Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020286.1 Corchorus olitorius cultivar O-4 contig20319, 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: 56242
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:4298 original size:21 final size:20
Alignment explanation
Indices: 4268--4329 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
4258 ATCTTTTAAC
4268 AATAATCTTATAAGATTTTTT
1 AATAA-CTTATAAGATTTTTT
4289 AATAAGCTTAGT-AGATTTTTT
1 AATAA-CTTA-TAAGATTTTTT
*
4310 AGTAACTTTATAAG-TTTTTT
1 AATAAC-TTATAAGATTTTTT
4330 TTGAAGTAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 8 0.22
21 27 0.75
22 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.52
Consensus pattern (20 bp):
AATAACTTATAAGATTTTTT
Found at i:5943 original size:3 final size:3
Alignment explanation
Indices: 5935--5985 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
5925 ACATCAGCAA
* * *
5935 CAT CAT CAT CGT CAT AAT CAT CAT CAT CAT CAT CAC CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
5983 CAT
1 CAT
5986 AACAAGAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:8801 original size:15 final size:16
Alignment explanation
Indices: 8781--8811 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8771 TCTACTTTTA
8781 TAATTT-AATTGCTTT
1 TAATTTAAATTGCTTT
8796 TAATTTAAATTGCTTT
1 TAATTTAAATTGCTTT
8812 GATTACTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
TAATTTAAATTGCTTT
Found at i:13365 original size:13 final size:12
Alignment explanation
Indices: 13336--13378 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
13326 CCTACGTCAA
13336 AAATTAGTTTTTG
1 AAATT-GTTTTTG
*
13349 AAATTGTTTTCTT
1 AAATTGTTTT-TG
13362 AAATTGTTTTTG
1 AAATTGTTTTTG
*
13374 GAATT
1 AAATT
13379 AACTTTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (12 bp):
AAATTGTTTTTG
Found at i:25638 original size:136 final size:135
Alignment explanation
Indices: 25484--25748 Score: 395
Period size: 136 Copynumber: 2.0 Consensus size: 135
25474 ATAAATAAAG
* * *
25484 TTGAATGACTAAATTGTATAGAATTAAATATTTGAGAGACTAAGTTGCATAAAATTAAAATGTCT
1 TTGAAGGACTAAATTGTATAAAATTAAATATTTCAGAGACTAAGTTGCATAAAATTAAAATGTCT
* * * * *
25549 AAGGGCTTTTGTATGAATGAAGTAAAGTCGAATGACTAAATCTTGAAAAAGAAATAATAAAAGGA
66 AAGAGCTTTTATATGAAT-AAATAAAATCGAAGGACTAAATCTTGAAAAAGAAATAATAAAAGGA
25614 ATACAC
130 ATACAC
* *
25620 TTGAAGGACTAAATTGTATAAAATTAAATATTTCAGGGGCTAAGTTGCATAAAATTAAAATGTCT
1 TTGAAGGACTAAATTGTATAAAATTAAATATTTCAGAGACTAAGTTGCATAAAATTAAAATGTCT
* * * *
25685 AAGAGCTTTTATATGAATAAATAAAATTGAAGGGCTAAATCTTGAAAAAGATATGATAAAAGGA
66 AAGAGCTTTTATATGAATAAATAAAATCGAAGGACTAAATCTTGAAAAAGAAATAATAAAAGGA
25749 CTAAACAAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
135 39 0.34
136 76 0.66
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.30
Consensus pattern (135 bp):
TTGAAGGACTAAATTGTATAAAATTAAATATTTCAGAGACTAAGTTGCATAAAATTAAAATGTCT
AAGAGCTTTTATATGAATAAATAAAATCGAAGGACTAAATCTTGAAAAAGAAATAATAAAAGGAA
TACAC
Found at i:27945 original size:14 final size:16
Alignment explanation
Indices: 27921--27953 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
27911 TAGTATACAA
27921 TATATATACATAT-TT
1 TATATATACATATCTT
27936 TATA-ATACATATCTT
1 TATATATACATATCTT
27951 TAT
1 TAT
27954 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATATACATATCTT
Found at i:32343 original size:19 final size:18
Alignment explanation
Indices: 32301--32349 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
32291 ATAGATCATA
*
32301 TTAACGTTATATTTGATT
1 TTAACGTTATATTTAATT
*
32319 TATAACATTATATTTAATT
1 T-TAACGTTATATTTAATT
32338 CTTAACGTTATA
1 -TTAACGTTATA
32350 CTCATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 24 0.92
20 1 0.04
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (18 bp):
TTAACGTTATATTTAATT
Found at i:37379 original size:3 final size:3
Alignment explanation
Indices: 37371--37434 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
37361 TAGCAAAATC
37371 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
37419 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
37435 ACCATTACTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:39392 original size:16 final size:17
Alignment explanation
Indices: 39373--39405 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39363 TTAGTATATC
*
39373 AAAAAATTAA-TAAAAT
1 AAAAAAGTAATTAAAAT
39389 AAAAAAGTAATTAAAAT
1 AAAAAAGTAATTAAAAT
39406 TTACAGCAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAAAGTAATTAAAAT
Found at i:48235 original size:28 final size:29
Alignment explanation
Indices: 48195--48258 Score: 67
Period size: 31 Copynumber: 2.2 Consensus size: 29
48185 TATGGGATTT
* *
48195 ATTTGTGCTAAAA-AAAGTTAAGGGGCCA
1 ATTTGTCCCAAAAGAAAGTTAAGGGGCCA
* *
48223 ATTTGTCCCAAAATGGATAGTTAAGGGGCTA
1 ATTTGTCCCAAAA--GAAAGTTAAGGGGCCA
48254 ATTTG
1 ATTTG
48259 GGTATTAAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 11 0.38
31 18 0.62
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (29 bp):
ATTTGTCCCAAAAGAAAGTTAAGGGGCCA
Done.