Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018635.1 Corchorus olitorius cultivar O-4 contig18668, 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: 13828
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:1494 original size:20 final size:20
Alignment explanation
Indices: 1469--1509 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1459 GTGGGCTTTT
*
1469 AAATCAACACTAAAGGAAGG
1 AAATCAACAATAAAGGAAGG
1489 AAATCAACAATAAAGGAAGG
1 AAATCAACAATAAAGGAAGG
1509 A
1 A
1510 GATGGGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.12, G:0.20, T:0.10
Consensus pattern (20 bp):
AAATCAACAATAAAGGAAGG
Found at i:2315 original size:15 final size:17
Alignment explanation
Indices: 2283--2317 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2273 CAAAAATCAC
2283 AAGACAAGAAAAAGAAA
1 AAGACAAGAAAAAGAAA
2300 AAGACAA-AAAAA-AAA
1 AAGACAAGAAAAAGAAA
2315 AAG
1 AAG
2318 GGGGGGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 5 0.28
17 7 0.39
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (17 bp):
AAGACAAGAAAAAGAAA
Found at i:4751 original size:2 final size:2
Alignment explanation
Indices: 4744--4790 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4734 GTGCTACATT
4744 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4786 TG TG T
1 TG TG T
4791 AGGCTAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:11412 original size:23 final size:23
Alignment explanation
Indices: 11359--11415 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
11349 TTGAATATTT
*
11359 TTATGAAA-TTTTGATTACCATC
1 TTATGAAATTTTTGATAACCATC
* * *
11381 CTATTAAATTTTTGATAACCATG
1 TTATGAAATTTTTGATAACCATC
11404 TTATGAAATTTT
1 TTATGAAATTTT
11416 AATAATTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 6 0.21
23 22 0.79
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (23 bp):
TTATGAAATTTTTGATAACCATC
Found at i:11495 original size:23 final size:22
Alignment explanation
Indices: 11360--11515 Score: 86
Period size: 22 Copynumber: 7.1 Consensus size: 22
11350 TGAATATTTT
* * *
11360 TATGAAATTTTGATTACCATCC
1 TATGAAATTTTAATAACCTTCC
* * * **
11382 TATTAAATTTTTGATAACCATGT
1 TATGAAA-TTTTAATAACCTTCC
* *
11405 TATGAAATTTTAATAA-TTTATC
1 TATGAAATTTTAATAACCTT-CC
* * * *
11427 TATAAAATTATGATAA-ATTCC
1 TATGAAATTTTAATAACCTTCC
* ***
11448 -ATGAAACTTTAATAACCTAAT
1 TATGAAATTTTAATAACCTTCC
11469 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTAAT-AACCTTCC
*
11492 TATGAAATTTT-GTAACCTTCC
1 TATGAAATTTTAATAACCTTCC
11513 TAT
1 TAT
11516 ATATGATTTT
Statistics
Matches: 101, Mismatches: 28, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
20 11 0.11
21 14 0.14
22 42 0.42
23 34 0.34
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTAATAACCTTCC
Found at i:11510 original size:21 final size:23
Alignment explanation
Indices: 11444--11515 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
11434 TTATGATAAA
*
11444 TTCC-ATGAAACTTTAAT-AACC
1 TTCCTATGAAATTTTAATAAACC
***
11465 TAATTATGAAATTTTAATAAACC
1 TTCCTATGAAATTTTAATAAACC
*
11488 TTCCTATGAAATTTT-GT-AACC
1 TTCCTATGAAATTTTAATAAACC
11509 TTCCTAT
1 TTCCTAT
11516 ATATGATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 12 0.29
22 13 0.32
23 16 0.39
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.40
Consensus pattern (23 bp):
TTCCTATGAAATTTTAATAAACC
Done.