Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010694.1 Corchorus capsularis cultivar CVL-1 contig10715, 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: 17173
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:842 original size:331 final size:327
Alignment explanation
Indices: 25--3587 Score: 2105
Period size: 331 Copynumber: 11.0 Consensus size: 327
15 TCGGGTCAGT
* * * * * ** * *
25 TTTTAGCCGAAATCGTGTACATTA-CATCACGGTTTTTAGCTGAAAACGCGTTTCGGGGCCTCGA
1 TTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTCTGGCTAAAAACGCGTTCCGTAGCCCCGG
* * * * * * *
89 CTCAATTTTGC-TTGGTTTTTGGCATAGAGACTCGTTTAAATATCTATATTCATCTAACCAAATC
65 CTCAA-TTTGCATT--ATTTTGTCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATC
* * * * * * * *
153 TCAGCCGCAATAGATTCAAGGATTTGTTTTTACGAGCATATGAATCTTATTTCGATTCAATCAGA
127 TCAGCCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * * *
218 AATAAATTCAAAAAAAAAACGACAAACGATATTAAAAGCGTGAAAACCGTTCAATTTTTTTGGCG
192 AATAAATTCGAAAAAAAAATGAAAAACGATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGG-A
* * * ** *
283 TTGAATCATATTTATTTTTTCTAAGTATTGTGGCAAAGAATTGAGGAAAAATTTTTCGGATCAGT
256 TTGAAT-ATATAT-TTTTTTCTGAGTATTGTGG-AAAAAATTGAGGAAAAAAATTTCGGGTCAGT
**
348 CATTGCAAAA
318 TTTTGCAAAA
* * *
358 TTTTAGCCAAAATTGTGTACT-ACCATCACGGTTT-TCGGC-AAAAACCCGTTCCGTAGCCCCGG
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCT-GGCTAAAAACGCGTTCCGTAGCCCCGG
* * ** *
420 CTCAATTTGCGTTATTTTTTACGGGAAGGCTCCTTGAAATATCTATATTCATCAAACCAAATCTC
65 CTCAATTTGCATTATTTTGT-CGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTC
* * *
485 AGACACATTAGATTTAA-AACTTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAATTAGAA
129 AGCCACATTAGATTTAAGAA-TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
*
549 ATAAATTCGAAAAAAAAATCGAAAAACGATATTAAAAGCGTGAAAACCCTTCATTTTTTTTGGAT
193 ATAAATTCGAAAAAAAAAT-GAAAAACGATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGGAT
614 TGAAGTATATATTTTTTTCTGAGTATTGTGGAAAAGAATTGAGGAAAAAAATTTCGGGTCAGTTT
257 TGAA-TATATATTTTTTTCTGAGTATTGTGGAAAA-AATTGAGGAAAAAAATTTCGGGTCAGTTT
*
679 TTACAAAA
320 TTGCAAAA
* * * *
687 TTTTAGCCGAAATCATGTACTAACCGTCACGGTTTCTGGCTAAAAACACGTTACGTAGCCCCGGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTAAAAACGCGTTCCGTAGCCCCGGC
* * * * * * * *
752 TCCATTTGCATTATTATGTCGTAAAGGCTCCTTGAATTATTTATATTCATCAAATCAAATTTTAG
66 TCAATTTGCATTATTTTGTCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAG
* * * *
817 CCACGATTAGATTTAAAAATTTGTTTTTACGAGCATATAAATCTTGTTTCGATTTATTTAGAAAT
131 CCAC-ATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * *
882 TAATTCG-GAAAAAAATG-GAAACTGATATTAAAAGCGTGGAAAACCTTTCAATCTTTTTATTTT
195 AAATTCGAAAAAAAAATGAAAAAC-GATATTAAAAGCGT-GAAAACCCTTCAA----TTT-TTTT
* * * *
945 TG-TTGAATCATATTTTTTTTTTCAGAGTATTGTGGCAAAAAATTGA-GAAAAAAA-TTCGGGTA
253 GGATTGAAT-ATA-TATTTTTTTCTGAGTATTGTGG-AAAAAATTGAGGAAAAAAATTTCGGGTC
1007 AG----T------
315 AGTTTTTGCAAAA
* * * * ** *
1010 TTTTAGCCGAAATCGTGTAATAACCATCACGGTTTCTGGCTAAAAACGCATTTCG-GGACATCGA
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTAAAAACGCGTTCCGTAG-CCCCGG
* * * *
1074 CT-AAGTTTTGC-TTGGTTCTTGGCATAGAGACTCCTTGAAATATCTATATTCATCAAACCAAAT
65 CTCAA--TTTGCATT-ATT-TTGTCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAAT
* * * * * * *
1137 CTCAGTCACAATGGATTCAAGGATTTGTTTTTACGAGCATCTGAGTCTTATTTCGATTTAATTAG
126 CTCAGCCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
*
1202 AAATAAATTCGGAAAAGAAAAATCGAAAAACAATATTAAAAGCGTGAAAACCCTTCAATTTTTTT
191 AAATAAATTC-GAAAA-AAAAAT-GAAAAACGATATTAAAAGCGTGAAAACCCTTCAATTTTTTT
* * * * * * **
1267 GGCATTGAAT-TA-GTTTTTTT-T-ATTATTGTCGCAAACAATT--TGCATTAAA---C----CA
253 GG-ATTGAATATATATTTTTTTCTGAGTATTGT-GGAAAAAATTGAGGAAAAAAATTTCGGGTCA
**
1319 ---TTTGCATTA
316 GTTTTTGCAAAA
** * * * ** * * *** *
1328 -CGTAGCCCCGGATCAGTCATTGCAAAAACCGTCGAAACGCGTTTCGAGGCT-TCGACTCAGTT-
1 TTTTAG--CC-GA--AATC-GTGTACTAACCATC---ACG-GTTTC-TGGCTAAAAACGC-GTTC
* ** * *** * * * * * **
1390 --TTG-CTTGG-T--TTTTGTCATTGAGACT-CCTTGAAATA-T-CTAG-ATTCATC-A-AACCA
54 CGTAGCCCCGGCTCAATTTG-CATT-ATTTTGTCGT-AAAGACTCCTTGAAAT-ATCTATATTC-
* ** * * * * * * ** * * * *
1443 AATCTCAACCACAAT-GGATTCAAGGATTTGTTTTTACG-A---GCATCTA-AATCTTATTTCG-
114 -ATC-AAACCA-AATCTCA-GCCA-CATTAG-ATTTAAGAATTTGTTTTTACGAGC--ATCT-GA
** * * * * * *
1501 AT-TTAATTAGAAATAAATTCGAAAAAAAATCG---AAA--------AACGATATTAAAAGCGTG
170 ATCTTGTTTCG-ATTTAATTAGAAATAAATTCGAAAAAAAAATGAAAAACGATATTAAAAGCGTG
* *
1554 AAAACCCTTCATTTCTTTTTGGATTGAAGTATATATTTTTTTCTGAGTATTGTGGCAAAGAATTG
234 AAAACCCTTCAATT-TTTTTGGATTGAA-TATATATTTTTTTCTGAGTATTGTGG-AAAAAATTG
* **
1619 AGGACAAATTTTTCGGGTCAGTTTTTGCAAAA
296 AGGAAAAAAATTTCGGGTCAGTTTTTGCAAAA
*
1651 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTAAAAACGCGTTACGTAGCCCCGGC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTAAAAACGCGTTCCGTAGCCCCGGC
* * * *
1716 TCCATTTGCATTATTTTGTCGTAAAGGCTCATTGAATTATCTATATTCATCAAACCAAATCTCAG
66 TCAATTTGCATTATTTTGTCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAG
* * * *
1781 CCACAATTAGATTTAAAAATTTGTTTTTACGAGCATCTAAATCTTGTTTTGATTTATTTAGAAAT
131 CCAC-ATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * * * * *
1846 TAATTCGGAAAAAAAATG-GAAACTAATATTAGAAGCGTGGAAAACCTTTCAATCTTTTTTTTTT
195 AAATTCGAAAAAAAAATGAAAAAC-GATATTAAAAGCGT-GAAAACCCTTCAA----TTTTTTTG
*
1910 G-TTGAAT-TATATTTTTTT-TAGAGTATTGTGGCAAAAAATTGA-GAAAAAAA-TTCGGGTAAG
254 GATTGAATATATATTTTTTTCT-GAGTATTGTGG-AAAAAATTGAGGAAAAAAATTTCGGGTCAG
1970 ----T------
317 TTTTTGCAAAA
* * * * ** ** *
1971 TTTTAGCCGAAATCATGTAATAACCATCATGGTTTCTGGCTAAAAACGCGTTTCGGGGCATCGAC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTAAAAACGCGTTCCGTAGCCCCGGC
* * * * * *
2036 TCAGTTTTGC-TTGGTTCTTGGCATAGAGACTCCTTAAAATATCTATATTCATCAAACCAAATCT
66 TCA-ATTTGCATT-ATT-TTGTCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCT
* * * * * * *
2100 CAGTCACAATGGATTCAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTTGATTTAATTAGAA
128 CAGCCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
*
2165 ATAAATTCGGAAAAGAAAAATCGAAAAACAATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGG
193 ATAAATTC-GAAAA-AAAAAT-GAAAAACGATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGG
* * * * ** **
2230 CATTGAAT-TATATTTTTCTT-TTATTATTGTCGCAAACAATTGAGG-AAAATTTTTCTTGTCAG
255 -ATTGAATATATATTTTT-TTCTGAGTATTGT-GGAAAAAATTGAGGAAAAAAATTTCGGGTCAG
2292 TTTTTGCAAAA
317 TTTTTGCAAAA
* * * *
2303 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGTGTTCCATAGCCCCGAC
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTAAAAACGCGTTCCGTAGCCCCGGC
*
2368 TCAATTTGCATTATTTTTGTCGTAAAGACTCCTTAAAATATCTATATTCATCAAACCAAATCTCA
66 TCAATTTGCATTA-TTTTGTCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCA
* * * * * * *
2433 GCCACATTAGGTTTAAGAAGTTGTTTTTACTAGCATCTAAATCTTGTTTCGTTTTAATGAAAAAT
130 GCCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * * *
2498 TAATTCG---GAAAAATGGAAAACTGATATTAGAAGCGTGGAAAACCCTTCAATTGTTTTGGCAT
195 AAATTCGAAAAAAAAATGAAAAAC-GATATTAAAAGCGT-GAAAACCCTTCAATTTTTTTGG-AT
* * * * *
2560 TGAAT-TATATATTTTTTCTGAGTTTTGTGGCAAAAAATTCATG-AAAAATTCTTCAGGTCAG--
257 TGAATATATAT-TTTTTTCTGAGTATTGTGG-AAAAAATTGAGGAAAAAAAT-TTCGGGTCAGTT
2621 --T------
319 TTTGCAAAA
* * ** * * * * * ** *
2622 TTTTAGCCGAATTCGTGTAATAACCATCACAATTTTTTTAGCTAAAAACACATTTCGGGGACCCG
1 TTTTAGCCGAAATCGTGTACTAACCATCAC--GGTTTCTGGCTAAAAACGCGTTCCGTAGCCCCG
** * * * * *
2687 GCTCAATTTTAAATGATTTTTGACAG-AAAGACTTCTTGAAATATTTATATTCATCTAACCAAAT
64 GCTCAA-TTTGCATTA-TTTTGTC-GTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAAT
* * * * * *
2751 ATCAGCCACAATGGATTTAAGGATCTGCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
126 CTCAGCCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* * * * * * *
2816 AAATTAATTCGAAAAAAAAAAGGAAAACGATATTAGAAGCGTCAAAAACACTTCAATTGTTTTGG
191 AAATAAATTCGAAAAAAAAATGAAAAACGATATTAAAAGCGT-GAAAACCCTTCAATTTTTTTGG
* * * * * *
2881 AGCTGGATTATATATTTTGTAC-GAGTATTGTGGCAGAGAATTGAGGAAAAAAATTTCGGGTCAG
255 A--TTGAATATATATTTTTTTCTGAGTATTGTGG-AAAAAATTGAGGAAAAAAATTTCGGGTCAG
2945 TTTTTGCAAAA
317 TTTTTGCAAAA
* *
2956 TTTTAGCCGAAATCGTGTACTAACCATCACGATATT-TGGCTAAAAACGCATTCCG-AGGCCCCG
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGT-TTCTGGCTAAAAACGCGTTCCGTA-GCCCCG
* * * * * * * *
3019 ACTCAGTTTTGCATTATTTTTGGCATAAAAACTCCTTGTAATATCTATATTCATCGAATCAAATC
64 GCTCA-ATTTGCATTA-TTTTGTCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATC
* * * * * *
3084 CCAACCACATTGGATTCAAGAATTT-TTTTTACGAGCATCTGAATCTTGTTTCGATTTACTTTGA
127 TCAGCCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
* * * *
3148 AATTAATTC---AGAAAAATGGTAAAACGATATTAGAAGCGTGAAAAACCCTTCAACCTTTATTT
192 AATAAATTCGAAAAAAAAAT-GAAAAACGATATTAAAAGCGTG-AAAACCCTTCAA--TTT-TTT
* * *
3210 T-G-TTGAATA-ATATATTTTTTCAGAGTATTGTGGCAAAAAATTGAGAAAAAAAAATT-GGG-C
252 TGGATTGAATATATAT-TTTTTTCTGAGTATTGTGG-AAAAAATTGAGGAAAAAAATTTCGGGTC
*
3270 --------C-AAT
315 AGTTTTTGCAAAA
* * * * * * *
3274 TTTTACCCGAAATCGTGTACT----ATCACGGTTTTTGGCTAAAAACGCGTTTCAGGA-TCTCGA
1 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTAAAAACGCG-TTCCGTAGCCCCGG
* * * * *
3334 CTCAATTTTTC-TTGGTTTT-TGGCATAGACTCCTTGAAATATCTATATTCATCAAACCAAATCT
65 CTCAA-TTTGCATT-ATTTTGTCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCT
* * * *
3397 TAGCCAAATTGGATTTAAGGATTTG----T--GAGCATCTGAATCTTGTTTCGATTTAATTAGAA
128 CAGCCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * ** * * * *
3456 ATTAATTC--AGAAAAAATGGAAAAAAAAAATTAGAAGCGTGAAAATCCCATCAATCTTTTTGGC
193 ATAAATTCGAAAAAAAAAT-GAAAAACGATATTAAAAGCGTGAAAA-CCCTTCAATTTTTTTGG-
* * * * * *
3519 GTTTAAT-TATATATTTTTGCTGAG-ACTTGTGGCGAAAAGTTCA-GAAAAAAATCTTTCGGGTC
255 ATTGAATATATAT-TTTTTTCTGAGTA-TTGTGG-AAAAAATTGAGGAAAAAAA--TTTCGGGTC
*
3581 TGTTTTT
315 AGTTTTT
3588 AGCGGAATTC
Statistics
Matches: 2520, Mismatches: 490, Indels: 455
0.73 0.14 0.13
Matches are distributed among these distances:
305 4 0.00
306 39 0.02
307 59 0.02
308 67 0.03
309 10 0.00
310 5 0.00
311 16 0.01
312 54 0.02
313 17 0.01
314 40 0.02
315 10 0.00
316 5 0.00
317 17 0.01
318 66 0.03
319 76 0.03
320 134 0.05
321 151 0.06
322 197 0.08
323 104 0.04
324 149 0.06
325 82 0.03
326 31 0.01
327 68 0.03
328 73 0.03
329 161 0.06
330 208 0.08
331 337 0.13
332 214 0.08
333 31 0.01
334 52 0.02
335 37 0.01
336 6 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (327 bp):
TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTAAAAACGCGTTCCGTAGCCCCGGC
TCAATTTGCATTATTTTGTCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAG
CCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATA
AATTCGAAAAAAAAATGAAAAACGATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGGATTGAA
TATATATTTTTTTCTGAGTATTGTGGAAAAAATTGAGGAAAAAAATTTCGGGTCAGTTTTTGCAA
AA
Found at i:1911 original size:964 final size:964
Alignment explanation
Indices: 449--2270 Score: 3208
Period size: 964 Copynumber: 1.9 Consensus size: 964
439 TACGGGAAGG
* * *
449 CTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGACACATTAGATTTAAAACTTTGTTTTT
1 CTCCTTGAAATATCTAGATTCATCAAACCAAATCTCAGACACAATAGATTCAAAACTTTGTTTTT
*
514 ACAAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAAATCGAAAAACGAT
66 ACAAGCATCTAAATCTTATTTCGATTTAATTAGAAATAAATTCGAAAAAAAAATCGAAAAACGAT
579 ATTAAAAGCGTGAAAACCCTTCATTTTTTTTGGATTGAAGTATATATTTTTTTCTGAGTATTGTG
131 ATTAAAAGCGTGAAAACCCTTCATTTTTTTTGGATTGAAGTATATATTTTTTTCTGAGTATTGTG
644 GAAAAGAATTGAGGAAAAAAATTTCGGGTCAGTTTTTACAAAATTTTAGCCGAAATCATGTACTA
196 GAAAAGAATTGAGGAAAAAAATTTCGGGTCAGTTTTTACAAAATTTTAGCCGAAATCATGTACTA
*
709 ACCGTCACGGTTTCTGGCTAAAAACACGTTACGTAGCCCCGGCTCCATTTGCATTATTATGTCGT
261 ACCATCACGGTTTCTGGCTAAAAACACGTTACGTAGCCCCGGCTCCATTTGCATTATTATGTCGT
* * * * * *
774 AAAGGCTCCTTGAATTATTTATATTCATCAAATCAAATTTTAGCCACGATTAGATTTAAAAATTT
326 AAAGGCTCATTGAATTATCTATATTCATCAAACCAAATCTCAGCCACAATTAGATTTAAAAATTT
839 GTTTTTACGAGCATATAAATCTTGTTTCGATTTATTTAGAAATTAATTCGGAAAAAAATGGAAAC
391 GTTTTTACGAGCATATAAATCTTGTTTCGATTTATTTAGAAATTAATTCGGAAAAAAATGGAAAC
* *
904 TGATATTAAAAGCGTGGAAAACCTTTCAATCTTTTTATTTTTGTTGAATCATATTTTTTTTTTCA
456 TAATATTAAAAGCGTGGAAAACCTTTCAATCTTTTTATTTTTGTTGAAT--TATATTTTTTTT-A
*
969 GAGTATTGTGGCAAAAAATTGAGAAAAAAATTCGGGTAAGTTTTTAGCCGAAATCGTGTAATAAC
518 GAGTATTGTGGCAAAAAATTGAGAAAAAAATTCGGGTAAGTTTTTAGCCGAAATCATGTAATAAC
1034 CATCACGGTTTCTGGCTAAAAACGCATTTCGGGACATCGACTAAGTTTTGCTTGGTTCTTGGCAT
583 CATCACGGTTTCTGGCTAAAAACGCATTTCGGGACATCGACTAAGTTTTGCTTGGTTCTTGGCAT
*
1099 AGAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGTCACAATGGATTCAAGGATTTG
648 AGAGACTCCTTAAAATATCTATATTCATCAAACCAAATCTCAGTCACAATGGATTCAAGGATTTG
*
1164 TTTTTACGAGCATCTGAGTCTTATTTCGATTTAATTAGAAATAAATTCGGAAAAGAAAAATCGAA
713 TTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGAAAAGAAAAATCGAA
1229 AAACAATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGGCATTGAA-T-TAGTTTT-TTTTATT
778 AAACAATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGGCATTGAATTATAGTTTTCTTTTATT
1291 ATTGTCGCAAACAATTTGCATTAAACCATTTGCATTACGTAGCCCCGGATCAGTCATTGCAAAAA
843 ATTGTCGCAAACAATTTGCATTAAACCATTTGCATTACGTAGCCCCGGATCAGTCATTGCAAAAA
1356 CCGTCGAAACGCGTTTCGAGGCTTCGACTCAGTTTTGCTTGGTTTTTGTCATTGAGA
908 CCGTCGAAACGCGTTTCGAGGCTTCGACTCAGTTTTGCTTGGTTTTTGTCATTGAGA
* *
1413 CTCCTTGAAATATCTAGATTCATCAAACCAAATCTCA-ACCACAATGGATTCAAGGA-TTTGTTT
1 CTCCTTGAAATATCTAGATTCATCAAACCAAATCTCAGA-CACAATAGATTCAA-AACTTTGTTT
*
1476 TTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATAAATTCG-AAAAAAAATCGAAAAACG
64 TTACAAGCATCTAAATCTTATTTCGATTTAATTAGAAATAAATTCGAAAAAAAAATCGAAAAACG
1540 ATATTAAAAGCGTGAAAACCCTTCATTTCTTTTTGGATTGAAGTATATATTTTTTTCTGAGTATT
129 ATATTAAAAGCGTGAAAACCCTTCATTT-TTTTTGGATTGAAGTATATATTTTTTTCTGAGTATT
* * ** * *
1605 GTGGCAAAGAATTGAGGACAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
193 GTGGAAAAGAATTGAGGAAAAAAATTTCGGGTCAGTTTTTACAAAATTTTAGCCGAAATCATGTA
* *
1670 CTAACCATCACGGTTTCTGGCTAAAAACGCGTTACGTAGCCCCGGCTCCATTTGCATTATTTTGT
258 CTAACCATCACGGTTTCTGGCTAAAAACACGTTACGTAGCCCCGGCTCCATTTGCATTATTATGT
1735 CGTAAAGGCTCATTGAATTATCTATATTCATCAAACCAAATCTCAGCCACAATTAGATTTAAAAA
323 CGTAAAGGCTCATTGAATTATCTATATTCATCAAACCAAATCTCAGCCACAATTAGATTTAAAAA
* *
1800 TTTGTTTTTACGAGCATCTAAATCTTGTTTTGATTTATTTAGAAATTAATTCGGAAAAAAAATGG
388 TTTGTTTTTACGAGCATATAAATCTTGTTTCGATTTATTTAGAAATTAATTCGG-AAAAAAATGG
*
1865 AAACTAATATTAGAAGCGTGGAAAACCTTTCAATCTTTTT-TTTTTGTTGAATTATATTTTTTTT
452 AAACTAATATTAAAAGCGTGGAAAACCTTTCAATCTTTTTATTTTTGTTGAATTATATTTTTTTT
1929 AGAGTATTGTGGCAAAAAATTGAGAAAAAAATTCGGGTAAGTTTTTAGCCGAAATCATGTAATAA
517 AGAGTATTGTGGCAAAAAATTGAGAAAAAAATTCGGGTAAGTTTTTAGCCGAAATCATGTAATAA
* * * *
1994 CCATCATGGTTTCTGGCTAAAAACGCGTTTCGGGGCATCGACTCAGTTTTGCTTGGTTCTTGGCA
582 CCATCACGGTTTCTGGCTAAAAACGCATTTCGGGACATCGACTAAGTTTTGCTTGGTTCTTGGCA
2059 TAGAGACTCCTTAAAATATCTATATTCATCAAACCAAATCTCAGTCACAATGGATTCAAGGATTT
647 TAGAGACTCCTTAAAATATCTATATTCATCAAACCAAATCTCAGTCACAATGGATTCAAGGATTT
*
2124 GTTTTTACGAGCATCTGAATCTTATTTTGATTTAATTAGAAATAAATTCGGAAAAGAAAAATCGA
712 GTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGAAAAGAAAAATCGA
*
2189 AAAACAATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGGCATTGAATTATATTTTTCTTTTAT
777 AAAACAATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGGCATTGAATTATAGTTTTCTTTTAT
2254 TATTGTCGCAAACAATT
842 TATTGTCGCAAACAATT
2271 GAGGAAAATT
Statistics
Matches: 815, Mismatches: 36, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
961 300 0.37
962 12 0.01
963 53 0.07
964 401 0.49
965 49 0.06
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (964 bp):
CTCCTTGAAATATCTAGATTCATCAAACCAAATCTCAGACACAATAGATTCAAAACTTTGTTTTT
ACAAGCATCTAAATCTTATTTCGATTTAATTAGAAATAAATTCGAAAAAAAAATCGAAAAACGAT
ATTAAAAGCGTGAAAACCCTTCATTTTTTTTGGATTGAAGTATATATTTTTTTCTGAGTATTGTG
GAAAAGAATTGAGGAAAAAAATTTCGGGTCAGTTTTTACAAAATTTTAGCCGAAATCATGTACTA
ACCATCACGGTTTCTGGCTAAAAACACGTTACGTAGCCCCGGCTCCATTTGCATTATTATGTCGT
AAAGGCTCATTGAATTATCTATATTCATCAAACCAAATCTCAGCCACAATTAGATTTAAAAATTT
GTTTTTACGAGCATATAAATCTTGTTTCGATTTATTTAGAAATTAATTCGGAAAAAAATGGAAAC
TAATATTAAAAGCGTGGAAAACCTTTCAATCTTTTTATTTTTGTTGAATTATATTTTTTTTAGAG
TATTGTGGCAAAAAATTGAGAAAAAAATTCGGGTAAGTTTTTAGCCGAAATCATGTAATAACCAT
CACGGTTTCTGGCTAAAAACGCATTTCGGGACATCGACTAAGTTTTGCTTGGTTCTTGGCATAGA
GACTCCTTAAAATATCTATATTCATCAAACCAAATCTCAGTCACAATGGATTCAAGGATTTGTTT
TTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGGAAAAGAAAAATCGAAAAA
CAATATTAAAAGCGTGAAAACCCTTCAATTTTTTTGGCATTGAATTATAGTTTTCTTTTATTATT
GTCGCAAACAATTTGCATTAAACCATTTGCATTACGTAGCCCCGGATCAGTCATTGCAAAAACCG
TCGAAACGCGTTTCGAGGCTTCGACTCAGTTTTGCTTGGTTTTTGTCATTGAGA
Found at i:2282 original size:652 final size:643
Alignment explanation
Indices: 6--3536 Score: 3273
Period size: 653 Copynumber: 5.5 Consensus size: 643
1 GAGAA
* * * * *
6 AAAAAAACTTCGGGTCAGTTTTTAGCCGAAATCGTGTACATTA-CATCACGGTTTTTAGCTGAAA
1 AAAAAAA-TTCGGGTCAGTTTTTAGCCGAAATCATGTA-ATAACCATCACGGTTTCTGGCTAAAA
* * *
70 ACGCGTTTCGGGGCCTCGACTCAATTTTGCTTGGTTTTTGGCATAGAGACTCGTTTAAATATCTA
64 ACGCGTTTCGGGGCATCGACTCAATTTTGCTTGGTTTTTGGCATAGAGACTCCTTGAAATATCTA
* * * *
135 TATTCATCTAACCAAATCTCAGCCGCAATAGATTCAAGGATTTGTTTTTACGAGCATATGAATCT
129 TATTCATCAAACCAAATCTCAGCCACAATGGATTCAAGGATTTGTTTTTACGAGCATCTGAATCT
* * * * *
200 TATTTCGATTCAATCAGAAATAAATTCAAAAAAAAAACGACAAACGATATTAAAAGCGTGAAAAC
194 TATTTCGATTTAATTAGAAATAAATTCGAAAAAAAATCGAAAAACGATATTAAAAGCGTGAAAAC
* * *
265 CGTTCAATTTTTTTGGCGTTGAATCATATTTATTTTTTCTAAGTATTGTGGCAAAGAATTGAGGA
259 CCTTCAATTTTTTTGGCATTGAATTATATTT-TTTTTT-T-AGTATTGTGGCAAAGAATTGAGG-
* ** * *
330 AAAATTTTTCGGATCAGTCATTGCAAAATTTTAGCCAAAATTGTGTACT-ACCATCACGGTTTTC
320 AAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT-
* * * * ** *
394 GGC-AAAAACCCGTTCCGTAGCCCCGGCTCAATTTGCGTTATTTTTTACGGGAAGGCTCCTTGAA
384 GGCTAAAAACGCGTTCCGTAGCCCCGACTCAATTTGCATTATTTTGT-CGTAAAGACTCCTTGAA
* *
458 ATATCTATATTCATCAAACCAAATCTCAGACACATTAGATTTAA-AACTTTGTTTTTACAAGCAT
448 ATATCTATATTCATCAAACCAAATCTCAGCCACATTAGATTTAAGAA-TTTGTTTTTACGAGCAT
* * * *
522 CTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAAATCGAAAAACGATATTAAAAG
512 CTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAT-G-GAAACGATATTAGAAG
*
587 CGT-GAAAACCCTTC-A-TTTTTTTTGGATTGAAGTATATATTTTTTTCTGAGTATTGTGG-AAA
575 CGTGGAAAACCCTTCAATTTTTTTTTCG-TTGAA-T-TATATTTTTTT-TGAGTATTGTGGCAAA
648 AGAATTGAGG
636 A-AATTGA-G
* *
658 AAAAAAATTTCGGGTCAGTTTTTACAAAATTTTAGCCGAAATCATGTACTAACCGTCACGGTTTC
1 AAAAAAA-TTCGGGTCAG----T------TTTTAGCCGAAATCATGTAATAACCATCACGGTTTC
* * ** ** * * * * * * * *
723 TGGCTAAAAACACGTTACGTAGCCCCGGCTCCA-TTTGCATT--ATTATGTCGTAAAGGCTCCTT
55 TGGCTAAAAACGCGTTTCGGGGCATCGACTCAATTTTGC-TTGGTTTTTGGCATAGAGACTCCTT
* * * * * * * * **
785 GAATTATTTATATTCATCAAATCAAATTTTAGCCACGATTAGATTTAAAAATTTGTTTTTACGAG
119 GAAATATCTATATTCATCAAACCAAATCTCAGCCAC-AATGGATTCAAGGATTTGTTTTTACGAG
* * * * * * *
850 CATATAAATCTTGTTTCGATTTATTTAGAAATTAATTCGGAAAAAAAT-G-GAAACTGATATTAA
183 CATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCGAAAAAAAATCGAAAAAC-GATATTAA
* **** *
913 AAGCGTGGAAAACCTTTCAATCTTTTTATTTTTGTTGAATCATATTTTTTTTTTCAGAGTATTGT
247 AAGCGT-GAAAACCCTTCAA--TTTTT-TTGGCATTGAATTATATTTTTTTTTT---AGTATTGT
* *** * *
978 GGCAAAAAATTGA-GAAAAAAATTCGGGTAAG----T------TTTTAGCCGAAATCGTGTAATA
305 GGCAAAGAATTGAGGAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTA
* * * ** *
1032 ACCATCACGGTTTCTGGCTAAAAACGCATTTCG-GGACATCGACT-AAGTTTTGC-TTGGTTCTT
370 ACCATCACGGTTT-TGGCTAAAAACGCGTTCCGTAG-CCCCGACTCAA--TTTGCATT-ATT-TT
* * * * * * * *
1094 GGCATAGAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGTCACAATGGATTCAAGG
429 GTCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTAGATTTAAGA
* * * *
1159 ATTTGTTTTTACGAGCATCTGAGTCTTATTTCGATTTAATTAGAAATAAATTCGGAAAAGAAAAA
494 ATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAA-AAAAA
* * * ** * *
1224 TCGAAAAACAATATTAAAAGCGT-GAAAACCCTTCAATTTTTTTGGCATTGAATTA-GTTTTTTT
557 T-G-GAAACGATATTAGAAGCGTGGAAAACCCTTCAATTTTTTTTTCGTTGAATTATATTTTTTT
* * * *
1287 T-ATTATTGTCGCAAACAATTTGCAT
620 TGAGTATTGTGGCAAA-AAATTG-AG
* ** * ** * * ** * ** *
1312 TAAACCATT--TG-CA-TTACGTAGCCCCG-GATCA-GTCATTGCAAAAACCG--TC--G----A
1 AAAAAAATTCGGGTCAGTT-TTTAG--CCGAAATCATGTAATAACCATCACGGTTTCTGGCTAAA
* * * * *
1363 AACGCGTTTCGAGGCTTCGACTCAGTTTTGCTTGGTTTTTGTCATTGAGACTCCTTGAAATATCT
63 AACGCGTTTCGGGGCATCGACTCAATTTTGCTTGGTTTTTGGCATAGAGACTCCTTGAAATATCT
* * *
1428 AGATTCATCAAACCAAATCTCAACCACAATGGATTCAAGGATTTGTTTTTACGAGCATCTAAATC
128 ATATTCATCAAACCAAATCTCAGCCACAATGGATTCAAGGATTTGTTTTTACGAGCATCTGAATC
1493 TTATTTCGATTTAATTAGAAATAAATTCGAAAAAAAATCGAAAAACGATATTAAAAGCGTGAAAA
193 TTATTTCGATTTAATTAGAAATAAATTCGAAAAAAAATCGAAAAACGATATTAAAAGCGTGAAAA
* * *
1558 CCCTTCATTTCTTTTTGG-ATTGAAGTATATATTTTTTTCTGAGTATTGTGGCAAAGAATTGAGG
258 CCCTTCAATT-TTTTTGGCATTGAA-T-TATATTTTTTTTTTAGTATTGTGGCAAAGAATTGAGG
1622 ACAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTC
320 A-AAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT-
* * * * *
1687 TGGCTAAAAACGCGTTACGTAGCCCCGGCTCCATTTGCATTATTTTGTCGTAAAGGCTCATTGAA
383 TGGCTAAAAACGCGTTCCGTAGCCCCGACTCAATTTGCATTATTTTGTCGTAAAGACTCCTTGAA
* *
1752 TTATCTATATTCATCAAACCAAATCTCAGCCACAATTAGATTTAAAAATTTGTTTTTACGAGCAT
448 ATATCTATATTCATCAAACCAAATCTCAGCCAC-ATTAGATTTAAGAATTTGTTTTTACGAGCAT
* * *
1817 CTAAATCTTGTTTTGATTTATTTAGAAATTAATTCGGAAAAAAAATGGAAACTAATATTAGAAGC
512 CTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAC-GATATTAGAAGC
* *
1882 GTGGAAAACCTTTCAATCTTTTTTTTTTGTTGAATTATATTTTTTTTAGAGTATTGTGGCAAAAA
576 GTGGAAAACCCTTCAA--TTTTTTTTTCGTTGAATTATATTTTTTTT-GAGTATTGTGGCAAAAA
1947 ATTGAG
638 ATTGAG
* *
1953 AAAAAAATTCGGGTAAGTTTTTAGCCGAAATCATGTAATAACCATCATGGTTTCTGGCTAAAAAC
1 AAAAAAATTCGGGTCAGTTTTTAGCCGAAATCATGTAATAACCATCACGGTTTCTGGCTAAAAAC
* * *
2018 GCGTTTCGGGGCATCGACTCAGTTTTGCTTGGTTCTTGGCATAGAGACTCCTTAAAATATCTATA
66 GCGTTTCGGGGCATCGACTCAATTTTGCTTGGTTTTTGGCATAGAGACTCCTTGAAATATCTATA
*
2083 TTCATCAAACCAAATCTCAGTCACAATGGATTCAAGGATTTGTTTTTACGAGCATCTGAATCTTA
131 TTCATCAAACCAAATCTCAGCCACAATGGATTCAAGGATTTGTTTTTACGAGCATCTGAATCTTA
* *
2148 TTTTGATTTAATTAGAAATAAATTCGGAAAAGAAAAATCGAAAAACAATATTAAAAGCGTGAAAA
196 TTTCGATTTAATTAGAAATAAATTC-G-AAA-AAAAATCGAAAAACGATATTAAAAGCGTGAAAA
* * * *
2213 CCCTTCAATTTTTTTGGCATTGAATTATATTTTTCTTTTATTATTGTCGCAAACAATTGAGGAAA
258 CCCTTCAATTTTTTTGGCATTGAATTATATTTTTTTTTTAGTATTGTGGCAAAGAATTGAGGAAA
**
2278 ATTTTTCTTGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC
323 ATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTGGC
* * *
2343 TAAAAACGTGTTCCATAGCCCCGACTCAATTTGCATTATTTTTGTCGTAAAGACTCCTTAAAATA
387 TAAAAACGCGTTCCGTAGCCCCGACTCAATTTGCATTA-TTTTGTCGTAAAGACTCCTTGAAATA
* * *
2408 TCTATATTCATCAAACCAAATCTCAGCCACATTAGGTTTAAGAAGTTGTTTTTACTAGCATCTAA
451 TCTATATTCATCAAACCAAATCTCAGCCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTAA
* * *
2473 ATCTTGTTTCGTTTTAATGAAAAATTAATTCGG---AAAAATGGAAAACTGATATTAGAAGCGTG
516 ATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGG-AAAC-GATATTAGAAGCGTG
* ** * * *
2535 GAAAACCCTTCAATTGTTTTGGCATTGAATTATATATTTTTTCTGAGTTTTGTGGCAAAAAATTC
579 GAAAACCCTTCAATTTTTTTTTCGTTGAATTATAT-TTTTTT-TGAGTATTGTGGCAAAAAATTG
2600 ATG
642 A-G
** * * * ** * *
2603 AAAAATTCTTCAGGTCAGTTTTTAGCCGAATTCGTGTAATAACCATCACAATTTTTTTAGCTAAA
1 AAAAA-AATTCGGGTCAGTTTTTAGCCGAAATCATGTAATAACCATCAC--GGTTTCTGGCTAAA
* * * * *** * * * * * *
2668 AACACATTTCGGGG-ACCCGGCTCAATTTTAAATGATTTTTGACAGAAAGACTTCTTGAAATATT
63 AACGCGTTTCGGGGCA-TCGACTCAATTTTGCTTGGTTTTTGGCATAGAGACTCCTTGAAATATC
* * * * *
2732 TATATTCATCTAACCAAATATCAGCCACAATGGATTTAAGGATCTGCTTTTACGAGCATCTGAAT
127 TATATTCATCAAACCAAATCTCAGCCACAATGGATTCAAGGATTTGTTTTTACGAGCATCTGAAT
* * ** * * *
2797 CTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAAAAGGAAAACGATATTAGAAGCGTCAAA
192 CTTATTTCGATTTAATTAGAAATAAATTCGAAAAAAAATCGAAAAACGATATTAAAAGCGT-GAA
* * * * * *** *
2862 AACACTTCAATTGTTTTGG-AGCTGGATTATATATTTTGTACGAGTATTGTGGCAGAGAATTGAG
256 AACCCTTCAATTTTTTTGGCA-TTGAATTATAT-TTTTTTTTTAGTATTGTGGCAAAGAATTGAG
** *
2926 GAAAAAAATTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATAT
319 G-AAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT-T
* * * * *
2991 TTGGCTAAAAACGCATTCCG-AGGCCCCGACTCAGTTTTGCATTATTTTTGGCATAAAAACTCCT
382 TTGGCTAAAAACGCGTTCCGTA-GCCCCGACTCA-ATTTGCATTA-TTTTGTCGTAAAGACTCCT
* * * * * * *
3055 TGTAATATCTATATTCATCGAATCAAATCCCAACCACATTGGATTCAAGAATTT-TTTTTACGAG
444 TGAAATATCTATATTCATCAAACCAAATCTCAGCCACATTAGATTTAAGAATTTGTTTTTACGAG
* * * *
3119 CATCTGAATCTTGTTTCGATTTACTTTGAAATTAATTC---AGAAAAATGGTAAAACGATATTAG
509 CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGG--AAACGATATTAG
* * * **
3181 AAGCGTGAAAAACCCTTCAACCTTTATTTT-GTTGAATAATATATTTTTTCAGAGTATTGTGGCA
572 AAGCGTGGAAAACCCTTCAA-TTTTTTTTTCGTTGAAT--TATATTTTTTTTGAGTATTGTGGCA
3245 AAAAATTGAG
634 AAAAATTGAG
* * * * * *
3255 AAAAAAAAATT-GGGCCAATTTTTACCCGAAATC--GT-GT-ACTATCACGGTTTTTGGCTAAAA
1 --AAAAAAATTCGGGTCAGTTTTTAGCCGAAATCATGTAATAACCATCACGGTTTCTGGCTAAAA
** *
3315 ACGCGTTTCAGGATC-TCGACTCAATTTTTCTTGGTTTTTGGCAT--AGACTCCTTGAAATATCT
64 ACGCGTTTC-GGGGCATCGACTCAATTTTGCTTGGTTTTTGGCATAGAGACTCCTTGAAATATCT
* *
3377 ATATTCATCAAACCAAATCTTAGCCA-AATTGGATTTAAGGATTTG----T--GAGCATCTGAAT
128 ATATTCATCAAACCAAATCTCAGCCACAA-TGGATTCAAGGATTTGTTTTTACGAGCATCTGAAT
* * * * ** * *
3435 CTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAAAATGGAAAAAAAAAATTAGAAGCGTGAAA
192 CTTATTTCGATTTAATTAGAAATAAATTCGAAAAAAAATCGAAAAACGATATTAAAAGCGTGAAA
* * * * *
3499 ATCCCATCAATCTTTTTGGCGTTTAATTATATATTTTT
257 A-CCCTTCAATTTTTTTGGCATTGAATTATATTTTTTT
3537 GCTGAGACTT
Statistics
Matches: 2361, Mismatches: 400, Indels: 252
0.78 0.13 0.08
Matches are distributed among these distances:
629 20 0.01
630 7 0.00
631 17 0.01
632 33 0.01
633 82 0.03
634 59 0.02
635 5 0.00
636 13 0.01
637 59 0.02
638 61 0.03
639 51 0.02
640 90 0.04
641 78 0.03
642 13 0.01
643 19 0.01
644 66 0.03
645 3 0.00
646 42 0.02
647 2 0.00
648 25 0.01
649 35 0.01
650 66 0.03
651 68 0.03
652 382 0.16
653 446 0.19
654 131 0.06
655 169 0.07
656 9 0.00
657 39 0.02
658 7 0.00
659 10 0.00
660 57 0.02
661 82 0.03
662 67 0.03
663 12 0.01
664 36 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (643 bp):
AAAAAAATTCGGGTCAGTTTTTAGCCGAAATCATGTAATAACCATCACGGTTTCTGGCTAAAAAC
GCGTTTCGGGGCATCGACTCAATTTTGCTTGGTTTTTGGCATAGAGACTCCTTGAAATATCTATA
TTCATCAAACCAAATCTCAGCCACAATGGATTCAAGGATTTGTTTTTACGAGCATCTGAATCTTA
TTTCGATTTAATTAGAAATAAATTCGAAAAAAAATCGAAAAACGATATTAAAAGCGTGAAAACCC
TTCAATTTTTTTGGCATTGAATTATATTTTTTTTTTAGTATTGTGGCAAAGAATTGAGGAAAATT
TTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTGGCTAAA
AACGCGTTCCGTAGCCCCGACTCAATTTGCATTATTTTGTCGTAAAGACTCCTTGAAATATCTAT
ATTCATCAAACCAAATCTCAGCCACATTAGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTT
GTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAACGATATTAGAAGCGTGGAAAACC
CTTCAATTTTTTTTTCGTTGAATTATATTTTTTTTGAGTATTGTGGCAAAAAATTGAG
Found at i:9400 original size:16 final size:16
Alignment explanation
Indices: 9379--9425 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
9369 TAAGTACTCC
*
9379 TATGTGTATATGTATA
1 TATGTGTGTATGTATA
* *
9395 TATGTGTGTGTGTATG
1 TATGTGTGTATGTATA
*
9411 TATGTATGTATGTAT
1 TATGTGTGTATGTAT
9426 GATTTGATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (16 bp):
TATGTGTGTATGTATA
Found at i:9410 original size:20 final size:20
Alignment explanation
Indices: 9381--9419 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9371 AGTACTCCTA
9381 TGTGTATATGTATATATGTG
1 TGTGTATATGTATATATGTG
* *
9401 TGTGTGTATGTATGTATGT
1 TGTGTATATGTATATATGT
9420 ATGTATGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (20 bp):
TGTGTATATGTATATATGTG
Found at i:9412 original size:4 final size:4
Alignment explanation
Indices: 9387--9426 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
9377 CCTATGTGTA
* * *
9387 TATG TATA TATG TGTG TGTG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9427 ATTTGATTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:14371 original size:15 final size:15
Alignment explanation
Indices: 14348--14378 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14338 AGTTTAGTAT
14348 ATGAAATTGAGACCC
1 ATGAAATTGAGACCC
*
14363 ATGAGATTGAGACCC
1 ATGAAATTGAGACCC
14378 A
1 A
14379 AGACTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (15 bp):
ATGAAATTGAGACCC
Found at i:14704 original size:23 final size:22
Alignment explanation
Indices: 14669--14712 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
14659 ACTATCAATA
14669 TTACTAACTTTTAGTGTATTTTG
1 TTACTAACTTTTA-TGTATTTTG
*
14692 TTACTATAC-TTTATTTATTTT
1 TTACTA-ACTTTTATGTATTTT
14713 TTTTAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 10 0.53
24 2 0.11
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (22 bp):
TTACTAACTTTTATGTATTTTG
Found at i:14947 original size:3 final size:3
Alignment explanation
Indices: 14928--14982 Score: 92
Period size: 3 Copynumber: 17.7 Consensus size: 3
14918 ATCTTAATCT
14928 ATA ATA TATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA -ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
14975 ATA ATA AT
1 ATA ATA AT
14983 CTTATCTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:16219 original size:24 final size:24
Alignment explanation
Indices: 16192--16247 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
16182 AGGCATCACC
*
16192 ATAGACATGGGCATGGGAATGGGA
1 ATAGACATGGGCAGGGGAATGGGA
* * *
16216 ATAGTCAGGGGCAGGGGAATGGGC
1 ATAGACATGGGCAGGGGAATGGGA
*
16240 ATGGACAT
1 ATAGACAT
16248 CATCACAGGC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.43, T:0.16
Consensus pattern (24 bp):
ATAGACATGGGCAGGGGAATGGGA
Done.