Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022373.1 Corchorus olitorius cultivar O-4 contig22406, 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: 14688
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:3316 original size:15 final size:15
Alignment explanation
Indices: 3293--3358 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
3283 TATCATGCAT
*
3293 AATATATCCTTCAAA
1 AATAAATCCTTCAAA
*
3308 AATAAATCCTTTAAAA
1 AATAAATCC-TTCAAA
* *
3324 AATACATTCTT---A
1 AATAAATCCTTCAAA
3336 AAT--ATCCTTCAAA
1 AATAAATCCTTCAAA
3349 AATAAATCCT
1 AATAAATCCT
3359 AGGGAAGTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
10 5 0.12
12 4 0.10
13 4 0.10
15 15 0.38
16 12 0.30
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAATCCTTCAAA
Found at i:3736 original size:2 final size:2
Alignment explanation
Indices: 3729--3765 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3719 TAATTAGCGG
*
3729 AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3766 GTGGCGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:3902 original size:43 final size:43
Alignment explanation
Indices: 3852--3973 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
3842 ATTTAATTAC
* *
3852 ATATATAATTTGTAAATATTATTTCCTAATTATATTTTC-TAAA
1 ATATATAATTTATAAATATTATTTCCTAATTATA-ATTCATAAA
* * * * * *
3895 ATTTATAA-TTCTAAATATTATTTTCTAGTTATAATTCATTAT
1 ATATATAATTTATAAATATTATTTCCTAATTATAATTCATAAA
3937 ATATATAATTTATAAATATTATTTCCTAATTATAATT
1 ATATATAATTTATAAATATTATTTCCTAATTATAATT
3974 ATATCATTTC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 3 0.05
42 31 0.47
43 32 0.48
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (43 bp):
ATATATAATTTATAAATATTATTTCCTAATTATAATTCATAAA
Found at i:3920 original size:14 final size:14
Alignment explanation
Indices: 3816--3921 Score: 74
Period size: 14 Copynumber: 7.4 Consensus size: 14
3806 ATTTTGCTAA
*
3816 TTTCTAAATATTTT
1 TTTCTAAATATTAT
*
3830 TTTCTAAATAATAT
1 TTTCTAAATATTAT
* *
3844 TTAAT-TACATATATAA
1 TT--TCTAAATAT-TAT
*
3860 TTTGTAAATATTAT
1 TTTCTAAATATTAT
* *
3874 TTCCTAATTA-TAT
1 TTTCTAAATATTAT
3887 TTTCTAAA-ATTTAT
1 TTTCTAAATA-TTAT
*
3901 AATTCTAAATATTAT
1 -TTTCTAAATATTAT
3916 TTTCTA
1 TTTCTA
3922 GTTATAATTC
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
12 1 0.01
13 9 0.13
14 32 0.46
15 22 0.31
16 6 0.09
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.54
Consensus pattern (14 bp):
TTTCTAAATATTAT
Found at i:5667 original size:34 final size:35
Alignment explanation
Indices: 5627--5701 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
5617 AACTACTTAA
5627 ATATATTAAATAT-AAT-ACCATGTATATATATATAT
1 ATATATTAAATATAAATGA--ATGTATATATATATAT
* *
5662 A-ATATTAAATTTAAATGAATTTATATATATATAT
1 ATATATTAAATATAAATGAATGTATATATATATAT
5696 ATATAT
1 ATATAT
5702 ATTCAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 26 0.74
35 8 0.23
36 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (35 bp):
ATATATTAAATATAAATGAATGTATATATATATAT
Found at i:5689 original size:36 final size:36
Alignment explanation
Indices: 5649--5724 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
5639 TAATACCATG
5649 TATATATATATATA-ATATTAAATTTAAATGAATTTA
1 TATATATATATATATATATTAAATTTAAATG-ATTTA
* *
5685 TATATATATATATATATATTCAATTTAAATGATTTG
1 TATATATATATATATATATTAAATTTAAATGATTTA
5721 TATA
1 TATA
5725 ACATCATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 22 0.59
37 15 0.41
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TATATATATATATATATATTAAATTTAAATGATTTA
Found at i:5831 original size:32 final size:32
Alignment explanation
Indices: 5764--5878 Score: 149
Period size: 32 Copynumber: 3.6 Consensus size: 32
5754 AAAAAAAACA
* * ** *
5764 AAATAGCGGCGTTTCAGTACAGAAATGCCACT
1 AAATTGCGGCGTTTCTGTATGGAAACGCCACT
* * *
5796 AAATTGTGGTGTTTTTGTATGGAAACGCCACT
1 AAATTGCGGCGTTTCTGTATGGAAACGCCACT
5828 AAATTGCGGCGTTTCTGTATGGAAACGCCACT
1 AAATTGCGGCGTTTCTGTATGGAAACGCCACT
*
5860 AAATAGCGGCGTTTCTGTA
1 AAATTGCGGCGTTTCTGTA
5879 CTGAAATGCC
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (32 bp):
AAATTGCGGCGTTTCTGTATGGAAACGCCACT
Found at i:8176 original size:19 final size:19
Alignment explanation
Indices: 8154--8194 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
8144 TATTTATTAA
*
8154 TTATTT-TACTATTATATTT
1 TTATTTATA-TATTACATTT
8173 TTATTTATATATTACATTT
1 TTATTTATATATTACATTT
8192 TTA
1 TTA
8195 CTTAAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTATATATTACATTT
Found at i:9321 original size:17 final size:17
Alignment explanation
Indices: 9299--9341 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
9289 AATAATTGAG
9299 ATTTGAA-AATTGAGAAA
1 ATTTGAAGAATTGA-AAA
9316 ATTTGAGAGAATTGAAAA
1 ATTTGA-AGAATTGAAAA
*
9334 TTTTGAAG
1 ATTTGAAG
9342 TTTGAAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 9 0.39
19 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.33
Consensus pattern (17 bp):
ATTTGAAGAATTGAAAA
Found at i:10061 original size:2 final size:2
Alignment explanation
Indices: 10054--10080 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10044 ACCGACACTT
10054 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 T
10081 TACAGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.