Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015402.1 Corchorus olitorius cultivar O-4 contig15435, 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: 56656
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:693 original size:330 final size:327
Alignment explanation
Indices: 1--3008 Score: 2150
Period size: 330 Copynumber: 9.3 Consensus size: 327
* * * *
1 AATATAGATATTTCAGTGAGTCTTGGCGCCAAAAATCATACAAAACTGAG-TCGGGGCCTCGGAA
1 AATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCT-GGGGCCCCGGAA
* * ** * *
65 CGCGTTATTAGCC-AAAAGTCGTGATCATTAGTACACGGATTTCGGCTAAAATTTTTCAAAATCT
65 CGCGTTTTTAGCCAAAAACT-GTGATGGTTAGTACAC-GATTTCGGC-AAAATTTTGCAAAAACT
* * * * * * * *
129 AACCCGAAAAACTTTTCCT--TTTTTTTGCTACAATACTGGTAAAAAATATATAATTCAATGCTT
127 GACCCGAAAAATTTTTCCTCAATTTTTT-CCACAATACTCGTAAAAATTATA-AATTCAACGC-C
* * * *
192 AAAAA-ATTGAAGGGCTTTGCACGCTTCTAATATCGTTTTTCTT-TTTTT------T--TTTTTC
189 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCCGAAATAATTTCTA
** * *
247 CGAAAT--AAATTGGTTCTCTGATACTCGTAAAAACAAATTCTTAAAT-CAATGTTG-TTGAGAT
254 ATAAATCGAAATTGGTT-TCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCTT-AGAT
308 TTGGTCAGATG
317 TTGGTCAGATG
* * * * *
319 AATATAGATATTTAAATGAGTCTTGGCGTCAAAAATCATGCAAAACTGAGCTGGCGCCTCGGAAC
1 AATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCGGAAC
*
384 GCGTTTTTA-CCAAAAACTGTGATGGTTAGTACACGATTTTGGCAAATATTTTGCAAAAACTGAC
66 GCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCAAA-ATTTTGCAAAAACTGAC
*
448 CCGAAAAATTTTTCCTGAATCTTTTTCCACAATACTCGTAAAAATTATAAATATCAACGCCAAAA
130 CCGAAAAATTTTTCCTCAAT-TTTTTCCACAATACTCGTAAAAATTATAAAT-TCAACGCCAAAA
* * *
513 ATATTGAAAGGCTTTTCACGCTTCTAATATCATTTTTCTTATTTTTCCGAAATAATTTCTGATCA
193 AGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCCGAAATAATTTCTAAT-A
** * * *
578 AATCGAAATTGGTTTCTGATGCTCGTAAAAATGAATCCTTACATACAATGATGCTTAGATTTGGT
257 AATCGAAATTGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCTTAGATTTGGT
*
643 AAGATG
322 CAGATG
* * * *
649 AATATAGATATTTCAATGAGTCCTGACACCAAAAATCTTGCAAAACTGAGCTGGGGCCACGGAAC
1 AATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCGGAAC
*
714 GCGTTTTTA-CCAAAAACTGTGATGGTTAGTACACGATTTTGGCTAAAATTTTGCAAAAACTGAC
66 GCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGC-AAAATTTTGCAAAAACTGAC
** * * * *
778 CCG-AAAATATTTTCCTCAATCTCCTTCCACAATACTCATAAAAATTATAAATATTAACTCCATA
130 CCGAAAAAT-TTTTCCTCAAT-TTTTTCCACAATACTCGTAAAAATTATAAAT-TCAACGCCAAA
* **
842 AAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCCTAAATAAAATCTAATT
192 AAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCCGAAATAATTTCTAA-T
* * * *
907 AAATCAAAATCGGTTCTCTGATACTCGTAAAAACAAATTCTTAAAT-CAATGTTG-TTGAGATTT
256 AAATCGAAATTGGTT-TCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCTT-AGATTT
**
970 GGTTGGATG
319 GGTCAGATG
* * * * * * * * *
979 AATATAGATATTTCTATTAGTCTTGTCGCCAAAAAACATGCGAAATTAAGCTGGGACCCCGGAAT
1 AATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCGGAAC
* ** * * * *** *
1044 GCCTTTTTAATCAAAAACCGTGATGGTTAGTACAAGATTTCAGCAAATATTTCAAAAAAAAATGA
66 GCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCAAA-ATTT-TGCAAAAACTGA
* * * * * *
1109 CCTG-AATATATTTTCATTAATTTTTGGCCA-AA-A----T----A-TAT-AATTCAACGCCATA
129 CCCGAAAAAT-TTTTCCTCAATTTTT-TCCACAATACTCGTAAAAATTATAAATTCAACGCCAAA
* * * * * * * *
1161 AAGGTTGAAGGGTTTTTCTCGCTTCTGATATTGTTTTTCTTA-ATTTCCTG-AATTATATTCTAA
192 AAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCC-GAAATAAT-TTCT-A
* ** * * * * *
1224 ATAAATCGATATTTATTTCTGATGCTCATAAAAACAAATTCTTAAATCCATTTTTGCTGAGATTT
254 ATAAATCGAAATTGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCTTAGA-TT
*
1289 TGGTTAGATG
318 TGGTCAGATG
* * * * * *
1299 AATATAGATATTTCAATGAGCCATGGCGTCAAAAATCATGCGAAACTGAG-TCGGCGCCCCCGGA
1 AATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCT-GG-GGCCCCGGA
** * * *
1363 ACGCGTTAGTCGCCAAAAA--GTG-T-G--ACGTACACGATTGCGGCTAAAATTTTGTAAAAACT
64 ACGCGTTTTTAGCCAAAAACTGTGATGGTTA-GTACACGATTTCGGC-AAAATTTTGCAAAAACT
* ** * * ** **
1422 AATTCTAAAAACTTTTCCTCAATCCCTTGGCACAATACTCGTCAAAAA-TATATAATTCAACGCC
127 GACCCGAAAAATTTTTCCTCAAT-TTTTTCCACAATACTCGT-AAAAATTATA-AATTCAACGCC
* * *
1486 AAAAAGATTGAAAGACTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCTGAATTAATTT-TA
189 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCCGAAATAATTTCT-
** * *
1550 AATTAAATCGAAAACGGTTTCTGATGGTCGTAAAAACAAATCCTTAAATCCAATGTTGCTGAGAT
253 AA-TAAATCGAAATTGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCTTAGAT
* * *
1615 TTTGTCATATA
317 TTGGTCAGATG
* *
1626 AATATAGATATTTCAACGAGTCTTGACGCCAAAAATCATGCAAAACTGAG-TCAGGGCCCCGGAA
1 AATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCT-GGGGCCCCGGAA
** * * ** * * ** *
1690 CGCGTTACTAGCCAAAAATTGTGATGGTTAGTATATAATAATTTTGGTTAAAATTTTTTAAAAAT
65 CGCGTTTTTAGCCAAAAACTGTGATGGTTAG--TA-CACGATTTCGG-CAAAATTTTGCAAAAAC
* ** * *** *
1755 TGACTCGAAAAATTTTTCCTCAATTTTTTCCACAATACAGGTAAAAAAATATATAAGAAAACGCA
126 TGACCCGAAAAATTTTTCCTCAATTTTTTCCACAATACTCGT-AAAAATTATA-AATTCAACGCC
* * * * * * *
1820 AAAAAGATTGCAGGGCTTTTCACACTTCTAAAATTGTTTTCCTCTT-TTTTTCCGAATTAATTTG
189 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTT--TCTTATTTTTCCGAAATAATTTC
* * * *** *
1884 TAATTAAGTCGAAACCT-GTTTC-GGTGCTCGTTTCAA-AAATCCTTAAATCCAATGTTGCTGAG
252 TAA-TAAATCGAAA-TTGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCTTAG
* *
1946 ATTTTGTCGGATG
315 ATTTGGTCAGATG
* * * *
1959 AATATAGATATTCCAGTGAGTCTTGGA-ACCAAAAATCATGCAAAACTGAGAC-GGGGCCCGGGA
1 AATATAGATATTTCAATGAGTCTT-GACGCCAAAAATCATGCAAAACTGAG-CTGGGGCCCCGGA
** * * * * *
2022 ACGCGTAATTAGTCAAAAA-TCGTAATGGCTACTACACGATTTCGGCTAATACTTTT-CAAAAAC
64 ACGCGTTTTTAGCCAAAAACT-GTGATGGTTAGTACACGATTTCGGC-AA-AATTTTGCAAAAAC
* * * ** * * *
2085 TAACACGAAAAATTTTTACT-GTTTTTTTGCTACAATACTAGTAAAAGAATATATAATTCAACGC
126 TGACCCGAAAAATTTTTCCTCAATTTTTT-CCACAATACTCGTAAAA-ATTATA-AATTCAACGC
* * * ** *
2149 TAAAAA-ATTGAAGGGCTTTGCACGCTTCTAATATCGTTTACCCTT-TTTTTCC-AAATTACTTT
188 CAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTT-TTCTTATTTTTCCGAAA-TAATTT
* ** * * **
2211 GTAAATAAATCGAAA-CCGATTATGAATGCTCGTAAAAACAAATCCTTAAATCCAATGTTAATTG
251 CT-AATAAATCGAAATTGGTTTCTG-ATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCTT-
* *
2275 AGATTTGGTAATAAGAATATATATATAT
313 AGATTTGG---TCAG---------AT-G
* * * * ** *
2303 ATATATATATATTTCAATGAGTCTT-AGTGCCAAAAAT-AAGCAAAACTGAGCCGGGGATCTGGA
1 A-ATATAGATATTTCAATGAGTCTTGA-CGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCGGA
** * *
2366 ACGCGTTTTTAGCCAAAAA-TCGTGA----T-GTACAAAATTTCGACAATAATTTTGCAAAAAAT
64 ACGCGTTTTTAGCCAAAAACT-GTGATGGTTAGTACACGATTTCGGCAA-AATTTTGCAAAAACT
** ** * * * * *
2425 GGA-CCGAAAGTTTTTTCCTCAATTTATGACCAAAATACTCATGAAAATGTAT-AATGCAACGTC
127 -GACCCGAAAAATTTTTCCTCAATTT-TTTCCACAATACTCGTAAAAAT-TATAAATTCAACGCC
*
2488 AAAAAGATTGAAAGGCTTTTCACGCTTCT-A-ATCATTTTTCTTATTTTTCCG----AA----T-
189 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCCGAAATAATTTCTA
* *
2542 -T--A--G----T--TTT-TGATGCTCGTAAAAATAAATCCTTAAATCCAATGTTGCTGAGATTT
254 ATAAATCGAAATTGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCTTAGATTT
* * *
2595 AGTAAGATA
319 GGTCAGATG
* * * * *
2604 AATATAGATATTTCAATGAGTCTTGCCACTAAAAATCATGCAAAACTGAACTGGGGCCCCGGAAA
1 AATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCGGAAC
* * * *
2669 GCGTTTTTA-CCAAAAACTGTGA----CAATACACGATTTTGGCTAAAATTTTGCAAAAATTGAC
66 GCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGC-AAAATTTTGCAAAAACTGAC
* * *
2729 CCG-AAAA--TTT--T---TTTTTTCCACAATACTCGTCAATATTATGAATATCAACGCCAAAAA
130 CCGAAAAATTTTTCCTCAATTTTTTCCACAATACTCGTAAAAATTATAAAT-TCAACGCCAAAAA
* *
2786 GAATGAAAGGCTTTTCACGCTTCTAATATCGTTTCTT-TTATTTTTCCGAAATAATTTTTAATTA
194 GATTGAAAGGCTTTTCACGCTTCTAATATCGTTT-TTCTTATTTTTCCGAAATAATTTCTAA-TA
** ** * * *
2850 AATCGAAATCAGTTTCTGATGCTCGTAAAAACAAATTTTTAAATCCAACGTT-ATTGAGATTTAG
257 AATCGAAATTGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCTT-AGATTTGG
2914 TCAGATG
321 TCAGATG
* * *
2921 AATATAGATATTTCAATGAGTCTTTGA-GCCAAAAATCATGTAAAAGTGAGCTGGGGCCCCGTAA
1 AATATAGATATTTCAATGAGTC-TTGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCGGAA
* *
2985 CGCGCTTTTAGCCAAAAATTGTGA
65 CGCGTTTTTAGCCAAAAACTGTGA
3009 CATACACAAC
Statistics
Matches: 2151, Mismatches: 388, Indels: 302
0.76 0.14 0.11
Matches are distributed among these distances:
291 3 0.00
292 19 0.01
293 37 0.02
294 1 0.00
295 17 0.01
296 3 0.00
298 3 0.00
299 2 0.00
300 44 0.02
301 59 0.03
302 4 0.00
303 1 0.00
306 1 0.00
308 1 0.00
310 1 0.00
311 4 0.00
314 7 0.00
315 57 0.03
316 66 0.03
317 137 0.06
318 186 0.09
319 83 0.04
320 60 0.03
321 24 0.01
322 2 0.00
324 1 0.00
325 1 0.00
326 31 0.01
327 68 0.03
328 136 0.06
329 91 0.04
330 434 0.20
331 83 0.04
332 30 0.01
333 132 0.06
334 99 0.05
335 33 0.02
336 8 0.00
337 13 0.01
338 22 0.01
339 52 0.02
340 20 0.01
341 1 0.00
343 4 0.00
344 42 0.02
345 28 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (327 bp):
AATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCTGGGGCCCCGGAAC
GCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCAAAATTTTGCAAAAACTGACC
CGAAAAATTTTTCCTCAATTTTTTCCACAATACTCGTAAAAATTATAAATTCAACGCCAAAAAGA
TTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCCGAAATAATTTCTAATAAATC
GAAATTGGTTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTTGCTTAGATTTGGTCAGA
TG
Found at i:1522 original size:647 final size:643
Alignment explanation
Indices: 1--3002 Score: 1866
Period size: 647 Copynumber: 4.6 Consensus size: 643
* * * *
1 AATATAGATATTTCAGTGAGTCTTGGCGCCAAAAATCATACAAAACTGAGTCGGGGCCTCGGAAC
1 AATATAGATATTTCAATGAG-CCTGGCGCCAAAAATCATGCAAAACTGAGTCGGGGCCACGGAAC
*
66 GCGTTATTAGCC-AAAAGTCGTGATCATTAGTACACGGATTTCGGCTAAAATTTT-TCAAAATCT
65 GCGTTATTAGCCAAAAAGT-GTGA-C----GTACAC-GATTTCGGCTAAAATTTTGT-AAAAACT
* *** * * *
129 AACCCGAAAAACTTTTCCT--TTTTTTTGCTACAATACTGGTAAAAAATATATAATTCAATGCTT
122 AACCCGAAAAACTTTTCCTCAATCCCTTGC-ACAATACTCGT-AAAAATATATAATTCAACGC-C
* * ****
192 AAAAA-ATTGAAGGGCTTTGCACGCTTCTAATATCGTTTTTCTT-TTTTT-T--T--TTTTCCGA
184 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCTAATAATTTAATTA
*
250 AAT--AAATTGGTTCTCTGATACTCGTAAAAACAAATTCTTAAATCAATGTTGTTGAGATTTGGT
249 AATCAAAATCGGTTCTCTGATACTCGTAAAAACAAATTCTTAAATCAATGTTGTTGAGATTTGGT
* * * * *
313 CAGATGAATATAGATATTTAAATGAGTCTTGGCGTCAAAAATCATGCAAAACTGAGCTGGCGCCT
314 CAGATGAATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTAAGCTGGCGCCC
* * * ** ***
378 CGGAACGCGTTTTTACCAAAAACTGTGATGGTTAGTACACGATTTTGGCAAATATTTTGCAAAAA
379 CGGAACGCCTTTTTACCAAAAACCGTGATGGTTAGTACAAGATTTCAGCAAATATTTAAAAAAAA
* * *
443 CTGACCCGAAAAATTTTTCCTGAATCTTTTTCCACAATACTCGTAAAAATTATAAATATCAACGC
444 ATGACCCGAAAAATTTTTCATGAATCTTTTGCCACAATA--C-T---AATTATAAATATCAACGC
* *
508 CAAAAATATTGAAAGGCTTTTCACGCTTCTAATATCATTTTTCTTATTTTTCCGAAATAATTTCT
503 CAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCATTTTTCTTATATTTCCGAAATAATTTCT
* * * ** * *
573 GATCAAATCGAAATTGGTTTCTGATGCTCGTAAAAATGAATCCTTACATACAATGATGCTTAGAT
568 AATCAAATCGAAATTGATTTCTGATGCTCATAAAAACAAATCCTTAAATACAATGATGCTGAGAT
638 TTGGTAAGATG
633 TTGGTAAGATG
* * *
649 AATATAGATATTTCAATGAGTCCTGACACCAAAAATCTTGCAAAACTGAG-CTGGGGCCACGGAA
1 AATATAGATATTTCAATGAG-CCTGGCGCCAAAAATCATGCAAAACTGAGTC-GGGGCCACGGAA
* * * *
713 CGCGTTTTTA-CCAAAAACTGTGATGGTTA-GTACACGATTTTGGCTAAAATTTTGCAAAAACTG
64 CGCGTTATTAGCCAAAAA--GTG-T-G--ACGTACACGATTTCGGCTAAAATTTTGTAAAAACTA
* * * *
776 ACCCGAAAATA-TTTTCCTCAATCTCCTTCCACAATACTCATAAAAAT-TATAAATATTAACTCC
123 ACCCGAAAA-ACTTTTCCTCAATC-CCTTGCACAATACTCGTAAAAATATAT-AAT-TCAACGCC
* *
839 ATAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCCTAAATAAAATCTA
184 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTT-CT-AAT--AATTTA
904 ATTAAATCAAAATCGGTTCTCTGATACTCGTAAAAACAAATTCTTAAATCAATGTTGTTGAGATT
245 ATTAAATCAAAATCGGTTCTCTGATACTCGTAAAAACAAATTCTTAAATCAATGTTGTTGAGATT
** * * * * * *
969 TGGTTGGATGAATATAGATATTTCTATTAGTCTTGTCGCCAAAAAACATGCGAAATTAAGCTGG-
310 TGGTCAGATGAATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTAAGCTGGC
* *
1033 GACCCCGGAATGCCTTTTTAATCAAAAACCGTGATGGTTAGTACAAGATTTCAGCAAATATTTCA
375 G-CCCCGGAACGCCTTTTT-ACCAAAAACCGTGATGGTTAGTACAAGATTTCAGCAAATATTT-A
* * *
1098 AAAAAAAATGACCTG-AATATATTTTCATTAAT-TTTTGGCCA-AA-A-T-A-TAT-AAT-TCAA
437 AAAAAAAATGACCCGAAAAAT-TTTTCATGAATCTTTT-GCCACAATACTAATTATAAATATCAA
* * * * * * ** *
1154 CGCCATAAAGGTTGAAGGGTTTTTCTCGCTTCTGATATTGTTTTTCTTA-ATTTCCTG-AATTAT
500 CGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCATTTTTCTTATATTTCC-GAAATAAT
* * * * * **
1217 ATTCTAAAT-AAATCGATATTTATTTCTGATGCTCATAAAAACAAATTCTTAAATCCATTTTTGC
564 -TTCT-AATCAAATCGAAATTGATTTCTGATGCTCATAAAAACAAATCCTTAAATACAATGATGC
*
1281 TGAGATTTTGGTTAGATG
627 TGAGA-TTTGGTAAGATG
* * * *
1299 AATATAGATATTTCAATGAGCCATGGCGTCAAAAATCATGCGAAACTGAGTCGGCGCCCCCGGAA
1 AATATAGATATTTCAATGAGCC-TGGCGCCAAAAATCATGCAAAACTGAGTCGG-GGCCACGGAA
* * * ** *
1364 CGCGTTAGTCGCCAAAAAGTGTGACGTACACGATTGCGGCTAAAATTTTGTAAAAACTAATTCTA
64 CGCGTTATTAGCCAAAAAGTGTGACGTACACGATTTCGGCTAAAATTTTGTAAAAACTAACCCGA
1429 AAAACTTTTCCTCAATCCCTTGGCACAATACTCGTCAAAAATATATAATTCAACGCCAAAAAGAT
129 AAAACTTTTCCTCAATCCCTT-GCACAATACTCGT-AAAAATATATAATTCAACGCCAAAAAGAT
*
1494 TGAAAGACTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCTGAATTAATTTTAAATTAAATC
192 TGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCT-AA-TAA-TTT-AATTAAATC
** * * *
1559 GAAAA-CGGTT-TCTGATGGTCGTAAAAACAAATCCTTAAATCCAATGTTGCTGAGATTTTGTCA
253 -AAAATCGGTTCTCTGATACTCGTAAAAACAAATTCTTAAAT-CAATGTTGTTGAGATTTGGTCA
* * * * *
1622 TATAAATATAGATATTTCAACGAGTCTTGACGCCAAAAATCATGCAAAACTGAGTCAGG-GCCCC
316 GATGAATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTAAG-CTGGCGCCCC
* ** ** * * ** * ***
1686 GGAACGCGTTACTAGCCAAAAATTGTGATGGTTAGTATATAATAATTTTGGTTAAA-ATTTTTTA
380 GGAACGCCTTTTTA-CCAAAAACCGTGATGGTTAG--TACAA-GATTTCAG-CAAATATTTAAAA
* * * * * * *
1750 AAAATTGACTCGAAAAATTTTTCCTCAAT-TTTTTCCACAATACAGGTAA-AAAAATATATAAGA
440 AAAAATGACCCGAAAAATTTTTCATGAATCTTTTGCCACAATAC---TAATTATAA-ATAT----
* * * * * * ** * *
1813 AAACGCAAAAAAGATTGCAGGGCTTTTCACACTTCTAAAATTGTTTTCCTCTT-TTTTTCCGAAT
497 CAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCATTTT--TCTTATATTTCCGAAA
* * * * * * *** * *
1877 TAATTTGTAATTAAGTCGAAACCTG-TTTC-GGTGCTCGTTTCAA-AAATCCTTAAATCCAATGT
560 TAATTTCTAATCAAATCGAAA-TTGATTTCTGATGCTCATAAAAACAAATCCTTAAATACAATGA
* **
1939 TGCTGAGATTTTGTCGGATG
624 TGCTGAGATTTGGTAAGATG
* * * ** *
1959 AATATAGATATTCCAGTGAGTCTTGGAACCAAAAATCATGCAAAACTGAGACGGGGCC-CGGGAA
1 AATATAGATATTTCAATGAG-CCTGGCGCCAAAAATCATGCAAAACTGAGTCGGGGCCAC-GGAA
* * * * *
2023 CGCGTAATTAGTCAAAAATCGTAATGGCTAC-TACACGATTTCGGCTAATACTTTT-CAAAAACT
64 CGCGTTATTAGCCAAAAA--GT-GT-G--ACGTACACGATTTCGGCTAA-AATTTTGTAAAAACT
* * * ** *** * *
2086 AACACGAAAAATTTTTACT-GTTTTTTTGCTACAATACTAGTAAAAGAATATATAATTCAACGCT
122 AACCCGAAAAACTTTTCCTCAATCCCTTGC-ACAATACTCGT-AAA-AATATATAATTCAACGCC
* * ** * *
2150 AAAAA-ATTGAAGGGCTTTGCACGCTTCTAATATCGTTTACCCTT-TTTTTCCAAATTACTTTGT
184 AAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTT-TTCTTATTTTT-CTAA-TA-ATT-T
* * * * * * * *
2213 AAATAAATCGAAA-CCGAT-TATGAATGCTCGTAAAAACAAATCCTTAAATCCAATGTTAATTGA
244 AATTAAATCAAAATCGGTTCTCTG-ATACTCGTAAAAACAAATTCTTAAAT-CAATGTT-GTTGA
* * * *
2276 GATTTGGTAATAAGAATATATATATATATATATATATATTTCAATGAGTCTT-AGTGCCAAAAAT
306 GATTTGG---TCAG---------AT-GA-ATATAGATATTTCAATGAGTCTTGA-CGCCAAAAAT
* * * * ** * * * *
2340 -AAGCAAAACTGAGCCGGGGATCTGGAACGCGTTTTTAGCCAAAAATCGTGA----T-GTACAAA
356 CATGCAAAACTAAGCTGGCGCCCCGGAACGCCTTTTTA-CCAAAAACCGTGATGGTTAGTACAAG
*** ** * * * *
2399 ATTTC-G-ACAATAATTTTGCAAAAAATGGA-CCGAAAGTTTTTTCCTCAAT-TTATGACCAAAA
420 ATTTCAGCA-AAT-ATTTAAAAAAAAAT-GACCCGAAAAATTTTTCATGAATCTTTTG-CCACAA
* * * *
2460 TACTCATGAAAATGTATAATGCAACGTCAAAAAGATTGAAAGGCTTTTCACGCTTCT-A-ATCAT
481 TACTAATTATAA---AT-AT-CAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCAT
* * *
2523 TTTTCTTATTTTTCCG----AA----T--T---A--G----T--TTT-TGATGCTCGTAAAAATA
541 TTTTCTTATATTTCCGAAATAATTTCTAATCAAATCGAAATTGATTTCTGATGCTCATAAAAACA
* * * *
2566 AATCCTTAAATCCAATGTTGCTGAGATTTAGTAAGATA
606 AATCCTTAAATACAATGATGCTGAGATTTGGTAAGATG
* * * *
2604 AATATAGATATTTCAATGAGTCTTGC-CACTAAAAATCATGCAAAACTGA-ACTGGGGCCCCGGA
1 AATATAGATATTTCAATGAGCCTGGCGC-C-AAAAATCATGCAAAACTGAGTC-GGGGCCACGGA
* * * * * * * *
2667 AAGCGTTTTTA-CCAAAAACTGTGACAATACACGATTTTGGCTAAAATTTTGCAAAAATTGACCC
63 ACGCGTTATTAGCCAAAAAGTGTGAC-GTACACGATTTCGGCTAAAATTTTGTAAAAACTAACCC
** * * *
2731 G-AAAA-TTTT--T---T-TTTTCCACAATACTCGTCAATAT-TATGAATATCAACGCCAAAAAG
127 GAAAAACTTTTCCTCAATCCCTTGCACAATACTCGTAAAAATATAT-AAT-TCAACGCCAAAAAG
* *
2787 AATGAAAGGCTTTTCACGCTTCTAATATCGTTTCTT-TTATTTTTCCGAAATAATTTTTAATTAA
190 ATTGAAAGGCTTTTCACGCTTCTAATATCGTTT-TTCTTATTTTT-C-TAATAA--TTTAATTAA
* * * * * * *
2851 ATCGAAATCAGTT-TCTGATGCTCGTAAAAACAAATTTTTAAATCCAACGTTATTGAGATTTAGT
250 ATCAAAATCGGTTCTCTGATACTCGTAAAAACAAATTCTTAAAT-CAATGTTGTTGAGATTTGGT
* * * *
2915 CAGATGAATATAGATATTTCAATGAGTCTTTGA-GCCAAAAATCATGTAAAAGTGAGCTGGGGCC
314 CAGATGAATATAGATATTTCAATGAGTC-TTGACGCCAAAAATCATGCAAAACTAAGCTGGCGCC
*
2979 CCGTAACGCGC-TTTTAGCCAAAAA
378 CCGGAACGC-CTTTTTA-CCAAAAA
3003 TTGTGACATA
Statistics
Matches: 1890, Mismatches: 322, Indels: 314
0.75 0.13 0.12
Matches are distributed among these distances:
617 29 0.02
618 38 0.02
619 3 0.00
628 3 0.00
629 3 0.00
630 5 0.00
631 27 0.01
632 93 0.05
633 16 0.01
634 1 0.00
636 1 0.00
638 6 0.00
639 9 0.00
640 28 0.01
641 1 0.00
642 1 0.00
643 1 0.00
644 24 0.01
645 92 0.05
646 83 0.04
647 243 0.13
648 149 0.08
649 140 0.07
650 81 0.04
651 24 0.01
652 8 0.00
653 1 0.00
654 2 0.00
655 3 0.00
656 2 0.00
657 3 0.00
658 8 0.00
659 22 0.01
660 176 0.09
661 77 0.04
662 84 0.04
663 115 0.06
664 91 0.05
665 15 0.01
666 7 0.00
667 7 0.00
668 35 0.02
669 36 0.02
670 17 0.01
671 2 0.00
672 1 0.00
673 1 0.00
676 5 0.00
677 41 0.02
678 30 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (643 bp):
AATATAGATATTTCAATGAGCCTGGCGCCAAAAATCATGCAAAACTGAGTCGGGGCCACGGAACG
CGTTATTAGCCAAAAAGTGTGACGTACACGATTTCGGCTAAAATTTTGTAAAAACTAACCCGAAA
AACTTTTCCTCAATCCCTTGCACAATACTCGTAAAAATATATAATTCAACGCCAAAAAGATTGAA
AGGCTTTTCACGCTTCTAATATCGTTTTTCTTATTTTTCTAATAATTTAATTAAATCAAAATCGG
TTCTCTGATACTCGTAAAAACAAATTCTTAAATCAATGTTGTTGAGATTTGGTCAGATGAATATA
GATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTAAGCTGGCGCCCCGGAACGCCTTT
TTACCAAAAACCGTGATGGTTAGTACAAGATTTCAGCAAATATTTAAAAAAAAATGACCCGAAAA
ATTTTTCATGAATCTTTTGCCACAATACTAATTATAAATATCAACGCCAAAAAGATTGAAAGGCT
TTTCACGCTTCTAATATCATTTTTCTTATATTTCCGAAATAATTTCTAATCAAATCGAAATTGAT
TTCTGATGCTCATAAAAACAAATCCTTAAATACAATGATGCTGAGATTTGGTAAGATG
Found at i:4879 original size:20 final size:20
Alignment explanation
Indices: 4846--5249 Score: 263
Period size: 20 Copynumber: 19.8 Consensus size: 20
4836 TACGCGGCAT
4846 ATTCACATTCAACTTTCCCA
1 ATTCACATTCAACTTTCCCA
* * *
4866 A-TCAACATTGAACTTGCCTTA
1 ATTC-ACATTCAACTTTCC-CA
4887 ATTCACATTCAACTTTCCCA
1 ATTCACATTCAACTTTCCCA
* * *
4907 A-TCAACATTGAACTTGCCTTA
1 ATTC-ACATTCAACTTTCC-CA
*
4928 ATTCACATCCAACTTTCCCA
1 ATTCACATTCAACTTTCCCA
* * **
4948 ATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCC-CA
* *
4969 ATTCACATTCAAATTTCCTA
1 ATTCACATTCAACTTTCCCA
* * **
4989 ATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCC-CA
* *
5010 ATTCACATTCAAATTTCCTA
1 ATTCACATTCAACTTTCCCA
* * **
5030 ATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCC-CA
* *
5051 ATTCACATTCAAATTTCCTA
1 ATTCACATTCAACTTTCCCA
* * **
5071 ATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCC-CA
5092 ATTCACATTCAACTTTCCCA
1 ATTCACATTCAACTTTCCCA
* * **
5112 ATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCC-CA
*
5133 ATTCACATTCAACTTTTCCA
1 ATTCACATTCAACTTTCCCA
* * **
5153 ATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCC-CA
*
5174 ATTCACATTCAACTTTCCAA
1 ATTCACATTCAACTTTCCCA
* * * **
5194 ATTGACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCC-CA
* *
5215 ATTCATATTCAACTTTCCAA
1 ATTCACATTCAACTTTCCCA
* *
5235 ATTGACATTGAACTT
1 ATTCACATTCAACTT
5250 GCCTTCATTC
Statistics
Matches: 293, Mismatches: 78, Indels: 26
0.74 0.20 0.07
Matches are distributed among these distances:
19 4 0.01
20 149 0.51
21 136 0.46
22 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.37
Consensus pattern (20 bp):
ATTCACATTCAACTTTCCCA
Found at i:4892 original size:41 final size:41
Alignment explanation
Indices: 4846--5264 Score: 662
Period size: 41 Copynumber: 10.2 Consensus size: 41
4836 TACGCGGCAT
*
4846 ATTCACATTCAACTTTCCCAA-TCAACATTGAACTTGCCTTA
1 ATTCACATTCAACTTTCCCAATTC-ACATTGAACTTGCCTTG
*
4887 ATTCACATTCAACTTTCCCAA-TCAACATTGAACTTGCCTTA
1 ATTCACATTCAACTTTCCCAATTC-ACATTGAACTTGCCTTG
*
4928 ATTCACATCCAACTTTCCCAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
* *
4969 ATTCACATTCAAATTTCCTAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
* *
5010 ATTCACATTCAAATTTCCTAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
* *
5051 ATTCACATTCAAATTTCCTAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
5092 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
*
5133 ATTCACATTCAACTTTTCCAATTCACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
* *
5174 ATTCACATTCAACTTTCCAAATTGACATTGAACTTGCCTTG
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
* * * *
5215 ATTCATATTCAACTTTCCAAATTGACATTGAACTTGCCTTC
1 ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
5256 ATTCACATT
1 ATTCACATT
5265 GGCCCTTAAT
Statistics
Matches: 363, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
41 361 0.99
42 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (41 bp):
ATTCACATTCAACTTTCCCAATTCACATTGAACTTGCCTTG
Found at i:5549 original size:124 final size:121
Alignment explanation
Indices: 5331--5575 Score: 355
Period size: 124 Copynumber: 2.0 Consensus size: 121
5321 GTCGTGATAG
* * * *
5331 GAAGGCATTCCTTGCTGCCACAGGGATATGCTCAGATTCAATGAGGAGACAACTGCAGAAGAGAA
1 GAAGGCAATCCTTGCTGCAACAGGAATATGCTCAGATCCAATGAGGAGACAACTGCAGAAGAGAA
* * * *
5396 GAAACGTTAGCAAGAAATCGTCAGAGCAGAAAAAGGAAAATCACAGCAAGCAAATCT
66 GAAACATTAGCAAGAAACCATCAAAGCAG-AAAAGGAAAATCACAGCAAGCAAATCT
* *
5453 GAAGGCAATCCTTGCTGCAACAGGAATACATGCTCAGCTCCAATGGGGAGACAACTGCAGAAGAG
1 GAAGGCAATCCTTGCTGCAACAGGAAT--ATGCTCAGATCCAATGAGGAGACAACTGCAGAAGAG
* *
5518 AAGAAACATTATCAAGAAACCATTAAAGCAGAAAAGGAAAATCACAGCAAGCAAATCT
64 AAGAAACATTAGCAAGAAACCATCAAAGCAGAAAAGGAAAATCACAGCAAGCAAATCT
5576 ATGCAATGGC
Statistics
Matches: 109, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
122 24 0.22
123 27 0.25
124 58 0.53
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (121 bp):
GAAGGCAATCCTTGCTGCAACAGGAATATGCTCAGATCCAATGAGGAGACAACTGCAGAAGAGAA
GAAACATTAGCAAGAAACCATCAAAGCAGAAAAGGAAAATCACAGCAAGCAAATCT
Found at i:5696 original size:4 final size:4
Alignment explanation
Indices: 5687--5719 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
5677 TTACAGGCCC
5687 GAAA GAAA GAAA GAAA GAAA GAAA GAAA -AAA GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA
5720 GAGCGGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:44077 original size:43 final size:43
Alignment explanation
Indices: 44016--44103 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
44006 TGGCGTTTTA
44016 CAAGCTCTTCACTGCAAATTAATTCATGATTCCAAAGCAAAAT
1 CAAGCTCTTCACTGCAAATTAATTCATGATTCCAAAGCAAAAT
44059 CAAGCTCTTCACTGCAAATTAATTCATGATTCCAAAGCAAAAT
1 CAAGCTCTTCACTGCAAATTAATTCATGATTCCAAAGCAAAAT
44102 CA
1 CA
44104 TGCATAGGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (43 bp):
CAAGCTCTTCACTGCAAATTAATTCATGATTCCAAAGCAAAAT
Found at i:44098 original size:23 final size:23
Alignment explanation
Indices: 44029--44099 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
44019 GCTCTTCACT
44029 GCAAATTAATTCATGATTCCAAA
1 GCAAATTAATTCATGATTCCAAA
* * * **
44052 GC-AA--AA-TCAAGCTCTTCACT
1 GCAAATTAATTCATGAT-TCCAAA
44072 GCAAATTAATTCATGATTCCAAA
1 GCAAATTAATTCATGATTCCAAA
44095 GCAAA
1 GCAAA
44100 ATCATGCATA
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 2 0.06
22 2 0.06
23 12 0.36
24 5 0.15
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (23 bp):
GCAAATTAATTCATGATTCCAAA
Found at i:49413 original size:21 final size:23
Alignment explanation
Indices: 49370--49414 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
49360 CACTTGTGTG
49370 AATACTTATCACACATAACAAAAT
1 AATACTTAT-ACACATAACAAAAT
49394 AATACTTAT-CACATAA-AAAAT
1 AATACTTATACACATAACAAAAT
49415 CTTACTGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 7 0.33
24 9 0.43
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.27
Consensus pattern (23 bp):
AATACTTATACACATAACAAAAT
Found at i:54545 original size:2 final size:2
Alignment explanation
Indices: 54538--54562 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54528 TTTTCTCCAT
54538 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 T
54563 TTATTTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.