Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019778.1 Corchorus olitorius cultivar O-4 contig19811, 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: 28514
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:87 original size:29 final size:28
Alignment explanation
Indices: 48--103 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
38 GTTATTCCAC
*
48 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
77 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
104 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:10266 original size:19 final size:19
Alignment explanation
Indices: 10244--10281 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10234 GGTAATTACA
*
10244 AAAAAAAAATTGTTTTCAT
1 AAAAAAAAAGTGTTTTCAT
*
10263 AAAAAAGAAGTGTTTTCAT
1 AAAAAAAAAGTGTTTTCAT
10282 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (19 bp):
AAAAAAAAAGTGTTTTCAT
Found at i:14060 original size:770 final size:763
Alignment explanation
Indices: 12280--16091 Score: 6508
Period size: 770 Copynumber: 5.0 Consensus size: 763
12270 ATACAAATAA
*
12280 TTAGTGCAATGTAAATTACTTACAATCTTCTATGTATATCTTTAGCCCGTCTGTCGAAACAATAA
1 TTAGTGAAATGTAAATTACTTACAATCTTCTATGTATATCTTTAGCCCGTCTGTCGAAACAATAA
*
12345 ATATAAGAGAAACAAAATTAGTTTATTCTTCCTCGAAAATTCAAATTTTAATTTAACAATTTCGT
66 ATATAAGAGAAACAAAATTAGTTTATTCTTCCTCGAAAATTCAAATTTTAATTTAACAATTTCGA
* *
12410 CAGAAGACTAGTGTTTTACCTGCAATTTGCTGTTTTCTAGTCTCCAATTTCAGGAACGGTATCTC
131 CAGAAGACTAGTGTTTTACCTGCAATTTGCTGTTTTCTAGTCTCCATTTTTAGGAACGGTATCTC
* * *
12475 AACATTTTCTTCGAACTTTTTATCATAGAAAATCATAGACTCCATGTAGACTACCAATAGTCTCA
196 AACATTTTCTTCGAACTTTTTATCATAGAAAATCATAGCCTCCATGTAGACTACCAACAGTCTTA
* * * *
12540 GATCGCGATCATCTAAAACCATATGCTCACCAATAATACAAGTATCTCGTCCATTCCCAAATAAA
261 GATCGCGATCATCCAAAACGATATGCTCACCAATAATACAAGTATCTCGTCCATGCCCAAATACA
*
12605 TATTTTAAGGTATGGAAATGTATAAAAATTTCTTTATGATAACAAAAGGATATAAATAAAGAACA
326 TATTTTAAGGTATGGAAATGTATAAAAATGTCTTTATGATAACAAAAGGATATAAATAAAGAACA
* *
12670 TGCAGCTATTGTATTTGAAACATGCAGATGAAAAAACGTGATTCCTAACCAAATCATTGCGATAA
391 TGCAGCTATTGTATTAGAAACATGCAGATGAAAAAATGTGATTCCTAACCAAATCATTGCGATAA
*
12735 TTAGCAAAAGCAATATAATGTTATGCACGTTCATAACTTTAATTTAAATTTATTCATCAACTACA
456 TTAGCAAAAGCAATATAATGTTATGCACGTTCATAACTTTTATTTAAATTTATTCATCAACTACA
*
12800 ACCATTGCGATGTCAAAAAAAAATTATTTAAAATCAAAGTAAAGAATATGTTTGCATTACGATCA
521 ACCATTGCGATGTC-AAAAAAAA-TATTTAAAATCAAAGTAAAGAATATGTTCGCATTACGATCA
*
12865 AAATTTTCATGCGTTTGTCGTCCTTTATCAATGTATCAGAGCCTTTACATATACATGATAGTACC
584 AAATTTTCATGCGTTTGTCGTCCTTTATCAATGTATCAGAGCCTTTACATATACATGGTAGTACC
12930 AATTAAAAGTTGCATAAGCTTACATCCATCAATTTAATATATAAATATCTGCACAATTTGAAATG
649 AATTAAAAGTTGCATAAGCTTACATCCATCAATTTAATATATAAATATCTGCACAATTTGAAATG
*
12995 AAAACCAAATACCTTCTTCTGAACAAAAAAATGTATATCTTTGTATATCT
714 AAAACCAAATACCTTCTTCTGAACAAAGAAATGTATATCTTTGTATATCT
13045 TTAGTGAAATGTAAATTACTTACAATCTTCTATGTATATCTTTAGCCCGTCTGTCGAAACAATAA
1 TTAGTGAAATGTAAATTACTTACAATCTTCTATGTATATCTTTAGCCCGTCTGTCGAAACAATAA
13110 ATATAAGAGAAACAAAATTAGTTTATTCTTCCTCGAAAATTCAAATTTTAATTTAACAATTTCGA
66 ATATAAGAGAAACAAAATTAGTTTATTCTTCCTCGAAAATTCAAATTTTAATTTAACAATTTCGA
*
13175 CAGAAAACTAGTGTTTTACCTGCAATTTGCTGTTTTCTAGTCTCCATAGTCTCCATTTTCAGGAA
131 CAGAAGACTAGTGTTTTACCTGCAATTTGCTGTTTTCTAGTCTCC--A---T---TTTT-AGGAA
*
13240 CGGTATTTCAACATTTTCTTCGAACTTTTTATCATAGAAAATCATAGCCTCCATGTAGACTACCA
187 CGGTATCTCAACATTTTCTTCGAACTTTTTATCATAGAAAATCATAGCCTCCATGTAGACTACCA
** *
13305 ACAGTCTTAGATCGCGATCATCCAAAACGATATGCTCACCAATAATTTAAGTATTTCGTCCATGC
252 ACAGTCTTAGATCGCGATCATCCAAAACGATATGCTCACCAATAATACAAGTATCTCGTCCATGC
13370 CCAAATACATATTTTAAGGTATGGAAATGTATAAAAATGTCTTTATGATAACAAAAGGATATAAA
317 CCAAATACATATTTTAAGGTATGGAAATGTATAAAAATGTCTTTATGATAACAAAAGGATATAAA
*
13435 TAAAGAACATGCAGCTATTGTATTAGAAACATACAGATGAAAAAATGTGATTCCTAACCAAATCA
382 TAAAGAACATGCAGCTATTGTATTAGAAACATGCAGATGAAAAAATGTGATTCCTAACCAAATCA
* * **
13500 TTACGATAATTAGCAAAAGTAATATAATGTTATGCACGTTCATATTTTTTATTTAAATTTATTCA
447 TTGCGATAATTAGCAAAAGCAATATAATGTTATGCACGTTCATAACTTTTATTTAAATTTATTCA
*
13565 TCAACTACAACCATTGCGATGTC-AAAAAAATATTTAAAATCAAATTAAAGAATATGTTCGCATT
512 TCAACTACAACCATTGCGATGTCAAAAAAAATATTTAAAATCAAAGTAAAGAATATGTTCGCATT
* *
13629 ACGATCAAAATTTGCATGCATTTGTCGTCCTTTATCAATGTATCAGAGCCTTTACATATACATGG
577 ACGATCAAAATTTTCATGCGTTTGTCGTCCTTTATCAATGTATCAGAGCCTTTACATATACATGG
* *
13694 TAGTACCAATTAAAAGTTGTATAAGCTTACATCCATCAATTTAATATATAAATATCTACA-AATT
642 TAGTACCAATTAAAAGTTGCATAAGCTTACATCCATCAATTTAATATATAAATATCTGCACAATT
*
13758 TGAAATGAAAACCAAATACCTTCTTCTGAACAAAGAAATGTATATATTTGTATATCT
707 TGAAATGAAAACCAAATACCTTCTTCTGAACAAAGAAATGTATATCTTTGTATATCT
* *
13815 TTAGTGAAATGTAAATTACTTACAATCTTTTATGTATATTTTTAGCCCGTCTGTCGAAACAATAA
1 TTAGTGAAATGTAAATTACTTACAATCTTCTATGTATATCTTTAGCCCGTCTGTCGAAACAATAA
*
13880 ATATAAGAGAAACAAAATTAGTTTATTCTTCCTAGAAAATTCAAATTTTAATTTAACAATTTCGA
66 ATATAAGAGAAACAAAATTAGTTTATTCTTCCTCGAAAATTCAAATTTTAATTTAACAATTTCGA
* *
13945 CAGAAGACTAGTATTTTACCTGGAATTTGCTGTTTTCTAGTATCTATAGTCTCCATTTTTAGGAA
131 CAGAAGACTAGTGTTTTACCTGCAATTTGCTG---T-T--T-TC--TAGTCTCCATTTTTAGGAA
14010 CGGTATCTCAACATTTTCTTCGAACTTTTTATCATAGAAAATCATAGCCTCCATGTAGACTACCA
187 CGGTATCTCAACATTTTCTTCGAACTTTTTATCATAGAAAATCATAGCCTCCATGTAGACTACCA
* * *
14075 ACAGTCTTAAATCGCGATCATCCAAAACGATATGCTCACCAATAATTCAAGTATTTCGTCCATGC
252 ACAGTCTTAGATCGCGATCATCCAAAACGATATGCTCACCAATAATACAAGTATCTCGTCCATGC
*
14140 CCAAATACATATTTTAAGGTACGGAAATGTATAAAAATGTCTTTATGATAACAAAAGGATATAAA
317 CCAAATACATATTTTAAGGTATGGAAATGTATAAAAATGTCTTTATGATAACAAAAGGATATAAA
* * *
14205 TAAAGAACATGCAGCTTTTGTATTAGAAACATGCAGATGAAAAAATGTGATTCCTATCTAAATCA
382 TAAAGAACATGCAGCTATTGTATTAGAAACATGCAGATGAAAAAATGTGATTCCTAACCAAATCA
* * *
14270 TTGCGATAATTAGCAAAAGTAATATAATGTTATGCATGTTCATAACTCTTATTTAAATTTATTCA
447 TTGCGATAATTAGCAAAAGCAATATAATGTTATGCACGTTCATAACTTTTATTTAAATTTATTCA
* * *
14335 TCAACTACAACCATTGCGATGTTAAAAAAAAATATTTAAAATTAAAGTAAAGAATATATTCGCAT
512 TCAACTACAACCATTGCGATG-TCAAAAAAAATATTTAAAATCAAAGTAAAGAATATGTTCGCAT
* *
14400 TACGATCAAAATTTTCATGCGTTTGTCGTCCTTTACCAATGTATCAAAGCCTTTACATATACATG
576 TACGATCAAAATTTTCATGCGTTTGTCGTCCTTTATCAATGTATCAGAGCCTTTACATATACATG
*
14465 GTAGTACCAATTAAAAGTTGTATAAGCTTACATCCATCAATTTAATATATAAATATCTGCACAAT
641 GTAGTACCAATTAAAAGTTGCATAAGCTTACATCCATCAATTTAATATATAAATATCTGCACAAT
*
14530 TTGAAATGAAAACCAAATACCTTCTTCTGAACAAAGAAATGTATGTCTTTGTATATCT
706 TTGAAATGAAAACCAAATACCTTCTTCTGAACAAAGAAATGTATATCTTTGTATATCT
* *
14588 TTAGGGAAATGTAAATTACTTACAATCTTCTATATATATCTTTAGCCCGTCTGTCGAAACAATAA
1 TTAGTGAAATGTAAATTACTTACAATCTTCTATGTATATCTTTAGCCCGTCTGTCGAAACAATAA
*
14653 ATATAAGAAAAACAAAATTAGTTTATTCTTCCTCGAAAATTCAAATTTTAATTTAACAATTTCGA
66 ATATAAGAGAAACAAAATTAGTTTATTCTTCCTCGAAAATTCAAATTTTAATTTAACAATTTCGA
* * *
14718 CAGAAGGCTAGTGTTTTACCTGCAATTTGCTGTTTTCT--TCTCCATTTTCT-GAAACAGTATCT
131 CAGAAGACTAGTGTTTTACCTGCAATTTGCTGTTTTCTAGTCTCCATTTT-TAGGAACGGTATCT
*
14780 CAACATTTTCTTCGAACTTTTTATCATAGAAAATCATAGCCTCCATGTAGACAACCAACAGTCTT
195 CAACATTTTCTTCGAACTTTTTATCATAGAAAATCATAGCCTCCATGTAGACTACCAACAGTCTT
* ** *
14845 AGATCGCGATCATCAAAAACGATATGCTCATTAATAATACAAGTATCTCGTACATGCCCAAATAC
260 AGATCGCGATCATCCAAAACGATATGCTCACCAATAATACAAGTATCTCGTCCATGCCCAAATAC
* * * *
14910 ATATTTTAAGGTATGAAAATGTGTAAAAATGTCTTTATGATAA-AAAAAGATATAAATAGAGAAC
325 ATATTTTAAGGTATGGAAATGTATAAAAATGTCTTTATGATAACAAAAGGATATAAATAAAGAAC
** *
14974 ATG-TTCTATTGTATTAGAAACATGCAGATGAAAAATTGTGATTCCTAACCAAATCATTGCGATA
390 ATGCAGCTATTGTATTAGAAACATGCAGATGAAAAAATGTGATTCCTAACCAAATCATTGCGATA
15038 ATTAGCAAAAGCAATATAATGTTATGCACGTTCATAACTTTTATTTAAATTTATTCATCAACTAC
455 ATTAGCAAAAGCAATATAATGTTATGCACGTTCATAACTTTTATTTAAATTTATTCATCAACTAC
15103 AACCATTGCGATGTCAAAAAAAATTATTTAAAATCAAAGTAAAGAATATGTTCGCATTACGATCA
520 AACCATTGCGATGTCAAAAAAAA-TATTTAAAATCAAAGTAAAGAATATGTTCGCATTACGATCA
*
15168 AAATTTTCATGCGTTTGTCGTCCTTTATCAATATATCAGAGCCTTTACATATACATGGTAGTACC
584 AAATTTTCATGCGTTTGTCGTCCTTTATCAATGTATCAGAGCCTTTACATATACATGGTAGTACC
15233 AATTAAAAGTTGCATAAGCTTACATCCATCAATTTAATATATAAATATCTGCACAATTTGAAATG
649 AATTAAAAGTTGCATAAGCTTACATCCATCAATTTAATATATAAATATCTGCACAATTTGAAATG
15298 AAAACCAAATACCTTCTTCTGAACAAAGAAATGTATATCTTTGTATATCT
714 AAAACCAAATACCTTCTTCTGAACAAAGAAATGTATATCTTTGTATATCT
* * * *
15348 TTAGTGAAATATAAATTACTTACAATTTTCTATATATATCTTTTGCCCGTCTGTCGAAACAATAA
1 TTAGTGAAATGTAAATTACTTACAATCTTCTATGTATATCTTTAGCCCGTCTGTCGAAACAATAA
15413 ATATAAGAGAAACAAAATTAGTTTATTCTTCCTCGAAAATTCAAATTTTAATTTAACAATTTCGA
66 ATATAAGAGAAACAAAATTAGTTTATTCTTCCTCGAAAATTCAAATTTTAATTTAACAATTTCGA
*
15478 CAGAAGACTAGTGTTTTACCTGCAATTTGCTGTTTTCTAGTCTCAATTTTTAGGAACGGTATCTC
131 CAGAAGACTAGTGTTTTACCTGCAATTTGCTGTTTTCTAGTCTCCATTTTTAGGAACGGTATCTC
* * * * *
15543 AACTTTTTCTTCGAACTTTTTATCATAGAAAATCATGGACTCCATGTAGACTACCAATAGTCTCA
196 AACATTTTCTTCGAACTTTTTATCATAGAAAATCATAGCCTCCATGTAGACTACCAACAGTCTTA
* *
15608 AATCGCGATCATCCAAAACGATATGCTCACCAATAATACAAGTATCTCGTCCATGCCTAAATACA
261 GATCGCGATCATCCAAAACGATATGCTCACCAATAATACAAGTATCTCGTCCATGCCCAAATACA
* *
15673 TATTTTAAGGTA-GGTAAATGTTTAAAAATGTCTTTATGATAACAAAAGGATATAAATAGAGAAC
326 TATTTTAAGGTATGG-AAATGTATAAAAATGTCTTTATGATAACAAAAGGATATAAATAAAGAAC
15737 ATGCA-CTATTGTATTAGAAACATGCAGATGAAAAAATGTGATTCCTAACCAAATCATTGCGATA
390 ATGCAGCTATTGTATTAGAAACATGCAGATGAAAAAATGTGATTCCTAACCAAATCATTGCGATA
15801 ATTAGCAAAAGCAATATAATGTTATGCACGTTCATAACTTTTATTTAAATTTATTCATCAACTAC
455 ATTAGCAAAAGCAATATAATGTTATGCACGTTCATAACTTTTATTTAAATTTATTCATCAACTAC
* *
15866 AACCATTGCGATGTCAAAAAAAAATATTTAAAATTAAAGTAAAGAATATATTCGCATTACGATCA
520 AACCATTGCGATGTC-AAAAAAAATATTTAAAATCAAAGTAAAGAATATGTTCGCATTACGATCA
15931 AAATTTTCATGCGTTTGTCGTCCTTTATCAATGTATCAGAGCCTTTACATATACATGGTAGTACC
584 AAATTTTCATGCGTTTGTCGTCCTTTATCAATGTATCAGAGCCTTTACATATACATGGTAGTACC
*
15996 AATTAAAAGTTGCATAAGCTTACATCCATCAATTTAATATATAAATATCTGCACAATTTGAAATA
649 AATTAAAAGTTGCATAAGCTTACATCCATCAATTTAATATATAAATATCTGCACAATTTGAAATG
16061 AAAACCAAATACCTTCTTCTGAACAAAGAAA
714 AAAACCAAATACCTTCTTCTGAACAAAGAAA
16092 CAAATACAAA
Statistics
Matches: 2882, Mismatches: 135, Indels: 62
0.94 0.04 0.02
Matches are distributed among these distances:
759 9 0.00
760 506 0.18
761 24 0.01
762 358 0.12
763 360 0.12
764 9 0.00
765 172 0.06
766 2 0.00
767 2 0.00
769 1 0.00
770 554 0.19
771 157 0.05
772 165 0.06
773 216 0.07
774 335 0.12
776 1 0.00
777 3 0.00
779 8 0.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (763 bp):
TTAGTGAAATGTAAATTACTTACAATCTTCTATGTATATCTTTAGCCCGTCTGTCGAAACAATAA
ATATAAGAGAAACAAAATTAGTTTATTCTTCCTCGAAAATTCAAATTTTAATTTAACAATTTCGA
CAGAAGACTAGTGTTTTACCTGCAATTTGCTGTTTTCTAGTCTCCATTTTTAGGAACGGTATCTC
AACATTTTCTTCGAACTTTTTATCATAGAAAATCATAGCCTCCATGTAGACTACCAACAGTCTTA
GATCGCGATCATCCAAAACGATATGCTCACCAATAATACAAGTATCTCGTCCATGCCCAAATACA
TATTTTAAGGTATGGAAATGTATAAAAATGTCTTTATGATAACAAAAGGATATAAATAAAGAACA
TGCAGCTATTGTATTAGAAACATGCAGATGAAAAAATGTGATTCCTAACCAAATCATTGCGATAA
TTAGCAAAAGCAATATAATGTTATGCACGTTCATAACTTTTATTTAAATTTATTCATCAACTACA
ACCATTGCGATGTCAAAAAAAATATTTAAAATCAAAGTAAAGAATATGTTCGCATTACGATCAAA
ATTTTCATGCGTTTGTCGTCCTTTATCAATGTATCAGAGCCTTTACATATACATGGTAGTACCAA
TTAAAAGTTGCATAAGCTTACATCCATCAATTTAATATATAAATATCTGCACAATTTGAAATGAA
AACCAAATACCTTCTTCTGAACAAAGAAATGTATATCTTTGTATATCT
Found at i:16323 original size:29 final size:29
Alignment explanation
Indices: 16290--16421 Score: 129
Period size: 29 Copynumber: 4.5 Consensus size: 29
16280 TAGGATCACC
* * **
16290 CAGGGACATTATGGTCATTTTTGCATATT
1 CAGGGGCATTTTGGTCATTTCCGCATATT
* * *
16319 CAGGGGCATTTTTGTCATTTCTGCACATT
1 CAGGGGCATTTTGGTCATTTCCGCATATT
* * *
16348 CAGGGGGTATTCTAGTCATTTCCGCATATT
1 CA-GGGGCATTTTGGTCATTTCCGCATATT
* **
16378 CAGGGGCATTTTGGTCATTTTCGCATACC
1 CAGGGGCATTTTGGTCATTTCCGCATATT
*
16407 CAGGGGGATTTTGGT
1 CAGGGGCATTTTGGT
16422 TGTTTGTGCA
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
29 61 0.72
30 24 0.28
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (29 bp):
CAGGGGCATTTTGGTCATTTCCGCATATT
Found at i:26497 original size:2 final size:2
Alignment explanation
Indices: 26490--26527 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
26480 TCTTCTATTC
*
26490 CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
26528 AAACTTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:26694 original size:21 final size:19
Alignment explanation
Indices: 26652--26691 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
26642 GCCCTTTGGC
*
26652 CTTTTTTTTTCTTCTTCTT
1 CTTTTTTTATCTTCTTCTT
26671 CTTTTTTTATCTTC-TCTT
1 CTTTTTTTATCTTCTTCTT
26689 CTT
1 CTT
26692 CTTCTTTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (19 bp):
CTTTTTTTATCTTCTTCTT
Done.