Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011521.1 Corchorus capsularis cultivar CVL-1 contig11542, 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: 24805
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--71 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
72 CTTTTTTTTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2257 original size:59 final size:61
Alignment explanation
Indices: 2162--2277 Score: 157
Period size: 59 Copynumber: 1.9 Consensus size: 61
2152 TACTCTCATA
* *
2162 TTTTTGGAACTTTGTTGTTTCTGATACAAGTTAGACCATAATCA-AAATCAATTGTCATTTTC
1 TTTTTGGAAC-TTGTTGTTTCTAATACAAGTTAGACCATAA-AAGAAATCAATTGTCATTTTC
* *
2224 TTTTTGGAAC-T-TTGTTTCTAATATATGTTAGACCATAAAAGAAATCAATTGTCA
1 TTTTTGGAACTTGTTGTTTCTAATACAAGTTAGACCATAAAAGAAATCAATTGTCA
2278 CCACTTTTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 1 0.02
59 37 0.76
60 1 0.02
62 10 0.20
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (61 bp):
TTTTTGGAACTTGTTGTTTCTAATACAAGTTAGACCATAAAAGAAATCAATTGTCATTTTC
Found at i:3133 original size:2 final size:2
Alignment explanation
Indices: 3126--3150 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3116 TTTCTTTTCC
3126 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 A
3151 AAGAAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3609 original size:43 final size:43
Alignment explanation
Indices: 3541--3625 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
3531 CGGGTTACAA
**
3541 TGTGCTATACATTGCTTTTGCATATTATAATGTGCTTGATGGC
1 TGTGCTATACATTGCTTGCGCATATTATAATGTGCTTGATGGC
* *
3584 TGTGCTATGCATTGCTTGCGGATATTATAATGTGCTTGATGG
1 TGTGCTATACATTGCTTGCGCATATTATAATGTGCTTGATGG
3626 GGCTAAATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.42
Consensus pattern (43 bp):
TGTGCTATACATTGCTTGCGCATATTATAATGTGCTTGATGGC
Found at i:3870 original size:29 final size:28
Alignment explanation
Indices: 3816--3871 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
3806 ATGACGTGGG
*
3816 TTTTCTTTTTCTTTTCCTTTTTTTTCTGT
1 TTTTCTTTTTCTTTTCC-TTTCTTTCTGT
3845 TTTTCTTTTTCTCTTCTCC-TTCTTTCT
1 TTTTCTTTTTCT-TT-TCCTTTCTTTCT
3872 CAACCTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 19 0.79
30 2 0.08
31 3 0.12
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (28 bp):
TTTTCTTTTTCTTTTCCTTTCTTTCTGT
Found at i:5126 original size:52 final size:53
Alignment explanation
Indices: 5047--5156 Score: 186
Period size: 55 Copynumber: 2.1 Consensus size: 53
5037 GTGATTTATG
*
5047 TTTATAAAGGAATTTTTTT-TAATTTTTTTCCAAAAATCCACGTCATTTGGTC
1 TTTATAAAGGAATTTTTTTAAAATTTTTTTCCAAAAATCCACGTCATTTGGTC
5099 TTTATAAAGGAATTTTTTTAAAATTTTTTTTTCCAAAAATCCACGTCATTTGGTC
1 TTTATAAAGGAATTTTTTTAAAA--TTTTTTTCCAAAAATCCACGTCATTTGGTC
5154 TTT
1 TTT
5157 TAGCCACGTG
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
52 19 0.35
53 2 0.04
55 33 0.61
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (53 bp):
TTTATAAAGGAATTTTTTTAAAATTTTTTTCCAAAAATCCACGTCATTTGGTC
Found at i:5461 original size:17 final size:17
Alignment explanation
Indices: 5423--5455 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5413 CACCTTATCA
*
5423 AATTCTGATCATTATTC
1 AATTCTCATCATTATTC
5440 AATTCTCATCATTATT
1 AATTCTCATCATTATT
5456 AGATTCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.48
Consensus pattern (17 bp):
AATTCTCATCATTATTC
Found at i:8842 original size:142 final size:142
Alignment explanation
Indices: 8586--8869 Score: 568
Period size: 142 Copynumber: 2.0 Consensus size: 142
8576 AGGTCAGTGG
8586 TTCAAATGCTTTTGTTGTTACTGTTGTCTATGCTAGTACTGATAAAGATAGTAGGCATTTTTTAT
1 TTCAAATGCTTTTGTTGTTACTGTTGTCTATGCTAGTACTGATAAAGATAGTAGGCATTTTTTAT
8651 GGCGCTACCTTAAAGCTTTGGGTTCTAGTATTATTGCCTTGTTATGGATTGGAGACTTTAATGAA
66 GGCGCTACCTTAAAGCTTTGGGTTCTAGTATTATTGCCTTGTTATGGATTGGAGACTTTAATGAA
8716 GTTTTGAAATCT
131 GTTTTGAAATCT
8728 TTCAAATGCTTTTGTTGTTACTGTTGTCTATGCTAGTACTGATAAAGATAGTAGGCATTTTTTAT
1 TTCAAATGCTTTTGTTGTTACTGTTGTCTATGCTAGTACTGATAAAGATAGTAGGCATTTTTTAT
8793 GGCGCTACCTTAAAGCTTTGGGTTCTAGTATTATTGCCTTGTTATGGATTGGAGACTTTAATGAA
66 GGCGCTACCTTAAAGCTTTGGGTTCTAGTATTATTGCCTTGTTATGGATTGGAGACTTTAATGAA
8858 GTTTTGAAATCT
131 GTTTTGAAATCT
8870 GAGGACAAAC
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (142 bp):
TTCAAATGCTTTTGTTGTTACTGTTGTCTATGCTAGTACTGATAAAGATAGTAGGCATTTTTTAT
GGCGCTACCTTAAAGCTTTGGGTTCTAGTATTATTGCCTTGTTATGGATTGGAGACTTTAATGAA
GTTTTGAAATCT
Found at i:12932 original size:33 final size:33
Alignment explanation
Indices: 12843--12939 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 33
12833 GTGTTTTAAA
* * *
12843 TGTTGTTTGTGATGATACTAAACCTAATTTGAG
1 TGTTGTTTGTGATGAAACTAAATCTATTTTGAG
* * *
12876 TGTTTTTTGCGATGACACTAAATCTATTTT-AGG
1 TGTTGTTTGTGATGAAACTAAATCTATTTTGA-G
* *
12909 TGTTGTTTGTGATGAAACAAAATCTGTTTTG
1 TGTTGTTTGTGATGAAACTAAATCTATTTTG
12940 GTTGATCATA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
32 1 0.02
33 51 0.98
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGTGATGAAACTAAATCTATTTTGAG
Found at i:13372 original size:30 final size:30
Alignment explanation
Indices: 13336--13398 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
13326 TCTTCAAGGG
*
13336 GGAGGGAATGATGCGCCCAAGGA-TTATCAT
1 GGAGGGAATGATGC-ACCAAGGACTTATCAT
13366 GGAGGGAATGATGCACCAAGGACTTATCAT
1 GGAGGGAATGATGCACCAAGGACTTATCAT
13396 GGA
1 GGA
13399 CTTGAAGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.32, C:0.16, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCACCAAGGACTTATCAT
Found at i:13476 original size:9 final size:10
Alignment explanation
Indices: 13433--13479 Score: 57
Period size: 9 Copynumber: 5.1 Consensus size: 10
13423 GGAAAGCATG
*
13433 TGCATGG-GC
1 TGCATGGAGA
13442 TGCATGGAG-
1 TGCATGGAGA
13451 -GCATGGAGA
1 TGCATGGAGA
13460 TGCATGGAGA
1 TGCATGGAGA
13470 T-CATGGAGA
1 TGCATGGAGA
13479 T
1 T
13480 AACGATGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.23
9 16 0.46
10 11 0.31
ACGTcount: A:0.26, C:0.13, G:0.40, T:0.21
Consensus pattern (10 bp):
TGCATGGAGA
Done.