Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015826.1 Corchorus olitorius cultivar O-4 contig15859, 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: 46048
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1180 original size:2 final size:2
Alignment explanation
Indices: 1168--1206 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1158 ACCACGGGTG
1168 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1207 AGACCTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2038 original size:2 final size:2
Alignment explanation
Indices: 2031--2062 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
2021 CCTAATTGAT
2031 TA TA TA TA TA TA TGA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T
2063 TTGTCTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2053 original size:17 final size:16
Alignment explanation
Indices: 2027--2060 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
2017 TAACCCTAAT
2027 TGATTATATATATATA
1 TGATTATATATATATA
2043 TGATATATATATATATA
1 TGAT-TATATATATATA
2060 T
1 T
2061 ATTTGTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TGATTATATATATATA
Found at i:4322 original size:66 final size:66
Alignment explanation
Indices: 4240--4371 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
4230 TCTGACTAAC
*
4240 CATTATAAGAGACAAGTAGGTC-CAATTATTCATGCAATCAACTTTAGCATCTCAAATAATCCTT
1 CATTATAAGAGACAAGTAGG-CGCAATTATTCATGCAATCAACTTTAGCATATCAAATAATCCTT
4304 AA
65 AA
*
4306 CATTATAAGAGACAAGTAGGCGCAATTATTCATGCAATCAACTTTAGCATATCAAATCATCCTTA
1 CATTATAAGAGACAAGTAGGCGCAATTATTCATGCAATCAACTTTAGCATATCAAATAATCCTTA
4371 A
66 A
4372 GTTAACATCT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 1 0.02
66 62 0.98
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (66 bp):
CATTATAAGAGACAAGTAGGCGCAATTATTCATGCAATCAACTTTAGCATATCAAATAATCCTTA
A
Found at i:11202 original size:27 final size:27
Alignment explanation
Indices: 11172--11241 Score: 140
Period size: 27 Copynumber: 2.6 Consensus size: 27
11162 CTATTTCATC
11172 AATTCATGTTTTATGGTATTATAAAAA
1 AATTCATGTTTTATGGTATTATAAAAA
11199 AATTCATGTTTTATGGTATTATAAAAA
1 AATTCATGTTTTATGGTATTATAAAAA
11226 AATTCATGTTTTATGG
1 AATTCATGTTTTATGG
11242 ATATGGAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (27 bp):
AATTCATGTTTTATGGTATTATAAAAA
Found at i:18150 original size:60 final size:61
Alignment explanation
Indices: 18024--18153 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 61
18014 AAATATGTAC
* * * * *
18024 ATTTTCCCCCCTGAACTTTTAATTTGGAACTTTTACCCCCTAAACTATGAAAATTGAGACA
1 ATTTTCCCTCCTGAACTTTTAATTTGGAACTTTCACCACCTAAACTATCAAAACTGAGACA
* * * *
18085 A-TTTCCCTCCTGAATTTTTAATTTGGAACTTTCA-CATCTAAATTATCAAAACTGGGACA
1 ATTTTCCCTCCTGAACTTTTAATTTGGAACTTTCACCACCTAAACTATCAAAACTGAGACA
18144 ATTTTCCCTC
1 ATTTTCCCTC
18154 AGCCATTAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 20 0.34
60 38 0.64
61 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (61 bp):
ATTTTCCCTCCTGAACTTTTAATTTGGAACTTTCACCACCTAAACTATCAAAACTGAGACA
Found at i:19127 original size:59 final size:60
Alignment explanation
Indices: 18992--19130 Score: 185
Period size: 59 Copynumber: 2.4 Consensus size: 60
18982 TAATGTTTGC
* * *
18992 CAAAATGCTCAAATAA-AGACCGATCTTTTAATTTAACCAAATAAGAACCTAACGTTTGT
1 CAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTAACCAAATAAGAACCTAACGTTTAT
* ** *
19051 CAAAATGCTCAAATAAGGGTCCGATTTTTTAATTTGGCCAAATAAG-GCCTAACG-TTAT
1 CAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTAACCAAATAAGAACCTAACGTTTAT
19109 CAAAAATGCTCAAATAAGGGTC
1 C-AAAATGCTCAAATAAGGGTC
19131 TGGCGTCAGT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
58 4 0.06
59 43 0.61
60 24 0.34
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (60 bp):
CAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTAACCAAATAAGAACCTAACGTTTAT
Found at i:19273 original size:31 final size:31
Alignment explanation
Indices: 19238--19336 Score: 75
Period size: 31 Copynumber: 3.3 Consensus size: 31
19228 CCGGGTCTTT
19238 TTTAAGCATTTTAGAAAACATTAGACCCTTA
1 TTTAAGCATTTTAGAAAACATTAGACCCTTA
*
19269 TTTAA-CTATATTA-AAAGATCA-T-G-CCCTTA
1 TTTAAGC-ATTTTAGAAA-A-CATTAGACCCTTA
* * *
19298 TTTGAGCATTTT-GATAAACATTAAATCCTTA
1 TTTAAGCATTTTAGA-AAACATTAGACCCTTA
*
19329 TTTGAGCA
1 TTTAAGCA
19337 AGTAGCCAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
28 2 0.04
29 17 0.31
30 8 0.15
31 25 0.46
32 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (31 bp):
TTTAAGCATTTTAGAAAACATTAGACCCTTA
Found at i:21435 original size:19 final size:19
Alignment explanation
Indices: 21411--21448 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
21401 ACGTAGCAAC
21411 GCCACGTC-AGACCAAAAAT
1 GCCACGTCGA-ACCAAAAAT
21430 GCCACGTCGAACCAAAAAT
1 GCCACGTCGAACCAAAAAT
21449 ACCATGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.42, C:0.32, G:0.16, T:0.11
Consensus pattern (19 bp):
GCCACGTCGAACCAAAAAT
Found at i:36456 original size:22 final size:23
Alignment explanation
Indices: 36425--36478 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
36415 GGACTGTTTA
*
36425 TATATTATATATTATATAATCTATT
1 TATAATATAT-TTAT-TAATCTATT
*
36450 T-TAATATATTTATTTATCTATT
1 TATAATATATTTATTAATCTATT
36472 TATAATA
1 TATAATA
36479 ATATAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 9 0.35
23 9 0.35
24 7 0.27
25 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TATAATATATTTATTAATCTATT
Found at i:39080 original size:22 final size:22
Alignment explanation
Indices: 39055--39098 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
39045 TAAGCAACAT
39055 TGAGAAAAATATGTTTGAAGTA
1 TGAGAAAAATATGTTTGAAGTA
39077 TGAGAAAAATATGTTTGAAGTA
1 TGAGAAAAATATGTTTGAAGTA
39099 ATCTAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
TGAGAAAAATATGTTTGAAGTA
Found at i:43654 original size:11 final size:11
Alignment explanation
Indices: 43638--43668 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
43628 TATCAGTCCT
43638 AATAGATATTC
1 AATAGATATTC
43649 AATAGATATTC
1 AATAGATATTC
*
43660 AAGAGATAT
1 AATAGATAT
43669 AGCAAATCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (11 bp):
AATAGATATTC
Found at i:46014 original size:2 final size:2
Alignment explanation
Indices: 45998--46045 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
45988 CATCCTGTAC
*
45998 AT AT CT AT A- 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 AT AT AT AT
46039 AT AT AT A
1 AT AT AT A
46046 CAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.