Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016043.1 Corchorus capsularis cultivar CVL-1 contig16064, 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: 10209
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:587 original size:2 final size:2
Alignment explanation
Indices: 580--615 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
570 TCCGAAAAAC
580 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
616 GAGACAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:904 original size:27 final size:27
Alignment explanation
Indices: 868--928 Score: 104
Period size: 27 Copynumber: 2.2 Consensus size: 27
858 AACATAATAG
868 TCCCTCTGTTCCTTTTTAATTGTCCCTT
1 TCCCT-TGTTCCTTTTTAATTGTCCCTT
*
896 TCCCTTGTTCCTTTTTAATTGTCTCTT
1 TCCCTTGTTCCTTTTTAATTGTCCCTT
923 TCCCTT
1 TCCCTT
929 ATTTTCCAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.07, C:0.31, G:0.07, T:0.56
Consensus pattern (27 bp):
TCCCTTGTTCCTTTTTAATTGTCCCTT
Found at i:1125 original size:20 final size:20
Alignment explanation
Indices: 1100--1141 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1090 TAAATCAGTT
1100 AAAAGGGACAATTAAAAAGG
1 AAAAGGGACAATTAAAAAGG
1120 AAAAGGGACAATTAAAAAGG
1 AAAAGGGACAATTAAAAAGG
1140 AA
1 AA
1142 CAGAGGGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.24, T:0.10
Consensus pattern (20 bp):
AAAAGGGACAATTAAAAAGG
Found at i:3287 original size:9 final size:9
Alignment explanation
Indices: 3273--3306 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
3263 TATATATATG
3273 TGAAGAGAC
1 TGAAGAGAC
3282 TGAAGAGAC
1 TGAAGAGAC
3291 TGAAGAGA-
1 TGAAGAGAC
3299 -GAAGAGAC
1 TGAAGAGAC
3307 ACAATATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.29
9 17 0.71
ACGTcount: A:0.47, C:0.09, G:0.35, T:0.09
Consensus pattern (9 bp):
TGAAGAGAC
Found at i:3304 original size:16 final size:17
Alignment explanation
Indices: 3273--3306 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
3263 TATATATATG
3273 TGAAGAGACTGAAGAGAC
1 TGAAGAGAC-GAAGAGAC
3291 TGAAGAGA-GAAGAGAC
1 TGAAGAGACGAAGAGAC
3307 ACAATATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.47, C:0.09, G:0.35, T:0.09
Consensus pattern (17 bp):
TGAAGAGACGAAGAGAC
Found at i:6250 original size:7 final size:7
Alignment explanation
Indices: 6223--6274 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
6213 TTTTATTTGC
6223 TTATATA
1 TTATATA
*
6230 TATGTATA
1 T-TATATA
*
6238 TTATATT
1 TTATATA
6245 TTATATA
1 TTATATA
6252 TTATATA
1 TTATATA
*
6259 TTACTATT
1 TTA-TATA
6267 TTATATA
1 TTATATA
6274 T
1 T
6275 ATAGAGTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
7 25 0.68
8 12 0.32
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (7 bp):
TTATATA
Found at i:6251 original size:22 final size:23
Alignment explanation
Indices: 6223--6277 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 23
6213 TTTTATTTGC
*
6223 TTATATATATGTATATTA-TATT
1 TTATATATATATATATTACTATT
6245 TTATATAT-TATATATTACTATT
1 TTATATATATATATATTACTATT
6267 TTATATATATA
1 TTATATATATA
6278 GAGTAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 8 0.27
22 20 0.67
23 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATATATATATATATTACTATT
Found at i:7108 original size:52 final size:53
Alignment explanation
Indices: 7020--7124 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 53
7010 AGTATGAAAA
* * * *
7020 GGAAGTGGGGATAGTTTTTCCATAGAGTTTTACTACTTAACCTTCCAATTATT
1 GGAAGTGGAGATAGTTTTTCCATAAAGCTTTACTACTTAACCCTCCAATTATT
* * *
7073 GGAAGTGGAGATTG-TTTTCCATAAAGCTTTGCTACTTAACCCTCTAATTATT
1 GGAAGTGGAGATAGTTTTTCCATAAAGCTTTACTACTTAACCCTCCAATTATT
7125 TGACTCTCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 33 0.73
53 12 0.27
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (53 bp):
GGAAGTGGAGATAGTTTTTCCATAAAGCTTTACTACTTAACCCTCCAATTATT
Found at i:7382 original size:22 final size:22
Alignment explanation
Indices: 7357--7400 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
7347 AATCATTATT
*
7357 CTTTTCTTTACCAAAAACCAAA
1 CTTTTCTTCACCAAAAACCAAA
7379 CTTTTCTTCACCAAAAACCAAA
1 CTTTTCTTCACCAAAAACCAAA
7401 AGATTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.30
Consensus pattern (22 bp):
CTTTTCTTCACCAAAAACCAAA
Found at i:9442 original size:349 final size:355
Alignment explanation
Indices: 8740--9445 Score: 1034
Period size: 349 Copynumber: 2.0 Consensus size: 355
8730 TGTCCAAAAT
*
8740 TGAAGTTCGGGGGGCAAGTCCTCTAATTGGAATAAGTTCAGGGGGCAAAATGGACCTTTTGCCAA
1 TGAAGTTCGGGGGGCAAGTCCTCCAATTGGAATAAGTTCAGGGGGCAAAATGGACCTTTTGCCAA
*
8805 TAATACACTTTCTTTTTTGAGATACCAAATAATATAGGGGGAATTAATCATGACCTTATAGAAAA
66 TAATACACATTCTTTTTTGAGATACCAAATAATATAGGGGGAATTAATCATGACCTTATAGAAAA
* * *
8870 AAAGAAAATTTATTTTCTTAATTCATAATAAAGACACGTGGGTTTTTTTAGGTTTGGGTCGTGTT
131 AAAGAAAATTTATTTTCTTAATTCATAATAAAGACACCTGGGGTTTTTTACGTTTGGGTCGTGTT
* * *
8935 TTTAACTGCGTCAGTGTTTCGGAGTGTGACCCACTTAATCTGACGTGCCTATGCCATATGTGCGC
196 TTTAACCGCGTCAGTGTTTAGGAGTGGGACCCACTTAATCTGACGTGCCTATGCCATATGTGCGC
* * * * *
9000 CATGTCAGCACCGTAATGGTGTCGTTAGTCACGTGTGGTCATGTGACTAACGGTCCGTTACTGAG
261 CATGTCAACACCGCAACGGCGTCGTTAGTCACGTGTGGTCATGTGACTAACGGCCCGTTACTGAG
*
9065 GGGGCAACGCAAGCTTACATTGATAGTTCA
326 GGGGCAACGCAAGCTTAAATTGATAGTTCA
* * * * * **
9095 TGAAGTTTGGGGGG-AAGTCGTCCACTTGGTATAAGTTCAGGGGGCAGAATGGGTCTTTTGCCAA
1 TGAAGTTCGGGGGGCAAGTCCTCCAATTGGAATAAGTTCAGGGGGCAAAATGGACCTTTTGCCAA
*
9159 TAATATACATT-TTTTTT-AGATACCAAATAATATAGGGGGAATTAATCATGACCTTATAG-AAA
66 TAATACACATTCTTTTTTGAGATACCAAATAATATAGGGGGAATTAATCATGACCTTATAGAAAA
* * * *
9221 AATGAAATTTTATTTTCTTAATTCATAATAAAGAC-CCTGGGGTTTTTTACGTTTGTGTTG-GAT
131 AAAGAAAATTTATTTTCTTAATTCATAATAAAGACACCTGGGGTTTTTTACGTTTGGGTCGTG-T
* * * *
9284 TTTTAACCGGGTCAGTGTTTTAGG-GTGGGGCCCACTTAATCTGACGTGTCTATGCCATGTGTGC
195 TTTTAACCGCGTCAGTG-TTTAGGAGTGGGACCCACTTAATCTGACGTGCCTATGCCATATGTGC
*
9348 GCC-TGTCAACACCGCAACGGCGTCGTTAGTCACGTGTGGTCATGTGACTAATGGCCCGTTACTG
259 GCCATGTCAACACCGCAACGGCGTCGTTAGTCACGTGTGGTCATGTGACTAACGGCCCGTTACTG
*
9412 AGGGGGCAACAG-AGGCTTAAATTGATAGTTCA
324 AGGGGGCAAC-GCAAGCTTAAATTGATAGTTCA
9444 TG
1 TG
9446 GGGCAATTTG
Statistics
Matches: 316, Mismatches: 32, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
349 86 0.27
350 76 0.24
351 41 0.13
352 42 0.13
353 6 0.02
354 52 0.16
355 13 0.04
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (355 bp):
TGAAGTTCGGGGGGCAAGTCCTCCAATTGGAATAAGTTCAGGGGGCAAAATGGACCTTTTGCCAA
TAATACACATTCTTTTTTGAGATACCAAATAATATAGGGGGAATTAATCATGACCTTATAGAAAA
AAAGAAAATTTATTTTCTTAATTCATAATAAAGACACCTGGGGTTTTTTACGTTTGGGTCGTGTT
TTTAACCGCGTCAGTGTTTAGGAGTGGGACCCACTTAATCTGACGTGCCTATGCCATATGTGCGC
CATGTCAACACCGCAACGGCGTCGTTAGTCACGTGTGGTCATGTGACTAACGGCCCGTTACTGAG
GGGGCAACGCAAGCTTAAATTGATAGTTCA
Done.