Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016346.1 Corchorus olitorius cultivar O-4 contig16379, 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: 60479
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:376 original size:13 final size:13
Alignment explanation
Indices: 358--384 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
348 CCTACATAAT
358 AATAGCATATATA
1 AATAGCATATATA
371 AATAGCATATATA
1 AATAGCATATATA
384 A
1 A
385 GATTTGGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
AATAGCATATATA
Found at i:771 original size:30 final size:30
Alignment explanation
Indices: 735--795 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
725 TTAGTAAGAT
735 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
1 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
*
765 ATTAAAATTTGATGGTATAAGAGGAAAGTC
1 ATTAAAATTTGAGGGTATAAGAGGAAAGTC
795 A
1 A
796 AGATAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (30 bp):
ATTAAAATTTGAGGGTATAAGAGGAAAGTC
Found at i:1944 original size:17 final size:17
Alignment explanation
Indices: 1922--1955 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1912 AGAAAATGAG
*
1922 TCGGGTTACTCGGTTTT
1 TCGGGTCACTCGGTTTT
*
1939 TCGGGTCATTCGGTTTT
1 TCGGGTCACTCGGTTTT
1956 GAAAGTCGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.18, G:0.29, T:0.47
Consensus pattern (17 bp):
TCGGGTCACTCGGTTTT
Found at i:6469 original size:13 final size:13
Alignment explanation
Indices: 6451--6477 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6441 CCTACATAAT
6451 AATAGCATATATA
1 AATAGCATATATA
6464 AATAGCATATATA
1 AATAGCATATATA
6477 A
1 A
6478 GATTTGGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
AATAGCATATATA
Found at i:9890 original size:13 final size:13
Alignment explanation
Indices: 9872--9898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9862 ACTACTTAAT
9872 AATAGCATATATA
1 AATAGCATATATA
9885 AATAGCATATATA
1 AATAGCATATATA
9898 A
1 A
9899 GATTTGGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
AATAGCATATATA
Found at i:17968 original size:30 final size:30
Alignment explanation
Indices: 17932--17994 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
17922 GGAGTGTTTT
17932 TTTTTTTTTGGCATC-AATTTTCACATGGAG
1 TTTTTTTTTGGCA-CAAATTTTCACATGGAG
*
17962 TTTTTTTTTGGCACAAATTTTCACCTGGAG
1 TTTTTTTTTGGCACAAATTTTCACATGGAG
17992 TTT
1 TTT
17995 AACAGCTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (30 bp):
TTTTTTTTTGGCACAAATTTTCACATGGAG
Found at i:25882 original size:13 final size:13
Alignment explanation
Indices: 25864--25897 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
25854 TTAATTATTA
*
25864 GGAGGGTCAAGTT
1 GGAGGGTCAAATT
*
25877 GGAGGGACAAATT
1 GGAGGGTCAAATT
25890 GGAGGGTC
1 GGAGGGTC
25898 TGAAAGAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.47, T:0.18
Consensus pattern (13 bp):
GGAGGGTCAAATT
Found at i:26529 original size:24 final size:24
Alignment explanation
Indices: 26501--26550 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
26491 TTATAGGACC
*
26501 TGGGTCGTACGTTGAGGTCACCTG
1 TGGGTCGTACGTTAAGGTCACCTG
*
26525 TGGGTCGTACGTTAAGGTCACGTG
1 TGGGTCGTACGTTAAGGTCACCTG
26549 TG
1 TG
26551 AAGTGCCAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.18, G:0.38, T:0.30
Consensus pattern (24 bp):
TGGGTCGTACGTTAAGGTCACCTG
Found at i:40278 original size:42 final size:41
Alignment explanation
Indices: 40197--40276 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
40187 ATTTTCTCAT
*
40197 ATTTGCCTTAGTCATTTGCCTATCCAACTCATCATTTTTCC
1 ATTTGCCTTAGTCATTTACCTATCCAACTCATCATTTTTCC
40238 ATTTGCCTTTAG-CTATTTACCTATCCAACTCAT-ATTTTT
1 ATTTGCC-TTAGTC-ATTTACCTATCCAACTCATCATTTTT
40277 TCACAACCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
41 14 0.39
42 22 0.61
ACGTcount: A:0.21, C:0.26, G:0.06, T:0.46
Consensus pattern (41 bp):
ATTTGCCTTAGTCATTTACCTATCCAACTCATCATTTTTCC
Found at i:49971 original size:22 final size:22
Alignment explanation
Indices: 49946--49995 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
49936 AATTGAGTTT
49946 TTTTTTTTTTACTTTATT-AAGC
1 TTTTTTTTTTACTTT-TTAAAGC
* *
49968 TTTTCTTTTTCCTTTTTCAAAGC
1 TTTTTTTTTTACTTTTT-AAAGC
49991 TTTTT
1 TTTTT
49996 GGTTACCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.09
22 13 0.57
23 8 0.35
ACGTcount: A:0.14, C:0.14, G:0.04, T:0.68
Consensus pattern (22 bp):
TTTTTTTTTTACTTTTTAAAGC
Found at i:50131 original size:19 final size:19
Alignment explanation
Indices: 50093--50136 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
50083 TAAGTTTTTC
*
50093 AGTAATCTTAACAATTTTT
1 AGTAATCTTAACAATGTTT
* *
50112 AGTAATCTTGATAATGTTT
1 AGTAATCTTAACAATGTTT
50131 AGTAAT
1 AGTAAT
50137 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (19 bp):
AGTAATCTTAACAATGTTT
Found at i:50174 original size:21 final size:19
Alignment explanation
Indices: 50128--50181 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
50118 CTTGATAATG
* *
50128 TTTAGTAATTTTATTAAAT
1 TTTAGTAACTTTATGAAAT
*
50147 TGTAGTAACTTTATGAAACTT
1 TTTAGTAACTTTATGAAA--T
*
50168 TTTAGTAACATTAT
1 TTTAGTAACTTTAT
50182 CAATTTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 15 0.54
21 13 0.46
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (19 bp):
TTTAGTAACTTTATGAAAT
Found at i:50225 original size:20 final size:21
Alignment explanation
Indices: 50152--50223 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
50142 TAAATTGTAG
* * *
50152 TAACTTTATGAAACTTTTTAG
1 TAACATTATCAAACTTTTTAA
**
50173 TAACATTATCAATTTATTTTAA
1 TAACATTATCAAACT-TTTTAA
*
50195 TAATC-TTAT-AAACTTTTTAC
1 TAA-CATTATCAAACTTTTTAA
50215 TAACATTAT
1 TAACATTAT
50224 AATTTTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
19 1 0.03
20 12 0.30
21 14 0.35
22 12 0.30
23 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (21 bp):
TAACATTATCAAACTTTTTAA
Found at i:50231 original size:20 final size:20
Alignment explanation
Indices: 50166--50232 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
50156 TTTATGAAAC
*
50166 TTTTTAGTAACATTATCAATT
1 TTTTTAATAACATTAT-AATT
**
50187 TATTTTAATAATC-TTATAAAC
1 T-TTTTAATAA-CATTATAATT
*
50208 TTTTTACTAACATTATAATT
1 TTTTTAATAACATTATAATT
50228 TTTTT
1 TTTTT
50233 TTAGAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 19 0.51
21 4 0.11
22 12 0.32
23 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.01, T:0.55
Consensus pattern (20 bp):
TTTTTAATAACATTATAATT
Found at i:55347 original size:2 final size:2
Alignment explanation
Indices: 55334--55374 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
55324 GGTACTAAGC
*
55334 AT AT AT AA AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55375 GAAAATATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57889 original size:51 final size:54
Alignment explanation
Indices: 57798--57905 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 54
57788 CTTTTTCAAT
57798 TTCCTTGTTACTACTCATGTTACTACTTTTCTTAAAGATGCACACCGAAAGCAGG
1 TTCCTTGTTACTAC-CATGTTACTACTTTTCTTAAAGATGCACACCGAAAGCAGG
57853 TTCCTTGTTACTA-C-TGTTACTA-TTTTCTTAAAGATGCACACCGAAAGCAGG
1 TTCCTTGTTACTACCATGTTACTACTTTTCTTAAAGATGCACACCGAAAGCAGG
57904 TT
1 TT
57906 ACTTTTTTAC
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
51 31 0.58
52 8 0.15
53 1 0.02
55 13 0.25
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (54 bp):
TTCCTTGTTACTACCATGTTACTACTTTTCTTAAAGATGCACACCGAAAGCAGG
Found at i:58310 original size:33 final size:33
Alignment explanation
Indices: 58222--58310 Score: 80
Period size: 33 Copynumber: 2.8 Consensus size: 33
58212 CGGGGGGCAA
*
58222 GCACAGTCAGGTCA-AGCACCCCAA--G-TGGCC
1 GCACAGTCAGGTCATA-CACGCCAAGTGTTGGCC
* *
58252 GCACAGTCAGGTCATACGCGTCAAGTGTTGGCC
1 GCACAGTCAGGTCATACACGCCAAGTGTTGGCC
* *
58285 GCGCAGTTAGGTCA-ACCACGCCAAGT
1 GCACAGTCAGGTCATA-CACGCCAAGT
58311 AGAAGTCGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
30 19 0.40
31 1 0.02
32 2 0.04
33 25 0.53
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.16
Consensus pattern (33 bp):
GCACAGTCAGGTCATACACGCCAAGTGTTGGCC
Found at i:59312 original size:42 final size:43
Alignment explanation
Indices: 59261--59353 Score: 118
Period size: 45 Copynumber: 2.2 Consensus size: 43
59251 AGTGCATTAC
*
59261 CTAA-ATTCTA-CTACATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTACATCTCTAGATAATTCATCAAAATAAAG
* *
59302 CTAATATTCTAGTCCTCCATCTTTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTACATCTCTAGATAATTCATCAAAATAAAG
*
59347 GTAATAT
1 CTAATAT
59354 ATATTAATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.14
45 34 0.77
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTACATCTCTAGATAATTCATCAAAATAAAG
Done.