Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023788.1 Corchorus olitorius cultivar O-4 contig23821, 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: 12572
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:984 original size:30 final size:29
Alignment explanation
Indices: 920--999 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
910 TAGGGTCATC
* ** *
920 CAGGGGCATTTGGGTCATTTTTGCGTATT
1 CAGGGGCATTTTGGTCATTTTTGCACACT
*
949 CAGGGGTATTTTGGTCATTTTTGCACACT
1 CAGGGGCATTTTGGTCATTTTTGCACACT
*
978 CAAGGGGCATTGTGGTCATTTT
1 C-AGGGGCATTTTGGTCATTTT
1000 AAGCCCACTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 25 0.58
30 18 0.42
ACGTcount: A:0.16, C:0.15, G:0.29, T:0.40
Consensus pattern (29 bp):
CAGGGGCATTTTGGTCATTTTTGCACACT
Found at i:1643 original size:22 final size:22
Alignment explanation
Indices: 1617--1666 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1607 TTCAAAGAAG
1617 TCCTTTCTCCCCAAAGGCCACA
1 TCCTTTCTCCCCAAAGGCCACA
*
1639 TCCTTTCTCCCCAAAGGCCATA
1 TCCTTTCTCCCCAAAGGCCACA
1661 TCCTTT
1 TCCTTT
1667 GCTTGAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.42, G:0.08, T:0.30
Consensus pattern (22 bp):
TCCTTTCTCCCCAAAGGCCACA
Found at i:8810 original size:35 final size:35
Alignment explanation
Indices: 8720--9195 Score: 342
Period size: 36 Copynumber: 13.9 Consensus size: 35
8710 CTGAAAATTT
* *
8720 ATTTCAGTTGATCCAGGGCGATCTTTCCTTCCA-TTT
1 ATTTCAATTGATCCAGGGCGATCTTT-CTT-CAGTTC
*** *
8756 ATTTCGGCTGATCCAGGGCGATATTTCTTCAGTTC
1 ATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTC
* ** *
8791 ATTTTAATTGATCCAGGGCGATCTTTCCCCAATT-
1 ATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTC
* *
8825 ACTTCAGTTGATCCAGGGCGA----TC-T---TT-
1 ATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTC
* * *
8851 ATTTCAGTTGA-CCTAGGGCGGTCTTTCTTCAATTC
1 ATTTCAATTGATCC-AGGGCGATCTTTCTTCAGTTC
* *
8886 ATTTTAATGGATCCAGGGCGATCTTTTCTTCAG--C
1 ATTTCAATTGATCCAGGGCGATC-TTTCTTCAGTTC
* * * * *
8920 --TT-ACTTGACCCAGGGCGGTCTTTCTCCAGTTT
1 ATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTC
* * * *
8952 ATTTCAGTTGATCCAGGGCAATCTTTTATTCAGTTT
1 ATTTCAATTGATCCAGGGCGATC-TTTCTTCAGTTC
*
8988 ATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTTC
1 ATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTC
* *
9023 ATTTTAATTGATCCAGGGCGATCTTTCCTC-GATT-
1 ATTTCAATTGATCCAGGGCGATCTTTCTTCAG-TTC
** * *
9057 ACCTCAATTGATCCAGGGCGATCTTTATTTCAGTTG
1 ATTTCAATTGATCCAGGGCGATCTTT-CTTCAGTTC
* *
9093 ATTTCAATTGATCCAGGGCGATCTTTATTTCAGTTT
1 ATTTCAATTGATCCAGGGCGATCTTT-CTTCAGTTC
* * * * *
9129 ATTTCAGTTGACCCAGGGCGGTCTTTCTTCAATTT
1 ATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTC
* * * *
9164 ATTTTAATGGATCGAGGGCGATATTTTCTTCA
1 ATTTCAATTGATCCAGGGCGAT-CTTTCTTCA
9196 ATTTATCAAT
Statistics
Matches: 355, Mismatches: 61, Indels: 48
0.77 0.13 0.10
Matches are distributed among these distances:
25 2 0.01
26 18 0.05
30 12 0.03
31 15 0.04
32 2 0.01
34 49 0.14
35 127 0.36
36 130 0.37
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (35 bp):
ATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTC
Found at i:8856 original size:26 final size:26
Alignment explanation
Indices: 8827--8876 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
8817 CCCCAATTAC
8827 TTCAGTTGATCC-AGGGCGATCTTTAT
1 TTCAGTTGA-CCTAGGGCGATCTTTAT
*
8853 TTCAGTTGACCTAGGGCGGTCTTT
1 TTCAGTTGACCTAGGGCGATCTTT
8877 CTTCAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (26 bp):
TTCAGTTGACCTAGGGCGATCTTTAT
Found at i:9135 original size:141 final size:136
Alignment explanation
Indices: 8848--9195 Score: 457
Period size: 141 Copynumber: 2.5 Consensus size: 136
8838 CAGGGCGATC
8848 TTTATTTCAGTTGACCTAGGGCGGTCTTTCTTCAATTCATTTTAATGGATCCAGGGCGATCTTTT
1 TTTATTTCAGTTGACC-AGGGCGGTCTTTCTTCAATTCATTTTAATGGATCCAGGGCGATCTTTT
* * * * * *
8913 CTTCAGCTTACTTGACCCAGGGCGGTCTTTCTCCAGTTTATTTCAGTTGATCCAGGGCAATCTTT
65 CTTCACCTCAATTGACCCAGGGCGATCTTTCTCCAGTTGATTTCAATTGATCCAGGGCAATCTTT
8978 TATTCAG
130 TATTCAG
* * *
8985 TTTATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTTCATTTTAATTGATCCAGGGCGATCTTTC
1 TTTATTTCAGTTGA-CCAGGGCGGTCTTTCTTCAATTCATTTTAATGGATCCAGGGCGATCTTT-
* * * *
9050 CTCGATT-ACCTCAATTGATCCAGGGCGATCTTTATTTCAGTTGATTTCAATTGATCCAGGGCGA
64 -TC--TTCACCTCAATTGACCCAGGGCGATCTTT-CTCCAGTTGATTTCAATTGATCCAGGGCAA
9114 TC-TTTATTTCAG
125 TCTTTTA-TTCAG
* * *
9126 TTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAATTTATTTTAATGGATCGAGGGCGATATTTT
1 TTTATTTCAGTTGA-CCAGGGCGGTCTTTCTTCAATTCATTTTAATGGATCCAGGGCGATCTTTT
9191 CTTCA
65 CTTCA
9196 ATTTATCAAT
Statistics
Matches: 183, Mismatches: 20, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
137 60 0.33
138 3 0.02
139 4 0.02
140 25 0.14
141 91 0.50
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (136 bp):
TTTATTTCAGTTGACCAGGGCGGTCTTTCTTCAATTCATTTTAATGGATCCAGGGCGATCTTTTC
TTCACCTCAATTGACCCAGGGCGATCTTTCTCCAGTTGATTTCAATTGATCCAGGGCAATCTTTT
ATTCAG
Found at i:9615 original size:30 final size:30
Alignment explanation
Indices: 9539--9846 Score: 440
Period size: 30 Copynumber: 10.2 Consensus size: 30
9529 CTTTATCAGT
*
9539 TTTATTTTAAATCCTGTTCGAGGATCATTGC
1 TTTATTTT-AATCCTGTTTGAGGATCATTGC
9570 TTTATTTTAAATCCTGTTTGAGGATCATTGC
1 TTTATTTT-AATCCTGTTTGAGGATCATTGC
*
9601 TTTATTTTAATCCTGTTTGAGGATCGTTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
9631 TTCATGTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
9661 TTCATTTTTAATCCTGTTTGAGGATCATGGC
1 TTTA-TTTTAATCCTGTTTGAGGATCATTGC
*
9692 TTTATTTTAATCATGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* *
9722 TTTATTTTAATCTTGTTTGAGGATCATTAC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
* * *
9752 TTCATTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGTTTGAGGATCATTGC
*
9782 TTTATTATAATCCTGGTTT-AGGATCATTGC
1 TTTATTTTAATCCT-GTTTGAGGATCATTGC
9812 TTTATTTTAATCCTAGTTT-AGGATCATTGC
1 TTTATTTTAATCCT-GTTTGAGGATCATTGC
9842 TTTAT
1 TTTAT
9847 CAGTTAATCC
Statistics
Matches: 252, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
30 184 0.73
31 68 0.27
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (30 bp):
TTTATTTTAATCCTGTTTGAGGATCATTGC
Found at i:9654 original size:91 final size:90
Alignment explanation
Indices: 9539--9843 Score: 443
Period size: 91 Copynumber: 3.4 Consensus size: 90
9529 CTTTATCAGT
* *
9539 TTTATTTTAAATCCTGTTCGAGGATCATTGCTTTATTTTAAATCCTGTTTGAGGATCATTGCTTT
1 TTTATTTT-AATCCTGTTTGAGGATCATTGCTTCATTTT-AATCCTGTTTGAGGATCATTGCTTT
*
9604 ATTTTAATCCTGTTTGAGGATCGTTGC
64 ATTTTAATCCTGTTTGAGGATCATTGC
* * *
9631 TTCATGTTAATCCTGTTTGAGGATCATTGCTTCATTTTTAATCCTGTTTGAGGATCATGGCTTTA
1 TTTATTTTAATCCTGTTTGAGGATCATTGCTTCA-TTTTAATCCTGTTTGAGGATCATTGCTTTA
*
9696 TTTTAATCATGTTTGAGGATCATTGC
65 TTTTAATCCTGTTTGAGGATCATTGC
* * * *
9722 TTTATTTTAATCTTGTTTGAGGATCATTACTTCATTTTAATCCTGGTTGAGGATCGTTGCTTTAT
1 TTTATTTTAATCCTGTTTGAGGATCATTGCTTCATTTTAATCCTGTTTGAGGATCATTGCTTTAT
*
9787 TATAATCCTGGTTT-AGGATCATTGC
66 TTTAATCCT-GTTTGAGGATCATTGC
9812 TTTATTTTAATCCTAGTTT-AGGATCATTGCTT
1 TTTATTTTAATCCT-GTTTGAGGATCATTGCTT
9844 TATCAGTTAA
Statistics
Matches: 192, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
90 71 0.37
91 111 0.58
92 10 0.05
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (90 bp):
TTTATTTTAATCCTGTTTGAGGATCATTGCTTCATTTTAATCCTGTTTGAGGATCATTGCTTTAT
TTTAATCCTGTTTGAGGATCATTGC
Found at i:9866 original size:32 final size:30
Alignment explanation
Indices: 9559--9879 Score: 135
Period size: 30 Copynumber: 10.6 Consensus size: 30
9549 ATCCTGTTCG
* * *
9559 AGGATCATTGCTTTATTTTAAATCC-TGTTT
1 AGGATCATTGCTTTATGTT-AATCCGAGTGT
* * *
9589 GAGGATCATTGCTTTATTTTAATCC-TGTTT
1 -AGGATCATTGCTTTATGTTAATCCGAGTGT
* * * *
9619 GAGGATCGTTGCTTCATGTTAATCC-TGTTT
1 -AGGATCATTGCTTTATGTTAATCCGAGTGT
* * * *
9649 GAGGATCATTGCTTCATTTTTAATCC-TGTTT
1 -AGGATCATTGCTTTA-TGTTAATCCGAGTGT
* * *
9680 GAGGATCATGGCTTTATTTTAAT-C-ATGTTT
1 -AGGATCATTGCTTTATGTTAATCCGA-GTGT
* ** *
9710 GAGGATCATTGCTTTATTTTAAT-CTTGTTT
1 -AGGATCATTGCTTTATGTTAATCCGAGTGT
* * *
9740 GAGGATCATTACTTCATTTTAATCCTG-GT-T
1 -AGGATCATTGCTTTATGTTAATCC-GAGTGT
* *
9770 GAGGATCGTTGCTTTAT-TATAATCCTG-GTTT
1 -AGGATCATTGCTTTATGT-TAATCC-GAGTGT
* * *
9801 AGGATCATTGCTTTATTTTAATCCTAGTTT
1 AGGATCATTGCTTTATGTTAATCCGAGTGT
9831 AGGATCATTGCTTTATCAGTTAATCCCGA-TGT
1 AGGATCATTGCTTTAT--GTTAAT-CCGAGTGT
* *
9863 AGGATTATTGCATTATG
1 AGGATCATTGCTTTATG
9880 AGATAATTTC
Statistics
Matches: 255, Mismatches: 23, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.01
30 178 0.70
31 51 0.20
32 21 0.08
33 3 0.01
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (30 bp):
AGGATCATTGCTTTATGTTAATCCGAGTGT
Found at i:10431 original size:30 final size:29
Alignment explanation
Indices: 10360--10436 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
10350 GGTCATCCAT
* ** *
10360 GGGCATTTTGGCCATTTTTGCGTATTCAG
1 GGGCATTTTGGTCATTTTTGCACACTCAG
*
10389 GGGTATTTTGGTCATTTTTGCACACTCAAG
1 GGGCATTTTGGTCATTTTTGCACACTC-AG
*
10419 GGGCATTGTGGTCATTTT
1 GGGCATTTTGGTCATTTT
10437 AAGCCCACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 22 0.55
30 18 0.45
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.42
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTTGCACACTCAG
Done.