Multiple sequence alignment - TraesCS6A01G331700

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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 TraesCS6A01G331700 chr6A 100.000 3081 0 0 1 3081 563713357 563710277 0.000000e+00 5690.0
1 TraesCS6A01G331700 chr6A 86.139 202 26 2 2209 2409 197861722 197861922 1.860000e-52 217.0
2 TraesCS6A01G331700 chr6B 87.871 2564 178 48 598 3081 633917553 633915043 0.000000e+00 2889.0
3 TraesCS6A01G331700 chr6B 86.802 591 62 10 1 588 633918207 633917630 0.000000e+00 645.0
4 TraesCS6A01G331700 chr6D 90.521 2226 111 33 930 3081 420750126 420747927 0.000000e+00 2850.0
5 TraesCS6A01G331700 chr6D 88.841 233 20 3 1 228 420750759 420750528 6.500000e-72 281.0
6 TraesCS6A01G331700 chr6D 98.113 53 1 0 261 313 420750341 420750289 3.270000e-15 93.5
7 TraesCS6A01G331700 chr2B 84.949 1475 118 42 1116 2520 15784170 15782730 0.000000e+00 1399.0
8 TraesCS6A01G331700 chr2B 84.799 1467 120 40 1116 2520 15720065 15718640 0.000000e+00 1378.0
9 TraesCS6A01G331700 chr2B 84.542 1475 124 42 1116 2520 15856626 15855186 0.000000e+00 1365.0
10 TraesCS6A01G331700 chr2B 84.477 612 53 17 1116 1696 15955594 15954994 1.600000e-157 566.0
11 TraesCS6A01G331700 chr2B 96.907 291 9 0 2791 3081 15718640 15718350 3.570000e-134 488.0
12 TraesCS6A01G331700 chr2B 96.220 291 11 0 2791 3081 15782730 15782440 7.730000e-131 477.0
13 TraesCS6A01G331700 chr2B 95.876 291 12 0 2791 3081 15855186 15854896 3.600000e-129 472.0
14 TraesCS6A01G331700 chrUn 84.799 1467 120 40 1116 2520 333311842 333313267 0.000000e+00 1378.0
15 TraesCS6A01G331700 chrUn 84.477 612 53 17 1116 1696 380900515 380899915 1.600000e-157 566.0
16 TraesCS6A01G331700 chrUn 96.907 291 9 0 2791 3081 333313267 333313557 3.570000e-134 488.0
17 TraesCS6A01G331700 chrUn 89.030 237 20 3 1611 1845 259180123 259180355 3.890000e-74 289.0
18 TraesCS6A01G331700 chrUn 85.714 210 18 2 1831 2028 259180782 259180991 8.660000e-51 211.0
19 TraesCS6A01G331700 chrUn 86.096 187 11 7 2041 2216 124974236 124974418 1.460000e-43 187.0
20 TraesCS6A01G331700 chrUn 85.561 187 12 7 2041 2216 259181286 259181468 6.790000e-42 182.0
21 TraesCS6A01G331700 chr7A 86.334 1061 79 26 1499 2520 11677928 11676895 0.000000e+00 1096.0
22 TraesCS6A01G331700 chr7A 96.220 291 11 0 2791 3081 11676895 11676605 7.730000e-131 477.0
23 TraesCS6A01G331700 chr7A 94.595 74 3 1 1116 1189 11678003 11677931 2.510000e-21 113.0
24 TraesCS6A01G331700 chr3B 82.979 987 91 31 1256 2204 745703907 745704854 0.000000e+00 821.0
25 TraesCS6A01G331700 chr3B 87.204 211 22 5 2204 2409 380277498 380277708 5.140000e-58 235.0
26 TraesCS6A01G331700 chr4D 96.296 243 9 0 2839 3081 508464387 508464145 1.720000e-107 399.0
27 TraesCS6A01G331700 chr4D 85.804 317 30 6 1048 1355 508472500 508472190 3.830000e-84 322.0
28 TraesCS6A01G331700 chr4D 95.455 176 6 1 2654 2829 508471998 508471825 2.340000e-71 279.0
29 TraesCS6A01G331700 chr4D 87.624 202 24 1 2209 2409 366045035 366044834 1.850000e-57 233.0
30 TraesCS6A01G331700 chr4D 82.400 125 16 4 478 598 46180187 46180065 1.510000e-18 104.0
31 TraesCS6A01G331700 chr1B 86.603 209 25 3 2204 2409 514932166 514931958 8.590000e-56 228.0
32 TraesCS6A01G331700 chr2A 86.473 207 26 2 2204 2409 381732809 381733014 3.090000e-55 226.0
33 TraesCS6A01G331700 chr3A 86.139 202 27 1 2209 2409 361577361 361577562 1.860000e-52 217.0
34 TraesCS6A01G331700 chr3D 81.119 143 21 6 617 758 527684758 527684621 3.250000e-20 110.0
35 TraesCS6A01G331700 chr7B 83.607 122 12 5 478 593 6919998 6919879 1.170000e-19 108.0
36 TraesCS6A01G331700 chr7B 82.353 102 15 3 494 595 6797640 6797738 5.470000e-13 86.1
37 TraesCS6A01G331700 chr4B 84.404 109 13 2 490 598 654709446 654709550 1.510000e-18 104.0
38 TraesCS6A01G331700 chr4A 82.203 118 19 2 479 595 54725361 54725245 1.950000e-17 100.0
39 TraesCS6A01G331700 chr4A 80.342 117 20 3 481 595 626545477 626545592 5.470000e-13 86.1
40 TraesCS6A01G331700 chr4A 90.000 60 6 0 598 657 626545695 626545636 9.160000e-11 78.7
41 TraesCS6A01G331700 chr1D 82.906 117 11 9 478 589 478165588 478165700 2.530000e-16 97.1
42 TraesCS6A01G331700 chr5B 79.839 124 12 12 481 596 684199571 684199453 9.160000e-11 78.7


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 TraesCS6A01G331700 chr6A 563710277 563713357 3080 True 5690.000000 5690 100.000000 1 3081 1 chr6A.!!$R1 3080
1 TraesCS6A01G331700 chr6B 633915043 633918207 3164 True 1767.000000 2889 87.336500 1 3081 2 chr6B.!!$R1 3080
2 TraesCS6A01G331700 chr6D 420747927 420750759 2832 True 1074.833333 2850 92.491667 1 3081 3 chr6D.!!$R1 3080
3 TraesCS6A01G331700 chr2B 15782440 15784170 1730 True 938.000000 1399 90.584500 1116 3081 2 chr2B.!!$R3 1965
4 TraesCS6A01G331700 chr2B 15718350 15720065 1715 True 933.000000 1378 90.853000 1116 3081 2 chr2B.!!$R2 1965
5 TraesCS6A01G331700 chr2B 15854896 15856626 1730 True 918.500000 1365 90.209000 1116 3081 2 chr2B.!!$R4 1965
6 TraesCS6A01G331700 chr2B 15954994 15955594 600 True 566.000000 566 84.477000 1116 1696 1 chr2B.!!$R1 580
7 TraesCS6A01G331700 chrUn 333311842 333313557 1715 False 933.000000 1378 90.853000 1116 3081 2 chrUn.!!$F3 1965
8 TraesCS6A01G331700 chrUn 380899915 380900515 600 True 566.000000 566 84.477000 1116 1696 1 chrUn.!!$R1 580
9 TraesCS6A01G331700 chrUn 259180123 259181468 1345 False 227.333333 289 86.768333 1611 2216 3 chrUn.!!$F2 605
10 TraesCS6A01G331700 chr7A 11676605 11678003 1398 True 562.000000 1096 92.383000 1116 3081 3 chr7A.!!$R1 1965
11 TraesCS6A01G331700 chr3B 745703907 745704854 947 False 821.000000 821 82.979000 1256 2204 1 chr3B.!!$F2 948
12 TraesCS6A01G331700 chr4D 508471825 508472500 675 True 300.500000 322 90.629500 1048 2829 2 chr4D.!!$R4 1781

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
420 600 0.104304 AGTCTTTCTTGCCACGACGT 59.896 50.0 0.00 0.00 0.0 4.34 F
456 643 0.179062 GGCCTCACTCATGCTTCGAT 60.179 55.0 0.00 0.00 0.0 3.59 F
908 1167 0.179073 CGGGCCTAGACATGTCCAAG 60.179 60.0 22.21 18.45 0.0 3.61 F
1599 1962 0.106819 AGAGCATGATTGGCCCTGAC 60.107 55.0 0.00 0.00 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1959 0.179032 AGTTGTTGCACCATCCGTCA 60.179 50.000 0.00 0.00 0.00 4.35 R
1599 1962 0.442310 CGTAGTTGTTGCACCATCCG 59.558 55.000 0.00 0.00 0.00 4.18 R
1994 2814 1.226311 CTTTCCTCCCTTATGGCCCT 58.774 55.000 0.00 0.00 0.00 5.19 R
2733 3898 1.670811 CAAGAATCGCTAATGGCCGTT 59.329 47.619 16.02 16.02 37.74 4.44 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
68 70 1.135431 TGGCAAAGCAATGATGTACGC 60.135 47.619 0.00 0.00 0.00 4.42
82 84 1.253999 GTACGCGACTAACCGAAGTG 58.746 55.000 15.93 0.00 0.00 3.16
107 109 6.481954 AACCAAGAGATGTACGTGAATTTC 57.518 37.500 0.00 0.00 0.00 2.17
132 134 5.982890 CTGAATTTGTGGGGTTTCAGTAT 57.017 39.130 0.00 0.00 39.97 2.12
143 145 7.094631 GTGGGGTTTCAGTATTTGATTTAACC 58.905 38.462 0.00 0.00 40.88 2.85
145 147 6.071784 GGGGTTTCAGTATTTGATTTAACCGT 60.072 38.462 0.00 0.00 41.82 4.83
146 148 7.025365 GGGTTTCAGTATTTGATTTAACCGTC 58.975 38.462 0.00 0.00 41.82 4.79
147 149 7.308710 GGGTTTCAGTATTTGATTTAACCGTCA 60.309 37.037 0.00 0.00 41.82 4.35
194 196 7.264947 AGTGTTTGGTTCTTTTCATTTTCGAT 58.735 30.769 0.00 0.00 0.00 3.59
240 420 2.545946 GCCATTTTATGACTCCGAGCTC 59.454 50.000 2.73 2.73 0.00 4.09
331 511 7.291182 ACTTGGAGCTATGATTTCACCTACTAT 59.709 37.037 0.00 0.00 0.00 2.12
333 513 7.671302 TGGAGCTATGATTTCACCTACTATTC 58.329 38.462 0.00 0.00 0.00 1.75
334 514 6.809196 GGAGCTATGATTTCACCTACTATTCG 59.191 42.308 0.00 0.00 0.00 3.34
335 515 7.309255 GGAGCTATGATTTCACCTACTATTCGA 60.309 40.741 0.00 0.00 0.00 3.71
346 526 3.572682 CCTACTATTCGAGCATACCCACA 59.427 47.826 0.00 0.00 0.00 4.17
392 572 1.888512 ACAACATTCAGGCAATCGCTT 59.111 42.857 0.00 0.00 38.60 4.68
415 595 1.996191 CGCTCTAGTCTTTCTTGCCAC 59.004 52.381 0.00 0.00 0.00 5.01
416 596 1.996191 GCTCTAGTCTTTCTTGCCACG 59.004 52.381 0.00 0.00 0.00 4.94
417 597 2.352814 GCTCTAGTCTTTCTTGCCACGA 60.353 50.000 0.00 0.00 0.00 4.35
418 598 3.246619 CTCTAGTCTTTCTTGCCACGAC 58.753 50.000 0.00 0.00 0.00 4.34
419 599 1.986378 CTAGTCTTTCTTGCCACGACG 59.014 52.381 0.00 0.00 0.00 5.12
420 600 0.104304 AGTCTTTCTTGCCACGACGT 59.896 50.000 0.00 0.00 0.00 4.34
421 601 0.507358 GTCTTTCTTGCCACGACGTC 59.493 55.000 5.18 5.18 0.00 4.34
422 602 0.937699 TCTTTCTTGCCACGACGTCG 60.938 55.000 34.58 34.58 46.33 5.12
423 603 0.937699 CTTTCTTGCCACGACGTCGA 60.938 55.000 41.52 19.00 43.02 4.20
424 604 0.319211 TTTCTTGCCACGACGTCGAT 60.319 50.000 41.52 23.81 43.02 3.59
425 605 0.319211 TTCTTGCCACGACGTCGATT 60.319 50.000 41.52 20.19 43.02 3.34
426 606 1.006825 TCTTGCCACGACGTCGATTG 61.007 55.000 41.52 29.30 43.02 2.67
427 607 2.548587 CTTGCCACGACGTCGATTGC 62.549 60.000 41.52 34.41 43.02 3.56
428 608 3.849953 GCCACGACGTCGATTGCC 61.850 66.667 41.52 18.77 43.02 4.52
429 609 2.431771 CCACGACGTCGATTGCCA 60.432 61.111 41.52 0.00 43.02 4.92
446 633 2.225467 GCCAATGATAAGGCCTCACTC 58.775 52.381 5.23 3.73 45.18 3.51
448 635 3.749954 GCCAATGATAAGGCCTCACTCAT 60.750 47.826 5.23 12.19 45.18 2.90
453 640 2.698855 TAAGGCCTCACTCATGCTTC 57.301 50.000 5.23 0.00 0.00 3.86
456 643 0.179062 GGCCTCACTCATGCTTCGAT 60.179 55.000 0.00 0.00 0.00 3.59
460 647 2.606725 CCTCACTCATGCTTCGATTGTC 59.393 50.000 0.00 0.00 0.00 3.18
463 650 3.056607 TCACTCATGCTTCGATTGTCTCA 60.057 43.478 0.00 0.00 0.00 3.27
470 657 2.208431 CTTCGATTGTCTCAGCATCCC 58.792 52.381 0.00 0.00 0.00 3.85
476 663 1.451028 GTCTCAGCATCCCAGCCAC 60.451 63.158 0.00 0.00 34.23 5.01
529 716 4.568152 AGAAAACTTCGTGAAACCCATG 57.432 40.909 0.00 0.00 34.02 3.66
539 726 3.566322 CGTGAAACCCATGTTTGGAAGTA 59.434 43.478 0.00 0.00 46.92 2.24
588 777 9.950496 GATATGTTAGGATGGTGATGTTCTATT 57.050 33.333 0.00 0.00 0.00 1.73
589 778 9.730705 ATATGTTAGGATGGTGATGTTCTATTG 57.269 33.333 0.00 0.00 0.00 1.90
590 779 5.822519 TGTTAGGATGGTGATGTTCTATTGC 59.177 40.000 0.00 0.00 0.00 3.56
595 784 2.689471 TGGTGATGTTCTATTGCCATGC 59.311 45.455 0.00 0.00 0.00 4.06
608 864 1.334556 TGCCATGCGACTATTCATTGC 59.665 47.619 0.00 0.00 33.52 3.56
636 892 9.289303 GAATTTATTCTTTTCATAGCTCGCAAA 57.711 29.630 0.00 0.00 34.05 3.68
666 922 6.232581 TGTGTTTGAACTTGGGAATTTCAT 57.767 33.333 0.00 0.00 31.36 2.57
698 954 8.738645 ATAGAACATCACACTCTTAAAATCCC 57.261 34.615 0.00 0.00 0.00 3.85
699 955 5.643777 AGAACATCACACTCTTAAAATCCCG 59.356 40.000 0.00 0.00 0.00 5.14
710 966 6.150474 ACTCTTAAAATCCCGTATGTTTGTGG 59.850 38.462 0.00 0.00 0.00 4.17
716 972 3.085533 TCCCGTATGTTTGTGGGATTTG 58.914 45.455 0.00 0.00 45.66 2.32
723 979 6.143758 CGTATGTTTGTGGGATTTGTTTGAAG 59.856 38.462 0.00 0.00 0.00 3.02
753 1009 6.582437 AACATCATTTTTCACGTGGTTTTC 57.418 33.333 17.00 0.00 0.00 2.29
754 1010 5.655488 ACATCATTTTTCACGTGGTTTTCA 58.345 33.333 17.00 0.00 0.00 2.69
783 1039 7.650104 GGTTTTCACCGAAACTTGATTTTCATA 59.350 33.333 0.00 0.00 39.05 2.15
784 1040 9.191995 GTTTTCACCGAAACTTGATTTTCATAT 57.808 29.630 0.00 0.00 36.75 1.78
786 1042 7.680442 TCACCGAAACTTGATTTTCATATGA 57.320 32.000 0.00 0.00 35.54 2.15
787 1043 7.526608 TCACCGAAACTTGATTTTCATATGAC 58.473 34.615 4.48 0.00 35.54 3.06
788 1044 7.174080 TCACCGAAACTTGATTTTCATATGACA 59.826 33.333 4.48 0.00 35.54 3.58
789 1045 7.970061 CACCGAAACTTGATTTTCATATGACAT 59.030 33.333 4.48 0.27 35.54 3.06
790 1046 8.522830 ACCGAAACTTGATTTTCATATGACATT 58.477 29.630 4.48 0.00 35.54 2.71
791 1047 9.013490 CCGAAACTTGATTTTCATATGACATTC 57.987 33.333 4.48 5.91 35.54 2.67
792 1048 9.778993 CGAAACTTGATTTTCATATGACATTCT 57.221 29.630 4.48 0.00 35.54 2.40
804 1060 1.002430 TGACATTCTCTCCAGCCACAC 59.998 52.381 0.00 0.00 0.00 3.82
807 1063 1.833630 CATTCTCTCCAGCCACACCTA 59.166 52.381 0.00 0.00 0.00 3.08
810 1066 0.534412 CTCTCCAGCCACACCTACTG 59.466 60.000 0.00 0.00 0.00 2.74
815 1071 1.072331 CCAGCCACACCTACTGTTCTT 59.928 52.381 0.00 0.00 0.00 2.52
818 1074 1.610886 GCCACACCTACTGTTCTTCCC 60.611 57.143 0.00 0.00 0.00 3.97
819 1075 1.697432 CCACACCTACTGTTCTTCCCA 59.303 52.381 0.00 0.00 0.00 4.37
820 1076 2.289694 CCACACCTACTGTTCTTCCCAG 60.290 54.545 0.00 0.00 36.01 4.45
857 1116 0.671781 CAGCTTCGGAAGGGTGTGAG 60.672 60.000 18.73 0.00 0.00 3.51
903 1162 3.075005 ACGCGGGCCTAGACATGT 61.075 61.111 12.47 0.00 0.00 3.21
908 1167 0.179073 CGGGCCTAGACATGTCCAAG 60.179 60.000 22.21 18.45 0.00 3.61
936 1195 4.504916 CGAGCCCAGTCGCAGGAG 62.505 72.222 0.00 0.00 32.22 3.69
938 1197 4.704103 AGCCCAGTCGCAGGAGGA 62.704 66.667 0.00 0.00 0.00 3.71
939 1198 3.706373 GCCCAGTCGCAGGAGGAA 61.706 66.667 0.00 0.00 0.00 3.36
941 1200 2.581354 CCAGTCGCAGGAGGAAGG 59.419 66.667 0.00 0.00 0.00 3.46
943 1202 2.284258 AGTCGCAGGAGGAAGGCT 60.284 61.111 0.00 0.00 0.00 4.58
944 1203 1.915769 AGTCGCAGGAGGAAGGCTT 60.916 57.895 0.00 0.00 0.00 4.35
989 1290 2.700371 TCCTGTTCTGTTGAAGCAGAGA 59.300 45.455 0.00 0.00 45.03 3.10
990 1291 3.065655 CCTGTTCTGTTGAAGCAGAGAG 58.934 50.000 0.00 0.00 45.03 3.20
991 1292 3.244009 CCTGTTCTGTTGAAGCAGAGAGA 60.244 47.826 0.00 0.00 45.03 3.10
992 1293 3.987547 TGTTCTGTTGAAGCAGAGAGAG 58.012 45.455 0.00 0.00 45.03 3.20
993 1294 3.244009 TGTTCTGTTGAAGCAGAGAGAGG 60.244 47.826 0.00 0.00 45.03 3.69
994 1295 2.881734 TCTGTTGAAGCAGAGAGAGGA 58.118 47.619 0.00 0.00 40.23 3.71
995 1296 2.824936 TCTGTTGAAGCAGAGAGAGGAG 59.175 50.000 0.00 0.00 40.23 3.69
1191 1492 4.437587 CCCCAGCCTCAGCCCTTG 62.438 72.222 0.00 0.00 41.25 3.61
1194 1495 4.044439 CAGCCTCAGCCCTTGCCT 62.044 66.667 0.00 0.00 41.25 4.75
1195 1496 4.044439 AGCCTCAGCCCTTGCCTG 62.044 66.667 0.00 0.00 41.25 4.85
1233 1549 1.007387 CAACAAGAAGCCCAACGCC 60.007 57.895 0.00 0.00 38.78 5.68
1235 1551 1.040339 AACAAGAAGCCCAACGCCAA 61.040 50.000 0.00 0.00 38.78 4.52
1237 1553 0.318955 CAAGAAGCCCAACGCCAAAG 60.319 55.000 0.00 0.00 38.78 2.77
1238 1554 0.467290 AAGAAGCCCAACGCCAAAGA 60.467 50.000 0.00 0.00 38.78 2.52
1239 1555 1.172812 AGAAGCCCAACGCCAAAGAC 61.173 55.000 0.00 0.00 38.78 3.01
1240 1556 1.452145 GAAGCCCAACGCCAAAGACA 61.452 55.000 0.00 0.00 38.78 3.41
1241 1557 1.455383 AAGCCCAACGCCAAAGACAG 61.455 55.000 0.00 0.00 38.78 3.51
1242 1558 2.919494 GCCCAACGCCAAAGACAGG 61.919 63.158 0.00 0.00 0.00 4.00
1254 1579 2.011122 AAGACAGGAGGAAGGTTCGA 57.989 50.000 0.00 0.00 0.00 3.71
1270 1595 4.070552 GACCAGCGGCGGAAGAGT 62.071 66.667 9.78 0.00 0.00 3.24
1507 1866 3.848726 ACAAAAAGACTGGCTGTTGTTG 58.151 40.909 6.95 0.00 33.96 3.33
1530 1893 5.652014 TGGATAGATGCAAAATTTCGGTTCT 59.348 36.000 0.00 0.00 0.00 3.01
1531 1894 6.152661 TGGATAGATGCAAAATTTCGGTTCTT 59.847 34.615 0.00 0.00 0.00 2.52
1532 1895 6.473455 GGATAGATGCAAAATTTCGGTTCTTG 59.527 38.462 0.00 0.00 0.00 3.02
1565 1928 3.384789 AGCATGCTGAATTGCTGATCATT 59.615 39.130 21.98 0.00 46.96 2.57
1566 1929 3.490896 GCATGCTGAATTGCTGATCATTG 59.509 43.478 11.37 0.00 35.95 2.82
1596 1959 0.333993 ACAAGAGCATGATTGGCCCT 59.666 50.000 0.00 0.00 0.00 5.19
1599 1962 0.106819 AGAGCATGATTGGCCCTGAC 60.107 55.000 0.00 0.00 0.00 3.51
1696 2059 5.719085 AGCTCTCCTGATTTTAGTCTTCAGA 59.281 40.000 1.49 0.00 39.36 3.27
1742 2108 5.001237 TGATGCTGTTATGGCTGATTTTG 57.999 39.130 0.00 0.00 0.00 2.44
1849 2658 1.538876 ACAGGGAAGCCTGCAGGTA 60.539 57.895 32.81 0.00 41.12 3.08
1891 2711 5.396484 TGTTCGTGTATCTTAGTTCTTCGG 58.604 41.667 0.00 0.00 0.00 4.30
1922 2742 2.554142 TGATTTATCTGCTGCCTGTCG 58.446 47.619 0.00 0.00 0.00 4.35
1994 2814 3.136443 TCCTGAGCTTGGAAACTTCAAGA 59.864 43.478 6.90 0.00 42.94 3.02
1998 2818 1.270826 GCTTGGAAACTTCAAGAGGGC 59.729 52.381 7.86 0.00 42.94 5.19
2026 2846 4.407296 AGGGAGGAAAGTAGTAAGCATGAG 59.593 45.833 0.00 0.00 0.00 2.90
2057 3189 6.007936 TGAACGAGGTTAAATTGTTGGATG 57.992 37.500 0.00 0.00 0.00 3.51
2083 3215 7.634210 GCCACAAATACTACTGGTACCTGATTA 60.634 40.741 24.19 12.08 32.72 1.75
2146 3279 1.133915 CCGGGGCACAAATACTGGTAT 60.134 52.381 0.00 0.00 0.00 2.73
2204 3342 2.319844 TCCTGTTCTGCTCAGAGTTGA 58.680 47.619 0.00 0.00 38.88 3.18
2292 3453 8.026396 TGTTCTGAATGATATCATCTCTTGGA 57.974 34.615 18.44 13.12 35.10 3.53
2297 3459 9.339850 CTGAATGATATCATCTCTTGGACTTTT 57.660 33.333 18.44 0.00 35.10 2.27
2346 3508 7.789831 ACTTGGATATATAGTCCACCAGAAAGA 59.210 37.037 8.71 0.00 45.05 2.52
2398 3561 5.550232 TTCATCGTCCAATGACATTCAAG 57.450 39.130 0.00 0.00 41.85 3.02
2549 3714 6.432783 TCACGACCAAACCAAATTAGATCATT 59.567 34.615 0.00 0.00 0.00 2.57
2583 3748 9.118300 GATCTGTCTGGAATTGATTGATAGTTT 57.882 33.333 0.00 0.00 0.00 2.66
2601 3766 3.821033 AGTTTGACACTTATGACCAAGCC 59.179 43.478 0.00 0.00 27.32 4.35
2627 3792 9.599866 CATCTAATGATTAACAAGAGGTACACA 57.400 33.333 0.00 0.00 0.00 3.72
2733 3898 4.030913 CCTCCCTCTTAACCTGTCATGTA 58.969 47.826 0.00 0.00 0.00 2.29
2870 4035 7.013529 GTGCCTACACGTAGAAATAAAAACAG 58.986 38.462 5.77 0.00 36.98 3.16
2981 4146 9.802039 TGTAGAAAAAGATATACAAACCTTGGT 57.198 29.630 0.00 0.00 34.12 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.321122 CCAGTTCACCACTCTCTGCC 60.321 60.000 0.00 0.00 30.92 4.85
15 16 1.072331 ACAGGATCACCAGTTCACCAC 59.928 52.381 0.00 0.00 38.94 4.16
55 56 2.034001 GGTTAGTCGCGTACATCATTGC 60.034 50.000 5.77 0.00 0.00 3.56
56 57 2.215587 CGGTTAGTCGCGTACATCATTG 59.784 50.000 5.77 0.00 0.00 2.82
57 58 2.097954 TCGGTTAGTCGCGTACATCATT 59.902 45.455 5.77 0.00 0.00 2.57
68 70 2.746269 TGGTTTCACTTCGGTTAGTCG 58.254 47.619 0.00 0.00 0.00 4.18
82 84 6.481954 AATTCACGTACATCTCTTGGTTTC 57.518 37.500 0.00 0.00 0.00 2.78
121 123 6.916440 ACGGTTAAATCAAATACTGAAACCC 58.084 36.000 0.00 0.00 38.47 4.11
122 124 7.586747 TGACGGTTAAATCAAATACTGAAACC 58.413 34.615 0.00 0.00 38.39 3.27
132 134 8.994429 AAATATTGCATGACGGTTAAATCAAA 57.006 26.923 0.00 0.00 0.00 2.69
194 196 9.162764 GCTAGAAGAACCAACTCAACAATATTA 57.837 33.333 0.00 0.00 0.00 0.98
210 212 6.018669 CGGAGTCATAAAATGGCTAGAAGAAC 60.019 42.308 0.00 0.00 46.97 3.01
247 427 2.155279 GAGGTTCAAACAAGGAGGCTC 58.845 52.381 5.78 5.78 0.00 4.70
248 428 1.777272 AGAGGTTCAAACAAGGAGGCT 59.223 47.619 0.00 0.00 0.00 4.58
250 430 2.373502 AGGAGAGGTTCAAACAAGGAGG 59.626 50.000 0.00 0.00 0.00 4.30
251 431 3.326297 AGAGGAGAGGTTCAAACAAGGAG 59.674 47.826 0.00 0.00 0.00 3.69
331 511 1.138859 CAGGATGTGGGTATGCTCGAA 59.861 52.381 0.00 0.00 0.00 3.71
333 513 0.752658 TCAGGATGTGGGTATGCTCG 59.247 55.000 0.00 0.00 37.40 5.03
334 514 3.144506 CAATCAGGATGTGGGTATGCTC 58.855 50.000 0.00 0.00 37.40 4.26
335 515 2.779430 TCAATCAGGATGTGGGTATGCT 59.221 45.455 0.00 0.00 37.40 3.79
346 526 8.215736 TCAAGTCAATACATGATCAATCAGGAT 58.784 33.333 11.27 0.00 40.76 3.24
392 572 1.673033 GCAAGAAAGACTAGAGCGGCA 60.673 52.381 1.45 0.00 0.00 5.69
415 595 0.930310 ATCATTGGCAATCGACGTCG 59.070 50.000 31.30 31.30 41.45 5.12
416 596 3.059597 CCTTATCATTGGCAATCGACGTC 60.060 47.826 10.36 5.18 0.00 4.34
417 597 2.872245 CCTTATCATTGGCAATCGACGT 59.128 45.455 10.36 0.00 0.00 4.34
418 598 3.526385 CCTTATCATTGGCAATCGACG 57.474 47.619 10.36 0.00 0.00 5.12
427 607 3.565764 TGAGTGAGGCCTTATCATTGG 57.434 47.619 6.77 0.00 0.00 3.16
428 608 3.252701 GCATGAGTGAGGCCTTATCATTG 59.747 47.826 19.96 16.63 0.00 2.82
429 609 3.137913 AGCATGAGTGAGGCCTTATCATT 59.862 43.478 19.96 6.84 28.84 2.57
442 622 3.256558 TGAGACAATCGAAGCATGAGTG 58.743 45.455 0.00 0.00 37.45 3.51
446 633 2.004733 TGCTGAGACAATCGAAGCATG 58.995 47.619 1.68 0.00 35.70 4.06
448 635 2.274437 GATGCTGAGACAATCGAAGCA 58.726 47.619 8.05 8.05 41.49 3.91
453 640 1.579698 CTGGGATGCTGAGACAATCG 58.420 55.000 0.00 0.00 0.00 3.34
456 643 1.300963 GGCTGGGATGCTGAGACAA 59.699 57.895 0.00 0.00 0.00 3.18
460 647 2.513204 CGTGGCTGGGATGCTGAG 60.513 66.667 0.00 0.00 0.00 3.35
463 650 2.685017 TCTCGTGGCTGGGATGCT 60.685 61.111 0.00 0.00 0.00 3.79
470 657 3.443099 TGTGATATTCTCTCGTGGCTG 57.557 47.619 0.00 0.00 0.00 4.85
476 663 5.359756 TGGTTTCCATGTGATATTCTCTCG 58.640 41.667 0.00 0.00 0.00 4.04
517 704 2.360801 ACTTCCAAACATGGGTTTCACG 59.639 45.455 0.00 0.00 45.18 4.35
522 709 6.739331 TTTCAATACTTCCAAACATGGGTT 57.261 33.333 0.00 0.00 39.43 4.11
556 743 9.425248 ACATCACCATCCTAACATATCATTTTT 57.575 29.630 0.00 0.00 0.00 1.94
557 744 9.425248 AACATCACCATCCTAACATATCATTTT 57.575 29.630 0.00 0.00 0.00 1.82
558 745 9.071276 GAACATCACCATCCTAACATATCATTT 57.929 33.333 0.00 0.00 0.00 2.32
559 746 8.443176 AGAACATCACCATCCTAACATATCATT 58.557 33.333 0.00 0.00 0.00 2.57
560 747 7.982252 AGAACATCACCATCCTAACATATCAT 58.018 34.615 0.00 0.00 0.00 2.45
562 749 9.950496 AATAGAACATCACCATCCTAACATATC 57.050 33.333 0.00 0.00 0.00 1.63
563 750 9.730705 CAATAGAACATCACCATCCTAACATAT 57.269 33.333 0.00 0.00 0.00 1.78
571 760 3.554934 TGGCAATAGAACATCACCATCC 58.445 45.455 0.00 0.00 0.00 3.51
588 777 1.334556 GCAATGAATAGTCGCATGGCA 59.665 47.619 0.00 0.00 40.40 4.92
589 778 1.605710 AGCAATGAATAGTCGCATGGC 59.394 47.619 0.00 0.00 40.87 4.40
590 779 2.874086 TCAGCAATGAATAGTCGCATGG 59.126 45.455 0.00 0.00 0.00 3.66
595 784 9.941664 AAGAATAAATTCAGCAATGAATAGTCG 57.058 29.630 4.04 0.00 37.52 4.18
608 864 8.124823 TGCGAGCTATGAAAAGAATAAATTCAG 58.875 33.333 5.55 0.00 39.23 3.02
616 872 5.126061 ACCATTTGCGAGCTATGAAAAGAAT 59.874 36.000 10.67 0.00 0.00 2.40
625 881 4.199310 ACACATTACCATTTGCGAGCTAT 58.801 39.130 0.00 0.00 0.00 2.97
636 892 5.144100 TCCCAAGTTCAAACACATTACCAT 58.856 37.500 0.00 0.00 0.00 3.55
666 922 6.721704 AGAGTGTGATGTTCTATCAGCATA 57.278 37.500 0.00 0.00 36.17 3.14
698 954 5.524284 TCAAACAAATCCCACAAACATACG 58.476 37.500 0.00 0.00 0.00 3.06
699 955 6.073819 GCTTCAAACAAATCCCACAAACATAC 60.074 38.462 0.00 0.00 0.00 2.39
723 979 6.122125 CACGTGAAAAATGATGTTTTGAAGC 58.878 36.000 10.90 0.00 30.87 3.86
741 997 1.956297 AACCGATGAAAACCACGTGA 58.044 45.000 19.30 0.00 0.00 4.35
779 1035 3.969312 TGGCTGGAGAGAATGTCATATGA 59.031 43.478 0.00 0.00 0.00 2.15
783 1039 1.911357 TGTGGCTGGAGAGAATGTCAT 59.089 47.619 0.00 0.00 0.00 3.06
784 1040 1.002430 GTGTGGCTGGAGAGAATGTCA 59.998 52.381 0.00 0.00 0.00 3.58
786 1042 0.326264 GGTGTGGCTGGAGAGAATGT 59.674 55.000 0.00 0.00 0.00 2.71
787 1043 0.617413 AGGTGTGGCTGGAGAGAATG 59.383 55.000 0.00 0.00 0.00 2.67
788 1044 1.834263 GTAGGTGTGGCTGGAGAGAAT 59.166 52.381 0.00 0.00 0.00 2.40
789 1045 1.203187 AGTAGGTGTGGCTGGAGAGAA 60.203 52.381 0.00 0.00 0.00 2.87
790 1046 0.409876 AGTAGGTGTGGCTGGAGAGA 59.590 55.000 0.00 0.00 0.00 3.10
791 1047 0.534412 CAGTAGGTGTGGCTGGAGAG 59.466 60.000 0.00 0.00 0.00 3.20
792 1048 0.178932 ACAGTAGGTGTGGCTGGAGA 60.179 55.000 0.00 0.00 38.28 3.71
793 1049 0.687354 AACAGTAGGTGTGGCTGGAG 59.313 55.000 0.00 0.00 40.26 3.86
794 1050 0.685097 GAACAGTAGGTGTGGCTGGA 59.315 55.000 0.00 0.00 40.26 3.86
810 1066 3.119096 GCCGCGACTGGGAAGAAC 61.119 66.667 8.23 0.00 0.00 3.01
832 1091 0.453390 CCCTTCCGAAGCTGAAATGC 59.547 55.000 2.27 0.00 0.00 3.56
834 1093 1.073923 ACACCCTTCCGAAGCTGAAAT 59.926 47.619 2.27 0.00 0.00 2.17
857 1116 0.177141 TATACGTGGCCCAGCTTGAC 59.823 55.000 0.00 0.00 0.00 3.18
935 1194 1.004891 CCCCTCCCTAAGCCTTCCT 59.995 63.158 0.00 0.00 0.00 3.36
936 1195 0.402126 ATCCCCTCCCTAAGCCTTCC 60.402 60.000 0.00 0.00 0.00 3.46
938 1197 2.707554 CTTATCCCCTCCCTAAGCCTT 58.292 52.381 0.00 0.00 0.00 4.35
939 1198 1.766869 GCTTATCCCCTCCCTAAGCCT 60.767 57.143 2.84 0.00 40.80 4.58
941 1200 0.321996 CGCTTATCCCCTCCCTAAGC 59.678 60.000 3.96 3.96 42.39 3.09
943 1202 1.482553 CCTCGCTTATCCCCTCCCTAA 60.483 57.143 0.00 0.00 0.00 2.69
944 1203 0.114560 CCTCGCTTATCCCCTCCCTA 59.885 60.000 0.00 0.00 0.00 3.53
989 1290 1.719529 CATGAGCATCCTCCTCCTCT 58.280 55.000 0.00 0.00 37.29 3.69
990 1291 0.035176 GCATGAGCATCCTCCTCCTC 59.965 60.000 0.00 0.00 41.58 3.71
991 1292 0.400237 AGCATGAGCATCCTCCTCCT 60.400 55.000 0.00 0.00 45.49 3.69
992 1293 0.250381 CAGCATGAGCATCCTCCTCC 60.250 60.000 0.00 0.00 45.49 4.30
993 1294 0.885596 GCAGCATGAGCATCCTCCTC 60.886 60.000 0.00 0.00 45.49 3.71
994 1295 1.148723 GCAGCATGAGCATCCTCCT 59.851 57.895 0.00 0.00 45.49 3.69
995 1296 2.252346 CGCAGCATGAGCATCCTCC 61.252 63.158 10.58 0.00 45.49 4.30
1087 1388 3.210528 GGACGAGAGACCGGCGAT 61.211 66.667 9.30 0.00 38.74 4.58
1192 1493 4.292178 GATCTCGGAGCGCCCAGG 62.292 72.222 2.29 0.86 34.14 4.45
1193 1494 4.292178 GGATCTCGGAGCGCCCAG 62.292 72.222 2.29 0.00 34.14 4.45
1197 1498 4.292178 CTGGGGATCTCGGAGCGC 62.292 72.222 0.00 0.00 0.00 5.92
1198 1499 4.292178 GCTGGGGATCTCGGAGCG 62.292 72.222 0.00 0.00 0.00 5.03
1199 1500 2.735772 TTGCTGGGGATCTCGGAGC 61.736 63.158 8.05 8.05 0.00 4.70
1233 1549 2.037251 TCGAACCTTCCTCCTGTCTTTG 59.963 50.000 0.00 0.00 0.00 2.77
1235 1551 1.619332 GTCGAACCTTCCTCCTGTCTT 59.381 52.381 0.00 0.00 0.00 3.01
1237 1553 0.246910 GGTCGAACCTTCCTCCTGTC 59.753 60.000 0.00 0.00 34.73 3.51
1238 1554 0.471211 TGGTCGAACCTTCCTCCTGT 60.471 55.000 0.00 0.00 39.58 4.00
1239 1555 0.247736 CTGGTCGAACCTTCCTCCTG 59.752 60.000 0.00 0.00 39.58 3.86
1240 1556 1.545706 GCTGGTCGAACCTTCCTCCT 61.546 60.000 0.00 0.00 39.58 3.69
1241 1557 1.079057 GCTGGTCGAACCTTCCTCC 60.079 63.158 0.00 0.00 39.58 4.30
1242 1558 1.446272 CGCTGGTCGAACCTTCCTC 60.446 63.158 0.00 0.00 39.58 3.71
1254 1579 4.070552 GACTCTTCCGCCGCTGGT 62.071 66.667 1.97 0.00 0.00 4.00
1380 1711 3.952628 GAACTCGGGGCCCTTGTCG 62.953 68.421 24.38 17.29 0.00 4.35
1507 1866 6.136541 AGAACCGAAATTTTGCATCTATCC 57.863 37.500 8.63 0.00 0.00 2.59
1530 1893 4.271661 TCAGCATGCTCCATCATAAACAA 58.728 39.130 19.68 0.00 34.76 2.83
1531 1894 3.888583 TCAGCATGCTCCATCATAAACA 58.111 40.909 19.68 0.00 34.76 2.83
1532 1895 4.906065 TTCAGCATGCTCCATCATAAAC 57.094 40.909 19.68 0.00 34.76 2.01
1565 1928 0.667487 GCTCTTGTACAGCTGCGACA 60.667 55.000 15.27 15.74 33.75 4.35
1566 1929 0.667487 TGCTCTTGTACAGCTGCGAC 60.667 55.000 15.27 13.05 37.79 5.19
1596 1959 0.179032 AGTTGTTGCACCATCCGTCA 60.179 50.000 0.00 0.00 0.00 4.35
1599 1962 0.442310 CGTAGTTGTTGCACCATCCG 59.558 55.000 0.00 0.00 0.00 4.18
1674 2037 6.042143 GCTCTGAAGACTAAAATCAGGAGAG 58.958 44.000 2.76 0.00 40.71 3.20
1682 2045 4.453819 GTGCACTGCTCTGAAGACTAAAAT 59.546 41.667 10.32 0.00 0.00 1.82
1696 2059 2.260844 ACTTACACATGTGCACTGCT 57.739 45.000 25.68 7.68 0.00 4.24
1742 2108 1.612676 GGTCTACAACACCCCCAAAC 58.387 55.000 0.00 0.00 0.00 2.93
1849 2658 2.892852 ACAACAACACAATAGCCAGCAT 59.107 40.909 0.00 0.00 0.00 3.79
1858 2667 6.371809 AAGATACACGAACAACAACACAAT 57.628 33.333 0.00 0.00 0.00 2.71
1891 2711 6.150318 CAGCAGATAAATCAATTCAGCATCC 58.850 40.000 0.00 0.00 0.00 3.51
1922 2742 1.388547 TCCACACAAGCACTGGAAAC 58.611 50.000 0.00 0.00 30.81 2.78
1994 2814 1.226311 CTTTCCTCCCTTATGGCCCT 58.774 55.000 0.00 0.00 0.00 5.19
1998 2818 5.130477 TGCTTACTACTTTCCTCCCTTATGG 59.870 44.000 0.00 0.00 0.00 2.74
2026 2846 1.448985 TAACCTCGTTCATGCTTGCC 58.551 50.000 0.00 0.00 0.00 4.52
2057 3189 4.081309 TCAGGTACCAGTAGTATTTGTGGC 60.081 45.833 15.94 0.00 32.91 5.01
2083 3215 4.400567 GTGAGTACCCTACACTCCGTAATT 59.599 45.833 0.38 0.00 41.46 1.40
2130 3263 7.715249 TGAGAATTAGATACCAGTATTTGTGCC 59.285 37.037 0.00 0.00 0.00 5.01
2131 3264 8.552034 GTGAGAATTAGATACCAGTATTTGTGC 58.448 37.037 0.00 0.00 0.00 4.57
2180 3317 2.094286 ACTCTGAGCAGAACAGGATTCG 60.094 50.000 4.19 0.00 36.94 3.34
2221 3382 5.065090 TGTTATCATCAGAATTTGACAGCGG 59.935 40.000 0.00 0.00 38.99 5.52
2346 3508 1.308047 TGCTTGCGTGAGTTCATGTT 58.692 45.000 3.51 0.00 35.38 2.71
2398 3561 3.004106 GGATGGCAGAGTTCATGTATTGC 59.996 47.826 0.00 0.00 0.00 3.56
2455 3619 6.567687 TTCACCAACGATTATGAACACATT 57.432 33.333 0.00 0.00 0.00 2.71
2583 3748 3.264193 AGATGGCTTGGTCATAAGTGTCA 59.736 43.478 0.00 0.00 0.00 3.58
2601 3766 9.599866 TGTGTACCTCTTGTTAATCATTAGATG 57.400 33.333 0.00 0.00 33.90 2.90
2627 3792 9.686683 ACTGCTATCTTTGTATTGTAAATTCCT 57.313 29.630 0.00 0.00 0.00 3.36
2649 3814 4.322567 ACAGATCTGAGAAAAGGAACTGC 58.677 43.478 29.27 0.00 40.86 4.40
2733 3898 1.670811 CAAGAATCGCTAATGGCCGTT 59.329 47.619 16.02 16.02 37.74 4.44
2870 4035 6.503524 TCCAGTAAATGTTTTTGCTTCAGTC 58.496 36.000 0.00 0.00 35.85 3.51
2981 4146 8.593945 AAAATATGTTTGGAAAGGAGCTATCA 57.406 30.769 0.00 0.00 0.00 2.15
2986 4151 5.934043 AGCAAAAATATGTTTGGAAAGGAGC 59.066 36.000 18.08 3.31 38.64 4.70


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

AutoCloner maintained by Alex Coulton.