Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010122.1 Corchorus olitorius cultivar O-4 contig10154, 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: 13548
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Found at i:955 original size:437 final size:439
Alignment explanation
Indices: 136--987 Score: 1546
Period size: 437 Copynumber: 1.9 Consensus size: 439
126 ACTTTTATTT
*
136 CCCAAAGTTACCCATCTTTCTAGCGGCTATTCGGATCACTGCCCTATTTTGATTAATTTAATTTA
1 CCCAAAGTTACCCATCTTTCTAGCGGCCATTCGGATCACTGCCCTATTTTG---AATTTAATTTA
*
201 GACGCTGCTGGTCAAGTGAAGGGGGACAAACCATTTAGATTTCAAAAGATGTGGTTTCAACACCC
63 GACGCTGCTGGTCAAGTGAAGGCGGACAAACCATTTAGATTTCAAAAGATGTGGTTTCAACACCC
* **
266 AGATTTCTGTCTCTAATTCATAATAACTGGATGAATAGTGCTAACTCCTTTAATTAGGCCCTTGC
128 AGATTTCTGTCTCTAATTCATAATAACTGGATGAATAATGCTAACTCCTTTAACCAGGCCCTTGC
331 TAGACTTAGTGACTGTCTCACAATTTGGAATAAGGAGGAGTTTGGTAATGTTTTTAGGAGAAAGA
193 TAGACTTAGTGACTGTCTCACAATTTGGAATAAGGAGGAGTTTGGTAATGTTTTTAGGAGAAAGA
396 AGAGGGTTTTAGCCGGATTGGCTGGAGTGGATAAAGCTTTATGCTCGAGCCCCTCCCAATTCTTA
258 AGAGGGTTTTAGCCGGATTGGCTGGAGTGGATAAAGCTTTATGCTCGAGCCCCTCCCAATTCTTA
461 ATTGTCCTTCAAAAGAGTTTAAATATGGAATGTAAGGGTATTTTGAAGGAAGAAGAGGATCTGTG
323 ATTGTCCTTCAAAAGAGTTTAAATATGGAATGTAAGGGTATTTTGAAGGAAGAAGAGGATCTGTG
526 GGCACTCAAGTCCAGAGTGGACTGGACTGCCCTACATTCCATCTAGCGGCCA
388 GGCACTCAAGTCCAGAGTGGACTGGACTGCCCTACATTCCATCTAGCGGCCA
578 CCCAAAGTTACCCATCTTTCTAGCGGCCATTCGGATCACTGCCCTATTTTG-A-TTAATTTAGAC
1 CCCAAAGTTACCCATCTTTCTAGCGGCCATTCGGATCACTGCCCTATTTTGAATTTAATTTAGAC
*
641 GCTGCTGGTCAAGTGAAGGCGGACAAACCATTTAGATTTCAAAAGATGTGGTTTCAGCACCCAGA
66 GCTGCTGGTCAAGTGAAGGCGGACAAACCATTTAGATTTCAAAAGATGTGGTTTCAACACCCAGA
*
706 TTTCTGTCTCTAATTCGTAATAACTGGATGAATAATGCTAACTCCTTTAACCAGGCCCTTGCTAG
131 TTTCTGTCTCTAATTCATAATAACTGGATGAATAATGCTAACTCCTTTAACCAGGCCCTTGCTAG
*
771 ACTTAGTGACTGTCTCACAATTTGGAATAAGGAGGAGTTTGGTAATGTTTTTAGGAGGAAGAAGA
196 ACTTAGTGACTGTCTCACAATTTGGAATAAGGAGGAGTTTGGTAATGTTTTTAGGAGAAAGAAGA
*
836 GGGTTTTAGTCGGATTGGCTGGAGTGGATAAAGCTTTATGCTCGAGCCCCTCCCAATTCTTAATT
261 GGGTTTTAGCCGGATTGGCTGGAGTGGATAAAGCTTTATGCTCGAGCCCCTCCCAATTCTTAATT
* **
901 GTCCTTCAAAAGAGTTTAAATATGGAATGTAAGGGTATTTTGAAGGAAGAAGAGGATGTGTGGTT
326 GTCCTTCAAAAGAGTTTAAATATGGAATGTAAGGGTATTTTGAAGGAAGAAGAGGATCTGTGGGC
*
966 ACTCAAGTCCATAGTGGACTGG
391 ACTCAAGTCCAGAGTGGACTGG
988 CTTCTAGAAG
Statistics
Matches: 397, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
437 346 0.87
438 1 0.00
442 50 0.13
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (439 bp):
CCCAAAGTTACCCATCTTTCTAGCGGCCATTCGGATCACTGCCCTATTTTGAATTTAATTTAGAC
GCTGCTGGTCAAGTGAAGGCGGACAAACCATTTAGATTTCAAAAGATGTGGTTTCAACACCCAGA
TTTCTGTCTCTAATTCATAATAACTGGATGAATAATGCTAACTCCTTTAACCAGGCCCTTGCTAG
ACTTAGTGACTGTCTCACAATTTGGAATAAGGAGGAGTTTGGTAATGTTTTTAGGAGAAAGAAGA
GGGTTTTAGCCGGATTGGCTGGAGTGGATAAAGCTTTATGCTCGAGCCCCTCCCAATTCTTAATT
GTCCTTCAAAAGAGTTTAAATATGGAATGTAAGGGTATTTTGAAGGAAGAAGAGGATCTGTGGGC
ACTCAAGTCCAGAGTGGACTGGACTGCCCTACATTCCATCTAGCGGCCA
Found at i:1682 original size:22 final size:22
Alignment explanation
Indices: 1644--1688 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1634 AGTATTTTAG
*
1644 TAAAAAATTAGATTAATTATAA
1 TAAAAAATTAGATTAATCATAA
*
1666 TAAAAAATGTATA-TAATCATAA
1 TAAAAAAT-TAGATTAATCATAA
1688 T
1 T
1689 GTATTGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (22 bp):
TAAAAAATTAGATTAATCATAA
Found at i:1918 original size:30 final size:31
Alignment explanation
Indices: 1884--1941 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1874 ACAGTAAGGT
*
1884 TCCGGT-TCCAAATGGGCGG-TACGGTTTCGG
1 TCCGGTCT-CAAATAGGCGGTTACGGTTTCGG
*
1914 TCCGGTCTCGAATAGGCGGTTACGGTTT
1 TCCGGTCTCAAATAGGCGGTTACGGTTT
1942 GGTTCCACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.14, C:0.22, G:0.34, T:0.29
Consensus pattern (31 bp):
TCCGGTCTCAAATAGGCGGTTACGGTTTCGG
Found at i:4306 original size:19 final size:18
Alignment explanation
Indices: 4269--4308 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
4259 CTCTTGAGAT
*
4269 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
4287 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
4306 AAT
1 AAT
4309 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Done.