Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011940.1 Corchorus olitorius cultivar O-4 contig11973, 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: 30342
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2645 original size:16 final size:17
Alignment explanation
Indices: 2624--2660 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2614 AGAGCAAGGT
2624 CAATG-ACACACCAAAA
1 CAATGAACACACCAAAA
*
2640 CAATGAACACATCAAAA
1 CAATGAACACACCAAAA
2657 CAAT
1 CAAT
2661 ATTTTGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.57, C:0.27, G:0.05, T:0.11
Consensus pattern (17 bp):
CAATGAACACACCAAAA
Found at i:4179 original size:42 final size:42
Alignment explanation
Indices: 4120--4202 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
4110 AGCAACAATT
*
4120 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
4162 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTA
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTA
4203 CTAGAATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Found at i:5007 original size:16 final size:17
Alignment explanation
Indices: 4971--5010 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
4961 CGAACCCGTC
4971 TGACCCGAGATCCAACA
1 TGACCCGAGATCCAACA
4988 -GACCCGAGA-CTCAA-A
1 TGACCCGAGATC-CAACA
5003 TGACCCGA
1 TGACCCGA
5011 ACCTTGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.35, C:0.35, G:0.20, T:0.10
Consensus pattern (17 bp):
TGACCCGAGATCCAACA
Found at i:7438 original size:30 final size:30
Alignment explanation
Indices: 7404--7474 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
7394 GTCCATGACT
* * *
7404 CCACATAAGCAAATACATGTCATCA-AAGAG
1 CCACATAAGCAAACACAGGTAATCAGAA-AG
7434 CCACATAAGCAAACACAGGTAATCAGAAAG
1 CCACATAAGCAAACACAGGTAATCAGAAAG
7464 CCACATAAGCA
1 CCACATAAGCA
7475 TTAACAGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 35 0.95
31 2 0.05
ACGTcount: A:0.48, C:0.25, G:0.14, T:0.13
Consensus pattern (30 bp):
CCACATAAGCAAACACAGGTAATCAGAAAG
Found at i:11800 original size:23 final size:24
Alignment explanation
Indices: 11757--11818 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
11747 TAGTTGTTAG
* *
11757 TTATAACTTGGGC-CTGATTTGTC
1 TTATAATTTGGGCTTTGATTTGTC
*
11780 TTATAATTTGGGCTTTG-TTTGTT
1 TTATAATTTGGGCTTTGATTTGTC
*
11803 TTAGTTATTTGGGCTT
1 TTA-TAATTTGGGCTT
11819 GACCTTTCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 20 0.61
24 13 0.39
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.53
Consensus pattern (24 bp):
TTATAATTTGGGCTTTGATTTGTC
Found at i:12526 original size:40 final size:36
Alignment explanation
Indices: 12405--12544 Score: 147
Period size: 40 Copynumber: 3.7 Consensus size: 36
12395 TCAATTTAGT
* * * *
12405 TTTTCAAATT-GGGAAAGTTCCCATCAACTCTTCATAG
1 TTTTC-AATTAGGGAAAGATCCCATCCAGTTTTCA-AG
*
12442 TTTTTCAAATAGGGAAAGATCCCATCCAGTTTTCAAG
1 -TTTTCAATTAGGGAAAGATCCCATCCAGTTTTCAAG
*
12479 ATTTCAATTTAGGGAAAGATCCCATCCAGTCTTTTTCAAG
1 TTTTCAA-TTAGGGAAAGATCCCATCCAG---TTTTCAAG
12519 TTTTCAATTAGGGGAAAGATCCCATC
1 TTTTCAATTA-GGGAAAGATCCCATC
12545 AAAGTTTTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
36 6 0.07
37 25 0.28
38 25 0.28
39 3 0.03
40 29 0.33
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (36 bp):
TTTTCAATTAGGGAAAGATCCCATCCAGTTTTCAAG
Found at i:16200 original size:14 final size:14
Alignment explanation
Indices: 16183--16234 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
16173 AAAATTGAGG
16183 AATAATTATTGAAT
1 AATAATTATTGAAT
*
16197 AATAATAATT--AT
1 AATAATTATTGAAT
16209 CGAATAATTATTGAAT
1 --AATAATTATTGAAT
16225 AATAATTATT
1 AATAATTATT
16235 ATTAGCTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 2 0.06
14 28 0.88
16 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (14 bp):
AATAATTATTGAAT
Found at i:16205 original size:17 final size:17
Alignment explanation
Indices: 16183--16216 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16173 AAAATTGAGG
*
16183 AATAATTATTGAATAAT
1 AATAATTATCGAATAAT
16200 AATAATTATCGAATAAT
1 AATAATTATCGAATAAT
16217 TATTGAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (17 bp):
AATAATTATCGAATAAT
Found at i:16206 original size:28 final size:28
Alignment explanation
Indices: 16182--16236 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
16172 CAAAATTGAG
16182 GAATAATTATTGAATAATAATAATTATC
1 GAATAATTATTGAATAATAATAATTATC
*
16210 GAATAATTATTGAATAATAATTATTAT
1 GAATAATTATTGAATAATAATAATTAT
16237 TAGCTCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (28 bp):
GAATAATTATTGAATAATAATAATTATC
Found at i:27093 original size:39 final size:40
Alignment explanation
Indices: 27039--27114 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
27029 GAGAGGTTAC
*
27039 AATTCTAGATAATTAA-GGGGATAGGATTTATTATAAAAT
1 AATTCTAGATAATTAAGGGGGATAGGATTTATCATAAAAT
27078 AATTCTAGATAATTAAGGGGGATAGGATTTATCATAA
1 AATTCTAGATAATTAAGGGGGATAGGATTTATCATAA
27115 CATTTATGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 16 0.46
40 19 0.54
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (40 bp):
AATTCTAGATAATTAAGGGGGATAGGATTTATCATAAAAT
Found at i:28780 original size:653 final size:652
Alignment explanation
Indices: 27527--28810 Score: 2379
Period size: 653 Copynumber: 2.0 Consensus size: 652
27517 TCTATTTCAC
* *
27527 ATAATGAACTTTGGTTCATAGAAGTGATATACTTCACCAAAATTCAGTGAAATATTTTTCATTCT
1 ATAAAGAACTTTGGTTCATAGAAGTGATATACTTCACCAAAATTCAATGAAATATTTTTCATTCT
* * * *
27592 TTCTAAGACTGGTTCATAGCCCAAAAGGCACCAGTTCGATGCACTACATTCCATGGTGAATCCAG
66 TTCTAAGACTGGTTCATAACCCAAAAGGCACCAATGCGATGCACTACATTCCATGGTGAACCCAG
27657 CAAAAATTTTTATTTATTTTTAACCTTTGAAATATGTGGGGGATTGTTGGAAAATTATTTATTTC
131 CAAAAATTTTTATTTATTTTTAACCTTTGAAATATGTGGGGGATTGTTGGAAAATTATTTATTTC
27722 AAAGATTAAAAATATTAAATTACCTATTAAATGTTTTATAACCGTTATAGGTTTATTTGTAACCT
196 AAAGATTAAAAATATTAAATTACCTATTAAATGTTTTATAACCGTTATAGGTTTATTTGTAACCT
*
27787 ACCCTTAATCCTAATAATTTCTCTATTTATTATGAGTTATTACTACTTATTATATACATAACGGT
261 ACCCTTAATCCTAATAATTTCCCTATTTATTATGAGTTATTACTACTTATTATATACATAACGGT
* *
27852 TATAAAACTCACTACTATATATAGCTATCTAATCCTTATTTTTCATATGCAAGAGATGATTAATT
326 TATAAAACTCACTACTATATATAGCTATCTAATCCTTATTTTTCATATGCAAGAGAAGATCAATT
*
27917 CTATTTTTCCTCCACATTATTTTGCTGGTTCATTTTGTTTTAGTGTTGTTCCTGTAGCCTTGATA
391 CTATTTTTCCTCCACATTATTTTGCTGGTTCATTTTATTTTAGTGTTGTTCCTGTAGCCTTGATA
27982 GCTAGTGTAGGCTATCAAGAAGAGTCTGTTGAATCCTGGAGGATAGCCGCTATCAAACCTTTTAC
456 GCTAGTGTAGGCTATCAAGAAGAGTCTGTTGAATCCTGGAGGATAGCCGCTATCAAACCTTTTAC
*
28047 ACCGAGTTATAAACTCCGAGGGGCAGAAATTATCCTTAAGGACAGTGTCCTTCACGCCTCAGACT
521 ACCGAGTTATAAACTCCGAGGGGCAGAAATTATCCTTAAGGACAGTGTCATTCACGCCTCAGACT
*
28112 ATTGTCAGTGTTCTTGTGTTCTTGCTTATTCAATATTTTTCCAACAATTCAAGTAGAAAAAGAAT
586 ATTCTCAGTGTTCTTGTGTTCTTGCTTATTCAATATTTTTCCAACAATTCAAGTAGAAAAAGAAT
28177 GA
651 GA
*
28179 ATAAAGAATCTTTGGTTCATAGAAGTGATATACTTCACCAAAATTCAATGACATATTTTTCATTC
1 ATAAAGAA-CTTTGGTTCATAGAAGTGATATACTTCACCAAAATTCAATGAAATATTTTTCATTC
28244 TTTCTAAGACTGGTTCATAACCCAAAAGGCACCAATGCGATGCACTACATTCCATGGTGAACCCA
65 TTTCTAAGACTGGTTCATAACCCAAAAGGCACCAATGCGATGCACTACATTCCATGGTGAACCCA
28309 GCAAAAATTTTTATTTATTTTTAACCTTTGAAATATGTGGGGGATTGTTGGAAAATTATTTATTT
130 GCAAAAATTTTTATTTATTTTTAACCTTTGAAATATGTGGGGGATTGTTGGAAAATTATTTATTT
28374 CAAAGATTAAAAATATTAAATTACCTATTAAATGTTTTATAACCGTTATAGGTTTATTTGTAACC
195 CAAAGATTAAAAATATTAAATTACCTATTAAATGTTTTATAACCGTTATAGGTTTATTTGTAACC
28439 TACCCTTAATCCTAATAATTTCCCTATTTATTATGAGTTATTACTACTTATTATATACATAACGG
260 TACCCTTAATCCTAATAATTTCCCTATTTATTATGAGTTATTACTACTTATTATATACATAACGG
* *
28504 TTATAAAACTTACTACTATATATAGCTATCTAATCCTTATTTTTTATATGCAAGAGAAGATCAAT
325 TTATAAAACTCACTACTATATATAGCTATCTAATCCTTATTTTTCATATGCAAGAGAAGATCAAT
* *
28569 TCTATTTTTCCTCCTCATTATTTTGTTGGTTCATTTTATTTTAGTGTTGTTCCTGTAGCCTTGAT
390 TCTATTTTTCCTCCACATTATTTTGCTGGTTCATTTTATTTTAGTGTTGTTCCTGTAGCCTTGAT
28634 AGCTAGTGTAGGCTATCAAGAAGAGTCTGTTGAATCCTGGAGGATAGCCGCTATCAAACCTTTTA
455 AGCTAGTGTAGGCTATCAAGAAGAGTCTGTTGAATCCTGGAGGATAGCCGCTATCAAACCTTTTA
* *
28699 CACCGAGTTATAAACTCTGAGGGGCGGAAATTATCCTTAAGGACAGTGTCATTCACGCCTCAGAC
520 CACCGAGTTATAAACTCCGAGGGGCAGAAATTATCCTTAAGGACAGTGTCATTCACGCCTCAGAC
*
28764 TATTCTCGGTGTTCTTGTGTTCTTGCTTATTCAATATTTTTCCAACA
585 TATTCTCAGTGTTCTTGTGTTCTTGCTTATTCAATATTTTTCCAACA
28811 GTGACATACC
Statistics
Matches: 611, Mismatches: 20, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
652 7 0.01
653 604 0.99
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (652 bp):
ATAAAGAACTTTGGTTCATAGAAGTGATATACTTCACCAAAATTCAATGAAATATTTTTCATTCT
TTCTAAGACTGGTTCATAACCCAAAAGGCACCAATGCGATGCACTACATTCCATGGTGAACCCAG
CAAAAATTTTTATTTATTTTTAACCTTTGAAATATGTGGGGGATTGTTGGAAAATTATTTATTTC
AAAGATTAAAAATATTAAATTACCTATTAAATGTTTTATAACCGTTATAGGTTTATTTGTAACCT
ACCCTTAATCCTAATAATTTCCCTATTTATTATGAGTTATTACTACTTATTATATACATAACGGT
TATAAAACTCACTACTATATATAGCTATCTAATCCTTATTTTTCATATGCAAGAGAAGATCAATT
CTATTTTTCCTCCACATTATTTTGCTGGTTCATTTTATTTTAGTGTTGTTCCTGTAGCCTTGATA
GCTAGTGTAGGCTATCAAGAAGAGTCTGTTGAATCCTGGAGGATAGCCGCTATCAAACCTTTTAC
ACCGAGTTATAAACTCCGAGGGGCAGAAATTATCCTTAAGGACAGTGTCATTCACGCCTCAGACT
ATTCTCAGTGTTCTTGTGTTCTTGCTTATTCAATATTTTTCCAACAATTCAAGTAGAAAAAGAAT
GA
Done.