Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017517.1 Corchorus olitorius cultivar O-4 contig17550, 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: 11123
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Found at i:3530 original size:60 final size:60
Alignment explanation
Indices: 3463--3642 Score: 308
Period size: 60 Copynumber: 3.0 Consensus size: 60
3453 CATACTTATA
* * *
3463 TTCTAAATGCAACTAATAAAAACATTTTTGCAAACGAC-AACTAATGTTAAATTGATGGAG
1 TTCTAAATGCAACAAATGAAAACA-TTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
3523 TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
1 TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
*
3583 TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAATTAATGTTAAATTGATGGAG
1 TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
3643 GATTGCTAAA
Statistics
Matches: 115, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
59 12 0.10
60 103 0.90
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.29
Consensus pattern (60 bp):
TTCTAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
Found at i:3910 original size:28 final size:28
Alignment explanation
Indices: 3839--3944 Score: 122
Period size: 29 Copynumber: 3.7 Consensus size: 28
3829 AAATGAACTT
*
3839 AAAATGATCAAAATGCCCCTGAATATGCA
1 AAAATGACCAAAATGCCCCTGAATATG-A
* * *
3868 TAAATGACCATAATGCCCCTGAATGTGA
1 AAAATGACCAAAATGCCCCTGAATATGA
** * *
3896 AAAATGACCAAAATGCCCCTAGGTTTTTA
1 AAAATGACCAAAATGCCCCT-GAATATGA
3925 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
3945 AGGTGATCCT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
28 19 0.29
29 47 0.71
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAATATGA
Found at i:4252 original size:35 final size:35
Alignment explanation
Indices: 4206--4543 Score: 468
Period size: 35 Copynumber: 9.7 Consensus size: 35
4196 TGAGTCCATA
**
4206 TTGAAGATGCTACACCGAGTCATCCAAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* * *
4241 TTGAAGGTGCTACACCGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* * *
4276 TTGAAGATGTTACACCGAGTCATCTGAGTTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
4311 TTGAAGATGCTACACCGAGTCATCTGAATTCATAT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
4346 TTGAAGATGCTACACCGAGTCATCTGGATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT
* *
4381 TCGAAGATGCTACACCGAGTCATCTGGATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT
*
4416 TTGAAGATGCTACACCGAGTCATCTGGATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT
* *
4451 TTGAAGATGCTACACCGAGTCATCTGAGTTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
4486 TTGAAGATGCTACACCGAGTCATCTGAATAT-AACT
1 TTGAAGATGCTACACCGAGTCATCTGAAT-TCATCT
4521 TTGAAGATGCTACACCGAGTCAT
1 TTGAAGATGCTACACCGAGTCAT
4544 TTGAGAAGAT
Statistics
Matches: 280, Mismatches: 20, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
34 1 0.00
35 276 0.99
36 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
Found at i:4324 original size:105 final size:104
Alignment explanation
Indices: 4206--4543 Score: 522
Period size: 105 Copynumber: 3.2 Consensus size: 104
4196 TGAGTCCATA
** *
4206 TTGAAGATGCTACACCGAGTCATCCAAATTCATCTTTGAAGGTGCTACACCGAGTCATCTGGATT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAT-TTTGAAGATGCTACACCGAGTCATCTGGATT
*
4271 CAACTTTGAAGATGTTACACCGAGTCATCTGAGTTCAACT
65 CAACTTTGAAGATGCTACACCGAGTCATCTGAGTTCAACT
4311 TTGAAGATGCTACACCGAGTCATCTGAATTCATATTTGAAGATGCTACACCGAGTCATCTGGATT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAT-TTTGAAGATGCTACACCGAGTCATCTGGATT
*
4376 CAA-TTTCGAAGATGCTACACCGAGTCATCTG-GATTCAATT
65 CAACTTT-GAAGATGCTACACCGAGTCATCTGAG-TTCAACT
*
4416 TTGAAGATGCTACACCGAGTCATCTGGATTCAATTTTGAAGATGCTACACCGAGTCATCT-GAGT
1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATTTTGAAGATGCTACACCGAGTCATCTGGA-T
*
4480 TCAACTTTGAAGATGCTACACCGAGTCATCTGAATAT-AACT
64 TCAACTTTGAAGATGCTACACCGAGTCATCTGAGT-TCAACT
4521 TTGAAGATGCTACACCGAGTCAT
1 TTGAAGATGCTACACCGAGTCAT
4544 TTGAGAAGAT
Statistics
Matches: 217, Mismatches: 9, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
104 6 0.03
105 205 0.94
106 6 0.03
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (104 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCATTTTGAAGATGCTACACCGAGTCATCTGGATTC
AACTTTGAAGATGCTACACCGAGTCATCTGAGTTCAACT
Found at i:4642 original size:50 final size:50
Alignment explanation
Indices: 4563--4692 Score: 179
Period size: 50 Copynumber: 2.6 Consensus size: 50
4553 TGGTAATGTA
* * * *
4563 TCGTATGGAAATGAACTGTGGCTTATGGAAAAGCCCATGTTGATAATTAAC
1 TCGTATGGAAACG-AGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTAAC
* *
4614 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTAAC
* *
4664 TAGTATGGAAACGAGTTTGGTTTGTGGAA
1 TCGTATGGAAACGAGTTTGGCTTGTGGAA
4693 TGTTTCACTT
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 59 0.83
51 12 0.17
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (50 bp):
TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTAAC
Found at i:4810 original size:50 final size:50
Alignment explanation
Indices: 4767--4988 Score: 381
Period size: 50 Copynumber: 4.4 Consensus size: 50
4757 CAATCTAATA
4767 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
* * * *
4817 TTGAAAGGACCGTCTTCTGCTTATCCCTTGAATTGTCTACCAATTCAATC
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
*
4867 TTAAAAGGATCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
*
4917 TTAAAAAGGACCGTCTTCCGCTCATCCTTTGAACTGTCTACCAATTCAATC
1 TT-AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
4968 TTAAAAGGACCGTCTTCCGCT
1 TTAAAAGGACCGTCTTCCGCT
4989 GTATTGTCTT
Statistics
Matches: 160, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
50 112 0.70
51 48 0.30
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (50 bp):
TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
Found at i:4975 original size:101 final size:100
Alignment explanation
Indices: 4767--4988 Score: 381
Period size: 101 Copynumber: 2.2 Consensus size: 100
4757 CAATCTAATA
*
4767 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTGAAAGGACCGTCT
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCT
* * *
4832 TCTGCTTATCCCTTGAATTGTCTACCAATTCAATC
66 TCCGCTCATCCCTTGAACTGTCTACCAATTCAATC
*
4867 TTAAAAGGATCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAAGGACCGTC
1 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTT-AAAAGGACCGTC
*
4932 TTCCGCTCATCCTTTGAACTGTCTACCAATTCAATC
65 TTCCGCTCATCCCTTGAACTGTCTACCAATTCAATC
4968 TTAAAAGGACCGTCTTCCGCT
1 TTAAAAGGACCGTCTTCCGCT
4989 GTATTGTCTT
Statistics
Matches: 114, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
100 51 0.45
101 63 0.55
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (100 bp):
TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCT
TCCGCTCATCCCTTGAACTGTCTACCAATTCAATC
Found at i:5058 original size:54 final size:54
Alignment explanation
Indices: 4976--5100 Score: 205
Period size: 54 Copynumber: 2.3 Consensus size: 54
4966 TCTTAAAAGG
* * *
4976 ACCGTCTTCCGCTGTATTGTCTTCCAATCAACATTTGAAAATTTTTTCTAGCAA
1 ACCGTCTTCCGATGTATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAA
5030 ACCGTCTTCCGATGTATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAA
1 ACCGTCTTCCGATGTATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAA
* *
5084 ACCGTCTTTCGGTGTAT
1 ACCGTCTTCCGATGTAT
5101 CTAAAATCCT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (54 bp):
ACCGTCTTCCGATGTATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAACAA
Found at i:8921 original size:14 final size:14
Alignment explanation
Indices: 8902--8930 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8892 TGCACGTAAT
8902 TATGTAGCTGTCTG
1 TATGTAGCTGTCTG
8916 TATGTAGCTGTCTG
1 TATGTAGCTGTCTG
8930 T
1 T
8931 CTCCCCCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (14 bp):
TATGTAGCTGTCTG
Done.