Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018550.1 Corchorus olitorius cultivar O-4 contig18583, 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: 52186
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5140 original size:17 final size:17
Alignment explanation
Indices: 5096--5143 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
5086 TAATGATGCC
* *
5096 CTTAAATTGCATACTGT
1 CTTAAATTGCTTAATGT
5113 CTTAAATTGCTTAATGT
1 CTTAAATTGCTTAATGT
*
5130 CTTAAACTGCTTAA
1 CTTAAATTGCTTAA
5144 ATTGCAGGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CTTAAATTGCTTAATGT
Found at i:5280 original size:14 final size:15
Alignment explanation
Indices: 5260--5294 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5250 GTTTGATAAA
5260 ACTGAAA-ATTAAGT
1 ACTGAAAGATTAAGT
*
5274 GCTGAAAGATTAAGT
1 ACTGAAAGATTAAGT
5289 ACTGAA
1 ACTGAA
5295 TTTTTAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (15 bp):
ACTGAAAGATTAAGT
Found at i:5323 original size:16 final size:15
Alignment explanation
Indices: 5284--5328 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
5274 GCTGAAAGAT
**
5284 TAAGTACTGAATTTT
1 TAAGTACTGAATTCA
5299 TAA-TACTGAATCTCA
1 TAAGTACTGAAT-TCA
5314 TAAGTACTGAATTCA
1 TAAGTACTGAATTCA
5329 AACTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 8 0.31
15 10 0.38
16 8 0.31
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (15 bp):
TAAGTACTGAATTCA
Found at i:8119 original size:7 final size:7
Alignment explanation
Indices: 8106--8142 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
8096 AATATTTATT
8106 TATAGTA
1 TATAGTA
*
8113 CATAGTA
1 TATAGTA
8120 TATAGTA
1 TATAGTA
8127 TATAGTA
1 TATAGTA
8134 TATA-TA
1 TATAGTA
8140 TAT
1 TAT
8143 TGTGGTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (7 bp):
TATAGTA
Found at i:12915 original size:16 final size:16
Alignment explanation
Indices: 12890--12928 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
12880 GTTGCTTAAT
12890 TTTA-TTATTTTCTTG
1 TTTATTTATTTTCTTG
*
12905 TTTATTTATTTTTTTG
1 TTTATTTATTTTCTTG
*
12921 TTTCTTTA
1 TTTATTTA
12929 ATTCAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (16 bp):
TTTATTTATTTTCTTG
Found at i:12915 original size:24 final size:25
Alignment explanation
Indices: 12869--12916 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
12859 ATAGAAGTAT
*
12869 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
12894 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTGATTAATTTT
12917 TTTGTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:18946 original size:23 final size:23
Alignment explanation
Indices: 18916--18960 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
18906 ATAATTTTTC
18916 AGAGAGAGTGAAAGAAAATTTAA
1 AGAGAGAGTGAAAGAAAATTTAA
*
18939 AGAGAGAGTGAAAGGAAATTTA
1 AGAGAGAGTGAAAGAAAATTTA
18961 CCAGGTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.29, T:0.18
Consensus pattern (23 bp):
AGAGAGAGTGAAAGAAAATTTAA
Found at i:19118 original size:14 final size:14
Alignment explanation
Indices: 19069--19118 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
19059 GTCCGTCAAC
* *
19069 CGGTGAGCGGTGAC
1 CGGTGAGTGGTGAG
19083 CGGTGAGTGGTGAG
1 CGGTGAGTGGTGAG
* *
19097 TGATGAGTGGTGAG
1 CGGTGAGTGGTGAG
*
19111 CGGCGAGT
1 CGGTGAGT
19119 CGGGTTTTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.16, C:0.12, G:0.52, T:0.20
Consensus pattern (14 bp):
CGGTGAGTGGTGAG
Found at i:19385 original size:29 final size:30
Alignment explanation
Indices: 19352--19424 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
19342 ACAAATTATT
19352 CGTGGCAAAGCCCGCTG-AAACTCTAAAAC
1 CGTGGCAAAGCCCGCTGAAAACTCTAAAAC
19381 CGTGGCAAAGCCCGCTGAAAACTCTAAAAC
1 CGTGGCAAAGCCCGCTGAAAACTCTAAAAC
*
19411 CGTGGCAAGGCCCG
1 CGTGGCAAAGCCCG
19425 TGGCCAACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 17 0.40
30 25 0.60
ACGTcount: A:0.32, C:0.32, G:0.25, T:0.12
Consensus pattern (30 bp):
CGTGGCAAAGCCCGCTGAAAACTCTAAAAC
Found at i:24334 original size:29 final size:29
Alignment explanation
Indices: 24294--24361 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
24284 ACAAATAATT
24294 TTTTTCAATTTGGTCCTTACATTTTTCAA
1 TTTTTCAATTTGGTCCTTACATTTTTCAA
24323 TTTTTCAATTTGGTCCTTACATTTTTCAA
1 TTTTTCAATTTGGTCCTTACATTTTTCAA
24352 TTTTTCAATT
1 TTTTTCAATT
24362 CCATCCCCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.21, C:0.16, G:0.06, T:0.57
Consensus pattern (29 bp):
TTTTTCAATTTGGTCCTTACATTTTTCAA
Found at i:26841 original size:57 final size:56
Alignment explanation
Indices: 26758--26872 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 56
26748 TATCCGTTTC
*
26758 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATT
26814 CTTTCACACAATAAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATT
1 CTTTCACACAAT-AAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATT
26871 CT
1 CT
26873 ACAAAATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 12 0.21
57 45 0.79
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCATATCTCTACTTAATTATT
Found at i:26997 original size:42 final size:42
Alignment explanation
Indices: 26936--27018 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
26926 GTTAAGGATC
26936 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
*
26978 ATGATTTGAGTTGATTATTTCTTAATTTACAAAGAATTTTC
1 ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
27019 AAGACTTAGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCT
Found at i:30088 original size:11 final size:11
Alignment explanation
Indices: 30072--30105 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
30062 CAATTTTATG
30072 TTTTATACGGA
1 TTTTATACGGA
*
30083 TTTTATACGGT
1 TTTTATACGGA
*
30094 TTTTATATGGA
1 TTTTATACGGA
30105 T
1 T
30106 ATCCGCTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (11 bp):
TTTTATACGGA
Found at i:32839 original size:86 final size:86
Alignment explanation
Indices: 32738--32909 Score: 326
Period size: 86 Copynumber: 2.0 Consensus size: 86
32728 CTTACGTATT
32738 TATAGGCAAACCTAAGACACATCCTACCCTTATGACAATCAATACGAACCCTTAGATGAGGCGGC
1 TATAGGCAAACCTAAGACACATCCTACCCTTATGACAATCAATACGAACCCTTAGATGAGGCGGC
32803 ACAAAGGGCAAGATAGACATC
66 ACAAAGGGCAAGATAGACATC
* *
32824 TATAGGCAAACCTAAGACGCATCCTACCCTTATGACAATCAATACGAACCCTTAGATGAGGTGGC
1 TATAGGCAAACCTAAGACACATCCTACCCTTATGACAATCAATACGAACCCTTAGATGAGGCGGC
32889 ACAAAGGGCAAGATAGACATC
66 ACAAAGGGCAAGATAGACATC
32910 AAAATTCTAG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (86 bp):
TATAGGCAAACCTAAGACACATCCTACCCTTATGACAATCAATACGAACCCTTAGATGAGGCGGC
ACAAAGGGCAAGATAGACATC
Found at i:36932 original size:5 final size:5
Alignment explanation
Indices: 36922--36954 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
36912 TGAAGGAGCA
36922 TTGCC TTGCC TTGCC TTGCC TTGCC TTGCC TTG
1 TTGCC TTGCC TTGCC TTGCC TTGCC TTGCC TTG
36955 AAAGTTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.36, G:0.21, T:0.42
Consensus pattern (5 bp):
TTGCC
Found at i:40018 original size:22 final size:23
Alignment explanation
Indices: 39992--40035 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
39982 AAATCTGAGG
39992 CTACCAAGCCCCGGGT-ACCCCC
1 CTACCAAGCCCCGGGTGACCCCC
* *
40014 CTACCCAGCCCTGGGTGACCCC
1 CTACCAAGCCCCGGGTGACCCC
40036 AGAAGCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.16, C:0.52, G:0.20, T:0.11
Consensus pattern (23 bp):
CTACCAAGCCCCGGGTGACCCCC
Found at i:43032 original size:21 final size:21
Alignment explanation
Indices: 43008--43108 Score: 150
Period size: 21 Copynumber: 4.8 Consensus size: 21
42998 CTTAGGCAAT
* *
43008 TCCAATGAGCTTGAAATCTTC
1 TCCAATGAGCTTGGAACCTTC
43029 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
43050 TCCAATGAGCTTGGCACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
43071 TCCAATGAGCATGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
43092 TCCAATGAGCTTGGAAC
1 TCCAATGAGCTTGGAAC
43109 TTGTTCCAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.04
21 69 0.96
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:43109 original size:21 final size:20
Alignment explanation
Indices: 43008--43120 Score: 145
Period size: 21 Copynumber: 5.4 Consensus size: 20
42998 CTTAGGCAAT
*
43008 TCCAATGAGCTTGAAATCTTC
1 TCCAATGAGCTTGGAA-CTTC
43029 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAA-CTTC
*
43050 TCCAATGAGCTTGGCACCTTC
1 TCCAATGAGCTTGG-AACTTC
*
43071 TCCAATGAGCATGGAACTTGC
1 TCCAATGAGCTTGGAACTT-C
*
43092 TCCAATGAGCTTGGAACTTGT
1 TCCAATGAGCTTGGAACTT-C
43113 TCCAATGA
1 TCCAATGA
43121 TCTCCTAGCA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
20 4 0.05
21 78 0.94
22 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (20 bp):
TCCAATGAGCTTGGAACTTC
Found at i:51241 original size:22 final size:22
Alignment explanation
Indices: 51216--51257 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
51206 TCACGGGGCA
51216 TGGCCAAGTCATGACCGGGTTG
1 TGGCCAAGTCATGACCGGGTTG
** *
51238 TGGCCTGGTCATGTCCGGGT
1 TGGCCAAGTCATGACCGGGT
51258 GCCATCGAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.38, T:0.26
Consensus pattern (22 bp):
TGGCCAAGTCATGACCGGGTTG
Done.