Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006008.1 Corchorus capsularis cultivar CVL-1 contig06026, 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: 6183
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Found at i:404 original size:6 final size:5
Alignment explanation
Indices: 371--416 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
361 CAGTTTTCAC
* *
371 TTCTT TTCTC TTCTC TTCTT TTCTT TTCCTT TTC-T TT-TT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT-CTT TTCTT TTCTT TTCTT TT
417 TCATCTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 6 0.17
5 25 0.69
6 5 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTCTT
Found at i:411 original size:19 final size:20
Alignment explanation
Indices: 371--416 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
361 CAGTTTTCAC
371 TTCTTTTCTCTTCTCTTCTT
1 TTCTTTTCTCTTCTCTTCTT
* *
391 TTCTTTTC-CTTTTCTTTTT
1 TTCTTTTCTCTTCTCTTCTT
410 TTCTTTT
1 TTCTTTT
417 TCATCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTCTTTTCTCTTCTCTTCTT
Found at i:813 original size:12 final size:12
Alignment explanation
Indices: 798--839 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
788 ATTTACTTTT
798 TTTTAAAAACCA
1 TTTTAAAAACCA
810 TTTTATCAAAACC-
1 TTTTA--AAAACCA
*
823 TTTTGAAAACCA
1 TTTTAAAAACCA
835 TTTTA
1 TTTTA
840 TCAAAACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.24
12 9 0.36
13 4 0.16
14 6 0.24
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (12 bp):
TTTTAAAAACCA
Found at i:813 original size:14 final size:13
Alignment explanation
Indices: 803--851 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
793 CTTTTTTTTA
803 AAAACCATTTTATC
1 AAAACC-TTTTATC
*
817 AAAACC-TTT-TG
1 AAAACCTTTTATC
828 AAAACCATTTTATC
1 AAAACC-TTTTATC
842 AAAACCTTTT
1 AAAACCTTTT
852 GAAAATCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 7 0.23
12 3 0.10
13 7 0.23
14 13 0.43
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (13 bp):
AAAACCTTTTATC
Found at i:832 original size:25 final size:25
Alignment explanation
Indices: 798--856 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
788 ATTTACTTTT
*
798 TTTTAAAAACCATTTTATCAAAACC
1 TTTTGAAAACCATTTTATCAAAACC
823 TTTTGAAAACCATTTTATCAAAACC
1 TTTTGAAAACCATTTTATCAAAACC
848 TTTTGAAAA
1 TTTTGAAAA
857 TCATGACTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.37
Consensus pattern (25 bp):
TTTTGAAAACCATTTTATCAAAACC
Found at i:887 original size:18 final size:17
Alignment explanation
Indices: 866--935 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 17
856 ATCATGACTC
866 TTTTTCTTTTGTTTTC-T
1 TTTTTCTTTT-TTTTCTT
883 TTTTTCTTTCTTCTTTCTT
1 TTTTTCTTT-TT-TTTCTT
902 GTATTCTTCTTCTTCTTTTCTT
1 -T-TT-TTCTT-TT-TTTTCTT
*
924 TCTTTCTTTTTT
1 TTTTTCTTTTTT
936 CCTTCTATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
17 12 0.27
18 7 0.16
19 6 0.14
20 2 0.05
21 3 0.07
22 12 0.27
23 2 0.05
ACGTcount: A:0.01, C:0.19, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTTCTTTTTTTTCTT
Found at i:892 original size:11 final size:11
Alignment explanation
Indices: 868--953 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 11
858 CATGACTCTT
*
868 TTTCTTTTGT-
1 TTTCTTTTTTC
878 TTTCTTTTTTC
1 TTTCTTTTTTC
*
889 TTTCTTCTTTC
1 TTTCTTTTTTC
*
900 TTGTATTCTTCTTC
1 TT-TCTT-TT-TTC
914 -TTCTTTTCTTTC
1 TTTC-TTT-TTTC
926 TTTCTTTTTTC
1 TTTCTTTTTTC
* *
937 CTTCTATTTTTT
1 TTTCT-TTTTTC
949 TTTCT
1 TTTCT
954 GGGAAACTGT
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
10 9 0.15
11 20 0.33
12 20 0.33
13 8 0.13
14 3 0.05
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:935 original size:15 final size:15
Alignment explanation
Indices: 868--953 Score: 65
Period size: 14 Copynumber: 5.8 Consensus size: 15
858 CATGACTCTT
*
868 TTTCTTTTGT-TTTC
1 TTTCTTTTTTCTTTC
882 TTT-TTTCTTTC-TTC
1 TTTCTTT-TTTCTTTC
*
896 TTTCTTGTATTC-TTC
1 TTTCTT-TTTTCTTTC
911 -TTCTTCTTTTCTTTC
1 TTTCTT-TTTTCTTTC
*
926 TTTCTTTTTTCCTTC
1 TTTCTTTTTTCTTTC
*
941 TATTTTTTTTTCT
1 T-TTCTTTTTTCT
954 GGGAAACTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
13 3 0.05
14 20 0.34
15 20 0.34
16 15 0.26
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTCTTTTTTCTTTC
Found at i:949 original size:16 final size:15
Alignment explanation
Indices: 879--952 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
869 TTCTTTTGTT
879 TTCTTT-TTTCTTT-C
1 TTCTTTCTTT-TTTCC
*
893 TTCTTTCTTGTATT-C
1 TTCTTTCTT-TTTTCC
*
908 TTC-TTCTTCTTTTCT
1 TTCTTTCTT-TTTTCC
923 TTCTTTCTTTTTTCC
1 TTCTTTCTTTTTTCC
*
938 TTCTATTTTTTTTTC
1 TTCT-TTCTTTTTTC
953 TGGGAAACTG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
14 14 0.29
15 20 0.41
16 15 0.31
ACGTcount: A:0.03, C:0.22, G:0.01, T:0.74
Consensus pattern (15 bp):
TTCTTTCTTTTTTCC
Done.