Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016439.1 Corchorus olitorius cultivar O-4 contig16472, 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: 7861
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:741 original size:44 final size:44
Alignment explanation
Indices: 673--761 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
663 GTTGGCGGCT
* *
673 GTACAAGCCTTGCAGCATCAGGAACACGTGGAAACCCGAATGGA
1 GTACAAGCCTCGCAGCATCAGGAACACATGGAAACCCGAATGGA
** *
717 GTACAAGCCTCGCAGCATTGGGAACCCATGGAAACCCGAATGGA
1 GTACAAGCCTCGCAGCATCAGGAACACATGGAAACCCGAATGGA
761 G
1 G
762 AAACAGAGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.28, T:0.13
Consensus pattern (44 bp):
GTACAAGCCTCGCAGCATCAGGAACACATGGAAACCCGAATGGA
Found at i:858 original size:126 final size:128
Alignment explanation
Indices: 592--952 Score: 476
Period size: 126 Copynumber: 2.8 Consensus size: 128
582 TGGGCTGTAT
**
592 AAGCCTTGCAGCGTCAGGAACCCGTGGAAACCCGAATGGAGAGACAGAGGTTTAGGCAACCAACA
1 AAGCCTTGCAGCGTCAGGAACCCGTGGAAACCCGAATGGAGAGACAGAGGTAGAGGCAACCAAC-
* *
657 AAAGGAGTTGGCGGCTGTACAAGCCTTGCAGCATCAGGAACACGTGGAAACCCGAATGGAGTAC
65 AAAGGAGTTGGCGGCTGTACAAACCTTGCAGCATCAAGAACACGTGGAAACCCGAATGGAGTAC
* * ** * *
721 AAGCCTCGCAGCATTGGGAACCCATGGAAACCCGAATGGAGAAACAGAGGTAGAGGCAACCAAC-
1 AAGCCTTGCAGCGTCAGGAACCCGTGGAAACCCGAATGGAGAGACAGAGGTAGAGGCAACCAACA
* ** *
785 AA-GAGTTGGCGGCTAG-ACAAACCTTGCAGCGTCAAGTTCCCGTGGAAACCCGAATGGAGTAC
66 AAGGAGTTGGCGGCT-GTACAAACCTTGCAGCATCAAGAACACGTGGAAACCCGAATGGAGTAC
* * * * *
847 GAGCCTTGCAGCGTCACGAACTCGTGGAAACCCGAATGGAGAGGCAGAGGCAGAGGCAACCAACA
1 AAGCCTTGCAGCGTCAGGAACCCGTGGAAACCCGAATGGAGAGACAGAGGTAGAGGCAACCAAC-
* * *
912 AAAGGAGTTGGCGGTTGTACAAACTTTGCAGCATCAGGAAC
65 AAAGGAGTTGGCGGCTGTACAAACCTTGCAGCATCAAGAAC
953 CCCGAATGGA
Statistics
Matches: 196, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
126 105 0.54
127 3 0.02
128 3 0.02
129 85 0.43
ACGTcount: A:0.33, C:0.24, G:0.30, T:0.14
Consensus pattern (128 bp):
AAGCCTTGCAGCGTCAGGAACCCGTGGAAACCCGAATGGAGAGACAGAGGTAGAGGCAACCAACA
AAGGAGTTGGCGGCTGTACAAACCTTGCAGCATCAAGAACACGTGGAAACCCGAATGGAGTAC
Found at i:976 original size:35 final size:35
Alignment explanation
Indices: 928--998 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
918 GTTGGCGGTT
*
928 GTACAAACTTTGCAGCATCAGGAACCCCGAATGGA
1 GTACAAACCTTGCAGCATCAGGAACCCCGAATGGA
* ** * *
963 GTACAAGCCTTGCAGTTTCAGGAATCCGGAATGGA
1 GTACAAACCTTGCAGCATCAGGAACCCCGAATGGA
998 G
1 G
999 AGACAGAGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.20
Consensus pattern (35 bp):
GTACAAACCTTGCAGCATCAGGAACCCCGAATGGA
Found at i:5015 original size:25 final size:25
Alignment explanation
Indices: 4986--5035 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
4976 GCACTGTAAT
4986 AGTCTTATCTTATGATAATAATTAA
1 AGTCTTATCTTATGATAATAATTAA
5011 AGTCTTATCTTATGATAATAATTAA
1 AGTCTTATCTTATGATAATAATTAA
5036 TTACTGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (25 bp):
AGTCTTATCTTATGATAATAATTAA
Found at i:5570 original size:34 final size:35
Alignment explanation
Indices: 5525--5599 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 35
5515 TTGCTTTTGC
5525 TCTTCAATTCTTACCCACTCC-CCATCTCATATGA
1 TCTTCAATTCTTACCCACTCCTCCATCTCATATGA
*
5559 TTTTCAATTCTTACCCACTCCTCCATCTCATATGA
1 TCTTCAATTCTTACCCACTCCTCCATCTCATATGA
5594 TCTTCA
1 TCTTCA
5600 GGCTTTCACC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 20 0.53
35 18 0.47
ACGTcount: A:0.23, C:0.36, G:0.03, T:0.39
Consensus pattern (35 bp):
TCTTCAATTCTTACCCACTCCTCCATCTCATATGA
Found at i:5742 original size:27 final size:29
Alignment explanation
Indices: 5712--5765 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
5702 AGGCTCTTAC
5712 AAGGAG-AAGAAAA-ACACTCC-GGGATAA
1 AAGGAGCAAGAAAACA-ACTCCAGGGATAA
5739 AAGGAGCAAGAAAACAACTCCAGGGAT
1 AAGGAGCAAGAAAACAACTCCAGGGAT
5766 TCTGTTGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.25
28 12 0.50
29 6 0.25
ACGTcount: A:0.50, C:0.17, G:0.26, T:0.07
Consensus pattern (29 bp):
AAGGAGCAAGAAAACAACTCCAGGGATAA
Found at i:5885 original size:7 final size:7
Alignment explanation
Indices: 5873--5909 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
5863 GTTATAATTA
5873 TTCTTAG
1 TTCTTAG
5880 TTCTTAG
1 TTCTTAG
*
5887 TTATTA-
1 TTCTTAG
5893 TTCTTAG
1 TTCTTAG
5900 TTCTTAG
1 TTCTTAG
5907 TTC
1 TTC
5910 CTGCTCAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.59
Consensus pattern (7 bp):
TTCTTAG
Found at i:5894 original size:20 final size:20
Alignment explanation
Indices: 5869--5908 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5859 TGAAGTTATA
5869 ATTATTCTTAGTTCTTAGTT
1 ATTATTCTTAGTTCTTAGTT
5889 ATTATTCTTAGTTCTTAGTT
1 ATTATTCTTAGTTCTTAGTT
5909 CCTGCTCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (20 bp):
ATTATTCTTAGTTCTTAGTT
Found at i:7050 original size:128 final size:128
Alignment explanation
Indices: 6915--7169 Score: 406
Period size: 129 Copynumber: 2.0 Consensus size: 128
6905 CCCTCTCTGC
* *
6915 TTTTTTTT-TAATTATTCTCAATTTGTAGAAGTTGAGGTCAATATTTCTTTATTTTAGTTAATAA
1 TTTTTTTTCTAATTATTCTCAATTTATAGAAGTTGAGGTCAATATTTCTTT-GTTTAGTTAATAA
* *
6979 TGGATATTGAAA-TTTTTAAAATTTACATTTGACTCTTTTTGGCTTCTCATTTTTACTATTGTTT
65 TGGATATTGAAATTTTTTAAAATTCACATTTGACTC-TTTTGGCTTCTCATTTTAACTATTGTTT
* *
7043 TTTTTTTTCTAATTGTTCTCAATTTATAGAAGTTGAGGTCAGTATTTCTTTGTTTAGTTAATAAT
1 TTTTTTTTCTAATTATTCTCAATTTATAGAAGTTGAGGTCAATATTTCTTTGTTTAGTTAATAAT
* *
7108 GGATATTGAAATTTTTTAAAGTTCACATTTGACTCTTTTGGGTTCTCATTTTAACTATTGTT
66 GGATATTGAAATTTTTTAAAATTCACATTTGACTCTTTTGGCTTCTCATTTTAACTATTGTT
7170 GACTAATCGA
Statistics
Matches: 117, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
128 57 0.49
129 60 0.51
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.53
Consensus pattern (128 bp):
TTTTTTTTCTAATTATTCTCAATTTATAGAAGTTGAGGTCAATATTTCTTTGTTTAGTTAATAAT
GGATATTGAAATTTTTTAAAATTCACATTTGACTCTTTTGGCTTCTCATTTTAACTATTGTTT
Done.