Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014781.1 Corchorus capsularis cultivar CVL-1 contig14802, 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: 80146
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA TA TA TA 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 TA TA TA TA T
36 GGTTTGATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7812 original size:33 final size:33
Alignment explanation
Indices: 7770--7844 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
7760 AATTGCTCAT
* *
7770 GCCGCCCCAGGGGGGCGG-CTGAACCATGGTAGG
1 GCCGCCCCAGGGGAGCGGCCTG-ACCATGGTAAG
* *
7803 GCCGCCCCAGGGGAGCGGCCTGGCCATGGTAAT
1 GCCGCCCCAGGGGAGCGGCCTGACCATGGTAAG
7836 GCCGCCCCA
1 GCCGCCCCA
7845 TGGATAGGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 34 0.92
34 3 0.08
ACGTcount: A:0.15, C:0.36, G:0.40, T:0.09
Consensus pattern (33 bp):
GCCGCCCCAGGGGAGCGGCCTGACCATGGTAAG
Found at i:8322 original size:15 final size:15
Alignment explanation
Indices: 8302--8333 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
8292 TCAAATGTAC
*
8302 AACAACACTAGGAAA
1 AACAACACCAGGAAA
8317 AACAACACCAGGAAA
1 AACAACACCAGGAAA
8332 AA
1 AA
8334 GAGCAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.22, G:0.12, T:0.03
Consensus pattern (15 bp):
AACAACACCAGGAAA
Found at i:9287 original size:33 final size:33
Alignment explanation
Indices: 9249--9358 Score: 195
Period size: 33 Copynumber: 3.3 Consensus size: 33
9239 CCCACCCCTA
*
9249 TCCGCCGTGGCTA-AGCCGTCCTAGTGGGGAGGC
1 TCCGCCGTGGC-AGAGCCGCCCTAGTGGGGAGGC
9282 TCCGCCGTGGCAGAGCCGCCCTAGTGGGGAGGC
1 TCCGCCGTGGCAGAGCCGCCCTAGTGGGGAGGC
9315 TCCGCCGTGGCAGAGCCGCCCTAGTGGGGAGGC
1 TCCGCCGTGGCAGAGCCGCCCTAGTGGGGAGGC
9348 TCCGCCGTGGC
1 TCCGCCGTGGC
9359 TAAGGGCAAA
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
32 1 0.01
33 74 0.99
ACGTcount: A:0.11, C:0.34, G:0.41, T:0.15
Consensus pattern (33 bp):
TCCGCCGTGGCAGAGCCGCCCTAGTGGGGAGGC
Found at i:42736 original size:113 final size:113
Alignment explanation
Indices: 42535--42745 Score: 273
Period size: 113 Copynumber: 1.9 Consensus size: 113
42525 AAAGTTAGTC
* * * * *
42535 GATTCTCAAAATTATATACAATTTTTACATCACTTTCTAAAACTAGTCTCAACTTTACGTGACAT
1 GATTCTCAAAATTATATACAATTTTTACAACACTTACCAAAACTACTCTCAACTTTACGTAACAT
*
42600 ATGTTACTTTTTCTACATCTAATAAAGGTAAAAATAGTAAAAATGGTT
66 ATGTTACTTTCTCTACATCTAATAAAGGTAAAAATAGTAAAAATGGTT
* ** * * *
42648 GATTCTCAAAATTTTATATGATTTTTATAACACTTACCAAAATTACTCTCAATTTTAC-TAAACA
1 GATTCTCAAAATTATATACAATTTTTACAACACTTACCAAAACTACTCTCAACTTTACGT-AACA
*
42712 TATGTTACTCTTCT-TACATTTAATAAAGGTAAAA
65 TATGTTACT-TTCTCTACATCTAATAAAGGTAAAA
42746 GTAAAAATTG
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
112 1 0.01
113 79 0.95
114 3 0.04
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.39
Consensus pattern (113 bp):
GATTCTCAAAATTATATACAATTTTTACAACACTTACCAAAACTACTCTCAACTTTACGTAACAT
ATGTTACTTTCTCTACATCTAATAAAGGTAAAAATAGTAAAAATGGTT
Found at i:57965 original size:2 final size:2
Alignment explanation
Indices: 57958--57992 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
57948 AGAGGCATGA
57958 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
57993 TATTTTTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58211 original size:22 final size:22
Alignment explanation
Indices: 58183--58278 Score: 91
Period size: 22 Copynumber: 4.7 Consensus size: 22
58173 ATTGATATGT
58183 TAAGTGGGTTTTTAATATGTTA
1 TAAGTGGGTTTTTAATATGTTA
* *
58205 TAAGTGGGTTTTTAAT-TCCTTT
1 TAAGTGGGTTTTTAATAT-GTTA
* *
58227 TAA-----TTATTGATATG-T-
1 TAAGTGGGTTTTTAATATGTTA
58242 TAAGTGGGTTTTTAATATGTTA
1 TAAGTGGGTTTTTAATATGTTA
58264 TAAGTGGGTTTTTAA
1 TAAGTGGGTTTTTAA
58279 GACATCTCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
15 3 0.05
16 1 0.02
17 6 0.10
18 1 0.02
20 9 0.16
21 2 0.03
22 36 0.62
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.51
Consensus pattern (22 bp):
TAAGTGGGTTTTTAATATGTTA
Found at i:58258 original size:59 final size:59
Alignment explanation
Indices: 58161--58278 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
58151 TAATTTGAGG
58161 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
1 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
*
58220 TTCCTTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
1 TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
58279 GACATCTCAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.25, C:0.04, G:0.19, T:0.52
Consensus pattern (59 bp):
TTCCCTTTAATTATTGATATGTTAAGTGGGTTTTTAATATGTTATAAGTGGGTTTTTAA
Found at i:60413 original size:20 final size:19
Alignment explanation
Indices: 60371--60413 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
60361 TTTATTAAAT
* *
60371 AAAAGTAAAAAAGGGATGG
1 AAAAGTAAAAAAGGGAAGA
*
60390 AAAATTAAAAACAGGGAAGA
1 AAAAGTAAAAA-AGGGAAGA
60410 AAAA
1 AAAA
60414 CACATAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.65, C:0.02, G:0.23, T:0.09
Consensus pattern (19 bp):
AAAAGTAAAAAAGGGAAGA
Found at i:61759 original size:53 final size:53
Alignment explanation
Indices: 61655--61755 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
61645 ACATACATGT
*
61655 ATACTGCTAAGATTTTATCAAATACCTACATAAATTTTCAAGGTCCAAATTTC
1 ATACTGCTAAGATTTTATCAAATAACTACATAAATTTTCAAGGTCCAAATTTC
* *
61708 ATACTGCTAAGATTTTATCAAATATATTACA-AACTTTT-AAGGTCCAAA
1 ATACTGCTAAGATTTTATCAAATA-ACTACATAAATTTTCAAGGTCCAAA
61756 ATTTACATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 10 0.23
53 30 0.68
54 4 0.09
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (53 bp):
ATACTGCTAAGATTTTATCAAATAACTACATAAATTTTCAAGGTCCAAATTTC
Found at i:62719 original size:12 final size:13
Alignment explanation
Indices: 62702--62737 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
62692 TTTAAAAATG
62702 ATTATATATA-TT
1 ATTATATATACTT
62714 ATTATATATACTT
1 ATTATATATACTT
*
62727 ATAATATATAC
1 ATTATATATAC
62738 CAGTATGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTATATATACTT
Found at i:72664 original size:31 final size:31
Alignment explanation
Indices: 72629--72793 Score: 148
Period size: 31 Copynumber: 5.5 Consensus size: 31
72619 TTTGGCTAAT
*
72629 TGCTCAAATAAGGGCCTAACGTTTGACAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * **
72660 TGCTCATATAAGGGCCTGATC-TTT-TC-ATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCCAAAA
72689 TGAC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 TG-CTCAAATAAGGGCCTAACGTTTGCCAAAA
* * **
72720 TGCTCAAATAAGGGCCCCATC-TTTG--AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCCAAAA
72749 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
72780 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
72794 TCTGTATCAC
Statistics
Matches: 104, Mismatches: 18, Indels: 24
0.71 0.12 0.16
Matches are distributed among these distances:
28 6 0.06
29 35 0.34
30 8 0.08
31 49 0.47
32 6 0.06
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:72731 original size:60 final size:60
Alignment explanation
Indices: 72633--72793 Score: 259
Period size: 60 Copynumber: 2.7 Consensus size: 60
72623 GCTAATTGCT
* * ** **
72633 CAAATAAGGGCCTAACGTTTGACAAAATGCTCATATAAGGGCCTGATCTTTTCATTTGAC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC
*
72693 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC
72753 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
72794 TCTGTATCAC
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 94 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC
Found at i:72865 original size:31 final size:30
Alignment explanation
Indices: 72827--73022 Score: 127
Period size: 31 Copynumber: 6.5 Consensus size: 30
72817 TGACATTGGT
72827 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTT-GATAACGTTAGG
* *
72858 CCCTTATTTGAACATTTTTTATAACGTTAGG
1 CCCTTATTTGAGCA-TTTTGATAACGTTAGG
** * *
72889 CCCTTATTT-AGCCAAATTAAAAGACCG---GG
1 CCCTTATTTGAG-CATTTTGATA-A-CGTTAGG
*
72918 CCCTTATTTGAGCATTTTCGATAACATTAGG
1 CCCTTATTTGAGCATTTT-GATAACGTTAGG
* ** * **
72949 CCCTTATCTG-GCCAAATT-A-AAAGATCGGG
1 CCCTTATTTGAG-CATTTTGATAACG-TTAGG
* *
72978 TCCTTATTTGAGCATTTTGACAAACGTTAGG
1 CCCTTATTTGAGCATTTTGA-TAACGTTAGG
73009 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
73023 ATTAGCCTAT
Statistics
Matches: 123, Mismatches: 27, Indels: 30
0.68 0.15 0.17
Matches are distributed among these distances:
28 3 0.02
29 32 0.26
30 12 0.10
31 67 0.54
32 9 0.07
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGATAACGTTAGG
Found at i:72925 original size:60 final size:60
Alignment explanation
Indices: 72856--73017 Score: 227
Period size: 60 Copynumber: 2.7 Consensus size: 60
72846 GATAACGTTA
* *
72856 GGCCCTTATTTGAACATTTTTTATAACGTTAGGCCCTTATTTAGCCAAATTAAAAGACCG
1 GGCCCTTATTTGAGCATTTTTGATAACGTTAGGCCCTTATTTAGCCAAATTAAAAGACCG
* * * * *
72916 GGCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATCTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTTGATAACGTTAGGCCCTTATTTAGCCAAATTAAAAGACCG
* *
72976 GGTCCTTATTTGAGCA-TTTTGACAAACGTTAGGCCCTTATTT
1 GGCCCTTATTTGAGCATTTTTGA-TAACGTTAGGCCCTTATTT
73018 GAGCAATTAG
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 5 0.06
60 84 0.94
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTTGATAACGTTAGGCCCTTATTTAGCCAAATTAAAAGACCG
Found at i:75325 original size:21 final size:21
Alignment explanation
Indices: 75299--75339 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
75289 AAGACAATAA
*
75299 CAATCAAAGTAATTTATTGAG
1 CAATCAAAGTAATTGATTGAG
75320 CAATCAAAGTAATTGATTGA
1 CAATCAAAGTAATTGATTGA
75340 CTTGCCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.32
Consensus pattern (21 bp):
CAATCAAAGTAATTGATTGAG
Found at i:79962 original size:21 final size:21
Alignment explanation
Indices: 79936--79978 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
79926 TGAAGACAAT
*
79936 AGCAATCAAAGTAATTTATTG
1 AGCAATCAAAGTAATTGATTG
79957 AGCAATCAAAGTAATTGATTG
1 AGCAATCAAAGTAATTGATTG
79978 A
1 A
79979 CTTGCCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.30
Consensus pattern (21 bp):
AGCAATCAAAGTAATTGATTG
Found at i:80084 original size:17 final size:17
Alignment explanation
Indices: 80062--80096 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
80052 AATATAGCTA
*
80062 TGTGAATGTAATCCCAT
1 TGTGAACGTAATCCCAT
80079 TGTGAACGTAATCCCAT
1 TGTGAACGTAATCCCAT
80096 T
1 T
80097 AAGTTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (17 bp):
TGTGAACGTAATCCCAT
Done.