Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004410.1 Hibiscus syriacus cultivar Beakdansim tig00009665_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: 49300
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:600 original size:10 final size:11
Alignment explanation
Indices: 576--604 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
566 AGATTAGCAC
576 AGAACCGGTAA
1 AGAACCGGTAA
587 AGAACCGG-AA
1 AGAACCGGTAA
597 AGAACCGG
1 AGAACCGG
605 CTGAAAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.45, C:0.21, G:0.31, T:0.03
Consensus pattern (11 bp):
AGAACCGGTAA
Found at i:613 original size:21 final size:21
Alignment explanation
Indices: 576--629 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
566 AGATTAGCAC
*
576 AGAACCGGTAAAGAACCGGAA
1 AGAACCGGTGAAGAACCGGAA
*
597 AGAACCGGCTGAA-AACCGGGA
1 AGAACCGG-TGAAGAACCGGAA
618 A-AACCGGGTGAA
1 AGAACC-GGTGAA
630 CCGGCTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 8 0.28
21 18 0.62
22 3 0.10
ACGTcount: A:0.43, C:0.20, G:0.31, T:0.06
Consensus pattern (21 bp):
AGAACCGGTGAAGAACCGGAA
Found at i:621 original size:9 final size:9
Alignment explanation
Indices: 607--654 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
597 AGAACCGGCT
607 GAAAACCGG
1 GAAAACCGG
616 GAAAACCGG
1 GAAAACCGG
**
625 GTGAACCGG
1 GAAAACCGG
634 CTGAAAACCGG
1 --GAAAACCGG
*
645 CAAAACCGG
1 GAAAACCGG
654 G
1 G
655 GTGAACCGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
9 24 0.77
11 7 0.23
ACGTcount: A:0.38, C:0.25, G:0.33, T:0.04
Consensus pattern (9 bp):
GAAAACCGG
Found at i:632 original size:29 final size:30
Alignment explanation
Indices: 598--679 Score: 134
Period size: 29 Copynumber: 2.8 Consensus size: 30
588 GAACCGGAAA
*
598 GAACCGGCTGAAAACCGGGAAAACC-GGGT
1 GAACCGGCTGAAAACCGGCAAAACCGGGGT
627 GAACCGGCTGAAAACCGGCAAAACCGGGGT
1 GAACCGGCTGAAAACCGGCAAAACCGGGGT
657 GAACCGGCTG-AAACC-GCAAAACC
1 GAACCGGCTGAAAACCGGCAAAACC
680 AGTTTGAACC
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
28 8 0.16
29 29 0.57
30 14 0.27
ACGTcount: A:0.35, C:0.28, G:0.30, T:0.06
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGGCAAAACCGGGGT
Found at i:915 original size:24 final size:24
Alignment explanation
Indices: 882--937 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
872 TAGAAGTTCG
882 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
*
906 ATTGATGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
*
930 ATTAAAGC
1 ATTGAAGC
938 GAAAGAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:3566 original size:65 final size:64
Alignment explanation
Indices: 3477--3632 Score: 206
Period size: 65 Copynumber: 2.4 Consensus size: 64
3467 TACACTTGGG
* * * * *
3477 GTGCATCGGTACACTAATTACATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTC
1 GTGCATCAGTACACAAAATGCATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGGT-
3541 T
64 T
* * *
3542 TTGCATCAGTACATAAAATGCATTCGATGTTTCAATAAAATCAGGAGTGCATCGATGCATGGTT
1 GTGCATCAGTACACAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGTT
*
3606 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCAGTACACAAAATGCATTCGA
3633 ATTATGGTGT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 25 0.32
65 52 0.66
66 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (64 bp):
GTGCATCAGTACACAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGTT
Found at i:7988 original size:2 final size:2
Alignment explanation
Indices: 7981--8052 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
7971 ATCATAACCC
7981 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
8023 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
8053 ATAACTCACT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9107 original size:58 final size:59
Alignment explanation
Indices: 9012--9132 Score: 217
Period size: 58 Copynumber: 2.1 Consensus size: 59
9002 GGTCATGATA
* *
9012 TTGAACTATGGTTGTTTACACTATTAGTGTTTTAGTATTT-AACTATGCTTTCTTTTAT
1 TTGAACTATGGTTGTTTACACTATTAGTGTTTAAGTATTTGAACTATGATTTCTTTTAT
9070 TTGAACTATGGTTGTTTACACTATTAGTGTTTAAGTATTTGAACTATGATTTCTTTTAT
1 TTGAACTATGGTTGTTTACACTATTAGTGTTTAAGTATTTGAACTATGATTTCTTTTAT
9129 TTGA
1 TTGA
9133 TTTATGTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 39 0.65
59 21 0.35
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (59 bp):
TTGAACTATGGTTGTTTACACTATTAGTGTTTAAGTATTTGAACTATGATTTCTTTTAT
Found at i:12240 original size:16 final size:16
Alignment explanation
Indices: 12219--12252 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
12209 TTTTTAAAAA
12219 TAAAATGTGATGCACC
1 TAAAATGTGATGCACC
12235 TAAAATGTGATGCACC
1 TAAAATGTGATGCACC
12251 TA
1 TA
12253 TACAAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (16 bp):
TAAAATGTGATGCACC
Found at i:13130 original size:200 final size:201
Alignment explanation
Indices: 12641--13131 Score: 641
Period size: 200 Copynumber: 2.4 Consensus size: 201
12631 GATGTTGACG
* * * * * *
12641 CCTATTATCATTAAACCGGTAGATTTTTAACGTCTACATTGTAAATTTACTTATTACTTTAAAGT
1 CCTATTATCATTAAATCGATAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGT
* * * *
12706 AATCGAT-TTT-GAAAGTCTAACTATCGATACTTTATATATGTGTATCGATATTTTTTTGCGTGC
66 AAT--ATGTTTCGAAATTCTAAGTATCGATACTTTATATATGTGTATCGATATCTTTTTGCGTCC
* *
12769 AAATTGTTTGAGATGCATACTGGAATAAAAGTATCAATACTTATATAATAAATAGCGATACTTTA
129 AAATTGTTTGAGATCCATACTGGAATAAAAGTATCAATACATATATAATAAATAGCGATACTTTA
12834 TATTTACT
194 TATTTACT
*
12842 CCTATTATCATTAAATCGGTAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAG-
1 CCTATTATCATTAAATCGATAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGT
* * * * *
12906 ATATAGGTTTCGAATTTATAAGTATTGATACTTTATATATGTGTATTGATA-CTTTTTGCGTCCA
66 A-ATATGTTTCGAAATTCTAAGTATCGATACTTTATATATGTGTATCGATATCTTTTTGCGTCCA
* * * * *
12970 AATTGTTTGAGATCCATACTGGAATAACAGTATCGATACATATATAATAAGTATCGATTCTTTAT
130 AATTGTTTGAGATCCATACTGGAATAAAAGTATCAATACATATATAATAAATAGCGATACTTTAT
*
13035 ATTTTC-
195 ATTTACT
* * * * *
13041 CTCTATTATCATTCAATTGATAGTTTTTTACCGTTTACATTTTAAATTTACGTATTACTTTAAAG
1 C-CTATTATCATTAAATCGATAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAG
*
13106 TAATATGTTTCAAAATTCTAAGTATC
65 TAATATGTTTCGAAATTCTAAGTATC
13132 AAAATTTTGT
Statistics
Matches: 252, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
199 2 0.01
200 154 0.61
201 96 0.38
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (201 bp):
CCTATTATCATTAAATCGATAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGT
AATATGTTTCGAAATTCTAAGTATCGATACTTTATATATGTGTATCGATATCTTTTTGCGTCCAA
ATTGTTTGAGATCCATACTGGAATAAAAGTATCAATACATATATAATAAATAGCGATACTTTATA
TTTACT
Found at i:14246 original size:20 final size:20
Alignment explanation
Indices: 14153--14245 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
14143 TATTATAGGA
*
14153 ATCGATACTTATATGACAGT
1 ATCGATACTTGTATGACAGT
*
14173 ATCGATACTTGTATGATAGT
1 ATCGATACTTGTATGACAGT
14193 ATCGATACTTGTATGACAGT
1 ATCGATACTTGTATGACAGT
*
14213 ATCGATACTTGTACGACAGT
1 ATCGATACTTGTATGACAGT
*
14233 GTCGATACTTGTA
1 ATCGATACTTGTA
14246 CATTTACGCT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (20 bp):
ATCGATACTTGTATGACAGT
Found at i:14826 original size:199 final size:200
Alignment explanation
Indices: 14362--15149 Score: 832
Period size: 200 Copynumber: 3.9 Consensus size: 200
14352 TTATACATGT
* * * * * * ** *
14362 GTATCGATACTTGATGTTTATGCCTATTATCATTATATCAGTAGACTTTTAATGTTTTCATTGTA
1 GTATTGATACTTAATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTACCGTTTACATTGTA
* * * * * * *
14427 AATTAACATATTATTTTACAGTAATAGGTTTCGAAATTATAAGTATGGATACTTTATATATGTGT
66 AATTTACATATAACTTTAAAGTAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTGT
* * *
14492 ATCGATACTTTTTGCGTGCAAATTGTATGAGAAACATACTGGAATAAAAGTATCAATACTTATAT
131 ATCGATACTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCAATACATATA-
* *
14557 TAGACA
195 TAAAAA
* ** * * * * * *
14563 GTATCGATACTTGGTATTTACGTCTATTATTAATATACCAGTAGA-CTTTACCGTTTACATTGTA
1 GTATTGATACTTAATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTACCGTTTACATTGTA
* * * * ** *
14627 AATTTACATATAACTTTAAAGAAATCGGTTTCCAAATTCCGCGTATCGATAATTTATACATGTGT
66 AATTTACATATAACTTTAAAGTAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTGT
* * * *
14692 ATCGATA-TTTTGTGCGTGCAAATTG-TTGAGAAGCATACTGGATTAAAAGTATCGATCCCTATA
131 ATCGATACTTTT-TGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCAATACATATA
*
14755 CAAAAA
195 TAAAAA
* *
14761 CTATTGATACTAAATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTACCGTTTACATTGTA
1 GTATTGATACTTAATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTACCGTTTACATTGTA
* * * * * *
14826 AATTTACCTATTACTTTAAAGTAATCGGTTTCGAAAGTCCAAGTATCGATACTTTATATATGTGT
66 AATTTACATATAACTTTAAAGTAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTGT
* * *
14891 ATCTATATTTTTTGCGTGCAAATTGTTTGA-AATGCATACTGGAATAACAA-TATTAATACATAT
131 ATCGATACTTTTTGCGTGCAAATTGTTTGAGAA-GCATACTGGAATAA-AAGTATCAATACATAT
*
14954 ATAATAA
194 ATAAAAA
** * * * *
14961 GTATTGATACTTTGTCTTTACGCCTATTATAATTAAACAAGTAGATTTTTATCGTTTAC-TCTGT
1 GTATTGATACTTAATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTACCGTTTACAT-TGT
** * * * * *
15025 AAATTTATGTATAACTTTATAGTAATAGGTTTTGAGATTACAAGTATTGATACTTTGTACATGTG
65 AAATTTACATATAACTTTAAAGTAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTG
* * * * * *
15090 TATCAATACCTTTTGCGTGCAAAATGTTTGAGAAGCATATTGGAATAAATGTATCGATAC
130 TATCGATACTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCAATAC
15150 TTGATGTTGT
Statistics
Matches: 488, Mismatches: 90, Indels: 19
0.82 0.15 0.03
Matches are distributed among these distances:
198 38 0.08
199 133 0.27
200 275 0.56
201 42 0.09
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (200 bp):
GTATTGATACTTAATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTACCGTTTACATTGTA
AATTTACATATAACTTTAAAGTAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTGT
ATCGATACTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCAATACATATAT
AAAAA
Found at i:15088 original size:399 final size:389
Alignment explanation
Indices: 14375--15652 Score: 1268
Period size: 399 Copynumber: 3.3 Consensus size: 389
14365 TCGATACTTG
* * * * * * *
14375 ATGTTTATGCCTATTATCATTATATCAGTAGACTTTTAATGTTTTCATTGTAAATTAACATATTA
1 ATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTAACGTTTACATTGTAAATTTACATATTA
* * * * * *
14440 TTTTACAGTAATAGGTTTCGAAATTATAAGTATGGATACTTTATATATGTGTATCGATACTTTTT
66 CTTTAAAGTAATCGGTTTCGAAATTCTAAGTATCGATACTTTATATATGTGTATCGATATTTTTT
* * * *
14505 GCGTGCAAATTGTATGAGAA-ACATACTGGAATAAAAGTATCAATACTTATATTAGACAGTATCG
131 GCGTGCAAATTGTTTGA-AATGCATACTGGAATAAAAGTATCAATACTTATATAATA-AGTATCG
* * * *
14569 ATACTTGGTATTTACGTCTATTATTAA-TATACCAGTAGA-CTTTACCGTTTACATTGTAAATTT
194 ATACTTTGTATTTACGCCTATTA-TAATTA-AACAGTAGATTTTTACCGTTTAC-TTGTAAATTT
* ** * ** * * *
14632 ACATATAACTTTAAAGAAATCGGTTTCCAAATTCCGCGTATCGATAATTTATACATGTGTATCGA
256 ACATATAACTTTAAAG-AATAGGTTT-TGAATTACAAGTATTGATACTTTATACATGTGTATCAA
*
14697 TA-TTTTGTGCGTGCAAATTG-TTGAGAAGCATACTGGATTAAAAGTATCGATCCCTATACAAAA
319 TACTTTT-TGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGAT--CTAT--AAAA
14760 ACTATTGATACT
379 ACTATTGAT-CT
* *
14772 AAATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTACCGTTTACATTGTAAATTTACCTAT
1 --ATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTAACGTTTACATTGTAAATTTACATAT
* * *
14837 TACTTTAAAGTAATCGGTTTCGAAAGTCCAAGTATCGATACTTTATATATGTGTATCTATATTTT
64 TACTTTAAAGTAATCGGTTTCGAAATTCTAAGTATCGATACTTTATATATGTGTATCGATATTTT
* * *
14902 TTGCGTGCAAATTGTTTGAAATGCATACTGGAATAACAA-TATTAATACATATATAATAAGTATT
129 TTGCGTGCAAATTGTTTGAAATGCATACTGGAATAA-AAGTATCAATACTTATATAATAAGTATC
* *
14966 GATACTTTGTCTTTACGCCTATTATAATTAAACAAGTAGATTTTTATCGTTTACTCTGTAAATTT
193 GATACTTTGTATTTACGCCTATTATAATTAAAC-AGTAGATTTTTACCGTTTACT-TGTAAATTT
** * *
15031 ATGTATAACTTTATAGTAATAGGTTTTGAGATTACAAGTATTGATACTTTGTACATGTGTATCAA
256 ACATATAACTTTAAAG-AATAGGTTTTGA-ATTACAAGTATTGATACTTTATACATGTGTATCAA
* * * *
15096 TACCTTTTGCGTGCAAAATGTTTGAGAAGCATATTGGAATAAATGTATCG----AT----AC--T
319 TACTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATCTATAAAAACTAT
*
15151 TGATGT
384 TGATCT
* * * * *
15157 -TG--T-CGCCTATTATCATTAACCCGGTAGATTTTTAACGTCTGCATTGTAAATTTACTTATTA
1 ATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTAACGTTTACATTGTAAATTTACATATTA
*
15218 CTTTAAAGTAATCGATTTCGAAATTCTAAGTATCGATACTTTATATATGTGTATCGATATTTTTT
66 CTTTAAAGTAATCGGTTTCGAAATTCTAAGTATCGATACTTTATATATGTGTATCGATA-TTTTT
* * * * * *
15283 TGCGTGTAAATTGTTTGAGATGCATAATAGAATAAAAGTATCAATACTTATATAATAAATAGCGA
130 TGCGTGCAAATTGTTTGAAATGCATACTGGAATAAAAGTATCAATACTTATATAATAAGTATCGA
* * * * * * *
15348 TACTTTATATTTACTCCTATTATCATTAAATCGGTTGATTTTTACCGTTTATATTATAAATTTAC
195 TACTTTGTATTTACGCCTATTATAATTAAA-CAGTAGATTTTTACCGTTTA-CTTGTAAATTTAC
* * * * *
15413 CTATTACTTTAAAGATATAGGTTTTGAATTTATAAGTATTGATACTTTATATATGTGTATTAATA
258 ATATAACTTTAAAGA-ATAGGTTTTGAA-TTACAAGTATTGATACTTTATACATGTGTATCAATA
* * *
15478 CTTTTTGCGTCCAAATTGTTTGAGATGCATACTGGAATAAATA-TATCGATACATATATAATAAG
321 CTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAA-AGTATCGAT-C-TATA-AA-AAC
*
15542 TATCGATTCTTT
381 TATTGA-TC--T
* * * * ** * * **
15554 ATATTTTCTCCTATTATCATTCAA-TTGATAGATTTTTACCGTTTACATTTTAAATTTATGTATT
1 ATGTTTACGCCTATTATCATTAAACCAG-TAGATTTTTAACGTTTACATTGTAAATTTACATATT
* ** *
15618 ACATTAAAGTAATATGTTTCAAAATTCTAAGTATC
65 ACTTTAAAGTAATCGGTTTCGAAATTCTAAGTATC
15653 AAAATTTTGT
Statistics
Matches: 728, Mismatches: 113, Indels: 74
0.80 0.12 0.08
Matches are distributed among these distances:
379 111 0.15
380 205 0.28
381 2 0.00
382 2 0.00
385 1 0.00
386 7 0.01
388 2 0.00
392 1 0.00
394 5 0.01
395 1 0.00
397 6 0.01
398 39 0.05
399 239 0.33
400 33 0.05
401 74 0.10
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (389 bp):
ATGTTTACGCCTATTATCATTAAACCAGTAGATTTTTAACGTTTACATTGTAAATTTACATATTA
CTTTAAAGTAATCGGTTTCGAAATTCTAAGTATCGATACTTTATATATGTGTATCGATATTTTTT
GCGTGCAAATTGTTTGAAATGCATACTGGAATAAAAGTATCAATACTTATATAATAAGTATCGAT
ACTTTGTATTTACGCCTATTATAATTAAACAGTAGATTTTTACCGTTTACTTGTAAATTTACATA
TAACTTTAAAGAATAGGTTTTGAATTACAAGTATTGATACTTTATACATGTGTATCAATACTTTT
TGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATCTATAAAAACTATTGATCT
Found at i:15270 original size:179 final size:180
Alignment explanation
Indices: 14981--15331 Score: 413
Period size: 179 Copynumber: 2.0 Consensus size: 180
14971 TTTGTCTTTA
* * *
14981 CGCCTATTATAATTAAACAAGTAGATTTTTATCGTTTACTCTGTAAATTTATGTATAACTTTATA
1 CGCCTATTATAATTAAACAAGTAGATTTTTAACGTCTACTCTGTAAATTTATGTATAACTTTAAA
* * * * *
15046 GTAATAGGTTTTGAGATTACAAGTATTGATACTTTGTACATGTGTATCAATA-CCTTTTGCGTGC
66 GTAATAGATTTCGAAATTACAAGTATCGATACTTTATACATGTGTATCAATATCCTTTTGCGTGC
* * * *
15110 AAAATGTTTGAGAAGCATATTGGAATAAATGTATCGATACTTGATGTTGT
131 AAAATGTTTGAGAAGCATAATAGAATAAAAGTATCAATACTTGATGTTGT
* * ** * *
15160 CGCCTATTATCATTAACCCGGTAGATTTTTAACGTCTGCAT-TGTAAATTTACT-TATTACTTTA
1 CGCCTATTATAATTAAACAAGTAGATTTTTAACGTCTAC-TCTGTAAATTTA-TGTATAACTTTA
* * * **
15223 AAGTAATCGATTTCGAAATT-CTAAGTATCGATACTTTATATATGTGTATCGATATTTTTTTGCG
64 AAGTAATAGATTTCGAAATTAC-AAGTATCGATACTTTATACATGTGTATCAATATCCTTTTGCG
* * *
15287 TGTAAATTGTTTGAGATGCATAATAGAATAAAAGTATCAATACTT
128 TGCAAAATGTTTGAGAAGCATAATAGAATAAAAGTATCAATACTT
15332 ATATAATAAA
Statistics
Matches: 142, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
178 1 0.01
179 94 0.66
180 47 0.33
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (180 bp):
CGCCTATTATAATTAAACAAGTAGATTTTTAACGTCTACTCTGTAAATTTATGTATAACTTTAAA
GTAATAGATTTCGAAATTACAAGTATCGATACTTTATACATGTGTATCAATATCCTTTTGCGTGC
AAAATGTTTGAGAAGCATAATAGAATAAAAGTATCAATACTTGATGTTGT
Found at i:15486 original size:380 final size:379
Alignment explanation
Indices: 14781--15529 Score: 1031
Period size: 380 Copynumber: 2.0 Consensus size: 379
14771 TAAATGTTTA
* *
14781 CGCCTATTATCATTAAACCAGTAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAA
1 CGCCTATTATCATTAAACCAGTAGATTTTTAACGTCTACATTGTAAATTTACCTATTACTTTAAA
* *
14846 GTAATCGGTTTCGAAAGTCCAAGTATCGATACTTTATATATGTGTATCTATATTTTTTGCGTGCA
66 GTAATCGATTTCGAAAGTCCAAGTATCGATACTTTATATATGTGTATCGATATTTTTTGCGTGCA
* * * * ** *
14911 AATTGTTTGAAATGCATACTGGAATAACAATATTAATACATATATAATAAGTATTGATACTTTGT
131 AATTGTTTGAAATGCATAATAGAATAACAATATCAATACATATATAATAAATAGCGATACTTTAT
* * * **
14976 CTTTACGCCTATTATAATTAAACAAGTAGATTTTTATCGTTTACTCTGTAAATTTATGTATAACT
196 ATTTACGCCTATTATAATTAAACAAGTAGATTTTTACCGTTTACTCTATAAATTTACCTATAACT
* *
15041 TTATAGTAATAGGTTTTGAGATTACAAGTATTGATACTTTGTACATGTGTATCAATACCTTTTGC
261 TTAAAGTAATAGGTTTTGAGATTACAAGTATTGATACTTTATACATGTGTATCAATACCTTTTGC
* * *
15106 GTGCAAAATGTTTGAGAAGCATATTGGAATAAATGTATCGATACTTGATGTTGT
326 GTCCAAAATGTTTGAGAAGCATACTGGAATAAATATATCGATACTTGATGTTGT
* * * *
15160 CGCCTATTATCATTAACCCGGTAGATTTTTAACGTCTGCATTGTAAATTTACTTATTACTTTAAA
1 CGCCTATTATCATTAAACCAGTAGATTTTTAACGTCTACATTGTAAATTTACCTATTACTTTAAA
* * *
15225 GTAATCGATTTCGAAATTCTAAGTATCGATACTTTATATATGTGTATCGATATTTTTTTGCGTGT
66 GTAATCGATTTCGAAAGTCCAAGTATCGATACTTTATATATGTGTATCGATA-TTTTTTGCGTGC
* *
15290 AAATTGTTTGAGATGCATAATAGAATAA-AAGTATCAATACTTATATAATAAATAGCGATACTTT
130 AAATTGTTTGAAATGCATAATAGAATAACAA-TATCAATACATATATAATAAATAGCGATACTTT
* * * * *
15354 ATATTTACTCCTATTATCATTAAATC-GGTTGATTTTTACCGTTTA-TATTATAAATTTACCTAT
194 ATATTTACGCCTATTATAATTAAA-CAAGTAGATTTTTACCGTTTACT-CTATAAATTTACCTAT
* * * * *
15417 TACTTTAAAG-ATATAGGTTTTGA-ATTTATAAGTATTGATACTTTATATATGTGTATTAATACT
257 AACTTTAAAGTA-ATAGGTTTTGAGA-TTACAAGTATTGATACTTTATACATGTGTATCAATACC
* *
15480 TTTTGCGTCCAAATTGTTTGAGATGCATACTGGAATAAATATATCGATAC
320 TTTTGCGTCCAAAATGTTTGAGAAGCATACTGGAATAAATATATCGATAC
15530 ATATATAATA
Statistics
Matches: 322, Mismatches: 42, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
379 112 0.35
380 209 0.65
381 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (379 bp):
CGCCTATTATCATTAAACCAGTAGATTTTTAACGTCTACATTGTAAATTTACCTATTACTTTAAA
GTAATCGATTTCGAAAGTCCAAGTATCGATACTTTATATATGTGTATCGATATTTTTTGCGTGCA
AATTGTTTGAAATGCATAATAGAATAACAATATCAATACATATATAATAAATAGCGATACTTTAT
ATTTACGCCTATTATAATTAAACAAGTAGATTTTTACCGTTTACTCTATAAATTTACCTATAACT
TTAAAGTAATAGGTTTTGAGATTACAAGTATTGATACTTTATACATGTGTATCAATACCTTTTGC
GTCCAAAATGTTTGAGAAGCATACTGGAATAAATATATCGATACTTGATGTTGT
Found at i:15590 original size:200 final size:201
Alignment explanation
Indices: 15162--15652 Score: 585
Period size: 200 Copynumber: 2.4 Consensus size: 201
15152 GATGTTGTCG
** * * * * * *
15162 CCTATTATCATTAACCCGGTAGATTTTTAACGTCTGCATTGTAAATTTACTTATTACTTTAAAGT
1 CCTATTATCATTAAATCGATAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGT
* * * * **
15227 AATCGATTTCGAAATTCTAAGTATCGATACTTTATATATGTGTATCGATATTTTTTTGCGTGTAA
66 AATAGATTTCGAAATTATAAGTATCGATACTTTATATATGTGTATCAATATCTTTTTGCGTCCAA
*
15292 ATTGTTTGAGATGCATAATAGAATAAAAGTATCAATACTTATATAATAAATAGCGATACTTTATA
131 ATTGTTTGAGATGCATAATAGAATAAAAGTATCAATACATATATAATAAATAGCGATACTTTATA
15357 TTTACT
196 TTTACT
* * *
15363 CCTATTATCATTAAATCGGTTGATTTTTACCGTTTATATTATAAATTTACCTATTACTTTAAAG-
1 CCTATTATCATTAAATCGATAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGT
* * * * *
15427 ATATAGGTTTTGAATTTATAAGTATTGATACTTTATATATGTGTATTAATA-CTTTTTGCGTCCA
66 A-ATAGATTTCGAAATTATAAGTATCGATACTTTATATATGTGTATCAATATCTTTTTGCGTCCA
* * * * * *
15491 AATTGTTTGAGATGCATACTGGAATAAATA-TATCGATACATATATAATAAGTATCGATTCTTTA
130 AATTGTTTGAGATGCATAATAGAATAAA-AGTATCAATACATATATAATAAATAGCGATACTTTA
*
15555 TATTTTCT
194 TATTTACT
* * * ** *
15563 CCTATTATCATTCAATTGATAGATTTTTACCGTTTACATTTTAAATTTATGTATTACATTAAAGT
1 CCTATTATCATTAAATCGATAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGT
* *
15628 AATATG-TTTCAAAATTCTAAGTATC
66 AATA-GATTTCGAAATTATAAGTATC
15653 AAAATTTTGT
Statistics
Matches: 244, Mismatches: 42, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
200 145 0.59
201 99 0.41
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (201 bp):
CCTATTATCATTAAATCGATAGATTTTTACCGTTTACATTATAAATTTACCTATTACTTTAAAGT
AATAGATTTCGAAATTATAAGTATCGATACTTTATATATGTGTATCAATATCTTTTTGCGTCCAA
ATTGTTTGAGATGCATAATAGAATAAAAGTATCAATACATATATAATAAATAGCGATACTTTATA
TTTACT
Found at i:17201 original size:6 final size:6
Alignment explanation
Indices: 17190--17218 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17180 CTCAAATTGA
17190 AAATTC AAATTC AAATTC AAATTC AAATT
1 AAATTC AAATTC AAATTC AAATTC AAATT
17219 GAAAATTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATTC
Found at i:19816 original size:18 final size:18
Alignment explanation
Indices: 19782--19821 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
19772 AAGCCCTTAC
*
19782 TTGAGAAGAATACCTTGG
1 TTGAGAAGAATAACTTGG
19800 TTGAGAAG-ATGAACTTGG
1 TTGAGAAGAAT-AACTTGG
19818 TTGA
1 TTGA
19822 TAATAAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (18 bp):
TTGAGAAGAATAACTTGG
Found at i:20649 original size:180 final size:187
Alignment explanation
Indices: 20341--21144 Score: 567
Period size: 180 Copynumber: 4.2 Consensus size: 187
20331 GTTTAGATCG
* * * **
20341 AAAGTATCAATACCTATATAA-AACATATCGATACTTTATGTTTCCACCTATTATCATTAAAATG
1 AAAGTATCAATACCTATATAATAA-GTATCGATACTTTATGTTTACGCCTATTATCATTAAACCG
* * * * * * ** *
20405 ATAGATTTTTACCGTTTACATTGTAAATTTACCTATTAATTCAAAGCAATATGCATCAAAATTAT
65 GTAGATTTTTACCGTTTACATTGTAAATTTACATATTACTTTAAAGAAATAAGTTTCGAAATTAT
*
20470 AAGTATCAATACTTT-T-T-TGCAT-G-TA-AAT-TGTTTGAGATGCATACTGGAATA
130 AAGTATCGATACTTTATATGTGCATCGATATAATATGTTTGAGATGCATACTGGAATA
* * *
20521 AAAGTATCAATACTTATATAATAAGTACCGATACTTTATGTTTACGCCTATTATCATTCAACCGG
1 AAAGTATCAATACCTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCGG
* *
20586 TAGATTTTTACCGTTTACATTGTAAATTTACATATTACTTTAAAGAAATAAATTTTGAAATTATA
66 TAGATTTTTACCGTTTACATTGTAAATTTACATATTACTTTAAAGAAATAAGTTTCGAAATTATA
*
20651 AGTATCGATACTTGTTATATGTGTATCGATACTTTTTTGCGTGCAA-ATTGTTTGAGATGCATAC
131 AGTATCGATAC-T-TTATATGTGCATCGATA----------T--AATA-TGTTTGAGATGCATAC
20715 TGGAATA
181 TGGAATA
* *
20722 AAAGTATCGATACCTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATAATTAAACCGG
1 AAAGTATCAATACCTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCGG
* * * * *
20787 TAGATTTTTACAC-TTTACTTTGTAAACTTA-AGTATT-CTTTATAGTAATAGGTTTCGAAATTA
66 TAGATTTTTAC-CGTTTACATTGTAAATTTACA-TATTACTTTAAAGAAATAAGTTTCGAAATTA
* * * * * * *
20849 CAAGTATTGATACTTTGTACATGTGTATCGATACTTTTTGCGTGCAAAATGTTTGTGATTCATAC
129 TAAGTATCGATAC-TT-TATATGTGCATCGATA---------T--AATATGTTTGAGATGCATAC
20914 TGGAATA
181 TGGAATA
* ** * * *
20921 TAAGTATTGATACTTATATAATAAGTATCGATACTTTCTGTTTACACCTATTATCATTAAA-C--
1 AAAGTATCAATACCTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCGG
* * * * *
20983 T-G----GT-CCGTTTATATTGTAAATTTACCTATTACTTTAAA-ATAA-AAGGTTTCAAAATTC
66 TAGATTTTTACCGTTTACATTGTAAATTTACATATTACTTTAAAGA-AATAA-GTTTCGAAATTA
* *
21040 TAAGTATCGATACTTTTATATATGTATCGATATTTTTTGCGTGCAA-ATTGTTTGAGATGCATAC
129 TAAGTATCGATAC-TTTATATGTGCATCGATA---------T--AATA-TGTTTGAGATGCATAC
*
21104 TAGAATA
181 TGGAATA
* *
21111 AAAGTATCGATACCTATATAAAAAGTATCGATAC
1 AAAGTATCAATACCTATATAATAAGTATCGATAC
21145 CTATAGAAAA
Statistics
Matches: 524, Mismatches: 67, Indels: 56
0.81 0.10 0.09
Matches are distributed among these distances:
180 118 0.23
181 3 0.01
182 2 0.00
183 1 0.00
184 1 0.00
185 4 0.01
186 1 0.00
187 2 0.00
189 2 0.00
190 97 0.19
191 33 0.06
195 1 0.00
196 1 0.00
198 1 0.00
199 90 0.17
200 53 0.10
201 113 0.22
202 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (187 bp):
AAAGTATCAATACCTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCGG
TAGATTTTTACCGTTTACATTGTAAATTTACATATTACTTTAAAGAAATAAGTTTCGAAATTATA
AGTATCGATACTTTATATGTGCATCGATATAATATGTTTGAGATGCATACTGGAATA
Found at i:21136 original size:21 final size:21
Alignment explanation
Indices: 21110--21165 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
21100 ATACTAGAAT
*
21110 AAAAGTATCGATACCTATATA
1 AAAAGTATCGATACCTATAGA
21131 AAAAGTATCGATACCTATAGA
1 AAAAGTATCGATACCTATAGA
21152 AAAAGTATCGATAC
1 AAAAGTATCGATAC
21166 TTTATGTTTA
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:0.48, C:0.14, G:0.12, T:0.25
Consensus pattern (21 bp):
AAAAGTATCGATACCTATAGA
Found at i:21360 original size:21 final size:20
Alignment explanation
Indices: 21330--21368 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
21320 GCATACTGGA
21330 ATAAAAGTATCGATACTTAT
1 ATAAAAGTATCGATACTTAT
21350 ATAATAAGTATCGATACTT
1 ATAA-AAGTATCGATACTT
21369 TATGTTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
ATAAAAGTATCGATACTTAT
Found at i:21374 original size:201 final size:201
Alignment explanation
Indices: 20472--21569 Score: 1071
Period size: 201 Copynumber: 5.4 Consensus size: 201
20462 AAAATTATAA
* * * *
20472 GTATCAATACTTTTTTGCATGTAAATTGTTTGAGATGCATACTGGAATAAAAGTATCAATACTTA
1 GTATCGATACTTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTA
* * ***
20537 TATAATAAGTACCGATACTTTATGTTTACGCCTATTATCATTCAACCGGTAGATTTTTACCGTTT
66 TATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGTAGATTTTTATAATTT
* ** * *
20602 ACATTGTAAATTT-ACATATTACTTTAAAGAAATAAATTTTGAAATTATAAGTATCGATACTTGT
131 ACATTGTAAATTTAAC-TATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTTTT
20666 TATATGT
195 TATATGT
*
20673 GTATCGATACTTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACCTA
1 GTATCGATACTTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTA
* * *
20738 TATAATAAGTATCGATACTTTATGTTTACGCCTATTATAATTAAACCGGTAGATTTTTACACTTT
66 TATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGTAGATTTTTATAATTT
* * * * * * *
20803 ACTTTGTAAACTTAAGTATT-CTTTATAGTAATAGGTTTCGAAATTACAAGTATTGATACTTTGT
131 ACATTGTAAATTTAACTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTTTTT
*
20867 ACATGT
196 ATATGT
* * * * *
20873 GTATCGATAC-TTTTTGCGTGCAAAATGTTTGTGATTCATACTGGAATATAAGTATTGATACTTA
1 GTATCGATACTTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTA
* * * *
20937 TATAATAAGTATCGATACTTTCTGTTTACACCTATTATCATTAAACTGGTCCG----TT-T-A--
66 TATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGT-AGATTTTTATAATT
* * * * *
20994 T--ATTGTAAATTTACCTATTACTTTAAAATAAAAGGTTTCAAAATTCTAAGTATCGATAC-TTT
130 TACATTGTAAATTTAACTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTTTT
*
21056 TATATAT
195 TATATGT
* *
21063 GTATCGATA-TTTTTTGCGTGCAAATTGTTTGAGATGCATACTAGAATAAAAGTATCGATACCTA
1 GTATCGATACTTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTA
* * * ** *
21127 TATAAAAAGTATCGATACCTATAGAAAAAGTATCGATAC-TTTATGTTTACGCCCATTATCATTA
66 TATAATAAGTATCGATA-CT-T----TATGT-T---TACGCCTA---TTA---TCA-T-T-A--A
*** ** * * * *
21191 AATTGGTAGACGTTTATAATTTACATTGTAAATTTATCTATTACTTTAAAGGAGTAGGTTTCGGA
110 ACCG-GTAGATTTTTATAATTTACATTGTAAATTTAACTATTACTTTAAAGTAATAGGTTTCGAA
* * *
21256 ATTTTAAGTATCAATACTTTTTATATAT
174 ATTATAAGTATCGATACTTTTTATATGT
* *
21284 GTATTGATACTTTTTTGCGTGTAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTA
1 GTATCGATACTTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTA
* * * * * *
21349 TATAATAAGTATCGATACTTTATGTTTACACCCATTATCATTAAATCGATAGATTGTTATAGTTT
66 TATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGTAGATTTTTATAATTT
* * * * * ** *
21414 CCATTGTATATTTAAGTATTAATGTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTAT
131 ACATTGTAAATTTAACTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTTTTT
*
21479 ATATGG
196 ATATGT
* * * *
21485 GTATCGATACTTTGTTGC-TGCCAAATTGTTTGAGAT-CGATACTAGAATAAAAGTATCAATACG
1 GTATCGATACTTTTTTGCGTG-CAAATTGTTTGAGATGC-ATACTGGAATAAAAGTATCGATACT
* * *
21548 GATATAAAAAGTATCGAAACTT
64 TATATAATAAGTATCGATACTT
21570 GGACAATTTC
Statistics
Matches: 737, Mismatches: 119, Indels: 82
0.79 0.13 0.09
Matches are distributed among these distances:
190 93 0.13
191 34 0.05
192 2 0.00
196 4 0.01
197 1 0.00
199 96 0.13
200 57 0.08
201 274 0.37
202 6 0.01
204 1 0.00
205 3 0.00
206 2 0.00
207 3 0.00
208 1 0.00
210 7 0.01
211 2 0.00
212 3 0.00
213 1 0.00
214 2 0.00
215 2 0.00
216 4 0.01
218 1 0.00
220 50 0.07
221 20 0.03
222 68 0.09
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (201 bp):
GTATCGATACTTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATACTTA
TATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCGGTAGATTTTTATAATTT
ACATTGTAAATTTAACTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTTTTT
ATATGT
Found at i:23385 original size:38 final size:38
Alignment explanation
Indices: 23334--23406 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
23324 ATCCAATAGA
23334 AGAAGGAATTAGTAAAATACATATCAACGAGTTGAAAG
1 AGAAGGAATTAGTAAAATACATATCAACGAGTTGAAAG
* *
23372 AGAAGGAATTAGTAAAATGCATATCAACTAGTTGA
1 AGAAGGAATTAGTAAAATACATATCAACGAGTTGA
23407 TAGCGAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.48, C:0.08, G:0.21, T:0.23
Consensus pattern (38 bp):
AGAAGGAATTAGTAAAATACATATCAACGAGTTGAAAG
Found at i:31870 original size:11 final size:12
Alignment explanation
Indices: 31854--31886 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
31844 TAAGGGGGAG
31854 TAATTTCAAAC-
1 TAATTTCAAACT
31865 TAATTTCAAACT
1 TAATTTCAAACT
*
31877 TGATTTCAAA
1 TAATTTCAAA
31887 ATCTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (12 bp):
TAATTTCAAACT
Found at i:33360 original size:20 final size:20
Alignment explanation
Indices: 33312--33430 Score: 69
Period size: 20 Copynumber: 5.9 Consensus size: 20
33302 GTAGTTCTTT
* *
33312 ACTGGTTTTCTCAAATTGAA
1 ACTGGTTTTGTCAAATTTAA
* * *
33332 ACCGATTTTGTCAAATTTCA
1 ACTGGTTTTGTCAAATTTAA
* *
33352 ACTGGTTTTGTCAATTTTTA
1 ACTGGTTTTGTCAAATTTAA
* **
33372 A-TCGGTTTAGTCAAATTCTTT
1 ACT-GGTTTTGTCAAATT-TAA
* * *
33393 ACTTGTCTTGTCAAATTGAA
1 ACTGGTTTTGTCAAATTTAA
* **
33413 ATTGAATTTGTCAAATTT
1 ACTGGTTTTGTCAAATTT
33431 CATTATGTTA
Statistics
Matches: 72, Mismatches: 24, Indels: 6
0.71 0.24 0.06
Matches are distributed among these distances:
19 1 0.01
20 56 0.78
21 14 0.19
22 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (20 bp):
ACTGGTTTTGTCAAATTTAA
Found at i:41962 original size:14 final size:15
Alignment explanation
Indices: 41943--41974 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
41933 CCACCGACCG
41943 AATCGAATTATCA-T
1 AATCGAATTATCACT
41957 AATCGAATTATCACT
1 AATCGAATTATCACT
41972 AAT
1 AAT
41975 TGAAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (15 bp):
AATCGAATTATCACT
Found at i:43244 original size:16 final size:15
Alignment explanation
Indices: 43206--43253 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
43196 TATAAGGTAA
43206 TTTTATTATAA-TAT
1 TTTTATTATAATTAT
43220 TTTTAATTATAATTAT
1 TTTT-ATTATAATTAT
*
43236 TGTTTATTATCATTAT
1 T-TTTATTATAATTAT
43252 TT
1 TT
43254 GAAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.13
15 8 0.27
16 15 0.50
17 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:46456 original size:35 final size:34
Alignment explanation
Indices: 46371--46457 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
46361 ATTTGGTATT
*
46371 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
46405 TAAATGATAACCAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
46443 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
46458 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:48848 original size:10 final size:10
Alignment explanation
Indices: 48829--48859 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
48819 CTTAAACAGA
*
48829 GAGAGTATTT
1 GAGAGAATTT
48839 GAGAGAATTT
1 GAGAGAATTT
48849 GAGAGAATTT
1 GAGAGAATTT
48859 G
1 G
48860 GTGTGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:49085 original size:50 final size:50
Alignment explanation
Indices: 49016--49135 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 50
49006 TACCCCTATG
* ** * * **
49016 GCGTATAGCGTGGATCAGGGTCGCGCTATA-CTCACGTGTAACCTATGTCA
1 GCGTATAGCGCGGGGCAGGGACGCGCTATATCTCACGTGGAACC-AAATCA
* **
49066 GCGTATAGCGCGGGGCAGGGACGCGCTATATCTCATGTGGCGCCAAATCA
1 GCGTATAGCGCGGGGCAGGGACGCGCTATATCTCACGTGGAACCAAATCA
*
49116 GCATATAGCGCGGGGCAGGG
1 GCGTATAGCGCGGGGCAGGG
49136 GGCGCGCTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 49 0.84
51 9 0.16
ACGTcount: A:0.22, C:0.24, G:0.34, T:0.20
Consensus pattern (50 bp):
GCGTATAGCGCGGGGCAGGGACGCGCTATATCTCACGTGGAACCAAATCA
Done.