Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010918.1 Corchorus olitorius cultivar O-4 contig10950, 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: 59012
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1097 original size:332 final size:326
Alignment explanation
Indices: 426--2936 Score: 2275
Period size: 332 Copynumber: 7.7 Consensus size: 326
416 TACACCCATA
* *
426 ATCTTTATTCATCGAACCAAATCTCAGCCACATTGCATATAAGGATTTGTTTTTTCGGGCATCTG
1 ATCTATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGGATTTGTTTTTACGGGCATCTG
* * * * *
491 AATCTTGTTTCTATTTAA-TAACAAATTAATACGGGAAAAACGGAAAAAACGATATTAGAAACGT
66 AATCTTGTTTCCATTTAATTAA-AAATTAATTCGGAAAAAATGG-AAAAACGATATTAGAAGCGT
* * * *
555 GAAAAGCCCGTCAATTTTTCTGCCGTTGAAATATATATTATTTT-TGAGTATTGTGGTAAAAATT
129 GAAAAGCCCGTCAATTTTT-TGGCGTTGAATTATATATT-TTTTATGAGTATTGTGGCAAAAAAT
* * * *
619 TGAGAGAAAACTTTTCGGGCCAG---T----TTTTAGCTGAAATCGTGTACTAACCATCACAGTT
192 TGAGA-AAAAATTTTCGGGTCAGTTTTGCAATTTTAGCCGAAATCGTGTACTAACCATCAC-G-G
* *
677 TTTTTTGCTAAAAACGCATTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGACTC
254 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGACTC
742 CTTGAAAT
319 CTTGAAAT
*
750 ATCTATATTCATCGAACCAAATCTTAGCCACATTGCATATAAGGATTTGATTTTT-CGGGCATCT
1 ATCTATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGGATTTG-TTTTTACGGGCATCT
* * * * * *
814 GAATCTTGTTTCCATTTAATTAAAAATTGATTTGGGAAAAATGGAAAAACGATTTTAAAAGTGTG
65 GAATCTTGTTTCCATTTAATTAAAAATTAATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTG
* * * * * **
879 AAAATCCCGTCAATAATTTTGTCATTGAATTATATATTTTTTCTGAGTATTGTGAAAAAAAATTG
130 AAAAGCCCGTCAAT-TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTG
*
944 AGGAAAAAAAATTTTCGGGTCAGTTTTGCAAAATTTTAGCCGAAATCGTGTTCTAACCATCACGG
194 A-G--AAAAAATTTTCGGGTCAGTTTTGC--AATTTTAGCCGAAATCGTGTACTAACCATCACGG
* * * **
1009 TTTTTTGCTACAAACGCATTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTC
254 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGACTC
1074 CTTGAAAT
319 CTTGAAAT
* * * *
1082 ATTTATATTCATCGAACCAAATCCCAGCCACAATGGATATAAGGATTTGTTTTTACGGGGCATCT
1 ATCTATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGGATTTGTTTTTAC-GGGCATCT
* * *
1147 GAATCTTATTTCCATTTAATTAAAAATTAATTCAGGAAAAAATTGGAAAAACAATATTAGAAGTG
65 GAATCTTGTTTCCATTTAATTAAAAATTAATTC-GGAAAAAA-TGGAAAAACGATATTAGAAGCG
* *
1212 TGAAAAGCCCGTC-ATTCTTTTCGGCGTTGAATTATATATTTATTATGAGTATTGTGACAAAAAA
128 TGAAAAGCCCGTCAATT-TTTT-GGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAA
* * *
1276 TTGAGAAAAAATTTTTGGGTCAG---T----TTTTAGCTGAAATCGTGTACGT---TATCACGGT
191 TTGAGAAAAAATTTTCGGGTCAGTTTTGCAATTTTAGCCGAAATCGTGTAC-TAACCATCACGG-
* * * *
1331 TTTGAGAAAAAATTTCGGGTCAAAAACGCGTT-CGGAGCTCCGGGTCAGTTTTGCATGATTTTTT
254 -TT---------TTT-GGCT-AAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGA--TTTT
*
1395 GTGGC--AAA-ACT-TTGTGAAAT
305 -TGGCATAAAGACTCCT-TGAAAT
* * * * * * * * *
1415 ATCTAAATTCATCTAACCAAATCTTAGCCACATTGGATTTAACGATTTGCTTTTACGAGCATTTG
1 ATCTATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGGATTTGTTTTTACGGGCATCTG
* * * * * * * * *
1480 AATCATGTTTCGATTTAATTAGAAATAAATTTGGGAAAAAAGCAGGACAAACGATGTTAGAAGTG
66 AATCTTGTTTCCATTTAATTAAAAATTAA-TTCGGAAAAAA--TGGAAAAACGATATTAGAAGCG
* * ** *
1545 TGAGAAGCCCGTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGATTATTGTGGCTTATAAT
128 TGAAAAGCCCGTCAAT-TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAAT
* *
1609 TGAG-AAAAATATTTCGGGTCAATTTTTGC------AGTCGAAATCGTG---T-ACCATCACGGT
192 TGAGAAAAAAT-TTTCGGGTC-AGTTTTGCAATTTTAGCCGAAATCGTGTACTAACCATCACGG-
* * * * * *** * * * *
1663 TTTTTCGTTAAAAACGTGTTCCGGGGCCTCGAAGCAGTTTTGAATGGTTTTTTTGCATAAAGACT
254 TTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCAT-GATTTTTGGCATAAAGACT
1728 CCTTGAAAT
318 CCTTGAAAT
* * * * * * *
1737 ACCTATAATCATCTAACCAAATATCAGGCACAATTG-ATTTAAGGATTTGTTTTTACGAGCATCT
1 ATCTATATTCATCGAACCAAATCTCAGCCAC-ATTGCATATAAGGATTTGTTTTTACGGGCATCT
* * * * * * *
1801 GAATCTTGTTTCGATTCAATCAGAAAA-AAATTCGGAAAAGAATATGAAAAACTATAGTAGAAGC
65 GAATCTTGTTTCCATTTAATTA-AAAATTAATTCGGAAAA-AAT-GGAAAAACGATATTAGAAGC
** * ** * * *
1865 GTGAAAAATCCTTCAATTTTTTTGGCGTTGAATTATATATTTCATCTGAGTATTATGGCAAAGAA
127 GTGAAAAGCCCGTCAA-TTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAA
* * * * *
1930 TTGAAGAAAAATTTTTCGGTTCAATTTCTTGCAAATTTTTAACCGAAATCGTTTACT---CATCA
191 TTG-AGAAAAAATTTTCGGGTC-AGTT-TTGC-AA-TTTTAGCCGAAATCGTGTACTAACCATCA
* * * *
1992 CGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCTGCTCAGTTTTGCATGATTTTTGGCATAAAGA
251 CGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGA
*
2057 CTCCTTTAAAT
316 CTCCTTGAAAT
** * * *
2068 ATAAATATTCATCGAACCAAATCCCAGCCACATT-CGATTTAACGATTTGTTTTTACGAGCATGC
1 ATCTATATTCATCGAACCAAATCTCAGCCACATTGC-ATATAAGGATTTGTTTTTACG-G---GC
* * * * *
2132 ATCTGAATCTTATTTCTATTTAATTTAAAATTAATTCGGAAAAAATGGACAAACGATATTAAAAG
61 ATCTGAATCTTGTTTCCATTTAATTAAAAATTAATTCGGAAAAAATGGAAAAACGATATTAGAAG
* * *
2197 CGTGAAAAACTC-TGCAATGTTTTTGGCGTTGAATTATATATTTTTGATGAGTATTGTGGCAAAA
126 CGTGAAAAGCCCGT-CAAT-TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAA
* ** *
2261 AATTGAG-AAAAATTTTCGAGTCA-----GC---TTTAGCCGAAATCGTGTACTAATTATCACTG
189 AATTGAGAAAAAATTTTCGGGTCAGTTTTGCAATTTTAGCCGAAATCGTGTACTAACCATCACGG
* *** * * * *
2317 TTTTTGGCTAAAAACGCGTTTCAGG-GATTCGACTCAATTTTGCATGGA-TTTTGACATAAATAT
254 TTTTTGGCTAAAAACGCG-TTCCGGAGCCCCGGCTCAATTTTGCAT-GATTTTTGGCATAAAGAC
2380 TCCTTGAAAT
317 TCCTTGAAAT
* * ** * * * *
2390 ATCTAAATTCATCTAACCAAATCTCAGCCACATTTAATTTAAAGATTTGGTTTTACGAGCATCTG
1 ATCTATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGGATTTGTTTTTACGGGCATCTG
* * * *
2455 AATCTTATTTCCATTTAATTAGAAATAAATTCGGAAAAAATATGAAAAACGATATTAGAAGCGTG
66 AATCTTGTTTCCATTTAATTAAAAATTAATTCGGAAAAAAT-GGAAAAACGATATTAGAAGCGTG
* * *
2520 AAAAACCCTTCAATTTTTATGGCGTTGAA-TATATATATTTTTCTGAGTATTGTGGCAAAAAATT
130 AAAAGCCCGTCAATTTTT-TGGCGTTGAATTATATAT-TTTTTATGAGTATTGTGGCAAAAAATT
* * * *
2584 GAGGAAAAACTTTTCGGGTCAAATTTTGCAAAATTTTAGCAGAAACCGTGTACTTAA-CATCACG
193 GA-GAAAAAATTTTCGGGTC-AGTTTTGC--AATTTTAGCCGAAATCGTGTAC-TAACCATCACG
** *
2648 GTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAAACT
253 GTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGACT
2713 CCTTGAAAT
318 CCTTGAAAT
*
2722 ATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGGGCATCTG
1 ATCTATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGGATTTGTTTTTACGGGCATCTG
* *
2787 AATCTTGTTTCTATTTAATTAGAAATTAATTCTGGAAAAAA---AAAAACGATATTAGAAGCGTG
66 AATCTTGTTTCCATTTAATTAAAAATTAATTC-GGAAAAAATGGAAAAACGATATTAGAAGCGTG
* * * * * * * *
2849 AAAAGCCCGTCAATTTTTTGACGTTGGAA-TAAATAATATTTCTGCGTATTGTGTCAAAAGATTG
130 AAAAGCCCGTCAATTTTTTGGCGTT-GAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTG
* *
2913 AGAAAAACTTTTCGGGCCAGTTTT
194 AGAAAAAATTTTCGGGTCAGTTTT
2937 TAGCTTAAAT
Statistics
Matches: 1810, Mismatches: 261, Indels: 230
0.79 0.11 0.10
Matches are distributed among these distances:
318 55 0.03
319 89 0.05
320 16 0.01
321 97 0.05
322 220 0.12
323 115 0.06
324 107 0.06
325 23 0.01
326 6 0.00
327 18 0.01
328 32 0.02
329 46 0.03
330 5 0.00
331 101 0.06
332 426 0.24
333 259 0.14
334 78 0.04
335 112 0.06
336 5 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (326 bp):
ATCTATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGGATTTGTTTTTACGGGCATCTG
AATCTTGTTTCCATTTAATTAAAAATTAATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGA
AAAGCCCGTCAATTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAG
AAAAAATTTTCGGGTCAGTTTTGCAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
CTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAA
T
Found at i:2331 original size:654 final size:643
Alignment explanation
Indices: 434--2928 Score: 2298
Period size: 654 Copynumber: 3.8 Consensus size: 643
424 TAATCTTTAT
* * * * *
434 TCATCGAACCAAATCTCAGCCAC-ATTGCATATAAGGATTTGTTTTTTCGGGCATCTGAATCTTG
1 TCATCTAACCAAATCTCAGCCACAATTG-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTA
* * * ** * * ** * * *
498 TTTCTATTTAATAACAAATTAATACGGGAAAAA-CGGAAAAAACGATATTAGAAACGTGAAAAGC
65 TTTCCATTTAATTAGAAAAAAATTCGGAAAAAATATG-AAAAACAATATTAGAAGCGTGAAAAAC
* * * * * * * *
562 CCGTCAATTTTTCTGCCGTTGAAATATATATTATTTTTGAGTATTGTGGTAAAAATTTG-AGAGA
129 CCTTCAATTTTTTTGGCGTTGAATTATATATT-TATCTGAGTATTGTGGCAAAAAATTGAAGA-A
* * * * * *
626 AAACTTTTCGGG-C--------C-AGTTTTTAGCTGAAATCGTGTACTAACCATCACAGTTTTTT
192 AAATTTTTCGGGTCAATTTTTGCAAATTTTTAACCGAAATCGTTTACT---CATCAC-G-GTTTT
* *
681 TTGCTAAAAACGCATTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTG
252 TGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTG
* * * *
746 AAATATCTATATTCATCGAACCAAATCTTAGCCACATTGCATATAAGGATTTGATTTTT-CGGGC
317 AAATATCAATATTCATCGAACCAAATCTCAGCCACATTGGATATAACGATTTG-TTTTTACGGGC
* * * * * *
810 ATCTGAATCTTGTTTCCATTTAATTAAAAATTGATTTGGGAAAAATGGAAAAACGATTTTAAAAG
381 ATCTGAATCTTGTTTCTATTTAATTAGAAATTAATTCGGAAAAAATGGAAAAACGATATTAAAAG
* * * * * * **
875 TGTGAAAATCCCGTCAATAATTTTGTCATTGAATTATATATTTTTTCTGAGTATTGTGAAAAAAA
446 CGTGAAAAGCCCGTCAAT-TTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTGTGGCAAAAA
*
940 ATTGAGGAAAAAAAATTTTCGGGTCAGTTTTGCAAAATTTTAGCCGAAATCGTGTTCTAACCATC
509 ATTGA-G---AAAAATTTTCGGGTCA-----GC-----TTTAGCCGAAATCGTGTACTAA-CATC
* * * * * * * * **
1005 ACGGTTTTTTGCTACAAACGCATTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAG
559 ACGGTTTTTCGCTAAAAACGCGTTCCGGGGCCTCGACTCAATTTTGCATGGTTTTTTGCATAAAG
* *
1070 ACTCCTTGAAATATTTATAT
624 ACTCCTTGAAATATCTATAA
* * * * *
1090 TCATCGAACCAAATCCCAGCCACAATGGATATAAGGATTTGTTTTTACGGGGCATCTGAATCTTA
1 TCATCTAACCAAATCTCAGCCACAATTGATTTAAGGATTTGTTTTTAC-GAGCATCTGAATCTTA
* *
1155 TTTCCATTTAATTA-AAAATTAATTCAGGAAAAAAT-TGGAAAAACAATATTAGAAGTGTGAAAA
65 TTTCCATTTAATTAGAAAA-AAATTC-GGAAAAAATAT-GAAAAACAATATTAGAAGCGTGAAAA
* * * * *
1218 GCCCGTC-ATTCTTTTCGGCGTTGAATTATATATTTATTATGAGTATTGTGACAAAAAATTG-AG
127 ACCCTTCAATT-TTTTTGGCGTTGAATTATATATTTA-TCTGAGTATTGTGGCAAAAAATTGAAG
* * * ** * ** **
1281 AAAAAATTTTT-GGGTCAGTTTTTAGCTGAAATCGTGT-A-CGTTATCACGGTTT--TGAGAAAA
190 -AAAAATTTTTCGGGTCAATTTTT-GC--AAAT-TTTTAACCGAAAT--C-GTTTACTCATCACG
** * * * * *
1341 AATTTCGGGTCAAAAACGCGTT-CGGAGCTCCGGGTCAGTTTTGCATGATTTTTTGTGGC--AAA
247 GTTTTTGGCT-AAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGA--TTTT-TGGCATAAA
* * * * *
1403 -ACT-TTGTGAAATATCTAA-ATTCATCTAACCAAATCTTAGCCACATTGGATTTAACGATTTGC
308 GACTCCT-TGAAATATC-AATATTCATCGAACCAAATCTCAGCCACATTGGATATAACGATTTGT
* * * * * * * *
1465 TTTTACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATAAATTTGGGAAAAAAGCAGGACAA
371 TTTTACGGGCATCTGAATCTTGTTTCTATTTAATTAGAAATTAA-TTCGGAAAAAA--TGGAAAA
* * * * *
1530 ACGATGTTAGAAGTGTGAGAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTATGATTA
433 ACGATATTAAAAGCGTGAAAAGCCCGTCAAT-TTTTTGGCGTTGAATTATATATTTTTATGAGTA
** * ** *
1595 TTGTGGCTTATAATTGAGAAAAATATTTCGGGTCAATTTTTGCAGTCGAAATCGTGTAC---CAT
497 TTGTGGCAAAAAATTGAGAAAAAT-TTTCGGGTC-AGCTTT--AGCCGAAATCGTGTACTAACAT
* * ** * *
1657 CACGGTTTTTTCGTTAAAAACGTGTTCCGGGGCCTCGAAGCAGTTTTGAATGGTTTTTTTGCATA
558 CACGG-TTTTTCGCTAAAAACGCGTTCCGGGGCCTCGACTCAATTTTGCATGG-TTTTTTGCATA
*
1722 AAGACTCCTTGAAATACCTATAA
621 AAGACTCCTTGAAATATCTATAA
* * *
1745 TCATCTAACCAAATATCAGGCACAATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAACCAAATCTCAGCCACAATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTAT
* * * * * *
1810 TTCGATTCAATCAGAAAAAAATTCGGAAAAGAATATGAAAAACTATAGTAGAAGCGTGAAAAATC
66 TTCCATTTAATTAGAAAAAAATTCGGAAAA-AATATGAAAAACAATATTAGAAGCGTGAAAAACC
* *
1875 CTTCAATTTTTTTGGCGTTGAATTATATATTTCATCTGAGTATTATGGCAAAGAATTGAAGAAAA
130 CTTCAATTTTTTTGGCGTTGAATTATATATTT-ATCTGAGTATTGTGGCAAAAAATTGAAGAAAA
*
1940 ATTTTTCGGTTCAATTTCTTGCAAATTTTTAACCGAAATCGTTTACTCATCACGGTTTTTGGCTA
194 ATTTTTCGGGTCAATTT-TTGCAAATTTTTAACCGAAATCGTTTACTCATCACGGTTTTTGGCTA
* * * * *
2005 AAAACGCGTTTCGGGGCCCCTGCTCAGTTTTGCATGATTTTTGGCATAAAGACTCCTTTAAATAT
258 AAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATAT
* * * *
2070 AAATATTCATCGAACCAAATCCCAGCCACATTCGATTTAACGATTTGTTTTTACGAGCATGCATC
323 CAATATTCATCGAACCAAATCTCAGCCACATTGGATATAACGATTTGTTTTTACG-G---GCATC
* *
2135 TGAATCTTATTTCTATTTAATTTA-AAATTAATTCGGAAAAAATGGACAAACGATATTAAAAGCG
384 TGAATCTTGTTTCTATTTAA-TTAGAAATTAATTCGGAAAAAATGGAAAAACGATATTAAAAGCG
* *
2199 TGAAAAACTC-TGCAATGTTTTTGGCGTTGAATTATATATTTTTGATGAGTATTGTGGCAAAAAA
448 TGAAAAGCCCGT-CAAT-TTTTTGGCGTTGAATTATATATTTTT-ATGAGTATTGTGGCAAAAAA
* * * *
2263 TTGAGAAAAATTTTCGAGTCAGCTTTAGCCGAAATCGTGTACTAATTATCACTGTTTTTGGCTAA
510 TTGAGAAAAATTTTCGGGTCAGCTTTAGCCGAAATCGTGTACTAA-CATCACGGTTTTTCGCTAA
* * ** * * *
2328 AAACGCGTTTCAGGGATTCGACTCAATTTTGCATGG-ATTTTGACATAAATATTCCTTGAAATAT
574 AAACGCGTTCCGGGGCCTCGACTCAATTTTGCATGGTTTTTTG-CATAAAGACTCCTTGAAATAT
2392 CTA-AA
638 CTATAA
* * * *
2397 TTCATCTAACCAAATCTCAGCCACATTTAATTTAAAGATTTGGTTTTACGAGCATCTGAATCTTA
1 -TCATCTAACCAAATCTCAGCCACAATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTA
* *
2462 TTTCCATTTAATTAGAAATAAATTCGGAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAACC
65 TTTCCATTTAATTAGAAAAAAATTCGGAAAAAATATGAAAAACAATATTAGAAGCGTGAAAAACC
* * *
2527 CTTCAATTTTTATGGCGTTGAATATATATATTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAA
130 CTTCAATTTTTTTGGCGTTGAAT-TATATATTTATCTGAGTATTGTGGCAAAAAATTGAAGAAAA
* * * * * * *
2592 ACTTTTCGGGTCAAATTTTGCAAAATTTTAGCAGAAACCGTGTACTTAACATCACGGTTTTTGGC
194 ATTTTTCGGGTCAATTTTTGCAAATTTTTAACCGAAATCGTTTAC-T--CATCACGGTTTTTGGC
** *
2657 TAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAAACTCCTTGAAAT
256 TAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAAT
* *
2722 ATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGGGCATCTG
321 ATCAATATTCATCGAACCAAATCTCAGCCACATTGGATATAACGATTTGTTTTTACGGGCATCTG
*
2787 AATCTTGTTTCTATTTAATTAGAAATTAATTCTGGAAAAAA---AAAAACGATATTAGAAGCGTG
386 AATCTTGTTTCTATTTAATTAGAAATTAATTC-GGAAAAAATGGAAAAACGATATTAAAAGCGTG
* * * * * * *
2849 AAAAGCCCGTCAATTTTTTGACGTTGGAA-TAAATAATATTTCTGCGTATTGTGTCAAAAGATTG
450 AAAAGCCCGTCAATTTTTTGGCGTT-GAATTATAT-ATTTTTATGAGTATTGTGGCAAAAAATTG
2913 AGAAAAACTTTTCGGG
513 AGAAAAA-TTTTCGGG
2929 CCAGTTTTTA
Statistics
Matches: 1511, Mismatches: 245, Indels: 174
0.78 0.13 0.09
Matches are distributed among these distances:
647 40 0.03
648 44 0.03
649 4 0.00
650 38 0.03
651 54 0.04
652 122 0.08
653 226 0.15
654 375 0.25
655 127 0.08
656 56 0.04
657 83 0.05
658 89 0.06
659 2 0.00
663 6 0.00
664 14 0.01
665 112 0.07
666 24 0.02
667 29 0.02
668 54 0.04
669 3 0.00
670 3 0.00
671 3 0.00
672 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (643 bp):
TCATCTAACCAAATCTCAGCCACAATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTAT
TTCCATTTAATTAGAAAAAAATTCGGAAAAAATATGAAAAACAATATTAGAAGCGTGAAAAACCC
TTCAATTTTTTTGGCGTTGAATTATATATTTATCTGAGTATTGTGGCAAAAAATTGAAGAAAAAT
TTTTCGGGTCAATTTTTGCAAATTTTTAACCGAAATCGTTTACTCATCACGGTTTTTGGCTAAAA
ACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCAA
TATTCATCGAACCAAATCTCAGCCACATTGGATATAACGATTTGTTTTTACGGGCATCTGAATCT
TGTTTCTATTTAATTAGAAATTAATTCGGAAAAAATGGAAAAACGATATTAAAAGCGTGAAAAGC
CCGTCAATTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAT
TTTCGGGTCAGCTTTAGCCGAAATCGTGTACTAACATCACGGTTTTTCGCTAAAAACGCGTTCCG
GGGCCTCGACTCAATTTTGCATGGTTTTTTGCATAAAGACTCCTTGAAATATCTATAA
Found at i:4886 original size:332 final size:323
Alignment explanation
Indices: 3422--5386 Score: 1553
Period size: 332 Copynumber: 6.1 Consensus size: 323
3412 CCTTCAAGTC
* * * ** * * * *
3422 GAATTATATATTTTTTATGATTATTGTGTCTGAAAATTGAGAAAGATATTTCGGGTCAATTTTTT
1 GAATTATATA-TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTT-TGGTC-AGTTTTT
* *
3487 GCAAAATTTCAGCCGAAATCGTGTAC--CATTACCGTTTTTTTTGGCTAAAAACGCGTTCCAGGA
63 GCAAAATTTTAGCCGAAATCGTGTACTACATCA-CG--TTTTTT-GCTAAAAACGCGTTCC-GGA
* * * *** * * *
3550 -C-CTCGACGCAGTTTTCCATGGTTTTTGGTATAAAAGACTCCTTGAGATACCTATAATCATC-T
123 GCACT-G-CTCAGTTTTGCATGATTTTTGG-CGCAAAGACTCCTTGAAATATCTATATTCATCGT
* * * *
3612 AACCAAATCTCAGGCACATTGGATTTAAGGATTTGTTTTTACAAGCAAT-TGAATCTTGATTC--
185 -ACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGC-ATCTGAATCTTGTTTCTT
* * ** * *
3674 GATTTAGAAATAAATTCCGAAAAAAAAATGGAAAAAC-AGTATTAGAAGCGTGAAAAACCCTTCA
248 TAATTAGAAATAAATT-CG-GGAAAAAATGGAAAAACGA-TATTAGAAGCGTGAAAAGCCATTCA
*
3738 ATTTTTTTGGCGTT
310 ATCTTTTTGGCGTT
* *
3752 GAATTATATATTTCTTCTGAGTATTGTGGCAAAGAATTGA-ACAAAAATTTT--TCAAGTTTTTG
1 GAATTATATATTT-TTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTGGTC-AGTTTTTG
* * * * * * * *
3814 CAAGATTTTAGCTGAAATCGTTTACTA-ATCACAGTTTTTGGTTAAAAACGGGTTACAGG-GCCC
64 CAAAATTTTAGCCGAAATCGTGTACTACATCAC-GTTTTTTGCTAAAAACGCGTT-CCGGAG-CA
* ** **
3877 CTGCTCAGTTTTGCATGATTTTTGTCATAAAGACTCCTT-AAATTATAAATATTCATCG-ATCCA
126 CTGCTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAA-TATCTATATTCATCGTA-CCA
* * * * **
3940 ATTCCCAGCCACATTCGATTTATCGATTTGTTTTTACGAGCATGTATCTGAATCTTGTTTCGATT
189 AATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGC----ATCTGAATCTTGTTTC--TT
* * * * *
4005 TAATTAGAAATTAATTC-GGAAAAAA-GGGAAAACGATATTAGAAGCATGAAAA-ACACTGCAAT
248 TAATTAGAAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCA-TTCAAT
4067 CTTTTTGGCGTT
312 CTTTTTGGCGTT
* * * ** *
4079 AAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTAAG-AACGAATTTT--TC-G--TGT-C
1 GAATTATATA-TTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTGGTCAGTTTTTGC
** * * * * *
4137 -AGTTTTTAGCCGAAATCGTG---TACGTCACGGTTTTTGCCTGAAAACGCGTTTCGG-G-GC--
65 AAAATTTTAGCCGAAATCGTGTACTACATCACGTTTTTTG-CTAAAAACGCGTTCCGGAGCACTG
** * * * *
4194 CTC-G-ACT-CA-G--TTTTGGCACAAAGACTCTTTGAAATATCTATATTCATCGAATCAAATCT
129 CTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGTACCAAATCT
* * *
4253 CAGCCACATTGGATATAAGGATTTGTTTTTACTAGCATCTGAATCTTGTTTC--GATTTAGAAAT
194 CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCTTTAATTAGAAAT
** * * *
4316 AAATTCGACAAAAAAAAGGAAAAACGATATTAGAAGTGTGAAAA-CCCTTCAA-CTTTTTTGGCG
259 AAATTCG-GGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATTCAATC-TTTTTGGCG
4379 TT
322 TT
** *
4381 GAATTATATATTTTCTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTTTGTGTCAATTTTT
1 GAATTATATATTTT-TCTGAGTATTGTGGCAAAAAATTGAGAAAAA-AATTTTG-GTCAGTTTTT
4446 GCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCGGAGC
63 GCAAAATTTTAGCCGAAATCGTGTACT-A-CATCAC-GTTTTTTGCTAAAAACGCGTTCCGGAGC
* * * * *
4511 CCCGACTCAATTTTGCATGATTTTTGGCGCAAAAATTCCTTGAAATATCTATATTCATCGTACCA
125 ACTG-CTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGTACCA
* *
4576 AATCTTAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCCTTTCAAT
189 AATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT-CTTT-AAT
* * * *
4641 TAGAAATAAATTCGGGAAAAAATTGAAAAACGATATTAGAACCCTGAAAAGCCAGTCAATCTTTT
252 TAGAAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATTCAATCTTTT
4706 TGGCGTT
317 TGGCGTT
* *
4713 GAATTATATATTGTTTCTGAGTATTGTGACAAAAAATTGAGGAAAAAAATTTTAGGGTTAGTTTT
1 GAATTATATATT-TTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAAAATTTT--GGTCAGTTTT
* * *
4778 TGCAAAATTTTAGCTGAAATCGTATACTAACCATCACAGTTTTTTGCTACAAACGCGTTCCGGAG
62 TGCAAAATTTTAGCCGAAATCGTGTACT-A-CATCAC-GTTTTTTGCTAAAAACGCGTTCCGGAG
* ** *
4843 TCACAGCTCAAATTTGCATGA-TTTTGGC-CTAAAGACTCCTTGAAATATCTATATTCATCGAAC
124 -CACTGCTCAGTTTTGCATGATTTTTGGCGC-AAAGACTCCTTGAAATATCTATATTCATCGTAC
* * * * * *
4906 CAAATTTCAGCGACATTGGATATAATGATTTGTTTTCACGGGGCATCTAAATCTTGTTTCTATTT
187 CAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTAC-GAGCATCTGAATCTTGTTTC--TTT
* * * * *
4971 AATTAAAAATTAATTCGGG-AAAAATGGGAAAACGATATTAGAAGCGTGAAAAG-AACGTCAATC
249 AATTAGAAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCA-TTCAATC
5034 TTTTTGGCGTT
313 TTTTTGGCGTT
* * *
5045 GAATTATATATTGTTTTTGAGTATTGTGGCGAAAAATTGAG-AAAAACTTTTCGGGTCAG---TT
1 GAATTATATATT-TTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTT--GGTCAGTTTTT
* * * *
5106 ------TTTT-GCCGAAAT--TGT-GTACGTCACGGTTTTTGACTAAAAACGCGTT-CTGAGGCC
63 GCAAAATTTTAGCCGAAATCGTGTACTACATCACGTTTTTTG-CTAAAAACGCGTTCCGGA-G-C
* * * * *
5160 ACTGCTCTGTTTTGCATGATTTTTGGCGCCGAA-ACTCCTTGATATATCTTTATTCATC-TAATC
125 ACTGCTCAGTTTTGCATGATTTTTGGCG-CAAAGACTCCTTGAAATATCTATATTCATCGT-ACC
* * * * *
5223 AAATATCAGACACATTGGATTTAAGAATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAA
188 AAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTC--TTTAA
* * ** * *
5288 TTAGAAATTAATTC-AGAAATAAATATAAAGAACGATATTAAAAGCTTGAAAAGTCC-TTCAATC
251 TTAGAAATAAATTCGGGAAA-AAATGGAAA-AACGATATTAGAAGCGTGAAAAG-CCATTCAATC
5351 TTTTTGGCGTT
313 TTTTTGGCGTT
*
5362 GAATTATATATATTTTATGAGTATT
1 GAATTATATAT-TTTTCTGAGTATT
5387 TTTTCCAAAA
Statistics
Matches: 1338, Mismatches: 210, Indels: 187
0.77 0.12 0.11
Matches are distributed among these distances:
300 14 0.01
301 5 0.00
302 54 0.04
303 27 0.02
304 20 0.01
307 2 0.00
308 66 0.05
309 4 0.00
310 3 0.00
311 3 0.00
312 19 0.01
313 1 0.00
314 14 0.01
315 74 0.06
316 72 0.05
317 83 0.06
318 23 0.02
319 15 0.01
320 7 0.01
321 21 0.02
322 7 0.01
323 60 0.04
324 33 0.02
325 11 0.01
326 38 0.03
327 98 0.07
328 101 0.08
329 11 0.01
330 46 0.03
331 45 0.03
332 230 0.17
333 124 0.09
334 7 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (323 bp):
GAATTATATATTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTTGGTCAGTTTTTGCA
AAATTTTAGCCGAAATCGTGTACTACATCACGTTTTTTGCTAAAAACGCGTTCCGGAGCACTGCT
CAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGTACCAAATCTCA
GCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCTTTAATTAGAAATAA
ATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATTCAATCTTTTTGGCGTT
Found at i:5605 original size:305 final size:307
Alignment explanation
Indices: 4875--5612 Score: 803
Period size: 305 Copynumber: 2.4 Consensus size: 307
4865 TTTGGCCTAA
* * * * *
4875 AGACTCCTTGAAATATCTATATTCATCGAACCAAATTTCA-GCGACATTGGATATAATGATTTGT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATATCAGGC-ACATTGGATTTAAGGATTTGT
* * * * * * * *
4939 TTTCACGGGGCATCTAAATCTTGTTTCTATTTAATTAAAAATTAATTCGGGAAAAATGGGAAAAC
65 TTTTAC-GAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGAAAAAC
* *
5004 GATATTAGAAGCGTGAAAAGAACGTCAATCTTTTTGGCGTTGAATTATATATTGTTTTTGAGTAT
129 GATATTAAAAGCGTGAAAAGAACGTCAATCTTTTTGGCGTTGAATTATATATTGTTTATGAGTAT
* * * *
5069 TGTGGCGAAAAATTGAGAAAAACTTTTCGGGTCAGTTTTTTGCCGAAATTGTGTACGTCACGGTT
194 TGTGGCCAAAAATTGAGAAAAACTTTTCGGGTCA----TAT--C--AATTGTGTACATCACGATT
* * * * * * *
5134 TTTGACTAAAAACGCGTTCTGAGGCCACTGCTCTGTTTTGCATGATTTTTGGCGCCG
251 TTTGACTAAAAACGCATTCCGAGGCCACAGCTCAGTTTTACATGATTTTTGACACCG
* * * * *
5191 AAACTCCTTGATATATCTTTATTCATCTAATCAAATATCAGACACATTGGATTTAAGAATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATATCAGGCACATTGGATTTAAGGATTTGTT
* * *
5256 TTTACGTGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAATAAATATAAAGAAC
66 TTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAA-AAATAGAAA-AAC
* ** *
5321 GATATTAAAAGCTTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATAT-TTTATGAGTA
129 GATATTAAAAGCGTGAAAAGAACGTCAATCTTTTTGGCGTTGAATTATATAT-TGTTTATGAGTA
* ** * *
5385 TTTTTTCCAAAAATTGAGGAAAAATCTTTTCGGGTCA-AT-AATT-T-TATCATTATGATTTTTG
193 TTGTGGCCAAAAATTGA-GAAAAA-CTTTTCGGGTCATATCAATTGTGTA-CATCACGATTTTTG
**
5446 GTTAAAAACGCATTCCG-GGCC-CAGCTCAGTTTTACATGATTTTTGACACCG
255 ACTAAAAACGCATTCCGAGGCCACAGCTCAGTTTTACATGATTTTTGACACCG
* *
5497 AGACTCCTTGAAATATCTATATT-ATCTAATCAAATCTCAGGCATATTGGATTTAAGGATTTGTT
1 AGACTCCTTGAAATATCTATATTCATCTAATCAAATATCAGGCACATTGGATTTAAGGATTTGTT
* * * *
5561 TTTACGAGTATTTAAATTTTGTTTCGATTTAAATAGAAATTAATTCA-AAAAA
66 TTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAA
5613 TATGAAACAA
Statistics
Matches: 358, Mismatches: 57, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
303 2 0.01
304 3 0.01
305 78 0.22
306 45 0.13
307 6 0.02
308 24 0.07
309 4 0.01
314 1 0.00
315 40 0.11
316 63 0.18
317 73 0.20
318 7 0.02
319 12 0.03
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (307 bp):
AGACTCCTTGAAATATCTATATTCATCTAATCAAATATCAGGCACATTGGATTTAAGGATTTGTT
TTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGAAAAACGA
TATTAAAAGCGTGAAAAGAACGTCAATCTTTTTGGCGTTGAATTATATATTGTTTATGAGTATTG
TGGCCAAAAATTGAGAAAAACTTTTCGGGTCATATCAATTGTGTACATCACGATTTTTGACTAAA
AACGCATTCCGAGGCCACAGCTCAGTTTTACATGATTTTTGACACCG
Found at i:7916 original size:23 final size:24
Alignment explanation
Indices: 7890--7936 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
7880 TCTTAATTTC
*
7890 TGCAAATCTGT-ATCCAACTTGTT
1 TGCAAATCTGTAATCAAACTTGTT
*
7913 TGCAAGTCTGTAATCAAACTTGTT
1 TGCAAATCTGTAATCAAACTTGTT
7937 GAGCTGAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (24 bp):
TGCAAATCTGTAATCAAACTTGTT
Found at i:11448 original size:26 final size:26
Alignment explanation
Indices: 11419--11488 Score: 140
Period size: 26 Copynumber: 2.7 Consensus size: 26
11409 AATTGTTGCT
11419 AACTCTAATCTCTCACTAGTAGCAAA
1 AACTCTAATCTCTCACTAGTAGCAAA
11445 AACTCTAATCTCTCACTAGTAGCAAA
1 AACTCTAATCTCTCACTAGTAGCAAA
11471 AACTCTAATCTCTCACTA
1 AACTCTAATCTCTCACTA
11489 CTGTTTAGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.29
Consensus pattern (26 bp):
AACTCTAATCTCTCACTAGTAGCAAA
Found at i:25711 original size:15 final size:15
Alignment explanation
Indices: 25691--25750 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 15
25681 TTAGAAAGGT
25691 TATTAATTTATCGAG
1 TATTAATTTATCGAG
* *
25706 TATTAATTTATGGAAATTT
1 TATTAATTTATCG--A--G
25725 TATTAATTTATCGAG
1 TATTAATTTATCGAG
25740 TATTAATTTAT
1 TATTAATTTAT
25751 GGAAATCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 23 0.62
17 2 0.05
19 12 0.32
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (15 bp):
TATTAATTTATCGAG
Found at i:25729 original size:34 final size:34
Alignment explanation
Indices: 25690--25756 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
25680 TTTAGAAAGG
25690 TTATTAATTTATCGAGTATTAATTTATGGAAATT
1 TTATTAATTTATCGAGTATTAATTTATGGAAATT
25724 TTATTAATTTATCGAGTATTAATTTATGGAAAT
1 TTATTAATTTATCGAGTATTAATTTATGGAAAT
25757 CATAGTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (34 bp):
TTATTAATTTATCGAGTATTAATTTATGGAAATT
Found at i:25730 original size:19 final size:18
Alignment explanation
Indices: 25706--25775 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 18
25696 ATTTATCGAG
*
25706 TATTAATTTATGGAAATTT
1 TATTAATTTATGGAAA-TA
* *
25725 TATTAATTTATCG--A-G
1 TATTAATTTATGGAAATA
25740 TATTAATTTATGGAAATCA
1 TATTAATTTATGGAAAT-A
*
25759 TAGTAATTTATGGAAAT
1 TATTAATTTATGGAAAT
25776 CATAGATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 12 0.29
17 2 0.05
19 28 0.67
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.46
Consensus pattern (18 bp):
TATTAATTTATGGAAATA
Found at i:25766 original size:34 final size:34
Alignment explanation
Indices: 25694--25769 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
25684 GAAAGGTTAT
** *
25694 TAATTTATCGAGTATTAATTTATGGAAATTTTAT
1 TAATTTATCGAGTATTAATTTATGGAAATCATAG
25728 TAATTTATCGAGTATTAATTTATGGAAATCATAG
1 TAATTTATCGAGTATTAATTTATGGAAATCATAG
25762 TAATTTAT
1 TAATTTAT
25770 GGAAATCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (34 bp):
TAATTTATCGAGTATTAATTTATGGAAATCATAG
Found at i:25776 original size:19 final size:19
Alignment explanation
Indices: 25743--25780 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25733 TATCGAGTAT
25743 TAATTTATGGAAATCATAG
1 TAATTTATGGAAATCATAG
25762 TAATTTATGGAAATCATAG
1 TAATTTATGGAAATCATAG
25781 ATTTTGGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (19 bp):
TAATTTATGGAAATCATAG
Found at i:26667 original size:81 final size:80
Alignment explanation
Indices: 26554--26708 Score: 276
Period size: 81 Copynumber: 1.9 Consensus size: 80
26544 ATACCATGCC
26554 TTATGATCTAACATAACACAGCATTCGATTCCTACACCTCTAAAACATGCAGGCATTTATAACAG
1 TTATGATCTAACATAACACAGCATTCGATTCCTACACCTCTAAAACATGCAGGCATTTATAACAG
26619 CATAACTGAAAGCTG
66 CATAACTGAAAGCTG
*
26634 TTATGATCT-ACATAACTAACAGCATTTGATTCCTACACCTCTAAAACATGCAGGCATTTATAAC
1 TTATGATCTAACATAAC--ACAGCATTCGATTCCTACACCTCTAAAACATGCAGGCATTTATAAC
26698 AGCATAACTGA
64 AGCATAACTGA
26709 CTAGATTCCT
Statistics
Matches: 72, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
79 7 0.10
80 9 0.12
81 56 0.78
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (80 bp):
TTATGATCTAACATAACACAGCATTCGATTCCTACACCTCTAAAACATGCAGGCATTTATAACAG
CATAACTGAAAGCTG
Found at i:28448 original size:19 final size:19
Alignment explanation
Indices: 28424--28462 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28414 GTGTAGACAG
28424 AGAGCTGCCCAATCTCATA
1 AGAGCTGCCCAATCTCATA
28443 AGAGCTGCCCAATCTCATA
1 AGAGCTGCCCAATCTCATA
28462 A
1 A
28463 TTTCAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (19 bp):
AGAGCTGCCCAATCTCATA
Found at i:36534 original size:21 final size:21
Alignment explanation
Indices: 36508--36548 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
36498 AAATAACCCA
*
36508 TGACTAATCATCATGAGAGAT
1 TGACTAATCATCACGAGAGAT
36529 TGACTAATCATCACGAGAGA
1 TGACTAATCATCACGAGAGA
36549 GTACACACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (21 bp):
TGACTAATCATCACGAGAGAT
Found at i:38371 original size:13 final size:13
Alignment explanation
Indices: 38353--38378 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38343 AGAAACAAAC
38353 AAATGAAGAGGTT
1 AAATGAAGAGGTT
38366 AAATGAAGAGGTT
1 AAATGAAGAGGTT
38379 CAGGTAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (13 bp):
AAATGAAGAGGTT
Found at i:48383 original size:3 final size:3
Alignment explanation
Indices: 48375--48440 Score: 50
Period size: 3 Copynumber: 22.7 Consensus size: 3
48365 TCATGTGATT
* * *
48375 ATA ATA ATA ATA ATA ATA AT- ATA ATA ACA A-C ATA A-A TTA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
48418 ATA A-A AGTA ATA ATA GTA ATA AT
1 ATA ATA A-TA ATA ATA ATA ATA AT
48441 TTACCCAGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
2 6 0.12
3 39 0.78
4 5 0.10
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:55741 original size:17 final size:17
Alignment explanation
Indices: 55719--55751 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55709 TACTCACTAG
55719 CCACTTAATTTTTTTTA
1 CCACTTAATTTTTTTTA
*
55736 CCACTTTATTTTTTTT
1 CCACTTAATTTTTTTT
55752 TCAGCTATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (17 bp):
CCACTTAATTTTTTTTA
Found at i:58254 original size:14 final size:14
Alignment explanation
Indices: 58235--58268 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
58225 TTGTATTATT
58235 ATGTTCTAGAGACA
1 ATGTTCTAGAGACA
*
58249 ATGTTCTAGAGGCA
1 ATGTTCTAGAGACA
58263 ATGTTC
1 ATGTTC
58269 CAGTTCTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (14 bp):
ATGTTCTAGAGACA
Found at i:58584 original size:23 final size:22
Alignment explanation
Indices: 58554--58599 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
58544 GACAAAAGGA
*
58554 TGAATTTTGTTAGTCATATTATT
1 TGAATTTTATTAGTCAT-TTATT
*
58577 TGAATTTTATTATTCATTTATT
1 TGAATTTTATTAGTCATTTATT
58599 T
1 T
58600 ACTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (22 bp):
TGAATTTTATTAGTCATTTATT
Done.