Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009208.1 Corchorus capsularis cultivar CVL-1 contig09229, 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: 3615
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:704 original size:324 final size:322
Alignment explanation
Indices: 1--2066 Score: 2590
Period size: 324 Copynumber: 6.4 Consensus size: 322
* * * *
1 CTTAAATCCATTGTGACTGAGATTTGGTTAGAAGAATATAGATATTTCAAGGAGCCGTTCTGCCA
1 CTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCA
*
66 AAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCATTTCTAGCAAAAAACAGTGATGGTTAGT
66 AAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGATGGTTAGT
* * *
131 ACAC-ATTTTCGGTTAAAAATTAACCCGAAAAGGTTTTTTCTCAATATTTTT-AAAAATATTGAG
131 ACACGA-TTTCGGCTAAAAATTAACCCG-AAA-GTTTTTTCTCAAT-TTTTTGCAAAATATTCAG
* * * *
194 AAAAAAATATATAATTTAACGCCAAAAAGATTGACGGGCTTTTCACG-TATCTAATATCG-----
192 -AAAAAATATGTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCT-TCTAACATCGTTTTT
* * * **
253 -C-TT-TTTTTTTCAAATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTTGTAAAAACAA
255 TCATTATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAA
315 ATC
320 ATC
* * *
318 CTTAAATCTATTGTGACTGAGATTTGGTTAGATGAATATAGATATTAAAAGGAGTTTTTCTGCCA
1 CTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCA
* * * * * *
383 AAAATCATGCAAAACAGAGCCGGAGCCCCGTAATGCGTTTCTAACAAAAAACAATGATGCTTAAT
66 AAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGATGGTTAGT
*
448 ACACGATTTCGGCTAAAAATTAACCCGAAATGTTTTTTTCTCAATTTTTTGCAAAATGTTCAGAA
131 ACACGATTTCGGCTAAAAATTAACCCGAAA-G-TTTTTTCTCAATTTTTTGCAAAATATTCAGAA
* * *
513 AAAATATGTAATTCAATGCCAAAAAGATTGACACGCTTTTCACGCTTCTAACATTGTTTTTTCAT
194 AAAATATGTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAACATCGTTTTTTCAT
* ** * * *
578 TATTTTTTTCGACTTGCTTTAAAATTAATTCGAAACAAGATTCAGATGCGCTTAAAAACAAATC
259 TATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATC
* * * *
642 TTTAAATCCTTTGTGACTGAGATTTTGTTAGATGAATATAGATTTTTAAAGGAGTCTTTCTGCCA
1 CTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCA
* * * *
707 AAAATCATGCAAAACTA-AGCAAGG-GCCCCGAAACGCGTTTATAGCCAAAAACCGTGATGGTTA
66 AAAATCATGCAAAAC-AGAGC-CGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGATGGTTA
* * * * * * *
770 ATACACGATTTCAGCTAAAAACTGACCTGAAGAG-TTTTTCTCAATTTTTCAGGAAAATATTCAG
129 GTACACGATTTCGGCTAAAAATTAACCCGAA-AGTTTTTTCTCAATTTTT-TGCAAAATATTCAG
* ** * * * *
834 AAAAAATATAG-AATTCCACGCCAAAAAGATTGATGGGTTTTTCATGTTTCTAATATCGTTTTTT
192 AAAAAATAT-GTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAACATCGTTTTTT
** * * * *
898 TTTTCATTTTTTTCGAATTTATTTCAAATTAAGTCGAAAAAAAATTCAGATGCTCGTAAAAACAA
256 CATT-ATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAA
963 ATC
320 ATC
* * * * * *
966 CCTAAATCCATTGTGACTAAGATTTGGTTAGATGAATATAAATATTTCAAGGTGTCCTTCTGCCA
1 CTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCA
* * *
1031 AAAATCATGCAAAACAGAGTCGGAGCCCCGAAATGCGTTTCTAACAAAAAAACAGTGATGGTTAG
66 AAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGC-AAAAAACAGTGATGGTTAG
* * *
1096 TACACGATTTCGGCTAAAAATTAACCTGAAAATTTTTTTCTCAATTTTTTGCAAAATGTTCAGAA
130 TACACGATTTCGGCTAAAAATTAACCCG-AAAGTTTTTTCTCAATTTTTTGCAAAATATTCAGAA
*
1161 AAAATATGTAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAACATCGTTTTTTC--
194 AAAATATGTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAACATCGTTTTTTCAT
* * *
1224 -ATTTTTTTCGACTTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATC
259 TATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATC
*
1287 TTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCA
1 CTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCA
* * * * * * *
1352 AAAATCATGCAAAACTGAGCAGGGGCCCCAAAACGCATTTCTAGCCAAAAACCGTGATGGTTAGT
66 AAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGATGGTTAGT
** * * * * *
1417 ACACGATTTAAGCTAAAAACTGACCCGAGGAG-TTTTTCTCAATTTTTCTGGAAAATATTCAAAA
131 ACACGATTTCGGCTAAAAATTAACCCGA-AAGTTTTTTCTCAATTTTT-TGCAAAATATTCAGAA
* * * * * *
1481 AAAATATATAATTCAACGCCAATAAGATCGATAGGTTTTTCACGCTTCTAATATCGTTTTTTCA-
194 AAAATATGTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAACATCGTTTTTTCAT
* * *
1545 TGTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAACC
259 TATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATC
** * *
1609 CTTAAATCCATTGTGACTGAGATTTGGTTAGAAAAATATAGATATTTCAAGGAGTCGTTCTGCCA
1 CTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCA
* * *
1674 AAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCATTTCTAGCTAAAATCAGTGATGGTTAGT
66 AAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGATGGTTAGT
* * * *
1739 ACACGTTTTCGGTTAAAAATTAATCCGAAAAGATTTTTTCTCAATTTTTTGCAAAATGTTCAGAA
131 ACACGATTTCGGCTAAAAATTAACCCG-AAAG-TTTTTTCTCAATTTTTTGCAAAATATTCAGAA
* * * * * *
1804 ACAATATTTAATTTAACGCTAAAAAGATTGACAGGCTTTTAACGCTTTTAACATCGTTTTTTCAT
194 AAAATATGTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAACATCGTTTTTTCAT
* ** *
1869 TTTTTTTTTCGACGTTATTTCAAATTAAATCGAAACAATATTCAGATGCGCGTAAAAACAAATC
259 TATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATC
** * * *
1933 CTTAAATTTATTGTGACTGAGATTTGGTTATATGAATATACATATTTAAAGGAGTCCTTCTGCCA
1 CTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCA
* * * *
1998 AAAATCATGCAAAACTGAGCAGGGGCCCCGAAACGCGTTTCTAGCCAAAAACCA-TGATGGTTAG
66 AAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAG-CAAAAAACAGTGATGGTTAG
2062 TACAC
130 TACAC
2067 CCCAGCTCAG
Statistics
Matches: 1502, Mismatches: 214, Indels: 59
0.85 0.12 0.03
Matches are distributed among these distances:
316 58 0.04
317 162 0.11
318 1 0.00
319 16 0.01
320 110 0.07
321 151 0.10
322 213 0.14
323 137 0.09
324 517 0.34
325 120 0.08
326 17 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (322 bp):
CTTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCA
AAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGATGGTTAGT
ACACGATTTCGGCTAAAAATTAACCCGAAAGTTTTTTCTCAATTTTTTGCAAAATATTCAGAAAA
AATATGTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAACATCGTTTTTTCATTA
TTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATC
Found at i:1502 original size:645 final size:642
Alignment explanation
Indices: 2--2066 Score: 2945
Period size: 645 Copynumber: 3.2 Consensus size: 642
1 C
* * * *
2 TTAAATCCATTGTGACTGAGATTTGGTTAGAAGAATATAGATATTTCAAGGAGCCGTTCTGCCAA
1 TTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCAA
* * * * *
67 AAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCATTTCTAGCAAAAAACAGTGATGGTTAGTA
66 AAATCATGCAAAACTGAGCAGGGGCCCCGAAACGCATTTCTAGCCAAAAACCGTGATGGTTAGTA
* * * * * * *
132 CAC-ATTTTCGGTTAAAAATTAACCCGAAAAGGTTTTTTCTCAATATTTT-T-AAAAATATTGAG
131 CACGA-TTTCAGCTAAAAACTGACCCGAAGA-G-TTTTTCTCAAT-TTTTCTGGAAAATATTCA-
* * * *
194 AAAAAAATATATAATTTAACGCCAAAAAGATTGACGGGCTTTTCACGTATCTAATATCGCTTTTT
191 AAAAAAATATATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGTTTCTAATATCG-TTTTT
* * *
259 TTTTCA---------AATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTTGTAAAAACAA
255 TTTTCATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * ** **
315 ATCCTTAAATCTATTGTGACTGAGATTTGGTTAGATGAATATAGATATTAAAAGGAGTTTTTCTG
320 ATCCCTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCTTCTG
* * *
380 CCAAAAATCATGCAAAACAGAGCCGGAGCCCCGTAATGCGTTTCTAACAAAAAACAATGATGCTT
385 CCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAATGCGTTTCTAACAAAAAACAGTGATGGTT
* *
445 AATACACGATTTCGGCTAAAAATTAACCCGAAATGTTTTTTTCTCAATTTTTTGCAAAATGTTCA
450 AGTACACGATTTCGGCTAAAAATTAA-CCGAAA-ATTTTTTTCTCAATTTTTTGCAAAATGTTCA
* * *
510 GAAAAAATATGTAATTCAATGCCAAAAAGATTGACACGCTTTTCACGCTTCTAACATTGTTTTTT
513 GAAAAAATATGTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAACATCGTTTTTT
* * *
575 CATTATTTTTTTCGACTTGCTTTAAAATTAATTCGAAACAAGATTCAGATGCGCTTAAAAACAAA
578 C---ATTTTTTTCGACTTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAA
640 TCT
640 TCT
* * *
643 TTAAATCCTTTGTGACTGAGATTTTGTTAGATGAATATAGATTTTTAAAGGAGTCTTTCTGCCAA
1 TTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCAA
* * * * *
708 AAATCATGCAAAACTAAGCAAGGGCCCCGAAACGCGTTTATAGCCAAAAACCGTGATGGTTAATA
66 AAATCATGCAAAACTGAGCAGGGGCCCCGAAACGCATTTCTAGCCAAAAACCGTGATGGTTAGTA
* * *
773 CACGATTTCAGCTAAAAACTGACCTGAAGAGTTTTTCTCAATTTTTCAGGAAAATATTCAGAAAA
131 CACGATTTCAGCTAAAAACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATATTCAAAAAA
* * *
838 AATATAGAATTCCACGCCAAAAAGATTGATGGGTTTTTCATGTTTCTAATATCGTTTTTTTTTTC
196 AATATATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGTTTCTAATATCG-TTTTTTTTTC
* * *
903 ATTTTTTTCGAATTTATTTCAAATTAAGTCGAAAAAAAATTCAGATGCTCGTAAAAACAAATCCC
260 ATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCC
* * *
968 TAAATCCATTGTGACTAAGATTTGGTTAGATGAATATAAATATTTCAAGGTGTCCTTCTGCCAAA
325 TAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCTTCTGCCAAA
*
1033 AATCATGCAAAACAGAGTCGGAGCCCCGAAATGCGTTTCTAACAAAAAAACAGTGATGGTTAGTA
390 AATCATGCAAAACAGAGCCGGAGCCCCGAAATGCGTTTCTAAC-AAAAAACAGTGATGGTTAGTA
1098 CACGATTTCGGCTAAAAATTAACCTGAAAATTTTTTTCTCAATTTTTTGCAAAATGTTCAGAAAA
454 CACGATTTCGGCTAAAAATTAACC-GAAAATTTTTTTCTCAATTTTTTGCAAAATGTTCAGAAAA
*
1163 AATATGTAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAACATCGTTTTTTCATTT
518 AATATGTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAACATCGTTTTTTCATTT
1228 TTTTCGACTTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATCT
583 TTTTCGACTTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATCT
1288 TTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCAA
1 TTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCAA
*
1353 AAATCATGCAAAACTGAGCAGGGGCCCCAAAACGCATTTCTAGCCAAAAACCGTGATGGTTAGTA
66 AAATCATGCAAAACTGAGCAGGGGCCCCGAAACGCATTTCTAGCCAAAAACCGTGATGGTTAGTA
* *
1418 CACGATTTAAGCTAAAAACTGACCCGAGGAGTTTTTCTCAATTTTTCTGGAAAATATTCAAAAAA
131 CACGATTTCAGCTAAAAACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATATTCAAAAAA
* * * * ** *
1483 AATATATAATTCAACGCCAATAAGATCGATAGGTTTTTCACGCTTCTAATATCGTTTTTTCAT-G
196 AATATATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGTTTCTAATATCGTTTTTTTTTCA
1547 TTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA-CCCT
261 TTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCC-
** *
1611 TAAATCCATTGTGACTGAGATTTGGTTAGAAAAATATAGATATTTCAAGGAGTCGTTCTGCCAAA
325 TAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCTTCTGCCAAA
* * * * *
1676 AATCATGCAAAACAGAGCCGGAGCCCCGAAACGCATTTCTAGCTAAAATCAGTGATGGTTAGTAC
390 AATCATGCAAAACAGAGCCGGAGCCCCGAAATGCGTTTCTAACAAAAAACAGTGATGGTTAGTAC
* * * *
1741 ACGTTTTCGGTTAAAAATTAATCCGAAAAGATTTTTTCTCAATTTTTTGCAAAATGTTCAGAAAC
455 ACGATTTCGGCTAAAAATTAA-CCGAAAA-TTTTTTTCTCAATTTTTTGCAAAATGTTCAGAAAA
* * * * *
1806 AATATTTAATTTAACGCTAAAAAGATTGACAGGCTTTTAACGCTTTTAACATCGTTTTTTCATTT
518 AATATGTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAACATCGTTTTTTCA---
* * *
1871 TTTTTTTCGACGTT-ATTTCAAATTAAATCGAAACAATATTCAGATGCGCGTAAAAACAAATCC
580 TTTTTTTCGAC-TTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATCT
** * * *
1934 TTAAATTTATTGTGACTGAGATTTGGTTATATGAATATACATATTTAAAGGAGTCCTTCTGCCAA
1 TTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCAA
* *
1999 AAATCATGCAAAACTGAGCAGGGGCCCCGAAACGCGTTTCTAGCCAAAAACCATGATGGTTAGTA
66 AAATCATGCAAAACTGAGCAGGGGCCCCGAAACGCATTTCTAGCCAAAAACCGTGATGGTTAGTA
2064 CAC
131 CAC
2067 CCCAGCTCAG
Statistics
Matches: 1280, Mismatches: 123, Indels: 37
0.89 0.09 0.03
Matches are distributed among these distances:
638 4 0.00
639 73 0.06
640 10 0.01
641 135 0.11
642 48 0.04
643 246 0.19
644 7 0.01
645 289 0.23
646 182 0.14
647 2 0.00
648 240 0.19
649 44 0.03
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (642 bp):
TTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCAA
AAATCATGCAAAACTGAGCAGGGGCCCCGAAACGCATTTCTAGCCAAAAACCGTGATGGTTAGTA
CACGATTTCAGCTAAAAACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATATTCAAAAAA
AATATATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGTTTCTAATATCGTTTTTTTTTCA
TTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCCT
AAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCTTCTGCCAAAA
ATCATGCAAAACAGAGCCGGAGCCCCGAAATGCGTTTCTAACAAAAAACAGTGATGGTTAGTACA
CGATTTCGGCTAAAAATTAACCGAAAATTTTTTTCTCAATTTTTTGCAAAATGTTCAGAAAAAAT
ATGTAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTCTAACATCGTTTTTTCATTTTTT
TCGACTTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATCT
Found at i:1877 original size:967 final size:962
Alignment explanation
Indices: 3--2066 Score: 2711
Period size: 967 Copynumber: 2.1 Consensus size: 962
1 CT
* *
3 TAAATCCATTGTGACTGAGATTTGGTTAGAAGAATATAGATATTTCAAGGAG-CCGTTCTGCCAA
1 TAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGTCC-TTCTGCCAA
*
67 AAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCATTTCTAGCAAAAAACAGTGATGGTTAGTA
65 AAATCATGCAAAACAGAG-CGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGATGGTTAGTA
* *
132 CACATTTTCGGTTAAAAATTAACCCGAAAAGGTTTTTTCTCAATATTTTTAAAAATATTGAGAAA
129 CACATTTTCGGCTAAAAATTAACCCGAAAAGGTTTTTTCTCAATATTTTTAAAAATATTCAGAAA
* *
197 AAAATATATAATTTAACGCCAAAAAGATTGACGGGCTTTTCACGTATCTAATATCGCTTTTTTTT
194 AAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGTATCTAACATCGCTTTTTTTT
* * * * ** *
262 TCAAATTTATTTCAAATTAAATCGAAACACGATTCCGATGCTTGTAAAAACAAATCCTTAAATCT
259 TCAAATTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATCCTTAAATCC
*
327 ATTGTGACTGAGATTTGGTTAGATGAATATAGATATTAAAAGGAGTTTTTCTGCCAAAAATCATG
324 ATTGTGACTGAGATTTGGTTAGATGAATATAGATATTAAAAGGAGTCTTTCTGCCAAAAATCATG
* ** * *
392 CAAAACAGAGCCGGAGCCCCGTAATGCGTTTCTAACAAAAAACAATGATGCTTAATACACGATTT
389 CAAAACAGAGCAGGAGCCCCAAAACGCATTTCTAACAAAAAACAATGATGCTTAATACACGATTT
** * * * *
457 CGGCTAAAAATTAACCCGAAATGTTTTTTTCTCAATTTTTTGCAAAATGTTCAGAAAAAATATGT
454 AAGCTAAAAACTAACCCGAAATG-TTTTTTCTCAATTTTTTGCAAAATATTCAAAAAAAATATAT
* * *
522 AATTCAATGCCAAAAAGATTGACACGCTTTTCACGCTTCTAACATTGTTTTTTCATTATTTTTTT
518 AATTCAACGCCAAAAAGATCGACACGCTTTTCACGCTTCTAACATCGTTTTTTCATTATTTTTTT
* * * * * * *
587 CGACTTGCTTTAAAATTAATTCGAAACAAGATTCAGATGCGCTTAAAAACAAATCTTTAAATCCT
583 CGAATTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAACCCTTAAATCCA
* ** * *
652 TTGTGACTGAGATTTTGTTAGATGAATATAGATTTTTAAAGGAGTCTTTCTGCCAAAAATCATGC
648 TTGTGACTGAGATTTGGTTAGAAAAATATAGATATTTAAAGGAGTCGTTCTGCCAAAAATCATGC
* *
717 AAAACTAAGCAAGGGCCCCGAAACGCGTTTATAGCCAAAAACCGTGATGGTTAATACACGATTTC
713 AAAACTAAGCAAGGGCCCCGAAACGCATTTATAGCCAAAAACAGTGATGGTTAATACACGATTTC
* *
782 AGCTAAAAACTGACCTGAAGAGTTTTTCTCAATTTTTCAGGAAAATATTCAGAAAAAATATAGAA
778 AGCTAAAAACTAACCTGAAGAGTTTTTCTCAATTTTTCAGCAAAATATTCAGAAAAAATATAGAA
* ** * * * * *
847 TTCCACGCCAAAAAGATTGATGGGTTTTTCATGTTTCTAATATCGTTTTTTTTTTCATTTTTTTC
843 TTCAACGCCAAAAAGATTGACAGGCTTTTAACGTTTCTAACATCGTTTTTTATTT-ATTTTTTTC
* * *
912 GAATTTATTTCAAATTAAGTCGAAAAAAAATTCAGATGCTCGTAAAAACAAATCCC
907 GAAGTTATTTCAAATTAAATCGAAAAAAAATTCAGATGCGCGTAAAAACAAATCCC
* *
968 TAAATCCATTGTGACTAAGATTTGGTTAGATGAATATAAATATTTCAAGGTGTCCTTCTGCCAAA
1 TAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGTCCTTCTGCCAAA
* *
1033 AATCATGCAAAACAGAGTCGGAGCCCCGAAATGCGTTTCTAACAAAAAAACAGTGATGGTTAGTA
66 AATCATGCAAAACAGAG-CGGAGCCCCGAAACGCGTTTCTAGC-AAAAAACAGTGATGGTTAGTA
* * * *
1098 CACGA-TTTCGGCTAAAAATTAACCTGAAAA-TTTTTTTCTCAAT-TTTTTGCAAAATGTTCAG-
129 CAC-ATTTTCGGCTAAAAATTAACCCGAAAAGGTTTTTTCTCAATATTTTT-AAAAATATTCAGA
* *
1159 AAAAAATATGTAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCT-TCTAACATCGTTTTTT
192 AAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACG-TATCTAACATCG---CTT
* * *
1223 CATTTTTTTCGACTTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATCT
253 --TTTTTTTCAAATTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATCC
*
1288 TTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTTAAAGGAGTCTTTCTGCCAA
316 TTAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAGATATTAAAAGGAGTCTTTCTGCCAA
* * * * ** * *
1353 AAATCATGCAAAACTGAGCAGGGGCCCCAAAACGCATTTCTAGCCAAAAACCGTGATGGTTAGTA
381 AAATCATGCAAAACAGAGCAGGAGCCCCAAAACGCATTTCTAACAAAAAACAATGATGCTTAATA
* * *
1418 CACGATTTAAGCTAAAAACTGACCCGAGGA-G-TTTTTCTCAATTTTTCTGGAAAATATTCAAAA
446 CACGATTTAAGCTAAAAACTAACCCGA-AATGTTTTTTCTCAATTTTT-TGCAAAATATTCAAAA
* * * * *
1481 AAAATATATAATTCAACGCCAATAAGATCGATAGGTTTTTCACGCTTCTAATATCGTTTTTTCA-
509 AAAATATATAATTCAACGCCAAAAAGATCGACACGCTTTTCACGCTTCTAACATCGTTTTTTCAT
* * * *
1545 TGTTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAACCC
574 TATTTTTTTCGAATTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAACCC
*
1610 TTAAATCCATTGTGACTGAGATTTGGTTAGAAAAATATAGATATTTCAAGGAGTCGTTCTGCCAA
639 TTAAATCCATTGTGACTGAGATTTGGTTAGAAAAATATAGATATTTAAAGGAGTCGTTCTGCCAA
* * * * *
1675 AAATCATGCAAAAC-AGAGC-CGGAGCCCCGAAACGCATTTCTAGCTAAAATCAGTGATGGTTAG
704 AAATCATGCAAAACTA-AGCAAGG-GCCCCGAAACGCATTTATAGCCAAAAACAGTGATGGTTAA
* * * * * * *
1738 TACACGTTTTCGGTTAAAAATTAATCC-GAAAAGATTTTTTCTCAATTTTT-TGCAAAATGTTCA
767 TACACGATTTCAGCTAAAAACTAA-CCTG--AAGAGTTTTTCTCAATTTTTCAGCAAAATATTCA
* ** * *
1801 GAAACAATATTTAATTTAACGCTAAAAAGATTGACAGGCTTTTAACGCTTT-TAACATCGTTTTT
829 GAAAAAATATAGAATTCAACGCCAAAAAGATTGACAGGCTTTTAACG-TTTCTAACATCGTTTTT
* * *
1865 TCATTT-TTTTTTTCGACGTTATTTCAAATTAAATCGAAACAATATTCAGATGCGCGTAAAAACA
893 T-ATTTATTTTTTTCGAAGTTATTTCAAATTAAATCGAAAAAAAATTCAGATGCGCGTAAAAACA
*
1929 AATCCT
957 AATCCC
** * * *
1935 TAAATTTATTGTGACTGAGATTTGGTTATATGAATATACATATTTAAAGGAGTCCTTCTGCCAAA
1 TAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGTCCTTCTGCCAAA
* * *
2000 AATCATGCAAAACTGAGCAGGGGCCCCGAAACGCGTTTCTAGCCAAAAACCA-TGATGGTTAGTA
66 AATCATGCAAAACAGAGC-GGAGCCCCGAAACGCGTTTCTAG-CAAAAAACAGTGATGGTTAGTA
2064 CAC
129 CAC
2067 CCCAGCTCAG
Statistics
Matches: 953, Mismatches: 125, Indels: 41
0.85 0.11 0.04
Matches are distributed among these distances:
964 58 0.06
965 119 0.12
966 68 0.07
967 360 0.38
968 130 0.14
969 217 0.23
970 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (962 bp):
TAAATCCATTGTGACTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGTCCTTCTGCCAAA
AATCATGCAAAACAGAGCGGAGCCCCGAAACGCGTTTCTAGCAAAAAACAGTGATGGTTAGTACA
CATTTTCGGCTAAAAATTAACCCGAAAAGGTTTTTTCTCAATATTTTTAAAAATATTCAGAAAAA
AATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGTATCTAACATCGCTTTTTTTTTC
AAATTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAATCCTTAAATCCAT
TGTGACTGAGATTTGGTTAGATGAATATAGATATTAAAAGGAGTCTTTCTGCCAAAAATCATGCA
AAACAGAGCAGGAGCCCCAAAACGCATTTCTAACAAAAAACAATGATGCTTAATACACGATTTAA
GCTAAAAACTAACCCGAAATGTTTTTTCTCAATTTTTTGCAAAATATTCAAAAAAAATATATAAT
TCAACGCCAAAAAGATCGACACGCTTTTCACGCTTCTAACATCGTTTTTTCATTATTTTTTTCGA
ATTGATTTAAAATTAAATCGAAACAAGATTCAGATGCGCGTAAAAACAAACCCTTAAATCCATTG
TGACTGAGATTTGGTTAGAAAAATATAGATATTTAAAGGAGTCGTTCTGCCAAAAATCATGCAAA
ACTAAGCAAGGGCCCCGAAACGCATTTATAGCCAAAAACAGTGATGGTTAATACACGATTTCAGC
TAAAAACTAACCTGAAGAGTTTTTCTCAATTTTTCAGCAAAATATTCAGAAAAAATATAGAATTC
AACGCCAAAAAGATTGACAGGCTTTTAACGTTTCTAACATCGTTTTTTATTTATTTTTTTCGAAG
TTATTTCAAATTAAATCGAAAAAAAATTCAGATGCGCGTAAAAACAAATCCC
Found at i:2618 original size:288 final size:288
Alignment explanation
Indices: 2077--2642 Score: 748
Period size: 288 Copynumber: 2.0 Consensus size: 288
2067 CCCAGCTCAG
* * * *
2077 TTTTGCATAATTTTTGCCGTCAAGACTCACTGAAATACATATATTTATCTAACCGAATCTCAACC
1 TTTTGCATAATTTTTGCCGCCAAAACTCACTGAAATACATATATTCATCTAACCAAATCTCAACC
* *
2142 ACATTTGATTTAAGGATTTGTTATTACGAGTATCTAATTTATGTTTCGATTTAGTCAGAAATTAA
66 ACATTTGATTTAAGGATTTGTTATTACGAGTATCTAATTCATGTTTCGATTTAATCAGAAATTAA
* * *
2207 TTCGTAAAATATAGCAAATACGATATTAGAAGCGTGAAAAGCCTTTCATTTTTATGGCATTGAAT
131 TTCGTAAAATATAGCAAATACGAAATTAGAAGAGTGAAAAGCCCTTCATTTTTATGGCATTGAAT
* * * * * * *
2272 TATATGTTTTTTATGAGTATTGTGGATAAAAATTGAGGAAAATTCTTCCGGATCAGTTTTTTACA
196 TATATATTTTTTAAGAGTAATGTGGACAAAAATTAAGAAAAATTCTTCAGGATCAG-TTTTTA-A
2337 AAAATTT-AGCGGAAATCGTATACCAAAAA
259 AAAATTTAAGCGGAAATCGTATACCAAAAA
* * * ** * * **
2366 TTTTGCATGATTTTTGTCGCCAAAACTCATTGAAATATGTGTATTCATGTAACCAAATCTCAGTC
1 TTTTGCATAATTTTTGCCGCCAAAACTCACTGAAATACATATATTCATCTAACCAAATCTCAACC
* *
2431 ACATTTGATTTAAGG-TTTTTTTTTACGAGTATCTGAA-TCATGTTTCGATTTAATCAGAAATTA
66 ACATTTGATTTAAGGATTTGTTATTACGAGTATCT-AATTCATGTTTCGATTTAATCAGAAATTA
* *
2494 ATTC-TGAAAA-ATAGGAAATACGAAATTAGAAGAGTGAAAAGCCCTTCATTCTTTTTGGCATTG
130 ATTCGT-AAAATATAGCAAATACGAAATTAGAAGAGTGAAAAGCCCTTCATT-TTTATGGCATTG
* *
2557 AATTATATATTTTTTAAGAGTAATGTGGCCAAAAATTAAAGAAAAATTCTTTAGG-TCAGTTTTT
193 AATTATATATTTTTTAAGAGTAATGTGGACAAAAATT-AAGAAAAATTCTTCAGGATCAGTTTTT
*
2621 AAAAAATTTAAGCTGAAATCGT
257 AAAAAATTTAAGCGGAAATCGT
2643 GTACTAATCC
Statistics
Matches: 240, Mismatches: 32, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
286 8 0.03
287 54 0.22
288 96 0.40
289 82 0.34
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (288 bp):
TTTTGCATAATTTTTGCCGCCAAAACTCACTGAAATACATATATTCATCTAACCAAATCTCAACC
ACATTTGATTTAAGGATTTGTTATTACGAGTATCTAATTCATGTTTCGATTTAATCAGAAATTAA
TTCGTAAAATATAGCAAATACGAAATTAGAAGAGTGAAAAGCCCTTCATTTTTATGGCATTGAAT
TATATATTTTTTAAGAGTAATGTGGACAAAAATTAAGAAAAATTCTTCAGGATCAGTTTTTAAAA
AATTTAAGCGGAAATCGTATACCAAAAA
Found at i:2945 original size:333 final size:324
Alignment explanation
Indices: 2397--3614 Score: 1243
Period size: 333 Copynumber: 3.7 Consensus size: 324
2387 AAAACTCATT
* * * * * * * *
2397 GAAATATGTGTATTCATGTAACCAAATCTCAGTCACATTTGATTTAAGG-TTTTTTTTTACGAGT
1 GAAATATCTATATTCATCTAACCAAATATCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
*
2461 ATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCTG-AAAAATAGGAAATACGAAATTAGAA
66 ATCTGAATCATGTTTCGATTTAATCAGAAATTAATTC-GAAAAAATAGGAAATACGATATTAGAA
* *
2525 GAGTGAAAAGCCCTTCATTCTTTTTGGCATTGAATTATATATTTTTTAAGAGTAATGTGGCCAAA
130 GCGTGAAAAGCCCTTCATTCTTTTTGGCATTGAATTATATATTTTTTATGAGTAATGTGGCCAAA
* * *
2590 AATTAAAGAAAAATTCTTTAGGTCAGTTTTTAAAAAATTTAAGCTGAAATCGTGTACTAATCCAT
195 AATTAAGGAAAAAAT-TTTAGGTCAGTTTTTAAAAAATTT-AGCTGAAATCATGTACTAA-CCAT
* *
2655 CAAAGTTTTTGGCTAAAAACGTGTTCCGAGTCCCCGACTTAGTTTTGCATGATTTTTCGTACCGA
257 CACAGTTTTT-GCTAAAAACGCGTTCCGAGTCCCCGACTTAGTTTTGCATGATTTTTCG--CC-A
2720 GACTAAC
318 GACTAAC
* * * *
2727 GAAAATACCTATATTCATTTAACCAAATCTCAGCCACATTTGATTTAAGGATTTGTTTTTACGAG
1 G-AAATATCTATATTCATCTAACCAAATATCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* *
2792 TATCTGAATCATGTTTCAATTTAATCAGAAATTAATTCAGAAAAAATAGGAAATACGATATTAGA
65 CATCTGAATCATGTTTCGATTTAATCAGAAATTAATTC-GAAAAAATAGGAAATACGATATTAGA
* * * * *
2857 AGCGTGAAAAGGCCTTCATTTTTTTTGGCATTGAATTATATATCTTTTATGAGTATTGTTGCCAA
129 AGCGTGAAAAGCCCTTCATTCTTTTTGGCATTGAATTATATATTTTTTATGAGTAATGTGGCCAA
** * *
2922 AAATTAAGGAAAAAAATTTTAGGTCAGTGTTTGCAAAATTTTAGCTGAAATCATGTACTAACCGT
194 AAATTAAGG-AAAAAATTTTAGGTCAGT-TTTTAAAAAATTTAGCTGAAATCATGTACTAACCAT
* * * * *
2987 CACCGTTTTTTCAATTAAAAACGCGTTCCGAGGCCTCGATTATAG-TTTGCATGATTTTTGGCGC
257 CACAGTTTTTGC---TAAAAACGCGTTCCGAGTCCCCGACT-TAGTTTTGCATGATTTTT--CGC
3051 CA-A--AAC
316 CAGACTAAC
** * ** * ** *
3057 TCAATATGTGCATTCATCAAACCAAATAAAAGCCACATTGGATTTAAGGATTTGTTTTTACAAGC
1 GAAATATCTATATTCATCTAACCAAATATCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
*
3122 ATCTGAATCATGTTTCGATTTAATCAGAAATTAATTTCGAAAAAATAGAAAATACGATATTAGAA
66 ATCTGAATCATGTTTCGATTTAATCAGAAATTAA-TTCGAAAAAATAGGAAATACGATATTAGAA
* * * * * * * * * * **
3187 GTGTCAAAACCCCTTCATT-TTTTCGGCATTCAAGTATATGTTTTTAATGAGTATTCTGGATAAA
130 GCGTGAAAAGCCCTTCATTCTTTTTGGCATTGAATTATATATTTTTTATGAGTAATGTGGCCAAA
* * * * * * * ** *
3251 AATTGAGG--AAAATTCTTCCGAATTAGTTTTCGAAAAAATTTAGCCGAAATAATACACTAACTA
195 AATTAAGGAAAAAATT-TT-AG-GTCAGTTTT-TAAAAAATTTAGCTGAAATCATGTACTAACCA
* * *** * * *
3314 TCACAGTCTTTAGTTAAAAACGCGTGATGGGTCCCC-AGCTCAGTTTTGCATGGTTGTTGTCGCC
256 TCACAGT-TTTTGCTAAAAACGCGTTCCGAGTCCCCGA-CTTAGTTTTGCATGATT-TT-TCGCC
**
3378 AAGACTCATT
317 -AGACT-AAC
* * **
3388 GAAATATCTATAATT-ATCTAACCAAATATCAGCCACATTGGATTCACGGATTACTTTTTACGAG
1 GAAATATCTAT-ATTCATCTAACCAAATATCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* * *
3452 CATCTAAATCATGTTTCGATTTAATCAGAAATTTAATTCGGGAAAAATAGGAAATACGATATTAA
65 CATCTGAATCATGTTTCGATTTAATCAGAAA-TTAATTC-GAAAAAATAGGAAATACGATATTAG
* * * *
3517 AAACGTGAAAAACCCTTCATTCTTTTAGGCATTGAATTATATATTTTTTACGAGTAATGTGGCCA
128 AAGCGTGAAAAGCCCTTCATTCTTTTTGGCATTGAATTATATATTTTTTATGAGTAATGTGGCCA
* *
3582 AAAATTAAGGAAAAATTTTTTGGGTCAGTTTTT
193 AAAATTAAGGAAAAA-ATTTTAGGTCAGTTTTT
3615 G
Statistics
Matches: 731, Mismatches: 124, Indels: 64
0.80 0.13 0.07
Matches are distributed among these distances:
325 9 0.01
326 33 0.05
327 7 0.01
328 78 0.11
329 128 0.18
330 7 0.01
331 125 0.17
332 109 0.15
333 168 0.23
334 55 0.08
335 8 0.01
336 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (324 bp):
GAAATATCTATATTCATCTAACCAAATATCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
ATCTGAATCATGTTTCGATTTAATCAGAAATTAATTCGAAAAAATAGGAAATACGATATTAGAAG
CGTGAAAAGCCCTTCATTCTTTTTGGCATTGAATTATATATTTTTTATGAGTAATGTGGCCAAAA
ATTAAGGAAAAAATTTTAGGTCAGTTTTTAAAAAATTTAGCTGAAATCATGTACTAACCATCACA
GTTTTTGCTAAAAACGCGTTCCGAGTCCCCGACTTAGTTTTGCATGATTTTTCGCCAGACTAAC
Done.