Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014617.1 Corchorus capsularis cultivar CVL-1 contig14638, 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: 15570
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:7309 original size:108 final size:108
Alignment explanation
Indices: 7116--7335 Score: 422
Period size: 108 Copynumber: 2.0 Consensus size: 108
7106 GTGATTTTTT
7116 TAATGCTTTGTTTGTTCTCATTTTGCAAGGTCAACTCATACTTTATTGTGTTTATGTAGCATATG
1 TAATGCTTTGTTTGTTCTCATTTTGCAAGGTCAACTCATACTTTATTGTGTTTATGTAGCATATG
7181 AATGTTGTTGTCGATATAGCATTCTGTAATTCATTTCCTTTGG
66 AATGTTGTTGTCGATATAGCATTCTGTAATTCATTTCCTTTGG
7224 TAATGCTTTGTTTGTTCTCATTTTGCAAGGTCAACTCATACTTTATTGTGTTTATGTAGCATATG
1 TAATGCTTTGTTTGTTCTCATTTTGCAAGGTCAACTCATACTTTATTGTGTTTATGTAGCATATG
* *
7289 AATGTTGTTGTCGATGTAGCATTGTGTAATTCATTTCCTTTGG
66 AATGTTGTTGTCGATATAGCATTCTGTAATTCATTTCCTTTGG
7332 TAAT
1 TAAT
7336 TTAGTTGACT
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 110 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.47
Consensus pattern (108 bp):
TAATGCTTTGTTTGTTCTCATTTTGCAAGGTCAACTCATACTTTATTGTGTTTATGTAGCATATG
AATGTTGTTGTCGATATAGCATTCTGTAATTCATTTCCTTTGG
Found at i:7641 original size:13 final size:14
Alignment explanation
Indices: 7615--7921 Score: 128
Period size: 14 Copynumber: 21.0 Consensus size: 14
7605 TTAATGTTTT
*
7615 TAAATATTATTTTC
1 TAAATATTAATTTC
7629 TAAATA-TAATTTC
1 TAAATATTAATTTC
*
7642 ATTACATATTTAATTTC
1 --TAAATA-TTAATTTC
* *
7659 TTAATATT-TTATTC
1 TAAATATTAAT-TTC
* *
7673 TAATTA-TAATGTC
1 TAAATATTAATTTC
* *
7686 ATTAAATTTATAATTTT
1 --TAAATAT-TAATTTC
* *
7703 TAAATATTATTTTG
1 TAAATATTAATTTC
* *
7717 TAATTA-TAATATC
1 TAAATATTAATTTC
* *
7730 ATTACATTGTTAATTTC
1 --TA-AATATTAATTTC
*
7747 TAAATATTATTTTC
1 TAAATATTAATTTC
7761 TAAAT-TTAATTTC
1 TAAATATTAATTTC
* *
7774 AGTACATTTATAATTTC
1 --TAAATAT-TAATTTC
7791 TAAATA-TAATTTC
1 TAAATATTAATTTC
* *
7804 ATTACATATATAACTTC
1 --TAAATAT-TAATTTC
*
7821 TAAATATTATTTTC
1 TAAATATTAATTTC
7835 TAAATA-TAATTTC
1 TAAATATTAATTTC
*
7848 ATTACATATATAATTTC
1 --TAAATAT-TAATTTC
7865 TAAATA-TAATTTC
1 TAAATATTAATTTC
* *
7878 ATTACATTTATAATTTC
1 --TAAATAT-TAATTTC
*
7895 TAAATATTATTTTC
1 TAAATATTAATTTC
*
7909 TAATTA-TAATTTC
1 TAAATATTAATTTC
7922 ATTACATTTA
Statistics
Matches: 219, Mismatches: 44, Indels: 61
0.68 0.14 0.19
Matches are distributed among these distances:
13 47 0.21
14 62 0.28
15 61 0.28
16 4 0.02
17 45 0.21
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.52
Consensus pattern (14 bp):
TAAATATTAATTTC
Found at i:7681 original size:44 final size:43
Alignment explanation
Indices: 7617--7802 Score: 207
Period size: 44 Copynumber: 4.2 Consensus size: 43
7607 AATGTTTTTA
*
7617 AATATTATTTTCTAAATATAATTTCATTACATATTTAATTTCTT
1 AATATTATTTTCTAATTATAATTTCATTACAT-TTTAATTTCTT
* *
7661 AATATT-TTATTCTAATTATAATGTCATTAAATTTATAATTT-TT
1 AATATTATT-TTCTAATTATAATTTCATTACATTT-TAATTTCTT
* * *
7704 AAATATTATTTTGTAATTATAATATCATTACATTGTTAATTTCTA
1 -AATATTATTTTCTAATTATAATTTCATTACATT-TTAATTTCTT
* *
7749 AATATTATTTTCTAAATT-TAATTTCAGTACATTTATAATTTCTA
1 AATATTATTTTCT-AATTATAATTTCATTACATTT-TAATTTCTT
*
7793 AATATAATTT
1 AATATTATTT
7803 CATTACATAT
Statistics
Matches: 123, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
43 7 0.06
44 108 0.88
45 8 0.07
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (43 bp):
AATATTATTTTCTAATTATAATTTCATTACATTTTAATTTCTT
Found at i:7707 original size:88 final size:88
Alignment explanation
Indices: 7611--7802 Score: 255
Period size: 88 Copynumber: 2.2 Consensus size: 88
7601 AAATTTAATG
* *
7611 TTTTTAAATATTATTTTCTAAATATAATTTCATTACATAT-TTAATTTCTTAATATT-TTATTCT
1 TTTTTAAATATTATTTTCTAAATATAATATCATTACAT-TGTTAATTTCTAAATATTATT-TTCT
*
7674 -AATTATAATGTCATTAAATTTATAA
64 AAATT-TAATGTCAGTAAATTTATAA
* *
7699 TTTTTAAATATTATTTTGTAATTATAATATCATTACATTGTTAATTTCTAAATATTATTTTCTAA
1 TTTTTAAATATTATTTTCTAAATATAATATCATTACATTGTTAATTTCTAAATATTATTTTCTAA
* *
7764 ATTTAATTTCAGTACATTTATAA
66 ATTTAATGTCAGTAAATTTATAA
* *
7787 TTTCTAAATATAATTT
1 TTTTTAAATATTATTT
7803 CATTACATAT
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
87 1 0.01
88 85 0.92
89 6 0.07
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (88 bp):
TTTTTAAATATTATTTTCTAAATATAATATCATTACATTGTTAATTTCTAAATATTATTTTCTAA
ATTTAATGTCAGTAAATTTATAA
Found at i:7793 original size:30 final size:30
Alignment explanation
Indices: 7757--7834 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
7747 TAAATATTAT
*
7757 TTTCTAAATTTAATTTCAGTACATTTATAA
1 TTTCTAAATTTAATTTCAGTACATATATAA
* *
7787 TTTCTAAATATAATTTCATTACATATATAA
1 TTTCTAAATTTAATTTCAGTACATATATAA
* *
7817 CTTCTAAATATTATTTTC
1 TTTCTAAAT-TTAATTTC
7835 TAAATATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 35 0.85
31 6 0.15
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (30 bp):
TTTCTAAATTTAATTTCAGTACATATATAA
Found at i:7799 original size:74 final size:73
Alignment explanation
Indices: 7721--7951 Score: 338
Period size: 74 Copynumber: 3.1 Consensus size: 73
7711 ATTTTGTAAT
* *
7721 TATAATATCATTACATTGTTAATTTCTAAATATTATTTTCTAAATTTAATTTCAGTACATTTATA
1 TATAATTTCATTACATT-TTAATTTCTAAATATTATTTTCTAAATTTAATTTCATTACATTTATA
7786 ATTTCTAAA
65 ATTTCTAAA
* * * *
7795 TATAATTTCATTACATATATAACTTCTAAATATTATTTTCTAAATATAATTTCATTACATATATA
1 TATAATTTCATTACAT-TTTAATTTCTAAATATTATTTTCTAAATTTAATTTCATTACATTTATA
7860 ATTTCTAAA
65 ATTTCTAAA
7869 TATAATTTCATTACATTTATAATTTCTAAATATTATTTTCT-AATTATAATTTCATTACATTTAT
1 TATAATTTCATTACATTT-TAATTTCTAAATATTATTTTCTAAATT-TAATTTCATTACATTTAT
* *
7933 AATTTATAGA
64 AATTTCTAAA
*
7943 TATTATTTC
1 TATAATTTC
7952 CTGATTATAA
Statistics
Matches: 141, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
73 4 0.03
74 136 0.96
75 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.51
Consensus pattern (73 bp):
TATAATTTCATTACATTTTAATTTCTAAATATTATTTTCTAAATTTAATTTCATTACATTTATAA
TTTCTAAA
Found at i:7833 original size:118 final size:117
Alignment explanation
Indices: 7625--7988 Score: 409
Period size: 118 Copynumber: 3.1 Consensus size: 117
7615 TAAATATTAT
* *
7625 TTTCTAAATATAATTTCATTACATATT-TAATTTCTTAATATT-TTATTCTAATTATAATGTCAT
1 TTTCTAAATATAATTTCA-TACA-ATTATAATTTCTAAATATTATT-TTCTAATTATAATTTCAT
* * * * *
7688 TAAATTTATAATTTTTAAATATTATTTTGTAATTATAATATCATTACAT-TGTTAA
63 TACATTTATAATTTATAAATATTATTTTCTAATTATAATTTCATTACATAT-ATAA
* * *
7743 TTTCTAAATATTATTTTC-TA-AATT-TAATTTCAGTACAT-TTATAATTTCTAAATATAATTTC
1 TTTCTAAATA-TAATTTCATACAATTATAATTTC--TAAATATTAT--TTTCTAATTATAATTTC
* * * *
7804 ATTACATATATAACTTCTAAATATTATTTTCTAAATATAATTTCATTACATATATAA
61 ATTACATTTATAATTTATAAATATTATTTTCTAATTATAATTTCATTACATATATAA
*
7861 TTTCTAAATATAATTTCATTACATTTATAATTTCTAAATATTATTTTCTAATTATAATTTCATTA
1 TTTCTAAATATAATTTCA-TACAATTATAATTTCTAAATATTATTTTCTAATTATAATTTCATTA
* * * **
7926 CATTTATAATTTATAGATATTATTTCCTGATTATAATTTCATTATGTATATAA
65 CATTTATAATTTATAAATATTATTTTCTAATTATAATTTCATTACATATATAA
7979 TTTCTAAATA
1 TTTCTAAATA
7989 CTATTATTTT
Statistics
Matches: 208, Mismatches: 26, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
115 10 0.05
116 3 0.01
117 12 0.06
118 155 0.75
119 14 0.07
120 7 0.03
121 7 0.03
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.52
Consensus pattern (117 bp):
TTTCTAAATATAATTTCATACAATTATAATTTCTAAATATTATTTTCTAATTATAATTTCATTAC
ATTTATAATTTATAAATATTATTTTCTAATTATAATTTCATTACATATATAA
Found at i:7835 original size:44 final size:44
Alignment explanation
Indices: 7782--7876 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
7772 TCAGTACATT
7782 TATAA-TTTCTAAATATAATTTCATTACATATATAACTTCTAAA
1 TATAATTTTCTAAATATAATTTCATTACATATATAACTTCTAAA
* *
7825 TATTATTTTCTAAATATAATTTCATTACATATATAATTTCTAAA
1 TATAATTTTCTAAATATAATTTCATTACATATATAACTTCTAAA
7869 TATAATTT
1 TATAATTT
7877 CATTACATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 4 0.08
44 44 0.92
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (44 bp):
TATAATTTTCTAAATATAATTTCATTACATATATAACTTCTAAA
Found at i:7867 original size:30 final size:30
Alignment explanation
Indices: 7831--7988 Score: 134
Period size: 30 Copynumber: 5.3 Consensus size: 30
7821 TAAATATTAT
7831 TTTCTAAATATAATTTCATTACATATATAA
1 TTTCTAAATATAATTTCATTACATATATAA
*
7861 TTTCTAAATATAATTTCATTACATTTATAA
1 TTTCTAAATATAATTTCATTACATATATAA
*
7891 TTTCTAAATATTATTT--TCTA-AT-TATAA
1 TTTCTAAATATAATTTCAT-TACATATATAA
* *
7918 TTTCATTACATTTATAATTT-A-TAGATAT-T-A
1 TTTC--TA-A-ATATAATTTCATTACATATATAA
* * **
7948 TTTCCTGATTATAATTTCATTATGTATATAA
1 TTT-CTAAATATAATTTCATTACATATATAA
7979 TTTCTAAATA
1 TTTCTAAATA
7989 CTATTATTTT
Statistics
Matches: 106, Mismatches: 9, Indels: 26
0.75 0.06 0.18
Matches are distributed among these distances:
27 18 0.17
28 5 0.05
29 10 0.09
30 57 0.54
31 15 0.14
32 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (30 bp):
TTTCTAAATATAATTTCATTACATATATAA
Found at i:7909 original size:44 final size:44
Alignment explanation
Indices: 7861--8009 Score: 190
Period size: 44 Copynumber: 3.3 Consensus size: 44
7851 ACATATATAA
*
7861 TTTCTAAATATAATTTCATTACATTTATAATTTCTAAATATTAT
1 TTTCTAATTATAATTTCATTACATTTATAATTTCTAAATATTAT
* *
7905 TTTCTAATTATAATTTCATTACATTTATAATTTATAGATATTAT
1 TTTCTAATTATAATTTCATTACATTTATAATTTCTAAATATTAT
* * ** *
7949 TTCCTGATTATAATTTCATTATGTATATAATTTCTAAATACTATTAT
1 TTTCTAATTATAATTTCATTACATTTATAATTTCT-AA-A-TATTAT
*
7996 TTTCTCATTATAAT
1 TTTCTAATTATAAT
8010 CTATATTAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
44 70 0.78
45 1 0.01
46 1 0.01
47 18 0.20
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (44 bp):
TTTCTAATTATAATTTCATTACATTTATAATTTCTAAATATTAT
Found at i:7934 original size:17 final size:15
Alignment explanation
Indices: 7776--7937 Score: 78
Period size: 17 Copynumber: 10.9 Consensus size: 15
7766 TTAATTTCAG
7776 TACATTTATAATTTC
1 TACATTTATAATTTC
*
7791 TA-A-ATATAATTTC
1 TACATTTATAATTTC
* *
7804 ATTACATATATAACTTC
1 --TACATTTATAATTTC
*
7821 TAAATATTAT--TTTC
1 TACAT-TTATAATTTC
*
7835 TA-A-ATATAATTTC
1 TACATTTATAATTTC
*
7848 ATTACATATATAATTTC
1 --TACATTTATAATTTC
*
7865 TA-A-ATATAATTTC
1 TACATTTATAATTTC
7878 ATTACATTTATAATTTC
1 --TACATTTATAATTTC
*
7895 TAAATATTAT--TTTC
1 TACAT-TTATAATTTC
7909 TA-A-TTATAATTTC
1 TACATTTATAATTTC
7922 ATTACATTTATAATTT
1 --TACATTTATAATTT
7938 ATAGATATTA
Statistics
Matches: 117, Mismatches: 8, Indels: 42
0.70 0.05 0.25
Matches are distributed among these distances:
11 7 0.06
13 29 0.25
14 13 0.11
15 20 0.17
16 11 0.09
17 37 0.32
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.51
Consensus pattern (15 bp):
TACATTTATAATTTC
Found at i:14221 original size:22 final size:23
Alignment explanation
Indices: 14193--14235 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
14183 TAGAAGGAGT
14193 AGGTTTTACT-TTCCTACCAGAA
1 AGGTTTTACTATTCCTACCAGAA
14215 AGGTTTTACTATTCCTACCAG
1 AGGTTTTACTATTCCTACCAG
14236 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACCAGAA
Done.