Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013196.1 Corchorus olitorius cultivar O-4 contig13229, 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: 15602
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Found at i:2630 original size:19 final size:18
Alignment explanation
Indices: 2597--2632 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2587 TGGAAATAAT
2597 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
2615 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
2633 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:11495 original size:39 final size:39
Alignment explanation
Indices: 11452--11543 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
11442 ACATTCAAGT
*
11452 AAACCTGCTTAGGT-CTTCGTTTAGAAGTTTC-GTTTAATC
1 AAACCTGCTTAGGTCCTT-GTTTAGAA-TTTCTGTTTAAGC
11491 AAACCTGCTTAGGTCCTTGTTTAGAATTTCTGTTTAAGC
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTCTGTTTAAGC
*
11530 AAGCCTGCTTAGGT
1 AAACCTGCTTAGGT
11544 ATCTGTTCCG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
38 4 0.08
39 42 0.86
40 3 0.06
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (39 bp):
AAACCTGCTTAGGTCCTTGTTTAGAATTTCTGTTTAAGC
Found at i:11605 original size:147 final size:147
Alignment explanation
Indices: 11344--11665 Score: 416
Period size: 147 Copynumber: 2.2 Consensus size: 147
11334 CTGTTTAAGA
* ** * * * * *
11344 AAACCTGCTTAGATCCCCGCTTAGAATCTCGTTTAAGTAAACCTGCTTAGGTCGCTGTCTTGTTT
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTCGTTTAAGCAAACCTGCTTAGGTAGCTGTCTCGTTT
* *
11409 AGGTGAACCTGCTTAGGATCTCCGCTTAGAGTTACATTCAAGTAAACCTGCTTAGGTCTTCGTTT
66 AAGTAAACCTGCTTAGGATCTCCGCTTAGAGTTACATTCAAGTAAACCTGCTTAGGTCTTCGTTT
**
11474 AGAAGTTTCGTTTAATC
131 AGAAACTTCGTTTAATC
* *
11491 AAACCTGCTTAGGTCCTTGTTTAGAATTTCTGTTTAAGCAAGCCTGCTTAGGTATCTGT-TCCGT
1 AAACCTGCTTAGGTCCTTGTTTAGAATTTC-GTTTAAGCAAACCTGCTTAGGTAGCTGTCT-CGT
* * * *
11555 TTAAGTAAACCTGTTTAGGA-CTTCTGCTTTGAGTT-CATTCGAGTAAACCTGCTTAGGTCTTCG
64 TTAAGTAAACCTGCTTAGGATC-TCCGCTTAGAGTTACATTCAAGTAAACCTGCTTAGGTCTTCG
11618 TTTAGAAACTTCGTTTAATC
128 TTTAGAAACTTCGTTTAATC
* *
11638 AAACCCGCTTAGGTTCTTGTTTAGAATT
1 AAACCTGCTTAGGTCCTTGTTTAGAATT
11666 CCCACTTAAG
Statistics
Matches: 152, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
147 98 0.64
148 54 0.36
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (147 bp):
AAACCTGCTTAGGTCCTTGTTTAGAATTTCGTTTAAGCAAACCTGCTTAGGTAGCTGTCTCGTTT
AAGTAAACCTGCTTAGGATCTCCGCTTAGAGTTACATTCAAGTAAACCTGCTTAGGTCTTCGTTT
AGAAACTTCGTTTAATC
Found at i:12337 original size:20 final size:20
Alignment explanation
Indices: 12312--12350 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12302 TTTGAGCTTT
*
12312 TATCTATTCTTAGATTTATC
1 TATCTATTATTAGATTTATC
12332 TATCTATTATTAGATTTAT
1 TATCTATTATTAGATTTAT
12351 GTAGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.56
Consensus pattern (20 bp):
TATCTATTATTAGATTTATC
Found at i:12664 original size:5 final size:5
Alignment explanation
Indices: 12651--12684 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
12641 CGAAATCTGC
*
12651 AAAAA AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
12685 ATCTCAAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:15510 original size:2 final size:2
Alignment explanation
Indices: 15503--15585 Score: 112
Period size: 2 Copynumber: 41.5 Consensus size: 2
15493 TGGGGCATTG
* * *
15503 AT AT AT AT AT AT AT AT AT CT AT AT TT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
15545 AT AT AT AT CT AT AT TT AT AT TT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15586 CATGAACAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:15544 original size:32 final size:32
Alignment explanation
Indices: 15503--15584 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
15493 TGGGGCATTG
15503 ATATATATATATATATATCTATATTTATATTT
1 ATATATATATATATATATCTATATTTATATTT
15535 ATATATATATATATATATCTATATTTATATTT
1 ATATATATATATATATATCTATATTTATATTT
15567 ATATATATATATATATAT
1 ATATATATATATATATAT
15585 ACATGAACAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
ATATATATATATATATATCTATATTTATATTT
Done.