Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014556.1 Corchorus capsularis cultivar CVL-1 contig14577, 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: 30773
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3886 original size:24 final size:25
Alignment explanation
Indices: 3839--3897 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
3829 TCTGAAAGAA
*
3839 AATAAAATAATAATAAATCATTTTT
1 AATAAAAAAATAATAAATCATTTTT
3864 AATAAAAAAATAA-AAAT-ATTTTTT
1 AATAAAAAAATAATAAATCA-TTTTT
*
3888 AATTAAAAAA
1 AATAAAAAAA
3898 CAATTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 1 0.03
24 18 0.58
25 12 0.39
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
AATAAAAAAATAATAAATCATTTTT
Found at i:13116 original size:1 final size:1
Alignment explanation
Indices: 13110--13135 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
13100 CAAACTACAT
13110 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
13136 GAATGACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30273 original size:31 final size:31
Alignment explanation
Indices: 30192--30397 Score: 105
Period size: 31 Copynumber: 6.8 Consensus size: 31
30182 AATCATGTTC
*
30192 TTATCGAAAATGCTCAAATAAGGGCTCGATC-
1 TTATCGAAAATGCTCAAATAAGGGC-CGAACG
* **
30223 TT-T-TAATTTGGC-CAAATAAGGGTCC-AACG
1 TTATCGAAAAT-GCTCAAATAAGGG-CCGAACG
*
30252 TTATCGAAAATGCTCAAATAAGGGCCCGATC-
1 TTATCGAAAATGCTCAAATAAGGG-CCGAACG
* ** * *
30283 TT-T-TAATTTGGC-CAAAAAAGGGCCTAACG
1 TTATCGAAAAT-GCTCAAATAAGGGCCGAACG
*
30312 TTATCGAAAATGCTCAAATAAGGGCCTGATC-
1 TTATCGAAAATGCTCAAATAAGGGCC-GAACG
* ** *
30343 TT-T-TAATTTGGC-CAAATAAGGGCCTAACG
1 TTATCGAAAAT-GCTCAAATAAGGGCCGAACG
**
30372 TTATCGAAAATATTCAAATAAGGGCC
1 TTATCGAAAATGCTCAAATAAGGGCC
30398 TGACATCAGT
Statistics
Matches: 126, Mismatches: 31, Indels: 36
0.65 0.16 0.19
Matches are distributed among these distances:
28 8 0.06
29 47 0.37
30 17 0.13
31 50 0.40
32 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (31 bp):
TTATCGAAAATGCTCAAATAAGGGCCGAACG
Found at i:30362 original size:29 final size:29
Alignment explanation
Indices: 30206--30367 Score: 102
Period size: 29 Copynumber: 5.4 Consensus size: 29
30196 CGAAAATGCT
30206 CAAATAAGGG-CTCGATCTTTTAATTTGGC
1 CAAATAAGGGCCT-GATCTTTTAATTTGGC
* * **
30235 CAAATAAGGGTCC--AACGTTATCGAAAAT-GC
1 CAAATAAGGG-CCTGATC-TT-T-TAATTTGGC
*
30265 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCTGATCTTTTAATTTGGC
* * * **
30295 CAAAAAAGGGCCT-AACGTTATCGAAAAT-GC
1 CAAATAAGGGCCTGATC-TT-T-TAATTTGGC
30325 TCAAATAAGGGCCTGATCTTTTAATTTGGC
1 -CAAATAAGGGCCTGATCTTTTAATTTGGC
30355 CAAATAAGGGCCT
1 CAAATAAGGGCCT
30368 AACGTTATCG
Statistics
Matches: 99, Mismatches: 19, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
28 4 0.04
29 44 0.44
30 14 0.14
31 33 0.33
32 4 0.04
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (29 bp):
CAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:30398 original size:31 final size:31
Alignment explanation
Indices: 30235--30398 Score: 112
Period size: 31 Copynumber: 5.4 Consensus size: 31
30225 TTAATTTGGC
30235 CAAATAAGGGTCC-AACGTTATCGAAAATGCT
1 CAAATAAGGG-CCTAACGTTATCGAAAATGCT
* * * **
30266 CAAATAAGGGCCCGATC-TT-T-TAATTTGGC-
1 CAAATAAGGG-CCTAACGTTATCGAAAAT-GCT
*
30295 CAAAAAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * **
30326 CAAATAAGGGCCTGATC-TT-T-TAATTTGGC-
1 CAAATAAGGGCCT-AACGTTATCGAAAAT-GCT
**
30355 CAAATAAGGGCCTAACGTTATCGAAAATATT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
30386 CAAATAAGGGCCT
1 CAAATAAGGGCCT
30399 GACATCAGTT
Statistics
Matches: 99, Mismatches: 22, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
28 6 0.06
29 32 0.32
30 10 0.10
31 47 0.47
32 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:30398 original size:60 final size:60
Alignment explanation
Indices: 30192--30400 Score: 350
Period size: 60 Copynumber: 3.5 Consensus size: 60
30182 AATCATGTTC
30192 TTATCGAAAATGCTCAAATAAGGG-CTCGATCTTTTAATTTGGCCAAATAAGGGTCC-AACG
1 TTATCGAAAATGCTCAAATAAGGGCCT-GATCTTTTAATTTGGCCAAATAAGGG-CCTAACG
* *
30252 TTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAAAAAGGGCCTAACG
1 TTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCCAAATAAGGGCCTAACG
30312 TTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCCAAATAAGGGCCTAACG
1 TTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCCAAATAAGGGCCTAACG
**
30372 TTATCGAAAATATTCAAATAAGGGCCTGA
1 TTATCGAAAATGCTCAAATAAGGGCCTGA
30401 CATCAGTTTG
Statistics
Matches: 141, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
59 2 0.01
60 138 0.98
61 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (60 bp):
TTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCCAAATAAGGGCCTAACG
Found at i:30531 original size:60 final size:60
Alignment explanation
Indices: 30435--30600 Score: 253
Period size: 60 Copynumber: 2.8 Consensus size: 60
30425 ATTTTCGACG
* * *
30435 CCAGGCCCTTATTTGAGTATTTTGGCAAACGTTAGGCCAC-TATTTGGCCAAATTAAAAGA
1 CCAGGCCCTTATTTGAGCATTTTGCCAAACGTTAGGCC-CTTATTTGGCCAAATCAAAAGA
* * * *
30495 TCGGGCCCTTATTTGAGCATTTTGTCAAATGTTAGGCCCTTATTTGGCCAAATCAAAAGA
1 CCAGGCCCTTATTTGAGCATTTTGCCAAACGTTAGGCCCTTATTTGGCCAAATCAAAAGA
30555 CCAGGCCCTTATTTGAGCATTTTGCCAAACGTTAGGCCCTTATTTG
1 CCAGGCCCTTATTTGAGCATTTTGCCAAACGTTAGGCCCTTATTTG
30601 AGCAATTAAC
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 1 0.01
60 94 0.99
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (60 bp):
CCAGGCCCTTATTTGAGCATTTTGCCAAACGTTAGGCCCTTATTTGGCCAAATCAAAAGA
Found at i:30534 original size:31 final size:31
Alignment explanation
Indices: 30498--30604 Score: 105
Period size: 31 Copynumber: 3.5 Consensus size: 31
30488 TAAAAGATCG
*
30498 GGCCCTTATTTGAGCATTTTGTCAAATGTTA
1 GGCCCTTATTTGAGCATTTTGTCAAAAGTTA
** **
30529 GGCCCTTATTTG-GCCA---AATCAAAAGACCA
1 GGCCCTTATTTGAG-CATTTTGTCAAAAG-TTA
* *
30558 GGCCCTTATTTGAGCATTTTGCCAAACGTTA
1 GGCCCTTATTTGAGCATTTTGTCAAAAGTTA
30589 GGCCCTTATTTGAGCA
1 GGCCCTTATTTGAGCA
30605 ATTAACAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 6 0.10
29 15 0.25
30 2 0.03
31 31 0.53
32 5 0.08
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (31 bp):
GGCCCTTATTTGAGCATTTTGTCAAAAGTTA
Done.