Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014655.1 Corchorus capsularis cultivar CVL-1 contig14676, 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: 20930
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:324 original size:2 final size:2
Alignment explanation
Indices: 317--349 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
307 TCCGCCACTG
*
317 TA TA TA TA TA TA TA TA TA TA -A TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
350 AAACGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:358 original size:13 final size:13
Alignment explanation
Indices: 317--350 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
307 TCCGCCACTG
*
317 TATATAT-ATATA
1 TATATATAATAAA
329 TATATATAATAAA
1 TATATATAATAAA
342 TATATATAA
1 TATATATAA
351 AACGTATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATATATAATAAA
Found at i:1105 original size:2 final size:2
Alignment explanation
Indices: 1063--1095 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1053 CCATAAAATT
1063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1096 GAGCATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6165 original size:2 final size:2
Alignment explanation
Indices: 6160--6193 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6150 AAATCTTATG
6160 AT AT 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 AT AT
6194 TCTTAAGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9559 original size:104 final size:101
Alignment explanation
Indices: 9358--9549 Score: 222
Period size: 104 Copynumber: 1.8 Consensus size: 101
9348 AGAACAAGAT
* * * *
9358 GTTGATGATGAAATTCAATCCATTGTAATTTATGTTATGAACAATATAATTTCTTTTTTATAAAT
1 GTTGATGATGAAATTAAATACATTGTAATTTATGTTATAAACAATATAATTTCATTTTTATAAAT
* ****
9423 GAAAATTACATTTTCTTCAAAAAATAAAATTAATGGAAC
66 GAAAATTAAATCAGATTC---AAATAAAATTAATGGAAC
*
9462 GTTGATGATGAAATTAAATATATTGTAATTTATGTTATAAACAAACAGTATAATTTCATTTTTAT
1 GTTGATGATGAAATTAAATACATTGTAATTTATGTTATAAAC--A-A-TATAATTTCATTTTTAT
9527 AAATGAAAATTATAATCAGATTC
62 AAATGAAAATTA-AATCAGATTC
9550 GAAAAATTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
104 38 0.52
106 1 0.01
107 1 0.01
108 28 0.38
109 5 0.07
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (101 bp):
GTTGATGATGAAATTAAATACATTGTAATTTATGTTATAAACAATATAATTTCATTTTTATAAAT
GAAAATTAAATCAGATTCAAATAAAATTAATGGAAC
Found at i:9765 original size:30 final size:29
Alignment explanation
Indices: 9698--9767 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
9688 CTTGTAGCGT
9698 TTGGACGTTTTGCTCCCTGAACTTCAATC
1 TTGGACGTTTTGCTCCCTGAACTTCAATC
* *
9727 TTGGACGTTTTGC-CCTTTGAACTTCAATT
1 TTGGACGTTTTGCTCC-CTGAACTTCAATC
9756 TTGGGACGTTTT
1 TT-GGACGTTTT
9768 ACCCCTTCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 2 0.05
29 26 0.70
30 9 0.24
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (29 bp):
TTGGACGTTTTGCTCCCTGAACTTCAATC
Found at i:9946 original size:29 final size:29
Alignment explanation
Indices: 9899--9971 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
9889 GATTGTGGGG
9899 GCAAAACGTCCCAAAATTGAAGTTCAGAGA
1 GCAAAACGT-CCAAAATTGAAGTTCAGAGA
* * * *
9929 GCAAAATGTCCAAGATTGAAGTTCAGGGG
1 GCAAAACGTCCAAAATTGAAGTTCAGAGA
9958 GCAAAACGTCCAAA
1 GCAAAACGTCCAAA
9972 CGTTACAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 29 0.78
30 8 0.22
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.16
Consensus pattern (29 bp):
GCAAAACGTCCAAAATTGAAGTTCAGAGA
Found at i:15024 original size:14 final size:14
Alignment explanation
Indices: 15005--15034 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
14995 GGTTTGGAAG
15005 AAGTGTTTTTTTAA
1 AAGTGTTTTTTTAA
15019 AAGTGTTTTTTTAA
1 AAGTGTTTTTTTAA
15033 AA
1 AA
15035 TTGGGGTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (14 bp):
AAGTGTTTTTTTAA
Found at i:18717 original size:45 final size:45
Alignment explanation
Indices: 18653--18750 Score: 187
Period size: 45 Copynumber: 2.2 Consensus size: 45
18643 CCTTTTTGTC
*
18653 AGAAGCCCCCTGATTCAAATAAAACAACAGGGAAAAAATGAAATT
1 AGAAGCCCCCTGACTCAAATAAAACAACAGGGAAAAAATGAAATT
18698 AGAAGCCCCCTGACTCAAATAAAACAACAGGGAAAAAATGAAATT
1 AGAAGCCCCCTGACTCAAATAAAACAACAGGGAAAAAATGAAATT
18743 AGAAGCCC
1 AGAAGCCC
18751 ACCCACTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.50, C:0.20, G:0.16, T:0.13
Consensus pattern (45 bp):
AGAAGCCCCCTGACTCAAATAAAACAACAGGGAAAAAATGAAATT
Found at i:18763 original size:45 final size:45
Alignment explanation
Indices: 18653--18765 Score: 165
Period size: 45 Copynumber: 2.5 Consensus size: 45
18643 CCTTTTTGTC
* * *
18653 AGAAGCCCCCTGATTCAAATAAAACAACAGGGAAAAAATGAAATT
1 AGAAGCCCCCTCACTAAAATAAAACAACAGGGAAAAAATGAAATT
* *
18698 AGAAGCCCCCTGACTCAAATAAAACAACAGGGAAAAAATGAAATT
1 AGAAGCCCCCTCACTAAAATAAAACAACAGGGAAAAAATGAAATT
18743 AGAAGCCCACC-CACTAAAATAAA
1 AGAAGCCC-CCTCACTAAAATAAA
18766 CCATTGCTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 62 0.97
46 2 0.03
ACGTcount: A:0.51, C:0.21, G:0.14, T:0.13
Consensus pattern (45 bp):
AGAAGCCCCCTCACTAAAATAAAACAACAGGGAAAAAATGAAATT
Done.