Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005687.1 Corchorus capsularis cultivar CVL-1 contig05705, 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: 5165
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Found at i:2458 original size:66 final size:66
Alignment explanation
Indices: 2325--2716 Score: 653
Period size: 66 Copynumber: 5.9 Consensus size: 66
2315 CGTTGATGCA
* * *
2325 AACGTCTCCCTCAAGACCATTTTACCAAAAAAAAAAAAACGATCCTTGAATCGTAACTTAGGTAA
1 AACGTCTCCCTCGAGACCGTTTTACC---AAAATAAAAACGATCCTTGAATCGTAACTTAGGTAA
2390 GACG
63 GACG
*
2394 AACGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCTTAACTTAGGTAAGAC
1 AACGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGAC
2459 G
66 G
* *
2460 TACGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGAC
1 AACGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGAC
2525 G
66 G
*
2526 AACGTCTCCCTCGAGACCGTTTTATCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGAC
1 AACGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGAC
2591 G
66 G
* *
2592 AACGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCCTATCTTAGGTAAGAC
1 AACGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGAC
2657 G
66 G
*
2658 AACGTCTCCCT--TGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
1 AACGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
2717 CAAAATAAAA
Statistics
Matches: 307, Mismatches: 16, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
64 45 0.15
66 238 0.78
69 24 0.08
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (66 bp):
AACGTCTCCCTCGAGACCGTTTTACCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGAC
G
Found at i:2728 original size:36 final size:36
Alignment explanation
Indices: 2681--2752 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
2671 ACCGTTTTAC
2681 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
1 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
*
2717 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTA
1 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
2753 AGACGAACGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (36 bp):
CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
Found at i:2750 original size:100 final size:101
Alignment explanation
Indices: 2617--2818 Score: 352
Period size: 100 Copynumber: 2.0 Consensus size: 101
2607 ACCGTTTTAC
* *
2617 CAAAATAAAAACGATCCTTGAATCCTATCTTAGGTAAGACGAACGTCTCCCT-TGACCGTTTTAC
1 CAAAATAAAAACGATCCTTGAATCCTATCTTAGGTAAGACGAACGTCACCCTCAGACCGTTTTAC
2681 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
66 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
*
2717 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
1 CAAAATAAAAACGATCCTTGAATCCTATCTTAGGTAAGACGAACGTCACCCTC-AGACCGTTTTA
*
2782 TCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
65 CCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
2819 AGACGAACGT
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
100 50 0.52
102 46 0.48
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (101 bp):
CAAAATAAAAACGATCCTTGAATCCTATCTTAGGTAAGACGAACGTCACCCTCAGACCGTTTTAC
CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
Found at i:2798 original size:66 final size:66
Alignment explanation
Indices: 2717--2960 Score: 420
Period size: 66 Copynumber: 3.7 Consensus size: 66
2707 AACTTAGGTA
* *
2717 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
1 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTTA
*
2782 T
66 C
2783 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTTA
1 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTTA
2848 C
66 C
* *
2849 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCTCCCT--TGACCGTTTTA
1 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTTA
2912 C
66 C
*
2913 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGTACGTCT
1 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCT
2961 TTCCTTTGTA
Statistics
Matches: 171, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
64 57 0.33
66 114 0.67
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (66 bp):
CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTTA
C
Found at i:2825 original size:166 final size:167
Alignment explanation
Indices: 2551--2884 Score: 589
Period size: 166 Copynumber: 2.0 Consensus size: 167
2541 ACCGTTTTAT
*
2551 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTTA
1 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
* *
2616 CCAAAATAAAAACGATCCTTGAATCCTATCTTAGGTAAGACGAACGTCTCCCT-TGACCGTTTTA
66 CCAAAATAAAAACGATCCTTGAATCCTAACTTAGGTAAGACGAACGTCTCCCTCAGACCGTTTTA
2680 CCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
131 CCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
*
2717 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
1 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
* *
2782 TCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTT
66 CCAAAATAAAAACGATCCTTGAATCCTAACTTAGGTAAGACGAACGTCTCCCTC-AGACCGTTTT
*
2847 ACCAAAATAAAAACGATCCTTGAATCGTATCTTAGGTA
130 ACCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
2885 AGACGAACGT
Statistics
Matches: 159, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
166 113 0.71
168 46 0.29
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (167 bp):
CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
CCAAAATAAAAACGATCCTTGAATCCTAACTTAGGTAAGACGAACGTCTCCCTCAGACCGTTTTA
CCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
Found at i:2891 original size:232 final size:232
Alignment explanation
Indices: 2485--2948 Score: 910
Period size: 232 Copynumber: 2.0 Consensus size: 232
2475 ACCGTTTTAC
*
2485 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTTA
1 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
2550 TCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTT
66 TCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTT
2615 ACCAAAATAAAAACGATCCTTGAATCCTATCTTAGGTAAGACGAACGTCTCCCTTGACCGTTTTA
131 ACCAAAATAAAAACGATCCTTGAATCCTATCTTAGGTAAGACGAACGTCTCCCTTGACCGTTTTA
2680 CCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
196 CCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
2717 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
1 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
2782 TCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTT
66 TCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTT
*
2847 ACCAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCTCCCTTGACCGTTTTA
131 ACCAAAATAAAAACGATCCTTGAATCCTATCTTAGGTAAGACGAACGTCTCCCTTGACCGTTTTA
2912 CCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
196 CCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
2949 AGACGTACGT
Statistics
Matches: 230, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
232 230 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.26
Consensus pattern (232 bp):
CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
TCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTT
ACCAAAATAAAAACGATCCTTGAATCCTATCTTAGGTAAGACGAACGTCTCCCTTGACCGTTTTA
CCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTA
Found at i:2952 original size:130 final size:131
Alignment explanation
Indices: 2717--2960 Score: 436
Period size: 130 Copynumber: 1.9 Consensus size: 131
2707 AACTTAGGTA
2717 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTCGAGACCGTTTTA
1 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTC-AGACCGTTTTA
*
2782 TCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTT
65 CCAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTT
2847 AC
130 AC
* *
2849 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCTCCCT-TGACCGTTTTAC
1 CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTCAGACCGTTTTAC
*
2913 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGTACGTCT
66 CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCT
2961 TTCCTTTGTA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
130 57 0.53
132 51 0.47
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (131 bp):
CAAAATAAAAACGATCCTTGAATCGTATCTTAGGTAAGACGAACGTCACCCTCAGACCGTTTTAC
CAAAATAAAAACGATCCTTGAATCGTAACTTAGGTAAGACGAACGTCTCCCTCGAGACCGTTTTA
C
Done.