Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014128.1 Corchorus olitorius cultivar O-4 contig14161, 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: 14203
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:666 original size:332 final size:331
Alignment explanation
Indices: 171--1005 Score: 1218
Period size: 333 Copynumber: 2.5 Consensus size: 331
161 TATTTCTTGA
* * * * * ** * *
171 TAAAATACTCATAAAATATATA-ATTT-AACACCAAAAGGATTGGAGAACTTTTCACGCTTT-TA
1 TAAAATACTTATAAAAAATATATATTTCAACGCCAAAAAGATTGAAGGGCTTTTGACG-TTTCCA
* * * * *
233 ATATCGTTTTT-C-ATATTTTCCTGAATTAATTTCTAATAAAATCGGAATAAGATTCAGATGCTT
65 ATATCGTTTTTCCTATTTTTTCC-AAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG-TT
* * * *
296 -GTAAAAACAAATTCTTAAACCCTATGTGGTTGAGATTTGATTAGATGAATATGGATATCTCAAG
128 CGTAAAAACAAA-TCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAG
* *
360 GAGTCTTGGCGCCAAAAATCATGCAAAACTGAGACGGGGCCCCAGAAC-TTTTTTTAGCAAAAAA
192 GAGTCTTGGAGCAAAAAATCATGCAAAACTGAGACGGGGCCCCAGAACGTTTTTTTAGCAAAAAA
*
424 CTGTGATGGTTATTACACGATTTTGGCTAAAATTTTGTAAAAATTGATTAGAAAAATATTTCCTC
257 CTGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGATTAGAAAAATATTTCCTC
489 AATTTTAGGC
322 AATTTTAGGC
* *
499 TAAAATACTTATAAAAAATATATCTTTCAACGCCAAAAAGATTGAATGGCTTTTGACGTTTCCAA
1 TAAAATACTTATAAAAAATATATATTTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCCAA
* *
564 TATCGTTTTTCCTATTTTTTCCAAATTAATTTATAAATTAAATCTAAACAAGATTCAGATGTTCG
66 TATCGTTTTTCCTATTTTTTCCAAATTAATTTCT-AATTAAATCGAAACAAGATTCAGATGTTCG
** * **
629 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGACAAATATAGATATTTCAAGTT
130 TAAAAACAAAT-CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGA
* * *
694 GTCTTGGAGCAAAAAATCATGCAAAATTGAGCCGGGGCCCCAGAACGTTTTTTTAGCCAAAAACT
194 GTCTTGGAGCAAAAAATCATGCAAAACTGAGACGGGGCCCCAGAACGTTTTTTTAGCAAAAAACT
759 GTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGATTAGAAAAATATTTCCTCAA
259 GTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGATTAGAAAAATATTTCCTCAA
824 TTTTAGGC
324 TTTTAGGC
832 TAAAATACTTATAAAAAATATATATTTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCCAA
1 TAAAATACTTATAAAAAATATATATTTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCCAA
* *
897 TATCGTTTTTCCTATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
66 TATCGTTTTTCCTATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGTTCGT
* * *
962 AAAAA-AAATTTTAAATCCAATGTTGCTGAGATTTGGTTAGATGA
131 AAAAACAAATCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
1006 TGTAAAGTAT
Statistics
Matches: 454, Mismatches: 44, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
328 20 0.04
329 6 0.01
330 65 0.14
331 18 0.04
332 160 0.35
333 185 0.41
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (331 bp):
TAAAATACTTATAAAAAATATATATTTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCCAA
TATCGTTTTTCCTATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGTTCGT
AAAAACAAATCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGT
CTTGGAGCAAAAAATCATGCAAAACTGAGACGGGGCCCCAGAACGTTTTTTTAGCAAAAAACTGT
GATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGATTAGAAAAATATTTCCTCAATT
TTAGGC
Found at i:4085 original size:45 final size:44
Alignment explanation
Indices: 4035--4156 Score: 108
Period size: 42 Copynumber: 2.8 Consensus size: 44
4025 AACGCATGAA
*
4035 AATCAACCAACTAGTACAATCTGTAACGCCTGGAAATATTGTTAG
1 AATCAACCAACTAGTACAATCTGTAACGCCT-GAAATAATGTTAG
* * *
4080 AATCAACTAA-TCA-TAACAATTTGTAAAGCCT-AAA-AATGTTAG
1 AATCAACCAACT-AGT-ACAATCTGTAACGCCTGAAATAATGTTAG
* * ** *
4122 AATTAGCCAACCGGTATAATCTGTAACGCCTGAAA
1 AATCAACCAACTAGTACAATCTGTAACGCCTGAAA
4157 ATGTTAAAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
42 27 0.45
43 7 0.12
44 2 0.03
45 24 0.40
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (44 bp):
AATCAACCAACTAGTACAATCTGTAACGCCTGAAATAATGTTAG
Found at i:8998 original size:69 final size:69
Alignment explanation
Indices: 8887--9024 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
8877 GATCCTAAAA
8887 TTGGCTTGGAATGCATTCTATTACTTCATTTGGAAAGAACGCAATACAAAAGTGTTTAACAACAA
1 TTGGCTTGGAATGCATTCTATTACTTCATTTGGAAAGAACGCAATACAAAAGTGTTTAACAACAA
8952 GATG
66 GATG
*
8956 TTGGCTTGGAATGCATTCTGTTACTTCATTTGGAAAGAACGCAATACAAAAGTGTTTAACAACAA
1 TTGGCTTGGAATGCATTCTATTACTTCATTTGGAAAGAACGCAATACAAAAGTGTTTAACAACAA
9021 GATG
66 GATG
9025 CAAACTGTTA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (69 bp):
TTGGCTTGGAATGCATTCTATTACTTCATTTGGAAAGAACGCAATACAAAAGTGTTTAACAACAA
GATG
Found at i:9086 original size:38 final size:38
Alignment explanation
Indices: 9035--9109 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
9025 CAAACTGTTA
*
9035 ATCAATTTTTTCAAGTTTTATCTGATGTAATTAGATTG
1 ATCAACTTTTTCAAGTTTTATCTGATGTAATTAGATTG
9073 ATCAACTTTTTCAAGTTTTATCTGATGTAATTAGATT
1 ATCAACTTTTTCAAGTTTTATCTGATGTAATTAGATT
9110 TAGGTTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.49
Consensus pattern (38 bp):
ATCAACTTTTTCAAGTTTTATCTGATGTAATTAGATTG
Found at i:9456 original size:44 final size:42
Alignment explanation
Indices: 9406--9494 Score: 124
Period size: 44 Copynumber: 2.1 Consensus size: 42
9396 TAAGCACATC
*
9406 AGACATGGAATGATCCAACAAAACTTTGAATATATGATCAAAAG
1 AGACATGGAATGATCCAACAAAACTCTG-A-ATATGATCAAAAG
* * *
9450 AGACATGGAATTATCTAACAAGACTCTGAATATGATCAAAAG
1 AGACATGGAATGATCCAACAAAACTCTGAATATGATCAAAAG
9492 AGA
1 AGA
9495 AAGTCCCTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 16 0.39
43 1 0.02
44 24 0.59
ACGTcount: A:0.47, C:0.13, G:0.17, T:0.22
Consensus pattern (42 bp):
AGACATGGAATGATCCAACAAAACTCTGAATATGATCAAAAG
Found at i:9535 original size:32 final size:32
Alignment explanation
Indices: 9493--9558 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
9483 GATCAAAAGA
*
9493 GAAAGTCCCTGGTGGGAAGGTAGGGGTCAGAT
1 GAAAGACCCTGGTGGGAAGGTAGGGGTCAGAT
9525 GAAAGACCCTGGTGGGAAGGTAGGGGTCAGAT
1 GAAAGACCCTGGTGGGAAGGTAGGGGTCAGAT
9557 GA
1 GA
9559 TCTAATCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.44, T:0.17
Consensus pattern (32 bp):
GAAAGACCCTGGTGGGAAGGTAGGGGTCAGAT
Done.