Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020464.1 Corchorus olitorius cultivar O-4 contig20497, 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: 25103
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:1216 original size:31 final size:29
Alignment explanation
Indices: 1178--1251 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 29
1168 TTAATGCCCT
*
1178 TTTTGCCCCCTGAACTTTTACGATTTTGACG
1 TTTTGCCCCCTGAACTTTTA--ATTTGGACG
* * *
1209 TTTTGCCCTCTAAAC-TTTAATTTGGATG
1 TTTTGCCCCCTGAACTTTTAATTTGGACG
1237 -TTTGCCCCCTGAACT
1 TTTTGCCCCCTGAACT
1252 CGCAATTTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
27 12 0.33
28 7 0.19
30 4 0.11
31 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.42
Consensus pattern (29 bp):
TTTTGCCCCCTGAACTTTTAATTTGGACG
Found at i:2867 original size:22 final size:22
Alignment explanation
Indices: 2822--2868 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2812 TTTGTAAGCA
* **
2822 TTTTTAGTAACCTTATAATTTT
1 TTTTTAATAACCTTATAAAATT
*
2844 TTTTTAATAATCTTATAAAATT
1 TTTTTAATAACCTTATAAAATT
2866 TTT
1 TTT
2869 AACACTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTAATAACCTTATAAAATT
Found at i:13187 original size:183 final size:184
Alignment explanation
Indices: 12878--13239 Score: 532
Period size: 183 Copynumber: 2.0 Consensus size: 184
12868 ATCCTTGCTA
* * * *
12878 TTCAAGATTGTTTAAGAAAGGATTAGCTACCTCCTCGTGGGATTCAATCCTTGCTTACCATTTTA
1 TTCAAGATTGTTCAAGAAAGGATTAACTACCTCCTCATGGGATTCAATCCTTGCTTACCACTTTA
* * *
12943 CCTAAGTTTGCGAGGATAATTAAAACCGATTATTTCTTGTGATGACCAGGAGACACCATCAATAT
66 CCTAAGTTTACGAGGATAATTAAAACCGATTATTTCTTATGACGACCAGGAGACACCATCAATAT
*
13008 GTTCATCTCCTCACTTGTGAAGGTGACAGTCCAAACTTCCT-TTTTTCCTCTTT
131 GTCCATCTCCTCACTTGTGAAGGTGACAGTCCAAACTTCCTCTTTTTCCTCTTT
*
13061 TTCAAGATTGTTCAAGAAAGGATTAACTACCTCCTCATGGGATTCGA-CTCTTGCTTACCACTTT
1 TTCAAGATTGTTCAAGAAAGGATTAACTACCTCCTCATGGGATTCAATC-CTTGCTTACCACTTT
* * * *
13125 ACCTGAGTTTATGAGGATAATTAAAACTGATTGTTTCTTATGACGACCAGGAGA-ACCCATCAAT
65 ACCTAAGTTTACGAGGATAATTAAAACCGATTATTTCTTATGACGACCAGGAGACA-CCATCAAT
* * * *
13189 ATGTCCATCTCTTCACTTGTGATGGTGACGGTCCAATCTTCCTCTTTTTCC
129 ATGTCCATCTCCTCACTTGTGAAGGTGACAGTCCAAACTTCCTCTTTTTCC
13240 AACCTTTTGG
Statistics
Matches: 159, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
182 2 0.01
183 150 0.94
184 7 0.04
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (184 bp):
TTCAAGATTGTTCAAGAAAGGATTAACTACCTCCTCATGGGATTCAATCCTTGCTTACCACTTTA
CCTAAGTTTACGAGGATAATTAAAACCGATTATTTCTTATGACGACCAGGAGACACCATCAATAT
GTCCATCTCCTCACTTGTGAAGGTGACAGTCCAAACTTCCTCTTTTTCCTCTTT
Found at i:22999 original size:39 final size:39
Alignment explanation
Indices: 22945--23056 Score: 174
Period size: 39 Copynumber: 2.9 Consensus size: 39
22935 TATACTTAGA
*
22945 ATTGAAATTACTCAACTCCAATCATAAACTAAAAAAACC
1 ATTGAAATTACTCAACTCCAATCATAAACTGAAAAAACC
22984 ATTGAAATTACTCAACTCCAATCATAAACTGAAAAAACC
1 ATTGAAATTACTCAACTCCAATCATAAACTGAAAAAACC
* * *
23023 A--CAGAGTACTCAACTCCAATCATAAACTGAAAAA
1 ATTGAAATTACTCAACTCCAATCATAAACTGAAAAA
23057 TCACTGGGTT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 30 0.43
39 39 0.57
ACGTcount: A:0.50, C:0.23, G:0.05, T:0.21
Consensus pattern (39 bp):
ATTGAAATTACTCAACTCCAATCATAAACTGAAAAAACC
Found at i:23123 original size:75 final size:75
Alignment explanation
Indices: 23028--23167 Score: 271
Period size: 75 Copynumber: 1.9 Consensus size: 75
23018 AAACCACAGA
*
23028 GTACTCAACTCCAATCATAAACTGAAAAATCACTGGGTTAATATCCAGTTATAATTAATTTCATC
1 GTACTCAACTCCAATCATAAACTGAAAAACCACTGGGTTAATATCCAGTTATAATTAATTTCATC
23093 AATTTCATCT
66 AATTTCATCT
23103 GTACTCAACTCCAATCATAAACTGAAAAACCACTGGGTTAATATCCAGTTATAATTAATTTCATC
1 GTACTCAACTCCAATCATAAACTGAAAAACCACTGGGTTAATATCCAGTTATAATTAATTTCATC
23168 TGGGTCGGAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (75 bp):
GTACTCAACTCCAATCATAAACTGAAAAACCACTGGGTTAATATCCAGTTATAATTAATTTCATC
AATTTCATCT
Found at i:24875 original size:18 final size:19
Alignment explanation
Indices: 24835--24874 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
24825 ATAGCTTAGC
*
24835 AAAGCCCAATGAGAAATTA
1 AAAGCCCAATCAGAAATTA
24854 AAAGCCCAA-CAGAAAGTTA
1 AAAGCCCAATCAGAAA-TTA
24873 AA
1 AA
24875 GTCTACTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.55, C:0.17, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAGCCCAATCAGAAATTA
Done.