Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016371.1 Corchorus olitorius cultivar O-4 contig16404, 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: 24159
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--26 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
27 GAACCATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:658 original size:48 final size:49
Alignment explanation
Indices: 586--692 Score: 180
Period size: 48 Copynumber: 2.2 Consensus size: 49
576 GGCTAAATGC
586 TCAATTTGGGGCCAAACGTTTGCGGAGATGCTCGATTTGGGGCCAAACG-
1 TCAATTT-GGGCCAAACGTTTGCGGAGATGCTCGATTTGGGGCCAAACGT
*
635 TCAATTTGGGCCAAACGTTTGCGGGGATGCTCGATTTGGGGCCAAACGTT
1 TCAATTTGGGCCAAACGTTTGCGGAGATGCTCGATTTGGGGCCAAACG-T
685 TCAATTTG
1 TCAATTTG
693 AACAAAAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
48 40 0.73
49 7 0.13
50 8 0.15
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (49 bp):
TCAATTTGGGCCAAACGTTTGCGGAGATGCTCGATTTGGGGCCAAACGT
Found at i:851 original size:25 final size:26
Alignment explanation
Indices: 823--908 Score: 81
Period size: 25 Copynumber: 3.4 Consensus size: 26
813 GTAAATAACA
*
823 TATT-TTCTTCTTTTTTTCTTTTTTT
1 TATTCTTCTTCTTTTTTTCTTTTTTC
* * *
848 TATTCTTTTTC-TTTATTCATTTTTC
1 TATTCTTCTTCTTTTTTTCTTTTTTC
* *
873 TCTTCTTCTT-TCTTTTTCTTTTTTC
1 TATTCTTCTTCTTTTTTTCTTTTTTC
898 -ATTCTTTCTTC
1 TATTC-TTCTTC
909 CTCCCTCACT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
24 3 0.06
25 39 0.83
26 5 0.11
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.76
Consensus pattern (26 bp):
TATTCTTCTTCTTTTTTTCTTTTTTC
Found at i:873 original size:32 final size:31
Alignment explanation
Indices: 835--907 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
825 TTTTCTTCTT
* *
835 TTTTTCTTTTTTTTATTCTTTTTCTTTATTCA
1 TTTTTCTTTCTTCT-TTCTTTTTCTTTATTCA
*
867 TTTTTCTCTTCTTCTTTCTTTTTCTTTTTTCA
1 TTTTTCT-TTCTTCTTTCTTTTTCTTTATTCA
899 TTCTTTCTT
1 TT-TTTCTT
908 CCTCCCTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 26 0.72
33 10 0.28
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (31 bp):
TTTTTCTTTCTTCTTTCTTTTTCTTTATTCA
Found at i:894 original size:5 final size:6
Alignment explanation
Indices: 825--895 Score: 67
Period size: 6 Copynumber: 11.7 Consensus size: 6
815 AAATAACATA
*
825 TTTTCT TCTT-T TTTTCT TTTT-T TTATTCT TTTTCT TTATTCAT TTTTC-
1 TTTTCT TTTTCT TTTTCT TTTTCT TT-TTCT TTTTCT TT-TTC-T TTTTCT
*
873 TCTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT T-TTTCT TTTTCT TTTT
896 TCATTCTTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
5 11 0.20
6 26 0.48
7 14 0.26
8 3 0.06
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:9103 original size:22 final size:22
Alignment explanation
Indices: 8966--9696 Score: 192
Period size: 22 Copynumber: 32.8 Consensus size: 22
8956 TATTAATTTT
*
8966 CCTATGAAA-TTTGATAGCCTC
1 CCTATGAAATTTTGATAACCTC
* * * *
8987 CCAATGAAAATTTGAAAACCTT
1 CCTATGAAATTTTGATAACCTC
** *
9009 AATATGAAATTTTGATAACCTT
1 CCTATGAAATTTTGATAACCTC
* * *
9031 CATCTGAAATTTTGATAACCAC
1 CCTATGAAATTTTGATAACCTC
* * * *
9053 CATACGAAATTAATATTAATAGCCTC
1 CCTATGAAA-T--T-TTGATAACCTC
*
9079 CCTATGAAATTTTGATATCCTCCCTAATC
1 CCTATGAAATTTTGATA----ACC---TC
* * * *
9108 CCTATGAAATGTTGTTAAGC-A
1 CCTATGAAATTTTGATAACCTC
* * * *
9129 CATAATGTAGTTTTGATAACATC
1 CCT-ATGAAATTTTGATAACCTC
* * * * *
9152 CCGATAAAATGTT-AGTAATCAC
1 CCTATGAAATTTTGA-TAACCTC
* *
9174 ACTATCAAATTTTGATAA-CTAC
1 CCTATGAAATTTTGATAACCT-C
* * * *
9196 ACTTATTAAATTGTGATAACTTC
1 -CCTATGAAATTTTGATAACCTC
** *
9219 ATTATGAAATTTTTATTAACCTC
1 CCTATGAAATTTTGA-TAACCTC
* *
9242 CATATAAAATTTTGATAACCTC
1 CCTATGAAATTTTGATAACCTC
* *
9264 CATTTGAAATTTTGATAACCTTC
1 CCTATGAAATTTTGATAACC-TC
* *
9287 GC-ATGAAATTTTGATAA-CTAG
1 CCTATGAAATTTTGATAACCT-C
* *
9308 CTTATAAAATTTTGATAACCTC
1 CCTATGAAATTTTGATAACCTC
* *
9330 CTTATGCAAA-TTTGGTAACCTC
1 CCTATG-AAATTTTGATAACCTC
*
9352 CCTACGAAATTTTGATAA--TAC
1 CCTATGAAATTTTGATAACCT-C
*
9373 CATATGAAA--TT--TAACC-C
1 CCTATGAAATTTTGATAACCTC
* *
9390 CATATGAAATTTTGATAATTAACCAC
1 CCTATGAAATTTTG---A-TAACCTC
* **
9416 ACTATGAAATTACGATAACCTC
1 CCTATGAAATTTTGATAACCTC
* * * * *
9438 CTTCTA-AAAATTTTGTTTATCTA
1 C--CTATGAAATTTTGATAACCTC
* *
9461 CCTACGAAATTTTGATAACCAC
1 CCTATGAAATTTTGATAACCTC
* * * *
9483 GCTATCAAATTTTGTTAACTTC
1 CCTATGAAATTTTGATAACCTC
* *
9505 ACTATGAAATTTTGATTACC-C
1 CCTATGAAATTTTGATAACCTC
* * ** *
9526 CGCAATGAAAATGCGATAACCTT
1 C-CTATGAAATTTTGATAACCTC
* **
9549 CCAATGAAATTTT-AGTAACAAC
1 CCTATGAAATTTTGA-TAACCTC
* * * * *
9571 ACTATGAATTTTTTATAATCTT
1 CCTATGAAATTTTGATAACCTC
* *
9593 CCAATGAAATTTTTGATAACCAC
1 CCTATGAAA-TTTTGATAACCTC
** * * *
9616 ATTATTAGATTTTGATAATCT-
1 CCTATGAAATTTTGATAACCTC
*
9637 CCTATTGAAATTTCGATAACCT-
1 CCTA-TGAAATTTTGATAACCTC
* * *
9659 CATATTAAAATTTT-TTAACCT-
1 CCTA-TGAAATTTTGATAACCTC
*
9680 -CTATGATATTTTGATAA
1 CCTATGAAATTTTGATAA
9697 TTATACTATG
Statistics
Matches: 504, Mismatches: 158, Indels: 97
0.66 0.21 0.13
Matches are distributed among these distances:
17 13 0.03
19 11 0.02
20 7 0.01
21 37 0.07
22 309 0.61
23 70 0.14
24 4 0.01
25 8 0.02
26 28 0.06
29 17 0.03
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCTC
Found at i:9212 original size:23 final size:23
Alignment explanation
Indices: 9172--9229 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
9162 GTTAGTAATC
*
9172 ACAC-TATCAAATTTTGATAACT
1 ACACTTATCAAATTGTGATAACT
*
9194 ACACTTATTAAATTGTGATAACT
1 ACACTTATCAAATTGTGATAACT
* *
9217 TCA-TTATGAAATT
1 ACACTTATCAAATT
9230 TTTATTAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (23 bp):
ACACTTATCAAATTGTGATAACT
Found at i:9432 original size:26 final size:25
Alignment explanation
Indices: 9383--9433 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
9373 CATATGAAAT
* **
9383 TTAACCCCATATGAAATTTTGATAA
1 TTAACCACATATGAAATTACGATAA
9408 TTAACCACACTATGAAATTACGATAA
1 TTAACCACA-TATGAAATTACGATAA
9434 CCTCCTTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (25 bp):
TTAACCACATATGAAATTACGATAA
Found at i:20890 original size:13 final size:13
Alignment explanation
Indices: 20872--20898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20862 AGCAATATTG
20872 TGAACAAGTACAT
1 TGAACAAGTACAT
20885 TGAACAAGTACAT
1 TGAACAAGTACAT
20898 T
1 T
20899 TAAGGATTTT
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:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (13 bp):
TGAACAAGTACAT
Found at i:22888 original size:27 final size:27
Alignment explanation
Indices: 22836--22888 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
22826 TAGAATAAAT
****
22836 CCAATTTAAAGTTATGTTTTTTTTATA
1 CCAATTTAAAGTTATGTTACAATTATA
22863 CCAATTTAAAGTTATGTTACAATTAT
1 CCAATTTAAAGTTATGTTACAATTAT
22889 TAAAGTTCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (27 bp):
CCAATTTAAAGTTATGTTACAATTATA
Found at i:23143 original size:33 final size:33
Alignment explanation
Indices: 23103--23177 Score: 143
Period size: 32 Copynumber: 2.3 Consensus size: 33
23093 GCGAAAATAT
23103 ATACTTAATTTTTTTTTTTTTGGTAAAACGAAA
1 ATACTTAATTTTTTTTTTTTTGGTAAAACGAAA
23136 ATACTTAA-TTTTTTTTTTTTGGTAAAACGAAA
1 ATACTTAATTTTTTTTTTTTTGGTAAAACGAAA
23168 ATACTTAATT
1 ATACTTAATT
23178 AAGTACATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 32 0.78
33 9 0.22
ACGTcount: A:0.35, C:0.07, G:0.08, T:0.51
Consensus pattern (33 bp):
ATACTTAATTTTTTTTTTTTTGGTAAAACGAAA
Done.