Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020820.1 Corchorus olitorius cultivar O-4 contig20853, 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: 29886
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:871 original size:333 final size:331
Alignment explanation
Indices: 266--1581 Score: 1699
Period size: 333 Copynumber: 4.0 Consensus size: 331
256 TTTTCCAACC
* * *
266 ATCACGGTTTCTAGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTCGTATGATTTTTGACACC
1 ATCACGGTTTCTAGCTGAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTTGACGCC
* * *
331 GAGACTCCTTGTAATATCTATTTTCATCTAATCATGTCTTAGCCACATTGGATTTAAGAATATGT
65 GAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTTAGCCACATTGGATTTAAGGATATGT
* *
396 TTTTACGAGCTTCTGAATCTTGTTTCTATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAAA
130 TTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAA
* * * *
461 CCACATGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCATTGAATTATAAATTTTTTATGAGTA
195 CCATATGTGAAGCATGAAAAGCCCTTAAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTA
* * * *
526 CTGTGGCCAAAAATTGAGGAAAAATTTTCCGTTTCAGTTTTTGCAAAATTTTAGCTGAAATCGTG
260 CTGTGACCAAAAATTGAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTG
591 TAC-TAA
325 TACGTAA
** * * * * * *
597 CCATCATAGTTTCTGGCTGAAAACGCGTTCCGGGATCCCGGCTAAGTTTTACAGGATTTTTGGCG
1 --ATCACGGTTTCTAGCTGAAAACGCGTTCCGGG-CCCCGGCTCAGTTTTGCATGATTTTTGACG
* *
662 CCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTTATCCACATTGGACTTAAGGATAT
63 CCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTTAGCCACATTGGATTTAAGGATAT
** * *
727 GTTTTTATTAGCTTCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAATAAATAGGAAA
128 GTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAA
792 AACCATATGTGAAGCATGAAAAGCCCTTAAATATTTTTGGCGTTGAATTATA-ATTTTTTTATGA
193 AACCATATGTGAAGCATGAAAAGCCCTTAAATATTTTTGGCGTTGAATTATATA-TTTTTTATGA
* * **
856 GTACTGTGACCAAAAACTGAGGAAAAATTTTTCGCTTCAGTAATTGCAAAATTTTAGCCGAAATC
257 GTACTGTGACCAAAAATTGAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATC
921 GTGTACGT--
322 GTGTACGTAA
* * * * *
929 -T-ACGGTTTCTGGCTGAAAACACGTTCCGGGGCACCGACTCTGTTTTGCATGATTTTTG--GCA
1 ATCACGGTTTCTAGCTGAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTTGACGC-
* * * *
990 CGGGACTCTTTGTAATATCTATATTCATCTAATCAAGTCTTAGCCACGTTGGATTTAAGGATATT
64 CGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTTAGCCACATTGGATTTAAGGATATG
* *
1055 TTTTTACTAGCTTCTGAATCTTGTTTCGATTTAATCAAAAATTAATTTGG-AAAAAATAGGAAAA
129 TTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAA
* * * *
1119 ACCATATGTGAAGTATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATAATATATTTTTTATGAGT
194 ACCATATGTGAAGCATGAAAAGCCCTTAAATATTTTTGGCGTTGAATTATATATTTTTTATGAGT
** * *
1184 ACTGTGGTCAAAAATTGAGGAAAAATTTTTCGGTTCAGTTTTTGCAAGATTTTAGCCGAAATCGT
259 ACTGTGACCAAAAATTGAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGT
*
1249 GTACGTTA
324 GTACGTAA
* *
1257 ATCACGGTTTCTATCTGAAAACGCGTTCCGGGCCCCGGCTCAGTTTTTCATGATTTTTGACGCCG
1 ATCACGGTTTCTAGCTGAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGACGCCG
* * * * *
1322 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACGTTGGATTTAAGGATATGCT
66 AGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTTAGCCACATTGGATTTAAGGATATGTT
* * * * *
1387 GTTGCGAGCATCTGAATC----TTC-TTTTAATCAGAAATTAATTTGGAAAAAAAAGAAGGAAAA
131 TTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGG-AAAAAAA-TAGGAAAA
* * * *** * *
1447 CCCATATTTGAAGCATGAAAAACCCTTAAATATTTTTTTATGTTGAATTATATATTTTATGTGAG
194 ACCATATGTGAAGCATGAAAAGCCCTTAAATA-TTTTTGGCGTTGAATTATATATTTTTTATGAG
* * * * * * *
1512 TATTGTCACAAAAAATTAAGGATAAAA-TTTTCGAGTCAGTTTTTGCAAAATTTTAACTGAAATC
258 TACTGTGACCAAAAATTGAGGA-AAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATC
1576 GTGTAC
322 GTGTAC
1582 TTGTATATTT
Statistics
Matches: 861, Mismatches: 105, Indels: 38
0.86 0.10 0.04
Matches are distributed among these distances:
325 20 0.02
326 141 0.16
327 113 0.13
328 77 0.09
329 112 0.13
330 101 0.12
331 2 0.00
332 4 0.00
333 290 0.34
334 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (331 bp):
ATCACGGTTTCTAGCTGAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGACGCCG
AGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTTAGCCACATTGGATTTAAGGATATGTT
TTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAAAAAATAGGAAAAAC
CATATGTGAAGCATGAAAAGCCCTTAAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTAC
TGTGACCAAAAATTGAGGAAAAATTTTTCGATTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGT
ACGTAA
Found at i:9897 original size:21 final size:21
Alignment explanation
Indices: 9845--9898 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
9835 AAATGGCTTC
* *
9845 CCATGATCATCACCACCATGA
1 CCATGATCATGACCACCATCA
*
9866 CCATGAACATGACCACCATCA
1 CCATGATCATGACCACCATCA
*
9887 CCATCATCATGA
1 CCATGATCATGA
9899 TCATGACCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.37, G:0.09, T:0.19
Consensus pattern (21 bp):
CCATGATCATGACCACCATCA
Found at i:13739 original size:23 final size:23
Alignment explanation
Indices: 13696--13741 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
13686 GGAGAGATAT
* *
13696 GCTTCCACGTTGTTGTAACTACA
1 GCTTCCACATTGTTGCAACTACA
*
13719 GCTTCCACATTGTTGCCACTACA
1 GCTTCCACATTGTTGCAACTACA
13742 AAACTGCAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (23 bp):
GCTTCCACATTGTTGCAACTACA
Found at i:17061 original size:7 final size:7
Alignment explanation
Indices: 17044--17077 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
17034 AGTATGATCT
17044 TATACAGA
1 TATA-AGA
17052 TATAAGA
1 TATAAGA
17059 TATAAGA
1 TATAAGA
17066 TATAAGA
1 TATAAGA
17073 TATAA
1 TATAA
17078 TGTATTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (7 bp):
TATAAGA
Found at i:29866 original size:2 final size:2
Alignment explanation
Indices: 29855--29886 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29845 ATTATATTCA
29855 AT AT -T 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 A
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.