Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010886.1 Corchorus capsularis cultivar CVL-1 contig10907, 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: 190571
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:629 original size:332 final size:337
Alignment explanation
Indices: 1--684 Score: 1083
Period size: 332 Copynumber: 2.0 Consensus size: 337
* *
1 AAAACCGTGATGGTTAGTATACAATTTCAGCTAAAATTTTGCAAAATTTGACCCCGAAAATTTTT
1 AAAACCGTGATGGTTAGTACACAATTTCAGCTAAAATTTTGCAAAATTTGACCCCAAAAATTTTT
* *
66 TCCTCAATTCTTGGCGACAATACTAAAAATATATATATATATAATTCAACGCCAAAAAGATTTAA
66 TCCTCAATTCTTGGCCACAATACT-AAAATATATATATATACAATTCAACGCCAAAAAGATTTAA
* *
131 GGGCTTTTCATGCTAAAAATACGGTTATTCCTATTATTTTCTAAATTAATTTTTGATTAAATCGA
130 GGGCTTTTCATGCTAAAAATACGGTTATTCCTATTATTTTCCAAATTAATTTCTGATTAAATCGA
** * *
196 AAAAGGATTCAGATGCTCGTAAAAAGATATCCTTAATTCCAATATGGATGAGATTTGATTAGATA
195 AAAAGGATTCAGATGCTCAAAAAAACATATCCTTAAATCCAATATGGATGAGATTTGATTAGATA
* * * * *
261 AATATTTATATTTCAAGCAGTCTCGGCGCCAAAAATCATGTAAAATTGAGTCGG-GCCCCGGAAC
260 AATATTCATATTTCAAGCAGTCTCAGCGCAAAAAATCATGTAAAACTGAGCCGGAGCCCCGGAAC
325 GCGTTTTAAGCCA
325 GCGTTTTAAGCCA
* *
338 AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAATTTGACCCCAAAAATTTTT
1 AAAACCGTGATGGTTAGTACACAATTTCAGCTAAAATTTTGCAAAATTTGACCCCAAAAATTTTT
*
403 TCCTCAATTCTTGGCCACAATACT-AAA-A-ATATATATACAATTCAATGCCAAAAAGATTTAAG
66 TCCTCAATTCTTGGCCACAATACTAAAATATATATATATACAATTCAACGCCAAAAAGATTTAAG
* * *
465 GG-TTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAA
131 GGCTTTTCATGCTAAAAATACGGTTATTCCTATTATTTTCCAAATTAATTTCTGATTAAATCGAA
*
529 ACAGGATTCAGATGCTCAAAAAAACATATCCTTAAAT-CACATATGGATGAGATTTGATTAGATA
196 AAAGGATTCAGATGCTCAAAAAAACATATCCTTAAATCCA-ATATGGATGAGATTTGATTAGATA
* * *
593 AATATTCATATTTCAAGGAGTCTCAGTGCAAAAAATCATGTAAAACTGAGCCGGAGCCCTGGAAC
260 AATATTCATATTTCAAGCAGTCTCAGCGCAAAAAATCATGTAAAACTGAGCCGGAGCCCCGGAAC
658 GCGTTTTAAGCCA
325 GCGTTTTAAGCCA
671 AAAACCGTGATGGT
1 AAAACCGTGATGGT
685 CTGACCCGAA
Statistics
Matches: 320, Mismatches: 25, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
331 2 0.01
332 160 0.50
333 70 0.22
334 1 0.00
335 3 0.01
337 84 0.26
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (337 bp):
AAAACCGTGATGGTTAGTACACAATTTCAGCTAAAATTTTGCAAAATTTGACCCCAAAAATTTTT
TCCTCAATTCTTGGCCACAATACTAAAATATATATATATACAATTCAACGCCAAAAAGATTTAAG
GGCTTTTCATGCTAAAAATACGGTTATTCCTATTATTTTCCAAATTAATTTCTGATTAAATCGAA
AAAGGATTCAGATGCTCAAAAAAACATATCCTTAAATCCAATATGGATGAGATTTGATTAGATAA
ATATTCATATTTCAAGCAGTCTCAGCGCAAAAAATCATGTAAAACTGAGCCGGAGCCCCGGAACG
CGTTTTAAGCCA
Found at i:959 original size:300 final size:299
Alignment explanation
Indices: 386--1316 Score: 1026
Period size: 300 Copynumber: 3.0 Consensus size: 299
376 TTGCAAAATT
* * * *
386 TGACCCCAAAAATTTTTTCCTCAATTCTTGGCCACAAT-A-C-TAAAAATATATATACAATTCAA
1 TGACCCGAAAATTTTTTTCCTCAATTATTGGCCACAATAACCATAAGAA-ATATAT--AATTCAA
*
448 TGCCAAAAAGATTTAAGGGTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAAT
63 CGCCAAAAAGATTTAAGGGTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAAT
**
513 TTCTGATTAAATCGAAACAGGATTCAGATGCTCAAAAAAACATATCCTTAAAT-CACATATGGAT
128 TTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCA-ATATGGAT
* *
577 GAGATTTGATTAGATAAATATTCATATTTCAAGGAGTCTCAGTGCAAAAAATCATGTAAAACTGA
192 GAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCAGCGCAAAAAATCATGTAAAACTGA
*
642 GCCGGAGCCCTGGAACGCGTTTTAAGCCAAAAACCGTGATGGTC
257 GCCGGGGCCC-GGAACGCGTTTTAAGCCAAAAACCGTGATGGTC
* *
686 TGACCCGAAAATTTTTTTCTTCAATTATTGGCCACAATAACCATAAGAAATACATAATTCAACGC
1 TGACCCGAAAATTTTTTTCCTCAATTATTGGCCACAATAACCATAAGAAATATATAATTCAACGC
* *
751 CAAAAATATTTAAGGGTTTTCATGATTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTC
66 CAAAAAGATTTAAGGGTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTC
* * * * *
816 TAATTAAATCGAAATAGGATTCTGATGCTCGTAAAAACATATCCTTAATTCCAATGTGGATGAGA
131 TGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATATGGATGAGA
* * * * ** * **
881 TTTGATAAGATAAATATTGATATTCCGAGGAGTCTCGGCGCTGAAAATCATGTAAAACTAAGTAG
196 TTTGATTAGATAAATATTGATATTTCAAGGAGTCTCAGCGCAAAAAATCATGTAAAACTGAGCCG
* * *
946 GGGCTGCGGAACGCGTTTTTCAGCCAGACCCCGTGATTGGTACACTATTTCGTCTAAAATTTTGC
261 GGGC-CCGGAACGCG-TTTTAAGCCA-A-------A-----A-AC-----CG--T--GA---TG-
*
1011 AAAATC
297 ---GTC
* * * * *
1017 TGACCCGAAAATTTTTTTTCCCCAACTATAGGCCACAATAACCATAAGGAATATATAATTCAACA
1 TGACCCGAAAA-TTTTTTTCCTCAATTATTGGCCACAATAACCATAAGAAATATATAATTCAACG
* * *
1082 CCAAAAAGATCTAAAGGCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATAAATT
65 CCAAAAAGAT-TTAAGGGTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATT
* *
1147 T-TGATTCAATCGAAACAGGATTCAGATGCTTGTAAAAACATATCCTTAAATCCAATATGGATGA
129 TCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATATGGATGA
** * * * *
1211 GATTTGATTAGATAAATATTGATATTTCAAGGACCCCCCGCGCCAAAAATCATGTAAAATTGAGC
194 GATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCAGCGCAAAAAATCATGTAAAACTGAGC
*
1276 CGGGGCCCGGAACGCATTTTAAGCCAAAAAACCGTGATGGT
259 CGGGGCCCGGAACGCGTTTTAAGCC-AAAAACCGTGATGGT
1317 TAATACACGA
Statistics
Matches: 523, Mismatches: 69, Indels: 77
0.78 0.10 0.12
Matches are distributed among these distances:
300 226 0.43
301 14 0.03
302 7 0.01
303 5 0.01
305 2 0.00
308 1 0.00
309 1 0.00
310 1 0.00
312 2 0.00
314 1 0.00
315 2 0.00
317 2 0.00
318 1 0.00
320 2 0.00
322 1 0.00
323 1 0.00
324 1 0.00
327 2 0.00
330 9 0.02
331 22 0.04
332 169 0.32
333 51 0.10
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (299 bp):
TGACCCGAAAATTTTTTTCCTCAATTATTGGCCACAATAACCATAAGAAATATATAATTCAACGC
CAAAAAGATTTAAGGGTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTC
TGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATATGGATGAGA
TTTGATTAGATAAATATTGATATTTCAAGGAGTCTCAGCGCAAAAAATCATGTAAAACTGAGCCG
GGGCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTC
Found at i:1312 original size:632 final size:631
Alignment explanation
Indices: 106--1316 Score: 1741
Period size: 632 Copynumber: 1.9 Consensus size: 631
96 ATATATATAT
*
106 ATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGCTAAAAATACGGTTATTCCTATTATTTT
1 ATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGATAAAAATACGGTTATTCCTATTATTTT
* * * *
171 CTAAATTAATTTTTGATTAAATCGAAAAAGGATTCAGATGCTCGTAAAAAGATATCCTTAATTCC
66 CCAAATTAATTTCTAATTAAATCGAAAAAGGATTCAGATGCTCGTAAAAACATATCCTTAATTCC
* * *
236 AATATGGATGAGATTTGATTAGATAAATATTTATATTTCAAGCAGTCTCGGCGCCAAAAATCATG
131 AATATGGATGAGATTTGATAAGATAAATATTGATATTCCAAGCAGTCTCGGCGCCAAAAATCATG
* *
301 TAAAATTGAGTCGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACACGATTTC
196 TAAAACTAAGTCGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGA--GTTAGTACACGATTTC
* * * * * *
366 GGCTAAAATTTTGCAAAATTTGACCCCAAAAATTTTTTCCTCAATTCTTGGCCACAATACTAAAA
259 GGCTAAAATTTTGCAAAATCTGACCCCAAAAATTTTTTCCCCAACTATAGGCCACAATACCAAAA
* ** * *
431 ATATATATACAATTCAATGCCAAAAAGATTTAAGGGTTTTCATGCTTAAAATATGGTTATTCCTA
324 AGATATATACAATTCAACACCAAAAAGATTAAAGGCTTTTCATGCTTAAAATATGGTTATTCCTA
*
496 TTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCAAAAAAACATATCCT
389 TTCTTTTCCAAATAAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCAAAAAAACATATCCT
** * *
561 TAAATCACATATGGATGAGATTTGATTAGATAAATATTCATATTTCAAGGAGTCTCAGTGCAAAA
454 TAAATCACATATGGATGAGATTTGATTAGATAAATATTCATATTTCAAGGACCCCCAGCGCAAAA
*
626 AATCATGTAAAACTGAGCCGGAGCCCTGGAACGCGTTTTAAGCCAAAAACCGTGATGGTCTGACC
519 AATCATGTAAAACTGAGCCGGAGCCCTGGAACGCATTTTAAGCCAAAAACCGTGATGGTCTGACC
691 CGAAAATTTTTTTCTTCAATTATTGGCCACAATAACCATAAGAAATAC
584 CGAAAATTTTTTTCTTCAATTATTGGCCACAATAACCATAAGAAATAC
* * * *
739 ATAATTCAACGCCAAAAATATTTAAGGG-TTTTCATGATTAAAATATGGTTATTCCTATTCTTTT
1 ATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGATAAAAATACGGTTATTCCTATTATTTT
* *
803 CCAAATTAATTTCTAATTAAATCGAAATAGGATTCTGATGCTCGTAAAAACATATCCTTAATTCC
66 CCAAATTAATTTCTAATTAAATCGAAAAAGGATTCAGATGCTCGTAAAAACATATCCTTAATTCC
* * * **
868 AATGTGGATGAGATTTGATAAGATAAATATTGATATTCCGAGGAGTCTCGGCGCTGAAAATCATG
131 AATATGGATGAGATTTGATAAGATAAATATTGATATTCCAAGCAGTCTCGGCGCCAAAAATCATG
* ** * * ** * *
933 TAAAACTAAGTAGGGGCTGCGGAACGCGTTTTTCAGCCAGACCCCGTGA-TTGGTACACTATTTC
196 TAAAACTAAGT-CGGGCCCCGGAACGCG-TTTTAAGCCAAAAACCGTGAGTTAGTACACGATTTC
* * * *
997 GTCTAAAATTTTGCAAAATCTGACCCGAAAATTTTTTTTCCCCAACTATAGGCCACAATAACCAT
259 GGCTAAAATTTTGCAAAATCTGACCCCAAAA-ATTTTTTCCCCAACTATAGGCCACAAT-ACCAA
* *
1062 AAGGA-ATATATAATTCAACACCAAAAAGATCTAAAGGCTTTTCATGCTTAAAATATGGTTATTC
322 AAAGATATATACAATTCAACACCAAAAAGAT-TAAAGGCTTTTCATGCTTAAAATATGGTTATTC
* ***
1126 CTATTCTTTTCCAAATAAATTT-TGATTCAATCGAAACAGGATTCAGATGCTTGTAAAAACATAT
386 CTATTCTTTTCCAAATAAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCAAAAAAACATAT
* *
1190 CCTTAAATC-CAATATGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGACCCCCCGCGC
451 CCTTAAATCAC-ATATGGATGAGATTTGATTAGATAAATATTCATATTTCAAGGACCCCCAGCGC
* * *
1254 CAAAAATCATGTAAAATTGAGCCGGGGCCC-GGAACGCATTTTAAGCCAAAAAACCGTGATGGT
515 AAAAAATCATGTAAAACTGAGCCGGAGCCCTGGAACGCATTTTAAGCC-AAAAACCGTGATGGT
1317 TAATACACGA
Statistics
Matches: 509, Mismatches: 62, Indels: 15
0.87 0.11 0.03
Matches are distributed among these distances:
631 58 0.11
632 337 0.66
633 98 0.19
634 16 0.03
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (631 bp):
ATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGATAAAAATACGGTTATTCCTATTATTTT
CCAAATTAATTTCTAATTAAATCGAAAAAGGATTCAGATGCTCGTAAAAACATATCCTTAATTCC
AATATGGATGAGATTTGATAAGATAAATATTGATATTCCAAGCAGTCTCGGCGCCAAAAATCATG
TAAAACTAAGTCGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGAGTTAGTACACGATTTCGG
CTAAAATTTTGCAAAATCTGACCCCAAAAATTTTTTCCCCAACTATAGGCCACAATACCAAAAAG
ATATATACAATTCAACACCAAAAAGATTAAAGGCTTTTCATGCTTAAAATATGGTTATTCCTATT
CTTTTCCAAATAAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCAAAAAAACATATCCTTA
AATCACATATGGATGAGATTTGATTAGATAAATATTCATATTTCAAGGACCCCCAGCGCAAAAAA
TCATGTAAAACTGAGCCGGAGCCCTGGAACGCATTTTAAGCCAAAAACCGTGATGGTCTGACCCG
AAAATTTTTTTCTTCAATTATTGGCCACAATAACCATAAGAAATAC
Found at i:1910 original size:475 final size:475
Alignment explanation
Indices: 869--2300 Score: 2321
Period size: 476 Copynumber: 3.0 Consensus size: 475
859 CTTAATTCCA
* * * *
869 ATGTGGATGAGATTTGATAAGATAAATATTGATATTCCGAGGAGTCTCGGC-GCTGAAAATCATG
1 ATGTGGATGAGATTCGATTAGATAAATATTGATATTTCGAGGAGTCTCGGCATC-GAAAATCATG
* ** ** *
933 TAAAACTAAGTAGGGGCTGCGGAACGCGTTTTTCAGCCAGACCCCGTGATTGGTACACTATTTCG
65 TAAAACTAAGTCGGGGCCACGGAACGCGTTTTTCAGCCAGAAACCGTGATTAGTACACTATTTCG
* *
998 TCTAAAATTTTGCAAAATCTGACCCGAAAATTTTTTTTCCCCAACTATAGGCCACAATAACCATA
130 GCTAAAATTTTGCAAAATCTGACCCGAAAATTTTTTTTCCCCAACTATTGGCCACAATAACCATA
1063 AGGAATATATAATTCAACACCAAAAAGATCTAAAGGCTTTTCATGCTTAAAATATGGTTATTCCT
195 AGGAATATATAATTCAACACCAAAAAGATCTAAAGGCTTTTCATGCTTAAAATATGGTTATTCCT
* * *
1128 ATTCTTTTCCAAATAAATTT-TGATTCAATCGAAACAGGATTCAGATGCTTGTAAAAACATATCC
260 ATTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCC
* ** *
1192 TTAAATCCAATATGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGACCCCCCGCGCCAA
325 TTAAATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGA-GTCCAGCGCCAA
* *
1257 AAATCATGTAAAATTGAGCCGGGGCCCGGAACGCATTTTAAGCCAAAAAACCGTGATGGTTAATA
389 AAATCATGTAAAATTGAGCCGGGGCCCGGAACGCGTTTTAAGCC-AAAAACCGTGATGGTTAGTA
*
1322 CACGATTTCGACTAAAATTTTGC
453 CACGATTTCGGCTAAAATTTTGC
* *
1345 ATGTGGATGAGATTCGATTAGATAAATATTGATAATTCAAGGAGTCTCGGCATCGAAAATCATGT
1 ATGTGGATGAGATTCGATTAGATAAATATTGATATTTCGAGGAGTCTCGGCATCGAAAATCATGT
* *
1410 AAAACTAAGTCGGGGCCAAGGAACGCGTTTTTCAGCCAGAAACCGTGATTAGTACATTATTTCGG
66 AAAACTAAGTCGGGGCCACGGAACGCGTTTTTCAGCCAGAAACCGTGATTAGTACACTATTTCGG
* *
1475 CTAAAATTTTGCAAAATCTGACCCG-AATTTTTTTTTCTCCAACTATTGGCCACAATAACCATAA
131 CTAAAATTTTGCAAAATCTGACCCGAAAATTTTTTTTCCCCAACTATTGGCCACAATAACCATAA
* * ** * * * * *
1539 GGAATATTTAACTCAATGCCAAAAAGATTTAAGGGCTTTTCATACTTAAAATATGATTATTCTTA
196 GGAATATATAATTCAACACCAAAAAGATCTAAAGGCTTTTCATGCTTAAAATATGGTTATTCCTA
1604 TTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCT
261 TTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCT
* *
1669 TAAATCCAATGTGGATGAGATTTGATTAGATAAATATTCATATTTCAAGGAGTCCAGGTGCCAAA
326 TAAATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCCA-GCGCCAAA
*
1734 AATCATGTAAAATTGAGCCGGGGCCCGGAACGCGTTTTATGCCAAAAACCGTGATGGTTAGTACA
390 AATCATGTAAAATTGAGCCGGGGCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACA
1799 CGATTTCGGCTAAAATTTTGC
455 CGATTTCGGCTAAAATTTTGC
* *
1820 ATGTGGATGAGATTCGATTAGATAAATATTTATATTTCGAGGAGTCTCAGCATCGAAAATCATGT
1 ATGTGGATGAGATTCGATTAGATAAATATTGATATTTCGAGGAGTCTCGGCATCGAAAATCATGT
* *
1885 AAAACTAAGTCGGGGCCCCGGAACGCGTTTTTCAGCCAGAAACCGTGATTGTTAGTACACGATTT
66 AAAACTAAGTCGGGGCCACGGAACGCGTTTTTCAGCCAGAAACCGTGA---TTAGTACACTATTT
*
1950 CAGCTAAAATTTTGCAAAATCTGACCCGAAAATTTTTTTTCCCCAACTATTGGCCACAATAACCA
128 CGGCTAAAATTTTGCAAAATCTGACCCGAAAATTTTTTTTCCCCAACTATTGGCCACAATAACCA
*
2015 TAAGGAATATATAATTCAACAACAAAAAGATCTAAAGGCTTTTCATGCTTAAAATATGGTTATTC
193 TAAGGAATATATAATTCAACACCAAAAAGATCTAAAGGCTTTTCATGCTTAAAATATGGTTATTC
*
2080 CTATTCTTTTCCAATTTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATAT
258 CTATTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATAT
*
2145 CCTTAAATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCCCAGCGCA
323 CCTTAAATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGT-CCAGCGCC
*
2210 AAAAATCATGTAAAATTGAGCCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATAGTTAG
387 AAAAATCATGTAAAATTGAGCCGGGG-CCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAG
2275 TACACGATTTCGGCTAAAATTTTGC
451 TACACGATTTCGGCTAAAATTTTGC
2300 A
1 A
2301 AAATTTGACC
Statistics
Matches: 880, Mismatches: 67, Indels: 14
0.92 0.07 0.01
Matches are distributed among these distances:
475 260 0.30
476 278 0.32
477 1 0.00
478 39 0.04
479 237 0.27
480 65 0.07
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (475 bp):
ATGTGGATGAGATTCGATTAGATAAATATTGATATTTCGAGGAGTCTCGGCATCGAAAATCATGT
AAAACTAAGTCGGGGCCACGGAACGCGTTTTTCAGCCAGAAACCGTGATTAGTACACTATTTCGG
CTAAAATTTTGCAAAATCTGACCCGAAAATTTTTTTTCCCCAACTATTGGCCACAATAACCATAA
GGAATATATAATTCAACACCAAAAAGATCTAAAGGCTTTTCATGCTTAAAATATGGTTATTCCTA
TTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCT
TAAATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCCAGCGCCAAAA
ATCATGTAAAATTGAGCCGGGGCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACAC
GATTTCGGCTAAAATTTTGC
Found at i:2872 original size:333 final size:332
Alignment explanation
Indices: 1819--3269 Score: 2223
Period size: 333 Copynumber: 4.4 Consensus size: 332
1809 TAAAATTTTG
* * * * * *
1819 CATGTGGATGAGATTCGATTAGATAAATATTTATATTTCGAGGAGTCTCAGCATC-GAAAATCAT
1 CATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGC-GCAAAAAATCAT
* * * *
1883 GTAAAACTAAGTCGGGGCCCCGGAACGCGTTTTTCAGCCAGAAACCGTGATTGTTAGTACACGAT
65 GTAAAACTGAGTCGGGGCCCCGGAACGCG-TTTTAAGCCAAAAACCGTGATGGTTAGTACACGAT
* * *
1948 TTCAGCTAAAATTTTGCAAAATCTGACCCGAAAATTTTTTTTCCCCAACTATTGGCCACAATAAC
129 TTCGGCTAAAATTTTGCAAAATCTGACCCGAAAA--TTTTTTCCTCAATTATTGG-CACAATAAC
* * *
2013 CATAAGGAATATATAATTCAACAACAAAAAGATCTAAAGGCTTTTCATGCTTAAAATATGGTTAT
191 CATAAGGAATATATAATTCAACACCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTAT
*
2078 TCCTATTCTTTTCCAATTTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACAT
256 TCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACAT
2143 ATCCTTAAATCC
321 ATCCTTAAATCC
* * *
2155 AATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCCCAGCGCAAAAAATCATG
1 CATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCAAAAAATCATG
* * *
2220 TAAAATTGAGCCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATAGTTAGTACACGATTT
66 TAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACACGATTT
* * * *
2285 CGGCTAAAATTTTGCAAAATTTGACCCCGAAAATTTTTTCCTAAATTCTTGGCGACAAT-ACTA-
131 CGGCTAAAATTTTGCAAAATCTGA-CCCGAAAATTTTTTCCTCAATTATTGGC-ACAATAACCAT
** ** *
2348 AAAAAATATATACAATTCAATGCCAAAAAGATTTAATGG-TTTTCATGCTTAAAATATGGTTATT
194 AAGGAATATAT--AATTCAACACCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATT
2412 CCTATTCTTTTCC-AATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATA
257 CCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATA
2476 TCCTTAAATCC
322 TCCTTAAATCC
* * *
2487 CATGTGGATGAAATTTGATTAGATAAATATTGATATTTCAAGGAGGCTCGGCGCAAAAAATCTTG
1 CATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCAAAAAATCATG
* * *
2552 T-AAACTGAGTCGGGGCCCCAGAACGCGTTTTAAGCAAAAAACCGTGATGGTTAATACACGATTT
66 TAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACACGATTT
* * *
2616 CGGCTACAATTTTGCAAAATTTGACCCCGAAAATTTTTTCCTCAATTCTTGGCAACAATAACCAT
131 CGGCTAAAATTTTGCAAAATCTGA-CCCGAAAATTTTTTCCTCAATTATTGGC-ACAATAACCAT
* *
2681 AAGGAATATATAATTCAACGCCTAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCC
194 AAGGAATATATAATTCAACACCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCC
*
2746 TATTCTTTTCCAAATTAATTTCTAATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATC
259 TATTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATC
2811 CTTAAATCC
324 CTTAAATCC
* *
2820 CATGTGGATGAGATTTGATTAGATAAATATTGATAATTCAAGG-GCTCTCGGCGCCAAAAATCAT
1 CATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAG-TCTCGGCGCAAAAAATCAT
* *
2884 GTAAAACTGAGTCGGGGGCCCGGAACGCGTTTTAAGCCAAAAACAGTGATGGTTAGTACACGATT
65 GTAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACACGATT
*
2949 TCGGCTAAAATTTTGCAAAATCTGACCCGAAATTTTTTTCCTCAATTATTCGGCACAATAACCAT
130 TCGGCTAAAATTTTGCAAAATCTGACCCGAAAATTTTTTCCTCAATTATT-GGCACAATAACCAT
*
3014 AAGGAATATATAATTCAACACCTAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCC
194 AAGGAATATATAATTCAACACCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCC
* *
3079 TATTCTTTTCCAAATTAATTTCTGATTAAATCGAAATAGGATTCAGATGCTCGTAAAAACATATT
259 TATTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATC
3144 CTTAAATCC
324 CTTAAATCC
3153 CATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCAAAAAATCATG
1 CATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCAAAAAATCATG
* * * * *
3218 TAAAATTGAGCCGGAGCCCCGGATCGCGTTTTAAACCAAAAACCGTGATGGT
66 TAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGT
3270 CTGACCCGAA
Statistics
Matches: 1025, Mismatches: 77, Indels: 29
0.91 0.07 0.03
Matches are distributed among these distances:
331 136 0.13
332 172 0.17
333 446 0.44
334 125 0.12
335 57 0.06
336 89 0.09
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (332 bp):
CATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCAAAAAATCATG
TAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACACGATTT
CGGCTAAAATTTTGCAAAATCTGACCCGAAAATTTTTTCCTCAATTATTGGCACAATAACCATAA
GGAATATATAATTCAACACCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTA
TTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCT
TAAATCC
Found at i:3514 original size:300 final size:300
Alignment explanation
Indices: 2969--3569 Score: 981
Period size: 300 Copynumber: 2.0 Consensus size: 300
2959 TTTTGCAAAA
* * *
2969 TCTGACCCGAAATTTTTTTCCTCAATTATTCGGCACAATAACCATAAGGAATATATAATTCAACA
1 TCTGACCCGAAATTTTTTTCCTCAATTATTCGCCACAATAACCATAAGAAATACATAATTCAACA
*
3034 CCTAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATT
66 CCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATT
* *
3099 TCTGATTAAATCGAAATAGGATTCAGATGCTCGTAAAAACATATTCTTAAATCCCATGTGGATGA
131 TCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCCATGTGGATGA
*
3164 GATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCAAAAAATCATGTAAAA-TTGAG
196 GATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCACAAAAAATCATGTAAAACTT-AG
*
3228 CCGGAGCCCCGGATCGCGTTTTAAACCAAAAACCGTGATGG
260 CCGGAGCCCCGGAACGCGTTTTAAACCAAAAACCGTGATGG
* * * *
3269 TCTGACCCGAAAATTTTTTTCTTCAATTGTTTGCCACAGTAACCATAAGAAATACATAATTCAAC
1 TCTGACCCG-AAATTTTTTTCCTCAATTATTCGCCACAATAACCATAAGAAATACATAATTCAAC
* *
3334 GCCAAAAAGATTTAAGGG-TTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCGAAATTAAT
65 ACCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAAT
3398 TTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCCATGTGGATG
130 TTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCCATGTGGATG
*
3463 AGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCACCAAAAATCATGTAAAACTTAG
195 AGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCACAAAAAATCATGTAAAACTTAG
* * * * * *
3528 TCGGGGGCGCGGAACGCGTTTTAAGCCAAAAATCGTGATGG
260 CCGGAGCCCCGGAACGCGTTTTAAACCAAAAACCGTGATGG
3569 T
1 T
3570 TAGTACACGA
Statistics
Matches: 278, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
300 212 0.76
301 66 0.24
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (300 bp):
TCTGACCCGAAATTTTTTTCCTCAATTATTCGCCACAATAACCATAAGAAATACATAATTCAACA
CCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATT
TCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCCATGTGGATGA
GATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCACAAAAAATCATGTAAAACTTAGC
CGGAGCCCCGGAACGCGTTTTAAACCAAAAACCGTGATGG
Found at i:4000 original size:214 final size:214
Alignment explanation
Indices: 3620--4034 Score: 704
Period size: 214 Copynumber: 1.9 Consensus size: 214
3610 GAAAATTGTT
* * ** *
3620 TTTTCCTCAATTATTGGCCACAATAACCATAAGGAATATATAATTCAACACCAAAAAGATTTAAG
1 TTTTCCCCAACTATTGGCCACAATAACCATAAGGAATATATAATTCAACACCAAAAAGATCAAAA
*
3685 GGCTTTTCGTGCTTAAAATATGGTTATTCCTACTCTTTTCCAAATTAATTTCTGATTAAATCGAA
66 GGCTTTTCATGCTTAAAATATGGTTATTCCTACTCTTTTCCAAATTAATTTCTGATTAAATCGAA
* * *
3750 ATAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCCATGTGGATGAGATTTGATTAGATAA
131 ACAGGATTAAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGATGAGATTTGATTAGATAA
3815 ATATTGGAGTCTCGGCGCC
196 ATATTGGAGTCTCGGCGCC
*
3834 TTTTCCCCAACTATTGGCCACAATAACCATAAGGAATATATAATTCAACTCCAAAAAGATCAAAA
1 TTTTCCCCAACTATTGGCCACAATAACCATAAGGAATATATAATTCAACACCAAAAAGATCAAAA
** * *
3899 GTTTTTTCATGCTTAAAATATTGTTATTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAA
66 GGCTTTTCATGCTTAAAATATGGTTATTCCTACTCTTTTCCAAATTAATTTCTGATTAAATCGAA
3964 ACAGGATTAAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGATGAGATTTGATTAGATAA
131 ACAGGATTAAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGATGAGATTTGATTAGATAA
4029 ATATTG
196 ATATTG
4035 ATATTTCAAG
Statistics
Matches: 187, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
214 187 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (214 bp):
TTTTCCCCAACTATTGGCCACAATAACCATAAGGAATATATAATTCAACACCAAAAAGATCAAAA
GGCTTTTCATGCTTAAAATATGGTTATTCCTACTCTTTTCCAAATTAATTTCTGATTAAATCGAA
ACAGGATTAAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGATGAGATTTGATTAGATAA
ATATTGGAGTCTCGGCGCC
Found at i:5638 original size:334 final size:332
Alignment explanation
Indices: 3868--6206 Score: 3300
Period size: 334 Copynumber: 7.0 Consensus size: 332
3858 AACCATAAGG
* ** * ** *
3868 AATATATAATTCAACTCCAAAAAGATCAAAAGTTTTTTCATGCTTAAAATATTGTTATTCCTATT
1 AATATATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATT
*
3933 CTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTAAGATGCTCGTAAAAACATATCCTTA
66 CTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTA
* *
3998 AATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCCCGGCACCAAAAA
131 AATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCCAAAAA
* * * * *
4063 TCATGTAAAATTAAGCCGGGTCCCCGGAGCGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACAC
196 TCATGTAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACAC
* * *
4128 GATTTTGGCTAAAATCTTGCAAAATTTGACCCCGAAAATCTTTTTTCCTCAAATTCTTGGCGACA
261 GATTTCGGCTAAAATTTTGCAAAATTTGA-CCCGAAAA--TTTTTTCCTC-AATTCTTGGCCACA
4193 ATACTAAAAATA
322 ATACTAAAAA-A
*
4205 TATATATATAATTCAACGCCAAAAAGATTTAAGGCCTTTTCATGCTTAAAATATGGTTATTCCTA
1 -A-ATATATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTA
4270 TTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCT
64 TTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCT
* * * *
4335 TAATTCCAATGTTGATGAGATTTGTTTAGATAAATATTGATATTTAAAGGAGTCTCGGCGCCAAA
129 TAAATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCCAAA
* *
4400 AATCATGTAAAACTGAG-CCGGG-CCCGGAAAGCGTTTTAAGCCAAAAACCGTGATGGTTAGTAC
194 AATCATGTAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTAC
* * *
4463 ACGATTTCGGCTAAAATTTTGCAAAATCTGACCCGAAATTTTTTTTTCCTCAATTATTGGCCACA
259 ACGATTTCGGCTAAAATTTTGCAAAATTTGACCCGAAA--ATTTTTTCCTCAATTCTTGGCCACA
* * **
4528 ATAACCATAAGG
322 AT-ACTAAAAAA
* * * *
4540 AATATATAACTCAACGCCAAAAAGATTTAAGGGCTTTTCATGCTTAAACTATGGTTGTTCTTATT
1 AATATATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATT
4605 CTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTA
66 CTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTA
* * *
4670 AATCCCATGTGGATTAGATTTGATTAGATAAATATTGATATTTCAAAGAGTCTCGGCGCCAAAAA
131 AATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCCAAAAA
** * *
4735 TCATGTAAAACTGAGTCGGGGCCTTGGAACGCGTTTTAAGTCAAAAACTGTGATGGTTAGTACAC
196 TCATGTAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACAC
*
4800 GATTTCGGCTAAAGTTTTGCAAAATTTGACCC-AAAATTTTTTTCCTCAATTCTTGGCCACAATA
261 GATTTCGGCTAAAATTTTGCAAAATTTGACCCGAAAA-TTTTTTCCTCAATTCTTGGCCACAATA
* *
4864 CT-CATAA
325 CTAAAAAA
* * **
4871 GA-A-A-AATTCAACGCCAAAATGATTTAATGGG-TTTTCATGCTTAAAATATGGTTATTTATAT
1 AATATATAATTCAACGCCAAAAAGATTTAA-GGGCTTTTCATGCTTAAAATATGGTTATTCCTAT
* * * *
4932 TCTTTTGCAAATTAATTTCTGATTAAATCGAAACATGATTCAGATACTCGTAAAAACATATCTTT
65 TCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTT
* * *
4997 AAATCCAATATGGCTGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCCGAAA
130 AAATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCCAAAA
* *
5062 ATCATGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTCAA-CCAGAAACCGTGATGGTTAGTAC
195 ATCATGTAAAACTGAGTCGGGGCCCCGGAACGCGTTTT-AAGCCAAAAACCGTGATGGTTAGTAC
* * * *
5126 ACGATTTCGGCTAAAATTTTGCAAAATCTGA--CTAAATTTTTTTTCTTCAATTCTTGGCCACAA
259 ACGATTTCGGCTAAAATTTTGCAAAATTTGACCCGAAA-ATTTTTTCCTCAATTCTTGGCCACAA
5189 TACTCAAAAAA
323 TACT-AAAAAA
* *
5200 AA-ATATAATTCAACGCCAAAAAGATTTAAGTGATTTTCATGCTTAAAATATGGTTATTCCTATT
1 AATATATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATT
5264 CTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTA
66 CTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTA
* * * *
5329 AATCCAATGTGGATGAGATTTGATTAGATAAATATTTATATTTCAAGGAGTCCCGGTG-CGAAAA
131 AATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCCAAAAA
* * *
5393 TCATATAAAATTGAGTC-GGGCCCCGGAACGCGTTTTAAGCCAAAAATCGTGATGGTTAGTACAC
196 TCATGTAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACAC
*
5457 GATTTCGGCTAAAATTTTGCAAAATTTGACCCCGAAAATTTTTTCCTCAATTCTTGGCAACAATA
261 GATTTCGGCTAAAATTTTGCAAAATTTGA-CCCGAAAATTTTTTCCTCAATTCTTGGCCACAATA
5522 CTAAAAATA
325 CTAAAAA-A
* *
5531 TATATATATAATTCAATGCCAAAAAGATATAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTA
1 -A-ATATATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTA
* *
5596 TTATTTTCCAAATTAATTTCTGATTAAATCGAAATAGGATTCAGATGCTCGTAAAAACATATCCT
64 TTCTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCT
* * * *
5661 TAAATCCCATGTGGATGAGATTTTATTAGATAAATATTGATATTTCGAGGAGTCTCGGCACCAAA
129 TAAATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCCAAA
* * * * *
5726 AATCATGTAAAACTAAGTCGGGGGCCCGAAACGCGTTTTAAACCAAAAACCTTGATGGTTAGTAC
194 AATCATGTAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTAC
* * * *
5791 ACGATTTCGGCTAAAATTTTCCAAAATCTGACCCGAAATTTTTTTTCCTCAATTATTCGG-CACA
259 ACGATTTCGGCTAAAATTTTGCAAAATTTGACCCGAAA-ATTTTTTCCTCAATTCTT-GGCCACA
* * **
5855 ATAGCCATAAGG
322 ATA-CTAAAAAA
*
5867 AATATATAATTCAACACCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATT
1 AATATATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATT
*
5932 CTTTTCCAAATTAATTTCTTATTAAATCGAAACAGGATTCAGATGCTACGTAAAAACATATCCTT
66 CTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCT-CGTAAAAACATATCCTT
* * * *
5997 AAATCCCATGTGGCATGAGATTTGATTAGATAAATATAGATATTTCTAGGAGTCTCGGCGTCAAA
130 AAATCCAATGTGG-ATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCCAAA
* ** * *
6062 AATCATGTAAAACTAAGTCAAGGCCCCGGAACGCGTTTTCAGCCAGAAACCGTGAT-G---GTAC
194 AATCATGTAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTAC
*
6123 ACGATTTCGGCTAAAATTTTGCAAAATCTT-A-CC-AAAATTTTTTTTCCTCAATTCTTGGCCGC
259 ACGATTTCGGCTAAAATTTTGCAAAAT-TTGACCCGAAAA--TTTTTTCCTCAATTCTTGGCCAC
6185 AATACTCATAAAAAA
321 AATA--C-TAAAAAA
6200 AATATAT
1 AATATAT
6207 TCTCATGATC
Statistics
Matches: 1794, Mismatches: 170, Indels: 79
0.88 0.08 0.04
Matches are distributed among these distances:
326 1 0.00
327 31 0.02
328 253 0.14
329 81 0.05
330 34 0.02
331 219 0.12
332 39 0.02
333 234 0.13
334 285 0.16
335 140 0.08
336 207 0.12
337 73 0.04
338 4 0.00
339 193 0.11
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (332 bp):
AATATATAATTCAACGCCAAAAAGATTTAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATT
CTTTTCCAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTA
AATCCAATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAGGAGTCTCGGCGCCAAAAA
TCATGTAAAACTGAGTCGGGGCCCCGGAACGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACAC
GATTTCGGCTAAAATTTTGCAAAATTTGACCCGAAAATTTTTTCCTCAATTCTTGGCCACAATAC
TAAAAAA
Found at i:5832 original size:993 final size:998
Alignment explanation
Indices: 3834--6205 Score: 3521
Period size: 1000 Copynumber: 2.4 Consensus size: 998
3824 TCTCGGCGCC
* * * * **
3834 TTTTCCCCAACTATT-GGCCACAATAACCATAAGGAATATATAATTCAACTCCAAAAAGATCAAA
1 TTTTCCTCAATTATTCGG-CACAATAGCCATAAGGAATATATAATTCAACACCAAAAAGATTTAA
* ** *
3898 AGTTTTTTCATGCTTAAAATATTGTTATTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGA
65 GGGCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGA
* *
3963 AACAGGATTAAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGATGAGATTTGATTAGATA
130 AACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATA
* * * * * *
4028 AATATTGATATTTCAAGGAGTCCCGGCACCAAAAATCATGTAAAATTAAGCCGGGTCCCCGGAGC
195 AATATTGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTAAGTCGGGGCCCCGGAAC
* * * *
4093 GCGTTTT-AAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAATCTTGCAAAATTTGA
260 GCGTTTTCAA-CCAGAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAATCTGA
* *
4157 CCCCGAAAATCTTTTTTCCTCAAATTCTTGGCGACAATACT-AAAAATATATATATATAATTCAA
324 --CC-AAAATTTTTTTTCCTC-AATTCTTGGCCACAATACTCAAAAA-A-A-A-ATATAATTCAA
*
4221 CGCCAAAAAGATTTAAGGCCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAA
381 CGCCAAAAAGATTTAAGGCATTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAA
* *
4286 TTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAATTCCAATGTTGAT
446 TTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGAT
* * *
4351 GAGATTTGTTTAGATAAATATTGATATTTAAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTGA
511 GAGATTTGATTAGATAAATATTGATATTTAAAGGAGTCCCGGCGCCAAAAATCATATAAAACTGA
4416 GCCGGGCCCGGAAAGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATT
576 GCCGGGCCCGGAAAGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATT
* * * * *
4481 TTGCAAAATCTGACCCGAAATTTTTTTTTCCTCAATTATTGGCCACAATAACCATAAGGAATATA
641 TTGCAAAATCTGACCCGAAA-TATTTTTTCCTCAATTATTGGCAACAATAACAAAAAAGAATATA
* * * * *
4546 TAACTCAACGCCAAAAAGATTTAAGGGCTTTTCATGCTTAAACTATGGTTGTTCTTATTCTTTTC
705 TAACTCAACGCCAAAAAGATATAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATTATTTTC
4611 CAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCC
770 CAAATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCC
* *
4676 ATGTGGATTAGATTTGATTAGATAAATATTGATATTTCAAAGAGTCTCGGCGCCAAAAATCATGT
835 ATGTGGATGAGATTTGATTAGATAAATATTGATATTTCAAAGAGTCTCGGCACCAAAAATCATGT
* * * **
4741 AAAACTGAGTCGGGGCCTTGGAACGCGTTTTAAGTCAAAAACTGTGATGGTTAGTACACGATTTC
900 AAAACTAAGTCGGGGCCTCGAAACGCGTTTTAAACCAAAAACTGTGATGGTTAGTACACGATTTC
* * *
4806 GGCTAAAGTTTTGCAAAATTTGACCCAAAA-TTT
965 GGCTAAAATTTTCCAAAATCTGACCCAAAATTTT
* * *
4839 TTTTCCTCAATTCTT-GGCCACAATA-CTCATAA-G-A-A-A-AATTCAACGCCAAAATGATTTA
1 TTTTCCTCAATTATTCGG-CACAATAGC-CATAAGGAATATATAATTCAACACCAAAAAGATTTA
** *
4897 ATGGG-TTTTCATGCTTAAAATATGGTTATTTATATTCTTTTGCAAATTAATTTCTGATTAAATC
64 A-GGGCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTCTGATTAAATC
* * * *
4961 GAAACATGATTCAGATACTCGTAAAAACATATCTTTAAATCCAATATGGCTGAGATTTGATTAGA
128 GAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGA
* * *
5026 TAAATATTGATATTTCAAGGAGTCTCGGCGCCGAAAATCATGCAAAACTGAGTCGGGGCCCCGGA
193 TAAATATTGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTAAGTCGGGGCCCCGGA
5091 ACGCGTTTTCAACCAGAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAATCTG
258 ACGCGTTTTCAACCAGAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAATCTG
* *
5156 A-CTAAATTTTTTTTCTTCAATTCTTGGCCACAATACTCAAAAAAAAATATAATTCAACGCCAAA
323 ACCAAAATTTTTTTTCCTCAATTCTTGGCCACAATACTCAAAAAAAAATATAATTCAACGCCAAA
5220 AAGATTTAAGTG-ATTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTCTG
388 AAGATTTAAG-GCATTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTCTG
5284 ATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGATGAGATT
452 ATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGATGAGATT
* * * * * *
5349 TGATTAGATAAATATTTATATTTCAAGGAGTCCCGGTG-CGAAAATCATATAAAATTGAGTCGGG
517 TGATTAGATAAATATTGATATTTAAAGGAGTCCCGGCGCCAAAAATCATATAAAACTGAGCCGGG
* *
5413 CCCCGGAACGCGTTTTAAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
582 -CCCGGAAAGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
* * *
5478 AAATTTGACCCCGAAA-ATTTTTTCCTCAATTCTTGGCAACAAT-ACTAAAAATATATATATATA
646 AAATCTGA-CCCGAAATATTTTTTCCTCAATTATTGGCAACAATAAC-AAAAA-AGA-ATATATA
* *
5541 ATTCAATGCCAAAAAGATATAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATTATTTTCCA
707 ACTCAACGCCAAAAAGATATAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATTATTTTCCA
*
5606 AATTAATTTCTGATTAAATCGAAATAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCCAT
772 AATTAATTTCTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCCAT
* * *
5671 GTGGATGAGATTTTATTAGATAAATATTGATATTTCGAGGAGTCTCGGCACCAAAAATCATGTAA
837 GTGGATGAGATTTGATTAGATAAATATTGATATTTCAAAGAGTCTCGGCACCAAAAATCATGTAA
5736 AACTAAGTCGGGGGCC-CGAAACGCGTTTTAAACCAAAAACCT-TGATGGTTAGTACACGATTTC
902 AACTAAGTC-GGGGCCTCGAAACGCGTTTTAAACCAAAAA-CTGTGATGGTTAGTACACGATTTC
*
5799 GGCTAAAATTTTCCAAAATCTGACCCGAAATTTT
965 GGCTAAAATTTTCCAAAATCTGACCCAAAATTTT
5833 TTTTCCTCAATTATTCGGCACAATAGCCATAAGGAATATATAATTCAACACCAAAAAGATTTAAG
1 TTTTCCTCAATTATTCGGCACAATAGCCATAAGGAATATATAATTCAACACCAAAAAGATTTAAG
*
5898 GGCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTCTTATTAAATCGAA
66 GGCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAA
*
5963 ACAGGATTCAGATGCTACGTAAAAACATATCCTTAAATCCCATGTGGCATGAGATTTGATTAGAT
131 ACAGGATTCAGATGCT-CGTAAAAACATATCCTTAAATCCAATGTGGC-TGAGATTTGATTAGAT
* * * **
6028 AAATATAGATATTTCTAGGAGTCTCGGCGTCAAAAATCATGTAAAACTAAGTCAAGGCCCCGGAA
194 AAATATTGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTAAGTCGGGGCCCCGGAA
* *
6093 CGCGTTTTCAGCCAGAAACCGTGAT-G---GTACACGATTTCGGCTAAAATTTTGCAAAATCTTA
259 CGCGTTTTCAACCAGAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAATCTGA
*
6154 CCAAAATTTTTTTTCCTCAATTCTTGGCCGCAATACTCATAAAAAAAATATA
324 CCAAAATTTTTTTTCCTCAATTCTTGGCCACAATACTCA-AAAAAAAATATA
6206 TTCTCATGAT
Statistics
Matches: 1237, Mismatches: 105, Indels: 56
0.88 0.08 0.04
Matches are distributed among these distances:
990 2 0.00
991 49 0.04
992 245 0.20
993 272 0.22
994 38 0.03
995 23 0.02
996 19 0.02
997 36 0.03
998 39 0.03
999 105 0.08
1000 277 0.22
1001 101 0.08
1002 1 0.00
1003 1 0.00
1004 2 0.00
1005 27 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (998 bp):
TTTTCCTCAATTATTCGGCACAATAGCCATAAGGAATATATAATTCAACACCAAAAAGATTTAAG
GGCTTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTCTGATTAAATCGAA
ACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATAA
ATATTGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGTAAAACTAAGTCGGGGCCCCGGAACG
CGTTTTCAACCAGAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAATCTGACC
AAAATTTTTTTTCCTCAATTCTTGGCCACAATACTCAAAAAAAAATATAATTCAACGCCAAAAAG
ATTTAAGGCATTTTCATGCTTAAAATATGGTTATTCCTATTCTTTTCCAAATTAATTTCTGATTA
AATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCAATGTGGATGAGATTTGAT
TAGATAAATATTGATATTTAAAGGAGTCCCGGCGCCAAAAATCATATAAAACTGAGCCGGGCCCG
GAAAGCGTTTTAAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAATC
TGACCCGAAATATTTTTTCCTCAATTATTGGCAACAATAACAAAAAAGAATATATAACTCAACGC
CAAAAAGATATAAGGGCTTTTCATGCTTAAAATATGGTTATTCCTATTATTTTCCAAATTAATTT
CTGATTAAATCGAAACAGGATTCAGATGCTCGTAAAAACATATCCTTAAATCCCATGTGGATGAG
ATTTGATTAGATAAATATTGATATTTCAAAGAGTCTCGGCACCAAAAATCATGTAAAACTAAGTC
GGGGCCTCGAAACGCGTTTTAAACCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTT
TCCAAAATCTGACCCAAAATTTT
Found at i:15443 original size:17 final size:16
Alignment explanation
Indices: 15416--15451 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
15406 CTACTATATT
15416 TTAATTATAAATGTAA
1 TTAATTATAAATGTAA
*
15432 TTAATGTATAAATTTAA
1 TTAAT-TATAAATGTAA
15449 TTA
1 TTA
15452 CGTTGACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TTAATTATAAATGTAA
Found at i:28114 original size:2 final size:2
Alignment explanation
Indices: 28109--28135 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28099 ACACACACAC
28109 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28136 ATCTAGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30237 original size:27 final size:27
Alignment explanation
Indices: 30169--30232 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
30159 ATTTCTGGAA
*
30169 AACAAGGGAAATGGACAATTAAAAAGG
1 AACAAGGGAAATAGACAATTAAAAAGG
30196 AACAAGGGAAATAGACAATTAAAAAGG
1 AACAAGGGAAATAGACAATTAAAAAGG
30223 AACAGAGGGA
1 AACA-AGGGA
30233 GTAGATAGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 30 0.86
28 5 0.14
ACGTcount: A:0.56, C:0.08, G:0.27, T:0.09
Consensus pattern (27 bp):
AACAAGGGAAATAGACAATTAAAAAGG
Found at i:66556 original size:2 final size:2
Alignment explanation
Indices: 66549--66575 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
66539 AATGCTATTC
66549 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
66576 TTAAGTTGTA
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:72066 original size:21 final size:21
Alignment explanation
Indices: 72037--72079 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
72027 GCAGCTCGGC
72037 TATT-TTTTTAAAAAAAATAAT
1 TATTATTTTTAAAAAAAA-AAT
72058 TATTATTTTTAAAAAAAAAAT
1 TATTATTTTTAAAAAAAAAAT
72079 T
1 T
72080 TTGGTCTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTATTTTTAAAAAAAAAAT
Found at i:79416 original size:16 final size:15
Alignment explanation
Indices: 79395--79442 Score: 60
Period size: 17 Copynumber: 3.0 Consensus size: 15
79385 GAATAGATTT
79395 TAAAATGCTAAAAAAA
1 TAAAATGC-AAAAAAA
*
79411 TAAAATTCACCAAAAAA
1 TAAAATGCA--AAAAAA
79428 TAAAATGCAAAAAAA
1 TAAAATGCAAAAAAA
79443 ATTACTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 7 0.25
16 7 0.25
17 14 0.50
ACGTcount: A:0.69, C:0.10, G:0.04, T:0.17
Consensus pattern (15 bp):
TAAAATGCAAAAAAA
Found at i:79443 original size:16 final size:16
Alignment explanation
Indices: 79395--79444 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
79385 GAATAGATTT
*
79395 TAAAATGCTAAAAAAA
1 TAAAATGCAAAAAAAA
* *
79411 TAAAATTCACCAAAAAA
1 TAAAATGCA-AAAAAAA
79428 TAAAATGCAAAAAAAA
1 TAAAATGCAAAAAAAA
79444 T
1 T
79445 TACTAATTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.68, C:0.10, G:0.04, T:0.18
Consensus pattern (16 bp):
TAAAATGCAAAAAAAA
Found at i:86080 original size:254 final size:254
Alignment explanation
Indices: 85631--86138 Score: 1016
Period size: 254 Copynumber: 2.0 Consensus size: 254
85621 TTCCTTTTCT
85631 TCATAATATTTGGTGTTATATGACTCAATTATCAGCTCATTTCAGTGTTATAATTGTTTCATAGG
1 TCATAATATTTGGTGTTATATGACTCAATTATCAGCTCATTTCAGTGTTATAATTGTTTCATAGG
85696 AATGTATAAGGCAACTTGTTTCATAATTCTTATTATATCTTGTACCTTGGTTTATGTTCATAATT
66 AATGTATAAGGCAACTTGTTTCATAATTCTTATTATATCTTGTACCTTGGTTTATGTTCATAATT
85761 GGAGCCATTTGAGTGGCCAAAAGGCTTAAGAAAATGATGCTGCTTATCTAAAACAGTGATCATTC
131 GGAGCCATTTGAGTGGCCAAAAGGCTTAAGAAAATGATGCTGCTTATCTAAAACAGTGATCATTC
85826 TTTGCTAAAACACCGCTATCTTTTAAAGAGTGTCATCTCTGTGAAAGAAAGAAAGAAAG
196 TTTGCTAAAACACCGCTATCTTTTAAAGAGTGTCATCTCTGTGAAAGAAAGAAAGAAAG
85885 TCATAATATTTGGTGTTATATGACTCAATTATCAGCTCATTTCAGTGTTATAATTGTTTCATAGG
1 TCATAATATTTGGTGTTATATGACTCAATTATCAGCTCATTTCAGTGTTATAATTGTTTCATAGG
85950 AATGTATAAGGCAACTTGTTTCATAATTCTTATTATATCTTGTACCTTGGTTTATGTTCATAATT
66 AATGTATAAGGCAACTTGTTTCATAATTCTTATTATATCTTGTACCTTGGTTTATGTTCATAATT
86015 GGAGCCATTTGAGTGGCCAAAAGGCTTAAGAAAATGATGCTGCTTATCTAAAACAGTGATCATTC
131 GGAGCCATTTGAGTGGCCAAAAGGCTTAAGAAAATGATGCTGCTTATCTAAAACAGTGATCATTC
86080 TTTGCTAAAACACCGCTATCTTTTAAAGAGTGTCATCTCTGTGAAAGAAAGAAAGAAAG
196 TTTGCTAAAACACCGCTATCTTTTAAAGAGTGTCATCTCTGTGAAAGAAAGAAAGAAAG
86139 AAACAAGGCA
Statistics
Matches: 254, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
254 254 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (254 bp):
TCATAATATTTGGTGTTATATGACTCAATTATCAGCTCATTTCAGTGTTATAATTGTTTCATAGG
AATGTATAAGGCAACTTGTTTCATAATTCTTATTATATCTTGTACCTTGGTTTATGTTCATAATT
GGAGCCATTTGAGTGGCCAAAAGGCTTAAGAAAATGATGCTGCTTATCTAAAACAGTGATCATTC
TTTGCTAAAACACCGCTATCTTTTAAAGAGTGTCATCTCTGTGAAAGAAAGAAAGAAAG
Found at i:112157 original size:73 final size:73
Alignment explanation
Indices: 112038--112326 Score: 355
Period size: 73 Copynumber: 3.8 Consensus size: 73
112028 TCTACGTCAA
* * * *
112038 ATTCTCACATGAAATCAAGGATCCCTCCAACCAAACACGCCCTTAATGTTTTCTTCTTTCGTATT
1 ATTCTCACATGAAATCAAGGATTCCTCCAACCAAACGCGCCCTTAATGTTTTATTCTTTCGCATT
112103 TCCTACTT
66 TCCTACTT
* * *
112111 ATTCTCACATGAAATCAAGGATTCCTCCAACCAAACGCACCCTTAATATTTTATTCTTTTGCATT
1 ATTCTCACATGAAATCAAGGATTCCTCCAACCAAACGCGCCCTTAATGTTTTATTCTTTCGCATT
*
112176 TCCTACAT
66 TCCTACTT
*
112184 ATTCTCACATGAAATCAAGGATTCCTCCAACCAAACGCGCCCTTAATGTTTTATTCTTACGCATT
1 ATTCTCACATGAAATCAAGGATTCCTCCAACCAAACGCGCCCTTAATGTTTTATTCTTTCGCATT
112249 TCCTACATCAGTGAT
66 TCCT--A-C--T--T
** * *
112264 CAGGTTCTCGTAGGAAATCAAGGA-TCTCTCCAACCAAACGCGCCCTTAATGTTTTCTTCTTTC
1 -A--TTCTCACATGAAATCAAGGATTC-CTCCAACCAAACGCGCCCTTAATGTTTTATTCTTTC
112327 TCAAGCTTTG
Statistics
Matches: 187, Mismatches: 18, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
73 130 0.70
75 1 0.01
76 1 0.01
80 1 0.01
81 1 0.01
82 2 0.01
83 51 0.27
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.34
Consensus pattern (73 bp):
ATTCTCACATGAAATCAAGGATTCCTCCAACCAAACGCGCCCTTAATGTTTTATTCTTTCGCATT
TCCTACTT
Found at i:119025 original size:3 final size:3
Alignment explanation
Indices: 119017--119076 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
119007 AATTTTTATA
* * * * * *
119017 AAT AAT AAT AAT GAT GAT GAT GAT GAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
119065 AAT AATT AAT AA
1 AAT AA-T AAT AA
119077 AGTTAATTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:126383 original size:23 final size:23
Alignment explanation
Indices: 126353--126398 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
126343 AAATGGCAGA
126353 AATCTTATTAATTTAGATTATGT
1 AATCTTATTAATTTAGATTATGT
126376 AATCTTATTAATTTAGATTATGT
1 AATCTTATTAATTTAGATTATGT
126399 CACAGTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (23 bp):
AATCTTATTAATTTAGATTATGT
Found at i:138811 original size:17 final size:16
Alignment explanation
Indices: 138789--138837 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
138779 CTAAGGTACA
138789 AATATAGACCAAACAAT
1 AATATAGACCAAA-AAT
138806 AATAT--ACCAAGAAA-
1 AATATAGACCAA-AAAT
138820 AATATAGACCAAATAAT
1 AATATAGACCAAA-AAT
138837 A
1 A
138838 CAAACTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 8 0.30
17 6 0.22
ACGTcount: A:0.61, C:0.14, G:0.06, T:0.18
Consensus pattern (16 bp):
AATATAGACCAAAAAT
Found at i:145282 original size:94 final size:92
Alignment explanation
Indices: 145173--145342 Score: 288
Period size: 94 Copynumber: 1.8 Consensus size: 92
145163 TGTTTCATCA
* *
145173 TCTTTTAGTTTTAAGTGTTTGTAGGACTTCAACTACATTTTTGGTTTTCGGCC-AAAAAAAAACT
1 TCTTTTAGTTTTAAGTGTTTGTACGACTTCAACTAC---TTTGGGTTTCGGCCAAAAAAAAAACT
145237 ACTTTTTTGGGTAAGTGTTTGTAGGACTAC
63 ACTTTTTTGGGTAAGTGTTTGTAGGACTAC
145267 TCTTTTAGTTTTAAGTGTTTGTACGACTTCAACTACTTTGGGTTTCGGCCAAAAAAAAAACTACT
1 TCTTTTAGTTTTAAGTGTTTGTACGACTTCAACTACTTTGGGTTTCGGCCAAAAAAAAAACTACT
145332 TTTTTGGGTAA
66 TTTTTGGGTAA
145343 CCATGCTAAG
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
91 13 0.18
92 25 0.34
94 35 0.48
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (92 bp):
TCTTTTAGTTTTAAGTGTTTGTACGACTTCAACTACTTTGGGTTTCGGCCAAAAAAAAAACTACT
TTTTTGGGTAAGTGTTTGTAGGACTAC
Found at i:150077 original size:2 final size:2
Alignment explanation
Indices: 150070--150095 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
150060 AGTTACATAA
150070 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
150096 TTTGTTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:160728 original size:12 final size:12
Alignment explanation
Indices: 160711--160755 Score: 81
Period size: 12 Copynumber: 3.8 Consensus size: 12
160701 GTATATCTTA
160711 TGGTGGAAGGGG
1 TGGTGGAAGGGG
*
160723 TGGTGGAAGAGG
1 TGGTGGAAGGGG
160735 TGGTGGAAGGGG
1 TGGTGGAAGGGG
160747 TGGTGGAAG
1 TGGTGGAAG
160756 AGGCAGGGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.20, C:0.00, G:0.62, T:0.18
Consensus pattern (12 bp):
TGGTGGAAGGGG
Found at i:160741 original size:24 final size:24
Alignment explanation
Indices: 160711--160758 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
160701 GTATATCTTA
160711 TGGTGGAAGGGGTGGTGGAAGAGG
1 TGGTGGAAGGGGTGGTGGAAGAGG
160735 TGGTGGAAGGGGTGGTGGAAGAGG
1 TGGTGGAAGGGGTGGTGGAAGAGG
160759 CAGGGGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.62, T:0.17
Consensus pattern (24 bp):
TGGTGGAAGGGGTGGTGGAAGAGG
Found at i:160769 original size:24 final size:24
Alignment explanation
Indices: 160712--160771 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
160702 TATATCTTAT
*
160712 GGTGGAAGGGGTGGTGGAAGAGGT
1 GGTGGAAGGGGTGGTGGAAGAGGA
160736 GGTGGAAGGGGTGGTGGAAGAGGCA
1 GGTGGAAGGGGTGGTGGAAGAGG-A
*
160761 GG-GGGAGGGGT
1 GGTGGAAGGGGT
160772 TGGGGAGGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.20, C:0.02, G:0.65, T:0.13
Consensus pattern (24 bp):
GGTGGAAGGGGTGGTGGAAGAGGA
Found at i:168520 original size:20 final size:20
Alignment explanation
Indices: 168495--168532 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
168485 AACAGAGATA
168495 TTATCATCAGACATATCAAT
1 TTATCATCAGACATATCAAT
*
168515 TTATCATCAGAGATATCA
1 TTATCATCAGACATATCA
168533 TTCCAATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (20 bp):
TTATCATCAGACATATCAAT
Found at i:168836 original size:44 final size:44
Alignment explanation
Indices: 168787--168893 Score: 214
Period size: 44 Copynumber: 2.4 Consensus size: 44
168777 GTCTCGGGAA
168787 AGTTCTTTATTGATGCTCTTTGTTCGTGAATGAAGAAAATTTTG
1 AGTTCTTTATTGATGCTCTTTGTTCGTGAATGAAGAAAATTTTG
168831 AGTTCTTTATTGATGCTCTTTGTTCGTGAATGAAGAAAATTTTG
1 AGTTCTTTATTGATGCTCTTTGTTCGTGAATGAAGAAAATTTTG
168875 AGTTCTTTATTGATGCTCT
1 AGTTCTTTATTGATGCTCT
168894 ATTCTTCATG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (44 bp):
AGTTCTTTATTGATGCTCTTTGTTCGTGAATGAAGAAAATTTTG
Found at i:169376 original size:21 final size:24
Alignment explanation
Indices: 169347--169397 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
169337 TTTTGAACTC
169347 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
169370 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
169393 ATTAT
1 ATTAT
169398 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:169392 original size:25 final size:25
Alignment explanation
Indices: 169347--169395 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
169337 TTTTGAACTC
*
169347 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
169372 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
169396 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:173842 original size:22 final size:21
Alignment explanation
Indices: 173818--174095 Score: 140
Period size: 22 Copynumber: 12.9 Consensus size: 21
173808 TAGTTACCCA
173818 AAAATTTCATAGGGGGTTACC
1 AAAATTTCATAGGGGGTTACC
* * *
173839 AAAATTTCACAAGGAGGATTACT
1 AAAATTTCA-TAGG-GGGTTACC
* * *
173862 GAAATTTCATAGGGTGTTATC
1 AAAATTTCATAGGGGGTTACC
* * *
173883 AGAATTTCATCGGGATGTTACC
1 AAAATTTCATAGGG-GGTTACC
173905 AAAATTTCAT------TTACC
1 AAAATTTCATAGGGGGTTACC
*
173920 AAAATTTCATAGTGAGGTTACC
1 AAAATTTCATAG-GGGGTTACC
* *** *
173942 AAATTTTCATATTAAGGTTACT
1 AAAATTTCATA-GGGGGTTACC
* *
173964 GAAATTTCATAAGGAAGTTAGGTTATC
1 AAAATTTCAT-AGG--G---GGTTACC
*
173991 AACATTTCATAGGGGGATTACC
1 AAAATTTCATAGGGGG-TTACC
174013 AAAATTTCATA--GGGTTACC
1 AAAATTTCATAGGGGGTTACC
* * *
174032 AACATTTCATTGGGGGATTAAC
1 AAAATTTCATAGGGGG-TTACC
* **
174054 AAAATTTGATAGTAAGGTTACC
1 AAAATTTCATAG-GGGGTTACC
*
174076 AAAATTTCATAAGGAGGTTA
1 AAAATTTCAT-AGGGGGTTA
174096 GTAAAATTCA
Statistics
Matches: 194, Mismatches: 40, Indels: 45
0.70 0.14 0.16
Matches are distributed among these distances:
15 15 0.08
19 14 0.07
20 3 0.02
21 29 0.15
22 97 0.50
23 19 0.10
24 1 0.01
26 3 0.02
27 13 0.07
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (21 bp):
AAAATTTCATAGGGGGTTACC
Found at i:173860 original size:23 final size:21
Alignment explanation
Indices: 173818--173875 Score: 53
Period size: 23 Copynumber: 2.7 Consensus size: 21
173808 TAGTTACCCA
* *
173818 AAAATTTCATAGGGGGTTACC
1 AAAATTTCAAAGGGGATTACC
*
173839 AAAATTTCACAAGGAGGATTACT
1 AAAATTTCA-AAGG-GGATTACC
* *
173862 GAAATTTCATAGGG
1 AAAATTTCAAAGGG
173876 TGTTATCAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 10 0.33
22 6 0.20
23 14 0.47
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (21 bp):
AAAATTTCAAAGGGGATTACC
Found at i:173920 original size:15 final size:15
Alignment explanation
Indices: 173900--173929 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
173890 CATCGGGATG
173900 TTACCAAAATTTCAT
1 TTACCAAAATTTCAT
173915 TTACCAAAATTTCAT
1 TTACCAAAATTTCAT
173930 AGTGAGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
TTACCAAAATTTCAT
Found at i:174041 original size:41 final size:42
Alignment explanation
Indices: 173983--174086 Score: 138
Period size: 41 Copynumber: 2.5 Consensus size: 42
173973 TAAGGAAGTT
* *
173983 AGGTTATCAACATTTCATAGGGGGATTACCAAAATTTCATAG
1 AGGTTACCAACATTTCATAGGGGGATTAACAAAATTTCATAG
* *
174025 -GGTTACCAACATTTCATTGGGGGATTAACAAAATTTGATAG
1 AGGTTACCAACATTTCATAGGGGGATTAACAAAATTTCATAG
*
174066 TAAGGTTACCAAAATTTCATA
1 --AGGTTACCAACATTTCATA
174087 AGGAGGTTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 37 0.70
44 16 0.30
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (42 bp):
AGGTTACCAACATTTCATAGGGGGATTAACAAAATTTCATAG
Found at i:174577 original size:22 final size:22
Alignment explanation
Indices: 174483--175107 Score: 370
Period size: 22 Copynumber: 28.8 Consensus size: 22
174473 GAATAGTGGG
* **
174483 GGTTACTAAAATTTCATAATGA
1 GGTTACCAAAATTTCATAGGGA
* *
174505 GGTTACC-AAATTTTATACTGG-
1 GGTTACCAAAATTTCATA-GGGA
* *
174526 GGTTACTAAAATCTCATAGGG-
1 GGTTACCAAAATTTCATAGGGA
* *
174547 GTTTACCAAAATTTCATGGGGA
1 GGTTACCAAAATTTCATAGGGA
*
174569 GGTTACCAAAATTTCATATGG-
1 GGTTACCAAAATTTCATAGGGA
* ***
174590 GGTTACCAATATTTCA-AAATA
1 GGTTACCAAAATTTCATAGGGA
* * *
174611 GGTTATCAAAATTACATAGTGA
1 GGTTACCAAAATTTCATAGGGA
* * * *
174633 GTTTACGAAATTTTCATAGTGA
1 GGTTACCAAAATTTCATAGGGA
* ***
174655 GGTTA-CATCAATTTCATAGTCC
1 GGTTACCA-AAATTTCATAGGGA
* * * *
174677 GGCTACAAAAATTTCACAGTGA
1 GGTTACCAAAATTTCATAGGGA
*
174699 GGTTA-CAGAAATTTCATATGGA
1 GGTTACCA-AAATTTCATAGGGA
* *
174721 --TTACCAAAATTTCATTGTGA
1 GGTTACCAAAATTTCATAGGGA
*
174741 GGTTACCAATATTTCATA-GG-
1 GGTTACCAAAATTTCATAGGGA
* ** *
174761 GGTTACCAATATTTTTTAGGAA
1 GGTTACCAAAATTTCATAGGGA
* * *
174783 GGCTACAAAAATTTCATAGTGA
1 GGTTACCAAAATTTCATAGGGA
* * * * *
174805 GCTTACAAAAATTTAATTGTGA
1 GGTTACCAAAATTTCATAGGGA
* * *
174827 GGTTATCGAAATTTCATA-AG-
1 GGTTACCAAAATTTCATAGGGA
* * *
174847 GGTTATCC-GAATTCCATAGTGA
1 GGTTA-CCAAAATTTCATAGGGA
* *
174869 GGTTACAAAAATTTCATA-GTA
1 GGTTACCAAAATTTCATAGGGA
*
174890 CAGTTACCAAAATTTCATA-GG-
1 -GGTTACCAAAATTTCATAGGGA
* * *
174911 GGTAACCAAAATTTCCTATGGA
1 GGTTACCAAAATTTCATAGGGA
*
174933 GGTTTCCAAAATTTCATAGGG-
1 GGTTACCAAAATTTCATAGGGA
* * * *
174954 TGTTACTAAAATTTCATAAGAA
1 GGTTACCAAAATTTCATAGGGA
* *
174976 GGTTGCCAGAATTTTCATAGTGTCGA
1 GGTTACCA-AAATTTCATAG-G--GA
* * **
175002 CGTTACCCAAATTTCATAATGA
1 GGTTACCAAAATTTCATAGGGA
175024 GGTTACCAAAATTTCATAGGGA
1 GGTTACCAAAATTTCATAGGGA
* **
175046 GGTTACCAAAATTCCATAGTCA
1 GGTTACCAAAATTTCATAGGGA
*
175068 GGTTACCAAAATTTCATAGTGTA
1 GGTTACCAAAATTTCATAG-GGA
*
175091 -GTTATCAAAATTTCATA
1 GGTTACCAAAATTTCATA
175108 AAATGTGACA
Statistics
Matches: 456, Mismatches: 121, Indels: 52
0.72 0.19 0.08
Matches are distributed among these distances:
20 59 0.13
21 91 0.20
22 279 0.61
23 11 0.02
24 1 0.00
25 9 0.02
26 6 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGGGA
Found at i:174657 original size:86 final size:84
Alignment explanation
Indices: 174483--175107 Score: 319
Period size: 86 Copynumber: 7.2 Consensus size: 84
174473 GAATAGTGGG
* * * * * * *
174483 GGTTACTAAAATTTCATAATGAGGTTACCAA-ATTTTATACTGGGGTTACTAAAATCTCATAGGG
1 GGTTACCAAAATTTCAT-ATGGGGTTACCAATATTTCAAAATGAGGTTAC-AAAAT-TCATAGTG
* *
174547 GTTTACCAAAATTTCATGGGGA
63 GTTTACCAAAATTTCATAGTGA
174569 GGTTACCAAAATTTCATATGGGGTTACCAATATTTCAAAAT-AGGTTATCAAAATTACATAGTGA
1 GGTTACCAAAATTTCATATGGGGTTACCAATATTTCAAAATGAGGTTA-CAAAATT-CATAGTG-
* *
174633 GTTTACGAAATTTTCATAGTGA
63 GTTTACCAAAATTTCATAGTGA
* ** * * * * *
174655 GGTTA-CATCAATTTCATAGTCCGGCTACAAAAATTTCACAGTGAGGTTACAGAAATTTCATA-T
1 GGTTACCA-AAATTTCATA-TGGGGTTACCAATATTTCAAAATGAGGTTACA-AAA-TTCATAGT
* *
174718 GGATTACCAAAATTTCATTGTGA
62 GGTTTACCAAAATTTCATAGTGA
* *** * *
174741 GGTTACCAATATTTCATA-GGGGTTACCAATATTT-TTTAGGAAGGCTACAAAAATTTCATAGTG
1 GGTTACCAAAATTTCATATGGGGTTACCAATATTTCAAAATG-AGGTTAC-AAAA-TTCATAGTG
* * * *
174804 AGCTTACAAAAATTTAATTGTGA
63 -GTTTACCAAAATTTCATAGTGA
* * * * * * *
174827 GGTTATCGAAATTTCATA-AGGGTTATCCGA-ATTCCATAGTGAGGTTACAAAAATTTCATAGTA
1 GGTTACCAAAATTTCATATGGGGTTA-CCAATATTTCAAAATGAGGTTAC-AAAA-TTCATAGT-
*
174890 CAG-TTACCAAAATTTCATAG-G-
62 -GGTTTACCAAAATTTCATAGTGA
* * * * * *
174911 GGTAACCAAAATTTCCTATGGAGGTTTCCAAAATTTC-ATA-GGGTGTTACTAAAATTTCATAAG
1 GGTTACCAAAATTTCATATGG-GGTTACCAATATTTCAAAATGAG-GTTAC-AAAA-TTCAT-AG
* * *
174974 AAGG-TTGCCAGAATTTTCATAGTGTCGA
61 -TGGTTTACCA-AAATTTCATA--GT-GA
* * * * * **
175002 CGTTACCCAAATTTCATAATGAGGTTACCAAAATTTCATAGGGAGGTTACCAAAATTCCATAGTC
1 GGTTACCAAAATTTCAT-ATGGGGTTACCAATATTTCAAAATGAGGTTA-CAAAATT-CATAGT-
175067 AGG-TTACCAAAATTTCATAGTGTA
62 -GGTTTACCAAAATTTCATAGTG-A
*
175091 -GTTATCAAAATTTCATA
1 GGTTACCAAAATTTCATA
175108 AAATGTGACA
Statistics
Matches: 415, Mismatches: 86, Indels: 75
0.72 0.15 0.13
Matches are distributed among these distances:
83 1 0.00
84 44 0.11
85 59 0.14
86 183 0.44
87 29 0.07
88 29 0.07
89 5 0.01
90 1 0.00
91 40 0.10
92 21 0.05
93 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (84 bp):
GGTTACCAAAATTTCATATGGGGTTACCAATATTTCAAAATGAGGTTACAAAATTCATAGTGGTT
TACCAAAATTTCATAGTGA
Found at i:174755 original size:64 final size:64
Alignment explanation
Indices: 174483--175108 Score: 375
Period size: 64 Copynumber: 9.6 Consensus size: 64
174473 GAATAGTGGG
* * * * * * *
174483 GGTTACTAAAATTTCATAATGAGGTTACC-AAATTTTATACTGGGGTTACTAAAATCTCATAG-G
1 GGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATA--AGGATTACCAAAATTTCATAGTG
174546 -
64 A
* * * * * * *
174546 GGTTTACCAAAATTTCATGGGGAGGTTACCAAAATTTCATATGGGGTTACCAATATTTCAAAAT-
1 GG-TTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATA-AGGATTACCAAAATTTCATAGTG
174610 A
64 A
* * * * * *
174611 GGTTATCAAAATTACATAGTGAGTTTACGAAATTTTCAT-AGTGAGGTTA-CATCAATTTCATAG
1 GGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAAG-GA--TTACCA-AAATTTCATAG
**
174674 TCC
62 TGA
* * * * *
174677 GGCTACAAAAATTTCACAGTGAGGTTA-CAGAAATTTCATATGGATTACCAAAATTTCATTGTGA
1 GGTTACCAAAATTTCATAGTGAGGTTACCA-AAATTTCATAAGGATTACCAAAATTTCATAGTGA
* * * * * *
174741 GGTTACCAATATTTCATAG-G-GGTTACCAATATTT-TTTAGGAAGGCTACAAAAATTTCATAGT
1 GGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAAGG-A--TTACCAAAATTTCATAGT
174803 GA
63 GA
* * * * * * * * *
174805 GCTTACAAAAATTTAATTGTGAGGTTATCGAAATTTCATAAGGGTTATCC-GAATTCCATAGTGA
1 GGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAAGGATTA-CCAAAATTTCATAGTGA
* * * * * *
174869 GGTTACAAAAATTTCATAGT-ACAGTTACCAAAATTTCATAGGGGTAACCAAAATTTCCTA-TGG
1 GGTTACCAAAATTTCATAGTGA-GGTTACCAAAATTTCATAAGGATTACCAAAATTTCATAGT-G
174932 A
64 A
* * * * *
174933 GGTTTCCAAAATTTCATAG-G-GTGTTACTAAAATTTCATAAGAAGGTTGCCAGAATTTTCATAG
1 GGTTACCAAAATTTCATAGTGAG-GTTACCAAAATTTCATAAG--GATTACCA-AAATTTCATA-
174996 TGTCGA
61 -GT-GA
* * * * * *
175002 CGTTACCCAAATTTCATAATGAGGTTACCAAAATTTCATAGGGAGGTTACCAAAATTCCATAGTC
1 GGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAAGGA--TTACCAAAATTTCATAGTG
175067 A
64 A
*
175068 GGTTACCAAAATTTCATAGTGTA-GTTATCAAAATTTCATAA
1 GGTTACCAAAATTTCATAGTG-AGGTTACCAAAATTTCATAA
175109 AATGTGACAA
Statistics
Matches: 427, Mismatches: 100, Indels: 69
0.72 0.17 0.12
Matches are distributed among these distances:
61 3 0.01
62 12 0.03
63 27 0.06
64 208 0.49
65 33 0.08
66 85 0.20
67 8 0.02
68 1 0.00
69 26 0.06
70 23 0.05
71 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (64 bp):
GGTTACCAAAATTTCATAGTGAGGTTACCAAAATTTCATAAGGATTACCAAAATTTCATAGTGA
Found at i:175345 original size:34 final size:34
Alignment explanation
Indices: 175302--175369 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
175292 ATCCTCTTGA
175302 AAATAAATCCAAACACAATATTTAGTATTAATAG
1 AAATAAATCCAAACACAATATTTAGTATTAATAG
175336 AAATAAATCCAAACACAATATTTAGTATTAATAG
1 AAATAAATCCAAACACAATATTTAGTATTAATAG
175370 TTAAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (34 bp):
AAATAAATCCAAACACAATATTTAGTATTAATAG
Found at i:182950 original size:24 final size:23
Alignment explanation
Indices: 182906--182952 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
182896 CCGGTAAGAG
182906 GTTTATTTTAATTTTTCTTGGTT
1 GTTTATTTTAATTTTTCTTGGTT
182929 GTTTATTTTAAAATTTTT-TTGGTT
1 GTTTATTTT--AATTTTTCTTGGTT
182953 ATGAATTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 6 0.27
25 7 0.32
ACGTcount: A:0.17, C:0.02, G:0.13, T:0.68
Consensus pattern (23 bp):
GTTTATTTTAATTTTTCTTGGTT
Found at i:183553 original size:28 final size:28
Alignment explanation
Indices: 183500--183554 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
183490 AAAAAGCAAT
*
183500 AAAAAACCCCTCATAACTTGATGCCAAA
1 AAAAAACCCCTCATAACTTGAGGCCAAA
183528 AAAAAACCCCTCATAACTTTG-GGCCAA
1 AAAAAACCCCTCATAAC-TTGAGGCCAA
183555 GGCAAACAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.44, C:0.29, G:0.09, T:0.18
Consensus pattern (28 bp):
AAAAAACCCCTCATAACTTGAGGCCAAA
Found at i:186994 original size:22 final size:22
Alignment explanation
Indices: 186948--187001 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
186938 ATGATCCCAT
* ** *
186948 TATGAAATTTTGATAATTTTTC
1 TATGAAATTTTAATAATAATAC
186970 TATGAAATTTTAATAATAATAC
1 TATGAAATTTTAATAATAATAC
*
186992 TATGGAATTT
1 TATGAAATTT
187002 CGAGATTCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (22 bp):
TATGAAATTTTAATAATAATAC
Found at i:187221 original size:23 final size:22
Alignment explanation
Indices: 187204--187484 Score: 68
Period size: 22 Copynumber: 12.9 Consensus size: 22
187194 GAATTGTTAG
* *
187204 TAATTACACTTTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
**
187226 TAATCACACTATGAAATAGTGA
1 TAATCACACTATGAAATTTTGA
* * * *
187248 TAACCTCGCTATAAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
187270 TAAAT-ATTC-CTATAAAATTTTGA
1 T-AATCA--CACTATGAAATTTTGA
* * * * *
187293 TAAACCTCCCAATGAAATTTTAA
1 T-AATCACACTATGAAATTTTGA
** *
187316 TAACTTTC-TTATGAAATTTTG-
1 TAA-TCACACTATGAAATTTTGA
187337 --AT-A-ACTAT-AAATTTTGA
1 TAATCACACTATGAAATTTTGA
**
187354 TAA-CATTC-CTTATGATTTTTTGA
1 TAATCA--CAC-TATGAAATTTTGA
* * * *
187377 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* * *
187399 TAATCTCCCTATGATATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
187421 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * *
187443 TAA-CCCTCTTATAAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* *
187465 -AAACTAAACTATGAAATTTT
1 TAATC-ACACTATGAAATTTT
187485 TTATTGCCAA
Statistics
Matches: 186, Mismatches: 50, Indels: 46
0.66 0.18 0.16
Matches are distributed among these distances:
16 8 0.04
17 3 0.02
18 1 0.01
19 3 0.02
21 6 0.03
22 118 0.63
23 45 0.24
24 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:187270 original size:22 final size:21
Alignment explanation
Indices: 187215--187464 Score: 132
Period size: 22 Copynumber: 11.5 Consensus size: 21
187205 AATTACACTT
* *
187215 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTC-CTA
**
187237 TGAAATAGTGATAACCTCGCTA
1 TGAAATTTTGATAACCTC-CTA
* **
187259 TAAAATTTTGATAAATATTCCTA
1 TGAAATTTTGAT-AA-CCTCCTA
* *
187282 TAAAATTTTGATAAACCTCCCAA
1 TGAAATTTTGAT-AACCT-CCTA
* * *
187305 TGAAATTTTAATAACTTTCTTA
1 TGAAATTTTGATAAC-CTCCTA
187327 TGAAATTTTGATAA----CTA
1 TGAAATTTTGATAACCTCCTA
*
187344 T-AAATTTTGATAACATTCCTTA
1 TGAAATTTTGATAAC-CTCC-TA
** *
187366 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTC-CTA
* *
187388 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCT-CCTA
* * * *
187410 TGATATTTTGATCTACATACTA
1 TGAAATTTTGAT-AACCTCCTA
*
187432 TGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAA-CCTCCTA
*
187454 TAAAATTTTGA
1 TGAAATTTTGA
187465 AAACTAAACT
Statistics
Matches: 172, Mismatches: 41, Indels: 30
0.71 0.17 0.12
Matches are distributed among these distances:
16 12 0.07
17 3 0.02
21 2 0.01
22 105 0.61
23 48 0.28
24 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:187334 original size:45 final size:46
Alignment explanation
Indices: 187234--187340 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 46
187224 GATAATCACA
** * * *
187234 CTATGAAATAGTGAT-AACCTCGCTATAAAATTTTGATAAATATTC
1 CTATGAAATTTTGATAAACCTCCCAATAAAATTTTAATAAATATTC
* * *
187279 CTATAAAATTTTGATAAACCTCCCAATGAAATTTTAATAACT-TTC
1 CTATGAAATTTTGATAAACCTCCCAATAAAATTTTAATAAATATTC
*
187324 TTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
187341 CTATAAATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 30 0.59
46 21 0.41
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (46 bp):
CTATGAAATTTTGATAAACCTCCCAATAAAATTTTAATAAATATTC
Found at i:187375 original size:39 final size:38
Alignment explanation
Indices: 187307--187380 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
187297 CCTCCCAATG
*
187307 AAATTTTAATAACTTTCTTATGAAATTTTGATAACTAT
1 AAATTTTAATAACTTCCTTATGAAATTTTGATAACTAT
* **
187345 AAATTTTGATAACATTCCTTATGATTTTTTGATAAC
1 AAATTTTAATAAC-TTCCTTATGAAATTTTGATAAC
187381 CTCATTATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 12 0.39
39 19 0.61
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.47
Consensus pattern (38 bp):
AAATTTTAATAACTTCCTTATGAAATTTTGATAACTAT
Found at i:187655 original size:22 final size:22
Alignment explanation
Indices: 187625--187676 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
187615 TCACATTTTG
187625 AAAA-TTTGATAAACTCTTTAT
1 AAAATTTTGATAAACTCTTTAT
** *
187646 GGAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAAACTCTTTAT
187668 AAAATTTTG
1 AAAATTTTG
187677 TTGACCCCTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAAACTCTTTAT
Found at i:187857 original size:38 final size:38
Alignment explanation
Indices: 187815--187897 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
187805 ACAATCAGAG
*
187815 ACAAAAACAAAAA-ATAAAATTAAATACA-ACGATTGGAA
1 ACAAAAACAAAAAGACAAAATTAAATA-AGACG-TTGGAA
* *
187853 ACAAAGACAAAAAGGCAAAATTAAATAAGACGTTGGAA
1 ACAAAAACAAAAAGACAAAATTAAATAAGACGTTGGAA
187891 ACAAAAA
1 ACAAAAA
187898 GTCAAATTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 25 0.64
39 14 0.36
ACGTcount: A:0.64, C:0.11, G:0.12, T:0.13
Consensus pattern (38 bp):
ACAAAAACAAAAAGACAAAATTAAATAAGACGTTGGAA
Found at i:188078 original size:31 final size:31
Alignment explanation
Indices: 188023--188085 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
188013 ATTTAGAAAT
* * *
188023 ATATTTTTTGAAAAAAATGGTACAATTGGAA
1 ATATGTTTTGAAAAAAAGGGTACAATCGGAA
188054 ATATGTTTT-AAAAATAAGGGTACAATCGGAA
1 ATATGTTTTGAAAAA-AAGGGTACAATCGGAA
188085 A
1 A
188086 ACATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (31 bp):
ATATGTTTTGAAAAAAAGGGTACAATCGGAA
Done.