Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023861.1 Corchorus olitorius cultivar O-4 contig23894, 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: 3709
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:750 original size:320 final size:320
Alignment explanation
Indices: 22--3705 Score: 2978
Period size: 320 Copynumber: 11.5 Consensus size: 320
12 CTAATATCAT
* * * * *
22 TTTTTCGGAATTAATTTCAATTTAAATCGAAATAAGATTCAGTTGCTCGTAAAAACAAATCGTTA
1 TTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * *
87 AATCGAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTC-AAGAAGCCTTTACGCCAAAA
66 AATCCAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAAG-AGTCTTTACGACAAAA
* * * * *
151 ATCATGTAAAATTGAGCCGTGGACCCGGAACGTGTTTTTAGCAAAAAAACCGTGTTGGTTAGTAC
130 ATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGC-AAAAAACCGTGATGGTTAGTAC
* * * *
216 ACGATTTCGGCTAAAATTTTGTAAAAACTGA-TCCGAAAAATTTATCCTCAGTTTTTTTGCCACA
194 ACGATTTAGGC----------TAAAAACTGACT-CGAAAAATTTTTTCTCA-ATTTTTTGCCACA
* * ** * * * * *
280 ATAGGT-AGGACCAATATATAATTCAAAG-C-AAAAGAAATAAAGGGTTTTTCAAGCTTCTAATA
247 ATA-CTCAGAAAAAATATATAATTCAACGCCAAAAAG-ATTGACGGGTTTTTCACGCTTCTAATA
*
342 TCGTTTTTCCA
310 TCATTTTTCCA
* * * * * *
353 TTTTTTCGGATTTAATTTCTATTTAAATCGAAATAAGATTTAGATACTCGTAAAAACAAATTCTT
1 -TTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * * *
418 AAATCGAATGTGGCTGGGATTTGGTTCGATAAATATAGATATTTCAAAGAGTCTTTACAATAAAG
65 AAATCCAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTTACGACAAAA
** * *
483 ATCATGCAAAACTGAATCGGGGACCCAGAACGAGTTTTTAGCAAAAAACCGTGATGGTTAGTACA
130 ATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACA
* * * * * *
548 CGATTTAGGCTAAAAACTGAGTCGAAAATTTTTTTATGAATCTTTTGCCACAATACTTAGAAAAA
195 CGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA
* *
613 ATATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTACTATCATCTTTCCA
260 ATATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCA
* *
674 TTTTTAGGAATTATTTTCTATTTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
1 TTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * *
739 TATCCAATGTGGCTGGGATTTGGATCGA-AGAATATAAATATTT-TAAGAAGTCTTTACGCCAAA
66 AATCCAATGTGGCTGGGATTTGGTTAGATA-AATATAGATATTTCAAAG-AGTCTTTACGACAAA
* *
802 AATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAAACCGTGATGGTTAGTGC
129 AATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTAC
* * * * * *
867 AAGATTTCGGCTAAAATTTTGTAAAAACTGACACAAAAAATTTATCCTCAATTTTTTTGCCACAA
194 ACGATTTAGGC----------TAAAAACTGACTCGAAAAATTTTTTCTCAA-TTTTTTGCCACAA
* * * * * * * *
932 TAGTCGGGAACAATATATAATTCAATG-GAAAAA-AATGAAGGG--TTT-A-G------------
248 TACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCA
**
979 GGTTT--A
313 TTTTTCCA
*** * * * * * *
985 GGGTTAGG-GTTTATTTTTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCTTA
1 TTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * * * * *
1049 ACTCAAATGTAGCTGAGACTTGGTTAGATGAATATAAATATTTCAAGGAGTCTTT-CTGCCAAAA
66 AATCCAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTTAC-GACAAAA
** * * * * * * * * * *
1113 AT-ATTTAAACCTGAGCTGGGGCCCCGAAACGCGCTTTTGGCCCAAAAACCATGAT-G--AATAT
130 ATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAG-CAAAAAACCGTGATGGTTAGTAC
* * * *
1174 A-GA--TAGGC-AAAAACTAACTCGAAAAAAATTTTTCTGAATTTTTTTCCACAATACTCAGAAA
194 ACGATTTAGGCTAAAAACTGACTCG-AAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAA
* * * *
1235 AAATATATAATTCAACGCAAAAAAGATTGACGGGCTTTTCACGCTTCAAATATCATTTTTCAA
258 AAATATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCA
* * *
1298 TTTCTTCGGAATTAATATCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATT
1 TTT-TTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * *
1363 ATATCCAATGTGGCTGGGATTTGGATCGA-AGAATATAGATATTTC-AAGAAGTCTTTACGCCAA
65 AAATCCAATGTGGCTGGGATTTGGTTAGATA-AATATAGATATTTCAAAG-AGTCTTTACGACAA
* * * *
1426 AAATCATGCAAAACTGAGCCGGGGACCCGGAACGTGTTTTTAGCAAGAAACCGTGTTCGTTAGTA
128 AAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTA
* * * * *
1491 CACGATATCGGCTAAAATTTTGTAAAAACTGACCCGAAAAATTTATCCTCAATTTTTTTGCCACA
193 CACGATTTAGGC----------TAAAAACTGACTCGAAAAATTTTTTCTCAA-TTTTTTGCCACA
* * * ** * * * * *
1556 ATAGTTAGGAGCAATATATAATTCAATGCAAAAATAAAATGAAGGGTTTTTCACGCTTCTAATAT
247 ATACTCAGAAAAAATATATAATTCAACGCCAAAA-AGATTGACGGGTTTTTCACGCTTCTAATAT
* *
1621 CGTTTTCCCA
311 CATTTTTCCA
** * * * * *
1631 TTTTT-TCAGTTTATTTCTAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACAAA--C---
1 TTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * * *
1690 ---CC--TGTAGCTGAGAATTGGTTAGATGAATATAGATATTTCAAGGAATCTTT-CTG-CCAAA
66 AATCCAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTTAC-GACAAAA
* * ** * * * **
1748 ATTATTCAAAACTGAGCTAGGGCCCCGAAACACGTTTTTAGCCCCAAAACCGTGATGGTTAGTAC
130 ATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAG-CAAAAAACCGTGATGGTTAGTAC
* * * *
1813 ACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTGAATTTTTTGCGACAACACTCAGAGAA
194 ACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAA
* * * *
1878 AATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCATGCTTGTAATATCATTTTTCAA
259 AATATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCA
* * * *
1940 TTTTTTCGGAATTAATTTCTATTTATATCGAAACAAGATTCAGATGCTCGTTAAAACAAATCATT
1 -TTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * * * *
2005 ATATCCAATGTGGCTGGGATTTGGTTCGATAAATATGGATATTTCAAGGAGTCTTTACAAGAAAA
65 AAATCCAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTTACGACAAAA
* *
2070 ATCATGCAAAACTGAGTCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTATA
130 ATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACA
* * * * * * *
2135 CAATTTCGACTAAAATTTTGTAAATAATGACCCGAAAAATTTATCCTCAATTTTTTTTGCCACAA
195 CGATTTAGGCT---A------AAA-ACTGACTCGAAAAATTTTTTCTCAA--TTTTTTGCCACAA
* * * ** * * * * *
2200 TAGTTAGGAGCAATATATGATTCAATGCAAAAAAGATAAAAAATTAAGGGTTTTTCACGCTTCTA
248 TACTCAGAAAAAATATATAATTCAACGCCAAAAAGAT------TGACGGGTTTTTCACGCTTCTA
*
2265 ATATC--GTTT---
307 ATATCATTTTTCCA
* * *
2274 TTTTT-----TT-ATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAA-CCGTT
1 TTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC-TT
* * * * * ** *
2332 AAATCCAATGTGGTTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAA
65 AAATCCAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTTACGACAAAA
* * * * * *
2397 AT-ATTCAAAACTGAG-CTGTGACTCCGAAACGCGTTTTTAGCACCAAAACCGTGATGGTTACTA
130 ATCATGCAAAACTGAGCCGGGGAC-CCGGAACGCGTTTTTAGCA-AAAAACCGTGATGGTTAGTA
* *
2460 CACGATTTAGGCTCAAAACTGACTCGAGAAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGA
193 CACGATTTAGGCTAAAAACTGACTCGA-AAAA-TTTTTTCTCAATTTTTTGCCACAATACTCAGA
* *
2525 AAAAATATATAATTCAACAG-CAAAAAGATTGACGGGCTTTTCATGCTTCTAATATCATTTTTCC
256 AAAAATATATAATTCAAC-GCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCC
2589 A
320 A
*** * * * *
2590 TTTTTTCAATATTAATTTCTATTTAAATTGAAATAAGATTTAGATGCTCGTAAAAAAAAAATCCT
1 TTTTTAGGA-ATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGT-AAAAACAAATCCT
* * * * * *
2655 TAAATCGAATTTCGCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTACAACAAA
64 TAAATCCAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTTACGACAAA
* * * * *
2720 AATCATGCAAAACAGAGTCGGGGAGCCGGAACGCGTTCTTAGCAAAAAACC--G-T-G--CGTAC
129 AATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTAC
* * * * *
2779 ACGATTTAGGCTAAAAACTGAGTCGAAAATTTTTTTTTCTGAATCTTTTGCCACAATACTTAGAA
194 ACGATTTAGGCTAAAAACTGACTCGAAAA--ATTTTTTCTCAATTTTTTGCCACAATACTCAGAA
* * *
2844 AAAATATACAATTCAATGCCAAAAAGATTGACGAGTTTTTCACGCTTCTAATATCATTTTTCCA
257 AAAATATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCA
*
2908 TTTTTTAGGAATT-ATTCTCTATTTAAATCGAAACAAGATTCAGATGCTCGTGAAAACAAATCCT
1 -TTTTTAGGAATTAATT-TCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
* * * * *
2972 TATATCCAATGTGGCTGGGATTTGGATCGA-ATAATATAGATATTTC-AAGAAGTCTTTATGCCA
64 TAAATCCAATGTGGCTGGGATTTGGTTAGATA-AATATAGATATTTCAAAG-AGTCTTTACGACA
* * * *
3035 AAACTCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAAACAGTGATGGTCGAT
127 AAAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGT-TA-
* * ** * * * * * *
3100 TTCGGCTAAAATTT-TG-TAAAAACTGACCCAAAAAATTTATCCTCAATTTTTTTGCCACAATAG
190 GT--AC-ACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTCAA-TTTTTTGCCACAATAC
* * * * * * * *
3163 TCAGGAACAATATATAATTCAATG-CAAAAAAAATGAAGGGTTTTTCACGATTCTAATATCGTTT
251 TCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTT
3227 TTCCA
316 TTCCA
** * * * * ** * *
3232 TTTTT-TCAGTTTATTACAAAATAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCTTA
1 TTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * * * ** *
3296 ACTCAAATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAAA
66 AATCCAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTTACGACAAAAA
** * * * * *
3361 T-ATTTAAAAC-GAGCTGGGGCCCCGAAACGCGTTTTTAGCCCAAAATA-CGTGATGGTTAGGAC
131 TCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAG--CAAAAAACCGTGATGGTTAGTAC
** * * *
3423 ACGATTTAAACTAAAAACTGAGTCGAAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAA
194 ACGATTTAGGCTAAAAACTGACTCGAAAA-ATTTTTTCTCAATTTTTTGCCACAATACTCAGAAA
* * * *
3488 AGATATATAATTCAACGTCAAAAAGATTGACGGGATTTTCATGCTTCTAATATCA----T---
258 AAATATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCA
* * * * *
3544 TTTTTCGGAATTAATTTCTATTTAAATCGAAATAAGATTCAGTTGCTCGCAAAAACAAATCATTA
1 TTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * *
3609 AATCGAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTC-AAGAAGCCTTTACGCCAAAA
66 AATCCAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAAG-AGTCTTTACGACAAAA
* *
3673 ATCATGTAAAACTGAGCCGGGGACCCGAAACGC
130 ATCATGCAAAACTGAGCCGGGGACCCGGAACGC
3706 ATTT
Statistics
Matches: 2663, Mismatches: 531, Indels: 333
0.76 0.15 0.09
Matches are distributed among these distances:
293 44 0.02
294 17 0.01
295 7 0.00
297 3 0.00
298 1 0.00
299 1 0.00
304 4 0.00
306 2 0.00
307 3 0.00
309 62 0.02
310 150 0.06
311 104 0.04
312 7 0.00
313 105 0.04
314 14 0.01
315 126 0.05
316 44 0.02
317 162 0.06
318 210 0.08
319 62 0.02
320 270 0.10
321 209 0.08
322 149 0.06
323 45 0.02
324 119 0.04
325 71 0.03
326 51 0.02
327 130 0.05
328 7 0.00
329 7 0.00
330 30 0.01
331 141 0.05
332 199 0.07
333 82 0.03
337 3 0.00
339 22 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (320 bp):
TTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
AATCCAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTTACGACAAAAA
TCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACAC
GATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAA
TATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCA
Found at i:2024 original size:642 final size:639
Alignment explanation
Indices: 20--2773 Score: 3160
Period size: 642 Copynumber: 4.3 Consensus size: 639
10 TTCTAATATC
* * * *
20 ATTTTTTCGGAATTAATTTCAATTTAAATCGAAATAAGATTCAGTTGCTCGTAAAAACAAATCGT
1 ATTTTTTCGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCAT
* * * * * **
85 TAAATCGAATGTGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAGAAGCCTTTACGCCAAA
66 TATATCCAATGTGGCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTACAACAAA
* * * * * * *
150 AATCATGTAAAATTGAGCCGTGGACCCGGAACGTGTTTTTAGCAAAAAAACCGTGTTGGTTAGTA
131 AATCATGCAAAACTGAGTCGGGGACCCGGAACGCGTTTTTAGC-AAAAAACCGTGATCGTTAGTA
* * * * *
215 CACGATTTCGGCTAAAATTTTGTAAA-AACTGATCCGAAAAATTTATCCTC-AGTTTTTTTGCCA
195 CACAATATCGACTAAAATTTTGTAAATAA-TGACCCGAAAAATTTATCCTCAATTTTTTTTGCCA
* * * * *
278 CAATAGGTAGGACCAATATATAATTCAAAGC-AAAAG----AAATAAAGGGTTTTTCAAGCTTCT
259 CAATAGTTAGGAGCAATATATAATTCAATGCAAAAAGATAAAAATGAAGGGTTTTTCACGCTTCT
* * *
338 AATATCGTTTTTCCATTTTTTCGGATTTAATTTCTATTTAAATCGAAATAAGATTTAGATACTCG
324 AATATCG----T---TTTTTT--G-TTT-ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG
* * * * * * * *
403 TAAAAACAAATTCTTAAATCGAATGTGGCTGGGATTTGGTTCGATAAATATAGATATTTCAAAGA
378 TAAAAACAAA--C---CA-C-CATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGA
* * * * * * * **
468 GTC-TT-TACAATAAAGATCATGCAAAACTGAATCGGGGACCC-AGAACGAGTTTTTAG-CAAAA
436 GTCTTTCTGCCA-AAA-AT-ATTCAAAACTG-AGCTGGGCCCCGA-AACGCGTTTTTAGCCCCAA
* * * * *
529 AACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGAGTCGAAAATTTTTTTATGAATCTTTT
496 AACCGTGATGGTTAATACACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTGAATTTTTT
* * *
594 GCCACAATACTTAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCT
561 GCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCATGCTTCT
* * *
659 ACTATCATCTTTCC
626 AATATCATTTTTCA
* * * *
673 A-TTTTTAGGAATTATTTTCTATTTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
1 ATTTTTTCGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCAT
* * * * **
737 TATATCCAATGTGGCTGGGATTTGGATCGA-AGAATATAAATATTTTAAGAAGTCTTTACGCCAA
66 TATATCCAATGTGGCTGGGATTTGGTTCGATA-AATATAGATATTTCAAGGAGTCTTTACAACAA
* * * *
801 AAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAAACCGTGATGGTTAGTG
130 AAATCATGCAAAACTGAGTCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATCGTTAGTA
* * * *
866 CA-AGATTTCGGCTAAAATTTTGTAAA-AACTGACACAAAAAATTTATCCTCAA-TTTTTTTGCC
195 CACA-ATATCGACTAAAATTTTGTAAATAA-TGACCCGAAAAATTTATCCTCAATTTTTTTTGCC
** * * **
928 ACAATAGTCGGGAACAATATATAATTCAATG------GAAAAAAATGAAGGG--TTT-A-GGGT-
258 ACAATAGTTAGGAGCAATATATAATTCAATGCAAAAAGATAAAAATGAAGGGTTTTTCACGCTTC
** *** *
982 T--TA--GGGTTAGGGTTTATTTTTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAA
323 TAATATCGTTTTTTTGTTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAA
*
1043 CCCTTAACTCAAATGTAGCTGAGACTTGGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGC
388 -CC---AC-C--ATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC
* * * * * *
1108 CAAAAATATTTAAACCTGAGCTGGGGCCCCGAAACGCGCTTTTGGCCCAAAAACCATGAT-G--A
446 CAAAAATATTCAAAACTGAGCT-GGGCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTA
* * * *
1170 ATATA-GA--TAGGC-AAAAACTAACTCGAAAAAAATTTTTCTGAATTTTTTTCCACAATACTCA
510 ATACACGATTTAGGCTAAAAACTGACTCG-AAAAATTTTTTCTGAATTTTTTGCCACAATACTCA
* * *
1231 GAAAAAATATATAATTCAACGCAAAAAAGATTGACGGGCTTTTCACGCTTCAAATATCATTTTTC
574 GAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCATGCTTCTAATATCATTTTTC
1296 A
639 A
* *
1297 ATTTCTTCGGAATTAATATCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCAT
1 ATTTTTTCGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCAT
* * **
1362 TATATCCAATGTGGCTGGGATTTGGATCGA-AGAATATAGATATTTCAAGAAGTCTTTACGCCAA
66 TATATCCAATGTGGCTGGGATTTGGTTCGATA-AATATAGATATTTCAAGGAGTCTTTACAACAA
* * * *
1426 AAATCATGCAAAACTGAGCCGGGGACCCGGAACGTGTTTTTAGCAAGAAACCGTGTTCGTTAGTA
130 AAATCATGCAAAACTGAGTCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATCGTTAGTA
* *
1491 CACGATATCGGCTAAAATTTTGTAAA-AACTGACCCGAAAAATTTATCCTCAA-TTTTTTTGCCA
195 CACAATATCGACTAAAATTTTGTAAATAA-TGACCCGAAAAATTTATCCTCAATTTTTTTTGCCA
1554 CAATAGTTAGGAGCAATATATAATTCAATGC-AAAA-AT-AAAATGAAGGGTTTTTCACGCTTCT
259 CAATAGTTAGGAGCAATATATAATTCAATGCAAAAAGATAAAAATGAAGGGTTTTTCACGCTTCT
*
1616 AATATCGTTTTCCCATTTTTTCAGTTTATTTCTAATTAAATCAAAACAAGATTTAGATGCTCGTA
324 AATATCG---T----TTTTTT--GTTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
* *
1681 AAAACAAA-C-CC-TGTAGCTGAGAATTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTG
380 AAAACAAACCACCATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTG
* *
1743 CCAAAATTATTCAAAACTGAGCTAGGGCCCCGAAACACGTTTTTAGCCCCAAAACCGTGATGGTT
445 CCAAAAATATTCAAAACTGAGCT-GGGCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTT
* * *
1808 AGTACACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTGAATTTTTTGCGACAACACTCA
509 AATACACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTGAATTTTTTGCCACAATACTCA
* *
1873 GAGAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCATGCTTGTAATATCATTTTTC
574 GAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCATGCTTCTAATATCATTTTTC
1938 A
639 A
* *
1939 ATTTTTTCGGAATTAATTTCTATTTATATCGAAACAAGATTCAGATGCTCGTTAAAACAAATCAT
1 ATTTTTTCGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCAT
* *
2004 TATATCCAATGTGGCTGGGATTTGGTTCGATAAATATGGATATTTCAAGGAGTCTTTACAAGAAA
66 TATATCCAATGTGGCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTACAACAAA
* *
2069 AATCATGCAAAACTGAGTCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTAT
131 AATCATGCAAAACTGAGTCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATCGTTAGTAC
*
2134 ACAATTTCGACTAAAATTTTGTAAATAATGACCCGAAAAATTTATCCTCAATTTTTTTTGCCACA
196 ACAATATCGACTAAAATTTTGTAAATAATGACCCGAAAAATTTATCCTCAATTTTTTTTGCCACA
* *
2199 ATAGTTAGGAGCAATATATGATTCAATGCAAAAAAGATAAAAAATTAAGGGTTTTTCACGCTTCT
261 ATAGTTAGGAGCAATATATAATTCAATGC-AAAAAGAT-AAAAATGAAGGGTTTTTCACGCTTCT
*
2264 AATATCGTTTTTTT-TTTATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAAC
324 AATATCGTTTTTTTGTTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAAC
* * *
2328 CGTTAAATCCAATGTGGTTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCC
389 C-----A-CC-ATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCC
* * * *
2393 AAAAATATTCAAAACTGAGCTGTGACTCCGAAACGCGTTTTTAGCACCAAAACCGTGATGGTTAC
447 AAAAATATTCAAAACTGAGCTG-GGCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAA
* *
2458 TACACGATTTAGGCTCAAAACTGACTCGAGAAAATTTTTTTCTAAATTTTTTGCCACAATACTCA
511 TACACGATTTAGGCTAAAAACTGACTCGA-AAAA-TTTTTTCTGAATTTTTTGCCACAATACTCA
2523 GAAAAAATATATAATTCAACAG-CAAAAAGATTGACGGGCTTTTCATGCTTCTAATATCATTTTT
574 GAAAAAATATATAATTCAAC-GCCAAAAAGATTGACGGGCTTTTCATGCTTCTAATATCATTTTT
*
2587 CC
638 CA
* * * * *
2589 ATTTTTTC-AATATTAATTTCTATTTAAATTGAAATAAGATTTAGATGCTCGTAAAAAAAAAATC
1 ATTTTTTCGGA-ATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGT-AAAAACAAATC
* * * * *
2653 CTTAAATCGAATTTCGCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTACAACA
64 ATTATATCCAATGTGGCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTACAACA
* * *
2718 AAAATCATGCAAAACAGAGTCGGGGAGCCGGAACGCGTTCTTAGCAAAAAACCGTG
129 AAAATCATGCAAAACTGAGTCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTG
2774 CGTACACGAT
Statistics
Matches: 1832, Mismatches: 195, Indels: 150
0.84 0.09 0.07
Matches are distributed among these distances:
623 11 0.01
624 95 0.05
625 263 0.14
626 2 0.00
627 4 0.00
628 14 0.01
629 28 0.02
630 99 0.05
631 9 0.00
632 6 0.00
633 1 0.00
634 2 0.00
635 2 0.00
636 100 0.05
637 2 0.00
638 47 0.03
639 6 0.00
640 3 0.00
641 7 0.00
642 319 0.17
643 58 0.03
644 3 0.00
645 6 0.00
646 55 0.03
647 2 0.00
648 167 0.09
649 5 0.00
650 142 0.08
651 222 0.12
652 151 0.08
653 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (639 bp):
ATTTTTTCGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCAT
TATATCCAATGTGGCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTACAACAAA
AATCATGCAAAACTGAGTCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATCGTTAGTAC
ACAATATCGACTAAAATTTTGTAAATAATGACCCGAAAAATTTATCCTCAATTTTTTTTGCCACA
ATAGTTAGGAGCAATATATAATTCAATGCAAAAAGATAAAAATGAAGGGTTTTTCACGCTTCTAA
TATCGTTTTTTTGTTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCA
CCATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATATT
CAAAACTGAGCTGGGCCCCGAAACGCGTTTTTAGCCCCAAAACCGTGATGGTTAATACACGATTT
AGGCTAAAAACTGACTCGAAAAATTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATAT
AATTCAACGCCAAAAAGATTGACGGGCTTTTCATGCTTCTAATATCATTTTTCA
Found at i:2931 original size:968 final size:946
Alignment explanation
Indices: 20--3705 Score: 2838
Period size: 968 Copynumber: 3.8 Consensus size: 946
10 TTCTAATATC
* * * * * *
20 ATTTTTTCGGAATTAATTTCAATTTAAATCGAAATAAGATTCAGTTGCTCGTAAAAACAAATCGT
1 ATTTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTGAAAACAAATCAT
* * * * * **
85 TAAATCGAATGTGGCTGGGATTTGGTTAG-ATAAATATAGATATTTCAAGAAGCCTTTACGCCAA
66 TATATCCAATGTGGCTGGGATTTGGATCGAAT-AATATAGATATTTCAAGAAGTCTTTACAACAA
* * * * * * *
149 AAATCATGTAAAATTGAGCCGTGGACCCGGAACGTGTTTTTAGCAAAAAAACCGTGTTGGTTAGT
130 AAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAAC-AAAAAACAGTGAT-G---GT
* * * *
214 ACACGATTTCGGCTAAAATTTTGTAAAAACTGATCCGAAAAATTTATCCTCAGTTTTTTTGCCAC
190 -CA--ATTTCGACTAAAATTTTGTAAAAACTGACCCAAAAAATTTATCCTCAATTTTTTTGCCAC
* * * * * *
279 AATAGGT-AGGACCAATATATAATTCAAAGCAAAAGAAATAAAGGGTTTTTCAAGCTTCTAATAT
252 AATA-GTCAGGAACAATATATAATTCAATGCAAAAAAAATGAAGGGTTTTTCACGATTCTAATAT
* * ** *
343 CGTTTTTCCATTTTTTCGGATTTAATTTCTATTTAAATCGAAATAAGATTTAGATACTCGTAAAA
316 CGTTTTT-C-TTTTTTC--A-TT-ATTACAAAATAAATCGAAACAAGATTTAGATACTCGTAAAA
** * * * * * * *
408 ACAAATTCTTAAATCGAATGTGGCTGGGATTTGGTTCGATAAATATAGATATTTCAAAGAGTC--
375 ACAAACCCTTAAATCAAATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
* * * * * * * *
471 TTTACAATAAAGATCATGCAAAACTGAATCGGGGACCCAG-AACGAGTTTTTAG--CAAAAAACC
440 TTTGCCA-AAA-AT-ATTCAAAAC-G-AGCTGGGACCCCGAAACGCGTTTTTAGCCCAAAATA-C
** * * * *
533 GTGATGGTTA-GTACACGATTTAGGCTAAAAACTGAGTCG-AAAATTTTTTTATGAATCTTTTGC
499 GTGATGGTTACG-ACACGATTTAAACTAAAAACTGACTCGAAAAATTTTTTTCTAAATTTTTTGC
* * * *
596 CACAATACTTAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAC
563 CACAATACTCAGAAAAAATATATAATTCAACGTCAAAAAGATTGACGGGATTTTCATGCTTCTA-
* * * * * * *
661 TATCATCTTTCCATTTTTAGGAATTATTTTCTATTTAAATTGAAACAAGATTCAGATGCTCGTAA
627 -AT-ATC-AT---TTTTTCGAAATTAATTTCTATTTAAATCGAAATAAGATTCAGATGCTCGAAA
* * * * * * * * * *
726 AAACAAATCCTTATATCCAATGTGGCTGGGATTTGGATCGA-AGAATATAAATATTTTAAGAAGT
686 AAAAAAATCATTAAATCGAATGTCGCTGGGATTTGGTTAGATA-AATATAGATATTTCAAGAAGC
** * * * *
790 CTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAAACCGT
750 CTTTACAACAAAAATCATGCAAAACAGAGCCGGGGACCCGAAACGCGTTCTTAGCAAAAAACCGT
* * * * * * * *
855 GATGGTTAGTGCAAGATTTCGGCTAAAATTTTGTAAAAACTGACACAAAAAATTTATCCTCAATT
815 G--CG-TA---CACGATTTAGGC----------TAAAAACTGACTCGAAAAATTTTTTCTGAA-T
* * * * * * * * * *
920 TTTTTGCCACAATAGTCGGGAACAATATATAATTCAATG-GAAAAA-AATGA--AG--------G
863 CTTTTGCCACAACACTCAGAAAAAATATACAATTCAACGCCAAAAAGATTGACGAGCTTTTCACG
* ***
973 -GT-T--TA--GGGTTT--
928 CTTCTAATATCATTTTTCA
*** * * * * * * * *
984 A-GGGTTAGG-GTTTATTTTTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCT
1 ATTTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTGAAAACAAATCAT
* * * * * * * * **
1047 TA-ACTCAAATGTAGCTGAGACTTGGTTAG-ATGAATATAAATATTTCAAGGAGTCTTT-CTGCC
66 TATA-TCCAATGTGGCTGGGATTTGGATCGAAT-AATATAGATATTTCAAGAAGTCTTTAC-AAC
** * * * * *** *
1109 AAAAAT-ATTTAAACCTGAGCTGGGGCCCCGAAACGCGCTTTTGGCCCAAAAACCA-TGAT-G--
128 AAAAATCATGCAAAACTGAGCCGGGGACCCGGAACGCG-TTTT-TAACAAAAAACAGTGATGGTC
* ** * * * * *
1169 AA--T--A-T-AGA-TAGGCAAAAACTAACTCGAAAAAAATTT-TTCTGAATTTTTTT-CCACAA
191 AATTTCGACTAAAATTTTGTAAAAACTGAC-C-CAAAAAATTTATCCTCAATTTTTTTGCCACAA
* * * * * * * * * *
1225 TACTCAGAAAAAATATATAATTCAACGCAAAAAAGATTGACGGGCTTTTCACGCTTCAAATATCA
254 TAGTCAGGAACAATATATAATTCAATGCAAAAAA-AATGAAGGGTTTTTCACGATTCTAATATCG
* * * ** * *
1290 TTTTTCAATTTCTTCGGAATTAATATCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
318 TTTTTC--TTTTTTC---ATTATTA-CAAAATAAATCGAAACAAGATTTAGATACTCGTAAAAAC
* * * * * * * * * * * *
1355 AAATCATTATATCCAATGTGGCTGGGATTTGGATCGAAGAATATAGATATTTCAAGAAGTCTTTA
377 AAACCCTTAAATCAAATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTT
* * * * *
1420 CGCCAAAAATCATGCAAAACTGAGCCGGGGA-CCCGGAACGTGTTTTTAG--CAAGAA-ACCGTG
442 TGCCAAAAAT-ATTCAAAAC-GAG-CTGGGACCCCGAAACGCGTTTTTAGCCCAA-AATA-CGTG
* * * * * * *
1481 TTCGTTA-GTACACGATATCGGCTAAAATTTTGTAAAAACTGACCCGAAAAA-TTTATCCTCAAT
502 ATGGTTACG-ACACGAT-T----T-AAA----CTAAAAACTGACTCGAAAAATTTTTTTCT-AAA
* * * ** * * * * *
1544 TTTTTTGCCACAATAGTTAGGAGCAATATATAATTCAATG-CAAAAATAAAATGAAGGGTTTTTC
555 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGTC-AAAA-AGATTGACGGGATTTTC
* * * * * * *
1608 ACGCTTCTAATATCGTTTTCCCATTTTTTC--AGTTTATTTCTAATTAAATCAAAACAAGATTTA
618 ATGCTTCTAATA------T--CATTTTTTCGAAATTAATTTCTATTTAAATCGAAATAAGATTCA
* ** * * * *
1671 GATGCTCG----TAAAAA-C---AAA-C-CCTGTAGCTGAGAATTGGTTAGATGAATATAGATAT
675 GATGCTCGAAAAAAAAAATCATTAAATCGAATGTCGCTGGGATTTGGTTAGATAAATATAGATAT
* ** * * * * ** * * *
1726 TTCAAGGAA-TCTTT-CTGCCAAAATTATTCAAAACTGAGCTAGGGCCCCGAAACACGTTTTTAG
740 TTCAA-GAAGCCTTTACAACAAAAATCATGCAAAACAGAGCCGGGGACCCGAAACGCGTTCTTAG
** *
1789 CCCCAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTGAA
804 -CAAAAAACC--G-T-G--CGTACACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTGAA
* * * * * *
1854 TTTTTTGCGACAACACTCAGAGAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCAT
862 TCTTTTGCCACAACACTCAGAAAAAATATACAATTCAACGCCAAAAAGATTGACGAGCTTTTCAC
*
1919 GCTTGTAATATCATTTTTCA
927 GCTTCTAATATCATTTTTCA
* * *
1939 ATTTTTTCGGAATTAATTTCTATTTATATCGAAACAAGATTCAGATGCTCGTTAAAACAAATCAT
1 ATTTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTGAAAACAAATCAT
* * * *
2004 TATATCCAATGTGGCTGGGATTTGGTTCG-ATAAATATGGATATTTCAAGGAGTCTTTACAAGAA
66 TATATCCAATGTGGCTGGGATTTGGATCGAAT-AATATAGATATTTCAAGAAGTCTTTACAACAA
* * *
2068 AAATCATGCAAAACTGAGTCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTA
130 AAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAAACAGTGAT-G---G--
*
2133 TACAATTTCGACTAAAATTTTGTAAATAA-TGACCCGAAAAATTTATCCTCAATTTTTTTTGCCA
189 T-CAATTTCGACTAAAATTTTGTAAA-AACTGACCCAAAAAATTTATCCTCAA-TTTTTTTGCCA
* * * * *
2197 CAATAGTTAGGAGCAATATATGATTCAATGCAAAAAAGATAAAAAATTAAGGGTTTTTCACGCTT
251 CAATAGTCAGGAACAATATATAATTCAATGC-----A-A-AAAAAATGAAGGGTTTTTCACGATT
* *
2262 CTAATATCG-TTTT-TTTTTT-A-T-TT-CTAATTAAATCGAAACAAGATTTAGATACTCGTAAA
309 CTAATATCGTTTTTCTTTTTTCATTATTACAAAATAAATCGAAACAAGATTTAGATACTCGTAAA
* * * *
2321 AACAAACCGTTAAATCCAATGTGGTTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
374 AACAAACCCTTAAATCAAATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
* * *
2386 TTTTGCCAAAAATATTCAAAACTGAGCTGTGACTCCGAAACGCGTTTTTAGCACCAAAA-CCGTG
439 TTTTGCCAAAAATATTCAAAAC-GAGCTGGGACCCCGAAACGCGTTTTTAGC-CCAAAATACGTG
* ** *
2450 ATGGTTACTACACGATTTAGGCTCAAAACTGACTCGAGAAAATTTTTTTCTAAATTTTTTGCCAC
502 ATGGTTACGACACGATTTAAACTAAAAACTGACTCGA-AAAATTTTTTTCTAAATTTTTTGCCAC
*
2515 AATACTCAGAAAAAATATATAATTCAACAG-CAAAAAGATTGACGGGCTTTTCATGCTTCTAATA
566 AATACTCAGAAAAAATATATAATTCAAC-GTCAAAAAGATTGACGGGATTTTCATGCTTCT-A-A
* *
2579 TCATTTTTCCATTTTTTC-AATATTAATTTCTATTTAAATTGAAATAAGATTTAGATGCTCGTAA
628 T-A----T-CATTTTTTCGAA-ATTAATTTCTATTTAAATCGAAATAAGATTCAGATGCTCG-AA
* * * * *
2643 AAAAAAAATCCTTAAATCGAATTTCGCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGT
685 AAAAAAAATCATTAAATCGAATGTCGCTGGGATTTGGTTAGATAAATATAGATATTTCAAGAAGC
* * *
2708 CTTTACAACAAAAATCATGCAAAACAGAGTCGGGGAGCCGGAACGCGTTCTTAGCAAAAAACCGT
750 CTTTACAACAAAAATCATGCAAAACAGAGCCGGGGACCCGAAACGCGTTCTTAGCAAAAAACCGT
* * *
2773 GCGTACACGATTTAGGCTAAAAACTGAGTCGAAAATTTTTTTTTCTGAATCTTTTGCCACAATAC
815 GCGTACACGATTTAGGCTAAAAACTGACTCGAAAA--ATTTTTTCTGAATCTTTTGCCACAACAC
* * *
2838 TTAGAAAAAATATACAATTCAATGCCAAAAAGATTGACGAGTTTTTCACGCTTCTAATATCATTT
878 TCAGAAAAAATATACAATTCAACGCCAAAAAGATTGACGAGCTTTTCACGCTTCTAATATCATTT
*
2903 TTCC
943 TTCA
*
2907 ATTTTTTAGGAATT-ATTCTCTATTTAAATCGAAACAAGATTCAGATGCTCGTGAAAACAAATCC
1 ATTTTTTAGGAATTAATT-TCTATTTAAATCGAAACAAGATTCAGATGCTCGTGAAAACAAATCA
***
2971 TTATATCCAATGTGGCTGGGATTTGGATCGAATAATATAGATATTTCAAGAAGTCTTTATGCCAA
65 TTATATCCAATGTGGCTGGGATTTGGATCGAATAATATAGATATTTCAAGAAGTCTTTACAACAA
* *
3036 AACTCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAAACAGTGATGGTCGATT
130 AAATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAAACAGTGATGGTCAATT
*
3101 TCGGCTAAAATTTTGTAAAAACTGACCCAAAAAATTTATCCTCAATTTTTTTGCCACAATAGTCA
195 TCGACTAAAATTTTGTAAAAACTGACCCAAAAAATTTATCCTCAATTTTTTTGCCACAATAGTCA
3166 GGAACAATATATAATTCAATGCAAAAAAAATGAAGGGTTTTTCACGATTCTAATATCGTTTTTCC
260 GGAACAATATATAATTCAATGCAAAAAAAATGAAGGGTTTTTCACGATTCTAATATCGTTTTT-C
*
3231 ATTTTTTCAGTTTATTACAAAATAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCTTA
324 -TTTTTTCA--TTATTACAAAATAAATCGAAACAAGATTTAGATACTCGTAAAAACAAACCCTTA
*
3296 ACTCAAATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAAA
386 AATCAAATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAAA
* * *
3361 TATTTAAAACGAGCTGGGGCCCCGAAACGCGTTTTTAGCCCAAAATACGTGATGGTTAGGACACG
451 TATTCAAAACGAGCTGGGACCCCGAAACGCGTTTTTAGCCCAAAATACGTGATGGTTACGACACG
* * * *
3426 ATTTAAACTAAAAACTGAGTCGAAAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAGA
516 ATTTAAACTAAAAACTGACTCGAAAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAA
*
3491 TATATAATTCAACGTCAAAAAGATTGACGGGATTTTCATGCTTCTAATATCATTTTTTCGGAATT
581 TATATAATTCAACGTCAAAAAGATTGACGGGATTTTCATGCTTCTAATATCATTTTTTCGAAATT
* * * *
3556 AATTTCTATTTAAATCGAAATAAGATTCAGTTGCTCGCAAAAACAAATCATTAAATCGAATGTGG
646 AATTTCTATTTAAATCGAAATAAGATTCAGATGCTCGAAAAAAAAAATCATTAAATCGAATGTCG
** * *
3621 CTGGGATTTGGTTAGATAAATATAGATATTTCAAGAAGCCTTTACGCCAAAAATCATGTAAAACT
711 CTGGGATTTGGTTAGATAAATATAGATATTTCAAGAAGCCTTTACAACAAAAATCATGCAAAACA
3686 GAGCCGGGGACCCGAAACGC
776 GAGCCGGGGACCCGAAACGC
3706 ATTT
Statistics
Matches: 2198, Mismatches: 381, Indels: 298
0.76 0.13 0.10
Matches are distributed among these distances:
935 32 0.01
936 30 0.01
937 4 0.00
939 1 0.00
943 1 0.00
944 49 0.02
945 232 0.11
946 69 0.03
947 8 0.00
948 4 0.00
949 5 0.00
950 4 0.00
951 5 0.00
952 102 0.05
953 82 0.04
954 8 0.00
955 22 0.01
956 89 0.04
957 135 0.06
958 33 0.02
959 45 0.02
960 93 0.04
961 205 0.09
962 177 0.08
963 120 0.05
964 3 0.00
966 37 0.02
967 11 0.01
968 277 0.13
969 119 0.05
970 6 0.00
971 8 0.00
972 55 0.03
973 44 0.02
974 15 0.01
975 29 0.01
977 5 0.00
980 5 0.00
981 25 0.01
982 4 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (946 bp):
ATTTTTTAGGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTGAAAACAAATCAT
TATATCCAATGTGGCTGGGATTTGGATCGAATAATATAGATATTTCAAGAAGTCTTTACAACAAA
AATCATGCAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAAACAGTGATGGTCAATTT
CGACTAAAATTTTGTAAAAACTGACCCAAAAAATTTATCCTCAATTTTTTTGCCACAATAGTCAG
GAACAATATATAATTCAATGCAAAAAAAATGAAGGGTTTTTCACGATTCTAATATCGTTTTTCTT
TTTTCATTATTACAAAATAAATCGAAACAAGATTTAGATACTCGTAAAAACAAACCCTTAAATCA
AATGTAGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAAATATTC
AAAACGAGCTGGGACCCCGAAACGCGTTTTTAGCCCAAAATACGTGATGGTTACGACACGATTTA
AACTAAAAACTGACTCGAAAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATAT
AATTCAACGTCAAAAAGATTGACGGGATTTTCATGCTTCTAATATCATTTTTTCGAAATTAATTT
CTATTTAAATCGAAATAAGATTCAGATGCTCGAAAAAAAAAATCATTAAATCGAATGTCGCTGGG
ATTTGGTTAGATAAATATAGATATTTCAAGAAGCCTTTACAACAAAAATCATGCAAAACAGAGCC
GGGGACCCGAAACGCGTTCTTAGCAAAAAACCGTGCGTACACGATTTAGGCTAAAAACTGACTCG
AAAAATTTTTTCTGAATCTTTTGCCACAACACTCAGAAAAAATATACAATTCAACGCCAAAAAGA
TTGACGAGCTTTTCACGCTTCTAATATCATTTTTCA
Found at i:2932 original size:318 final size:316
Alignment explanation
Indices: 995--3705 Score: 2188
Period size: 318 Copynumber: 8.5 Consensus size: 316
985 GGGTTAGGGT
* * * * * *
995 TTATTTTTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCTTAACTCAAATGTA
1 TTATTTCTATTTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * ** *
1060 GCTGAGACTTGGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCCAAAAAT-ATTTAAACC
66 GCTGGGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAAC
* * * * * ** *
1124 TGAGCTGGGGCCCCGAAACGCGCTTTTGGCCCAAAAACCATGATGAATATA-GA--TAGGC-AAA
131 TGAGC-GGGGACCCGAAACGCGTTTTTAG-CAAAAAACCGTGA-GGTTACACGATTTAGGCTAAA
* * ** *
1185 AACTAACTCGA-AAAAAATTTTTCTGAATTTTTTTCCACAATACTCAGAAAAAATATATAATTCA
193 AACTGAGTCGACAAAATTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCA
* * * * * *
1249 ACGCAAAAAAGATTGACGGGCTTTTCACGCTTCAAATATCATTTTTCAATTTCTTCGGAA
258 ATGC-AAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCAGAA
* * * *
1309 TTAATATCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTATATCCAATGT
1 TT-ATTTCTATTTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * *
1374 GGCTGGGATTTGGATCGA-AGAATATAGATATTTCAAGAAGTCTTTACGCCAAAAATCATGCAAA
65 GGCTGGGATTTGGTTAGATA-AATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAA
* * * * * * *
1438 ACTGAGCCGGGGACCCGGAACGTGTTTTTAGCAAGAAACCGTGTTCGTTAGTACACGATATCGGC
129 ACTGAG-CGGGGACCCGAAACGCGTTTTTAGCAAAAAACCGTG--AGGT--TACACGATTTAGGC
** ** * * * * * * * **
1503 TAAAATTTTGTAAAAACTGACCCGAAAAATTTATCCTCAATTTTTTTGCCACAATAGTTAGGAGC
189 TAAAA-ACTG---AGTC-GA--C-AAAATTTTTTTCTGAA-TTTTTTGCCACAATACTCAGAAAA
* * * * *
1568 AATATATAATTCAATGCAAAAATAAAATGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATT
245 AATATATAATTCAATGC-AAAA-AGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCATT
*
1633 TTTTCAG-T
308 TTTTCAGAA
* * *
1641 TTATTTCTAATTAAATCAAAACAAGATTTAGATGCTCGTAAAAACAAA--C------CC--TGTA
1 TTATTTCTATTTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * * *
1696 GCTGAGAATTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTGCC-AAAATTATTCAAAAC
66 GCTGGGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAAC
* * * **
1760 TGAGCTAGGGCCCCGAAACACGTTTTTAGCCCCAAAACCGTGATGGTTAGTACACGATTTAGGCT
131 TGAGC-GGGGACCCGAAACGCGTTTTTAG-CAAAAAACCGTGA-GG-T--TACACGATTTAGGCT
* * * *
1825 AAAAACTGACTCGA-AAAA-TTTTTTCTGAATTTTTTGCGACAACACTCAGAGAAAATATATAAT
190 AAAAACTGAGTCGACAAAATTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
* * * * * *
1888 TCAACGCCAAAAAGATTGACGGGCTTTTCATGCTTGTAATATCATTTTTCAATTTTTTCGGAA
255 TCAATG-CAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCAGAA
* * * * *
1951 TTAATTTCTATTTATATCGAAACAAGATTCAGATGCTCGTTAAAACAAATCATTATATCCAATGT
1 TT-ATTTCTATTTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * ****
2016 GGCTGGGATTTGGTTCGATAAATATGGATATTTCAAGGAGTCTTTACAAGAAAAATCATGCAAAA
65 GGCTGGGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAA
* * * * *
2081 CTGAGTCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTATACAATTTCGACT
130 CTGAG-CGGGGACCCGAAACGCGTTTTTAGCAAAAAACCGTGA-GG-T--TACACGATTTAGGCT
** * * * * * * * * * **
2146 AAAATTTTGTAAATAATGACCCGAAAAATTTATCCTCAATTTTTTTTGCCACAATAGTTAGGAGC
190 AAAA-ACTG--AGT--CGA--C-AAAATTTTTTTCTGAA--TTTTTTGCCACAATACTCAGAAAA
* * * *
2211 AATATATGATTCAATGCAAAAAAGATAAAAAATTAAGGGTTTTTCACGCTTCTAATATC---GTT
245 AATATATAATTCAATGC-AAAAAGAT------TGACGGGTTTTTCACGCTTCTAATATCATTTTT
2273 ---TTTTTT-----
303 CCATTTTTTCAGAA
* *
2279 TTATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAA-CCGTTAAATCCAATGT
1 TTATTTCTATTTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCC-TTAAATCCAATGT
* * * * * *
2343 GGTTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAAAT-ATTCAAAA
65 GGCTGGGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAA
* * *
2407 CTGAGCTGTGACTCCGAAACGCGTTTTTAGCACCAAAACCGTGATGGTTACTACACGATTTAGGC
130 CTGAGCGGGGAC-CCGAAACGCGTTTTTAGCA-AAAAACCGTGA-GG-T--TACACGATTTAGGC
* * * *
2472 TCAAAACTGACTCGAGAAAATTTTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAA
189 TAAAAACTGAGTCGACAAAATTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAA
* * *
2537 TTCAACAGCAAAAAGATTGACGGGCTTTTCATGCTTCTAATATCATTTTTCCATTTTTTCA-ATA
254 TTCAA-TGCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCAGA-A
* * * * *
2601 TTAATTTCTATTTAAATTGAAATAAGATTTAGATGCTCGTAAAAAAAAAATCCTTAAATCGAATT
1 TT-ATTTCTATTTAAATCGAAACAAGATTTAGATGCTCGT-AAAAACAAATCCTTAAATCCAATG
* * ***
2666 TCGCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTACAACAAAAATCATGCAAA
64 TGGCTGGGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAA
* * * * *
2731 ACAGAGTCGGGGAGCCGGAACGCGTTCTTAGCAAAAAACCGTG-CG-TACACGATTTAGGCTAAA
129 ACTGAG-CGGGGACCCGAAACGCGTTTTTAGCAAAAAACCGTGAGGTTACACGATTTAGGCTAAA
* * * *
2794 AACTGAGTCGA-AAATTTTTTTTTCTGAATCTTTTGCCACAATACTTAGAAAAAATATACAATTC
193 AACTGAGTCGACAAA-ATTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC
*
2858 AATGCCAAAAAGATTGACGAGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTT-AGGAA
257 AATG-CAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCA-GAA
* * *
2919 TTATTCTCTATTTAAATCGAAACAAGATTCAGATGCTCGTGAAAACAAATCCTTATATCCAATGT
1 TTATT-TCTATTTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * *
2984 GGCTGGGATTTGGATCGA-ATAATATAGATATTTCAAGAAGTCTTTATGCCAAAACTCATGCAAA
65 GGCTGGGATTTGGTTAGATA-AATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAA
* * * *
3048 ACTGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAAACAGTGATGG-T---CGATTTCGGCTAA
129 ACTGAG-CGGGGACCCGAAACGCGTTTTTAGCAAAAAACCGTGA-GGTTACACGATTTAGGCTAA
** ** * * * * * * *
3109 AATTTTGTAAAAACTGACCCAAAAAATTTATCCTCAATTTTTTTGCCACAATAGTCAGGAACAAT
192 AA-ACTG---AGTC-GA--C-AAAATTTTTTTCTGAA-TTTTTTGCCACAATACTCAGAAAAAAT
* * * * *
3174 ATATAATTCAATGCAAAAAAAATGAAGGGTTTTTCACGATTCTAATATCGTTTTTCCATTTTTTC
248 ATATAATTCAATGCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTC
*
3239 AG-T
313 AGAA
* * ** * * * *
3242 TTATTACAAAATAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCTTAACTCAAATGTA
1 TTATTTCTATTTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * **
3307 GCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAAAT-ATTTAAAAC
66 GCTGGGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAAC
* * **
3371 -GAGCTGGGGCCCCGAAACGCGTTTTTAGCCCAAAATA-CGTGATGGTTAGGACACGATTTAAAC
131 TGAGC-GGGGACCCGAAACGCGTTTTTAG--CAAAAAACCGTGA-GGTT---ACACGATTTAGGC
* *
3434 TAAAAACTGAGTCGA-AAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAGATATATAA
189 TAAAAACTGAGTCGACAAAATTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAA
* * * *
3498 TTCAACGTCAAAAAGATTGACGGGATTTTCATGCTTCT-A-AT-A----T-CATTTTTTCGGAA
254 TTCAATG-CAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCAGAA
* * * * * *
3554 TTAATTTCTATTTAAATCGAAATAAGATTCAGTTGCTCGCAAAAACAAATCATTAAATCGAATGT
1 TT-ATTTCTATTTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * *
3619 GGCTGGGATTTGGTTAGATAAATATAGATATTTCAAGAAGCCTTTACGCCAAAAATCATGTAAAA
65 GGCTGGGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAA
3684 CTGAGCCGGGGACCCGAAACGC
130 CTGAG-CGGGGACCCGAAACGC
3706 ATTT
Statistics
Matches: 1902, Mismatches: 377, Indels: 235
0.76 0.15 0.09
Matches are distributed among these distances:
309 39 0.02
310 37 0.02
311 83 0.04
312 7 0.00
313 98 0.05
314 12 0.01
315 124 0.07
316 47 0.02
317 173 0.09
318 196 0.10
319 56 0.03
320 63 0.03
321 165 0.09
322 149 0.08
323 44 0.02
324 134 0.07
325 73 0.04
326 41 0.02
327 132 0.07
328 14 0.01
330 4 0.00
331 62 0.03
332 42 0.02
333 83 0.04
336 2 0.00
339 22 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (316 bp):
TTATTTCTATTTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
GCTGGGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAAC
TGAGCGGGGACCCGAAACGCGTTTTTAGCAAAAAACCGTGAGGTTACACGATTTAGGCTAAAAAC
TGAGTCGACAAAATTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAATG
CAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCAGAA
Done.