Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021784.1 Corchorus olitorius cultivar O-4 contig21817, 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: 4713
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Found at i:307 original size:27 final size:27
Alignment explanation
Indices: 265--338 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 27
255 AAGTGGACTT
* *
265 AAAATGACCAACATGCCCCTGAATATG
1 AAAATGACCAAAATGCCCCTGAATATA
* * * *
292 CAAATGACCAAAATG-CCCTTAGTGTA
1 AAAATGACCAAAATGCCCCTGAATATA
318 AAAATGACCAAAATGCCCCTG
1 AAAATGACCAAAATGCCCCTG
339 GGTGACACTA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATATA
Found at i:787 original size:35 final size:34
Alignment explanation
Indices: 742--986 Score: 321
Period size: 35 Copynumber: 7.0 Consensus size: 34
732 ATCTTAAAGG
*
742 TGCTACACCGAGTCATCTGAATTCATCTTTGAAGA
1 TGCTACACCGAGTCATCTG-ATTCAACTTTGAAGA
* * **
777 TGCTACACCGAGTCATCCGAGATCATTTTTGAAGA
1 TGCTACACCGAGTCATCTGA-TTCAACTTTGAAGA
* *
812 TGCTACACCGAGTCTTCTGGATTCAACTGTGAAGA
1 TGCTACACCGAGTCATCT-GATTCAACTTTGAAGA
*
847 TGCTACACCGAGTCATCTGAAGTCATA-TTTGAAGA
1 TGCTACACCGAGTCATCTG-ATTCA-ACTTTGAAGA
882 TGCTACACCGAGTCATCTGATTCTAACTTTGAAGA
1 TGCTACACCGAGTCATCTGATTC-AACTTTGAAGA
* *
917 TGCTACACTGAGTCATCCGATTCTAACTTTGAAGA
1 TGCTACACCGAGTCATCTGATTC-AACTTTGAAGA
952 TGCTACACCGAGTCATCTGATTCTAACTTTGAAGA
1 TGCTACACCGAGTCATCTGATTC-AACTTTGAAGA
987 AATTTCATTT
Statistics
Matches: 187, Mismatches: 17, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
34 6 0.03
35 178 0.95
36 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (34 bp):
TGCTACACCGAGTCATCTGATTCAACTTTGAAGA
Found at i:1274 original size:64 final size:64
Alignment explanation
Indices: 1168--1446 Score: 328
Period size: 64 Copynumber: 4.5 Consensus size: 64
1158 TCCGGTGTAT
* * *
1168 CAAGATCGTCCTCTGATCAACTTCT-AGAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
1 CAAGATCGTCTTCCGATCAATTTCTGA-AAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
* * *
1232 CAATATCGTCTTCCGATCAATTTCTGAAAATTCTTGAAAAACCATCTTCTGGTGTACTTCTTGA
1 CAAGATCGTCTTCCGATCAATTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
* * * * *
1296 CCAGATCGTCTTCCGATCAATTTCTAAAAACTCTTGATAAACCATCTTCTGGTGTACTTTTTAA
1 CAAGATCGTCTTCCGATCAATTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
* * * *
1360 TAAGATCGTCTTCCGATC-ATCTTTTGAAAATTATTGAGAAACCATCTTCT-G-G-------TGA
1 CAAGATCGTCTTCCGATCAAT-TTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
1415 CAAGATCGTCTTCCGATCAATTTCTGAAAACT
1 CAAGATCGTCTTCCGATCAATTTCTGAAAACT
1447 GTTTCTAGCA
Statistics
Matches: 188, Mismatches: 24, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
55 28 0.15
56 2 0.01
62 1 0.01
63 3 0.02
64 153 0.81
65 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (64 bp):
CAAGATCGTCTTCCGATCAATTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
Found at i:1327 original size:128 final size:128
Alignment explanation
Indices: 1170--1413 Score: 364
Period size: 128 Copynumber: 1.9 Consensus size: 128
1160 CGGTGTATCA
* * *
1170 AGATCGTCCTCTGATCAACTTCTAGAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAA
1 AGATCGTCCTCCGATCAACTTCTAAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTAACAA
* *
1235 TATCGTCTTCCGATCAAT-TTCTGAAAATTCTTGAAAAACCATCTTCTGGTGTACTTCTTGACC
66 GATCGTCTTCCGATC-ATCTTCTGAAAATTATTGAAAAACCATCTTCTGGTGTACTTCTTGACC
* * * * *
1298 AGATCGTCTTCCGATCAATTTCTAAAAACTCTTGATAAACCATCTTCTGGTGTACTTTTTAATAA
1 AGATCGTCCTCCGATCAACTTCTAAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTAACAA
* *
1363 GATCGTCTTCCGATCATCTTTTGAAAATTATTGAGAAACCATCTTCTGGTG
66 GATCGTCTTCCGATCATCTTCTGAAAATTATTGAAAAACCATCTTCTGGTG
1414 ACAAGATCGT
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
127 2 0.02
128 101 0.98
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.36
Consensus pattern (128 bp):
AGATCGTCCTCCGATCAACTTCTAAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTAACAA
GATCGTCTTCCGATCATCTTCTGAAAATTATTGAAAAACCATCTTCTGGTGTACTTCTTGACC
Found at i:1530 original size:67 final size:66
Alignment explanation
Indices: 1439--1676 Score: 354
Period size: 67 Copynumber: 3.6 Consensus size: 66
1429 GATCAATTTC
* *
1439 TGAAAACTGTTTCTAGCAAACCGTCTTCCGATGTATTCTTTAATGAGATTGTCTTCCAATCAGCA
1 TGAAAACTCTTTCTAGCAAACCGTCTTCCGATGTGTTC-TTAATGAGATTGTCTTCCAATCAGCA
*
1504 CT
65 TT
* * *
1506 TGAAAACTCTTCCTAGCAAACCGTCCTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATCAGCA
1 TGAAAACTCTTTCTAGCAAACCGTCTTCCGATGTGTT-CTTAATGAGATTGTCTTCCAATCAGCA
1571 TT
65 TT
* * *
1573 TGAAAACTGTTTCTAGCAAACCGTCTTCCGATGTGTTCTTAATGAGATTGTCTTCCAATCAACTT
1 TGAAAACTCTTTCTAGCAAACCGTCTTCCGATGTGTTCTTAATGAGATTGTCTTCCAATCAGCAT
1638 T
66 T
*
1639 TGAAAATTCTTTCTAGCAAACCGTCTTCCG--GTGTTCTT
1 TGAAAACTCTTTCTAGCAAACCGTCTTCCGATGTGTTCTT
1677 CTAAAATCCT
Statistics
Matches: 156, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
64 8 0.05
66 55 0.35
67 92 0.59
68 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (66 bp):
TGAAAACTCTTTCTAGCAAACCGTCTTCCGATGTGTTCTTAATGAGATTGTCTTCCAATCAGCAT
T
Done.