Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016313.1 Corchorus olitorius cultivar O-4 contig16346, 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: 3051
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:1203 original size:100 final size:99
Alignment explanation
Indices: 1007--1882 Score: 534
Period size: 100 Copynumber: 8.8 Consensus size: 99
997 AGACCTAATC
* * * *
1007 AATTTAATAAATAGATCTCTTATTCACAAAACACGATGCAACAAAAATTAAGATATGATTCGAAT
1 AATTGAATAAATAGATCTCTTATTCA-TAAACACGATGCGACAAAAATGAAGATATGATTCGAAT
* *
1072 TTGTCG-TTT-AAAGTAATACAAAAACAATATCCACT
65 TTGTCGTTTTAAAAG-AATACAAAAA-AGTATCCATT
* * *
1107 AATTCAATAAATAGATCTCTTATTCATGAAACACTATGTGACAAAAATGAAGATATGATTCGAAT
1 AATTGAATAAATAGATCTCTTATTCAT-AAACACGATGCGACAAAAATGAAGATATGATTCGAAT
1172 TTGTCGTTTTAAAAGAATACAAAAAAGTATCCATT
65 TTGTCGTTTTAAAAGAATACAAAAAAGTATCCATT
* * * * * *
1207 AATTGACTAAATAGATATCTTATTCATGAGACATGATGCGACAAAAACGAAGATATGA-TCTGGA
1 AATTGAATAAATAGATCTCTTATTCAT-AAACACGATGCGACAAAAATGAAGATATGATTC-GAA
* * * *
1271 TTTGTCATTTTTAAATATTA-AAAAAA--ATCCATT
64 TTTGTCGTTTTAAAAGAATACAAAAAAGTATCCATT
* * *
1304 AATTGAATAAATATATCT-TTATTCATAAGGCACGATGCGAC--------------GATTCAAAT
1 AATTGAATAAATAGATCTCTTATTCATAA-ACACGATGCGACAAAAATGAAGATATGATTCGAAT
* * * * *
1354 TTCTCTTTTTAATATGATATATAAAAGAAAGTATTCATT
65 TTGTCGTTTTAA-AAGA-ATA-CAAA-AAAGTATCCATT
* * * ** * * **
1393 AATTAAATAAATCGATCTCTTATTTATAAGACATAATCCAACAAAAACAAAAGATATGATTCGAA
1 AATTGAATAAATAGATCTCTTATTCATAA-ACACGATGCGACAAAAA-TGAAGATATGATTCGAA
* * *
1458 TTTGTCGTTTTAGAATAATACAAAAAAGTATCCATC
64 TTTGTCGTTTTAAAAGAATACAAAAAAGTATCCATT
* * *
1494 AATTCAATAAAATAGATCT-TTATTCATAAGACACGATGCGACAAAAAT-AAGTTATGATTTGAA
1 AATTGAAT-AAATAGATCTCTTATTCATAA-ACACGATGCGACAAAAATGAAGATATGATTCGAA
* *
1557 TTTGTCGTTTTAAAATAATACAAAAAAGTAT-AATTT
64 TTTGTCGTTTTAAAAGAATACAAAAAAGTATCCA-TT
* * * * * *
1593 AATTGAATAAAGAGATCCCTTATTCATAAGACGCGATGTGACAAAAATAAAGATACGATTCGAAT
1 AATTGAATAAATAGATCTCTTATTCATAA-ACACGATGCGACAAAAATGAAGATATGATTCGAAT
* * * * * **
1658 CTCTCTTTTTAATATG-ATACAATAAAGTATTTATTTATT
65 TTGTCGTTTTAA-AAGAATACAA-AAA--A-GTATCCATT
* * * ** * * * *
1697 AATTAAATAAATCGATCTCTTATTTATATAAGGCATAATCCCACAAAAAAGAAGATATGATTCAA
1 AATTGAATAAATAGATCTCTTATTCATA-AA--CACGATGCGACAAAAATGAAGATATGATTCGA
* * * * *
1762 ATTTCTCTTTTTAACATG-ATACAAGTAGAAGGTATACATT
63 ATTTGTCGTTTTAA-AAGAATACAA--A-AAAGTATCCATT
* * ** **
1802 AATTAAATAAATCAG-TCTCTTATTTATAAGACATAAT-C--CAAAAAAAAAGATATGATTCGAA
1 AATTGAATAAAT-AGATCTCTTATTCATAA-ACACGATGCGACAAAAATGAAGATATGATTCGAA
* * *
1863 TTATTTTGTTTTAAATGAAT
64 TT-TGTCGTTTTAAAAGAAT
1883 TTTTCTGCAA
Statistics
Matches: 619, Mismatches: 109, Indels: 95
0.75 0.13 0.12
Matches are distributed among these distances:
82 13 0.02
83 4 0.01
84 2 0.00
86 3 0.00
87 3 0.00
89 21 0.03
90 17 0.03
95 1 0.00
96 18 0.03
97 22 0.04
98 9 0.01
99 86 0.14
100 194 0.31
101 67 0.11
102 17 0.03
103 10 0.02
104 32 0.05
105 51 0.08
106 45 0.07
107 2 0.00
108 2 0.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.34
Consensus pattern (99 bp):
AATTGAATAAATAGATCTCTTATTCATAAACACGATGCGACAAAAATGAAGATATGATTCGAATT
TGTCGTTTTAAAAGAATACAAAAAAGTATCCATT
Found at i:1524 original size:101 final size:99
Alignment explanation
Indices: 1381--1864 Score: 357
Period size: 99 Copynumber: 4.8 Consensus size: 99
1371 TATATAAAAG
* * * * *
1381 AAAGTATTCATTAATTAAATAAATCGATCTCTTATTTATAAGACATAATCCAACAAAAACAAAAG
1 AAAGTATCCATCAATTAAATAAATAGATCTCTTATTCATAAGACACAATCCAAC-AAAA-AAAAG
*
1446 ATATGATTCGAATTTGTCGTTTTAGAATAATACAAA
64 ATATGATTCGAATTTGTCGTTTTAAAATAATACAAA
* * * * * *
1482 AAAGTATCCATCAATTCAATAAAATAGATCT-TTATTCATAAGACACGATGCGACAAAAATAAGT
1 AAAGTATCCATCAATTAAAT-AAATAGATCTCTTATTCATAAGACACAATCCAACAAAAAAAAGA
*
1546 TATGATTTGAATTTGTCGTTTTAAAATAATACAAA
65 TATGATTCGAATTTGTCGTTTTAAAATAATACAAA
* * * * * * * ***
1581 AAAGTAT-AATTTAATTGAATAAAGAGATCCCTTATTCATAAGACGCGATGTGACAAAAATAAAG
1 AAAGTATCCA-TCAATTAAATAAATAGATCTCTTATTCATAAGACACAATCCAACAAAAA-AAAG
* * * * * *
1645 ATACGATTCGAATCTCTCTTTTTAATATGATACAATA
64 ATATGATTCGAATTTGTCGTTTTAAAATAATACAA-A
* ** * * * * * *
1682 AAGTATTTATTTATTAATTAAATAAATCGATCTCTTATTTATATAAGGCATAATCCCACAAAAAA
1 AA--A-GTATCCATCAATTAAATAAATAGATCTCTTA-TT-CATAAGACACAATCCAACAAAAAA
* * * * *
1747 GAAGATATGATTCAAATTTCTCTTTTTAACATGATACAAGTA
61 -AAGATATGATTCGAATTTGTCGTTTTAAAATAATACAA--A
* * * * *
1789 GAAGGTATACATTAATTAAATAAATCAG-TCTCTTATTTATAAGACATAATCC-A-AAAAAAAAG
1 -AAAGTATCCATCAATTAAATAAAT-AGATCTCTTATTCATAAGACACAATCCAACAAAAAAAAG
1851 ATATGATTCGAATT
64 ATATGATTCGAATT
1865 ATTTTGTTTT
Statistics
Matches: 314, Mismatches: 54, Indels: 31
0.79 0.14 0.08
Matches are distributed among these distances:
98 9 0.03
99 78 0.25
100 50 0.16
101 44 0.14
102 10 0.03
103 15 0.05
104 25 0.08
105 29 0.09
106 50 0.16
107 2 0.01
108 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (99 bp):
AAAGTATCCATCAATTAAATAAATAGATCTCTTATTCATAAGACACAATCCAACAAAAAAAAGAT
ATGATTCGAATTTGTCGTTTTAAAATAATACAAA
Done.