Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014943.1 Corchorus olitorius cultivar O-4 contig14976, 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: 49407
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1769 original size:334 final size:331
Alignment explanation
Indices: 33--2132 Score: 2387
Period size: 333 Copynumber: 6.4 Consensus size: 331
23 GCTGAAATCG
* * *
33 TTTGGCTGAAAACACGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACCCCT
1 TTTGGCTAAAAACGCGTTTC-GGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
* * * * * ** * *
98 CGAAATATATGTATTTATCTAAACAAATATCAGCCACTTTGGATTTACAGATTTGTTTTTACGAG
65 CGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTACGGATTTATTTTTACGAG
*
163 CATCTGAATCTTGTTTCGATTTAATTAG------A-----AAAAAATGGAAAAACGATATTAAAA
130 CATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAAAACGATATTAGAA
* ** *
217 TCGTGAAAAACATTAAAAT-TGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAA
195 GCGTGAAAAACCCTAATATAT-TTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAA
* **
281 AAATTGGGAAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCA
259 AAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACC-
*
346 AT-ACGATT
323 ATCACGGTT
* * *** *
354 TGTGGCTAAAAACACGTTTCGGGGCCCT-ACCTCAGTTTTGCATGATTTTACACAGAAAGACTGC
1 TTTGGCTAAAAACGCGTTTC-GGGCCCTGA-CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCC
* * * * * * *
418 TTGAAATATTTATATTCAACTAACAAAATCTCACCCACATTGGATTTAC-GAGTTTGTTTTTACG
64 TCGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTACGGA-TTTATTTTTACG
* * * * *
482 AGCATCTGAATCTTGTTTCGATTTAATAAGAAATTAATAT-GGAAAAAAAGGGAAAACGAAATTA
128 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT-TCGGAAAAAATGGAAAAACGATATTA
* * * * * * *
546 TAAGCGT-AAAAATCCTTCAAT-T-TTTTTGACGTTTAATTATA-CATTTTTTCTGAGTATTTTT
192 GAAGCGTGAAAAA-CCCT-AATATATTTTTGGCGTTGAATTATATGA-TTTTTCTGAGTATTGTG
* * * * * *
607 CCAAAGAATTGAGGAAAAATTTTTCGGGCCAG-----T------TTTTAGCTGAAATTGTGTACG
254 GCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTAC-
*
661 T-----T-ATGGTT
318 TAACCATCACGGTT
* * * **
669 TTTCGCTAAAAACGCGTTTCAGGGCCCT-ATCTCAGTTTTGCAAGACTTTTGGCAGAAAGACGGC
1 TTTGGCTAAAAACGCGTTTC-GGGCCCTGA-CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCC
* *
733 TCGAAATATCTATATTCATCTAACCAAAATCTCTGCCACAATGGATTTACGGATTTTTTTTTTAC
64 TCGAAATATCTATATTCATCTAACC-AAATCTCAGCCACAATGGATTTACGGA-TTTATTTTTAC
* * *
798 GAGAATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAAATTTGGAAAAACGATATT
127 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAA-ATGGAAAAACGATATT
* * * *
863 AGAAGCATG-AAAACCCT-ATAGTACTTTTGGCTTTGAATTATATGATTTTACTGAGTATTGTGG
191 AGAAGCGTGAAAAACCCTAATA-TATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGG
*
926 CAAAAAATTGGGGAAAAACTTTTCAGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
255 CAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTA
* *
991 ACTATCACAGTT
320 ACCATCACGGTT
* * ** * * *
1003 TTTGGCTAAAAACGCGTCTCGGGGCTCTGGTTCAGTTTTTCATGATTTTTGGAAAAAAGACTCCT
1 TTTGGCTAAAAACGCGTTTC-GGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
* * ** * * *
1068 CGAAATATATTTATTCATCTAGTCAAATCTTAGCCACAATGGATTTAAGGATTTATTTTTACCAG
65 CGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTACGGATTTATTTTTACGAG
* * * *
1133 TATCTGAATGTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAAATGGAAAAATGATATTAG
130 CATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-G-GAAAAAATGGAAAAACGATATTAG
* *
1198 AAGCGTG-AAAACCCTTCAT-TGTTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCA
193 AAGCGTGAAAAACCC-TAATATATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCA
* * *
1261 AAAAGTTGGGGAAAAACTTTTCAGGTCATTTTTTTGCAAAATTTTAGCTGAAATCGTGTAC-AAC
257 AAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAAC
1325 CATCACGGTT
322 CATCACGGTT
* * *
1335 TTTGGCTAAAAATGCGTTTCAGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGGCTTCT
1 TTTGGCTAAAAACGCGTTTC-GGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
*
1400 CGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACG
65 CGAAATATCTATATTCATCTAACCAAA--TCTCAGCCACAATGGATTTACGGATTTATTTTTACG
* * * ** *
1465 AGTATCCGAATCTTGTTTCGATTTAATTAAAAATGTATTGTGGCAAAAAATGGAAAAACGATATT
128 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT-CGG-AAAAAATGGAAAAACGATATT
* * *
1530 AGAAGCGTGAAAAACCCTAATATATTTTTGGCATTGAATTATATGATTTTTTTGAGTGTTGTGGC
191 AGAAGCGTGAAAAACCCTAATATATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC
* *
1595 AAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTCAGCTGAAATCGTGTACTAA
256 AAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAA
1660 CCATCACGGTT
321 CCATCACGGTT
* * * *
1671 TTTGGCTGAAAACGTGTTTCGGGATCCTGACTCAGTTTTGCATGACTTTTGGCAGAAAGACTCCT
1 TTTGGCTAAAAACGCGTTTCGGG-CCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
* * * ** ** *
1736 CAAAATATCTGTATTCATCTAACCATATCTCAGCCACGTTGGATTTATAGATTTGTTTTTACGAG
65 CGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTACGGATTTATTTTTACGAG
* * *
1801 CATTTGAATCTTGTTTCGATTTATTTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTAGA
130 CATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GGAAAAAATGGAAAAACGATATTAGA
** * * * *
1866 AGCGTGAAAAACATTAAAAAAATTTTGGCGTTGAATTATATGATTTTTCAGAGTATTGTGGCAAA
194 AGCGTGAAAAACCCTAATATATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAA
* *
1931 GAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
259 AAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCA
1996 TCACGGTT
324 TCACGGTT
* * *
2004 TTTGGCTAAAAATGCGTTTCGCGGCCCTGACTTAGTTTTGCATGATTTTTGGCAGAAAGACTTCT
1 TTTGGCTAAAAACGCGTTTCG-GGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCT
* * *
2069 TGAAATATCTATATTCATCTAATCAAATCTCTTAGACACAATGGATTTACGGATTTATTTTTAC
65 CGAAATATCTATATTCATCTAACCAAATCTC--AGCCACAATGGATTTACGGATTTATTTTTAC
2133 TAAGACTTAG
Statistics
Matches: 1502, Mismatches: 217, Indels: 106
0.82 0.12 0.06
Matches are distributed among these distances:
315 81 0.05
316 22 0.01
317 58 0.04
318 77 0.05
319 1 0.00
320 20 0.01
321 136 0.09
323 1 0.00
326 1 0.00
327 1 0.00
328 1 0.00
329 19 0.01
330 1 0.00
331 62 0.04
332 165 0.11
333 386 0.26
334 247 0.16
335 133 0.09
336 90 0.06
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (331 bp):
TTTGGCTAAAAACGCGTTTCGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTC
GAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTACGGATTTATTTTTACGAGC
ATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAAAACGATATTAGAAG
CGTGAAAAACCCTAATATATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAA
ATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATC
ACGGTT
Found at i:1940 original size:668 final size:657
Alignment explanation
Indices: 33--2132 Score: 2492
Period size: 668 Copynumber: 3.2 Consensus size: 657
23 GCTGAAATCG
* * * **
33 TTTGGCTGAAAACACGTTTCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACCCCT
1 TTTGGCTAAAAACGCGTTTCAGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTTCT
* * * * * ** * *
98 CGAAATATATGTATTTATCTAAACAAA--TATCAGCCACTTTGGATTTACAGATTTGTTTTTACG
66 CGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACG
* * *
161 AGCATCTGAATCTTGTTTCGATTTAATT---A-GA----AAAAAATGGAAAAACGATATTAAAAT
131 AGAATCTGAATCTTGTTTCGATTTAATTAAAATGATTGGAAAAAATGGAAAAACGATATTAGAAG
** * *
218 CGTGAAAAACATTAAAAT-TGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAA
196 CGTGAAAAACCCTAATATAT-TTTTGGCATTGAATTATATGATTTTTCTGAGTATTGTGGCAAAA
* **
282 AATTGGGAAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCAA
260 AATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACC-A
* * * **
347 T-ACGATTTGTGGCTAAAAACACGTTTCGGGGCCCT-ACCTCAGTTTTGCATGATTTTACACAGA
324 TCACGGTTTTTGGCTAAAAACGCGTTTC-GGGCCCTGA-CTCAGTTTTGCATGATTTT-GGCAGA
* * * * * * *
410 AAGACTGCTTGAAATATTTATATTCAACTAACAAAATCTCACCCACATTGGATTTACGAGTTTGT
386 AAGACTCCTCGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGA-TTTGT
* * * *
475 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATAAGAAATTAATAT-GGAAAAAAA-GGGAAAA
450 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT-TCAGAAAAAAATGGAAAAA
* * * * * *
538 CGAAATTATAAGCGT-AAAAATCCTTCAATTTTTTTGACGTTTAATTATA-CATTTTTTCTGAGT
514 CGATATTAGAAGCGTGAAAAA-CCTTCAATATTTTTGGCGTTGAATTATATGA-TTTTTCTGAGT
* ** * * * ** *
601 ATTTTTCCAAAGAATTGAGGAAAAATTTTTCGG---------GCCAGTTTTTAGCTGAAATTGTG
577 ATTGTGGCAAAGAATTGGGGAAAAACTTTTCGGTCATTTTTTGCAAAATTTTAGCTGAAATCGTG
* * *
657 T---A-CGTTATGGTT
642 TACAACCATCACGGTT
* * * **
669 TTTCGCTAAAAACGCGTTTCAGGGCCCT-ATCTCAGTTTTGCAAGACTTTTGGCAGAAAGACGGC
1 TTTGGCTAAAAACGCGTTTCAGGGCCCTGA-CTCAGTTTTGCATGATTTTTGGCAGAAAGACTTC
* *
733 TCGAAATATCTATATTCATCTAACCAAAATCTCT--GCCACAATGGATTTACGGATTTTTTTTTT
65 TCGAAATATCTATATTCATCTAATC-AAATCTCTCAGCCACAATGGATTTACGGA-TTTATTTTT
* * *
796 ACGAGAATCTGAATCTTGTTTCGATTAAATTAGAAATAAATTCGGAAAAATTTGGAAAAACGATA
128 ACGAGAATCTGAATCTTGTTTCGATTTAATTA-AAAT-GATT-GGAAAAA-ATGGAAAAACGATA
* * * *
861 TTAGAAGCATG-AAAACCCT-ATAGTACTTTTGGCTTTGAATTATATGATTTTACTGAGTATTGT
189 TTAGAAGCGTGAAAAACCCTAATA-TATTTTTGGCATTGAATTATATGATTTTTCTGAGTATTGT
*
924 GGCAAAAAATTGGGGAAAAACTTTTCAGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTAC
253 GGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTAC
* * * * ** *
989 TAACTATCACAGTTTTTGGCTAAAAACGCGTCTCGGGGCTCTGGTTCAGTTTTTCATGATTTTTG
318 TAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGCCCTGACTCAGTTTTGCATGA-TTTTG
* * * ** * *
1054 GAAAAAAGACTCCTCGAAATATATTTATTCATCTAGTCAAATCTTAGCCACAATGGATTTAAGGA
381 GCAGAAAGACTCCTCGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAA-GA
* * * *
1119 TTTATTTTTACCAGTATCTGAATGTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAAATGG
445 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG-AAAAAAATGG
* * * *
1184 AAAAATGATATTAGAAGCGTGAAAACCCTTCATTGTTTTTGGCGTTGAATTATATGATTTTTCTG
509 AAAAACGATATTAGAAGCGTGAAAAACCTTCAATATTTTTGGCGTTGAATTATATGATTTTTCTG
1249 AGTATTGTGGCAAA-AAGTTGGGGAAAAACTTTTCAGGTCATTTTTTTGCAAAATTTTAGCTGAA
574 AGTATTGTGGCAAAGAA-TTGGGGAAAAACTTTTC-GGTCA-TTTTTTGCAAAATTTTAGCTGAA
1313 ATCGTGTACAACCATCACGGTT
636 ATCGTGTACAACCATCACGGTT
* *
1335 TTTGGCTAAAAATGCGTTTCAGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGGCTTCT
1 TTTGGCTAAAAACGCGTTTCAGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTTCT
1400 CGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACG
66 CGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACG
* *
1465 AGTATCCGAATCTTGTTTCGATTTAATTAAAAATGTATTGTGGCAAAAAATGGAAAAACGATATT
131 AGAATCTGAATCTTGTTTCGATTTAATT-AAAATG-A-T-TGG-AAAAAATGGAAAAACGATATT
* *
1530 AGAAGCGTGAAAAACCCTAATATATTTTTGGCATTGAATTATATGATTTTTTTGAGTGTTGTGGC
191 AGAAGCGTGAAAAACCCTAATATATTTTTGGCATTGAATTATATGATTTTTCTGAGTATTGTGGC
* *
1595 AAAAAATTGGGGAAAATCTTTTCGGGTCAGTTTTTTGCAAAATTTCAGCTGAAATCGTGTACTAA
256 AAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAA
* * *
1660 CCATCACGGTTTTTGGCTGAAAACGTGTTTCGGGATCCTGACTCAGTTTTGCATGACTTTTGGCA
321 CCATCACGGTTTTTGGCTAAAAACGCGTTTCGGG-CCCTGACTCAGTTTTGCATGA-TTTTGGCA
* * * * *
1725 GAAAGACTCCTCAAAATATCTGTATTCATCTAACCATATCTCAGCCACGTTGGATTTATAGATTT
384 GAAAGACTCCTCGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTA-AGATTT
* *
1790 GTTTTTACGAGCATTTGAATCTTGTTTCGATTTATTTAGAAATAAATTCAGAAAAAAATGGAAAA
448 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAA
* * * * *
1855 ACGATATTAGAAGCGTGAAAAACATTAAAAAAATTTTGGCGTTGAATTATATGATTTTTCAGAGT
513 ACGATATTAGAAGCGTGAAAAACCTT-CAATATTTTTGGCGTTGAATTATATGATTTTTCTGAGT
*
1920 ATTGTGGCAAAGAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAATCG
577 ATTGTGGCAAAGAATTGGGGAAAAACTTTTC-GGTCA-TTTTTTGCAAAATTTTAGCTGAAATCG
1985 TGTACTAACCATCACGGTT
640 TGTAC-AACCATCACGGTT
* *
2004 TTTGGCTAAAAATGCGTTTC-GCGGCCCTGACTTAGTTTTGCATGATTTTTGGCAGAAAGACTTC
1 TTTGGCTAAAAACGCGTTTCAG-GGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTTC
* * *
2068 TTGAAATATCTATATTCATCTAATCAAATCTCTTAGACACAATGGATTTACGGATTTATTTTTAC
65 TCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTAC
2133 TAAGACTTAG
Statistics
Matches: 1247, Mismatches: 157, Indels: 87
0.84 0.11 0.06
Matches are distributed among these distances:
635 1 0.00
636 75 0.06
637 19 0.02
638 37 0.03
639 2 0.00
642 1 0.00
644 1 0.00
648 5 0.00
649 245 0.20
650 36 0.03
651 76 0.06
652 7 0.01
662 20 0.02
665 9 0.01
666 127 0.10
667 87 0.07
668 358 0.29
669 141 0.11
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (657 bp):
TTTGGCTAAAAACGCGTTTCAGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTTCT
CGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACG
AGAATCTGAATCTTGTTTCGATTTAATTAAAATGATTGGAAAAAATGGAAAAACGATATTAGAAG
CGTGAAAAACCCTAATATATTTTTGGCATTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAA
ATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATC
ACGGTTTTTGGCTAAAAACGCGTTTCGGGCCCTGACTCAGTTTTGCATGATTTTGGCAGAAAGAC
TCCTCGAAATATATATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGATTTGTTTTTAC
GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATT
AGAAGCGTGAAAAACCTTCAATATTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCA
AAGAATTGGGGAAAAACTTTTCGGTCATTTTTTGCAAAATTTTAGCTGAAATCGTGTACAACCAT
CACGGTT
Found at i:2165 original size:18 final size:19
Alignment explanation
Indices: 2124--2167 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2114 TTTACGGATT
2124 TATTTTTACTAAGACTTAG
1 TATTTTTACTAAGACTTAG
*
2143 AATTTTTACTAAGACTTA-
1 TATTTTTACTAAGACTTAG
2161 TATTTTT
1 TATTTTT
2168 TGTTTCCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (19 bp):
TATTTTTACTAAGACTTAG
Found at i:10445 original size:36 final size:36
Alignment explanation
Indices: 10398--10467 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
10388 TTCAATAACC
* *
10398 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
10434 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
10468 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:11335 original size:202 final size:202
Alignment explanation
Indices: 10983--11391 Score: 748
Period size: 202 Copynumber: 2.0 Consensus size: 202
10973 GCTTAATAAC
10983 TTTATAAATGGTGAATGTTATTAATTCTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATAAATGGTGAATGTTATTAATTCTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
11048 GATACAACACATTATTATTATATATTAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATTAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
*
11113 AATTATTAAATTAAATTAGATCAATGTCAAATAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 AATTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
*
11178 CGATTTA
196 CAATTTA
* *
11185 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATAAATGGTGAATGTTATTAATTCTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
11250 GATACAACACATTACTATTATATA-TAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTT
66 GATACAACACATTACTATTATATATTA-AACTATACCAAAAAAAATTAGTTGAACATTAGTGGTT
*
11314 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
130 GAATTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
11379 CCAATTTA
195 CCAATTTA
11387 TTTAT
1 TTTAT
11392 TATTAAGGAA
Statistics
Matches: 200, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
201 2 0.01
202 198 0.99
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (202 bp):
TTTATAAATGGTGAATGTTATTAATTCTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATTAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
AATTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
CAATTTA
Found at i:11494 original size:25 final size:24
Alignment explanation
Indices: 11460--11506 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
11450 ACGTTTGCAC
11460 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
11485 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
11507 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:11551 original size:39 final size:40
Alignment explanation
Indices: 11497--11577 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
11487 ATACCTAAGA
*
11497 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
11536 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
11576 AT
1 AT
11578 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:44953 original size:35 final size:35
Alignment explanation
Indices: 44901--44971 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 35
44891 CTTTGTTCAA
*
44901 GTTCGGCTCGTGTTCGTTTATAAAGTTT-G-GTGTTC
1 GTTCGGCTCGTGCTCGTTTA-AAA-TTTAGAGTGTTC
44936 GTTCGAGCTCG-GCTCGTTTAAAATTTAGAGTGTTC
1 GTTCG-GCTCGTGCTCGTTTAAAATTTAGAGTGTTC
44971 G
1 G
44972 AAGCTCGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
33 3 0.09
34 4 0.12
35 20 0.62
36 5 0.16
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.41
Consensus pattern (35 bp):
GTTCGGCTCGTGCTCGTTTAAAATTTAGAGTGTTC
Found at i:45088 original size:18 final size:18
Alignment explanation
Indices: 45065--45099 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
45055 ACAAAAACTG
45065 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
45083 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
45100 TGTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:45348 original size:35 final size:35
Alignment explanation
Indices: 45302--45376 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
45292 TTATATAAAC
*
45302 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATAAACAATAAACGAGCCTGTTCGT
* *
45337 GAACACTTAAATAAACAATAAATGAGTCTGTTCGT
1 GAACACTTAAATAAACAATAAACGAGCCTGTTCGT
45372 GAACA
1 GAACA
45377 TAAACGAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (35 bp):
GAACACTTAAATAAACAATAAACGAGCCTGTTCGT
Found at i:45521 original size:24 final size:23
Alignment explanation
Indices: 45476--45521 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
45466 ACGAACATAA
* *
45476 ACGAGCTTTAATCGAGCCCGTTC
1 ACGAGCTTTAATCGAACACGTTC
*
45499 ACGAGCTGTTCATCGAACACGTT
1 ACGAGCT-TTAATCGAACACGTT
45522 GTTCATTTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (23 bp):
ACGAGCTTTAATCGAACACGTTC
Done.