Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009220.1 Corchorus capsularis cultivar CVL-1 contig09241, 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: 2958
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Found at i:858 original size:333 final size:333
Alignment explanation
Indices: 1--2958 Score: 4349
Period size: 333 Copynumber: 8.9 Consensus size: 333
* * * * *
1 CTAAAAACGTGTTTCGGGGCCCCGGTTCATTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
* ** *
66 TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTCAATTTTCCGAGCATCT
66 TATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
* *
131 AAACCTTGTTTAGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAAAACAATATAAAAA
131 GAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATG----AAAAA-AATATAAAAA
* * * * *
196 CCGTGAAATGTCCTCCAATCTTTTTGGTGTTGAATTATATCTATTTCATGAATATTTAAGCTAAA
191 GCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAA
* *
261 ATTTGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGTCGAAATCGAGTACTAACCAT
256 ATTTGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
326 CACGACTTTTTTTG
321 CACGAC-TTTTTTG
* * * * * * *
340 CTGAAAACGCGTTTCGGTGCTCCCCGACTCAGTTTTGCATGATCTCTAGCATCGAGACTTCTTGA
1 CTAAAAACGCGTTTCGG-G-GCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGA
* *
405 AATATCTATATCTATAAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGGAT
64 AATATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCAT
* * * *
470 CTGAACCTTGATTCGATTTAATTAAAAATTCGTTCAGAAGAAATATGAAAAAAATATAAATAGCG
129 CTGAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAATATAAAAAGCG
535 TGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATT
194 TGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATT
* * * *
600 TGAAGAAAAATTTTTCGCGTTATTTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAATCATCAC
259 TGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC
665 GACTTTTTTG
324 GACTTTTTTG
* *
675 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
*
740 TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
66 TATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
* * *
805 GAACCTTGATTCGATTTAATTAGAAATTCGTTAAGAAAAAATATGAAAAAAATATAAAAGGCGTG
131 GAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAATATAAAAAGCGTG
* * * *
870 AAAAGTCCTCCAATCTTTTTGGTGTTAAATTATATCTATTTCATAAACATTTTAGCCAAAATTTT
196 AAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATTTG
* * *
935 AGGAAAAATTTTTCGCGTCATTTGTTGGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGA
261 AGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGA
*
1000 ATTTTTTG
326 CTTTTTTG
*
1008 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCGAGACTTCTTGAAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
* *
1073 TATCTATATCT-TACAAATCAAATATTAGGCACGTTGCATTTAAGAATTCGTTTTTGCGAGCATC
66 TATCTATATCTAT-CAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATC
* *
1137 TGAACCTTGTTTCGATTTAATTAAAAATTTGTTC---------A-G-AAAAAATATAAAAAGCGT
130 TGAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAATATAAAAAGCGT
*
1191 GAAATA-TCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCAGGAATATTTTAGCCAAAATT
195 GAAA-AGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATT
* *
1255 TGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCAC
259 TGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC
1320 GA-TCTTTTTG
324 GACT-TTTTTG
1330 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
* *
1395 TAACTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCAG-TTTTGCGAGCATC
66 TATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTC-GTTTTTACGAGCATC
* *
1459 TGAACCTTGTTTCAATTTAATTAGAAATTTGTTCAGAAAAAATATGAAAAAAAAATATATAAAAA
130 TGAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATG---AAAAAA-ATATAAAAA
* * * *
1524 GCGTGAAAAATCCTCCAATATTTTTGGAGTTCAATTATATCTATTTCATGAATATTTTAGCCGAA
191 GCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAA
* *
1589 ATTTGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCAT
256 ATTTGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCAT
* *
1654 CACGATTTATTTTTT
321 CACGA-CT-TTTTTG
* *
1669 CTAAAAACGTGTTTCGGGCCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
* * * *
1734 TATCTATATCTATCAAATCAAATATCAGGCATGTTGCATTTAAGAACTCGCTTTTACGAGTATCT
66 TATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
* * *
1799 GAACCTTCTTTCGATTTAATTA-ACAATTCGTTCAGAAAAAATATGAAAAAAAAAATAAAAAGTG
131 GAACCTTGTTTCGATTTAATTAGA-AATTCGTTCAGAAAAAATATG-AAAAAAATATAAAAAGCG
* * *
1863 TGAAAAGTCGTCCAATCTTTTTGTTGTTCAATTATATCTATTTTATGAATATTTTAGCCAAAATT
194 TGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATT
* * * * * *
1928 TCAGGAAAATTTTTTTGCGTCATTTTTTTGCAAAATTTAAGACGAAATCATGTACTAACCATCAC
259 TGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC
*
1993 GATTTTTTTG
324 GACTTTTTTG
* *
2003 CTAAAAACGCGTTTC-GGGCCCCTGGCTCAGTTTTGCATGATTTTTTGCATCGAGACTTCTTGAA
1 CTAAAAACGCGTTTCGGGGCCCC-GGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAA
* * * *
2067 ATATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAACTCGCTTTTGCGAGTATC
65 ATATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATC
* * *
2132 TGAACCTTGTTTCGATTTCATTAAAAATTCGTTCAGAAAAAATATGAAAAATATATAAAAAGCGT
130 TGAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAATATAAAAAGCGT
*
2197 GAAAAGTCCTCCAATCTTTTTGCTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATTT
195 GAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATTT
* *
2262 GAGGAAAAATTTTTCGCGTCA-TTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATTACG
260 GAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACG
*
2326 ATTTTTTTG
325 ACTTTTTTG
* ** * *
2335 CTAAAAACGCGTTTTGGGGCCCCGTTTCAGTTTTGAATGACTTTTGGCGTCGAGACTTCTTGAAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
* * * *
2400 TATCTATATCTATCTAATCAAATATCTGGCACGTTGCATTTAAGAATTTGTTTTTGCGAGCATCT
66 TATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
* *
2465 AAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAATAAATATAAATAGCG
131 GAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATG-AAAA-AAATATAAAAAGCG
* *
2530 TGAAAAGTCCTCCAATATTTTTGGTGTTCAATTATATCTATTTCATGAATATCTTAGCCAAAATT
194 TGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATT
* *
2595 TGAGGAAAAATTTTTCGCGTCATTTTTTTTTTTGCAAAATTTTAGTCGAAATCGTGTACGT---T
259 TGAGGAAAAATTTTTCGCGTCA----TTTTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAACC
*
2657 ATCACGACTTGTTTG
319 ATCACGACTTTTTTG
* * *
2672 CTAAAAACGCGTTTCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
* *
2737 TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTTGTTTTTACGAGCATCT
66 TATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
* * *
2802 GAACCTTGATTCGATTTAATTAGAAATTCGTCCAGAAAAAATATGAAAAAAATATAAAAAGTGTG
131 GAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAATATAAAAAGCGTG
* *
2867 AAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCAT-AAAAATTTAGCCAAAATTTG
196 AAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATTTG
*
2931 AGGAAAAAATTTTTCGCGTTATTTTTTT
261 AGG-AAAAATTTTTCGCGTCATTTTTTT
Statistics
Matches: 2387, Mismatches: 193, Indels: 86
0.90 0.07 0.03
Matches are distributed among these distances:
321 1 0.00
322 296 0.12
323 4 0.00
324 1 0.00
331 8 0.00
332 200 0.08
333 551 0.23
334 280 0.12
335 99 0.04
336 273 0.11
337 322 0.13
338 2 0.00
339 212 0.09
340 2 0.00
341 136 0.06
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (333 bp):
CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
TATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
GAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAATATAAAAAGCGTG
AAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATTTG
AGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGA
CTTTTTTG
Found at i:1850 original size:337 final size:334
Alignment explanation
Indices: 1173--2958 Score: 2685
Period size: 337 Copynumber: 5.3 Consensus size: 334
1163 ATTTGTTCAG
*
1173 AAAAAATATAAAAAGCGTGAAATA-TCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCAGG
1 AAAAAATATAAAAAGCGTGAAA-AGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATG
*
1237 AATATTTTAGCCAAAATTTGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAGCTGAAA
65 AATATTTTAGCCAAAATTTGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAA
* *
1302 TCGTGTACTAACCATCACGATCTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCA
130 TCGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGCCCCCGGCTCAGTTTTGCA
*
1367 TGATTTTTGGCGTCGAGACTTCTTGAAATAACTATATCTATCAAATCAAATATCAGGCACGTTGC
195 TGATTTTTGGCGTCGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCACGTTGC
* *
1432 ATTTAAGAATTCAG-TTTTGCGAGCATCTGAACCTTGTTTCAATTTAATTAGAAATTTGTTCAGA
260 ATTTAAGAATTC-GCTTTTGCGAGCATCTGAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGA
1496 AAAAATATGAAAA
324 AAAAATATG--AA
* * *
1509 AAAAATATATAAAAAGCGTGAAAAATCCTCCAATATTTTTGGAGTTCAATTATATCTATTTCATG
1 AAAAA-ATATAAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATG
* *
1574 AATATTTTAGCCGAAATTTGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAACCGAAA
65 AATATTTTAGCCAAAATTTGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAA
* *
1639 TCGTGTACTAACCATCACGATTTATTTTTTCTAAAAACGTGTTTCGGGCCCCCGGCTCAGTTTTG
130 TCGTGTACTAACCATCACGA-TT-TTTTTGCTAAAAACGCGTTTCGGGCCCCCGGCTCAGTTTTG
*
1704 CATGATTTTTGGCGTCGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCATGTT
193 CATGATTTTTGGCGTCGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCACGTT
* * * *
1769 GCATTTAAGAACTCGCTTTTACGAGTATCTGAACCTTCTTTCGATTTAATTA-ACAATTCGTTCA
258 GCATTTAAGAATTCGCTTTTGCGAGCATCTGAACCTTGTTTCGATTTAATTAGA-AATTCGTTCA
1833 GAAAAAATATGAA
322 GAAAAAATATGAA
* * * * *
1846 AAAAAAAATAAAAAGTGTGAAAAGTCGTCCAATCTTTTTGTTGTTCAATTATATCTATTTTATGA
1 AAAAAATATAAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGA
* ** * * *
1911 ATATTTTAGCCAAAATTTCAGGAAAATTTTTTTGCGTCATTTTTTTGCAAAATTTAAGACGAAAT
66 ATATTTTAGCCAAAATTTGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAAT
* *
1976 CATGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGCCCCTGGCTCAGTTTTGCAT
131 CGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGCCCCCGGCTCAGTTTTGCAT
* *
2041 GATTTTTTGCATCGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCACGTTGCA
196 GATTTTTGGCGTCGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCACGTTGCA
* * * *
2106 TTTAAGAACTCGCTTTTGCGAGTATCTGAACCTTGTTTCGATTTCATTAAAAATTCGTTCAGAAA
261 TTTAAGAATTCGCTTTTGCGAGCATCTGAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAA
2171 AAATATG-A
326 AAATATGAA
* *
2179 AAAATATATAAAAAGCGTGAAAAGTCCTCCAATCTTTTTGCTGTTCAATTATATCTATTTCATGA
1 AAAAAATATAAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGA
*
2244 ATATTTTAGCCAAAATTTGAGGAAAAATTTTTCGCGTCA-TTTTTTGCAAAATTTTAGCCGAAAT
66 ATATTTTAGCCAAAATTTGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAAT
* * * * ** *
2308 CGTATACTAACCATTACGATTTTTTTGCTAAAAACGCGTTTTGGGGCCCCGTTTCAGTTTTGAAT
131 CGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGCCCCCGGCTCAGTTTTGCAT
* * *
2373 GACTTTTGGCGTCGAGACTTCTTGAAATATCTATATCTATCTAATCAAATATCTGGCACGTTGCA
196 GATTTTTGGCGTCGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCACGTTGCA
* * *
2438 TTTAAGAATTTGTTTTTGCGAGCATCTAAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAA
261 TTTAAGAATTCGCTTTTGCGAGCATCTGAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAA
2503 AAATATGAA
326 AAATATGAA
* *
2512 AAATAAATATAAATAGCGTGAAAAGTCCTCCAATATTTTTGGTGTTCAATTATATCTATTTCATG
1 AAA-AAATATAAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATG
* * *
2577 AATATCTTAGCCAAAATTTGAGGAAAAATTTTTCGCGTCATTTTTTTTTTTGCAAAATTTTAGTC
65 AATATTTTAGCCAAAATTTGAGGAAAAAATTTTCGCGTCA----TTTTTTTGCAAAATTTTAGCC
* * *
2642 GAAATCGTGTACGT---TATCACGACTTGTTTGCTAAAAACGCGTTTCGGTG-CCCCGGCTCAGT
126 GAAATCGTGTAC-TAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGG-GCCCCCGGCTCAGT
* * *
2703 TTTGCATGATTTTTGGCGTCGAGACTTCTCGTAATATCTATATCTATCTAATCAAATATCAGGCA
189 TTTGCATGATTTTTGGCGTCGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCA
* * * *
2768 CGTTGCATTTAAGAATTTGTTTTTACGAGCATCTGAACCTTGATTCGATTTAATTAGAAATTCGT
254 CGTTGCATTTAAGAATTCGCTTTTGCGAGCATCTGAACCTTGTTTCGATTTAATTAGAAATTCGT
*
2833 CCAGAAAAAATATG-A
319 TCAGAAAAAATATGAA
*
2848 AAAAAATATAAAAAGTGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCAT-A
1 AAAAAATATAAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGA
* * *
2912 AAAATTTAGCCAAAATTTGAGGAAAAAATTTTTCGCGTTATTTTTTT
66 ATATTTTAGCCAAAATTTGAGGAAAAAA-TTTTCGCGTCATTTTTTT
Statistics
Matches: 1326, Mismatches: 107, Indels: 39
0.90 0.07 0.03
Matches are distributed among these distances:
331 7 0.01
332 204 0.15
333 100 0.08
334 291 0.22
335 70 0.05
336 137 0.10
337 316 0.24
338 4 0.00
339 196 0.15
340 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (334 bp):
AAAAAATATAAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGA
ATATTTTAGCCAAAATTTGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAGCCGAAAT
CGTGTACTAACCATCACGATTTTTTTGCTAAAAACGCGTTTCGGGCCCCCGGCTCAGTTTTGCAT
GATTTTTGGCGTCGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCACGTTGCA
TTTAAGAATTCGCTTTTGCGAGCATCTGAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAA
AAATATGAA
Found at i:2701 original size:669 final size:665
Alignment explanation
Indices: 1--2957 Score: 4387
Period size: 669 Copynumber: 4.4 Consensus size: 665
* * *
1 CTAAAAACGTGTTTCGGGGCCCCGGTTCATTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
** *
66 TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTCAATTTTCCGAGCATCT
66 TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
* *
131 AAACCTTGTTTAGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAAAACAATATAAAAA
131 GAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATG----AAAAA-AATATAAAAA
* * * * *
196 CCGTGAAATGTCCTCCAATCTTTTTGGTGTTGAATTATATCTATTTCATGAATATTTAAGCTAAA
191 GCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAA
*
261 ATTTGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGTCGAAATCG-AGTACTAACCA
256 ATTTGAGGAAAAATTTTTCGCGTCA-TTTTTTGCAAAATTTTAGCCGAAATCGTA-TACTAACCA
* * * * * *
325 TCACGACTTTTTTTGCTGAAAACGCGTTTCGGTGCTCCCCGACTCAGTTTTGCATGATCTCTAGC
319 TCACGACTTTTTTTGCTAAAAACGCGTTTCGG-G-GCCCCGGCTCAGTTTTGCATGATTTTTGGC
*
390 ATCGAGACTTCTTGAAATATCTATATCTATAAAATCAAATATCAGGCACGTTGCATTTAAGAATT
382 ATCGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATT
* * *
455 CGTTTTTACGAGGATCTGAACCTTGATTCGATTTAATTAAAAATTCGTTCAGAAGAAATATG-AA
447 CGTTTTTACGAGCATCTGAACCTTGTTTCGATTTAATTAAAAATTCGTTCAGAAAAAATATGAAA
519 AAAAATATAAATAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAA
512 AAAAATATAAATAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAA
* *
584 TATTTTAGCCAAAATTTGAAGAAAAATTTTTCGCGTTATTTTTTTGCAAAATTTTAGTCGAAATC
577 TATTTTAGCCAAAATTTGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGTCGAAATC
649 GTGTACTAATCATCACGACTTTTTTG
642 GTGTACT-A-CATCACGACTTTTTTG
675 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
740 TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
66 TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
* * *
805 GAACCTTGATTCGATTTAATTAGAAATTCGTTAAGAAAAAATATGAAAAAAATATAAAAGGCGTG
131 GAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAATATAAAAAGCGTG
* * * *
870 AAAAGTCCTCCAATCTTTTTGGTGTTAAATTATATCTATTTCATAAACATTTTAGCCAAAATTTT
196 AAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATTTG
*
935 AGGAAAAATTTTTCGCGTCATTTGTTGGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGA
261 AGGAAAAATTTTTCGCGTCATTT-TTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGA
*
1000 -ATTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCGAGAC
325 CTTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCGAGAC
*
1064 TTCTTGAAATATCTATATCT-TACAAATCAAATATTAGGCACGTTGCATTTAAGAATTCGTTTTT
390 TTCTTGAAATATCTATATCTAT-CAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTT
* *
1128 GCGAGCATCTGAACCTTGTTTCGATTTAATTAAAAATTTGTTCAG-AAAAA-AT--------ATA
454 ACGAGCATCTGAACCTTGTTTCGATTTAATTAAAAATTCGTTCAGAAAAAATATGAAAAAAAATA
*
1183 -AAA-AGCGTGAAATA-TCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCAGGAATATTTT
519 TAAATAGCGTGAAA-AGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTT
*
1245 AGCCAAAATTTGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAG-CTGAAATCGTGTA
583 AGCCAAAATTTGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGTC-GAAATCGTGTA
1309 CTAACCATCACGA-TCTTTTTG
647 CT-A-CATCACGACT-TTTTTG
* *
1330 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTTGAAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
* * *
1395 TAACTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCAG-TTTTGCGAGCATC
66 TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTC-GTTTTTACGAGCATC
* *
1459 TGAACCTTGTTTCAATTTAATTAGAAATTTGTTCAGAAAAAATATGAAAAAAAAATATATAAAAA
130 TGAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATG---AAAAAA-ATATAAAAA
* * * *
1524 GCGTGAAAAATCCTCCAATATTTTTGGAGTTCAATTATATCTATTTCATGAATATTTTAGCCGAA
191 GCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAA
* * *
1589 ATTTGAGGAAAAAATTTTCGCGTCATTTTTTTGCAAAATTTTAACCGAAATCGTGTACTAACCAT
256 ATTTGAGGAAAAATTTTTCGCGTCA-TTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCAT
* * * * *
1654 CACGATTTATTTTTTCTAAAAACGTGTTTCGGGCCCCCGGCTCAGTTTTGCATGATTTTTGGCGT
320 CACGACTT-TTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAT
* *
1719 CGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCATGTTGCATTTAAGAACTCG
384 CGAGACTTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCG
* * * *
1784 CTTTTACGAGTATCTGAACCTTCTTTCGATTTAATTAACAATTCGTTCAGAAAAAATATGAAAAA
449 TTTTTACGAGCATCTGAACCTTGTTTCGATTTAATTAAAAATTCGTTCAGAAAAAATATGAAAAA
* * * * * *
1849 AAAAATAAAAAGTGTGAAAAGTCGTCCAATCTTTTTGTTGTTCAATTATATCTATTTTATGAATA
514 AAATATAAATAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATA
* * * * * *
1914 TTTTAGCCAAAATTTCAGGAAAATTTTTTTGCGTCATTTTTTTGCAAAATTTAAGACGAAATCAT
579 TTTTAGCCAAAATTTGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGTCGAAATCGT
*
1979 GTACTAACCATCACGATTTTTTTG
644 GTACT-A-CATCACGACTTTTTTG
* * * *
2003 CTAAAAACGCGTTTC-GGGCCCCTGGCTCAGTTTTGCATGATTTTTTGCATCGAGACTTCTTGAA
1 CTAAAAACGCGTTTCGGGGCCCC-GGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTA
* * * * *
2067 ATATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAACTCGCTTTTGCGAGTATC
65 ATATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATC
* * *
2132 TGAACCTTGTTTCGATTTCATTAAAAATTCGTTCAGAAAAAATATGAAAAATATATAAAAAGCGT
130 TGAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAATATAAAAAGCGT
*
2197 GAAAAGTCCTCCAATCTTTTTGCTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATTT
195 GAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATTT
*
2262 GAGGAAAAATTTTTCGCGTCATTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATTACGA
260 GAGGAAAAATTTTTCGCGTCATTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGA
* ** * * *
2327 -TTTTTTTGCTAAAAACGCGTTTTGGGGCCCCGTTTCAGTTTTGAATGACTTTTGGCGTCGAGAC
325 CTTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCGAGAC
* * * *
2391 TTCTTGAAATATCTATATCTATCTAATCAAATATCTGGCACGTTGCATTTAAGAATTTGTTTTTG
390 TTCTTGAAATATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTA
* *
2456 CGAGCATCTAAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAATAAATA
455 CGAGCATCTGAACCTTGTTTCGATTTAATTAAAAATTCGTTCAGAAAAAATATGAAAAA-AAATA
* *
2521 TAAATAGCGTGAAAAGTCCTCCAATATTTTTGGTGTTCAATTATATCTATTTCATGAATATCTTA
519 TAAATAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTA
2586 GCCAAAATTTGAGGAAAAATTTTTCGCGTCATTTTTTTTTTTGCAAAATTTTAGTCGAAATCGTG
584 GCCAAAATTTGAGGAAAAATTTTTCGCGTCA----TTTTTTTGCAAAATTTTAGTCGAAATCGTG
* *
2651 TACGT-TATCACGACTTGTTTG
645 TAC-TACATCACGACTTTTTTG
*
2672 CTAAAAACGCGTTTCGGTGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
*
2737 TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTTGTTTTTACGAGCATCT
66 TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
* * *
2802 GAACCTTGATTCGATTTAATTAGAAATTCGTCCAGAAAAAATATGAAAAAAATATAAAAAGTGTG
131 GAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAATATAAAAAGCGTG
* *
2867 AAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCAT-AAAAATTTAGCCAAAATTTG
196 AAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATTTG
*
2931 AGGAAAAAATTTTTCGCGTTATTTTTT
261 AGG-AAAAATTTTTCGCGTCATTTTTT
2958 T
Statistics
Matches: 2078, Mismatches: 165, Indels: 85
0.89 0.07 0.04
Matches are distributed among these distances:
654 2 0.00
655 297 0.14
656 5 0.00
657 3 0.00
658 6 0.00
659 127 0.06
660 4 0.00
661 156 0.08
662 6 0.00
663 2 0.00
664 2 0.00
665 5 0.00
666 300 0.14
667 93 0.04
668 88 0.04
669 470 0.23
670 17 0.01
671 32 0.02
672 13 0.01
673 283 0.14
674 167 0.08
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (665 bp):
CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTTCTCGTAA
TATCTATATCTATCTAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTACGAGCATCT
GAACCTTGTTTCGATTTAATTAGAAATTCGTTCAGAAAAAATATGAAAAAAATATAAAAAGCGTG
AAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGCCAAAATTTG
AGGAAAAATTTTTCGCGTCATTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGAC
TTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCATCGAGACT
TCTTGAAATATCTATATCTATCAAATCAAATATCAGGCACGTTGCATTTAAGAATTCGTTTTTAC
GAGCATCTGAACCTTGTTTCGATTTAATTAAAAATTCGTTCAGAAAAAATATGAAAAAAAATATA
AATAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTCAATTATATCTATTTCATGAATATTTTAGC
CAAAATTTGAGGAAAAATTTTTCGCGTCATTTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAC
ATCACGACTTTTTTG
Done.