Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010290.1 Corchorus capsularis cultivar CVL-1 contig10311, 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: 29046
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:1439 original size:329 final size:330
Alignment explanation
Indices: 1--2909 Score: 4220
Period size: 329 Copynumber: 8.9 Consensus size: 330
* * *
1 TTAGATTTGGTCAGATGAATATAAATACTTCATGGAGTCTTTCCGCCAAAGATCATGCAAAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
*
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACGATTTCGGCTAAA
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
*
131 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATATTAAAAACGATATA
131 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATATA
*
196 TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGGTTTTCCTATTTTTTCC
196 TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTATTTTTTCC
* * *
261 GAATTAATTTCTAATTAAATCAAAACATAATTCACATGCTGTAAAAGCAAATCCTTAAATCCAAT
261 GAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAATCCAAT
326 GTGGT
326 GTGGT
** *
331 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATTTAGAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
* * * *
396 AGTCCGGGGCCTCGGAACGCGTTTTTAGCTAAAAATCGTGATTGTTAGTACAAGATTTCGGCTAA
66 AGT-CGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
* * *
461 ATTTTTTGCAAAAATTGACCCGAAATATGTTTCCTTAAATCTTTTGGCAATAATACTAAAAACGA
130 A-ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAAT-TTTT-GCAATAATACTAAAAACGA
*
526 TATATAACTCAACGCCAAAAATATTAAA-GGCTTTTCACGCTTCTAAGATCGATTTTCCTATTTT
192 TATATAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTATTTT
*
590 TGT--GAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAATT
257 T-TCCGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAAT
653 CCAATGTGGT
321 CCAATGTGGT
* * *
663 TTAGATTTGGTTAGATGAATATAGATACTTCAAGGAGTCTTGCCGCCAAAAATCATGCAAAATTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
* * * *
728 AGTCGGGGCCACGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTACTACAGGATTTCAGCTAAA
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * * * *
793 ATTTTGCAAAAATTGACCCAAAATATGTTTCCTTAATTTTTTGCTCATAATACTAAAAA--A-AT
131 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGC-AATAATACTAAAAACGATAT
* * * * * *
855 TTAATTCAACGCCAAAAATATTACAGGG-TTTTCACGCCTCTAAGATCGGTTTTCCTATTTTTTC
195 ATAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTATTTTTTC
* * * * *
919 CGAATTAATTTCTAATTAATTCGAAACGTAATTCACAGGCTGTAAAAGCAAATCCTTAAATCCAA
260 CGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAATCCAA
984 TGTGGT
325 TGTGGT
*
990 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGAC-TTCCGCCAAAAATCATGCAAAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
* *
1054 AGCCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCTAAA
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
*
1119 ATTTTGGAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATATA
131 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATATA
1184 TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTAATTTTTTC
196 TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCT-ATTTTTTC
* * *
1249 CTAATTAA-TT-TAGTTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAATTCCAA
260 CGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAATCCAA
*
1312 AGTGGT
325 TGTGGT
*
1318 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTGCCGCCAAAAATCATGCAAAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
*
1383 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTCCACGATTTCGGCTAAA
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * * *
1448 ATTTTGCAAAAAATGACCCGAAATATTTTTCCTTAAAATTTTGCAATAATACTAAAAACAATATA
131 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATATA
* *
1513 TAACTCAATGCCAAAAATACTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTAATTTTTTC
196 TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCT-ATTTTTTC
* *
1578 CGAATTAA-TT-TAGTTAAATCGAAACATGATTGACATGCTGTAAAACCAAATCCTTAAATCCAA
260 CGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAATCCAA
1641 TGTGGT
325 TGTGGT
* * * * * *
1647 TTAGATTTTGTTAGATGAATATAGATACTTCAAGGACTCTTTTCTCCAAAAATGATGCAAAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
*
1712 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGA-----CGTACACGATTTCGGC----
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* ** *
1768 ----T---AAAATTGACCTGAAAGATTTTTCCTTATTTTTTTTGGTC-ATAATACTAAAAA-TAT
131 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTA-AATTTTT-G-CAATAATACTAAAAACGAT
* * * * *
1824 ATATCATTTAACGCCAAAAATTTTAAAGGGCTTTTCGCACTTCTAAGATCGATTTTCCTATTTTT
193 ATATAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTATTTTT
* * * * *
1889 TCCGAATTAATTTCTAATTAAATCGAAATATAATTCACATGTTGTAAAAGCAAATCCTTAAATGC
258 TCCGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAATCC
1954 AATGTGGT
323 AATGTGGT
* *
1962 TTAGATTTTGTTAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
* *
2027 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACATGATTTCGGGTAA
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
*
2092 AATTTTGCAAATATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATAT
130 AATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATAT
* *
2157 ATAACTCAACCCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATGGATTTTCCTAATTTTTT
195 ATAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCT-ATTTTTT
* * * * *
2222 CCTAATTAA-TT-TAGTTAAATCGAGACGTGATTCACATGCTGTAAAACCAAATCCTTAATTCCA
259 CCGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAATCCA
2285 ATGTGGT
324 ATGTGGT
2292 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
*
2357 AGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* ** *
2422 ATTTTGCAAAAATTGACCTGAAAGATTTTTCCTTATTTTTTTGGTC-ATAATACTAAAAA-AATA
131 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTT-G-CAATAATACTAAAAACGATA
* * *
2485 TATAATTTAACGCCAAAAATATAAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTATTTTTT
194 TATAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTATTTTTT
* * * *
2550 CCGAATTAATTTCTAATTAAATCGAAATATAATTCACATGCTGTAAAAGCAAATCCTTAAATGCA
259 CCGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAATCCA
2615 ATGTGGT
324 ATGTGGT
* * * *
2622 TTAGATTTTGTTAGATGAATATAGATACTTCAAGGAGTCTTTCTGCCAAAAATAATGCAAAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
* * * * * *
2687 AGTCGGGGCCCCGGAACGCGTTTTTAGCTAAAAATCGTGATTGTTAGCACAAC-ATTTCGTCTAA
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTAC-ACGATTTCGGCTAA
* * * * * *
2751 AATTTTGCAAAAATTGACCCAAAATATGTTTCCTTAATTTTTTGGCCATAATACTAAAAA-AATA
130 AATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTT-GCAATAATACTAAAAACGATA
* * * * * * *
2815 CATAATTCAATGCCAGAAATATTACAGGG-TTTTCACGCTTCTAAGATCGGTTTTCCTA-TTTTT
194 TATAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTATTTTTT
*
2878 CTGAATTAATTTCTAATTAAATCGAAACATGA
259 CCGAATTAATTTCTAATTAAATCGAAACATGA
2910 GGGTTTTCAC
Statistics
Matches: 2330, Mismatches: 203, Indels: 94
0.89 0.08 0.04
Matches are distributed among these distances:
313 40 0.02
314 60 0.03
315 156 0.07
316 13 0.01
321 13 0.01
324 14 0.01
325 14 0.01
326 178 0.08
327 105 0.05
328 167 0.07
329 576 0.25
330 529 0.23
331 176 0.08
332 203 0.09
333 39 0.02
334 47 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (330 bp):
TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATATA
TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTATTTTTTCC
GAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAATCCAAT
GTGGT
Found at i:2255 original size:974 final size:979
Alignment explanation
Indices: 1--2907 Score: 4472
Period size: 974 Copynumber: 3.0 Consensus size: 979
* * *
1 TTAGATTTGGTCAGATGAATATAAATACTTCATGGAGTCTTTCCGCCAAAGATCATGCAAAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
*
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTACACGATTTCGGCTAAA
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
*
131 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATATTAAAAACGATATA
131 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATATA
196 TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGG-TTTTCCT-ATTTTTT
196 TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGAT-GGATTTTCCTAATTTTTT
* * * * * *
259 CCGAATTAATTTCTAATTAAATCAAAACATAATTCACATGCTGTAAAAGCAAATCCTTAAATCCA
260 CCTAATTAA-TT-TAGTTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAATTCCA
**
324 ATGTGGTTTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATTT
323 ATGTGGTTTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGC
* * * * *
389 AGAACTGAGTCCGGGGCCTCGGAACGCGTTTTTAGCTAAAAATCGTGATTGTTAGTACAAGATTT
388 AAAACTGAGT-CGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT
* * *
454 CGGCTAAATTTTTTGCAAAAATTGACCCGAAATATGTTTCCTTAAATCTTTTGGCAATAATACTA
452 CGGCTAAA-ATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAAA-ATTTTGGCAATAATACTA
* *
519 AAAACGATATATAACTCAACGCCAAAAATATTAAA-GGCTTTTCACGCTTCTAAGATCGATTTTC
515 AAAACAATATATAACTCAACGCCAAAAATA-TAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTC
583 CTATTTTTGT--GAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATC
579 CTATTTTT-TCCGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATC
* * ** *
646 CTTAATTCCAATGTGGTTTAGATTTGGTTAGATGAATATAGATACTTCAAGGAGTCTTGCCGCCA
643 CTTAAATCCAATGTGGTTTAGATTTTGTTAGATGAATATAGATACTTCAAGGAGTCTTTTCTCCA
* * *
711 AAAATCATGCAAAATTGAGTCGGGGCCACGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTACT
708 AAAATAATGCAAAACTGAGTCGGGGCCACGGAACGCGTTTTTAGCCAAAAACCGTGATCGTTAC-
* *
776 ACAGGATTTCAGCTAAAATTTTGCAAAAATTGACCCAAAATATGTTTCCTTAATTTTTTGCTCAT
772 ACA-GATTTCGGCTAAAA-TTTG---AAATTGA--CAAAATATGTTTCCTTAATTTTTTGGTCAT
* *
841 AATACTAAAAAA-ATTTAATTCAACGCCAAAAATATTACAGGGTTTTCACGCCTCTAAGATCGGT
830 AATACTAAAAAATATATAATTCAACGCCAAAAATATTACAGGGTTTTCACGCTTCTAAGATCGGT
* *
905 TTTCCTATTTTTTCCGAATTAATTTCTAATTAATTCGAAACGTAATTCACAGGCTGTAAAAGCAA
895 TTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTCACAGGCTGTAAAAGCAA
970 ATCCTTAAATCCAATGTGGT
960 ATCCTTAAATCCAATGTGGT
*
990 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGAC-TTCCGCCAAAAATCATGCAAAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
* *
1054 AGCCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCTAAA
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
*
1119 ATTTTGGAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATATA
131 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATATA
*
1184 TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTAATTTTTTC
196 TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATGGATTTTCCTAATTTTTTC
*
1249 CTAATTAATTTAGTTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAATTCCAAAG
261 CTAATTAATTTAGTTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAATTCCAATG
*
1314 TGGTTTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTGCCGCCAAAAATCATGCAAA
326 TGGTTTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAA
*
1379 ACTGAGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTCCACGATTTCGGC
391 ACTGAGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
*
1444 TAAAATTTTGCAAAAAATGACCCGAAATATTTTTCCTTAAAATTTT-GCAATAATACTAAAAACA
456 TAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAAAATTTTGGCAATAATACTAAAAACA
*
1508 ATATATAACTCAATGCCAAAAATACTAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTAATT
521 ATATATAACTCAACGCCAAAAATA-TAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCT-ATT
* *
1573 TTTTCCGAATTAA-TT-TAGTTAAATCGAAACATGATTGACATGCTGTAAAACCAAATCCTTAAA
584 TTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAA
* *
1636 TCCAATGTGGTTTAGATTTTGTTAGATGAATATAGATACTTCAAGGACTCTTTTCTCCAAAAATG
649 TCCAATGTGGTTTAGATTTTGTTAGATGAATATAGATACTTCAAGGAGTCTTTTCTCCAAAAATA
*
1701 ATGCAAAACTGAGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGA-CG-TACAC-GATT
714 ATGCAAAACTGAGTCGGGGCCACGGAACGCGTTTTTAGCCAAAAACCGTGATCGTTACACAGATT
** * *
1763 TCGGCTAAAA-TTG-ACCTGA-AAGAT-T-TTTCCTTATTTTTTTTGGTCATAATACTAAAAATA
779 TCGGCTAAAATTTGAAATTGACAAAATATGTTTCCTTA-ATTTTTTGGTCATAATACTAAAAA-A
* * * * * * *
1823 TATATCATTTAACGCCAAAAATTTTAAAGGGCTTTTCGCACTTCTAAGATCGATTTTCCTATTTT
842 TATATAATTCAACGCCAAAAATATTACAGGG-TTTTCACGCTTCTAAGATCGGTTTTCCTATTTT
* * * *
1888 TTCCGAATTAATTTCTAATTAAATCGAAATATAATTCACATGTTGTAAAAGCAAATCCTTAAATG
906 TTCCGAATTAATTTCTAATTAAATCGAAACATAATTCACAGGCTGTAAAAGCAAATCCTTAAATC
1953 CAATGTGGT
971 CAATGTGGT
* *
1962 TTAGATTTTGTTAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
1 TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
* *
2027 AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACATGATTTCGGGTAA
66 AGTCGGGGCCTCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
*
2092 AATTTTGCAAATATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATAT
130 AATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATAT
*
2157 ATAACTCAACCCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATGGATTTTCCTAATTTTTT
195 ATAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATGGATTTTCCTAATTTTTT
* *
2222 CCTAATTAATTTAGTTAAATCGAGACGTGATTCACATGCTGTAAAACCAAATCCTTAATTCCAAT
260 CCTAATTAATTTAGTTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAATTCCAAT
2287 GTGGTTTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAA
325 GTGGTTTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAA
*
2352 AACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGG
390 AACTGAGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGG
* * ***
2417 CTAAAATTTTGCAAAAATTGACCTGAAAGATTTTTCCTTATTTTTTTGGTC-ATAATACTAAAAA
455 CTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAAAATTTTGG-CAATAATACTAAAAA
* *
2481 -AATATATAATTTAACGCCAAAAATATAAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTAT
519 CAATATATAACTCAACGCCAAAAATAT-AAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTAT
* * *
2545 TTTTTCCGAATTAATTTCTAATTAAATCGAAATATAATTCACATGCTGTAAAAGCAAATCCTTAA
583 TTTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAA
*
2610 ATGCAATGTGGTTTAGATTTTGTTAGATGAATATAGATACTTCAAGGAGTC-TTTCTGCCAAAAA
648 ATCCAATGTGGTTTAGATTTTGTTAGATGAATATAGATACTTCAAGGAGTCTTTTCT-CCAAAAA
* * * *
2674 TAATGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCTAAAAATCGTGATTGTTAGCACAA
712 TAATGCAAAACTGAGTCGGGGCCACGGAACGCGTTTTTAGCCAAAAACCGTGATCGTTA-CAC-A
* * *
2739 CATTTCGTCTAAAATTTTGCAAAAATTGACCCAAAATATGTTTCCTTAATTTTTTGGCCATAATA
775 GATTTCGGCTAAAA-TTTG---AAATTGA--CAAAATATGTTTCCTTAATTTTTTGGTCATAATA
* * *
2804 CTAAAAAAATACATAATTCAATGCCAGAAATATTACAGGGTTTTCACGCTTCTAAGATCGGTTTT
834 CT-AAAAAATATATAATTCAACGCCAAAAATATTACAGGGTTTTCACGCTTCTAAGATCGGTTTT
*
2869 CCTA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAT
898 CCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAT
2908 GAGGGTTTTC
Statistics
Matches: 1759, Mismatches: 124, Indels: 71
0.90 0.06 0.04
Matches are distributed among these distances:
968 8 0.00
969 23 0.01
970 5 0.00
971 25 0.01
972 133 0.08
973 74 0.04
974 452 0.26
975 161 0.09
976 2 0.00
977 5 0.00
978 3 0.00
979 13 0.01
980 12 0.01
981 2 0.00
982 6 0.00
983 45 0.03
984 188 0.11
985 42 0.02
986 68 0.04
987 118 0.07
988 237 0.13
989 81 0.05
990 43 0.02
991 13 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (979 bp):
TTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAAACTG
AGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAAATTTTTGCAATAATACTAAAAACGATATA
TAACTCAACGCCAAAAATATTAAAGGGCTTTTCGCGCTTCTAAGATGGATTTTCCTAATTTTTTC
CTAATTAATTTAGTTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAATTCCAATG
TGGTTTAGATTTGGTCAGATGAATATAGATACTTCAAGGAGTCTTTCCGCCAAAAATCATGCAAA
ACTGAGTCGGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
TAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAAAATTTTGGCAATAATACTAAAAACA
ATATATAACTCAACGCCAAAAATATAAAGGGCTTTTCGCGCTTCTAAGATCGATTTTCCTATTTT
TTCCGAATTAATTTCTAATTAAATCGAAACATGATTCACATGCTGTAAAACCAAATCCTTAAATC
CAATGTGGTTTAGATTTTGTTAGATGAATATAGATACTTCAAGGAGTCTTTTCTCCAAAAATAAT
GCAAAACTGAGTCGGGGCCACGGAACGCGTTTTTAGCCAAAAACCGTGATCGTTACACAGATTTC
GGCTAAAATTTGAAATTGACAAAATATGTTTCCTTAATTTTTTGGTCATAATACTAAAAAATATA
TAATTCAACGCCAAAAATATTACAGGGTTTTCACGCTTCTAAGATCGGTTTTCCTATTTTTTCCG
AATTAATTTCTAATTAAATCGAAACATAATTCACAGGCTGTAAAAGCAAATCCTTAAATCCAATG
TGGT
Found at i:2951 original size:69 final size:69
Alignment explanation
Indices: 2840--2978 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
2830 GAAATATTAC
*
2840 AGGGTTTTCACGCTTCTAAGATCGGTTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAA
1 AGGGTTTTCACGCTTCTAAGATCGATTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAA
2905 CATG
66 CATG
*
2909 AGGGTTTTCACGCTTCTAAGATCGATTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAG
1 AGGGTTTTCACGCTTCTAAGATCGATTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAA
2974 CATG
66 CATG
2978 A
1 A
2979 TTGAGATGCT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (69 bp):
AGGGTTTTCACGCTTCTAAGATCGATTTTCCTATTTTTCTGAATTAATTTCTAATTAAATCGAAA
CATG
Found at i:14076 original size:2 final size:2
Alignment explanation
Indices: 14069--14097 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
14059 TCGGTGGCAT
14069 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14098 CTTGACAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15491 original size:51 final size:51
Alignment explanation
Indices: 15424--15689 Score: 152
Period size: 51 Copynumber: 5.3 Consensus size: 51
15414 TAGTTTCGAT
* *
15424 GTTCTCACGATGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
** * * * *
15475 GTTCTCACAAAGAGTCC--AT-G-GCT-TACGTTC--A-ACCAACTTAGTTTCGAT
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAG---C--C
* * *
15523 GTTCTCACGATGAGTCCGGATCGAAATCTAAGGTTAAATACGAACTTAGCC
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
* * * * *
15574 GTTCTCACAAAGAGTCCAGG---G--CT-TACGTTC--A-ACCAACTTAGTTTCGAT
1 GTTCTCACAAAGAGTCC-GGATCGAAATCTAAGGTCAAATACGAACTTAG---C--C
* *
15622 GTTCTCACGATGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
15673 GTTCTCACAAAGAGTCC
1 GTTCTCACAAAGAGTCC
15690 AGGGCTTACG
Statistics
Matches: 153, Mismatches: 34, Indels: 56
0.63 0.14 0.23
Matches are distributed among these distances:
43 18 0.12
44 2 0.01
46 11 0.07
47 4 0.03
48 31 0.20
49 3 0.02
50 3 0.02
51 46 0.30
52 4 0.03
53 11 0.07
55 2 0.01
56 18 0.12
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (51 bp):
GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
Found at i:15538 original size:48 final size:48
Alignment explanation
Indices: 15475--15638 Score: 122
Period size: 48 Copynumber: 3.4 Consensus size: 48
15465 GAACTTAGCC
15475 GTTCTCACAAAGAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGAT
1 GTTCTCACAAAGAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGAT
* * * * * * * *
15523 GTTCTCACGATGAGTCCGGATCGAAATCTAAGGTTAAATACGAACTTAG---C--C
1 GTTCTCACAAAGAGTCC--AT-G---GCTTACGTT-CA-ACCAACTTAGTTTCGAT
*
15574 GTTCTCACAAAGAGTCCAGGGCTTACGTTCAACCAACTTAGTTTCGAT
1 GTTCTCACAAAGAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGAT
* *
15622 GTTCTCACGATGAGTCC
1 GTTCTCACAAAGAGTCC
15639 GGATCGAAAT
Statistics
Matches: 84, Mismatches: 19, Indels: 26
0.65 0.15 0.20
Matches are distributed among these distances:
43 9 0.11
44 1 0.01
45 6 0.07
46 1 0.01
48 31 0.37
49 1 0.01
50 2 0.02
51 16 0.19
53 1 0.01
54 6 0.07
55 1 0.01
56 9 0.11
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (48 bp):
GTTCTCACAAAGAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGAT
Found at i:15858 original size:99 final size:99
Alignment explanation
Indices: 14866--15856 Score: 1531
Period size: 99 Copynumber: 10.0 Consensus size: 99
14856 ACTTAGGTTG
* * *
14866 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGACTTACGTTCGGCCAACTTAGTTTAGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
* *
14931 TCTCACGAAGAGTCCAGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* *
14965 AATACGAACTTAGCCGTTCTTACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
*
15030 TCTCACGATGAGTCTGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * *
15064 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCTAACTTAGTTTCAATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
15129 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * * *
15163 ATTACGAACGTT-GTCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGGCAACTTAGTTTCGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATG
* ** *
15227 TTCTCATGGGGAGTTCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
** * *
15262 GTTACGAACGTT-GCCGTTCTCACAAAAAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATG
*
15326 TTCTCACGATGAGTGCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * * * * *
15361 ATTACAAACGTT-GCTGTTTTCACAAAGAGTCCATGGCTTACATTCAGCCAACTTAGTTTCGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATG
15425 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* *
15460 AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
*
15525 TCTCACGATGAGTCCGGATCGAAATCTAAGGTTA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
*
15559 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAACCAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
15624 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* *
15658 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCTAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
**
15723 TCTCACGGGGAGTCCGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * *
15757 ATTACGAACGTT-GCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCAACTTAGTTTTGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATG
**
15821 TTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
15856 A
1 A
15857 TTCGGAAATT
Statistics
Matches: 832, Mismatches: 57, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
98 2 0.00
99 826 0.99
100 4 0.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (99 bp):
AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCAGCCAACTTAGTTTCGATGT
TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
Found at i:16639 original size:231 final size:232
Alignment explanation
Indices: 16224--16650 Score: 671
Period size: 231 Copynumber: 1.8 Consensus size: 232
16214 CCACATACAG
*** *
16224 CTTCGTGGATCTCCTTCAACACATAGTTGGCTTCATCTGGGTCTACAAACTTCAAAAAAGAAAAG
1 CTTCGTGGATCTCCTTCAACACATAGACAGCTTCATCTGAGTCTACAAACTTCAAAAAAGAAAAG
16289 GTGAAGGATTTCTTATATAGTTCATCATCAATCAACACATACCTTGCCGCTCTTCATGGTCTAGC
66 GTGAAGGATTTCTTATATAGTTCATCATCAATCAACACATACCTTGCCGCTCTTCATGGTCTAGC
* * *
16354 TGCCATGACTTTTGGATCAAATGGAGGATTGATCCCTTTCAAATACTCCACTATCTCGATCATCC
131 TGCCACGACTCTTGGATCAAATGGAGGATCGATCCCTTTCAAATACTCCACTATCTCGATCATCC
16419 ACCTTCGTGGATCAGACTTACATTCGGGGGTTTCCAC
196 ACCTTCGTGGATCAGACTTACATTCGGGGGTTTCCAC
* * *
16456 CTTCGTGGATCTCCCTT-AACACATAGACAGCTTCATCT-AGTCTACATACTTCAAAAAAGGAAG
1 CTTCGTGGATCT-CCTTCAACACATAGACAGCTTCATCTGAGTCTACAAACTTCAAAAAAGAAAA
16519 GGTGAAGGATATT-TTATATAGTTCATCATCAATCAACACATACCTTGCCGCTCTTCATGGTCTA
65 GGTGAAGGAT-TTCTTATATAGTTCATCATCAATCAACACATACCTTGCCGCTCTTCATGGTCTA
* * * * * *
16583 GCTGTCGCGACTCTTGGATCAGATGGAGGATCGATTCCTTTCAAGTACTTCACTATCTCGATCAT
129 GCTGCCACGACTCTTGGATCAAATGGAGGATCGATCCCTTTCAAATACTCCACTATCTCGATCAT
16648 CCA
194 CCA
16651 GTTAGATCAT
Statistics
Matches: 177, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
231 141 0.80
232 32 0.18
233 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (232 bp):
CTTCGTGGATCTCCTTCAACACATAGACAGCTTCATCTGAGTCTACAAACTTCAAAAAAGAAAAG
GTGAAGGATTTCTTATATAGTTCATCATCAATCAACACATACCTTGCCGCTCTTCATGGTCTAGC
TGCCACGACTCTTGGATCAAATGGAGGATCGATCCCTTTCAAATACTCCACTATCTCGATCATCC
ACCTTCGTGGATCAGACTTACATTCGGGGGTTTCCAC
Found at i:18215 original size:66 final size:66
Alignment explanation
Indices: 18107--18354 Score: 392
Period size: 66 Copynumber: 3.8 Consensus size: 66
18097 ACCAACATAA
18107 GGATCTCCATATCTG-ACAC-TCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTA
1 GGATCTCCATATC-GAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTA
18170 CG
65 CG
** * *
18172 GGATCTCCATATCGAACACTTCTGTTGATCTTCGATGTTGTCGTTTTACCTTGTTCATGTTCTAC
1 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTAC
18237 G
66 G
* *
18238 GGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
1 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTAC
18303 G
66 G
* **
18304 AGATCTCCATATCTCACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCA
1 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCA
18355 ACATAAGGAT
Statistics
Matches: 170, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
64 1 0.01
65 17 0.10
66 152 0.89
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.39
Consensus pattern (66 bp):
GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTAC
G
Found at i:18540 original size:287 final size:292
Alignment explanation
Indices: 18172--18768 Score: 918
Period size: 287 Copynumber: 2.0 Consensus size: 292
18162 ATGTTCTACG
** *
18172 GGATCTCCATATCGAACACTTCTGTTGATCTTCGATGTTGTCGTTTTACCTTGTTCATGTTCTAC
1 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
18237 GGGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTA
66 GGGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTA
**
18302 CGAGATCTCCATATCTCACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCA-ACA-TA-AGGA
131 CGAGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATACATTACAGGA
* * * **
18364 TCTCCATATCTGACAC-TCTGCCGATCTTCGATGTTGTTGTTCTTCCATGTTTGGGTTCTATCAC
196 TCTCCATATCTCACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCAGGTTCTATCAC
* *
18428 CATCAGATCTTTCAAGCTTGTAACCAACGTAA
261 CATCAAATCTTTCAAGCTTGTAACCAACGCAA
18460 GGATCTCCATATCTG-ACAC-TCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTA
1 GGATCTCCATATC-GAACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTA
18523 CGGGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCT
65 CGGGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCT
* * * *
18588 ACGGGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTC
130 ACGAGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCA--TACA---T-
* *
18653 TACGGGATCTCCATATCTCACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTT
189 TACAGGATCTCCATATCTCACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCAGGTT
*
18718 CTATCACCATCAAATCTTTCAAGTTTGTAACCAACGCAA
254 CTATCACCATCAAATCTTTCAAGCTTGTAACCAACGCAA
18757 GGATCTCCATAT
1 GGATCTCCATAT
18769 GTGAAGTTCT
Statistics
Matches: 279, Mismatches: 19, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
287 155 0.56
288 17 0.06
289 1 0.00
290 2 0.01
295 2 0.01
296 18 0.06
297 84 0.30
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.38
Consensus pattern (292 bp):
GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
GGGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTA
CGAGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATACATTACAGGA
TCTCCATATCTCACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCAGGTTCTATCAC
CATCAAATCTTTCAAGCTTGTAACCAACGCAA
Found at i:18567 original size:66 final size:66
Alignment explanation
Indices: 18460--18720 Score: 454
Period size: 66 Copynumber: 4.0 Consensus size: 66
18450 ACCAACGTAA
18460 GGATCTCCATATCTG-ACAC-TCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTA
1 GGATCTCCATATC-GAACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTA
18523 CG
65 CG
*
18525 GGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
1 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
18590 G
66 G
*
18591 GGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
1 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
18656 G
66 G
** *
18657 GGATCTCCATATCTCACACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTA
1 GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTA
18721 TCACCATCAA
Statistics
Matches: 189, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
64 1 0.01
65 17 0.09
66 171 0.90
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.39
Consensus pattern (66 bp):
GGATCTCCATATCGAACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
G
Found at i:18673 original size:353 final size:354
Alignment explanation
Indices: 18008--18707 Score: 1294
Period size: 353 Copynumber: 2.0 Consensus size: 354
17998 TTGTGGGGAA
* *
18008 GATCTTCATATCTGACACTTCTGCCGATCTTTGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
1 GATCTCCATATCTGACACTTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
18073 ACCATCAAACCTTTCAAGCTTGTAACCAACATAAGGATCTCCATATCTGACACTCTGCCGATCTT
66 ACCATCAAACCTTTCAAGCTTGTAACCAACATAAGGATCTCCATATCTGACACTCTGCCGATCTT
*
18138 CGATGTTGTCGTTCTACCATGTTCATGTTCTACGGGATCTCCATATCGAACACTTCTGTTGATCT
131 CGATGTTGTCGTTCTACCATGTTCATGTTCTACGGGATCTCCATATCGAACACTTCTGTCGATCT
*
18203 TCGATGTTGTCGTTTTACCTTGTTCATGTTCTACGGGATCTCCATATCGAACACTTCTGTCGATC
196 TCGATGTTGTCGTTTTACCATGTTCATGTTCTACGGGATCTCCATATCGAACACTTCTGTCGATC
18268 TTCGATGTTGTCGTTTTACCATGTTCATGTTCTACGAGATCTCCATATCTCACACTTCTGCCGAT
261 TTCGATGTTGTCGTTTTACCATGTTCATGTTCTACGAGATCTCCATATCTCACACTTCTGCCGAT
18333 CTTCGATGTTGTCGTTCTACCAACATAAG
326 CTTCGATGTTGTCGTTCTACCAACATAAG
* *
18362 GATCTCCATATCTGACAC-TCTGCCGATCTTCGATGTTGTTGTTCTTCCATGTTTGGGTTCTATC
1 GATCTCCATATCTGACACTTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
* * *
18426 ACCATCAGATCTTTCAAGCTTGTAACCAACGTAAGGATCTCCATATCTGACACTCTGCCGATCTT
66 ACCATCAAACCTTTCAAGCTTGTAACCAACATAAGGATCTCCATATCTGACACTCTGCCGATCTT
*
18491 CGATGTTGTCGTTTTACCATGTTCATGTTCTACGGGATCTCCATATCGAACACTTCTGTCGATCT
131 CGATGTTGTCGTTCTACCATGTTCATGTTCTACGGGATCTCCATATCGAACACTTCTGTCGATCT
18556 TCGATGTTGTCGTTTTACCATGTTCATGTTCTACGGGATCTCCATATCGAACACTTCTGTCGATC
196 TCGATGTTGTCGTTTTACCATGTTCATGTTCTACGGGATCTCCATATCGAACACTTCTGTCGATC
*
18621 TTCGATGTTGTCGTTTTACCATGTTCATGTTCTACGGGATCTCCATATCTCACACTTCTGCCGAT
261 TTCGATGTTGTCGTTTTACCATGTTCATGTTCTACGAGATCTCCATATCTCACACTTCTGCCGAT
18686 CTTCGATGTTGTCGTTCTACCA
326 CTTCGATGTTGTCGTTCTACCA
18708 TGTTCATGTT
Statistics
Matches: 335, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
353 318 0.95
354 17 0.05
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (354 bp):
GATCTCCATATCTGACACTTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
ACCATCAAACCTTTCAAGCTTGTAACCAACATAAGGATCTCCATATCTGACACTCTGCCGATCTT
CGATGTTGTCGTTCTACCATGTTCATGTTCTACGGGATCTCCATATCGAACACTTCTGTCGATCT
TCGATGTTGTCGTTTTACCATGTTCATGTTCTACGGGATCTCCATATCGAACACTTCTGTCGATC
TTCGATGTTGTCGTTTTACCATGTTCATGTTCTACGAGATCTCCATATCTCACACTTCTGCCGAT
CTTCGATGTTGTCGTTCTACCAACATAAG
Found at i:25222 original size:6 final size:6
Alignment explanation
Indices: 25211--25237 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
25201 TAATTATCAA
25211 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
25238 TTTAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:28289 original size:44 final size:44
Alignment explanation
Indices: 28239--28423 Score: 146
Period size: 44 Copynumber: 4.2 Consensus size: 44
28229 TTGTCACATT
28239 TTATGAAATTTTGGTAACTACACTATGAAATTTTGGTAACCT-CA
1 TTATGAAATTTTGGTAA-TACACTATGAAATTTTGGTAACCTCCA
* * * * * *
28283 TTATGAAATTTGGGTAAAATCACTATGAAAATTCTAGCAACCTTC-
1 TTATGAAATTTTGGTAATA-CACTATG-AAATTTTGGTAACCTCCA
* * ** * * *
28328 TTGTGAAATTTTAGTAACCCTCTATGAAGTTTTGGAAACCTCCA
1 TTATGAAATTTTGGTAATACACTATGAAATTTTGGTAACCTCCA
* * * * *
28372 -TATGAAATTTTGTTTAT-CCCTATGAAATTTTGGTAA-TTGCA
1 TTATGAAATTTTGGTAATACACTATGAAATTTTGGTAACCTCCA
28413 TTATGAAATTT
1 TTATGAAATTT
28424 AAATTGAAAA
Statistics
Matches: 110, Mismatches: 26, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
41 3 0.03
42 26 0.24
43 25 0.23
44 29 0.26
45 26 0.24
46 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (44 bp):
TTATGAAATTTTGGTAATACACTATGAAATTTTGGTAACCTCCA
Found at i:28382 original size:22 final size:22
Alignment explanation
Indices: 28240--28407 Score: 114
Period size: 22 Copynumber: 7.7 Consensus size: 22
28230 TGTCACATTT
28240 TATGAAATTTTGGTAA-CTACAC
1 TATGAAATTTTGGTAACCT-CAC
*
28262 TATGAAATTTTGGTAACCTCAT
1 TATGAAATTTTGGTAACCTCAC
* **
28284 TATGAAATTTGGGTAAAATCAC
1 TATGAAATTTTGGTAACCTCAC
* * * *
28306 TATGAAAATTCTAGCAACCTTC-T
1 TATG-AAATTTTGGTAACC-TCAC
* * *
28329 TGTGAAATTTTAGTAACC-CTC
1 TATGAAATTTTGGTAACCTCAC
* *
28350 TATGAAGTTTTGGAAACCTC-C
1 TATGAAATTTTGGTAACCTCAC
* * *
28371 ATATGAAATTTTGTTTA--TCCC
1 -TATGAAATTTTGGTAACCTCAC
28392 TATGAAATTTTGGTAA
1 TATGAAATTTTGGTAA
28408 TTGCATTATG
Statistics
Matches: 113, Mismatches: 26, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
20 17 0.15
21 16 0.14
22 65 0.58
23 13 0.12
24 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGGTAACCTCAC
Found at i:28471 original size:68 final size:69
Alignment explanation
Indices: 28392--28529 Score: 224
Period size: 68 Copynumber: 2.0 Consensus size: 69
28382 TGTTTATCCC
* * * *
28392 TATGAAATTTTGGTAATTGCATTATGAAATTTAAATTGAAAATTG-TAGTTTTTTGCCCACAATG
1 TATGAAATTTTGGTAATTGCACTATGAAATTTAAATTGAAAATTGCAAATTTCTTGCCCACAATG
28456 ACAG
66 ACAG
28460 TATGAAATTTTGGTAATTGCACTATGAAATTTAAATTGAAAATTGCAAATTTCTTGCCCACAATG
1 TATGAAATTTTGGTAATTGCACTATGAAATTTAAATTGAAAATTGCAAATTTCTTGCCCACAATG
*
28525 GCAG
66 ACAG
28529 T
1 T
28530 GATGGATAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
68 44 0.69
69 20 0.31
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (69 bp):
TATGAAATTTTGGTAATTGCACTATGAAATTTAAATTGAAAATTGCAAATTTCTTGCCCACAATG
ACAG
Found at i:28500 original size:34 final size:34
Alignment explanation
Indices: 28394--28500 Score: 78
Period size: 34 Copynumber: 3.1 Consensus size: 34
28384 TTTATCCCTA
*
28394 TGAAATTTTGGTAATTGCATTATGAAATTTAAAT
1 TGAAATTTTGGTAATTGCACTATGAAATTTAAAT
* * ** * * *
28428 TGAAAATTGTAGTTTTTTGCCCACAATGACA-GT--A-
1 TG-AAATT-TTGGTAATTG--CACTATGAAATTTAAAT
28462 TGAAATTTTGGTAATTGCACTATGAAATTTAAAT
1 TGAAATTTTGGTAATTGCACTATGAAATTTAAAT
28496 TGAAA
1 TGAAA
28501 ATTGCAAATT
Statistics
Matches: 50, Mismatches: 15, Indels: 16
0.62 0.19 0.20
Matches are distributed among these distances:
30 8 0.16
31 1 0.02
32 6 0.12
33 6 0.12
34 9 0.18
35 6 0.12
36 6 0.12
37 1 0.02
38 7 0.14
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.39
Consensus pattern (34 bp):
TGAAATTTTGGTAATTGCACTATGAAATTTAAAT
Found at i:28585 original size:2 final size:2
Alignment explanation
Indices: 28580--28615 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28570 AATGTGTGTG
28580 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28616 AGACTAAGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.