Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016024.1 Corchorus capsularis cultivar CVL-1 contig16045, 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, 780
Length: 1300
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:570 original size:12 final size:12
Alignment explanation
Indices: 553--586 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
543 TGTAATTTGT
*
553 ATTTTTTTGTTA
1 ATTTTTATGTTA
565 ATTTTTAT-TTA
1 ATTTTTATGTTA
576 ATTTTTATGTT
1 ATTTTTATGTT
587 GTAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
ATTTTTATGTTA
Found at i:617 original size:6 final size:6
Alignment explanation
Indices: 606--636 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
596 TTAGTTCAAT
606 TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA T
1 TCCAAA TCCAAA TCCAAA TCCAAA TCCAAA T
637 ATCAGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.19
Consensus pattern (6 bp):
TCCAAA
Found at i:886 original size:23 final size:23
Alignment explanation
Indices: 819--944 Score: 102
Period size: 23 Copynumber: 5.6 Consensus size: 23
809 AATCGCACTT
*
819 TGAAATTTTGAT-AATC-ACACTA
1 TGAAATTTTGATAAATCTTC-CTA
*
841 TG-AATTTGTGAT-AA-CCTCGCTA
1 TGAAATTT-TGATAAATCTTC-CTA
863 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
886 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
909 TAAAATTTTGATAACT-TTCTTA
1 TGAAATTTTGATAAATCTTCCTA
*
931 TGAAATCTTGATAA
1 TGAAATTTTGATAA
945 CTACAAATTT
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
21 6 0.07
22 34 0.39
23 44 0.51
24 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (23 bp):
TGAAATTTTGATAAATCTTCCTA
Found at i:915 original size:46 final size:45
Alignment explanation
Indices: 843--944 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 45
833 TCACACTATG
* *
843 AATTTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTCCTATAA
1 AATTT-TGATAAACCTCCCTATAAAATTTTGATAAAT-TTCCTATAA
* * *
889 AATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGA
1 AATTTTGATAAACCTCCCTATAAAATTTTGATAAATTTCCTATAA
*
934 AATCTTGATAA
1 AATTTTGATAA
945 CTACAAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
45 21 0.43
46 28 0.57
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (45 bp):
AATTTTGATAAACCTCCCTATAAAATTTTGATAAATTTCCTATAA
Found at i:1013 original size:45 final size:44
Alignment explanation
Indices: 819--1046 Score: 168
Period size: 45 Copynumber: 5.2 Consensus size: 44
809 AATCGCACTT
* * * *
819 TGAAATTTTGATAATCACACTATG-AATTTGTGATAA-CCTCGCTA
1 TGAAATTTTGATAACCTCCCTATGAAATTT-TGATAACCCTC-TTA
* * * * *
863 TGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTCCCTATGAAATTTTGATAACCCT-CTTA
* * * * *
909 TAAAATTTTGATAACTTTCTTATGAAATCTTGATAA----C-TA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCCTCTTA
* **
948 -CAAATTTTGATAACCTCCCTATGATTTTTTGATAA-CCTCATTA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCCTC-TTA
* *
991 TGGAAATTTTGTTAATCTCCCTATGAAATTTTGATAACCCTCTTA
1 T-GAAATTTTGATAACCTCCCTATGAAATTTTGATAACCCTCTTA
1036 TGAAATTTTGA
1 TGAAATTTTGA
1047 AAACTAAACT
Statistics
Matches: 149, Mismatches: 23, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
38 28 0.19
39 2 0.01
40 1 0.01
41 1 0.01
43 2 0.01
44 21 0.14
45 67 0.45
46 26 0.17
47 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (44 bp):
TGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCCTCTTA
Found at i:1015 original size:23 final size:22
Alignment explanation
Indices: 819--1109 Score: 185
Period size: 22 Copynumber: 13.5 Consensus size: 22
809 AATCGCACTT
* * *
819 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCCCTA
*
841 TG-AATTTGTGATAACCTCGCTA
1 TGAAATTT-TGATAACCTCCCTA
* *
863 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGAT-AACCTCCCTA
*
886 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTCCCTA
* * * *
909 TAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAACCTCCCTA
*
931 TGAAATCTTGATAA-----CTA
1 TGAAATTTTGATAACCTCCCTA
*
948 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCCCTA
** **
969 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTCCCTA
* *
991 TGGAAATTTTGTTAATCTCCCTA
1 T-GAAATTTTGATAACCTCCCTA
*
1014 TGAAATTTTGATAACC-CTCTTA
1 TGAAATTTTGATAACCTC-CCTA
* **
1036 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT-CCCTA
* * *
1058 TTAAATTTTAATATCCTCCC--
1 TGAAATTTTGATAACCTCCCTA
**
1078 TGAAATTTTGATATGCTCCC--
1 TGAAATTTTGATAACCTCCCTA
1098 TGAAATTTTGAT
1 TGAAATTTTGAT
1110 TACTCCATAA
Statistics
Matches: 211, Mismatches: 44, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
16 11 0.05
17 2 0.01
20 29 0.14
21 12 0.06
22 94 0.45
23 63 0.30
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCCTA
Found at i:1107 original size:20 final size:20
Alignment explanation
Indices: 1060--1109 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1050 CTAAACTATT
*
1060 AAATTTTAATATCCTCCCTG
1 AAATTTTGATATCCTCCCTG
*
1080 AAATTTTGATATGCTCCCTG
1 AAATTTTGATATCCTCCCTG
1100 AAATTTTGAT
1 AAATTTTGAT
1110 TACTCCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (20 bp):
AAATTTTGATATCCTCCCTG
Done.