Multiple sequence alignment - TraesCS1B01G361600

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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 TraesCS1B01G361600 chr1B 100.000 3485 0 0 1 3485 589975502 589978986 0.000000e+00 6436.0
1 TraesCS1B01G361600 chr1B 81.564 1432 221 23 1082 2475 590091037 590092463 0.000000e+00 1142.0
2 TraesCS1B01G361600 chr1A 93.726 2343 115 17 930 3257 533323258 533325583 0.000000e+00 3483.0
3 TraesCS1B01G361600 chr1A 80.949 1433 207 29 1082 2475 533409286 533410691 0.000000e+00 1074.0
4 TraesCS1B01G361600 chr1A 91.638 287 20 3 3133 3418 533325622 533325905 9.070000e-106 394.0
5 TraesCS1B01G361600 chr1A 93.333 60 2 1 881 940 533321467 533321524 1.720000e-13 87.9
6 TraesCS1B01G361600 chr1D 93.979 1827 71 15 885 2685 436112628 436114441 0.000000e+00 2728.0
7 TraesCS1B01G361600 chr1D 80.152 1184 193 23 1318 2475 436120172 436121339 0.000000e+00 846.0
8 TraesCS1B01G361600 chr1D 89.691 388 27 3 2880 3261 436114636 436115016 1.880000e-132 483.0
9 TraesCS1B01G361600 chr1D 82.986 288 22 16 3133 3419 436115051 436115312 5.820000e-58 235.0
10 TraesCS1B01G361600 chr7A 96.000 775 30 1 5 778 540868503 540869277 0.000000e+00 1258.0
11 TraesCS1B01G361600 chr3B 95.536 784 33 2 5 786 780862901 780863684 0.000000e+00 1253.0
12 TraesCS1B01G361600 chr3B 95.385 780 35 1 5 783 672958255 672957476 0.000000e+00 1240.0
13 TraesCS1B01G361600 chr3B 95.128 780 37 1 5 783 429581608 429580829 0.000000e+00 1229.0
14 TraesCS1B01G361600 chr3B 84.580 441 68 0 2008 2448 24901736 24901296 4.130000e-119 438.0
15 TraesCS1B01G361600 chr6B 95.958 767 30 1 5 770 719752412 719751646 0.000000e+00 1243.0
16 TraesCS1B01G361600 chr5B 95.844 770 30 2 5 773 614364843 614364075 0.000000e+00 1243.0
17 TraesCS1B01G361600 chrUn 95.367 777 34 2 5 780 371064520 371065295 0.000000e+00 1234.0
18 TraesCS1B01G361600 chrUn 95.238 777 35 2 5 780 43163354 43164129 0.000000e+00 1229.0
19 TraesCS1B01G361600 chrUn 95.238 777 35 2 5 780 43167100 43167875 0.000000e+00 1229.0
20 TraesCS1B01G361600 chr6D 79.671 1397 244 22 1100 2461 417775873 417777264 0.000000e+00 970.0
21 TraesCS1B01G361600 chr6D 79.679 935 163 16 1100 2016 417752057 417751132 0.000000e+00 649.0
22 TraesCS1B01G361600 chr7B 77.809 1442 250 47 1079 2474 59078727 59080144 0.000000e+00 826.0
23 TraesCS1B01G361600 chr7D 80.085 944 167 13 1551 2474 101780794 101779852 0.000000e+00 682.0
24 TraesCS1B01G361600 chr3D 79.728 957 170 16 1081 2016 17343131 17342178 0.000000e+00 671.0
25 TraesCS1B01G361600 chr3D 77.322 926 183 17 1080 1990 17698280 17699193 3.990000e-144 521.0
26 TraesCS1B01G361600 chr3D 83.559 444 67 4 2008 2448 17342156 17341716 9.000000e-111 411.0
27 TraesCS1B01G361600 chr3D 82.424 165 29 0 2084 2248 387709335 387709171 1.010000e-30 145.0
28 TraesCS1B01G361600 chr6A 79.325 948 169 16 1087 2016 560192871 560191933 1.050000e-179 640.0


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 TraesCS1B01G361600 chr1B 589975502 589978986 3484 False 6436.000000 6436 100.000000 1 3485 1 chr1B.!!$F1 3484
1 TraesCS1B01G361600 chr1B 590091037 590092463 1426 False 1142.000000 1142 81.564000 1082 2475 1 chr1B.!!$F2 1393
2 TraesCS1B01G361600 chr1A 533321467 533325905 4438 False 1321.633333 3483 92.899000 881 3418 3 chr1A.!!$F2 2537
3 TraesCS1B01G361600 chr1A 533409286 533410691 1405 False 1074.000000 1074 80.949000 1082 2475 1 chr1A.!!$F1 1393
4 TraesCS1B01G361600 chr1D 436112628 436115312 2684 False 1148.666667 2728 88.885333 885 3419 3 chr1D.!!$F2 2534
5 TraesCS1B01G361600 chr1D 436120172 436121339 1167 False 846.000000 846 80.152000 1318 2475 1 chr1D.!!$F1 1157
6 TraesCS1B01G361600 chr7A 540868503 540869277 774 False 1258.000000 1258 96.000000 5 778 1 chr7A.!!$F1 773
7 TraesCS1B01G361600 chr3B 780862901 780863684 783 False 1253.000000 1253 95.536000 5 786 1 chr3B.!!$F1 781
8 TraesCS1B01G361600 chr3B 672957476 672958255 779 True 1240.000000 1240 95.385000 5 783 1 chr3B.!!$R3 778
9 TraesCS1B01G361600 chr3B 429580829 429581608 779 True 1229.000000 1229 95.128000 5 783 1 chr3B.!!$R2 778
10 TraesCS1B01G361600 chr6B 719751646 719752412 766 True 1243.000000 1243 95.958000 5 770 1 chr6B.!!$R1 765
11 TraesCS1B01G361600 chr5B 614364075 614364843 768 True 1243.000000 1243 95.844000 5 773 1 chr5B.!!$R1 768
12 TraesCS1B01G361600 chrUn 371064520 371065295 775 False 1234.000000 1234 95.367000 5 780 1 chrUn.!!$F1 775
13 TraesCS1B01G361600 chrUn 43163354 43167875 4521 False 1229.000000 1229 95.238000 5 780 2 chrUn.!!$F2 775
14 TraesCS1B01G361600 chr6D 417775873 417777264 1391 False 970.000000 970 79.671000 1100 2461 1 chr6D.!!$F1 1361
15 TraesCS1B01G361600 chr6D 417751132 417752057 925 True 649.000000 649 79.679000 1100 2016 1 chr6D.!!$R1 916
16 TraesCS1B01G361600 chr7B 59078727 59080144 1417 False 826.000000 826 77.809000 1079 2474 1 chr7B.!!$F1 1395
17 TraesCS1B01G361600 chr7D 101779852 101780794 942 True 682.000000 682 80.085000 1551 2474 1 chr7D.!!$R1 923
18 TraesCS1B01G361600 chr3D 17341716 17343131 1415 True 541.000000 671 81.643500 1081 2448 2 chr3D.!!$R2 1367
19 TraesCS1B01G361600 chr3D 17698280 17699193 913 False 521.000000 521 77.322000 1080 1990 1 chr3D.!!$F1 910
20 TraesCS1B01G361600 chr6A 560191933 560192871 938 True 640.000000 640 79.325000 1087 2016 1 chr6A.!!$R1 929

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
808 4556 0.096976 CGCTTTATCTGCCCACAACG 59.903 55.0 0.0 0.0 0.0 4.10 F
809 4557 0.451783 GCTTTATCTGCCCACAACGG 59.548 55.0 0.0 0.0 0.0 4.44 F
1649 7222 0.467290 GAGGACCCTGAGAGCGAGAT 60.467 60.0 0.0 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 7469 0.667792 AGAGGAAAACGACGCTGCTC 60.668 55.0 0.00 0.0 0.00 4.26 R
1879 7470 0.946221 CAGAGGAAAACGACGCTGCT 60.946 55.0 0.00 0.0 0.00 4.24 R
2875 8523 0.034337 TAGTTCCAACCACGTCTGGC 59.966 55.0 3.43 0.0 42.08 4.85 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
61 62 3.210012 AACGCCCATCACCTGCCTT 62.210 57.895 0.00 0.00 0.00 4.35
95 96 1.336755 GCAGCCACCGAAGAAAAGAAA 59.663 47.619 0.00 0.00 0.00 2.52
114 115 2.864885 AGATGGATCACCTCCTCACT 57.135 50.000 0.00 0.00 45.21 3.41
290 291 0.609151 TCGCGGAAGGAAACCATACA 59.391 50.000 6.13 0.00 0.00 2.29
324 325 0.667993 CACGAACCCAGCACATGTTT 59.332 50.000 0.00 0.00 0.00 2.83
507 4254 4.918810 ACAGACTGGTTTCCAAATTCAC 57.081 40.909 7.51 0.00 30.80 3.18
531 4278 0.261696 AACCATAGGACCAATGGCCC 59.738 55.000 0.00 0.00 46.63 5.80
680 4427 2.989824 CCCTCACCACCGACGACT 60.990 66.667 0.00 0.00 0.00 4.18
735 4482 0.539051 CGCTGGAAGATTGGGTCTCT 59.461 55.000 0.00 0.00 35.67 3.10
783 4531 2.027100 AGGACAGGAGGAAAACGATTCC 60.027 50.000 14.33 14.33 38.86 3.01
784 4532 2.000447 GACAGGAGGAAAACGATTCCG 59.000 52.381 15.61 7.21 43.23 4.30
794 4542 4.496670 CGATTCCGTCTCCGCTTT 57.503 55.556 0.00 0.00 0.00 3.51
795 4543 3.635433 CGATTCCGTCTCCGCTTTA 57.365 52.632 0.00 0.00 0.00 1.85
796 4544 2.135664 CGATTCCGTCTCCGCTTTAT 57.864 50.000 0.00 0.00 0.00 1.40
797 4545 2.052157 CGATTCCGTCTCCGCTTTATC 58.948 52.381 0.00 0.00 0.00 1.75
798 4546 2.287668 CGATTCCGTCTCCGCTTTATCT 60.288 50.000 0.00 0.00 0.00 1.98
799 4547 2.579207 TTCCGTCTCCGCTTTATCTG 57.421 50.000 0.00 0.00 0.00 2.90
800 4548 0.102481 TCCGTCTCCGCTTTATCTGC 59.898 55.000 0.00 0.00 0.00 4.26
801 4549 0.876342 CCGTCTCCGCTTTATCTGCC 60.876 60.000 0.00 0.00 0.00 4.85
802 4550 0.876342 CGTCTCCGCTTTATCTGCCC 60.876 60.000 0.00 0.00 0.00 5.36
803 4551 0.178068 GTCTCCGCTTTATCTGCCCA 59.822 55.000 0.00 0.00 0.00 5.36
804 4552 0.178068 TCTCCGCTTTATCTGCCCAC 59.822 55.000 0.00 0.00 0.00 4.61
805 4553 0.107703 CTCCGCTTTATCTGCCCACA 60.108 55.000 0.00 0.00 0.00 4.17
806 4554 0.326595 TCCGCTTTATCTGCCCACAA 59.673 50.000 0.00 0.00 0.00 3.33
807 4555 0.451783 CCGCTTTATCTGCCCACAAC 59.548 55.000 0.00 0.00 0.00 3.32
808 4556 0.096976 CGCTTTATCTGCCCACAACG 59.903 55.000 0.00 0.00 0.00 4.10
809 4557 0.451783 GCTTTATCTGCCCACAACGG 59.548 55.000 0.00 0.00 0.00 4.44
819 4567 2.325583 CCCACAACGGCAGTATATGT 57.674 50.000 0.00 0.00 0.00 2.29
820 4568 3.462483 CCCACAACGGCAGTATATGTA 57.538 47.619 0.00 0.00 0.00 2.29
821 4569 3.799366 CCCACAACGGCAGTATATGTAA 58.201 45.455 0.00 0.00 0.00 2.41
822 4570 4.193090 CCCACAACGGCAGTATATGTAAA 58.807 43.478 0.00 0.00 0.00 2.01
823 4571 4.636648 CCCACAACGGCAGTATATGTAAAA 59.363 41.667 0.00 0.00 0.00 1.52
824 4572 5.448089 CCCACAACGGCAGTATATGTAAAAC 60.448 44.000 0.00 0.00 0.00 2.43
825 4573 5.122554 CCACAACGGCAGTATATGTAAAACA 59.877 40.000 0.00 0.00 0.00 2.83
826 4574 6.183360 CCACAACGGCAGTATATGTAAAACAT 60.183 38.462 0.00 0.00 42.35 2.71
827 4575 7.011576 CCACAACGGCAGTATATGTAAAACATA 59.988 37.037 2.45 2.45 44.29 2.29
828 4576 8.391859 CACAACGGCAGTATATGTAAAACATAA 58.608 33.333 4.02 0.00 43.50 1.90
829 4577 9.116067 ACAACGGCAGTATATGTAAAACATAAT 57.884 29.630 4.02 0.00 43.50 1.28
830 4578 9.944663 CAACGGCAGTATATGTAAAACATAATT 57.055 29.630 4.02 0.00 43.50 1.40
832 4580 9.332502 ACGGCAGTATATGTAAAACATAATTCA 57.667 29.630 4.02 0.00 43.50 2.57
843 4591 9.486497 TGTAAAACATAATTCATGCATTGTTGT 57.514 25.926 11.80 9.51 38.29 3.32
844 4592 9.743937 GTAAAACATAATTCATGCATTGTTGTG 57.256 29.630 11.80 10.43 38.29 3.33
845 4593 7.966246 AAACATAATTCATGCATTGTTGTGT 57.034 28.000 11.80 10.94 38.29 3.72
846 4594 6.954616 ACATAATTCATGCATTGTTGTGTG 57.045 33.333 13.47 4.78 38.29 3.82
847 4595 6.457355 ACATAATTCATGCATTGTTGTGTGT 58.543 32.000 13.47 5.27 38.29 3.72
848 4596 7.600960 ACATAATTCATGCATTGTTGTGTGTA 58.399 30.769 13.47 0.00 38.29 2.90
849 4597 8.252417 ACATAATTCATGCATTGTTGTGTGTAT 58.748 29.630 13.47 0.00 38.29 2.29
850 4598 9.089601 CATAATTCATGCATTGTTGTGTGTATT 57.910 29.630 0.00 0.00 0.00 1.89
851 4599 7.966246 AATTCATGCATTGTTGTGTGTATTT 57.034 28.000 0.00 0.00 0.00 1.40
852 4600 7.966246 ATTCATGCATTGTTGTGTGTATTTT 57.034 28.000 0.00 0.00 0.00 1.82
853 4601 9.486497 AATTCATGCATTGTTGTGTGTATTTTA 57.514 25.926 0.00 0.00 0.00 1.52
854 4602 8.877808 TTCATGCATTGTTGTGTGTATTTTAA 57.122 26.923 0.00 0.00 0.00 1.52
855 4603 8.518151 TCATGCATTGTTGTGTGTATTTTAAG 57.482 30.769 0.00 0.00 0.00 1.85
856 4604 8.355913 TCATGCATTGTTGTGTGTATTTTAAGA 58.644 29.630 0.00 0.00 0.00 2.10
857 4605 7.922505 TGCATTGTTGTGTGTATTTTAAGAC 57.077 32.000 0.00 0.00 0.00 3.01
858 4606 7.484140 TGCATTGTTGTGTGTATTTTAAGACA 58.516 30.769 0.00 0.00 0.00 3.41
859 4607 7.976175 TGCATTGTTGTGTGTATTTTAAGACAA 59.024 29.630 0.00 0.00 31.17 3.18
860 4608 8.977505 GCATTGTTGTGTGTATTTTAAGACAAT 58.022 29.630 0.00 0.00 36.09 2.71
990 6482 2.724977 TTGCTCCGTCACTGAACTAG 57.275 50.000 0.00 0.00 0.00 2.57
1002 6494 5.795939 GTCACTGAACTAGTACGAGACAATG 59.204 44.000 10.22 9.33 37.60 2.82
1387 6915 1.204941 GCGACTTCCTCTGCTCCTTTA 59.795 52.381 0.00 0.00 0.00 1.85
1647 7220 2.477176 CGAGGACCCTGAGAGCGAG 61.477 68.421 0.00 0.00 0.00 5.03
1649 7222 0.467290 GAGGACCCTGAGAGCGAGAT 60.467 60.000 0.00 0.00 0.00 2.75
1890 7481 4.421479 CCGGAGAGCAGCGTCGTT 62.421 66.667 0.00 0.00 0.00 3.85
2017 7647 1.461091 TTTCAGCGACGACCAGGACT 61.461 55.000 0.00 0.00 0.00 3.85
2042 7672 1.446272 CTCTCTTGCCGAACGGGTC 60.446 63.158 15.01 0.00 38.44 4.46
2046 7676 2.604079 TTGCCGAACGGGTCCCTA 60.604 61.111 15.01 0.00 38.44 3.53
2386 8016 2.972505 CACACAAGGAAGGCGCGT 60.973 61.111 8.43 0.00 0.00 6.01
2451 8081 1.445582 GTTCTTGGCCGACGTCGAT 60.446 57.895 37.65 0.00 43.02 3.59
2649 8282 6.765989 CGATTTTATGTGGAGATTCCTGGTTA 59.234 38.462 0.00 0.00 37.46 2.85
2657 8290 4.522789 TGGAGATTCCTGGTTACTTTTTGC 59.477 41.667 0.00 0.00 37.46 3.68
2658 8291 4.379499 GGAGATTCCTGGTTACTTTTTGCG 60.379 45.833 0.00 0.00 32.53 4.85
2659 8292 4.142038 AGATTCCTGGTTACTTTTTGCGT 58.858 39.130 0.00 0.00 0.00 5.24
2660 8293 3.701532 TTCCTGGTTACTTTTTGCGTG 57.298 42.857 0.00 0.00 0.00 5.34
2662 8295 1.679153 CCTGGTTACTTTTTGCGTGGT 59.321 47.619 0.00 0.00 0.00 4.16
2664 8297 3.112580 CTGGTTACTTTTTGCGTGGTTG 58.887 45.455 0.00 0.00 0.00 3.77
2666 8299 2.099427 GGTTACTTTTTGCGTGGTTGGA 59.901 45.455 0.00 0.00 0.00 3.53
2685 8318 5.089970 TGGAGAGATTCCTGTTGTGTATG 57.910 43.478 0.00 0.00 46.92 2.39
2686 8319 4.532126 TGGAGAGATTCCTGTTGTGTATGT 59.468 41.667 0.00 0.00 46.92 2.29
2746 8394 6.016610 TGTTTTCATCGGGGTTTTCTTCTTAG 60.017 38.462 0.00 0.00 0.00 2.18
2769 8417 7.417496 AGAACTCCAACAACGATTAAGTTAC 57.583 36.000 0.00 0.00 32.35 2.50
2776 8424 7.601886 TCCAACAACGATTAAGTTACCGAATAA 59.398 33.333 9.92 0.00 32.35 1.40
2819 8467 6.938507 AGAGCTGCAAATTTCATTTATTGGA 58.061 32.000 1.02 0.00 0.00 3.53
2851 8499 9.800433 AATCATTACGTCATGCAAAAATATGAA 57.200 25.926 4.81 0.00 35.29 2.57
2861 8509 6.040209 TGCAAAAATATGAAAGCACATCCT 57.960 33.333 0.00 0.00 0.00 3.24
2863 8511 6.935771 TGCAAAAATATGAAAGCACATCCTTT 59.064 30.769 0.00 0.00 37.73 3.11
2864 8512 8.093307 TGCAAAAATATGAAAGCACATCCTTTA 58.907 29.630 0.00 0.00 35.31 1.85
2892 8621 0.889186 ATGCCAGACGTGGTTGGAAC 60.889 55.000 13.03 0.00 46.96 3.62
2906 8635 6.696148 CGTGGTTGGAACTATCTATCTGTTAC 59.304 42.308 0.00 0.00 0.00 2.50
3034 8770 1.022735 AACGATCTATGACGCGTCCT 58.977 50.000 34.34 27.40 35.74 3.85
3037 8773 2.159282 ACGATCTATGACGCGTCCTTTT 60.159 45.455 34.34 19.22 30.15 2.27
3058 8794 0.105039 GACGCCCGGATCTCAAAGAT 59.895 55.000 0.73 0.00 37.73 2.40
3063 8799 2.486191 GCCCGGATCTCAAAGATGTGAT 60.486 50.000 0.73 0.00 41.26 3.06
3068 8804 5.407691 CCGGATCTCAAAGATGTGATACATG 59.592 44.000 0.00 0.00 39.27 3.21
3103 8839 1.875514 CATACCATCGTTCCCATGCAG 59.124 52.381 0.00 0.00 0.00 4.41
3104 8840 1.199615 TACCATCGTTCCCATGCAGA 58.800 50.000 0.00 0.00 0.00 4.26
3105 8841 0.548031 ACCATCGTTCCCATGCAGAT 59.452 50.000 0.00 0.00 0.00 2.90
3106 8842 0.949397 CCATCGTTCCCATGCAGATG 59.051 55.000 0.00 0.00 38.61 2.90
3107 8843 0.309922 CATCGTTCCCATGCAGATGC 59.690 55.000 0.00 0.00 42.50 3.91
3201 8937 2.700897 ACACTCCCCTATGATGTAGCAC 59.299 50.000 0.00 0.00 0.00 4.40
3213 8949 7.384932 CCTATGATGTAGCACGACAATTATTGA 59.615 37.037 12.28 0.00 31.83 2.57
3215 8951 7.371126 TGATGTAGCACGACAATTATTGAAA 57.629 32.000 12.28 0.00 31.83 2.69
3238 8974 6.764308 AGCATATATGACAACTTTTGTGCT 57.236 33.333 17.10 0.00 45.52 4.40
3257 9154 2.289002 GCTTAGCATGTCAATTCTCCCG 59.711 50.000 0.00 0.00 0.00 5.14
3261 9158 4.000331 AGCATGTCAATTCTCCCGATAG 58.000 45.455 0.00 0.00 0.00 2.08
3289 9324 3.900601 TGGCAATTTCTAAACATGTGGGT 59.099 39.130 0.00 0.00 0.00 4.51
3295 9330 7.655732 GCAATTTCTAAACATGTGGGTAACTTT 59.344 33.333 0.00 0.00 0.00 2.66
3312 9347 5.594199 AACTTTCCCCTTTTCTTAGCCTA 57.406 39.130 0.00 0.00 0.00 3.93
3325 9360 5.712084 TCTTAGCCTACCAGTTCTCTCTA 57.288 43.478 0.00 0.00 0.00 2.43
3328 9363 3.626930 AGCCTACCAGTTCTCTCTACTG 58.373 50.000 0.00 0.00 42.06 2.74
3412 9448 6.670695 TTCTATAGCATGGCTCAACATAGA 57.329 37.500 0.00 0.00 40.44 1.98
3419 9455 4.500375 GCATGGCTCAACATAGAAATTCCC 60.500 45.833 0.00 0.00 0.00 3.97
3420 9456 3.278574 TGGCTCAACATAGAAATTCCCG 58.721 45.455 0.00 0.00 0.00 5.14
3421 9457 2.618709 GGCTCAACATAGAAATTCCCGG 59.381 50.000 0.00 0.00 0.00 5.73
3422 9458 2.033424 GCTCAACATAGAAATTCCCGGC 59.967 50.000 0.00 0.00 0.00 6.13
3423 9459 3.545703 CTCAACATAGAAATTCCCGGCT 58.454 45.455 0.00 0.00 0.00 5.52
3424 9460 3.947834 CTCAACATAGAAATTCCCGGCTT 59.052 43.478 0.00 0.00 0.00 4.35
3425 9461 3.945285 TCAACATAGAAATTCCCGGCTTC 59.055 43.478 0.00 0.00 0.00 3.86
3426 9462 3.644966 ACATAGAAATTCCCGGCTTCA 57.355 42.857 0.00 0.00 0.00 3.02
3427 9463 4.170468 ACATAGAAATTCCCGGCTTCAT 57.830 40.909 0.00 0.00 0.00 2.57
3428 9464 4.536765 ACATAGAAATTCCCGGCTTCATT 58.463 39.130 0.00 0.00 0.00 2.57
3429 9465 4.580580 ACATAGAAATTCCCGGCTTCATTC 59.419 41.667 0.00 0.00 0.00 2.67
3430 9466 2.379005 AGAAATTCCCGGCTTCATTCC 58.621 47.619 0.00 0.00 0.00 3.01
3431 9467 1.409064 GAAATTCCCGGCTTCATTCCC 59.591 52.381 0.00 0.00 0.00 3.97
3432 9468 0.631212 AATTCCCGGCTTCATTCCCT 59.369 50.000 0.00 0.00 0.00 4.20
3433 9469 1.518367 ATTCCCGGCTTCATTCCCTA 58.482 50.000 0.00 0.00 0.00 3.53
3434 9470 0.544697 TTCCCGGCTTCATTCCCTAC 59.455 55.000 0.00 0.00 0.00 3.18
3435 9471 0.326238 TCCCGGCTTCATTCCCTACT 60.326 55.000 0.00 0.00 0.00 2.57
3436 9472 0.106894 CCCGGCTTCATTCCCTACTC 59.893 60.000 0.00 0.00 0.00 2.59
3437 9473 0.249489 CCGGCTTCATTCCCTACTCG 60.249 60.000 0.00 0.00 0.00 4.18
3438 9474 0.460311 CGGCTTCATTCCCTACTCGT 59.540 55.000 0.00 0.00 0.00 4.18
3439 9475 1.536284 CGGCTTCATTCCCTACTCGTC 60.536 57.143 0.00 0.00 0.00 4.20
3440 9476 1.480954 GGCTTCATTCCCTACTCGTCA 59.519 52.381 0.00 0.00 0.00 4.35
3441 9477 2.103263 GGCTTCATTCCCTACTCGTCAT 59.897 50.000 0.00 0.00 0.00 3.06
3442 9478 3.321111 GGCTTCATTCCCTACTCGTCATA 59.679 47.826 0.00 0.00 0.00 2.15
3443 9479 4.551388 GCTTCATTCCCTACTCGTCATAG 58.449 47.826 0.00 0.00 0.00 2.23
3444 9480 4.038162 GCTTCATTCCCTACTCGTCATAGT 59.962 45.833 0.00 0.00 0.00 2.12
3445 9481 5.452077 GCTTCATTCCCTACTCGTCATAGTT 60.452 44.000 0.00 0.00 0.00 2.24
3446 9482 6.238953 GCTTCATTCCCTACTCGTCATAGTTA 60.239 42.308 0.00 0.00 0.00 2.24
3447 9483 7.524038 GCTTCATTCCCTACTCGTCATAGTTAT 60.524 40.741 0.00 0.00 0.00 1.89
3448 9484 8.929260 TTCATTCCCTACTCGTCATAGTTATA 57.071 34.615 0.00 0.00 0.00 0.98
3449 9485 9.529823 TTCATTCCCTACTCGTCATAGTTATAT 57.470 33.333 0.00 0.00 0.00 0.86
3450 9486 9.175312 TCATTCCCTACTCGTCATAGTTATATC 57.825 37.037 0.00 0.00 0.00 1.63
3451 9487 9.179909 CATTCCCTACTCGTCATAGTTATATCT 57.820 37.037 0.00 0.00 0.00 1.98
3452 9488 8.789825 TTCCCTACTCGTCATAGTTATATCTC 57.210 38.462 0.00 0.00 0.00 2.75
3453 9489 7.337167 TCCCTACTCGTCATAGTTATATCTCC 58.663 42.308 0.00 0.00 0.00 3.71
3454 9490 7.182387 TCCCTACTCGTCATAGTTATATCTCCT 59.818 40.741 0.00 0.00 0.00 3.69
3455 9491 7.496591 CCCTACTCGTCATAGTTATATCTCCTC 59.503 44.444 0.00 0.00 0.00 3.71
3456 9492 6.971527 ACTCGTCATAGTTATATCTCCTCG 57.028 41.667 0.00 0.00 0.00 4.63
3457 9493 5.875910 ACTCGTCATAGTTATATCTCCTCGG 59.124 44.000 0.00 0.00 0.00 4.63
3458 9494 5.183969 TCGTCATAGTTATATCTCCTCGGG 58.816 45.833 0.00 0.00 0.00 5.14
3459 9495 4.942483 CGTCATAGTTATATCTCCTCGGGT 59.058 45.833 0.00 0.00 0.00 5.28
3460 9496 6.070596 TCGTCATAGTTATATCTCCTCGGGTA 60.071 42.308 0.00 0.00 0.00 3.69
3461 9497 6.036953 CGTCATAGTTATATCTCCTCGGGTAC 59.963 46.154 0.00 0.00 0.00 3.34
3475 9511 4.109675 GTACCACCCATGCCGCCT 62.110 66.667 0.00 0.00 0.00 5.52
3476 9512 3.792736 TACCACCCATGCCGCCTC 61.793 66.667 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.205464 TGTTCTGCTATCTTTTCAGTTTGAGG 59.795 38.462 0.00 0.00 0.00 3.86
2 3 7.663081 AGATGTTCTGCTATCTTTTCAGTTTGA 59.337 33.333 0.00 0.00 29.64 2.69
3 4 7.814642 AGATGTTCTGCTATCTTTTCAGTTTG 58.185 34.615 0.00 0.00 29.64 2.93
61 62 4.662961 CTGCTGTCGTGGTGCCGA 62.663 66.667 0.00 0.00 33.79 5.54
290 291 1.745115 CGTGGTTCGTGGATGGCAT 60.745 57.895 0.00 0.00 34.52 4.40
398 399 1.598130 GACGGTGTTTGCTCCAGCT 60.598 57.895 0.00 0.00 42.66 4.24
507 4254 0.933700 ATTGGTCCTATGGTTGGGGG 59.066 55.000 0.00 0.00 0.00 5.40
531 4278 2.497675 TCTTCGGATCCTTCCTTGACAG 59.502 50.000 10.75 0.24 40.17 3.51
710 4457 1.448540 CAATCTTCCAGCGCCGTCT 60.449 57.895 2.29 0.00 0.00 4.18
735 4482 3.078836 AACCCTAGCCGCCGCTAA 61.079 61.111 8.14 0.00 46.89 3.09
784 4532 0.178068 TGGGCAGATAAAGCGGAGAC 59.822 55.000 0.00 0.00 0.00 3.36
785 4533 0.178068 GTGGGCAGATAAAGCGGAGA 59.822 55.000 0.00 0.00 0.00 3.71
786 4534 0.107703 TGTGGGCAGATAAAGCGGAG 60.108 55.000 0.00 0.00 0.00 4.63
787 4535 0.326595 TTGTGGGCAGATAAAGCGGA 59.673 50.000 0.00 0.00 0.00 5.54
788 4536 0.451783 GTTGTGGGCAGATAAAGCGG 59.548 55.000 0.00 0.00 0.00 5.52
789 4537 0.096976 CGTTGTGGGCAGATAAAGCG 59.903 55.000 0.00 0.00 0.00 4.68
790 4538 0.451783 CCGTTGTGGGCAGATAAAGC 59.548 55.000 0.00 0.00 0.00 3.51
800 4548 2.325583 ACATATACTGCCGTTGTGGG 57.674 50.000 0.00 0.00 38.63 4.61
801 4549 5.122554 TGTTTTACATATACTGCCGTTGTGG 59.877 40.000 0.00 0.00 42.50 4.17
802 4550 6.171932 TGTTTTACATATACTGCCGTTGTG 57.828 37.500 0.00 0.00 0.00 3.33
803 4551 6.995511 ATGTTTTACATATACTGCCGTTGT 57.004 33.333 0.00 0.00 36.99 3.32
804 4552 9.944663 AATTATGTTTTACATATACTGCCGTTG 57.055 29.630 0.77 0.00 40.41 4.10
806 4554 9.332502 TGAATTATGTTTTACATATACTGCCGT 57.667 29.630 0.77 0.00 40.41 5.68
817 4565 9.486497 ACAACAATGCATGAATTATGTTTTACA 57.514 25.926 9.01 0.00 39.08 2.41
818 4566 9.743937 CACAACAATGCATGAATTATGTTTTAC 57.256 29.630 12.29 0.00 39.08 2.01
819 4567 9.486497 ACACAACAATGCATGAATTATGTTTTA 57.514 25.926 12.29 0.00 39.08 1.52
820 4568 8.283992 CACACAACAATGCATGAATTATGTTTT 58.716 29.630 12.29 1.83 39.08 2.43
821 4569 7.441760 ACACACAACAATGCATGAATTATGTTT 59.558 29.630 12.29 6.02 39.08 2.83
822 4570 6.930164 ACACACAACAATGCATGAATTATGTT 59.070 30.769 12.29 2.83 39.08 2.71
823 4571 6.457355 ACACACAACAATGCATGAATTATGT 58.543 32.000 0.00 10.03 39.08 2.29
824 4572 6.954616 ACACACAACAATGCATGAATTATG 57.045 33.333 0.00 4.36 39.88 1.90
825 4573 9.656040 AAATACACACAACAATGCATGAATTAT 57.344 25.926 0.00 0.00 0.00 1.28
826 4574 9.486497 AAAATACACACAACAATGCATGAATTA 57.514 25.926 0.00 0.00 0.00 1.40
827 4575 7.966246 AAATACACACAACAATGCATGAATT 57.034 28.000 0.00 0.00 0.00 2.17
828 4576 7.966246 AAAATACACACAACAATGCATGAAT 57.034 28.000 0.00 0.00 0.00 2.57
829 4577 8.877808 TTAAAATACACACAACAATGCATGAA 57.122 26.923 0.00 0.00 0.00 2.57
830 4578 8.355913 TCTTAAAATACACACAACAATGCATGA 58.644 29.630 0.00 0.00 0.00 3.07
831 4579 8.427012 GTCTTAAAATACACACAACAATGCATG 58.573 33.333 0.00 0.00 0.00 4.06
832 4580 8.140628 TGTCTTAAAATACACACAACAATGCAT 58.859 29.630 0.00 0.00 0.00 3.96
833 4581 7.484140 TGTCTTAAAATACACACAACAATGCA 58.516 30.769 0.00 0.00 0.00 3.96
834 4582 7.922505 TGTCTTAAAATACACACAACAATGC 57.077 32.000 0.00 0.00 0.00 3.56
904 4652 1.200519 TGGACCTACCTACCACATGC 58.799 55.000 0.00 0.00 39.86 4.06
956 6448 2.031682 GGAGCAATAATGACATGGTCGC 60.032 50.000 0.00 0.00 41.28 5.19
990 6482 4.624452 GGTTCACCTAACATTGTCTCGTAC 59.376 45.833 0.00 0.00 40.08 3.67
1002 6494 2.291465 GGTTTTCACGGGTTCACCTAAC 59.709 50.000 0.00 0.00 36.97 2.34
1465 7017 1.625616 GAGGTGAACATGACGTACCG 58.374 55.000 0.00 0.00 32.27 4.02
1547 7120 2.105128 CGCCTAGCTCCTGGAACG 59.895 66.667 0.00 0.00 0.00 3.95
1647 7220 1.883084 CACCGCCGCCTTGTAGATC 60.883 63.158 0.00 0.00 0.00 2.75
1649 7222 2.992689 TCACCGCCGCCTTGTAGA 60.993 61.111 0.00 0.00 0.00 2.59
1878 7469 0.667792 AGAGGAAAACGACGCTGCTC 60.668 55.000 0.00 0.00 0.00 4.26
1879 7470 0.946221 CAGAGGAAAACGACGCTGCT 60.946 55.000 0.00 0.00 0.00 4.24
1933 7533 1.360551 CGACGGCGATCTCCTTGAT 59.639 57.895 16.62 0.00 40.82 2.57
2017 7647 2.126463 CGGCAAGAGAGCGTCGAA 60.126 61.111 0.00 0.00 34.64 3.71
2042 7672 2.427245 CCTCTGGTGCGGTCTAGGG 61.427 68.421 0.00 0.00 0.00 3.53
2070 7700 1.961277 CACCCACTGCTTGACGACC 60.961 63.158 0.00 0.00 0.00 4.79
2311 7941 1.222936 CCATGACCAGCCTCACCTC 59.777 63.158 0.00 0.00 0.00 3.85
2649 8282 1.676006 CTCTCCAACCACGCAAAAAGT 59.324 47.619 0.00 0.00 0.00 2.66
2664 8297 5.091261 ACATACACAACAGGAATCTCTCC 57.909 43.478 0.00 0.00 45.81 3.71
2666 8299 8.928448 ACATATACATACACAACAGGAATCTCT 58.072 33.333 0.00 0.00 0.00 3.10
2746 8394 6.596703 GGTAACTTAATCGTTGTTGGAGTTC 58.403 40.000 0.00 0.00 0.00 3.01
2769 8417 8.682710 TCCTCCTAACATTTGAAAATTATTCGG 58.317 33.333 0.00 0.00 0.00 4.30
2776 8424 6.376581 CAGCTCTCCTCCTAACATTTGAAAAT 59.623 38.462 0.00 0.00 0.00 1.82
2833 8481 5.345472 TGTGCTTTCATATTTTTGCATGACG 59.655 36.000 0.00 0.00 32.98 4.35
2871 8519 0.249120 TCCAACCACGTCTGGCATAG 59.751 55.000 3.43 0.00 42.08 2.23
2872 8520 0.687920 TTCCAACCACGTCTGGCATA 59.312 50.000 3.43 0.00 42.08 3.14
2874 8522 1.525077 GTTCCAACCACGTCTGGCA 60.525 57.895 3.43 0.00 42.08 4.92
2875 8523 0.034337 TAGTTCCAACCACGTCTGGC 59.966 55.000 3.43 0.00 42.08 4.85
2877 8525 3.594603 AGATAGTTCCAACCACGTCTG 57.405 47.619 0.00 0.00 0.00 3.51
2878 8526 5.067936 CAGATAGATAGTTCCAACCACGTCT 59.932 44.000 0.00 0.00 0.00 4.18
2984 8715 0.706433 ATCCCATGGACAGTTGGCTT 59.294 50.000 15.22 0.00 32.98 4.35
3012 8748 1.779724 GACGCGTCATAGATCGTTTCC 59.220 52.381 33.09 1.28 35.12 3.13
3014 8750 1.404391 AGGACGCGTCATAGATCGTTT 59.596 47.619 37.26 8.98 35.12 3.60
3034 8770 0.035598 TGAGATCCGGGCGTCAAAAA 59.964 50.000 0.00 0.00 0.00 1.94
3037 8773 0.391130 CTTTGAGATCCGGGCGTCAA 60.391 55.000 0.00 5.36 0.00 3.18
3058 8794 2.934887 CAGGGATTGCCATGTATCACA 58.065 47.619 0.00 0.00 40.98 3.58
3126 8862 5.010282 GGTGTATGGGAGAGAATGTTTGTT 58.990 41.667 0.00 0.00 0.00 2.83
3213 8949 7.605449 AGCACAAAAGTTGTCATATATGCTTT 58.395 30.769 7.92 8.65 43.23 3.51
3215 8951 6.764308 AGCACAAAAGTTGTCATATATGCT 57.236 33.333 7.92 0.00 43.23 3.79
3238 8974 3.904800 TCGGGAGAATTGACATGCTAA 57.095 42.857 0.00 0.00 34.75 3.09
3257 9154 5.443185 TTAGAAATTGCCATGCTGCTATC 57.557 39.130 0.00 0.00 0.00 2.08
3261 9158 3.587923 TGTTTAGAAATTGCCATGCTGC 58.412 40.909 0.00 0.00 0.00 5.25
3289 9324 5.594199 AGGCTAAGAAAAGGGGAAAGTTA 57.406 39.130 0.00 0.00 0.00 2.24
3295 9330 2.844348 CTGGTAGGCTAAGAAAAGGGGA 59.156 50.000 0.00 0.00 0.00 4.81
3312 9347 1.548269 GCTGCAGTAGAGAGAACTGGT 59.452 52.381 16.64 0.00 43.71 4.00
3325 9360 3.570975 TCAAAGATTTGACATGCTGCAGT 59.429 39.130 16.64 6.46 41.88 4.40
3328 9363 5.854157 CATTTCAAAGATTTGACATGCTGC 58.146 37.500 17.00 0.00 45.99 5.25
3389 9425 6.670695 TCTATGTTGAGCCATGCTATAGAA 57.329 37.500 3.21 0.00 39.88 2.10
3390 9426 6.670695 TTCTATGTTGAGCCATGCTATAGA 57.329 37.500 3.21 3.38 39.88 1.98
3410 9446 2.379005 GGAATGAAGCCGGGAATTTCT 58.621 47.619 2.18 0.00 0.00 2.52
3412 9448 1.007118 AGGGAATGAAGCCGGGAATTT 59.993 47.619 2.18 0.00 0.00 1.82
3419 9455 0.460311 ACGAGTAGGGAATGAAGCCG 59.540 55.000 0.00 0.00 0.00 5.52
3420 9456 1.480954 TGACGAGTAGGGAATGAAGCC 59.519 52.381 0.00 0.00 0.00 4.35
3421 9457 2.961526 TGACGAGTAGGGAATGAAGC 57.038 50.000 0.00 0.00 0.00 3.86
3422 9458 5.776173 ACTATGACGAGTAGGGAATGAAG 57.224 43.478 0.00 0.00 0.00 3.02
3423 9459 7.834881 ATAACTATGACGAGTAGGGAATGAA 57.165 36.000 0.00 0.00 0.00 2.57
3424 9460 9.175312 GATATAACTATGACGAGTAGGGAATGA 57.825 37.037 0.00 0.00 0.00 2.57
3425 9461 9.179909 AGATATAACTATGACGAGTAGGGAATG 57.820 37.037 0.00 0.00 0.00 2.67
3426 9462 9.398538 GAGATATAACTATGACGAGTAGGGAAT 57.601 37.037 0.00 0.00 0.00 3.01
3427 9463 7.828223 GGAGATATAACTATGACGAGTAGGGAA 59.172 40.741 0.00 0.00 0.00 3.97
3428 9464 7.182387 AGGAGATATAACTATGACGAGTAGGGA 59.818 40.741 0.00 0.00 0.00 4.20
3429 9465 7.340256 AGGAGATATAACTATGACGAGTAGGG 58.660 42.308 0.00 0.00 0.00 3.53
3430 9466 7.223193 CGAGGAGATATAACTATGACGAGTAGG 59.777 44.444 0.00 0.00 0.00 3.18
3431 9467 7.223193 CCGAGGAGATATAACTATGACGAGTAG 59.777 44.444 0.00 0.00 0.00 2.57
3432 9468 7.040494 CCGAGGAGATATAACTATGACGAGTA 58.960 42.308 0.00 0.00 0.00 2.59
3433 9469 5.875910 CCGAGGAGATATAACTATGACGAGT 59.124 44.000 0.00 0.00 0.00 4.18
3434 9470 5.294799 CCCGAGGAGATATAACTATGACGAG 59.705 48.000 0.00 0.00 0.00 4.18
3435 9471 5.183969 CCCGAGGAGATATAACTATGACGA 58.816 45.833 0.00 0.00 0.00 4.20
3436 9472 4.942483 ACCCGAGGAGATATAACTATGACG 59.058 45.833 0.00 0.00 0.00 4.35
3437 9473 6.318396 GGTACCCGAGGAGATATAACTATGAC 59.682 46.154 0.00 0.00 0.00 3.06
3438 9474 6.012245 TGGTACCCGAGGAGATATAACTATGA 60.012 42.308 10.07 0.00 0.00 2.15
3439 9475 6.095160 GTGGTACCCGAGGAGATATAACTATG 59.905 46.154 10.07 0.00 0.00 2.23
3440 9476 6.186234 GTGGTACCCGAGGAGATATAACTAT 58.814 44.000 10.07 0.00 0.00 2.12
3441 9477 5.515534 GGTGGTACCCGAGGAGATATAACTA 60.516 48.000 10.07 0.00 30.04 2.24
3442 9478 4.405548 GTGGTACCCGAGGAGATATAACT 58.594 47.826 10.07 0.00 0.00 2.24
3443 9479 3.509184 GGTGGTACCCGAGGAGATATAAC 59.491 52.174 10.07 0.00 30.04 1.89
3444 9480 3.771216 GGTGGTACCCGAGGAGATATAA 58.229 50.000 10.07 0.00 30.04 0.98
3445 9481 3.446442 GGTGGTACCCGAGGAGATATA 57.554 52.381 10.07 0.00 30.04 0.86
3446 9482 2.305858 GGTGGTACCCGAGGAGATAT 57.694 55.000 10.07 0.00 30.04 1.63
3447 9483 3.835810 GGTGGTACCCGAGGAGATA 57.164 57.895 10.07 0.00 30.04 1.98
3448 9484 4.701286 GGTGGTACCCGAGGAGAT 57.299 61.111 10.07 0.00 30.04 2.75
3458 9494 4.109675 AGGCGGCATGGGTGGTAC 62.110 66.667 13.08 0.00 0.00 3.34
3459 9495 3.792736 GAGGCGGCATGGGTGGTA 61.793 66.667 13.08 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.