Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014780.1 Corchorus olitorius cultivar O-4 contig14813, 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: 76347
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:13174 original size:18 final size:18
Alignment explanation
Indices: 13151--13186 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13141 ACAAGACATA
13151 TTTACCCTCTCAACAATT
1 TTTACCCTCTCAACAATT
13169 TTTACCCTCTCAACAATT
1 TTTACCCTCTCAACAATT
13187 CAAGATTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTACCCTCTCAACAATT
Found at i:27540 original size:123 final size:123
Alignment explanation
Indices: 27340--27594 Score: 377
Period size: 123 Copynumber: 2.0 Consensus size: 123
27330 CATTGCTTAA
* *
27340 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATGAT
**
27405 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTATAATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
27463 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-AC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATGA-
27527 CTATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
65 -T-TTTTA----TA--ATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
27592 AT
122 AT
27594 A
1 A
27595 TTTCTTAAAT
Statistics
Matches: 118, Mismatches: 5, Indels: 10
0.89 0.04 0.08
Matches are distributed among these distances:
122 1 0.01
123 59 0.50
124 1 0.01
125 5 0.04
131 52 0.44
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (123 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATGAT
TTTTATAATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:27582 original size:131 final size:123
Alignment explanation
Indices: 27340--27594 Score: 411
Period size: 131 Copynumber: 2.0 Consensus size: 123
27330 CATTGCTTAA
*
27340 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
27405 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
*
27463 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T---
*
27528 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
60 TA--TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
27593 T
123 T
27594 A
1 A
27595 TTTCTTAAAT
Statistics
Matches: 121, Mismatches: 3, Indels: 8
0.92 0.02 0.06
Matches are distributed among these distances:
123 54 0.45
124 1 0.01
125 1 0.01
126 1 0.01
129 2 0.02
131 62 0.51
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (123 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:27616 original size:14 final size:13
Alignment explanation
Indices: 27580--27618 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
27570 TATATATTAG
27580 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
27593 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
27607 AATTTTTTAAAT
1 AATTTTTTAAAT
27619 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:35218 original size:6 final size:7
Alignment explanation
Indices: 35200--35224 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35190 TTCATCCTTA
35200 CTTTTTC
1 CTTTTTC
35207 CTTTTTC
1 CTTTTTC
35214 CTTTTTC
1 CTTTTTC
35221 CTTT
1 CTTT
35225 CCCTTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
CTTTTTC
Found at i:42154 original size:34 final size:34
Alignment explanation
Indices: 42111--42178 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
42101 TAAACTCCAG
42111 AACTCTAGTTTATTAAACTCCACCGATGGCGTAT
1 AACTCTAGTTTATTAAACTCCACCGATGGCGTAT
*
42145 AACTCTAGTTTATTAAACTTCACCGATGGCGTAT
1 AACTCTAGTTTATTAAACTCCACCGATGGCGTAT
42179 TGAATAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (34 bp):
AACTCTAGTTTATTAAACTCCACCGATGGCGTAT
Found at i:43263 original size:24 final size:24
Alignment explanation
Indices: 43234--43283 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
43224 CATTCACAGT
*
43234 AAGATCTCCGGTTCGAGTCTTGTA
1 AAGATCTCCAGTTCGAGTCTTGTA
43258 AAGATCTCCAGTTCGAGTCTTGTA
1 AAGATCTCCAGTTCGAGTCTTGTA
43282 AA
1 AA
43284 TAGCGAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (24 bp):
AAGATCTCCAGTTCGAGTCTTGTA
Found at i:44102 original size:17 final size:18
Alignment explanation
Indices: 44066--44105 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
44056 AAAAGATTTT
*
44066 GATTTGTATGTAATATTA
1 GATTTATATGTAATATTA
*
44084 GATTTATATGTTA-ATTA
1 GATTTATATGTAATATTA
44101 GATTT
1 GATTT
44106 TAAACACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (18 bp):
GATTTATATGTAATATTA
Found at i:55012 original size:7 final size:7
Alignment explanation
Indices: 55002--55038 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
54992 TTTCATCTTC
55002 TTTCCTT
1 TTTCCTT
55009 TTTCCTT
1 TTTCCTT
55016 TTTCCTT
1 TTTCCTT
55023 TTTCCTT
1 TTTCCTT
55030 TTTCCTT
1 TTTCCTT
55037 TT
1 TT
55039 CCTCGTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTCCTT
Found at i:65903 original size:28 final size:28
Alignment explanation
Indices: 65861--65918 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
65851 ATAAGAACTT
*
65861 ATACGCTACTGGGACACTCATTAATAAA
1 ATACGCTACTCGGACACTCATTAATAAA
*
65889 ATACTCTACTCGGACACTCATTAATAAA
1 ATACGCTACTCGGACACTCATTAATAAA
65917 AT
1 AT
65919 CCTATTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (28 bp):
ATACGCTACTCGGACACTCATTAATAAA
Found at i:75928 original size:39 final size:40
Alignment explanation
Indices: 75850--75930 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
75840 TTTAATTCCT
* *
75850 ATGTAATATATATAATAACTAAAATACTTATATCGATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
* * *
75890 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
75929 AT
1 AT
75931 TCTTAGGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
Found at i:75957 original size:25 final size:24
Alignment explanation
Indices: 75921--75967 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
75911 AATACTTACA
*
75921 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGATATTTTT
75945 TTAATTCAAATTCTTAGATATTT
1 TTAATT-AAATTCTTAGATATTT
75968 GTGCAAACGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGATATTTTT
Done.