Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024798.1 Corchorus olitorius cultivar O-4 contig24831, 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: 27207
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:821 original size:439 final size:434
Alignment explanation
Indices: 1--1008 Score: 1169
Period size: 439 Copynumber: 2.3 Consensus size: 434
* ** * * *
1 CATTTTTTAGAATTG-AAATATAGGAATTAGCTTTTGAGTCTTTCATGAAAGTTGTAGATCATAA
1 CATTTTTTAGAATTGAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGA
* * * *
65 AATTACCTTTTAATAGATACCTGAATTACCTTAATTGGACAAATAGAACAAAGAAATTAAAAA-A
66 AATTACCTTTTAATAGATACATGAATCAACTTAA-TCGACAAATAGAACAAAG-AA-TAAAAATA
129 CACGAAGTATTAAATCGAGTAAGATAGAATTTGGAAAGGACTAAGTAGCATAAAATAGAAAAGTA
128 -A--AAGTATTAAATCGAGTAAGATAGAATTTGGAAAGGACTAAGTAGCATAAAATAGAAAAGTA
* * *
194 TGAGGGTGATTTATAACTAATTCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAA
190 TGAGGGTCATTTATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAA
* * * *
259 ATTTCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCAAGAAAGTC
255 ATTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTAACTTTCGGCTCCTTCAAGAAAGTC
* * * ** **** * * * * *
324 GTAGATTTTCTTTCGGGTTCTTTAACCGACACTTGAATAACTTTAATTGGACATGTGGATC-GAA
320 GTAAATATGCAATCAACCTCTTTAACCGACACTTCAATAACTTCAATCGGAAATGTGGA-CAAAA
* * *
388 AATTAGATGGTATTAAAT-AGACCAACAATCGAAACAA-ACAAATTTAGGAAG
384 AATTAGACGATATTAAATCA-ACCAACAATCAAAACAACA-AAATTTAGGAAG
*
439 CATTTTTTTGAATTGAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGA
1 CATTTTTTAGAATTGAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGA
* * *
504 AACTACCTTTTAATAGACACATGAATCAACTTAATCAGACACATAGAACAAAGAATAAAAATATA
66 AATTACCTTTTAATAGATACATGAATCAACTTAATC-GACAAATAGAACAAAGAATAAAAATA-A
* * * *
569 AAG-CTTAAA-CGTTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAGTA
129 AAGTATTAAATCG--AG--TAAGATAGAATTTGGAAAGGACTAAGTAGCATAAAATAGAAAAGTA
*
632 TGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAGA
190 TGAGGGTCATTT-ATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATA-A
* *
697 AAA-TCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTTAGCTTTCGGCTCCTTCATGAAA
253 AAATTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAA-TTAACTTTCGGCTCCTTCAAGAAA
*
761 GTCGTAAATCATGCAAT-AACCT-TTTAACCTACACTTCAATAACTTCAATCGGAAATGTGGACA
317 GTCGTAAAT-ATGCAATCAACCTCTTTAACCGACACTTCAATAACTTCAATCGGAAATGTGGACA
* ** * *
824 AAAAATTATACGATATTAAATCAACCGGCAATCAAAACCACAAAATTTCGGAAG
381 AAAAATTAGACGATATTAAATCAACCAACAATCAAAACAACAAAATTTAGGAAG
* * * * * * *
878 TATTTTTTAGGA-TCAAAACATTAAAA-TTGACTTTTGAGTTCTTAATGAAAATTGTAGATCATG
1 CATTTTTTAGAATTGAAAACATAAAAATTTG-CTTTTGAGTCCTTCATGAAAGTTGTAGATCATG
* * * *
941 AAATTACCTTTTAATAGATACTTGAATC-ACATTAATCGAACAAATAGAAAAAAGTACAAAAATA
65 AAATTACCTTTTAATAGATACATGAATCAAC-TTAATCG-ACAAATAGAACAAAGAATAAAAATA
1005 AAAG
128 AAAG
1009 GCAACGCGTT
Statistics
Matches: 486, Mismatches: 67, Indels: 35
0.83 0.11 0.06
Matches are distributed among these distances:
434 2 0.00
435 5 0.01
436 5 0.01
437 16 0.03
438 168 0.35
439 252 0.52
440 35 0.07
441 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (434 bp):
CATTTTTTAGAATTGAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGA
AATTACCTTTTAATAGATACATGAATCAACTTAATCGACAAATAGAACAAAGAATAAAAATAAAA
GTATTAAATCGAGTAAGATAGAATTTGGAAAGGACTAAGTAGCATAAAATAGAAAAGTATGAGGG
TCATTTATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAAATTCCC
TTTTGAACCCTTCACGAAACTCGTAGATCAAATTAACTTTCGGCTCCTTCAAGAAAGTCGTAAAT
ATGCAATCAACCTCTTTAACCGACACTTCAATAACTTCAATCGGAAATGTGGACAAAAAATTAGA
CGATATTAAATCAACCAACAATCAAAACAACAAAATTTAGGAAG
Found at i:1121 original size:439 final size:437
Alignment explanation
Indices: 1--1121 Score: 1094
Period size: 439 Copynumber: 2.6 Consensus size: 437
* * ** * * * * *
1 CATTTTTTAGAATT-GAAATATAGGAATTAGCTTTTGAGTCTTTCATGAAAGTTGTAGATCATAA
1 CATTTTTTAGAATTCAAAACATAAAAATTTGCTTTTGAGTCCTTAATGAAAATTGTAGATCATGA
* * * * * ** *
65 AATTACCTTTTAATAGATACCTGAATTACCTTAATTGGACAAATAGAACAAAGAA-ATTAAAA-A
66 AACTACCTTTTAATAGACACATGAATCAACTTAATCAGACAAATAGAAAAAAGAACA--AAAATA
* * *** * * *
128 -ACA-CGAAGTATTAAATCGAGTAAGATAGAATTTGGAAAGGACTAAGTAGCATAAAATAGAAAA
129 TAAAGCTAAACGTTAAAT----TAACATAGAATTTGTAAAGGACTAAGTAGCATAAAGTAGAAAA
* * * *
191 GTATGAGGGTGATTTATAACTAATTCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATA
190 GTATGAGGGTCATTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATA
* * * *
256 AAAATTTCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCAAGAAA
255 AAAATTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTAACTTTCGGCTCCTTCAAGAAA
* * * ** **** * * * * *
321 GTCGTAGATTTTCTTTCGGGTTCTTTAACCGACACTTGAATAACTTTAATTGGACATGTGGATCG
320 GTCGTAAATATGCAATCAACCTCTTTAACCGACACTTCAATAACTTCAATCGGAAATGTGGATCA
* * *
386 AAAATTAGATGGTATTAAATAGACCAACAATCGAAACAAACAAATTTAGGAAG
385 AAAATTAGACGATATTAAATAGACCAACAATCAAAACAAACAAATTTAGGAAG
* * * *
439 CATTTTTTTGAATTGAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGA
1 CATTTTTTAGAATTCAAAACATAAAAATTTGCTTTTGAGTCCTTAATGAAAATTGTAGATCATGA
* * *
504 AACTACCTTTTAATAGACACATGAATCAACTTAATCAGACACATAGAACAAAGAATAAAAATATA
66 AACTACCTTTTAATAGACACATGAATCAACTTAATCAGACAAATAGAAAAAAGAACAAAAATATA
* * *
569 AAGCTTAAACGTTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAGTATG
131 AAGC-TAAACGTTAAATTAACATAGAATTTGTAAAGGACTAAGTAGCATAAAGTAGAAAAGTATG
*
634 AGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAGAAA
195 AGGGTCA-TTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATA-AAA
* *
699 A-TCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTTAGCTTTCGGCTCCTTCATGAAAGT
258 ATTCCCTTTTGAACCCTTCACGAAACTCGTAGATCAAA-TTAACTTTCGGCTCCTTCAAGAAAGT
*
763 CGTAAATCATGCAAT-AACCT-TTTAACCTACACTTCAATAACTTCAATCGGAAATGTGGA-CAA
322 CGTAAAT-ATGCAATCAACCTCTTTAACCGACACTTCAATAACTTCAATCGGAAATGTGGATC-A
* ** * *
825 AAAATTATACGATATTAAATCA-ACCGGCAATCAAAAC-CACAAAATTTCGGAAG
385 AAAATTAGACGATATTAAAT-AGACCAACAATCAAAACAAAC-AAATTTAGGAAG
* * * *
878 TATTTTTTAGGA-TCAAAACATTAAAA-TTGACTTTTGAGTTCTTAATGAAAATTGTAGATCATG
1 CATTTTTTAGAATTCAAAACATAAAAATTTG-CTTTTGAGTCCTTAATGAAAATTGTAGATCATG
* * * *
941 AAATTACCTTTTAATAGATACTTGAATC-ACATTAATC-GAACAAATAGAAAAAAGTACAAAAAT
65 AAACTACCTTTTAATAGACACATGAATCAAC-TTAATCAG-ACAAATAGAAAAAAGAACAAAAAT
* * * * * *
1004 A-AAAGGC-AACGCGTTAAATTGTTCAACCTATAA-TTGTAAAGGACTAAATAGCATACAGTATA
128 ATAAA-GCTAA-ACGTTAAA---TT-AACATAGAATTTGTAAAGGACTAAGTAGCATAAAGTAGA
** * *
1066 AAAGTATGAGAATCATTAGATAAATAATCCAACA-AA-AAAATATTAGTTTATGGAGA
187 AAAGTATGAGGGTCATT-GATAAATAATCCAA-ATAAGAAAATATTTGTTAATGGAGA
1122 ATGGGACCCA
Statistics
Matches: 571, Mismatches: 88, Indels: 47
0.81 0.12 0.07
Matches are distributed among these distances:
436 2 0.00
437 15 0.03
438 167 0.29
439 276 0.48
440 93 0.16
441 11 0.02
442 7 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (437 bp):
CATTTTTTAGAATTCAAAACATAAAAATTTGCTTTTGAGTCCTTAATGAAAATTGTAGATCATGA
AACTACCTTTTAATAGACACATGAATCAACTTAATCAGACAAATAGAAAAAAGAACAAAAATATA
AAGCTAAACGTTAAATTAACATAGAATTTGTAAAGGACTAAGTAGCATAAAGTAGAAAAGTATGA
GGGTCATTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTGAAACATAAAAATT
CCCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTAACTTTCGGCTCCTTCAAGAAAGTCGTA
AATATGCAATCAACCTCTTTAACCGACACTTCAATAACTTCAATCGGAAATGTGGATCAAAAATT
AGACGATATTAAATAGACCAACAATCAAAACAAACAAATTTAGGAAG
Found at i:1834 original size:37 final size:38
Alignment explanation
Indices: 1793--1868 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
1783 TGAAACATAA
*
1793 AAATTC-CCTTTTGAACCCTTCATGAAACTCGTAGATC
1 AAATTCACCTTTCGAACCCTTCATGAAACTCGTAGATC
* * * *
1830 AAATTCAGCTTTCGGATCCTTCATGAAAGTCGTAGATC
1 AAATTCACCTTTCGAACCCTTCATGAAACTCGTAGATC
1868 A
1 A
1869 TGCAATAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
37 6 0.18
38 27 0.82
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (38 bp):
AAATTCACCTTTCGAACCCTTCATGAAACTCGTAGATC
Found at i:2527 original size:15 final size:15
Alignment explanation
Indices: 2507--2549 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2497 ATATATTGTA
*
2507 TTATAAAAATTATAT
1 TTATAAAAATTATAG
* *
2522 TTATAAAAAATATGG
1 TTATAAAAATTATAG
*
2537 TTAAAAAAATTAT
1 TTATAAAAATTAT
2550 TATCATGTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
TTATAAAAATTATAG
Found at i:2957 original size:62 final size:62
Alignment explanation
Indices: 2883--3006 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
2873 TCAATTCATG
*
2883 AGAAGAGAGGGTTAGA-CCGATTTTTTT-GTCATTTCACTCCTTACTCCTTATTGTTTTGTATA
1 AGAAAAGAGGGTTAGACCCG-TTTTTTTGGTCATTTCACTCCTTACT-CTTATTGTTTTGTATA
*
2945 AGAAAAGAGGGTTAGACCCGTTTTTTTGGTCATTTCACTTCTTACTCTTATTGTTTTGTATA
1 AGAAAAGAGGGTTAGACCCGTTTTTTTGGTCATTTCACTCCTTACTCTTATTGTTTTGTATA
3007 TTTGTATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
62 38 0.66
63 20 0.34
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (62 bp):
AGAAAAGAGGGTTAGACCCGTTTTTTTGGTCATTTCACTCCTTACTCTTATTGTTTTGTATA
Found at i:4071 original size:41 final size:42
Alignment explanation
Indices: 3999--4080 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
3989 AGCAACAATT
* * *
3999 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATAAATTACCTAGAGATGAAGTAG
4041 AATATTAGCTTTA-TTTGATAAATTACCTAGAGATGAAGTA
1 AATATTAGCTTTATTTTGATAAATTACCTAGAGATGAAGTA
4081 CTAGAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 24 0.65
42 13 0.35
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATAAATTACCTAGAGATGAAGTAG
Found at i:5529 original size:296 final size:293
Alignment explanation
Indices: 4961--5550 Score: 946
Period size: 296 Copynumber: 2.0 Consensus size: 293
4951 TTTTTAGTGA
*
4961 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCTTTTTTTGGT
1 CTATGGAAATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCTTTTTTTGGT
* *
5026 CTTTTCTCACTTTTCGGGAGACTAAAAAGGCCCTTGATAAATTTTCTCCCTTACCTTTCATCCTG
66 CTTTTCTCACTTTTCGGGAGACTAAAAAGGCCCTCGATAAATTTGCTCCCTTACCTTTCATCCTG
* * **
5091 CCCTTTTTTGTAATTTACTATTTTTGTATTTATGATTAAGTGTGTTTTAATAATGTATTAATTGT
131 CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTATTTTAATAACATATTAATTGT
*
5156 GTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTGGTGCTATAAA
196 GTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTATAAA
*
5221 TGTATCTACCCGAGTTCATTAATTTAACAATTG
261 AGTATCTACCCGAGTTCATTAATTTAACAATTG
* *
5254 CTATGGAAATTACCTAAAAGGCCAAATTGAGGATTAGTGTGGTGCTTCCTTTTAGGCTTTTTTTT
1 CTATGGAAATTA-CTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTT-GGC-TTTTTTT
* * * * * * *
5319 TGTCTTTTCTCACTTTTCGGGTGACTAAAAAGGCTCTCGATGAATTTGCTCCCTTACTTTTCCTG
63 GGTCTTTTCTCACTTTTCGGGAGACTAAAAAGGCCCTCGATAAATTTGCTCCCTTACCTTTCATC
* *
5384 CTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTATTTTAATTACATATTGAT
128 CTGCCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTATTTTAATAACATATTAAT
*
5449 TGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTGT
193 TGTGTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTAT
* *
5514 AAAAGTGTTTACCCGAGTTCATTAATTTAACAATTG
258 AAAAGTATCTACCCGAGTTCATTAATTTAACAATTG
5550 C
1 C
5551 AATCAAGATT
Statistics
Matches: 271, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
293 12 0.04
294 37 0.14
295 3 0.01
296 219 0.81
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.42
Consensus pattern (293 bp):
CTATGGAAATTACTAAAAGGCCAAATTGAGGATTAATGTGGTGCCTCCTTTTGGCTTTTTTTGGT
CTTTTCTCACTTTTCGGGAGACTAAAAAGGCCCTCGATAAATTTGCTCCCTTACCTTTCATCCTG
CCCTTTTTTGTAATTTACTATTTTTATATTTATGATTAAGTGTATTTTAATAACATATTAATTGT
GTGTGGATATTAGGATTTACCGGTTCAACTCCTCTGCCGGAATTCCAAAGGATTAGTGCTATAAA
AGTATCTACCCGAGTTCATTAATTTAACAATTG
Found at i:6875 original size:42 final size:42
Alignment explanation
Indices: 6829--6919 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
6819 AGCAACAATT
* *
6829 AATATTAGTTTTATTTTGATGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
*
6871 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGTGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
6913 AAT-TTAG
1 AATATTAG
6920 GTAATGCACT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 42 0.91
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Found at i:12283 original size:36 final size:36
Alignment explanation
Indices: 12230--12470 Score: 209
Period size: 36 Copynumber: 6.8 Consensus size: 36
12220 TTGCAGTTAA
* *
12230 CTGAAATAAACTTAAGAACGACCACCCTCGATCATT
1 CTGACATAAACTGAAGAACGACCACCCTCGATCATT
* * * * * *
12266 CCGACATATACTGAAGAAGGACCACCCTGGGTCA-A
1 CTGACATAAACTGAAGAACGACCACCCTCGATCATT
* *
12301 CTGAGATAAACTCAAGAACGACCACCCTCGATCATT
1 CTGACATAAACTGAAGAACGACCACCCTCGATCATT
* * * * *
12337 CTGACATAAACTGGAGAAAGACCACCCTGGGTCA-A
1 CTGACATAAACTGAAGAACGACCACCCTCGATCATT
* * *
12372 CCGAAATAAACTTAAGAACGACCACCCTCGATCATT
1 CTGACATAAACTGAAGAACGACCACCCTCGATCATT
* * * * * *
12408 CTGATATAAACTGGAGAAAGACCACCCTGGGTCA-A
1 CTGACATAAACTGAAGAACGACCACCCTCGATCATT
* * * *
12443 CTGAAATAAATTGAAGAATGACCGCCCT
1 CTGACATAAACTGAAGAACGACCACCCT
12471 GGGTCAATTG
Statistics
Matches: 159, Mismatches: 44, Indels: 5
0.76 0.21 0.02
Matches are distributed among these distances:
35 77 0.48
36 82 0.52
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.18
Consensus pattern (36 bp):
CTGACATAAACTGAAGAACGACCACCCTCGATCATT
Found at i:12324 original size:35 final size:35
Alignment explanation
Indices: 12228--12483 Score: 233
Period size: 35 Copynumber: 7.2 Consensus size: 35
12218 ATTTGCAGTT
* * *
12228 AACTGAAATAAACTTAAGAACGACCACCCTCGATC
1 AACTGAAATAAACTGAAGAACGACCACCCTGGGTC
* * * * *
12263 ATTCCGACATATACTGAAGAAGGACCACCCTGGGTC
1 A-ACTGAAATAAACTGAAGAACGACCACCCTGGGTC
* * * *
12299 AACTGAGATAAACTCAAGAACGACCACCCTCGATC
1 AACTGAAATAAACTGAAGAACGACCACCCTGGGTC
* * * *
12334 ATTCTGACATAAACTGGAGAAAGACCACCCTGGGTC
1 A-ACTGAAATAAACTGAAGAACGACCACCCTGGGTC
* * * *
12370 AACCGAAATAAACTTAAGAACGACCACCCTCGATC
1 AACTGAAATAAACTGAAGAACGACCACCCTGGGTC
* * * *
12405 ATTCTGATATAAACTGGAGAAAGACCACCCTGGGTC
1 A-ACTGAAATAAACTGAAGAACGACCACCCTGGGTC
* * *
12441 AACTGAAATAAATTGAAGAATGACCGCCCTGGGTC
1 AACTGAAATAAACTGAAGAACGACCACCCTGGGTC
*
12476 AATTGAAA
1 AACTGAAA
12484 AAGGATCGCC
Statistics
Matches: 172, Mismatches: 46, Indels: 6
0.77 0.21 0.03
Matches are distributed among these distances:
35 90 0.52
36 82 0.48
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (35 bp):
AACTGAAATAAACTGAAGAACGACCACCCTGGGTC
Found at i:12344 original size:71 final size:71
Alignment explanation
Indices: 12228--12470 Score: 380
Period size: 71 Copynumber: 3.4 Consensus size: 71
12218 ATTTGCAGTT
* * * *
12228 AACTGAAATAAACTTAAGAACGACCACCCTCGATCATTCCGACATATACTGAAGAAGGACCACCC
1 AACTGAAATAAACTTAAGAACGACCACCCTCGATCATTCTGACATAAACTGGAGAAAGACCACCC
12293 TGGGTC
66 TGGGTC
* *
12299 AACTGAGATAAACTCAAGAACGACCACCCTCGATCATTCTGACATAAACTGGAGAAAGACCACCC
1 AACTGAAATAAACTTAAGAACGACCACCCTCGATCATTCTGACATAAACTGGAGAAAGACCACCC
12364 TGGGTC
66 TGGGTC
* *
12370 AACCGAAATAAACTTAAGAACGACCACCCTCGATCATTCTGATATAAACTGGAGAAAGACCACCC
1 AACTGAAATAAACTTAAGAACGACCACCCTCGATCATTCTGACATAAACTGGAGAAAGACCACCC
12435 TGGGTC
66 TGGGTC
* *
12441 AACTGAAATAAA-TTGAAGAATGACCGCCCT
1 AACTGAAATAAACTT-AAGAACGACCACCCT
12471 GGGTCAATTG
Statistics
Matches: 158, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
70 2 0.01
71 156 0.99
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (71 bp):
AACTGAAATAAACTTAAGAACGACCACCCTCGATCATTCTGACATAAACTGGAGAAAGACCACCC
TGGGTC
Found at i:12509 original size:26 final size:26
Alignment explanation
Indices: 12450--12509 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
12440 CAACTGAAAT
* * *
12450 AAATTGAAGAATGACCGCCCTGGGTC
1 AAATTGAAAAAGGACCGCCCTGGATC
* *
12476 -AATTGAAAAAGGATCGCCTTGGATC
1 AAATTGAAAAAGGACCGCCCTGGATC
12501 AAATTGAAA
1 AAATTGAAA
12510 TTCATTGTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 20 0.71
26 8 0.29
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (26 bp):
AAATTGAAAAAGGACCGCCCTGGATC
Found at i:14279 original size:21 final size:21
Alignment explanation
Indices: 14245--14286 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
14235 TTAGAAATTT
14245 CTACCCCTAAAAAAATTGTTGG
1 CTACCCCTAAAAAAATT-TTGG
14267 CTACCCC-AAAAAAATTTTGG
1 CTACCCCTAAAAAAATTTTGG
14287 TTAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (21 bp):
CTACCCCTAAAAAAATTTTGG
Found at i:15220 original size:41 final size:41
Alignment explanation
Indices: 15140--15221 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
15130 TTGTATAGAC
*
15140 ATCTATGATTTTTCATTATATATTATTGTTTCTGGTAAGAT
1 ATCTATGATTTTTCATTATATATTATTGTTTCTGATAAGAT
* *
15181 ATCTAT-AGTTTTTCATTATATGTTATTGTTTCTTATAAGAT
1 ATCTATGA-TTTTTCATTATATATTATTGTTTCTGATAAGAT
15222 GTTGATGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (41 bp):
ATCTATGATTTTTCATTATATATTATTGTTTCTGATAAGAT
Found at i:20253 original size:2 final size:2
Alignment explanation
Indices: 20246--20286 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
20236 TATTACTATC
20246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20287 AGTAGAAGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26757 original size:5 final size:5
Alignment explanation
Indices: 26713--26755 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
26703 ATAACCTCTG
26713 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT -TTTT -TTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT
26756 TTCTAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.21
5 30 0.79
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
GTTTT
Found at i:27182 original size:2 final size:2
Alignment explanation
Indices: 27175--27207 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27165 ATATTTAGTG
27175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.