Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022200.1 Corchorus olitorius cultivar O-4 contig22233, 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: 24801
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:415 original size:27 final size:27
Alignment explanation
Indices: 380--454 Score: 141
Period size: 27 Copynumber: 2.8 Consensus size: 27
370 TGTGAACTTA
380 AAAAATGACCAAAATGCCCCTGAATGC
1 AAAAATGACCAAAATGCCCCTGAATGC
*
407 AAAAATGACCAAAATGCCCCTGAATGT
1 AAAAATGACCAAAATGCCCCTGAATGC
434 AAAAATGACCAAAATGCCCCT
1 AAAAATGACCAAAATGCCCCT
455 AGGTGATCCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.45, C:0.25, G:0.13, T:0.16
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGAATGC
Found at i:10878 original size:74 final size:73
Alignment explanation
Indices: 10747--10897 Score: 198
Period size: 74 Copynumber: 2.1 Consensus size: 73
10737 CAATTTAGAA
* *
10747 ATATGTTTTAAAAAAAAGCTACAATCGGAAAACGTAAAGTTTCCCATTATTCGTGCTTTTATAGT
1 ATATGTTTTAAAAAAAAGCTACAATCGGAAAAAGTAAAATTTCCCATTATTCGTGCTTTTATAGT
*
10812 TAGTTTAG
66 TAGTATAG
* * * *
10820 ATATGTTTTCTAAAAAAAGGGTACAATC-GAAAAAGATAAAATTTCTCA-TATTCTTGCTTTTAT
1 ATATG-TTT-TAAAAAAAAGCTACAATCGGAAAAAG-TAAAATTTCCCATTATTCGTGCTTTTAT
10883 AGTTAGTATAG
63 AGTTAGTATAG
10894 ATAT
1 ATAT
10898 AGATAATCGA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
73 5 0.07
74 37 0.54
75 26 0.38
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (73 bp):
ATATGTTTTAAAAAAAAGCTACAATCGGAAAAAGTAAAATTTCCCATTATTCGTGCTTTTATAGT
TAGTATAG
Found at i:14481 original size:21 final size:23
Alignment explanation
Indices: 14440--14610 Score: 78
Period size: 22 Copynumber: 7.8 Consensus size: 23
14430 AAATGTGACA
* *
14440 GAAAGATTATCAAAA-ATCATAG
1 GAAAGTTTATCAAAATTTCATAG
*
14462 GAATG-TTA-CAAAATTTCATAG
1 GAAAGTTTATCAAAATTTCATAG
*
14483 GAAAGTTTATTAAAATTTCATA-
1 GAAAGTTTATCAAAATTTCATAG
** * *
14505 GTTAGGTTATCAAAGTTT-ATTATG
1 GAAAGTTTATCAAAATTTCA-TA-G
* *
14529 G--AGTTTATCACAATTTTATAG
1 GAAAGTTTATCAAAATTTCATAG
* *
14550 GTAA--TTATTAAAATTTCATATG
1 GAAAGTTTATCAAAATTTCATA-G
* * *
14572 G--TGGTTATCAAAATTTAATAG
1 GAAAGTTTATCAAAATTTCATAG
**
14593 GGTAG-TTATCAAAATTTC
1 GAAAGTTTATCAAAATTTC
14611 GTAAAAATAT
Statistics
Matches: 115, Mismatches: 20, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
20 5 0.04
21 31 0.27
22 64 0.56
23 14 0.12
24 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.39
Consensus pattern (23 bp):
GAAAGTTTATCAAAATTTCATAG
Found at i:14584 original size:22 final size:21
Alignment explanation
Indices: 14466--14610 Score: 87
Period size: 22 Copynumber: 6.7 Consensus size: 21
14456 TCATAGGAAT
*
14466 GTTA-CAAAATTTCATAGGAAAG
1 GTTATCAAAATTTCATAGG--TG
* * *
14488 TTTATTAAAATTTCATAGTTAG
1 GTTATCAAAATTTCATAGGT-G
* *
14510 GTTATCAAAGTTT-ATTATGGAG
1 GTTATCAAAATTTCA-TA-GGTG
* * * *
14532 TTTATCACAATTTTATAGGTA
1 GTTATCAAAATTTCATAGGTG
* *
14553 ATTATTAAAATTTCATATGGTG
1 GTTATCAAAATTTCATA-GGTG
* *
14575 GTTATCAAAATTTAATAGGGTA
1 GTTATCAAAATTTCATA-GGTG
14597 GTTATCAAAATTTC
1 GTTATCAAAATTTC
14611 GTAAAAATAT
Statistics
Matches: 92, Mismatches: 25, Indels: 12
0.71 0.19 0.09
Matches are distributed among these distances:
21 16 0.17
22 62 0.67
23 14 0.15
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.41
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGTG
Found at i:16495 original size:22 final size:22
Alignment explanation
Indices: 16467--16510 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
16457 TACTCTTGTT
16467 GCCTTAGATCTACGTTGAGCAC
1 GCCTTAGATCTACGTTGAGCAC
16489 GCCTTAGATCTACGTTGAGCAC
1 GCCTTAGATCTACGTTGAGCAC
16511 ATGGGCAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (22 bp):
GCCTTAGATCTACGTTGAGCAC
Found at i:19393 original size:41 final size:41
Alignment explanation
Indices: 19336--19417 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
19326 GAACCCGATC
19336 CAAAAAATAATGAGGAAAAATAAATCTTGTGAGAGTGAGAA
1 CAAAAAATAATGAGGAAAAATAAATCTTGTGAGAGTGAGAA
*
19377 CAAAAAATAATGAGGAAGAATAAATCTTGTGAGAGTGAGAA
1 CAAAAAATAATGAGGAAAAATAAATCTTGTGAGAGTGAGAA
19418 ATGTAAGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.52, C:0.05, G:0.23, T:0.20
Consensus pattern (41 bp):
CAAAAAATAATGAGGAAAAATAAATCTTGTGAGAGTGAGAA
Found at i:19502 original size:13 final size:13
Alignment explanation
Indices: 19484--19511 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19474 TATAGATCTC
19484 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
19497 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
19510 AA
1 AA
19512 CATCCTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (13 bp):
AAGAGGTGTGTTA
Found at i:23232 original size:29 final size:29
Alignment explanation
Indices: 23199--23436 Score: 228
Period size: 29 Copynumber: 8.1 Consensus size: 29
23189 TCGCACGCTC
* *
23199 AGGGGAATTTTGGTCATTTTTGCATATAT
1 AGGGGCATTTTGGTCATTTTTGCATATCT
* * *
23228 GGGGGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCT
* ***
23257 GGAGGGCATTTTGGTCATTTCCACATATCT
1 AG-GGGCATTTTGGTCATTTTTGCATATCT
* *
23287 AGGGGCATTCTGGTCATTTTCGCATA-CT
1 AGGGGCATTTTGGTCATTTTTGCATATCT
*
23315 CAGGGGCATTTTGGTCATTTTTGCACATCT
1 -AGGGGCATTTTGGTCATTTTTGCATATCT
* * *
23345 AGGAGCATTTTGGTCATTCTTGCATATCC
1 AGGGGCATTTTGGTCATTTTTGCATATCT
* * * *
23374 AGGGGCATTTCGGTCATCTTTACACATTCT
1 AGGGGCATTTTGGTCATTTTTGCATA-TCT
* *
23404 -GGGGCAGTTTGGTTATTTTTTGCATATTCT
1 AGGGGCATTTTGGTCA-TTTTTGCATA-TCT
23434 AGG
1 AGG
23437 TTCTCTTTGG
Statistics
Matches: 169, Mismatches: 34, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
28 2 0.01
29 127 0.75
30 38 0.22
31 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCATATCT
Done.