Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019757.1 Corchorus olitorius cultivar O-4 contig19790, 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: 11359
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Found at i:1127 original size:2 final size:2
Alignment explanation
Indices: 1122--1150 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1112 TTTGTTGAAT
1122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1151 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6210 original size:100 final size:100
Alignment explanation
Indices: 6037--6736 Score: 1131
Period size: 100 Copynumber: 7.0 Consensus size: 100
6027 ATTTTTATCT
6037 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
1 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
*
6102 CCCTGGACTCTTTGAGAGAACGGCAACGTTCGTAA
66 CCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
* * * *
6137 TTGACTTTTGAATTCAATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGTCGAACGTAAAG
1 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
*
6202 CCCTGGACTCTTTGAGAGAACGGCAACGTTCGTAA
66 CCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
* *
6237 TTGACCTTAGAATTTGATCCGGACTCCACGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
1 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
* *
6302 CCCTAGACTCTTTGTGAGAATGGCAACGTTCGTAA
66 CCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
6337 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
1 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
6402 CCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
66 CCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
6437 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
1 TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
*
6502 CCCTGGACTCTTTGTGAGAACGGCAACGTTCGTGA
66 CCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
** * * *
6537 TTGACCTTAGACCTCGATCTGGACT--CCGATGAGAACATCGAATCTAAGTTTGCTGAACGTAAA
1 TTGACCTTAGAATTCGATCCGGACTCCCCG-TGAGAACATCGAATCTAAGTTGGCCGAACGTAAA
* *
6600 GCCCTGGACTCTTTGTGAGAGCGGCAACGTTCGTGA
65 GCCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
** *
6636 TTGACCTTAGACCTCGATCTGGACT--CCGATGAGAACATCGAATCTAAGTTGGCCGAACGTAAA
1 TTGACCTTAGAATTCGATCCGGACTCCCCG-TGAGAACATCGAATCTAAGTTGGCCGAACGTAAA
* * *
6699 G-CCTGGACTCTTTGAGAGAACGACAATGTTCGTAA
65 GCCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
6734 TTG
1 TTG
6737 TAACAAACAA
Statistics
Matches: 568, Mismatches: 31, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
98 35 0.06
99 129 0.23
100 404 0.71
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (100 bp):
TTGACCTTAGAATTCGATCCGGACTCCCCGTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAG
CCCTGGACTCTTTGTGAGAACGGCAACGTTCGTAA
Found at i:6419 original size:49 final size:49
Alignment explanation
Indices: 6266--6522 Score: 129
Period size: 49 Copynumber: 5.2 Consensus size: 49
6256 CGGACTCCAC
*
6266 GTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCCCTAGACTCTTT
1 GTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCCCTGGACTCTTT
* * * ** * * ***
6315 GTGAGAATGGCAACG-TTCGTAA-TTGACCTTA-G-AATTCGATCC-GGACTCCCC
1 GTGAGAA---CATCGAATC-TAAGTTGGCCGAACGTAA--AG-CCCTGGACTCTTT
6366 GTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCCCTGGACTCTTT
1 GTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCCCTGGACTCTTT
* * * ** * * ***
6415 GTGAGAACGGCAACG-TTCGTAA-TTGACCTTA-G-AATTCGATCC-GGACTCCCC
1 GTGAGAA---CATCGAATC-TAAGTTGGCCGAACGTAA--AG-CCCTGGACTCTTT
6466 GTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCCCTGGACTCTTT
1 GTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCCCTGGACTCTTT
6515 GTGAGAAC
1 GTGAGAAC
6523 GGCAACGTTC
Statistics
Matches: 143, Mismatches: 41, Indels: 48
0.62 0.18 0.21
Matches are distributed among these distances:
48 18 0.13
49 56 0.39
50 4 0.03
51 47 0.33
52 18 0.13
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (49 bp):
GTGAGAACATCGAATCTAAGTTGGCCGAACGTAAAGCCCTGGACTCTTT
Found at i:6470 original size:51 final size:51
Alignment explanation
Indices: 6315--6473 Score: 125
Period size: 51 Copynumber: 3.2 Consensus size: 51
6305 TAGACTCTTT
*
6315 GTGAGAATGGCAACGTTCGTAATTGACCTTAGAATTCGATCCGGACTCCCC
1 GTGAGAACGGCAACGTTCGTAATTGACCTTAGAATTCGATCCGGACTCCCC
* * * * ** * ***
6366 GTGAGAA---CATCGAATC-TAAGTTGGCC---GAACGTAAAGCCCTGGACTCTTT
1 GTGAGAACGGCAACG-TTCGTAA-TTGACCTTAGAA-TTCGA-TCC-GGACTCCCC
6415 GTGAGAACGGCAACGTTCGTAATTGACCTTAGAATTCGATCCGGACTCCCC
1 GTGAGAACGGCAACGTTCGTAATTGACCTTAGAATTCGATCCGGACTCCCC
6466 GTGAGAAC
1 GTGAGAAC
6474 ATCGAATCTA
Statistics
Matches: 76, Mismatches: 20, Indels: 24
0.63 0.17 0.20
Matches are distributed among these distances:
46 3 0.04
47 2 0.03
48 9 0.12
49 20 0.26
51 28 0.37
52 9 0.12
53 2 0.03
54 3 0.04
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.24
Consensus pattern (51 bp):
GTGAGAACGGCAACGTTCGTAATTGACCTTAGAATTCGATCCGGACTCCCC
Found at i:6562 original size:51 final size:51
Alignment explanation
Indices: 6504--6661 Score: 118
Period size: 51 Copynumber: 3.2 Consensus size: 51
6494 ACGTAAAGCC
6504 CTGGACTCTTTGTGAGAACGGCAACGTTCGTGATTGACCTTAGACCTCGAT
1 CTGGACTCTTTGTGAGAACGGCAACGTTCGTGATTGACCTTAGACCTCGAT
* ** * * * * *
6555 CTGGACTC--CGATGAGAACATCGAATCTAAGTT--TG-CTGAACGTAAAGC-C---
1 CTGGACTCTTTG-TGAGAACGGC-AA-C---GTTCGTGATTGACCTTAGACCTCGAT
*
6603 CTGGACTCTTTGTGAGAGCGGCAACGTTCGTGATTGACCTTAGACCTCGAT
1 CTGGACTCTTTGTGAGAACGGCAACGTTCGTGATTGACCTTAGACCTCGAT
6654 CTGGACTC
1 CTGGACTC
6662 CGATGAGAAC
Statistics
Matches: 75, Mismatches: 17, Indels: 30
0.61 0.14 0.25
Matches are distributed among these distances:
44 3 0.04
46 2 0.03
47 9 0.12
48 11 0.15
49 8 0.11
50 9 0.12
51 19 0.25
52 9 0.12
53 2 0.03
55 3 0.04
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.27
Consensus pattern (51 bp):
CTGGACTCTTTGTGAGAACGGCAACGTTCGTGATTGACCTTAGACCTCGAT
Found at i:10397 original size:2 final size:2
Alignment explanation
Indices: 10390--10419 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10380 GACTAGTATG
10390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10420 TATTACCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.