Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009837.1 Corchorus capsularis cultivar CVL-1 contig09858, 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: 52788
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:276 original size:167 final size:168
Alignment explanation
Indices: 1--381 Score: 712
Period size: 167 Copynumber: 2.3 Consensus size: 168
1 GAATTATATA-TTTTTTCGAGTATTGTGGAAGAAATTTCAGGAAAACAATGGATTTAAGAATTTG
1 GAATTATATATTTTTTTCGAGTATTGTGGAAGAAATTTCAGGAAAACAATGGATTTAAGAATTTG
65 TTTTTACGAGCATCTAACTTTTGTTTCGATTTAATTAGAAACAAATTCAGAAAAATGGAAAAAAA
66 TTTTTACGAGCATCTAACTTTTGTTTCGATTTAATTAGAAACAAATTCAGAAAAATGGAAAAAAA
130 AATTGAAAGCGTGAAAAACCCTTCAA-TTTTTGGCATT
131 AATTGAAAGCGTGAAAAACCCTTCAATTTTTTGGCATT
167 GAATTATATATTTTTTTCGAGTATTGTGGAAGAAATTTCAGGAAAACAATGGATTTAAGAATTTG
1 GAATTATATATTTTTTTCGAGTATTGTGGAAGAAATTTCAGGAAAACAATGGATTTAAGAATTTG
232 TTTTTACGAGCATCTAACTTTTGTTTCGATTTAATTAGAAACAAATTCAGAAAAATGGAAAAAAA
66 TTTTTACGAGCATCTAACTTTTGTTTCGATTTAATTAGAAACAAATTCAGAAAAATGGAAAAAAA
*
297 TATTGAAAGCGTGAAAAACCCTTCAATTTTTTGGCATT
131 AATTGAAAGCGTGAAAAACCCTTCAATTTTTTGGCATT
* *
335 CAATTATATATTTTTTTCCGAGTATTGTGGAAAAAATTTCAGGAAAA
1 GAATTATATATTTTTTT-CGAGTATTGTGGAAGAAATTTCAGGAAAA
382 TTTTTTTCGG
Statistics
Matches: 209, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
166 10 0.05
167 144 0.69
168 27 0.13
169 28 0.13
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (168 bp):
GAATTATATATTTTTTTCGAGTATTGTGGAAGAAATTTCAGGAAAACAATGGATTTAAGAATTTG
TTTTTACGAGCATCTAACTTTTGTTTCGATTTAATTAGAAACAAATTCAGAAAAATGGAAAAAAA
AATTGAAAGCGTGAAAAACCCTTCAATTTTTTGGCATT
Found at i:1170 original size:322 final size:319
Alignment explanation
Indices: 216--3087 Score: 3205
Period size: 322 Copynumber: 9.0 Consensus size: 319
206 AGGAAAACAA
* *
216 TGGATTTAAGAATTTGTTTTTACGAGCATCT-AACTTTTGTTTCGATTTAATTAGAAACAAATTC
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAA-TTTTGTTTCGATTTAATTAGAAATAAATTC
* * * *
280 AGAAAAATGGAAAAAA--ATATTGAAAGCGTGAAAAACCCTTCAA-TTTTTTGGCATTCAATTAT
65 GGAAAAAT-GAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTAT
* * * *
342 ATATTTTTTTCCGAGTATTGTGGAAAAAATTTCAGGAAAATTTTTTTCGGATTCCATTCTTAGCC
129 ATA-TTTTTTCCGAGTATTGTGGCAAAAATTTCAGAAAAAATTTTTTCGG-GTCCATTCTTAGCC
* * *
407 GAAA---G-AGT--GT-ACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGC
192 AAAACGTGTACTACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGC
* *
465 ATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTAATCATCGAACCAAATCTCAGCCACAA
257 ATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAT
* * *
528 TGGATATAAGAATTTGTTTTTACGAGCATCT-AACTTTTGTTTCGATTTAATTAGAAACAAATTC
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAA-TTTTGTTTCGATTTAATTAGAAATAAATTC
* ** * * *
592 AGAAAAATGGAAAAAAAAATATTGAAAGCGTGAAAAACCTTTCAA-TTTTTTGGCATTGAATTAT
65 GGAAAAAT-GAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTAT
* * * * *
656 ATATTTTTTTCGAGTATTGTGG-AAGAAATTTCAGGAAAAATTTTTTCGGATCCATTCTTAGTCG
129 ATATTTTTTCCGAGTATTGTGGCAA-AAATTTCAGAAAAAATTTTTTCGGGTCCATTCTTAGCCA
* *
720 AAA---G-AGT--GT-ACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCA
193 AAACGTGTACTACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCA
* *
778 TGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATGGAACTAAATCTCAGCCACAT
258 TGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAT
* *
840 TGGATTTAAGGATTTGTTTTTACGCGCATCTGAATTATGTTTCGATTTAATTAGAAATAAATTCG
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCG
905 GAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATAT
66 GAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATAT
* ** *
970 ATTTTTTCCGAGTATTGTGGCAAAAATTTCAGGAAATTTTTTTTCGGGTGCATTCTTAGCCAAAA
131 ATTTTTTCCGAGTATTGTGGCAAAAATTTCAGAAAAAATTTTTTCGGGTCCATTCTTAGCCAAAA
*
1035 CAGTGTACTAAACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCTCCGACTCAGTTTTGCA
196 C-GTGTACT--ACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCA
*
1100 TGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAA
258 TGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAT
* * * * * *
1162 TGGATTTAAGGATTTGTTTTTACAAGCATTTGACTTTTGTTTCAATTTAATTAGAAATAGATTCA
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCG
*
1227 GAAAAATGGACAAAAA--ATATTGAAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTAT
66 GAAAAAT-GA-AAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTAT
* * * * *
1290 GTATTTTTTCCGAGTATTGTGGTAAAAATTTTAGAAAAAAAAAATTTTCCGGGTCCATTCTTAGC
129 ATATTTTTTCCGAGTATTGTGGCAAAAATTTCAG---AAAAAATTTTTTCGGGTCCATTCTTAGC
* *
1355 CGAAAGCCCGAAACACTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGTCCCG
191 C---A-----AAAC-GTGTACT-A-CATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCG
* * * * * *
1420 GCTCAGTTTTTCATGATTTTTGGCAAAAATCCTCCTTGAAATATCTCTATTCATCAAACTAAATC
245 ACTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATC
1485 TCAGCCACAT
310 TCAGCCACAT
* * ** *
1495 TCGATGTAAGGATTTGTTTTTACGAGCATCTGAATTTCCTTTCAATTTAATTAGAAATAAATTCG
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCG
* ** * * * * * ** *
1560 AAAAAATGGGAAAACGATATTGGAAGCATTAAAAATCCTTCACTTTTTTTTTGCGTTGAATTATT
66 GAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCA-ATTTTTTTGGTATTGAATTATA
* * * * * *
1625 TATTTTTTCCAAGTATTGCGACAAAAA-TTCAGAAAAAAATGTTTT-GGCTCAATT-TTAAGCCG
130 TATTTTTTCCGAGTATTGTGGCAAAAATTTCAG-AAAAAATTTTTTCGGGTCCATTCTT-AGCC-
* * * *
1687 AAATCGTGTACTAATCATCACTGCTATTGGGCTAAAAACGCGTTTCGAGGCCCCGACTCAATTTT
192 AAAACGTGTACT-A-CATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTT
* * * *
1752 GCATGATTTTTGGCATG-TAGTCTCTCTT-AAATATCTTTATTCATCGTACCAAATCTCAGCCAC
255 GCATGATTTTTGGCA-GAAAGCCTC-CTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCAC
1815 AT
318 AT
* * *
1817 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGTAATAAATTTG
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCG
* * *
1882 GAAAAATGGAAAAACGTTATTTGAAGCGTGAAAAACCCTTCAATTTTTTTTGGTATTGAATTATA
66 GAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAA-TTTTTTTGGTATTGAATTATA
* * * *
1947 TATTTTTTCAGAGTATTGTGGCAAAAATTTTAGAAAAAA-ATTTTCGGGTTCCA-TCTTAGCTGA
130 TATTTTTTCCGAGTATTGTGGCAAAAATTTCAGAAAAAATTTTTTCGGG-TCCATTCTTAGC-CA
* * * * * ** *
2010 AACCGTGTACTAACCATCATTATTATTAGGCTAAAAATGCGTTTCAAGGCCCCGGCTCAGTTTTG
193 AAACGTGTACT-A-CATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTG
* *
2075 CATGATTTTTGCCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATTTCAGCCACAT
256 CATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAT
* *
2139 TGGATTTAAGGATTTGTTTTTACGATCATCTGAATTATG-TTCTGATTTAATTAGAAATAAATTC
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTC-GATTTAATTAGAAATAAATTC
* *
2203 GGAAAAATGAAAAAACTATATTGGTAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATA
65 GGAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATA
* * * * *
2268 TATTTTTTCCGAGTATCGTGGCAAAATTTTTCAG-AAAATTTTTTTGCGGATCCATTCTTAGTCG
130 TATTTTTTCCGAGTATTGTGGCAAAA-ATTTCAGAAAAAATTTTTT-CGGGTCCATTCTTAG-CC
* ** *
2332 AAATCGTG---TA-ATCACTGTTATTCAGCTAAAAACGCGTTTCGGGG-CCCGGCTCAGTTTTGC
192 AAAACGTGTACTACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGC
* *
2392 ATGATTTTTGCCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAATCAAATCTCAGCCACAT
257 ATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAT
*
2455 TGGATTTAAGGATTT-TTTTTACGAGCATCTGAATTTTATTTCGATTTAATTAGAAATAAATTCG
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCG
* * * * * * ** *
2519 GAAAAAT-AGGAAAACGATATTAGAAGCATGAAAAACCATTCATTTTTTCTTTGCGTTGAATAAT
66 GAAAAATGA-AAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTT-TTGGTATTGAATTAT
* * * * ** *
2583 ATA-TTTTTCCTAGTATTATGGCAGAAATTTCACAAAAAATAAAAATAAAAATTCGGGTCTATTC
129 ATATTTTTTCCGAGTATTGTGGCAAAAATTTCAGAAAAAAT-----T---TTTTCGGGTCCATTC
* * * ** * ** * *
2647 TTAGCCGAAATCGTATACGT-TATCACTGTTATTGCTCTAAAAATGCGTTTCGAAGCTCCGGCTC
186 TTAGCC-AAAACGTGTAC-TACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTC
* * * * *
2711 AATTTTGCATGATTTTTGGTAGAAAGCCTCCTTGAAATATCTCTATTTATCGAATCAAAGCTCAG
249 AGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAG
*
2776 TCACAT
314 CCACAT
* * * * *
2782 TGGATTTAAGGATTTGTCTTTACAAGCATATGAATTTTGTTTTGATTTAATTAGAAATAAATACG
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCG
* ** * * *
2847 GAAAAAAGGGAAATCGATATTGGAAGTGTGAAAAAATCCCTTC--TTTTTTT-TTACGTTGAATT
66 GAAAAATGAAAAAACGATATTGGAAGCGTG-AAAAA-CCCTTCAATTTTTTTGGTA--TTGAATT
** * * * * *
2909 ATATATTTTTTCCGAGTATTGCAGCGAAAATTT-A-AAAAAA---ATTCAGGTCAATTCTAAGCC
127 ATATATTTTTTCCGAGTATTGTGGCAAAAATTTCAGAAAAAATTTTTTCGGGTCCATTCTTAGCC
* * * *
2969 GAAATCGTGTACTAACAATCACTATTATTTGGCTAAAAACGCGTTTCGGGGGCCCGACTCAGTTT
192 -AAAACGTGTACT-AC-ATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTT
*
3034 TGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGTACCAAA
254 TGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAA
3088 ATTTTTTTAA
Statistics
Matches: 2216, Mismatches: 265, Indels: 152
0.84 0.10 0.06
Matches are distributed among these distances:
311 32 0.01
312 348 0.16
313 45 0.02
314 53 0.02
315 106 0.05
316 138 0.06
317 29 0.01
318 87 0.04
319 1 0.00
320 2 0.00
321 62 0.03
322 733 0.33
323 36 0.02
324 6 0.00
325 23 0.01
326 29 0.01
327 95 0.04
328 85 0.04
329 28 0.01
330 16 0.01
331 14 0.01
332 3 0.00
333 205 0.09
334 40 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (319 bp):
TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCG
GAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATAT
ATTTTTTCCGAGTATTGTGGCAAAAATTTCAGAAAAAATTTTTTCGGGTCCATTCTTAGCCAAAA
CGTGTACTACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGA
TTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAT
Found at i:1986 original size:655 final size:634
Alignment explanation
Indices: 216--3087 Score: 3218
Period size: 655 Copynumber: 4.5 Consensus size: 634
206 AGGAAAACAA
* * *
216 TGGATTTAAGAATTTGTTTTTACGAGCATCT-AACTTTTGTTTCGATTTAATTAGAAACAAATTC
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAA-TTATGTTTCGATTTAATTAGAAATAAATTC
* *
280 -AGAAAAATGGAAAAAA--ATATTGAAAGCGTGAAAAACCCTTCAA-TTTTTTGGCATTCAATTA
65 GA-AAAAAT-GAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTA
* * * *
341 TATATTTTTTTCCGAGTATTGTGGA-AAAAATTTCAGGAAAATTTTTTTCGGATTCCATTCTTAG
128 TATA-TTTTTTCCGAGTATTG-CGACAAAAA-TTCAGAAAAAATTTTTTCGG--TCAATTCTTAG
* *
405 CCGAAA----G-AGT---GT-ACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTT
188 CCGAAATCGTGTACTAACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTT
*
461 TTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTAATCATCGAACCAAATCTCAGCCAC
253 TTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCAC
* * *
526 AATGGATATAAGAATTTGTTTTTACGAGCATCT-AACTTTTGTTTCGATTTAATTAGAAACAAAT
318 AATGGATTTAAGGATTTGTTTTTACGAGCATCTGAA-TTTTGTTTCGATTTAATTAGAAATAAAT
* * *
590 TCAGAAAAATGGAAAAAAAAATATTGAAAGCGTGAAAAACCTTTCAA-TTTTTTGGCATTGAATT
382 TCAGAAAAATGGAAAAAAATAT-TTGAAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATT
* ** * *
654 ATATATTTTTTTCGAGTATTGTGG-AAGAAATTTCAGGAAAAATTTTTTCGGATCCATTCTTAGT
446 ATATATTTTTTCCGAGTATTGTGGCAA-AAATTTCA-GAAAAAAATTTTCGGGTCCATTCTTAGC
* * *
718 CGAAA--GAG-TGT-ACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCAT
509 CGAAACCGAGTTATCACTGTTATTGGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCAT
*
779 GATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATGGAACTAAATCTCAGCCACAT
574 GATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACTAAATCTCAGCCACAT
*
840 TGGATTTAAGGATTTGTTTTTACGCGCATCTGAATTATGTTTCGATTTAATTAGAAATAAATTCG
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATAAATTCG
* *
905 GAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATAT
66 AAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTATAT
* * * **
970 ATTTTTTCCGAGTATTGTGGCAAAAATTTCAGGAAATTTTTTTTCGGGTGC-ATTCTTAGCC-AA
131 ATTTTTTCCGAGTATTGCGACAAAAA-TTCAGAAAAAATTTTTTC-GGT-CAATTCTTAGCCGAA
* *
1033 AACAGTGTACTAAACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCTCCGACTCAGTTTTG
193 ATC-GTGTACT-AACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTG
1098 CATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAAT
256 CATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAAT
* * * * *
1163 GGATTTAAGGATTTGTTTTTACAAGCATTTGACTTTTGTTTCAATTTAATTAGAAATAGATTCAG
321 GGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAG
*
1228 AAAAATGGACAAAAAATA-TTGAAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATGT
386 AAAAATGGA-AAAAAATATTTGAAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATAT
* *
1292 ATTTTTTCCGAGTATTGTGGTAAAAATTTTAGAAAAAAAAAATTTTCCGGGTCCATTCTTAGCCG
450 ATTTTTTCCGAGTATTGTGGCAAAAATTTCAG---AAAAAAATTTT-CGGGTCCATTCTTAGCCG
* *
1357 AAAGCCCGAAACACTGTACTAACCATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGTCCCGGC
511 AAA--CCG----A--GT--T----ATCACTGTTATTGGGCTAAAAACGCGTTTCGAGGCCCCGGC
* * * *
1422 TCAGTTTTTCATGATTTTTGGCAAAAATCCTCCTTGAAATATCTCTATTCATCAAACTAAATCTC
562 TCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACTAAATCTC
1487 AGCCACAT
627 AGCCACAT
* * * *
1495 TCGATGTAAGGATTTGTTTTTACGAGCATCTGAATT-TCCTTTCAATTTAATTAGAAATAAATTC
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTAT-GTTTCGATTTAATTAGAAATAAATTC
** * * * * * *
1559 GAAAAAATGGGAAAACGATATTGGAAGCATTAAAAATCCTTCACTTTTTTTTTGCGTTGAATTAT
65 GAAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCA-ATTTTTTTGGCATTGAATTAT
* * *
1624 TTATTTTTTCCAAGTATTGCGACAAAAATTCAGAAAAAAATGTTTT-GGCTCAATT-TTAAGCCG
129 ATATTTTTTCCGAGTATTGCGACAAAAATTCAG-AAAAAATTTTTTCGG-TCAATTCTT-AGCCG
* * *
1687 AAATCGTGTACTAATCATCACTGCTATTGGGCTAAAAACGCGTTTCGAGGCCCCGACTCAATTTT
191 AAATCGTGTACTAA-CATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTT
* * * *
1752 GCATGATTTTTGGCATG-TAGTCTCTCTT-AAATATCTTTATTCATCGTACCAAATCTCAGCCAC
255 GCATGATTTTTGGCA-GAAAGCCTC-CTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCAC
* * *
1815 ATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGTAATAAATT
318 AATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATT
** **
1880 TGGAAAAATGGAAAAACGTTATTTG-AAGCGTGAAAAACCCTTCAATTTTTTTTGGTATTGAATT
383 CAGAAAAATGGAAAAA-AATATTTGAAAGCGTGAAAAACCCTTCAA-TTTTTTTGGTATTGAATT
* * *
1944 ATATATTTTTTCAGAGTATTGTGGCAAAAATTTTAGAAAAAAATTTTCGGGTTCCA-TCTTAGCT
446 ATATATTTTTTCCGAGTATTGTGGCAAAAATTTCAGAAAAAAATTTTCGGG-TCCATTCTTAGCC
* * * * * *
2008 GAAACCGTGTACTAACCATCATTATTATTAGGCTAAAAATGCGTTTCAAGGCCCCGGCTCAGTTT
510 GAAACCGAGT--T----ATCACTGTTATTGGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAGTTT
* * *
2073 TGCATGATTTTTGCCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATTTCAGCCACA
569 TGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACTAAATCTCAGCCACA
2138 T
634 T
*
2139 TGGATTTAAGGATTTGTTTTTACGATCATCTGAATTATG-TTCTGATTTAATTAGAAATAAATTC
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTATGTTTC-GATTTAATTAGAAATAAATTC
* * * *
2203 GGAAAAATGAAAAAACTATATTGGTAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATA
65 GAAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTATA
* * * * * * *
2268 TATTTTTTCCGAGTATCGTGGCAAAATTTTTCAG-AAAATTTTTTTGCGGATCCATTCTTAGTCG
130 TATTTTTTCCGAGTATTGCGACAAAA--ATTCAGAAAAAATTTTTT-CGG-TCAATTCTTAGCCG
** *
2332 AAATCGTG---T-A-ATCACTGTTATTCAGCTAAAAACGCGTTTCGGGG-CCCGGCTCAGTTTTG
191 AAATCGTGTACTAACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTG
* * *
2391 CATGATTTTTGCCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATT
256 CATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAAT
* *
2456 GGATTTAAGGATTT-TTTTTACGAGCATCTGAATTTTATTTCGATTTAATTAGAAATAAATTCGG
321 GGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAG
** * * * * * ** *
2520 AAAAATAGGAAAACGATATTAG-AAGCATGAAAAACCATTCATTTTTTCTTTGCGTTGAATAATA
386 AAAAAT-GGAAAAAAATATTTGAAAGCGTGAAAAACCCTTCAATTTTT-TTGGTATTGAATTATA
* * * * * *
2584 TA-TTTTTCCTAGTATTATGGCAGAAATTTCACAAAAAATAAAAATAAAAATTCGGGTCTATTCT
449 TATTTTTTCCGAGTATTGTGGCAAAAATTT--C--AGAA-AAAAAT----TTTCGGGTCCATTCT
* ** * * * *
2648 TAGCCGAAATCGTATACGTTATCACTGTTATTGCTCTAAAAATGCGTTTCGAAGCTCCGGCTCAA
505 TAGCCGAAACCG---A-GTTATCACTGTTATTGGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAG
* * * *
2713 TTTTGCATGATTTTTGGTAGAAAGCCTCCTTGAAATATCTCTATTTATCGAA-TCAAAGCTCAGT
566 TTTTGCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACT-AAATCTCAGC
2777 CACAT
630 CACAT
* * * * * *
2782 TGGATTTAAGGATTTGTCTTTACAAGCATATGAATTTTGTTTTGATTTAATTAGAAATAAATACG
1 TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATAAATTC-
** * * * ** *
2847 GAAAAAA-GGGAAATCGATATTGGAAGTGTGAAAAAATCCCTTC-TTTTTTTTTACGTTGAATTA
65 GAAAAAATGAAAAAACGATATTGGAAGCGTG-AAAAA-CCCTTCAATTTTTTTGGCATTGAATTA
* * * *
2910 TATATTTTTTCCGAGTATTGC-AGCGAAAATTTA-AAAAAA---ATTCAGGTCAATTCTAAGCCG
128 TATATTTTTTCCGAGTATTGCGA-CAAAAATTCAGAAAAAATTTTTTC-GGTCAATTCTTAGCCG
* * *
2970 AAATCGTGTACTAACAATCACTATTATTTGGCTAAAAACGCGTTTCGGGGGCCCGACTCAGTTTT
191 AAATCGTGTACTAAC-ATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTT
*
3035 GCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGTACCAAA
255 GCATGATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAA
3088 ATTTTTTTAA
Statistics
Matches: 1927, Mismatches: 222, Indels: 177
0.83 0.10 0.08
Matches are distributed among these distances:
623 10 0.01
624 75 0.04
625 68 0.04
626 22 0.01
628 1 0.00
629 2 0.00
633 25 0.01
634 219 0.11
635 10 0.01
636 37 0.02
637 112 0.06
638 106 0.06
639 34 0.02
640 3 0.00
641 9 0.00
642 9 0.00
643 219 0.11
644 282 0.15
645 114 0.06
646 2 0.00
647 2 0.00
649 2 0.00
650 4 0.00
652 15 0.01
653 15 0.01
654 13 0.01
655 406 0.21
656 111 0.06
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (634 bp):
TGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTATGTTTCGATTTAATTAGAAATAAATTCG
AAAAAATGAAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTATAT
ATTTTTTCCGAGTATTGCGACAAAAATTCAGAAAAAATTTTTTCGGTCAATTCTTAGCCGAAATC
GTGTACTAACATCACTGTTATTGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGA
TTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGAACCAAATCTCAGCCACAATGGATT
TAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
TGGAAAAAAATATTTGAAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTT
TCCGAGTATTGTGGCAAAAATTTCAGAAAAAAATTTTCGGGTCCATTCTTAGCCGAAACCGAGTT
ATCACTGTTATTGGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG
AAAGCCTCCTTGAAATATCTCTATTCATCGAACTAAATCTCAGCCACAT
Found at i:10220 original size:6 final size:6
Alignment explanation
Indices: 10209--10247 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
10199 CTTCTGCTAT
** *
10209 ATCCTC ATCCTC ATCCTC CCCCTC ATCATC ATCCTC ATC
1 ATCCTC ATCCTC ATCCTC ATCCTC ATCCTC ATCCTC ATC
10248 ATCCTCCCCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.51, G:0.00, T:0.31
Consensus pattern (6 bp):
ATCCTC
Found at i:10240 original size:24 final size:24
Alignment explanation
Indices: 10213--10262 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
10203 TGCTATATCC
*
10213 TCATCCTCATCCTCC-CCCTCATCA
1 TCATCCTCATCATCCTCCC-CATCA
10237 TCATCCTCATCATCCTCCCCATCA
1 TCATCCTCATCATCCTCCCCATCA
10261 TC
1 TC
10263 TGCCATGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.18, C:0.52, G:0.00, T:0.30
Consensus pattern (24 bp):
TCATCCTCATCATCCTCCCCATCA
Found at i:10248 original size:12 final size:12
Alignment explanation
Indices: 10213--10284 Score: 58
Period size: 12 Copynumber: 6.0 Consensus size: 12
10203 TGCTATATCC
*
10213 TCATCCTCATCC
1 TCATCCTCATCA
**
10225 TCCCCCTCATCA
1 TCATCCTCATCA
10237 TCATCCTCATCA
1 TCATCCTCATCA
* *
10249 TCCTCCCCATCA
1 TCATCCTCATCA
*
10261 TC-TGCCAT-GTCA
1 TCAT-CC-TCATCA
10273 TCATCCTCATCA
1 TCATCCTCATCA
10285 CCCATATCAT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
11 2 0.04
12 43 0.93
13 1 0.02
ACGTcount: A:0.19, C:0.47, G:0.03, T:0.31
Consensus pattern (12 bp):
TCATCCTCATCA
Found at i:10296 original size:36 final size:36
Alignment explanation
Indices: 10234--10302 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
10224 CTCCCCCTCA
* *
10234 TCATCATCCTCATCATCCTCCCCATCATCTGCCATG
1 TCATCATCCTCATCACCCTCACCATCATCTGCCATG
*
10270 TCATCATCCTCATCACCCAT-ATCATCATCTGCC
1 TCATCATCCTCATCACCC-TCACCATCATCTGCC
10303 CTATTATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 28 0.97
37 1 0.03
ACGTcount: A:0.22, C:0.43, G:0.04, T:0.30
Consensus pattern (36 bp):
TCATCATCCTCATCACCCTCACCATCATCTGCCATG
Found at i:16586 original size:39 final size:39
Alignment explanation
Indices: 16532--16610 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
16522 ATAAGAATGC
16532 AACCAGAACTTTAAAGCATACAGTTCTACCATTACGATT
1 AACCAGAACTTTAAAGCATACAGTTCTACCATTACGATT
** *
16571 AACCAGAACTTTAAAGCATATTGTTCTACTATTACGATT
1 AACCAGAACTTTAAAGCATACAGTTCTACCATTACGATT
16610 A
1 A
16611 TAGAAAATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (39 bp):
AACCAGAACTTTAAAGCATACAGTTCTACCATTACGATT
Found at i:18987 original size:106 final size:112
Alignment explanation
Indices: 18849--19061 Score: 321
Period size: 106 Copynumber: 2.0 Consensus size: 112
18839 GGTCTTCATT
* *
18849 TTTTTTCTTCTACTTTTTTTAGTATGACAAATTATTTAATC-AA-ATATTAA-TAATAACAATAA
1 TTTTTGCTTCTACTTCTTTTAGTATGACAAATTATTTAATCAAATATATTAATTAATAACAATAA
18911 TAAT-T-TT-AATTTTATCAATATATGGAATTATAATTATGATTTTG
66 TAATATATTCAATTTTATCAATATATGGAATTATAATTATGATTTTG
* ***
18955 TTTTTGCTTCTACTTCTTTTAGTATGGCAAATTATTTAATCAAATATATTAATTAATGTTAATAA
1 TTTTTGCTTCTACTTCTTTTAGTATGACAAATTATTTAATCAAATATATTAATTAATAACAATAA
*
19020 TAATATATTCAATTTTATCAATATATTGAATTATAATTATGA
66 TAATATATTCAATTTTATCAATATATGGAATTATAATTATGA
19062 GAATTTTGAT
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
106 38 0.40
107 2 0.02
108 7 0.07
109 13 0.14
110 1 0.01
111 2 0.02
112 31 0.33
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (112 bp):
TTTTTGCTTCTACTTCTTTTAGTATGACAAATTATTTAATCAAATATATTAATTAATAACAATAA
TAATATATTCAATTTTATCAATATATGGAATTATAATTATGATTTTG
Found at i:19648 original size:14 final size:14
Alignment explanation
Indices: 19629--19660 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
19619 TAAAAGGTCT
19629 CAAGTCTCGACCCA
1 CAAGTCTCGACCCA
19643 CAAGTCTCGACCCA
1 CAAGTCTCGACCCA
19657 -AAGT
1 CAAGT
19661 AACAATGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.31, C:0.38, G:0.16, T:0.16
Consensus pattern (14 bp):
CAAGTCTCGACCCA
Found at i:22954 original size:6 final size:6
Alignment explanation
Indices: 22943--22971 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
22933 GTTTAATCCG
22943 AAATAA AAATAA AAATAA AAATAA AAATA
1 AAATAA AAATAA AAATAA AAATAA AAATA
22972 GTAGTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:33071 original size:5 final size:5
Alignment explanation
Indices: 33061--33086 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
33051 TTAGCGCTTA
33061 AAACC AAACC AAACC AAACC AAACC A
1 AAACC AAACC AAACC AAACC AAACC A
33087 GTAATAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACC
Found at i:34655 original size:3 final size:3
Alignment explanation
Indices: 34647--34673 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34637 TCTTTCTTGA
34647 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
34674 CTCCCCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Done.