Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001063.1 Corchorus olitorius cultivar O-4 contig01063, 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: 7477
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Found at i:4799 original size:45 final size:45
Alignment explanation
Indices: 4735--4823 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
4725 TACTAAAATA
*
4735 AAGGCATCCAATAATTTTGCACTGGTGGGCACTTGTCTTTAATTC
1 AAGGCATCCAATAATTTTGCACTGGTGGGCACTTGTCTTCAATTC
4780 AAGGCATCCAATAATTTTGCACTGGTGGGCACTTGTCTTCAATT
1 AAGGCATCCAATAATTTTGCACTGGTGGGCACTTGTCTTCAATT
4824 TTTCTTTTAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (45 bp):
AAGGCATCCAATAATTTTGCACTGGTGGGCACTTGTCTTCAATTC
Found at i:6046 original size:41 final size:43
Alignment explanation
Indices: 5967--6055 Score: 155
Period size: 41 Copynumber: 2.1 Consensus size: 43
5957 ATAATATTCA
5967 AATTAAGTATATTAAACAAATTACTAATAATTTCTCAAACTAAT
1 AATTAAGTATATTAAACAAA-TACTAATAATTTCTCAAACTAAT
6011 AATTAAGTATATTAAAC-AA-ACTAATAATTTCTCAAACTAAT
1 AATTAAGTATATTAAACAAATACTAATAATTTCTCAAACTAAT
6052 AATT
1 AATT
6056 TCTGCTAGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
41 26 0.58
43 2 0.04
44 17 0.38
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (43 bp):
AATTAAGTATATTAAACAAATACTAATAATTTCTCAAACTAAT
Found at i:6048 original size:16 final size:16
Alignment explanation
Indices: 6027--6058 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6017 GTATATTAAA
6027 CAAACTAATAATTTCT
1 CAAACTAATAATTTCT
6043 CAAACTAATAATTTCT
1 CAAACTAATAATTTCT
6059 GCTAGCTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
CAAACTAATAATTTCT
Found at i:6194 original size:93 final size:92
Alignment explanation
Indices: 6090--6271 Score: 294
Period size: 93 Copynumber: 2.0 Consensus size: 92
6080 TTTAACTATT
* * *
6090 GCTATCATATGATATTTGA-TTTCATTAATTTATATTATTATGGGGGCGGCAGGTTGTAATTTTC
1 GCTATCATATGATATTT-ACTTTCATTAATTTATATTATTATGGGGACGACAGGTTGAAATTTTC
*
6154 ACGTTCGGGTAATAAAATTAATATGCTAA
65 ACGTTC-GGTAATAAAATTAACATGCTAA
*
6183 GCTATCTTATGATATTTACTTTCATTAATTTATATTATTATGGGGACGACAGGTTGAAATTTTCA
1 GCTATCATATGATATTTACTTTCATTAATTTATATTATTATGGGGACGACAGGTTGAAATTTTCA
6248 CGTTCGGTAATAAAATTAACATGC
66 CGTTCGGTAATAAAATTAACATGC
6272 AGTTAGCATT
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
92 19 0.23
93 64 0.77
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.41
Consensus pattern (92 bp):
GCTATCATATGATATTTACTTTCATTAATTTATATTATTATGGGGACGACAGGTTGAAATTTTCA
CGTTCGGTAATAAAATTAACATGCTAA
Found at i:7350 original size:29 final size:28
Alignment explanation
Indices: 7313--7413 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 28
7303 CCAAAATGCT
7313 CAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGG-CCGATCTTTTAATTTGGC
* * * **
7342 CAAATAAGGGCCTAACGTTAATGAAAAT-GC
1 CAAATAAGGGCCGATC-TT--TTAATTTGGC
7372 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGG-CCGATCTTTTAATTTGGC
7402 CAAATAAGGGCC
1 CAAATAAGGGCC
7414 TAACGTTTGC
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
28 6 0.11
29 26 0.46
30 4 0.07
31 16 0.29
32 4 0.07
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (28 bp):
CAAATAAGGGCCGATCTTTTAATTTGGC
Found at i:7376 original size:60 final size:59
Alignment explanation
Indices: 7283--7444 Score: 245
Period size: 60 Copynumber: 2.7 Consensus size: 59
7273 CTAATTGCTA
* ** *
7283 AAATAAGGGCCCAACGTTTACCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACG-TTATGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCC
7343 AAATAAGGGCCTAACGTTAATGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACGTT-ATGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCC
7403 AAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCC
1 AAATAAGGGCCTAACGTTATG--AAAATGCTCAAATAAGGGCC
7445 TGGCATCAGT
Statistics
Matches: 95, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
58 2 0.02
59 2 0.02
60 91 0.96
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (59 bp):
AAATAAGGGCCTAACGTTATGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCC
Found at i:7445 original size:31 final size:29
Alignment explanation
Indices: 7278--7445 Score: 101
Period size: 31 Copynumber: 5.6 Consensus size: 29
7268 ATAGGCTAAT
* *
7278 TGCTAAAATAAGGGCCCAACGTTTACCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT--CAAAA
* * * **
7309 TGCTCAAATAAGGGTCCGATC-TTTTAATT
1 TGCTCAAATAAGGG-CCTAACGTTTCAAAA
*
7338 TGGC-CAAATAAGGGCCTAACGTTAATGAAAA
1 T-GCTCAAATAAGGGCCTAACGTT--TCAAAA
* * * **
7369 TGCTCAAATAAGGGCCCGATC-TTTTAATT
1 TGCTCAAATAAGGG-CCTAACGTTTCAAAA
7398 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTT--CAAAA
7429 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
7446 GGCATCAGTT
Statistics
Matches: 104, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 8 0.08
29 32 0.31
30 8 0.08
31 48 0.46
32 8 0.08
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (29 bp):
TGCTCAAATAAGGGCCTAACGTTTCAAAA
Done.