Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 147 of 204
Found at i:44325153 original size:216 final size:217
Alignment explanation
Indices: 44324778--44325189 Score: 630
Period size: 216 Copynumber: 1.9 Consensus size: 217
44324768 CTACTCCTGG
* *
44324778 TGCAACTTCAGGGAGATTAGACTAAATACGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCA
1 TGCAACTTCAGAGAGATAAGACTAAATACGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCA
* * ** *
44324843 ATGTTTTAAACCACTCCACTACAAATTTAGGAAGATAGGATTATCGACTTTAATCTGCTCCACTG
66 AGGTTTTAAACCACTCCACTACAAATTCAACAAGATAGGATTACCGACTTTAATCTGCTCCACTG
*
44324908 CAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGATAAGAC
131 CAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGATAAGAC
44324973 TTGCCCACTTAGTCTGCTCCAC
196 TTGCCCACTTAGTCTGCTCCAC
* * * *
44324995 TGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTA
1 TGCAACTTCAGAGAGATAAGACTAAATACGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCA
* * * * *
44325060 AGGTTTTAATCCGCT-CACTACAACTTCAACAAGATTGGATTACC-AGTTTTAATCTGCTCCACT
66 AGGTTTTAAACCACTCCACTACAAATTCAACAAGATAGGATTACCGA-CTTTAATCTGCTCCACT
* *
44325123 GCAACTTCAGGAAGATAAGATTTGCCATCTTTAGTCTGCCTCACTGCAACTTCAGGAGGATAAGA
130 GCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGATAAGA
44325188 CT
195 CT
44325190 AGATGCGATC
Statistics
Matches: 175, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
215 1 0.01
216 103 0.59
217 71 0.41
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (217 bp):
TGCAACTTCAGAGAGATAAGACTAAATACGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCA
AGGTTTTAAACCACTCCACTACAAATTCAACAAGATAGGATTACCGACTTTAATCTGCTCCACTG
CAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGATAAGAC
TTGCCCACTTAGTCTGCTCCAC
Found at i:44325346 original size:216 final size:214
Alignment explanation
Indices: 44324778--44325358 Score: 496
Period size: 216 Copynumber: 2.7 Consensus size: 214
44324768 CTACTCCTGG
* * * * * ** * * *
44324778 TGCAACTTCAGGGAGATTAGACTAAATACGATCTGCTCTCTACAACTTCAGAGAGATAAGATCCA
1 TGCAACTTCAGAGAGATAAGACTAGATGCAATCCACTCACTGCAACTTCAGAGAGATAAGATCTA
* * * * * ** * * * *
44324843 ATG-TTTTAAACCACTCCACTACAAATTTAGGAAGATAGGATTATCGACTTT-AATCTGCTCCAC
66 A-GACTTTAATCCGCT-CACTACAACTTCAACAAGATAAGATTA-CCAGTTTCAATCTCCTCCAC
*
44324906 TGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGATAAG
128 TGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGATAAG
* *
44324971 ACTTGCCCACTTAGTCTGCTCCAC
193 ACTAG--CACTGAGTCTGCTCCAC
* ** *
44324995 TGCAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTA
1 TGCAACTTCAGAGAGATAAGACTAGATGCAATCCACTCACTGCAACTTCAGAGAGATAAGATCTA
** ** * *
44325060 AGGTTTTAATCCGCTCACTACAACTTCAACAAGATTGGATTACCAGTTTTAATCTGCTCCACTGC
66 AGACTTTAATCCGCTCACTACAACTTCAACAAGATAAGATTACCAGTTTCAATCTCCTCCACTGC
* *
44325125 AACTTCAGGAAGATAAGATTTGCCATCTTTAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACT
131 AACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGATAAGACT
* *
44325190 AG-A-TGCGATCTGCT-CTC
196 AGCACTGAG-TCTGCTCCAC
* ** * *
44325207 TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCACTCACTGCAACTT-AGCGAGATAGGAT
1 TGCAACTTCAGAGAGATAAGA-CT-A-GATGCAATCCACTCACTGCAACTTCAGAGAGATAAGAT
* * * *** * *
44325271 -TATCGACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTTCCA-TCTTCAGTCTACC
63 CTA-AGACTTTAATCCGCT-CACTACAACTTCAACAAGATAAGA-TTACCAGT-TTCAATCT-CC
* *
44325334 T-CACTACAACTTCAGGAGGATAAGA
123 TCCACTGCAACTTCAGGAAGATAAGA
44325359 CTAGATGCGA
Statistics
Matches: 306, Mismatches: 47, Indels: 23
0.81 0.12 0.06
Matches are distributed among these distances:
212 25 0.08
213 11 0.04
214 23 0.08
215 41 0.13
216 134 0.44
217 72 0.24
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (214 bp):
TGCAACTTCAGAGAGATAAGACTAGATGCAATCCACTCACTGCAACTTCAGAGAGATAAGATCTA
AGACTTTAATCCGCTCACTACAACTTCAACAAGATAAGATTACCAGTTTCAATCTCCTCCACTGC
AACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGATAAGACT
AGCACTGAGTCTGCTCCAC
Found at i:44325353 original size:171 final size:171
Alignment explanation
Indices: 44324891--44325532 Score: 859
Period size: 172 Copynumber: 3.7 Consensus size: 171
44324881 GATTATCGAC
* * * * * * * *
44324891 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGC-CTCACTACA
1 TTTAATCCGCT-CACTGCAACTTCAGCGAGATAGGA-TTACGA-CTTTAATCTGCTC-CACTGCA
*
44324955 ACTTCA-GGAGGATAAGACTTGCCCA-CTT-AGTCTG-CTCCACTGCAACTTCA-GAGAGATAAG
62 ACTTCAGGGA-GATAAGATTTG-CCATCTTCAGTCTGCCT-CACTGCAACTTCAGGAG-GATAAG
44325015 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGT
123 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGT
* * * * * *
44325064 TTTAATCCGCTCACTACAACTTCAACAAGATTGGATTACCAGTTTTAATCTGCTCCACTGCAACT
1 TTTAATCCGCTCACTGCAACTTCAGCGAGATAGGATTACGA-CTTTAATCTGCTCCACTGCAACT
* *
44325129 TCAGGAAGATAAGATTTGCCATCTTTAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTAGAT
65 TCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTAGAT
44325194 GCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGT
130 GCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGT
*
44325236 TTTAATCCACTCACTGCAACTT-AGCGAGATAGGATTATCGACTTTAATCTGCTCCACTGCAACT
1 TTTAATCCGCTCACTGCAACTTCAGCGAGATAGGATTA-CGACTTTAATCTGCTCCACTGCAACT
* *
44325300 TCAGGGAGATAAGACTTT-CCATCTTCAGTCTACCTCACTACAACTTCAGGAGGATAAGACTAGA
65 TCAGGGAGATAAGA-TTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTAGA
* * * * *
44325364 TGCGATCTACTTTCTGAAACTTCAGAGAAATAAGATCTAAAGT
129 TGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGT
* * *
44325407 TTTAATCCGCTCACTGCAACTTCAGAGAGATAGGATTACCGGCTTTAATCTGCTCTACTGCAACT
1 TTTAATCCGCTCACTGCAACTTCAGCGAGATAGGATTA-CGACTTTAATCTGCTCCACTGCAACT
*
44325472 TCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTTAGGAGGATAAGACT
65 TCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACT
44325533 TACCTACTTA
Statistics
Matches: 420, Mismatches: 39, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
170 3 0.01
171 190 0.45
172 212 0.50
173 15 0.04
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (171 bp):
TTTAATCCGCTCACTGCAACTTCAGCGAGATAGGATTACGACTTTAATCTGCTCCACTGCAACTT
CAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTAGATG
CGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGT
Found at i:44325572 original size:44 final size:43
Alignment explanation
Indices: 44324896--44325576 Score: 246
Period size: 45 Copynumber: 15.8 Consensus size: 43
44324886 TCGACTTTAA
* *
44324896 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACCA-CTT-AG
* *
44324941 TCTGC-CTCACTACAACTTCA-GGAGGATAAGACTTGCCCACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTT-ACCACTTAG
* * **
44324985 TCTGCTCCACTGCAACTTCAGAGAGATAAGAC-TA-GA-TGCG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACCACTTAG
* * * **** *
44325025 ATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTTACCACTTAG
* * *** ** * *
44325069 TCCGCT-CACTACAACTTCAACAAGATTGGA-TTACCAGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACCA--CTTAG
* * *
44325112 TCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTTAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACCA-C-TTAG
* **
44325157 TCTGC-CTCACTGCAACTTCA-GGAGGATAAGAC-TA-GA-TGCG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTACCACTTAG
* * * **** *
44325197 ATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTTACCACTTAG
** * * * *
44325241 TCCACT-CACTGCAACTT-AGCGAGATAGGA-TTATCGACTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTA-CCAC-TTAG
*
44325283 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTTCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACCA-CTT-AG
* * * **
44325328 TCTAC-CTCACTACAACTTCA-GGAGGATAAGAC-TA-GA-TGCG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTACCACTTAG
* ** * * * * **** *
44325368 ATCTACT-TTCTGAAACTTCAGAGAAATAAGATCTAAAGTTTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTTACCACTTAG
* * * * *
44325412 TCCGCT-CACTGCAACTTCAGAGAGATAGGA-TTACCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACC-AC-TTAG
* * *
44325455 TCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACCA-CTT-AG
*
44325500 TCTGC-CTCACTGCAACTTTA-GGAGGATAAGACTTACCTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTACC-ACTTAG
*
44325544 TTTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT
44325577 CGATCTGTTT
Statistics
Matches: 478, Mismatches: 107, Indels: 103
0.69 0.16 0.15
Matches are distributed among these distances:
40 64 0.13
41 30 0.06
42 21 0.04
43 95 0.20
44 131 0.27
45 133 0.28
46 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTACCACTTAG
Found at i:44333588 original size:24 final size:24
Alignment explanation
Indices: 44333559--44333604 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
44333549 ATCATCTTTT
* *
44333559 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
44333583 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
44333605 GGATTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:44333794 original size:19 final size:20
Alignment explanation
Indices: 44333757--44333794 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
44333747 TATAAGAAAA
*
44333757 CTTTACTATAAATTAAATTC
1 CTTTACTATAAAGTAAATTC
*
44333777 CTTTAC-ATAAAGTGAATT
1 CTTTACTATAAAGTAAATT
44333795 ACAAATAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.42
Consensus pattern (20 bp):
CTTTACTATAAAGTAAATTC
Found at i:44337475 original size:15 final size:15
Alignment explanation
Indices: 44337438--44337479 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
44337428 AACATAAATC
44337438 AACAAACAAATAA-ATA
1 AACAAA-AAA-AATATA
44337454 AACAAAAAAAATATA
1 AACAAAAAAAATATA
*
44337469 AAGAAAAAAAA
1 AACAAAAAAAA
44337480 AGGTGCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 2 0.08
15 16 0.67
16 6 0.25
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.10
Consensus pattern (15 bp):
AACAAAAAAAATATA
Found at i:44337657 original size:16 final size:17
Alignment explanation
Indices: 44337615--44337661 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
44337605 GATAGAAAGT
44337615 ATAACATATATATACGTAC
1 ATAA-ATATATA-ACGTAC
* *
44337634 ATATATATATAAGGTA-
1 ATAAATATATAACGTAC
44337650 ATAAATATATAA
1 ATAAATATATAA
44337662 ATCATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 11 0.44
17 4 0.16
18 7 0.28
19 3 0.12
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (17 bp):
ATAAATATATAACGTAC
Found at i:44342436 original size:39 final size:39
Alignment explanation
Indices: 44342382--44342463 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
44342372 CATAACACCC
44342382 CATACCCAACCTGGTTGCTAGGTCTGAGCTACGGGATAT
1 CATACCCAACCTGGTTGCTAGGTCTGAGCTACGGGATAT
*
44342421 CATACCCAACCTGGTTGCTAGGTTTGAGCTACGGGATAT
1 CATACCCAACCTGGTTGCTAGGTCTGAGCTACGGGATAT
44342460 CATA
1 CATA
44342464 TCCATTACCG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (39 bp):
CATACCCAACCTGGTTGCTAGGTCTGAGCTACGGGATAT
Found at i:44349012 original size:76 final size:75
Alignment explanation
Indices: 44348877--44349297 Score: 405
Period size: 76 Copynumber: 5.5 Consensus size: 75
44348867 CAAGTTTTAC
* * * *
44348877 ACCCAGCGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCATCACTAGTCAGATTAATCGA
1 ACCCAACGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCA-AACTAGTCGGATTAACCGA
44348942 CAAAGATTTGT
65 CAAAGATTTGT
* * * *
44348953 TCCCAACGCTAGTTGGATAAACTGATGATATTAAGTGTGTGCCCAGAACTAGTCGGATTAACCGA
1 ACCCAACGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCA-AACTAGTCGGATTAACCGA
44349018 CAAAGA-TT-T
65 CAAAGATTTGT
* * * * *
44349027 ACGCCAAGTGCTAGTTGGATAAACCGACAATATTAAATGTTTGCCCAGCACTAGTCCGATTAACC
1 AC-CCAA-CGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCA-AACTAGTCGGATTAACC
44349092 GACAAAGATTTGT
63 GACAAAGATTTGT
* ** * * * * * *
44349105 GCCCAGTGCTAGTCGGATAAACCGACGATACTAAATATGTGTCCAACAGTCGTCGGATTAACCGA
1 ACCCAACGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCAA-ACTAGTCGGATTAACCGA
* * *
44349170 AAAATATTTGC
65 CAAAGATTTGT
* ** * ** *
44349181 ACCCAGCATTGGTCAGATAAACCAACGATATTAAATGTGTGCCCAACACTAGTCGGATTAACCGA
1 ACCCAACGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCAA-ACTAGTCGGATTAACCGA
*
44349246 CAAAGATTTAT
65 CAAAGATTTGT
* *** * * *
44349257 GCCCAACGCTAGTCAAATAAACTGACAATATTAAATATGTG
1 ACCCAACGCTAGTTGGATAAACCGACGATATTAAATGTGTG
44349298 TTATGTCCTA
Statistics
Matches: 281, Mismatches: 59, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
74 2 0.01
75 6 0.02
76 266 0.95
77 5 0.02
78 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (75 bp):
ACCCAACGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCAAACTAGTCGGATTAACCGAC
AAAGATTTGT
Found at i:44349041 original size:36 final size:35
Alignment explanation
Indices: 44348992--44349130 Score: 116
Period size: 36 Copynumber: 3.8 Consensus size: 35
44348982 ATTAAGTGTG
** *
44348992 TGCCCAGAACTAGTCGGATTAACCGACAAAGATTT
1 TGCCCAGTGCTAGTCGGATAAACCGACAAAGATTT
* * * *
44349027 ACGCCAAGTGCTAGTTGGATAAACCGACAATATTAAATGTT
1 -TGCCCAGTGCTAGTCGGATAAACCGAC-A-A--AGAT-TT
** * *
44349068 TGCCCAGCACTAGTCCGATTAACCGACAAAGATTT
1 TGCCCAGTGCTAGTCGGATAAACCGACAAAGATTT
44349103 GTGCCCAGTGCTAGTCGGATAAACCGAC
1 -TGCCCAGTGCTAGTCGGATAAACCGAC
44349131 GATACTAAAT
Statistics
Matches: 78, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
35 2 0.03
36 47 0.60
37 1 0.01
38 2 0.03
39 1 0.01
40 23 0.29
41 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (35 bp):
TGCCCAGTGCTAGTCGGATAAACCGACAAAGATTT
Found at i:44349160 original size:152 final size:152
Alignment explanation
Indices: 44348872--44349298 Score: 514
Period size: 152 Copynumber: 2.8 Consensus size: 152
44348862 GTAACCAAGT
* *
44348872 TTTACACCCAGCGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCATCACTAGTCAGATTA
1 TTTACACCAAGCGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCAACACTAGTCAGATTA
* * * * * * *
44348937 ATCGACAAAGATTTGTTCCCAACGCTAGTTGGATAAACTGATGATATTAAGTGTGTGCCCAGAAC
66 ACCGACAAAGATTTGTGCCCAACGCTAGTCGGATAAACTGACGATATTAAATATGTGTCCAGAAC
*
44349002 TAGTCGGATTAACCGACAAAGA
131 TAGTCGGATTAACCGAAAAAGA
* * * * * *
44349024 TTTACGCCAAGTGCTAGTTGGATAAACCGACAATATTAAATGTTTGCCCAGCACTAGTCCGATTA
1 TTTACACCAAGCGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCAACACTAGTCAGATTA
** * *
44349089 ACCGACAAAGATTTGTGCCCAGTGCTAGTCGGATAAACCGACGATACTAAATATGTGTCCA-ACA
66 ACCGACAAAGATTTGTGCCCAACGCTAGTCGGATAAACTGACGATATTAAATATGTGTCCAGA-A
* * *
44349153 GTCGTCGGATTAACCGAAAAATA
130 CTAGTCGGATTAACCGAAAAAGA
* * ** * ** * *
44349176 TTTGCACCCAGCATTGGTCAGATAAACCAACGATATTAAATGTGTGCCCAACACTAGTCGGATTA
1 TTTACACCAAGCGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCAACACTAGTCAGATTA
* ** *
44349241 ACCGACAAAGATTTATGCCCAACGCTAGTCAAATAAACTGACAATATTAAATATGTGT
66 ACCGACAAAGATTTGTGCCCAACGCTAGTCGGATAAACTGACGATATTAAATATGTGT
44349299 TATGTCCTAC
Statistics
Matches: 230, Mismatches: 44, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
151 1 0.00
152 229 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (152 bp):
TTTACACCAAGCGCTAGTTGGATAAACCGACGATATTAAATGTGTGCCCAACACTAGTCAGATTA
ACCGACAAAGATTTGTGCCCAACGCTAGTCGGATAAACTGACGATATTAAATATGTGTCCAGAAC
TAGTCGGATTAACCGAAAAAGA
Found at i:44352571 original size:28 final size:28
Alignment explanation
Indices: 44352539--44352600 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
44352529 ATAAGAAGGA
*
44352539 GACGATGGCTTCTGGTGAGGGAGGTGAT
1 GACGATGGCTTCTGGTGAGGGAAGTGAT
44352567 GACGATGGCTTCTGGTGAGGGAAGTGAT
1 GACGATGGCTTCTGGTGAGGGAAGTGAT
44352595 GACGAT
1 GACGAT
44352601 CTTGAGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.21, C:0.11, G:0.44, T:0.24
Consensus pattern (28 bp):
GACGATGGCTTCTGGTGAGGGAAGTGAT
Found at i:44363676 original size:19 final size:18
Alignment explanation
Indices: 44363652--44363694 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
44363642 TGGGCCTCAT
44363652 TGGGCCAAAATGGGCTGTG
1 TGGGCCAAAATGGGCT-TG
* *
44363671 TGGGCC-CAGTGGGCTTG
1 TGGGCCAAAATGGGCTTG
44363688 TGGGCCA
1 TGGGCCA
44363695 CACAGATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 7 0.33
19 6 0.29
ACGTcount: A:0.14, C:0.21, G:0.44, T:0.21
Consensus pattern (18 bp):
TGGGCCAAAATGGGCTTG
Found at i:44364075 original size:27 final size:27
Alignment explanation
Indices: 44364044--44364377 Score: 222
Period size: 27 Copynumber: 12.4 Consensus size: 27
44364034 CCCAATATTT
44364044 GTAAAATGACCATAATACCCCTATAGG
1 GTAAAATGACCATAATACCCCTATAGG
* *
44364071 GTAAAATGACCGA-AAAACCCAC-ATAGC
1 GTAAAATGACC-ATAATACCC-CTATAGG
* * * *
44364098 GTAAAATGACCGTAATGCCCCTGTAAG
1 GTAAAATGACCATAATACCCCTATAGG
*
44364125 GTAAAAATGA-CAGTAATGCCCCTATAGG
1 GT-AAAATGACCA-TAATACCCCTATAGG
* *
44364153 GTAAAATGACCGA-AA-AGCCCCCATAAG
1 GTAAAATGACC-ATAATA-CCCCTATAGG
* * *
44364180 GTAAAATGACCGTAAT-GCCCTCGTAGG
1 GTAAAATGACCATAATACCCCT-ATAGG
* * * *
44364207 GTAAAATGACCGTAATGCCCCTGTAAG
1 GTAAAATGACCATAATACCCCTATAGG
* * *
44364234 GTAAAATAACCGTAATACCCCTGTAGG
1 GTAAAATGACCATAATACCCCTATAGG
* *
44364261 GTAAAATGATCGA-AA-AACCCTCATAGG
1 GTAAAATGA-CCATAATACCCCT-ATAGG
* * * * *
44364288 GTAAAATGATCGTAATGCCCTTGTAGG
1 GTAAAATGACCATAATACCCCTATAGG
* *
44364315 GTAAAATGA-C-TGAAGTACCCCTGTAAG
1 GTAAAATGACCAT-AA-TACCCCTATAGG
* *
44364342 GTAAAATGACCATAATGCCCCTAAAGG
1 GTAAAATGACCATAATACCCCTATAGG
44364369 GT-AAATGAC
1 GTAAAATGAC
44364378 TATTTTGCCC
Statistics
Matches: 243, Mismatches: 43, Indels: 43
0.74 0.13 0.13
Matches are distributed among these distances:
25 1 0.00
26 19 0.08
27 185 0.76
28 36 0.15
29 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (27 bp):
GTAAAATGACCATAATACCCCTATAGG
Found at i:44364108 original size:54 final size:54
Alignment explanation
Indices: 44364044--44364377 Score: 272
Period size: 54 Copynumber: 6.2 Consensus size: 54
44364034 CCCAATATTT
* * * *
44364044 GTAAAATGACCATAATACCCCTATAGGGTAAAATGACCGAAAAACCCAC-ATAGC
1 GTAAAATGACCATAATACCCCTATAAGGTAAAATGACCGTAATACCC-CTATAGG
* * * * *
44364098 GTAAAATGACCGTAATGCCCCTGTAAGGTAAAAATGACAGTAATGCCCCTATAGG
1 GTAAAATGACCATAATACCCCTATAAGGT-AAAATGACCGTAATACCCCTATAGG
* * *
44364153 GTAAAATGACCGA-AA-AGCCCCCATAAGGTAAAATGACCGTAAT-GCCCTCGTAGG
1 GTAAAATGACC-ATAATA-CCCCTATAAGGTAAAATGACCGTAATACCCCT-ATAGG
* * * * *
44364207 GTAAAATGACCGTAATGCCCCTGTAAGGTAAAATAACCGTAATACCCCTGTAGG
1 GTAAAATGACCATAATACCCCTATAAGGTAAAATGACCGTAATACCCCTATAGG
* * * * * * *
44364261 GTAAAATGATCGA-AA-AACCCTCATAGGGTAAAATGATCGTAATGCCCTTGTAGG
1 GTAAAATGA-CCATAATACCCCT-ATAAGGTAAAATGACCGTAATACCCCTATAGG
* * * *
44364315 GTAAAATGA-C-TGAAGTACCCCTGTAAGGTAAAATGACCATAATGCCCCTAAAGG
1 GTAAAATGACCAT-AA-TACCCCTATAAGGTAAAATGACCGTAATACCCCTATAGG
44364369 GT-AAATGAC
1 GTAAAATGAC
44364378 TATTTTGCCC
Statistics
Matches: 224, Mismatches: 41, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
53 16 0.07
54 157 0.70
55 51 0.23
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (54 bp):
GTAAAATGACCATAATACCCCTATAAGGTAAAATGACCGTAATACCCCTATAGG
Found at i:44364264 original size:81 final size:80
Alignment explanation
Indices: 44364044--44364361 Score: 336
Period size: 81 Copynumber: 3.9 Consensus size: 80
44364034 CCCAATATTT
* *
44364044 GTAAAATGACCATAATACCCCTATAGGGTAAAATGACCGAAAAACCCAC-AT-AGCGTAAAATGA
1 GTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCG-AAAACCC-CTATAAG-GTAAAATGA
*
44364107 CCGTAATGCCC-CTGTAAG
63 CCGTAATGCCCTC-GTAGG
* *
44364125 GTAAAAATGACAGTAATGCCCCTATAGGGTAAAATGACCGAAAAGCCCCCATAAGGTAAAATGAC
1 GT-AAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGAAAA-CCCCTATAAGGTAAAATGAC
44364190 CGTAATGCCCTCGTAGG
64 CGTAATGCCCTCGTAGG
* * * * * * *
44364207 GTAAAATGACCGTAATGCCCCTGTAAGGTAAAATAACCGTAATACCCCTGTAGGGTAAAATGATC
1 GTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCG-AAAACCCCTATAAGGTAAAATGACC
* ** *
44364272 GAAAAACCCTCATAGG
65 GTAATGCCCTCGTAGG
* * * * * *
44364288 GTAAAATGATCGTAATGCCCTTGTAGGGTAAAATGACTGAAGTACCCCTGTAAGGTAAAATGACC
1 GTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGAA-AACCCCTATAAGGTAAAATGACC
*
44364353 ATAATGCCC
65 GTAATGCCC
44364362 CTAAAGGGTA
Statistics
Matches: 202, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
80 2 0.01
81 129 0.64
82 68 0.34
83 3 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.20
Consensus pattern (80 bp):
GTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGAAAACCCCTATAAGGTAAAATGACCG
TAATGCCCTCGTAGG
Found at i:44364425 original size:24 final size:24
Alignment explanation
Indices: 44364394--44364457 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
44364384 GCCCCTCGAG
* *
44364394 TGTAAATGATTTATTTTTCCGTGA
1 TGTAAATGACTGATTTTTCCGTGA
**
44364418 TGTAAATGACTGATTTTTTTGTGA
1 TGTAAATGACTGATTTTTCCGTGA
*
44364442 TTTAAATGACTGATTT
1 TGTAAATGACTGATTT
44364458 GTTTGTGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (24 bp):
TGTAAATGACTGATTTTTCCGTGA
Found at i:44364431 original size:28 final size:25
Alignment explanation
Indices: 44364400--44364466 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 25
44364390 CGAGTGTAAA
44364400 TGATTTATTTTTCCGTGATGTAAATGAC
1 TGATTT-TTTTT--GTGATGTAAATGAC
*
44364428 TGA-TTTTTTTGTGATTTAAATGAC
1 TGATTTTTTTTGTGATGTAAATGAC
*
44364452 TGA-TTTGTTTGTGAT
1 TGATTTTTTTTGTGAT
44364467 TGGTATGACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 27 0.73
26 5 0.14
27 2 0.05
28 3 0.08
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.52
Consensus pattern (25 bp):
TGATTTTTTTTGTGATGTAAATGAC
Found at i:44364462 original size:24 final size:24
Alignment explanation
Indices: 44364414--44364504 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 24
44364404 TTATTTTTCC
* *
44364414 GTGATGTAAATGACTGATTTTTTT
1 GTGATTTAAATGACTGATTTGTTT
44364438 GTGATTTAAATGACTGATTTGTTT
1 GTGATTTAAATGACTGATTTGTTT
*** *
44364462 GTGATTGGTATGACTGATTTGTCT
1 GTGATTTAAATGACTGATTTGTTT
* **
44364486 ATGATTTGTATGACTGATT
1 GTGATTTAAATGACTGATT
44364505 CTGAGTATGG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.48
Consensus pattern (24 bp):
GTGATTTAAATGACTGATTTGTTT
Found at i:44364686 original size:32 final size:32
Alignment explanation
Indices: 44364645--44364737 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 32
44364635 GCTACAATGC
*
44364645 TACTGATGGCTTTGTGCCAATCATATTACCAT
1 TACTGATGGCTTTGTGTCAATCATATTACCAT
* * * *
44364677 TACTGATGGCTGTGTGTCGATCATATCACTAT
1 TACTGATGGCTTTGTGTCAATCATATTACCAT
*
44364709 TGCTGATGGCTTTGTGTCAATCATATTAC
1 TACTGATGGCTTTGTGTCAATCATATTAC
44364738 TGTACTTATG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (32 bp):
TACTGATGGCTTTGTGTCAATCATATTACCAT
Found at i:44364768 original size:22 final size:20
Alignment explanation
Indices: 44364743--44364812 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 20
44364733 ATTACTGTAC
44364743 TTATGGCTTGTAGTCATTCTGT
1 TTATGGCTT-TAG-CATTCTGT
* *
44364765 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTT-TAGC-ATTCTGT
* *
44364787 TTACGGCTCTTAGCCATTCTGG
1 TTATGGCT-TTAG-CATTCTGT
44364809 TTAT
1 TTAT
44364813 TGGCAGCTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
21 1 0.03
22 34 0.92
23 2 0.05
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.46
Consensus pattern (20 bp):
TTATGGCTTTAGCATTCTGT
Found at i:44366760 original size:2 final size:2
Alignment explanation
Indices: 44366753--44366816 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
44366743 GATGCACCTT
44366753 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
44366795 TA AA TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
44366817 GTATGTGTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44368258 original size:10 final size:11
Alignment explanation
Indices: 44368232--44368257 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44368222 AAAAATTTAA
44368232 AAAAATATTTT
1 AAAAATATTTT
44368243 AAAAATATTTT
1 AAAAATATTTT
44368254 AAAA
1 AAAA
44368258 TTAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:44368289 original size:38 final size:40
Alignment explanation
Indices: 44368208--44368282 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
44368198 ACTAAAAATT
44368208 TATTTTAAAAATAAAAAAATTTAAAAAAATATTTTAAAAA
1 TATTTTAAAAATAAAAAAATTTAAAAAAATATTTTAAAAA
*
44368248 TATTTT-AAAATTAAAAAA-TTAAAAAAATATATTTA
1 TATTTTAAAAATAAAAAAATTTAAAAAAATAT-TTTA
44368283 TTATATTCGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
38 12 0.36
39 15 0.45
40 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (40 bp):
TATTTTAAAAATAAAAAAATTTAAAAAAATATTTTAAAAA
Found at i:44368620 original size:28 final size:29
Alignment explanation
Indices: 44368563--44368629 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
44368553 TTTTTTATTG
44368563 AAATAATAT-GAAAAACAATTAATTACCT
1 AAATAATATAGAAAAACAATTAATTACCT
* *
44368591 AAATAATATAGAATGAA-AATTATTTA-CT
1 AAATAATATAGAA-AAACAATTAATTACCT
44368619 AAAGTAATATA
1 AAA-TAATATA
44368630 TTTACATAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 14 0.41
29 18 0.53
30 2 0.06
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATAATATAGAAAAACAATTAATTACCT
Found at i:44368832 original size:21 final size:21
Alignment explanation
Indices: 44368803--44368866 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
44368793 TCAAGCCCAG
*
44368803 AAAGTATTTGAAGAACTAAGGC
1 AAAG-ATTTGAAGAACAAAGGC
* *
44368825 AAAGATTTGAAGAACAAAAGT
1 AAAGATTTGAAGAACAAAGGC
44368846 AAAGATTTGAAGAACAAAGGC
1 AAAGATTTGAAGAACAAAGGC
44368867 TAAGTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 33 0.89
22 4 0.11
ACGTcount: A:0.52, C:0.08, G:0.22, T:0.19
Consensus pattern (21 bp):
AAAGATTTGAAGAACAAAGGC
Found at i:44371919 original size:2 final size:2
Alignment explanation
Indices: 44371912--44371950 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
44371902 AGTAAAGTTA
44371912 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
44371951 ATGATGAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44372243 original size:20 final size:21
Alignment explanation
Indices: 44372213--44372262 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
44372203 TAAAAATTAA
* *
44372213 AAAAAATATGTATATAGATAT
1 AAAATATATGTATACAGATAT
*
44372234 -AAATATATGTATACAGTTAT
1 AAAATATATGTATACAGATAT
44372254 AAAATATAT
1 AAAATATAT
44372263 AAAATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (21 bp):
AAAATATATGTATACAGATAT
Found at i:44372624 original size:3 final size:3
Alignment explanation
Indices: 44372618--44372673 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
44372608 GATGATGATG
44372618 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44372666 ATA ATA AT
1 ATA ATA AT
44372674 CATCATCATC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:44372678 original size:3 final size:3
Alignment explanation
Indices: 44372672--44372711 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
44372662 AATAATAATA
44372672 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
44372712 ATAACATAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:44374284 original size:44 final size:44
Alignment explanation
Indices: 44374216--44374371 Score: 142
Period size: 44 Copynumber: 3.6 Consensus size: 44
44374206 TGGTTTTAGT
* *
44374216 CTGCTCCACTGCAACGTCA-AGGAGATAAGACTTATATTTTCAAC
1 CTGCTCCACTGCAACTTCAGA-GAGATAAGACTTGTATTTTCAAC
* * * * * *
44374260 CTGCTCCACTGCAACTTCAGGGAGATAAG-GTTGGA--TGCGAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTATTTTCAAC
* * * * *
44374301 CTGCTCTACTGCAACTGCAGAGAGATAAGATTTGTGTTTTTAATC
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTATTTTCAA-C
44374346 C-GCTCCACTGCAACTTCAGAGAGATA
1 CTGCTCCACTGCAACTTCAGAGAGATA
44374372 TGATTAGTTT
Statistics
Matches: 87, Mismatches: 20, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
41 29 0.33
42 3 0.03
43 3 0.03
44 51 0.59
45 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTATTTTCAAC
Found at i:44374326 original size:85 final size:85
Alignment explanation
Indices: 44374215--44374371 Score: 212
Period size: 85 Copynumber: 1.8 Consensus size: 85
44374205 GTGGTTTTAG
44374215 TCTGCTCCACTGCAACGTCAAGGAGATAAGACTTATATTTTCAA-CCTGCTCCACTGCAACTTCA
1 TCTGCTCCACTGCAACGTCAAGGAGATAAGACTTATATTTTCAATCC-GCTCCACTGCAACTTCA
*
44374279 GGGAGATAAGGTTGGATGCGA
65 GAGAGATAAGGTTGGATGCGA
* * * * *
44374300 TCTGCTCTACTGCAAC-TGC-AGAGAGATAAGATTTGTGTTTTTAATCCGCTCCACTGCAACTTC
1 TCTGCTCCACTGCAACGT-CAAG-GAGATAAGACTTATATTTTCAATCCGCTCCACTGCAACTTC
44374363 AGAGAGATA
64 AGAGAGATA
44374372 TGATTAGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
84 3 0.05
85 58 0.92
86 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (85 bp):
TCTGCTCCACTGCAACGTCAAGGAGATAAGACTTATATTTTCAATCCGCTCCACTGCAACTTCAG
AGAGATAAGGTTGGATGCGA
Found at i:44374950 original size:24 final size:24
Alignment explanation
Indices: 44374889--44374953 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
44374879 TTGCCCCCCA
* *
44374889 CTGTAATCTTCAAAGTTCAATCCG
1 CTGTACTCTTCAAGGTTCAATCCG
44374913 CTGTACTCTTCAAGGTTCAATCCG
1 CTGTACTCTTCAAGGTTCAATCCG
44374937 CTGTACTCTTCAAGGTT
1 CTGTACTCTTCAAGGTT
44374954 TAGTCCACTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.35
Consensus pattern (24 bp):
CTGTACTCTTCAAGGTTCAATCCG
Found at i:44374964 original size:24 final size:24
Alignment explanation
Indices: 44374886--44374965 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
44374876 AGATTGCCCC
* *
44374886 CCACTGTAATCTTCAAAGTTCAAT
1 CCACTGTACTCTTCAAGGTTCAAT
*
44374910 CCGCTGTACTCTTCAAGGTTCAAT
1 CCACTGTACTCTTCAAGGTTCAAT
* * *
44374934 CCGCTGTACTCTTCAAGGTTTAGT
1 CCACTGTACTCTTCAAGGTTCAAT
44374958 CCACTGTA
1 CCACTGTA
44374966 ATAAAATTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.34
Consensus pattern (24 bp):
CCACTGTACTCTTCAAGGTTCAAT
Found at i:44375821 original size:5 final size:5
Alignment explanation
Indices: 44375802--44375856 Score: 53
Period size: 5 Copynumber: 11.4 Consensus size: 5
44375792 GGCCTCTCCT
* * *
44375802 TTTTC TTTT- TCTTC TTTTC TTTT- ATTTC TTTTC TTTT- TTTCTT TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT-TC TTTTC
44375850 TTTTC TT
1 TTTTC TT
44375857 CTTTATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
4 9 0.22
5 29 0.71
6 3 0.07
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:44375821 original size:8 final size:8
Alignment explanation
Indices: 44375808--44375860 Score: 55
Period size: 7 Copynumber: 7.4 Consensus size: 8
44375798 TCCTTTTTCT
44375808 TTTTCTTC
1 TTTTCTTC
44375816 TTTTCTT-
1 TTTTCTTC
*
44375823 TTAT-TTC
1 TTTTCTTC
44375830 TTTTC-T-
1 TTTTCTTC
44375836 TTTT-TTC
1 TTTTCTTC
44375843 TTTT-TTC
1 TTTTCTTC
44375850 TTTTCTTC
1 TTTTCTTC
44375858 TTT
1 TTT
44375861 ATTTTTTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 7 0.18
7 18 0.47
8 13 0.34
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTCTTC
Found at i:44375823 original size:20 final size:20
Alignment explanation
Indices: 44375801--44375860 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 20
44375791 TGGCCTCTCC
44375801 TTTTTCTTTTTCTTCTTTTCTT
1 TTTTTC-TTTTCTTCTTTTC-T
*
44375823 TTATTTCTTTTCTTTTTTTCT
1 TT-TTTCTTTTCTTCTTTTCT
44375844 TTTTTCTTTTCTTCTTT
1 TTTTTCTTTTCTTCTTT
44375861 ATTTTTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.40
21 3 0.09
22 14 0.40
23 4 0.11
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTCTTCTTTTCT
Found at i:44375867 original size:14 final size:13
Alignment explanation
Indices: 44375802--44375856 Score: 76
Period size: 14 Copynumber: 4.2 Consensus size: 13
44375792 GGCCTCTCCT
44375802 TTTTCTTTTTCTTC
1 TTTTCTTTTT-TTC
44375816 TTTTCTTTTATTTC
1 TTTTCTTTT-TTTC
44375830 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
*
44375843 TTTT-TTCTTTTC
1 TTTTCTTTTTTTC
44375855 TT
1 TT
44375857 CTTTATTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
12 9 0.23
13 8 0.21
14 21 0.54
15 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:44380786 original size:20 final size:19
Alignment explanation
Indices: 44380758--44380806 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
44380748 AAAAATTAAA
*
44380758 AAAATATGTATATAGATAT
1 AAAATATGTATACAGATAT
*
44380777 AAATATATGTATACAGTTAT
1 AAA-ATATGTATACAGATAT
44380797 AAAATATGTA
1 AAAATATGTA
44380807 AAATATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (19 bp):
AAAATATGTATACAGATAT
Found at i:44381217 original size:3 final size:3
Alignment explanation
Indices: 44381211--44381272 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
44381201 AAATATGATG
* *
44381211 ATA ATA ACA ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44381259 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
44381273 CATCATCATC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:44390933 original size:3 final size:3
Alignment explanation
Indices: 44390920--44390960 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
44390910 TTTTATAGTC
44390920 TCT TC- TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
44390961 GTTATTAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:44391055 original size:21 final size:21
Alignment explanation
Indices: 44391029--44391070 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
44391019 ATCCAACATG
*
44391029 GCTAGTTAATTGGCCACGTCA
1 GCTAGTTAACTGGCCACGTCA
44391050 GCTAGTTAACTGGCCACGTCA
1 GCTAGTTAACTGGCCACGTCA
44391071 CCTGTCCCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (21 bp):
GCTAGTTAACTGGCCACGTCA
Found at i:44392283 original size:30 final size:31
Alignment explanation
Indices: 44392244--44392303 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
44392234 GGAGGTGGGA
*
44392244 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
44392275 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
44392304 TAAAATGTTT
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:44392473 original size:21 final size:21
Alignment explanation
Indices: 44392439--44392479 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44392429 GGGGGAAAGT
*
44392439 GGGAAAGAGTAAAAGTTTTGA
1 GGGAAAGAGTAAAAGGTTTGA
44392460 GGGAAA-AGTAAAAAGGTTTG
1 GGGAAAGAGT-AAAAGGTTTG
44392480 GGAATTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAAGAGTAAAAGGTTTGA
Found at i:44392474 original size:29 final size:30
Alignment explanation
Indices: 44392415--44392474 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
44392405 GAGGGGAGGG
* * **
44392415 GAGTAAAAGTTTTGGGGGGAAAGTGGGAAA
1 GAGTAAAAGTTTTGAGGGAAAAGTGAAAAA
44392445 GAGTAAAAGTTTTGAGGGAAAAGT-AAAAA
1 GAGTAAAAGTTTTGAGGGAAAAGTGAAAAA
44392474 G
1 G
44392475 GTTTGGGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (30 bp):
GAGTAAAAGTTTTGAGGGAAAAGTGAAAAA
Found at i:44392901 original size:3 final size:3
Alignment explanation
Indices: 44392893--44392952 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
44392883 CTCACAAAAT
44392893 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44392941 TTA TTA TTA TTA
1 TTA TTA TTA TTA
44392953 ACTTTTTATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:44394711 original size:5 final size:5
Alignment explanation
Indices: 44394701--44394726 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44394691 GAAATAAATA
44394701 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
44394727 CAAAATTTAA
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:44394871 original size:20 final size:19
Alignment explanation
Indices: 44394846--44394885 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
44394836 GATTAAAATT
*
44394846 AAAAATAAATATTTTTTTAA
1 AAAAATAAAT-TTTTATTAA
*
44394866 AAAAATTAATTTTTATTAA
1 AAAAATAAATTTTTATTAA
44394885 A
1 A
44394886 TGGAAGCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAATAAATTTTTATTAA
Found at i:44421898 original size:50 final size:50
Alignment explanation
Indices: 44421813--44421945 Score: 187
Period size: 50 Copynumber: 2.7 Consensus size: 50
44421803 AAAGAGTAAA
* * *
44421813 CTCAGTTCGGTAGCCTTTCAGA-CTATTTTGACTGATGTGTTCAACTCTG
1 CTCAGTTCAGCAGCCTTTCAGATCTATTTTGACTGATGTGCTCAACTCTG
* **
44421862 TTCAGTTCAGCAGCCTTTTGGATCTATTTTGACTGATGTGCTCAACTCTG
1 CTCAGTTCAGCAGCCTTTCAGATCTATTTTGACTGATGTGCTCAACTCTG
* *
44421912 CTCAGTTCAGCAGTCTTTCAGATCTATTCTGACT
1 CTCAGTTCAGCAGCCTTTCAGATCTATTTTGACT
44421946 AGAGCGCTCC
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 17 0.24
50 55 0.76
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (50 bp):
CTCAGTTCAGCAGCCTTTCAGATCTATTTTGACTGATGTGCTCAACTCTG
Found at i:44422150 original size:21 final size:23
Alignment explanation
Indices: 44422103--44422151 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
44422093 GAGAAAACTA
*
44422103 AAGTGAGTGAGAGAGGAATGTTG
1 AAGTGAGTGAGAGAGGAATGTAG
*
44422126 -AGTGA-TGAGAGATGAATG-AG
1 AAGTGAGTGAGAGAGGAATGTAG
44422146 AAGTGA
1 AAGTGA
44422152 AAGATGGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (23 bp):
AAGTGAGTGAGAGAGGAATGTAG
Found at i:44422703 original size:21 final size:20
Alignment explanation
Indices: 44422648--44422703 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
44422638 ATATATACAT
*
44422648 TAATA-AATTAA-CATGAAT
1 TAATATAATTAAGCATGAAA
* *
44422666 TAATATAAAATATGCATGAAAA
1 TAATAT-AATTAAGCATG-AAA
44422688 TAATATAATTAAGCAT
1 TAATATAATTAAGCAT
44422704 AATTTCACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.17
20 4 0.14
21 12 0.41
22 8 0.28
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAATATAATTAAGCATGAAA
Found at i:44428552 original size:3 final size:3
Alignment explanation
Indices: 44428546--44428573 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
44428536 TTTCTTCTAC
44428546 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
44428574 GACCCACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:44432409 original size:17 final size:18
Alignment explanation
Indices: 44432378--44432412 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44432368 GATTGATGAC
*
44432378 CAAATTTAACTAAAAAAT
1 CAAATTTAACAAAAAAAT
44432396 CAAA-TTAACAAAAAAAT
1 CAAATTTAACAAAAAAAT
44432413 ATTAACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (18 bp):
CAAATTTAACAAAAAAAT
Found at i:44434515 original size:3 final size:3
Alignment explanation
Indices: 44434507--44434535 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
44434497 CCTAAAATTA
44434507 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
44434536 AGGGTGTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:44447045 original size:23 final size:23
Alignment explanation
Indices: 44446981--44447091 Score: 111
Period size: 23 Copynumber: 5.0 Consensus size: 23
44446971 TACCAGATAC
44446981 GCCACAAAGGTTA-ACAGAATGT
1 GCCACAAAGGTTATACAGAATGT
* * * * *
44447003 -CAAGAAA-GCTACACAAAATGT
1 GCCACAAAGGTTATACAGAATGT
*
44447024 GCCACAAAGGCTATACAGAATGT
1 GCCACAAAGGTTATACAGAATGT
* * *
44447047 GCCATAAAGGTTATACAGAGTGC
1 GCCACAAAGGTTATACAGAATGT
*
44447070 GCCACAAAAGTTATACAGAATG
1 GCCACAAAGGTTATACAGAATG
44447092 CTACAAAAGC
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
20 3 0.04
21 13 0.18
22 5 0.07
23 50 0.70
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (23 bp):
GCCACAAAGGTTATACAGAATGT
Found at i:44448394 original size:21 final size:19
Alignment explanation
Indices: 44448366--44448408 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
44448356 GAATAGGAGG
*
44448366 TCTTCTAACCTTATCTTCAC
1 TCTTCTAAACTTATCTTC-C
*
44448386 TCTTACTAAAGTTATCTTCC
1 TCTT-CTAAACTTATCTTCC
44448406 TCT
1 TCT
44448409 CCTCCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.21, C:0.30, G:0.02, T:0.47
Consensus pattern (19 bp):
TCTTCTAAACTTATCTTCC
Found at i:44457612 original size:25 final size:25
Alignment explanation
Indices: 44457584--44457690 Score: 110
Period size: 25 Copynumber: 4.4 Consensus size: 25
44457574 CACATAAATG
44457584 GGAAGCTCTTCCGAGCCATATAACA
1 GGAAGCTCTTCCGAGCCATATAACA
*
44457609 GGAAGCTCTTCCGAGCCATATAACG
1 GGAAGCTCTTCCGAGCCATATAACA
* ** * *
44457634 GGAAGCTCATGAGAGCCATA-ATCT
1 GGAAGCTCTTCCGAGCCATATAACA
* * **
44457658 GGAAGCTCATACGAGCCA-ATATTA
1 GGAAGCTCTTCCGAGCCATATAACA
44457682 GGAAGCTCT
1 GGAAGCTCT
44457691 GGAGAGCCAT
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
23 1 0.01
24 28 0.40
25 41 0.59
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (25 bp):
GGAAGCTCTTCCGAGCCATATAACA
Found at i:44457711 original size:49 final size:50
Alignment explanation
Indices: 44457608--44457724 Score: 136
Period size: 49 Copynumber: 2.4 Consensus size: 50
44457598 GCCATATAAC
* *
44457608 AGGAAGCTCTTCCGAGCC-ATATAACGGGAAGCTCATGAGAGCCATAATCT
1 AGGAAGCTCATACGAGCCAATATAAC-GGAAGCTCATGAGAGCCATAATCT
*
44457658 -GGAAGCTCATACGAGCCAATATTA-GGAAGCTC-TGGAGAGCCATAAAT-T
1 AGGAAGCTCATACGAGCCAATATAACGGAAGCTCAT-GAGAGCCAT-AATCT
*
44457706 AGGAAGCTCATAAGAGCCA
1 AGGAAGCTCATACGAGCCA
44457725 TAAACGAGAC
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
47 1 0.02
48 18 0.31
49 35 0.59
50 5 0.08
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (50 bp):
AGGAAGCTCATACGAGCCAATATAACGGAAGCTCATGAGAGCCATAATCT
Found at i:44457712 original size:25 final size:25
Alignment explanation
Indices: 44457634--44457728 Score: 110
Period size: 24 Copynumber: 3.9 Consensus size: 25
44457624 CCATATAACG
44457634 GGAAGCTCATGAGAGCCAT-AATCT-
1 GGAAGCTCATGAGAGCCATAAAT-TA
*
44457658 GGAAGCTCAT-ACGAGCCA-ATATTA
1 GGAAGCTCATGA-GAGCCATAAATTA
44457682 GGAAGCTC-TGGAGAGCCATAAATTA
1 GGAAGCTCAT-GAGAGCCATAAATTA
*
44457707 GGAAGCTCATAAGAGCCATAAA
1 GGAAGCTCATGAGAGCCATAAA
44457729 CGAGACTTAA
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
23 3 0.05
24 32 0.52
25 25 0.41
26 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (25 bp):
GGAAGCTCATGAGAGCCATAAATTA
Found at i:44459068 original size:20 final size:20
Alignment explanation
Indices: 44459043--44459086 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
44459033 ATCTTGTTTT
*
44459043 ATTTGATTCCAATCAATTTG
1 ATTTGATTCCAATCAAATTG
**
44459063 ATTTGATTTTAATCAAATTG
1 ATTTGATTCCAATCAAATTG
44459083 ATTT
1 ATTT
44459087 AATGGATCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
ATTTGATTCCAATCAAATTG
Found at i:44463516 original size:20 final size:20
Alignment explanation
Indices: 44463491--44463534 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
44463481 ATCTTGTTTT
*
44463491 ATTTGATTCTAATCCAATTG
1 ATTTGATTCTAATCAAATTG
*
44463511 ATTTGATTTTAATCAAATTG
1 ATTTGATTCTAATCAAATTG
44463531 ATTT
1 ATTT
44463535 AATGGCAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
ATTTGATTCTAATCAAATTG
Found at i:44463990 original size:20 final size:21
Alignment explanation
Indices: 44463944--44463990 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
44463934 TTATTCAATT
44463944 TATA-TTTTATTTCATATAAA
1 TATATTTTTATTTCATATAAA
**
44463964 TAT-TTTTTATTT-ATATTTA
1 TATATTTTTATTTCATATAAA
44463983 TATATTTT
1 TATATTTT
44463991 GTCCGCTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TATATTTTTATTTCATATAAA
Found at i:44471199 original size:34 final size:35
Alignment explanation
Indices: 44471155--44471221 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
44471145 CAGTAAAATG
*
44471155 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
44471189 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
44471222 CTGCTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:44472915 original size:24 final size:24
Alignment explanation
Indices: 44472865--44472916 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
44472855 TTTCTAGAAA
* *
44472865 ATTTAGCATTTATTAGTATCATAT
1 ATTTAGCATTTATTAGCATAATAT
*
44472889 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
44472913 ATTT
1 ATTT
44472917 GACTTACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:44481723 original size:20 final size:20
Alignment explanation
Indices: 44481698--44481737 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44481688 CAAATTATGC
44481698 AAAAATAAAATATAAAATAT
1 AAAAATAAAATATAAAATAT
* *
44481718 AAAAATTAAATATCAAATAT
1 AAAAATAAAATATAAAATAT
44481738 GAGTATAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATAAAATATAAAATAT
Found at i:44489542 original size:24 final size:25
Alignment explanation
Indices: 44489478--44489529 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
44489468 GCTATTAATG
*
44489478 GGAAGCTCATGAGAGCCATATATCA
1 GGAAACTCATGAGAGCCATATATCA
*
44489503 GGAAACTCAAGAGAGCCA-ATATCA
1 GGAAACTCATGAGAGCCATATATCA
44489527 GGA
1 GGA
44489530 TGCTTATGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.15
Consensus pattern (25 bp):
GGAAACTCATGAGAGCCATATATCA
Found at i:44495675 original size:12 final size:12
Alignment explanation
Indices: 44495658--44495691 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
44495648 TTCGTCACAC
44495658 GGCCGTGTGGTA
1 GGCCGTGTGGTA
*
44495670 GGCCGTATGGTA
1 GGCCGTGTGGTA
*
44495682 GACCGTGTGG
1 GGCCGTGTGG
44495692 CTGGTCGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.18, G:0.47, T:0.24
Consensus pattern (12 bp):
GGCCGTGTGGTA
Found at i:44499129 original size:118 final size:117
Alignment explanation
Indices: 44498908--44499134 Score: 287
Period size: 118 Copynumber: 1.9 Consensus size: 117
44498898 AGTGTTATTG
* * *
44498908 AAGCGGTGTTTGGGCAGTGGATGGTGGTGAGAAGAAATCCTGGTGTCGATAAAGAGAATCAAAGG
1 AAGCGGCGTTTGGGCAGTGGATGGTGGTGAGAAGAAATCCTGGTGTCGATAAAGAAAATCAAAAG
** * * *
44498973 CTATGGAATAGATGAAAATAGAAAAAAAATTTTAAGGTTCAAGGTGCAGCTA
66 CTAAAGAACAAACGAAAATAGAAAAAAAATTTTAAGGTTCAAGGTGCAGCTA
* *
44499025 AAGCGGCGTTTGGGCAGTGGATGGTGGTG-GAAAGGAAAT-CTCGGTGTGGATAAGGAAAATCAA
1 AAGCGGCGTTTGGGCAGTGGATGGTGGTGAG-AA-GAAATCCT-GGTGTCGATAAAGAAAATCAA
* * * *
44499088 AAGCTAAAGAACAAACGAAAATAGAGAAAGAGTTTTGAGGTTCAAGG
63 AAGCTAAAGAACAAACGAAAATAGAAAAAAAATTTTAAGGTTCAAGG
44499135 ATTTCGGCAT
Statistics
Matches: 93, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
116 1 0.01
117 32 0.34
118 60 0.65
ACGTcount: A:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (117 bp):
AAGCGGCGTTTGGGCAGTGGATGGTGGTGAGAAGAAATCCTGGTGTCGATAAAGAAAATCAAAAG
CTAAAGAACAAACGAAAATAGAAAAAAAATTTTAAGGTTCAAGGTGCAGCTA
Found at i:44506388 original size:17 final size:16
Alignment explanation
Indices: 44506367--44506397 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
44506357 AAAATAGGTT
44506367 TTTTTTTTTGGAAATA
1 TTTTTTTTTGGAAATA
44506383 TTTTTTTTTGGAAAT
1 TTTTTTTTTGGAAAT
44506398 TTTCAAAATT
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:0.23, C:0.00, G:0.13, T:0.65
Consensus pattern (16 bp):
TTTTTTTTTGGAAATA
Found at i:44511731 original size:15 final size:16
Alignment explanation
Indices: 44511711--44511740 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44511701 TGGTGCCTTA
44511711 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
44511726 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
44511741 AGTATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:44512660 original size:67 final size:67
Alignment explanation
Indices: 44512588--44512723 Score: 218
Period size: 67 Copynumber: 2.0 Consensus size: 67
44512578 CACGGCCATG
** * *
44512588 TGTCCCTTGTAAATTTTTATAGGTTACATTTCGAGTGTTACACGGCCTGGCACATGGGCATGTGG
1 TGTCCCTTGTAAATTTTTATAGGTTACATTTCGAAAGTTACACAGCCTGGCACACGGGCATGTGG
44512653 CT
66 CT
* *
44512655 TGTCCCTTGTAAGTTTTTATAGGTTACATTTCGAAAGTTACACAGCCTGGCACACGGGCGTGTGG
1 TGTCCCTTGTAAATTTTTATAGGTTACATTTCGAAAGTTACACAGCCTGGCACACGGGCATGTGG
44512720 CT
66 CT
44512722 TG
1 TG
44512724 CTGTGTGAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (67 bp):
TGTCCCTTGTAAATTTTTATAGGTTACATTTCGAAAGTTACACAGCCTGGCACACGGGCATGTGG
CT
Found at i:44520340 original size:19 final size:19
Alignment explanation
Indices: 44520287--44520358 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
44520277 TTTTTTTCAT
* *
44520287 TTTATTTAATATTTTTATAAT
1 TTTA-TTAAT-TTTTTAAAAA
* *
44520308 TTTAATAATGTTTTAAAAA
1 TTTATTAATTTTTTAAAAA
44520327 TTTATTAATTTTTTTCAAAAA
1 TTTATTAA-TTTTTT-AAAAA
*
44520348 ATTA-TAATTTT
1 TTTATTAATTTT
44520359 AAATAAATCT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 18 0.43
20 12 0.29
21 12 0.29
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (19 bp):
TTTATTAATTTTTTAAAAA
Found at i:44520341 original size:20 final size:20
Alignment explanation
Indices: 44520287--44520358 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
44520277 TTTTTTTCAT
* * *
44520287 TTTATTTAATATTTTTATAAT
1 TTTA-TTAATTTTTTTAAAAA
* *
44520308 TTTAATAA-TGTTTTAAAAA
1 TTTATTAATTTTTTTAAAAA
44520327 TTTATTAATTTTTTTCAAAAA
1 TTTATTAATTTTTTT-AAAAA
*
44520348 ATTA-TAATTTT
1 TTTATTAATTTT
44520359 AAATAAATCT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 14 0.34
20 15 0.37
21 12 0.29
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
TTTATTAATTTTTTTAAAAA
Found at i:44524230 original size:25 final size:26
Alignment explanation
Indices: 44524202--44524293 Score: 73
Period size: 25 Copynumber: 3.5 Consensus size: 26
44524192 ATATTATACA
*
44524202 AAAAAATTAAAAATTA-AAAAATTAT
1 AAAAAATTAAAAATTACAAAAATCAT
44524227 AAAAAGA-TAGAAAATTACAAAAATCAT
1 AAAAA-ATTA-AAAATTACAAAAATCAT
* * * *
44524254 -ATAAATGAAAATTTATAAAAATCATT
1 AAAAAATTAAAAATTACAAAAATCA-T
* *
44524280 TAAAAAGTAAAAAT
1 AAAAAATTAAAAAT
44524294 AAAAATAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
25 22 0.42
26 13 0.25
27 17 0.33
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.26
Consensus pattern (26 bp):
AAAAAATTAAAAATTACAAAAATCAT
Found at i:44524327 original size:22 final size:22
Alignment explanation
Indices: 44524300--44524347 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
44524290 AAATAAAAAT
*
44524300 AAAAATTAT-ATAATTATGAAGA
1 AAAAATTATAAAAATTATGAA-A
*
44524322 AAAAATTGTAAAAATTATGAAA
1 AAAAATTATAAAAATTATGAAA
44524344 AAAA
1 AAAA
44524348 TTAAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (22 bp):
AAAAATTATAAAAATTATGAAA
Found at i:44524790 original size:51 final size:49
Alignment explanation
Indices: 44524694--44524790 Score: 115
Period size: 51 Copynumber: 1.9 Consensus size: 49
44524684 AAAATTGTAG
* *
44524694 ATAATTTTTATAATTTTATAATTTTCTATTTTTTTAAATAATTTTGAATA
1 ATAATTTTAATAATTTTATAATTTTCTAATTTTTT-AATAATTTTGAATA
* *
44524744 ATAATTTGTAATAATTTTGTAATTTTTTACATTTTTT-ATAACTTTTG
1 ATAATTT-TAATAATTTTATAATTTTCTA-ATTTTTTAATAA-TTTTG
44524791 CACTTTCCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
50 11 0.28
51 23 0.57
52 6 0.15
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (49 bp):
ATAATTTTAATAATTTTATAATTTTCTAATTTTTTAATAATTTTGAATA
Found at i:44526921 original size:23 final size:23
Alignment explanation
Indices: 44526890--44526949 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
44526880 TTAGGTCGTG
*
44526890 TAGA-CCCATTTTGGTCTAATTG
1 TAGAGCCCATTTTGGTCTAATTA
* *
44526912 TAGTGCCCATTTTGGTCTGATTA
1 TAGAGCCCATTTTGGTCTAATTA
44526935 TAGAGCCCATTTTGG
1 TAGAGCCCATTTTGG
44526950 GCCGGGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 3 0.09
23 30 0.91
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (23 bp):
TAGAGCCCATTTTGGTCTAATTA
Found at i:44529441 original size:243 final size:244
Alignment explanation
Indices: 44529011--44529486 Score: 801
Period size: 243 Copynumber: 2.0 Consensus size: 244
44529001 AAGCTACACG
* * *
44529011 ATGCTGGTCACACGAGCTATGGAGAATCCTCAACAAATGTAGGACCTCAGCCATCGGTAGGAAAT
1 ATGCTGGTCACACGAGCTATGGAGAATCCTCAAAAAATGTAGGACCTCAGCCATCAGTAGCAAAT
** * *
44529076 TCAAGACCAGCACTTGGAACATGAAATCCCTAATGACATGTCATTTGTATCTTAAGAATTCTTAA
66 TCAAGACCAGCACCCGAAACATGAAATCCCTAATGACATGTCATTTGTATCCTAAGAATTCTTAA
* *
44529141 GGTTCAACCGGGACTTGATATCTGTCAATTCATCACAATGTGGATACATTTTCATATATA-TGAT
131 GGTTCAACCGGGACTTGATATCCGTCAATTCATCACAATGTGGATACATTCTCATATATATTGAT
44529205 TCATTTACATTAAAAACAACATAGTAAACATTTAATTTGGTAAGTTCGT
196 TCATTTACATTAAAAACAACATAGTAAACATTTAATTTGGTAAGTTCGT
* * *
44529254 ATGCTGGTCATACGAGCTGTGGAGAATCCTCAAAAAATGTAGGACCTCAGCCATCAGTAGCACAT
1 ATGCTGGTCACACGAGCTATGGAGAATCCTCAAAAAATGTAGGACCTCAGCCATCAGTAGCAAAT
*
44529319 TCAAGACCAGCACCCGAAACATGAAATCCTTAATGACATGTCATTTGTATCCTAAGAATTCTTAA
66 TCAAGACCAGCACCCGAAACATGAAATCCCTAATGACATGTCATTTGTATCCTAAGAATTCTTAA
* *
44529384 GGTTCAACCGGGACTTGATATCCGTCGATTCGTCACAATGTGGATACATTCTCATATATATTGAT
131 GGTTCAACCGGGACTTGATATCCGTCAATTCATCACAATGTGGATACATTCTCATATATATTGAT
*
44529449 TCATTTACATTAAAAACAACGTAGTAAACATTTAATTT
196 TCATTTACATTAAAAACAACATAGTAAACATTTAATTT
44529487 AAATAATATT
Statistics
Matches: 216, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
243 175 0.81
244 41 0.19
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (244 bp):
ATGCTGGTCACACGAGCTATGGAGAATCCTCAAAAAATGTAGGACCTCAGCCATCAGTAGCAAAT
TCAAGACCAGCACCCGAAACATGAAATCCCTAATGACATGTCATTTGTATCCTAAGAATTCTTAA
GGTTCAACCGGGACTTGATATCCGTCAATTCATCACAATGTGGATACATTCTCATATATATTGAT
TCATTTACATTAAAAACAACATAGTAAACATTTAATTTGGTAAGTTCGT
Found at i:44531593 original size:16 final size:16
Alignment explanation
Indices: 44531572--44531608 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
44531562 TTGGTTCGCT
44531572 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
44531588 GTAATGGATTAGAGGC
1 GTAATGGAATAGAGGC
44531604 GTAAT
1 GTAAT
44531609 ATCAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.24
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:44531639 original size:45 final size:44
Alignment explanation
Indices: 44531588--44531685 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
44531578 GAATAGAGGC
*
44531588 GTAATGGATTAGAGGCGTAATA-TCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGT--ATTC-ATGTGTTTGGTTGAAT
*
44531633 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGTATTCATGTGTTTGGTTGAAT
*
44531677 GGAATGGAA
1 GTAATGGAA
44531686 GTGTAATAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
43 1 0.02
44 25 0.52
45 21 0.44
46 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.36
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGTATTCATGTGTTTGGTTGAAT
Found at i:44531922 original size:61 final size:59
Alignment explanation
Indices: 44531856--44532176 Score: 231
Period size: 61 Copynumber: 5.3 Consensus size: 59
44531846 TTTTAATTAA
44531856 AATATATAATTTGATAAAATTCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTT-ATAAAA-TCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
* * * * * * * * ** * *
44531917 AATATATGATACTATAAAAT-ATAAT-TTGAAATAATTATTAT-TAAATATATTTTAATTAA
1 AATATATAAT-TTATAAAATCTTAGTATT-AAAT-ATTCTTATATGAATTTACTAAAATCAT
44531976 AATATATAATTTAATAAAATTCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTT-ATAAAA-TCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
* * * * ** * * * ** * *
44532037 AATATATGATACTATAAAAT-ATAAT-TTGAAATAATAATTAT-TAAATATATTTTAATTAA
1 AATATATAAT-TTATAAAATCTTAGTATT-AAAT-ATTCTTATATGAATTTACTAAAATCAT
* *
44532096 AATTTATAATTTAATGAAACTCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTT-AT-AAAATCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
*
44532157 AATATATAATACTATAAAAT
1 AATATATAAT-TTATAAAAT
44532177 ATAATTTAAA
Statistics
Matches: 188, Mismatches: 55, Indels: 35
0.68 0.20 0.13
Matches are distributed among these distances:
58 6 0.03
59 61 0.32
60 37 0.20
61 77 0.41
62 7 0.04
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (59 bp):
AATATATAATTTATAAAATCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:44531982 original size:18 final size:17
Alignment explanation
Indices: 44531961--44531995 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
44531951 TTATTATTAA
*
44531961 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
44531979 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
44531996 TCTTAGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:44532040 original size:120 final size:120
Alignment explanation
Indices: 44531827--44532264 Score: 759
Period size: 120 Copynumber: 3.6 Consensus size: 120
44531817 ATATTTTAAC
*
44531827 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTGATAAAATTCTTAGTATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
44531892 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
44531947 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
44532012 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * * *
44532067 ATAATAATTATTAAATATATTTTAATTAAAATTTATAATTTAATGAAACTCTTAGTATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
* *
44532132 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAA
66 TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
* * ** *
44532187 ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAACATCAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
*
44532252 TCTTATATAAATT
66 TCTTATATGAATT
44532265 CTTAACATTA
Statistics
Matches: 301, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 301 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (120 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
TCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAA
Found at i:44532319 original size:42 final size:42
Alignment explanation
Indices: 44532260--44532339 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
44532250 ATTCTTATAT
44532260 AAATTCTTAACATTAAATATAATTGTGTTATAAAAAAATTTA
1 AAATTCTTAACATTAAATATAATTGTGTTATAAAAAAATTTA
44532302 AAATTCTTAACATTAAATATAATTGTGTTATAAAAAAA
1 AAATTCTTAACATTAAATATAATTGTGTTATAAAAAAA
44532340 AACAAGGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (42 bp):
AAATTCTTAACATTAAATATAATTGTGTTATAAAAAAATTTA
Found at i:44537026 original size:29 final size:28
Alignment explanation
Indices: 44536993--44537079 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 28
44536983 GGAGGGGAGG
* **
44536993 GGAGTAAAAGTTTAGGGGGAAAGTGGGAA
1 GGAGTAAAAGTTTTGGGGGAAAGT-AAAA
*
44537022 GGAGTAAAAGTTTTGAGGGAAAAGTAAAA
1 GGAGTAAAAGTTTTG-GGGGAAAGTAAAA
*
44537051 GGAGTAAAAGTTTTGAGGGAAAAGTAAAA
1 GGAGTAAAAGTTTTG-GGGGAAAGTAAAA
44537080 AGATTTGGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 45 0.85
30 8 0.15
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.20
Consensus pattern (28 bp):
GGAGTAAAAGTTTTGGGGGAAAGTAAAA
Found at i:44537093 original size:30 final size:29
Alignment explanation
Indices: 44537023--44537082 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
44537013 AAGTGGGAAG
*
44537023 GAGTAAAAGTTTTGAGGGAAAAGTAAAAG
1 GAGTAAAAGTTTTGAGGGAAAAGTAAAAA
44537052 GAGTAAAAGTTTTGAGGGAAAAGTAAAAA
1 GAGTAAAAGTTTTGAGGGAAAAGTAAAAA
44537081 GA
1 GA
44537083 TTTGGGAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (29 bp):
GAGTAAAAGTTTTGAGGGAAAAGTAAAAA
Found at i:44537138 original size:9 final size:9
Alignment explanation
Indices: 44537124--44537160 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44537114 TATAGTTTGA
44537124 TATTCGAAT
1 TATTCGAAT
44537133 TATTCGAAT
1 TATTCGAAT
*
44537142 TATTCGAGT
1 TATTCGAAT
44537151 TATTCGAAT
1 TATTCGAAT
44537160 T
1 T
44537161 TGAAAACTCA
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:44538858 original size:2 final size:2
Alignment explanation
Indices: 44538851--44538876 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44538841 TGGTGGTTCG
44538851 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
44538877 TTTATAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44545249 original size:52 final size:49
Alignment explanation
Indices: 44545143--44545321 Score: 168
Period size: 52 Copynumber: 3.7 Consensus size: 49
44545133 AAACGAAACA
* * * * * *
44545143 AAATAATATATAGAACAATTTGAAGTAAATAGTATAAAACAATTTAAAGT
1 AAATAATATATAAAACAAATTAAAATAAATAATATAAAA-AATTTAAAAT
* *
44545193 AAATAATGTGTAAAACAAATTAAAATAAATAATATACAAAGAAATTTAAAAT
1 AAATAATATATAAAACAAATTAAAATAAATAATAT--AAA-AAATTTAAAAT
* * * *
44545245 AAATAACATATAAGACAATTTAAAAT-AAT-ATATAAAAAGTTTAAAAT
1 AAATAATATATAAAACAAATTAAAATAAATAATATAAAAAATTTAAAAT
* *
44545292 AAATGATATACAAAAC-AATTAAAA-AAATAA
1 AAATAATATATAAAACAAATTAAAATAAATAA
44545322 ATGATATATA
Statistics
Matches: 105, Mismatches: 19, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
46 10 0.10
47 23 0.22
48 3 0.03
50 32 0.30
51 3 0.03
52 33 0.31
53 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (49 bp):
AAATAATATATAAAACAAATTAAAATAAATAATATAAAAAATTTAAAAT
Found at i:44545287 original size:21 final size:22
Alignment explanation
Indices: 44545245--44545293 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
44545235 AATTTAAAAT
44545245 AAATAACATATAAGACAATTTA
1 AAATAACATATAAGACAATTTA
*
44545267 AAATAATATATAA-A-AAGTTTA
1 AAATAACATATAAGACAA-TTTA
44545288 AAATAA
1 AAATAA
44545294 ATGATATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 11 0.44
22 12 0.48
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (22 bp):
AAATAACATATAAGACAATTTA
Found at i:44545310 original size:47 final size:47
Alignment explanation
Indices: 44545219--44545320 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 47
44545209 AAATTAAAAT
* *
44545219 AAATAATATACAAAGAAATTTAAAATAAATAACATATAAGACAATTTA
1 AAATAATATACAAAGAAATTTAAAATAAATAACATACAAAACAA-TTA
* * * *
44545267 AAATAATATATAAA-AAGTTTAAAATAAATGATATACAAAACAATTA
1 AAATAATATACAAAGAAATTTAAAATAAATAACATACAAAACAATTA
*
44545313 AAAAAATA
1 AAATAATA
44545321 AATGATATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 10 0.21
47 24 0.51
48 13 0.28
ACGTcount: A:0.65, C:0.05, G:0.04, T:0.26
Consensus pattern (47 bp):
AAATAATATACAAAGAAATTTAAAATAAATAACATACAAAACAATTA
Found at i:44545316 original size:26 final size:26
Alignment explanation
Indices: 44545143--44545321 Score: 144
Period size: 26 Copynumber: 7.2 Consensus size: 26
44545133 AAACGAAACA
* * * *
44545143 AAATAATATATAGAACAATTTGAAGT
1 AAATAATATACAAAACAATTTAAAAT
* *
44545169 AAATAGTAT--AAAACAATTTAAAGT
1 AAATAATATACAAAACAATTTAAAAT
* ** *
44545193 AAATAATGTGTAAAACAAATTAAAAT
1 AAATAATATACAAAACAATTTAAAAT
44545219 AAATAATATACAAAGA-AATTTAAAAT
1 AAATAATATACAAA-ACAATTTAAAAT
* * *
44545245 AAATAACATATAAGACAATTTAAAAT
1 AAATAATATACAAAACAATTTAAAAT
*
44545271 -AAT-ATAT--AAAA-AGTTTAAAAT
1 AAATAATATACAAAACAATTTAAAAT
*
44545292 AAATGATATACAAAACAA-TTAAAA-
1 AAATAATATACAAAACAATTTAAAAT
44545316 AAATAA
1 AAATAA
44545322 ATGATATATA
Statistics
Matches: 125, Mismatches: 19, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.07
22 6 0.05
23 4 0.03
24 28 0.22
25 14 0.11
26 63 0.50
27 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (26 bp):
AAATAATATACAAAACAATTTAAAAT
Found at i:44545483 original size:29 final size:30
Alignment explanation
Indices: 44545450--44545518 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
44545440 GGAAAACTTA
*
44545450 AAATAAATAATAAAACA-ATTTAAAATAAAT
1 AAATAAATAAGAAAA-ATATTTAAAATAAAT
* * *
44545480 -AATATATGAGAAAAATGTTTAAAATAAAT
1 AAATAAATAAGAAAAATATTTAAAATAAAT
44545509 AAATAAATAA
1 AAATAAATAA
44545519 CAAATTTGCG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
28 1 0.03
29 23 0.74
30 7 0.23
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (30 bp):
AAATAAATAAGAAAAATATTTAAAATAAAT
Found at i:44548592 original size:31 final size:30
Alignment explanation
Indices: 44548557--44548619 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 30
44548547 AAAAGAAAAG
44548557 TTTAA-ATTCTTAAAATAAAATTTTGATCTTT
1 TTTAACATT-TTAAAATAAAATTTTGAT-TTT
* *
44548588 TTTAACTATTTTGAAATAAAGTTTTGATTTT
1 TTTAAC-ATTTTAAAATAAAATTTTGATTTT
44548619 T
1 T
44548620 AAGAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 9 0.32
32 16 0.57
33 3 0.11
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTAACATTTTAAAATAAAATTTTGATTTT
Found at i:44548709 original size:154 final size:153
Alignment explanation
Indices: 44548503--44548780 Score: 407
Period size: 154 Copynumber: 1.8 Consensus size: 153
44548493 TTTTAAAAAT
*
44548503 AAAGTTTAGATTTTTAAAATAAAAATTTTTTTCGTAGTCATATTAAAAGAAAAGTTTAAA-TTCT
1 AAAGTTTAAATTTTTAAAATAAAAATTTTTTTCGTAGTCATATTAAAAGAAAAGTTTAAATTTCT
* * *
44548567 TAAAATAAAATTTTGATCTTTTTT-AACTATTTTGAAATAAAGTTTTGATTTTTAAGAAAAATAG
66 TAAAA-AAAATTTTGAT-TTTTTTCAACCATTTCGAAATAAAGTTTTAATTTTTAAGAAAAATAG
44548631 TGATTTTTTTTTAAAAAAAAAAGAG
129 TGATTTTTTTTTAAAAAAAAAAGAG
** * * *
44548656 AAAGTTTAAATTTTTAAAATAAAAATTTGTTTTTTTAGTCATTTTAAAGGAAAAGTTTAAATTTT
1 AAAGTTTAAATTTTTAAAATAAAAATTT-TTTTCGTAGTCATATTAAAAGAAAAGTTTAAATTTC
** *
44548721 TTTCAAAAAGTTTTGATTTTTTTCAACCATTTCGAAATAAAGTTTTAATTTTTAAGAAAA
65 TTAAAAAAAATTTTGATTTTTTTCAACCATTTCGAAATAAAGTTTTAATTTTTAAGAAAA
44548781 GTAATGACTT
Statistics
Matches: 110, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
153 33 0.30
154 71 0.65
155 6 0.05
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (153 bp):
AAAGTTTAAATTTTTAAAATAAAAATTTTTTTCGTAGTCATATTAAAAGAAAAGTTTAAATTTCT
TAAAAAAAATTTTGATTTTTTTCAACCATTTCGAAATAAAGTTTTAATTTTTAAGAAAAATAGTG
ATTTTTTTTTAAAAAAAAAAGAG
Found at i:44548711 original size:51 final size:52
Alignment explanation
Indices: 44548495--44548721 Score: 166
Period size: 50 Copynumber: 4.4 Consensus size: 52
44548485 TGATTTTTTT
* **
44548495 TTAAAA-ATAAAGTTTAGATTTTTAAAATAAAAATTT--TTTTCGTAGTCATA
1 TTAAAAGA-AAAGTTTAAATTTTTAAAATAAAAATTTGATTTTTTTAGTCATA
* * * *
44548545 TTAAAAGAAAAGTTTAAATTCTTAAAATAAAATTTTGATCTTTTTTA-ACTATT
1 TTAAAAGAAAAGTTTAAATTTTTAAAATAAAAATTTGAT-TTTTTTAGTC-ATA
* * ** * * * * *
44548598 TTGAAA-TAAAGTTTTGATTTTT--AAGAAAAATAGTGATTTTTTT-TTAAAA
1 TTAAAAGAAAAGTTTAAATTTTTAAAATAAAAAT-TTGATTTTTTTAGTCATA
** *
44548647 AAAAAAGAGAAAGTTTAAATTTTTAAAATAAAAATTTG-TTTTTTTAGTCATT
1 TTAAAAGA-AAAGTTTAAATTTTTAAAATAAAAATTTGATTTTTTTAGTCATA
*
44548699 TTAAAGGAAAAGTTTAAATTTTT
1 TTAAAAGAAAAGTTTAAATTTTT
44548722 TTCAAAAAGT
Statistics
Matches: 131, Mismatches: 34, Indels: 23
0.70 0.18 0.12
Matches are distributed among these distances:
49 4 0.03
50 44 0.34
51 40 0.31
52 23 0.18
53 20 0.15
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (52 bp):
TTAAAAGAAAAGTTTAAATTTTTAAAATAAAAATTTGATTTTTTTAGTCATA
Found at i:44548729 original size:20 final size:20
Alignment explanation
Indices: 44548706--44548746 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
44548696 ATTTTAAAGG
44548706 AAAAGTTTAAATTTTTTTCA
1 AAAAGTTTAAATTTTTTTCA
**
44548726 AAAAGTTTTGATTTTTTTCA
1 AAAAGTTTAAATTTTTTTCA
44548746 A
1 A
44548747 CCATTTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (20 bp):
AAAAGTTTAAATTTTTTTCA
Found at i:44552830 original size:5 final size:6
Alignment explanation
Indices: 44552815--44552845 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
44552805 TATTTTGAGA
44552815 AAAAAT AAAAAT AAAAAT AAAAAT AATAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AA-AAAT
44552846 TTGGTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:44557525 original size:205 final size:200
Alignment explanation
Indices: 44557172--44557777 Score: 733
Period size: 205 Copynumber: 3.0 Consensus size: 200
44557162 AATTAGAAAA
* * * *
44557172 TTGAATGCCTTAATAAGGATGCATGGTATGGTG-TTTCTATCTTGTAATGCTTGAAAAATGTGTA
1 TTGAATGCCTTAATATGGATGCATGATATAGTGTTTTC-ATCTTGTAATGCTTG-AAAA-CTGTA
* * *
44557236 TAAACCAAAATGGATGAAAGTATAATTGCATCTTGTG--TTT-T-AAAATTAGTAATATTTCTGT
63 TAAACCAGAGTGGATGAAAGTATAATTGCAT-TTGTGTTTTTGTCAAAATTAGCAATATTTCTGT
* * * * *
44557297 CATTAACTGTTGATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTAGATGATTTTACCATAT
127 CATTAACTGCTGATTTTCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTATACCATAT
44557362 ATAATGTAAG
192 A-AATGTAAG
*
44557372 TTGAATGCCTTAATATGGATTCATGATATAGTGTTTTCATCTTGTAATGCTTGAAAACTGTATAA
1 TTGAATGCCTTAATATGGATGCATGATATAGTGTTTTCATCTTGTAATGCTTGAAAACTGTATAA
* *
44557437 ACCAGAGTGGATTG-AAGTATTATTGCATATTGTGTTTTGTGTACCAAAATTAGCAATATTTCTA
66 ACCAGAGTGGA-TGAAAGTATAATTGCAT-TTGTGTTTT-TGT--CAAAATTAGCAATATTTCTG
** * *
44557501 TCATTAACTGCAAATTTTCATGTTCTGTTGCTCTCCCTTGTTTTCATTTGGATAATTATACCATA
126 TCATTAACTGCTGATTTTCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTATACCATA
44557566 TAAGATGTAAG
191 TAA-ATGTAAG
* *
44557577 TTGAATTCCTTAATATGGATGCATGATATAGTGTTTTCATCTTATAATGCTTGAAAACTGTATAT
1 TTGAATGCCTTAATATGGATGCATGATATAGTGTTTTCATCTTGTAATGCTTGAAAACTG--TAT
44557642 AAACCAGAGTGGATGAAAGTATAATTGCATTTGTGTTTTATGTTTCAAAACTTA-CTAATATTTC
64 AAACCAGAGTGGATGAAAGTATAATTGCATTTGTGTTTT-TG--TCAAAA-TTAGC-AATATTTC
* ** * * *
44557706 TGTAATTGAACTGCTGATTTT-ATTGTTCCACTGCTCTGCCTTGATTTCTTTTGGATAATTGTAC
124 TGTCATT-AACTGCTGATTTTCA-TGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTATAC
44557770 CATATAAA
187 CATATAAA
44557778 ATGCAAGAGA
Statistics
Matches: 351, Mismatches: 36, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
198 34 0.10
199 6 0.02
200 46 0.13
201 5 0.01
202 1 0.00
204 1 0.00
205 139 0.40
206 19 0.05
207 47 0.13
208 53 0.15
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.42
Consensus pattern (200 bp):
TTGAATGCCTTAATATGGATGCATGATATAGTGTTTTCATCTTGTAATGCTTGAAAACTGTATAA
ACCAGAGTGGATGAAAGTATAATTGCATTTGTGTTTTTGTCAAAATTAGCAATATTTCTGTCATT
AACTGCTGATTTTCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTATACCATATAAAT
GTAAG
Found at i:44557914 original size:40 final size:40
Alignment explanation
Indices: 44557859--44557941 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
44557849 GAGGAAACAA
44557859 AAGAAATATATAGAGAACATC-AGAAAGGAATCAACAGAGT
1 AAGAAATATATAGAGAACATCGA-AAAGGAATCAACAGAGT
*
44557899 AAGAAATATATAGAGAATATCGAAAAGGAATCAACAGAGT
1 AAGAAATATATAGAGAACATCGAAAAGGAATCAACAGAGT
44557939 AAG
1 AAG
44557942 GAATCAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 40 0.98
41 1 0.02
ACGTcount: A:0.55, C:0.08, G:0.20, T:0.16
Consensus pattern (40 bp):
AAGAAATATATAGAGAACATCGAAAAGGAATCAACAGAGT
Found at i:44560154 original size:32 final size:32
Alignment explanation
Indices: 44560115--44560204 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
44560105 TTAGATATTG
* *
44560115 ATTATGTTTTAAGCTTGTTAGATATTTAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
*
44560147 ATTATGTTTTAAGCTTGTTGGTTATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
44560179 ATTATGTTTTAAGCTTGTTGGATATT
1 ATTATGTTTTAAGCTTGTTGGATATT
44560205 AAAATGATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.24, C:0.03, G:0.17, T:0.56
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTGGATATTGAATTT
Found at i:44562210 original size:58 final size:59
Alignment explanation
Indices: 44562111--44562273 Score: 186
Period size: 58 Copynumber: 2.8 Consensus size: 59
44562101 AACTTTTAAA
* ** * *
44562111 ATTAGAATTAAATTGATAAGTTTTGTAAATGTTCAGAGCTAAATTTATTGAATTTTTAG
1 ATTAGAATTAAATTGATAAATTTTGTAAACATTGAGGGCTAAATTTATTGAATTTTTAG
* * *
44562170 ATTAGAATTAGA-TGACAAATTTTGTAAACATTGAGGGCTAAA-TTATTGAGTTTTTAG
1 ATTAGAATTAAATTGATAAATTTTGTAAACATTGAGGGCTAAATTTATTGAATTTTTAG
* * * * *
44562227 ATTAGGATCAAATTGATAAATTGTGTAAACATGGAATGGCTAAATTT
1 ATTAGAATTAAATTGATAAATTTTGTAAACATTG-AGGGCTAAATTT
44562274 GTTATTAGGT
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
57 23 0.27
58 42 0.49
59 19 0.22
60 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (59 bp):
ATTAGAATTAAATTGATAAATTTTGTAAACATTGAGGGCTAAATTTATTGAATTTTTAG
Found at i:44562520 original size:21 final size:21
Alignment explanation
Indices: 44562496--44562535 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44562486 ATTTAATTTA
*
44562496 ATAAATTAATATATAATTATG
1 ATAAATCAATATATAATTATG
* *
44562517 ATAAGTCAATGTATAATTA
1 ATAAATCAATATATAATTA
44562536 CAGTTTGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (21 bp):
ATAAATCAATATATAATTATG
Found at i:44567542 original size:89 final size:89
Alignment explanation
Indices: 44567322--44567542 Score: 250
Period size: 89 Copynumber: 2.5 Consensus size: 89
44567312 CTTAAGGAAG
* * * * *
44567322 CAAAAAG-CCTTCAAACTTTTTCAAAAAAAGCAATTAAGCCTCAGCTCTCTTTATTTGCACTCAT
1 CAAAAAGACCCTCAAACTTTTTC-AAAAAAGCAATTAAACC-CA-CCCACTTTATTTGCACTCAA
*
44567386 TTGGGTACTTAAACTTTTAAAATGCAT
63 TTGGGTACTTAAACTTTCAAAATGCAT
* * * * * * *
44567413 AAAAAAAAGCCTGAAACCTTTTCAAAAGAAGTAATT-AACCC-CCCACTTTCTTTTGCACTCAAT
1 CAAAAAGACCCTCAAACTTTTTCAAAA-AAGCAATTAAACCCACCCACTTT-ATTTGCACTCAAT
*
44567476 TGGGTACTTGAACTTTCAAAATGCAT
64 TGGGTACTTAAACTTTCAAAATGCAT
44567502 CAAAAAGACCCTCAAACTTTTTCAAAAAAGCAATTAAACCC
1 CAAAAAGACCCTCAAACTTTTTCAAAAAAGCAATTAAACCC
44567543 TTGCTTTTAT
Statistics
Matches: 106, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
88 13 0.12
89 62 0.58
90 1 0.01
91 12 0.11
92 18 0.17
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (89 bp):
CAAAAAGACCCTCAAACTTTTTCAAAAAAGCAATTAAACCCACCCACTTTATTTGCACTCAATTG
GGTACTTAAACTTTCAAAATGCAT
Found at i:44567627 original size:13 final size:13
Alignment explanation
Indices: 44567609--44567651 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
44567599 AAATTTTATT
*
44567609 AAAATTCAATAAA
1 AAAATTTAATAAA
*
44567622 AAAATTTAATATTA
1 AAAATTTAATA-AA
*
44567636 AAAATTTATTAAA
1 AAAATTTAATAAA
44567649 AAA
1 AAA
44567652 TAGAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAATTTAATAAA
Found at i:44567687 original size:28 final size:27
Alignment explanation
Indices: 44567646--44567715 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
44567636 AAAATTTATT
* *
44567646 AAAAAATAGAAAAAAATATA-AGAATCGTA
1 AAAAAATA-TAAAAAATATAGA-AAT-ATA
*
44567675 AAAAAATATAAAATATATAGAAATATA
1 AAAAAATATAAAAAATATAGAAATATA
44567702 AAAAAATTATAAAA
1 AAAAAA-TATAAAA
44567716 TTTTATAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.22
28 19 0.53
29 9 0.25
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (27 bp):
AAAAAATATAAAAAATATAGAAATATA
Found at i:44568181 original size:84 final size:85
Alignment explanation
Indices: 44568085--44568246 Score: 202
Period size: 85 Copynumber: 1.9 Consensus size: 85
44568075 GAGCAGGGGA
* * * *
44568085 TTAATTGC-TTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAA-CTCAAGTACCCA
1 TTAATTGCTTTTTTTGAAAAAGTTTGAGAGCCCTTTTGATGCATTTT-AAAAGCTCAAGTACCCA
44568148 ATTGAGTGAAAAAACAGTTGC
65 ATTGAGTGAAAAAACAGTTGC
* * * * * *
44568169 TTAATTGCTTTTTTTGAAGAAGTTTGAGAGCCCTTTTGATGTATTTTAAAAGTTTAAGTGCTCAA
1 TTAATTGCTTTTTTTGAAAAAGTTTGAGAGCCCTTTTGATGCATTTTAAAAGCTCAAGTACCCAA
*
44568234 TTGAGTGCAAAAA
66 TTGAGTGAAAAAA
44568247 GAAAAGAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
84 12 0.18
85 53 0.82
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (85 bp):
TTAATTGCTTTTTTTGAAAAAGTTTGAGAGCCCTTTTGATGCATTTTAAAAGCTCAAGTACCCAA
TTGAGTGAAAAAACAGTTGC
Found at i:44569421 original size:17 final size:17
Alignment explanation
Indices: 44569399--44569432 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44569389 GGAGTTCTAC
44569399 AAATAAAAATAATTATA
1 AAATAAAAATAATTATA
* *
44569416 AAATAAGAATCATTATA
1 AAATAAAAATAATTATA
44569433 TAAAAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATAAAAATAATTATA
Found at i:44569510 original size:27 final size:27
Alignment explanation
Indices: 44569466--44569524 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
44569456 ATTAGATTTG
*
44569466 TAAAATTTTATAAATATTATGAATAAAA
1 TAAAATTTTATAAATATT-GGAATAAAA
*
44569494 TAAAA-TTTA-AATATATTGGAATTAAA
1 TAAAATTTTATAA-ATATTGGAATAAAA
44569520 TAAAA
1 TAAAA
44569525 ATTAGTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 14 0.50
27 9 0.32
28 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (27 bp):
TAAAATTTTATAAATATTGGAATAAAA
Found at i:44575208 original size:59 final size:61
Alignment explanation
Indices: 44575145--44575259 Score: 148
Period size: 59 Copynumber: 1.9 Consensus size: 61
44575135 GTTAAATTTA
44575145 TTAAATTTTTAGAATTAGAA-CTAAA-TGAAAAAATT-TGTAAACATT-GAGGGCTAAAATTG
1 TTAAATTTTTAGAATTAGAATC-AAATTG-AAAAATTATGTAAACATTAGAGGGCTAAAATTG
* * * *
44575204 TTAAATTTTTATATTTAGGATCAAATTGATAAATTATGTAAACATTAGAGGGCTAA
1 TTAAATTTTTAGAATTAGAATCAAATTGAAAAATTATGTAAACATTAGAGGGCTAA
44575260 TTTGTTATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 26 0.54
60 13 0.27
61 9 0.19
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.37
Consensus pattern (61 bp):
TTAAATTTTTAGAATTAGAATCAAATTGAAAAATTATGTAAACATTAGAGGGCTAAAATTG
Found at i:44575509 original size:21 final size:20
Alignment explanation
Indices: 44575483--44575522 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
44575473 ATTTAGTTCA
44575483 ATAAATCAATATATAATTATG
1 ATAAATCAATATAT-ATTATG
*
44575504 ATAAATCAATGTATATTAT
1 ATAAATCAATATATATTAT
44575523 AGTTTGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (20 bp):
ATAAATCAATATATATTATG
Found at i:44578313 original size:43 final size:43
Alignment explanation
Indices: 44578265--44578387 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 43
44578255 GGCTCGTACA
* * *
44578265 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAC-AGATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACAAG-TCG
* * * *
44578308 ATGCC-ACTATCCCAAACAGGGTCTTACACGAAAACACAAGTTG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAAACACAAGTCG
*
44578351 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACAC
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAAACAC
44578388 TTTTTGAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 2 0.03
43 60 0.91
44 4 0.06
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAAACACAAGTCG
Found at i:44580266 original size:143 final size:143
Alignment explanation
Indices: 44580003--44580272 Score: 360
Period size: 143 Copynumber: 1.9 Consensus size: 143
44579993 ATTTTAAGAA
* * * **
44580003 TCTTTACAGTTTGCTGATTTACAATCGCAACTGATATCATTAAAGCTTGTTGATTTACGATCATG
1 TCTTAACAGTTTGCTGATTTACAATCGCAACTGATATCATTAAAGCTCGTTGATTTACAATCACA
** ** * * *
44580068 TTTTAAGTTCATTGATATATGATCATGAGCAATTCATCTAAAGTTCACTGGTTTACTATCACGAC
66 ACTTAAGTTCATTGATATACAATCATGAACAATTCATCTAAAGTTCACTGATTTACGATCACGAC
44580133 TCCTCTTGACTCC
131 TCCTCTTGACTCC
* * *
44580146 TCTTAACAGTTTGCTGATTTACGATCGCAACTGGTATCATTAAAGCTCGTTGATTTACAATCGCA
1 TCTTAACAGTTTGCTGATTTACAATCGCAACTGATATCATTAAAGCTCGTTGATTTACAATCACA
* * * **
44580211 ACTTAAGTTCATTGATTTACAATCATGAATAATTCATCTAGAGTTCGTTGATTTACGATCAC
66 ACTTAAGTTCATTGATATACAATCATGAACAATTCATCTAAAGTTCACTGATTTACGATCAC
44580273 AACTTGTAAT
Statistics
Matches: 107, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
143 107 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (143 bp):
TCTTAACAGTTTGCTGATTTACAATCGCAACTGATATCATTAAAGCTCGTTGATTTACAATCACA
ACTTAAGTTCATTGATATACAATCATGAACAATTCATCTAAAGTTCACTGATTTACGATCACGAC
TCCTCTTGACTCC
Found at i:44584444 original size:44 final size:42
Alignment explanation
Indices: 44584322--44584480 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 42
44584312 GTAATAATGT
* * * * * * *
44584322 CATATCCCAGATATGCTCTTACATGTAATCTCGTATTGATGGC
1 CATATCCCAGACATGGTCTTACACGAAATCACATATCGAT-GC
* * * * *
44584365 AATAGCTCAGCCATGATCTTACACGAAATCACATATCGATGC
1 CATATCCCAGACATGGTCTTACACGAAATCACATATCGATGC
* * *
44584407 CAATGTCCCAGACATGGGTCTTACACGAACTCTCATATCGATGC
1 C-ATATCCCAGACAT-GGTCTTACACGAAATCACATATCGATGC
* *
44584451 CATATCCCAGATATGGTCTTACACGTAATC
1 CATATCCCAGACATGGTCTTACACGAAATC
44584481 TCGGTAACCC
Statistics
Matches: 91, Mismatches: 23, Indels: 5
0.76 0.19 0.04
Matches are distributed among these distances:
42 16 0.18
43 49 0.54
44 26 0.29
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (42 bp):
CATATCCCAGACATGGTCTTACACGAAATCACATATCGATGC
Found at i:44585788 original size:22 final size:22
Alignment explanation
Indices: 44585753--44585809 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
44585743 ATAATCAAAT
* *
44585753 TGGTGTTGCAACATCTAGGGTG
1 TGGTGTTGCGACATCCAGGGTG
*
44585775 TGGTGTCGCGACATCCAGGGTG
1 TGGTGTTGCGACATCCAGGGTG
44585797 TGGTGTTGCGACA
1 TGGTGTTGCGACA
44585810 CTCAAGATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.16, C:0.18, G:0.39, T:0.28
Consensus pattern (22 bp):
TGGTGTTGCGACATCCAGGGTG
Found at i:44588571 original size:23 final size:23
Alignment explanation
Indices: 44588540--44588590 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
44588530 ACCTACTTTC
* *
44588540 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
44588563 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
44588586 TTACA
1 TTACA
44588591 ACATAACCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:44590807 original size:22 final size:22
Alignment explanation
Indices: 44590782--44590835 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
44590772 AAGTACGAAT
44590782 CAGTAGGCACCATAGTGCAAA-A
1 CAGTAGGCACCATAGTG-AAAGA
* *
44590804 CAGTAGGCATCATAGTGAAAGT
1 CAGTAGGCACCATAGTGAAAGA
44590826 CAGTAGGCAC
1 CAGTAGGCAC
44590836 TGAAGTGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (22 bp):
CAGTAGGCACCATAGTGAAAGA
Found at i:44593855 original size:39 final size:39
Alignment explanation
Indices: 44593812--44594085 Score: 358
Period size: 39 Copynumber: 7.1 Consensus size: 39
44593802 ATCGAGTATT
* * * *
44593812 CTGAATTATTGCTCAATCAAGCAAGACTTACTAAATATA
1 CTGAATTGTTGCTCAATCGAGCAAAACTTACTGAATATA
* * *
44593851 CTGAA-TGCTGCTCAATTGAGCAAAA-TCTACTGAACATA
1 CTGAATTGTTGCTCAATCGAGCAAAACT-TACTGAATATA
44593889 CTGAATTGTTGCTCAATCGAGCAAAACTTACTGAATATA
1 CTGAATTGTTGCTCAATCGAGCAAAACTTACTGAATATA
* * * **
44593928 CT-AAATGCTGCTCAATCGAGCAAAA-TCTACTAAACGTA
1 CTGAATTGTTGCTCAATCGAGCAAAACT-TACTGAATATA
*
44593966 CTGAATTGTTGCTCAATCAAGCAAAACTTACTGAATATA
1 CTGAATTGTTGCTCAATCGAGCAAAACTTACTGAATATA
* *
44594005 CGGAATTGTTGCTCAATCGAGCAAAATTTACTGAATATA
1 CTGAATTGTTGCTCAATCGAGCAAAACTTACTGAATATA
*
44594044 CTGAATTGTTGCTCAATCGAGAAAAACTTACTGAATATA
1 CTGAATTGTTGCTCAATCGAGCAAAACTTACTGAATATA
44594083 CTG
1 CTG
44594086 TGTAATACCC
Statistics
Matches: 202, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.01
38 60 0.30
39 138 0.68
40 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (39 bp):
CTGAATTGTTGCTCAATCGAGCAAAACTTACTGAATATA
Found at i:44593905 original size:77 final size:77
Alignment explanation
Indices: 44593812--44594085 Score: 413
Period size: 77 Copynumber: 3.5 Consensus size: 77
44593802 ATCGAGTATT
* * * *
44593812 CTGAATTATTGCTCAATCAAGCAAGACTTACTAAATATACTGAATGCTGCTCAATTGAGCAAAAT
1 CTGAATTGTTGCTCAATCAAGCAAAACTTACTGAATATACTGAATGCTGCTCAATCGAGCAAAAT
44593877 CTACTGAACATA
66 CTACTGAACATA
* *
44593889 CTGAATTGTTGCTCAATCGAGCAAAACTTACTGAATATACTAAATGCTGCTCAATCGAGCAAAAT
1 CTGAATTGTTGCTCAATCAAGCAAAACTTACTGAATATACTGAATGCTGCTCAATCGAGCAAAAT
* *
44593954 CTACTAAACGTA
66 CTACTGAACATA
* *
44593966 CTGAATTGTTGCTCAATCAAGCAAAACTTACTGAATATACGGAATTGTTGCTCAATCGAGCAAAA
1 CTGAATTGTTGCTCAATCAAGCAAAACTTACTGAATATACTGAA-TGCTGCTCAATCGAGCAAAA
* *
44594031 TTTACTGAATATA
65 TCTACTGAACATA
* *
44594044 CTGAATTGTTGCTCAATCGAGAAAAACTTACTGAATATACTG
1 CTGAATTGTTGCTCAATCAAGCAAAACTTACTGAATATACTG
44594086 TGTAATACCC
Statistics
Matches: 177, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
77 110 0.62
78 67 0.38
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (77 bp):
CTGAATTGTTGCTCAATCAAGCAAAACTTACTGAATATACTGAATGCTGCTCAATCGAGCAAAAT
CTACTGAACATA
Done.