Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013273.1 Corchorus olitorius cultivar O-4 contig13306, 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: 49206
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:9355 original size:91 final size:91
Alignment explanation
Indices: 9213--9382 Score: 207
Period size: 91 Copynumber: 1.9 Consensus size: 91
9203 AATTTTTCGA
* * * * * * * * *
9213 ATTAAGATTAACCCAGAAATATTTAATAATCCATTTTCGAGTTAAACTTAATCTAAAAATCAGAT
1 ATTAAGATTAACCCAAAAAGACTTAATAATCAATTTCCAAATTAAACTTAATCCAAAAATCA-AA
9278 CTTTGAA-TCAAGGACTTGATTTTCAC
65 CTTTGAATTCAAGGACTTGATTTTCAC
* **
9304 ATTAAGATTAACCCAAAAAGACTTAATGATCAATTTCCAAATTAATTTTAATCCAAAAATCAAAC
1 ATTAAGATTAACCCAAAAAGACTTAATAATCAATTTCCAAATTAAACTTAATCCAAAAATCAAAC
*
9369 TTTTAATTCAAGGA
66 TTTGAATTCAAGGA
9383 ATTAATAAAC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
90 7 0.11
91 58 0.89
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (91 bp):
ATTAAGATTAACCCAAAAAGACTTAATAATCAATTTCCAAATTAAACTTAATCCAAAAATCAAAC
TTTGAATTCAAGGACTTGATTTTCAC
Found at i:15470 original size:77 final size:78
Alignment explanation
Indices: 15329--15481 Score: 256
Period size: 77 Copynumber: 2.0 Consensus size: 78
15319 TGAAAAATAG
* *
15329 TAAAATGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTGAATAAAAATAGAGTTTTTA
1 TAAAATGGTAAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA
15394 ATAGAATAAAACT
66 ATAGAATAAAACT
*
15407 TAAAATGGTAAAAATAAAATAATTATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTT
1 TAAAATGGTAAAAATAAAATAATTATAAAGATATTAG-ATTTAATTAAATAAAAATAGAGTTTTT
15470 AATAGAATAAAA
65 AATAGAATAAAA
15482 ATGTATGTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
76 1 0.01
77 42 0.59
78 28 0.39
ACGTcount: A:0.56, C:0.01, G:0.10, T:0.33
Consensus pattern (78 bp):
TAAAATGGTAAAAATAAAATAATTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA
ATAGAATAAAACT
Found at i:33948 original size:14 final size:12
Alignment explanation
Indices: 33929--33972 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
33919 TTATTATTAT
33929 TTTTCCTTCTGTCC
1 TTTTCCTT-T-TCC
*
33943 TTTTCCTTTCCC
1 TTTTCCTTTTCC
33955 TTTTCCTTTTTCC
1 TTTTCC-TTTTCC
33968 TTTTC
1 TTTTC
33973 TTTCGTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 8 0.30
13 11 0.41
14 8 0.30
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (12 bp):
TTTTCCTTTTCC
Found at i:33951 original size:6 final size:6
Alignment explanation
Indices: 33929--33972 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
33919 TTATTATTAT
*
33929 TTTTCC TTCTGTCC TTTTCC TTTCCC TTTTCC TTTTTCC TTTTC
1 TTTTCC TT-T-TCC TTTTCC TTTTCC TTTTCC -TTTTCC TTTTC
33973 TTTCGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 20 0.61
7 8 0.24
8 5 0.15
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (6 bp):
TTTTCC
Found at i:34708 original size:20 final size:20
Alignment explanation
Indices: 34683--34722 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
34673 ATAGGGGTTT
*
34683 ATTCAAAATTTCATAGTGTG
1 ATTCAAAACTTCATAGTGTG
34703 ATTCAAAACTTCATAGTGTG
1 ATTCAAAACTTCATAGTGTG
34723 CAGATCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (20 bp):
ATTCAAAACTTCATAGTGTG
Found at i:34737 original size:22 final size:20
Alignment explanation
Indices: 34685--34740 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
34675 AGGGGTTTAT
* *
34685 TCAAAATTTCATAGTGTGAT
1 TCAAAACTTCATAGTGTGAA
34705 TCAAAACTTCATAGTGTGCAGA
1 TCAAAACTTCATAGTGTG-A-A
*
34727 TCAAAAGTTCATAG
1 TCAAAACTTCATAG
34741 GGAGGTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 17 0.55
21 1 0.03
22 13 0.42
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TCAAAACTTCATAGTGTGAA
Found at i:34825 original size:23 final size:23
Alignment explanation
Indices: 34781--34869 Score: 80
Period size: 23 Copynumber: 3.9 Consensus size: 23
34771 TTAAAAAATC
* *
34781 ATAAGGAGGTTAT-AAAAATTTA
1 ATAAGGATGTTATCAAAATTTTA
34803 ATAAGGATGTTATCAAAATTTTA
1 ATAAGGATGTTATCAAAATTTTA
34826 TAGTAAGG-T-TTATCAAAATTTT-
1 -A-TAAGGATGTTATCAAAATTTTA
*
34848 AT-AGGAAGCTTTATCAAAATTT
1 ATAAGGATG--TTATCAAAATTT
34870 CATAGTGAGA
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
19 3 0.05
20 1 0.02
21 1 0.02
22 12 0.21
23 33 0.58
24 2 0.04
25 5 0.09
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (23 bp):
ATAAGGATGTTATCAAAATTTTA
Found at i:34874 original size:23 final size:22
Alignment explanation
Indices: 34790--34895 Score: 90
Period size: 23 Copynumber: 4.7 Consensus size: 22
34780 CATAAGGAGG
* * *
34790 TTATAAAAATTTAATAAGGATG-
1 TTATCAAAATTTCAT-AGGAAGT
* *
34812 TTATCAAAATTTTATAGTAAGGT
1 TTATCAAAATTTCATAGGAA-GT
*
34835 TTATCAAAATTTTATAGGAAGCT
1 TTATCAAAATTTCATAGGAAG-T
*
34858 TTATCAAAATTTCATAGTG-AGA
1 TTATCAAAATTTCATAG-GAAGT
*
34880 TTATCACAATTTCATA
1 TTATCAAAATTTCATA
34896 CTGTGATTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.04
22 30 0.42
23 38 0.53
24 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAAGT
Found at i:34890 original size:22 final size:22
Alignment explanation
Indices: 34663--35065 Score: 142
Period size: 22 Copynumber: 18.4 Consensus size: 22
34653 ATTCTAGTTT
* * *
34663 TCAAAATATCATAG-GGGTTTA
1 TCAAAATTTCATAGTGTGATTA
34684 TTCAAAATTTCATAGTGTGA-T-
1 -TCAAAATTTCATAGTGTGATTA
* *
34705 TCAAAACTTCATAGTGTGCA-GA
1 TCAAAATTTCATAGTGTG-ATTA
* * * *
34727 TCAAAAGTTCATAGGGAGGTTAA
1 TCAAAATTTCATAGTGTGATT-A
* * *
34750 T-AAAATTTCATAATGAGGTTA
1 TCAAAATTTCATAGTGTGATTA
* ** * *
34771 TTAAAAAATCATAAG-GAGGTTA
1 TCAAAATTTCAT-AGTGTGATTA
* *
34793 TAAAAATTTAATAAG-GATG-TTA
1 TCAAAATTTCAT-AGTG-TGATTA
* *
34815 TCAAAATTTTATAGTAAG-GTTTA
1 TCAAAATTTCATAGT--GTGATTA
* * *
34838 TCAAAATTTTATAG-GAAGCTTTA
1 TCAAAATTTCATAGTG-TG-ATTA
*
34861 TCAAAATTTCATAGTGAGATTA
1 TCAAAATTTCATAGTGTGATTA
* *
34883 TCACAATTTCATACTGTGATTA
1 TCAAAATTTCATAGTGTGATTA
*
34905 TCAAAATTTCACAGTGTGATTA
1 TCAAAATTTCATAGTGTGATTA
* * *
34927 -CTAACATTTCAT-GTGCATG-CTC
1 TC-AAAATTTCATAGTG--TGATTA
*
34949 CCAAAATTTCATAGTGT--TCTA
1 TCAAAATTTCATAGTGTGAT-TA
* * ** *
34970 CCAACATTTCACGGGGAT-ATTA
1 TCAAAATTTCATAGTG-TGATTA
34992 TCAAAATTTCATAGTGTTG-TTA
1 TCAAAATTTCATAGTG-TGATTA
*
35014 TCAAAATTTCAT-TTG-GAGGTTA
1 TCAAAATTTCATAGTGTGA--TTA
* * *
35036 TCAAAATTTCATAGTGAGGTTT
1 TCAAAATTTCATAGTGTGATTA
35058 TCAAAATT
1 TCAAAATT
35066 ACATGGGGAG
Statistics
Matches: 299, Mismatches: 52, Indels: 60
0.73 0.13 0.15
Matches are distributed among these distances:
19 1 0.00
20 18 0.06
21 25 0.08
22 201 0.67
23 51 0.17
24 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAGTGTGATTA
Found at i:35076 original size:22 final size:22
Alignment explanation
Indices: 34726--35199 Score: 178
Period size: 22 Copynumber: 21.7 Consensus size: 22
34716 TAGTGTGCAG
*
34726 ATCAAAAGTTCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
34748 AAT-AAAATTTCATAATGAGGTT
1 -ATCAAAATTTCATAGGGAGGTT
* ** *
34770 ATTAAAAAATCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
34792 ATAAAAATTTAATAAGGATGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
34814 ATCAAAATTTTATAGTAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* * *
34837 ATCAAAATTTTATAGGAAGCTTT
1 ATCAAAATTTCATAGGGAG-GTT
* *
34860 ATCAAAATTTCATAGTGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* ** * *
34882 ATCACAATTTCATACTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
34904 ATCAAAATTTCACAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
34926 A-CTAACATTTCAT-GTGCATGCT
1 ATC-AAAATTTCATAG-GGAGGTT
** * *
34948 CCCAAAATTTCATA--GTGTTCT
1 ATCAAAATTTCATAGGGAGGT-T
* * ** **
34969 ACCAACATTTCACGGGGATATT
1 ATCAAAATTTCATAGGGAGGTT
* **
34991 ATCAAAATTTCATAGTGTTGTT
1 ATCAAAATTTCATAGGGAGGTT
**
35013 ATCAAAATTTCATTTGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
35035 ATCAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
35057 TTCAAAATTACATGGGGAGG--
1 ATCAAAATTTCATAGGGAGGTT
* * *
35077 ---AAATTTTCATAGGAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
35096 AACAAAATTTCATAGAAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * ** **
35118 CTCGAAATTTCTTAATGTCGTT
1 ATCAAAATTTCATAGGGAGGTT
*
35140 ATCAAAATTTAATAGAGG-GGTT
1 ATCAAAATTTCATAG-GGAGGTT
* * * **
35162 ATCGAAATTCCATAGTGTCGTT
1 ATCAAAATTTCATAGGGAGGTT
35184 ATCAAAATTTCATAGG
1 ATCAAAATTTCATAGG
35200 AAAGATCAAA
Statistics
Matches: 332, Mismatches: 102, Indels: 35
0.71 0.22 0.07
Matches are distributed among these distances:
17 12 0.04
21 16 0.05
22 260 0.78
23 44 0.13
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:36281 original size:435 final size:433
Alignment explanation
Indices: 35446--36301 Score: 1235
Period size: 435 Copynumber: 2.0 Consensus size: 433
35436 AGTTGAAACG
* * *
35446 TTAAATCGAATAAGATAGAATTGGTAAAGGACTAAGTAGTATAATATAGAAAAGTATGAGGGTCA
1 TTAAATCGAATAAGATAGAATTAGTAAAGGACTAAGTAGTACAATATAGAAAAATATGAGGGTCA
* *
35511 TTTGATAAATAATCCAATTAAAAAAAATGTTTGTTGATAGGGATCTTGAAACATAAAAATTCCCT
66 TTTGATAAATAACCCAA-TAAAAAAAATGTTTGATGATAGGGATCTTGAAACATAAAAATTCCCT
* * * *
35576 TTTGAACCCTTCATGAAACTTGTAGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAGAT
130 TTTGAACCCTTAATGAAACTCGTAGATCAAATTTAGCTCTCGGGTCCTTCATGAAAGTCGCAGAT
* * *
35641 CACGCAATAACCTTTTAACCGACACTTAAATAACTTTAATTGGACATATGGATCCAAAATTATAT
195 CACGCAATAACCTTTTAACCGACACTTAAATAACATTAATCGGACATATGGATCAAAAATTATAT
*
35706 GGTATTAAATACCGGCAATCGAAACTACCAAATTTGGAAAGATTTTTTTTTTTGAATTGAAACAT
260 GATATTAAATACCGGCAATCGAAACTACCAAATTTGGAAAGA---TTTTTTTTGAATTGAAACAT
35771 AAAAATTGACATTTAAGTCCTTCATGAAAGTTGGAAATCATGAAATTACCTTTTAATAGACACCT
322 AAAAATTGACATTTAAGTCCTTCATGAAAGTTGGAAATCATGAAATTACCTTTTAATAGACACCT
* *
35836 CTTGACCTTAATCGGATAAATAGAAAAAAAACTAATATGCTTAAGCA
387 ATTGACCTTAATCGGACAAATAGAAAAAAAACTAATATGCTTAAGCA
* *
35883 TTAAATC-AATTAGGATAGATTTAGTAAAGGACTAAGTAGTACAA-AGTAGAAAAATATGAGGGT
1 TTAAATCGAA-TAAGATAGAATTAGTAAAGGACTAAGTAGTACAATA-TAGAAAAATATGAGGGT
* * * *
35946 CATTTGATAAATAACCCAA-ACAAACAAATGTTTGATGAT-GGAGATTTTGAAATAT-AAAATTT
64 CATTTGATAAATAACCCAATA-AAAAAAATGTTTGATGATAGG-GATCTTGAAACATAAAAATTC
*
36008 CCTTTTGAATCCTTAATGAAACTCGTAGATCAAATTTAGCTCTCGGGTCCTTCATGAAAGTCGCA
127 CCTTTTGAACCCTTAATGAAACTCGTAGATCAAATTTAGCTCTCGGGTCCTTCATGAAAGTCGCA
* *
36073 GATCATGCAATAACCTTTTAACCGACACTTAAATAACATTAATCGGACATGTGGATCAAAAATTA
192 GATCACGCAATAACCTTTTAACCGACACTTAAATAACATTAATCGGACATATGGATCAAAAATTA
*
36138 TATGATATTAAATAAACCGGCAATCGAAA-TCGCCAAATTTCGG-AAGCA-TTTTTTTGAATTGA
257 TATGATATTAAAT--ACCGGCAATCGAAACT-ACCAAATTT-GGAAAG-ATTTTTTTTGAATTGA
* * * * *
36200 AACATAAAAATTGGCTTTTGAGTCCTTTATGAAAGTTGTAAATCATGAAATTACCTTTTAATAGA
317 AACATAAAAATTGACATTTAAGTCCTTCATGAAAGTTGGAAATCATGAAATTACCTTTTAATAGA
*
36265 CACCTGGATT-ACCTTAATCGGACAAATAGGAAAAAAA
382 CACCT--ATTGACCTTAATCGGACAAATAGAAAAAAAA
36302 TACATAAAGC
Statistics
Matches: 377, Mismatches: 31, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
434 79 0.21
435 166 0.44
436 33 0.09
437 96 0.25
438 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (433 bp):
TTAAATCGAATAAGATAGAATTAGTAAAGGACTAAGTAGTACAATATAGAAAAATATGAGGGTCA
TTTGATAAATAACCCAATAAAAAAAATGTTTGATGATAGGGATCTTGAAACATAAAAATTCCCTT
TTGAACCCTTAATGAAACTCGTAGATCAAATTTAGCTCTCGGGTCCTTCATGAAAGTCGCAGATC
ACGCAATAACCTTTTAACCGACACTTAAATAACATTAATCGGACATATGGATCAAAAATTATATG
ATATTAAATACCGGCAATCGAAACTACCAAATTTGGAAAGATTTTTTTTGAATTGAAACATAAAA
ATTGACATTTAAGTCCTTCATGAAAGTTGGAAATCATGAAATTACCTTTTAATAGACACCTATTG
ACCTTAATCGGACAAATAGAAAAAAAACTAATATGCTTAAGCA
Found at i:48722 original size:4 final size:4
Alignment explanation
Indices: 48715--48740 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
48705 CCTTTTTTTT
48715 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
48741 CGTTTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Done.