Multiple sequence alignment - TraesCS6A01G390700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G390700 chr6A 100.000 2894 0 0 1 2894 605392812 605389919 0.000000e+00 5345.0
1 TraesCS6A01G390700 chr6D 93.180 2302 98 31 606 2894 459735963 459733708 0.000000e+00 3326.0
2 TraesCS6A01G390700 chr6D 82.985 1005 117 34 1877 2857 459715725 459714751 0.000000e+00 859.0
3 TraesCS6A01G390700 chr6D 91.317 357 21 5 113 466 459736403 459736054 2.020000e-131 479.0
4 TraesCS6A01G390700 chr6B 90.280 2068 93 44 133 2177 699019537 699017555 0.000000e+00 2606.0
5 TraesCS6A01G390700 chr2B 85.714 182 25 1 1110 1290 211614099 211614280 1.060000e-44 191.0
6 TraesCS6A01G390700 chr2A 82.075 212 34 4 1110 1318 146825246 146825036 8.240000e-41 178.0
7 TraesCS6A01G390700 chr1D 82.171 129 17 4 1120 1245 366475660 366475535 3.940000e-19 106.0
8 TraesCS6A01G390700 chr1A 82.171 129 17 4 1120 1245 465496876 465497001 3.940000e-19 106.0
9 TraesCS6A01G390700 chr1B 81.395 129 18 4 1120 1245 491232555 491232680 1.830000e-17 100.0
10 TraesCS6A01G390700 chr4D 90.625 64 6 0 1184 1247 479525271 479525334 5.140000e-13 86.1
11 TraesCS6A01G390700 chr4D 91.228 57 4 1 2831 2887 4000035 3999980 3.090000e-10 76.8
12 TraesCS6A01G390700 chr4D 91.228 57 4 1 2831 2887 4002742 4002687 3.090000e-10 76.8
13 TraesCS6A01G390700 chr4D 91.228 57 4 1 2831 2887 4005453 4005398 3.090000e-10 76.8
14 TraesCS6A01G390700 chr4D 91.228 57 4 1 2831 2887 4008162 4008107 3.090000e-10 76.8
15 TraesCS6A01G390700 chr4D 91.228 57 4 1 2831 2887 4010873 4010818 3.090000e-10 76.8
16 TraesCS6A01G390700 chr4D 91.228 57 4 1 2831 2887 4013585 4013530 3.090000e-10 76.8
17 TraesCS6A01G390700 chr4D 91.228 57 4 1 2831 2887 4021718 4021663 3.090000e-10 76.8
18 TraesCS6A01G390700 chr4D 91.228 57 4 1 2831 2887 4024429 4024374 3.090000e-10 76.8
19 TraesCS6A01G390700 chr4B 90.625 64 6 0 1184 1247 606755246 606755309 5.140000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G390700 chr6A 605389919 605392812 2893 True 5345.0 5345 100.0000 1 2894 1 chr6A.!!$R1 2893
1 TraesCS6A01G390700 chr6D 459733708 459736403 2695 True 1902.5 3326 92.2485 113 2894 2 chr6D.!!$R2 2781
2 TraesCS6A01G390700 chr6D 459714751 459715725 974 True 859.0 859 82.9850 1877 2857 1 chr6D.!!$R1 980
3 TraesCS6A01G390700 chr6B 699017555 699019537 1982 True 2606.0 2606 90.2800 133 2177 1 chr6B.!!$R1 2044

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
975 1039 0.171455 GACCAGACTACACCAGCTCG 59.829 60.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2391 2479 0.398318 CTTGCCTAGGCCTGGTATCC 59.602 60.0 30.81 0.44 41.09 2.59 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 8.699130 ACACATATCTCAATGTAAGATCTGACA 58.301 33.333 15.55 15.55 38.01 3.58
89 90 9.538508 CACATATCTCAATGTAAGATCTGACAA 57.461 33.333 17.11 0.34 38.01 3.18
104 105 9.486497 AAGATCTGACAAATATAGCATGTACTG 57.514 33.333 0.00 0.00 0.00 2.74
105 106 8.864087 AGATCTGACAAATATAGCATGTACTGA 58.136 33.333 0.00 0.00 0.00 3.41
106 107 9.138062 GATCTGACAAATATAGCATGTACTGAG 57.862 37.037 0.00 0.00 0.00 3.35
107 108 8.237811 TCTGACAAATATAGCATGTACTGAGA 57.762 34.615 0.00 0.00 0.00 3.27
108 109 8.138074 TCTGACAAATATAGCATGTACTGAGAC 58.862 37.037 0.00 0.00 0.00 3.36
109 110 7.781056 TGACAAATATAGCATGTACTGAGACA 58.219 34.615 0.00 0.00 0.00 3.41
110 111 8.424133 TGACAAATATAGCATGTACTGAGACAT 58.576 33.333 0.00 0.00 40.78 3.06
111 112 9.914131 GACAAATATAGCATGTACTGAGACATA 57.086 33.333 0.00 0.00 37.99 2.29
120 121 7.503902 AGCATGTACTGAGACATAACTGAGATA 59.496 37.037 0.00 0.00 37.99 1.98
122 123 9.623350 CATGTACTGAGACATAACTGAGATATG 57.377 37.037 8.02 8.02 37.99 1.78
123 124 7.652727 TGTACTGAGACATAACTGAGATATGC 58.347 38.462 9.33 3.59 34.75 3.14
148 149 7.202011 GCCAAGACTGATATTTCTAAGGGTCTA 60.202 40.741 0.00 0.00 33.30 2.59
249 250 3.179939 GACGAAGAGAACGCCGGC 61.180 66.667 19.07 19.07 0.00 6.13
250 251 3.628280 GACGAAGAGAACGCCGGCT 62.628 63.158 26.68 6.32 0.00 5.52
251 252 2.262471 GACGAAGAGAACGCCGGCTA 62.262 60.000 26.68 0.00 0.00 3.93
252 253 1.586564 CGAAGAGAACGCCGGCTAG 60.587 63.158 26.68 12.89 0.00 3.42
253 254 1.227002 GAAGAGAACGCCGGCTAGG 60.227 63.158 26.68 12.04 44.97 3.02
254 255 1.946475 GAAGAGAACGCCGGCTAGGT 61.946 60.000 26.68 12.81 43.70 3.08
255 256 1.946475 AAGAGAACGCCGGCTAGGTC 61.946 60.000 26.68 18.34 43.70 3.85
281 283 0.459063 CTACCGGCCGAGTGGTTTAC 60.459 60.000 30.73 0.00 39.70 2.01
313 317 2.056577 CACGGACGAAGAACCACTAAC 58.943 52.381 0.00 0.00 0.00 2.34
418 428 3.119245 ACTGATTGCAACTGCCAATCATC 60.119 43.478 20.06 0.00 42.11 2.92
421 431 2.728690 TGCAACTGCCAATCATCAAC 57.271 45.000 0.00 0.00 41.18 3.18
422 432 1.962100 TGCAACTGCCAATCATCAACA 59.038 42.857 0.00 0.00 41.18 3.33
443 453 2.046285 CCTGACAAATGGCGTCCCC 61.046 63.158 0.00 0.00 32.15 4.81
463 473 5.541868 TCCCCAAAAGAAGCATCAATAAACA 59.458 36.000 0.00 0.00 0.00 2.83
466 476 7.228308 CCCCAAAAGAAGCATCAATAAACAAAA 59.772 33.333 0.00 0.00 0.00 2.44
467 477 8.069574 CCCAAAAGAAGCATCAATAAACAAAAC 58.930 33.333 0.00 0.00 0.00 2.43
468 478 8.829612 CCAAAAGAAGCATCAATAAACAAAACT 58.170 29.630 0.00 0.00 0.00 2.66
469 479 9.853921 CAAAAGAAGCATCAATAAACAAAACTC 57.146 29.630 0.00 0.00 0.00 3.01
470 480 7.858052 AAGAAGCATCAATAAACAAAACTCG 57.142 32.000 0.00 0.00 0.00 4.18
471 481 6.970484 AGAAGCATCAATAAACAAAACTCGT 58.030 32.000 0.00 0.00 0.00 4.18
489 499 3.418047 TCGTTGGTCATCACTACTCAGA 58.582 45.455 0.00 0.00 0.00 3.27
519 530 2.489971 CGGGCTCTAACACACAAGAAA 58.510 47.619 0.00 0.00 0.00 2.52
536 547 9.559958 ACACAAGAAATAATGAATCAATTCGAC 57.440 29.630 0.00 0.00 39.62 4.20
568 579 3.039526 CCTCCCTCCCTCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
622 655 0.247974 CGTCGCTCGTCGTCCTTAAT 60.248 55.000 1.17 0.00 39.67 1.40
637 671 2.056577 CTTAATAATCCGTCGGTCGCC 58.943 52.381 11.88 0.00 38.35 5.54
791 833 5.118990 CCACATCAAACATCGAGATAACCT 58.881 41.667 0.00 0.00 0.00 3.50
794 836 5.977725 ACATCAAACATCGAGATAACCTACG 59.022 40.000 0.00 0.00 0.00 3.51
800 842 4.587684 ACATCGAGATAACCTACGGGATTT 59.412 41.667 0.00 0.00 36.25 2.17
801 843 4.579454 TCGAGATAACCTACGGGATTTG 57.421 45.455 0.00 0.00 36.25 2.32
802 844 3.057734 CGAGATAACCTACGGGATTTGC 58.942 50.000 0.00 0.00 36.25 3.68
935 977 3.382546 CCCTCCCTTAAATTCATGCACAG 59.617 47.826 0.00 0.00 0.00 3.66
963 1027 2.222027 CACCCAAAGTTCAGACCAGAC 58.778 52.381 0.00 0.00 0.00 3.51
964 1028 2.127708 ACCCAAAGTTCAGACCAGACT 58.872 47.619 0.00 0.00 0.00 3.24
965 1029 3.071023 CACCCAAAGTTCAGACCAGACTA 59.929 47.826 0.00 0.00 0.00 2.59
966 1030 3.071167 ACCCAAAGTTCAGACCAGACTAC 59.929 47.826 0.00 0.00 0.00 2.73
967 1031 3.071023 CCCAAAGTTCAGACCAGACTACA 59.929 47.826 0.00 0.00 0.00 2.74
968 1032 4.058817 CCAAAGTTCAGACCAGACTACAC 58.941 47.826 0.00 0.00 0.00 2.90
969 1033 4.058817 CAAAGTTCAGACCAGACTACACC 58.941 47.826 0.00 0.00 0.00 4.16
970 1034 2.958818 AGTTCAGACCAGACTACACCA 58.041 47.619 0.00 0.00 0.00 4.17
971 1035 2.894126 AGTTCAGACCAGACTACACCAG 59.106 50.000 0.00 0.00 0.00 4.00
972 1036 1.257743 TCAGACCAGACTACACCAGC 58.742 55.000 0.00 0.00 0.00 4.85
973 1037 1.203063 TCAGACCAGACTACACCAGCT 60.203 52.381 0.00 0.00 0.00 4.24
974 1038 1.203523 CAGACCAGACTACACCAGCTC 59.796 57.143 0.00 0.00 0.00 4.09
975 1039 0.171455 GACCAGACTACACCAGCTCG 59.829 60.000 0.00 0.00 0.00 5.03
976 1040 0.251209 ACCAGACTACACCAGCTCGA 60.251 55.000 0.00 0.00 0.00 4.04
977 1041 0.453793 CCAGACTACACCAGCTCGAG 59.546 60.000 8.45 8.45 0.00 4.04
978 1042 1.454201 CAGACTACACCAGCTCGAGA 58.546 55.000 18.75 0.00 0.00 4.04
979 1043 1.400142 CAGACTACACCAGCTCGAGAG 59.600 57.143 18.75 7.53 0.00 3.20
980 1044 1.279558 AGACTACACCAGCTCGAGAGA 59.720 52.381 18.75 0.00 39.12 3.10
1126 1193 2.029964 GCAAGTTCGTCGGGGTGA 59.970 61.111 0.00 0.00 0.00 4.02
1128 1195 1.663739 CAAGTTCGTCGGGGTGAGA 59.336 57.895 0.00 0.00 0.00 3.27
1431 1498 1.220749 GCCCGCTGTTACCATCAGA 59.779 57.895 0.00 0.00 35.20 3.27
1454 1521 1.160329 GCCACGGCAGCTAGTAATGG 61.160 60.000 2.36 0.00 41.49 3.16
1546 1613 4.567597 ACCACACCCCGACTCCCA 62.568 66.667 0.00 0.00 0.00 4.37
1547 1614 4.016706 CCACACCCCGACTCCCAC 62.017 72.222 0.00 0.00 0.00 4.61
1548 1615 4.016706 CACACCCCGACTCCCACC 62.017 72.222 0.00 0.00 0.00 4.61
1549 1616 4.567597 ACACCCCGACTCCCACCA 62.568 66.667 0.00 0.00 0.00 4.17
1635 1702 2.195139 GAGCATCAGCCATGGCCT 59.805 61.111 33.14 21.98 43.56 5.19
1644 1711 4.124351 CCATGGCCTGCAACGCTG 62.124 66.667 3.32 0.00 0.00 5.18
1731 1798 1.524482 GAGGCCGGAGAAGCAAGAT 59.476 57.895 5.05 0.00 0.00 2.40
1732 1799 0.531753 GAGGCCGGAGAAGCAAGATC 60.532 60.000 5.05 0.00 0.00 2.75
1733 1800 1.221840 GGCCGGAGAAGCAAGATCA 59.778 57.895 5.05 0.00 0.00 2.92
1808 1875 2.216750 GACGGGTTCGACATCGGGAA 62.217 60.000 0.73 0.00 40.29 3.97
1948 2022 1.838112 TTCTCGCTCGGTTTAGGGTA 58.162 50.000 0.00 0.00 0.00 3.69
2068 2154 6.205464 TGAGATGAGTGGATTTTGAAGTGTTC 59.795 38.462 0.00 0.00 0.00 3.18
2398 2486 1.079681 GTTGTCACGCCGGATACCA 60.080 57.895 5.05 0.00 0.00 3.25
2408 2496 1.837051 CGGATACCAGGCCTAGGCA 60.837 63.158 34.09 14.82 44.11 4.75
2412 2500 1.346068 GATACCAGGCCTAGGCAAGAG 59.654 57.143 34.09 21.05 44.11 2.85
2414 2502 0.980231 ACCAGGCCTAGGCAAGAGAG 60.980 60.000 34.09 17.98 44.11 3.20
2419 2507 1.970352 GCCTAGGCAAGAGAGCTGCT 61.970 60.000 29.33 0.00 41.49 4.24
2481 2572 8.049117 AGGTGAGATTAAGCAGACATAAATCAA 58.951 33.333 0.00 0.00 0.00 2.57
2482 2573 8.341173 GGTGAGATTAAGCAGACATAAATCAAG 58.659 37.037 0.00 0.00 0.00 3.02
2575 2666 1.229082 ACTAGTCGCTTCCCACCCA 60.229 57.895 0.00 0.00 0.00 4.51
2603 2694 6.825721 AGTCAAGCCTATTATTGGAAGTCTTG 59.174 38.462 0.00 1.45 0.00 3.02
2872 2970 2.225091 ACATGACCATCAAGCTTCCCAA 60.225 45.455 0.00 0.00 0.00 4.12
2873 2971 2.673775 TGACCATCAAGCTTCCCAAA 57.326 45.000 0.00 0.00 0.00 3.28
2880 2978 1.202927 TCAAGCTTCCCAAACCAGGAG 60.203 52.381 0.00 0.00 34.08 3.69
2888 2986 1.561542 CCCAAACCAGGAGTCATAGCT 59.438 52.381 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 8.699130 TGTCAGATCTTACATTGAGATATGTGT 58.301 33.333 5.61 0.00 41.36 3.72
63 64 9.538508 TTGTCAGATCTTACATTGAGATATGTG 57.461 33.333 10.46 0.00 41.36 3.21
78 79 9.486497 CAGTACATGCTATATTTGTCAGATCTT 57.514 33.333 0.00 0.00 0.00 2.40
79 80 8.864087 TCAGTACATGCTATATTTGTCAGATCT 58.136 33.333 0.00 0.00 0.00 2.75
80 81 9.138062 CTCAGTACATGCTATATTTGTCAGATC 57.862 37.037 0.00 0.00 0.00 2.75
81 82 8.864087 TCTCAGTACATGCTATATTTGTCAGAT 58.136 33.333 0.00 0.00 0.00 2.90
82 83 8.138074 GTCTCAGTACATGCTATATTTGTCAGA 58.862 37.037 0.00 0.00 0.00 3.27
83 84 7.922811 TGTCTCAGTACATGCTATATTTGTCAG 59.077 37.037 0.00 0.00 0.00 3.51
84 85 7.781056 TGTCTCAGTACATGCTATATTTGTCA 58.219 34.615 0.00 0.00 0.00 3.58
85 86 8.824159 ATGTCTCAGTACATGCTATATTTGTC 57.176 34.615 0.00 0.00 38.65 3.18
89 90 9.920133 CAGTTATGTCTCAGTACATGCTATATT 57.080 33.333 0.00 0.00 40.29 1.28
90 91 9.301897 TCAGTTATGTCTCAGTACATGCTATAT 57.698 33.333 0.00 0.00 40.29 0.86
91 92 8.691661 TCAGTTATGTCTCAGTACATGCTATA 57.308 34.615 0.00 0.00 40.29 1.31
92 93 7.503902 TCTCAGTTATGTCTCAGTACATGCTAT 59.496 37.037 0.00 0.00 40.29 2.97
93 94 6.828785 TCTCAGTTATGTCTCAGTACATGCTA 59.171 38.462 0.00 0.00 40.29 3.49
94 95 5.654209 TCTCAGTTATGTCTCAGTACATGCT 59.346 40.000 0.00 0.00 40.29 3.79
95 96 5.895928 TCTCAGTTATGTCTCAGTACATGC 58.104 41.667 0.00 0.00 40.29 4.06
96 97 9.623350 CATATCTCAGTTATGTCTCAGTACATG 57.377 37.037 0.00 0.00 40.29 3.21
97 98 8.303156 GCATATCTCAGTTATGTCTCAGTACAT 58.697 37.037 4.92 0.00 42.62 2.29
98 99 7.255625 GGCATATCTCAGTTATGTCTCAGTACA 60.256 40.741 4.92 0.00 30.69 2.90
99 100 7.087639 GGCATATCTCAGTTATGTCTCAGTAC 58.912 42.308 4.92 0.00 30.69 2.73
100 101 6.777580 TGGCATATCTCAGTTATGTCTCAGTA 59.222 38.462 8.49 0.00 33.74 2.74
101 102 5.600069 TGGCATATCTCAGTTATGTCTCAGT 59.400 40.000 8.49 0.00 33.74 3.41
102 103 6.094193 TGGCATATCTCAGTTATGTCTCAG 57.906 41.667 8.49 0.00 33.74 3.35
103 104 6.324770 TCTTGGCATATCTCAGTTATGTCTCA 59.675 38.462 8.49 1.87 33.74 3.27
104 105 6.644592 GTCTTGGCATATCTCAGTTATGTCTC 59.355 42.308 8.49 0.00 33.74 3.36
105 106 6.326064 AGTCTTGGCATATCTCAGTTATGTCT 59.674 38.462 8.49 0.00 33.74 3.41
106 107 6.423302 CAGTCTTGGCATATCTCAGTTATGTC 59.577 42.308 0.93 0.93 33.30 3.06
107 108 6.098838 TCAGTCTTGGCATATCTCAGTTATGT 59.901 38.462 4.92 0.00 31.13 2.29
108 109 6.519382 TCAGTCTTGGCATATCTCAGTTATG 58.481 40.000 0.00 0.00 0.00 1.90
109 110 6.737720 TCAGTCTTGGCATATCTCAGTTAT 57.262 37.500 0.00 0.00 0.00 1.89
110 111 6.737720 ATCAGTCTTGGCATATCTCAGTTA 57.262 37.500 0.00 0.00 0.00 2.24
111 112 5.627182 ATCAGTCTTGGCATATCTCAGTT 57.373 39.130 0.00 0.00 0.00 3.16
120 121 6.126361 ACCCTTAGAAATATCAGTCTTGGCAT 60.126 38.462 0.00 0.00 0.00 4.40
122 123 5.685728 ACCCTTAGAAATATCAGTCTTGGC 58.314 41.667 0.00 0.00 0.00 4.52
123 124 7.130681 AGACCCTTAGAAATATCAGTCTTGG 57.869 40.000 0.00 0.00 29.31 3.61
148 149 9.284968 GGTCAAACACCATATATTAAGTAGCAT 57.715 33.333 0.00 0.00 45.98 3.79
195 196 5.304778 GCATAAGGGAAACAAAAACCATGT 58.695 37.500 0.00 0.00 0.00 3.21
199 200 3.738791 CACGCATAAGGGAAACAAAAACC 59.261 43.478 0.00 0.00 0.00 3.27
249 250 2.161030 GCCGGTAGACCTATGACCTAG 58.839 57.143 1.90 0.00 0.00 3.02
250 251 1.202976 GGCCGGTAGACCTATGACCTA 60.203 57.143 1.90 0.00 0.00 3.08
251 252 0.469518 GGCCGGTAGACCTATGACCT 60.470 60.000 1.90 0.00 0.00 3.85
252 253 1.803366 CGGCCGGTAGACCTATGACC 61.803 65.000 20.10 0.00 0.00 4.02
253 254 0.820891 TCGGCCGGTAGACCTATGAC 60.821 60.000 27.83 0.00 0.00 3.06
254 255 0.536687 CTCGGCCGGTAGACCTATGA 60.537 60.000 27.83 0.00 0.00 2.15
255 256 0.822532 ACTCGGCCGGTAGACCTATG 60.823 60.000 27.83 5.33 0.00 2.23
281 283 1.198867 TCGTCCGTGCATTTCAAATGG 59.801 47.619 12.14 0.00 0.00 3.16
313 317 2.898840 ATGCATCTGCCCGCTTCG 60.899 61.111 0.00 0.00 41.18 3.79
418 428 1.600164 CGCCATTTGTCAGGTGTGTTG 60.600 52.381 0.00 0.00 0.00 3.33
421 431 2.330254 ACGCCATTTGTCAGGTGTG 58.670 52.632 0.00 0.00 46.20 3.82
422 432 4.898607 ACGCCATTTGTCAGGTGT 57.101 50.000 0.00 0.00 43.41 4.16
443 453 9.853921 GAGTTTTGTTTATTGATGCTTCTTTTG 57.146 29.630 0.88 0.00 0.00 2.44
463 473 4.957296 AGTAGTGATGACCAACGAGTTTT 58.043 39.130 0.00 0.00 0.00 2.43
466 476 3.154710 TGAGTAGTGATGACCAACGAGT 58.845 45.455 0.00 0.00 0.00 4.18
467 477 3.440522 TCTGAGTAGTGATGACCAACGAG 59.559 47.826 0.00 0.00 0.00 4.18
468 478 3.418047 TCTGAGTAGTGATGACCAACGA 58.582 45.455 0.00 0.00 0.00 3.85
469 479 3.850122 TCTGAGTAGTGATGACCAACG 57.150 47.619 0.00 0.00 0.00 4.10
470 480 5.140747 ACTTCTGAGTAGTGATGACCAAC 57.859 43.478 0.00 0.00 33.32 3.77
471 481 6.516739 CTACTTCTGAGTAGTGATGACCAA 57.483 41.667 1.72 0.00 46.74 3.67
489 499 1.601419 TTAGAGCCCGCGCACTACTT 61.601 55.000 8.75 0.00 37.82 2.24
519 530 6.905076 CGTTTTCCGTCGAATTGATTCATTAT 59.095 34.615 0.00 0.00 36.61 1.28
536 547 1.670083 GAGGGGGTCACGTTTTCCG 60.670 63.158 0.00 0.00 44.03 4.30
568 579 2.516227 AGAAGATGTGACGAGGAGGA 57.484 50.000 0.00 0.00 0.00 3.71
609 623 3.303329 CGACGGATTATTAAGGACGACGA 60.303 47.826 0.00 0.00 40.58 4.20
610 624 2.969306 CGACGGATTATTAAGGACGACG 59.031 50.000 0.00 0.00 34.09 5.12
611 625 3.243201 ACCGACGGATTATTAAGGACGAC 60.243 47.826 23.38 0.00 0.00 4.34
612 626 2.951642 ACCGACGGATTATTAAGGACGA 59.048 45.455 23.38 0.00 0.00 4.20
794 836 2.534903 GCGCTAGACGGCAAATCCC 61.535 63.158 0.00 0.00 43.93 3.85
802 844 1.389609 TTTCTAGGGGCGCTAGACGG 61.390 60.000 33.19 13.71 43.93 4.79
935 977 0.609406 GAACTTTGGGTGGAGGAGGC 60.609 60.000 0.00 0.00 0.00 4.70
963 1027 1.939934 CTCTCTCTCGAGCTGGTGTAG 59.060 57.143 7.81 0.00 37.19 2.74
964 1028 1.555533 TCTCTCTCTCGAGCTGGTGTA 59.444 52.381 7.81 0.00 37.19 2.90
965 1029 0.326595 TCTCTCTCTCGAGCTGGTGT 59.673 55.000 7.81 0.00 37.19 4.16
966 1030 1.679139 ATCTCTCTCTCGAGCTGGTG 58.321 55.000 7.81 0.00 37.19 4.17
967 1031 3.569194 TTATCTCTCTCTCGAGCTGGT 57.431 47.619 7.81 0.00 37.19 4.00
968 1032 6.757897 ATAATTATCTCTCTCTCGAGCTGG 57.242 41.667 7.81 0.00 37.19 4.85
988 1052 9.507329 GAACTGGAGCTCCATTGATTAATATAA 57.493 33.333 35.11 7.70 46.46 0.98
989 1053 8.103305 GGAACTGGAGCTCCATTGATTAATATA 58.897 37.037 35.11 8.17 46.46 0.86
990 1054 6.944862 GGAACTGGAGCTCCATTGATTAATAT 59.055 38.462 35.11 12.44 46.46 1.28
991 1055 6.126507 TGGAACTGGAGCTCCATTGATTAATA 60.127 38.462 35.11 12.93 46.46 0.98
1431 1498 4.135153 CTAGCTGCCGTGGCGAGT 62.135 66.667 6.37 0.00 45.51 4.18
1454 1521 3.350612 TGTTGTTACCGGCGCTGC 61.351 61.111 11.81 0.00 0.00 5.25
1539 1606 0.033011 TAGAGAGGCTGGTGGGAGTC 60.033 60.000 0.00 0.00 0.00 3.36
1546 1613 1.556911 CATGTGGTTAGAGAGGCTGGT 59.443 52.381 0.00 0.00 0.00 4.00
1547 1614 1.833630 TCATGTGGTTAGAGAGGCTGG 59.166 52.381 0.00 0.00 0.00 4.85
1548 1615 2.499289 AGTCATGTGGTTAGAGAGGCTG 59.501 50.000 0.00 0.00 0.00 4.85
1549 1616 2.826488 AGTCATGTGGTTAGAGAGGCT 58.174 47.619 0.00 0.00 0.00 4.58
1948 2022 1.755179 CTCCCGATGGCAGAAAATGT 58.245 50.000 0.00 0.00 0.00 2.71
2079 2165 6.316390 ACGGCACAAGATAAATTTCTCTTAGG 59.684 38.462 15.98 12.58 30.70 2.69
2180 2266 1.032014 GCATCCCCGTACCGTAACTA 58.968 55.000 0.00 0.00 0.00 2.24
2181 2267 1.818555 GCATCCCCGTACCGTAACT 59.181 57.895 0.00 0.00 0.00 2.24
2182 2268 1.589727 CGCATCCCCGTACCGTAAC 60.590 63.158 0.00 0.00 0.00 2.50
2183 2269 2.784356 CCGCATCCCCGTACCGTAA 61.784 63.158 0.00 0.00 0.00 3.18
2184 2270 3.218470 CCGCATCCCCGTACCGTA 61.218 66.667 0.00 0.00 0.00 4.02
2187 2273 3.222354 CTAGCCGCATCCCCGTACC 62.222 68.421 0.00 0.00 0.00 3.34
2188 2274 2.143594 CTCTAGCCGCATCCCCGTAC 62.144 65.000 0.00 0.00 0.00 3.67
2189 2275 1.901948 CTCTAGCCGCATCCCCGTA 60.902 63.158 0.00 0.00 0.00 4.02
2190 2276 3.227276 CTCTAGCCGCATCCCCGT 61.227 66.667 0.00 0.00 0.00 5.28
2191 2277 2.912542 TCTCTAGCCGCATCCCCG 60.913 66.667 0.00 0.00 0.00 5.73
2192 2278 1.403687 AAGTCTCTAGCCGCATCCCC 61.404 60.000 0.00 0.00 0.00 4.81
2224 2310 8.475331 AAAGAAACATACTAACGTCATTCGAT 57.525 30.769 0.00 0.00 42.86 3.59
2314 2401 8.236586 TGTAACCTCGATTGAAAAAGAATCATG 58.763 33.333 0.00 0.00 31.26 3.07
2346 2433 8.638565 GTGCTGAATTACATTAACACATTTCAC 58.361 33.333 0.00 0.00 0.00 3.18
2391 2479 0.398318 CTTGCCTAGGCCTGGTATCC 59.602 60.000 30.81 0.44 41.09 2.59
2398 2486 1.002792 AGCTCTCTTGCCTAGGCCT 59.997 57.895 30.81 15.55 41.09 5.19
2408 2496 2.741598 GCACGCAGCAGCTCTCTT 60.742 61.111 0.00 0.00 44.79 2.85
2419 2507 1.119684 ACCTGATGTATAGGCACGCA 58.880 50.000 0.00 0.00 38.96 5.24
2575 2666 7.345914 AGACTTCCAATAATAGGCTTGACTAGT 59.654 37.037 0.00 0.00 0.00 2.57
2619 2712 9.400638 CCTCTATTTTCTTATGTAGTCATCGAC 57.599 37.037 0.00 0.00 35.70 4.20
2674 2769 3.887621 AGTGAAGTATCCGCTTGCTAA 57.112 42.857 0.00 0.00 0.00 3.09
2872 2970 2.683768 CCCTAGCTATGACTCCTGGTT 58.316 52.381 0.00 0.00 0.00 3.67
2873 2971 1.133009 CCCCTAGCTATGACTCCTGGT 60.133 57.143 0.00 0.00 0.00 4.00


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.