Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009178.1 Hibiscus syriacus cultivar Beakdansim tig00112743_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 75759
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:2842 original size:22 final size:22
Alignment explanation
Indices: 2797--2844 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2787 AATAACATAT
*
2797 TAGGTAGCGCTTAATAATGTAA
1 TAGGTAGCGCTTAATAATGAAA
2819 TAGGTAGCGCTTATATAAT-AAA
1 TAGGTAGCGCTTA-ATAATGAAA
2841 TAGG
1 TAGG
2845 CATTTAACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (22 bp):
TAGGTAGCGCTTAATAATGAAA
Found at i:3518 original size:192 final size:192
Alignment explanation
Indices: 2848--3518 Score: 641
Period size: 194 Copynumber: 3.4 Consensus size: 192
2838 AAATAGGCAT
* * * *
2848 TTAACTGGTATTTATACCGG-TAGCATTGCAAATTTACCTATTGCATTATAATTATTGGTTTCGT
1 TTAACTGGTATATATACCGGTTA-CATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGA
*
2912 TGTTTTTTGGATCGATACAATTTTAAATGTATCGACACTTATGCTTGCACCTCGTTGGGCATTCC
65 TGTTTTTGGGATCGATACAATTTTAAATGTATCGACACTTATGCTTGCACCTCGTTGGGCATT-C
* * *
2977 TAATTCATTCTGGAAAAAGTATCGACACAAAC-TATAAAGGTGTCGATACATTTATTTAGACTTA
129 --A-T--TT-TGGAAAAAGTATCGACACAAACTTACAAAAGTGTCGATAC-TTTATTT-GACAT-
* *
3041 TTTTCTCA
185 TTTTATAA
* * * * * * *
3049 TAAAATCGGTATATTTATATCGGGTACATTGTAAATTTACCTATAACATTGTAATT-TTTGTTTC
1 TTAACT-GGTATA--TATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTC
* *
3113 GATGTTTTTGAGATCGATACAATTTTAAATGTATCGACACGTTATTCTTGCACCTCGTTGGGCAT
63 GATGTTTTTGGGATCGATACAATTTTAAATGTATCGACAC-TTATGCTTGCACCTCGTTGGGCAT
* * **
3178 TCATTATGGAAAATGTATCGACACAAA-TTACGCAAGTGT---TACTTTATTCTGACCAATTTTC
127 TCATTTTGGAAAAAGTATCGACACAAACTTACAAAAGTGTCGATACTTTATT-TGA-C-ATTTT-
3239 TCATAA
188 T-ATAA
* * * * *
3245 --AACCGGTAAATTTAAACCGGTTACATTGTAAATTGACCTATTACATTATAATTATCGGTTTCG
1 TTAACTGGT--ATATATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCG
** * * *
3308 ATGTTTTTGTAATCGATACAATTTTAAATGTATCGACACTTTATGCGTGAACCT-GTTTGTGC-T
64 ATGTTTTTGGGATCGATACAATTTTAAATGTATCGACAC-TTATGCTTGCACCTCG-TTGGGCAT
3371 TC-TTTTGGAAAAAAGTATCGACACAAACTTA-AAAAGTGTCGATAC-TTATGTTGACATGTTTT
127 TCATTTTGG-AAAAAGTATCGACACAAACTTACAAAAGTGTCGATACTTTAT-TTGACAT-TTTT
3433 ATAA
189 ATAA
* * ** * *
3437 TTAACTGGTATATATACTGGTTACATTGTTAATTTAAATATTACATTATAATTATTTGTTTCAAT
1 TTAACTGGTATATATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGAT
*
3502 GTTTTTGGGGTCGATAC
66 GTTTTTGGGATCGATAC
3519 TTTTTGAAAA
Statistics
Matches: 388, Mismatches: 58, Indels: 57
0.77 0.12 0.11
Matches are distributed among these distances:
192 69 0.18
193 76 0.20
194 83 0.21
195 11 0.03
196 6 0.02
197 27 0.07
198 1 0.00
200 1 0.00
201 5 0.01
202 5 0.01
203 45 0.12
204 57 0.15
205 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (192 bp):
TTAACTGGTATATATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGAT
GTTTTTGGGATCGATACAATTTTAAATGTATCGACACTTATGCTTGCACCTCGTTGGGCATTCAT
TTTGGAAAAAGTATCGACACAAACTTACAAAAGTGTCGATACTTTATTTGACATTTTTATAA
Found at i:5398 original size:293 final size:292
Alignment explanation
Indices: 4833--5417 Score: 971
Period size: 293 Copynumber: 2.0 Consensus size: 292
4823 TTTGAATACA
4833 AGCACGCAATCTACTTCAACTGATTTTTTTGAAGACGGAATGGAATGGTTATGAACCTCCAGCAC
1 AGCACGCAATCTACTTCAACTGATTTTTTTGAAGACGGAATGGAATGGTTATGAACCTCCAGCAC
* *
4898 ATGATGTTTGACATTTGGTTATAATTATGTTTTCAATGTTTTTGGGATCGACAATTGTTTAAATG
66 ATGATGTTAGACATTTGGTTATAATTATGTTTTCAATGTTTTTGGGATCAACAATTGTTTAAATG
4963 TATCGAAACTTTATTGTGCACTTGGTTTTTAAAATATAGTATGGACAAAAATATATCGAAACTTG
131 TATCGAAACTTTATTGTGCACTTGGTTTTTAAAATATAGTATGGACAAAAATATATCGAAACTTG
* *
5028 ATGTATTTGTGTCGATACTTCATGTATACATGTTTTCTCATAAACCGGTACATTTAGACCGGTTA
196 ATGTATTTGTGTCGATACTTCATGTATACATGTTTTCTCATAAACCGGTACATTTAGACCAGCTA
*
5093 CATTGTTAATTTACCTATTAAATTATAATTAT
261 CATTGCTAATTTACCTATTAAATTATAATTAT
* *
5125 AGCACGTAGTCTACTTCAACTGAATTTTTTTGAAGACGGAATGGAATGGTTATGAACCTCCAGCA
1 AGCACGCAATCTACTTCAACTG-ATTTTTTTGAAGACGGAATGGAATGGTTATGAACCTCCAGCA
* *
5190 CATGATGTTAGAGACATTTGGTTATAATTAT-TTTTCGATGTTTTTGGGATTAACAATTGTTATA
65 CATGATGTT--AGACATTTGGTTATAATTATGTTTTCAATGTTTTTGGGATCAACAATTGTT-TA
* * *
5254 AATGTATCGAAA--TT-TTGTTGCACTTGGTTTTTAAAATATAGTCTGGACAAAAATGTTTCGAA
127 AATGTATCGAAACTTTATTG-TGCACTTGGTTTTTAAAATATAGTATGGACAAAAATATATCGAA
5316 ACTTGATGTATTTGTGTCGATACTTCATGTATACATGTTTTCTCATAAACCGGTACATTTAGACC
191 ACTTGATGTATTTGTGTCGATACTTCATGTATACATGTTTTCTCATAAACCGGTACATTTAGACC
* *
5381 AGCTATATTGCTAATTTACCTATTACATTATAATTAT
256 AGCTACATTGCTAATTTACCTATTAAATTATAATTAT
5418 GGTTTTCGAG
Statistics
Matches: 274, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
292 23 0.08
293 191 0.70
294 27 0.10
295 33 0.12
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (292 bp):
AGCACGCAATCTACTTCAACTGATTTTTTTGAAGACGGAATGGAATGGTTATGAACCTCCAGCAC
ATGATGTTAGACATTTGGTTATAATTATGTTTTCAATGTTTTTGGGATCAACAATTGTTTAAATG
TATCGAAACTTTATTGTGCACTTGGTTTTTAAAATATAGTATGGACAAAAATATATCGAAACTTG
ATGTATTTGTGTCGATACTTCATGTATACATGTTTTCTCATAAACCGGTACATTTAGACCAGCTA
CATTGCTAATTTACCTATTAAATTATAATTAT
Found at i:6063 original size:396 final size:397
Alignment explanation
Indices: 5211--6421 Score: 1906
Period size: 396 Copynumber: 3.1 Consensus size: 397
5201 AGACATTTGG
* ** * * *
5211 TTATAATTA--TTTTTCGATGTTTTTGGGATTAACAATTGTTATAAATGTATCGA-AATTT-TGT
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTATG-
* * * * * * * *
5272 TGCACTTGGTTTTTAAAATA-TAGTCTGGACAAAAATGTTTCGAAACTTGATGTATTTGTGTCGA
65 TGCACTTGG-TTCTGAAATACT-TTCTGGACCAAAA-GTATCGACACTTGTTCTATTTGTGTCGA
* * * * *
5336 TACT-TCATGTATACATGTTTTCTCATAAACCGGTACATTTAGACCAGCTATATTGCTAATTTAC
127 TACTGT-TTGTACACATGTTTTCTCAAAAACCGGTACATTTAGACCGGTTATATTGCTAATTTAC
*
5400 CTATTACATTATAATTATGGTTTTCGA-GTTTTTGGGATCGACACTTGTTATATATGTATCTACA
191 CTATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATATATGTATCGACA
* *
5464 C-TTTTAGTGCACTTGGTTTTGAAATACATTCTGGAG-AAAAGTATCGACACTTGTTATATTTGT
256 CTTTTTAGTGCACTTGGTTTTGAAATACAATATGGAGAAAAAGTATCGACACTTGTTATATTTGT
*
5527 GTCGATACTTTTTATACA-CTATTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAAT
321 GTCGATACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAAT
5591 TTACCTATTACA
386 TTACCTATTACA
5603 TTATAATTATGTTTTTCGAT-TTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTTATG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACAC-TTTATG
5667 TGCACTTGGTTCTGAAATACTTTCTGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATAC
65 TGCACTTGGTTCTGAAATACTTTCTGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATAC
* * *
5732 TGTTTGTACACTTGTTTTCTCAAAAACCGGTAGATTTAGACCGGTTATATTGTTAATTTACCTAT
130 TGTTTGTACACATGTTTTCTCAAAAACCGGTACATTTAGACCGGTTATATTGCTAATTTACCTAT
*
5797 TACATTATAATTATGGTTTTTGATGTTTTTGGGATCGACACTTGTTATATATGTATCGACACTTT
195 TACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATATATGTATCGACACTTT
* *
5862 TTAGTGCACTTGGTTTTAAAATACAGT-TGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCG
260 TTAGTGCACTTGGTTTTGAAATACAATATGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCG
5926 ATACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTAC
325 ATACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTAC
5991 CTATTACA
390 CTATTACA
5999 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTATGT
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTATGT
*
6064 GCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
66 GCACTTGGTTCTGAAATACTTTCTGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
* * * *
6129 GTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGATTATTTTGCTAATTTACTTATT
131 GTTTGTACACATGTTTTCTCAAAAACCGGTACATTTAGACCGGTTATATTGCTAATTTACCTATT
* *
6194 ACATTATAATTATGGTTTTCGATGTTTTTGGGATCAACACTTGTTATATATGTATTGACACTTTT
196 ACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATATATGTATCGACACTTTT
* *
6259 TAGTGCACTTGGATTTGAAATACAATATGGAGAAAAAGTATCGACACTTGTTAGATTTGTGTCGA
261 TAGTGCACTTGGTTTTGAAATACAATATGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCGA
* * *
6324 TACTTTTTGTACACATGTTTTCTCAAAAACAGGTATATTTAGACCGTTTACATGAATAATTTACC
326 TACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACC
6389 TATTACA
391 TATTACA
*
6396 TTATAATTATATTTTTCGATGTTTTC
1 TTATAATTATGTTTTTCGATGTTTTC
6422 AATACTTATA
Statistics
Matches: 761, Mismatches: 45, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
392 9 0.01
393 133 0.17
394 72 0.09
395 84 0.11
396 295 0.39
397 168 0.22
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (397 bp):
TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTATGT
GCACTTGGTTCTGAAATACTTTCTGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATACT
GTTTGTACACATGTTTTCTCAAAAACCGGTACATTTAGACCGGTTATATTGCTAATTTACCTATT
ACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATATATGTATCGACACTTTT
TAGTGCACTTGGTTTTGAAATACAATATGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCGA
TACTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACC
TATTACA
Found at i:6361 original size:199 final size:199
Alignment explanation
Indices: 5211--6420 Score: 1617
Period size: 198 Copynumber: 6.1 Consensus size: 199
5201 AGACATTTGG
** * *
5211 TTATAATTAT--TTTTCGATGTTTTTGGGATTAACAATTGTTATAAATGTATCGA-A-ATTTT-G
1 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
* * * * * * *
5271 TTGCACTTGGTTTTTAAAATATAGTCTGGACAAAAATGTTTCGAAACTTGATGTATTTGTGTCGA
66 -TGCACTTGG-TTTTGAAATACATTCTGGACAAAAA-GTATCGACACTTGTTATATTTGTGTCGA
** * * * * * *
5336 TACTTCATGTATACATGTTTTCTCATAAACCGGTACATTTAGACCAGCTATA-TTG-CTAATTTA
128 TACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACC-G-TTTACATGAATAATTTA
5399 CCTATTACA
191 CCTATTACA
* *
5408 TTATAATTATGGTTTTCGA-GTTTTTGGGATCGACACTTGTTATATATGTATCTACAC-TTTTAG
1 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
*
5471 TGCACTTGGTTTTGAAATACATTCTGGA-GAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
66 TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
* *
5535 TTTTTATACAC-TATTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
131 TTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
5599 TACA
196 TACA
* * *
5603 TTATAATTATGTTTTTCGAT-TTTTCGGGATCGACACTTGTTTTAAATGTATCGACAC-TTTTAT
1 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA-
* * * *
5666 GTGCACTTGGTTCTGAAATACTTTCTGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATA
65 GTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATA
* * * * * *
5731 CTGTTTGTACACTTGTTTTCTCAAAAACCGGTAGATTTAGACCGGTTATATTG-TTAATTTACCT
130 CTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACA-TGAATAATTTACCT
5795 ATTACA
194 ATTACA
* *
5801 TTATAATTATGGTTTTTGATGTTTTTGGGATCGACACTTGTTATATATGTATCGACACTTTTTAG
1 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
* * *
5866 TGCACTTGGTTTTAAAATACAGT-TGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
66 TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
* *
5930 TTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
131 TTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
5995 TACA
196 TACA
* * * *
5999 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTAT-G
1 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
* * *
6063 TGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATAC
66 TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
* * ** * *
6128 TGTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGATTATTTTG-CTAATTTACTTA
131 TTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTA-CATGAATAATTTACCTA
6192 TTACA
195 TTACA
* * *
6197 TTATAATTATGGTTTTCGATGTTTTTGGGATCAACACTTGTTATATATGTATTGACACTTTTTAG
1 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
* * * * *
6262 TGCACTTGGATTTGAAATACAATATGGAGAAAAAGTATCGACACTTGTTAGATTTGTGTCGATAC
66 TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
*
6327 TTTTTGTACACATGTTTTCTCAAAAACAGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
131 TTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
6392 TACA
196 TACA
**
6396 TTATAATTATATTTTTCGATGTTTT
1 TTATAATTATGGTTTTCGATGTTTT
6421 CAATACTTAT
Statistics
Matches: 892, Mismatches: 102, Indels: 36
0.87 0.10 0.03
Matches are distributed among these distances:
193 3 0.00
194 3 0.00
195 99 0.11
196 61 0.07
197 80 0.09
198 421 0.47
199 219 0.25
200 6 0.01
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (199 bp):
TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
TTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGTTTACATGAATAATTTACCTAT
TACA
Found at i:6496 original size:20 final size:21
Alignment explanation
Indices: 6471--6509 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
6461 GTAGCGTTTT
6471 ACCGGTTTTGTCAT-TTTGGG
1 ACCGGTTTTGTCATATTTGGG
6491 ACCGGTTTTGTCATATTTG
1 ACCGGTTTTGTCATATTTG
6510 TACATGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.26, T:0.46
Consensus pattern (21 bp):
ACCGGTTTTGTCATATTTGGG
Found at i:14568 original size:64 final size:63
Alignment explanation
Indices: 14495--14635 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
14485 TCTTTAACAT
* * *
14495 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAATGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
14558 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
14622 GTGCATCGATGCAC
1 GTGCATCGATGCAC
14636 ATTGAATATG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:15467 original size:20 final size:20
Alignment explanation
Indices: 15444--15482 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
15434 TACTCAATCT
15444 TCGGCATGGAGACTAGTCCC
1 TCGGCATGGAGACTAGTCCC
*
15464 TCGGTATGGAGACTAGTCC
1 TCGGCATGGAGACTAGTCC
15483 ACCAACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (20 bp):
TCGGCATGGAGACTAGTCCC
Found at i:18467 original size:32 final size:30
Alignment explanation
Indices: 18403--18467 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
18393 TTAGATTTTG
*
18403 AAATTATTTTCATGTATAATATAAAATTTT
1 AAATTATTTTCATGTATAATATAAAATATT
*
18433 AAATTATTTTTCAT-TATAATCTTTAAAATATT
1 AAATTA-TTTTCATGTATAA--TATAAAATATT
18465 AAA
1 AAA
18468 AAACTAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 11 0.37
31 7 0.23
32 12 0.40
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.49
Consensus pattern (30 bp):
AAATTATTTTCATGTATAATATAAAATATT
Found at i:18721 original size:20 final size:21
Alignment explanation
Indices: 18696--18747 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
18686 TTTTTCCAAT
*
18696 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
18716 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
18737 TCGCAATGCGA
1 TCGCAATGCGA
18748 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:18761 original size:20 final size:20
Alignment explanation
Indices: 18736--18836 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
18726 AATTGGGAAA
18736 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
18756 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
18776 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
18797 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
18817 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
18837 TTCTCAACGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 51 0.75
21 13 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:18837 original size:20 final size:20
Alignment explanation
Indices: 18798--18850 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
18788 TAATACAAAA
* *
18798 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
18818 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
18838 TCTCAACGCGATT
1 TCGCAACGCGATT
18851 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:18849 original size:61 final size:61
Alignment explanation
Indices: 18733--18849 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
18723 GCGAATTGGG
* * * * *
18733 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
18794 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCTCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
18850 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:19430 original size:19 final size:19
Alignment explanation
Indices: 19406--19446 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
19396 CGAGAGAATT
*
19406 GCAACGCGAAATAAAAATC
1 GCAACGCGAAACAAAAATC
*
19425 GCAACGCGAAACCAAAATC
1 GCAACGCGAAACAAAAATC
19444 GCA
1 GCA
19447 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.27, G:0.17, T:0.07
Consensus pattern (19 bp):
GCAACGCGAAACAAAAATC
Found at i:19464 original size:19 final size:19
Alignment explanation
Indices: 19442--19587 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
19432 GAAACCAAAA
*
19442 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19461 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19480 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
19494 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
19513 TCGCGTTGC-A-ATTC---
1 TCGCGTTGCGATTTTCATT
* **
19527 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
19546 TCTGCGTTGCGATTCTCATT
1 TC-GCGTTGCGATTTTCATT
*
19566 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
19586 TC
1 TC
19588 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 17 0.17
15 1 0.01
16 5 0.05
17 6 0.06
18 1 0.01
19 40 0.40
20 29 0.29
21 2 0.02
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:19512 original size:33 final size:33
Alignment explanation
Indices: 19475--19562 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
19465 GTTGCGATTT
19475 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
19508 TCATTTCGCGTTGCAATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
19541 TCATTTCTGCGTTGCGATTCTC
1 TCATTTC-GCGTTGCGATTCTC
19563 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 38 0.75
34 13 0.25
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:21688 original size:21 final size:21
Alignment explanation
Indices: 21664--21730 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
21654 TCATTCCTCG
21664 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
21685 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
21706 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
21727 AGAG
1 AGAG
21731 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:21688 original size:42 final size:42
Alignment explanation
Indices: 21612--21730 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
21602 GACTCGCCTG
* * * *
21612 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
21654 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
21696 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
21731 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:23100 original size:14 final size:14
Alignment explanation
Indices: 23081--23112 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
23071 TTTAATTGAA
23081 TTGTAAAAGGTGAT
1 TTGTAAAAGGTGAT
*
23095 TTGTAAAAGTTGAT
1 TTGTAAAAGGTGAT
23109 TTGT
1 TTGT
23113 TTAATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTGTAAAAGGTGAT
Found at i:23295 original size:19 final size:19
Alignment explanation
Indices: 23271--23329 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
23261 GAAATTAGCG
23271 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
23290 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
23304 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
23323 TTGCGAT
1 TTGCGAT
23330 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:26615 original size:20 final size:20
Alignment explanation
Indices: 26590--26640 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
26580 TGTATTATCT
*
26590 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAAAATCG
26610 CGTTGCGAAAGTCAAAATCG
1 CGTTGCGAAAGTCAAAATCG
*
26630 TGTTGCGAAAG
1 CGTTGCGAAAG
26641 GCAATCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (20 bp):
CGTTGCGAAAGTCAAAATCG
Found at i:26905 original size:19 final size:20
Alignment explanation
Indices: 26853--26921 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
26843 ATTCATTTGA
26853 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
26873 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
26893 CTA-CGCAATGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
26911 CTATCGCAACG
1 CTATCGCAACG
26922 ACAAAATCGC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 9 0.20
19 14 0.30
20 23 0.50
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:27155 original size:14 final size:14
Alignment explanation
Indices: 27136--27172 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
27126 CATCAATTAA
27136 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
27150 ACAAATCATCTTTT
1 ACAAATCAACATTT
27164 ACAAATCAA
1 ACAAATCAA
27173 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:29054 original size:20 final size:20
Alignment explanation
Indices: 29031--29098 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
29021 GAAACTTAAA
29031 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
29051 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
* **
29071 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
29090 ATCGCAACG
1 ATCGCAACG
29099 ACAAAATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 13 0.31
20 29 0.69
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:29106 original size:14 final size:14
Alignment explanation
Indices: 29087--29144 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
29077 ATGCGAAATG
29087 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
29101 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
29117 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
29133 AAAATCGCAACG
1 AAAATCGCAACG
29145 CGAAACCCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:29129 original size:32 final size:33
Alignment explanation
Indices: 29071--29149 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
29061 GAAAATGGCT
29071 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
29104 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
29136 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
29150 CCCAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:29197 original size:14 final size:14
Alignment explanation
Indices: 29178--29235 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
29168 TTTCATTTCG
29178 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
29192 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
29208 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
29224 CGTTGCGATTTT
1 CGTTGCGATTTT
29236 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:29242 original size:33 final size:33
Alignment explanation
Indices: 29161--29251 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
29151 CCAAATCGCA
*
29161 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
29194 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
29226 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
29252 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:29270 original size:20 final size:19
Alignment explanation
Indices: 29236--29290 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
29226 TTGCGATTTT
*
29236 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
29255 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
29275 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
29291 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:29812 original size:17 final size:18
Alignment explanation
Indices: 29769--29812 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
29759 GTCGATCAGA
*
29769 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
29787 TGATAGCTCTGGGCGA-G
1 TGATGGCTCTGGGCGAGG
29804 TGATGGCTC
1 TGATGGCTC
29813 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.14, C:0.16, G:0.43, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:31179 original size:18 final size:18
Alignment explanation
Indices: 31150--31222 Score: 88
Period size: 18 Copynumber: 4.4 Consensus size: 18
31140 ACCGGTCACA
31150 ACCCGA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
31167 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
31184 ----TA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
31197 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
31215 ACCCGACC
1 ACCCGACC
31223 GTTGACCGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
12 10 0.21
13 1 0.02
17 7 0.15
18 29 0.62
ACGTcount: A:0.18, C:0.49, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:31191 original size:12 final size:13
Alignment explanation
Indices: 31171--31206 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
31161 CCGTTGACCC
31171 GACCCGACCCGTT
1 GACCCGACCCGTT
*
31184 TA-CCGACCCGTT
1 GACCCGACCCGTT
31196 GACCCGACCCG
1 GACCCGACCCG
31207 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:31191 original size:30 final size:30
Alignment explanation
Indices: 31154--31229 Score: 127
Period size: 30 Copynumber: 2.5 Consensus size: 30
31144 GTCACAACCC
31154 GACCGACCCGTTGACCCGACCCGACCCGTT
1 GACCGACCCGTTGACCCGACCCGACCCGTT
*
31184 TACCGACCCGTTGACCCGACCCGACCCGTT
1 GACCGACCCGTTGACCCGACCCGACCCGTT
31214 GACCCGA-CCGTTGACC
1 GA-CCGACCCGTTGACC
31230 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 39 0.91
31 4 0.09
ACGTcount: A:0.17, C:0.46, G:0.22, T:0.14
Consensus pattern (30 bp):
GACCGACCCGTTGACCCGACCCGACCCGTT
Found at i:31231 original size:7 final size:7
Alignment explanation
Indices: 31219--31249 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
31209 CCGTTGACCC
31219 GACCGTT
1 GACCGTT
31226 GACCGTT
1 GACCGTT
31233 GACCGTT
1 GACCGTT
31240 GACCGTT
1 GACCGTT
31247 GAC
1 GAC
31250 GGAGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:33785 original size:24 final size:24
Alignment explanation
Indices: 33691--33797 Score: 90
Period size: 24 Copynumber: 4.5 Consensus size: 24
33681 ATATTTTATC
* *
33691 TGATTTCTGATTTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
* * * *
33715 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTATGTTT
* * * * *
33739 TGAT-TCCTAACCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTATGTTT
33763 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTATGTTT
*
33787 TGATTTCTGAT
1 TGATATCTGAT
33798 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 61 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (24 bp):
TGATATCTGATCTGAATTATGTTT
Found at i:33964 original size:2 final size:2
Alignment explanation
Indices: 33957--34071 Score: 230
Period size: 2 Copynumber: 57.5 Consensus size: 2
33947 CGGATGGGGG
33957 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
33999 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
34041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34072 GTTTTAAATA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 113 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36039 original size:18 final size:18
Alignment explanation
Indices: 36016--36105 Score: 102
Period size: 18 Copynumber: 5.2 Consensus size: 18
36006 ACCGGTCACA
36016 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
36034 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
36051 ----TA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
36064 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
36082 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
36103 ACC
1 ACC
36106 GTTGACCGGA
Statistics
Matches: 61, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
12 10 0.16
13 1 0.02
17 1 0.02
18 37 0.61
21 12 0.20
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:36058 original size:12 final size:13
Alignment explanation
Indices: 36038--36099 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
36028 CCGTTGACCC
36038 GACCCGACCCGTT
1 GACCCGACCCGTT
*
36051 TA-CCGACCCGTT
1 GACCCGACCCGTT
36063 GACCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
36081 GACCCGACCCGTT
1 GACCCGACCCGTT
36094 GACCCG
1 GACCCG
36100 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
12 10 0.24
13 19 0.46
17 1 0.02
18 11 0.27
ACGTcount: A:0.16, C:0.47, G:0.23, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:36059 original size:30 final size:31
Alignment explanation
Indices: 36020--36099 Score: 144
Period size: 30 Copynumber: 2.6 Consensus size: 31
36010 GTCACAACCC
36020 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
36051 TA-CCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
36081 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
36100 TTGACCGTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 29 0.63
31 17 0.37
ACGTcount: A:0.16, C:0.47, G:0.23, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:36084 original size:8 final size:8
Alignment explanation
Indices: 36073--36112 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
36063 GACCCGACCC
36073 GACCCGTT
1 GACCCGTT
36081 GACCC---
1 GACCCGTT
36086 GACCCGTT
1 GACCCGTT
36094 GACCCGTT
1 GACCCGTT
36102 GA-CCGTT
1 GACCCGTT
36109 GACC
1 GACC
36113 GGAGTTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:38660 original size:24 final size:23
Alignment explanation
Indices: 38567--38671 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 23
38557 ATATTTTATC
* *
38567 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTG-TT
* *
38591 TGACATCTGATCTGAAATCTGTT
1 TGATATCTGATCTGAATTCTGTT
* *
38614 CTGAT-TCCT-AACTGGATTCTGTT
1 -TGATAT-CTGATCTGAATTCTGTT
*
38637 ATGATATCTGATCTGAATTATGTT
1 -TGATATCTGATCTGAATTCTGTT
*
38661 TGATTTCTGAT
1 TGATATCTGAT
38672 ATCTCCGTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 9
0.74 0.15 0.10
Matches are distributed among these distances:
23 30 0.47
24 34 0.53
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (23 bp):
TGATATCTGATCTGAATTCTGTT
Found at i:38840 original size:2 final size:2
Alignment explanation
Indices: 38833--38891 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
38823 CGGATGGGGG
38833 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
38875 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
38892 GTTTTAAAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40239 original size:20 final size:20
Alignment explanation
Indices: 40214--40267 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
40204 AATAGTTTCT
40214 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
40234 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
40254 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
40268 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:40519 original size:20 final size:21
Alignment explanation
Indices: 40494--40541 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
40484 TCTGAGAGAT
40494 GGAGATA-GACGGATTTCGCC
1 GGAGATAGGACGGATTTCGCC
*
40514 GGAGATAGGGACGGATTTCGTC
1 GGAGATA-GGACGGATTTCGCC
40536 GGAGAT
1 GGAGAT
40542 GGGTGAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 7 0.28
22 18 0.72
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.21
Consensus pattern (21 bp):
GGAGATAGGACGGATTTCGCC
Found at i:40775 original size:41 final size:41
Alignment explanation
Indices: 40712--40825 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
40702 CGCTTTGAAA
* *
40712 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
* * * *
40753 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
*
40794 ATCGCATTGCGA-TA-GTCAGTATCGCATTGCGA
1 ATCGCATTGCGATTATGT-ATTATCGCATTGCGA
40826 TTTTCCCAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 2 0.03
40 15 0.24
41 45 0.73
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
Found at i:40798 original size:20 final size:20
Alignment explanation
Indices: 40773--40826 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
40763 GATTTTGTAT
40773 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
40793 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
40813 TATCGCATTGCGAT
1 TATCGCATTGCGAT
40827 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:40811 original size:61 final size:62
Alignment explanation
Indices: 40712--40829 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 62
40702 CGCTTTGAAA
* * * *
40712 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
*
40774 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
40830 CCCAATTCGC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 2 0.04
61 36 0.72
62 12 0.24
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (62 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:40844 original size:21 final size:21
Alignment explanation
Indices: 40815--40870 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
40805 ATAGTCAGTA
*
40815 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
40836 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
40857 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
40871 ACTTATTCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:40845 original size:61 final size:61
Alignment explanation
Indices: 40712--40847 Score: 150
Period size: 61 Copynumber: 2.2 Consensus size: 61
40702 CGCTTTGAAA
* * * * ** *
40712 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
*
40774 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
*
40836 -TCGCGTTGCGAT
1 ATCGCATTGCGAT
40848 TTTCCCAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
60 2 0.03
61 47 0.75
62 14 0.22
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:40880 original size:20 final size:21
Alignment explanation
Indices: 40815--40887 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
40805 ATAGTCAGTA
* *
40815 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTACCAAT
*
40836 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTACCAAT
**
40857 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTACCAAT
*
40877 TCGCATTGCGA
1 TCGCGTTGCGA
40888 ATTGGGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 16 0.34
21 31 0.66
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTACCAAT
Found at i:40958 original size:21 final size:21
Alignment explanation
Indices: 40918--40958 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40908 ACTGTAGACC
** *
40918 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
40939 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
40959 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:45677 original size:20 final size:22
Alignment explanation
Indices: 45635--45678 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
45625 AAAACAGATA
45635 AAGATTAGCCGTCCCTGATGGC
1 AAGATTAGCCGTCCCTGATGGC
*
45657 AAGATTAG-CGT-CCTTATGGC
1 AAGATTAGCCGTCCCTGATGGC
45677 AA
1 AA
45679 CATGAGTGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
AAGATTAGCCGTCCCTGATGGC
Found at i:52605 original size:2 final size:2
Alignment explanation
Indices: 52598--52626 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52588 ACATAAATAC
52598 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 A
52627 ATTAGCGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55474 original size:2 final size:2
Alignment explanation
Indices: 55467--55498 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
55457 ATGAGATAGG
55467 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
55499 CACACATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62102 original size:6 final size:6
Alignment explanation
Indices: 62087--62153 Score: 80
Period size: 6 Copynumber: 11.2 Consensus size: 6
62077 GACACGTATT
* * * * * *
62087 ACCACA ACCACG ACCACA ACCTCG ACCACG ACCACG ACCTCG ACCTCA
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
62135 ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG A
62154 GCCGAGCTGA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.34, C:0.49, G:0.12, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:62165 original size:5 final size:5
Alignment explanation
Indices: 62151--62199 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
62141 ACCACGACCA
* * *
62151 CGAGC CGAGC TGAGC CGAGC C-ATGC CGTGC CGAGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGA-GC CGAGC CGAGC CGAGC CGAGC CGAG
62200 ACGGACGGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
4 1 0.03
5 36 0.97
ACGTcount: A:0.20, C:0.35, G:0.39, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:68089 original size:6 final size:6
Alignment explanation
Indices: 68066--68126 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
68056 GACACGTATT
* * *
68066 ACCACG ACCTCA ACCACG ACCACG ACCACG ACCTCG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
68114 ACCACG ACCACG A
1 ACCACG ACCACG A
68127 GCCGAGCTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.33, C:0.49, G:0.15, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:68093 original size:24 final size:24
Alignment explanation
Indices: 68066--68122 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
68056 GACACGTATT
68066 ACCACGACCTCAACCACGACCACG
1 ACCACGACCTCAACCACGACCACG
*
68090 ACCACGACCTCGACCACGACCACG
1 ACCACGACCTCAACCACGACCACG
68114 ACCACGACC
1 ACCACGACC
68123 ACGAGCCGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.51, G:0.14, T:0.04
Consensus pattern (24 bp):
ACCACGACCTCAACCACGACCACG
Found at i:73815 original size:6 final size:6
Alignment explanation
Indices: 73804--73924 Score: 120
Period size: 6 Copynumber: 20.2 Consensus size: 6
73794 TTACCAGACC
* ** *
73804 ACCACG ACCACG ACCACG ACC-CG ACCAAG AAAGATAG A-CACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG -ACCA-CG ACCACG ACCACG
* * *
73852 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * *
73900 ACCTCG ACCTCG ACCTCG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
73925 GCCGAGCCGA
Statistics
Matches: 104, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
5 7 0.07
6 92 0.88
7 3 0.03
8 2 0.02
ACGTcount: A:0.31, C:0.45, G:0.17, T:0.06
Consensus pattern (6 bp):
ACCACG
Found at i:73932 original size:5 final size:5
Alignment explanation
Indices: 73922--73980 Score: 64
Period size: 5 Copynumber: 11.8 Consensus size: 5
73912 ACCTCGACCA
* * * * *
73922 CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
*
73972 CGAGA CGAG
1 CGAGC CGAG
73981 ACGGACGGCG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.17, C:0.36, G:0.41, T:0.07
Consensus pattern (5 bp):
CGAGC
Done.