Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011930.1 Corchorus olitorius cultivar O-4 contig11963, 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: 3803
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Found at i:297 original size:154 final size:154
Alignment explanation
Indices: 1--1304 Score: 1970
Period size: 154 Copynumber: 8.4 Consensus size: 154
* * *
1 ATTAGTTCCGTTTTGAAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAGTGCTAAT
1 ATTAGTTCCGTTTTG-AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
* *
66 GGCCAAACTATAATCATTTTGGTGAGATTAGGCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
65 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
* *
131 GGTTATTTTGGGCCTATCGAGGCCC
130 TGTTATTTTGGGCCTATCGGGGCCC
* * *
156 ATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTCTTAATG
1 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
* * *
221 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAACTTTTTAGTTCATTTGGAACACTT
66 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
*
286 GTTATTTTGGGCCTATCGGGGTCC
131 GTTATTTTGGGCCTATCGGGGCCC
** * *
310 ATTAGTGACGTATTGAATCGTCTTCGATTTAGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
1 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
375 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
66 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
*
440 GTTA-TTTGAGGCCTTTCGGGGCCC
131 GTTATTTTG-GGCCTATCGGGGCCC
* *
464 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC-AACCTACGATGCTTTTC-TTCCATCGTTTAT
1 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCT-CAATGCTTTTCTTTCCATTGTTTAT
* *
527 GGCCTAACTATATTCATTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTTAGCTCTTTTGGAACA
65 GGCCTAACTATAATCA-TTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCTCATTTGGAACA
*
592 CTTGTTATTTTGGGCCTATCGGGGCGTC
128 CTTGTTATTTTGGGCCTATCGGGGC-CC
*
620 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC-AACCGTCATTGCTTTTCTTTCCATTGTTTAT
1 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTAT
*
684 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTCGGAACACT
65 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
749 TGTTATTTTGGGCCTATCGGGGCCC
130 TGTTATTTTGGGCCTATCGGGGCCC
* * * *
774 ATTAGTTCCGTATTGAATCGTATACGATTTGGCAAACCTCAAGGCTTTTCTTTCCATTGTTTATG
1 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
* * ** * *
839 GCATAACTATAATAATTTCAGTGAGATTAGTCCACTGTGAACTTTTTAGCTAATTTGGAACACTT
66 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
904 GTTATTTTGGGCCTATCGGGGCCC
131 GTTATTTTGGGCCTATCGGGGCCC
*** * * * * * *
928 ATTAGGAACGTATTGAATCTTCTACGAATTGGCAAGCCTCAATGCTTTTGTTTCCATTGTTTATG
1 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
* * * * *
993 GCCTACCTATAATCATTTTGTTTAGATTAGTCCACTTTGAAGTTTTTAGCTCATTCGGAACACTT
66 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
* *
1058 GTTATGTTGGGCCTATCGGGGCTC
131 GTTATTTTGGGCCTATCGGGGCCC
* *
1082 ATTAGTTCCGTTTTGAATCGTTTTAGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
1 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
* *
1147 CCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTT
66 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
*
1212 GTTATTTTGCGG-CTATCGAGGCCC
131 GTTATTTTG-GGCCTATCGGGGCCC
* *
1236 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTATCCATTGTTTATG
1 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
1301 GCCT
66 GCCT
1305 GCCTATCGGG
Statistics
Matches: 1038, Mismatches: 101, Indels: 21
0.89 0.09 0.02
Matches are distributed among these distances:
153 36 0.03
154 795 0.77
155 101 0.10
156 78 0.08
157 28 0.03
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
GTTATTTTGGGCCTATCGGGGCCC
Found at i:1266 original size:462 final size:462
Alignment explanation
Indices: 1--3799 Score: 3212
Period size: 462 Copynumber: 8.0 Consensus size: 462
* * * *
1 ATTAGTTCCGTTTTGAAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCAGTGCTAAT
1 ATTAGTTACGTTTTG-AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTAT
* *
66 GGCCAAACTATAATCATTTTGGTGAGATTAGGCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
65 GGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACT
* * *
131 GGTTATTTTGGGCCTATCGAGGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAAACCTC
130 TGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTC
* *
196 AATGCTTTTCTTTCCATTCTTAATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT-A
195 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGA
* *
260 AACTTTTTAGTTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTATTG
260 AA-TTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTG
*
325 AATCGTCTTCGATTTAGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
324 AATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCA
*
390 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTA-TTTGAGGCCT
389 TTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTG-GGCCT
*
454 TTCGGGGCCC
453 ATCGGGGCCC
* * *
464 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC-AACCTACGATGCTTTTC-TTCCATCGTTTAT
1 ATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCT-CAATGCTTTTCTTTCCATTGTTTAT
* *
527 GGCCTAACTATATTCATTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTTAGCTCTTTTGGAACA
65 GGCCTAACTATAATCA-TTTTGGTGAGATTAGTCCACTGTGAAG-TTTTTAGCTCATTTGGAACA
*
592 CTTGTTATTTTGGGCCTATCGGGGCGTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGC-AAC
128 CTTGTTATTTTGGGCCTATCGGGGC-CCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAAC
*
656 CGTCATTGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
192 C-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* * **
721 GTGAAGTTTTTAGCTCATTCGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTA
256 GTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTA
* * * *
786 TTGAATCGTATACGATTTGGCAAACCTCAAGGCTTTTCTTTCCATTGTTTATGGCATAACTATAA
321 TTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
* ** *
851 TAATTTCAGTGAGATTAGTCCACTGTGAACTTTTTAGCTAATTTGGAACACTTGTTATTTTGGGC
386 TCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
916 CTATCGGGGCCC
451 CTATCGGGGCCC
** * * * * * *
928 ATTAGGAACGTATTGAATCTTCTACGAATTGGCAAGCCTCAATGCTTTTGTTTCCATTGTTTATG
1 ATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
* * * * *
993 GCCTACCTATAATCATTTTGTTTAGATTAGTCCACTTTGAAGTTTTTAGCTCATTCGGAACACTT
66 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
* * * *
1058 GTTATGTTGGGCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTTTTAGATTTGGCAAACCTCA
131 GTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
*
1123 ATGCTTTTCTTTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
196 ATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
* ** *
1188 ATTTTTAGCTCATTTGGAACACTTGTTATTTTGCGG-CTATCGAGGCCCATTAGTTCCGTTTTGA
261 ATTTTTAGCTCATTTGGAACACTTGTTATTTTG-GGCCTATCGGGGCCCATTAGTGACGTATTGA
* * * *
1252 ATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTATCCATTGTTTATGGCCT-GC-CT-ATC--
325 ATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCAT
* ** ** * * * *
1312 ---GGGGCTCATTAGTTCCGTTTTGAATCGTCTT--C-GATTTGGCAA-ACCTCAATGCTT-TTC
390 TTTGGTG-AGATTAG-TCCACTGTGAA-CTTTTTAGCTCATTTGG-AACA-CT---TG-TTATT-
* * * *
1369 TT--TCC-ATTGTTTATGGCCTA
445 TTGGGCCTATCG----GGGCC-C
* * * * * ** ** **** *
1389 ACTA-TAATCATTTTGGTGAGATTAGTC--C-A-CTGTG-AAATTTTTA-GCTCATTGGGAATAC
1 ATTAGTTA-C-GTTT--TGA-A-TCGTCTTCGATTTG-GCAAACCTCAATGCT--TT-TCTTTCC
* * ****** * * **
1447 -TTGTTATTTTGGGCCTATCGGGGCCCA--TTAGTGACGTATTGAATCGTCT-TCG-A-TTTGGC
56 ATTG-T-TTAT-GGCCTAACTATAATCATTTTGGTGA-G-ATT-AGTCCACTGT-GAAGTTT---
** * **** * * * * ** *
1506 AAACCTCAATGCTTTCTTTCCACTTG-T-TTATGGCCTAACCATAATCAATTTGGTCAGATTA-A
111 TTAGCTC-A---TTT-GGAACACTTGTTATTTTGG----GCC-T-ATC----GGGGCCCATTAGT
* * * * * * * ** * * ***
1568 TCCATTTTGAA-CTTTTTAGCTTATTGG-AAAACT---TG-TTAT-TTTGGACCT-ATCGGGGCC
161 TCCGTTTTGAATCGTCTTCG-AT-TTGGCAAACCTCAATGCTTTTCTTTCCA-TTGTTTATGGCC
* * * * *** * * * * * **
1625 TATTAGTGACGTATTGATTCTT-CTTCCATTTGGCAGAC-CT-CAATGCTTTTATTTCCATTGTT
223 TA--ACT-A--TAATCATT-TTGGTGAGATTAGTC-CACTGTGAAAT--TTTTAGCT-CA----T
* * * ** ** * * * * *
1687 TATGG-CCTAATTATAATCATTTTGGTG-AGAT--TAGTCCACT-GTGAAGT-TT--TTAG-C-T
274 T-TGGAAC-ACTTGT--T-ATTTTGG-GCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTT
* * * * * *
1742 C-ATTTAG--AACACT---TG-TTATT-TTAGGCCTATCG---A-GGCC-CA-T-TAGTTCCGTT
333 CGATTTGGCAAAC-CTCAATGCTT-TTCTT--TCC-ATTGTTTATGGCCTAACTATA-AT-CATT
** * * * * * * **
1792 TTGAATCGTCTTCGATTTGGCAAATCTCAATGCTTTTCTTTC-CATTGTTTATGGCCTAACTA-T
391 TTG----G--TGAGATTAGTCCACTGTGAA--CTTTT-TAGCTCA----TT-TGG---AAC-ACT
** * ** ** *
1855 AATCATTTTGGTG-AGAT--TAGTCC
438 TGTTATTTTGG-GCCTATCGGGGCCC
* * * * * * * *
1878 ACTGTGAACTTTTTCGCTCATTTGGAA-C-ACTTGCTATTTTGGGTCTATCGGGGCCCATTAG--
1 A-T-T--A--GTTACG-T--TTT-GAATCGTCTT-CGA-TTT-GG-CAAAC----CTCAAT-GCT
* ** * * **
1939 TTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATTCTTTTCTTTCCAGTGTTTATGGCCAA
47 TTTC--TTTCCATTGT-TT--A--TGG----CCT-AA--C-TAT-AAT-CA---TTT-TGG----
*
2004 ACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
87 -------TGA---------GATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTAT
* *
2069 TTTGGGCCTATCTGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCT
136 TTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCT
* *
2134 TTTCTTTCCATTCTTAATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGT-AAACTTT
201 TTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAA-TTT
* *
2198 TTAGTTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGTCCATTAGTGACGTATTGAATCGT
265 TTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGT
*
2263 CTTCGATTTAGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
330 CTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGG
* *
2328 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACATTTGTTATTTTGGGCCTATCGGGG
395 TGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGG
2393 CCC
460 CCC
*
2396 ATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCGTTTCTTTCCATTGTTTATG
1 ATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
*
2461 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTGTAGCTCATTTGGAACACTT
66 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
*
2526 GTTATTTTGGGCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
131 GTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
2591 ATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
196 ATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
* * * *
2656 GTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGACCATTAGTGACGTTTTGAA
261 ATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAA
**
2721 TCGTCTTCGATTTGGCAAACCTCAATGCGATTCTTTCCATTGTTTATGGCCTAACTATAATCATT
326 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
* *
2786 TTGGTGAGATTAGTCCACTGTGAAATTTTTAGCTCATTTGGAACTCTTGTTATTTTGGGCCTATC
391 TTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
**
2851 GGGGCTT
456 GGGGCCC
* *
2858 ATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
1 ATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
* * *
2923 GCCTAACTATAATCATTTTGGTGAGATGAGTCCACTGTAAAATTTTTAGCTCATTTGGAACACTT
66 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
2988 GTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
131 GTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
* * *
3053 ATGCTTTTCTTTCCATTCTTAATGGCCTAACTGTAATCATTTTGGTGAGATTAGTCCACTGTGAA
196 ATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
*
3118 CTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAA
261 ATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAA
3183 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
326 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
* *
3248 TTGGTGAGATGAGTCCACTGTGAAATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
391 TTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
3313 GGGGCCC
456 GGGGCCC
* * * *
3320 ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCATTTCTTTCCAATGTTGATG
1 ATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
* *
3385 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAATACTT
66 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
** *
3450 GTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCA
131 GTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
*
3515 ATGCTTTTCTTACCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
196 ATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
* * * ** *
3580 GTTTTTAGCTCATTTGGAACACATGTTATTTTGGTCCTATCGGGGCCCATTAGTTCCGTTTTGAA
261 ATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAA
* *
3645 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACCATAATCAAT
326 TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
* * * * * *
3710 TTGGTCAGATTAGTCCATTGTGAACTTTATAGCTTATTTGGAAAACTTGTTATTTTGGGCCTCTC
391 TTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
3775 GGGGCCC
456 GGGGCCC
* *
3782 ATTAGTGACGTATTGAAT
1 ATTAGTTACGTTTTGAAT
3800 TTTC
Statistics
Matches: 2691, Mismatches: 402, Indels: 487
0.75 0.11 0.14
Matches are distributed among these distances:
454 9 0.00
455 10 0.00
456 11 0.00
457 6 0.00
458 4 0.00
459 6 0.00
460 7 0.00
461 36 0.01
462 1504 0.56
463 118 0.04
464 346 0.13
465 44 0.02
466 17 0.01
467 6 0.00
468 4 0.00
469 1 0.00
471 6 0.00
472 3 0.00
473 6 0.00
474 1 0.00
475 16 0.01
476 10 0.00
477 11 0.00
478 3 0.00
479 16 0.01
480 31 0.01
481 26 0.01
482 8 0.00
483 4 0.00
484 2 0.00
486 13 0.00
487 19 0.01
488 8 0.00
489 4 0.00
490 14 0.01
491 3 0.00
492 4 0.00
493 4 0.00
494 4 0.00
495 8 0.00
496 9 0.00
497 5 0.00
498 3 0.00
499 2 0.00
500 3 0.00
501 8 0.00
502 6 0.00
503 7 0.00
504 2 0.00
506 6 0.00
507 3 0.00
508 6 0.00
509 6 0.00
510 6 0.00
511 2 0.00
512 4 0.00
513 1 0.00
514 1 0.00
515 3 0.00
516 26 0.01
517 2 0.00
518 10 0.00
519 16 0.01
520 7 0.00
521 1 0.00
522 4 0.00
523 3 0.00
524 10 0.00
525 29 0.01
526 45 0.02
527 12 0.00
528 4 0.00
529 11 0.00
530 10 0.00
531 17 0.01
532 7 0.00
533 10 0.00
534 6 0.00
535 5 0.00
537 1 0.00
538 4 0.00
539 6 0.00
540 5 0.00
541 4 0.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (462 bp):
ATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATG
GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
GTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCA
ATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA
ATTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTGACGTATTGAA
TCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATT
TTGGTGAGATTAGTCCACTGTGAACTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATC
GGGGCCC
Found at i:1366 original size:83 final size:83
Alignment explanation
Indices: 1224--1387 Score: 292
Period size: 83 Copynumber: 2.0 Consensus size: 83
1214 TATTTTGCGG
1224 CTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTAT
1 CTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTAT
1289 CCATTGTTTATGGCCTGC
66 CCATTGTTTATGGCCTGC
* * * *
1307 CTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTT
1 CTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTAT
1372 CCATTGTTTATGGCCT
66 CCATTGTTTATGGCCT
1388 AACTATAATC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (83 bp):
CTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAAGCTTTTCTAT
CCATTGTTTATGGCCTGC
Found at i:1491 original size:237 final size:237
Alignment explanation
Indices: 1068--1541 Score: 817
Period size: 237 Copynumber: 2.0 Consensus size: 237
1058 GTTATGTTGG
*
1068 GCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTTTTAGATTTGGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTAGATTTGGCAAACCTCAATGCTTTTCT
1133 TTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCT
66 TTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCT
* ** *
1198 CATTTGGAACACTTGTTATTTTGCGGCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGA
131 CATTGGGAACACTTGTTATTTTGCGGCTATCGAGGCCCATTAGTGACGTATTGAATCGTCTTCGA
1263 TTTGGCAAACCTCAAAGCTTTTCTATCCA-TTGTTTATGGCCT
196 TTTGGCAAACCTCAAAGC-TTTCTATCCACTTGTTTATGGCCT
*
1305 GCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTAGATTTGGCAAACCTCAATGCTTTTCT
*
1370 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCT
66 TTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCT
* *
1435 CATTGGGAATACTTGTTATTTTG-GGCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCG
131 CATTGGGAACACTTGTTATTTTGCGG-CTATCGAGGCCCATTAGTGACGTATTGAATCGTCTTCG
* *
1499 ATTTGGCAAACCTCAATGCTTTCTTTCCACTTGTTTATGGCCT
195 ATTTGGCAAACCTCAAAGCTTTCTATCCACTTGTTTATGGCCT
1542 AACCATAATC
Statistics
Matches: 224, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
236 11 0.05
237 213 0.95
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (237 bp):
GCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTAGATTTGGCAAACCTCAATGCTTTTCT
TTCCATTGTTTATGCCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCT
CATTGGGAACACTTGTTATTTTGCGGCTATCGAGGCCCATTAGTGACGTATTGAATCGTCTTCGA
TTTGGCAAACCTCAAAGCTTTCTATCCACTTGTTTATGGCCT
Found at i:3799 original size:154 final size:154
Alignment explanation
Indices: 1305--3787 Score: 4061
Period size: 154 Copynumber: 16.1 Consensus size: 154
1295 TTTATGGCCT
*
1305 GCCTATCGGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
*
1370 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
* *
1435 CATTGGGAATACTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
** *
1459 GCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGC-TTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* * * * * *
1523 TTCCACTTGTTTATGGCCTAACCATAATCAATTTGGTCAGATTAATCCATTTTGAACTTTTTAGC
66 TTCCA-TTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGC
* *
1588 TTA-TTGGAAAACTTGTTATTTTGG
130 TCATTTGGAACACTTGTTATTTTGG
* * ** * * * * * *
1612 ACCTATCGGGGCCTATTAGTGACGTATTGATTCTTCTTCCATTTGGCAGACCTCAATGCTTTTAT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* *
1677 TTCCATTGTTTATGGCCTAATTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
* *
1742 CATTTAGAACACTTGTTATTTTAG
131 CATTTGGAACACTTGTTATTTTGG
* *
1766 GCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAATCTCAATGCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
*
1831 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTCGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
*
1896 CATTTGGAACACTTGCTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
* *
1920 GTCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATTCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* * *
1985 TTCCAGTGTTTATGGCCAAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
2050 CATTTGGAACACTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
* *
2074 GCCTATCTGGGCTCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* * * *
2139 TTCCATTCTTAATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAACTTTTTAGTT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
2204 CATTTGGAACACTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
* ** * *
2228 GCCTATCGGGGTCCATTAGTGACGTATTGAATCGTCTTCGATTTAGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
*
2293 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
*
2358 CATTTGGAACATTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
* *
2382 GCCTATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCGTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* *
2447 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTGTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
2512 CATTTGGAACACTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
*
2536 GCCTATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
*
2601 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
2666 CATTTGGAACACTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
* * ** **
2690 GCCTATCGAGGACCATTAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCGATTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
*
2755 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAATTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
*
2820 CATTTGGAACTCTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
** *
2844 GCCTATCGGGGCTTATTAGTTCCGTTTTGAATCATCTTCGATTTGGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* * *
2909 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATGAGTCCACTGTAAAATTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
2974 CATTTGGAACACTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
2998 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* * *
3063 TTCCATTCTTAATGGCCTAACTGTAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
3128 CATTTGGAACACTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
** *
3152 GCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* *
3217 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATGAGTCCACTGTGAAATTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
3282 CATTTGGAACACTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
*
3306 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCATTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* *
3371 TTCCAATGTTGATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
*
3436 CATTTGGAATACTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
** *
3460 GCCTATCGGGGCCCATTAGTGACGTATTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* *
3525 TACCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
*
3590 CATTTGGAACACATGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
*
3614 TCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
1 GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
* * * * *
3679 TTCCATTGTTTATGGCCTAACCATAATCAATTTGGTCAGATTAGTCCATTGTGAACTTTATAGCT
66 TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
* *
3744 TATTTGGAAAACTTGTTATTTTGG
131 CATTTGGAACACTTGTTATTTTGG
*
3768 GCCTCTCGGGGCCCATTAGT
1 GCCTATCGGGGCCCATTAGT
3788 GACGTATTGA
Statistics
Matches: 2160, Mismatches: 166, Indels: 6
0.93 0.07 0.00
Matches are distributed among these distances:
153 135 0.06
154 2025 0.94
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
GCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCT
TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAACTTTTTAGCT
CATTTGGAACACTTGTTATTTTGG
Done.