Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018870.1 Corchorus olitorius cultivar O-4 contig18903, 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: 12532
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1204 original size:12 final size:12
Alignment explanation
Indices: 1189--1223 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
1179 CTAATAGTTG
1189 AACTTGAAAGGC
1 AACTTGAAAGGC
1201 AACTTGAAAGGC
1 AACTTGAAAGGC
1213 AACTTGAAAGG
1 AACTTGAAAGG
1224 AGAGTGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (12 bp):
AACTTGAAAGGC
Found at i:4438 original size:2 final size:2
Alignment explanation
Indices: 4431--4464 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
4421 TCACATCTAT
*
4431 TA TA TA TA TA TA TA TA TA TA TA TT TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4465 CAATGTCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6917 original size:25 final size:25
Alignment explanation
Indices: 6888--6938 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
6878 AGATATATAT
6888 ATATAAATCAAAAGATAATTAATTG
1 ATATAAATCAAAAGATAATTAATTG
6913 ATATAAATCAAAAGATAATTAATTG
1 ATATAAATCAAAAGATAATTAATTG
6938 A
1 A
6939 ATTGAATTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (25 bp):
ATATAAATCAAAAGATAATTAATTG
Found at i:11693 original size:22 final size:22
Alignment explanation
Indices: 11663--11713 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
11653 CCCTTCGTCA
*
11663 TATTTTCTTCTTCTCCATA-TTC
1 TATTATCTT-TTCTCCATACTTC
11685 TATTATC-TTTCTCCATACTTC
1 TATTATCTTTTCTCCATACTTC
*
11706 AATTATCT
1 TATTATCT
11714 ACTCCCTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 9 0.36
21 10 0.40
22 6 0.24
ACGTcount: A:0.20, C:0.25, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTATCTTTTCTCCATACTTC
Found at i:11698 original size:20 final size:21
Alignment explanation
Indices: 11673--11713 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11663 TATTTTCTTC
*
11673 TTCTCCATA-TTCTATTATCT
1 TTCTCCATACTTCAATTATCT
11693 TTCTCCATACTTCAATTATCT
1 TTCTCCATACTTCAATTATCT
11714 ACTCCCTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (21 bp):
TTCTCCATACTTCAATTATCT
Found at i:11718 original size:20 final size:20
Alignment explanation
Indices: 11671--11718 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
11661 CATATTTTCT
*
11671 TCTT-CTCCATATTCTATTA
1 TCTTACTCCATATTCAATTA
*
11690 TCTTTCTCCATACTTCAATTA
1 TCTTACTCCATA-TTCAATTA
11711 TC-TACTCC
1 TCTTACTCC
11719 CTTGCTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (20 bp):
TCTTACTCCATATTCAATTA
Found at i:12060 original size:5 final size:5
Alignment explanation
Indices: 12050--12074 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12040 CATTTTAAAT
12050 TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA
12075 CATATTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:12470 original size:180 final size:178
Alignment explanation
Indices: 12148--12471 Score: 449
Period size: 180 Copynumber: 1.8 Consensus size: 178
12138 CCAATCAAGA
*
12148 TGATTCAAGTGTCTATTAAAAGGTTGTTCCATAATCTACAACTTTCATGAAAGACTCGAAAACTA
1 TGATTCAAGTGTCTATTAAAAGGTTATTCCATAATCTACAACTTTCATGAAAGACTCGAAAACTA
* * * * *
12213 AATTTAATGTTTCAAGTATCAAAAAAGCTTCCGAATAATTAGTTATTTCGGTTAACGGGAATGAA
66 AATTTAATGTTTCAAGTATCAAAAAAACTTCCAAAAAATTAATTATTTCGGTTAACGAGAATGAA
12278 CGATCCACTTAATATAACATTACTTTTGATCCAAATGTCTTATTGAGC
131 CGATCCACTTAATATAACATTACTTTTGATCCAAATGTCTTATTGAGC
** * *
12326 TGATTCAAGTGTC-ATATAAAAGGTTATTTTATATGATCTACAACTTTCATGCAAGACTCGAAAG
1 TGATTCAAGTGTCTAT-TAAAAGGTTATTCCATA--ATCTACAACTTTCATGAAAGACTCGAAAA
**
12390 CTAAATTTAATGTTTTTAGTAT-AAAAAATACTTCCAAAAAATTAATT-TTTCGGTT-ACGAGAA
63 CTAAATTTAATGTTTCAAGTATCAAAAAA-ACTTCCAAAAAATTAATTATTTCGGTTAACGAGAA
*
12452 TAGAACGGTCCTACTTAATA
127 T-GAACGATCC-ACTTAATA
12472 ATATATAATT
Statistics
Matches: 127, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
177 2 0.02
178 34 0.27
179 22 0.17
180 69 0.54
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (178 bp):
TGATTCAAGTGTCTATTAAAAGGTTATTCCATAATCTACAACTTTCATGAAAGACTCGAAAACTA
AATTTAATGTTTCAAGTATCAAAAAAACTTCCAAAAAATTAATTATTTCGGTTAACGAGAATGAA
CGATCCACTTAATATAACATTACTTTTGATCCAAATGTCTTATTGAGC
Done.