Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006058.1 Corchorus capsularis cultivar CVL-1 contig06076, 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: 61757
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:63 original size:2 final size:2
Alignment explanation
Indices: 2--49 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1 C
2 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44 TA TA TA
1 TA TA TA
50 GATCTTGCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1965 original size:3 final size:3
Alignment explanation
Indices: 1945--1993 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
1935 TCTTTATACA
*
1945 AAG AAG -AG AGG AAG -AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1991 AAG
1 AAG
1994 GGAAGGAGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31756 original size:3 final size:3
Alignment explanation
Indices: 31748--31791 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
31738 TATTTTCTAG
*
31748 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31792 TAAGGGTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:44609 original size:32 final size:32
Alignment explanation
Indices: 44573--44686 Score: 153
Period size: 32 Copynumber: 3.6 Consensus size: 32
44563 TCAGTTATAT
44573 GAATAATTTATGATAAATTGCTCAAAAAAAGA
1 GAATAATTTATGATAAATTGCTCAAAAAAAGA
*** *
44605 GAATAATTTATGATAAATT--T-ATAAGTTATA
1 GAATAATTTATGATAAATTGCTCA-AAAAAAGA
44635 TGAATAATTTATGATAAATTGCTCAAAAAAAGA
1 -GAATAATTTATGATAAATTGCTCAAAAAAAGA
44668 GAATAATTTATGATAAATT
1 GAATAATTTATGATAAATT
44687 TATAATTAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
29 1 0.01
30 5 0.07
31 19 0.28
32 38 0.55
33 5 0.07
34 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (32 bp):
GAATAATTTATGATAAATTGCTCAAAAAAAGA
Found at i:44633 original size:63 final size:63
Alignment explanation
Indices: 44565--44691 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
44555 ATACTAAATC
44565 AGTTATATGAATAATTTATGATAAATTGCTCAAAAAAAGAGAATAATTTATGATAAATTTATA
1 AGTTATATGAATAATTTATGATAAATTGCTCAAAAAAAGAGAATAATTTATGATAAATTTATA
44628 AGTTATATGAATAATTTATGATAAATTGCTCAAAAAAAGAGAATAATTTATGATAAATTTATA
1 AGTTATATGAATAATTTATGATAAATTGCTCAAAAAAAGAGAATAATTTATGATAAATTTATA
44691 A
1 A
44692 TTAGTAATTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (63 bp):
AGTTATATGAATAATTTATGATAAATTGCTCAAAAAAAGAGAATAATTTATGATAAATTTATA
Found at i:45873 original size:126 final size:128
Alignment explanation
Indices: 45727--45961 Score: 375
Period size: 134 Copynumber: 1.8 Consensus size: 128
45717 TATATCTAAG
*
45727 TTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAAT-AG-GTATAAGGATATTAGATTTAATTA
1 TTTTTTAATTAAAGTAGTAAAATGGTAAAAATAAAATAAGAGTATAAGGATATTAGATTTAATTA
45790 AATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAATTCAATAAGTT
66 AATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAATTCAATAAGTT
*
45853 TTTTTTAATTAAAGTAGTAAAATGGTAAAAATAAAATAAGTTATAACTTATAAGGATATTAGATT
1 TTTTTTAATTAAAGTAGTAAAATGGTAAAAATAAAATAAG-----A-GTATAAGGATATTAGATT
*
45918 TAATTAAATTAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
60 TAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
45962 ATTAAGCAAA
Statistics
Matches: 98, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
126 36 0.37
127 2 0.02
134 60 0.61
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (128 bp):
TTTTTTAATTAAAGTAGTAAAATGGTAAAAATAAAATAAGAGTATAAGGATATTAGATTTAATTA
AATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAATTCAATAAGTT
Found at i:47644 original size:23 final size:23
Alignment explanation
Indices: 47601--47644 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
47591 AAATGGAGCA
* *
47601 ATAGATATAGTAAATATAGATAG
1 ATAGATAGAGTAAATAAAGATAG
47624 ATAGATAGA-TAAATTAAAGAT
1 ATAGATAGAGTAAA-TAAAGAT
47645 TGTCCCCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.30
Consensus pattern (23 bp):
ATAGATAGAGTAAATAAAGATAG
Found at i:49402 original size:331 final size:325
Alignment explanation
Indices: 48094--49407 Score: 1296
Period size: 331 Copynumber: 4.0 Consensus size: 325
48084 TTAAGAATTT
* * * * *
48094 TCTCAGCAATATTGAATTTAAGAATTTGTTTTTATGAGTATCTGAATCTTTGTTTCGATTTAATT
1 TCTCAGC-ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATC-TTATTTCGATTTAATT
* ** * * * * *
48159 AGGAACAAATTTAGAAAAAATAAGAAATACGATATTAAAAGCATAAAAAGCCCTCCAATCTTTTT
64 AGAAATTAATTCAG-AAAAATATGAAAAACGATA-T-AAAGCGTGAAAAGCCCTCCAATCTTTTT
* * * *
48224 GACGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAAATGA-G-AAT-CTTTCGTGTCAAT
126 GGCGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATTTTCGGGTCAAT
* * * * * * * *
48286 TTTTGCAGAATTTAAACTGAAATCGTCTACAAACAAACCATCACGATTTATGGCTAAAAACGCAT
191 TTTTGCAAAATTTTAGCCGAAATCGTGTAC---TAAA-CATCACGATTTTTGGCTAAAAACGCGT
* * * * * * *
48351 TCCAGGGACCTGTCTCAATTTTGCATGATTTTTGGCTCCGAG-GTTACTTGAAATATCTATATTC
252 TTC-GGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTT-CTTGAAATATCTATATTC
* *
48415 ATATAATCAAA
315 ATCTAATAAAA
* * * * * *
48426 TCTTAGCCACATTGGATTTAAGGATTTGTTTTTTATGAGCATATGAATCTTGTTCCGATTTAATT
1 TCTCAG-CACATTGGATTTAAGAATTTG-TTTTTACGAGCATCTGAATCTTATTTCGATTTAATT
* * ** * * * * *
48491 ATAAATGAATTTGGAAAAAATAGGAAAAACGATATTAGAAACGTAAAAAACCCTTCAATCTTTTT
64 AGAAATTAATTCAG-AAAAATATGAAAAACGATA-TA-AAGCGTGAAAAGCCCTCCAATCTTTTT
* * *
48556 GGCGTTGAATTATATATTTTTTATGAGTGTTTTAGCCAAAAATTGAGGAAATATCTTTTGGGTCA
126 GGCGTTAAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATAT-TTTCGGGTCA
* * * * *
48621 ATTTTTGCAAAATTCTAGTCGAAATCGTG---TAATCATCACGGTTTTTGGCTAAAAACGCGTAT
189 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAACATCACGATTTTTGGCTAAAAACGCGTTT
* * * * * * *
48683 CGGGACCCCAGCTAAGTTTTGCATGATTTTTGACGCCAAGAC-TCTTTGAGATATCCATATTCAT
254 CGGG-GCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTTC-TTGAAATATCTATATTCAT
48747 CTAATAAAA
317 CTAATAAAA
* * *
48756 TCTCAGCTACATTGGATTTAAGAATTTATTTTTACGAGTATCTTAATCTTATTTCGATTTAATTA
1 TCTCAGC-ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTA
* * *
48821 GAAATTAATTCAGAAAAATATGAAAAACGATATTAAGCGTGAAAAAGTCCTCCAATGTTTTTGGC
65 GAAATTAATTCAGAAAAATATGAAAAACGATATAAAGCGTG-AAAAGCCCTCCAATCTTTTTGGC
** * * * *
48886 GTTGAATTATGTATATATTTTTATGAGTATTTTAGCCAAAAACAGACAGAAAAATTCTTTGGGTT
129 GTT-AA--AT-TATATATTTTTATGAGTATTTTAGCCAAAAATTGA-GGAAATATT-TTCGGGTC
* * * **
48951 ATTTTTTGCAAAATTTTAGCCGAAATTGTGTACTAACCATCACGATTTTTGGCTAAAAACATGTT
188 AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAACATCACGATTTTTGGCTAAAAACGCGTT
* * * * * *
49016 TCGGGGCCATGGCTCTGTTTTGCATGATTTTTGGCACCGAGACTCCTTAAAATATCTTTATTCAT
253 TCGGGGCC-CGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTTCTTGAAATATCTATATTCAT
*
49081 CTAATGAAA
317 CTAATAAAA
* * * *
49090 TCCCAGACAGATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAATCTTATTTCAATTTATAAA
1 TCTCAG-CACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTATTTCGA-TT-T-AA
* * *
49155 TTAGAAATTAATTCAGAAAAATATGAAAAACAATACTAAAGTGTGAAAAGTCCTCCAATCTTTTT
62 TTAGAAATTAATTCAGAAAAATATGAAAAACGATA-TAAAGCGTGAAAAGCCCTCCAATCTTTTT
* * *
49220 GGCGTTAAATTTTATA-TTTTATGAGTATTTTATCCAAAAATTGAGGAAATATTTTCGGGTCATT
126 GGCGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATTTTCGGGTCA-A
* * *
49284 TTTTTGCATAATTTTAGCCAAAATCATGTACTAAACATCACGATTTTTGGCTAAAAACGCGTTTC
190 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAACATCACGATTTTTGGCTAAAAACGCGTTTC
* * * *
49349 GCGGTCCCGGTTCAGTTTTACATGATTTTTGGCGCCGACACTTCTTGAAATATCTATAT
255 G-GGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTTCTTGAAATATCTATAT
49408 ATATACTATA
Statistics
Matches: 811, Mismatches: 140, Indels: 63
0.80 0.14 0.06
Matches are distributed among these distances:
326 5 0.01
327 23 0.03
328 19 0.02
329 45 0.06
330 135 0.17
331 158 0.19
332 132 0.16
333 53 0.07
334 133 0.16
335 7 0.01
336 3 0.00
337 91 0.11
338 7 0.01
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (325 bp):
TCTCAGCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAG
AAATTAATTCAGAAAAATATGAAAAACGATATAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGT
TAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATTTTCGGGTCAATTTTTG
CAAAATTTTAGCCGAAATCGTGTACTAAACATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCC
CGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTTCTTGAAATATCTATATTCATCTAATAAAA
Found at i:49579 original size:11 final size:11
Alignment explanation
Indices: 49563--49605 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
49553 CTATATATAT
49563 CTAATTAATAG
1 CTAATTAATAG
*
49574 CTAATTAATAT
1 CTAATTAATAG
*
49585 TTAATTAATAG
1 CTAATTAATAG
*
49596 TTAATTAATA
1 CTAATTAATA
49606 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:49584 original size:22 final size:22
Alignment explanation
Indices: 49559--49605 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
49549 TATACTATAT
49559 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
* *
49581 ATATTTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
49603 ATA
1 ATA
49606 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:53052 original size:349 final size:343
Alignment explanation
Indices: 52207--53417 Score: 1407
Period size: 349 Copynumber: 3.5 Consensus size: 343
52197 CCCCAGCTAA
** ** * * ** * * *
52207 GTTTTGCATGATTTTTCACGCTAAGACTCTTTGAGATATCCATATTCTTCTAATAAAATCTCAGC
1 GTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATC-CAAC
* * * * * * * * * * *
52272 TAC-TTGGATTTAAGAATTT-TTTTTACGAGTATCTCAATCTTATTTCGATTTAATAAGAAATTA
65 CACATTGGATTTAAGGATTTGTTTTTATGTGCATATGAATTTTGTTTCTATTTAATTAGAAATTA
* * * *
52335 ATTCAG-AAAAATATGAAAAACGATATTAGAAGCGTGAAAATTCCTCCAATTTTTTTGGCATT--
130 ATTCAGAAAAAATATGAAAAACAATATTA-AAGCGTGAAAAATCCTCCAATCTTTTTGCCATTCA
* * *
52397 G--------A-AT-TACATATATA-TTATGAGTATTTTATCGAAAAATTGACGGAAAAATTTTTC
194 GTTAAATATATATATATATATATATTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTTTC
* **
52451 -GGCACATTTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGACATTTGGCTAAAA
259 GGGTA-A-TTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAA
*
52515 CTGTGTTTC-GGGATCACAG-CTCA
322 C-GTGTTTCGGGGA-CA-AGACTCT
* * **
52538 GTTTTGCATGATTTTTGACGCCGAGACTCCTTGAAATATCTTTATGCATCTAATCAAATCCCAGT
1 GTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAAT-CCAAC
* * *
52603 CACATTGGATTTAAGGA-TTGTTTTTATGTGCATATAAATCTTTTTTTCCATTTAATTAGAAATT
65 CACATTGGATTTAAGGATTTGTTTTTATGTGCATATGAAT-TTTGTTTCTATTTAATTAGAAATT
52667 AATTCAGAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAATCCTCCAATCTTTTTGCCATCT
129 AATTCAGAAAAAATATGAAAAACAATATT-AAAGCGTGAAAAATCCTCCAATCTTTTTGCCAT-T
* *
52732 CA-TTAAATATATATATATATATATATTTAATGAGTATTTTAGCTAAAAATTGACGGAAGCAATT
192 CAGTTAAATATATATATATATATATATTT-ATGAGTATTTTAGCCAAAAATTGACGGAA-AAATT
* * * *
52796 TTTCGGGTAATTTTTTACAGAATTTTAG-CTAAAATCGTGTACTAACCATCACGTTTTTTTGGCT
255 TTTCGGGTAATTTTTTGCAAAATTTTAGTC-GAAATCGTGTACTAACCATCACG-ATTTTTGGCT
52860 AATAACGTGTTTCGGGGACAAGACTCT
318 AA-AACGTGTTTCGGGGACAAGACTCT
* *
52887 GTTTTACATGATTTTTGGCGCCGAGATTCCTTGAAATATCTTTATTCATCTAATCAAATCCTAAC
1 GTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCC-AAC
52952 CACATTGGATTTAAGGATTTGTTTTTATGTGCATATGAATTTTGTTTCTATTTAATTAGAAATTA
65 CACATTGGATTTAAGGATTTGTTTTTATGTGCATATGAATTTTGTTTCTATTTAATTAGAAATTA
* * ** * * *
53017 ATTCAGAAAAAATTATGAAAAAGAATATTAAAGCGTGGAATGTCCTCCAATCTTTTTGGCGTTGA
130 ATTCAGAAAAAA-TATGAAAAACAATATTAAAGCGTGAAAAATCCTCCAATCTTTTTGCCATTCA
*
53082 GTTATATATATATATATATATTATATTTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTT
194 GTTAAATATATATATATATA-TATA-TTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTT
* *
53147 TCGAGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTACT---CATCACGATTTTTGGCTAAAA
257 TCGGGTAATTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGATTTTTGGCT-AAA
* *
53209 ACGTGTTTCGGGG-CTACGACTTT
321 ACGTGTTTCGGGGAC-AAGACTCT
* *
53232 GTTTTGCATGCTTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCACACC
1 GTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATC-CAAC
* *
53297 CACATTGGATTTAAGGATTTGTTTTTATGTGCATATGAATCTTGTTTCTATTTAATTAAAAATTA
65 CACATTGGATTTAAGGATTTGTTTTTATGTGCATATGAATTTTGTTTCTATTTAATTAGAAATTA
* *
53362 ATATCAGAAGAAATATG-AAAACAATATCAAAAGCGTGAAAAATCCTCCAA-CTTTTT
130 AT-TCAGAAAAAATATGAAAAACAATAT-TAAAGCGTGAAAAATCCTCCAATCTTTTT
53418 TGGCGTTGAA
Statistics
Matches: 763, Mismatches: 77, Indels: 67
0.84 0.08 0.07
Matches are distributed among these distances:
331 56 0.07
332 27 0.04
333 27 0.04
334 49 0.06
335 2 0.00
344 17 0.02
345 177 0.23
346 28 0.04
347 3 0.00
348 71 0.09
349 224 0.29
350 79 0.10
351 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (343 bp):
GTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCCAACC
ACATTGGATTTAAGGATTTGTTTTTATGTGCATATGAATTTTGTTTCTATTTAATTAGAAATTAA
TTCAGAAAAAATATGAAAAACAATATTAAAGCGTGAAAAATCCTCCAATCTTTTTGCCATTCAGT
TAAATATATATATATATATATATTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTTTCGG
GTAATTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAACGTG
TTTCGGGGACAAGACTCT
Found at i:55039 original size:29 final size:30
Alignment explanation
Indices: 54997--55072 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 30
54987 TTTATATAAC
* * *
54997 GTTTAGTACTAAATTGGACGAAATA-AAAG
1 GTTTGGTACCAAATTGGACGAAACATAAAG
** **
55026 GTTTGGTACCAAATTACTATTAAACATAAAG
1 GTTTGGTACCAAATT-GGACGAAACATAAAG
55057 GTTTGGTACCAAATTG
1 GTTTGGTACCAAATTG
55073 AGATTTCAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 13 0.35
30 5 0.14
31 19 0.51
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (30 bp):
GTTTGGTACCAAATTGGACGAAACATAAAG
Found at i:55806 original size:335 final size:331
Alignment explanation
Indices: 55122--56515 Score: 2071
Period size: 335 Copynumber: 4.2 Consensus size: 331
55112 GAGTACACGA
* * * * *
55122 TTTTGGCTAAAAATATGTTTCGGGCCCACGACTCTATTTTGCATTATTTTTGGTGCCGAGACTCC
1 TTTTGGCTAAAAACATGTTTCGGG-CCACGACTCTCTTTTGCATGACTTTTGGCGCCGAGACTCC
* * *
55187 TTGAAATATCTTTGTTCATCTAATCAAATCCCAGCCACGTTGAATTTAAGAATTTGTTTTTATGT
65 TTGAAATATCTTTATTCATCTAATCAAATCCCAGCCACATTGGATTTAAGAATTTGTTTTTATGT
55252 GCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAAAAAATATGAAAAACAATATTAAAA
130 GCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAAAAAATATGAAAAACAATATTAAAA
* *
55317 GCGTGAAAAGTCTTTCAATCTTTTTGGCATTG-A-ATATATATATATATA-TA-GAGTATTTTAG
195 GCGTGAAAAGTCCTCCAATCTTTTTGGCATTGAATATATATATATATATATTATGAGTATTTTAG
* * * *
55378 CCAAAAATTGACGGAAAAATTTTCGGTTAATTTTTTGAAAAATTTTAGCCGAAATCGTGTACTCA
260 CCAAAAATTGACGGAAAAATTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTCA
55443 TCACAAT
325 TCACAAT
* * * *
55450 TTTTGGCTAAAAACGTGTTTCGAGGCCACAACTCTCTTTTGCATGACTTTTGGCACTGAGACTCC
1 TTTTGGCTAAAAACATGTTTCG-GGCCACGACTCTCTTTTGCATGACTTTTGGCGCCGAGACTCC
* * * *
55515 TTAAAATATCTTTATTCATCTAATCAAATCCCAGCCACATTGGACTTAAGGATTTATTTTTATGT
65 TTGAAATATCTTTATTCATCTAATCAAATCCCAGCCACATTGGATTTAAGAATTTGTTTTTATGT
*
55580 GCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAATAATATTAA
130 GCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTT--AAAAAATATGAAAAACAATATTAA
* *
55645 AAACGTGAAAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATATATATATTATGAGGATTT
193 AAGCGTGAAAAGTCCTCCAATCTTTTTGGCATTGAA-TATATATATATATATATTATGAGTATTT
*
55710 TAGTCAAAAATTGACGGAAAAATTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTAC
257 TAGCCAAAAATTGACGGAAAAATTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTAC
**
55775 TCATCATTAT
322 TCATCACAAT
* * * * * * *
55785 TTTTGGCTAAAAATATGTTTCGGGCCCCGGCTCTATTTTGTATGATTTTTGGCGCCGAGATTCCT
1 TTTTGGCTAAAAACATGTTTCGGGCCACGACTCTCTTTTGCATGACTTTTGGCGCCGAGACTCCT
* *
55850 TGAAATATCTTTATTCATCTAATCAAATCCCAACCACGTTGGATTTAAGAATTTGTTTTTATGTG
66 TGAAATATCTTTATTCATCTAATCAAATCCCAGCCACATTGGATTTAAGAATTTGTTTTTATGTG
55915 CATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAAAAAATATGAAAAACAATATTAAAAG
131 CATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAAAAAATATGAAAAACAATATTAAAAG
* *
55980 CGTGAAAAGTCCTTCAATATTTTTGGCATTGAATTATATATATATATATATTATGAGTATTTTAG
196 CGTGAAAAGTCCTCCAATCTTTTTGGCATTGAA-TATATATATATATATATTATGAGTATTTTAG
* *
56045 CCAAAAATTGACGGAAAAATTTTCGGTTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTCA
260 CCAAAAATTGACGGAAAAATTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTCA
*
56110 TCATAAT
325 TCACAAT
*
56117 TTTTGGCTAAAAACGTGTTTCGGGGCCACGACTCTCTTTTGCATGACTTTTGGCGCCGAGACTCC
1 TTTTGGCTAAAAACATGTTTC-GGGCCACGACTCTCTTTTGCATGACTTTTGGCGCCGAGACTCC
* **
56182 TTGAAATATCGTTATTCATCTAATCAAATCCCAGCCACATTGGATTTAAGTTTTTGTTTTTATGT
65 TTGAAATATCTTTATTCATCTAATCAAATCCCAGCCACATTGGATTTAAGAATTTGTTTTTATGT
* * *
56247 GCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTCAGAATAAATATGAAAAAGAACATTAA
130 GCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTA-AA-AAATATGAAAAACAATATTAA
* *
56312 AAGCGTGAAAAGTCATCCAATCTTTTTGACGA-TGAATATATATATATATATATATATGAGTATT
193 AAGCGTGAAAAGTCCTCCAATCTTTTTGGC-ATTGAATATATATATATATATAT-TATGAGTATT
* ** *
56376 TTAGCCAAAAATTGACGGAAAAATTTTCGAGTCATTTTTTGCAAAATTTTAGTAAAAATTGTGTA
256 TTAGCCAAAAATTGACGGAAAAATTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTA
* *
56441 CTTATCACGAT
321 CTCATCACAAT
* * * * *
56452 TTTTTGCTAAAAAGATATTTCGAGGCCACGACTCTCTTTTGCATGA-TATTTGGTGTCGAGACTC
1 TTTTGGCTAAAAACATGTTTCG-GGCCACGACTCTCTTTTGCATGACT-TTTGGCGCCGAGACTC
56516 TTCGAGAAAA
Statistics
Matches: 962, Mismatches: 89, Indels: 23
0.90 0.08 0.02
Matches are distributed among these distances:
328 150 0.16
329 2 0.00
330 54 0.06
331 1 0.00
332 174 0.18
333 151 0.16
334 154 0.16
335 275 0.29
336 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (331 bp):
TTTTGGCTAAAAACATGTTTCGGGCCACGACTCTCTTTTGCATGACTTTTGGCGCCGAGACTCCT
TGAAATATCTTTATTCATCTAATCAAATCCCAGCCACATTGGATTTAAGAATTTGTTTTTATGTG
CATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAAAAAATATGAAAAACAATATTAAAAG
CGTGAAAAGTCCTCCAATCTTTTTGGCATTGAATATATATATATATATATTATGAGTATTTTAGC
CAAAAATTGACGGAAAAATTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTCAT
CACAAT
Found at i:56421 original size:667 final size:662
Alignment explanation
Indices: 55117--56515 Score: 2273
Period size: 667 Copynumber: 2.1 Consensus size: 662
55107 GAGATGAGTA
* *
55117 CACGA-TTTTGGCTAAAAATATGTTTCGGGCCCACGACTCTATTTTGCATTATTTTTGGTGCCGA
1 CACGATTTTTGGCTAAAAATATGTTTCGGGCCC-CGACTCTATTTTGCATGATTTTTGGCGCCGA
* *
55181 GACTCCTTGAAATATCTTTGTTCATCTAATCAAATCCCAGCCACGTTGAATTTAAGAATTTGTTT
65 GACTCCTTGAAATATCTTTATTCATCTAATCAAATCCCAACCACGTTGAATTTAAGAATTTGTTT
55246 TTATGTGCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAAAAAATATGAAAAACAATA
130 TTATGTGCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAAAAAATATGAAAAACAATA
* *
55311 TTAAAAGCGTGAAAAGTCTTTCAATCTTTTTGGCATTGAATATATATATATATATAGAGTATTTT
195 TTAAAAGCGTGAAAAGTCCTTCAATATTTTTGGCATTGAATATATATATATATATAGAGTATTTT
55376 AGCCAAAAATTGACGGAAAAATTTTCGGTTAATTTTTTGAAAAATTTTAGCCGAAATCGTGTACT
260 AGCCAAAAATTGACGGAAAAATTTTCGGTTAATTTTTTGAAAAATTTTAGCCGAAATCGTGTACT
55441 CATCACAATTTTTGGCTAAAAACGTGTTTCGAGGCCACAACTCTCTTTTGCATGACTTTTGGCAC
325 CATCACAATTTTTGGCTAAAAACGTGTTTCGAGGCCACAACTCTCTTTTGCATGACTTTTGGCAC
* *
55506 TGAGACTCCTTAAAATATCTTTATTCATCTAATCAAATCCCAGCCACATTGGACTTAAGGATTTA
390 CGAGACTCCTTAAAATATCGTTATTCATCTAATCAAATCCCAGCCACATTGGACTTAAGGATTTA
*
55571 TTTTTATGTGCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAGAAAAAATATGAAAAA
455 TTTTTATGTGCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAA
* * * *
55636 TAATATTAAAAACGTGAAAAGTCCTCCAATCTTTTTGGCATTGAATTATATATATATATATATTA
520 GAACATTAAAAACGTGAAAAGTCATCCAATCTTTTTGACATTGAATTATATATATATATATATTA
* * *
55701 TGAGGATTTTAGTCAAAAATTGACGGAAAAATTTTCGGGTCATTTTTTGCAAAATTTTAGCCAAA
585 TGAGGATTTTAGCCAAAAATTGACGGAAAAATTTTCGAGTCATTTTTTGCAAAATTTTAGCAAAA
55766 ATCGTGTACTCAT
650 ATCGTGTACTCAT
** * *
55779 CATTATTTTTGGCTAAAAATATGTTTCGGGCCCCGGCTCTATTTTGTATGATTTTTGGCGCCGAG
1 CACGATTTTTGGCTAAAAATATGTTTCGGGCCCCGACTCTATTTTGCATGATTTTTGGCGCCGAG
* *
55844 ATTCCTTGAAATATCTTTATTCATCTAATCAAATCCCAACCACGTTGGATTTAAGAATTTGTTTT
66 ACTCCTTGAAATATCTTTATTCATCTAATCAAATCCCAACCACGTTGAATTTAAGAATTTGTTTT
55909 TATGTGCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAAAAAATATGAAAAACAATAT
131 TATGTGCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAAAAAATATGAAAAACAATAT
55974 TAAAAGCGTGAAAAGTCCTTCAATATTTTTGGCATTGAATTATATATATATATATATTATGAGTA
196 TAAAAGCGTGAAAAGTCCTTCAATATTTTTGGCATTG-A--ATATATATATATATA-TA-GAGTA
* *
56039 TTTTAGCCAAAAATTGACGGAAAAATTTTCGGTTCATTTTTTGCAAAATTTTAGCCGAAATCGTG
256 TTTTAGCCAAAAATTGACGGAAAAATTTTCGGTTAATTTTTTGAAAAATTTTAGCCGAAATCGTG
* * *
56104 TACTCATCATAATTTTTGGCTAAAAACGTGTTTCGGGGCCACGACTCTCTTTTGCATGACTTTTG
321 TACTCATCACAATTTTTGGCTAAAAACGTGTTTCGAGGCCACAACTCTCTTTTGCATGACTTTTG
* * * **
56169 GCGCCGAGACTCCTTGAAATATCGTTATTCATCTAATCAAATCCCAGCCACATTGGATTTAAGTT
386 GCACCGAGACTCCTTAAAATATCGTTATTCATCTAATCAAATCCCAGCCACATTGGACTTAAGGA
* *
56234 TTTGTTTTTATGTGCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTCAGAATAAATATGA
451 TTTATTTTTATGTGCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTCAGAAAAAATATGA
*
56299 AAAAGAACATTAAAAGCGTGAAAAGTCATCCAATCTTTTTGACGA-TGAA-TATATATATATATA
516 AAAAGAACATTAAAAACGTGAAAAGTCATCCAATCTTTTTGAC-ATTGAATTATATATATATATA
*
56362 TATATATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTTCGAGTCATTTTTTGCAAAATTTTA
580 TAT-TATGAGGATTTTAGCCAAAAATTGACGGAAAAATTTTCGAGTCATTTTTTGCAAAATTTTA
* * *
56427 GTAAAAATTGTGTACTTAT
644 GCAAAAATCGTGTACTCAT
* * * * * * * *
56446 CACGATTTTTTGCTAAAAAGATATTTCGAGGCCACGACTCTCTTTTGCATGATATTTGGTGTCGA
1 CACGATTTTTGGCTAAAAATATGTTTCG-GGCCCCGACTCTATTTTGCATGATTTTTGGCGCCGA
56511 GACTC
65 GACTC
56516 TTCGAGAAAA
Statistics
Matches: 676, Mismatches: 52, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
662 192 0.28
663 28 0.04
665 15 0.02
666 19 0.03
667 388 0.57
668 34 0.05
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (662 bp):
CACGATTTTTGGCTAAAAATATGTTTCGGGCCCCGACTCTATTTTGCATGATTTTTGGCGCCGAG
ACTCCTTGAAATATCTTTATTCATCTAATCAAATCCCAACCACGTTGAATTTAAGAATTTGTTTT
TATGTGCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTTAAAAAATATGAAAAACAATAT
TAAAAGCGTGAAAAGTCCTTCAATATTTTTGGCATTGAATATATATATATATATAGAGTATTTTA
GCCAAAAATTGACGGAAAAATTTTCGGTTAATTTTTTGAAAAATTTTAGCCGAAATCGTGTACTC
ATCACAATTTTTGGCTAAAAACGTGTTTCGAGGCCACAACTCTCTTTTGCATGACTTTTGGCACC
GAGACTCCTTAAAATATCGTTATTCATCTAATCAAATCCCAGCCACATTGGACTTAAGGATTTAT
TTTTATGTGCATATGAATCTTGTTTCTATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAAG
AACATTAAAAACGTGAAAAGTCATCCAATCTTTTTGACATTGAATTATATATATATATATATTAT
GAGGATTTTAGCCAAAAATTGACGGAAAAATTTTCGAGTCATTTTTTGCAAAATTTTAGCAAAAA
TCGTGTACTCAT
Found at i:57196 original size:18 final size:18
Alignment explanation
Indices: 57173--57208 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57163 TGTGATTAAC
*
57173 AGAAGATGATGATGATGA
1 AGAAGAAGATGATGATGA
*
57191 AGAAGAAGATGTTGATGA
1 AGAAGAAGATGATGATGA
57209 TGCTTGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (18 bp):
AGAAGAAGATGATGATGA
Found at i:61384 original size:101 final size:100
Alignment explanation
Indices: 61210--61406 Score: 304
Period size: 101 Copynumber: 2.0 Consensus size: 100
61200 TTTAGGCTTT
* * *
61210 TGGGTTACACTAACACGTATATGGGCTACCTGGTGGCGTTGCTAAAGCAGACAGGGCCCTGGTTC
1 TGGGTTACACCAACACGTATATGGGCTACATGGTGGCCTTGCTAAAGCAGACAGGGCCCTGGTTC
* *
61275 CTCTCCCAACAAGTGATATCAGAACTCGGTTGTAC
66 CTCTCCCAACAAATGATATCAAAACTCGGTTGTAC
* * *
61310 TGGGTTACACCAACATGTATATGGGCTACATGTTGGGCCTTGCTGAAGCAGACAGGGCCCTGGTT
1 TGGGTTACACCAACACGTATATGGGCTACATGGT-GGCCTTGCTAAAGCAGACAGGGCCCTGGTT
*
61375 CCTCTCCCAACAAATGGTATCAAAACTCGGTT
65 CCTCTCCCAACAAATGATATCAAAACTCGGTT
61407 AGACTAGGAC
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
100 30 0.34
101 57 0.66
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (100 bp):
TGGGTTACACCAACACGTATATGGGCTACATGGTGGCCTTGCTAAAGCAGACAGGGCCCTGGTTC
CTCTCCCAACAAATGATATCAAAACTCGGTTGTAC
Done.