Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015882.1 Corchorus olitorius cultivar O-4 contig15915, 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: 8747
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:861 original size:199 final size:199
Alignment explanation
Indices: 521--2187 Score: 1880
Period size: 199 Copynumber: 8.5 Consensus size: 199
511 AATAAGCGCC
* *
521 AAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGTCTAT
1 AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
* * * * *
586 TGTATAATTGTTCTTATAGGATTATTATACAATA-AACTGTTAATGTAAAATTTGGACTCCATAA
66 AGTATAATTTTTCTTATAGGATTATTATACAATACAA-TGTCAATGTAAATTTTGAACTCCATAA
* *
650 GCGGGTTAAGAAGTTGACACATACACCATTACATAATTAATTAAATATTTAATATTAATACATAG
130 GCGGGTTAAGAAGTTGACACATACACCATTTCATAATTAATTAAATATTTAATATTAATACATAT
*
715 TCCTT
195 TCCCT
* * * *
720 AAGGGGACACATGTTAACCCTTAAACCCCGCACGTACAGTCTGCTAAACTCGACTGATGGTGTAT
1 AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
* * *
785 AGTATAATTTTTCTTATAGGATTATTATACAATACAATGTCAATGTAAATTTTGTAGTCTATAAG
66 AGTATAATTTTTCTTATAGGATTATTATACAATACAATGTCAATGTAAATTTTGAACTCCATAAG
* * * * *
850 CAGGATAAGAAGTTGACACATACAACATTTTATAATTAATAAAATATTTAATATTAATACATATT
131 CGGGTTAAGAAGTTGACACATACACCATTTCATAATTAATTAAATATTTAATATTAATACATATT
*
915 CTCT
196 CCCT
* *
919 AAGGGGAAACATGTCAACCCTTAAACCCCGCACTTGCAGTCTGCTAAACTCCACTGACGGTGTAT
1 AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
* * * * *
984 TGTATAATTGTTCTTATAGGATTAATATACAATACATTGTCAATGTAAATTTTGAACTCTATAAG
66 AGTATAATTTTTCTTATAGGATTATTATACAATACAATGTCAATGTAAATTTTGAACTCCATAAG
* *
1049 CGGGTTAAGAAGTTGACATATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATT
131 CGGGTTAAGAAGTTGACACATACACCATTTCATAATTAATTAAATATTTAATATTAATACATATT
1114 CCCT
196 CCCT
* * * * * *
1118 AAGGGGACAAATGTCAACCATTATATCTCGCACGTGCAGTCTGCTAAAATCCACTGACGGTGTAT
1 AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
* * *
1183 AGTATAATTTTTCTTATAGGATTATTGTAGAATA-AACTTTCAATGTAAATTTTGAACTCCATAA
66 AGTATAATTTTTCTTATAGGATTATTATACAATACAA-TGTCAATGTAAATTTTGAACTCCATAA
* * * *
1247 GCGGGGTAAGAAATTG--ACATATATCA--T--TAATTAATT--ATA--TAATATTAATACATAT
130 GCGGGTTAAGAAGTTGACACATACACCATTTCATAATTAATTAAATATTTAATATTAATACATAT
*
1302 TCTCT
195 TCCCT
* * * * * **
1307 ATGGGGACACATGTC-A--C-T----CTC-CATGTGCAGTTTCCTAAACTCCACTGACAATGTAT
1 AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
* * * * * * *
1363 AATATAATTTTTCTTATAGGATTATTACACAATACACTGTCAGTGTAAAATTTGGACTCCATCAG
66 AGTATAATTTTTCTTATAGGATTATTATACAATACAATGTCAATGTAAATTTTGAACTCCATAAG
* * * *
1428 CGGGTTAAGAAGTTGACATATACCCCATTTTATAATTAATTAAATATTTATTATTAATACATATT
131 CGGGTTAAGAAGTTGACACATACACCATTTCATAATTAATTAAATATTTAATATTAATACATATT
1493 CCCT
196 CCCT
* * *
1497 AAGGGGGCACATGTCAACCCTTAAACCCCACACGTGCAGTCTGCTAAAATCCACTGACGGTGTAT
1 AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA-
* * ** ** * * *
1562 TA-TATAATTTTTTTTATAGGATTATTATACAACACGCTCCCAGTGTAAATTTTGGACTCTATAA
65 TAGTATAATTTTTCTTATAGGATTATTATACAATACAATGTCAATGTAAATTTTGAACTCCATAA
* * * * *
1626 GCGGGTTAAAAAGTTGACACAAAC-CTCATTTCATCATTAATTAAATATATAATATTAATACGTA
130 GCGGGTTAAGAAGTTGACACATACAC-CATTTCATAATTAATTAAATATTTAATATTAATACATA
1690 TTCCCT
194 TTCCCT
* * * ** * * *
1696 AAGGAGACACATGTCAACTCTTAAATCTTGCACATGCAGTCTGCTAAGCTCCACTGACAGTGTAT
1 AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
* * * *
1761 TGTATAATTGTTCTTATAGGATTATCATACAATACACTGTCAATGTAAATTTTGAACTCCATAAG
66 AGTATAATTTTTCTTATAGGATTATTATACAATACAATGTCAATGTAAATTTTGAACTCCATAAG
** *
1826 CGGGTTAAGAAGTTGACACATACTTCTTTTCATGATTATTTAAATATTAAATATTTAATATTAAT
131 CGGGTTAAGAAGTTGACACATACACCATTTCAT-A--A-TT--A-ATTAAATATTTAATATTAAT
1891 ACATATTCCCT
189 ACATATTCCCT
* * *
1902 AAGGGGACACATGTCAACCTTTAAACCCCGCACGTGCAGTCTGTTAAAATCCACTGACGGTGTAT
1 AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTA-
* * * *
1967 TA-TATAATTTTTCTTATAGGATTATTATTC-A-AC-ACG-C--TGT-CA----G-ACTCTATAA
65 TAGTATAATTTTTCTTATAGGATTATTATACAATACAATGTCAATGTAAATTTTGAACTCCATAA
* * * * * * *
2019 ACGGGTTAAGAATTTGACACATTTC-TCATTTCATCATCAATTAAATATATAATATTAATACATA
130 GCGGGTTAAGAAGTTGACACA-TACACCATTTCATAATTAATTAAATATTTAATATTAATACATA
2083 -TCGCCT
194 TTC-CCT
* * * * * * *
2089 AAGGGGACACATGTTAACCCTTAAACCCAGAACGTCCAGTTTGTTAAACTCCACTTACGGTGTAT
1 AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
*
2154 ACTATAATTTTTCTTATAGGATTATTATACAATA
66 AGTATAATTTTTCTTATAGGATTATTATACAATA
2188 AACTGCTAGT
Statistics
Matches: 1247, Mismatches: 182, Indels: 88
0.82 0.12 0.06
Matches are distributed among these distances:
180 95 0.08
181 4 0.00
182 6 0.00
184 1 0.00
185 1 0.00
186 13 0.01
187 110 0.09
188 6 0.00
189 34 0.03
190 33 0.03
191 5 0.00
193 10 0.01
194 36 0.03
195 4 0.00
197 6 0.00
198 5 0.00
199 754 0.60
200 7 0.01
202 2 0.00
203 3 0.00
204 2 0.00
205 2 0.00
206 107 0.09
207 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (199 bp):
AAGGGGACACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTAT
AGTATAATTTTTCTTATAGGATTATTATACAATACAATGTCAATGTAAATTTTGAACTCCATAAG
CGGGTTAAGAAGTTGACACATACACCATTTCATAATTAATTAAATATTTAATATTAATACATATT
CCCT
Found at i:2476 original size:13 final size:14
Alignment explanation
Indices: 2458--2498 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
2448 ATAATTGTTG
2458 CTTCATCTTTTAA-
1 CTTCATCTTTTAAT
2471 CTTCATCTTTTAATTT
1 CTTCATCTTTTAA--T
2487 CTTCATCTTTTA
1 CTTCATCTTTTA
2499 GTTTTTGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.52
16 12 0.48
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.59
Consensus pattern (14 bp):
CTTCATCTTTTAAT
Found at i:3244 original size:17 final size:17
Alignment explanation
Indices: 3222--3257 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3212 ATACAAAGAG
3222 CTATCTAGTATAACAAA
1 CTATCTAGTATAACAAA
* *
3239 CTATCTGGTGTAACAAA
1 CTATCTAGTATAACAAA
3256 CT
1 CT
3258 TTACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (17 bp):
CTATCTAGTATAACAAA
Found at i:5462 original size:2 final size:2
Alignment explanation
Indices: 5455--5486 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5445 TTTTATCAAA
5455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5487 CTACATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7530 original size:15 final size:15
Alignment explanation
Indices: 7510--7539 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7500 AATATTTGCG
7510 ATTCTTTATGATCAT
1 ATTCTTTATGATCAT
7525 ATTCTTTATGATCAT
1 ATTCTTTATGATCAT
7540 TATATATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTCTTTATGATCAT
Done.