Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018193.1 Corchorus olitorius cultivar O-4 contig18226, 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: 11766
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:525 original size:154 final size:154
Alignment explanation
Indices: 1--2889 Score: 4621
Period size: 154 Copynumber: 18.8 Consensus size: 154
*** * *
1 TCGAAGACGATTTCAAAACATCACTAATGGTCCCCGATAGGCCCATAATAACAAGTGTTCCAAAT
1 TCGAAGACGA-TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
*
66 GAGTTAAAAACTTCACAGTTGGACTAATCTCACC-AAATGTAATTATAGTTAGGCCATAAACAAT
65 GAGCTAAAAACTTCACAG-TGGACTAATCTCACCAAAATG--ATTATAGTTAGGCCATAAACAAT
*
130 GGTAAAGAAAAGCATTGAGGTTTGCCAAA
127 GG-AAAGAAAAGCATTGAGGGTTGCCAAA
* *
159 TCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTTTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
224 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
289 A-AAAAGCATTGAGGGTTGCCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
* * * * *
312 TCGAAGACGATTCAAAATGGAACTAGTGGGTCCCGAGAGGCCTAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
*
377 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
*
442 CGAAAAGCATTGAGGGTTGCCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
466 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
*
531 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAGTGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
* * *
596 CGAAAGGCATTGAGGGTTGTCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
* *
620 TCGAAGACGATACAAAACGGAACTAATGGGCCCCGAGAGGCCCAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * *
685 AGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACATTGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
750 AGAAAAGCATTGAGGGTT-CCTAAA
131 AGAAAAGCATTGAGGGTTGCC-AAA
* * *
774 TCGAAGATGATTCAAAACGGAACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
*
839 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAGTGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
* *
904 CGAAAAGCATTGAGGGTTGTCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
*
928 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAGAGGCCCAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * *
993 AGCTATAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
*
1058 AGAAAAAGCATTGAGGGTTACCAAA
131 AG-AAAAGCATTGAGGGTTGCCAAA
** * *
1083 TCGAAGACGATTCAAAACGTCATTAATAGG----GATAGGCCCAAAAGT-ACAAGTGTTCCAAAT
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA-TAACAAGTGTTCCAAAT
*
1143 GAGCTAAAAACTTCAACAGTGGACTAATCTCACC-AAATGAATTATAGTTAGGCCATAAGCAATG
65 GAGCTAAAAACTTC-ACAGTGGACTAATCTCACCAAAATG-ATTATAGTTAGGCCATAAACAATG
1207 GAAA-AAAAGCAATTGAGGGTTTGCCAAA
128 GAAAGAAAAGC-ATTGAGGG-TTGCCAAA
*
1235 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAACTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * *
1300 AGCTAAAAACTTCACTGTGGACTAATCTCACCATAATAATTATAGTTAGGCCATAAACAATGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
*
1365 CGAAAAGCATTGAGGGTTGCCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
* * *
1389 TCGAAGACGATTCAAAACGGAACTAATGGG-CCCGAGAGGCACAAAATTACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * *
1453 AGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTATGCCATAAACAATGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
1518 AGAAAAGCATTGAGGGTTGCCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
* * * *
1542 TCGAAGACGATTCAAAACGGAACTAATGGTCCTCGAGAGGCCGAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * * *
1607 AGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATAGGTAGGCCATAAACATTGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
1672 AGAAAAGCATTGAGGGTTGCCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
* * *
1696 TCGAAGACGATTCAAAACGGAACTAATGGTCCTCGATAGGCCGAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
*
1761 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
*
1826 CGAAAAGCATTGAGGGTTGCCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
* ** * *
1850 TCGAAGACGATTCAAAACGGAACTAATGGTCCTAGATAGGCCGAAAATAACAAGTGTTCTAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
*
1915 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAGTGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
* *
1980 CGAAAAGCATTGAGGGTTGTCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
*
2004 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAGAGGCCCAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * *
2069 AGCTATAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
2134 AGAAAAGCATTGAGGGTTGCCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
* * *
2158 TCGAAGACGATTCAAAACGGAACTAATGGTCCTCGATAGGCCCAAAATAACAAGTGTTCGAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* *
2223 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACATTGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
*
2288 AGAAAAGCATTGAGGGTTGCCGAA
131 AGAAAAGCATTGAGGGTTGCCAAA
** *
2312 TCGAAGACGATTCAAAACGGAACTAATGGATCCCG--A-G-ACAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* *
2373 AGCTAAATACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACATTGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
*
2438 AGAAAAGCATTGAGGGTTACCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
** * * *
2462 TCGAAGACGATTCAAAACGTCATTAATAGG----GTTAGGCCCAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
2523 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
2588 A-AAAAGCATTGAGGGTTGCCAAA
131 AGAAAAGCATTGAGGGTTGCCAAA
2611 TCGAAGACGATTCAAAACGGAACTAATGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
1 TCGAAGACGATTCAAAACGGAACTAAT-GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
*
2676 GAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCATAAACAATGGA
65 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
2741 AAGAAAAGCATTGAGGGTTGCCAAA
130 AAGAAAAGCATTGAGGGTTGCCAAA
* *
2766 TCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * *
2831 AGCTAAAAACTTCACAGTGGACGAATCTTACCAAAGTGATTATAGTTAGGCCATAAACA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACA
2890 TTGATGCGCC
Statistics
Matches: 2549, Mismatches: 154, Indels: 60
0.92 0.06 0.02
Matches are distributed among these distances:
146 1 0.00
148 1 0.00
149 46 0.02
150 227 0.09
151 54 0.02
152 79 0.03
153 285 0.11
154 1538 0.60
155 173 0.07
156 65 0.03
157 70 0.03
158 10 0.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (154 bp):
TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
AGAAAAGCATTGAGGGTTGCCAAA
Found at i:11170 original size:2 final size:2
Alignment explanation
Indices: 11163--11198 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11153 GATTATGTAC
11163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11199 GTATGTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11203 original size:4 final size:4
Alignment explanation
Indices: 11196--11244 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
11186 TATATATATA
11196 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11244 T
1 T
11245 GTGTGTATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:11510 original size:5 final size:5
Alignment explanation
Indices: 11497--11535 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
11487 GGACTAGTAA
* * *
11497 GGGAC GGGAT GGGAC GGGAT GGGAC GGGAT GGGAT GGGA
1 GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGGA
11536 AGTCCTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.08, G:0.62, T:0.10
Consensus pattern (5 bp):
GGGAT
Found at i:11510 original size:10 final size:10
Alignment explanation
Indices: 11497--11535 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
11487 GGACTAGTAA
11497 GGGACGGGAT
1 GGGACGGGAT
11507 GGGACGGGAT
1 GGGACGGGAT
11517 GGGACGGGAT
1 GGGACGGGAT
*
11527 GGGATGGGA
1 GGGACGGGA
11536 AGTCCTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.21, C:0.08, G:0.62, T:0.10
Consensus pattern (10 bp):
GGGACGGGAT
Done.