Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015192.1 Corchorus capsularis cultivar CVL-1 contig15213, 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: 21203
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Found at i:12284 original size:35 final size:36
Alignment explanation
Indices: 12234--12359 Score: 145
Period size: 35 Copynumber: 3.6 Consensus size: 36
12224 TATAACATAT
12234 TTCATCATTCAAC-ACTTGGGGACTCCAACAACTCC
1 TTCATCATTCAACAACTTGGGGACTCCAACAACTCC
*
12269 TTCCTCATTCAAC-ACTTGGGGACTCCAACAAC-CAC
1 TTCATCATTCAACAACTTGGGGACTCCAACAACTC-C
* * * *
12304 TTCATCATTCAACAACTAGGTG-CTCCAGCAACTCA
1 TTCATCATTCAACAACTTGGGGACTCCAACAACTCC
* *
12339 TTCTTCATTC-ACTACTTGGGG
1 TTCATCATTCAACAACTTGGGG
12360 GTTTCAATAA
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
34 9 0.12
35 62 0.79
36 7 0.09
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.28
Consensus pattern (36 bp):
TTCATCATTCAACAACTTGGGGACTCCAACAACTCC
Found at i:12842 original size:72 final size:71
Alignment explanation
Indices: 12723--13215 Score: 609
Period size: 72 Copynumber: 6.9 Consensus size: 71
12713 TGGTCTTCTT
* *
12723 CTTCATTGCGATTGTAGCCGAGACAGTTCCCACATTTGGCAGCCCTTCGCACAATCCTTACATGA
1 CTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGA
*
12788 TCATCAC
66 TTAT-AC
* * *
12795 CTTCATTGTGATTGTAGCTGAGGCAGTTCCCACATGTGGCAGTCCTTCGCACAATCCTTACATGA
1 CTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGA
*
12860 TAATATTC
66 T--TATAC
* *
12868 CAT-ATTGC-AGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCTTTCGCACAATCCTTACATG
1 CTTCATTGCGA-TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATG
*
12931 ATAAT-C
65 ATTATAC
* * * ***
12937 TTTCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTATGC
1 CTTC--ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACAT
*
13002 GATTATATT
64 GATTATA-C
* * **
13011 CATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTATGTGA
1 CTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGA
*
13076 TTATATT
66 TTATA-C
* * * **
13083 CATCATTGCGATTGTAGCCAAGGCAGTTCCCACATTTGACAGTCCTTCGCACAATCCTTATGTGA
1 CTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGA
13148 TTAT-C
66 TTATAC
*
13153 TTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCTTACA
1 --CTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
13216 ACTACCTTCC
Statistics
Matches: 374, Mismatches: 36, Indels: 23
0.86 0.08 0.05
Matches are distributed among these distances:
69 2 0.01
70 2 0.01
71 25 0.07
72 338 0.90
73 3 0.01
74 4 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.31
Consensus pattern (71 bp):
CTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGA
TTATAC
Found at i:12987 original size:144 final size:145
Alignment explanation
Indices: 12725--13215 Score: 701
Period size: 144 Copynumber: 3.4 Consensus size: 145
12715 GTCTTCTTCT
* * *
12725 TCATTGCGATTGTAGCCGAGACAGTTCCCACATTTGGCAGCCCTTCGCACAATCCTTACATGATC
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
* * *
12790 ATCACCTTC--ATTGTGATTGTAGCTGAGGCAGTTCCCACATGTGGCAGTCCTTCGCACAATCCT
66 ATCA--TTCATATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCT
** *
12853 TACATGATAATATTCCA
129 TATGTGATTATATTCCA
*
12870 T-ATTGC-AGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCTTTCGCACAATCCTTACATGAT
1 TCATTGCGA-TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGAT
* * *
12933 AATCTTTCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTT
65 AATCATTCATATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
*
12998 ATGCGATTATATT-CA
130 ATGTGATTATATTCCA
* ** *
13013 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTATGTGATT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
* *
13078 AT-ATTCATCATTGCGATTGTAGCCAAGGCAGTTCCCACATTTGACAGTCCTTCGCACAATCCTT
66 ATCATTCAT-ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
*
13142 ATGTGATTATCTTCC-
130 ATGTGATTATATTCCA
13157 TCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCTTACA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
13216 ACTACCTTCC
Statistics
Matches: 310, Mismatches: 29, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
142 3 0.01
143 33 0.11
144 271 0.87
145 3 0.01
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (145 bp):
TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
ATCATTCATATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
TGTGATTATATTCCA
Found at i:13109 original size:216 final size:216
Alignment explanation
Indices: 12719--13215 Score: 698
Period size: 216 Copynumber: 2.3 Consensus size: 216
12709 CCTATGGTCT
* * *
12719 TCTTCTTCATTGCGATTGTAGCCGAGACAGTTCCCACATTTGGCAGCCCTTCGCACAATCCTTAC
1 TCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
* * * *
12784 ATGATCATCACCTTCATTGTGATTGTAGCTGAGGCAGTTCCCACATGTGGCAGTCCTTCGCACAA
66 ACGATCATCACCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATGTGGCAGTCCTTCGCACAA
* * * *
12849 TCCTTACATGATAATATTCCATATTGCAGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCTTT
131 CCCTTACATGATAATATTCCATATTGCAGTTGTAGCCAAGGCAGTTCCCACATTTGACAGTCCTT
12914 CGCACAATCCTTACATGATAA
196 CGCACAATCCTTACATGATAA
* *
12935 TCTTTCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTA
1 TC-TTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
** * * *
12999 TGCGATTAT-ATTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCAC
65 CACGATCATCA-CCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATGTGGCAGTCCTTCGCAC
** *
13063 AACCCTTATGTGATTATATT-CATCATTGC-GATTGTAGCCAAGGCAGTTCCCACATTTGACAGT
129 AACCCTTACATGATAATATTCCAT-ATTGCAG-TTGTAGCCAAGGCAGTTCCCACATTTGACAGT
** *
13126 CCTTCGCACAATCCTTATGTGATTA
192 CCTTCGCACAATCCTTACATGATAA
*
13151 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCTTAC
1 TCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
13215 A
66 A
13216 ACTACCTTCC
Statistics
Matches: 247, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
215 33 0.13
216 210 0.85
217 4 0.02
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.31
Consensus pattern (216 bp):
TCTTCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
ACGATCATCACCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATGTGGCAGTCCTTCGCACAA
CCCTTACATGATAATATTCCATATTGCAGTTGTAGCCAAGGCAGTTCCCACATTTGACAGTCCTT
CGCACAATCCTTACATGATAA
Found at i:14020 original size:20 final size:20
Alignment explanation
Indices: 13995--14032 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13985 TCGAAGTGTC
*
13995 ATAGTTGCGGCAGGGACAAT
1 ATAGTTGCGGCAGAGACAAT
14015 ATAGTTGCGGCAGAGACA
1 ATAGTTGCGGCAGAGACA
14033 GAAGCATGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.34, T:0.18
Consensus pattern (20 bp):
ATAGTTGCGGCAGAGACAAT
Found at i:16243 original size:39 final size:42
Alignment explanation
Indices: 16149--16255 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
16139 CTCTCTCCCC
* * * *
16149 AAAGTCCCCAAACACATATAACACAAGGGCAATTCTCCTTCT
1 AAAGTCCCTAAACACATATAACACAAAGGCAATTCTCATACT
* *
16191 AAAGTCCTTAAACACATATTACACAAAGGC-A-TCT-ATACT
1 AAAGTCCCTAAACACATATAACACAAAGGCAATTCTCATACT
**
16230 AAAGTCCCTAAACACATGCAACACAA
1 AAAGTCCCTAAACACATATAACACAA
16256 CACAAGGGCA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
39 25 0.45
40 3 0.05
41 1 0.02
42 26 0.47
ACGTcount: A:0.43, C:0.28, G:0.08, T:0.21
Consensus pattern (42 bp):
AAAGTCCCTAAACACATATAACACAAAGGCAATTCTCATACT
Found at i:17946 original size:109 final size:108
Alignment explanation
Indices: 17734--17945 Score: 331
Period size: 109 Copynumber: 2.0 Consensus size: 108
17724 TAATCGGATT
** *
17734 TATTAATTCTTCAACAAAATAATCTGACATTACATTATAAATTTTAACGCTGAGATATTCGGAAA
1 TATTAATTCTTCAACAAAATAATCCAACATTACATTATAAATTATAACGCTGAGATATTCGGAAA
17799 AAAGAAAACAAAAAAATTGATTTAAGGATATTGTTAATTAATCA
66 AAAGAAAACAAAAAAATTGA-TTAAGGATATTGTTAATTAATCA
* * * *
17843 TATTAATTCTTGAACAAAATAATCCAACTTTACATTATAAATTATAAGGCTGAGATATTC-GAGA
1 TATTAATTCTTCAACAAAATAATCCAACATTACATTATAAATTATAACGCTGAGATATTCGGAAA
17907 AAA-AAAACAAAAAAATTGA-TAAGGATATTGTTAATTAAT
66 AAAGAAAACAAAAAAATTGATTAAGGATATTGTTAATTAAT
17946 TTTTACATTA
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
105 20 0.21
107 16 0.17
108 6 0.06
109 54 0.56
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (108 bp):
TATTAATTCTTCAACAAAATAATCCAACATTACATTATAAATTATAACGCTGAGATATTCGGAAA
AAAGAAAACAAAAAAATTGATTAAGGATATTGTTAATTAATCA
Found at i:18901 original size:67 final size:68
Alignment explanation
Indices: 18793--18920 Score: 215
Period size: 67 Copynumber: 1.9 Consensus size: 68
18783 TTAATTGCCC
18793 TTTTGTCCCTATACCTTACAAAAATAGATAATTTGCCCTTTTCA-TTTTTTGGGACATTTTGGTT
1 TTTTGTCCCTATACCTTACAAAAATAGATAATTTGCCCTTTTCATTTTTTTGGGACATTTTGGTT
18857 CCT
66 CCT
* *
18860 TTTTGTCCCTATTA-CTTACAAAAATAGATATTTTTCCCTTTTCATTTTTTTGGGACATTTT
1 TTTTGTCCCTA-TACCTTACAAAAATAGATAATTTGCCCTTTTCATTTTTTTGGGACATTTT
18921 AGTTACTTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
67 39 0.68
68 18 0.32
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (68 bp):
TTTTGTCCCTATACCTTACAAAAATAGATAATTTGCCCTTTTCATTTTTTTGGGACATTTTGGTT
CCT
Found at i:19205 original size:20 final size:21
Alignment explanation
Indices: 19180--19220 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
19170 TTCCATTAGC
*
19180 AAATTACTTAGC-CCGTTAAT
1 AAATTACTTAACACCGTTAAT
19200 AAATTACTTAACACCGTTAAT
1 AAATTACTTAACACCGTTAAT
19221 TTTACCCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (21 bp):
AAATTACTTAACACCGTTAAT
Done.