Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019946.1 Corchorus olitorius cultivar O-4 contig19979, 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: 47133
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:3188 original size:20 final size:20
Alignment explanation
Indices: 3160--3200 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3150 TTCATATTGT
* *
3160 AATGCTATCTTGATTTATGA
1 AATGATATCCTGATTTATGA
*
3180 AATGATATCCTGATTTTTGA
1 AATGATATCCTGATTTATGA
3200 A
1 A
3201 TTAACTCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.44
Consensus pattern (20 bp):
AATGATATCCTGATTTATGA
Found at i:9901 original size:43 final size:42
Alignment explanation
Indices: 9804--10090 Score: 242
Period size: 41 Copynumber: 6.8 Consensus size: 42
9794 TTATAGAGAT
* * *
9804 TGCCCTTGTGTTATAATTGTG-TTTAGGGACTTT--AATATGGA
1 TGCCCCTGTGTTATAAATGTGCTTGA-GGACTTTGAAATA-GGA
* * *
9845 CGCCTCTGTGTTATAAATGTGCTTGAGGACTTTGAAATAGCGG
1 TGCCCCTGTGTTATAAATGTGCTTGAGGACTTTGAAATAG-GA
* * * *
9888 TGCCCCTGTGTTATAATTGTGCTTGGGGACCTTGATATA-GA
1 TGCCCCTGTGTTATAAATGTGCTTGAGGACTTTGAAATAGGA
* * * * *
9929 TGCCTCTGTGTTATAAATGTGCTTGAAGACTTTTAAAAAGAA
1 TGCCCCTGTGTTATAAATGTGCTTGAGGACTTTGAAATAGGA
* * * *
9971 TTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGATATA-GA
1 -TGCCCCTGTGTTATAAATGTGCTTGAGGACTTTGAAATAGGA
* * * * *
10013 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAGAGAGAA
1 TGCCCCTGTGTTATAAATGTGCTTGAGGACTTT-GAAATAGGA
* * *
10056 TTGCCCCTATGTTATAAATGTGTTTGGGGACTTTG
1 -TGCCCCTGTGTTATAAATGTGCTTGAGGACTTTG
10091 GGGAGGGAGA
Statistics
Matches: 197, Mismatches: 40, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
41 86 0.44
42 10 0.05
43 71 0.36
44 30 0.15
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (42 bp):
TGCCCCTGTGTTATAAATGTGCTTGAGGACTTTGAAATAGGA
Found at i:9945 original size:84 final size:84
Alignment explanation
Indices: 9802--10090 Score: 407
Period size: 84 Copynumber: 3.4 Consensus size: 84
9792 CCTTATAGAG
* * * * *
9802 ATTGCCCTTGTGTTATAATTGTGTTTAGGGACTTTAATATGGACGCCTCTGTGTTATAAATGTGC
1 ATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGC
* *
9867 TTGAGGACTTTGAAATAGC
66 TTGAGGACTTTGAAAAAGA
** * *
9886 GGTGCCCCTGTGTTATAATTGTGCTTGGGGACCTTGATATAGATGCCTCTGTGTTATAAATGTGC
1 ATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGC
* *
9951 TTGAAGACTTTTAAAAAGA
66 TTGAGGACTTTGAAAAAGA
*
9970 ATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGT
1 ATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGC
* *
10035 TTGAGGACTTTAGAGAGAGA
66 TTGAGGACTTT-GAAAAAGA
* *
10055 ATTGCCCCTATGTTATAAATGTGTTTGGGGACTTTG
1 ATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTG
10091 GGGAGGGAGA
Statistics
Matches: 180, Mismatches: 24, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
84 141 0.78
85 39 0.22
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (84 bp):
ATTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGC
TTGAGGACTTTGAAAAAGA
Found at i:11918 original size:60 final size:60
Alignment explanation
Indices: 11817--11981 Score: 188
Period size: 60 Copynumber: 2.8 Consensus size: 60
11807 TTTCCGATAC
* * * *
11817 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCTCTTATTTGGCCAAATTAAAATAT
1 CAGGCCCTTATTTGAGCATTTTGGAAAACGTTAAGCTCTTATTTGGCCAAATTAAAAGAT
* * *
11877 CGGGCCCTTATTTGAGCATTTTGGAAAACGTTAA-ATCCTTATTTGGCCAAATTAAAGGAT
1 CAGGCCCTTATTTGAGCATTTTGGAAAACGTTAAGCT-CTTATTTGGCCAAATTAAAAGAT
** * * * **
11937 CAACCCCTTATTTGAACATTTTGGTAAATGTTTTGCTCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGAAAACGTTAAGCTCTTATTTG
11982 AGCAATTAGT
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
59 1 0.01
60 85 0.98
61 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGAAAACGTTAAGCTCTTATTTGGCCAAATTAAAAGAT
Found at i:22144 original size:31 final size:31
Alignment explanation
Indices: 22106--22170 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
22096 TAGGGGTGAG
* *
22106 CATCGGGTCGGGT-TGGTCCTAATCGGTTGGT
1 CATCGGGTCGGGTCT-ATCCTAATCGGTTGAT
22137 CATCGGGTCGGGTCTATCCTAATCGGTTGAT
1 CATCGGGTCGGGTCTATCCTAATCGGTTGAT
22168 CAT
1 CAT
22171 TGATCTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.32, T:0.32
Consensus pattern (31 bp):
CATCGGGTCGGGTCTATCCTAATCGGTTGAT
Found at i:38838 original size:15 final size:15
Alignment explanation
Indices: 38815--38844 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38805 ACAGTATAAC
*
38815 CTCTTTAAAATAATA
1 CTCTATAAAATAATA
38830 CTCTATAAAATAATA
1 CTCTATAAAATAATA
38845 TTTTTGTCCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
CTCTATAAAATAATA
Found at i:39617 original size:21 final size:21
Alignment explanation
Indices: 39577--39617 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39567 TACTACTACT
** *
39577 ATATATATATATTATTATATA
1 ATATATATATAAAATAATATA
39598 ATATATATATAAAATAATAT
1 ATATATATATAAAATAATAT
39618 TGTTATTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATATATATAAAATAATATA
Found at i:43818 original size:25 final size:25
Alignment explanation
Indices: 43784--43847 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
43774 GTGTTTTCTC
*
43784 TTCTCTTAGAGTTGTTAGTTGATTT
1 TTCTCTTAGAGTTGTTAGCTGATTT
43809 TTCTCTTAGAGTTGTTAGCTGATTT
1 TTCTCTTAGAGTTGTTAGCTGATTT
43834 TTCTCTTAGAGTTG
1 TTCTCTTAGAGTTG
43848 ATTGATTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.53
Consensus pattern (25 bp):
TTCTCTTAGAGTTGTTAGCTGATTT
Found at i:44830 original size:41 final size:41
Alignment explanation
Indices: 44718--45048 Score: 352
Period size: 41 Copynumber: 7.9 Consensus size: 41
44708 CCATAAGGAG
44718 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTG-TAAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGAT-AT
44760 AGAGATG-CTCCTGTGTTATATATGTGTTTGAGGACTTTGATAT
1 A-A-ATGCCT-CTGTGTTATATATGTGTTTGAGGACTTTGATAT
*
44803 AAATGCCTCTTTGTTATATATGTGTTTGAGGACTTTG-TAAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT
* * *
44844 AGAGTTGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATAT
1 A-A-ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATAT
* *
44887 AGATGTCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT
* * * *
44928 AAAGGCGCCCATGTG-T-TATATGTGTTTGGGGACTTGGATAT
1 AAATGC-CTC-TGTGTTATATATGTGTTTGAGGACTTTGATAT
**
44969 AGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGA-AT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTT-GATAT
* *
45011 AGAATTGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 A-AA-TGCCTCTGTGTTATATATGTGTTTGAGGACTTT
45049 TTGGTTATTG
Statistics
Matches: 244, Mismatches: 26, Indels: 37
0.79 0.08 0.12
Matches are distributed among these distances:
39 4 0.02
40 5 0.02
41 110 0.45
42 14 0.06
43 53 0.22
44 58 0.24
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.43
Consensus pattern (41 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATAT
Found at i:44879 original size:84 final size:85
Alignment explanation
Indices: 44718--45048 Score: 499
Period size: 84 Copynumber: 3.9 Consensus size: 85
44708 CCATAAGGAG
* *
44718 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCTCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
*
44783 GTGTTTGAGGACTTTGATAT
66 GTGTTTGGGGACTTTGATAT
*
44803 AAATGCCTCTTTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGTTGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
44867 GTGTTTGGGGACTTTGATAT
66 GTGTTTGGGGACTTTGATAT
* * * ** *
44887 AGATGTCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAAAGGCGCCCATGTG-T-TATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
*
44949 GTGTTTGGGGACTTGGATAT
66 GTGTTTGGGGACTTTGATAT
** * *
44969 AGGTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAATTGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
45034 GTGTTTGGGGACTTT
66 GTGTTTGGGGACTTT
45049 TTGGTTATTG
Statistics
Matches: 222, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
82 55 0.25
83 18 0.08
84 98 0.44
85 51 0.23
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.43
Consensus pattern (85 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGTTGCCCCTGTGTTATATAT
GTGTTTGGGGACTTTGATAT
Found at i:45828 original size:45 final size:42
Alignment explanation
Indices: 45764--45859 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 42
45754 AGCAACAATT
* *
45764 AATATTAGATTTATTTTGATGAATTATCTAGAGATGGAGGAGTAG
1 AATATTAGGTTTATTTTGATGAATTACCTAGAGAT-GA--AGTAG
45809 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGAAGTAG
1 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGAAGTAG
45851 AAT-TTAGGT
1 AATATTAGGT
45860 AATGCGCTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
41 6 0.12
42 8 0.16
44 2 0.04
45 33 0.67
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (42 bp):
AATATTAGGTTTATTTTGATGAATTACCTAGAGATGAAGTAG
Found at i:46242 original size:23 final size:24
Alignment explanation
Indices: 46197--46293 Score: 169
Period size: 24 Copynumber: 4.1 Consensus size: 24
46187 TTCTGAGTAC
**
46197 TTTGCAACGGAATCAAAAACGGAA
1 TTTGCAATAGAATCAAAAACGGAA
46221 TTTGCAATAGAATC-AAAACGGAA
1 TTTGCAATAGAATCAAAAACGGAA
46244 TTTGCAATAGAATCAAAAACGGAA
1 TTTGCAATAGAATCAAAAACGGAA
46268 TTTGCAATAGAATCAAAAACGGAA
1 TTTGCAATAGAATCAAAAACGGAA
46292 TT
1 TT
46294 CTATCTATGA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
23 23 0.33
24 47 0.67
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (24 bp):
TTTGCAATAGAATCAAAAACGGAA
Found at i:46257 original size:47 final size:48
Alignment explanation
Indices: 46197--46293 Score: 169
Period size: 47 Copynumber: 2.0 Consensus size: 48
46187 TTCTGAGTAC
*
46197 TTTGCAACGGAATCAAAAACGGAATTTGCAATAGAATC-AAAACGGAA
1 TTTGCAACAGAATCAAAAACGGAATTTGCAATAGAATCAAAAACGGAA
*
46244 TTTGCAATAGAATCAAAAACGGAATTTGCAATAGAATCAAAAACGGAA
1 TTTGCAACAGAATCAAAAACGGAATTTGCAATAGAATCAAAAACGGAA
46292 TT
1 TT
46294 CTATCTATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 36 0.77
48 11 0.23
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (48 bp):
TTTGCAACAGAATCAAAAACGGAATTTGCAATAGAATCAAAAACGGAA
Found at i:46619 original size:45 final size:45
Alignment explanation
Indices: 46566--46670 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
46556 AAAACTAAAC
** * * *
46566 CCTATACAAAATAAAGGCCTTTTCTAGATCATTGCAAGTT-AGTGA
1 CCTATACAAAATAAAGGCCTCGTCTAGATAATGGCAAATTAAG-GA
* *
46611 TCTATACAAAATAAATGCCTCGTCTAGATAATGGCAAATTAAGGA
1 CCTATACAAAATAAAGGCCTCGTCTAGATAATGGCAAATTAAGGA
46656 CCTATACAAAATAAA
1 CCTATACAAAATAAA
46671 AGGCTGCCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 49 0.96
46 2 0.04
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (45 bp):
CCTATACAAAATAAAGGCCTCGTCTAGATAATGGCAAATTAAGGA
Done.