Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017444.1 Corchorus olitorius cultivar O-4 contig17477, 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: 3775
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Found at i:35 original size:16 final size:16
Alignment explanation
Indices: 1--34 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1 TTTCTAGTTTAATTGT
1 TTTCTAGTTTAATTGT
17 TTTCT-GTTTAATTGT
1 TTTCTAGTTTAATTGT
32 TTT
1 TTT
35 TGTCAACCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.68
Consensus pattern (16 bp):
TTTCTAGTTTAATTGT
Found at i:3398 original size:71 final size:71
Alignment explanation
Indices: 3302--3775 Score: 456
Period size: 71 Copynumber: 6.7 Consensus size: 71
3292 ATTTCAGATG
* * * * * *
3302 CTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTTATTCAGTTTATTTCAATTGATCCAGGGCGA
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGA
*
3367 TCTTTT
66 TCCTTT
* * * * * * * * * *
3373 CTTCAATTCACTTCAGTTGATCCA-GGTGATCCTTATTCAATTCATTTCAGTTGACCCAGGGTGG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGA
*
3437 TCCTAT
66 TCCTTT
* * * * *
3443 -TTCAGTTTATTTCAGTTTGATCCAGGGCAATCCTTGTTCAATTTATTTCAGTTGACCCAGGGTG
1 CTTCAGTTTATTTCAG-TTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* *
3507 GTCCTAT
65 ATCCTTT
* * * *
3514 -TTCAGTTTATTTCAGTTGATCCAAGGCGATCCGTTCTTCAGTTTATATT-AATTGATCCAGGGC
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTTTAT-TTCAGTTGACCCAGGGC
3577 GATCCTTT
64 GATCCTTT
* **
3585 CTTCAGTTTATATT-AATTGATCCAGGGCGATCCTCCCTTCAGTTTATTTCAGTTGACCCAGGGC
1 CTTCAGTTTAT-TTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTTTATTTCAGTTGACCCAGGGC
* *
3649 GGT-CTTC
64 GATCCTTT
* ** *
3656 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCATTTTACCTCAGTTGATCCAGGGCG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
*
3721 ATCTTTT
65 ATCCTTT
* * * *
3728 CTTTAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTCAGTTTATT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCAGTTTATT
Statistics
Matches: 336, Mismatches: 57, Indels: 19
0.82 0.14 0.05
Matches are distributed among these distances:
69 12 0.04
70 59 0.18
71 166 0.49
72 97 0.29
73 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (71 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGA
TCCTTT
Found at i:3488 original size:36 final size:35
Alignment explanation
Indices: 3302--3775 Score: 438
Period size: 36 Copynumber: 13.3 Consensus size: 35
3292 ATTTCAGATG
* * * *
3302 CTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTT
* * *
3337 ATTCAGTTTATTTCAATTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATC-CTT
* * * *
3373 CTTCAATTCACTTCAGTTGATCCA-GGTGATCCTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTT
* * * * * *
3407 ATTCAATTCATTTCAGTTGACCCAGGGTGGTCCTAT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCCT-T
*
3443 -TTCAGTTTATTTCAGTTTGATCCAGGGCAATCCTT
1 CTTCAGTTTATTTCAG-TTGATCCAGGGCGATCCTT
* * * * *
3478 GTTCAATTTATTTCAGTTGACCCAGGGTGGTCCTAT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCCT-T
*
3514 -TTCAGTTTATTTCAGTTGATCCAAGGCGATCCGTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCC-TT
*
3549 CTTCAGTTTATATT-AATTGATCCAGGGCGATCCTTT
1 CTTCAGTTTAT-TTCAGTTGATCCAGGGCGATCC-TT
* *
3585 CTTCAGTTTATATT-AATTGATCCAGGGCGATCCTCC
1 CTTCAGTTTAT-TTCAGTTGATCCAGGGCGATCCT-T
* *
3621 CTTCAGTTTATTTCAGTTGACCCAGGGCGGT-CTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTT
*
3655 CCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
1 -CTTCAGTTTATTTCAGTTGATCCAGGGCGATC-CTT
* ** *
3692 CTTCATTTTACCTCAGTTGATCCAGGGCGATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATC-CTT
* * * * *
3728 CTTTAGTTTATTTCAATTGATCCGGGGCAATCTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATC-CTT
3764 CTTCAGTTTATT
1 CTTCAGTTTATT
Statistics
Matches: 371, Mismatches: 54, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
34 23 0.06
35 131 0.35
36 213 0.57
37 4 0.01
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (35 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTT
Found at i:3639 original size:143 final size:140
Alignment explanation
Indices: 3302--3775 Score: 468
Period size: 143 Copynumber: 3.3 Consensus size: 140
3292 ATTTCAGATG
* * * ** * * * * *
3302 CTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTTATTCAGTTTATTTCAATTGATCCAGGGCGA
1 CTTCAGTTTATTTCAATTGATCCAGGGCAATCCTTCTTCAGTTTATTTCAGTTGACCCAGGGCGG
* * * * * * * *
3367 TCTTTTCTTCAATTCACTTCAGTTGATCC-AGGTGATCCTTATTCAATTCATTTCAGTTGACCCA
66 TCTTAT-TTCAGTTTATTTCAGTTGATCCAAGGCGATCCTTCTTCAATTTATTT-AGTTGATCCA
* * *
3431 GGGTGGTCCTAT
129 GGGCGATCCTTT
* * * *
3443 -TTCAGTTTATTTCAGTTTGATCCAGGGCAATCCTTGTTCAATTTATTTCAGTTGACCCAGGGTG
1 CTTCAGTTTATTTCA-ATTGATCCAGGGCAATCCTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* * *
3507 GTCCTATTTCAGTTTATTTCAGTTGATCCAAGGCGATCCGTTCTTCAGTTTATATTAATTGATCC
65 GTCTTATTTCAGTTTATTTCAGTTGATCCAAGGCGATCC-TTCTTCAATTTAT-TTAGTTGATCC
3572 AGGGCGATCCTTT
128 AGGGCGATCCTTT
* *
3585 CTTCAGTTTATATT-AATTGATCCAGGGCGATCCTCCCTTCAGTTTATTTCAGTTGACCCAGGGC
1 CTTCAGTTTAT-TTCAATTGATCCAGGGCAATCCT-TCTTCAGTTTATTTCAGTTGACCCAGGGC
** * * * * *
3649 GGTCTTCCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCATTTTACCTCAGTTGATC
64 GGTCTTATTTCAGTTTATTTCAGTTGATCCAAGGCGATC-CTTCTTCAATTTA-TTTAGTTGATC
*
3714 CAGGGCGATCTTTT
127 CAGGGCGATCCTTT
* * *
3728 CTTTAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTCAGTTTATT
1 CTTCAGTTTATTTCAATTGATCCAGGGCAATC-CTTCTTCAGTTTATT
Statistics
Matches: 275, Mismatches: 47, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
140 32 0.12
141 51 0.19
142 46 0.17
143 143 0.52
144 3 0.01
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (140 bp):
CTTCAGTTTATTTCAATTGATCCAGGGCAATCCTTCTTCAGTTTATTTCAGTTGACCCAGGGCGG
TCTTATTTCAGTTTATTTCAGTTGATCCAAGGCGATCCTTCTTCAATTTATTTAGTTGATCCAGG
GCGATCCTTT
Done.