Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010007.1 Corchorus olitorius cultivar O-4 contig10039, 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: 4443
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Found at i:864 original size:333 final size:333
Alignment explanation
Indices: 53--4439 Score: 5411
Period size: 333 Copynumber: 13.1 Consensus size: 333
43 AAACTGTGAT
*
53 GTACACGATTTCGGCTAAAAATTTGCAAAAA-TGACCCGAAATA-TTTTCCTCAATTTTTGGCCG
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTGGCCG
* * * *
116 AAATACTGATGAAAAATATATAATTCAACACCGAAAAGATATAAGGGTTTTTCACTCTTCTAACA
66 AAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTAACA
* * * *
181 TCGATTTTCGTACTTTTTGT-TGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATACTCGT
131 TCGATTTTCCTA-TTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTCGT
*
245 AAAAACAAATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAATTTT
195 AAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTC------
* * * * * ** *
310 GAAGGAGTCTTGGCACCAAAAATCGTGCAAAACTGAGCCGAGGCCCTGAAACTTGTTTTTAACCA
254 -AAGGAGTCTCGGCACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCA
*
375 AAAACCGTGATAGTTA
318 AAAACCGTGATGGTTA
* * *
391 GTACACGATTTTGAG-TAAAATTCTGCAAAAATTGAACCCGAAATATTTTTCCTCAATTTTTGGT
1 GTACACGATTTCG-GCTAAAATTTTGCAAAAATTG-ACCCGAAATATTTTTCCTCAATTTTTGGC
** *
455 CGAAATACTCATAAAAAATATATAATTCAACGAGAAAAA-ACTATAAGTGTTTTTCACTCTTCTA
64 CGAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGA-TATAAGGGTTTTTCACTCTTCTA
* *
519 ACATCAATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATTTCTGATGCTC
128 ACATCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTC
* * * *
584 GTAAAAATAAATCCTTAAATCCAATGTGGCTGAGAATTGGTTAGATGAATATAGATATTTCAAGG
193 GTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAAGG
* * *
649 AGTCTCGGCACCAAAAATCACGAAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGACAAAAAC
258 AGTCTCGGCACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAC
714 CGTGATGGTTA
323 CGTGATGGTTA
* * *
725 GTACACGATTTCGGCTAAAATTTTACAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGTCG
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTGGCCG
* *
790 AAATACTCATAAAAAATATATAATTCAATGCCAAAAAGATATAAGGGCTTTTCACTCTTCTAACA
66 AAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTAACA
* * * *
855 TCGATTTTCCTATTTTTTTTTGAATTAATTTCTAATGAAATTGAAAACAGTTTCGGATGCTCGTA
131 TCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTCGTA
* * *
920 AAAAC-AATCCTTAAATCCAATGTGACTGGGATTTGGTTACATGAATATATATA-TTCTTAGGAG
196 AAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTC-AAGGAG
* * * * **
983 TCTCGGCACTAAAAATCATGCAAAACTGAGCCGGGACACCGGTACGCGTTTTTAGCC-AAAACCG
260 TCTCGGCACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCG
1047 TGATGGTTA
325 TGATGGTTA
* * * * *
1056 CTACACGATTTCGGCTAATATTTTGCAAAAACTGACCCGAAATATTTTTCCTTAATTTTTGTCC-
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTGGCCG
* *
1120 ATAATACTCATGAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCGTCTAAC
66 A-AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTAAC
* * * *
1185 ATCGATTTTCGTATTTTTTTTTCTGAATTAATTTCTAATGAAATTGAAAACGGTTTCGGATACTC
130 ATCGATTTTCCTA--TTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTC
*
1250 GTAAAAAAAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAATT
193 GTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAG--A--T--A-T
* * * * * * * *
1315 TTCAAGGAGTCTTGACACCAAAAATCATG-AAAACTGAGCCAGGGTCCCGGAACGCATTTTTATC
251 TTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGC
*
1379 CAAAAACCGTTATGGTTA
316 CAAAAACCGTGATGGTTA
* * *
1397 GTACACGATTTCGTCTAAAATTTTACAAAAATTGAACCAGAAATATTTTTCCTCAATTTTTGGCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTG-ACCCGAAATATTTTTCCTCAATTTTTGGCC
* * * *
1462 AAAATACTCA-AAAAACATATATTATTCAACGACAAAAAGATATAAGGGGTTTTCACTCTTCTAA
65 GAAATACTCATAAAAA-ATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTAA
* * *
1526 CATCGATTTTCCCA-TTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATTTCTGATGGTCG
129 CATCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTCG
* * * * *
1590 TAAAAACAAATCTTTAAATCCAATATGGCTGCGATTTGGTTAGATGAATATAGATATTTCAAGGA
194 TAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAAGGA
* * * * * * *
1655 GTCTCGGCACCAAAAATCACGGAAAATTGAGTCGGGGACCGGAAACACGTTTTTAGCAAAAAACC
259 GTCTCGGCACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACC
*
1720 GTGAT-G-CA
324 GTGATGGTTA
* * * * *
1728 -TACATGATTTCGGC-AAAATTTTTTCAAAAATTGACTCGAAATATATCTT-CTCAATTCTTGGC
1 GTACACGATTTCGGCTAAAA-TTTTGCAAAAATTGACCCGAAATAT-TTTTCCTCAATTTTTGGC
* *
1790 CGAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAGATATAAGGGCTTTTCACTCTTCTAA
64 CGAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTAA
* * *
1855 CATCGATTTTCCTA-TTTTTTCTGAATTAATTGCTAATGAACATGAAAACGGTTTCTGATGCTCA
129 CATCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTCG
* * * * *
1919 TAAAAACAAATCGTTAAATCCAATGTG-CTTGAGATTCGGTTACAGGAATAAAGATATTTCCAGG
194 TAAAAACAAATCCTTAAATCCAATGTGAC-TGAGATTTGGTTACATGAATATAGATATTTCAAGG
* * * *
1983 AGTCTCGGCACCAAAAATCATGCAAAACTGAGCCGTGGCCGC-AGAACGCGTTTTTAGCCAGAAA
258 AGTCTCGGCACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGA-AACGCGTTTTTAGCCAAAAA
2047 CCGTGAT-G---
322 CCGTGATGGTTA
* *
2055 GTACACGATTTCGGCTAAAATTTTGCAGATATTGACCCGAAAGGT-TCTTTTCCTCAATTTTTGG
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA--TAT-TTTTCCTCAATTTTTGG
* * * * *
2119 CTGCAATACTTATAAAAAGTATATAATTCAACGCC-AAAAGTTATAAGGGTTTTTCACTCTTCTA
63 CCGAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTA
* * * * * *
2183 ACATCGATTTTCGTACTTTTTT-TGAATTAATTTATAGTGAAATTGAAAACGGTTTCTGATACTC
128 ACATCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTC
*
2247 G-AAAAATCAAATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAAT
193 GTAAAAA-CAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAG--A--T--A-
* * *
2311 TTTCAAGGAGTCT-TG-ACCAAAAATCATGCAAAACTGAGAT-GGGGTCCCGGAACGCGTTTTTA
250 TTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAACTGAG-TCGGGGCCCCGAAACGCGTTTTTA
*
2373 GCCAAAAACCGTTATGGTTA
314 GCCAAAAACCGTGATGGTTA
* *
2393 GTACACGATTTCGGCTAAAATTTTGCAAAAATCGAACCCGAAATATTATTCCTCAATTTTTGGCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTG-ACCCGAAATATTTTTCCTCAATTTTTGGCC
* * * *
2458 AAAATACTCATAAAAGATATATAATTCAACGACAAAAAGATATAAGGGTTTTTCAATCTTCTAAC
65 GAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTAAC
* *
2523 ATCGATTTTCCTA-TTTTTTCTGAATCAATTTCTAATGAAAATGAAAACGATTTCTGATGCTCGT
130 ATCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTCGT
** * * * *
2587 AAAAACAAATCCTTAAATGAAATGTAACTGAGATTTAGTTAGATAAATATAGATATTTCAAGGAG
195 AAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAAGGAG
* * ** *
2652 TCTCGGCACCAAAAATCACGGAAAACTGAGTCGGGTACCCGAAACGCGTTTTTGGCCAAAAA-C-
260 TCTCGGCACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCG
***
2715 TG-TAACTA
325 TGATGGTTA
* * *
2723 GTATACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATAATTTTCCTCAATTTTTGGCCG
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTGGCCG
* *
2788 AAATACTCATAAAAAAATATATAATTCAACGCC-AAAAGATATAAGGACTTTTTCACTCTTCCAA
66 AAATACTCAT-AAAAAATATATAATTCAACGCCAAAAAGATATAAGG-GTTTTTCACTCTTCTAA
* * * *
2852 CATCTATTTTTCCTATTTTTTTCTGAATTAATTGCAAATGAAAATGAAAACGGTTTCCGATGCTC
129 CATCGA-TTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTC
* *
2917 GTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTCGGTTACA-GAATAAAGATATTTCAAGG
193 GTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAAGG
* * *
2981 AGTCTCGGCCCCAAAAATTCATGCAAAACT-ATGACGGGGCCCCCG-AATGCGTTTTTAGCCAAA
258 AGTCTCGGCACCAAAAA-TCATGCAAAACTGA-GTCGGGG-CCCCGAAACGCGTTTTTAGCCAAA
3044 AACCGTGAT-G--A
320 AACCGTGATGGTTA
* * *
3055 GTACACGATTTTGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTTTCCTCAATTTTTGGC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA--TATTTTTCCTCAATTTTTGGC
* * * * * * *
3120 TGTAATAATTATAAAAAAAATATAATTTAATGCC-AAAAGATATAAGGGTTTTTCACTCTTCTAA
64 CGAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTAA
* * *
3184 CATCGATTTTCCTA-TTTTTTCTGAATGAATTTTTAATGAAAATGAAAACGGTTTCTGATTCTCG
129 CATCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTCG
* *
3248 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTACATGAATATAGATATTTCAAGGA
194 TAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAAGGA
* * * *
3313 GTCTCAGCACCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGGGTTTTTAGCCAAAAACT
259 GTCTCGGCACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACC
3378 GTGATGGTTA
324 GTGATGGTTA
* * *
3388 TTAAACGATTTCGGCTAAAATTTTGC-AAAATCTGACCGGAAATATTTTTCCTCAATTTTTGGCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAAT-TGACCCGAAATATTTTTCCTCAATTTTTGGCC
**
3452 GAAATACTCATAAAAAATATATAATTCAATTCCAAAAAGATATAAGGGTTTTTTTTCACTCTTCT
65 GAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGG---TTTTTCACTCTTCT
* * * *
3517 AACATTGATTTT-CTAATTTTTTTTCTGCATTAATTTCTAATGAAAATGAAAACGATTTATGATG
127 AACATCGATTTTCCT-A-TTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATG
* * * *
3581 CTCGTAAAAACAAATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGAGATATGA
190 CTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCA
* * * * *
3646 AGGAGTCTCGGCGCCAAAAATCACGCAAAACTGAGTCGGGGCCTCGGAACGCATTTTTAGCCAAA
255 AGGAGTCTCGGCACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCC-AA
*
3711 AAACTGTGATGG--A
319 AAACCGTGATGGTTA
* * * *
3724 ATACACGATTACGGCAAAAATTTTGCAAAAATTGACACGAAATATATTTT-CTCAATTTTTGGCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATAT-TTTTCCTCAATTTTTGGCC
** **
3788 GAAATACTCATAAAAAATATATAATTCAAATCCAAAAAGATATAAGGACTTTTCACTCTTCTAAC
65 GAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTAAC
* * * *
3853 ATCGATTTT-CTAATTTTTTTCTGAATTAATTGCTAATGAACATGAAAACGGTTTCTGATTCTCA
130 ATCGATTTTCCT-ATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTCG
* * * * * * *
3917 TAAAAACAAATCCTTAAATCCAATGTGCCTTAGAATCGGTTACAGGAATAAAGATATTTCCAGGA
194 TAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAAGGA
* * * * *
3982 GTCTCGACACCAAAAATCATGCAAAACTGAGAT-GGGGCCCAGGAATGCGTTTTTAGCCAGAAAC
259 GTCTCGGCACCAAAAATCATGCAAAACTGAG-TCGGGGCCCCGAAACGCGTTTTTAGCCAAAAAC
*
4046 CGTGATGGTTT
323 CGTGATGGTTA
* ** *
4057 GTACACGATTTCGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTCTTCAATTTTTGGCCG
1 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTGGCCG
* * * *
4122 CAATACTTATAAAAAATATATAAATCAACGCC-AAAAGATATAAGGGGTTTTTCACTTTTCTAAC
66 AAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAA-GGGTTTTTCACTCTTCTAAC
** ** * * *
4186 ATCGATTTTTGTACTTTTTTT-AAAATTAATTTCTTATGAAATTGAAAACGGTTTCTGATACTCG
130 ATCGATTTTCCTA-TTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTCG
* * **
4250 -AAAAACAAATCCATAAATCCAATGTTACTGAGATTTGGTTACATGATTATATATTTCAATTTTC
194 TAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGA--ATATAGAT--A-TTTC
* ** * *
4314 AAGGAGTCTTGGCATCC-AAAATCATGCAAAACTGAGTTAGGGCCTCGGAACGCGTTTTTAGCCA
254 AAGGAGTCTCGGCA-CCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCA
*
4378 AAAACC--G-T--TAA
318 AAAACCGTGATGGTTA
*
4389 CGTACACGATTTCGGCTAAAATTTTGCAAAAATTAAACCCGAAATATTTTT
1 -GTACACGATTTCGGCTAAAATTTTGCAAAAATT-GACCCGAAATATTTTT
4440 TATC
Statistics
Matches: 3509, Mismatches: 435, Indels: 214
0.84 0.10 0.05
Matches are distributed among these distances:
328 38 0.01
329 431 0.12
330 283 0.08
331 307 0.09
332 523 0.15
333 565 0.16
334 252 0.07
335 32 0.01
336 110 0.03
337 275 0.08
338 193 0.06
339 108 0.03
340 47 0.01
341 250 0.07
342 94 0.03
343 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (333 bp):
GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTGGCCG
AAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTAACA
TCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTCGTA
AAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAAGGAGT
CTCGGCACCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGT
GATGGTTA
Found at i:2661 original size:667 final size:658
Alignment explanation
Indices: 1--4436 Score: 5277
Period size: 667 Copynumber: 6.7 Consensus size: 658
* * * * * *
1 CATGCAAAATTAAGCCGGGGCCCTGCAACGCGTTTTTAG-CTAAAACTGTGAT-GTACACGATTT
1 CATGCAAAACTGAGCCGGGGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGATGGTACACGATTT
* * * *
64 CGGCTAAAAATTTGCAAAAA-TGACCCGAAATATTTTCCTCAATTTTTGGCCGAAATACTGATGA
66 CGGCTAAAATTTTGCAAAAATTGACCCGAAATTTTTTCCTCAATTTTTGGCCGAAATACTCATAA
* *
128 AAAATATATAATTCAACACCGAAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTTTCGTA
131 AAAATATATAATTCAACGCC-AAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTTTCCTA
*
193 CTTTTTGTTGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATACTCGTAAAAACAAATCCA
195 CTTTTT-TTGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATGCTCGTAAAAACAAATCCA
* *
258 TAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAATTTTGAAGGAGTCTTGG
259 TAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATA-TTC-A-TTTCAAGGAGTCTCGG
* * * * ** *
323 CACCAAAAATCGTGCAAAACTGAGCCGAGGCCCTGAAACTTGTTTTTAACCAAAAACCGTGATAG
321 CACCAAAAATCATGCAAAACTGAG-TGGGGCCC-GGAACGCGTTTTTAGCCAAAAACCGTGAT-G
* * *
388 TTAGTACACGATTTTGAG-TAAAATTCTGCAAAAATTGAACCCGAAATATTTTTCCTCAATTTTT
383 --AGTACACGATTTCG-GCTAAAATTTTGCAAAAATTG-ACCCGAAATATTATTCCTCAATTTTT
* ** *
452 GGTCGAAATACTCATAAAAAATATATAATTCAACGAGAAAAA-ACTATAAGTGTTTTTCACTCTT
444 GGCCGAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGA-TATAAGGGTTTTTCACTCTT
* *
516 CTAACATCAATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATTTCTGATG
508 CTAACATCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATG
* * *
581 CTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGAATTGGTTAGATGAATATAGATATTTCA
573 CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGAATATAGATATTTCA
646 AGGAGTCTCGGCACCAAAAAT
638 AGGAGTCTCGGCACCAAAAAT
* * * * *
667 CACGAAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGACAAAAACCGTGATGGTTAGTACACG
1 CATGCAAAACTGAGCCGGGGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGAT-G---GTACACG
* * *
732 ATTTCGGCTAAAATTTTACAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGTCGAAATACT
62 ATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAT-TTTTTCCTCAATTTTTGGCCGAAATACT
* *
797 CATAAAAAATATATAATTCAATGCCAAAAAGATATAAGGGCTTTTCACTCTTCTAACATCGATTT
126 CATAAAAAATATATAATTCAACGCC-AAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTT
* * *
862 TCCTATTTTTTTTTGAATTAATTTCTAATGAAATTGAAAACAGTTTCGGATGCTCGTAAAAAC-A
190 TCCTA-CTTTTTTTGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATGCTCGTAAAAACAA
* * *
926 ATCCTTAAATCCAATGTGACTGGGATTTGGTTACATGAATATATATATTC--TT--AGGAGTCTC
254 ATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTCATTTCAAGGAGTCTC
* * * *
987 GGCACTAAAAATCATGCAAAACTGAGCCGGGACACCGGTACGCGTTTTTAGCC-AAAACCGTGAT
319 GGCACCAAAAATCATGCAAAACTGAG-TGGGGC-CCGGAACGCGTTTTTAGCCAAAAACCGTGAT
* * * * *
1051 GGTTACTACACGATTTCGGCTAATATTTTGCAAAAACTGACCCGAAATATTTTTCCTTAATTTTT
382 -G--AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTATTCCTCAATTTTT
* * *
1116 GTCC-ATAATACTCATGAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCGT
444 GGCCGA-AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTT
* * *
1180 CTAACATCGATTTTCGTATTTTTTTTTCTGAATTAATTTCTAATGAAATTGAAAACGGTTTCGGA
508 CTAACATCGATTTTCCTA--TTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGA
* * *
1245 TACTCGTAAAAAAAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTT
571 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGAATATAG--A--T
* *
1310 CAATTTTCAAGGAGTCTTGACACCAAAAAT
632 --A-TTTCAAGGAGTCTCGGCACCAAAAAT
* * * * *
1340 CATG-AAAACTGAGCCAGGGTCCC-GGAACGCATTTTTATCCAAAAACCGTTATGGTTAGTACAC
1 CATGCAAAACTGAGCC-GGGGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGAT-G---GTACAC
* * * *
1403 GATTTCGTCTAAAATTTTACAAAAATTGAACCAGAAATATTTTTCCTCAATTTTTGGCCAAAATA
61 GATTTCGGCTAAAATTTTGCAAAAATTG-ACCCGAAAT-TTTTTCCTCAATTTTTGGCCGAAATA
* * *
1468 CTCA-AAAAACATATATTATTCAACGACAAAAAGATATAAGGGGTTTTCACTCTTCTAACATCGA
124 CTCATAAAAA-ATATATAATTCAACG-CCAAAAGATATAAGGGTTTTTCACTCTTCTAACATCGA
* * * *
1532 TTTTCCCA-TTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATTTCTGATGGTCGTAAAAA
187 TTTTCCTACTTTTTT-TGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATGCTCGTAAAAA
** * * * *
1596 CAAATCTTTAAATCCAATATGGCTGCGATTTGGTTAGATGAATATAG--A-T-ATTTCAAGGAGT
251 CAAATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTCATTTCAAGGAGT
* * * * * *
1657 CTCGGCACCAAAAATCACGGAAAATTGAGTCGGGGACCGGAAACACGTTTTTAGCAAAAAACCGT
316 CTCGGCACCAAAAATCATGCAAAACTGAGT-GGGGCCCGG-AACGCGTTTTTAGCCAAAAACCGT
* * * *
1722 GATGCA-TACATGATTTCGGC-AAAATTTTTTCAAAAATTGACTCGAAATA-TATCTTCTCAATT
379 GATG-AGTACACGATTTCGGCTAAAA-TTTTGCAAAAATTGACCCGAAATATTAT-TCCTCAATT
* * *
1784 CTTGGCCGAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAGATATAAGGGCTTTTCACTC
441 TTTGGCCGAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTC
* *
1849 TTCTAACATCGATTTTCCTA-TTTTTTCTGAATTAATTGCTAATGAACATGAAAACGGTTTCTGA
506 TTCTAACATCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGA
* * * * *
1913 TGCTCATAAAAACAAATCGTTAAATCCAATGT-GCTTGAGATTCGGTTACAGGAATAAAGATATT
571 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC-TGAGATTTGGTTACATGAATATAGATATT
*
1977 TCCAGGAGTCTCGGCACCAAAAAT
635 TCAAGGAGTCTCGGCACCAAAAAT
* *
2001 CATGCAAAACTGAGCCGTGGCCGCAG-AACGCGTTTTTAGCCAGAAACCGTGATGGTACACGATT
1 CATGCAAAACTGAGCCGGGGCC-CAGAAACGCGTTTTTAGCCAAAAACCGTGATGGTACACGATT
* * * * *
2065 TCGGCTAAAATTTTGCAGATATTGACCCGAAAGGTTCTTTTCCTCAATTTTTGGCTGCAATACTT
65 TCGGCTAAAATTTTGCAAAAATTGACCCGAAA--TT-TTTTCCTCAATTTTTGGCCGAAATACTC
* *
2130 ATAAAAAGTATATAATTCAACGCCAAAAGTTATAAGGGTTTTTCACTCTTCTAACATCGATTTTC
127 ATAAAAAATATATAATTCAACGCCAAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTTTC
* * * *
2195 GTACTTTTTTTGAATTAATTTATAGTGAAATTGAAAACGGTTTCTGATACTCG-AAAAATCAAAT
192 CTACTTTTTTTGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATGCTCGTAAAAA-CAAAT
2259 CCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAATTTTCAAGGAGTCT
256 CCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATA-TTC-A-TTTCAAGGAGTCT
* *
2324 -TG-ACCAAAAATCATGCAAAACTGAGATGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTTA
318 CGGCACCAAAAATCATGCAAAACTGAG-TGGGG-CCCGGAACGCGTTTTTAGCCAAAAACCGTGA
*
2387 TGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATCGAACCCGAAATATTATTCCTCAATTT
381 T-G--AGTACACGATTTCGGCTAAAATTTTGCAAAAATTG-ACCCGAAATATTATTCCTCAATTT
* * * *
2452 TTGGCCAAAATACTCATAAAAGATATATAATTCAACGACAAAAAGATATAAGGGTTTTTCAATCT
442 TTGGCCGAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCT
* *
2517 TCTAACATCGATTTTCCTA-TTTTTTCTGAATCAATTTCTAATGAAAATGAAAACGATTTCTGAT
507 TCTAACATCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGAT
** ** * * *
2581 GCTCGTAAAAACAAATCCTTAAATGAAATGTAACTGAGATTTAGTTAGATAAATATAGATATTTC
572 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGAATATAGATATTTC
2646 AAGGAGTCTCGGCACCAAAAAT
637 AAGGAGTCTCGGCACCAAAAAT
* * * * * * * * *
2668 CACGGAAAACTGAGTCGGGTACCC-GAAACGCGTTTTTGGCCAAAAACTGTAACTAGTATACGAT
1 CATGCAAAACTGAGCCGGG-GCCCAGAAACGCGTTTTTAGCCAAAAACCGTGA-TGGTACACGAT
* *
2732 TTCAGCTAAAATTTTGCAAAAATTGACCCGAAATAATTTTCCTCAATTTTTGGCCGAAATACTCA
64 TTCGGCTAAAATTTTGCAAAAATTGACCCGAAAT-TTTTTCCTCAATTTTTGGCCGAAATACTCA
* * *
2797 TAAAAAAATATATAATTCAACGCCAAAAGATATAAGGACTTTTTCACTCTTCCAACATCTATTTT
128 T-AAAAAATATATAATTCAACGCCAAAAGATATAAGG-GTTTTTCACTCTTCTAACATCGA-TTT
* * * * *
2862 TCCTATTTTTTTCTGAATTAATTGCAAATGAAAATGAAAACGGTTTCCGATGCTCGTAAAAACAA
190 TCCTACTTTTTT-TGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATGCTCGTAAAAACAA
* * *
2927 ATCCTTAAATCCAATGTGACTGAGATTCGGTTACA-GAATA-A-AGA-T-ATTTCAAGGAGTCTC
254 ATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTCATTTCAAGGAGTCTC
* * * *
2987 GGCCCCAAAAATTCATGCAAAACTATGACG-GGGCCCCCGAATGCGTTTTTAGCCAAAAACCGTG
319 GGCACCAAAAA-TCATGCAAAAC--TGA-GTGGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTG
* * * *
3051 ATGAGTACACGATTTTGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTTTCCTCAATTTT
380 ATGAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA--TATTATTCCTCAATTTT
* * * * * * *
3116 TGGCTGTAATAATTATAAAAAAAATATAATTTAATGCC-AAAAGATATAAGGGTTTTTCACTCTT
443 TGGCCGAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTT
* * *
3180 CTAACATCGATTTTCCTA-TTTTTTCTGAATGAATTTTTAATGAAAATGAAAACGGTTTCTGATT
508 CTAACATCGATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATG
*
3244 CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTACATGAATATAGATATTTCA
573 CTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGAATATAGATATTTCA
*
3309 AGGAGTCTCAGCACCAAAAAT
638 AGGAGTCTCGGCACCAAAAAT
* * * *
3330 CATGCAAAACTGAGCCGGGGCCCCGAAACGGGTTTTTAGCCAAAAACTGTGATGGTTATTAAACG
1 CATGCAAAACTGAGCCGGGGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGATGG----TACACG
*
3395 ATTTCGGCTAAAATTTTGC-AAAATCTGACCGGAAATATTTTTCCTCAATTTTTGGCCGAAATAC
62 ATTTCGGCTAAAATTTTGCAAAAAT-TGACCCGAAAT-TTTTTCCTCAATTTTTGGCCGAAATAC
** *
3459 TCATAAAAAATATATAATTCAATTCCAAAAAGATATAAGGGTTTTTTTTCACTCTTCTAACATTG
125 TCATAAAAAATATATAATTCAACGCC-AAAAGATATAAGGG---TTTTTCACTCTTCTAACATCG
* * * * *
3524 ATTTT-CTAATTTTTTTTCTGCATTAATTTCTAATGAAAATGAAAACGATTTATGATGCTCGTAA
186 ATTTTCCT-A-CTTTTTT-TGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATGCTCGTAA
* *
3588 AAACAAATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGAGA-T-A--TGAAGG
248 AAACAAATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTCATTTCAAGG
* * *
3649 AGTCTCGGCGCCAAAAATCACGCAAAACTGAGTCGGGGCCTCGGAACGCATTTTTAGCCAAAAAA
313 AGTCTCGGCACCAAAAATCATGCAAAACTGAGT-GGGGCC-CGGAACGCGTTTTTAGCC-AAAAA
* * * * * *
3714 CTGTGATGGAATACACGATTACGGCAAAAATTTTGCAAAAATTGACACGAAATA-TATTTTCTCA
375 CCGTGAT-GAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTA-TTCCTCA
** **
3778 ATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAAATCCAAAAAGATATAAGGACTTTTCA
438 ATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCA
* *
3843 CTCTTCTAACATCGATTTT-CTAATTTTTTTCTGAATTAATTGCTAATGAACATGAAAACGGTTT
503 CTCTTCTAACATCGATTTTCCT-ATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTT
* * * * * * * *
3907 CTGATTCTCATAAAAACAAATCCTTAAATCCAATGTGCCTTAGAATCGGTTACAGGAATAAAGAT
567 CTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGAATATAGAT
* *
3972 ATTTCCAGGAGTCTCGACACCAAAAAT
632 ATTTCAAGGAGTCTCGGCACCAAAAAT
** * * *
3999 CATGCAAAACTGAGATGGGGCCCAGGAATGCGTTTTTAGCCAGAAACCGTGATGGTTTGTACACG
1 CATGCAAAACTGAGCCGGGGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGAT-G---GTACACG
* * * *
4064 ATTTCGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTCTTCAATTTTTGGCCGCAATACT
62 ATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-TTTTTTCCTCAATTTTTGGCCGAAATACT
* * *
4129 TATAAAAAATATATAAATCAACGCCAAAAGATATAAGGGGTTTTTCACTTTTCTAACATCGATTT
126 CATAAAAAATATATAATTCAACGCCAAAAGATATAA-GGGTTTTTCACTCTTCTAACATCGATTT
** * * *
4194 TTGTACTTTTTTTAAAATTAATTTCTTATGAAATTGAAAACGGTTTCTGATACTCG-AAAAACAA
190 TCCTACTTTTTTT-GAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATGCTCGTAAAAACAA
* * *
4258 ATCCATAAATCCAATGTTACTGAGATTTGGTTACATGATTATATAT-TTCAATTTTCAAGGAGTC
254 ATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTC-A-TTTCAAGGAGTC
* *
4322 TTGGCATCC-AAAATCATGCAAAACTGAGTTAGGGCCTCGGAACGCGTTTTTAGCCAAAAACCGT
317 TCGGCA-CCAAAAATCATGCAAAACTGAG-TGGGGCC-CGGAACGCGTTTTTAGCCAAAAACCGT
* *
4386 --TAACGTACACGATTTCGGCTAAAATTTTGCAAAAATTAAACCCGAAATATT
379 GATGA-GTACACGATTTCGGCTAAAATTTTGCAAAAATT-GACCCGAAATATT
4437 TTTTATC
Statistics
Matches: 3258, Mismatches: 387, Indels: 248
0.84 0.10 0.06
Matches are distributed among these distances:
657 12 0.00
658 150 0.05
659 45 0.01
660 6 0.00
661 45 0.01
662 286 0.09
663 95 0.03
664 190 0.06
665 222 0.07
666 303 0.09
667 488 0.15
668 255 0.08
669 356 0.11
670 92 0.03
671 131 0.04
672 160 0.05
673 268 0.08
674 149 0.05
675 5 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (658 bp):
CATGCAAAACTGAGCCGGGGCCCAGAAACGCGTTTTTAGCCAAAAACCGTGATGGTACACGATTT
CGGCTAAAATTTTGCAAAAATTGACCCGAAATTTTTTCCTCAATTTTTGGCCGAAATACTCATAA
AAAATATATAATTCAACGCCAAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTTTCCTAC
TTTTTTTGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATGCTCGTAAAAACAAATCCATA
AATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTCATTTCAAGGAGTCTCGGCACCA
AAAATCATGCAAAACTGAGTGGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGAGTACACG
ATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTATTCCTCAATTTTTGGCCGAAATACT
CATAAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTT
TCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGGTTTCTGATGCTCGTAAAAACAA
ATCCTTAAATCCAATGTGGCTGAGATTTGGTTACATGAATATAGATATTTCAAGGAGTCTCGGCA
CCAAAAAT
Found at i:3638 original size:999 final size:992
Alignment explanation
Indices: 1--4439 Score: 5976
Period size: 999 Copynumber: 4.4 Consensus size: 992
* * * * * * *
1 CATGCAAAATTAAGCCGGGGCCCTGCAACGCGTTTTTAG-CTAAAACTGTGAT-GTACACGATTT
1 CATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTACACGATTT
* * * * *
64 CGGCTAAAAATTTGCAAA-AATGACCCGAAA---TATTTTCCTCAATTTTTGGCCGAAATACTGA
66 CGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTTTCCTCAATTTTTGGCCGCAATACTTA
* *
125 TGAAAAATATATAATTCAACACCGAAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTTTC
131 TAAAAAATATATAATTCAACGCC-AAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTTTC
190 GTACTTTTTGTTGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATACTCGTAAAAACAAAT
195 GTACTTTTT-TTGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATACTCGTAAAAACAAAT
*
255 CCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAATTTTGAAGGAGTCT
259 CCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAG--A--T-AATTTTCAAGGAGTC-
* * * * ** * *
320 TGGCACCAAAAATCGTGCAAAACTGAGCCGAGGCCCTGAAACTTGTTTTTAACCAAAAACCGTGA
318 TGGCACCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTTA
* * *
385 TAGTTAGTACACGATTTTGAG-TAAAATTCTGCAAAAATTGAACCCGAAATATTTTTCCTCAATT
383 TGGTTAGTACACGATTTCG-GCTAAAATTTTGCAAAAATTGAACCCGAAATATTTTTCCTCAATT
* * * *
449 TTTGGTCGAAATACTCATAAAAAATATATAATTCAACGAGAAAAA-ACTATAAGTGTTTTTCACT
447 TTTGGCCAAAATACTCATAAAAAATATATAATTCAACGACAAAAAGA-TATAAGGGTTTTTCACT
*
513 CTTCTAACATCAATTTTCCTATTTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATTTCTG
511 CTTCTAACATCGATTTTCCTA-TTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATTTCTG
* * *
578 ATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGAATTGGTTAGATGAATATAGATATT
575 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGATATT
* * *
643 TCAAGGAGTCTCGGCACCAAAAATCACGAAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGAC
640 TCAAGGAGTCTCGGCACCAAAAATCACGGAAAACTGAGTCGGGGACCCGAAACGCGTTTTTAGCC
* * *
708 AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTACAAAAAATGACCCGAAATAT-TT
705 AAAAA-C-TG-T-GATAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATATT
* * *
772 TTCCTCAATTTTTGGTCGAAATACTCATAAAAAATATATAATTCAATGCCAAAAAGATATAAGGG
766 TT-CTCAATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAGATATAAGGA
* * *
837 CTTTTCACTCTTCTAACATCGATTTTCCTATTTTTTTTTGAATTAATTTCTAATGAAATTGAAAA
830 CTTTTCACTCTTCTAACATCGATTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAAATGAAAA
* * * * * *
902 CAGTTTCGGATGCTCGTAAAAAC-AATCCTTAAATCCAATGTGACTGGGATTTGGTTACATGAAT
895 CGGTTTCTGATGCTCATAAAAACAAATCCTTAAATCCAATGTGACTGAGATTCGGTTACAGGAAT
* * * *
966 ATATATA-TTCTTAGGAGTCTCGGCACTAAAAAT
960 AAAGATATTTC-CAGGAGTCTCGGCACCAAAAAT
* * * *
999 CATGCAAAACTGAGCCGGGACACCGGTACGCGTTTTTAGCC-AAAACCGTGATGGTTACTACACG
1 CATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGG----TACACG
* * * * * * **
1063 ATTTCGGCTAATATTTTGCAAAAACTGACCCGAAA--TATTTTTCCTTAATTTTTGTCCATAATA
62 ATTTCGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTTTCCTCAATTTTTGGCCGCAATA
* * *
1126 CTCATGAAAAATATATAATTCAACGCCAAAAAGATATAAGGGTTTTTCACTCGTCTAACATCGAT
127 CTTATAAAAAATATATAATTCAACGCC-AAAAGATATAAGGGTTTTTCACTCTTCTAACATCGAT
* *
1191 TTTCGTATTTTTTTTTCTGAATTAATTTCTAATGAAATTGAAAACGGTTTCGGATACTCGTAAAA
191 TTTCGTA--CTTTTTT-TGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATACTCGTAAAA
* *
1256 AAAAATCCTTAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAATTTTCAAG
253 ACAAATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAG--A--T-AATTTTCAAG
* * * * *
1321 GAGTCTTGACACCAAAAATCATG-AAAACTGAGCCAGGGTCCCGGAACGCATTTTTATCCAAAAA
313 GAGTC-TGGCACCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAA
* * *
1385 CCGTTATGGTTAGTACACGATTTCGTCTAAAATTTTACAAAAATTGAACCAGAAATATTTTTCCT
377 CCGTTATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACCCGAAATATTTTTCCT
* *
1450 CAATTTTTGGCCAAAATACTCA-AAAAACATATATTATTCAACGACAAAAAGATATAAGGGGTTT
442 CAATTTTTGGCCAAAATACTCATAAAAA-ATATATAATTCAACGACAAAAAGATATAAGGGTTTT
*
1514 TCACTCTTCTAACATCGATTTTCCCATTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATT
506 TCACTCTTCTAACATCGATTTTCCTATTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATT
* * * * *
1579 TCTGATGGTCGTAAAAACAAATCTTTAAATCCAATATGGCTGCGATTTGGTTAGATGAATATAGA
571 TCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGA
* * *
1644 TATTTCAAGGAGTCTCGGCACCAAAAATCACGGAAAATTGAGTCGGGGACCGGAAACACGTTTTT
636 TATTTCAAGGAGTCTCGGCACCAAAAATCACGGAAAACTGAGTCGGGGACCCGAAACGCGTTTTT
* * * * *
1709 AGCAAAAAACCGTGAT-GCATACATGATTTCGGC-AAAATTTTTTCAAAAATTGACTCGAAATAT
701 AGCCAAAAACTGTGATAG--TACACGATTTCGGCTAAAA-TTTTGCAAAAATTGACCCGAAATAT
* *
1772 ATCTTCTCAATTCTTGGCCGAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAGATATAAG
763 ATTTTCTCAATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAGATATAAG
* *
1837 GGCTTTTCACTCTTCTAACATCGATTTTCCTA-TTTTTTCTGAATTAATTGCTAATGAACATGAA
828 GACTTTTCACTCTTCTAACATCGATTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAAATGAA
*
1901 AACGGTTTCTGATGCTCATAAAAACAAATCGTTAAATCCAATGTG-CTTGAGATTCGGTTACAGG
893 AACGGTTTCTGATGCTCATAAAAACAAATCCTTAAATCCAATGTGAC-TGAGATTCGGTTACAGG
1965 AATAAAGATATTTCCAGGAGTCTCGGCACCAAAAAT
957 AATAAAGATATTTCCAGGAGTCTCGGCACCAAAAAT
* * * * *
2001 CATGCAAAACTGAGCCGTGGCCGCAGAACGCGTTTTTAGCCAGAAACCGTGATGGTACACGATTT
1 CATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTACACGATTT
* * *
2066 CGGCTAAAATTTTGCAGATATTGACCCGAAAGGTTCTTTTCCTCAATTTTTGGCTGCAATACTTA
66 CGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTTTCCTCAATTTTTGGCCGCAATACTTA
* *
2131 TAAAAAGTATATAATTCAACGCCAAAAGTTATAAGGGTTTTTCACTCTTCTAACATCGATTTTCG
131 TAAAAAATATATAATTCAACGCCAAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTTTCG
* *
2196 TACTTTTTTTGAATTAATTTATAGTGAAATTGAAAACGGTTTCTGATACTCG-AAAAATCAAATC
196 TACTTTTTTTGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATACTCGTAAAAA-CAAATC
*
2260 CATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATATTTCAATTTTCAAGGAGTCTT
260 CATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAG--A--T-AATTTTCAAGGAGTCTG
** *
2325 G-ACCAAAAATCATGCAAAACTGAGATGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTTATG
320 GCACCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTTATG
* *
2389 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATCGAACCCGAAATATTATTCCTCAATTTTT
385 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACCCGAAATATTTTTCCTCAATTTTT
* *
2454 GGCCAAAATACTCATAAAAGATATATAATTCAACGACAAAAAGATATAAGGGTTTTTCAATCTTC
450 GGCCAAAATACTCATAAAAAATATATAATTCAACGACAAAAAGATATAAGGGTTTTTCACTCTTC
*
2519 TAACATCGATTTTCCTATTTTTTCTGAATCAATTTCTAATGAAAATGAAAACGATTTCTGATGCT
515 TAACATCGATTTTCCTATTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATTTCTGATGCT
** * * *
2584 CGTAAAAACAAATCCTTAAATGAAATGTAACTGAGATTTAGTTAGATAAATATAGATATTTCAAG
580 CGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAG
* *
2649 GAGTCTCGGCACCAAAAATCACGGAAAACTGAGTCGGGTACCCGAAACGCGTTTTTGGCCAAAAA
645 GAGTCTCGGCACCAAAAATCACGGAAAACTGAGTCGGGGACCCGAAACGCGTTTTTAGCCAAAAA
* * *
2714 CTGTAACTAGTATACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATA-ATTTTCCTCAA
710 CTGTGA-TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATATTTT-CTCAA
*
2778 TTTTTGGCCGAAATACTCATAAAAAAATATATAATTCAACGCC-AAAAGATATAAGGACTTTTTC
773 TTTTTGGCCGAAATACTCAT-AAAAAATATATAATTCAAAGCCAAAAAGATATAAGGAC-TTTTC
* * *
2842 ACTCTTCCAACATCTATTTTTCCTATTTTTTTCTGAATTAATTGCAAATGAAAATGAAAACGGTT
836 ACTCTTCTAACATCGA-TTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAAATGAAAACGGTT
* *
2907 TCCGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTCGGTTACA-GAATAAAGA
900 TCTGATGCTCATAAAAACAAATCCTTAAATCCAATGTGACTGAGATTCGGTTACAGGAATAAAGA
* *
2971 TATTTCAAGGAGTCTCGGCCCCAAAAATT
965 TATTTCCAGGAGTCTCGGCACCAAAAA-T
* *
3000 CATGCAAAACT-ATGACGGGGCCCCCGAATGCGTTTTTAGCCAAAAACCGTGATGAGTACACGAT
1 CATGCAAAACTGA-GACGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG-GTACACGAT
* * * *
3064 TTTGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTTTCCTCAATTTTTGGCTGTAATAAT
64 TTCGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTTTCCTCAATTTTTGGCCGCAATACT
* * *
3129 TATAAAAAAAATATAATTTAATGCCAAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTTT
129 TATAAAAAATATATAATTCAACGCCAAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTTT
* * * * *
3194 CCTA-TTTTTTCTGAATGAATTTTTAATGAAAATGAAAACGGTTTCTGATTCTCGTAAAAACAAA
194 CGTACTTTTTT-TGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATACTCGTAAAAACAAA
* * * *
3258 TCCTTAAATCCAATGTGGCTGAGATTTTGTTACATGAATATAGAT-A-TTTCAAGGAGTCTCAGC
258 TCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATAATTTTCAAGGAGTCT-GGC
* * * *
3321 ACCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGGGTTTTTAGCCAAAAACTGTGATGGT
322 ACCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTTATGGT
* * *
3386 TATTAAACGATTTCGGCTAAAATTTTGC-AAAATCTG-ACCGGAAATATTTTTCCTCAATTTTTG
387 TAGTACACGATTTCGGCTAAAATTTTGCAAAAAT-TGAACCCGAAATATTTTTCCTCAATTTTTG
* ***
3449 GCCGAAATACTCATAAAAAATATATAATTCAATTCCAAAAAGATATAAGGGTTTTTTTTCACTCT
451 GCCAAAATACTCATAAAAAATATATAATTCAACGACAAAAAGATATAAGGG---TTTTTCACTCT
* * *
3514 TCTAACATTGATTTT-CTAATTTTTTTTCTGCATTAATTTCTAATGAAAATGAAAACGATTTATG
513 TCTAACATCGATTTTCCT-A--TTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATTTCTG
* * * *
3578 ATGCTCGTAAAAACAAATCCATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGAGATA
575 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGATATT
* * * * *
3643 TGAAGGAGTCTCGGCGCCAAAAATCACGCAAAACTGAGTCGGGG-CCTCGGAACGCATTTTTAGC
640 TCAAGGAGTCTCGGCACCAAAAATCACGGAAAACTGAGTCGGGGACC-CGAAACGCGTTTTTAGC
* * * *
3707 CAAAAAACTGTGATGGAATACACGATTACGGCAAAAATTTTGCAAAAATTGACACGAAATATATT
704 C-AAAAACTGTGAT--AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATATT
*
3772 TTCTCAATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAAATCCAAAAAGATATAAGGAC
766 TTCTCAATTTTTGGCCGAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAGATATAAGGAC
*
3837 TTTTCACTCTTCTAACATCGATTTT-CTAATTTTTTTCTGAATTAATTGCTAATGAACATGAAAA
831 TTTTCACTCTTCTAACATCGATTTTCCT-ATTTTTTTCTGAATTAATTGCTAATGAAAATGAAAA
* * * *
3901 CGGTTTCTGATTCTCATAAAAACAAATCCTTAAATCCAATGTGCCTTAGAATCGGTTACAGGAAT
895 CGGTTTCTGATGCTCATAAAAACAAATCCTTAAATCCAATGTGACTGAGATTCGGTTACAGGAAT
*
3966 AAAGATATTTCCAGGAGTCTCGACACCAAAAAT
960 AAAGATATTTCCAGGAGTCTCGGCACCAAAAAT
* * * *
3999 CATGCAAAACTGAGATGGGGCCCAGGAATGCGTTTTTAGCCAGAAACCGTGATGGTTTGTACACG
1 CATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT-G---GTACACG
*
4064 ATTTCGGCTAAAATTTTGCAAATATTGACCCGAAAGG--TTTTTCTTCAATTTTTGGCCGCAATA
62 ATTTCGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTTTCCTCAATTTTTGGCCGCAATA
* *
4127 CTTATAAAAAATATATAAATCAACGCCAAAAGATATAAGGGGTTTTTCACTTTTCTAACATCGAT
127 CTTATAAAAAATATATAATTCAACGCCAAAAGATATAA-GGGTTTTTCACTCTTCTAACATCGAT
* * *
4192 TTTTGTACTTTTTTTAAAATTAATTTCTTATGAAATTGAAAACGGTTTCTGATACTCG-AAAAAC
191 TTTCGTACTTTTTTT-GAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATACTCGTAAAAAC
* **
4256 AAATCCATAAATCCAATGTTACTGAGATTTGGTTACATGATTATATATTTCAATTTTCAAGGAGT
255 AAATCCATAAATCCAATGTGACTGAGATTTGGTTACATGA--ATATAGAT-AATTTTCAAGGAGT
*** *
4321 CTTGGCATCC-AAAATCATGCAAAACTGAGTTAGGGCCTCGGAACGCGTTTTTAGCCAAAAACCG
317 C-TGGCA-CCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCG
*
4385 TTA-----ACGTACACGATTTCGGCTAAAATTTTGCAAAAATTAAACCCGAAATATTTTT
380 TTATGGTTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGAACCCGAAATATTTTT
4440 TATC
Statistics
Matches: 3065, Mismatches: 301, Indels: 145
0.87 0.09 0.04
Matches are distributed among these distances:
993 13 0.00
994 78 0.03
995 102 0.03
996 421 0.14
997 181 0.06
998 97 0.03
999 471 0.15
1000 398 0.13
1001 260 0.08
1002 335 0.11
1003 70 0.02
1004 12 0.00
1005 260 0.08
1006 228 0.07
1007 139 0.05
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (992 bp):
CATGCAAAACTGAGACGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTACACGATTT
CGGCTAAAATTTTGCAAATATTGACCCGAAAGGTTTTTTTCCTCAATTTTTGGCCGCAATACTTA
TAAAAAATATATAATTCAACGCCAAAAGATATAAGGGTTTTTCACTCTTCTAACATCGATTTTCG
TACTTTTTTTGAATTAATTTCTAATGAAATTGAAAACGGTTTCTGATACTCGTAAAAACAAATCC
ATAAATCCAATGTGACTGAGATTTGGTTACATGAATATAGATAATTTTCAAGGAGTCTGGCACCA
AAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTTATGGTTAGT
ACACGATTTCGGCTAAAATTTTGCAAAAATTGAACCCGAAATATTTTTCCTCAATTTTTGGCCAA
AATACTCATAAAAAATATATAATTCAACGACAAAAAGATATAAGGGTTTTTCACTCTTCTAACAT
CGATTTTCCTATTTTTTCTGAATTAATTTCTAATGAAAATGAAAACGATTTCTGATGCTCGTAAA
AACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
CGGCACCAAAAATCACGGAAAACTGAGTCGGGGACCCGAAACGCGTTTTTAGCCAAAAACTGTGA
TAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATATTTTCTCAATTTTTGGC
CGAAATACTCATAAAAAATATATAATTCAAAGCCAAAAAGATATAAGGACTTTTCACTCTTCTAA
CATCGATTTTCCTATTTTTTTCTGAATTAATTGCTAATGAAAATGAAAACGGTTTCTGATGCTCA
TAAAAACAAATCCTTAAATCCAATGTGACTGAGATTCGGTTACAGGAATAAAGATATTTCCAGGA
GTCTCGGCACCAAAAAT
Done.