Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008453.1 Corchorus capsularis cultivar CVL-1 contig08474, 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: 7352
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Found at i:3598 original size:67 final size:67
Alignment explanation
Indices: 3348--3828 Score: 717
Period size: 67 Copynumber: 7.3 Consensus size: 67
3338 TACCTTCAAG
* * *
3348 TACGATTCAAGGATCGTTTT-ATCTTAGTAAAACGGTCTCAAGGGAGGCGTTCGTCTCGCTTAAG
1 TACGATTCAAGGATCGTTTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
3412 TC
66 TC
* * *
3414 TACGATTCAGGGATCG--CTCATTTTAGCAAAACAGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
1 TACGATTCAAGGATCGTTTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
3477 TC
66 TC
* * * *
3479 TACTATTCAAGGAT--TGTTCATTTTAGCAAAATGGTCTCAAGGGAGGCGTTCGTCTCGCTTAAG
1 TACGATTCAAGGATCGTTTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
3542 TC
66 TC
* *
3544 TACGATTCAAGGATCGTTTTCATTTTAGCCAAACGGTCTCAAGGGAGGCGTTCGTCTCGCTTAAG
1 TACGATTCAAGGATCGTTTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
3609 TC
66 TC
*
3611 TACGATTCAAGGATCG--TTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCATCTCGCTTAAG
1 TACGATTCAAGGATCGTTTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
3674 TC
66 TC
* *
3676 TACGATTCAAGGATCGTTTTCATTTTAGCCAAACGGTCTCAAGGGAGACGTTCATCTCGCTTAAG
1 TACGATTCAAGGATCGTTTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
3741 TC
66 TC
* * * *
3743 TACGATTCAAGGATCGTTTTCATTTTAGCCAAACGGTCTCGAGGGAGACGTTTGTCGT-ACTTAA
1 TACGATTCAAGGATCGTTTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTC-TCGCTTAA
*
3807 GTT
65 GTC
3810 TACGATTCAAGGATCGTTT
1 TACGATTCAAGGATCGTTT
3829 GTTTGGTCCT
Statistics
Matches: 382, Mismatches: 25, Indels: 15
0.91 0.06 0.04
Matches are distributed among these distances:
64 1 0.00
65 174 0.46
66 15 0.04
67 191 0.50
68 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (67 bp):
TACGATTCAAGGATCGTTTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
TC
Found at i:3619 original size:132 final size:132
Alignment explanation
Indices: 3348--3828 Score: 725
Period size: 132 Copynumber: 3.6 Consensus size: 132
3338 TACCTTCAAG
* * * *
3348 TACGATTCAAGGATCGTTTTATCTTAGTAAAACGGTCTCAAGGGAGGCGTTCGTCTCGCTTAAGT
1 TACGATTCAAGGATCG-TTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAGT
* * * *
3413 CTACGATTCAGGGATCG--CTCATTTTAGCAAAACAGTCTCAAGGGAGACGTTCGTCTCGCTTAA
65 CTACGATTCAAGGATCGTTTTCATTTTAGCCAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAA
3476 GTC
130 GTC
* * * *
3479 TACTATTCAAGGATTGTTCATTTTAGCAAAATGGTCTCAAGGGAGGCGTTCGTCTCGCTTAAGTC
1 TACGATTCAAGGATCGTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAGTC
*
3544 TACGATTCAAGGATCGTTTTCATTTTAGCCAAACGGTCTCAAGGGAGGCGTTCGTCTCGCTTAAG
66 TACGATTCAAGGATCGTTTTCATTTTAGCCAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
3609 TC
131 TC
*
3611 TACGATTCAAGGATCGTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCATCTCGCTTAAGTC
1 TACGATTCAAGGATCGTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAGTC
*
3676 TACGATTCAAGGATCGTTTTCATTTTAGCCAAACGGTCTCAAGGGAGACGTTCATCTCGCTTAAG
66 TACGATTCAAGGATCGTTTTCATTTTAGCCAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
3741 TC
131 TC
* * * *
3743 TACGATTCAAGGATCGTTTTCATTTTAGCCAAACGGTCTCGAGGGAGACGTTTGTCGT-ACTTAA
1 TACGATTCAAGGATCG--TTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTC-TCGCTTAA
*
3807 GTTTACGATTCAAGGATCGTTT
63 GTCTACGATTCAAGGATCGTTT
3829 GTTTGGTCCT
Statistics
Matches: 321, Mismatches: 24, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
130 60 0.19
131 14 0.04
132 186 0.58
134 60 0.19
135 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (132 bp):
TACGATTCAAGGATCGTTCATTTTAGCAAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAGTC
TACGATTCAAGGATCGTTTTCATTTTAGCCAAACGGTCTCAAGGGAGACGTTCGTCTCGCTTAAG
TC
Found at i:3698 original size:35 final size:35
Alignment explanation
Indices: 3659--3765 Score: 93
Period size: 35 Copynumber: 3.1 Consensus size: 35
3649 AAGGGAGACG
3659 TTCATCTCGCTTAAGTCTACGATTCAAGGATCGTT
1 TTCATCTCGCTTAAGTCTACGATTCAAGGATCGTT
* * * *
3694 TTCAT-T---TT-AGCCAAACGGTCTCAAGGGAGACG--
1 TTCATCTCGCTTAAGTC-TACGAT-TCAA-GGA-TCGTT
3726 TTCATCTCGCTTAAGTCTACGATTCAAGGATCGTT
1 TTCATCTCGCTTAAGTCTACGATTCAAGGATCGTT
3761 TTCAT
1 TTCAT
3766 TTTAGCCAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 22
0.64 0.10 0.27
Matches are distributed among these distances:
30 3 0.06
31 6 0.11
32 9 0.17
33 6 0.11
34 6 0.11
35 14 0.26
36 6 0.11
37 3 0.06
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (35 bp):
TTCATCTCGCTTAAGTCTACGATTCAAGGATCGTT
Found at i:3730 original size:32 final size:32
Alignment explanation
Indices: 3625--3730 Score: 76
Period size: 32 Copynumber: 3.2 Consensus size: 32
3615 ATTCAAGGAT
*
3625 CGTTCATTTTAGCAAAACGGTCTCAAGGGAGA
1 CGTTCATTTTAGCCAAACGGTCTCAAGGGAGA
* * * *
3657 CGTTCATCTCGCTTAAGTC-TACGAT-TCAA-GGA-T
1 CGTTCAT-T---TT-AGCCAAACGGTCTCAAGGGAGA
3690 CGTTTTCATTTTAGCCAAACGGTCTCAAGGGAGA
1 CG--TTCATTTTAGCCAAACGGTCTCAAGGGAGA
3724 CGTTCAT
1 CGTTCAT
3731 CTCGCTTAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 22
0.64 0.11 0.26
Matches are distributed among these distances:
30 3 0.06
31 6 0.11
32 16 0.30
33 6 0.11
34 6 0.11
35 9 0.17
36 6 0.11
37 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (32 bp):
CGTTCATTTTAGCCAAACGGTCTCAAGGGAGA
Done.