GAAGGAAACAGT
1 GAAGGAAACAGT
17800111 GAA
1 GAA
17800114 TGTTGAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.33, T:0.07
Consensus pattern (12 bp):
GAAGGAAACAGT
Found at i:17800922 original size:2 final size:2
Alignment explanation
Indices: 17800915--17800941 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17800905 GGAATTCATA
17800915 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
17800942 AACACAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17807108 original size:18 final size:18
Alignment explanation
Indices: 17807085--17807121 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
17807075 ATGCAAACAC
17807085 AGCAATCTAAGAATTTAA
1 AGCAATCTAAGAATTTAA
17807103 AGCAATCTAAGAATTTAA
1 AGCAATCTAAGAATTTAA
17807121 A
1 A
17807122 ACATACTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (18 bp):
AGCAATCTAAGAATTTAA
Found at i:17814296 original size:24 final size:25
Alignment explanation
Indices: 17814269--17814320 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
17814259 AAAATTTCTT
17814269 AAAAATAAAACCAG-AAAAAAAATA
1 AAAAATAAAACCAGCAAAAAAAATA
** *
17814293 AAAAATAAAATGAGCTAAAAAAATA
1 AAAAATAAAACCAGCAAAAAAAATA
17814318 AAA
1 AAA
17814321 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.12
Consensus pattern (25 bp):
AAAAATAAAACCAGCAAAAAAAATA
Found at i:17814331 original size:19 final size:20
Alignment explanation
Indices: 17814309--17814350 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
17814299 AAAATGAGCT
17814309 AAAAAAAT-AAAATAAAAT-
1 AAAAAAATCAAAATAAAATG
17814327 AAAAAAATCAAAATAAAATG
1 AAAAAAATCAAAATAAAATG
17814347 AAAA
1 AAAA
17814351 TGAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.36
19 10 0.45
20 4 0.18
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAAAATCAAAATAAAATG
Found at i:17814358 original size:19 final size:18
Alignment explanation
Indices: 17814283--17814350 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
17814273 ATAAAACCAG
17814283 AAAA-AAAAT-AAAAAAT
1 AAAATAAAATAAAAAAAT
* **
17814299 AAAATGAGCTAAAAAAAT
1 AAAATAAAATAAAAAAAT
17814317 AAAATAAAATAAAAAAAT
1 AAAATAAAATAAAAAAAT
17814335 CAAAATAAAATGAAAA
1 -AAAATAAAAT-AAAA
17814351 TGAAAAAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
16 4 0.10
17 2 0.05
18 22 0.52
19 10 0.24
20 4 0.10
ACGTcount: A:0.78, C:0.03, G:0.04, T:0.15
Consensus pattern (18 bp):
AAAATAAAATAAAAAAAT
Found at i:17815198 original size:22 final size:20
Alignment explanation
Indices: 17815170--17815212 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
17815160 ATTGGAACAA
17815170 AAAAGGAAATAAGAAAATAAAG
1 AAAAGGAAA-AAGAAAA-AAAG
*
17815192 AAAAGGAAAAGGAAAAAAAG
1 AAAAGGAAAAAGAAAAAAAG
17815212 A
1 A
17815213 CGAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 6 0.30
22 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (20 bp):
AAAAGGAAAAAGAAAAAAAG
Found at i:17822172 original size:21 final size:19
Alignment explanation
Indices: 17822136--17822175 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
17822126 ATTGAGTGAT
17822136 TTTTTAAAATTGTTTTAGG
1 TTTTTAAAATTGTTTTAGG
*
17822155 TTTTTAACTATTGATTTTAGG
1 TTTTTAA-AATTG-TTTTAGG
17822176 GTTAATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (19 bp):
TTTTTAAAATTGTTTTAGG
Found at i:17834052 original size:226 final size:225
Alignment explanation
Indices: 17833610--17834052 Score: 652
Period size: 226 Copynumber: 2.0 Consensus size: 225
17833600 CAGAAACATC
* * * * * *
17833610 ATTTCCCCTATCTTTGATCCAAAGTTAGGAGGCTACCAATCAGTTGGGTCATGAGGGAAAATGGA
1 ATTTCCCCTATCTTCGATCCAAACTTAAGAGGCTACCAATCAATTGGCTCATGAGGGAAAATGAA
17833675 CAATAAGTTGGCAGTATCTAAATAGTTTAAAATTACTATTTCATCAAAAAAATCTTAAAATGTCC
66 CAATAAGTTGGCAGTATCTAAATAGTTTAAAATTACTATTTCATCAAAAAAATCTTAAAATGTCC
* * * *
17833740 AATTTTGGCAACCCAGTTGAAGGAATTCATGAATACACCACAAATACGCCTTCTATATTAGCATA
131 AATTTTAGCAACCCAATTGAAGAAATTCATGAATAAACCACAAATACGCCTTCTATATTAGCATA
17833805 AATAGATCAACCACCTTGGCTATATAGATA
196 AATAGATCAACCACCTTGGCTATATAGATA
* * * * * *
17833835 ATTTCCCTTGTCTTCGATCCAAACTTAAGAGGTTATCAATCAATTGGACTCATGAGTGCAAATGA
1 ATTTCCCCTATCTTCGATCCAAACTTAAGAGGCTACCAATCAATTGG-CTCATGAGGGAAAATGA
* * * **
17833900 ACAATAAGTTGTCCGTGTCTAAATAGTTTAAAATTACTATTTCATCAAAAGTATCTTAAAATGTC
65 ACAATAAGTTGGCAGTATCTAAATAGTTTAAAATTACTATTTCATCAAAAAAATCTTAAAATGTC
* ** *
17833965 CAATTTTAGCAACCCAATTGAAGAAATTCATGAATAAACTACTTATATGCCTTCTATATTAGCAT
130 CAATTTTAGCAACCCAATTGAAGAAATTCATGAATAAACCACAAATACGCCTTCTATATTAGCAT
17834030 AAATAGATCAACCACCTTGGCTA
195 AAATAGATCAACCACCTTGGCTA
17834053 CACGTACATT
Statistics
Matches: 192, Mismatches: 25, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
225 39 0.20
226 153 0.80
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (225 bp):
ATTTCCCCTATCTTCGATCCAAACTTAAGAGGCTACCAATCAATTGGCTCATGAGGGAAAATGAA
CAATAAGTTGGCAGTATCTAAATAGTTTAAAATTACTATTTCATCAAAAAAATCTTAAAATGTCC
AATTTTAGCAACCCAATTGAAGAAATTCATGAATAAACCACAAATACGCCTTCTATATTAGCATA
AATAGATCAACCACCTTGGCTATATAGATA
Found at i:17836257 original size:13 final size:13
Alignment explanation
Indices: 17836221--17836261 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
17836211 ATATTAATTA
17836221 TAATAAAATTTATT
1 TAATAAAATTT-TT
*
17836235 TAATATAATTTTT
1 TAATAAAATTTTT
*
17836248 TATTAAAATTTTT
1 TAATAAAATTTTT
17836261 T
1 T
17836262 TCAATTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATAAAATTTTT
Found at i:17843194 original size:1 final size:1
Alignment explanation
Indices: 17843188--17843220 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
17843178 TCTCTCATTT
*
17843188 AAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17843221 CTCTGACTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:17844898 original size:35 final size:32
Alignment explanation
Indices: 17844821--17844935 Score: 101
Period size: 33 Copynumber: 3.5 Consensus size: 32
17844811 AAAATCTTAC
17844821 CAAAAATCATGC-AATATAATAAGTAATCATG
1 CAAAAATCATGCAAATATAATAAGTAATCATG
* *
17844852 CAAGAAATCATGCAAATATAATTATAATTATTCATG
1 CAA-AAATCATGCAAATAT-A--ATAAGTAATCATG
* *
17844888 CAAAAATCATGAAAATATTAGGTAA-TAAATCATG
1 CAAAAATCATGCAAATA-TA-ATAAGT-AATCATG
*
17844922 C-AAATTCATGCAAA
1 CAAAAATCATGCAAA
17844936 ATGTTAAGCA
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
31 3 0.04
32 9 0.13
33 17 0.25
34 11 0.16
35 14 0.20
36 15 0.22
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (32 bp):
CAAAAATCATGCAAATATAATAAGTAATCATG
Found at i:17845069 original size:16 final size:17
Alignment explanation
Indices: 17845057--17845091 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
17845047 TATAAATATT
17845057 TAATCATGCAAATAAATAA
1 TAATCATGCAAAT--ATAA
17845076 TAATCATGCAAATATA
1 TAATCATGCAAATATA
17845092 TTATTATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
19 13 0.81
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATCATGCAAATATAA
Found at i:17845071 original size:20 final size:20
Alignment explanation
Indices: 17845019--17845128 Score: 86
Period size: 20 Copynumber: 5.6 Consensus size: 20
17845009 ATGCAAAATT
*
17845019 ATCATGCAAATAAAAATTTA
1 ATCATGCAAATAAATATTTA
* *
17845039 ATAAAT-CATATAAATATTTA
1 AT-CATGCAAATAAATATTTA
*
17845059 ATCATGCAAATAAATA-ATA
1 ATCATGCAAATAAATATTTA
*
17845078 ATCATGCAAATATAT-TATTA
1 ATCATGCAAATAAATAT-TTA
* * *
17845098 TTCACGC-AATAAA-ATTAA
1 ATCATGCAAATAAATATTTA
17845116 ATTCATGCAAATA
1 A-TCATGCAAATA
17845129 TATAAAAACT
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
18 2 0.03
19 29 0.42
20 36 0.52
21 2 0.03
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.33
Consensus pattern (20 bp):
ATCATGCAAATAAATATTTA
Found at i:17846819 original size:25 final size:26
Alignment explanation
Indices: 17846775--17846839 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 26
17846765 AAGATTCGAA
*
17846775 ACGTGAAAAGAG-TTGAAGGTTCAAG
1 ACGTGAAAAGAGATAGAAGGTTCAAG
**
17846800 ACGTGAAAAGAGATAG-AGGTTTGAG
1 ACGTGAAAAGAGATAGAAGGTTCAAG
* *
17846825 ACATGAAAAAAGATA
1 ACGTGAAAAGAGATA
17846840 AGCTTCGAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 32 0.94
26 2 0.06
ACGTcount: A:0.46, C:0.06, G:0.29, T:0.18
Consensus pattern (26 bp):
ACGTGAAAAGAGATAGAAGGTTCAAG
Found at i:17847069 original size:11 final size:11
Alignment explanation
Indices: 17847055--17847088 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
17847045 GATTTGTTTA
17847055 AGATTTATTAG
1 AGATTTATTAG
* *
17847066 AGATTTGTTTG
1 AGATTTATTAG
17847077 AGATTTATTAG
1 AGATTTATTAG
17847088 A
1 A
17847089 TATTACTTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (11 bp):
AGATTTATTAG
Found at i:17847073 original size:22 final size:22
Alignment explanation
Indices: 17847045--17847088 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
17847035 TCCCATAAGT
17847045 GATTTGTTTAAGATTTATTAGA
1 GATTTGTTTAAGATTTATTAGA
*
17847067 GATTTGTTTGAGATTTATTAGA
1 GATTTGTTTAAGATTTATTAGA
17847089 TATTACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (22 bp):
GATTTGTTTAAGATTTATTAGA
Found at i:17847175 original size:52 final size:51
Alignment explanation
Indices: 17847109--17847212 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 51
17847099 TGGATAAGAA
*
17847109 GACTTACAAAAGAAGAATTTTAAAAG-AAAGAAGATTCTTAATAAGTAAGTTT
1 GACTTACAAAAGAAGAATTCTAAAAGAAAAG-AGATTCTTAAT-AGTAAGTTT
* * *
17847161 GACTTACAAAAGAAGAGTTCTAAAAGAAAAGCGATTCTTAATGGTAAGTTT
1 GACTTACAAAAGAAGAATTCTAAAAGAAAAGAGATTCTTAATAGTAAGTTT
17847212 G
1 G
17847213 TATAGTTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
51 9 0.19
52 34 0.72
53 4 0.09
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (51 bp):
GACTTACAAAAGAAGAATTCTAAAAGAAAAGAGATTCTTAATAGTAAGTTT
Found at i:17848070 original size:203 final size:202
Alignment explanation
Indices: 17847698--17848092 Score: 544
Period size: 203 Copynumber: 2.0 Consensus size: 202
17847688 CTAAAAATTC
* *
17847698 TTGCTTGACTATTTTTGCATATGGTGTAGCTTATACTCTAGCTTTGAAATATTGATGTCTCTATG
1 TTGCTTGACTATTTTTGCATATGGTGTAGCTTATAATCAAGCTTTGAAATATTGATGTCTCTATG
* *
17847763 CTAAATCCCTGCTTCTTACTAATTTACCAAAACCCTCTTTGAAAATCTTTGCTTGATTGTTTCTT
66 CTAAATCCCTGCTTCTTACTAATTTACCAAAACCCTCTTTGAAAATCTTTGCTAGATTGCTTCTT
* * * * *
17847828 GTTTGATGCTTGATTGTTTGTCGTGTCTTTTTACTTTTTTTAGTCCCTTTTGTATTGCTTGAGTT
131 GGTTGATGCTTGATTGCTTGTCGTGTCTTATTACTTTTTTGAGTCCCTTTTATATTGCTTGAGTT
17847893 GCGATTT
196 GCGATTT
* * *
17847900 TTGCTTGACTATTTTTAG-AGATTGGTGTAGCTTGTAATCAAGCTTTGAAGTATTGATGTC-CAT
1 TTGCTTGACTATTTTT-GCATA-TGGTGTAGCTTATAATCAAGCTTTGAAATATTGATGTCTC-T
** * * ** *
17847963 ATGCTAAATTTCTGTTTCTTACTGATTTACTGAAACCC-CATTTGGAAATCTTTGCTAGATTGCT
63 ATGCTAAATCCCTGCTTCTTACTAATTTACCAAAACCCTC-TTTGAAAATCTTTGCTAGATTGCT
* *
17848027 TCTTGGTTGATGCTTGATTGCTTGTCGTGTCTTATTGCTTTTTTGAGTCCTTTTTATATTGCTTG
127 TCTTGGTTGATGCTTGATTGCTTGTCGTGTCTTATTACTTTTTTGAGTCCCTTTTATATTGCTTG
17848092 A
192 A
17848093 TCTTGTTGTT
Statistics
Matches: 168, Mismatches: 21, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
202 20 0.12
203 148 0.88
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (202 bp):
TTGCTTGACTATTTTTGCATATGGTGTAGCTTATAATCAAGCTTTGAAATATTGATGTCTCTATG
CTAAATCCCTGCTTCTTACTAATTTACCAAAACCCTCTTTGAAAATCTTTGCTAGATTGCTTCTT
GGTTGATGCTTGATTGCTTGTCGTGTCTTATTACTTTTTTGAGTCCCTTTTATATTGCTTGAGTT
GCGATTT
Found at i:17849995 original size:18 final size:16
Alignment explanation
Indices: 17849972--17850019 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
17849962 TACGAATATT
17849972 TAAAATATTTAAAAATAA
1 TAAAATA-TTAAAAA-AA
17849990 TAAAATATTAAAAAAA
1 TAAAATATTAAAAAAA
*
17850006 TAAAGATAATAAAA
1 TAAA-ATATTAAAA
17850020 TGATATTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 6 0.21
17 15 0.54
18 7 0.25
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
TAAAATATTAAAAAAA
Found at i:17851410 original size:22 final size:23
Alignment explanation
Indices: 17851382--17851425 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17851372 TATTTTTTTA
17851382 ATATAAATT-ATATTTTGATTAT
1 ATATAAATTAATATTTTGATTAT
*
17851404 ATATAAATTAATATTTTTATTA
1 ATATAAATTAATATTTTGATTA
17851426 AATTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATAAATTAATATTTTGATTAT
Found at i:17851432 original size:22 final size:22
Alignment explanation
Indices: 17851372--17851432 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
17851362 AAGTTGATCT
17851372 TATTTTT-TT-AATATAAATTA
1 TATTTTTATTAAATATAAATTA
* *
17851392 TATTTTGATTATATATAAATTAA
1 TATTTTTATTAAATATAAATT-A
17851415 TATTTTTATTAAAT-TAAA
1 TATTTTTATTAAATATAAA
17851433 ATTTTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 6 0.18
21 2 0.06
22 13 0.38
23 13 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTTTTATTAAATATAAATTA
Found at i:17851441 original size:13 final size:13
Alignment explanation
Indices: 17851421--17851454 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
17851411 TTAATATTTT
17851421 TATTAAATTAAAA
1 TATTAAATTAAAA
*
17851434 TTTTAAATTAAAA
1 TATTAAATTAAAA
17851447 TATTAAAT
1 TATTAAAT
17851455 AATAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATTAAATTAAAA
Found at i:17859070 original size:22 final size:22
Alignment explanation
Indices: 17859039--17859082 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17859029 TGTATATTTA
*
17859039 TATTTATATCTCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
*
17859061 TATTTGTATCCCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
17859083 GACAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTATATCCCTAGAATTAAG
Found at i:17861575 original size:27 final size:27
Alignment explanation
Indices: 17861544--17861596 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
17861534 TAAGATTACG
*
17861544 ATATGA-TAGAATAAAATGATATTATAA
1 ATATGATTA-AATAAAATAATATTATAA
*
17861571 ATATGATTAAATTAAATAATATTATA
1 ATATGATTAAATAAAATAATATTATA
17861597 TTATTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.38
Consensus pattern (27 bp):
ATATGATTAAATAAAATAATATTATAA
Found at i:17865157 original size:22 final size:20
Alignment explanation
Indices: 17865118--17865174 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
17865108 TGAAGATTCA
*
17865118 GATTTT-AGGATTTTGGG-TT
1 GATTTTAAGG-TTTAGGGTTT
17865137 GAGTTTTGAAGGCTTTAGGGTTT
1 GA-TTTT-AAGG-TTTAGGGTTT
17865160 GATTTTAAGGTTTAG
1 GATTTTAAGGTTTAG
17865175 AGGGTCTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 2 0.06
20 9 0.28
21 4 0.12
22 13 0.41
23 4 0.12
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.47
Consensus pattern (20 bp):
GATTTTAAGGTTTAGGGTTT
Found at i:17865244 original size:30 final size:29
Alignment explanation
Indices: 17865210--17865308 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 29
17865200 GTATGGAAGG
17865210 TTTAGGATTTTGGTTTTAGAGTTTGAAGAT
1 TTTAGGATTTTGGTTTTAGAGTTTG-AGAT
* * *
17865240 TTTAGGGTTTTGGTTTTAAAATTTGAGAT
1 TTTAGGATTTTGGTTTTAGAGTTTGAGAT
* * **
17865269 TTTAGGGGTTTTGATTAAAGAGTTTG-GAT
1 TTTA-GGATTTTGGTTTTAGAGTTTGAGAT
17865298 TTTAAGGATTT
1 TTT-AGGATTT
17865309 GAGGTTTTGG
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 19 0.33
30 39 0.67
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.49
Consensus pattern (29 bp):
TTTAGGATTTTGGTTTTAGAGTTTGAGAT
Found at i:17865301 original size:74 final size:73
Alignment explanation
Indices: 17865218--17865356 Score: 160
Period size: 74 Copynumber: 1.9 Consensus size: 73
17865208 GGTTTAGGAT
* * *
17865218 TTTGGTTTT-A-GAGTTTGAAGATTTTAGGGTTTTGGTTTTAAA-ATTTGA-GATTTTAGGGGTT
1 TTTGGTTTTAAGGA-TTTG-AGATTTT-GGGGTTTGGATTTAAAGATTAGAGGATTTTA-GGGTT
17865279 TTGATTAAAGAG
62 TTGATTAAAGAG
* *
17865291 TTTGGATTTTAAGGATTTGAGGTTTTGGGGTTTGGATTTAAAGATTAGAGGGTTTTAGGGTTTTG
1 TTTGG-TTTTAAGGATTTGAGATTTTGGGGTTTGGATTTAAAGATTAGAGGATTTTAGGGTTTTG
17865356 A
65 A
17865357 AATTTAAGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
73 19 0.34
74 24 0.43
75 11 0.20
76 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (73 bp):
TTTGGTTTTAAGGATTTGAGATTTTGGGGTTTGGATTTAAAGATTAGAGGATTTTAGGGTTTTGA
TTAAAGAG
Found at i:17865302 original size:44 final size:44
Alignment explanation
Indices: 17865248--17865334 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 44
17865238 ATTTTAGGGT
*
17865248 TTTGGTTTTAA-AATTTGAGATTTTAGGGGTTTTGA-TTAAAGAG
1 TTTGGTTTTAAGAATTTGAGATTTT-GGGGTTTGGATTTAAAGAG
* *
17865291 TTTGGATTTTAAGGATTTGAGGTTTTGGGGTTTGGATTTAAAGA
1 TTTGG-TTTTAAGAATTTGAGATTTTGGGGTTTGGATTTAAAGA
17865335 TTAGAGGGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 5 0.13
44 15 0.39
45 18 0.47
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (44 bp):
TTTGGTTTTAAGAATTTGAGATTTTGGGGTTTGGATTTAAAGAG
Found at i:17865341 original size:29 final size:31
Alignment explanation
Indices: 17865290--17865353 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
17865280 TGATTAAAGA
* * *
17865290 GTTTGGATTTTAAGGATTTGA-GGTTTTGGG
1 GTTTGGATTTTAAAGATTAGAGGGTTTTAGG
17865320 GTTTGGA-TTTAAAGATTAGAGGGTTTTAGG
1 GTTTGGATTTTAAAGATTAGAGGGTTTTAGG
17865350 GTTT
1 GTTT
17865354 TGAAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.45
Consensus pattern (31 bp):
GTTTGGATTTTAAAGATTAGAGGGTTTTAGG
Found at i:17865628 original size:21 final size:22
Alignment explanation
Indices: 17865604--17865645 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
17865594 TAAGAAAAAT
17865604 GATTATTATTATAATT-TTTTA
1 GATTATTATTATAATTATTTTA
*
17865625 GATTATTATTATTATTATTTT
1 GATTATTATTATAATTATTTT
17865646 TAAGCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
GATTATTATTATAATTATTTTA
Found at i:17865955 original size:25 final size:25
Alignment explanation
Indices: 17865896--17865955 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
17865886 GTTTGGCGCG
* *
17865896 CGGTTTGGTTGAGTCGACTGAAGAG
1 CGGTTTGGTTGAATCGACTGAAGAA
* * *
17865921 CGATTCGGTTGAATCGACTGAGGAA
1 CGGTTTGGTTGAATCGACTGAAGAA
17865946 CGGTTTGGTT
1 CGGTTTGGTT
17865956 TGGTCTAGGG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.20, C:0.13, G:0.37, T:0.30
Consensus pattern (25 bp):
CGGTTTGGTTGAATCGACTGAAGAA
Found at i:17872561 original size:15 final size:16
Alignment explanation
Indices: 17872541--17872578 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
17872531 GGAAATTGAC
*
17872541 ATTTTTTTTCAA-AAA
1 ATTTTTTATCAATAAA
*
17872556 ATTTTTTATCAATGAA
1 ATTTTTTATCAATAAA
17872572 ATTTTTT
1 ATTTTTT
17872579 GTTGGTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTTTTATCAATAAA
Found at i:17876949 original size:28 final size:29
Alignment explanation
Indices: 17876896--17876951 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
17876886 GAATGGAATA
* *
17876896 GAGATTATGGTAGTCTTTAAGATTAGTTC
1 GAGATTAGGGTAATCTTTAAGATTAGTTC
17876925 GAGATTAGGGTAAT-TTTAAGATTAGTT
1 GAGATTAGGGTAATCTTTAAGATTAGTT
17876952 TAGCTCTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.41
Consensus pattern (29 bp):
GAGATTAGGGTAATCTTTAAGATTAGTTC
Found at i:17880200 original size:28 final size:28
Alignment explanation
Indices: 17880158--17880216 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
17880148 GAAAAATATG
*
17880158 TTTGACTATGCTGTATATAACTTTAAAT
1 TTTGACTATGCTGTATATAACATTAAAT
*
17880186 TTTGACTATGGTGTATATAACATTAAAT
1 TTTGACTATGCTGTATATAACATTAAAT
17880214 TTT
1 TTT
17880217 TAATTTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.47
Consensus pattern (28 bp):
TTTGACTATGCTGTATATAACATTAAAT
Found at i:17888866 original size:46 final size:45
Alignment explanation
Indices: 17888790--17888880 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 45
17888780 TCTATCCTTT
*
17888790 ATAATTCAGTAGCCTAACATGACATGCTGATTTATTCCCTGATTA
1 ATAATTCAGTAGCCTAACATGACATACTGATTTATTCCCTGATTA
17888835 ATAAGTTCAGTAGCCTAACATGACATACTGATTTATTCCCTGATTA
1 ATAA-TTCAGTAGCCTAACATGACATACTGATTTATTCCCTGATTA
17888881 GTTCAACCAC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 4 0.09
46 40 0.91
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (45 bp):
ATAATTCAGTAGCCTAACATGACATACTGATTTATTCCCTGATTA
Found at i:17893528 original size:2 final size:2
Alignment explanation
Indices: 17893516--17893554 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
17893506 AGAGCTTAAC
*
17893516 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
17893555 GGCATACATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17893921 original size:3 final size:3
Alignment explanation
Indices: 17893913--17893937 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17893903 ATGCAACCAA
17893913 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
17893938 GTTCTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17894564 original size:26 final size:25
Alignment explanation
Indices: 17894534--17894613 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
17894524 TATATAATTA
17894534 ATAAATTAATTTTTTTATTAAAAAAT
1 ATAAATT-ATTTTTTTATTAAAAAAT
* *
17894560 ATAAATTATTATTTTAGATTAATTAAA-
1 ATAAATTATT-TTTT-TATTAA-AAAAT
* *
17894587 ATAAA-TATATTTTTATTAAAATAT
1 ATAAATTATTTTTTTATTAAAAAAT
17894611 ATA
1 ATA
17894614 TTAATAGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
23 2 0.05
24 8 0.18
25 7 0.16
26 14 0.32
27 10 0.23
28 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (25 bp):
ATAAATTATTTTTTTATTAAAAAAT
Found at i:17911287 original size:227 final size:228
Alignment explanation
Indices: 17910892--17911350 Score: 814
Period size: 227 Copynumber: 2.0 Consensus size: 228
17910882 CAAACAGTAA
*
17910892 AAATCGAGAAAAAGCAAGAAACCATAAGTAAAAATATATAATGTGAGATCGACTTGACTAAAGTG
1 AAATCGAGAAAAAGCAAGAAACCATAAGTAAAAATATATAATGTGAGATCGACTTGACTAAAATG
* * *
17910957 CACTCTTAAGCTGCTTCGAACTTCTAAGATCTAACAAAAAGACATCTTTTGTTCCATTTCTTAAA
66 CACTCTTAAGCTACTTCAAACTTCTAAGATCCAACAAAAAGACATCTTTTGTTCCATTTCTTAAA
* *
17911022 TTTTTAAAGTAATTCTAAAGATGACTGAGCTTTTAAACT-GTGTAAACAATTACATGTCATTTGA
131 ATTTTAAAGTAATTCTAAAGATGACTGAGCTTTTAAACTGGTGTAAACAATTACATATCATTTGA
17911086 ATCAAGCTAATACGCTGGCCAAAATATAGCTTG
196 ATCAAGCTAATACGCTGGCCAAAATATAGCTTG
17911119 AAATCGAGAAAAAGCAAGAAACCATAAGTAAAAATATATAATGTGAGATCGACTTGACTAAAATG
1 AAATCGAGAAAAAGCAAGAAACCATAAGTAAAAATATATAATGTGAGATCGACTTGACTAAAATG
*
17911184 CACTCTTAAGCTACTTCAAAC-TCTTAAGATCCAACAAAAAGACATTTTTTGTTCCATTTCTTAA
66 CACTCTTAAGCTACTTCAAACTTC-TAAGATCCAACAAAAAGACATCTTTTGTTCCATTTCTTAA
*
17911248 AATTTTGAAGTAATTCTAAAGATGACTGAGCTTTTAAACTGGTGTAAACAATTACATATCATTTG
130 AATTTTAAAGTAATTCTAAAGATGACTGAGCTTTTAAACTGGTGTAAACAATTACATATCATTTG
*
17911313 AATCAAGCTAATACGTTGGCCAAAATATAGCTTG
195 AATCAAGCTAATACGCTGGCCAAAATATAGCTTG
17911347 AAAT
1 AAAT
17911351 GAAAAATACA
Statistics
Matches: 221, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
226 2 0.01
227 159 0.72
228 60 0.27
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (228 bp):
AAATCGAGAAAAAGCAAGAAACCATAAGTAAAAATATATAATGTGAGATCGACTTGACTAAAATG
CACTCTTAAGCTACTTCAAACTTCTAAGATCCAACAAAAAGACATCTTTTGTTCCATTTCTTAAA
ATTTTAAAGTAATTCTAAAGATGACTGAGCTTTTAAACTGGTGTAAACAATTACATATCATTTGA
ATCAAGCTAATACGCTGGCCAAAATATAGCTTG
Found at i:17915761 original size:36 final size:36
Alignment explanation
Indices: 17915710--17915802 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 36
17915700 AATTTCATTG
* *
17915710 CCTCTGGTCAGAGGAGCTTTTTTTAAAATGTCATAA
1 CCTCTGGTCAAAGGAGCTTTTTTCAAAATGTCATAA
* * * * * *
17915746 CCTTTGGTTAAAGGAGCCTTTTTCAAAGTTTCATAG
1 CCTCTGGTCAAAGGAGCTTTTTTCAAAATGTCATAA
*
17915782 CCTCTGGTCAAAAGAGCTTTT
1 CCTCTGGTCAAAGGAGCTTTT
17915803 AATTTTAAGA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (36 bp):
CCTCTGGTCAAAGGAGCTTTTTTCAAAATGTCATAA
Found at i:17916143 original size:36 final size:36
Alignment explanation
Indices: 17915912--17916168 Score: 153
Period size: 36 Copynumber: 6.9 Consensus size: 36
17915902 AGTTCCTTTA
* * * *
17915912 CCTTTAGTTAGAGGAGCC-TTTTTAAAATTTCATAA
1 CCTTTGGTTAGATGAGCCTTTTTTAAAGTTTCATAG
* * * *
17915947 CCTCTAGTTAAATGAG-CTTTCTTTAAAGTCTT-ATTG
1 CCTTTGGTTAGATGAGCCTTT-TTTAAAGT-TTCATAG
* * * * * *
17915983 CCTCTAGTTAGATGAACCTTTTTTAAAATATCATAA
1 CCTTTGGTTAGATGAGCCTTTTTTAAAGTTTCATAG
* * * *
17916019 CCTCTT-GTTAGAGGAGCTTTTTTTCTAAAGTCTCATAA
1 CCT-TTGGTTAGATGAGC-CTTTTT-TAAAGTTTCATAG
* *
17916057 TCTTTGGTTAGAAGAGCCTTTTTTCTAAAGTAAACTCTCATAG
1 CCTTTGGTTAGATGAGCC-TTTTT-TAAAGT----T-TCATAG
*
17916100 CCATTGGTTAGATGAGCCTTTTTTAAAGTTTCATAG
1 CCTTTGGTTAGATGAGCCTTTTTTAAAGTTTCATAG
* ** *
17916136 CTTTTGGTTAGAAAAGCCTTCTTTAAAGTTTCA
1 CCTTTGGTTAGATGAGCCTTTTTTAAAGTTTCA
17916169 AAACCTCTTG
Statistics
Matches: 176, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
34 1 0.01
35 16 0.09
36 78 0.44
37 15 0.09
38 35 0.20
41 6 0.03
42 5 0.03
43 20 0.11
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (36 bp):
CCTTTGGTTAGATGAGCCTTTTTTAAAGTTTCATAG
Found at i:17917406 original size:24 final size:24
Alignment explanation
Indices: 17917378--17917433 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
17917368 TCAGTTTTCC
* *
17917378 TTTTTTTTTTTATTTCTTGTT-TTA
1 TTTTTTATTTTATTTATT-TTGTTA
17917402 TTTTTTATTTTATTTATTTTGTTA
1 TTTTTTATTTTATTTATTTTGTTA
17917426 TTTTTTAT
1 TTTTTTAT
17917434 GATATTACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (24 bp):
TTTTTTATTTTATTTATTTTGTTA
Done.