Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002387.1 Hibiscus syriacus cultivar Beakdansim tig00004885_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: 91409
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3270 original size:22 final size:20
Alignment explanation
Indices: 3229--3271 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
3219 ATACTCTTAT
*
3229 TATATACATGCCTATTACCA
1 TATATACATGCCTATCACCA
*
3249 TATATAGATGCCTTCATCACCA
1 TATATACATGCC-T-ATCACCA
3271 T
1 T
3272 TTCACCGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35
Consensus pattern (20 bp):
TATATACATGCCTATCACCA
Found at i:6793 original size:34 final size:34
Alignment explanation
Indices: 6696--6794 Score: 180
Period size: 34 Copynumber: 2.9 Consensus size: 34
6686 ATACACACAT
*
6696 ACGTATGATCTTAAATTTATGTATAAAACATTAA
1 ACGTATGATCTTAAATTTATGTATAAAACTTTAA
6730 ACGTATGATCTTAAATTTATGTATAAAACTTTAA
1 ACGTATGATCTTAAATTTATGTATAAAACTTTAA
*
6764 ACGTATGATCTTAAATTTATGTATTAAACTT
1 ACGTATGATCTTAAATTTATGTATAAAACTT
6795 GAAATTTGAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (34 bp):
ACGTATGATCTTAAATTTATGTATAAAACTTTAA
Found at i:8319 original size:20 final size:19
Alignment explanation
Indices: 8290--8330 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
8280 TCGAACAAGG
*
8290 GTATCAATACTTTTCTTACA
1 GTATCAATACTATTCTT-CA
*
8310 GTATCGATACTATTCTTCA
1 GTATCAATACTATTCTTCA
8329 GT
1 GT
8331 TAAGGCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.44
Consensus pattern (19 bp):
GTATCAATACTATTCTTCA
Found at i:24232 original size:54 final size:54
Alignment explanation
Indices: 24166--24347 Score: 283
Period size: 54 Copynumber: 3.4 Consensus size: 54
24156 TTCTTTGAGA
* * * *
24166 TGCACACGTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
* * * *
24220 TGCACACTTAGTGGCTATACGATCGTTCATTAACATATGATGAATTACGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
*
24274 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
24328 TGCACACTTAGTGCCTATAC
1 TGCACACTTAGTGCCTATAC
24348 TGTAACACTC
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 117 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
Found at i:25422 original size:2 final size:2
Alignment explanation
Indices: 25415--25441 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25405 CTTATTCATG
25415 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 T
25442 CCGCAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31234 original size:541 final size:542
Alignment explanation
Indices: 28642--34291 Score: 10525
Period size: 542 Copynumber: 10.4 Consensus size: 542
28632 CCAAATAATT
* * * *
28642 TCTATTATATAAAACGTATGG-TTTATCAAATTGATCAGAGTGTATCCAATAAAAATCTTATATC
1 TCTATTGTATAAAACGTATGGTTTTA-CAAATTGATCAGAGCGTATCCAATACAAATCTTTTATC
**
28706 TTACATAACAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATT
65 TTACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATT
* * *
28771 GTGGAAAGGAGAATATGACCTGTCTTACTCCTCTAAACTTCTCTTTTTGCTTTCCGGAACCTACG
130 GTGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACG
* *
28836 TGTGAAATACTCACACACTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAA
195 TGTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAA
28901 CTACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTA
260 CTACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTA
28966 ATCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTA
325 ATCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTA
*
29031 TCAACATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATG
390 TCAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATG
*
29096 ACTCATTAAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAA
455 ACTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAA
29161 GCATATACATCACTTGTAATATA
520 GCATATACATCACTTGTAATATA
* *
29184 TCTATTGTATAAAACGTATGGTTTTACAAATTGATTAGAGTGTATCCAATACAAATCTTTTATCT
1 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
29249 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
66 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
29314 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
131 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
29379 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
196 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
* *
29444 TTCTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATATAA
261 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
*
29509 TCAAATGTACACATATACATATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
326 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
*
29574 CAATATGATTAGTATTTATATCTTGTAACCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
391 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
*
29639 CTCATTTAACCATGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
456 CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
29704 CATATACATCACTTGTAATATA
521 CATATACATCACTTGTAATATA
* *
29726 TCTATTGTATAAAACGTATGGTTTTACAAATTGATTAGAGTGTATCCAATACAAATCTTTTATCT
1 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
29791 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
66 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
29856 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
131 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
*
29921 ATGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
196 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
*
29986 TTCTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
261 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
30051 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
326 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
*
30116 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACATTTTAACCAACATGA
391 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
*
30181 CTCATTTAACCACGCAATACACATGTCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
456 CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
30246 CATATACATCACTTGTAATATA
521 CATATACATCACTTGTAATATA
30268 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
1 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
30333 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
66 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
*
30398 TGGAAAGGAGAATCTGACCTATCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
131 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
*
30463 ATGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
196 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
30528 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
261 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
30593 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
326 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
*
30658 CAATATGATTAGTATTTATATCTTGTAACCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
391 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
*
30723 CTCATTTAACCATGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
456 CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
30788 CATATACATCACTTGTAATATA
521 CATATACATCACTTGTAATATA
* *
30810 TCTATTGTATAAAACATATGGTTTTACAAATTGATTAGAGCGTATCCAATACAAATCTTTTATCT
1 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
* *
30875 TACATGCCAACTACATTTCATAGGAC-AAATACATATAATTTAAACATATTTCTGATTTGAAATG
66 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
*
30939 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCATTCCGGAACCTACGT
131 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
31004 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
196 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
31069 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
261 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
* *
31134 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCAATCATTAACCTTACTTTATTAT
326 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
*
31199 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACATTTTAACCAACATGA
391 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
*
31264 CTCATTTAACCACGCAATACACATATCATCATTAAAACCATATGATACAATTCATCTCACAAAAG
456 CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
31329 CATATACATCACTTGTAATATA
521 CATATACATCACTTGTAATATA
*
31351 TCTATTGTATAAAACGCATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
1 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
*
31416 TACATGCCAACTACATTTCACATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
66 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
* * * * *
31481 TAGAAAGGAGAATCTGACCTGTATTGCTCCTTTAAACTTCTCTTTTTGCTTTCCGGAACCTACAT
131 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
* *
31546 GTGAAACACTCACACACTAAGTCTATGAATTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
196 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
* *
31611 TACTTAATCATGCATGAACATATCATATCATGTTATCACACAAAATAATATAGCATTTCATGTAA
261 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
*
31676 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTTCATCATTAACCTTACTTTACTAT
326 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
31741 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
391 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
*
31806 CTCATTTAACCACGCAATACACATGTCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
456 CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
31871 CATATACATCACTTGTAATATA
521 CATATACATCACTTGTAATATA
* *
31893 TCTATTGTATAAAACATATGGTTTTACAAATTGATCAGAGCATATCCAATACAAATCTTTTATCT
1 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
31958 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
66 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
32023 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
131 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
32088 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
196 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
32153 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
261 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
32218 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
326 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
*
32283 CATTATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
391 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
*
32348 CTCATTTAACCACGCAATACACATGTCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
456 CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
32413 CATATACATCACTTGTAATATA
521 CATATACATCACTTGTAATATA
32435 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
1 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
32500 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
66 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
*
32565 TGGAAAGGAGAATCTGACATGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
131 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
* * *
32630 ATGAAACACTCACACGCTAAGTCTATGACGTAGTGAGGCATTAAACACATAAAAGTAGCTCTAAC
196 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
* *
32695 TACTTAATCATACATGAAAATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
261 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
32760 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
326 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
*
32825 CATTATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
391 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
*
32890 CTCATTTAACCATGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
456 CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
32955 CATATACATCACTTGTAATATA
521 CATATACATCACTTGTAATATA
* *
32977 TCTATTGTATAAAACGTATGGTTTTACAAATTGATTAGAGTGTATCCAATACAAATCTTTTATCT
1 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
* *
33042 TACATGCCAACTACATTTCATATGAC-AAATACATATAATTTAAACATATTTCTGATTTAAATTA
66 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
*
33106 TGAAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
131 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
33171 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
196 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
*
33236 TACTTAATCATGCATGAACATATCATATCATACTATCACACAAAACAATATAGCATTTCATGTAA
261 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
*
33301 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTATTAT
326 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
*
33366 TAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
391 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
*
33431 CTCATTTAACCACACAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
456 CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
33496 CATATACATCACTTGTAATATA
521 CATATACATCACTTGTAATATA
*
33518 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAAAGCGTATCCAATACAAATCTTTTATCT
1 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
33583 TACATGCCAACT-CATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
66 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
33647 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
131 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
33712 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
196 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
33777 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
261 TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
* *
33842 TCAAATGTACACATATACACATCATTCATTCAACATTCGTTCCATCAATAACCTTACTTTACTAT
326 TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
* *
33907 CATTATGATTAGTATTTATATCTTGTAATCATATCCTTTCATACTTAACGTTTTAACCAACATGA
391 CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
33972 CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
456 CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
34037 CATATACATCACTTGTAATATA
521 CATATACATCACTTGTAATATA
*
34059 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCATATCCAATACAAATCTTTTATCT
1 TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
34124 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
66 TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
*
34189 TGGAAAGGAGAATCTGACCTATCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
131 TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
* *
34254 GTGAAACACTCACACTCTAAGTCTATGAATTAGTGAGG
196 GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGG
34292 TTGTGCACTA
Statistics
Matches: 4975, Mismatches: 129, Indels: 8
0.97 0.03 0.00
Matches are distributed among these distances:
540 13 0.00
541 1549 0.31
542 3409 0.69
543 4 0.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (542 bp):
TCTATTGTATAAAACGTATGGTTTTACAAATTGATCAGAGCGTATCCAATACAAATCTTTTATCT
TACATGCCAACTACATTTCATATGACAAAATACATATAATTTAAACATATTTCTGATTTGAATTG
TGGAAAGGAGAATCTGACCTGTCTTGCTCCTCTAAACTTCTCTTCTTGCTTTCCGGAACCTACGT
GTGAAACACTCACACGCTAAGTCTATGACTTAGTGAGGCATTAAACACATAAAAGTAACTCTAAC
TACTTAATCATGCATGAACATATCATATCATGCTATCACACAAAACAATATAGCATTTCATGTAA
TCAAATGTACACATATACACATCATTCATTCAACATTCTTTCCATCATTAACCTTACTTTACTAT
CAATATGATTAGTATTTATATCTTGTAATCATATCCTTTCGTACTTAACGTTTTAACCAACATGA
CTCATTTAACCACGCAATACACATATCATCATTAAAATCATATGATACAATTCATCTCACAAAAG
CATATACATCACTTGTAATATA
Found at i:36793 original size:23 final size:23
Alignment explanation
Indices: 36767--36811 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
36757 CGAAATACCA
*
36767 CGTAGAATTGCACTGAAGTGCTG
1 CGTAGAATTGCACCGAAGTGCTG
*
36790 CGTAGAATTGCACCGTAGTGCT
1 CGTAGAATTGCACCGAAGTGCT
36812 ATATAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCTG
Found at i:45340 original size:36 final size:36
Alignment explanation
Indices: 45293--45393 Score: 186
Period size: 36 Copynumber: 2.8 Consensus size: 36
45283 TCCAAAATAT
45293 CCAAGACCAACGCGAGCAACAATGCACCATCTTCAC
1 CCAAGACCAACGCGAGCAACAATGCACCATCTTCAC
45329 CCAAGACCAACGCGAGCAACAATGCACCATCTTCAC
1 CCAAGACCAACGCGAGCAACAATGCACCATCTTCAC
45365 CCAAGACCAAAC-CGAGCAACAATGCACCA
1 CCAAGACC-AACGCGAGCAACAATGCACCA
45394 AAGGCTAAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
36 61 0.95
37 3 0.05
ACGTcount: A:0.39, C:0.39, G:0.14, T:0.09
Consensus pattern (36 bp):
CCAAGACCAACGCGAGCAACAATGCACCATCTTCAC
Found at i:47380 original size:66 final size:66
Alignment explanation
Indices: 47274--47417 Score: 191
Period size: 66 Copynumber: 2.2 Consensus size: 66
47264 AAACCCTACC
* * *
47274 CCAACCCCTTCTCCATCCCCGCCCCCGAAGCCAACTCCTTCTCCGGCACCGGCATCGACCCCAAA
1 CCAACCCCATCTCCATCCCCACCCCCGAAGCCAACTCCTTCTCCAGCACCGGCATCGACCCCAAA
47339 G
66 G
* * * *
47340 CCAACCCCATCTCC-TACCCCATCCCCGAAGCCAACTCCTTCTCCAGCACCGGTATCGGCCCCTA
1 CCAACCCCATCTCCAT-CCCCACCCCCGAAGCCAACTCCTTCTCCAGCACCGGCATCGACCCCAA
47404 AG
65 AG
* *
47406 TCGACCCCATCT
1 CCAACCCCATCT
47418 TTGGCCCCGG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 1 0.01
66 67 0.99
ACGTcount: A:0.20, C:0.51, G:0.12, T:0.16
Consensus pattern (66 bp):
CCAACCCCATCTCCATCCCCACCCCCGAAGCCAACTCCTTCTCCAGCACCGGCATCGACCCCAAA
G
Found at i:47698 original size:72 final size:72
Alignment explanation
Indices: 47575--47777 Score: 167
Period size: 72 Copynumber: 2.8 Consensus size: 72
47565 CGACGTAAAA
* * * * * * * * *
47575 CTAAACCAAGCAACAATGGACCATCTTCATCCAAGACCAAATCGAGTAACAATGCACGATCTACA
1 CTAAACCAAGCAACAATGCACCACCTCCATCCAAGACCAAACCAAGCAACAATCCACCACCTACA
*
47640 CCCAATG
66 CCCAAGG
* * * *
47647 CTGAACCAAGCAACAATGCACCACCTCCATCCAACG-CTAACCCAAGCAACAATCCACCACCTCC
1 CTAAACCAAGCAACAATGCACCACCTCCATCCAA-GACCAAACCAAGCAACAATCCACCACCTAC
*
47711 ACCGAAGG
65 ACCCAAGG
* * * * * * **
47719 TTAAACCAAGC-ACTAGTGCACCACCTCCATCCCAGTCTAGACCAAGCATTAATCCACCA
1 CTAAACCAAGCAAC-AATGCACCACCTCCATCCAAGACCAAACCAAGCAACAATCCACCA
47778 TCTGAAGCTC
Statistics
Matches: 105, Mismatches: 23, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
71 3 0.03
72 101 0.96
73 1 0.01
ACGTcount: A:0.37, C:0.37, G:0.11, T:0.15
Consensus pattern (72 bp):
CTAAACCAAGCAACAATGCACCACCTCCATCCAAGACCAAACCAAGCAACAATCCACCACCTACA
CCCAAGG
Found at i:47745 original size:36 final size:36
Alignment explanation
Indices: 47575--47750 Score: 142
Period size: 36 Copynumber: 4.9 Consensus size: 36
47565 CGACGTAAAA
* * *
47575 CTAAACCAAGCAACAATGGACCATCTTCATCCAA-G
1 CTAAACCAAGCAACAATGCACCACCTCCATCCAACG
* * * * * * * * *
47610 ACCAAATCGAGTAACAATGCACGATCTACACCCAATG
1 -CTAAACCAAGCAACAATGCACCACCTCCATCCAACG
*
47647 CTGAACCAAGCAACAATGCACCACCTCCATCCAACG
1 CTAAACCAAGCAACAATGCACCACCTCCATCCAACG
* * *
47683 CTAACCCAAGCAACAATCCACCACCTCCA-CCGAAGG
1 CTAAACCAAGCAACAATGCACCACCTCCATCC-AACG
* *
47719 TTAAACCAAGC-ACTAGTGCACCACCTCCATCC
1 CTAAACCAAGCAAC-AATGCACCACCTCCATCC
47751 CAGTCTAGAC
Statistics
Matches: 110, Mismatches: 26, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
35 4 0.04
36 103 0.94
37 3 0.03
ACGTcount: A:0.37, C:0.38, G:0.11, T:0.14
Consensus pattern (36 bp):
CTAAACCAAGCAACAATGCACCACCTCCATCCAACG
Found at i:47777 original size:36 final size:36
Alignment explanation
Indices: 47650--47777 Score: 113
Period size: 36 Copynumber: 3.6 Consensus size: 36
47640 CCCAATGCTG
*
47650 AACCAAGCAACAATGCACCACCTCCATCCAACG-CT
1 AACCAAGCAACAATCCACCACCTCCATCCAACGTCT
*
47685 AACCCAAGCAACAATCCACCACCTCCA-CCGAAGGT-T
1 AA-CCAAGCAACAATCCACCACCTCCATCC-AACGTCT
* * *
47721 AAACCAAGC-ACTAGTGCACCACCTCCATCCCA-GTCT
1 -AACCAAGCAAC-AATCCACCACCTCCATCCAACGTCT
**
47757 AGACCAAGCATTAATCCACCA
1 A-ACCAAGCAACAATCCACCA
47778 TCTGAAGCTC
Statistics
Matches: 75, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
35 9 0.12
36 62 0.83
37 4 0.05
ACGTcount: A:0.36, C:0.41, G:0.10, T:0.13
Consensus pattern (36 bp):
AACCAAGCAACAATCCACCACCTCCATCCAACGTCT
Found at i:58530 original size:25 final size:25
Alignment explanation
Indices: 58500--58570 Score: 124
Period size: 25 Copynumber: 2.8 Consensus size: 25
58490 TAGGGGATTA
* *
58500 GGTTTGAAACCCTAATTTGTTTTAG
1 GGTTTGAAACCCTAATCTGATTTAG
58525 GGTTTGAAACCCTAATCTGATTTAG
1 GGTTTGAAACCCTAATCTGATTTAG
58550 GGTTTGAAACCCTAATCTGAT
1 GGTTTGAAACCCTAATCTGAT
58571 GGGTTGTTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (25 bp):
GGTTTGAAACCCTAATCTGATTTAG
Found at i:58628 original size:11 final size:10
Alignment explanation
Indices: 58611--58648 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
58601 GGGCTTCGGG
58611 TTGTTGGGCC
1 TTGTTGGGCC
58621 TCTGTTGGGCC
1 T-TGTTGGGCC
58632 TTGGTTGGGCC
1 TT-GTTGGGCC
58643 TTGTTG
1 TTGTTG
58649 TATTGGGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.00, C:0.18, G:0.39, T:0.42
Consensus pattern (10 bp):
TTGTTGGGCC
Found at i:58693 original size:3 final size:3
Alignment explanation
Indices: 58679--58731 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
58669 TATGTAAATG
* **
58679 TAA TAT TAA TAA TAAA TAA TAA TAA TAA TAA TAA -AA TAA CGA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
58724 TAA TAA TA
1 TAA TAA TA
58732 TACAAAAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:58696 original size:13 final size:13
Alignment explanation
Indices: 58680--58731 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
58670 ATGTAAATGT
*
58680 AATATTAATAATA
1 AATAATAATAATA
58693 AATAATAATAAT-
1 AATAATAATAATA
58705 AATAATAA-AATA
1 AATAATAATAATA
58717 ACGATAATAATAATA
1 A--ATAATAATAATA
58732 TACAAAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 3 0.09
12 9 0.26
13 11 0.32
14 7 0.21
15 4 0.12
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:59052 original size:46 final size:45
Alignment explanation
Indices: 58970--59216 Score: 151
Period size: 46 Copynumber: 5.7 Consensus size: 45
58960 TCGGGGAATG
* ** **
58970 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGTTCATACGTGATGAAGAGAGCTGGTTATCTAAAGG-GATA
* * *
59016 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT--AGGG-TG
1 ACACGGTTCATACGTGATGAAGA-GAGCTGGTTATCTAAAGGGATA
* * * * *
59058 ACACGGCTCATACGTGATGAAGAGATCTGG---TC--GAGGAATG
1 ACACGGTTCATACGTGATGAAGAGAGCTGGTTATCTAAAGGGATA
** **
59098 ACACGGTTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGTTCATACGTGATGAAGAGAGCTGGTTATCTAAAGG-GATA
* * * * *
59144 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT--ATGGTTG
1 ACACGGTTCATACGTGATGAAGA-GAGCTGGTTATCTAAAGGGATA
* *
59187 ACAC-GCTCATACGTGATGAAGAGATCTGGT
1 ACACGGTTCATACGTGATGAAGAGAGCTGGT
59217 CTGGGGATGA
Statistics
Matches: 160, Mismatches: 29, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
39 5 0.03
40 30 0.19
41 2 0.01
42 45 0.28
43 9 0.06
44 5 0.03
45 3 0.02
46 59 0.37
47 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (45 bp):
ACACGGTTCATACGTGATGAAGAGAGCTGGTTATCTAAAGGGATA
Found at i:59075 original size:42 final size:43
Alignment explanation
Indices: 58895--59216 Score: 157
Period size: 40 Copynumber: 7.6 Consensus size: 43
58885 ACGCCACTGC
** * *
58895 TCATACGTGATGAAGAG-TTTGGTTATCTATGG-TTGACACGGC
1 TCATACGTGATGAAGAGAGCTGGTTATCTA-GGAGTGACACGGT
* * * ** * *
58937 TCCTATGTGATGAAGAGATCTGG---TCGGGGAATGACACGGC
1 TCATACGTGATGAAGAGAGCTGGTTATCTAGGAGTGACACGGT
** ** * *
58977 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGT
1 TCATACGTGATGAAGAGAGCTGGTTATCT--AGGAG-TGACACGGT
* * *
59023 TCCTACGTGATGAGGACG-GCTGGTTATCTAGG-GTGACACGGC
1 TCATACGTGATGAAGA-GAGCTGGTTATCTAGGAGTGACACGGT
* * *
59065 TCATACGTGATGAAGAGATCTGG---TCGAGGAATGACACGGT
1 TCATACGTGATGAAGAGAGCTGGTTATCTAGGAGTGACACGGT
** ** * *
59105 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGT
1 TCATACGTGATGAAGAGAGCTGGTTATCT--AGGAG-TGACACGGT
* * * *
59151 TCCTACGTGATGAGGACG-GCTGGTTATCTATGG-TTGACAC-GC
1 TCATACGTGATGAAGA-GAGCTGGTTATCTA-GGAGTGACACGGT
*
59193 TCATACGTGATGAAGAGATCTGGT
1 TCATACGTGATGAAGAGAGCTGGT
59217 CTGGGGATGA
Statistics
Matches: 216, Mismatches: 44, Indels: 40
0.72 0.15 0.13
Matches are distributed among these distances:
39 7 0.03
40 61 0.28
41 2 0.01
42 60 0.28
43 14 0.06
44 4 0.02
45 7 0.03
46 59 0.27
47 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (43 bp):
TCATACGTGATGAAGAGAGCTGGTTATCTAGGAGTGACACGGT
Found at i:59111 original size:40 final size:41
Alignment explanation
Indices: 58893--59127 Score: 167
Period size: 40 Copynumber: 5.6 Consensus size: 41
58883 GGACGCCACT
* * *
58893 GCTCATACGTGATGAAGAG-TTTGGTTATCTATGG-TTGACACG
1 GCTCATACGTGATGAAGAGATCTGG--ATCGA-GGAATGACACG
* * *
58935 GCTCCTATGTGATGAAGAGATCTGG-TCGGGGAATGACACG
1 GCTCATACGTGATGAAGAGATCTGGATCGAGGAATGACACG
* * * *
58975 GCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
1 GCTCATACGTGATGAAGAGATCTGG--ATC--GAGG-AATGACACG
* * * * * *
59021 GTTCCTACGTGATGAGGACG-GCTGGTTATCTAGG-GTGACACG
1 GCTCATACGTGATGAAGA-GATCTGG--ATCGAGGAATGACACG
59063 GCTCATACGTGATGAAGAGATCTGG-TCGAGGAATGACACG
1 GCTCATACGTGATGAAGAGATCTGGATCGAGGAATGACACG
* *
59103 GTTCATACGTGATGAAGAGTTCTGG
1 GCTCATACGTGATGAAGAGATCTGG
59128 CCATCTAAAG
Statistics
Matches: 152, Mismatches: 30, Indels: 24
0.74 0.15 0.12
Matches are distributed among these distances:
39 7 0.05
40 61 0.40
41 1 0.01
42 42 0.28
43 6 0.04
44 3 0.02
45 2 0.01
46 29 0.19
47 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (41 bp):
GCTCATACGTGATGAAGAGATCTGGATCGAGGAATGACACG
Found at i:59261 original size:128 final size:128
Alignment explanation
Indices: 58914--59245 Score: 560
Period size: 128 Copynumber: 2.6 Consensus size: 128
58904 ATGAAGAGTT
* * *
58914 TGGTTATCTATGGTTGACACGGCTCCTATGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTC
1 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGG-ATGACACGGTTC
58979 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
65 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
* *
59043 TGGTTATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCGAGGAATGACACGGTTC
1 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCG-GGGATGACACGGTTC
59107 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
65 ATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
59171 TGGTTATCTATGGTTGACAC-GCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTC
1 TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGATGACACGGTTC
* *
59235 CTACATGATGA
65 ATACGTGATGA
59246 GGACGACTGG
Statistics
Matches: 191, Mismatches: 9, Indels: 7
0.92 0.04 0.03
Matches are distributed among these distances:
128 170 0.89
129 21 0.11
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (128 bp):
TGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGATGACACGGTTCA
TACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGC
Found at i:59620 original size:15 final size:15
Alignment explanation
Indices: 59596--59639 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
59586 AAGATGATCT
*
59596 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
59611 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
59626 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
59640 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:59835 original size:62 final size:62
Alignment explanation
Indices: 59756--59894 Score: 158
Period size: 62 Copynumber: 2.2 Consensus size: 62
59746 AAGGTGGGTA
* *
59756 TTTTCAAAAGAAGTTGTCTCGA-GAGACAAAATTTTGTTTCAAAGGAAACCA-ACTCAAAG-ATT
1 TTTTCAAAAGAAATTGTCTCGAGGAGA-AAAATTTT-TTTCAAAAGAAA-CAGACTCAAAGAATT
** * *
59818 TTTTCAAAAGAAATTGTCTTTAGGAGATAAATTTTTTTCAAAAGAAATAGACTCAAAGATATT
1 TTTTCAAAAGAAATTGTCTCGAGGAGAAAAATTTTTTTCAAAAGAAACAGACTCAAAGA-ATT
59881 TGTTTCAAAAGAAA
1 T-TTTCAAAAGAAA
59895 CAACTCAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
60 1 0.02
61 19 0.29
62 26 0.39
63 8 0.12
64 12 0.18
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (62 bp):
TTTTCAAAAGAAATTGTCTCGAGGAGAAAAATTTTTTTCAAAAGAAACAGACTCAAAGAATT
Found at i:59887 original size:30 final size:29
Alignment explanation
Indices: 59850--59935 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
59840 GGAGATAAAT
*
59850 TTTTTTCAAAAGAAATAGACTCAAAGATA
1 TTTTTTCAAAAGAAACAGACTCAAAGATA
59879 TTTGTTTCAAAAGAAACA-ACTCAAAGAT-
1 TTT-TTTCAAAAGAAACAGACTCAAAGATA
*
59907 TTTTATTCAAAAGGAACAGACTCAAAGAT
1 TTTT-TTCAAAAGAAACAGACTCAAAGAT
59936 TTATCTCAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
27 1 0.02
28 15 0.29
29 23 0.44
30 13 0.25
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.29
Consensus pattern (29 bp):
TTTTTTCAAAAGAAACAGACTCAAAGATA
Found at i:59929 original size:29 final size:28
Alignment explanation
Indices: 59848--59951 Score: 129
Period size: 28 Copynumber: 3.6 Consensus size: 28
59838 TAGGAGATAA
*
59848 ATTTTTTTCAAAAGAAATAGACTCAAAG
1 ATTTTTTTCAAAAGAAACAGACTCAAAG
59876 ATATTTGTTTCAAAAGAAACA-ACTCAAAG
1 AT-TTT-TTTCAAAAGAAACAGACTCAAAG
*
59905 ATTTTTATTCAAAAGGAACAGACTCAAAG
1 ATTTTT-TTCAAAAGAAACAGACTCAAAG
* * *
59934 ATTTATCTCAAGAGAAAC
1 ATTTTTTTCAAAAGAAAC
59952 TGTCTCCAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.02
28 26 0.39
29 26 0.39
30 13 0.20
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (28 bp):
ATTTTTTTCAAAAGAAACAGACTCAAAG
Found at i:60279 original size:36 final size:35
Alignment explanation
Indices: 60195--60298 Score: 120
Period size: 36 Copynumber: 3.0 Consensus size: 35
60185 GAGAAAATGA
* * *
60195 TGTCTCAAGCGAGACGAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
* **
60229 AGTCTCAAATGAGACAAAATTTGTTTTTATAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AGAAAT
* *
60265 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAA
60299 CGATTTCAAG
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
34 19 0.33
35 9 0.16
36 29 0.51
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAT
Found at i:60452 original size:105 final size:100
Alignment explanation
Indices: 60266--60497 Score: 259
Period size: 105 Copynumber: 2.3 Consensus size: 100
60256 TATAGAAATT
* * **
60266 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACGATTTCAAGTGAGATCAACTTTGTTTAATGT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAACAAAATCAAGTGAGATCAACTTTGTTTAATGT
* *
60331 GAAACAAATCCGAAATTTGGATCTCAAAGGGAAAAG
65 GAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
* *
60367 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTT-
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AGAAACAA-AATC-AA-GTGAGATCAACTTTGTTTA
* * * * *
60431 TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AT-GTGAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
**
60472 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
60498 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
100 5 0.05
101 21 0.19
102 7 0.06
103 2 0.02
104 3 0.03
105 72 0.65
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (100 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAACAAAATCAAGTGAGATCAACTTTGTTTAATGTG
AAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:60584 original size:21 final size:21
Alignment explanation
Indices: 60523--60584 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
60513 TGTGGAAAAA
* *
60523 TGTCTCAAGCGAGACATAATT
1 TGTCTCAAACGAGACAAAATT
* * *
60544 TGTTTTAAA-GAG---AAAGT
1 TGTCTCAAACGAGACAAAATT
60561 TGTCTCAAACGAGACAAAATT
1 TGTCTCAAACGAGACAAAATT
60582 TGT
1 TGT
60585 TTTTAAGAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
17 10 0.34
18 3 0.10
20 3 0.10
21 13 0.45
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (21 bp):
TGTCTCAAACGAGACAAAATT
Found at i:60611 original size:36 final size:38
Alignment explanation
Indices: 60525--60611 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
60515 TGGAAAAATG
* * *
60525 TCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTG
1 TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGCTA
* *
60563 TCTCAAACGAGACAAAATTTGTTTTTAAGA-AAA-CTA
1 TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGCTA
*
60599 TCTCAAGTGAGAC
1 TCTCAAGCGAGAC
60612 GACACTTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 12 0.29
37 3 0.07
38 27 0.64
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (38 bp):
TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGCTA
Found at i:60981 original size:16 final size:16
Alignment explanation
Indices: 60960--61035 Score: 60
Period size: 16 Copynumber: 5.2 Consensus size: 16
60950 TGTAACATGC
60960 ATGTATGTGTTGATGT
1 ATGTATGTGTTGATGT
*
60976 ATGTA--T-AT-ATGT
1 ATGTATGTGTTGATGT
*
60988 ATGTATGAGTTGATGT
1 ATGTATGTGTTGATGT
*
61004 ATGTA--T-AT-ATGT
1 ATGTATGTGTTGATGT
*
61016 ATGTATGAGTTGATGT
1 ATGTATGTGTTGATGT
61032 ATGT
1 ATGT
61036 TTCTCAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
12 18 0.40
13 2 0.04
14 1 0.02
15 2 0.04
16 22 0.49
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
ATGTATGTGTTGATGT
Found at i:60992 original size:28 final size:28
Alignment explanation
Indices: 60960--61035 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
60950 TGTAACATGC
*
60960 ATGTATGTGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
60988 ATGTATGAGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
61016 ATGTATGAGTTGATGTATGT
1 ATGTATGAGTTGATGTATGT
61036 TTCTCAATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (28 bp):
ATGTATGAGTTGATGTATGTATATATGT
Found at i:61035 original size:4 final size:4
Alignment explanation
Indices: 60972--61022 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
60962 GTATGTGTTG
* *
60972 ATGT ATGT ATAT ATGT ATGT ATG- A-GT -TG- ATGT ATGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
61016 ATGT ATG
1 ATGT ATG
61023 AGTTGATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 1 0.03
3 4 0.10
4 34 0.87
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:62928 original size:20 final size:20
Alignment explanation
Indices: 62847--62929 Score: 62
Period size: 20 Copynumber: 4.0 Consensus size: 20
62837 ATAAATACAG
**
62847 TGTTTCAAGGT-GGAAAGAA
1 TGTTTCAAGGTCTCAAAGAA
62866 TGTTTCAAGGTCTCAAGAGAGGGAA
1 TGTTTCAAGGTCTC-A-A-A--GAA
*
62891 TGTTTCAAGGT-TGAAAAGAA
1 TGTTTCAAGGTCT-CAAAGAA
*
62911 TATTTCAAGGTCTCAAAGA
1 TGTTTCAAGGTCTCAAAGA
62930 GATAGAATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
19 11 0.22
20 18 0.35
21 2 0.04
22 2 0.04
23 2 0.04
24 2 0.04
25 14 0.27
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.28
Consensus pattern (20 bp):
TGTTTCAAGGTCTCAAAGAA
Found at i:64394 original size:30 final size:31
Alignment explanation
Indices: 64341--64400 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
64331 TGACAAAATG
64341 ACACAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAACAAAAGAGAAGAAATAAGTTAGTAT
64372 ACACAA-ACAAAGAGAA-AAATAAGTTAGTA
1 ACACAACA-AAAGAGAAGAAATAAGTTAGTA
64401 CATGTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.15
Consensus pattern (31 bp):
ACACAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:64402 original size:28 final size:30
Alignment explanation
Indices: 64341--64402 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
64331 TGACAAAATG
64341 ACACAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAACAAAAGAGAAGAAATAAGTTAG-AT
64372 ACACAA-ACAAAGAGAA-AAATAAGTTAG-T
1 ACACAACA-AAAGAGAAGAAATAAGTTAGAT
64400 ACA
1 ACA
64403 TGTAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
28 4 0.13
30 12 0.40
31 14 0.47
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (30 bp):
ACACAACAAAAGAGAAGAAATAAGTTAGAT
Found at i:66331 original size:29 final size:29
Alignment explanation
Indices: 66299--66358 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
66289 TGGTAATAAT
* * *
66299 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
66328 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
66357 AA
1 AA
66359 TGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:68487 original size:25 final size:25
Alignment explanation
Indices: 68453--68527 Score: 132
Period size: 25 Copynumber: 3.0 Consensus size: 25
68443 GGATAGGGGA
* *
68453 TTAGGGTTTGAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
68478 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
68503 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
68528 GGGTTGTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:68585 original size:11 final size:10
Alignment explanation
Indices: 68568--68605 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
68558 GGGCTTCGGG
68568 TTGTTGGGCC
1 TTGTTGGGCC
68578 TCTGTTGGGCC
1 T-TGTTGGGCC
68589 TTGGTTGGGCC
1 TT-GTTGGGCC
68600 TTGTTG
1 TTGTTG
68606 TATTGGGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.00, C:0.18, G:0.39, T:0.42
Consensus pattern (10 bp):
TTGTTGGGCC
Found at i:68653 original size:3 final size:3
Alignment explanation
Indices: 68639--68689 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
68629 ATGTAAAATG
* * **
68639 TAA TAT TAA TAA TAAA TAA TAA TAA TAA TAA AAA TAA CGA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
68685 TAA TA
1 TAA TA
68690 TACAAAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:70431 original size:23 final size:23
Alignment explanation
Indices: 70379--70431 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
70369 TTGTTTACCG
* *
70379 CTTGAACTAACCTCGTTGATACA
1 CTTGAATTAACCCCGTTGATACA
70402 CTTGAATTAACCCCGTTGATACA
1 CTTGAATTAACCCCGTTGATACA
70425 CTTGAAT
1 CTTGAAT
70432 ATGCTTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (23 bp):
CTTGAATTAACCCCGTTGATACA
Found at i:78170 original size:23 final size:23
Alignment explanation
Indices: 78144--78204 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
78134 ATTTATATGT
*
78144 CACTTGGGTGCATTTCTACGCT-G
1 CACTTCGGTGCATTTCTACG-TGG
*
78167 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCATTTCTACGTGG
*
78190 CACATCGGTGCATTT
1 CACTTCGGTGCATTT
78205 ATATGAACTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.33
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGTGG
Found at i:84295 original size:15 final size:15
Alignment explanation
Indices: 84275--84303 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
84265 GAAAGGGGTA
84275 GTATCGATACCATAG
1 GTATCGATACCATAG
84290 GTATCGATACCATA
1 GTATCGATACCATA
84304 AGGCAAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (15 bp):
GTATCGATACCATAG
Found at i:85046 original size:23 final size:23
Alignment explanation
Indices: 85019--85071 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
85009 CATTTTATAT
* *
85019 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCAGTGCAATTCTACGC
* *
85042 GGCACTTCAGTGCAATTCTTCGT
1 GGCACTTCAGTGCAATTCTACGC
85065 GGCACTT
1 GGCACTT
85072 TGATGTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCAGTGCAATTCTACGC
Done.