Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015381.1 Corchorus olitorius cultivar O-4 contig15414, 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: 65035
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:874 original size:331 final size:329
Alignment explanation
Indices: 1--2041 Score: 2030
Period size: 331 Copynumber: 6.2 Consensus size: 329
* * * * **
1 TCACGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATT
1 TCACGCTTCGAATATCGTTTTTCCTATTTTTTCTAAATTAATTTCTAATAAATCG-AACAAGATT
* ** * * *
66 CAG-CGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAAT
65 CAGATGCTCGTAAAAACAAATCCTTAAATATATTGTGGCTGAGATTTGGTTAGATGAATATAAAT
* * * ** *
130 ATTCTAAAGAGTCTCATCGCAAAAAATTATGCAAAACTGAG-TCGGGGCCCAGAGACGCGTTTTT
130 ATTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCT-GGGG-CTTGAAACGCGTTTTT
*** ** *
194 AATTAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAA
193 AGCCAAAAACAGTGATGAATAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAA
* * * * * * * * * *
259 ATTTTCGTCAATTTTTGGCCACTATCCTCA-AAAAAACTGT-TTATTACAACAGTATAAAGATTG
258 TTTTTCATCAATTTTTGGCCACGATTCTCATAAAAAA-TATATAACT-CAACGGCAAAAAGATTG
**
322 AAAATCTTT
321 AAAGGCTTT
* * * * *
331 GCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATTTCTTATTAAATCAGAACAAGA
1 TCACGCTTCGAATATCGTTTTTCCTA-TTTTTTCTAAATTAATTTC-TAATAAATC-GAACAAGA
**
396 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAA
63 TTCAGATGCTCGTAAAAACAAATCCTTAAATATATTGTGGCTGAGATTTGGTTAGATGAATATAA
* * * ** *
461 ATATTC-AAAGAAGTCTCATTGCCAAAAATCATGCACAACAGACCCTGGTCCTCGAAACGCGTTT
128 ATATTCTAAAG-AGTCTCATCGCCAAAAATCATGCAAAACAGA-GCTGGGGCTTGAAACGCGTTT
* * * * *
525 TTAACCAAAAACAGTGATGAATAGTACACGATTTCGACTAAAGTTTTACAAAAATTGACCCGAAA
191 TTAGCCAAAAACAGTGATGAATAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAA
*
590 AATTTTTCATCAATTTTTGGCCACGATTCTCATGAAAAATATATAACTCAACGGCAAAAAGATTG
256 AATTTTTCATCAATTTTTGGCCACGATTCTCATAAAAAATATATAACTCAACGGCAAAAAGATTG
655 AAAGGCTTT
321 AAAGGCTTT
* * *
664 TCGCGCTTCGAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATAAATCGTAACAGGATT
1 TCACGCTTCGAATATCGTTTTTCCTATTTTTTCTAAATTAATTTCTAATAAATCG-AACAAGATT
* * * *
729 CAGATGCTTGTAAAAACAAATCCTTAAATATAATGCT-GATGAGATTTGGTTAGATGAATAAAAA
65 CAGATGCTCGTAAAAACAAATCCTTAAATATATTG-TGGCTGAGATTTGGTTAGATGAATATAAA
* * *** * * * *
793 TGTTCTAATGAGTCTTGGCGCCAAAAATCATGCAAAAGAAAGCTGGGGAATTGAAACACGTTTTT
129 TATTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCTGGGG-CTTGAAACGCGTTTTT
* * ** *
858 TGCCAAAAATAGTGATGGTTAGTATACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAA
193 AGCCAAAAACAGTGATGAATAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAA
* * * * * *
923 TTTTTCGTCAATTTTTTGCCACAATACTCATAAAAAATATATAACTCAACGCCAAAAATATTGAA
258 TTTTTCATCAATTTTTGGCCACGATTCTCATAAAAAATATATAACTCAACGGCAAAAAGATTGAA
988 AGGCTTT
323 AGGCTTT
* * * *
995 TCGCGCTTCGAATATCGTTTTTCCTATTTTTTATGAATTAAATTCTAATAAATCGTAAC-AGTAT
1 TCACGCTTCGAATATCGTTTTTCCTATTTTTTCTAAATTAATTTCTAATAAATCG-AACAAG-AT
* * * *
1059 TCACATGCTCGTAAAAACAAATCCTTAAATATAATGCT-GATGAGATTTGGTTAGATGAATAAAA
64 TCAGATGCTCGTAAAAACAAATCCTTAAATATATTG-TGGCTGAGATTTGGTTAGATGAATATAA
** ** * *
1123 ATATTCTATGGAGTCTCGGCGTCGAAAATCATGCAAAACAGAG-TCGGGGCTTCGAAACGCGTTT
128 ATATTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCT-GGGGCTT-GAAACGCGTTT
* * * * **
1187 TTTGCCAAAAATAGTGATG---AGTATACGATTTCGGCTGAAATTTTGCAGAAAA-TG--TTGAA
191 TTAGCCAAAAACAGTGATGAATAGTACACGATTTCGGCTAAAATTTTGCA-AAAACTGACCCGAA
*** ** ** * * * *
1246 AGGCTTTTCGAGCTTCTAATATCTTTTTTCC-C-ATT-TTTTAAAGTAATTTCTAATTCAATCGT
255 AAATTTTTC-A---TC--A-AT-TTTTGGCCACGATTCTCATAAA-AAATATATAACTCAA-CG-
*
1308 AACAAAAAGATTGAAAGGC---
309 -GCAAAAAGATTGAAAGGCTTT
* * * * **
1327 TCACGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATT
1 TCACGCTTCGAATATCGTTTTTCCTATTTTTTCTAAATTAATTTCTAATAAATCG-AACAAGATT
* ** * * *
1392 CAGATGCTCGTAAAAACAAATCATTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAAT
65 CAGATGCTCGTAAAAACAAATCCTTAAATATATTGTGGCTGAGATTTGGTTAGATGAATATAAAT
* * * * * * *
1457 ATTCTAAAGAGTCTCATCGCCAAAAATTATGCAAAACTGAGCCGAAGCCCTGAGACGCGTTTTTA
130 ATTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCTG-GGGCTTGAAACGCGTTTTTA
** * * * *
1522 GTTAAAAACAGTGAT-AA-CGTACACAATTTCGGCTAAATTTTTGCAAAAACTGATCCGAAAAAT
194 GCCAAAAACAGTGATGAATAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAAT
* * * * ** * * *
1585 TTTTCGTCAATTTTTGGCCACTATACTCA-AAAAAACTATGTATTTCAACAGTATAAAGATTGAA
259 TTTTCATCAATTTTTGGCCACGATTCTCATAAAAAA-TATATAACTCAACGGCAAAAAGATTGAA
*
1649 AGTCTTT
323 AGGCTTT
* * * *
1656 TCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATTTCTTATTAAATCAGAACAAGA
1 TCACGCTTCGAATATCGTTTTTCCTA-TTTTTTCTAAATTAATTTC-TAATAAATC-GAACAAGA
*
1721 TTCAGATGCTCGTAAAAACAAATCCTTAAAT-TCATTGTGGCTGA-ATTTGGTTATATGAATATA
63 TTCAGATGCTCGTAAAAACAAATCCTTAAATAT-ATTGTGGCTGAGATTTGGTTAGATGAATATA
* * * *
1784 AATATTCTGAAGAGTCTCATTGCCAAAAATCATGCAAAACAGAG-TCGGGTTTCCGAAACGCGTT
127 AATATTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCTGGGGCTT--GAAACGCGTT
* * * *
1848 TTTAGCCAAAAACAGTGATGAATATTACACGATTTCGACTAAAATTTTACAAAAATTGACCCGAA
190 TTTAGCCAAAAACAGTGATGAATAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAA
*
1913 AAATTTTTCATCAATTTTTGGCCACGATTCTCATGAAAAATATATAACTCAACGGCAAAAAGATT
255 AAATTTTTCATCAATTTTTGGCCACGATTCTCATAAAAAATATATAACTCAACGGCAAAAAGATT
1978 GAAAGGCTTT
320 GAAAGGCTTT
* * * *
1988 TCGCGCTTCGAATATCATTTTTCCTAATTTTTCTGAATTAATTTCTAATAAATC
1 TCACGCTTCGAATATCGTTTTTCCTATTTTTTCTAAATTAATTTCTAATAAATC
2042 ATGCAAAACA
Statistics
Matches: 1428, Mismatches: 229, Indels: 108
0.81 0.13 0.06
Matches are distributed among these distances:
326 23 0.02
327 6 0.00
328 37 0.03
329 44 0.03
330 144 0.10
331 521 0.36
332 342 0.24
333 268 0.19
334 17 0.01
335 26 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (329 bp):
TCACGCTTCGAATATCGTTTTTCCTATTTTTTCTAAATTAATTTCTAATAAATCGAACAAGATTC
AGATGCTCGTAAAAACAAATCCTTAAATATATTGTGGCTGAGATTTGGTTAGATGAATATAAATA
TTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCTGGGGCTTGAAACGCGTTTTTAGC
CAAAAACAGTGATGAATAGTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTT
TTCATCAATTTTTGGCCACGATTCTCATAAAAAATATATAACTCAACGGCAAAAAGATTGAAAGG
CTTT
Found at i:1520 original size:663 final size:652
Alignment explanation
Indices: 1--2031 Score: 2381
Period size: 663 Copynumber: 3.1 Consensus size: 652
1 TCACGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATT
1 TCACGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATT
*
66 CAG-CGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAAT
* * *
130 ATTCTAAAGAGTCTCATCGCAAAAAATTATGCAAAACTGAGTCGGGGCCCAGAGACGCGTTTTTA
131 ATTCTAAAGAGTCTCATCGCCAAAAATTATGCAAAACTGAGCCGGGGCCCTGAGACGCGTTTTTA
* *
195 ATTAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAAA
196 GTTAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAAT
* * *
260 TTTTCGTCAATTTTTGGCCACTATCCTCAAAAAAACTGTTTATTACAACAGTATAAAGATTGAAA
261 TTTTCGTCAATTTTTGGCCACTATACTCAAAAAAACTATTAATT-CAACAGTATAAAGATTGAAA
* *
325 ATCTTTGCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATTTCTTATTAAATCAGA
325 GTCTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATTTCTTATTAAATCAGA
*
390 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGA
390 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-TATTGTGGCTGAGATTTGGTTAGATGA
* * * ** * *
455 ATATAAATATTCAAAGAAGTCTCATTGCCAAAAATCATGCACAACAGACCCTGGTCCTCGAAACG
454 ATATAAATATTC-TAGGAGTCTCATTGCCAAAAATCATGCAAAACAGAGTC-GGGCTTCGAAACG
* *
520 CGTTTTTAACCAAAAACAGTGATGAATAGTACACGATTTCGACTAAAGTTTTACAAAAATTGACC
517 CGTTTTTAGCCAAAAACAGTGATG---AGTATACGATTTCGACTAAA-TTTTACAAAAA-TGA-C
* *
585 CGAAAAATTTTTCATCAATTTTTGGCCACGATTCTCATGAAAAATATATAACTCAACGGCAAAAA
576 CGAAAAACTTTTCATCAATTTTTGGCCACGATTCTCATGAAAAATATATAACTCAACGACAAAAA
650 GATTGAAAGGCTTT
641 GATTGAAAGGC--T
* * * * * * ** * *
664 TCGCGCTTCGAATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATAAATCGTAACAGGATT
1 TCACGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATT
* ** * * * * * *
729 CAGATGCTTGTAAAAACAAATCCTTAAATATAATGCT-GATGAGATTTGGTTAGATGAATAAAAA
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCATTG-TGGCTTACATTTGGTTTGATGAATATAAA
* * *** * *** * *** * *
793 TGTTCTAATGAGTCTTGGCGCCAAAAATCATGCAAAAGAAAGCTGGGGAATTGAAACACGTTTTT
130 TATTCTAAAGAGTCTCATCGCCAAAAATTATGCAAAACTGAGCCGGGGCCCTGAGACGCGTTTTT
* ** * * *
858 TGCCAAAAATAGTGATGGTTAGTATACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAA
195 AGTTAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAA
* * * * * *
923 TTTTTCGTCAATTTTTTGCCACAATACTCATAAAAAA-TATATAACTCAAC-GCCAAAAATATTG
260 TTTTTCGTCAATTTTTGGCCACTATACTCA-AAAAAACTAT-TAATTCAACAG-TATAAAGATTG
* * * * * * * * *
986 AAAGGCTTTTCGCGCTTCGAATATCGTTTTTCCTA-TTTTTTATGAATTAAATTC-TAATAAATC
322 AAAGTCTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATTTCTTATTAAATC
* * *
1049 -GTAAC-AGTATTCACATGCTCGTAAAAACAAATCCTTAAATATAATGCT-GATGAGATTTGGTT
387 AG-AACAAG-ATTCAGATGCTCGTAAAAACAAATCCTTAAAT-TATTG-TGGCTGAGATTTGGTT
* *** * *
1111 AGATGAATAAAAATATTCTATGGAGTCTCGGCGTCGAAAATCATGCAAAACAGAGTCGGGGCTTC
448 AGATGAATATAAATATTCTA-GGAGTCTCATTGCCAAAAATCATGCAAAACAGAGTC-GGGCTTC
* * * *
1176 GAAACGCGTTTTTTGCCAAAAATAGTGATGAGTATACGATTTCGGCTGAAATTTTGCAGAAAATG
511 GAAACGCGTTTTTAGCCAAAAACAGTGATGAGTATACGATTTCGACT-AAATTTTACA-AAAATG
** ** ** * * * * *
1241 -TTGAAAGGCTTTTCGAGCTTCTAATATCTTTTTTCC-C-ATT-T-TTTAAAGTAATTTCTAATT
574 ACCGAAAAACTTTTC-A---TC--A-AT-TTTTGGCCACGATTCTCATGAAA--AATATATAACT
1301 CAATCGTAACAAAAAGATTGAAAGGC-
629 CAA-CG--ACAAAAAGATTGAAAGGCT
1327 TCACGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATT
1 TCACGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATT
*
1392 CAGATGCTCGTAAAAACAAATCATTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAAT
66 CAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAAT
**
1457 ATTCTAAAGAGTCTCATCGCCAAAAATTATGCAAAACTGAGCCGAAGCCCTGAGACGCGTTTTTA
131 ATTCTAAAGAGTCTCATCGCCAAAAATTATGCAAAACTGAGCCGGGGCCCTGAGACGCGTTTTTA
* * *
1522 GTTAAAAACAGTGA---TAACGTACACAATTTCGGCTAAATTTTTGCAAAAACTGATCCGAAAAA
196 GTTAAAAACAGTGATGGTTA-GTACACGATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAA
*
1584 TTTTTCGTCAATTTTTGGCCACTATACTCAAAAAAACTATGTATTTCAACAGTATAAAGATTGAA
260 TTTTTCGTCAATTTTTGGCCACTATACTCAAAAAAACTAT-TAATTCAACAGTATAAAGATTGAA
1649 AGTCTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATTTCTTATTAAATCAG
324 AGTCTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATTTCTTATTAAATCAG
*
1714 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCATTGTGGCTGA-ATTTGGTTATATG
389 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATT-ATTGTGGCTGAGATTTGGTTAGATG
* *
1778 AATATAAATATTCTGAAGAGTCTCATTGCCAAAAATCATGCAAAACAGAGTCGGGTTTCCGAAAC
453 AATATAAATATTCT-AGGAGTCTCATTGCCAAAAATCATGCAAAACAGAGTCGGGCTT-CGAAAC
*
1843 GCGTTTTTAGCCAAAAACAGTGATGAATATTACACGATTTCGACTAAAATTTTACAAAAATTGAC
516 GCGTTTTTAGCCAAAAACAGTGATGAGTA-T--ACGATTTCGACT-AAATTTTACAAAAA-TGA-
* *
1908 CCGAAAAATTTTTCATCAATTTTTGGCCACGATTCTCATGAAAAATATATAACTCAACGGCAAAA
575 CCGAAAAACTTTTCATCAATTTTTGGCCACGATTCTCATGAAAAATATATAACTCAACGACAAAA
1973 AGATTGAAAGGCTTT
640 AGATTGAAAGGC--T
* * * * * * *
1988 TCGCGCTTCGAATATCATTTTTCCTAATTTTTCTGAATTAATTT
1 TCACGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTT
2032 CTAATAAATC
Statistics
Matches: 1114, Mismatches: 205, Indels: 100
0.79 0.14 0.07
Matches are distributed among these distances:
657 9 0.01
658 18 0.02
659 29 0.03
660 20 0.02
661 183 0.16
662 243 0.22
663 314 0.28
664 233 0.21
665 38 0.03
666 18 0.02
667 9 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (652 bp):
TCACGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATT
CAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAAT
ATTCTAAAGAGTCTCATCGCCAAAAATTATGCAAAACTGAGCCGGGGCCCTGAGACGCGTTTTTA
GTTAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAAT
TTTTCGTCAATTTTTGGCCACTATACTCAAAAAAACTATTAATTCAACAGTATAAAGATTGAAAG
TCTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATTTCTTATTAAATCAGAA
CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTATTGTGGCTGAGATTTGGTTAGATGAAT
ATAAATATTCTAGGAGTCTCATTGCCAAAAATCATGCAAAACAGAGTCGGGCTTCGAAACGCGTT
TTTAGCCAAAAACAGTGATGAGTATACGATTTCGACTAAATTTTACAAAAATGACCGAAAAACTT
TTCATCAATTTTTGGCCACGATTCTCATGAAAAATATATAACTCAACGACAAAAAGATTGAAAGG
CT
Found at i:2935 original size:898 final size:889
Alignment explanation
Indices: 1148--2939 Score: 3212
Period size: 898 Copynumber: 2.0 Consensus size: 889
1138 TCGGCGTCGA
* *
1148 AAATCATGCAAAACAGAGTCGGGGCTTCGAAACGCGTTTTTTGCCAAAAATAGTGATGAGTATAC
1 AAATCATGCAAAACAGAGTCGGGGCCTCGAAACACGTTTTTTGCCAAAAATAGTGATGAGTATAC
*
1213 GATTTCGGCTGAAATTTTGCAGAAAATGTTGAAAGGCTTTTCGAGCTTCTAATATCTTTTTTCCC
66 GATTTCGGCTAAAATTTTGCAGAAAATGTTGAAAGGCTTTTCGAGCTTCTAATATCTTTTTTCCC
1278 ATTTTTTAAAGTAATTTCTAATTCAATCGTAACAAAAAGATTGAAAGGCTCACGCTTCTAATATC
131 ATTTTTTAAAGTAATTTCTAATTCAATCGTAACAAAAAGATTGAAAGGCTCACGCTTCTAATATC
1343 GTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
196 GTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
1408 CAAATCATTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAATATTCTAAAGAGTCTCA
261 CAAATCATTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAATATTCTAAAGAGTCTCA
1473 TCGCCAAAAATTATGCAAAACTGAGCCGAAGCCCTGAGACGCGTTTTTAGTTAAAAACAGTGATA
326 TCGCCAAAAATTATGCAAAACTGAGCCGAAGCCCTGAGACGCGTTTTTAGTTAAAAACAGTGATA
*
1538 ACGTACACAATTTCGGCTAAATTTTTGCAAAAACTGATCCGAAAAATTTTTCGTCAATTTTTGGC
391 ACGTACACAATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGC
1603 CACTATACTCAAAAAAACTATGTATTTCAACAGTATAAAGATTGAAAGTCTTTTCACGATTCTAA
456 CACTATACTCAAAAAAACTATGTATTTCAACAGTATAAAGATTGAAAGTCTTTTCACGATTCTAA
*
1668 TATCGTTTTTGCTATTTTTTTCTAAATTAATTTCTTATTAAATCAGAACAAGATTCAGATGCTCG
521 TATCGTTTTTGCTATTTCTTTCTAAATTAATTTCTTATTAAATCAGAACAAGATTCAGATGCTCG
* *
1733 TAAAAACAAATCCTTAAATTCATTGTGGCTGAATTTGGTTATATGAATATAAATATTCTGAAGAG
586 TAAAAACAAATCCTTAAATCCATTGTGGCTGAATTTGGTTAGATGAATATAAATATTCTGAAGAG
* * *
1798 TCTCATTGCCAAAAATCATGCAAAACAGAGTCGGGTTTCCGAAACGCGTTTTTAGCCAAAAACAG
651 TCTCATTGCCAAAAATCATGCAAAACAGAGCCGGGCTCCCGAAACGCGTTTTTAGCCAAAAACAG
*
1863 TGATGAATATTACACGATTTCGACTAAAATTTTACAAAAATTGACCCGAAAAATTTTTCATCAAT
716 TGATGAATATTACACGATTTCAACTAAAATTTTACAAAAATTGACCCGAAAAATTTTTCATCAAT
* * *
1928 TTTTGGCCACGATTCTCATGAAAAATATATAACTCAACGGCAAAAAGATTGAAAGGCTTTTCGCG
781 TTTTGGCCACGATACTCATAAAAAATATATAACTCAACGACAAAAAGATTGAAAGGCTTTTCGCG
1993 CTTCGAATATCATTTTTCCTAATTTTTCTGAATTAATTTCTAAT
846 CTTCGAATATCATTTTTCCTAATTTTTCTGAATTAATTTCTAAT
*
2037 AAATCATGCAAAACAGAGTCGGGGCCTCGAAACACGTTTTTTGTCAAAAATAGTGATCGTTAGTA
1 AAATCATGCAAAACAGAGTCGGGGCCTCGAAACACGTTTTTTGCCAAAAATAGTGAT-G--AGTA
*
2102 TACGATTTCGGCTAAAATTTTTCA-AAATATGTTGAAAGGCTTTTCGAGCTTCTAATATCTTTTT
63 TACGATTTCGGCTAAAATTTTGCAGAAA-ATGTTGAAAGGCTTTTCGAGCTTCTAATATCTTTTT
*
2166 TCCCATTTTTTAAAGTAATTTCTAATTCAATCGTAACAAAAAGATTGAAAGGCTTTTCATGCTTC
127 TCCCATTTTTTAAAGTAATTTCTAATTCAATCGTAACAAAAAGATTGAAAGGC---TCACGCTTC
2231 TAATATCGTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATTCAGATGCTC
189 TAATATCGTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATTCAGATGCTC
*
2296 GTAAAAACAAATCCTTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAATATTCTAAAG
254 GTAAAAACAAATCATTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAATATTCTAAAG
* **
2361 AGTCTCATCGCCAAAAATTATGCAAAACTGAGTCGGGGCCCTGAGACGCGTTTTTAGTTAAAAAC
319 AGTCTCATCGCCAAAAATTATGCAAAACTGAGCCGAAGCCCTGAGACGCGTTTTTAGTTAAAAAC
* *
2426 AGTGATGGTGA-GTACACGATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAATTTTTCGTC
384 AGTGA---TAACGTACACAATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAATTTTTCGTC
*
2490 AATTTTTGGCCACTATACTCAAAAAAACTGTGTATTTCAACAGTATAAAGATTGAAAGTCTTTTC
446 AATTTTTGGCCACTATACTCAAAAAAACTATGTATTTCAACAGTATAAAGATTGAAAGTCTTTTC
2555 ACGATTCTAATATCGTTTTTGCTATTTCTTTCTAAATTAATTTCTTATTAAATCAGAACAAGATT
511 ACGATTCTAATATCGTTTTTGCTATTTCTTTCTAAATTAATTTCTTATTAAATCAGAACAAGATT
2620 CAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAAAT
576 CAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA-ATTTGGTTAGATGAATATAAAT
*
2685 ATTCTGAAGAGTCTCATTGCCAAAAATCATGCAAAACAGAGCCGGGCTCCCGAATCGCGTTTTTA
640 ATTCTGAAGAGTCTCATTGCCAAAAATCATGCAAAACAGAGCCGGGCTCCCGAAACGCGTTTTTA
2750 GCCAAAAACAGTGATGAATATTACACGATTTCAACTAAAATTTTACAAAAATTGACCCGAAAAAT
705 GCCAAAAACAGTGATGAATATTACACGATTTCAACTAAAATTTTACAAAAATTGACCCGAAAAAT
*
2815 TTTTCGTCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGACAAAAAGATTGAAA
770 TTTTCATCAATTTTTGGCCACGATACTCATAAAAAATATATAACTCAACGACAAAAAGATTGAAA
*
2880 GGCTTTTCGCGCTTCGAATATCGTTTTTCCT-ATATTTTCTGAATTAATTTCTAAT
835 GGCTTTTCGCGCTTCGAATATCATTTTTCCTAAT-TTTTCTGAATTAATTTCTAAT
2935 AAATC
1 AAATC
2940 GTAACAGGAT
Statistics
Matches: 864, Mismatches: 27, Indels: 15
0.95 0.03 0.02
Matches are distributed among these distances:
889 54 0.06
890 1 0.00
891 3 0.00
892 115 0.13
895 204 0.24
897 222 0.26
898 265 0.31
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (889 bp):
AAATCATGCAAAACAGAGTCGGGGCCTCGAAACACGTTTTTTGCCAAAAATAGTGATGAGTATAC
GATTTCGGCTAAAATTTTGCAGAAAATGTTGAAAGGCTTTTCGAGCTTCTAATATCTTTTTTCCC
ATTTTTTAAAGTAATTTCTAATTCAATCGTAACAAAAAGATTGAAAGGCTCACGCTTCTAATATC
GTTTTTGCTATTTTTTATAAATTAATTTTTGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
CAAATCATTAAATCCATTGTGGCTTACATTTGGTTTGATGAATATAAATATTCTAAAGAGTCTCA
TCGCCAAAAATTATGCAAAACTGAGCCGAAGCCCTGAGACGCGTTTTTAGTTAAAAACAGTGATA
ACGTACACAATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGC
CACTATACTCAAAAAAACTATGTATTTCAACAGTATAAAGATTGAAAGTCTTTTCACGATTCTAA
TATCGTTTTTGCTATTTCTTTCTAAATTAATTTCTTATTAAATCAGAACAAGATTCAGATGCTCG
TAAAAACAAATCCTTAAATCCATTGTGGCTGAATTTGGTTAGATGAATATAAATATTCTGAAGAG
TCTCATTGCCAAAAATCATGCAAAACAGAGCCGGGCTCCCGAAACGCGTTTTTAGCCAAAAACAG
TGATGAATATTACACGATTTCAACTAAAATTTTACAAAAATTGACCCGAAAAATTTTTCATCAAT
TTTTGGCCACGATACTCATAAAAAATATATAACTCAACGACAAAAAGATTGAAAGGCTTTTCGCG
CTTCGAATATCATTTTTCCTAATTTTTCTGAATTAATTTCTAAT
Found at i:3258 original size:331 final size:330
Alignment explanation
Indices: 2203--5450 Score: 3471
Period size: 332 Copynumber: 9.9 Consensus size: 330
2193 CAATCGTAAC
* *
2203 AAAAAGATTGAAAGGCTTTTCATGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTT-T
1 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTGCTATTTTTTCTAAATTAATTTCT
* * * * *
2267 TGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTACAT
66 TATTAAATCGTAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACATTGTGGCTGAGAT
* * * * *
2332 TTGGTTTGATGAATATAAATATTCTAAAGAGTCTCATCGCCAAAAATTATGCAAAACTGAGTCGG
131 TTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCCGG
** * *
2397 GGCCCTGAGACGCGTTTTTAGTTAAAAACAGTGATGGTGAGTACACGATTTCGGCTAAATTTTTG
196 GGCCCTGA-ACGCGTTTTTAGCCAAAAACAGTGATGGTAAGTACACGATTTCGGCTAAAATTTTG
* * * * *
2462 CAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACTATACTCAAAAAAACTGTGTATTT
260 CAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCATAAAAA-TATATAATT
2527 CAACAGT
324 CAACAGT
* * *
2534 ATAAAGATTGAAAGTCTTTTCACGATTCTAATATCGTTTTTGCTATTTCTTTCTAAATTAATTTC
1 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTGCTATTT-TTTCTAAATTAATTTC
*
2599 TTATTAAATCAG-AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAG
65 TTATTAAATC-GTAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACATTGTGGCTGAG
*
2663 ATTTGGTTAGATGAATATAAATATTCTGAA-GAGTCTCATTGCCAAAAATCATGCAAAACAGAGC
129 ATTTGGTTAGATGAATATAAATATTCT-AAGGAGTCTCATCGCCAAAAATCATGCAAAACAGAGC
* * * **
2727 C-GGGCTCCCGAATCGCGTTTTTAGCCAAAAACAGTGAT-GAATATTACACGATTTCAACTAAAA
193 CGGGGC-CCTGAA-CGCGTTTTTAGCCAAAAACAGTGATGGTA-AGTACACGATTTCGGCTAAAA
* *
2790 TTTTACAAAAATTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCATAAAAAATATA
255 TTTTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCAT-AAAAATATA
* *
2855 TAACTCAAC-GAC
319 TAATTCAACAG-T
* * * * *
2867 AAAAAGATTGAAAGGCTTTTCGCGCTTCGAATATCGTTTTTCCTATATTTTCTGAATTAATTTC-
1 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTGCTATTTTTTCTAAATTAATTTCT
* * * * * *
2931 TAATAAATCGTAACAGGATTCAGATCCTCGTAAAAACAAATCCTTAAATATAATGCT-GATGAGA
66 TATTAAATCGTAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACATTG-TGGCTGAGA
* * *** *
2995 TTTGGTTAGATGAATAAAAATGTTCTAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCG
130 TTTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCCG
** *
3060 GGGCCCTGACACGCGTTTTTA-TTAAAAATAGTGATGGTAAGTACACGATTTCGGCT-AAATTTA
195 GGGCCCTGA-ACGCGTTTTTAGCCAAAAACAGTGATGGTAAGTACACGATTTCGGCTAAAATTT-
* * * * * *
3123 TGCAAAAACTGACCCGAAATATTTTTCATCAATTTTGGGCCACGATACTCAATAAAACTATGTAT
258 TGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTC-ATAAAAATATATAA
3188 TTCAACAGT
322 TTCAACAGT
* * ** *
3197 ATAAAGATTGAATGTTTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATTTC
1 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTGCTA-TTTTTTCTAAATTAATTTC
* * *
3262 TTATTAAATCAG-AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTAC
65 TTATTAAATC-GTAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACATTGTGGCTGAG
* * * * * * *
3326 ATTTGGTTTGATGCATATAATTATTCTAAAGAGTCTCATCGCCAAAAATTATGCAAAACTGAGTC
129 ATTTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCC
* * ** * * * *
3391 GGAGCCCTAAGACGCGTTTTTAGTTACAAAC---GATGATAACGTACACAATTTCGGCTAAATTT
194 GGGGCCCTGA-ACGCGTTTTTAGCCAAAAACAGTGATGGTAA-GTACACGATTTCGGCTAAAATT
* * * * * *
3453 TTGCCAAAACTGACACGAAAAATTTTTCGTCAATTTTTGGCCACTATAC-CAAAAAAAACTGTGT
257 TTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTC-ATAAAAA-TATAT
* *
3517 ATTTCAACACT
320 AATTCAACAGT
* * * *
3528 ATAAAGATTGAAAGTCTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTTCTAAATTACTTT
1 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTGCTA--TTTTTTCTAAATTAATTT
* *
3593 CTTATTAAATCAG-AACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
64 CTTATTAAATC-GTAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACATTGTGGCTGA
* * * *
3657 GATTTGGTTCGATGAATATAAATATTCTGAGGAGTCTCATTGTCAAAAATCATGCAAAACAGAGC
128 GATTTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATCGCCAAAAATCATGCAAAACAGAGC
* * * * *
3722 CGGGTCCCCGAAACGCGTTTTTAGCCAAAAATAGTGATGGTTAGTATACGATTTCGGCTAAAATT
193 CGGGGCCCTG-AACGCGTTTTTAGCCAAAAACAGTGATGGTAAGTACACGATTTCGGCTAAAATT
3787 TTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCATAAAAAATATATA
257 TTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCAT-AAAAATATATA
* *
3852 ACTCAAC-GCC
321 ATTCAACAG-T
* * * * * * *
3862 AAAAATATTGAAAGGCTTTTCGCGCTT-TGAATATCGTTTTTCCTAATTTTTATGAATTAAATTC
1 AAAAAGATTGAAAGGCTTTTCACGCTTCT-AATATCGTTTTTGCTATTTTTTCTAAATTAATTTC
* * * * * * *
3926 -TAATAAATCATAAC-AGTATTCAGATACTCGTAAAAACAAATTCTTAAATATAATGCT-GATGA
65 TTATTAAATCGTAACAAG-ATTCAGATGCTCGTAAAAACAAATCCTTAAATACATTG-TGGCTGA
* ** * *
3988 GATTTGGTTAGATGAATAAAAATATTCTAAGGAGTCTCGGCGCCAAAAATCATGCAAAATAGAGT
128 GATTTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATCGCCAAAAATCATGCAAAACAGAGC
* * * * *
4053 CGGGGCCCCGGAATGCGTTTTTAG-CATAAAACACTGATAG-ATACTACACGATTTCGGCTAAAA
193 CGGGG-CCCTGAACGCGTTTTTAGCCA-AAAACAGTGATGGTA-AGTACACGATTTCGGCTAAAA
* *
4116 TTTTGCAAAAACTAACCCG-AAAATATTTTC-CCAATTTTTGGCCACGATACTCATAAAAAAATT
255 TTTTGCAAAAACTGACCCGAAAAAT-TTTTCGTCAATTTTTGGCCACGATACTCAT--AAAAA-T
*
4179 ATATAATTCAACAAT
316 ATATAATTCAACAGT
* *
4194 AAAAAGATTGAAAGGTTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTCTAAATTAATTTCT
1 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTGCTATTTTTTCTAAATTAATTTCT
* * * *
4259 TATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATCCTTGAATCCGTTGTGGCTGAGAT
66 TATTAAATCGTAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACATTGTGGCTGAGAT
* * *
4323 TTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATTGCAAAAAATCATGCAAAACAGATCC-G
131 TTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCCGG
* * * * * *
4387 GG---T---C-C----TT-G---GAACCGGTGATGAATAA-TACACGATTTCGACTAAAATTTTA
196 GGCCCTGAACGCGTTTTTAGCCAAAAACAGTGATG-GTAAGTACACGATTTCGGCTAAAATTTTG
* * * *
4436 CAAAAATTGACCTGAAAAATTTTTCATCAATTTTTGGCCACGATACTCATAAAATATATATAACT
260 CAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCATAAAA-ATATATAATT
4501 CAAC-G-
324 CAACAGT
* * * * *
4506 ACAAAAAATTTTAAAGG-TTTT-ACGTGCTTCTAATATCTTTTTTCCCA-TTTTT-T-AATTAAT
1 A-AAAAGA-TTGAAAGGCTTTTCAC--GCTTCTAATATCGTTTTTGCTATTTTTTCTAAATTAAT
* * * * * *
4566 TTCTAATTAAATCGTAACTAGATTCAGATGCTCGTAAAAAAAAAGATTCCTTAAATATAATGTTG
62 TTCTTATTAAATCGTAACAAGATTCAGATGCTCGT-AAAAACAA-A-TCCTTAAATACATTGTGG
* * * ** *
4631 ATGAGATTTGGTTAGATGAATAAAAAAATTCTAAGGAGTCTCGGCGCCGAAAATCATGCAAAACA
124 CTGAGATTTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATCGCCAAAAATCATGCAAAACA
* * * * *
4696 GAGACGGAGTCCC-GAAACGCGTTTTTAGCCAAAAATAGTTATGGT-A-TACA--ATTTCTGCTA
189 GAGCCGG-GGCCCTG-AACGCGTTTTTAGCCAAAAACAGTGATGGTAAGTACACGATTTCGGCTA
* *
4756 AAATTTTGCAAAAACTGACCCGAAAAATTTTTCGTTAATTTTTTGCCA-GAATACTCATAAAAAA
252 AAATTTTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACG-ATACTCAT-AAAAA
**
4820 TATATAACTT-AACACA
315 TATATAA-TTCAACAGT
* ** * *
4836 AAAAATATTGAAAGGCTTTTTGCTCTTCTAATATCGTTTTT-CTTATTTTTTCTGAATTAATTT-
1 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTGC-TATTTTTTCTAAATTAATTTC
* * ** * * * *
4899 ATAGTGTATCGTAACAGGATTCAGATGCTCGTAAAAACAAATCCTTAAATATAATGCT-GATGAG
65 TTATTAAATCGTAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACATTG-TGGCTGAG
**
4963 ATTTGGTTAGATGAATCA-AAATATTCTAAGGAGTCTCGGCGCCAAAAATCATGCAAAACAGAGC
129 ATTTGGTTAGATGAAT-ATAAATATTCTAAGGAGTCTCATCGCCAAAAATCATGCAAAACAGAGC
* * * * *
5027 CGGGGCTCCAGAATGCGCTTTGAG-CATAAAACAGTGATGG-ATAGTACACGATTTCGACTAAAA
193 CGGGGC-CCTGAACGCGTTTTTAGCCA-AAAACAGTGATGGTA-AGTACACGATTTCGGCTAAAA
* *
5090 TTTTGCAAAAACTAACCC-AAAAATATTTT-ATCAATTTTTGGCCACGATACTCATAAAAAATAT
255 TTTTGCAAAAACTGACCCGAAAAAT-TTTTCGTCAATTTTTGGCCACGATACTCAT-AAAAATAT
*
5153 ATAATTCAACGGT
318 ATAATTCAACAGT
* * *
5166 AAAAAGATTGAAATG-TTTTCACGCTTCTAATATCGTTTGTGTTATTGTTTTCTAAATTAATTTC
1 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTGCTATT-TTTTCTAAATTAATTTC
* * * *
5230 TTATTAAATCGAAATAAGATTCAGATGCTCGTAAAAATAAATCCTTAAAATCCATTGTAGG-TGA
65 TTATTAAATCGTAACAAGATTCAGATGCTCGTAAAAACAAATCCTT-AAATACATTGT-GGCTGA
* *
5294 GATTTGGTTAGATGAATATAAATATCCTAAGGAGTGTCATCGCCAAAAATCATGCAAAACAGAGC
128 GATTTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATCGCCAAAAATCATGCAAAACAGAGC
* ** * * * * * *
5359 CAGATCCCTGGAACGTGTTTTTAGGCAAAAACAGTGATGGTTAGTACACGATTTCAGTTAAAAGT
193 CGGGGCCCT-GAACGCGTTTTTAGCCAAAAACAGTGATGGTAAGTACACGATTTCGGCTAAAATT
5424 TTGCAAAAACTGACCCGAAAAATTTTT
257 TTGCAAAAACTGACCCGAAAAATTTTT
5451 AAATCCAATG
Statistics
Matches: 2446, Mismatches: 356, Indels: 229
0.81 0.12 0.08
Matches are distributed among these distances:
311 39 0.02
312 9 0.00
313 16 0.01
314 42 0.02
315 118 0.05
316 30 0.01
317 2 0.00
318 1 0.00
319 2 0.00
323 2 0.00
324 1 0.00
326 4 0.00
327 108 0.04
328 100 0.04
329 64 0.03
330 273 0.11
331 568 0.23
332 624 0.26
333 309 0.13
334 122 0.05
335 12 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (330 bp):
AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTGCTATTTTTTCTAAATTAATTTCT
TATTAAATCGTAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACATTGTGGCTGAGAT
TTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATCGCCAAAAATCATGCAAAACAGAGCCGG
GGCCCTGAACGCGTTTTTAGCCAAAAACAGTGATGGTAAGTACACGATTTCGGCTAAAATTTTGC
AAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCATAAAAATATATAATTCA
ACAGT
Found at i:4153 original size:995 final size:988
Alignment explanation
Indices: 2203--5353 Score: 4243
Period size: 995 Copynumber: 3.2 Consensus size: 988
2193 CAATCGTAAC
* * * *
2203 AAAAAGATTGAAAGGCTTTTCATGCTTCTAATATCGTTTTTGCTATTTTTTATAAATTAATTT-T
1 AAAAAGATTGAAAGGTTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTCTAAATTAATTTCT
* *
2267 TGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTACAT
66 TATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGACAT
* *
2332 TTGGTTTGATGAATATAAATATTCTAAAGAGTCTCATCGCCAAAAATTATGCAAAACTGAGTCGG
131 TTGGTTAGATGAATATAAATATTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAACTGAGTC-G
* * *
2397 GGCCCTGAGACGCGTTTTTAGTTAAAAACAGTGATGGTGAGTACACGATTTCGGCTAAATTTTTG
195 GGCCCTAAGACGCGTTTTTAGTT-AAAAC---GATGATAAGTACACGATTTCGGCTAAATTTTTG
2462 CAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACTATACTC-AAAAAAACTGTGTATT
256 CAAAAACTGA-CCGAAAAATTTTTCGTCAATTTTTGGCCACTATACTCAAAAAAAACTGTGTATT
* *
2526 TCAACAGTATAAAGATTGAAAGTCTTTTCACGATTCTAATATCGTTTTTGCTATTTCTTTCTAAA
320 TCAACACTATAAAGATTGAAAGTCTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAA
2591 TTAATTTCTTATTAAATCAGAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGT
385 TTAATTTCTTATTAAATCAGAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGT
*
2656 GGCTGAGATTTGGTTAGATGAATATAAATATTCTGAAGAGTCTCATTGCCAAAAATCATGCAAAA
450 GGCTGAGATTTGGTTAGATGAATATAAATATTCTGAGGAGTCTCATTGCCAAAAATCATGCAAAA
* * * * * *
2721 CAGAGCCGGG-CTCCCGAATCGCGTTTTTAGCCAAAAACAGTGATGAATATTACACGATTTCAAC
515 CAGAGCCGGGTC-CCCGAAACGCGTTTTTAGCCAAAAATAGTGATG-GTAGTATACGATTTCAGC
* *
2785 TAAAATTTTACAAAAATTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCATAAAAA
578 TAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCATAAAAA
* * *
2850 ATATATAACTCAACGACAAAAAGATTGAAAGGCTTTTCGCGCTTCGAATATCGTTTTTCCT-ATA
643 ATATATAACTCAACGCCAAAAATATTGAAAGGCTTTTCGCGCTTTGAATATCGTTTTTCCTAAT-
*
2914 TTTTCTGAATTAATTTCTAATAAATCGTAACAGGATTCAGATCCTCGTAAAAACAAATCCTTAAA
707 TTTTCTGAATTAATTTCTAATAAATCGTAACAGGATTCAGATACTCGTAAAAACAAATCCTTAAA
* *
2979 TATAATGCTGATGAGATTTGGTTAGATGAATAAAAATGTTCTAAGGAGTCTTGGCGCCAAAAATC
772 TATAATGCTGATGAGATTTGGTTAGATGAATAAAAATATTCTAAGGAGTCTCGGCGCCAAAAATC
* * ** * *
3044 ATGCAAAACT-GAGCCGGGG-CCCTGACACGCGTTTTTATTA-AAAATAGTGATGGTAAGTACAC
837 ATGCAAAA-TAGAGCCGGGGCCCCAGA-ATGCGTTTTTAGCATAAAACAGTGATGAT-AGTACAC
* *
3106 GATTTCGGCT-AAATTTATGCAAAAACTGACCCG-AAATATTTTTCATCAATTTTGGGCCACGAT
899 GATTTCGGCTAAAATTT-TGCAAAAACTAACCCGAAAATA-TTTTC-TCAATTTTTGGCCACGAT
* * *
3169 ACTCAATAAAACTATGTATTTCAACAGT
961 ACTCAATAAAAATATATAATTCAACAGT
* * *
3197 ATAAAGATTGAATGTTTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATTTC
1 AAAAAGATTGAAAGGTTTTTCACGATTCTAATATCGTTTTTGCTA-TTTTTTCTAAATTAATTTC
*
3262 TTATTAAATC-AGAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTTAC
65 TTATTAAATCGA-AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAC
* * * *
3326 ATTTGGTTTGATGCATATAATTATTCTAAAGAGTCTCATCGCCAAAAATTATGCAAAACTGAGTC
129 ATTTGGTTAGATGAATATAAATATTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAACTGAGTC
*
3391 GGAGCCCTAAGACGCGTTTTTAGTTACAAACGATGATAACGTACACAATTTCGGCTAAATTTTTG
194 GG-GCCCTAAGACGCGTTTTTAGTTA-AAACGATGATAA-GTACACGATTTCGGCTAAATTTTTG
*
3456 CCAAAACTGACACGAAAAATTTTTCGTCAATTTTTGGCCACTATAC-CAAAAAAAACTGTGTATT
256 CAAAAACTGAC-CGAAAAATTTTTCGTCAATTTTTGGCCACTATACTCAAAAAAAACTGTGTATT
3520 TCAACACTATAAAGATTGAAAGTCTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTTCTAA
320 TCAACACTATAAAGATTGAAAGTCTTTTCACGATTCTAATATCGTTTTTGCTA-TTTTTTTCTAA
* *
3585 ATTACTTTCTTATTAAATCAGAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCATTG
384 ATTAATTTCTTATTAAATCAGAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTG
* *
3650 TGGCTGAGATTTGGTTCGATGAATATAAATATTCTGAGGAGTCTCATTGTCAAAAATCATGCAAA
449 TGGCTGAGATTTGGTTAGATGAATATAAATATTCTGAGGAGTCTCATTGCCAAAAATCATGCAAA
*
3715 ACAGAGCCGGGTCCCCGAAACGCGTTTTTAGCCAAAAATAGTGATGGTTAGTATACGATTTCGGC
514 ACAGAGCCGGGTCCCCGAAACGCGTTTTTAGCCAAAAATAGTGATGG-TAGTATACGATTTCAGC
3780 TAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCATAAAAA
578 TAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCATAAAAA
3845 ATATATAACTCAACGCCAAAAATATTGAAAGGCTTTTCGCGCTTTGAATATCGTTTTTCCTAATT
643 ATATATAACTCAACGCCAAAAATATTGAAAGGCTTTTCGCGCTTTGAATATCGTTTTTCCTAATT
* * * * *
3910 TTTATGAATTAAATTCTAATAAATCATAACAGTATTCAGATACTCGTAAAAACAAATTCTTAAAT
708 TTTCTGAATTAATTTCTAATAAATCGTAACAGGATTCAGATACTCGTAAAAACAAATCCTTAAAT
3975 ATAATGCTGATGAGATTTGGTTAGATGAATAAAAATATTCTAAGGAGTCTCGGCGCCAAAAATCA
773 ATAATGCTGATGAGATTTGGTTAGATGAATAAAAATATTCTAAGGAGTCTCGGCGCCAAAAATCA
* * * *
4040 TGCAAAATAGAGTCGGGGCCCCGGAATGCGTTTTTAGCATAAAACACTGATAGATACTACACGAT
838 TGCAAAATAGAGCCGGGGCCCCAGAATGCGTTTTTAGCATAAAACAGTGAT-GATAGTACACGAT
*
4105 TTCGGCTAAAATTTTGCAAAAACTAACCCGAAAATATTTTCCCAATTTTTGGCCACGATACTCAT
902 TTCGGCTAAAATTTTGCAAAAACTAACCCGAAAATATTTTCTCAATTTTTGGCCACGATACTCA-
* *
4170 AAAAAAATTATATAATTCAACAAT
966 ATAAAAA-TATATAATTCAACAGT
4194 AAAAAGATTGAAAGGTTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTCTAAATTAATTTCT
1 AAAAAGATTGAAAGGTTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTCTAAATTAATTTCT
* * *
4259 TATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATCCTTGAATCCGTTGTGGCTGAGAT
66 TATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGACAT
* * * *
4323 TTGGTTAGATGAATATAAATATTCTAAGGAGTCTCATTGCAAAAAATCATGCAAAACAGA-TCCG
131 TTGGTTAGATGAATATAAATATTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAACTGAGT-CG
* ** * * *
4387 GGTCCTTGGAAC-CG------G-T-----GATGAATAA-TACACGATTTCGACTAAAATTTTACA
195 GGCCCTAAG-ACGCGTTTTTAGTTAAAACGATG-ATAAGTACACGATTTCGGCTAAATTTTTGCA
* * * * * * * **
4438 AAAATTGACCTGAAAAATTTTTCATCAATTTTTGGCCACGATACTCATAAAATA-TATATAACTC
258 AAAACTGACC-GAAAAATTTTTCGTCAATTTTTGGCCACTATACTCAAAAAAAACTGTGTATTTC
* * * * * * *
4502 AACGAC-A-AAAAATTTTAAAG-GTTTT-ACGTGCTTCTAATATCTTTTTTCCCA--TTTTT-T-
322 AAC-ACTATAAAGA-TTGAAAGTCTTTTCAC--GATTCTAATATCGTTTTTGCTATTTTTTTCTA
* * * *
4559 AATTAATTTCTAATTAAATC-GTAACTAGATTCAGATGCTCGTAAAAAAAAAGATTCCTTAAATA
383 AATTAATTTCTTATTAAATCAG-AACAAGATTCAGATGCTCGT-AAAAACAA-A-TCCTTAAATC
* * * * * * * *** *
4623 TAATGTTGATGAGATTTGGTTAGATGAATAAAAAAATTCTAAGGAGTCTCGGCGCCGAAAATCAT
444 CATTGTGGCTGAGATTTGGTTAGATGAATATAAATATTCTGAGGAGTCTCATTGCCAAAAATCAT
* * *
4688 GCAAAACAGAGACGGAGT-CCCGAAACGCGTTTTTAGCCAAAAATAGTTAT-G--GTATACAATT
509 GCAAAACAGAGCCGG-GTCCCCGAAACGCGTTTTTAGCCAAAAATAGTGATGGTAGTATACGATT
* * *
4749 TCTGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCGTTAATTTTTTGCCA-GAATACTCA
573 TCAGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACG-ATACTCA
* * * * *
4813 TAAAAAATATATAACTTAACACAAAAAATATTGAAAGGCTTTTTGCTCTTCT-AATATCGTTTTT
637 TAAAAAATATATAACTCAACGCCAAAAATATTGAAAGGCTTTTCGCGCTT-TGAATATCGTTTTT
* * * * ** *
4877 CTTATTTTTTCTGAATTAATTTATAGTGTATCGTAACAGGATTCAGATGCTCGTAAAAACAAATC
701 CCTAATTTTTCTGAATTAATTTCTAATAAATCGTAACAGGATTCAGATACTCGTAAAAACAAATC
*
4942 CTTAAATATAATGCTGATGAGATTTGGTTAGATGAATCAAAATATTCTAAGGAGTCTCGGCGCCA
766 CTTAAATATAATGCTGATGAGATTTGGTTAGATGAATAAAAATATTCTAAGGAGTCTCGGCGCCA
* * * *
5007 AAAATCATGCAAAACAGAGCCGGGGCTCCAGAATGCGCTTTGAGCATAAAACAGTGATGGATAGT
831 AAAATCATGCAAAATAGAGCCGGGGCCCCAGAATGCGTTTTTAGCATAAAACAGTGAT-GATAGT
* * *
5072 ACACGATTTCGACTAAAATTTTGCAAAAACTAACCCAAAAATATTTTATCAATTTTTGGCCACGA
895 ACACGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAATATTTTCTCAATTTTTGGCCACGA
*
5137 TACTC-ATAAAAAATATATAATTCAACGGT
960 TACTCAAT-AAAAATATATAATTCAACAGT
* * * *
5166 AAAAAGATTGAAATG-TTTTCACGCTTCTAATATCGTTTGTGTTATTGTTTTCTAAATTAATTTC
1 AAAAAGATTGAAAGGTTTTTCACGATTCTAATATCGTTTTTGCTATT-TTTTCTAAATTAATTTC
* *
5230 TTATTAAATCGAAATAAGATTCAGATGCTCGTAAAAATAAATCCTTAAAATCCATTGTAGG-TGA
65 TTATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT-AAATCCATTGT-GGCTGA
* * * *
5294 GATTTGGTTAGATGAATATAAATATCCTAAGGAGTGTCATCGCCAAAAATCATGCAAAAC
128 CATTTGGTTAGATGAATATAAATATTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAAC
5354 AGAGCCAGAT
Statistics
Matches: 1947, Mismatches: 168, Indels: 104
0.88 0.08 0.05
Matches are distributed among these distances:
971 28 0.01
972 82 0.04
973 14 0.01
974 433 0.22
975 39 0.02
976 8 0.00
977 7 0.00
978 108 0.06
979 11 0.01
980 94 0.05
981 13 0.01
982 4 0.00
987 1 0.00
988 1 0.00
993 8 0.00
994 183 0.09
995 583 0.30
996 261 0.13
997 69 0.04
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (988 bp):
AAAAAGATTGAAAGGTTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTCTAAATTAATTTCT
TATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGACAT
TTGGTTAGATGAATATAAATATTCTAAAGAGTCTCATCGCCAAAAATCATGCAAAACTGAGTCGG
GCCCTAAGACGCGTTTTTAGTTAAAACGATGATAAGTACACGATTTCGGCTAAATTTTTGCAAAA
ACTGACCGAAAAATTTTTCGTCAATTTTTGGCCACTATACTCAAAAAAAACTGTGTATTTCAACA
CTATAAAGATTGAAAGTCTTTTCACGATTCTAATATCGTTTTTGCTATTTTTTTCTAAATTAATT
TCTTATTAAATCAGAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
GATTTGGTTAGATGAATATAAATATTCTGAGGAGTCTCATTGCCAAAAATCATGCAAAACAGAGC
CGGGTCCCCGAAACGCGTTTTTAGCCAAAAATAGTGATGGTAGTATACGATTTCAGCTAAAATTT
TGCAAAAACTGACCCGAAAAATTTTTCGTCAATTTTTGGCCACGATACTCATAAAAAATATATAA
CTCAACGCCAAAAATATTGAAAGGCTTTTCGCGCTTTGAATATCGTTTTTCCTAATTTTTCTGAA
TTAATTTCTAATAAATCGTAACAGGATTCAGATACTCGTAAAAACAAATCCTTAAATATAATGCT
GATGAGATTTGGTTAGATGAATAAAAATATTCTAAGGAGTCTCGGCGCCAAAAATCATGCAAAAT
AGAGCCGGGGCCCCAGAATGCGTTTTTAGCATAAAACAGTGATGATAGTACACGATTTCGGCTAA
AATTTTGCAAAAACTAACCCGAAAATATTTTCTCAATTTTTGGCCACGATACTCAATAAAAATAT
ATAATTCAACAGT
Found at i:10230 original size:26 final size:26
Alignment explanation
Indices: 10200--10284 Score: 111
Period size: 26 Copynumber: 3.3 Consensus size: 26
10190 AAATACTCGA
* *
10200 GCAACTACATGAGACCTATTGAATAT
1 GCAACTACATGAGACCTACTGATTAT
10226 GCAACTACATGA-ACCCTACTGATTAT
1 GCAACTACATGAGA-CCTACTGATTAT
*
10252 GCAACTACATG-GCCCCTACTGATTAT
1 GCAACTACATGAG-ACCTACTGATTAT
10278 GCAACTA
1 GCAACTA
10285 AAAGAGGAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
25 1 0.02
26 52 0.98
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (26 bp):
GCAACTACATGAGACCTACTGATTAT
Found at i:31551 original size:329 final size:322
Alignment explanation
Indices: 30946--31597 Score: 1124
Period size: 329 Copynumber: 2.0 Consensus size: 322
30936 GACAAGAAAA
*
30946 TAGCTGAAACAATATTCAATTTAGATTTTAATGTGATTCAATCTCGAATTAATCAGAATCCAATA
1 TAGCTGAAACAATATTCAATTTAAATTTTAATGTGATTCAATCTCGAATTAATCAGAATCCAATA
31011 AGTATGTGGAATGACTCAAACCATCAAAAAAGATAGTATATACTCAATGAAATGAGAGGTTGATA
66 AGTATGTGGAATGACTCAAACCATCAAAAAAGATAGTATATACTCAATGAAATGAGAGGTTGATA
*
31076 ATTTGCAGAAAAGAAGTGATATCGAAGTGCAAACCAATGAAAGGCCAATATTTGATATATAATTT
131 ATTTGCAGAAAAGAAGTGATATCGAAGTGCAAACCAATGAAAGGCCAATAATTGATATATAATTT
* *
31141 GTTTGGCCCAAACTTTAAGCAAGTTATTTTTGTAGTAAATTAGGTTTGAGAGTTATATTCTCTTA
196 ATTTGGCCCAAACTTTAAGCAAGTTATTTTCGTAGTAAATTAGGTTTGAGAGTTATATTCTCTTA
* * **
31206 ATTTTTTAAAGTGACATATATTTTTGGGAAAAAAAATCTCTATGGTGCCATCGGGCATTTGG
261 ATTTCTTAAAGTGACATATATTTTTGGGAAAAAAAATATCTACCGTGCCATCGGGCATTTGG
*
31268 TAGCTGAAACAATATTCAATTTAAATTTTAATGTGATTCAATCTCGAATTAATCATAATCCAATA
1 TAGCTGAAACAATATTCAATTTAAATTTTAATGTGATTCAATCTCGAATTAATCAGAATCCAATA
*
31333 AGTATGTGGAATGACTCAAACCACATCAAAAAAGATAGTATATACTCAATGAAATGAGAGGTTGG
66 AGTATGTGGAATGACTCAAA-C-CATCAAAAAAGATAGTATATACTCAATGAAATGAGAGGTTGA
31398 TAATTTGCAGAAAAGAAGTGATATCGAAGTGCAAACCAATGAAAGTGCCAATAATTGATATATGT
129 TAATTTGCAGAAAAGAAGTGATATCGAAGTGCAAACCAATGAAAG-GCCAATAATTG--ATA--T
*
31463 ATAATTTATTTGGCCCAAACTTTATGCAAGTTATTTTCGTAGTAAATTAGGTTTGAGAGTTATAT
189 ATAATTTATTTGGCCCAAACTTTAAGCAAGTTATTTTCGTAGTAAATTAGGTTTGAGAGTTATAT
* *
31528 TCTCTTAATTTCTTAAAGTGACATATATTTTTGTGAAAAAAAATATCTACCGTGCCATCGGGTAT
254 TCTCTTAATTTCTTAAAGTGACATATATTTTTGGGAAAAAAAATATCTACCGTGCCATCGGGCAT
31593 TTGG
319 TTGG
31597 T
1 T
31598 CTGGTGGTAG
Statistics
Matches: 310, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
322 83 0.27
323 1 0.00
324 86 0.28
325 10 0.03
327 3 0.01
329 127 0.41
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (322 bp):
TAGCTGAAACAATATTCAATTTAAATTTTAATGTGATTCAATCTCGAATTAATCAGAATCCAATA
AGTATGTGGAATGACTCAAACCATCAAAAAAGATAGTATATACTCAATGAAATGAGAGGTTGATA
ATTTGCAGAAAAGAAGTGATATCGAAGTGCAAACCAATGAAAGGCCAATAATTGATATATAATTT
ATTTGGCCCAAACTTTAAGCAAGTTATTTTCGTAGTAAATTAGGTTTGAGAGTTATATTCTCTTA
ATTTCTTAAAGTGACATATATTTTTGGGAAAAAAAATATCTACCGTGCCATCGGGCATTTGG
Found at i:34620 original size:22 final size:23
Alignment explanation
Indices: 34594--34680 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 23
34584 TCCATAGTGT
*
34594 GGTTACCAAAATTTCATATGGAA
1 GGTTACCAAAATTTCATAGGGAA
*
34617 -GTTATCAAAAATTTCAT-GGGAA
1 GGTTA-CCAAAATTTCATAGGGAA
* * * *
34639 GGTCATCAAAATTTCATAGTG-T
1 GGTTACCAAAATTTCATAGGGAA
* *
34661 GGTTGCCAAACTTTCATAGG
1 GGTTACCAAAATTTCATAGG
34681 ATCAAGTTTA
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
22 33 0.67
23 16 0.33
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (23 bp):
GGTTACCAAAATTTCATAGGGAA
Found at i:34631 original size:23 final size:23
Alignment explanation
Indices: 34600--34657 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
34590 GTGTGGTTAC
* *
34600 CAAAATTTCATATGGAA-GTTAT
1 CAAAATTTCATAGGGAAGGTCAT
34622 CAAAAATTTCAT-GGGAAGGTCAT
1 C-AAAATTTCATAGGGAAGGTCAT
34645 CAAAATTTCATAG
1 CAAAATTTCATAG
34658 TGTGGTTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (23 bp):
CAAAATTTCATAGGGAAGGTCAT
Found at i:34647 original size:67 final size:67
Alignment explanation
Indices: 34523--34888 Score: 187
Period size: 67 Copynumber: 5.3 Consensus size: 67
34513 ACTTGTCTCT
* * * *
34523 GTGTGGTTATCAAAATTTCATAAGATTGTTATTATAATTTCATGAGGAGGTTAATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATAAAAATTTCATGAGGAGGTTAATCAAAATTCCA
34588 TA
66 TA
* *
34590 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAAATTTCATG-GGAAGG-TCATCAAAATT
1 GTGTGGTTACCAAAATTTCATA-AGATAGTTAT-AAAAATTTCATGAGG-AGGTTAATCAAAATT
*
34652 TCATA
63 CCATA
* * * * * * **
34657 GTGTGGTTGCCAAACTTTCATAGGATCAAGTTTATTAAAATTTC-TTAGAAAGGTT-ATTGAAAT
1 GTGTGGTTACCAAAATTTCATAAGAT--AG-TTATAAAAATTTCATGAG-GAGGTTAATCAAAAT
*
34720 TTCATA
62 TCCATA
* * * * *
34726 GTCTGGTTATCACAATTTTATAA-AAAGGTTATCAAAGAGATTATCAAAATGTCATAGCGAGGTT
1 GTGTGGTTACCAAAATTTCATAAGATA-GTTAT-AAA-A-ATT-TC---ATG----AG-GAGGTT
*
34790 -AT-AAGAATTTCATA
53 AATCAA-AATTCCATA
* * * *
34804 GTGTGGTTAACAAAATTTCATAAGGA-GGTTACTAATATTTTCAT-AGGGAGGTT-ATCAAAATT
1 GTGTGGTTACCAAAATTTCATAA-GATAGTTA-TAAAAATTTCATGA-GGAGGTTAATCAAAATT
*
34866 TCATA
63 CCATA
*
34871 GTGTGGTTATCAAAATTT
1 GTGTGGTTACCAAAATTT
34889 TTTCGTTTGG
Statistics
Matches: 235, Mismatches: 35, Indels: 58
0.72 0.11 0.18
Matches are distributed among these distances:
66 8 0.03
67 100 0.43
68 21 0.09
69 45 0.19
70 7 0.03
72 2 0.01
74 1 0.00
75 2 0.01
76 2 0.01
77 2 0.01
78 43 0.18
79 1 0.00
80 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (67 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATAAAAATTTCATGAGGAGGTTAATCAAAATTCCA
TA
Found at i:34802 original size:22 final size:21
Alignment explanation
Indices: 34766--34928 Score: 105
Period size: 22 Copynumber: 7.4 Consensus size: 21
34756 ATCAAAGAGA
* *
34766 TTATCAAAATGTCATAGCGAGG
1 TTAT-AAAATTTCATAGTGAGG
*
34788 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAGTGAGG
*
34810 TTAACAAAATTTCATAAG-GAGG
1 TT-ATAAAATTTCAT-AGTGAGG
* *
34832 TTACTAATATTTTCATAGGGAGG
1 TTA-TAA-AATTTCATAGTGAGG
*
34855 TTATCAAAATTTCATAGTGTGG
1 TTAT-AAAATTTCATAGTGAGG
** * **
34877 TTATCAAAATTTTTTCGTTTGG
1 TTAT-AAAATTTCATAGTGAGG
*
34899 TTATCAAAACTTCATA-TGAAGG
1 TTAT-AAAATTTCATAGTG-AGG
34921 TTATAAAA
1 TTATAAAA
34929 GTCTCATTTT
Statistics
Matches: 113, Mismatches: 20, Indels: 17
0.75 0.13 0.11
Matches are distributed among these distances:
21 8 0.07
22 84 0.74
23 21 0.19
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (21 bp):
TTATAAAATTTCATAGTGAGG
Found at i:34863 original size:45 final size:45
Alignment explanation
Indices: 34766--34870 Score: 133
Period size: 45 Copynumber: 2.4 Consensus size: 45
34756 ATCAAAGAGA
* * *
34766 TTATCAAAATGTCAT-AGCGAGGTTATAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAAGCGAGGTTATAAGAATTTCATAGGGAGG
* * *
34810 TTAACAAAATTTCATAAG-GAGGTTACTAATATTTTCATAGGGAGG
1 TTATCAAAATTTCATAAGCGAGGTTA-TAAGAATTTCATAGGGAGG
34855 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
34871 GTGTGGTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 20 0.38
45 32 0.62
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (45 bp):
TTATCAAAATTTCATAAGCGAGGTTATAAGAATTTCATAGGGAGG
Found at i:34879 original size:45 final size:43
Alignment explanation
Indices: 34766--34888 Score: 131
Period size: 45 Copynumber: 2.8 Consensus size: 43
34756 ATCAAAGAGA
* * *
34766 TTATCAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTATAAGAATTTCATAGGGAGG
* * *
34810 TTAACAAAATTTCATAAGGAGGTTACTAATATTTTCATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTA-TAAGAATTTCATAGGGAGG
*
34855 TTATCAAAATTTCATAGTGTGGTTATCAA-AATTT
1 TTATCAAAATTTCATAG-GAGGTTAT-AAGAATTT
34889 TTTCGTTTGG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
44 27 0.41
45 39 0.59
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.37
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGAGGTTATAAGAATTTCATAGGGAGG
Found at i:34889 original size:45 final size:44
Alignment explanation
Indices: 34766--35805 Score: 210
Period size: 44 Copynumber: 24.1 Consensus size: 44
34756 ATCAAAGAGA
* * *
34766 TTATCAAAATGTCATAGCGAGGTTAT-AAGAA-TTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTATCAA-AATTTTCATAGGGAGG
* *
34810 TTAACAAAATTTCATAAGGAGGTTA-CTAATATTTTCATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTATC-AAAATTTTCATAGGGAGG
* * * ***
34855 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTT-TTCGTTTGG
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTTCATAGGGAGG
* * * *
34899 TTATCAAAACTTCATATGAAGGTTATAAAAGTCTCATTTTCATAAGGA-G
1 TTATCAAAATTTCATA-GGAGGTTATCAAA-----ATTTTCATAGGGAGG
* * * * * * * *
34948 -TACCAAAATTTGATAGAAGGTTATC-AAA-TCTAATAGAGTGA
1 TTATCAAAATTTCATAGGAGGTTATCAAAATTTTCATAGGGAGG
* * * *
34989 TTATCAAAATTTCATTAAGATTGGATTAACGAAA-TTT-ATA-GGATGA
1 TTATCAAAATTTCA-TAGGA--GG-TTATCAAAATTTTCATAGGGA-GG
** * * ** * *
35035 TTATCAAAATTTCATAGTGTTGTTATC-AAAGTTACATAATGTGA
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTTCATAGGGAGG
* * * * *
35079 TTATCAAAATTTTATAGAGGGGTCAACAAAATTTT-ATAGAGAGG
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTTCATAGGGAGG
* * * ** * *
35123 TTTATCAAAATTTCGTAAAGAGGTTATC-AAATTTTCAAAATGTGA
1 -TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTTCATAGGGAGG
* *
35168 TTATCAAAATTTCATA--A--TGAT----A-TTTC-T-GTGAAGG
1 TTATCAAAATTTCATAGGAGGTTATCAAAATTTTCATAG-GGAGG
* * * *
35202 TTATCAAAATTTCAAAGTATGGTTA-CCAAA---T--TAGGAAGG
1 TTATCAAAATTTCATAGGA-GGTTATCAAAATTTTCATAGGGAGG
* * * * * *
35241 TTATTAAACTTTTATTATGGA-GTAATCAAAA-TATC--AGTGAGG
1 TTATCAAAATTTCA-TA-GGAGGTTATCAAAATTTTCATAGGGAGG
* * * * **
35283 ATATCAAAATTTTATATGAAGGTTATCAGAA-TTTCATAGTTTA-G
1 TTATCAAAATTTCATA-GGAGGTTATCAAAATTTTCATAG-GGAGG
* * * * *
35327 TTTTCAAAATTTCATAAGAGGGTTAGCAAAA-TTTCATA-GTATG
1 TTATCAAAATTTCATAGGA-GGTTATCAAAATTTTCATAGGGAGG
* * * * * **
35370 TAGATCAAAATTCCATGGGGAGATTAACAAAA-TTTCATAATGAGG
1 T-TATCAAAATTTCAT-AGGAGGTTATCAAAATTTTCATAGGGAGG
** *
35415 TTATCAAAAAAATCATAGGGAGGTTATCAAAA--TT--T--GTA-G
1 TTATC-AAAATTTCATA-GGAGGTTATCAAAATTTTCATAGGGAGG
* *
35454 TTATCAAGATTTCATAAGGAGGTTATCAAAA--TT--T--GTA-G
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTTCATAGGGAGG
*
35492 TTATCAAGATTTCATAAGGAGGTTATCAAAATTTT-ATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTTCATAGGGAGG
* *
35536 TTTATCAAAATTTTATAGGAAGGTTTATCAAAA-TTTCATAGCGAGG
1 -TTATCAAAATTTCATAGG-AGG-TTATCAAAATTTTCATAGGGAGG
* * * * * * *
35582 TTATCACAATTTCATAGTGTGATTATCAAAA-TTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTTCATAGGGAGG
* ** * *
35626 TTA-CTAACAA-TTCATATGGAGGTT-TTAAAATTTTCATAACGTGA
1 TTATC-AA-AATTTCATA-GGAGGTTATCAAAATTTTCATAGGGAGG
* * * ** * **
35670 TTATCAATATATCATATAGAGGTTATC-AACGTCTCATAGTGTTGG
1 TTATCAAAATTTCATA-GGAGGTTATCAAAATTTTCATAG-GGAGG
* * *
35715 TTATCAAAATTTCATTGGGAAGTTATCAAAA-TTTCATAGTGAGG
1 TTATCAAAATTTCA-TAGGAGGTTATCAAAATTTTCATAGGGAGG
* * * * *
35759 TCT-TCAAAATTCCTTAGGGAGGTTAACAAAA-TTTCATAAGAAGG
1 T-TATCAAAATTTCATA-GGAGGTTATCAAAATTTTCATAGGGAGG
35803 TTA
1 TTA
35806 AAGAAATTTA
Statistics
Matches: 738, Mismatches: 176, Indels: 164
0.68 0.16 0.15
Matches are distributed among these distances:
34 16 0.02
35 4 0.01
36 2 0.00
38 59 0.08
39 32 0.04
40 16 0.02
41 10 0.01
42 46 0.06
43 24 0.03
44 274 0.37
45 173 0.23
46 49 0.07
47 14 0.02
48 12 0.02
49 6 0.01
50 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGAGGTTATCAAAATTTTCATAGGGAGG
Found at i:35135 original size:23 final size:22
Alignment explanation
Indices: 34761--35157 Score: 102
Period size: 22 Copynumber: 17.8 Consensus size: 22
34751 AGGTTATCAA
* * *
34761 AGAGATTATCAAAATGTCATAG
1 AGAGGTTATCAAAATTTTATAG
* *
34783 CGAGGTTAT-AAGAATTTCATAG
1 AGAGGTTATCAA-AATTTTATAG
* * * *
34805 TGTGGTTAACAAAATTTCATA-
1 AGAGGTTATCAAAATTTTATAG
*
34826 AGGAGGTTA-CTAATATTTTCATAG
1 A-GAGGTTATC-AAAATTTT-ATAG
* *
34850 GGAGGTTATCAAAATTTCATAG
1 AGAGGTTATCAAAATTTTATAG
* * * *
34872 TGTGGTTATCAAAATTTTTTCG
1 AGAGGTTATCAAAATTTTATAG
*** * *
34894 TTTGGTTATCAAAACTTCATATG
1 AGAGGTTATCAAAATTTTATA-G
*
34917 A-AGGTTATAAAAGTCTCATTTTCATA-
1 AGAGGTTATCAAA-----ATTTT-ATAG
* *
34943 AG-GAG-TACCAAAATTTGATAG
1 AGAG-GTTATCAAAATTTTATAG
* *
34964 A-AGGTTATC-AAATCTAATAG
1 AGAGGTTATCAAAATTTTATAG
* * *
34984 AGTGATTATCAAAATTTCATTA-
1 AGAGGTTATCAAAATTTTA-TAG
* *
35006 AGATTGGATTAACGAAA-TTTATAG
1 AGA--GG-TTATCAAAATTTTATAG
* *
35030 -GATGATTATCAAAATTTCATAG
1 AGA-GGTTATCAAAATTTTATAG
* ** * **
35052 TGTTGTTATCAAAGTTACATA-
1 AGAGGTTATCAAAATTTTATAG
* *
35073 ATGTGATTATCAAAATTTTATAG
1 A-GAGGTTATCAAAATTTTATAG
* * *
35096 AGGGGTCAACAAAATTTTATAG
1 AGAGGTTATCAAAATTTTATAG
** *
35118 AGAGGTTTATCAAAATTTCGTAA
1 AGAGG-TTATCAAAATTTTATAG
35141 AGAGGTTATC-AAATTTT
1 AGAGGTTATCAAAATTTT
35158 CAAAATGTGA
Statistics
Matches: 275, Mismatches: 69, Indels: 63
0.68 0.17 0.15
Matches are distributed among these distances:
20 14 0.05
21 31 0.11
22 160 0.58
23 44 0.16
24 5 0.02
25 7 0.03
26 7 0.03
27 4 0.01
28 3 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
AGAGGTTATCAAAATTTTATAG
Found at i:35186 original size:22 final size:22
Alignment explanation
Indices: 34985--35186 Score: 101
Period size: 22 Copynumber: 9.0 Consensus size: 22
34975 ATCTAATAGA
34985 GTGATTATCAAAATTTCATTAA-
1 GTGATTATCAAAATTTCA-TAAT
* * *
35007 GATTGGATTAACGAAATTT-AT-AG
1 G--T-GATTATCAAAATTTCATAAT
*
35030 GATGATTATCAAAATTTCATAGT
1 G-TGATTATCAAAATTTCATAAT
* *
35053 GTTG-TTATCAAAGTTACATAAT
1 G-TGATTATCAAAATTTCATAAT
*
35075 GTGATTATCAAAATTTTATAGA-
1 GTGATTATCAAAATTTCATA-AT
* * * * *
35097 GGGGTCAACAAAATTTTATAGA-
1 GTGATTATCAAAATTTCATA-AT
* * * *
35119 GAGGTTTATCAAAATTTCGTAAA
1 G-TGATTATCAAAATTTCATAAT
* * * *
35142 GAGGTTATCAAATTTTCAAAAT
1 GTGATTATCAAAATTTCATAAT
35164 GTGATTATCAAAATTTCATAAT
1 GTGATTATCAAAATTTCATAAT
35186 G
1 G
35187 ATATTTCTGT
Statistics
Matches: 137, Mismatches: 33, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
21 14 0.10
22 88 0.64
23 21 0.15
24 2 0.01
25 12 0.09
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (22 bp):
GTGATTATCAAAATTTCATAAT
Found at i:35422 original size:22 final size:22
Alignment explanation
Indices: 35276--35796 Score: 286
Period size: 22 Copynumber: 24.0 Consensus size: 22
35266 TCAAAATATC
* *
35276 AGTGAGGATATCAAAATTTTAT
1 AGTGAGGTTATCAAAATTTCAT
*
35298 A-TGAAGGTTATCAGAATTTCAT
1 AGTG-AGGTTATCAAAATTTCAT
* *
35320 AGTTTA-GTTTTCAAAATTTCAT
1 AG-TGAGGTTATCAAAATTTCAT
* *
35342 A-AGAGGGTTAGCAAAATTTCAT
1 AGTGA-GGTTATCAAAATTTCAT
* * *
35364 AGT-ATGTAGATCAAAATTCCAT
1 AGTGAGGT-TATCAAAATTTCAT
* * * *
35386 GGGGAGATTAACAAAATTTCAT
1 AGTGAGGTTATCAAAATTTCAT
* **
35408 AATGAGGTTATCAAAAAAATCAT
1 AGTGAGGTTATC-AAAATTTCAT
*
35431 AGGGAGGTTATCAAAA-TT--T
1 AGTGAGGTTATCAAAATTTCAT
*
35450 -GT-A-GTTATCAAGATTTCAT
1 AGTGAGGTTATCAAAATTTCAT
35469 AAG-GAGGTTATCAAAA-TT--T
1 -AGTGAGGTTATCAAAATTTCAT
*
35488 -GT-A-GTTATCAAGATTTCAT
1 AGTGAGGTTATCAAAATTTCAT
*
35507 AAG-GAGGTTATCAAAATTTTAT
1 -AGTGAGGTTATCAAAATTTCAT
* *
35529 AGGGAGGTTTATCAAAATTTTAT
1 AGTGAGG-TTATCAAAATTTCAT
35552 AG-GAAGGTTTATCAAAATTTCAT
1 AGTG-AGG-TTATCAAAATTTCAT
* *
35575 AGCGAGGTTATCACAATTTCAT
1 AGTGAGGTTATCAAAATTTCAT
* * *
35597 AGTGTGATTATCAAAATTTCAG
1 AGTGAGGTTATCAAAATTTCAT
* *
35619 AGTGTGATTA-CTAACAA-TTCAT
1 AGTGAGGTTATC-AA-AATTTCAT
*
35641 A-TGGAGGTT-TTAAAATTTTCAT
1 AGT-GAGGTTATCAAAA-TTTCAT
* *
35663 AACGTGA--TTATCAATATATCAT
1 -A-GTGAGGTTATCAAAATTTCAT
** *
35685 A-TAGAGGTTATCAACGTCTCAT
1 AGT-GAGGTTATCAAAATTTCAT
*
35707 AGTGTTGGTTATCAAAATTTCAT
1 AGTG-AGGTTATCAAAATTTCAT
* * *
35730 TGGGAAGTTATCAAAATTTCAT
1 AGTGAGGTTATCAAAATTTCAT
* *
35752 AGTGAGGTCT-TCAAAATTCCTT
1 AGTGAGGT-TATCAAAATTTCAT
* *
35774 AGGGAGGTTAACAAAATTTCAT
1 AGTGAGGTTATCAAAATTTCAT
35796 A
1 A
35797 AGAAGGTTAA
Statistics
Matches: 382, Mismatches: 72, Indels: 90
0.70 0.13 0.17
Matches are distributed among these distances:
16 18 0.05
17 7 0.02
18 1 0.00
19 5 0.01
20 5 0.01
21 19 0.05
22 236 0.62
23 86 0.23
24 4 0.01
25 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (22 bp):
AGTGAGGTTATCAAAATTTCAT
Found at i:35458 original size:16 final size:16
Alignment explanation
Indices: 35437--35503 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 16
35427 TCATAGGGAG
35437 GTTATCAAAATTTGTA
1 GTTATCAAAATTTGTA
* *
35453 GTTATCAAGATTTCATAAGGA
1 GTTATCAA-AATT--T--GTA
35474 GGTTATCAAAATTTGTA
1 -GTTATCAAAATTTGTA
*
35491 GTTATCAAGATTT
1 GTTATCAAAATTT
35504 CATAAGGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
16 20 0.50
17 5 0.12
19 2 0.05
21 5 0.12
22 8 0.20
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40
Consensus pattern (16 bp):
GTTATCAAAATTTGTA
Found at i:35475 original size:38 final size:38
Alignment explanation
Indices: 35427--35525 Score: 189
Period size: 38 Copynumber: 2.6 Consensus size: 38
35417 ATCAAAAAAA
*
35427 TCATAGGGAGGTTATCAAAATTTGTAGTTATCAAGATT
1 TCATAAGGAGGTTATCAAAATTTGTAGTTATCAAGATT
35465 TCATAAGGAGGTTATCAAAATTTGTAGTTATCAAGATT
1 TCATAAGGAGGTTATCAAAATTTGTAGTTATCAAGATT
35503 TCATAAGGAGGTTATCAAAATTT
1 TCATAAGGAGGTTATCAAAATTT
35526 TATAGGGAGG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (38 bp):
TCATAAGGAGGTTATCAAAATTTGTAGTTATCAAGATT
Found at i:35823 original size:21 final size:22
Alignment explanation
Indices: 35778--35825 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
35768 TTCCTTAGGG
*
35778 AGGTTAACAAAATTTCATAAGA
1 AGGTTAACAAAATTTCATAAAA
35800 AGGTTAA-AGAAATTT-ATAAAA
1 AGGTTAACA-AAATTTCATAAAA
35821 AGGTT
1 AGGTT
35826 CTCGAAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.29
Consensus pattern (22 bp):
AGGTTAACAAAATTTCATAAAA
Found at i:35870 original size:22 final size:22
Alignment explanation
Indices: 35845--35898 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
35835 CCATAGTATC
*
35845 GTTATTAAAATTTCCTAAAAAG
1 GTTATCAAAATTTCCTAAAAAG
* *
35867 GTTATCAAAATTTCTTAAGAAG
1 GTTATCAAAATTTCCTAAAAAG
*
35889 GTCATCAAAA
1 GTTATCAAAA
35899 ATAGTGTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (22 bp):
GTTATCAAAATTTCCTAAAAAG
Found at i:36723 original size:26 final size:27
Alignment explanation
Indices: 36680--36730 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
36670 TTTTTGAATT
* *
36680 ATAATAAAAATTAGCAAAAA-AAAATA
1 ATAATAAAAATAAACAAAAACAAAATA
*
36706 ATAATAATAATAAACAAAAACAAAA
1 ATAATAAAAATAAACAAAAACAAAA
36731 ACAAAGAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.18
Consensus pattern (27 bp):
ATAATAAAAATAAACAAAAACAAAATA
Found at i:42065 original size:20 final size:21
Alignment explanation
Indices: 42042--42082 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
42032 TTTTTAGGTA
42042 TTGTTGTCATTTT-ATGTTTT
1 TTGTTGTCATTTTCATGTTTT
42062 TTGTTGTCATTTTCATGTTTT
1 TTGTTGTCATTTTCATGTTTT
42083 GAAAACAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.10, C:0.07, G:0.15, T:0.68
Consensus pattern (21 bp):
TTGTTGTCATTTTCATGTTTT
Found at i:45992 original size:2 final size:2
Alignment explanation
Indices: 45985--46013 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45975 CTATTTAGTG
45985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46014 TACTTGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47737 original size:13 final size:13
Alignment explanation
Indices: 47719--47745 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
47709 TTGAGCATTT
47719 GATTCAATATTAA
1 GATTCAATATTAA
47732 GATTCAATATTAA
1 GATTCAATATTAA
47745 G
1 G
47746 GTGCATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (13 bp):
GATTCAATATTAA
Found at i:48414 original size:35 final size:35
Alignment explanation
Indices: 48370--48451 Score: 155
Period size: 35 Copynumber: 2.3 Consensus size: 35
48360 ATTTTGATTA
48370 TATTTCCGTAAGGTTTCTTCTTCAAAAAAACAAAT
1 TATTTCCGTAAGGTTTCTTCTTCAAAAAAACAAAT
*
48405 TATTTCCGTAAGGTTTCTTCTTCGAAAAAACAAAT
1 TATTTCCGTAAGGTTTCTTCTTCAAAAAAACAAAT
48440 TATTTCCGTAAG
1 TATTTCCGTAAG
48452 AATATGTACC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (35 bp):
TATTTCCGTAAGGTTTCTTCTTCAAAAAAACAAAT
Found at i:49397 original size:31 final size:31
Alignment explanation
Indices: 49348--49535 Score: 184
Period size: 31 Copynumber: 6.2 Consensus size: 31
49338 ACGGTGTTCG
* *
49348 ACGTGGCATGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
49379 ATGTGGCACGCCACGTGTA-CAAAAAGCGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* **
49409 ACGTGACACGCCATATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * * *
49440 ACATGGCACGTCACATGTACCAAAAAATGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* ** * *
49471 ATGTATCACGCCATGTGTACCAAAAAGTGAT
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * *
49502 ACGTGGCATGCCTCGTGCA-CAAAAAG-GAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
49531 ACGTG
1 ACGTG
49536 TCACATGTCA
Statistics
Matches: 125, Mismatches: 31, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
29 7 0.06
30 32 0.26
31 86 0.69
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:49428 original size:61 final size:60
Alignment explanation
Indices: 49348--49535 Score: 216
Period size: 61 Copynumber: 3.1 Consensus size: 60
49338 ACGGTGTTCG
* * *
49348 ACGTGGCATGCCATGTGTACCAAAAAGTGACATGTGGCACGCCACGTGTACAAAAAGCGAC
1 ACGTGACACGCCATGTGTACCAAAAAGTGACACGTGGCACGCCACGTGTACAAAAAG-GAC
* * * * *
49409 ACGTGACACGCCATATGTACCAAAAAGTGACACATGGCACGTCACATGTACCAAAAAATGAC
1 ACGTGACACGCCATGTGTACCAAAAAGTGACACGTGGCACGCCACGTGTA-C-AAAAAGGAC
* * * * *
49471 ATGT-ATCACGCCATGTGTACCAAAAAGTGATACGTGGCATGCCTCGTGCACAAAAAGGAC
1 ACGTGA-CACGCCATGTGTACCAAAAAGTGACACGTGGCACGCCACGTGTACAAAAAGGAC
49531 ACGTG
1 ACGTG
49536 TCACATGTCA
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
60 11 0.11
61 45 0.43
62 43 0.41
63 5 0.05
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (60 bp):
ACGTGACACGCCATGTGTACCAAAAAGTGACACGTGGCACGCCACGTGTACAAAAAGGAC
Found at i:49525 original size:92 final size:91
Alignment explanation
Indices: 49363--49532 Score: 209
Period size: 92 Copynumber: 1.9 Consensus size: 91
49353 GCATGCCATG
* * *
49363 TGTACCAAAAAGTGACATGTGGCACGCCACGTGTACAAAAAGCGACACGTGACACGCCATATGTA
1 TGTACCAAAAAATGACATGTAGCACGCCACGTGTACAAAAAGCGACACGTGACACGCCATATGCA
49428 CCAAAAAGTGACACATGGCACGTCACA
66 CCAAAAAG-GACACATGGCACGTCACA
* * * * * * *
49455 TGTACCAAAAAATGACATGTATCACGCCATGTGTACCAAAAAGTGATACGTGGCATGCC-TCGTG
1 TGTACCAAAAAATGACATGTAGCACGCCACGTGTA-CAAAAAGCGACACGTGACACGCCAT-ATG
49519 CA-CAAAAAGGACAC
64 CACCAAAAAGGACAC
49533 GTGTCACATG
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
91 5 0.08
92 39 0.59
93 22 0.33
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (91 bp):
TGTACCAAAAAATGACATGTAGCACGCCACGTGTACAAAAAGCGACACGTGACACGCCATATGCA
CCAAAAAGGACACATGGCACGTCACA
Found at i:60108 original size:13 final size:13
Alignment explanation
Indices: 60090--60126 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 13
60080 TAAATTTTCC
60090 AAAATTTATTTTA
1 AAAATTTATTTTA
60103 AAAA-TT-TTTTA
1 AAAATTTATTTTA
60114 AAAATTATATTTT
1 AAAATT-TATTTT
60127 TGTAATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 9 0.43
12 3 0.14
13 5 0.24
14 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAATTTATTTTA
Found at i:60116 original size:23 final size:25
Alignment explanation
Indices: 60081--60126 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
60071 TGTAAGTTTT
60081 AAATTTTCC-AAAATT-TATTTTAA
1 AAATTTTCCAAAAATTATATTTTAA
**
60104 AAATTTTTTAAAAATTATATTTT
1 AAATTTTCCAAAAATTATATTTT
60127 TGTAATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 6 0.32
25 6 0.32
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (25 bp):
AAATTTTCCAAAAATTATATTTTAA
Done.