Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021180.1 Corchorus olitorius cultivar O-4 contig21213, 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: 10782
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Found at i:1945 original size:41 final size:41
Alignment explanation
Indices: 1845--2174 Score: 292
Period size: 43 Copynumber: 7.8 Consensus size: 41
1835 CCAATAACCA
* * * *
1845 AAAGTCCCCAAACACAATTATAACACAG-GGCCAATTCTCTCTCC
1 AAAGTCCTCAAACACATTTATAACACAGAGG-C-A-TCTATAT-C
1889 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATC
1 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATC
* * * * *
1930 AAAGTCC-CTTAACACATTTGTTACACAGGGGCATCTCTATTCC
1 AAAGTCCTC-AAACACATTTATAACACAGAGGCATCTATA-T-C
* * **
1973 AAAGTCGTCAAATACATTTATAACACAGAAACATCTATATC
1 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATC
* * * * *
2014 AAAGTCCCCAAACACAATTATAACACA-AGGGCAATTCTCTCTA
1 AAAGTCCTCAAACACATTTATAACACAGA-GGC-A-TCTATATC
* *
2057 AAAGTCCTCAAACACATTTATAACATAGAGACATCTATATC
1 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATC
* * *
2098 AAAGTCC-CTAAAAACATTTATAACACAG-GGACACCTTTATCTC
1 AAAGTCCTC-AAACACATTTATAACACAGAGG-CA--TCTATATC
2141 AAAGTCCTCAAACACATTTATAACACAGAGGCAT
1 AAAGTCCTCAAACACATTTATAACACAGAGGCAT
2175 TTCTCTTTAT
Statistics
Matches: 231, Mismatches: 40, Indels: 33
0.76 0.13 0.11
Matches are distributed among these distances:
40 4 0.02
41 90 0.39
42 9 0.04
43 94 0.41
44 32 0.14
45 2 0.01
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.25
Consensus pattern (41 bp):
AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATATC
Found at i:1990 original size:43 final size:41
Alignment explanation
Indices: 1853--2174 Score: 244
Period size: 41 Copynumber: 7.6 Consensus size: 41
1843 CAAAAGTCCC
* * *
1853 CAAACACAATTATAACACAG-GGCCAATTCTCTCTCCAAAGTCCT
1 CAAACACATTTATAACACAGAGG-C-A-TCTATATCCAAAGT-CT
*
1897 CAAACACATTTATAACACAGAGGCATCTATAT-CAAAGTCC
1 CAAACACATTTATAACACAGAGGCATCTATATCCAAAGTCT
* * * * *
1937 CTTAACACATTTGTTACACAGGGGCATCTCTATTCCAAAGTCGT
1 C-AAACACATTTATAACACAGAGGCATCTATA-TCCAAAGTC-T
* ** *
1981 CAAATACATTTATAACACAGAAACATCTATAT-CAAAGTCCC
1 CAAACACATTTATAACACAGAGGCATCTATATCCAAAGT-CT
* * * *
2022 CAAACACAATTATAACACA-AGGGCAAT-TCTCTCTAAAAGTCCT
1 CAAACACATTTATAACACAGA-GGC-ATCTATATC-CAAAGT-CT
* * *
2065 CAAACACATTTATAACATAGAGACATCTATAT-CAAAGTCC
1 CAAACACATTTATAACACAGAGGCATCTATATCCAAAGTCT
* * *
2105 CTAAAAACATTTATAACACAG-GGACACCTTTATCTCAAAGTCCT
1 C-AAACACATTTATAACACAGAGG-CATCTATATC-CAAAGT-CT
2149 CAAACACATTTATAACACAGAGGCAT
1 CAAACACATTTATAACACAGAGGCAT
2175 TTCTCTTTAT
Statistics
Matches: 218, Mismatches: 42, Indels: 37
0.73 0.14 0.12
Matches are distributed among these distances:
40 6 0.03
41 87 0.40
42 12 0.06
43 85 0.39
44 26 0.12
45 2 0.01
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (41 bp):
CAAACACATTTATAACACAGAGGCATCTATATCCAAAGTCT
Found at i:1993 original size:84 final size:84
Alignment explanation
Indices: 1845--2170 Score: 406
Period size: 84 Copynumber: 3.9 Consensus size: 84
1835 CCAATAACCA
* * * *
1845 AAAGTCCCCAAACACAATTATAACACAGGGCCAAT-TCTCTCTCCAAAGTCCTCAAACACATTTA
1 AAAGTCCCTAAACACATTTATAACACAGGGGC-ATCTCTATCT-CAAAGTCCTCAAACACATTTA
*
1909 TAACACAGAGGCATCTATATC
64 TAACACAGAGACATCTATATC
* * * * *
1930 AAAGTCCCTTAACACATTTGTTACACAGGGGCATCTCTAT-TCCAAAGTCGTCAAATACATTTAT
1 AAAGTCCCTAAACACATTTATAACACAGGGGCATCTCTATCT-CAAAGTCCTCAAACACATTTAT
*
1994 AACACAGAAACATCTATATC
65 AACACAGAGACATCTATATC
* * * * *
2014 AAAGTCCCCAAACACAATTATAACACAAGGGCAAT-TCTCTCTAAAAGTCCTCAAACACATTTAT
1 AAAGTCCCTAAACACATTTATAACACAGGGGC-ATCTCTATCTCAAAGTCCTCAAACACATTTAT
*
2078 AACATAGAGACATCTATATC
65 AACACAGAGACATCTATATC
* * * *
2098 AAAGTCCCTAAAAACATTTATAACACAGGGACACCTTTATCTCAAAGTCCTCAAACACATTTATA
1 AAAGTCCCTAAACACATTTATAACACAGGGGCATCTCTATCTCAAAGTCCTCAAACACATTTATA
2163 ACACAGAG
66 ACACAGAG
2171 GCATTTCTCT
Statistics
Matches: 204, Mismatches: 33, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
83 1 0.00
84 170 0.83
85 33 0.16
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.25
Consensus pattern (84 bp):
AAAGTCCCTAAACACATTTATAACACAGGGGCATCTCTATCTCAAAGTCCTCAAACACATTTATA
ACACAGAGACATCTATATC
Found at i:2126 original size:168 final size:169
Alignment explanation
Indices: 1845--2169 Score: 503
Period size: 168 Copynumber: 1.9 Consensus size: 169
1835 CCAATAACCA
*
1845 AAAGTCCCCAAACACAATTATAACACAGGGCCAATTCTCTCTCCAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGCCAATTCTCTCTCAAAAGTCCTCAAACACATTTAT
* * * * * * *
1910 AACACAGAGGCATCTATATCAAAGTCCCTTAACACATTTGTTACACAGGGGCATCTCTAT-TCCA
66 AACACAGAGACATCTATATCAAAGTCCCTAAAAACATTTATAACACAGGGACACCTCTATCT-CA
* *
1974 AAGTCGTCAAATACATTTATAACACAGAAACATCTATATC
130 AAGTCCTCAAACACATTTATAACACAGAAACATCTATATC
2014 AAAGTCCCCAAACACAATTATAACACAAGGG-CAATTCTCTCT-AAAAGTCCTCAAACACATTTA
1 AAAGTCCCCAAACACAATTATAACAC-AGGGCCAATTCTCTCTCAAAAGTCCTCAAACACATTTA
* *
2077 TAACATAGAGACATCTATATCAAAGTCCCTAAAAACATTTATAACACAGGGACACCTTTATCTCA
65 TAACACAGAGACATCTATATCAAAGTCCCTAAAAACATTTATAACACAGGGACACCTCTATCTCA
2142 AAGTCCTCAAACACATTTATAACACAGA
130 AAGTCCTCAAACACATTTATAACACAGA
2170 GGCATTTCTC
Statistics
Matches: 142, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
168 100 0.70
169 38 0.27
170 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.25
Consensus pattern (169 bp):
AAAGTCCCCAAACACAATTATAACACAGGGCCAATTCTCTCTCAAAAGTCCTCAAACACATTTAT
AACACAGAGACATCTATATCAAAGTCCCTAAAAACATTTATAACACAGGGACACCTCTATCTCAA
AGTCCTCAAACACATTTATAACACAGAAACATCTATATC
Found at i:2248 original size:2 final size:2
Alignment explanation
Indices: 2241--2265 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2231 TCCTATCTTG
2241 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2266 GTAGCAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4581 original size:16 final size:15
Alignment explanation
Indices: 4543--4584 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
4533 ACAGAGGTTG
*
4543 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
4558 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
4573 ACTAGAAAACAA
1 AC-AGAAAACAA
4585 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.