Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021907.1 Corchorus olitorius cultivar O-4 contig21940, 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: 29233
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:15471 original size:54 final size:54
Alignment explanation
Indices: 15407--15517 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
15397 GATGAAGGTG
*
15407 ATGTCGGTGAA-TTGAAGCTGAACT-CCCCTTTGTCTGAGGCTGAGTC-GATTCTCA
1 ATGTCGGTGAAGTT-AAGCTGAA-TGCCACTTTGTCTGAGGCTGAGTCAG-TTCTCA
* *
15461 ATGTTGGTGAAGTTAAGCTGAATGCCACTTTGTCTGAGGTTGAGTCAGTTCTCA
1 ATGTCGGTGAAGTTAAGCTGAATGCCACTTTGTCTGAGGCTGAGTCAGTTCTCA
15515 ATG
1 ATG
15518 AGGCAACAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
53 1 0.02
54 47 0.92
55 3 0.06
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (54 bp):
ATGTCGGTGAAGTTAAGCTGAATGCCACTTTGTCTGAGGCTGAGTCAGTTCTCA
Found at i:21855 original size:406 final size:406
Alignment explanation
Indices: 21096--21903 Score: 1474
Period size: 406 Copynumber: 2.0 Consensus size: 406
21086 GTCAGTTTCC
*
21096 GACTCAAATTGAACTTCTTTAGGAAACGGCAGCTTCAAGTGAGGAGATGACTTCATCTTCTGGAA
1 GACTCAAATTGAACTTCTTTAGGAAACGACAGCTTCAAGTGAGGAGATGACTTCATCTTCTGGAA
* *
21161 ACTTCTTAAAACTTTACTGAGATGGCATCTAGACTAACCTCTGACGCCATATATCTTCTAGAAAT
66 ACTTCTTAAAACTTTACTGAGATGGCATCTAGACTAACCTCTGACGCCACATAACTTCTAGAAAT
21226 CACGTTGAGACCTTCCTTAATATGTAGTTGGCGCAATCCTCACCTTTCTAGCATGATTCAACATG
131 CACGTTGAGACCTTCCTTAATATGTAGTTGGCGCAATCCTCACCTTTCTAGCATGATTCAACATG
* * *
21291 TCTTGTTGTCTCCTTCGAGCTTGCAACAACTAATTTAGCAAGGAGATGGCTCTAAAACATTAAGG
196 TCTTGTTGCCTCCTTCGAGCTTGCAACAACTAATTCAGCAAGAAGATGGCTCTAAAACATTAAGG
* *
21356 ATTGAACCTTAAACATTTAAGCCACGAAATTCTCCATACTTATTCATATTAAGCACATCAAATCC
261 ATTGAACCTTAAACATTTAAGCCACAAAATTCTCCATACTTATTCATATTAAACACATCAAATCC
* * *
21421 TAAAAATATCATTCAACTAAGTAAATGGCCAAAATCGAGGTGTAAAAGCCATATGTCCTTAATTG
326 TAAAAATATCATTCAACTAAGAAAATGGCCAAAACCGAGGTATAAAAGCCATATGTCCTTAATTG
21486 AAAAGAGTGTAATTCT
391 AAAAGAGTGTAATTCT
21502 GACTCAAATTGAACTTCTTTAGGAAACGACAGCTTCAAGTGAGGAGATGACTTCATCTTCTGGAA
1 GACTCAAATTGAACTTCTTTAGGAAACGACAGCTTCAAGTGAGGAGATGACTTCATCTTCTGGAA
*
21567 ACTTC-TAGAAACTTTACTGAGATGGCATCTGGACTAACCTCTGACGCCACATAACTTCTAGAAA
66 ACTTCTTA-AAACTTTACTGAGATGGCATCTAGACTAACCTCTGACGCCACATAACTTCTAGAAA
*
21631 TCACGTTGAGACCTTCCTTAATATGTAGTTGGCGCAATCCTCACCTTTCTAGCATGATTCAGCAT
130 TCACGTTGAGACCTTCCTTAATATGTAGTTGGCGCAATCCTCACCTTTCTAGCATGATTCAACAT
21696 GTCTTGTTGCCTCCTTCGAGCTTGCAACAACTAATTCAGCAAGAAGATGGCTCTAAAACATTAAG
195 GTCTTGTTGCCTCCTTCGAGCTTGCAACAACTAATTCAGCAAGAAGATGGCTCTAAAACATTAAG
21761 GATTGAACCTTAAACATTTAAGCCACAAAATTCTCCATACTTATTCATATTAAACACATCAAATC
260 GATTGAACCTTAAACATTTAAGCCACAAAATTCTCCATACTTATTCATATTAAACACATCAAATC
*
21826 CTAAAAATATCATTCAACTAAGAAAATGGCCAAAACCGGGGTATAAAAGCCATATGTCCTTAATT
325 CTAAAAATATCATTCAACTAAGAAAATGGCCAAAACCGAGGTATAAAAGCCATATGTCCTTAATT
21891 GAAAAGAGTGTAA
390 GAAAAGAGTGTAA
21904 AAGTTATCAC
Statistics
Matches: 387, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
405 2 0.01
406 385 0.99
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (406 bp):
GACTCAAATTGAACTTCTTTAGGAAACGACAGCTTCAAGTGAGGAGATGACTTCATCTTCTGGAA
ACTTCTTAAAACTTTACTGAGATGGCATCTAGACTAACCTCTGACGCCACATAACTTCTAGAAAT
CACGTTGAGACCTTCCTTAATATGTAGTTGGCGCAATCCTCACCTTTCTAGCATGATTCAACATG
TCTTGTTGCCTCCTTCGAGCTTGCAACAACTAATTCAGCAAGAAGATGGCTCTAAAACATTAAGG
ATTGAACCTTAAACATTTAAGCCACAAAATTCTCCATACTTATTCATATTAAACACATCAAATCC
TAAAAATATCATTCAACTAAGAAAATGGCCAAAACCGAGGTATAAAAGCCATATGTCCTTAATTG
AAAAGAGTGTAATTCT
Found at i:22754 original size:13 final size:13
Alignment explanation
Indices: 22730--22756 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22720 AATCTTGACC
22730 ACTCATCTTGATA
1 ACTCATCTTGATA
22743 ACTCATCTTGATA
1 ACTCATCTTGATA
22756 A
1 A
22757 TATTTATGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ACTCATCTTGATA
Found at i:23058 original size:19 final size:18
Alignment explanation
Indices: 23017--23072 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
23007 AAAATAAAGT
* * *
23017 TAAAAATTATATTTTTAAG
1 TAAAAA-TATAATATTAAA
23036 TAAAAATATAATATATAAA
1 TAAAAATATAATAT-TAAA
*
23055 TAAAAATTTAATATTAAA
1 TAAAAATATAATATTAAA
23073 ACAATTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 10 0.31
19 22 0.69
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAAAATATAATATTAAA
Found at i:25134 original size:60 final size:60
Alignment explanation
Indices: 25041--25224 Score: 233
Period size: 60 Copynumber: 3.1 Consensus size: 60
25031 GCAACAGCAG
* * *
25041 CAGGTGCTCCCTCTGCATCCTCAGAAGGAGCAAAGGAGACGACACCGGCTACCGGTAGCT
1 CAGGTACTCCCTCTGCATCCTCAGAAGGAGCAAAGGAGATGACACCGGATACCGGTAGCT
* * * **
25101 CAGGTACTCCTTCTGCATCCTCAGAAGGAGCAAAGGAGGTGACACCAGATATTGGTAGCT
1 CAGGTACTCCCTCTGCATCCTCAGAAGGAGCAAAGGAGATGACACCGGATACCGGTAGCT
* * * * * * *
25161 CAGATACTCCCTCTGCATCCTCAGGAGCAGCAAAGGATATGACACCGGTTCCCGATAGCT
1 CAGGTACTCCCTCTGCATCCTCAGAAGGAGCAAAGGAGATGACACCGGATACCGGTAGCT
25221 CAGG
1 CAGG
25225 CTCTCCAGTG
Statistics
Matches: 103, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 103 1.00
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (60 bp):
CAGGTACTCCCTCTGCATCCTCAGAAGGAGCAAAGGAGATGACACCGGATACCGGTAGCT
Found at i:27302 original size:56 final size:57
Alignment explanation
Indices: 27209--27321 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
27199 ATTAATCAAA
*
27209 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAA-ACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCT
* * * *
27265 TATCGAGTGACATGTTTTTTTATTAGATGCCTAAAAAAGACGTTTTAGGACCGAGGC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGC
27322 ATGATGCTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
56 13 0.26
57 21 0.42
58 16 0.32
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (57 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCAAGGCT
Done.