Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008103.1 Corchorus capsularis cultivar CVL-1 contig08124, 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: 5174
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Found at i:440 original size:36 final size:36
Alignment explanation
Indices: 398--498 Score: 161
Period size: 36 Copynumber: 2.8 Consensus size: 36
388 CTCTTTTTAG
398 ATTAAGT-TCTTTATTGACT-TCACTTAATTACCCTGA
1 ATTAAGTCT-TTTATTGACTCT-ACTTAATTACCCTGA
*
434 ATTAAGTCTTTTATTGACTCTACTTAATTACCTTGA
1 ATTAAGTCTTTTATTGACTCTACTTAATTACCCTGA
470 ATTAAGTCTTTTATTGACTCTACTTAATT
1 ATTAAGTCTTTTATTGACTCTACTTAATT
499 TCCTTTTCTG
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
36 60 0.97
37 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.48
Consensus pattern (36 bp):
ATTAAGTCTTTTATTGACTCTACTTAATTACCCTGA
Found at i:580 original size:36 final size:35
Alignment explanation
Indices: 507--772 Score: 290
Period size: 36 Copynumber: 7.5 Consensus size: 35
497 TTTCCTTTTC
*
507 TGAAATTAAGCCTATGTC-TT-TTTACTTAATTTCCT
1 TGAAATTAAGCC-A-GTCTTTCTTTACCTAATTTCCT
*
542 TGAAATTAAGCCAGTCTTATCTTCACCTAATTTCCT
1 TGAAATTAAGCCAGTCTT-TCTTTACCTAATTTCCT
* *
578 TGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCG
1 TGAAATTAAGCCAGTC-TTTCTTTACCTAATTTCCT
* * * *
614 TGAAACTAAGCCAGTCTTTGTTTACTTAATTTTCT
1 TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
* *
649 TGAAATTAAGCTAGTCTTTTCTTTACCTAATTTCCC
1 TGAAATTAAGCCAGTC-TTTCTTTACCTAATTTCCT
* * * *
685 TAAAACTAAGCCAATCTTGT-TTTACTTAATTTCCT
1 TGAAATTAAGCCAGTCTT-TCTTTACCTAATTTCCT
* *
720 TGCAATTAAGCCCGTC-TTCTTTA-CTCAATTTCCT
1 TGAAATTAAGCCAGTCTTTCTTTACCT-AATTTCCT
754 TGAAATTAAGCCAGTCTTT
1 TGAAATTAAGCCAGTCTTT
773 TATCAGTCCA
Statistics
Matches: 191, Mismatches: 31, Indels: 18
0.80 0.13 0.08
Matches are distributed among these distances:
33 5 0.03
34 29 0.15
35 69 0.36
36 86 0.45
37 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (35 bp):
TGAAATTAAGCCAGTCTTTCTTTACCTAATTTCCT
Found at i:651 original size:107 final size:105
Alignment explanation
Indices: 507--771 Score: 325
Period size: 107 Copynumber: 2.5 Consensus size: 105
497 TTTCCTTTTC
*
507 TGAAATTAAGCCTATGTCTT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTATCTTCACCTA
1 TGAAACTAAGCC-A-GTCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTATCTTCACCTA
* * * * * *
571 ATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCG
64 ATTTCCCTAAAACTAAGCCAATCTTGT-TTTACCTAATTTCCG
* * * * *
614 TGAAACTAAGCCAGTCTTTGTTTACTTAATTTTCTTGAAATTAAGCTAGTCTTTTCTTTACCTAA
1 TGAAACTAAGCCAGTC-TTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTATCTTCACCTAA
* *
679 TTTCCCTAAAACTAAGCCAATCTTGTTTTACTTAATTTCCT
65 TTTCCCTAAAACTAAGCCAATCTTGTTTTACCTAATTTCCG
* * * *
720 TGCAATTAAGCCCGTCTTCTTTACTCAATTTCCTTGAAATTAAGCCAGTCTT
1 TGAAACTAAGCCAGTCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTT
772 TTATCAGTCC
Statistics
Matches: 136, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
105 35 0.26
106 28 0.21
107 73 0.54
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.43
Consensus pattern (105 bp):
TGAAACTAAGCCAGTCTTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTATCTTCACCTAAT
TTCCCTAAAACTAAGCCAATCTTGTTTTACCTAATTTCCG
Found at i:652 original size:71 final size:69
Alignment explanation
Indices: 507--772 Score: 295
Period size: 71 Copynumber: 3.8 Consensus size: 69
497 TTTCCTTTTC
* * * * *
507 TGAAATTAAGCCTATGTCTT-TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTATCTTCACCTA
1 TGAAATTAAGCC-A-GTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTT-TGTTTACTTA
571 ATTTCCT
63 ATTTCCT
* *
578 TGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCGTGAAACTAAGCCAGTCTTTGTTTACTTAA
1 TGAAATTAAGCCAGTC--TTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTGTTTACTTAA
*
643 TTTTCT
64 TTTCCT
* * * *
649 TGAAATTAAGCTAGTCTTTTCTTTACCTAATTTCCCTAAAACTAAGCCAATC-TTGTTTTACTTA
1 TGAAATTAAGCCAGTC--TTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTG-TTTACTTA
713 ATTTCCT
63 ATTTCCT
* * *
720 TGCAATTAAGCCCGTCTTCTTTA-CTCAATTTCCTTGAAATTAAGCCAGTCTTT
1 TGAAATTAAGCCAGTCTTCTTTACCT-AATTTCCTTGAAACTAAGCCAGTCTTT
773 TATCAGTCCA
Statistics
Matches: 168, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
68 2 0.01
69 30 0.18
70 6 0.04
71 101 0.60
72 29 0.17
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (69 bp):
TGAAATTAAGCCAGTCTTCTTTACCTAATTTCCTTGAAACTAAGCCAGTCTTTGTTTACTTAATT
TCCT
Found at i:804 original size:33 final size:33
Alignment explanation
Indices: 765--834 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
755 GAAATTAAGC
765 CAGTCTTTTATCAGTCCAATTTCAGTCTAATAT
1 CAGTCTTTTATCAGTCCAATTTCAGTCTAATAT
* * * *
798 CAGTCTTTTTTCAGTCTAATTTTAGTCTAATTT
1 CAGTCTTTTATCAGTCCAATTTCAGTCTAATAT
831 CAGT
1 CAGT
835 ATGATGTCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (33 bp):
CAGTCTTTTATCAGTCCAATTTCAGTCTAATAT
Found at i:824 original size:11 final size:11
Alignment explanation
Indices: 775--882 Score: 83
Period size: 11 Copynumber: 9.6 Consensus size: 11
765 CAGTCTTTTA
*
775 TCAGTCCAATT
1 TCAGTCTAATT
*
786 TCAGTCTAATA
1 TCAGTCTAATT
**
797 TCAGTCTTTTT
1 TCAGTCTAATT
808 TCAGTCTAATT
1 TCAGTCTAATT
*
819 TTAGTCTAATT
1 TCAGTCTAATT
* * *
830 TCAGTATGATG
1 TCAGTCTAATT
841 TCAGTCTAACTT
1 TCAGTCTAA-TT
*
853 TCTAGTCT-TTT
1 TC-AGTCTAATT
**
864 GTCAGTCTTCTT
1 -TCAGTCTAATT
876 TCAGTCT
1 TCAGTCT
883 TCTTTTGCCT
Statistics
Matches: 76, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
11 64 0.84
12 7 0.09
13 5 0.07
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.47
Consensus pattern (11 bp):
TCAGTCTAATT
Found at i:883 original size:11 final size:11
Alignment explanation
Indices: 850--887 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
840 GTCAGTCTAA
850 CTTTCTAGTCTT
1 CTTTC-AGTCTT
862 -TTGTCAGTCTT
1 CTT-TCAGTCTT
873 CTTTCAGTCTT
1 CTTTCAGTCTT
884 CTTT
1 CTTT
888 TGCCTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.08, C:0.24, G:0.11, T:0.58
Consensus pattern (11 bp):
CTTTCAGTCTT
Found at i:989 original size:36 final size:35
Alignment explanation
Indices: 949--1105 Score: 170
Period size: 35 Copynumber: 4.1 Consensus size: 35
939 TTGGATTGAA
949 TCTTTGCTGATTTTACTTAATTCTTGTGAAATTAAG
1 TCTTTGCT-ATTTTACTTAATTCTTGTGAAATTAAG
*
985 TCTTTGCTAATTTTACCTAATTTTACTTAATTCTTTTGAAATTAAG
1 TCTTTG----------CT-ATTTTACTTAATTCTTGTGAAATTAAG
* *
1031 TCTTTGATAATTTACTTAATTCTTGTGAAATTAAG
1 TCTTTGCTATTTTACTTAATTCTTGTGAAATTAAG
1066 TCTTTGCTATTTTAACTTAATTCTTGTGAAATTAAG
1 TCTTTGCTATTTT-ACTTAATTCTTGTGAAATTAAG
1102 TCTT
1 TCTT
1106 AGAACTTACT
Statistics
Matches: 103, Mismatches: 7, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
35 36 0.35
36 33 0.32
46 34 0.33
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.51
Consensus pattern (35 bp):
TCTTTGCTATTTTACTTAATTCTTGTGAAATTAAG
Found at i:1010 original size:46 final size:45
Alignment explanation
Indices: 958--1051 Score: 152
Period size: 46 Copynumber: 2.1 Consensus size: 45
948 ATCTTTGCTG
*
958 ATTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACCTA
1 ATTTTACTTAATTCTTGTGAAATTAAGTCTTTGATAA-TTTACCTA
* *
1004 ATTTTACTTAATTCTTTTGAAATTAAGTCTTTGATAATTTACTTA
1 ATTTTACTTAATTCTTGTGAAATTAAGTCTTTGATAATTTACCTA
1049 ATT
1 ATT
1052 CTTGTGAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 10 0.22
46 35 0.78
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (45 bp):
ATTTTACTTAATTCTTGTGAAATTAAGTCTTTGATAATTTACCTA
Found at i:2141 original size:9 final size:9
Alignment explanation
Indices: 2127--2151 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2117 CTGCAGAGTT
2127 TTTTTTTCC
1 TTTTTTTCC
2136 TTTTTTTCC
1 TTTTTTTCC
2145 TTTTTTT
1 TTTTTTT
2152 TTCCTGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:2141 original size:11 final size:11
Alignment explanation
Indices: 2125--2156 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2115 TTCTGCAGAG
2125 TTTTTTTTTCC
1 TTTTTTTTTCC
2136 --TTTTTTTCC
1 TTTTTTTTTCC
2145 TTTTTTTTTCC
1 TTTTTTTTTCC
2156 T
1 T
2157 GAAGAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTTTTCC
Done.