Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010897.1 Corchorus capsularis cultivar CVL-1 contig10918, 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: 5389
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Found at i:1307 original size:322 final size:321
Alignment explanation
Indices: 1--5382 Score: 5973
Period size: 322 Copynumber: 16.8 Consensus size: 321
* * *
1 TATTCATCGAAGCAAATCTCAGCCTTGTTGGATATAAGGATTTGTTTTACGAGCATCTCAATCTT
1 TATTCATCGAAGCAAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCATCTCAATCTT
*
66 GTTTCGATTTAATTAGAAATTAATTC-GAAAAAAATGGAAAAACGATATTAAAAGCGTAGAAAA-
66 GTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGT-GAAAAG
* *
129 CCCGGCCAATC-TTATGGCTTTGAATTATATA-TTTTTCTGTCTATTGTGGCAAAAAAATTGAGA
130 CCC-GCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGC-AAAAAATTGAGA
* * *
192 AAAAAC-TTTCGGGTTAGTCTTTTTTTG-CGAAATTGTGTATTAACCATCACGGTTTTTGGCTAA
193 AAAAACTTTTCGGGTCAG---TTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
* * ** * *
255 AAATGTGTTCCGGAGCCCCCGGCTCAATTTTGCCCGATTTTTGGCGCAAA-ACTTCTTAGAATAT
255 AAACGCGTTCCGGAG-CCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATAT
319 CTA
319 CTA
* * *
322 TATTCATCGAAGCAAAATCTAAGCGTGATTGGATATAAGGATTTTTTTTACGAGCATCTCATTCT
1 TATTCATCGAAGC-AAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCATCTCAATCT
*
387 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAA
65 TGTTTCGATTTAATTAGAAATTAATTCGG--AAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * * *
452 TGCCCGTCAGTCTTTTTGACTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAG-
128 AGCCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAGA
* * *
516 -AAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGCACGTTA--ATCACGGTTTTTGGCAAAAA
193 AAAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTAC-TAACCATCACGGTTTTTGGCTAAAA
* * * * *
578 ACGCATTCCAGAGCCCCGACTCAATTTTACATGATTTTTGGTGCAAAGACTCCTTAAAATATCTA
257 ACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
** * * * * *
643 TATAAATCAAATCAAATCTCAGCCTTGTTGGATATAAGGATTTGTTTTTACGAGTATCTCAATCT
1 TATTCATCGAAGCAAATCTCAGCGTTATTGGATATAAGGATTT-TTTTTACGAGCATCTCAATCT
* *
708 TGTTTCAATTTAATTAGAAATTAATTCGG-AAAAAATGGAAAAACGATATTAAAAGCGTGAAAAG
65 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG
* *
772 CCCGCCAATCTTTATGGCTTTGAATTATATATTTTTTCTGTCTATTGTGGCAAAAAAATTGAGAA
130 CCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGC-AAAAAATTGAGAA
* * *
837 AAAAC-TTTCGGGTTAGTTTTTTGTCGAAATCGTGTACTAACCATCACGGTTTATGGCTAAAAAC
194 AAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
* *
901 GCGTTCCGGAGCCACGGCTCTATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
259 GCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
*
964 TATTCATCGAAGCAAAATCTCAGCGTTATTAGATATAAGGATTTTTTTTACGAGCATCTCAATCT
1 TATTCATCGAAGC-AAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCATCTCAATCT
* * *
1029 TGTTTCGATATAATTAGAAATTAATTCGGAAAAAAATGGAAAAACAATATTAGAAGCATGAAAAG
65 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG
* * * *
1094 CCCGCCAATATTTTTCGCTTTGAATTATATATTTTTTCAGTGTATTGTGGGAAAAAATTGAGAAA
130 CCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAG-AA
* * *
1159 AAAACTTTTCGGGTAAGTTTTTTGCCTAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAAC
194 AAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
* ** * * * *
1224 GCATTCTAGAGCCCCGACTCAATTTTGCATGATTTTTGGTGCAATGACTCCTTAAAACATCTA
259 GCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
* * * *
1287 TATTCATCGAAGCAAATCTCAGCCTTGTTGGATAGAAGGATTTGTTTTTACGAGTATCTCAATCT
1 TATTCATCGAAGCAAATCTCAGCGTTATTGGATATAAGGATTT-TTTTTACGAGCATCTCAATCT
*
1352 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTAAAAAG
65 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG
* *
1417 -CCGCCAATCTTTCTGGCTTTGAATTATATATTTTTTTCTGTCTATTGTGGCAAAAAAATTTGAG
130 CCCGCCAATCTTTTTGGCTTTGAATTATATA-TTTTTTCTGTGTATTGTGGC-AAAAAA-TTGAG
* * ** * *
1481 AAAAAAAC-TCTCGGGTTAGTTTTTTTGCCGAAATTATTTACTAACCAACACGGTTTTT-GCTAA
192 -AAAAAACTTTTCGGGTCAG-TTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
* ** *
1544 AAACGCGTTCCGGAGCACCGGCTCAATTTTGCCCGATTTTTGGCGCAAAGGCTCCTTAAAATATC
255 AAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATC
1609 TA
320 TA
* * *
1611 TATGCATCGACGCAAAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCACCTCAATCT
1 TATTCATCGAAGC-AAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCATCTCAATCT
** *
1676 AATTTCGATTTAATTAGAAATCAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG
65 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG
* * * * *
1741 CCCG---ATCTCTATGGCTTTGAATTATATTTTTTTTCTGTCTATTGTAGCAAAAAAATTGAGAA
130 CCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGC-AAAAAATTGAGAA
* * * *
1803 AAAAC-TCTCGGGTTAGTTTTTTTGCCGAAATCGTGTACTAACCAACACGGTTTTTTGCTAAAAA
194 AAAACTTTTCGGGTCAG-TTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
* * ** * *
1867 CGCGTTCCGGAGCTCCAGCTCAATTTTGCCCGATTTTTGGCACAAAGGCTCCTTAAAATATCTA
258 CGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
* * *
1931 TCTTCATCGAAGCAAAATCTCAGTGTGATTGGATATAAGGATTTTTTTTACGAGCATCTCAATCT
1 TATTCATCGAAGC-AAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAG-----C-ATCT
* * * *
1996 CAATCTTTTTTCGATTTAATTAGAAATCAATTCGGAAAAAAATGAAAAAACGATATTAGAAGTGT
59 CAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGT
* * *
2061 GAAAAGCCCGCCAATCTTTATGGCTTTGAATTATATATTTTTTCTGTCTATTGTGGAAAAAAAAT
124 GAAAAGCCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGG-CAAAAAAT
**
2126 TGAG--AAAACTTTTCGGGTCAGTTTTTTTATCGAAATCGTGTACTAACCATCACGGTTTTTGGC
188 TGAGAAAAAACTTTTCGGGTCAG-TTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC
* * ** * *
2189 TAAAAACGTGTTCCGGAGCCCCGGCTCAACTTTGCCGGATTCTTGCCGCAAAGACTCCTTAAAAT
252 TAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAAT
2254 ATCTA
317 ATCTA
*
2259 TATTCATC-AACGTAAAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCATCTCAATC
1 TATTCATCGAA-G-CAAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCATCTCAATC
* * * * *
2323 TAGTTTCGATTTAATTAGAAATCAATTTAGAAAAAAAATGGAAAAATGATATTAGAAGCGTGAAA
64 TTGTTTCGATTTAATTAGAAATTAA-TTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * *
2388 AGCCCGCCAATCTTTATGGCTTTGAATAATATATTTTTCCTGTGTATTGTGGCAAAAAATTGAG-
128 AGCCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAGA
* * ** * *
2452 AAAAACCTTTCAGGTTTGTTTTTTTGTCTAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
193 AAAAACTTTTCGGGTCAG-TTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
* * * ** * * * *
2517 ACGCGTTCC-GATGCCACGGCTTAGTTTTATATGATTTTTGACACAAAGACTCCTTAATATACCT
257 ACGCGTTCCGGA-GCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCT
2581 A
321 A
*
2582 TATTCATCGAAGCAAAATCTCAGCGTGATTGGATATAAGGA-TTTTTTTACGAGCATCTCAATCT
1 TATTCATCGAAGC-AAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCATCTCAATCT
* * *
2646 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAACGTTATTAGAAGCATGAAAA
65 TGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * *
2711 GCCCGACAATCTTTTTGGCTTTGAATTATAAATTTTTTCTGTGTATTGTGGGAAAAAATTGGGAA
129 GCCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAGAA
* * * * *
2776 AAAACTTTTCGGGTAAGTTTTTTGCCGAGATCGTGTATTTAACCATCACGGATTTTGGCAAAAAA
194 AAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTA-CTAACCATCACGGTTTTTGGCTAAAAA
* ** * * * * * *
2841 CGCATTCCATAGCCCCGGCCCAATTTTGCTTGATTTTTGGTGCAAAGACTACTTAATATATCCA
258 CGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
* * *
2905 TATTCATCAAAAG-AAATCTCAGCCTTGTTGGATATAAGGATTTGTTTTTACGAGCATCTCAATC
1 TATTCATC-GAAGCAAATCTCAGCGTTATTGGATATAAGGATTT-TTTTTACGAGCATCTCAATC
* * * *
2969 TTATTAT-GATTTAATTAGAAATTAATTCGGAAAAAATTGG-AAAGCGATATTAGAAGCATGAAA
64 TTGTT-TCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * * ** * *
3032 AGCCCGTCAATCTTATTGGCGTTGAATTATATATTGATTCTGTGTATCGT-GCTAAAAAATTAAG
128 AGCCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGC-AAAAAATTGAG
* * *
3096 AAAAAACTTTTCGGGTCAGTTTTTTGCCGAAATCTTGTATTAACTATCACGGTTTTTGGCTAAAA
192 AAAAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
* * * **
3161 ACGCGTTCCGAAGTCCCGACTCAATTTTGCCCGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
257 ACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
*
3226 TATTCATC---G---A----AGC--------AT-TAAGGATTTTTTTTACGAGTATCTCAATCTT
1 TATTCATCGAAGCAAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCATCTCAATCTT
* * * *
3272 GTTTCGATTTTATTAGAAATTAATTCGG-AAAAAATGGGAAAATGATATTAGAAGCATGAAAAGC
66 GTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGC
*
3336 CCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAGTAAA
131 CCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAGAAAA
* *
3401 AA-TTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCATGGTTTTTGGCAAAAAACGC
196 AACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGC
* * * * *
3465 ATTCCAGAGCCCCGGCTCAATTTTGCATGATTTTTTGTGCAAAGACTCCTTAAAATATTTA
261 GTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
* * * *
3526 TATTCATCGAAGGAAATCTCAGCCTTGTTGGATATAAGGATTTGCTTTTACGAGCATCTCAATCT
1 TATTCATCGAAGCAAATCTCAGCGTTATTGGATATAAGGATTT-TTTTTACGAGCATCTCAATCT
*
3591 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGGTATTAGAAGCGTGAAAA
65 TGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* *
3656 GCCCGTCAATCTGTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAG-A
129 GCCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAGAA
*
3720 AAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTATCCATCACGGTTTTTGGC-AAAAGA
194 AAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA-A
* * * ** *
3784 CGCATTCCAGAGCCCCAGCTCAATTTTGCATGATTTTTGATGCAAAGACTCATTAAAATATCTA
258 CGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
* * * *
3848 TATTCATCGAAGCAAATCTCAACCTTGTTGGATATAAGGATTTGTTTTTACGAGCATCTTAATCT
1 TATTCATCGAAGCAAATCTCAGCGTTATTGGATATAAGGATTT-TTTTTACGAGCATCTCAATCT
* *
3913 CGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACAATATTAGAAGCGTGAAAAG
65 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG
* * ** * *
3978 CCCGCCAAT-TTGTATGACTTTGAATTATATATTGATTGTGTCTATTGTGGCAAAAAATTGAGAA
130 CCCGCCAATCTT-TTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAG-A
* * * * *
4042 AAAAAC-TTTCGAGTTAGTTTTTTGTCAAAATGGTGTACTAACCATCACGGTTTTTGGCTAAAAA
193 AAAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
* * * *
4106 CGCGTTCCGGAGTCACGACTTAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
258 CGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
* * *
4170 TATTCATTGAAGCAAAATCTCTGCGTGATTGGATATAAGGA-TTTTTTTACGAGCATCTCAATCT
1 TATTCATCGAAGC-AAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCATCTCAATCT
*
4234 TGTTTCGATTTTATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG
65 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG
* * *
4299 CCCGCCAATCTTTTTGGCTTTAAATTCTATATTTTTTCTGTGTATTATGGCAAAAAATTGAGAAA
130 CCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAG-AA
* ** * ** * * * ***
4364 AAAACTTTTCGGGTCAGTTTTTGGCAAAAAAACGCATTCCAGAGCC-CCGACTCAATTTT-GCAT
194 AAAACTTTTCGGGTCAGTTTTTTGC-CGAAATCGTGTACTA-A-CCATC-AC-GGTTTTTGGC-T
***** * ** * * * ** * * *
4427 GATTTTTG-G-TGCAAAGACTCC--TTAAAATATTT--AT-ATTCAT--CG-AAGGAAAT-CTCA
253 -AAAAACGCGTTCCGGAG-CCCCGGCT-CAAT-TTTGCATGATTTTTGGCGCAAAG-ACTCCTTA
*** *
4481 GCCT-TGT-
313 AAATATCTA
* * * * * * * * *
4488 TGGA-T-AT--AAG--TAT-T-TG-TTTTTATGAGCATTTCA--ATCTTGTTT-C--G-AT-TTA
1 T--ATTCATCGAAGCAAATCTCAGCGTTAT-TG-G-ATATAAGGATTTTTTTTACGAGCATCTCA
* * * * ** * * * *
4537 AT-TAG----AAATTAATTCGGAAAAAAAAAT-GGAAAAACGATAT-TAGAAGCG-TGA--A-AA
61 ATCTTGTTTCGATTTAATT-AG-AAATTAATTCGGAAAAA--A-ATGGAAAAACGAT-ATTAGAA
** * * ****** *** * * * * * **
4591 GCCCGCCAATGTTATTGAAGT-TGAAT---TAT--A-TAT-TGATTCTGTCTAT-T-GTG-GCAA
120 GCGTG-AAAAGCCCGCCAA-TCTTTTTGGCTTTGAATTATAT-ATTTTTTCTGTGTATTGTGGCA
* *
4645 AAAAATTGAGAAAAAAAAC-TTTCGGGTTAGTTTTTTGTCGAAATCGTGTACTAACCATCACGGT
182 AAAAATTGAG--AAAAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGT
* * * **
4709 TTTTGGCAAAAAAACGCGTTCCGGTGTCATGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTC
245 TTTTGGC-TAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTC
4774 CTTAAAATATCTA
309 CTTAAAATATCTA
* * *
4787 TATTCATCGAAGCAAAATCTCAGTGTGATTGGATATAAGGTATTTTTTTTTACGAGAATCTCAAT
1 TATTCATCGAAGC-AAATCTCAGCGTTATTGGATATAAGG-A-TTTTTTTTACGAGCATCTCAAT
*
4852 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCATGAAA
63 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * * *
4917 AGCCTGCCAATCTTTTTGACTTTGAATTATATATTTTTTCTGTCTATTGTGACAAAAAAATTGAA
128 AGCCCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGC-AAAAAATTG--
* * *
4982 AAAAAAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAATCATCACGGTTTTTGGCAAA
190 AGAAAAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC-TA
* * * *
5047 AAAACGCATTCCAGAGCCCCGGCTCAATTTTGCATGATTTTTTGTGCAAAGACTCCTTAAAATAT
254 AAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATAT
*
5112 TTA
319 CTA
* * * *
5115 TATTCATCGAAGGAAATCTCAGCCTTGTTGGATATAAGGATTTGCTTTTACGAGCATCTCAATCT
1 TATTCATCGAAGCAAATCTCAGCGTTATTGGATATAAGGATTT-TTTTTACGAGCATCTCAATCT
5180 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
65 TGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
** * *** * **
5245 GCTTGCCAATCTTATTGG-TGTTGAATTATATATTGACTATGTGTATTGTGGCAAAAAATCAAGA
129 GCCCGCCAATCTTTTTGGCT-TTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAGA
* * *
5309 AAAAACTTTTCGGGTCAATTTTTTGTCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAA
193 AAAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
*
5374 CGAGTTCCG
258 CGCGTTCCG
5383 AAACCCC
Statistics
Matches: 4293, Mismatches: 588, Indels: 358
0.82 0.11 0.07
Matches are distributed among these distances:
290 6 0.00
291 11 0.00
292 8 0.00
293 11 0.00
294 32 0.01
295 9 0.00
296 6 0.00
297 18 0.00
298 4 0.00
299 3 0.00
300 127 0.03
301 128 0.03
302 22 0.01
303 19 0.00
304 14 0.00
305 9 0.00
306 8 0.00
307 7 0.00
308 8 0.00
309 2 0.00
310 5 0.00
311 10 0.00
312 9 0.00
313 10 0.00
314 4 0.00
315 8 0.00
316 11 0.00
317 17 0.00
318 95 0.02
319 79 0.02
320 265 0.06
321 620 0.14
322 1018 0.24
323 621 0.14
324 302 0.07
325 156 0.04
326 160 0.04
327 122 0.03
328 277 0.06
329 52 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (321 bp):
TATTCATCGAAGCAAATCTCAGCGTTATTGGATATAAGGATTTTTTTTACGAGCATCTCAATCTT
GTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGC
CCGCCAATCTTTTTGGCTTTGAATTATATATTTTTTCTGTGTATTGTGGCAAAAAATTGAGAAAA
AACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGC
GTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTA
Found at i:4889 original size:327 final size:326
Alignment explanation
Indices: 4380--5373 Score: 1516
Period size: 327 Copynumber: 3.0 Consensus size: 326
4370 TTTCGGGTCA
*
4380 GTTTTTGGCAAAAAAACGCATTCCAGAGCCCCGACTCAATTTTGCATGATTTTTGGTGCAAAGAC
1 GTTTTTGGCAAAAAAACGCATTCCAGAGCCCCGGCTCAATTTTGCATGATTTTTGGTGCAAAGAC
4445 TCCTTAAAATATTTATATTCATCGAAGGAAATCTCAGCCTTGTTGGATATAA-GTATTTGTTTTT
66 TCCTTAAAATATTTATATTCATCGAAGGAAATCTCAG-CTTGTTGGATATAAGGTATTTGTTTTT
* *
4509 ATGAGCATTTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAATGGAAAAACGA
130 ACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAAATGGAAAAACGA
* *
4574 TATTAGAAGCGTGAAAAGCCCGCCAATGTTATTGAAGTTGAATTATATATTGATTCTGTCTATTG
194 TATTAGAAGCGTGAAAAGCCTGCCAATCTTATTGAAGTTGAATTATATATTGATTCTGTCTATTG
*
4639 TGGCAAAAAAATTGAGAAAAAAAAC-TTTCGGGTTAGTTTTTTGTCGAAATCGTGTACTAACCAT
259 TGGCAAAAAAATTGA-AAAAAAAACTTTTCGGGTCAGTTTTTTGTCGAAATCGTGTACTAACCAT
4703 CACG
323 CACG
* * * * ** *
4707 GTTTTTGGCAAAAAAACGCGTTCCGGTGTCATGGCTCAATTTTGCATGATTTTTGGCGCAAAGAC
1 GTTTTTGGCAAAAAAACGCATTCCAGAGCCCCGGCTCAATTTTGCATGATTTTTGGTGCAAAGAC
* * *
4772 TCCTTAAAATATCTATATTCATCGAAGCAAAATCTCAG-TGTGATTGGATATAAGGTATTTTTTT
66 TCCTTAAAATATTTATATTCATCGAAG-GAAATCTCAGCT-TG-TTGGATATAAGGTATTTGTTT
*
4836 TTACGAGAATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAATGGAAAAACG
128 TTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACG
* * ** **
4900 ATATTAGAAGCATGAAAAGCCTGCCAATCTTTTTGACTTTGAATTATATATTTTTTCTGTCTATT
193 ATATTAGAAGCGTGAAAAGCCTGCCAATCTTATTGAAGTTGAATTATATATTGATTCTGTCTATT
* * *
4965 GTGACAAAAAAATTGAAAAAAAAAACTTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAATCA
258 GTGGCAAAAAAATTG-AAAAAAAAACTTTTCGGGTCAGTTTTTTGTCGAAATCGTGTACTAACCA
5030 TCACG
322 TCACG
*
5035 GTTTTTGGCAAAAAAACGCATTCCAGAGCCCCGGCTCAATTTTGCATGATTTTTTGTGCAAAGAC
1 GTTTTTGGCAAAAAAACGCATTCCAGAGCCCCGGCTCAATTTTGCATGATTTTTGGTGCAAAGAC
*
5100 TCCTTAAAATATTTATATTCATCGAAGGAAATCTCAGCCTTGTTGGATATAAGG-ATTTGCTTTT
66 TCCTTAAAATATTTATATTCATCGAAGGAAATCTCAG-CTTGTTGGATATAAGGTATTTGTTTTT
5164 ACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGAT
130 ACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGAT
* ** * * *
5229 ATTAGAAGCGTGAAAAGCTTGCCAATCTTATTGGTGTTGAATTATATATTGACTATGTGTATTGT
195 ATTAGAAGCGTGAAAAGCCTGCCAATCTTATTGAAGTTGAATTATATATTGATTCTGTCTATTGT
* * *
5294 GGC-AAAAAA-TCAAGAAAAAACTTTTCGGGTCAATTTTTTGTCGAAATCGTGTACTAACCATCA
260 GGCAAAAAAATTGAAAAAAAAACTTTTCGGGTCAGTTTTTTGTCGAAATCGTGTACTAACCATCA
*
5357 CT
325 CG
*
5359 GTTTTTGGCTAAAAA
1 GTTTTTGGCAAAAAA
5374 CGAGTTCCGA
Statistics
Matches: 600, Mismatches: 58, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
324 63 0.10
325 1 0.00
326 59 0.10
327 278 0.46
328 145 0.24
329 54 0.09
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (326 bp):
GTTTTTGGCAAAAAAACGCATTCCAGAGCCCCGGCTCAATTTTGCATGATTTTTGGTGCAAAGAC
TCCTTAAAATATTTATATTCATCGAAGGAAATCTCAGCTTGTTGGATATAAGGTATTTGTTTTTA
CGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGATA
TTAGAAGCGTGAAAAGCCTGCCAATCTTATTGAAGTTGAATTATATATTGATTCTGTCTATTGTG
GCAAAAAAATTGAAAAAAAAACTTTTCGGGTCAGTTTTTTGTCGAAATCGTGTACTAACCATCAC
G
Done.