Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011981.1 Corchorus olitorius cultivar O-4 contig12014, 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: 31811
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6079 original size:36 final size:36
Alignment explanation
Indices: 6032--6101 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
6022 TTCAATAACC
* * *
6032 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATAATTCTTA
*
6068 TTACATTTTTTGTAATTTTGATTATCATAATTCT
1 TTACATCTTTTGTAATTTTGATTATCATAATTCT
6102 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.09, T:0.59
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATAATTCTTA
Found at i:6994 original size:202 final size:202
Alignment explanation
Indices: 6608--7005 Score: 719
Period size: 202 Copynumber: 2.0 Consensus size: 202
6598 CTTACATGCT
*
6608 TGAATGCTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACG
1 TGAATGCTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACA
*
6673 TTATTATTATATATAAAACTATACCAAAAAATAGTAGTTGAACATTAGTGGTTGATTTATTAAAT
66 TTACTATTATATATAAAACTATACCAAAAAATAGTAGTTGAACATTAGTGGTTGATTTATTAAAT
6738 TAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTA
131 TAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTA
6803 TCAATGG
196 TCAATGG
*
6810 TGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACA
1 TGAATGCTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACA
*
6875 TTACTATTATATATATAGAACTATACCAAAAAA-ATTAGTTGAACATTAGTGGTTGATTTATTAA
66 TTACTATTATATATA-A-AACTATACCAAAAAATAGTAGTTGAACATTAGTGGTTGATTTATTAA
*
6939 ATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATGTT-AAGATCCGATTTATT
129 ATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATT
7003 TAT
194 TAT
7006 TATTAAGGAA
Statistics
Matches: 189, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
202 95 0.50
203 79 0.42
204 15 0.08
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (202 bp):
TGAATGCTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACA
TTACTATTATATATAAAACTATACCAAAAAATAGTAGTTGAACATTAGTGGTTGATTTATTAAAT
TAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTTATTTA
TCAATGG
Found at i:7166 original size:39 final size:40
Alignment explanation
Indices: 7112--7192 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
7102 ATACCTAAGA
*
7112 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
7151 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
7191 AT
1 AT
7193 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:13466 original size:31 final size:31
Alignment explanation
Indices: 13428--13529 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 31
13418 AAAGTACCTG
*
13428 TTTAGTCCCTGTACTATTGAAAAAGGATCAA
1 TTTAGTCCCTCTACTATTGAAAAAGGATCAA
* * ***
13459 TTTAGTCCCTCCATTA-TGAAATCTG-TCAA
1 TTTAGTCCCTCTACTATTGAAAAAGGATCAA
13488 TTTAGTCCCTCTACTATTG-AAAAGAGATCAA
1 TTTAGTCCCTCTACTATTGAAAAAG-GATCAA
*
13519 TTTAATCCCTC
1 TTTAGTCCCTC
13530 CGTGAAACGG
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
29 20 0.36
30 9 0.16
31 27 0.48
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (31 bp):
TTTAGTCCCTCTACTATTGAAAAAGGATCAA
Found at i:15162 original size:31 final size:30
Alignment explanation
Indices: 15127--15227 Score: 116
Period size: 31 Copynumber: 3.3 Consensus size: 30
15117 TCCTGTTTCA
15127 TAGAGGGACTAAATTGATCTCTTTTCAATAG
1 TAGAGGGACTAAATTGATCT-TTTTCAATAG
** *
15158 TAGAGGGACTAAATTGATAGATTTT--ATAA
1 TAGAGGGACTAAATTGAT-CTTTTTCAATAG
*
15187 TGGAGGGACTAAATTGATCATTTTTCAATAG
1 TAGAGGGACTAAATTGATC-TTTTTCAATAG
*
15218 TACAGGGACT
1 TAGAGGGACT
15228 TAACAGGTAC
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
29 24 0.42
31 33 0.58
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.34
Consensus pattern (30 bp):
TAGAGGGACTAAATTGATCTTTTTCAATAG
Found at i:19922 original size:25 final size:25
Alignment explanation
Indices: 19872--19924 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
19862 AAGATGATTA
* ** *
19872 AAATTAAAGTTTTCTTTTTGGCAAT
1 AAATTAAAGTTTACTTAGTGGAAAT
19897 AAATTAAAGTTTACTTAGTGGAAAT
1 AAATTAAAGTTTACTTAGTGGAAAT
19922 AAA
1 AAA
19925 AGGAGAGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.40
Consensus pattern (25 bp):
AAATTAAAGTTTACTTAGTGGAAAT
Found at i:27240 original size:18 final size:18
Alignment explanation
Indices: 27217--27251 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27207 CAAAGCATGG
*
27217 CATCGTGTGCTCTTATGA
1 CATCGTGCGCTCTTATGA
27235 CATCGTGCGCTCTTATG
1 CATCGTGCGCTCTTATG
27252 GCGTTATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.37
Consensus pattern (18 bp):
CATCGTGCGCTCTTATGA
Found at i:27830 original size:59 final size:59
Alignment explanation
Indices: 27738--27852 Score: 221
Period size: 59 Copynumber: 1.9 Consensus size: 59
27728 TGAATGGATA
27738 CCGTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACTACG
1 CCGTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACTACG
*
27797 CCGTGCGACCGAGGGATGGTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACT
1 CCGTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACT
27853 CGGTCGTACG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.13, C:0.26, G:0.35, T:0.26
Consensus pattern (59 bp):
CCGTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACTACG
Found at i:27865 original size:59 final size:59
Alignment explanation
Indices: 27738--27867 Score: 208
Period size: 59 Copynumber: 2.2 Consensus size: 59
27728 TGAATGGATA
*
27738 CCGTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACTACG
1 CCGTACGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACTACG
* *
27797 CCGTGCGACCGAGGGATGGTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACT-CGG
1 CCGTACGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACTAC-G
*
27856 TCGTACGACCGA
1 CCGTACGACCGA
27868 ATACGGAGCA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
58 1 0.01
59 66 0.99
ACGTcount: A:0.14, C:0.27, G:0.35, T:0.25
Consensus pattern (59 bp):
CCGTACGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACTACG
Found at i:30285 original size:15 final size:16
Alignment explanation
Indices: 30261--30300 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
30251 AGAGGTTGAA
*
30261 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
30276 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
30292 AGAAAACAA
1 AGAAAACAA
30301 AGCAGAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:31696 original size:29 final size:30
Alignment explanation
Indices: 31659--31717 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
31649 CAATTCTTCC
*
31659 TCTTGAAATAAATCTTCAAA-GTCTTCAAG
1 TCTTCAAATAAATCTTCAAAGGTCTTCAAG
*
31688 TCTTCAAATAAGTCTTCAAATGGTCTTCAA
1 TCTTCAAATAAATCTTCAAA-GGTCTTCAA
31718 ACACGAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 18 0.69
31 8 0.31
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (30 bp):
TCTTCAAATAAATCTTCAAAGGTCTTCAAG
Found at i:31715 original size:11 final size:12
Alignment explanation
Indices: 31685--31718 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
31675 CAAAGTCTTC
31685 AAGTCTTCAAAT
1 AAGTCTTCAAAT
31697 AAGTCTTCAAAT
1 AAGTCTTCAAAT
*
31709 -GGTCTTCAAA
1 AAGTCTTCAAA
31719 CACGAACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (12 bp):
AAGTCTTCAAAT
Done.