Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024443.1 Corchorus olitorius cultivar O-4 contig24476, 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: 52803
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1202 original size:22 final size:22
Alignment explanation
Indices: 1172--1229 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
1162 GATTGAAGAA
*
1172 AATGTTCTGCAAAGTGGAAAAT
1 AATGCTCTGCAAAGTGGAAAAT
1194 AATGCTCTGCAAAGTGGAAAAT
1 AATGCTCTGCAAAGTGGAAAAT
1216 AATGCTCTGCAAAG
1 AATGCTCTGCAAAG
1230 ATGTTTCCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (22 bp):
AATGCTCTGCAAAGTGGAAAAT
Found at i:1327 original size:20 final size:22
Alignment explanation
Indices: 1269--1331 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
1259 CTGAAGTTGA
1269 AGAAAATAATGCTCTGCAAAGT
1 AGAAAATAATGCTCTGCAAAGT
*
1291 GGAAAATAATGCTCTGCAAAGT
1 AGAAAATAATGCTCTGCAAAGT
1313 AGAAAA-AAT-CTCTGCAAAG
1 AGAAAATAATGCTCTGCAAAG
1332 ATGTTTCCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
21 3 0.08
22 26 0.67
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (22 bp):
AGAAAATAATGCTCTGCAAAGT
Found at i:1643 original size:60 final size:60
Alignment explanation
Indices: 1549--1675 Score: 236
Period size: 60 Copynumber: 2.1 Consensus size: 60
1539 TACTCTTTAA
1549 AGTATCAATTAGCTTCCAAACTCTGGTATCCTCAGATCCTCAGATCCTTCGGGTTTGTCT
1 AGTATCAATTAGCTTCCAAACTCTGGTATCCTCAGATCCTCAGATCCTTCGGGTTTGTCT
* *
1609 GGTATCAATTAGCTTCCAAACTCTGGTATCCTCAGATCCTCAGCTCCTTCGGGTTTGTCT
1 AGTATCAATTAGCTTCCAAACTCTGGTATCCTCAGATCCTCAGATCCTTCGGGTTTGTCT
1669 AGTATCA
1 AGTATCA
1676 GAGCCAGGGA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (60 bp):
AGTATCAATTAGCTTCCAAACTCTGGTATCCTCAGATCCTCAGATCCTTCGGGTTTGTCT
Found at i:1746 original size:19 final size:20
Alignment explanation
Indices: 1718--1772 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1708 CAGCTCCGTT
* *
1718 TATTATATATCTATAATA-A
1 TATTAGATATATATAATATA
1737 TATTAGATATATATAATATA
1 TATTAGATATATATAATATA
*
1757 TATTCAAATATATATA
1 TATT-AGATATATATA
1773 TTAATAAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 5 0.16
21 10 0.32
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (20 bp):
TATTAGATATATATAATATA
Found at i:1748 original size:21 final size:21
Alignment explanation
Indices: 1722--1779 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
1712 TCCGTTTATT
*
1722 ATATATCTATAATAATATT-AG
1 ATATAT-TATAATAATATTCAA
1743 ATATA-TATAATATATATTCAA
1 ATATATTATAATA-ATATTCAA
1764 ATATATATATTAATAA
1 ATATAT-TA-TAATAA
1780 ACGGTCGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 7 0.23
20 5 0.16
21 11 0.35
23 3 0.10
24 5 0.16
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATATTATAATAATATTCAA
Found at i:10053 original size:5 final size:5
Alignment explanation
Indices: 10043--10071 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
10033 ATCTTCTTTT
10043 AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
10072 AATTTAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:13721 original size:24 final size:24
Alignment explanation
Indices: 13694--13751 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
13684 TCTTTAAATT
13694 TTACAATTTTTAATATTATTACAA
1 TTACAATTTTTAATATTATTACAA
13718 TTACAATTTTTAATATTATTACAA
1 TTACAATTTTTAATATTATTACAA
13742 TTACAATTTT
1 TTACAATTTT
13752 ACAAAACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.52
Consensus pattern (24 bp):
TTACAATTTTTAATATTATTACAA
Found at i:13738 original size:18 final size:16
Alignment explanation
Indices: 13686--13719 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
13676 CTTTTTTCTC
13686 TTTAAATTTTACAATT
1 TTTAAATTTTACAATT
13702 TTTAATATTATTACAATT
1 TTTAA-ATT-TTACAATT
13720 ACAATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAATTTTACAATT
Found at i:38954 original size:22 final size:23
Alignment explanation
Indices: 38920--38965 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
38910 TTTGGGGGCT
38920 GTTTCACCCTTTTCCA-GGTTGA
1 GTTTCACCCTTTTCCAGGGTTGA
* * *
38942 GTTTGACCTTTTTGCAGGGTTGA
1 GTTTCACCCTTTTCCAGGGTTGA
38965 G
1 G
38966 ACATGAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.13, C:0.20, G:0.26, T:0.41
Consensus pattern (23 bp):
GTTTCACCCTTTTCCAGGGTTGA
Found at i:43211 original size:74 final size:74
Alignment explanation
Indices: 43085--43233 Score: 280
Period size: 74 Copynumber: 2.0 Consensus size: 74
43075 CTTTATTACA
43085 TGTTCTAAAACTGAAGATGCCATTAATGTAGCTAACTTGTTCTTTAGGGAAATTGTTAGATTGCA
1 TGTTCTAAAACTGAAGATGCCATTAATGTAGCTAACTTGTTCTTTAGGGAAATTGTTAGATTGCA
43150 TGGAATGCC
66 TGGAATGCC
* *
43159 TGTTGTAAAACTGATGATGCCATTAATGTAGCTAACTTGTTCTTTAGGGAAATTGTTAGATTGCA
1 TGTTCTAAAACTGAAGATGCCATTAATGTAGCTAACTTGTTCTTTAGGGAAATTGTTAGATTGCA
43224 TGGAATGCC
66 TGGAATGCC
43233 T
1 T
43234 AGAACCATTG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (74 bp):
TGTTCTAAAACTGAAGATGCCATTAATGTAGCTAACTTGTTCTTTAGGGAAATTGTTAGATTGCA
TGGAATGCC
Found at i:48466 original size:16 final size:16
Alignment explanation
Indices: 48445--48483 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
48435 CTTTTCTCTC
*
48445 TCAATTGGGCCAGTTG
1 TCAATTGGACCAGTTG
48461 TCAATTGGACCAGTTG
1 TCAATTGGACCAGTTG
*
48477 ACAATTG
1 TCAATTG
48484 ATCAGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (16 bp):
TCAATTGGACCAGTTG
Found at i:52072 original size:37 final size:38
Alignment explanation
Indices: 52006--52239 Score: 255
Period size: 37 Copynumber: 6.1 Consensus size: 38
51996 AAGGAATTTC
* * *
52006 TTTCAAAGATTTTCAAATT-GGGAAGGATCCCGTCAAGT
1 TTTCAAAG-TTTTCAATTTAGGGAAAGATCCCATCAAGT
52044 TTTC-AAGTTTTCAATTTAGGGAAAGATCCCATC-AGTT
1 TTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAG-T
* * *
52081 TCTTCAAAATTTTCAATTTAGGGAAAGATCCCGTCGAGT
1 T-TTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGT
52120 TTTC-AAGTTTTCAATTTAGGGAAAGATCCCATC-AGT
1 TTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGT
** * *
52156 GTTTTTAAGTTTCCAATTTAGGGAAAGATCCCATCTAGTCTT
1 -TTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAG---T
52198 TTTCAAAGTTTTCAA-TTAGGGGAAAGATCCCATCAAAGT
1 TTTCAAAGTTTTCAATTTA-GGGAAAGATCCCATC-AAGT
52237 TTT
1 TTT
52240 TAAAATTGAG
Statistics
Matches: 170, Mismatches: 13, Indels: 25
0.82 0.06 0.12
Matches are distributed among these distances:
36 14 0.08
37 48 0.28
38 38 0.22
39 35 0.21
40 5 0.03
41 27 0.16
42 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (38 bp):
TTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCAAGT
Found at i:52111 original size:76 final size:76
Alignment explanation
Indices: 52002--52232 Score: 290
Period size: 76 Copynumber: 3.0 Consensus size: 76
51992 TCAAAAGGAA
* *
52002 TTTCTTTCAAAGATTTTCAAATT-GGGAAGGATCCCGTCAAGTTTTCAAGTTTTCAATTTAGGGA
1 TTTC-TTCAAA-ATTTTCAATTTAGGGAAAGATCCCGTCAAGTTTTCAAGTTTTCAATTTAGGGA
52066 AAGATCCCATCAG
64 AAGATCCCATCAG
*
52079 TTTCTTCAAAATTTTCAATTTAGGGAAAGATCCCGTCGAGTTTTCAAGTTTTCAATTTAGGGAAA
1 TTTCTTCAAAATTTTCAATTTAGGGAAAGATCCCGTCAAGTTTTCAAGTTTTCAATTTAGGGAAA
52144 GATCCCATCAG
66 GATCCCATCAG
* * * * *
52155 TGTT-TT-TAAGTTTCCAATTTAGGGAAAGATCCCATCTAGTCTTTTTCAAAGTTTTCAA-TTAG
1 T-TTCTTCAAAATTTTCAATTTAGGGAAAGATCCCGTCAAG---TTTTC-AAGTTTTCAATTTA-
52217 GGGAAAGATCCCATCA
60 GGGAAAGATCCCATCA
52233 AAGTTTTTAA
Statistics
Matches: 139, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
75 38 0.27
76 61 0.44
77 6 0.04
78 8 0.06
79 26 0.19
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (76 bp):
TTTCTTCAAAATTTTCAATTTAGGGAAAGATCCCGTCAAGTTTTCAAGTTTTCAATTTAGGGAAA
GATCCCATCAG
Done.