Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009655.1 Corchorus capsularis cultivar CVL-1 contig09676, 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: 145088
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:970 original size:334 final size:334
Alignment explanation
Indices: 1--2972 Score: 3500
Period size: 334 Copynumber: 8.9 Consensus size: 334
* * * *
1 ATTGAGTCGGGGCCCCGGAACGCGTTTTTATCCAAAAACTGTGATGGTTAGTACACGATTTCGGC
1 ATTGAGTCGGGGCCCCGGAACGCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGAC
* *
66 TAAAATTTTGCAGAAATTGAACTGTTTGATTTTTCTTCATTTTTTAGCCACAATACTAATATGGA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
* * * *
131 ATATATATGATTCAATTCCAAAAAGATTGAAAGGCCTTTCAAGCATCTAATATCGTTTTTCCTAT
131 ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCATCTAATATCGTTTTTCCTA-
* * * *
196 TTTTTTCTGAATTAATTTATAATGAAATCTAAATAAGATTTAAATGCTCGTAAATACAAATCCTC
195 TTTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTT
* * * ** *
261 AAATACATTGTGATTGAGATTTCATAAGATTAATATAGATATTTCAAGGATTCTCAACGCCAAAA
260 AAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTTAAGGATTCTTGACACCAAAA
326 ATCATGCAAA
325 ATCATGCAAA
* * * *
336 ATGGAGCCGGTGCCCCGGAAC-CAATTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTTCG
1 ATTGAGTCGGGGCCCCGGAACGC-ATTTTCAGCC-AAAAACTGTGATGGTTAGTACACGATTTCG
* * ** ** * *
400 GCTAAAATTTTGC-AAAATTGACCCATAAGATTTTTCCTCAATTTTTAGCCACAATACTCATA--
64 ACTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATG
* * * * * * * * * * * *
462 AAAAACATATAATTCAACGCCAGAAATATTGAAGGGTTTTTGATGCTTATAATATCGTATTTCC-
129 GAATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCATCTAATATCGTTTTTCCT
* * * * *
526 ATTATTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCC
194 ATT-TTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCC
*** * * * * * *
591 TTAAATCCCA-TGTGGCAGAGATTTTGTTAA-ATGAATTTTGATATTTTAAGGAGTCTTGGCACC
258 TTAAAT-CCATTGTGATTGAGATTTCG-TAAGATTAATATAGATATTTTAAGGATTCTTGACACC
654 AAAAATCATGCAAA
321 AAAAATCATGCAAA
* * * *
668 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGTCAAAAACTGTGATGGTTAGTACACGATTTAGAC
1 ATTGAGTCGGGGCCCCGGAACGCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGAC
733 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
* * * * * *
798 ATATATATGATTCAATTCCAAAAAGATTTAAAGGCCTTTCACGCATCTAATATCCTTTTTCCTAT
131 ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCATCTAATATCGTTTTTCCTAT
* * *
863 TTTTCCTGAATTAATTTATAATTAAATCTAAATAAGATTTAAATGCTCGTAAAAACAAATCCTGA
196 TTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTA
* ** *
928 AATCCATTGTGATTGAGATTTTGTAAGATTAATATAGATATTTTAAGGATTCTCAACGCCAAAAA
261 AATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTTAAGGATTCTTGACACCAAAAA
993 TCATGCAAA
326 TCATGCAAA
* * *
1002 ATTGAGCCGGTGCCCCGGAACCCA--TT--G--------T-T-A---TTA-T--ACGATTTCGAC
1 ATTGAGTCGGGGCCCCGGAACGCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGAC
* * ** ** * * *
1047 TAAAATTTTGCAAAACTTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAATACTCATA--AA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
* * * * * * *
1110 AAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTTATGCTTCTAATAACGTTTTTCC-AT
131 ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCATCTAATATCGTTTTTCCTAT
* * * * *
1174 TATTTTCCGAATTAATTTCA-AATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAGAA-CC
196 T-TTTTCTGAATTAATTT-ATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACA-AATCC
*** * * * * * *
1237 TTAAATCCCA-TGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAGGAGTCTTGTA-ACC
258 TTAAAT-CCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTTAAGGATTCTTG-ACACC
1300 AAAAATCATGCAAA
321 AAAAATCATGCAAA
* *
1314 ATTGATTCGGGGCCCCGGAACGCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGAC
1 ATTGAGTCGGGGCCCCGGAACGCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGAC
*
1379 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCATTTTTTAGCCACAATACTAATATGGA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
*
1444 ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCATCTAATATCGTTTTTCCTAT
131 ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCATCTAATATCGTTTTTCCTAT
1509 TTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAATAA-AAATCCTT
196 TTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAA-AACAAATCCTT
* * ** *
1573 AAATACATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTCAACGCCAAAA
260 AAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTTAAGGATTCTTGACACCAAAA
1638 ATCATGCAAA
325 ATCATGCAAA
* * * *
1648 ATTGAGCCGGTGCCCCGGAACCCATTTTTAGCCAAAAAACTGTGATGGTTAGTACACGATTTCTG
1 ATTGAGTCGGGGCCCCGGAACGCATTTTCAGCC-AAAAACTGTGATGGTTAGTACACGATTTC-G
* ** ** ** *
1713 -CTAAAATTTTGCAAAAATTGACCCATAAGATTTTTCCTCAACTTTTAGCCACAATACTCAT-T-
64 ACTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATG
* * * * * * *
1775 AAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATCGTTTTTCC-
129 GAATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCATCTAATATCGTTTTTCCT
* * * * *
1839 ATTATTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
194 ATT-TTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCC
* * * * * * * *
1904 TTAAATCC-TTAAATCCCATTTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAGGAGTCT
258 TTAAATCCATT--GT--GA-TT----GAGATTTCGTAAGATTAATATAGATATTTTAAGGATTCT
*
1968 TGGCACCAAAAATCATGCAAA
314 TGACACCAAAAATCATGCAAA
* * * *
1989 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTATGATGGTTAGTACACGATTTCGGC
1 ATTGAGTCGGGGCCCCGGAACGCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGAC
2054 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
* * * *
2119 ATATATATGATTCAATTCCAAAAAGATTGAAAGGCCTTTCAAGCATCTAATATCGTTTTTCCTAT
131 ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCATCTAATATCGTTTTTCCTAT
* *
2184 TTTTTCTGAATTAATTTATAATTAAATCTAAATAAGATTTAAATGCTCGTAAAAACAAATCCTCA
196 TTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTA
* * * *
2249 AATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTC-TCAAACCCAATA
261 AATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTTAAGGATTCTTGACA-CCAAAA
2313 ATCATGCAAA
325 ATCATGCAAA
* * * * * *
2323 ATTGAGCCGGTGCCCCTGAACCCATTTTTAGCCAAGAAACTGTGATGGTTAGTACACAATTTCGA
1 ATTGAGTCGGGGCCCCGGAACGCATTTTCAGCCAA-AAACTGTGATGGTTAGTACACGATTTCGA
* ** ** *
2388 CTAAAATTTTGCAAAAATTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAATACTAATATGG
65 CTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGG
* * * *
2453 AATATATATTAGTCAATGCCAAAAAGATTGAAGGG-TTTATGATGCTTCTAATATCGTTTTTCC-
130 AATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTT-TCATGCATCTAATATCGTTTTTCCT
* * * * *
2516 ATTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
194 ATT-TTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCC
* * ** * * * *
2581 TTAAATCTCA-TGTAGCA--GAGATTTGGTTAGAAGAATTTTGATATTTTAAGGAGTCTTGAAAC
258 TTAAATC-CATTGT-G-ATTGAGATTTCGTAAGATTAATATAGATATTTTAAGGATTCTTGACAC
2643 CAAAAATCATGCAAA
320 CAAAAATCATGCAAA
* * *
2658 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGAC
1 ATTGAGTCGGGGCCCCGGAACGCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGAC
*
2723 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCATTTTTTAGCCACAATACTAATATGGA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
* *
2788 ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCATATAATATCGTTTTTCCTAT
131 ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCATCTAATATCGTTTTTCCTA-
*
2853 TTTTTTCTGAATTAATTTATAATTAAATCTAAATC-AGATTTAAATGCTCGTAAAAACAAATTCT
195 TTTTTTCTGAATTAATTTATAATTAAATCTAAA-CAAGATTTAAATGCTCGTAAAAACAAATCCT
* *
2917 CAAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTT
259 TAAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTTAAGGATTCTT
2973 ACCGCCAAAA
Statistics
Matches: 2196, Mismatches: 363, Indels: 156
0.81 0.13 0.06
Matches are distributed among these distances:
311 3 0.00
312 177 0.08
313 7 0.00
314 65 0.03
316 2 0.00
317 3 0.00
320 1 0.00
321 1 0.00
322 1 0.00
324 1 0.00
325 1 0.00
326 1 0.00
329 3 0.00
330 2 0.00
331 43 0.02
332 245 0.11
333 185 0.08
334 588 0.27
335 526 0.24
336 55 0.03
337 3 0.00
338 2 0.00
339 2 0.00
340 81 0.04
341 78 0.04
342 115 0.05
343 5 0.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (334 bp):
ATTGAGTCGGGGCCCCGGAACGCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTCGAC
TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCATCTAATATCGTTTTTCCTAT
TTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTTA
AATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTTAAGGATTCTTGACACCAAAAA
TCATGCAAA
Found at i:1647 original size:646 final size:654
Alignment explanation
Indices: 1--2984 Score: 4601
Period size: 646 Copynumber: 4.5 Consensus size: 654
* * * * *
1 ATTGAGTCGGGGCCCCGGAACGCGTTTTTATCCAAAAACTGTGATGGTTAGTACACGATTTCGGC
1 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGAC
* *
66 TAAAATTTTGCAGAAATTGAACTGTTTGATTTTTCTTCATTTTTTAGCCACAATACTAATATGGA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCATTTTTTAGCCACAATACTAATATGGA
* *
131 ATATATATGATTCAATTCCAAAAAGATTGAAAGGCCTTTCAAGCATCTAATATCGTTTTTCCTAT
131 ATATATATGATTCAATGCCAAAAAGATTGAAAGGCCTTTCACGCATCTAATATCGTTTTTCCTA-
* * *
196 TTTTTTCTGAATTAATTTATAATGAAATCTAAATAAGATTTAAATGCTCGTAAATACAAATCCTC
195 TTTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTC
* *
261 AAATACATTGTGATTGAGATTTCATAAGATTAATATAGATATTTCAAGGATTCTCAACGCCAAAA
260 AAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTCAACGCCAAAA
* *
326 ATCATGCAAAATGGAGCCGGTGCCCCGGAACCAATTTTTAGCCAAAAAACTGTGATGGTTAGTAC
325 ATCATGCAAAATTGAGCCGGTGCCCCGGAACCCA--TTTAG-------A-TGTGA--GTTAGTA-
*
391 ACGATTTCGGCTAAAATTTTGC-AAAATTGACCCATAAGATTTTTCCTCAATTTTTAGCCACAAT
377 ACGATTTCGACTAAAATTTTGCAAAAATTGACCCATAAGATTTTTCCTCAATTTTTAGCCACAAT
* * * *
455 ACTCATAAAAAACATATAATTCAACGCCAGAAATATTGAAGGGTTTTTGATGCTTATAATATCGT
442 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATCGT
* * * *
520 ATTTCCATTATTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGTTCGTAAAAAC
507 TTTTCCATTATTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* *
585 AAATCCTTAAATCCCATGTGGCAGAGATTTTGTTAAATGAATTTTGATATTTTAAGGAGTCTTGG
572 AAATCCTTAAATCCCATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAGGAGTCTTGG
*
650 CACCAAAAATCATGCAAA
637 AACCAAAAATCATGCAAA
*
668 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGTCAAAAACTGTGATGGTTAGTACACGATTTAGAC
1 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGAC
*
733 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCATTTTTTAGCCACAATACTAATATGGA
* * *
798 ATATATATGATTCAATTCCAAAAAGATTTAAAGGCCTTTCACGCATCTAATATCCTTTTTCCTAT
131 ATATATATGATTCAATGCCAAAAAGATTGAAAGGCCTTTCACGCATCTAATATCGTTTTTCCTAT
* * *
863 TTTTCCTGAATTAATTTATAATTAAATCTAAATAAGATTTAAATGCTCGTAAAAACAAATCCTGA
196 TTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTCA
* *
928 AATCCATTGTGATTGAGATTTTGTAAGATTAATATAGATATTTTAAGGATTCTCAACGCCAAAAA
261 AATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTCAACGCCAAAAA
993 TCATGCAAAATTGAGCCGGTGCCCCGGAACCCA-TT-G-T-T-A-TTA-T-ACGATTTCGACTAA
326 TCATGCAAAATTGAGCCGGTGCCCCGGAACCCATTTAGATGTGAGTTAGTAACGATTTCGACTAA
* *
1050 AATTTTGCAAAACTTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATA
391 AATTTTGCAAAAATTGACCCATAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATA
* *
1115 TATAATTCAACGCCAAAAAGATTGAAGGGTTTTTTATGCTTCTAATAACGTTTTTCCATTATTTT
456 TATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATCGTTTTTCCATTATTTT
* * *
1180 CCGAATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAGAA-CCTTAAATC
521 ACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA-AATCCTTAAATC
*
1244 CCATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAGGAGTCTTGTAACCAAAAATCAT
585 CCATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAGGAGTCTTGGAACCAAAAATCAT
1309 GCAAA
650 GCAAA
*
1314 ATTGATTCGGGGCCCCGGAACGCATTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGAC
1 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGAC
1379 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCATTTTTTAGCCACAATACTAATATGGA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCATTTTTTAGCCACAATACTAATATGGA
* *
1444 ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCATCTAATATCGTTTTTCCTAT
131 ATATATATGATTCAATGCCAAAAAGATTGAAAGGCCTTTCACGCATCTAATATCGTTTTTCCTAT
*
1509 TTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAATAA-AAATCCTT
196 TTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAA-AACAAATCCTC
*
1573 AAATACATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTCAACGCCAAAA
260 AAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTCAACGCCAAAA
1638 ATCATGCAAAATTGAGCCGGTGCCCCGGAACCCATTTTTAGCCAAAAAACTGTGATGGTTAGTAC
325 ATCATGCAAAATTGAGCCGGTGCCCCGGAACCCA--TTTAG-------A-TGTGA--GTTAGTA-
*
1703 ACGATTTCTG-CTAAAATTTTGCAAAAATTGACCCATAAGATTTTTCCTCAACTTTTAGCCACAA
377 ACGATTTC-GACTAAAATTTTGCAAAAATTGACCCATAAGATTTTTCCTCAATTTTTAGCCACAA
*
1767 TACTCATTAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATCG
441 TACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATCG
*
1832 TTTTTCCATTATTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
506 TTTTTCCATTATTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT---AA
*
1897 CAAATCCTTAAATCCTTAAATCCCATTTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAG
568 -AAA--C--AAATCCTTAAATCCCATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAG
*
1962 GAGTCTTGGCACCAAAAATCATGCAAA
628 GAGTCTTGGAACCAAAAATCATGCAAA
* * *
1989 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTATGATGGTTAGTACACGATTTCGGC
1 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGAC
*
2054 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTCATTTTTTAGCCACAATACTAATATGGA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCATTTTTTAGCCACAATACTAATATGGA
* *
2119 ATATATATGATTCAATTCCAAAAAGATTGAAAGGCCTTTCAAGCATCTAATATCGTTTTTCCTAT
131 ATATATATGATTCAATGCCAAAAAGATTGAAAGGCCTTTCACGCATCTAATATCGTTTTTCCTAT
*
2184 TTTTTCTGAATTAATTTATAATTAAATCTAAATAAGATTTAAATGCTCGTAAAAACAAATCCTCA
196 TTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTCA
*
2249 AATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTCAAAC-CCAATA
261 AATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTC-AACGCCAAAA
*
2313 ATCATGCAAAATTGAGCCGGTGCCCCTGAACCCATTTTTAGCCAAGAAACTGTGATGGTTAGTAC
325 ATCATGCAAAATTGAGCCGGTGCCCCGGAACCCA--TTT-----AG--A-TGTGA--GTTAGTA-
* *
2378 ACAATTTCGACTAAAATTTTGCAAAAATTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAAT
377 ACGATTTCGACTAAAATTTTGCAAAAATTGACCCATAAGATTTTTCCTCAATTTTTAGCCACAAT
* * * * * * *
2443 ACTAATATGGAATATATATTAGTCAATGCCAAAAAGATTGAAGGGTTTATGATGCTTCTAATATC
442 ACTCATA--AAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATC
*
2508 GTTTTTCCATTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
505 GTTTTTCCATTATTTTACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * *
2573 ACAAATCCTTAAATCTCATGTAGCAGAGATTTGGTTAGAAGAATTTTGATATTTTAAGGAGTCTT
570 ACAAATCCTTAAATCCCATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAGGAGTCTT
*
2638 GAAACCAAAAATCATGCAAA
635 GGAACCAAAAATCATGCAAA
2658 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGAC
1 ATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGAC
2723 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCATTTTTTAGCCACAATACTAATATGGA
66 TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCATTTTTTAGCCACAATACTAATATGGA
* * *
2788 ATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCATATAATATCGTTTTTCCTAT
131 ATATATATGATTCAATGCCAAAAAGATTGAAAGGCCTTTCACGCATCTAATATCGTTTTTCCTA-
*
2853 TTTTTTCTGAATTAATTTATAATTAAATCTAAATC-AGATTTAAATGCTCGTAAAAACAAATTCT
195 TTTTTTCTGAATTAATTTATAATTAAATCTAAA-CAAGATTTAAATGCTCGTAAAAACAAATCCT
* *
2917 CAAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTTACCGCCAAA
259 CAAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTCAACGCCAAA
2982 AAT
324 AAT
2985 TTTTTGGTTA
Statistics
Matches: 2155, Mismatches: 115, Indels: 91
0.91 0.05 0.04
Matches are distributed among these distances:
645 21 0.01
646 574 0.27
647 5 0.00
648 3 0.00
649 2 0.00
650 1 0.00
651 1 0.00
652 1 0.00
653 1 0.00
659 1 0.00
660 1 0.00
661 1 0.00
662 1 0.00
663 2 0.00
664 3 0.00
665 1 0.00
666 154 0.07
667 360 0.17
668 1 0.00
669 264 0.12
670 125 0.06
671 4 0.00
673 4 0.00
674 7 0.00
675 503 0.23
676 3 0.00
677 109 0.05
680 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (654 bp):
ATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAACTGTGATGGTTAGTACACGATTTAGAC
TAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCATTTTTTAGCCACAATACTAATATGGA
ATATATATGATTCAATGCCAAAAAGATTGAAAGGCCTTTCACGCATCTAATATCGTTTTTCCTAT
TTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATTTAAATGCTCGTAAAAACAAATCCTCA
AATCCATTGTGATTGAGATTTCGTAAGATTAATATAGATATTTCAAGGATTCTCAACGCCAAAAA
TCATGCAAAATTGAGCCGGTGCCCCGGAACCCATTTAGATGTGAGTTAGTAACGATTTCGACTAA
AATTTTGCAAAAATTGACCCATAAGATTTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATA
TATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATCGTTTTTCCATTATTTT
ACGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
CATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAGGAGTCTTGGAACCAAAAATCATG
CAAA
Found at i:2173 original size:675 final size:675
Alignment explanation
Indices: 1036--2984 Score: 3299
Period size: 675 Copynumber: 2.9 Consensus size: 675
1026 TTGTTATTAT
*
1036 ACGATTTCGACTAAAATTTTGCAAAACTTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAAT
1 ACGATTTCGACTAAAATTTTGCAAAAATTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAAT
* * *
1101 ACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTTATGCTTCTAATAACGT
66 ACTCATTAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATCGT
* *
1166 TTTTCCATTATTTTCCGAATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAAC
131 TTTTCCATTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
*
1231 --A-----GAA-CCTTAAATCCCATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAGG
196 AAATCCTTAAATCCTTAAATCCCATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAGG
* *
1288 AGTCTTGTAACCAAAAATCATGCAAAATTGATTCGGGGCCCCGGAACGCATTTTCAGCCAAAAAC
261 AGTCTTGAAACCAAAAATCATGCAAAATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAAC
1353 TGTGATGGTTAGTACACGATTTAGACTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCA
326 TGTGATGGTTAGTACACGATTTAGACTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCA
1418 TTTTTTAGCCACAATACTAATATGGAATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTT
391 TTTTTTAGCCACAATACTAATATGGAATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTT
1483 CACGCATCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATT
456 CACGCATCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATT
* *
1548 TAAATGCTCGTAAATAA-AAATCCTTAAATACATTGTGATTGAGATTTCGTAAGATTAATATAGA
521 TAAATGCTCGTAAA-AACAAATCCTCAAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGA
1612 TATTTCAAGGATTCTCAACGCCAAAAATCATGCAAAATTGAGCCGGTGCCCCGGAACCCATTTTT
585 TATTTCAAGGATTCTCAACGCCAAAAATCATGCAAAATTGAGCCGGTGCCCCGGAACCCATTTTT
1677 AGCCAAAAAACTGTGATGGTTAGTAC
650 AGCCAAAAAACTGTGATGGTTAGTAC
* *
1703 ACGATTTCTG-CTAAAATTTTGCAAAAATTGACCCATAAGATTTTTCCTCAACTTTTAGCCACAA
1 ACGATTTC-GACTAAAATTTTGCAAAAATTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAA
1767 TACTCATTAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATCG
65 TACTCATTAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATCG
**
1832 TTTTTCCATTATTTTATGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
130 TTTTTCCATTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
*
1897 CAAATCCTTAAATCCTTAAATCCCATTTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAG
195 CAAATCCTTAAATCCTTAAATCCCATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAG
**
1962 GAGTCTTGGCACCAAAAATCATGCAAAATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAA
260 GAGTCTTGAAACCAAAAATCATGCAAAATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAA
* * * *
2027 CTATGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCCTC
325 CTGTGATGGTTAGTACACGATTTAGACTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATC
* * *
2092 ATTTTTTAGCCACAATACTAATATGGAATATATATGATTCAATTCCAAAAAGATTGAAAGGCCTT
390 ATTTTTTAGCCACAATACTAATATGGAATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTT
* *
2157 TCAAGCATCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTATAATTAAATCTAAATAAGAT
455 TCACGCATCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTATAATTAAATCTAAACAAGAT
2222 TTAAATGCTCGTAAAAACAAATCCTCAAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGA
520 TTAAATGCTCGTAAAAACAAATCCTCAAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGA
* *
2287 TATTTCAAGGATTCTCAAAC-CCAATAATCATGCAAAATTGAGCCGGTGCCCCTGAACCCATTTT
585 TATTTCAAGGATTCTC-AACGCCAAAAATCATGCAAAATTGAGCCGGTGCCCCGGAACCCATTTT
*
2351 TAGCCAAGAAACTGTGATGGTTAGTAC
649 TAGCCAAAAAACTGTGATGGTTAGTAC
*
2378 ACAATTTCGACTAAAATTTTGCAAAAATTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAAT
1 ACGATTTCGACTAAAATTTTGCAAAAATTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAAT
* * * * * * *
2443 ACTAATATGGAATATATATTAGTCAATGCCAAAAAGATTGAAGGGTTTATGATGCTTCTAATATC
66 ACTCAT-T-AAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATC
2508 GTTTTTCCATTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
129 GTTTTTCCATTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* *
2573 ACAAATCCTTAAAT-C-----T--CATGTAGCAGAGATTTGGTTAGAAGAATTTTGATATTTTAA
194 ACAAATCCTTAAATCCTTAAATCCCATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAA
2630 GGAGTCTTGAAACCAAAAATCATGCAAAATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAA
259 GGAGTCTTGAAACCAAAAATCATGCAAAATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAA
2695 ACTGTGATGGTTAGTACACGATTTAGACTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCAT
324 ACTGTGATGGTTAGTACACGATTTAGACTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCAT
2760 CATTTTTTAGCCACAATACTAATATGGAATATATATGATTCAATGCCAAAAAGATTGAAGGGCTT
389 CATTTTTTAGCCACAATACTAATATGGAATATATATGATTCAATGCCAAAAAGATTGAAGGGCTT
*
2825 TTCACGCATATAATATCGTTTTTCCTATTTTTTTCTGAATTAATTTATAATTAAATCTAAATC-A
454 TTCACGCATCTAATATCGTTTTTCCTA-TTTTTTCTGAATTAATTTATAATTAAATCTAAA-CAA
*
2889 GATTTAAATGCTCGTAAAAACAAATTCTCAAATCCATTGTGATTGAGATTTCGTAAGATTAATAT
517 GATTTAAATGCTCGTAAAAACAAATCCTCAAATCCATTGTGATTGAGATTTCGTAAGATTAATAT
* *
2954 AGATATTTCAAGGATTCTTACCGCCAAAAAT
582 AGATATTTCAAGGATTCTCAACGCCAAAAAT
2985 TTTTTGGTTA
Statistics
Matches: 1205, Mismatches: 60, Indels: 31
0.93 0.05 0.02
Matches are distributed among these distances:
667 183 0.15
668 1 0.00
669 252 0.21
670 123 0.10
671 1 0.00
674 5 0.00
675 508 0.42
676 5 0.00
677 127 0.11
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (675 bp):
ACGATTTCGACTAAAATTTTGCAAAAATTGACCCATCAGATTTTTCCTCAATTTTTAGCCACAAT
ACTCATTAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTGATGCTTCTAATATCGT
TTTTCCATTATTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
AAATCCTTAAATCCTTAAATCCCATGTGGCAGAGATTTGGTTAGATGAATTTTGATATTTTAAGG
AGTCTTGAAACCAAAAATCATGCAAAATTGATTCGGGGCCCCGGAACGCGTTTTCAGCCAAAAAC
TGTGATGGTTAGTACACGATTTAGACTAAAATTTTGCAAAAATTGAACTGTTTGATTTTTCATCA
TTTTTTAGCCACAATACTAATATGGAATATATATGATTCAATGCCAAAAAGATTGAAGGGCTTTT
CACGCATCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTTATAATTAAATCTAAACAAGATT
TAAATGCTCGTAAAAACAAATCCTCAAATCCATTGTGATTGAGATTTCGTAAGATTAATATAGAT
ATTTCAAGGATTCTCAACGCCAAAAATCATGCAAAATTGAGCCGGTGCCCCGGAACCCATTTTTA
GCCAAAAAACTGTGATGGTTAGTAC
Found at i:4685 original size:21 final size:21
Alignment explanation
Indices: 4659--4702 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
4649 TTATGTGGCG
4659 CACTCACCTTGAACATTACCT
1 CACTCACCTTGAACATTACCT
*
4680 CACTCACCTTGAACCTTACCT
1 CACTCACCTTGAACATTACCT
4701 CA
1 CA
4703 ACATAACCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.41, G:0.05, T:0.27
Consensus pattern (21 bp):
CACTCACCTTGAACATTACCT
Found at i:6855 original size:28 final size:28
Alignment explanation
Indices: 6824--6887 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
6814 AAAAGGTCTT
* *
6824 ATAAAA-TCAATCAATTTCGCAGGTTCCA
1 ATAAAACT-AATCAAATTCCCAGGTTCCA
* *
6852 ATAAAACTTATGAAATTCCCAGGTTCCA
1 ATAAAACTAATCAAATTCCCAGGTTCCA
6880 ATAAAACT
1 ATAAAACT
6888 TATGAATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.28
Consensus pattern (28 bp):
ATAAAACTAATCAAATTCCCAGGTTCCA
Found at i:6888 original size:28 final size:28
Alignment explanation
Indices: 6843--6899 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
6833 ATCAATTTCG
6843 CAGGTTCCAATAAAACTTATGAAATTCC
1 CAGGTTCCAATAAAACTTATGAAATTCC
*
6871 CAGGTTCCAATAAAACTTATGAATTTCC
1 CAGGTTCCAATAAAACTTATGAAATTCC
6899 C
1 C
6900 TAATCACCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.30
Consensus pattern (28 bp):
CAGGTTCCAATAAAACTTATGAAATTCC
Found at i:7150 original size:2 final size:2
Alignment explanation
Indices: 7145--7171 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7135 GGAAAGGGGG
7145 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
7172 TTGTTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:15156 original size:45 final size:46
Alignment explanation
Indices: 15090--15222 Score: 182
Period size: 45 Copynumber: 3.0 Consensus size: 46
15080 ATTACTTCTT
* * *
15090 CAGCTTATCATTAATCCGGGGTAGGGATGTTTTAGTAATTCCACCA
1 CAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCACCA
* * *
15136 -AGCTCATCACTAATTCGGGGTATGGATCTTTTAGTAATTCC-GCA
1 CAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCACCA
*
15180 CAGCTCATCATTAATTC-GGGTAGGGATCTTTTAGCAATTCCAC
1 CAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
15223 TACTCTATTA
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 24 0.32
45 51 0.68
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (46 bp):
CAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCACCA
Found at i:39606 original size:135 final size:134
Alignment explanation
Indices: 39445--39700 Score: 476
Period size: 135 Copynumber: 1.9 Consensus size: 134
39435 TGAACAGGTG
*
39445 AACCCTAAACATAGTGATGCATTTATATAGGATTTGGAATAAGAAATCTCCAAAAACCCAAAAGG
1 AACCCTAAACATAGTGATGCATTTATATAGGATTTGAAATAAGAAATCTCCAAAAACCCAAAA-G
39510 TAAATTAATGAAAGTTTGAGAGAAGTAAGGGTGTTTAGTAATTTCACCATGAACTTTATGTGTTT
65 TAAATTAATGAAAGTTTGAGAGAAGTAAGGGTGTTTAGTAATTTCACCATGAACTTTATGTGTTT
39575 TTATT
130 TTATT
* *
39580 AACCCTAAACATAGTGATGCCTTTATATAGGATTTGAAATAAGAAATCTCCAAAAACCTAAAAGT
1 AACCCTAAACATAGTGATGCATTTATATAGGATTTGAAATAAGAAATCTCCAAAAACCCAAAAGT
39645 AAATTAATGAAAGTTTGAGAGAAGTAAGGGTGTTTAGTAATTTCACCATGAACTTT
66 AAATTAATGAAAGTTTGAGAGAAGTAAGGGTGTTTAGTAATTTCACCATGAACTTT
39701 CCCAAAAACC
Statistics
Matches: 118, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
134 58 0.49
135 60 0.51
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (134 bp):
AACCCTAAACATAGTGATGCATTTATATAGGATTTGAAATAAGAAATCTCCAAAAACCCAAAAGT
AAATTAATGAAAGTTTGAGAGAAGTAAGGGTGTTTAGTAATTTCACCATGAACTTTATGTGTTTT
TATT
Found at i:39820 original size:77 final size:77
Alignment explanation
Indices: 39630--39856 Score: 399
Period size: 77 Copynumber: 3.0 Consensus size: 77
39620 AAGAAATCTC
* *
39630 CAAAAACCTAAAA-GTAAATTAATGAAAGTTTGAGAGAAGTAAGGGTGTTTAGTAATTTCACCAT
1 CAAAAACCCAAAAGGTAAATTAATGAAAGTTTGAGAGAAGTAAGTGTGTTTAGTAATTTCACCAT
*
39694 GAACTTTC---C
66 GAACTTTCTGTG
39703 CAAAAACCCAAAAGGTAAATTAATGAAAGTTTGAGAGAAGTAAGTGTGTTTAGTAATTTCACCAT
1 CAAAAACCCAAAAGGTAAATTAATGAAAGTTTGAGAGAAGTAAGTGTGTTTAGTAATTTCACCAT
39768 GAACTTTCTGTG
66 GAACTTTCTGTG
39780 CAAAAACCCAAAAGGTAAATTAATGAAAGTTTGAGAGAAGTAAGTGTGTTTAGTAATTTCACCAT
1 CAAAAACCCAAAAGGTAAATTAATGAAAGTTTGAGAGAAGTAAGTGTGTTTAGTAATTTCACCAT
39845 GAACTTTCTGTG
66 GAACTTTCTGTG
39857 TTTTTATTAA
Statistics
Matches: 147, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
73 12 0.08
74 58 0.39
77 77 0.52
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (77 bp):
CAAAAACCCAAAAGGTAAATTAATGAAAGTTTGAGAGAAGTAAGTGTGTTTAGTAATTTCACCAT
GAACTTTCTGTG
Found at i:54208 original size:7 final size:7
Alignment explanation
Indices: 54196--54224 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
54186 ACCCGCTAAA
54196 TTCTTTT
1 TTCTTTT
54203 TTCTTTT
1 TTCTTTT
54210 TTC-TTT
1 TTCTTTT
54216 TTCTTTT
1 TTCTTTT
54223 TT
1 TT
54225 TTAACTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTCTTTT
Found at i:54218 original size:13 final size:13
Alignment explanation
Indices: 54200--54224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54190 GCTAAATTCT
54200 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
54213 TTTTTCTTTTTT
1 TTTTTCTTTTTT
54225 TTAACTTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:56394 original size:2 final size:2
Alignment explanation
Indices: 56389--56418 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
56379 TTTAATAACT
*
56389 TA TA TA TA TA CA 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
56419 CCCACCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:59483 original size:19 final size:20
Alignment explanation
Indices: 59438--59483 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
59428 AGTGATCAGC
* *
59438 TTCTTTTGTTCTTTTTCCTT
1 TTCTTTTGTTATTTTTACTT
59458 TGT-TTTT-TTATTTTTACTT
1 T-TCTTTTGTTATTTTTACTT
59477 TTCTTTT
1 TTCTTTT
59484 AATCTAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 1 0.05
19 15 0.68
20 5 0.23
21 1 0.05
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.78
Consensus pattern (20 bp):
TTCTTTTGTTATTTTTACTT
Found at i:60555 original size:44 final size:44
Alignment explanation
Indices: 60492--60637 Score: 220
Period size: 44 Copynumber: 3.2 Consensus size: 44
60482 AGTCTTAGAG
60492 AGGATTTACAGTAGTATTTACAGATCATCCACCAATGAGGATCA
1 AGGATTTACAGTAGTATTTACAGATCATCCACCAATGAGGATCA
*
60536 AGGATTTACAGTAGTATTTACAGATCATCCACCAATGAGAATCA
1 AGGATTTACAGTAGTATTTACAGATCATCCACCAATGAGGATCA
* * * *
60580 GTAAGACTCTACGGTAGTATTTACAGATCATCCACCAATGAAGATCA
1 --AGGA-TTTACAGTAGTATTTACAGATCATCCACCAATGAGGATCA
60627 AGGATTTACAG
1 AGGATTTACAG
60638 ATCATCCACC
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
44 48 0.53
45 3 0.03
46 3 0.03
47 36 0.40
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (44 bp):
AGGATTTACAGTAGTATTTACAGATCATCCACCAATGAGGATCA
Found at i:78623 original size:147 final size:147
Alignment explanation
Indices: 78356--78657 Score: 604
Period size: 147 Copynumber: 2.1 Consensus size: 147
78346 AACGACCTTC
78356 CACCTGCAGTATGAAATTTGATTGGAGGTGGCTTGGGGACTGAATCAAATATTTCAGAATGCAGC
1 CACCTGCAGTATGAAATTTGATTGGAGGTGGCTTGGGGACTGAATCAAATATTTCAGAATGCAGC
78421 GGTGTTGAGCCACTTTCTCTGGCTAGTGTACTTCCTACTAAACTATTCCCAGAGTTTAACAAGTG
66 GGTGTTGAGCCACTTTCTCTGGCTAGTGTACTTCCTACTAAACTATTCCCAGAGTTTAACAAGTG
78486 CCTTGGTTCTGATGCGA
131 CCTTGGTTCTGATGCGA
78503 CACCTGCAGTATGAAATTTGATTGGAGGTGGCTTGGGGACTGAATCAAATATTTCAGAATGCAGC
1 CACCTGCAGTATGAAATTTGATTGGAGGTGGCTTGGGGACTGAATCAAATATTTCAGAATGCAGC
78568 GGTGTTGAGCCACTTTCTCTGGCTAGTGTACTTCCTACTAAACTATTCCCAGAGTTTAACAAGTG
66 GGTGTTGAGCCACTTTCTCTGGCTAGTGTACTTCCTACTAAACTATTCCCAGAGTTTAACAAGTG
78633 CCTTGGTTCTGATGCGA
131 CCTTGGTTCTGATGCGA
78650 CACCTGCA
1 CACCTGCA
78658 ACTCCATTAC
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 155 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (147 bp):
CACCTGCAGTATGAAATTTGATTGGAGGTGGCTTGGGGACTGAATCAAATATTTCAGAATGCAGC
GGTGTTGAGCCACTTTCTCTGGCTAGTGTACTTCCTACTAAACTATTCCCAGAGTTTAACAAGTG
CCTTGGTTCTGATGCGA
Found at i:83213 original size:6 final size:6
Alignment explanation
Indices: 83204--83232 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
83194 TGAATGACCA
83204 CCAAAC CCAAAC CCAAAC CCAAAC CCAAA
1 CCAAAC CCAAAC CCAAAC CCAAAC CCAAA
83233 GGTACTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAAAC
Found at i:92977 original size:24 final size:24
Alignment explanation
Indices: 92949--92997 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
92939 AGCATATATA
92949 ATCTGTTAAAAGACATGGGATTTC
1 ATCTGTTAAAAGACATGGGATTTC
92973 ATCTGTTAAAAGACATGGGATTTC
1 ATCTGTTAAAAGACATGGGATTTC
92997 A
1 A
92998 GATGCTACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (24 bp):
ATCTGTTAAAAGACATGGGATTTC
Found at i:109008 original size:13 final size:13
Alignment explanation
Indices: 108986--109017 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
108976 TCAAAATGCA
*
108986 ATTTGTGCATTCC
1 ATTTGGGCATTCC
108999 ATTTGGGCATTCC
1 ATTTGGGCATTCC
109012 ATTTGG
1 ATTTGG
109018 CATCCAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (13 bp):
ATTTGGGCATTCC
Found at i:112899 original size:28 final size:27
Alignment explanation
Indices: 112836--112900 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 27
112826 ATTTCTGGAA
112836 AATAAGGGAAAAGAACAATTAAAAAAG
1 AATAAGGGAAAAGAACAATTAAAAAAG
* *
112863 AAACAAGGGAAAAGAACAATTAAAAAGG
1 -AATAAGGGAAAAGAACAATTAAAAAAG
112891 AATAGAGGGA
1 AATA-AGGGA
112901 GTATTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 3 0.09
28 30 0.91
ACGTcount: A:0.63, C:0.05, G:0.23, T:0.09
Consensus pattern (27 bp):
AATAAGGGAAAAGAACAATTAAAAAAG
Found at i:124996 original size:6 final size:6
Alignment explanation
Indices: 124980--125009 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
124970 TGCTCAGGCC
*
124980 AGGCAG TGGCAG AGGCAG AGGCAG AGGCAG
1 AGGCAG AGGCAG AGGCAG AGGCAG AGGCAG
125010 GCCACTCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.50, T:0.03
Consensus pattern (6 bp):
AGGCAG
Found at i:141885 original size:9 final size:9
Alignment explanation
Indices: 141873--141897 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
141863 GTTTGCTACT
141873 GCTGCTGCA
1 GCTGCTGCA
141882 GCTGCTGCA
1 GCTGCTGCA
141891 GCTGCTG
1 GCTGCTG
141898 GAGTTTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (9 bp):
GCTGCTGCA
Found at i:144571 original size:32 final size:31
Alignment explanation
Indices: 144529--144588 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
144519 TTTTTCCTTT
**
144529 CTTTCCTTTGCTGTGCCTGTAATAAAATTGTC
1 CTTTCCTTTGCTGT-AATGTAATAAAATTGTC
*
144561 CTTTCTTTTGCTGTAATGTAATAAAATT
1 CTTTCCTTTGCTGTAATGTAATAAAATT
144589 TGTAATCAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (31 bp):
CTTTCCTTTGCTGTAATGTAATAAAATTGTC
Done.