Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001446.1 Corchorus capsularis cultivar CVL-1 contig01446, 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: 5214
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3967 original size:29 final size:29
Alignment explanation
Indices: 3933--4034 Score: 93
Period size: 29 Copynumber: 3.4 Consensus size: 29
3923 GTTAATTGCT
3933 CAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTGATCTTTTAATTTGGC
* * * *
3962 CAAATAAAGGCCT-AACGTTATCGAAAATT--C
1 CAAATAAGGGCCTGATC-TT-T--TAATTTGGC
*
3992 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCTGATCTTTTAATTTGGC
4022 CAAATAAGGGCCT
1 CAAATAAGGGCCT
4035 AACGTTATTG
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
28 6 0.11
29 26 0.47
30 4 0.07
31 13 0.24
32 6 0.11
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:3997 original size:31 final size:31
Alignment explanation
Indices: 3962--4096 Score: 143
Period size: 31 Copynumber: 4.4 Consensus size: 31
3952 TTAATTTGGC
* *
3962 CAAATAAAGGCCTAACGTTATCGAAAATTCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * **
3993 CAAATAAGGGCCCGATC-TT-T-TAATTTGGC-
1 CAAATAAGGG-CCTAACGTTATCGAAAAT-GCT
*
4022 CAAATAAGGGCCTAACGTTATTGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
*
4053 CAAATAAGGGTCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
4084 CAAATAAGGGCCT
1 CAAATAAGGGCCT
4097 GGTTTCAGTT
Statistics
Matches: 83, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
28 4 0.05
29 15 0.18
30 5 0.06
31 55 0.66
32 4 0.05
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:4024 original size:60 final size:60
Alignment explanation
Indices: 3926--4062 Score: 229
Period size: 60 Copynumber: 2.3 Consensus size: 60
3916 AAATACGGTT
*
3926 AATTGCTCAAATAAGGGCCTGATCTTTTAATTTGGCCAAATAAAGGCCTAACGTTATCGAA
1 AATT-CTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAAGGCCTAACGTTATCGAA
* *
3987 AATTCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGGCCTAACGTTATTGAA
1 AATTCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAAGGCCTAACGTTATCGAA
*
4047 AATGCTCAAATAAGGG
1 AATTCTCAAATAAGGG
4063 TCTAACGTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
60 68 0.94
61 4 0.06
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (60 bp):
AATTCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAAGGCCTAACGTTATCGAA
Found at i:4158 original size:31 final size:31
Alignment explanation
Indices: 4123--4351 Score: 158
Period size: 31 Copynumber: 7.6 Consensus size: 31
4113 ACGTATGAGA
4123 TAGGCCCTTATTTGAGCATTTTGACAAACGT
1 TAGGCCCTTATTTGAGCATTTTGACAAACGT
**
4154 TAGGCCCTTATTTG-GCTAAATT--CAAA-GAT
1 TAGGCCCTTATTTGAGC-ATTTTGACAAACG-T
** *
4183 CGGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGACAAACGT
** *
4214 TAGGCCCTTATTTG-GCCAAATT-A-AAATAG-
1 TAGGCCCTTATTTGAG-CATTTTGACAAA-CGT
* * *
4243 CAGACCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGACAAACGT
** *
4274 TAGGCCCTTATTTG-GCCAAATT-A-AAATAG-
1 TAGGCCCTTATTTGAG-CATTTTGACAAA-CGT
* * * *
4303 CAGACCCTTATTTGAGCATTTTGGCAAGCGT
1 TAGGCCCTTATTTGAGCATTTTGACAAACGT
4334 TAGGCCCTTATTTGAGCA
1 TAGGCCCTTATTTGAGCA
4352 ATAAGTCTAT
Statistics
Matches: 147, Mismatches: 33, Indels: 36
0.68 0.15 0.17
Matches are distributed among these distances:
28 1 0.01
29 58 0.39
30 12 0.08
31 75 0.51
32 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (31 bp):
TAGGCCCTTATTTGAGCATTTTGACAAACGT
Found at i:4198 original size:60 final size:60
Alignment explanation
Indices: 4127--4347 Score: 370
Period size: 60 Copynumber: 3.7 Consensus size: 60
4117 ATGAGATAGG
* * * * * * *
4127 CCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCTAAATTCAAAGATCGGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAATAGCAGA
4187 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAATAGCAGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAATAGCAGA
4247 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAATAGCAGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAATAGCAGA
*
4307 CCCTTATTTGAGCATTTTGGCAAGCGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
4348 AGCAATAAGT
Statistics
Matches: 153, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 153 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAATAGCAGA
Found at i:4316 original size:29 final size:29
Alignment explanation
Indices: 4218--4316 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
4208 AAACGTTAGG
4218 CCCTTATTTGGCCAAATTAAAATAGCAGA
1 CCCTTATTTGGCCAAATTAAAATAGCAGA
** * * * *
4247 CCCTTATTTGAG-CATTTTGGCAAA-CGTTAGG
1 CCCTTATTTG-GCCAAATT--AAAATAG-CAGA
4278 CCCTTATTTGGCCAAATTAAAATAGCAGA
1 CCCTTATTTGGCCAAATTAAAATAGCAGA
4307 CCCTTATTTG
1 CCCTTATTTG
4317 AGCATTTTGG
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
29 29 0.56
30 4 0.08
31 19 0.37
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAATAGCAGA
Done.