Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024649.1 Corchorus olitorius cultivar O-4 contig24682, 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: 18876
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6130 original size:27 final size:27
Alignment explanation
Indices: 6092--6197 Score: 203
Period size: 27 Copynumber: 3.9 Consensus size: 27
6082 GATTGTTGCC
6092 GCAGTGGATCCTCCCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
6119 GCAGTGGATCCTCCCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
*
6146 GCAGTGGATCCTCTCACTTCGACCCCA
1 GCAGTGGATCCTCCCACTTCGACCCCA
6173 GCAGTGGATCCTCCCACTTCGACCC
1 GCAGTGGATCCTCCCACTTCGACCC
6198 GGGTCGGTTC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.18, C:0.43, G:0.19, T:0.20
Consensus pattern (27 bp):
GCAGTGGATCCTCCCACTTCGACCCCA
Found at i:7034 original size:17 final size:17
Alignment explanation
Indices: 7012--7046 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
7002 GAAAAAGTGC
7012 ATTCTTGTTGGTACATT
1 ATTCTTGTTGGTACATT
*
7029 ATTCTTGTTGGTATATT
1 ATTCTTGTTGGTACATT
7046 A
1 A
7047 ACATTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (17 bp):
ATTCTTGTTGGTACATT
Found at i:8397 original size:3 final size:3
Alignment explanation
Indices: 8389--8430 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
8379 CATTGATTTG
8389 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
8431 TGCTAGTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9295 original size:22 final size:21
Alignment explanation
Indices: 9267--9329 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 21
9257 TGGCCCGAAC
*
9267 AAGGAAAAAAAACGAGAGA-GA
1 AAGGAAAAAAAA-GAGAAAGGA
9288 TAAGGAAAAGAAAAAGAGAAAGGA
1 -AAGG-AAA-AAAAAGAGAAAGGA
9312 AGAGGAAAAAAAAGAGAA
1 A-AGGAAAAAAAAGAGAA
9330 CAAGAAGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 14 0.39
23 12 0.33
24 10 0.28
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.02
Consensus pattern (21 bp):
AAGGAAAAAAAAGAGAAAGGA
Found at i:10203 original size:13 final size:13
Alignment explanation
Indices: 10187--10225 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
10177 ATTGTTTTGG
10187 TATTTTGGTTTAT
1 TATTTTGGTTTAT
* *
10200 TATTCTGGTTTGT
1 TATTTTGGTTTAT
*
10213 TACTTTGGTTTAT
1 TATTTTGGTTTAT
10226 GACTTAGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.13, C:0.05, G:0.18, T:0.64
Consensus pattern (13 bp):
TATTTTGGTTTAT
Found at i:15911 original size:22 final size:21
Alignment explanation
Indices: 15881--15922 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
15871 TTTCAAAAAT
* *
15881 AATTATCATTATTTTTATTTA
1 AATTATCATTAGTTGTATTTA
15902 AATTATTCATTAGTTGTATTT
1 AATTA-TCATTAGTTGTATTT
15923 TGTCCATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (21 bp):
AATTATCATTAGTTGTATTTA
Found at i:16128 original size:2 final size:2
Alignment explanation
Indices: 16123--16158 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
16113 ACACAGATAG
16123 AT AT AT AT AT AT AT AT AT AT AT AT CAT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
16159 TTAATTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16974 original size:115 final size:117
Alignment explanation
Indices: 16848--17087 Score: 412
Period size: 115 Copynumber: 2.1 Consensus size: 117
16838 AATTAAAATA
*
16848 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATTAAATAAAAGTAGAGTTTTTA
1 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATAAAATAAAAGTAGAGTTTTTA
* * *
16913 ATATAGTAAAACTATAATAGTTT-A-AACAATGGAACTTAAGAAATATGTTT
66 ATACAATAAAACTATAATAGTTTAACAACAATGAAACTTAAGAAATATGTTT
16963 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATAAAATAAAAGTAGAGTTTTTA
1 GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATAAAATAAAAGTAGAGTTTTTA
17028 ATACAATAAAACTATAATAGTTTGAACAACAATGAAACTTAAGAAATATGTTT
66 ATACAATAAAACTATAATAGTTT-AACAACAATGAAACTTAAGAAATATGTTT
*
17081 GAAAAAT
1 GTAAAAT
17088 AAGTATATAA
Statistics
Matches: 117, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
115 85 0.73
117 1 0.01
118 31 0.26
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.30
Consensus pattern (117 bp):
GTAAAATGGTAAAAATAAAAACAGTTATAAAGATAAGATTTAATAAAATAAAAGTAGAGTTTTTA
ATACAATAAAACTATAATAGTTTAACAACAATGAAACTTAAGAAATATGTTT
Found at i:17740 original size:24 final size:26
Alignment explanation
Indices: 17689--17740 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
17679 TACCCATTTC
17689 AATTATAATATAAACTAATTTGAAAAAAA
1 AATTATAATATAAACTAA-TT--AAAAAA
17718 AATTATAATATAAACTAA-TAAAA
1 AATTATAATATAAACTAATTAAAA
17741 GTCTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.17
27 1 0.04
29 18 0.78
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (26 bp):
AATTATAATATAAACTAATTAAAAAA
Found at i:18593 original size:24 final size:24
Alignment explanation
Indices: 18566--18621 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
18556 ACTAGTATAG
18566 TATAAATATAGATATAAATAGAT-A
1 TATAAA-ATAGATATAAATAGATAA
**
18590 TATAGAAATAGATATTGATAGATAA
1 TATA-AAATAGATATAAATAGATAA
18615 TATAAAA
1 TATAAAA
18622 AGAAAAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (24 bp):
TATAAAATAGATATAAATAGATAA
Done.