Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024812.1 Corchorus olitorius cultivar O-4 contig24845, 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: 40743
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3078 original size:2 final size:2
Alignment explanation
Indices: 3071--3109 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3061 TACTCACAAA
3071 AT AT AT AT AT AT 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 AT AT AT A
3110 CTAAATAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5842 original size:25 final size:25
Alignment explanation
Indices: 5789--5842 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
5779 TTATTTAAGT
* *
5789 TTAAAATTTTCAATAAATTTTTCAG
1 TTAAAATTTTCAAGAAATTTTTCAC
5814 TTAAAA-TTTCAAGAATATTTCTTC-C
1 TTAAAATTTTCAAGAA-ATTT-TTCAC
5839 TTAA
1 TTAA
5843 TTCTCTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 8 0.32
25 14 0.56
26 3 0.12
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (25 bp):
TTAAAATTTTCAAGAAATTTTTCAC
Found at i:5930 original size:33 final size:33
Alignment explanation
Indices: 5888--5954 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
5878 TCAACTTTTG
*
5888 GAAAATTATTCAATACATTGTCAGTAAAGTTTA
1 GAAAATTATTCAATACACTGTCAGTAAAGTTTA
*
5921 GAAAATTATTCAATACACTGTCAGTGAAGTTTA
1 GAAAATTATTCAATACACTGTCAGTAAAGTTTA
5954 G
1 G
5955 CAGACTACGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (33 bp):
GAAAATTATTCAATACACTGTCAGTAAAGTTTA
Found at i:7323 original size:178 final size:178
Alignment explanation
Indices: 7006--7461 Score: 444
Period size: 178 Copynumber: 2.6 Consensus size: 178
6996 CCGAAATAAC
* * * * * * * * * **
7006 AAATTTTTCAGAAGAATTTTTGGTATTTGAAAAATCAAATTCAGATTTCGAGTCCTTCATGAAAG
1 AAATTTTT-GGAAGCATTTTTGATACTCGAAACATTAAATTCAGCTTTCGAATCCTAAATGAAAG
* * * ** * * * * * *
7071 TCGCAGATCATGGAACAACCTTTTGACAGGTACTTGAATCAGCTCAATTGGACATCTGGAGCAAA
65 TTGTAGATAATAAAACAACCTTTTAACAGGCACTTGAATCACCTCAATTAGACATATGAAGCAAA
* * * * *
7136 AATTATGTAATATTAAGTGGACCGTCCATTCTCGCTAACCGAAACAACT
130 AATTATGTAATATTAAGTGGAACGACCATTCCCACTAACCAAAACAACT
* * **
7185 AAATTTTTGGAAGCATTTTTTATACTCGAAACATTAAATTTAGCTTTCGAATCCTATCTGAAAGT
1 AAATTTTTGGAAGCATTTTTGATACTCGAAACATTAAATTCAGCTTTCGAATCCTAAATGAAAGT
* * * *
7250 TGTAGATAATAAAACAACCTTTTAAGAGGCAGTTGAATCACCTTAATTAGACATATGAAGCAACA
66 TGTAGATAATAAAACAACCTTTTAACAGGCACTTGAATCACCTCAATTAGACATATGAAGCAAAA
* * * *
7315 GTTATGTAATATTAAGTGGAACGACCATTCCCATTAACCAAAATAATT
131 ATTATGTAATATTAAGTGGAACGACCATTCCCACTAACCAAAACAACT
* * * * * * *
7363 AATTTTTTGGAAGTATTTTTGATACTTGAAACATTAAATTCAGTTTTTGAGTCTTAAATGAAAGT
1 AAATTTTTGGAAGCATTTTTGATACTCGAAACATTAAATTCAGCTTTCGAATCCTAAATGAAAGT
* ** * *
7428 TGTAGATTATGGAACAACCTTTTAATAGACACTT
66 TGTAGATAATAAAACAACCTTTTAACAGGCACTT
7462 AAATAATCTT
Statistics
Matches: 222, Mismatches: 55, Indels: 1
0.80 0.20 0.00
Matches are distributed among these distances:
178 214 0.96
179 8 0.04
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (178 bp):
AAATTTTTGGAAGCATTTTTGATACTCGAAACATTAAATTCAGCTTTCGAATCCTAAATGAAAGT
TGTAGATAATAAAACAACCTTTTAACAGGCACTTGAATCACCTCAATTAGACATATGAAGCAAAA
ATTATGTAATATTAAGTGGAACGACCATTCCCACTAACCAAAACAACT
Found at i:8009 original size:32 final size:33
Alignment explanation
Indices: 7964--8034 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
7954 ATAGACTAGG
*
7964 CCATGGTTCAGTCGGGACCGGATCACGAC-TGA
1 CCATGGTTCAGTCGCGACCGGATCACGACTTGA
* *
7996 CCATGG-TCTAGTCGCGACCGTATCGCGACTTGA
1 CCATGGTTC-AGTCGCGACCGGATCACGACTTGA
8029 CCATGG
1 CCATGG
8035 CCTGGTCGCG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 2 0.06
32 23 0.68
33 9 0.26
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.21
Consensus pattern (33 bp):
CCATGGTTCAGTCGCGACCGGATCACGACTTGA
Found at i:8043 original size:33 final size:32
Alignment explanation
Indices: 7973--8049 Score: 91
Period size: 33 Copynumber: 2.4 Consensus size: 32
7963 GCCATGGTTC
* *
7973 AGTCGGGACCGGATCACGACTGACCATGGTCT
1 AGTCGCGACCGGATCACGACTGACCATGGCCT
* *
8005 AGTCGCGACCGTATCGCGACTTGACCATGGCCT
1 AGTCGCGACCGGATCACGAC-TGACCATGGCCT
* *
8038 GGTCGCGTCCGG
1 AGTCGCGACCGG
8050 GCCATGGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 17 0.46
33 20 0.54
ACGTcount: A:0.17, C:0.31, G:0.32, T:0.19
Consensus pattern (32 bp):
AGTCGCGACCGGATCACGACTGACCATGGCCT
Found at i:13551 original size:13 final size:13
Alignment explanation
Indices: 13533--13557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13523 TTTTAAAATC
13533 ATAATAATAATAT
1 ATAATAATAATAT
13546 ATAATAATAATA
1 ATAATAATAATA
13558 AACTAAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAATAATAT
Found at i:19579 original size:25 final size:24
Alignment explanation
Indices: 19528--19584 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
19518 GCCAGTCTTG
*
19528 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
19551 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
19576 AATTTATTT
1 AATTTATTT
19585 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:30404 original size:89 final size:89
Alignment explanation
Indices: 30299--30464 Score: 255
Period size: 89 Copynumber: 1.9 Consensus size: 89
30289 TTATTTAAAG
*
30299 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTAT-TTAATTAAGTCTAATATCCTTATAAC
1 TTTTATAGTTTTACTCAACTAAAAACTCTA-TTTTTATCTT-ATTAAATCTAATATCCTTATAAC
30363 TA-TTTTATTTTTAGTAGTTTACTAT
64 TATTTTTATTTTTAGTAGTTTACTAT
* ** *
30388 TTTTATAGTTTTACTCAATTAAAAACTCTATTTTTATCTTATTAAATCTAATATTTTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATCTTATTAAATCTAATATCCTTATAACTA
30453 TTTTTATTTTTA
66 TTTTTATTTTTA
30465 CCATTTTACT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
88 28 0.40
89 42 0.60
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.55
Consensus pattern (89 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATCTTATTAAATCTAATATCCTTATAACTA
TTTTTATTTTTAGTAGTTTACTAT
Found at i:35422 original size:39 final size:39
Alignment explanation
Indices: 35368--35447 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
35358 CTCTCTTTAG
35368 TTTATTTGAATTGCACATTTTTCAACTTGGTATTTCACT
1 TTTATTTGAATTGCACATTTTTCAACTTGGTATTTCACT
35407 TTTATTTGAATTGCACATTTTTCAACTTGGTATTTCACT
1 TTTATTTGAATTGCACATTTTTCAACTTGGTATTTCACT
35446 TT
1 TT
35448 ATGCAGTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (39 bp):
TTTATTTGAATTGCACATTTTTCAACTTGGTATTTCACT
Done.