Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019524.1 Corchorus olitorius cultivar O-4 contig19557, 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: 56046
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:98 original size:62 final size:62
Alignment explanation
Indices: 1--352 Score: 551
Period size: 62 Copynumber: 5.5 Consensus size: 62
* *
1 CTTCCTCTGTCTTCCCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCTTGCGGAGGCCTCTTC
1 CTTCCTCTGTCTTCTCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
* *
63 CTTCCTCTGTCTTCTCGTGTACCTCCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGTCTTCCTTCC
1 CTTCCTCTGTCTTCTCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG--------CC
128 TCTTC
58 TCTTC
*
133 CTTCCTCTGTCTTCCCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTCTTCTCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
*
195 CTTCCTCTGTCTTCACGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTCTTCTCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
*
257 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
1 CTTCCTCTGTCTTCTCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
* *
319 CTTCCTCTGTCTTCTCGTGTACCTTCGTGTCTGT
1 CTTCCTCTGTCTTCTCGTCTACCTTCGTGCCTGT
353 CGTGCCTTCA
Statistics
Matches: 271, Mismatches: 11, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
62 212 0.78
70 59 0.22
ACGTcount: A:0.03, C:0.39, G:0.21, T:0.36
Consensus pattern (62 bp):
CTTCCTCTGTCTTCTCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
Found at i:238 original size:132 final size:124
Alignment explanation
Indices: 1--352 Score: 569
Period size: 132 Copynumber: 2.8 Consensus size: 124
*
1 CTTCCTCTGTCTTCCCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCTTGCGGAGGCCTCTTCCTT
1 CTTCCTCTGTCTTCCCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
*
66 CCTCTGTCTTCTCGTGTACCTCCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGTCTTCCTTCCTCT
66 CCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGG--------CCTCT
131 TC
123 TC
133 CTTCCTCTGTCTTCCCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
1 CTTCCTCTGTCTTCCCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
* *
198 CCTCTGTCTTCACGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
66 CCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
* *
257 CTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
1 CTTCCTCTGTCTTCCCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
*
322 CCTCTGTCTTCTCGTGTACCTTCGTGTCTGT
66 CCTCTGTCTTCTCGTGTACCTTCGTGCCTGT
353 CGTGCCTTCA
Statistics
Matches: 211, Mismatches: 9, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
124 98 0.46
132 113 0.54
ACGTcount: A:0.03, C:0.39, G:0.21, T:0.36
Consensus pattern (124 bp):
CTTCCTCTGTCTTCCCGTCTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
CCTCTGTCTTCTCGTGTACCTTCGTGCCTGTTGGCCTCGCCTCCTGCGGAGGCCTCTTC
Found at i:1596 original size:12 final size:12
Alignment explanation
Indices: 1579--1604 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1569 TCCAATGAGG
1579 TCAATTTACTTT
1 TCAATTTACTTT
1591 TCAATTTACTTT
1 TCAATTTACTTT
1603 TC
1 TC
1605 CAAAATTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (12 bp):
TCAATTTACTTT
Found at i:2083 original size:25 final size:26
Alignment explanation
Indices: 2055--2103 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
2045 TGCTATTGAA
*
2055 TATGGAATTATATGAC-CCCTACTAG
1 TATGGAACTATATGACGCCCTACTAG
* *
2080 TATGTAACTGTATGACGCCCTACT
1 TATGGAACTATATGACGCCCTACT
2104 GAATATAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (26 bp):
TATGGAACTATATGACGCCCTACTAG
Found at i:2153 original size:25 final size:25
Alignment explanation
Indices: 2122--2221 Score: 110
Period size: 25 Copynumber: 3.8 Consensus size: 25
2112 AACATGCCCT
*
2122 TACTGAATATGCAATTATAGGACCC
1 TACTGAATATGCAACTATAGGACCC
* * *
2147 TATTGAATATGCAACTACATGACCC
1 TACTGAATATGCAACTATAGGACCC
2172 TACTGAATATGCAACTATATGATTATGACCC
1 TACTGAATATGCAACTATA-G-----GACCC
2203 TACTGAATATGCAACTATA
1 TACTGAATATGCAACTATA
2222 TGATAATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
25 38 0.61
31 24 0.39
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (25 bp):
TACTGAATATGCAACTATAGGACCC
Found at i:2200 original size:31 final size:31
Alignment explanation
Indices: 2165--2225 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
2155 ATGCAACTAC
2165 ATGACCCTACTGAATATGCAACTATATGATT
1 ATGACCCTACTGAATATGCAACTATATGATT
2196 ATGACCCTACTGAATATGCAACTATATGAT
1 ATGACCCTACTGAATATGCAACTATATGAT
2226 AATATAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (31 bp):
ATGACCCTACTGAATATGCAACTATATGATT
Found at i:2695 original size:45 final size:45
Alignment explanation
Indices: 2631--2716 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
2621 GTTTGGTGTT
2631 GTGAAGGAGTAGGGAAAGTTGATTAGCAAATTTAATGCAATTTAA
1 GTGAAGGAGTAGGGAAAGTTGATTAGCAAATTTAATGCAATTTAA
2676 GTGAAGGAGTAGGGAAAGTTGATTAGCAAATTTAATGCAAT
1 GTGAAGGAGTAGGGAAAGTTGATTAGCAAATTTAATGCAAT
2717 AAATTGATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.40, C:0.05, G:0.28, T:0.28
Consensus pattern (45 bp):
GTGAAGGAGTAGGGAAAGTTGATTAGCAAATTTAATGCAATTTAA
Found at i:9899 original size:24 final size:24
Alignment explanation
Indices: 9871--9917 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
9861 TTCTTTAAGG
*
9871 GTAGAAAATGGGTGAAAGCCGATT
1 GTAGAAAATGGGAGAAAGCCGATT
9895 GTAGAAAATGGGAGAAAGCCGAT
1 GTAGAAAATGGGAGAAAGCCGAT
9918 GATGAGGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.34, T:0.17
Consensus pattern (24 bp):
GTAGAAAATGGGAGAAAGCCGATT
Found at i:11025 original size:6 final size:6
Alignment explanation
Indices: 11014--11061 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
11004 ACTTCAATTT
* *
11014 AAAAAA AAAAAA AACAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
1 AAAAAC AAAAAC AA-AAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
11062 ACACTTCAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 35 0.88
7 5 0.12
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:11048 original size:22 final size:20
Alignment explanation
Indices: 11014--11062 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
11004 ACTTCAATTT
11014 AAAAAAAAAAAAAACAAACA
1 AAAAAAAAAAAAAACAAACA
11034 AAAACAAAAACAAAAACAAA-A
1 AAAA-AAAAA-AAAAACAAACA
11055 ACAAAAAA
1 A-AAAAAA
11063 CACTTCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.15
21 10 0.38
22 12 0.46
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAACAAACA
Found at i:14100 original size:2 final size:2
Alignment explanation
Indices: 14095--14125 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14085 AACGTGAGGA
14095 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14126 ATTCAATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15372 original size:66 final size:66
Alignment explanation
Indices: 15283--15407 Score: 205
Period size: 66 Copynumber: 1.9 Consensus size: 66
15273 TTGCGCCTCC
*
15283 AGAGGTTGTGCTGGAGCCACCTGACCCAGTTCTTGCACCACCACTCCTGCCAGAGGAGCCGGTGC
1 AGAGGTTGTGCTGGAGCCACCTGACCCAGTTCTCGCACCACCACTCCTGCCAGAGGAGCCGGTGC
15348 T
66 T
* * * *
15349 AGAGTTTGTGTTGGAGCCACCTGAGCCAGTTCTCGCACCACCACTTCTGCCAGAGGAGC
1 AGAGGTTGTGCTGGAGCCACCTGACCCAGTTCTCGCACCACCACTCCTGCCAGAGGAGC
15408 TTGCTCACGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.19, C:0.32, G:0.28, T:0.21
Consensus pattern (66 bp):
AGAGGTTGTGCTGGAGCCACCTGACCCAGTTCTCGCACCACCACTCCTGCCAGAGGAGCCGGTGC
T
Found at i:15685 original size:24 final size:24
Alignment explanation
Indices: 15619--15677 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
15609 TGCATGTTAG
* *
15619 ACCAGCACCACCTCGCTATGTTTT
1 ACCAGCACCACCTCGCTATATTTC
15643 ACCAGCACCACCTCGCTATATTTC
1 ACCAGCACCACCTCGCTATATTTC
15667 ACCAGCACCAC
1 ACCAGCACCAC
15678 TTTGCTATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.42, G:0.10, T:0.22
Consensus pattern (24 bp):
ACCAGCACCACCTCGCTATATTTC
Found at i:22662 original size:73 final size:73
Alignment explanation
Indices: 22542--22683 Score: 232
Period size: 73 Copynumber: 1.9 Consensus size: 73
22532 AGAAAGAATG
* *
22542 CAATCAATTTCGGTTACTAATCATCAGACATCTGGTCTGGTGATAGAGTGCT-AGAATTTTAGTA
1 CAATCAATTTCGGTTACTAACCATCAGACATCTGATCTGGTGATAGAGTGCTGA-AATTTTAGTA
22606 ACAGTAATA
65 ACAGTAATA
* *
22615 CAATCAATTTCGGTTACTAACCATCAGACATCTGATCTGGTGGTAGAGTGCTGAAATTTTAGTTA
1 CAATCAATTTCGGTTACTAACCATCAGACATCTGATCTGGTGATAGAGTGCTGAAATTTTAGTAA
22680 CAGT
66 CAGT
22684 GATTAGCATT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
73 63 0.98
74 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (73 bp):
CAATCAATTTCGGTTACTAACCATCAGACATCTGATCTGGTGATAGAGTGCTGAAATTTTAGTAA
CAGTAATA
Found at i:26931 original size:4 final size:4
Alignment explanation
Indices: 26922--26946 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
26912 GATGAGAAAA
26922 AAAC AAAC AAAC AAAC AAAC AAAC A
1 AAAC AAAC AAAC AAAC AAAC AAAC A
26947 TAAGCCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:27115 original size:12 final size:12
Alignment explanation
Indices: 27098--27122 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27088 ATACATCCTC
27098 CAATGATTCCAA
1 CAATGATTCCAA
27110 CAATGATTCCAA
1 CAATGATTCCAA
27122 C
1 C
27123 CTTTGGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (12 bp):
CAATGATTCCAA
Found at i:28850 original size:36 final size:36
Alignment explanation
Indices: 28799--28875 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 36
28789 GCATCTCCTG
*
28799 AAACAGATGAGATTGATAATCATAGTCCAATTAAGC
1 AAACAGATGAGATTGATAATCATAATCCAATTAAGC
*
28835 AAACAGAT-AGCATTGATAGTCATAATCCAATTAAGC
1 AAACAGATGAG-ATTGATAATCATAATCCAATTAAGC
28871 AAACA
1 AAACA
28876 AGGCCTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 2 0.05
36 36 0.95
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (36 bp):
AAACAGATGAGATTGATAATCATAATCCAATTAAGC
Found at i:54657 original size:31 final size:30
Alignment explanation
Indices: 54622--54702 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 30
54612 CATGCCACGT
* *
54622 AAATGACACGTGGCATGTCATGTGTACCAAA
1 AAATGACACGTGGCACGCCATGTGTA-CAAA
**
54653 AAATGACATATGGCACGCCATGTGTACAAA
1 AAATGACACGTGGCACGCCATGTGTACAAA
* *
54683 AAAGGACACGTGACACGCCA
1 AAATGACACGTGGCACGCCA
54703 CGTGCTAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 20 0.48
31 22 0.52
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (30 bp):
AAATGACACGTGGCACGCCATGTGTACAAA
Done.