Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013338.1 Corchorus capsularis cultivar CVL-1 contig13359, 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: 14925
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:64 original size:7 final size:7
Alignment explanation
Indices: 23--180 Score: 70
Period size: 7 Copynumber: 21.6 Consensus size: 7
13 AAGAGTTAGT
23 ATTATTA
1 ATTATTA
*
30 AATATTA
1 ATTATTA
*
37 ATTTAATA
1 A-TTATTA
*
45 A-TATGA
1 ATTATTA
*
51 TTTATTA
1 ATTATTA
58 ATTATTA
1 ATTATTA
65 ATTATTA
1 ATTATTA
*
72 TTTTATTA
1 -ATTATTA
* *
80 ATAATTT
1 ATTATTA
**
87 ACGAGTTA
1 ATTA-TTA
95 GGATTATTA
1 --ATTATTA
*
104 ATGATTA
1 ATTATTA
111 A-T-TTA
1 ATTATTA
116 ATTATTTA
1 ATTA-TTA
124 ATTTATTA
1 A-TTATTA
*
132 ATTATTG
1 ATTATTA
*
139 ATTAATA
1 ATTATTA
* *
146 TTATATTC
1 AT-TATTA
*
154 ATAATTTA
1 ATTA-TTA
162 ATTTATTA
1 A-TTATTA
170 ATTATTA
1 ATTATTA
177 ATTA
1 ATTA
181 AATAATAATA
Statistics
Matches: 109, Mismatches: 29, Indels: 26
0.66 0.18 0.16
Matches are distributed among these distances:
5 4 0.04
6 4 0.04
7 59 0.54
8 32 0.29
9 8 0.07
10 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (7 bp):
ATTATTA
Found at i:130 original size:74 final size:74
Alignment explanation
Indices: 9--162 Score: 211
Period size: 74 Copynumber: 2.1 Consensus size: 74
1 TATTGGTT
* * *
9 ATTTAAGAGTTAGTATTATTAAATATTAATTTAATAATATGATTTATTAATTATTAATTATTATT
1 ATTTAAGAGTTAGGATTATTAAATATTAATTTAATAATATAATTTATTAATTATTAATTAATATT
*
74 TTATTAATA
66 ATATTAATA
* * * *
83 ATTTACGAGTTAGGATTATT-AATGATTAATTTAATTATTTAATTTATTAATTATTGATTAATAT
1 ATTTAAGAGTTAGGATTATTAAAT-ATTAATTTAATAATATAATTTATTAATTATTAATTAATAT
*
147 TATATTCATA
65 TATATTAATA
157 ATTTAA
1 ATTTAA
163 TTTATTAATT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
73 3 0.04
74 66 0.96
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.52
Consensus pattern (74 bp):
ATTTAAGAGTTAGGATTATTAAATATTAATTTAATAATATAATTTATTAATTATTAATTAATATT
ATATTAATA
Found at i:697 original size:108 final size:108
Alignment explanation
Indices: 555--858 Score: 380
Period size: 108 Copynumber: 2.8 Consensus size: 108
545 ACAATAATTC
* *
555 AGGTTTAGCCCCAATTGTAAATATATTTTA-TTTTTTAAGGGTAAATCTCAAATTTTAAGACCCA
1 AGGTTTAGCCCCAATT-AAAATATGTTTTATTTTTTTAAGGGTAAATCTCAAATTTTAAGACCCA
* *
619 TTATTTTAGAATTTTAGAAAAATAAGTTTGAAAACTTTTAAATA
65 TTATCTTAGAATTTTAGAAAAATAAGTTTGAAAACTTATAAATA
* * ** * *
663 AGGTTTAGCCCCAACTAAAATATGTTTTATTTTTTTAAGGGTAAATCTTAAATGGTAAGATCCAC
1 AGGTTTAGCCCCAATTAAAATATGTTTTATTTTTTTAAGGGTAAATCTCAAATTTTAAGACCCAT
* *
728 TATCTTAGATTTTTAGAAAAATAAGTTTGAACACTTATAAATA
66 TATCTTAGAATTTTAGAAAAATAAGTTTGAAAACTTATAAATA
* * * *
771 AGGTTTAGCCCCAATTATAAAGT-TGTTTTATTTTTTAAAAGTGTAAATCTCAATTTTTAATACC
1 AGGTTTAGCCCCAATTA-AAA-TATGTTTTATTTTTT-TAAGGGTAAATCTCAAATTTTAAGACC
**
835 CATTATCATT-GTGTTTTAGAAAAA
63 CATTATC-TTAGAATTTTAGAAAAA
859 AAAATTGTAA
Statistics
Matches: 167, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
107 11 0.07
108 100 0.60
109 16 0.10
110 38 0.23
111 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (108 bp):
AGGTTTAGCCCCAATTAAAATATGTTTTATTTTTTTAAGGGTAAATCTCAAATTTTAAGACCCAT
TATCTTAGAATTTTAGAAAAATAAGTTTGAAAACTTATAAATA
Found at i:1481 original size:16 final size:17
Alignment explanation
Indices: 1455--1487 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1445 TTCTCTCTTT
*
1455 CTTTTTCTATTTTTATA
1 CTTTTTCTATTATTATA
1472 CTTTTT-TATTATTATA
1 CTTTTTCTATTATTATA
1488 GGGTTTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (17 bp):
CTTTTTCTATTATTATA
Found at i:1662 original size:107 final size:107
Alignment explanation
Indices: 1476--1770 Score: 481
Period size: 107 Copynumber: 2.8 Consensus size: 107
1466 TTTATACTTT
1476 TTTATTATTATAGGGTTTTACAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTA
1 TTTATTATTATAGGGTTTTACAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTA
*
1541 AAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATAA
66 AAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAA
1583 TTTATTATTATAGGGTTTTACAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTA
1 TTTATTATTATAGGGTTTTACAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTA
*
1648 AAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAA
66 AAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAA
* * * *
1690 --TATTGTTATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAG-CCCAAATTA
1 TTTATTATTATAGGGTTTTACAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTA
** *
1751 AAATTAAAATTTTATTTTAA
66 AAATTTTATTTTTATTTTAA
1771 AGGTTAGAAA
Statistics
Matches: 179, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
103 26 0.15
104 14 0.08
105 34 0.19
107 105 0.59
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (107 bp):
TTTATTATTATAGGGTTTTACAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTA
AAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAA
Done.