Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016771.1 Corchorus olitorius cultivar O-4 contig16804, 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: 46919
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:55 original size:20 final size:20
Alignment explanation
Indices: 30--68 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
20 AAATTTTTTA
30 ATTTTTTTAT-GACGCAAAAT
1 ATTTTTTT-TCGACGCAAAAT
50 ATTTTTTTTCGACGCAAAA
1 ATTTTTTTTCGACGCAAAA
69 CACAAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (20 bp):
ATTTTTTTTCGACGCAAAAT
Found at i:9968 original size:16 final size:15
Alignment explanation
Indices: 9930--9971 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
9920 ACAGAGGTTG
9930 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
9945 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
9960 ACTAGAAAACAA
1 AC-AGAAAACAA
9972 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:13201 original size:30 final size:31
Alignment explanation
Indices: 13162--13221 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
13152 CTCGTTGAGT
*
13162 GGAAGTGATGTGCCCAAAG-CTTATCATGGAG
1 GGAAGTGATGCG-CCAAAGACTTATCATGGAG
*
13193 GGAA-TGATGCGCCAAGGACTTATCATGGA
1 GGAAGTGATGCGCCAAAGACTTATCATGGA
13222 CTTGAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
30 17 0.65
31 4 0.15
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.22
Consensus pattern (31 bp):
GGAAGTGATGCGCCAAAGACTTATCATGGAG
Found at i:14238 original size:41 final size:43
Alignment explanation
Indices: 14179--14289 Score: 140
Period size: 43 Copynumber: 2.6 Consensus size: 43
14169 CAAGATGAGG
*
14179 CCCAAACACATTTATAACACAGAGTCATCC-ATA-CT-AAAGTC
1 CCCAAACACATTTATAACACAGAGGCA-CCTATATCTCAAAGTC
* *
14220 CCCAAACACATTTGTAACACA-AGGGCACCTCTATCTCAAAGTC
1 CCCAAACACATTTATAACACAGA-GGCACCTATATCTCAAAGTC
*
14263 CTCAAACACATTTATAACACAGAGGCA
1 CCCAAACACATTTATAACACAGAGGCA
14290 TTTCTCTTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
40 3 0.05
41 25 0.42
42 2 0.03
43 29 0.48
44 1 0.02
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.21
Consensus pattern (43 bp):
CCCAAACACATTTATAACACAGAGGCACCTATATCTCAAAGTC
Found at i:19359 original size:6 final size:6
Alignment explanation
Indices: 19351--19386 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
19341 CTACTTTTAT
*
19351 ATATAT ATATAA ATATAA ATATAA ATATAA TATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA -ATATA
19387 TAAAAGTACG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:20983 original size:29 final size:31
Alignment explanation
Indices: 20918--20990 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 31
20908 AATTAATATA
*
20918 TATATATATATATACATATAAATTATTCAAAT
1 TATAT-TATATATAAATATAAATTATTCAAAT
* *
20950 T-TATTATGTATAAATAT-AATTATT-TAAT
1 TATATTATATATAAATATAAATTATTCAAAT
*
20978 TATATTATTTATA
1 TATATTATATATA
20991 TAATTTCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.11
29 17 0.47
30 11 0.31
31 3 0.08
32 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (31 bp):
TATATTATATATAAATATAAATTATTCAAAT
Found at i:25767 original size:16 final size:16
Alignment explanation
Indices: 25746--25806 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
25736 TCGTTATTTC
25746 CCCTTTCTTTTTCTTT
1 CCCTTTCTTTTTCTTT
*
25762 CCCTTT-TTTTT-ATT
1 CCCTTTCTTTTTCTTT
25776 -CC-TTCTCTTTTCTTT
1 CCCTTTCT-TTTTCTTT
* *
25791 TCTTTTCTTTTTCTTT
1 CCCTTTCTTTTTCTTT
25807 TCGGCTTGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 2 0.05
13 3 0.08
14 6 0.16
15 7 0.19
16 15 0.41
17 4 0.11
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (16 bp):
CCCTTTCTTTTTCTTT
Found at i:25796 original size:10 final size:11
Alignment explanation
Indices: 25749--25808 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
25739 TTATTTCCCC
25749 TTTCTTTTTCT
1 TTTCTTTTTCT
* *
25760 TTCCCTTTTTTT
1 TT-TCTTTTTCT
* *
25772 TATTCCTTCTCT
1 T-TTCTTTTTCT
25784 TTTC-TTTTCT
1 TTTCTTTTTCT
25794 TTTCTTTTTCT
1 TTTCTTTTTCT
25805 TTTC
1 TTTC
25809 GGCTTGGGCC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
10 9 0.23
11 15 0.38
12 14 0.36
13 1 0.03
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:28230 original size:22 final size:22
Alignment explanation
Indices: 28204--28250 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
28194 TGTTTGTTGA
*
28204 TCTTCGATACTCGTGGTGGACT
1 TCTTCGATACTCATGGTGGACT
28226 TCTTCGATACTCATGGTGGACT
1 TCTTCGATACTCATGGTGGACT
28248 TCT
1 TCT
28251 GCTACAGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (22 bp):
TCTTCGATACTCATGGTGGACT
Found at i:32280 original size:18 final size:18
Alignment explanation
Indices: 32257--32294 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
32247 GACTTGTTTG
*
32257 TTTGCATTTAGCCTCTGT
1 TTTGCATTTAACCTCTGT
32275 TTTGCATTTAACCTCTGT
1 TTTGCATTTAACCTCTGT
32293 TT
1 TT
32295 GTCGTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.13, T:0.53
Consensus pattern (18 bp):
TTTGCATTTAACCTCTGT
Found at i:40189 original size:18 final size:17
Alignment explanation
Indices: 40166--40206 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
40156 TTTTTTTGTA
40166 TTTTTTGCTATTTCCATT
1 TTTTTTGC-ATTTCCATT
*
40184 TTTTTTGCATTTGCATT
1 TTTTTTGCATTTCCATT
40201 TTTTTT
1 TTTTTT
40207 ATTTTCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.10, C:0.12, G:0.07, T:0.71
Consensus pattern (17 bp):
TTTTTTGCATTTCCATT
Found at i:43000 original size:31 final size:30
Alignment explanation
Indices: 42940--43000 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
42930 ATTACTTCAC
*
42940 TGCTTTCTGATTAATTGTTTCCTTTAATTT
1 TGCTTTCTGATTAATTGTTTCATTTAATTT
*
42970 TGCTTTCT-AGTTAATTGTTTTGATTTAATTT
1 TGCTTTCTGA-TTAATTG-TTTCATTTAATTT
43001 AGTGTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 1 0.04
30 15 0.56
31 11 0.41
ACGTcount: A:0.18, C:0.10, G:0.11, T:0.61
Consensus pattern (30 bp):
TGCTTTCTGATTAATTGTTTCATTTAATTT
Done.