Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012124.1 Corchorus capsularis cultivar CVL-1 contig12145, 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: 41172
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:18622 original size:35 final size:35
Alignment explanation
Indices: 18576--18657 Score: 164
Period size: 35 Copynumber: 2.3 Consensus size: 35
18566 CGAAAACTGT
18576 TTTATGATCATTTGAAATATCATTCTTTCAAACAG
1 TTTATGATCATTTGAAATATCATTCTTTCAAACAG
18611 TTTATGATCATTTGAAATATCATTCTTTCAAACAG
1 TTTATGATCATTTGAAATATCATTCTTTCAAACAG
18646 TTTATGATCATT
1 TTTATGATCATT
18658 GTAGGTCAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (35 bp):
TTTATGATCATTTGAAATATCATTCTTTCAAACAG
Found at i:30905 original size:16 final size:16
Alignment explanation
Indices: 30878--30990 Score: 67
Period size: 16 Copynumber: 7.1 Consensus size: 16
30868 GTTTTCTTTC
*
30878 GTCATTTGGGTTTCGG
1 GTCATCTGGGTTTCGG
* *
30894 GTCATCTAGG-TTCGA
1 GTCATCTGGGTTTCGG
*
30909 GTTAT-TCGGGTTTCGG
1 GTCATCT-GGGTTTCGG
30925 GTCATTCT-GGTCTT-GG
1 GTCA-TCTGGGT-TTCGG
30941 GTCATAC-GGGTTTCGG
1 GTCAT-CTGGGTTTCGG
* *
30957 GTCAT-TCGGATTCTGG
1 GTCATCTGGGTTTC-GG
* *
30973 GTCATTTGGGTCTCGG
1 GTCATCTGGGTTTCGG
30989 GT
1 GT
30991 TTACCGGGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
14 1 0.01
15 18 0.24
16 46 0.62
17 8 0.11
18 1 0.01
ACGTcount: A:0.10, C:0.17, G:0.35, T:0.39
Consensus pattern (16 bp):
GTCATCTGGGTTTCGG
Found at i:30989 original size:32 final size:31
Alignment explanation
Indices: 30878--30990 Score: 113
Period size: 32 Copynumber: 3.6 Consensus size: 31
30868 GTTTTCTTTC
* * *
30878 GTCATTTGGGTTTCGGGTCATCTAGGTTC-GA
1 GTCATTCGGGTTTCGGGTCAT-TCGGTTCTGG
*
30909 GTTATTCGGGTTTCGGGTCATTCTGG-TCTTGG
1 GTCATTCGGGTTTCGGGTCATTC-GGTTC-TGG
*
30941 GTCATACGGGTTTCGGGTCATTCGGATTCTGG
1 GTCATTCGGGTTTCGGGTCATTCGG-TTCTGG
* *
30973 GTCATTTGGGTCTCGGGT
1 GTCATTCGGGTTTCGGGT
30991 TTACCGGGTC
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
30 3 0.04
31 23 0.34
32 40 0.59
33 2 0.03
ACGTcount: A:0.10, C:0.17, G:0.35, T:0.39
Consensus pattern (31 bp):
GTCATTCGGGTTTCGGGTCATTCGGTTCTGG
Found at i:31812 original size:9 final size:9
Alignment explanation
Indices: 31798--31886 Score: 59
Period size: 9 Copynumber: 10.8 Consensus size: 9
31788 TATAATATTC
31798 TCGGGTCAT
1 TCGGGTCAT
*
31807 TCGGGTTAT
1 TCGGGTCAT
31816 TCGGGT--T
1 TCGGGTCAT
*
31823 TCGGGTGAT
1 TCGGGTCAT
*
31832 ACGGGTC--
1 TCGGGTCAT
*
31839 TCGGGTCAA
1 TCGGGTCAT
*
31848 TCGAGT--T
1 TCGGGTCAT
*
31855 ACGGGTCAT
1 TCGGGTCAT
*
31864 TCCGGT--T
1 TCGGGTCAT
31871 TCGGGTCAT
1 TCGGGTCAT
31880 TCGGGTC
1 TCGGGTC
31887 TCCGGTCATC
Statistics
Matches: 61, Mismatches: 11, Indels: 16
0.69 0.12 0.18
Matches are distributed among these distances:
7 23 0.38
9 38 0.62
ACGTcount: A:0.11, C:0.20, G:0.36, T:0.33
Consensus pattern (9 bp):
TCGGGTCAT
Found at i:31827 original size:16 final size:16
Alignment explanation
Indices: 31806--31924 Score: 105
Period size: 16 Copynumber: 7.4 Consensus size: 16
31796 TCTCGGGTCA
*
31806 TTCGGGTTATTCGGGT
1 TTCGGGTCATTCGGGT
* *
31822 TTCGGGTGATACGGGT
1 TTCGGGTCATTCGGGT
* * *
31838 CTCGGGTCAATCGAGT
1 TTCGGGTCATTCGGGT
* *
31854 TACGGGTCATTCCGGT
1 TTCGGGTCATTCGGGT
31870 TTCGGGTCATTCGGGT
1 TTCGGGTCATTCGGGT
* *
31886 CTCCGGTCA-TCTGGGT
1 TTCGGGTCATTC-GGGT
* *
31902 TGCGTGTCATTCGGGT
1 TTCGGGTCATTCGGGT
*
31918 CTCGGGT
1 TTCGGGT
31925 TGGGCGAGTT
Statistics
Matches: 78, Mismatches: 23, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
15 2 0.03
16 74 0.95
17 2 0.03
ACGTcount: A:0.09, C:0.21, G:0.36, T:0.34
Consensus pattern (16 bp):
TTCGGGTCATTCGGGT
Found at i:31911 original size:48 final size:48
Alignment explanation
Indices: 31808--31924 Score: 137
Period size: 48 Copynumber: 2.4 Consensus size: 48
31798 TCGGGTCATT
* * *
31808 CGGGTTATTCGGGTTTCGGGTGATACGGGTCTCGGGTCAATCGAGTTA
1 CGGGTCATTCGGGTTTCGGGTCATACGGGTCTCCGGTCAATCGAGTTA
* * * *
31856 CGGGTCATTCCGGTTTCGGGTCATTCGGGTCTCCGGTC-ATCTGGGTTG
1 CGGGTCATTCGGGTTTCGGGTCATACGGGTCTCCGGTCAATC-GAGTTA
* *
31904 CGTGTCATTCGGGTCTCGGGT
1 CGGGTCATTCGGGTTTCGGGT
31925 TGGGCGAGTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 3 0.05
48 55 0.95
ACGTcount: A:0.09, C:0.21, G:0.37, T:0.32
Consensus pattern (48 bp):
CGGGTCATTCGGGTTTCGGGTCATACGGGTCTCCGGTCAATCGAGTTA
Found at i:33826 original size:2 final size:2
Alignment explanation
Indices: 33819--33896 Score: 59
Period size: 2 Copynumber: 43.5 Consensus size: 2
33809 GTTTAATAAT
*
33819 TA TA TA TA TA T- TA T- TA TA TA TA -A TCA TA TA TA T- TA GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
*
33858 T- TA T- TA T- TA TA TA TA TA TA -A AA TA TA TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33894 TA T
1 TA T
33897 TACTAAACGG
Statistics
Matches: 62, Mismatches: 3, Indels: 22
0.71 0.03 0.25
Matches are distributed among these distances:
1 10 0.16
2 50 0.81
3 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33859 original size:26 final size:24
Alignment explanation
Indices: 33814--33896 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
33804 GAACTGTTTA
*
33814 ATAATTATATATATATTATTATAT
1 ATAATTATATATATAATATTATAT
*
33838 ATAATCATATATATTAGATATTAT-T
1 ATAATTATATATA-TA-ATATTATAT
*
33863 ATTA-TATATATATAA-A--ATAT
1 ATAATTATATATATAATATTATAT
33883 ATAATTATATATAT
1 ATAATTATATATAT
33897 TACTAAACGG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
19 2 0.04
20 4 0.08
21 10 0.20
22 1 0.02
23 2 0.04
24 19 0.38
25 6 0.12
26 6 0.12
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (24 bp):
ATAATTATATATATAATATTATAT
Found at i:39211 original size:258 final size:257
Alignment explanation
Indices: 38333--39350 Score: 1539
Period size: 256 Copynumber: 4.0 Consensus size: 257
38323 TAATATCCTG
38333 AACTTTCAAAATTGTCA-TT-CATATATGAACTTGT-AAAAATGGACAAATTATCCATTTTGGAC
1 AACTTTCAAAATTGTCATTTGCATATATGAACTTGTAAAAAATGGACAAATTATCCATTTTGGAC
* * *
38395 CGAAATTGATTAAATTTTGCTAATAATTGGATAGAAATTGAACGAAATTTATTAGAGAGTCATAC
66 CGAAATTGGTTAAATTATGCTAATAATTGGACAGAAATTGAACGAAATTTATT--AGAGTCATAC
* * * * * * *
38460 CGATTTCTCCCCAAAATGACTAATGTCCGTCCAACTGTTAATGAAATTTAACCAATTTCCATCCA
129 CAATTTCTCTCCAAAAGGGCTAATTTCCGTCCAATTGTTAACGAAATTTAACCAATTTCCATCCA
** ** *
38525 AAATGGCT-CGTCGTCTCTTTTTTTACAACTTCAGGTTTGCAATTGGCAATTTATCCATTTTAC
194 AAATGGCTAATTTATCCCTTTTTTTACAACTTCAGGTTTGCAATTGGCAATTTATCCATTTTAC
38588 AACTTTCAAAATTGTCATTTGCATATATGAACTTGTAAAAAATGGACAAATTATCCATTTTGGAC
1 AACTTTCAAAATTGTCATTTGCATATATGAACTTGTAAAAAATGGACAAATTATCCATTTTGGAC
*
38653 CGAAATTGGTTAAATTATGCTAATAATTGGACAAAAATTGAACGAAATTTATTAGAGTCATACCA
66 CGAAATTGGTTAAATTATGCTAATAATTGGACAGAAATTGAACGAAATTTATTAGAGTCATACCA
* *
38718 ATTTCTCTCCAAAAGGGCTAATTTTCAG-CCAATTGTTAACGAAATTTAATCAATTTCCATCCAA
131 ATTTCTCTCCAAAAGGGCTAA-TTTCCGTCCAATTGTTAACGAAATTTAACCAATTTCCATCCAA
* *
38782 AATGGCTAATTTATCCCTTTTTTTACAACTTCAGGTTTGCAATTGGCAATTTATCCA-TTAAA
195 AATGGCTAATTTATCCCTTTTTTTACAACTTCAGGTTTGCAATTGGCAATTTATCCATTTTAC
* *
38844 AACTTTCAAAATTGTCATTTGTATATCTGAACTTGTAAAAAATGGACAAATTATCCATTTTGGAC
1 AACTTTCAAAATTGTCATTTGCATATATGAACTTGTAAAAAATGGACAAATTATCCATTTTGGAC
* * *
38909 TGAAATTGGTTAAATTATGCTAATAATTGGACAGAAATTGAACGAAAATTATTAGAGTCGTACCA
66 CGAAATTGGTTAAATTATGCTAATAATTGGACAGAAATTGAACGAAATTTATTAGAGTCATACCA
* *
38974 ATTTATCTCCAAAAGGGCTAATTTCCGTCCAATTGTTAACGAAATTTAACTAATTTCCATCCAAA
131 ATTTCTCTCCAAAAGGGCTAATTTCCGTCCAATTGTTAACGAAATTTAACCAATTTCCATCCAAA
*
39039 ATGGCTAATTTGTCCCTTTTTTTTACAACTTCAGGTTTGCAATTGGCAATTTATCCATTTTAC
196 ATGGCTAATTTATCCC-TTTTTTTACAACTTCAGGTTTGCAATTGGCAATTTATCCATTTTAC
**
39102 AACTTTCAAAATTGTCATTTGCATATCCGAACTTGTAAAAAATGGACAAATTATCCATTTTGGAC
1 AACTTTCAAAATTGTCATTTGCATATATGAACTTGTAAAAAATGGACAAATTATCCATTTTGGAC
*
39167 CGAAATTGGTTAAATTATGCTAATAATTGGACTGAAATTGAACGAAATTTATTAGAGTCATATAT
66 CGAAATTGGTTAAATTATGCTAATAATTGGACAGAAATTGAACGAAATTTATTAGAGTC----AT
* * *
39232 ACCAATTTCTCTCCAAAAGGGCTAATTTCCGTCCAATTATTAACGAAATTTAACCAATTTTCATT
127 ACCAATTTCTCTCCAAAAGGGCTAATTTCCGTCCAATTGTTAACGAAATTTAACCAATTTCCATC
** * * **
39297 CAAAATAACCAATTTAT-CCTTCTTATTACAACTTCAGACTTGCAA-TGGCAATTT
192 CAAAATGGCTAATTTATCCCTT-TTTTTACAACTTCAGGTTTGCAATTGGCAATTT
39351 TCGAAGTTCA
Statistics
Matches: 699, Mismatches: 51, Indels: 21
0.91 0.07 0.03
Matches are distributed among these distances:
255 22 0.03
256 268 0.38
257 103 0.15
258 199 0.28
260 11 0.02
261 22 0.03
262 74 0.11
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (257 bp):
AACTTTCAAAATTGTCATTTGCATATATGAACTTGTAAAAAATGGACAAATTATCCATTTTGGAC
CGAAATTGGTTAAATTATGCTAATAATTGGACAGAAATTGAACGAAATTTATTAGAGTCATACCA
ATTTCTCTCCAAAAGGGCTAATTTCCGTCCAATTGTTAACGAAATTTAACCAATTTCCATCCAAA
ATGGCTAATTTATCCCTTTTTTTACAACTTCAGGTTTGCAATTGGCAATTTATCCATTTTAC
Found at i:40780 original size:21 final size:21
Alignment explanation
Indices: 40756--40798 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40746 ATAATGTGAA
40756 TTACTAAATACCGCCCCCTTT
1 TTACTAAATACCGCCCCCTTT
** *
40777 TTACTAGGTACCGCCCTCTTT
1 TTACTAAATACCGCCCCCTTT
40798 T
1 T
40799 GGACAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (21 bp):
TTACTAAATACCGCCCCCTTT
Done.