Multiple sequence alignment - TraesCS3B01G313500

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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 TraesCS3B01G313500 chr3B 100.000 3431 0 0 1 3431 504066565 504069995 0.000000e+00 6336
1 TraesCS3B01G313500 chr3B 76.895 1082 226 20 1307 2376 503984633 503985702 2.950000e-165 592
2 TraesCS3B01G313500 chr3B 97.059 340 10 0 311 650 589557433 589557772 1.070000e-159 573
3 TraesCS3B01G313500 chr3B 98.662 299 4 0 1 299 589556888 589557186 6.520000e-147 531
4 TraesCS3B01G313500 chr3D 93.193 1954 116 13 858 2804 387710498 387708555 0.000000e+00 2856
5 TraesCS3B01G313500 chr3D 91.077 594 49 4 2840 3431 539552714 539552123 0.000000e+00 800
6 TraesCS3B01G313500 chr3D 76.623 1386 290 28 1008 2378 387770580 387769214 0.000000e+00 734
7 TraesCS3B01G313500 chr3A 93.363 1823 102 12 990 2804 509021669 509019858 0.000000e+00 2678
8 TraesCS3B01G313500 chr3A 76.521 1397 291 31 999 2378 509122486 509121110 0.000000e+00 728
9 TraesCS3B01G313500 chr3A 89.105 257 22 4 699 955 509021921 509021671 7.150000e-82 315
10 TraesCS3B01G313500 chr6B 91.694 614 46 3 2816 3425 640129508 640128896 0.000000e+00 846
11 TraesCS3B01G313500 chr6B 99.331 299 2 0 1 299 501126700 501126998 3.010000e-150 542
12 TraesCS3B01G313500 chrUn 90.792 619 52 5 2816 3431 412860344 412860960 0.000000e+00 822
13 TraesCS3B01G313500 chrUn 90.291 618 56 4 2816 3431 36298506 36297891 0.000000e+00 806
14 TraesCS3B01G313500 chr1B 90.747 616 53 2 2816 3427 391420020 391420635 0.000000e+00 819
15 TraesCS3B01G313500 chr1B 96.784 342 11 0 311 652 552308259 552307918 3.840000e-159 571
16 TraesCS3B01G313500 chr1B 98.997 299 2 1 1 299 552308803 552308506 5.040000e-148 534
17 TraesCS3B01G313500 chr7B 90.291 618 54 4 2816 3431 611349715 611349102 0.000000e+00 804
18 TraesCS3B01G313500 chr4B 90.209 623 50 10 2816 3431 595287806 595287188 0.000000e+00 802
19 TraesCS3B01G313500 chr4B 97.633 338 8 0 311 648 103053237 103053574 6.380000e-162 580
20 TraesCS3B01G313500 chr4B 96.746 338 10 1 311 648 462209389 462209725 2.310000e-156 562
21 TraesCS3B01G313500 chr4B 98.997 299 3 0 1 299 103052692 103052990 1.400000e-148 536
22 TraesCS3B01G313500 chr2B 90.145 619 56 5 2816 3431 111464825 111464209 0.000000e+00 800
23 TraesCS3B01G313500 chr2B 97.067 341 10 0 311 651 44906560 44906220 2.970000e-160 575
24 TraesCS3B01G313500 chr2B 99.331 299 2 0 1 299 44907105 44906807 3.010000e-150 542
25 TraesCS3B01G313500 chr2B 98.662 299 4 0 1 299 151498425 151498127 6.520000e-147 531
26 TraesCS3B01G313500 chr2B 72.968 1058 230 46 1309 2333 728269714 728268680 5.530000e-83 318
27 TraesCS3B01G313500 chr5B 89.408 642 53 11 2800 3431 401135016 401134380 0.000000e+00 795
28 TraesCS3B01G313500 chr5B 96.765 340 11 0 311 650 495831805 495832144 4.970000e-158 568
29 TraesCS3B01G313500 chr5B 96.746 338 10 1 311 648 299599837 299600173 2.310000e-156 562
30 TraesCS3B01G313500 chr5B 95.942 345 14 0 311 655 633969659 633970003 8.320000e-156 560
31 TraesCS3B01G313500 chr5B 96.450 338 12 0 311 648 45647188 45647525 2.990000e-155 558
32 TraesCS3B01G313500 chr5B 99.666 299 1 0 1 299 633969115 633969413 6.470000e-152 547
33 TraesCS3B01G313500 chr5B 99.331 299 2 0 1 299 299599292 299599590 3.010000e-150 542
34 TraesCS3B01G313500 chr5B 98.328 299 5 0 1 299 495831260 495831558 3.030000e-145 525
35 TraesCS3B01G313500 chr1D 77.519 1032 204 22 1264 2281 436098380 436097363 2.280000e-166 595
36 TraesCS3B01G313500 chr1D 73.999 1423 298 55 1005 2388 436087217 436085828 2.360000e-141 512
37 TraesCS3B01G313500 chr1A 76.357 1032 213 25 1264 2281 533265735 533264721 3.030000e-145 525
38 TraesCS3B01G313500 chr2A 73.507 1072 222 51 1295 2331 733132465 733131421 1.960000e-92 350
39 TraesCS3B01G313500 chr2D 73.066 1073 229 48 1295 2331 598898333 598897285 3.300000e-85 326


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 TraesCS3B01G313500 chr3B 504066565 504069995 3430 False 6336.0 6336 100.0000 1 3431 1 chr3B.!!$F2 3430
1 TraesCS3B01G313500 chr3B 503984633 503985702 1069 False 592.0 592 76.8950 1307 2376 1 chr3B.!!$F1 1069
2 TraesCS3B01G313500 chr3B 589556888 589557772 884 False 552.0 573 97.8605 1 650 2 chr3B.!!$F3 649
3 TraesCS3B01G313500 chr3D 387708555 387710498 1943 True 2856.0 2856 93.1930 858 2804 1 chr3D.!!$R1 1946
4 TraesCS3B01G313500 chr3D 539552123 539552714 591 True 800.0 800 91.0770 2840 3431 1 chr3D.!!$R3 591
5 TraesCS3B01G313500 chr3D 387769214 387770580 1366 True 734.0 734 76.6230 1008 2378 1 chr3D.!!$R2 1370
6 TraesCS3B01G313500 chr3A 509019858 509021921 2063 True 1496.5 2678 91.2340 699 2804 2 chr3A.!!$R2 2105
7 TraesCS3B01G313500 chr3A 509121110 509122486 1376 True 728.0 728 76.5210 999 2378 1 chr3A.!!$R1 1379
8 TraesCS3B01G313500 chr6B 640128896 640129508 612 True 846.0 846 91.6940 2816 3425 1 chr6B.!!$R1 609
9 TraesCS3B01G313500 chrUn 412860344 412860960 616 False 822.0 822 90.7920 2816 3431 1 chrUn.!!$F1 615
10 TraesCS3B01G313500 chrUn 36297891 36298506 615 True 806.0 806 90.2910 2816 3431 1 chrUn.!!$R1 615
11 TraesCS3B01G313500 chr1B 391420020 391420635 615 False 819.0 819 90.7470 2816 3427 1 chr1B.!!$F1 611
12 TraesCS3B01G313500 chr1B 552307918 552308803 885 True 552.5 571 97.8905 1 652 2 chr1B.!!$R1 651
13 TraesCS3B01G313500 chr7B 611349102 611349715 613 True 804.0 804 90.2910 2816 3431 1 chr7B.!!$R1 615
14 TraesCS3B01G313500 chr4B 595287188 595287806 618 True 802.0 802 90.2090 2816 3431 1 chr4B.!!$R1 615
15 TraesCS3B01G313500 chr4B 103052692 103053574 882 False 558.0 580 98.3150 1 648 2 chr4B.!!$F2 647
16 TraesCS3B01G313500 chr2B 111464209 111464825 616 True 800.0 800 90.1450 2816 3431 1 chr2B.!!$R1 615
17 TraesCS3B01G313500 chr2B 44906220 44907105 885 True 558.5 575 98.1990 1 651 2 chr2B.!!$R4 650
18 TraesCS3B01G313500 chr2B 728268680 728269714 1034 True 318.0 318 72.9680 1309 2333 1 chr2B.!!$R3 1024
19 TraesCS3B01G313500 chr5B 401134380 401135016 636 True 795.0 795 89.4080 2800 3431 1 chr5B.!!$R1 631
20 TraesCS3B01G313500 chr5B 633969115 633970003 888 False 553.5 560 97.8040 1 655 2 chr5B.!!$F4 654
21 TraesCS3B01G313500 chr5B 299599292 299600173 881 False 552.0 562 98.0385 1 648 2 chr5B.!!$F2 647
22 TraesCS3B01G313500 chr5B 495831260 495832144 884 False 546.5 568 97.5465 1 650 2 chr5B.!!$F3 649
23 TraesCS3B01G313500 chr1D 436097363 436098380 1017 True 595.0 595 77.5190 1264 2281 1 chr1D.!!$R2 1017
24 TraesCS3B01G313500 chr1D 436085828 436087217 1389 True 512.0 512 73.9990 1005 2388 1 chr1D.!!$R1 1383
25 TraesCS3B01G313500 chr1A 533264721 533265735 1014 True 525.0 525 76.3570 1264 2281 1 chr1A.!!$R1 1017
26 TraesCS3B01G313500 chr2A 733131421 733132465 1044 True 350.0 350 73.5070 1295 2331 1 chr2A.!!$R1 1036
27 TraesCS3B01G313500 chr2D 598897285 598898333 1048 True 326.0 326 73.0660 1295 2331 1 chr2D.!!$R1 1036

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
304 306 0.032678 ATCCTCACATAGGCGCTTCG 59.967 55.0 7.64 0.0 46.1 3.79 F
817 1055 0.040336 CGTCCCGTGATGATACTCCG 60.040 60.0 0.00 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 2223 1.600916 AGGAAGCAACGCCTCCAAC 60.601 57.895 6.4 0.0 41.28 3.77 R
2487 2762 0.388649 GTGAATCCAGCACGACTCGT 60.389 55.000 0.0 0.0 42.36 4.18 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
81 82 5.188948 TCACACTATGCATTAACCACCTACT 59.811 40.000 3.54 0.00 0.00 2.57
299 301 1.575244 CACACATCCTCACATAGGCG 58.425 55.000 0.00 0.00 46.10 5.52
300 302 0.179073 ACACATCCTCACATAGGCGC 60.179 55.000 0.00 0.00 46.10 6.53
301 303 0.105593 CACATCCTCACATAGGCGCT 59.894 55.000 7.64 0.00 46.10 5.92
302 304 0.833287 ACATCCTCACATAGGCGCTT 59.167 50.000 7.64 0.52 46.10 4.68
303 305 1.202580 ACATCCTCACATAGGCGCTTC 60.203 52.381 7.64 0.00 46.10 3.86
304 306 0.032678 ATCCTCACATAGGCGCTTCG 59.967 55.000 7.64 0.00 46.10 3.79
305 307 1.592669 CCTCACATAGGCGCTTCGG 60.593 63.158 7.64 0.00 38.97 4.30
308 310 0.101759 TCACATAGGCGCTTCGGTAC 59.898 55.000 7.64 0.00 0.00 3.34
309 311 0.874607 CACATAGGCGCTTCGGTACC 60.875 60.000 7.64 0.16 0.00 3.34
434 672 2.577059 CGAAGCCTACCGCCTCAA 59.423 61.111 0.00 0.00 38.78 3.02
607 845 4.846940 AGTTTTAGACAGGGGTCAGATCTT 59.153 41.667 0.00 0.00 46.80 2.40
655 893 4.692228 ACACGAAATTTTGCCTCAAATGT 58.308 34.783 5.27 0.00 33.19 2.71
656 894 4.744631 ACACGAAATTTTGCCTCAAATGTC 59.255 37.500 5.27 0.00 33.19 3.06
657 895 4.150451 CACGAAATTTTGCCTCAAATGTCC 59.850 41.667 5.27 0.00 33.19 4.02
658 896 4.039124 ACGAAATTTTGCCTCAAATGTCCT 59.961 37.500 5.27 0.00 33.19 3.85
659 897 4.622740 CGAAATTTTGCCTCAAATGTCCTC 59.377 41.667 0.00 0.00 33.19 3.71
660 898 5.565439 CGAAATTTTGCCTCAAATGTCCTCT 60.565 40.000 0.00 0.00 33.19 3.69
661 899 5.397142 AATTTTGCCTCAAATGTCCTCTC 57.603 39.130 0.00 0.00 33.19 3.20
662 900 2.099141 TTGCCTCAAATGTCCTCTCG 57.901 50.000 0.00 0.00 0.00 4.04
663 901 1.266178 TGCCTCAAATGTCCTCTCGA 58.734 50.000 0.00 0.00 0.00 4.04
664 902 1.066858 TGCCTCAAATGTCCTCTCGAC 60.067 52.381 0.00 0.00 42.33 4.20
665 903 1.914634 CCTCAAATGTCCTCTCGACG 58.085 55.000 0.00 0.00 45.23 5.12
666 904 1.472878 CCTCAAATGTCCTCTCGACGA 59.527 52.381 0.00 0.00 45.23 4.20
667 905 2.094700 CCTCAAATGTCCTCTCGACGAA 60.095 50.000 0.00 0.00 45.23 3.85
668 906 3.429547 CCTCAAATGTCCTCTCGACGAAT 60.430 47.826 0.00 0.00 45.23 3.34
669 907 3.770666 TCAAATGTCCTCTCGACGAATC 58.229 45.455 0.00 0.00 45.23 2.52
670 908 3.192633 TCAAATGTCCTCTCGACGAATCA 59.807 43.478 0.00 0.00 45.23 2.57
671 909 4.115516 CAAATGTCCTCTCGACGAATCAT 58.884 43.478 0.00 0.00 45.23 2.45
672 910 4.392921 AATGTCCTCTCGACGAATCATT 57.607 40.909 0.00 3.43 45.23 2.57
673 911 3.422417 TGTCCTCTCGACGAATCATTC 57.578 47.619 0.00 0.00 45.23 2.67
674 912 2.752903 TGTCCTCTCGACGAATCATTCA 59.247 45.455 0.00 0.00 45.23 2.57
675 913 3.381590 TGTCCTCTCGACGAATCATTCAT 59.618 43.478 0.00 0.00 45.23 2.57
676 914 3.733224 GTCCTCTCGACGAATCATTCATG 59.267 47.826 0.00 0.00 0.00 3.07
677 915 3.055591 CCTCTCGACGAATCATTCATGG 58.944 50.000 0.00 0.00 0.00 3.66
678 916 3.055591 CTCTCGACGAATCATTCATGGG 58.944 50.000 0.00 0.00 0.00 4.00
679 917 2.430694 TCTCGACGAATCATTCATGGGT 59.569 45.455 0.00 0.00 0.00 4.51
680 918 3.634910 TCTCGACGAATCATTCATGGGTA 59.365 43.478 0.00 0.00 0.00 3.69
681 919 4.280929 TCTCGACGAATCATTCATGGGTAT 59.719 41.667 0.00 0.00 0.00 2.73
682 920 4.306600 TCGACGAATCATTCATGGGTATG 58.693 43.478 0.00 0.00 35.57 2.39
683 921 3.433274 CGACGAATCATTCATGGGTATGG 59.567 47.826 0.00 0.00 34.97 2.74
684 922 3.149196 ACGAATCATTCATGGGTATGGC 58.851 45.455 0.00 0.00 34.97 4.40
685 923 2.489329 CGAATCATTCATGGGTATGGCC 59.511 50.000 0.00 0.00 34.97 5.36
686 924 2.205022 ATCATTCATGGGTATGGCCG 57.795 50.000 0.00 0.00 38.44 6.13
687 925 0.110295 TCATTCATGGGTATGGCCGG 59.890 55.000 0.00 0.00 38.44 6.13
688 926 1.228552 ATTCATGGGTATGGCCGGC 60.229 57.895 21.18 21.18 38.44 6.13
689 927 2.005606 ATTCATGGGTATGGCCGGCA 62.006 55.000 30.85 15.30 38.44 5.69
690 928 2.005606 TTCATGGGTATGGCCGGCAT 62.006 55.000 30.85 21.27 38.44 4.40
691 929 1.531365 CATGGGTATGGCCGGCATT 60.531 57.895 30.85 17.47 38.44 3.56
692 930 0.251121 CATGGGTATGGCCGGCATTA 60.251 55.000 30.85 16.30 38.44 1.90
693 931 0.251165 ATGGGTATGGCCGGCATTAC 60.251 55.000 30.85 26.09 38.44 1.89
694 932 1.602605 GGGTATGGCCGGCATTACC 60.603 63.158 33.28 33.28 38.44 2.85
695 933 1.454539 GGTATGGCCGGCATTACCT 59.545 57.895 33.51 14.35 35.61 3.08
696 934 0.179001 GGTATGGCCGGCATTACCTT 60.179 55.000 33.51 17.56 35.61 3.50
697 935 1.687563 GTATGGCCGGCATTACCTTT 58.312 50.000 30.85 5.36 35.61 3.11
703 941 0.814010 CCGGCATTACCTTTCTCCCG 60.814 60.000 0.00 0.00 35.61 5.14
708 946 2.421529 GCATTACCTTTCTCCCGGTCAT 60.422 50.000 0.00 0.00 34.76 3.06
716 954 1.358152 TCTCCCGGTCATGTCCTTTT 58.642 50.000 7.41 0.00 0.00 2.27
721 959 2.350522 CCGGTCATGTCCTTTTCTCAG 58.649 52.381 7.41 0.00 0.00 3.35
745 983 0.740737 GCATGGGCTGATTGTACACC 59.259 55.000 0.00 0.00 36.96 4.16
748 986 0.327924 TGGGCTGATTGTACACCTGG 59.672 55.000 0.00 0.00 0.00 4.45
778 1016 2.095415 CGGTCGTCTGATTGACAGTGTA 60.095 50.000 12.91 0.00 45.60 2.90
786 1024 4.162888 TCTGATTGACAGTGTATGGCTGAT 59.837 41.667 0.00 0.00 45.86 2.90
787 1025 5.363580 TCTGATTGACAGTGTATGGCTGATA 59.636 40.000 0.00 0.00 45.86 2.15
797 1035 4.818546 GTGTATGGCTGATATATGATGGCC 59.181 45.833 0.00 0.00 39.93 5.36
798 1036 3.589951 ATGGCTGATATATGATGGCCC 57.410 47.619 0.00 0.00 38.89 5.80
799 1037 1.210234 TGGCTGATATATGATGGCCCG 59.790 52.381 0.00 0.00 38.89 6.13
800 1038 1.210478 GGCTGATATATGATGGCCCGT 59.790 52.381 0.00 0.00 34.19 5.28
801 1039 2.555199 GCTGATATATGATGGCCCGTC 58.445 52.381 0.00 0.00 0.00 4.79
804 1042 0.830648 ATATATGATGGCCCGTCCCG 59.169 55.000 0.00 0.00 0.00 5.14
816 1054 0.314302 CCGTCCCGTGATGATACTCC 59.686 60.000 0.00 0.00 0.00 3.85
817 1055 0.040336 CGTCCCGTGATGATACTCCG 60.040 60.000 0.00 0.00 0.00 4.63
828 1066 0.177373 GATACTCCGGTTCACCACCC 59.823 60.000 0.00 0.00 43.83 4.61
849 1087 3.251972 CCCTCACTCTTGCAAACTTTCTC 59.748 47.826 0.00 0.00 0.00 2.87
850 1088 3.251972 CCTCACTCTTGCAAACTTTCTCC 59.748 47.826 0.00 0.00 0.00 3.71
919 1157 2.288666 TCACTCTTGCAAACCACACTC 58.711 47.619 0.00 0.00 0.00 3.51
931 1169 2.049063 ACACTCGAGTTCGCCAGC 60.049 61.111 17.26 0.00 39.60 4.85
941 1179 1.270550 AGTTCGCCAGCTTTCCATTTG 59.729 47.619 0.00 0.00 0.00 2.32
1066 1304 2.440147 TGAACCCCATGGTGCAGG 59.560 61.111 11.73 7.13 45.96 4.85
1245 1483 1.001406 GAGCAGTACTCCAACACAGCT 59.999 52.381 0.00 0.00 39.75 4.24
1300 1538 2.119611 TGCTCCGGGAGTTCCTCA 59.880 61.111 24.30 11.13 35.95 3.86
1301 1539 2.283529 TGCTCCGGGAGTTCCTCAC 61.284 63.158 24.30 7.22 35.95 3.51
1305 1543 1.609501 CCGGGAGTTCCTCACCTCA 60.610 63.158 0.00 0.00 35.95 3.86
1345 1586 1.284297 CGTGCTCGACATGTTCTGCA 61.284 55.000 13.86 13.86 39.71 4.41
1352 1593 1.350193 GACATGTTCTGCATCGACGT 58.650 50.000 0.00 0.00 35.19 4.34
1448 1689 1.209019 CCTCCAGGTTCCTGATGTCTG 59.791 57.143 19.12 2.81 36.24 3.51
1489 1733 3.026707 TCAAGGATATGGGAGACACGA 57.973 47.619 0.00 0.00 0.00 4.35
1869 2127 1.666054 CTCAGCTGAAAGAGATGGCC 58.334 55.000 18.85 0.00 38.72 5.36
2519 2794 4.630940 GCTGGATTCACTCTTTCTCAGAAG 59.369 45.833 0.00 0.00 0.00 2.85
2522 2797 6.462500 TGGATTCACTCTTTCTCAGAAGAAG 58.538 40.000 0.00 0.00 42.36 2.85
2523 2798 6.268617 TGGATTCACTCTTTCTCAGAAGAAGA 59.731 38.462 5.38 0.00 42.36 2.87
2524 2799 7.158021 GGATTCACTCTTTCTCAGAAGAAGAA 58.842 38.462 5.38 5.17 42.36 2.52
2525 2800 7.659390 GGATTCACTCTTTCTCAGAAGAAGAAA 59.341 37.037 5.38 0.00 42.36 2.52
2526 2801 8.970859 ATTCACTCTTTCTCAGAAGAAGAAAA 57.029 30.769 5.38 1.00 42.36 2.29
2527 2802 8.792830 TTCACTCTTTCTCAGAAGAAGAAAAA 57.207 30.769 5.38 0.00 42.36 1.94
2545 2820 3.518634 AAAAAGGCGTCTGCTCAAAAA 57.481 38.095 0.00 0.00 42.25 1.94
2589 2864 2.555325 TCAAAAGAGATGCAGTGGCTTG 59.445 45.455 0.00 0.00 41.91 4.01
2592 2867 0.035630 AGAGATGCAGTGGCTTGTCC 60.036 55.000 0.00 0.00 37.96 4.02
2607 2909 0.603707 TGTCCTTGCCTCTTTCGCAG 60.604 55.000 0.00 0.00 37.57 5.18
2656 2958 6.255020 TGTCGAATTCGTAATTTAGCTCTTCC 59.745 38.462 25.93 0.00 40.80 3.46
2670 2972 3.360956 CTTCCGCAGCATTTGGCCC 62.361 63.158 0.00 0.00 46.50 5.80
2674 2976 2.420568 CGCAGCATTTGGCCCTCAT 61.421 57.895 0.00 0.00 46.50 2.90
2677 2979 0.177141 CAGCATTTGGCCCTCATTGG 59.823 55.000 0.00 0.00 46.50 3.16
2740 3042 1.612950 AGCCTCATATGCTCGTCTCAG 59.387 52.381 0.00 0.00 32.41 3.35
2747 3049 0.453793 ATGCTCGTCTCAGTCCTTCG 59.546 55.000 0.00 0.00 0.00 3.79
2757 3059 5.044558 GTCTCAGTCCTTCGGTATTGATTC 58.955 45.833 0.00 0.00 0.00 2.52
2772 3075 7.148573 CGGTATTGATTCGAAAATAGGATCCTG 60.149 40.741 25.28 6.34 0.00 3.86
2806 3109 0.546988 GGGGACAGGTGACCTTAGGT 60.547 60.000 2.34 2.34 39.44 3.08
2848 3156 3.055602 GTCCAGACCCATACGTTTAGGTT 60.056 47.826 0.00 0.00 31.10 3.50
2854 3162 6.819649 CAGACCCATACGTTTAGGTTAAATGA 59.180 38.462 0.00 0.00 37.92 2.57
2962 3271 3.671262 GTTTTTGGGGTGAAACGGG 57.329 52.632 0.00 0.00 38.12 5.28
2964 3273 0.688087 TTTTTGGGGTGAAACGGGCT 60.688 50.000 0.00 0.00 38.12 5.19
3091 3402 1.001406 CACACTCCACTCTTCTCCACC 59.999 57.143 0.00 0.00 0.00 4.61
3098 3409 0.193574 ACTCTTCTCCACCCTTCCCA 59.806 55.000 0.00 0.00 0.00 4.37
3159 3482 3.702555 GTGCAACTCGAACGCGCT 61.703 61.111 5.73 0.00 37.46 5.92
3160 3483 2.964925 TGCAACTCGAACGCGCTT 60.965 55.556 5.73 0.00 37.46 4.68
3175 3498 1.603739 GCTTTCGCCCAGTCCCTTT 60.604 57.895 0.00 0.00 0.00 3.11
3225 3548 2.906897 CACCTGGTTTGCGCACCT 60.907 61.111 11.12 0.00 37.75 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 9.755804 TGTGAAGATGTATGTTTTGCAAAATTA 57.244 25.926 26.24 18.56 0.00 1.40
305 307 1.823041 CTCCCCTCGACTCGGGTAC 60.823 68.421 7.41 0.00 40.24 3.34
308 310 4.124943 TCCTCCCCTCGACTCGGG 62.125 72.222 1.12 1.12 41.59 5.14
309 311 2.517402 CTCCTCCCCTCGACTCGG 60.517 72.222 0.00 0.00 0.00 4.63
421 659 1.003718 ACAGTTTGAGGCGGTAGGC 60.004 57.895 0.00 0.00 44.19 3.93
554 792 2.322658 TCTGACCCTTTTGACTACCGT 58.677 47.619 0.00 0.00 0.00 4.83
607 845 9.726438 TTTTGACCCTTTTTACAAAGAAATTCA 57.274 25.926 2.86 0.00 41.97 2.57
655 893 3.243535 CCATGAATGATTCGTCGAGAGGA 60.244 47.826 0.00 0.00 0.00 3.71
656 894 3.055591 CCATGAATGATTCGTCGAGAGG 58.944 50.000 0.00 0.00 0.00 3.69
657 895 3.055591 CCCATGAATGATTCGTCGAGAG 58.944 50.000 0.00 0.00 0.00 3.20
658 896 2.430694 ACCCATGAATGATTCGTCGAGA 59.569 45.455 0.00 0.00 0.00 4.04
659 897 2.826428 ACCCATGAATGATTCGTCGAG 58.174 47.619 0.00 0.00 0.00 4.04
660 898 2.979814 ACCCATGAATGATTCGTCGA 57.020 45.000 0.00 0.00 0.00 4.20
661 899 3.433274 CCATACCCATGAATGATTCGTCG 59.567 47.826 0.00 0.00 33.67 5.12
662 900 3.189287 GCCATACCCATGAATGATTCGTC 59.811 47.826 0.00 0.00 33.67 4.20
663 901 3.149196 GCCATACCCATGAATGATTCGT 58.851 45.455 0.18 0.00 33.67 3.85
664 902 2.489329 GGCCATACCCATGAATGATTCG 59.511 50.000 0.00 0.00 33.67 3.34
665 903 2.489329 CGGCCATACCCATGAATGATTC 59.511 50.000 2.24 0.00 33.67 2.52
666 904 2.517959 CGGCCATACCCATGAATGATT 58.482 47.619 2.24 0.00 33.67 2.57
667 905 1.272092 CCGGCCATACCCATGAATGAT 60.272 52.381 2.24 0.00 33.67 2.45
668 906 0.110295 CCGGCCATACCCATGAATGA 59.890 55.000 2.24 0.00 33.67 2.57
669 907 1.526575 GCCGGCCATACCCATGAATG 61.527 60.000 18.11 0.00 33.67 2.67
670 908 1.228552 GCCGGCCATACCCATGAAT 60.229 57.895 18.11 0.00 33.67 2.57
671 909 2.005606 ATGCCGGCCATACCCATGAA 62.006 55.000 26.77 0.00 33.67 2.57
672 910 2.005606 AATGCCGGCCATACCCATGA 62.006 55.000 26.77 0.00 33.67 3.07
673 911 0.251121 TAATGCCGGCCATACCCATG 60.251 55.000 26.77 0.00 32.67 3.66
674 912 0.251165 GTAATGCCGGCCATACCCAT 60.251 55.000 26.77 5.51 32.67 4.00
675 913 1.149627 GTAATGCCGGCCATACCCA 59.850 57.895 26.77 2.60 32.67 4.51
676 914 1.602605 GGTAATGCCGGCCATACCC 60.603 63.158 32.54 20.35 32.67 3.69
677 915 0.179001 AAGGTAATGCCGGCCATACC 60.179 55.000 34.20 34.20 43.70 2.73
678 916 1.607148 GAAAGGTAATGCCGGCCATAC 59.393 52.381 26.77 24.76 43.70 2.39
679 917 1.493022 AGAAAGGTAATGCCGGCCATA 59.507 47.619 26.77 14.44 43.70 2.74
680 918 0.258774 AGAAAGGTAATGCCGGCCAT 59.741 50.000 26.77 15.63 43.70 4.40
681 919 0.393808 GAGAAAGGTAATGCCGGCCA 60.394 55.000 26.77 12.96 43.70 5.36
682 920 1.101635 GGAGAAAGGTAATGCCGGCC 61.102 60.000 26.77 8.13 43.70 6.13
683 921 1.101635 GGGAGAAAGGTAATGCCGGC 61.102 60.000 22.73 22.73 43.70 6.13
684 922 0.814010 CGGGAGAAAGGTAATGCCGG 60.814 60.000 0.00 0.00 43.33 6.13
685 923 0.814010 CCGGGAGAAAGGTAATGCCG 60.814 60.000 0.00 0.00 46.19 5.69
686 924 0.255033 ACCGGGAGAAAGGTAATGCC 59.745 55.000 6.32 0.00 39.30 4.40
687 925 1.065709 TGACCGGGAGAAAGGTAATGC 60.066 52.381 6.32 0.00 41.51 3.56
688 926 3.206150 CATGACCGGGAGAAAGGTAATG 58.794 50.000 6.32 0.00 41.51 1.90
689 927 2.844348 ACATGACCGGGAGAAAGGTAAT 59.156 45.455 6.32 0.00 41.51 1.89
690 928 2.235402 GACATGACCGGGAGAAAGGTAA 59.765 50.000 6.32 0.00 41.51 2.85
691 929 1.829222 GACATGACCGGGAGAAAGGTA 59.171 52.381 6.32 0.00 41.51 3.08
692 930 0.613777 GACATGACCGGGAGAAAGGT 59.386 55.000 6.32 0.00 44.64 3.50
693 931 0.107654 GGACATGACCGGGAGAAAGG 60.108 60.000 6.32 0.00 0.00 3.11
694 932 0.905357 AGGACATGACCGGGAGAAAG 59.095 55.000 6.32 0.00 34.73 2.62
695 933 1.358152 AAGGACATGACCGGGAGAAA 58.642 50.000 6.32 0.00 34.73 2.52
696 934 1.358152 AAAGGACATGACCGGGAGAA 58.642 50.000 6.32 0.00 34.73 2.87
697 935 1.278127 GAAAAGGACATGACCGGGAGA 59.722 52.381 6.32 0.00 34.73 3.71
703 941 4.006319 CCTTCTGAGAAAAGGACATGACC 58.994 47.826 6.05 6.05 45.15 4.02
708 946 1.774254 TGCCCTTCTGAGAAAAGGACA 59.226 47.619 13.51 0.54 45.15 4.02
716 954 1.617536 AGCCCATGCCCTTCTGAGA 60.618 57.895 0.00 0.00 38.69 3.27
721 959 0.685458 ACAATCAGCCCATGCCCTTC 60.685 55.000 0.00 0.00 38.69 3.46
778 1016 2.158711 CGGGCCATCATATATCAGCCAT 60.159 50.000 4.39 0.00 42.29 4.40
799 1037 0.314302 CCGGAGTATCATCACGGGAC 59.686 60.000 0.00 0.00 40.79 4.46
800 1038 2.728397 CCGGAGTATCATCACGGGA 58.272 57.895 0.00 0.00 40.79 5.14
804 1042 2.167693 TGGTGAACCGGAGTATCATCAC 59.832 50.000 9.46 10.25 39.43 3.06
828 1066 3.251972 GGAGAAAGTTTGCAAGAGTGAGG 59.748 47.826 0.00 0.00 0.00 3.86
849 1087 4.060900 GTCATATATCAGCCACACACTGG 58.939 47.826 0.00 0.00 44.08 4.00
850 1088 3.737774 CGTCATATATCAGCCACACACTG 59.262 47.826 0.00 0.00 36.44 3.66
919 1157 1.021390 ATGGAAAGCTGGCGAACTCG 61.021 55.000 0.00 0.00 43.27 4.18
931 1169 7.149569 TGATTAGCAGAGAACAAATGGAAAG 57.850 36.000 0.00 0.00 0.00 2.62
983 1221 3.939837 ATGCCGGCTCACAGTCACG 62.940 63.158 29.70 0.00 0.00 4.35
1245 1483 2.729675 CTCGTCGAGCATGCGCAAA 61.730 57.895 21.59 5.82 42.27 3.68
1300 1538 2.997897 GACGGCAGGGAGTGAGGT 60.998 66.667 0.00 0.00 0.00 3.85
1301 1539 4.135153 CGACGGCAGGGAGTGAGG 62.135 72.222 0.00 0.00 0.00 3.86
1707 1951 2.233676 CAGTGGCCCGATGCAGTATATA 59.766 50.000 0.00 0.00 43.89 0.86
1869 2127 2.413765 GAGTTCTCTAGCCCGCCG 59.586 66.667 0.00 0.00 0.00 6.46
1953 2223 1.600916 AGGAAGCAACGCCTCCAAC 60.601 57.895 6.40 0.00 41.28 3.77
2055 2325 2.338984 GTCACGAACGCTCCCACT 59.661 61.111 0.00 0.00 0.00 4.00
2160 2430 3.271225 TCTCCTCCACCAGGTGTATCTTA 59.729 47.826 18.82 0.00 43.95 2.10
2224 2494 2.581354 CACCTCCTCGGCCTTCAG 59.419 66.667 0.00 0.00 35.61 3.02
2487 2762 0.388649 GTGAATCCAGCACGACTCGT 60.389 55.000 0.00 0.00 42.36 4.18
2501 2776 8.970859 TTTTCTTCTTCTGAGAAAGAGTGAAT 57.029 30.769 0.00 0.00 41.19 2.57
2525 2800 3.518634 TTTTTGAGCAGACGCCTTTTT 57.481 38.095 0.00 0.00 39.83 1.94
2553 2828 8.958506 CATCTCTTTTGATTTCCATCTTCTTCT 58.041 33.333 0.00 0.00 0.00 2.85
2562 2837 4.219070 CCACTGCATCTCTTTTGATTTCCA 59.781 41.667 0.00 0.00 0.00 3.53
2589 2864 1.301677 CCTGCGAAAGAGGCAAGGAC 61.302 60.000 0.00 0.00 40.39 3.85
2592 2867 1.457346 AATCCTGCGAAAGAGGCAAG 58.543 50.000 0.00 0.00 40.39 4.01
2607 2909 1.800681 GCCTGCACCGTACAAATCC 59.199 57.895 0.00 0.00 0.00 3.01
2656 2958 1.952102 AATGAGGGCCAAATGCTGCG 61.952 55.000 6.18 0.00 40.92 5.18
2670 2972 4.336433 AGAAATATGCAACGTCCCAATGAG 59.664 41.667 0.00 0.00 0.00 2.90
2674 2976 5.123186 CAGTAAGAAATATGCAACGTCCCAA 59.877 40.000 0.00 0.00 0.00 4.12
2677 2979 4.495844 GCCAGTAAGAAATATGCAACGTCC 60.496 45.833 0.00 0.00 0.00 4.79
2718 3020 3.425659 TGAGACGAGCATATGAGGCTAT 58.574 45.455 6.97 0.00 42.78 2.97
2747 3049 7.661847 ACAGGATCCTATTTTCGAATCAATACC 59.338 37.037 15.67 0.00 0.00 2.73
2757 3059 2.874701 CAGCCACAGGATCCTATTTTCG 59.125 50.000 15.67 3.14 0.00 3.46
2772 3075 3.041940 CCCGTGAACGTCAGCCAC 61.042 66.667 1.75 0.00 37.74 5.01
2806 3109 1.630369 CAGAATGGGGTCTGGAGTTGA 59.370 52.381 0.00 0.00 41.21 3.18
2823 3130 1.933021 AACGTATGGGTCTGGACAGA 58.067 50.000 0.00 0.00 34.56 3.41
2848 3156 1.133407 GCCGCCCGATTTGTTCATTTA 59.867 47.619 0.00 0.00 0.00 1.40
2875 3183 2.951475 AAAGTCCGTTTGCTCCCGCA 62.951 55.000 0.00 0.00 46.24 5.69
3017 3326 1.526575 AAAAGCCCGTCATGTGCCAG 61.527 55.000 0.00 0.00 0.00 4.85
3072 3383 1.343069 GGTGGAGAAGAGTGGAGTGT 58.657 55.000 0.00 0.00 0.00 3.55
3091 3402 0.621082 GAGGGGAAGAGTTGGGAAGG 59.379 60.000 0.00 0.00 0.00 3.46
3098 3409 4.083862 GCGGCGAGGGGAAGAGTT 62.084 66.667 12.98 0.00 0.00 3.01
3159 3482 1.074248 GGAAAGGGACTGGGCGAAA 59.926 57.895 0.00 0.00 40.86 3.46
3160 3483 2.754375 GGAAAGGGACTGGGCGAA 59.246 61.111 0.00 0.00 40.86 4.70
3169 3492 3.387947 GGCGACGAGGGAAAGGGA 61.388 66.667 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.