Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014460.1 Corchorus capsularis cultivar CVL-1 contig14481, 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: 7567
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4812 original size:5 final size:6
Alignment explanation
Indices: 4775--4825 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
4765 TTGTTTGGCA
* *
4775 TCGTTT TCGTTTT TCTGTTTT TTGTTT TTG-TT TCGTTT TCGTTT TCGTTT
1 TCGTTT TCG-TTT TC-G-TTT TCGTTT TCGTTT TCGTTT TCGTTT TCGTTT
4825 T
1 T
4826 ATTTTTGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 4 0.10
6 24 0.60
7 6 0.15
8 6 0.15
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.73
Consensus pattern (6 bp):
TCGTTT
Found at i:4818 original size:11 final size:12
Alignment explanation
Indices: 4775--4825 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 12
4765 TTGTTTGGCA
4775 TCGTTTTCGTTTT
1 TCGTTTTCG-TTT
*
4788 TCTGTTTTTTGTTT
1 TC-G-TTTTCGTTT
*
4802 TTG-TTTCGTTT
1 TCGTTTTCGTTT
4813 TCGTTTTCGTTT
1 TCGTTTTCGTTT
4825 T
1 T
4826 ATTTTTGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
11 9 0.29
12 9 0.29
13 3 0.10
14 5 0.16
15 5 0.16
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.73
Consensus pattern (12 bp):
TCGTTTTCGTTT
Found at i:6743 original size:142 final size:140
Alignment explanation
Indices: 6583--7030 Score: 421
Period size: 149 Copynumber: 3.0 Consensus size: 140
6573 GGTCAATCAC
*
6583 AATAATCTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAAATAT-AAGTTT-TT-AATG
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAAATATCAA-TTTATTAAATG
* * *
6645 -A-AA-A-TAGAATCAAACTATATATTAAAAAATTTTAATACTCCAATATCTAAGTTTTTAATGA
65 AAGAATAGTAGAATCAAAATATATATTAAAAAATTTT-A-A-T---ATATCCAAGTTTTAAATGA
6706 AAAATAGTAAAATGGTAAA
124 AAAATAGT--AATGGTAAA
6725 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTAT-AAAAATATCGAATTTAATTAAAT
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAAATATC-AATTT-ATTAAAT
6789 GCAAATAGAATTTTTAGTAGAATCAAAATATATATTAAAAAATTTTAATATATCCAAGTTTTAAA
64 G---A-AGAA----TAGTAGAATCAAAATATATATTAAAAAATTTTAATATATCCAAGTTTTAAA
6854 TGAAAAATAGTAATGGTAAA
121 TGAAAAATAGTAATGGTAAA
* * * *
6874 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAGTCAT-AAAAATATTGAATTTAATTAGAT
1 AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAAATA-TCAATTT-ATTAAAT
* * * * *
6938 GAA-AATAGAGTTTTTAATAGAATCAAACTATATATTAAAATATTTTAATATATTCAATTTTTTA
64 GAAGAAT--AG-------TAGAATCAAAATATATATTAAAAAATTTTAATATATCCAAGTTTTAA
7002 ATGAAAAATAGTAAAATGGTAAA
120 ATGAAAAATAGT--AATGGTAAA
7025 AATAAA
1 AATAAA
7031 GTAATTATAA
Statistics
Matches: 264, Mismatches: 13, Indels: 49
0.81 0.04 0.15
Matches are distributed among these distances:
140 1 0.00
141 8 0.03
142 45 0.17
143 2 0.01
144 4 0.02
145 5 0.02
146 1 0.00
149 122 0.46
150 2 0.01
151 42 0.16
154 1 0.00
155 1 0.00
156 2 0.01
157 28 0.11
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (140 bp):
AATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAAATATCAATTTATTAAATGA
AGAATAGTAGAATCAAAATATATATTAAAAAATTTTAATATATCCAAGTTTTAAATGAAAAATAG
TAATGGTAAA
Found at i:6757 original size:14 final size:14
Alignment explanation
Indices: 6713--6759 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
6703 TGAAAAATAG
6713 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
* * * *
6727 TAAACT-TTTAAAT
1 TAAAATGGTAAAAA
6740 TAAAATGGTAAAAA
1 TAAAATGGTAAAAA
6754 TAAAAT
1 TAAAAT
6760 AATTATAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (14 bp):
TAAAATGGTAAAAA
Found at i:6825 original size:157 final size:152
Alignment explanation
Indices: 6647--7030 Score: 587
Period size: 149 Copynumber: 2.5 Consensus size: 152
6637 TTTTAATGAA
6647 AATAGAATCAAACTATATATTAAAAAATTTTAATACTCCAATATCTAAGTTTTTAATGAAAAATA
1 AATAGAATCAAACTATATATTAAAAAATTTTAATA-T---ATATC-AAGTTTTTAATGAAAAATA
*
6712 GTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATTATAAAAATATCGA
61 GTAAAATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATCATAAAAATATCGA
*
6777 ATTTAATTAAATGCAAATAGAATTTTT
126 ATTTAATTAAATGAAAATAGAATTTTT
* * * *
6804 AGTAGAATCAAAATATATATTAAAAAATTTTAATATAT-CCAAGTTTTAAATGAAAAATAGT--A
1 AATAGAATCAAACTATATATTAAAAAATTTTAATATATATCAAGTTTTTAATGAAAAATAGTAAA
* *
6866 ATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAATAAAATAGTCATAAAAATATTGAATTTA
66 ATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATCATAAAAATATCGAATTTA
* *
6931 ATTAGATGAAAATAGAGTTTTT
131 ATTAAATGAAAATAGAATTTTT
* *
6953 AATAGAATCAAACTATATATTAAAATATTTTAATATAT-TCAATTTTTTAATGAAAAATAGTAAA
1 AATAGAATCAAACTATATATTAAAAAATTTTAATATATATCAAGTTTTTAATGAAAAATAGTAAA
7017 ATGGTAAAAATAAA
66 ATGGTAAAAATAAA
7031 GTAATTATAA
Statistics
Matches: 209, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
149 137 0.66
151 35 0.17
152 1 0.00
153 2 0.01
156 1 0.00
157 33 0.16
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (152 bp):
AATAGAATCAAACTATATATTAAAAAATTTTAATATATATCAAGTTTTTAATGAAAAATAGTAAA
ATGGTAAAAATAAACTTTTAAATTAAAATGGTAAAAATAAAATAATCATAAAAATATCGAATTTA
ATTAAATGAAAATAGAATTTTT
Done.