Multiple sequence alignment - TraesCS3B01G343500

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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 TraesCS3B01G343500 chr3B 100.000 3441 0 0 1 3441 552474702 552478142 0.000000e+00 6355.0
1 TraesCS3B01G343500 chr3B 92.840 810 32 7 1 784 409279270 409278461 0.000000e+00 1151.0
2 TraesCS3B01G343500 chr4D 95.672 1340 31 7 794 2115 183382749 183384079 0.000000e+00 2128.0
3 TraesCS3B01G343500 chr4D 97.134 314 7 2 2241 2552 183384086 183384399 2.350000e-146 529.0
4 TraesCS3B01G343500 chr4A 95.063 1357 41 16 783 2115 310239423 310240777 0.000000e+00 2111.0
5 TraesCS3B01G343500 chr4A 95.238 441 20 1 2113 2552 310240807 310241247 0.000000e+00 697.0
6 TraesCS3B01G343500 chr4A 95.604 91 4 0 2606 2696 741977194 741977284 2.770000e-31 147.0
7 TraesCS3B01G343500 chr3D 97.268 1208 20 7 921 2115 424002688 424001481 0.000000e+00 2036.0
8 TraesCS3B01G343500 chr3D 96.825 441 12 1 2116 2554 424001448 424001008 0.000000e+00 736.0
9 TraesCS3B01G343500 chr3D 97.260 219 6 0 2395 2613 424001001 424000783 4.190000e-99 372.0
10 TraesCS3B01G343500 chr3D 94.643 56 2 1 2693 2748 424000786 424000732 6.120000e-13 86.1
11 TraesCS3B01G343500 chr4B 96.360 1099 27 5 1018 2115 200657993 200656907 0.000000e+00 1796.0
12 TraesCS3B01G343500 chr4B 94.558 441 23 1 2113 2552 200656877 200656437 0.000000e+00 680.0
13 TraesCS3B01G343500 chr3A 95.326 813 14 10 963 1753 565042049 565042859 0.000000e+00 1269.0
14 TraesCS3B01G343500 chr3A 93.061 807 31 5 1 782 712722886 712723692 0.000000e+00 1157.0
15 TraesCS3B01G343500 chr3A 92.857 812 32 6 1 786 597968675 597969486 0.000000e+00 1155.0
16 TraesCS3B01G343500 chr3A 92.831 809 33 4 1 784 12178276 12177468 0.000000e+00 1149.0
17 TraesCS3B01G343500 chr3A 92.089 809 36 11 1 783 688890620 688891426 0.000000e+00 1114.0
18 TraesCS3B01G343500 chr3A 90.111 809 31 13 1 783 696640103 696639318 0.000000e+00 1005.0
19 TraesCS3B01G343500 chr3A 94.379 427 21 3 1753 2177 565042819 565043244 0.000000e+00 652.0
20 TraesCS3B01G343500 chr3A 96.144 389 15 0 2225 2613 565043247 565043635 1.350000e-178 636.0
21 TraesCS3B01G343500 chr7B 97.701 696 13 2 2748 3441 68096713 68097407 0.000000e+00 1194.0
22 TraesCS3B01G343500 chr7B 93.795 693 23 11 2749 3441 528878817 528879489 0.000000e+00 1024.0
23 TraesCS3B01G343500 chr5B 93.612 814 25 6 1 787 550170430 550171243 0.000000e+00 1190.0
24 TraesCS3B01G343500 chr5B 97.258 693 18 1 2749 3441 420716498 420717189 0.000000e+00 1173.0
25 TraesCS3B01G343500 chr5B 93.651 693 24 11 2749 3441 406871282 406870610 0.000000e+00 1018.0
26 TraesCS3B01G343500 chr5B 93.372 694 25 13 2749 3441 179226334 179227007 0.000000e+00 1007.0
27 TraesCS3B01G343500 chr6B 93.086 810 31 5 1 785 213304871 213305680 0.000000e+00 1162.0
28 TraesCS3B01G343500 chr6B 93.237 695 25 13 2749 3441 408661274 408661948 0.000000e+00 1003.0
29 TraesCS3B01G343500 chr6B 93.218 693 26 12 2749 3441 704851369 704850698 0.000000e+00 1000.0
30 TraesCS3B01G343500 chr1B 92.963 810 30 7 1 784 569979204 569980012 0.000000e+00 1155.0
31 TraesCS3B01G343500 chr1B 92.698 808 33 6 1 783 27083418 27084224 0.000000e+00 1142.0
32 TraesCS3B01G343500 chr1B 89.815 108 7 3 2591 2697 77543003 77543107 5.990000e-28 135.0
33 TraesCS3B01G343500 chr5A 92.822 808 33 5 1 783 143593738 143594545 0.000000e+00 1147.0
34 TraesCS3B01G343500 chr5A 90.566 106 7 3 2591 2694 450225342 450225446 1.670000e-28 137.0
35 TraesCS3B01G343500 chr2A 93.362 693 25 12 2749 3441 719453111 719453782 0.000000e+00 1005.0
36 TraesCS3B01G343500 chr7A 92.929 693 28 12 2749 3441 171417966 171418637 0.000000e+00 989.0
37 TraesCS3B01G343500 chr7A 91.114 709 35 11 105 786 202741132 202741839 0.000000e+00 935.0
38 TraesCS3B01G343500 chr7A 95.247 547 26 0 1 547 108783896 108784442 0.000000e+00 867.0
39 TraesCS3B01G343500 chrUn 94.845 97 5 0 2606 2702 17148595 17148691 5.950000e-33 152.0
40 TraesCS3B01G343500 chr2D 95.604 91 4 0 2610 2700 35026578 35026488 2.770000e-31 147.0
41 TraesCS3B01G343500 chr1A 93.000 100 4 3 2598 2694 572633046 572633145 3.580000e-30 143.0
42 TraesCS3B01G343500 chr6A 91.346 104 7 2 2597 2699 101438265 101438367 1.290000e-29 141.0
43 TraesCS3B01G343500 chr2B 91.429 105 5 4 2592 2694 736103138 736103240 1.290000e-29 141.0
44 TraesCS3B01G343500 chr7D 89.286 112 10 2 2591 2702 252265177 252265286 4.630000e-29 139.0


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 TraesCS3B01G343500 chr3B 552474702 552478142 3440 False 6355.000000 6355 100.0000 1 3441 1 chr3B.!!$F1 3440
1 TraesCS3B01G343500 chr3B 409278461 409279270 809 True 1151.000000 1151 92.8400 1 784 1 chr3B.!!$R1 783
2 TraesCS3B01G343500 chr4D 183382749 183384399 1650 False 1328.500000 2128 96.4030 794 2552 2 chr4D.!!$F1 1758
3 TraesCS3B01G343500 chr4A 310239423 310241247 1824 False 1404.000000 2111 95.1505 783 2552 2 chr4A.!!$F2 1769
4 TraesCS3B01G343500 chr3D 424000732 424002688 1956 True 807.525000 2036 96.4990 921 2748 4 chr3D.!!$R1 1827
5 TraesCS3B01G343500 chr4B 200656437 200657993 1556 True 1238.000000 1796 95.4590 1018 2552 2 chr4B.!!$R1 1534
6 TraesCS3B01G343500 chr3A 712722886 712723692 806 False 1157.000000 1157 93.0610 1 782 1 chr3A.!!$F3 781
7 TraesCS3B01G343500 chr3A 597968675 597969486 811 False 1155.000000 1155 92.8570 1 786 1 chr3A.!!$F1 785
8 TraesCS3B01G343500 chr3A 12177468 12178276 808 True 1149.000000 1149 92.8310 1 784 1 chr3A.!!$R1 783
9 TraesCS3B01G343500 chr3A 688890620 688891426 806 False 1114.000000 1114 92.0890 1 783 1 chr3A.!!$F2 782
10 TraesCS3B01G343500 chr3A 696639318 696640103 785 True 1005.000000 1005 90.1110 1 783 1 chr3A.!!$R2 782
11 TraesCS3B01G343500 chr3A 565042049 565043635 1586 False 852.333333 1269 95.2830 963 2613 3 chr3A.!!$F4 1650
12 TraesCS3B01G343500 chr7B 68096713 68097407 694 False 1194.000000 1194 97.7010 2748 3441 1 chr7B.!!$F1 693
13 TraesCS3B01G343500 chr7B 528878817 528879489 672 False 1024.000000 1024 93.7950 2749 3441 1 chr7B.!!$F2 692
14 TraesCS3B01G343500 chr5B 550170430 550171243 813 False 1190.000000 1190 93.6120 1 787 1 chr5B.!!$F3 786
15 TraesCS3B01G343500 chr5B 420716498 420717189 691 False 1173.000000 1173 97.2580 2749 3441 1 chr5B.!!$F2 692
16 TraesCS3B01G343500 chr5B 406870610 406871282 672 True 1018.000000 1018 93.6510 2749 3441 1 chr5B.!!$R1 692
17 TraesCS3B01G343500 chr5B 179226334 179227007 673 False 1007.000000 1007 93.3720 2749 3441 1 chr5B.!!$F1 692
18 TraesCS3B01G343500 chr6B 213304871 213305680 809 False 1162.000000 1162 93.0860 1 785 1 chr6B.!!$F1 784
19 TraesCS3B01G343500 chr6B 408661274 408661948 674 False 1003.000000 1003 93.2370 2749 3441 1 chr6B.!!$F2 692
20 TraesCS3B01G343500 chr6B 704850698 704851369 671 True 1000.000000 1000 93.2180 2749 3441 1 chr6B.!!$R1 692
21 TraesCS3B01G343500 chr1B 569979204 569980012 808 False 1155.000000 1155 92.9630 1 784 1 chr1B.!!$F3 783
22 TraesCS3B01G343500 chr1B 27083418 27084224 806 False 1142.000000 1142 92.6980 1 783 1 chr1B.!!$F1 782
23 TraesCS3B01G343500 chr5A 143593738 143594545 807 False 1147.000000 1147 92.8220 1 783 1 chr5A.!!$F1 782
24 TraesCS3B01G343500 chr2A 719453111 719453782 671 False 1005.000000 1005 93.3620 2749 3441 1 chr2A.!!$F1 692
25 TraesCS3B01G343500 chr7A 171417966 171418637 671 False 989.000000 989 92.9290 2749 3441 1 chr7A.!!$F2 692
26 TraesCS3B01G343500 chr7A 202741132 202741839 707 False 935.000000 935 91.1140 105 786 1 chr7A.!!$F3 681
27 TraesCS3B01G343500 chr7A 108783896 108784442 546 False 867.000000 867 95.2470 1 547 1 chr7A.!!$F1 546

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
465 466 0.686789 TCAGCTGAGCTAACTGCCAA 59.313 50.0 13.74 0.0 44.23 4.52 F
549 550 0.836606 TCCTTTGCAGTGGACTCACA 59.163 50.0 5.76 0.0 45.91 3.58 F
925 954 0.905357 AACATAAGTCCGCAGCCTCT 59.095 50.0 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2051 2.028748 AGCCATGAAAAGACATGTTGCC 60.029 45.455 0.0 0.0 44.0 4.52 R
2169 2281 3.225940 TGCATTTTCCACATGTACACCA 58.774 40.909 0.0 0.0 0.0 4.17 R
2677 3138 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.0 0.0 0.0 4.00 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
181 182 2.223525 GCGCCGACAGATAGTAAAGAGT 60.224 50.000 0.00 0.00 0.00 3.24
231 232 4.736473 ACACTAGCCATTAAGGTTTTGGT 58.264 39.130 0.00 0.00 40.61 3.67
277 278 4.479156 ACCCAAAGGACCAATAAGGAAA 57.521 40.909 0.00 0.00 37.45 3.13
305 306 1.073923 ACATGTGGAGGAAACCAGGAC 59.926 52.381 0.00 0.00 40.85 3.85
465 466 0.686789 TCAGCTGAGCTAACTGCCAA 59.313 50.000 13.74 0.00 44.23 4.52
470 471 5.734550 AGCTGAGCTAACTGCCAACAGAG 62.735 52.174 4.49 0.00 41.31 3.35
522 523 8.095792 TGGATGCAACAACATAGAAATTGAATT 58.904 29.630 0.00 0.00 0.00 2.17
547 548 1.211703 TGTTCCTTTGCAGTGGACTCA 59.788 47.619 8.96 8.83 31.24 3.41
549 550 0.836606 TCCTTTGCAGTGGACTCACA 59.163 50.000 5.76 0.00 45.91 3.58
550 551 1.421268 TCCTTTGCAGTGGACTCACAT 59.579 47.619 5.76 0.00 45.91 3.21
614 640 3.270877 ACTTTGCGTCCATATCCTTCAC 58.729 45.455 0.00 0.00 0.00 3.18
742 768 6.408869 TCTCATCTGCTTGTAAATGACATGA 58.591 36.000 0.00 0.00 38.07 3.07
820 849 3.368843 GGATAGATCACCCATCGTCCATG 60.369 52.174 0.00 0.00 39.34 3.66
842 871 1.686115 CGCCCTCCCCATCTGAAAAAT 60.686 52.381 0.00 0.00 0.00 1.82
925 954 0.905357 AACATAAGTCCGCAGCCTCT 59.095 50.000 0.00 0.00 0.00 3.69
960 989 3.647771 AAACCCCTCACCCCTCGC 61.648 66.667 0.00 0.00 0.00 5.03
1971 2051 7.605691 ACTCTTCAGTCTTGAATATGGAACTTG 59.394 37.037 0.00 0.00 42.19 3.16
2064 2144 4.096382 TCTTCAAACTTGAAACCAGCAGTC 59.904 41.667 6.36 0.00 45.61 3.51
2069 2149 3.825328 ACTTGAAACCAGCAGTCTCAAT 58.175 40.909 0.00 0.00 0.00 2.57
2146 2258 5.752892 ATCAGCAGCATTCTCAACATTAG 57.247 39.130 0.00 0.00 0.00 1.73
2158 2270 9.694520 CATTCTCAACATTAGTATGAAACGAAG 57.305 33.333 0.00 0.00 35.65 3.79
2165 2277 8.019656 ACATTAGTATGAAACGAAGGGAGTAT 57.980 34.615 0.00 0.00 35.65 2.12
2169 2281 7.125792 AGTATGAAACGAAGGGAGTATCATT 57.874 36.000 0.00 0.00 36.25 2.57
2170 2282 6.986817 AGTATGAAACGAAGGGAGTATCATTG 59.013 38.462 0.00 0.00 36.25 2.82
2191 2303 3.831333 TGGTGTACATGTGGAAAATGCAT 59.169 39.130 9.11 0.00 33.78 3.96
2221 2333 9.313118 AGAAACCAAATAAAGTGTTCAACATTC 57.687 29.630 0.00 0.00 0.00 2.67
2342 2637 4.612412 GTGGTGGTCGCGGTGGAA 62.612 66.667 6.13 0.00 0.00 3.53
2343 2638 4.308458 TGGTGGTCGCGGTGGAAG 62.308 66.667 6.13 0.00 0.00 3.46
2344 2639 3.998672 GGTGGTCGCGGTGGAAGA 61.999 66.667 6.13 0.00 0.00 2.87
2462 2923 8.372459 TCTAGGATGTAGTTTTAAGTTTGCTGA 58.628 33.333 0.00 0.00 0.00 4.26
2599 3060 6.261381 GGTCAAGTGTTGAGTTAATGTTGGTA 59.739 38.462 0.00 0.00 41.01 3.25
2618 3079 8.822805 TGTTGGTATATCATAATTACTCCCTCC 58.177 37.037 0.00 0.00 0.00 4.30
2619 3080 7.655521 TGGTATATCATAATTACTCCCTCCG 57.344 40.000 0.00 0.00 0.00 4.63
2620 3081 7.186972 TGGTATATCATAATTACTCCCTCCGT 58.813 38.462 0.00 0.00 0.00 4.69
2621 3082 7.341256 TGGTATATCATAATTACTCCCTCCGTC 59.659 40.741 0.00 0.00 0.00 4.79
2622 3083 6.793505 ATATCATAATTACTCCCTCCGTCC 57.206 41.667 0.00 0.00 0.00 4.79
2623 3084 3.236896 TCATAATTACTCCCTCCGTCCC 58.763 50.000 0.00 0.00 0.00 4.46
2624 3085 1.696063 TAATTACTCCCTCCGTCCCG 58.304 55.000 0.00 0.00 0.00 5.14
2625 3086 0.325016 AATTACTCCCTCCGTCCCGT 60.325 55.000 0.00 0.00 0.00 5.28
2626 3087 0.552848 ATTACTCCCTCCGTCCCGTA 59.447 55.000 0.00 0.00 0.00 4.02
2627 3088 0.331278 TTACTCCCTCCGTCCCGTAA 59.669 55.000 0.00 0.00 0.00 3.18
2628 3089 0.552848 TACTCCCTCCGTCCCGTAAT 59.447 55.000 0.00 0.00 0.00 1.89
2629 3090 1.041447 ACTCCCTCCGTCCCGTAATG 61.041 60.000 0.00 0.00 0.00 1.90
2630 3091 1.000739 TCCCTCCGTCCCGTAATGT 59.999 57.895 0.00 0.00 0.00 2.71
2631 3092 0.258484 TCCCTCCGTCCCGTAATGTA 59.742 55.000 0.00 0.00 0.00 2.29
2632 3093 1.113788 CCCTCCGTCCCGTAATGTAA 58.886 55.000 0.00 0.00 0.00 2.41
2633 3094 1.068127 CCCTCCGTCCCGTAATGTAAG 59.932 57.143 0.00 0.00 0.00 2.34
2634 3095 2.026641 CCTCCGTCCCGTAATGTAAGA 58.973 52.381 0.00 0.00 0.00 2.10
2635 3096 2.223665 CCTCCGTCCCGTAATGTAAGAC 60.224 54.545 0.00 0.00 0.00 3.01
2636 3097 2.424601 CTCCGTCCCGTAATGTAAGACA 59.575 50.000 0.00 0.00 0.00 3.41
2637 3098 3.025978 TCCGTCCCGTAATGTAAGACAT 58.974 45.455 0.00 0.00 41.31 3.06
2639 3100 4.081531 TCCGTCCCGTAATGTAAGACATTT 60.082 41.667 9.92 0.00 45.80 2.32
2640 3101 4.632688 CCGTCCCGTAATGTAAGACATTTT 59.367 41.667 9.92 0.00 45.80 1.82
2641 3102 5.122711 CCGTCCCGTAATGTAAGACATTTTT 59.877 40.000 9.92 0.00 45.80 1.94
2642 3103 6.245724 CGTCCCGTAATGTAAGACATTTTTC 58.754 40.000 9.92 2.25 45.80 2.29
2643 3104 6.245724 GTCCCGTAATGTAAGACATTTTTCG 58.754 40.000 9.92 11.63 45.80 3.46
2644 3105 6.091169 GTCCCGTAATGTAAGACATTTTTCGA 59.909 38.462 9.92 0.00 45.80 3.71
2645 3106 6.091169 TCCCGTAATGTAAGACATTTTTCGAC 59.909 38.462 9.92 2.02 45.80 4.20
2646 3107 6.128499 CCCGTAATGTAAGACATTTTTCGACA 60.128 38.462 9.92 0.00 45.80 4.35
2647 3108 6.735063 CCGTAATGTAAGACATTTTTCGACAC 59.265 38.462 9.92 0.78 45.80 3.67
2648 3109 7.359765 CCGTAATGTAAGACATTTTTCGACACT 60.360 37.037 9.92 0.00 45.80 3.55
2649 3110 8.641155 CGTAATGTAAGACATTTTTCGACACTA 58.359 33.333 9.92 0.00 45.80 2.74
2650 3111 9.953825 GTAATGTAAGACATTTTTCGACACTAG 57.046 33.333 9.92 0.00 45.80 2.57
2651 3112 8.603242 AATGTAAGACATTTTTCGACACTAGT 57.397 30.769 0.00 0.00 45.80 2.57
2652 3113 7.402811 TGTAAGACATTTTTCGACACTAGTG 57.597 36.000 21.44 21.44 0.00 2.74
2653 3114 7.656137 ATGTAAGACATTTTTCGACACTAGTGT 59.344 33.333 28.27 28.27 40.45 3.55
2654 3115 8.136800 TGTAAGACATTTTTCGACACTAGTGTA 58.863 33.333 27.98 11.50 45.05 2.90
2655 3116 7.639162 AAGACATTTTTCGACACTAGTGTAG 57.361 36.000 27.98 26.46 45.05 2.74
2656 3117 6.746120 AGACATTTTTCGACACTAGTGTAGT 58.254 36.000 27.98 15.18 45.05 2.73
2686 3147 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2687 3148 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2688 3149 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2689 3150 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2690 3151 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2691 3152 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2692 3153 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2693 3154 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
2694 3155 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2695 3156 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
2696 3157 0.338814 ATGGGACGGAGGGAGTACTT 59.661 55.000 0.00 0.00 0.00 2.24
2697 3158 0.613853 TGGGACGGAGGGAGTACTTG 60.614 60.000 0.00 0.00 0.00 3.16
2698 3159 0.614134 GGGACGGAGGGAGTACTTGT 60.614 60.000 0.00 0.00 0.00 3.16
2699 3160 0.531200 GGACGGAGGGAGTACTTGTG 59.469 60.000 0.00 0.00 0.00 3.33
2728 3189 9.372369 GGTGCTTATATAGTGATAACATTCTCC 57.628 37.037 0.00 0.00 0.00 3.71
2833 3295 4.386711 CCGAAAAGGTAAGTTTCTGTCCT 58.613 43.478 0.00 0.00 33.63 3.85
2914 3376 4.895889 TCACGTGATTCTCTTCCATCCTAT 59.104 41.667 15.76 0.00 0.00 2.57
2984 3446 6.000840 GTCCCAAAAGAGAGACATCTTCTTT 58.999 40.000 10.63 10.63 38.59 2.52
3048 3510 1.086696 GCTTCAAGCCTGCAATACGA 58.913 50.000 0.00 0.00 34.48 3.43
3175 3637 3.295093 CCTCTCCAGCATCTTCTGTAGA 58.705 50.000 0.00 0.00 37.28 2.59
3216 3679 7.587037 TCTTGATTTTCTCCATCTGTGTTTT 57.413 32.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 182 1.440938 CCGGCGTTTGGACTTTGACA 61.441 55.000 6.01 0.00 0.00 3.58
220 221 6.834451 TGAGGTAATTTGTCACCAAAACCTTA 59.166 34.615 11.04 6.33 45.43 2.69
231 232 9.391006 GTATATTTGACCTGAGGTAATTTGTCA 57.609 33.333 2.97 0.00 35.25 3.58
305 306 6.260714 TCAACATTTATCTTCACGATCCCATG 59.739 38.462 0.00 0.00 33.48 3.66
356 357 2.203394 AGCACCACAAGCACCTGG 60.203 61.111 0.00 0.00 0.00 4.45
433 434 2.036992 CTCAGCTGAGTCAACTCCACTT 59.963 50.000 31.71 0.00 42.20 3.16
465 466 2.628657 GCCAAGTATATCCCGTCTCTGT 59.371 50.000 0.00 0.00 0.00 3.41
470 471 3.181469 TGAGTTGCCAAGTATATCCCGTC 60.181 47.826 0.00 0.00 0.00 4.79
522 523 4.072131 GTCCACTGCAAAGGAACAATCTA 58.928 43.478 8.27 0.00 35.29 1.98
547 548 4.655649 TGTGATGATAGCTACCTCCAATGT 59.344 41.667 0.00 0.00 0.00 2.71
549 550 5.150715 TCTGTGATGATAGCTACCTCCAAT 58.849 41.667 0.00 0.00 0.00 3.16
550 551 4.546674 TCTGTGATGATAGCTACCTCCAA 58.453 43.478 0.00 0.00 0.00 3.53
577 603 5.088739 CGCAAAGTCCATCATAAGTTGTTC 58.911 41.667 0.00 0.00 0.00 3.18
614 640 3.758755 TGGCCTCTCTATAGCAATGTG 57.241 47.619 3.32 0.00 0.00 3.21
694 720 9.878737 AGAAATAAAATCAGGGATCTCATCATT 57.121 29.630 0.00 0.00 0.00 2.57
792 818 0.686789 TGGGTGATCTATCCATGCGG 59.313 55.000 0.00 0.00 0.00 5.69
842 871 2.344981 TTTCTCGGCCGTCGGATCA 61.345 57.895 27.15 1.93 39.77 2.92
925 954 4.894705 GGGTTTGTTAGGGTTTTAGTGGAA 59.105 41.667 0.00 0.00 0.00 3.53
1247 1321 2.050351 AACGTCGACACCTCTGCG 60.050 61.111 17.16 0.88 0.00 5.18
1492 1567 2.234908 AGTGGTAAACTGCTAGCTCCAG 59.765 50.000 17.23 7.68 37.88 3.86
1540 1615 5.704515 AGAATCAAACTCAGTTCTCACATGG 59.295 40.000 0.00 0.00 0.00 3.66
1971 2051 2.028748 AGCCATGAAAAGACATGTTGCC 60.029 45.455 0.00 0.00 44.00 4.52
2138 2250 6.594159 ACTCCCTTCGTTTCATACTAATGTTG 59.406 38.462 0.00 0.00 34.50 3.33
2140 2252 6.295719 ACTCCCTTCGTTTCATACTAATGT 57.704 37.500 0.00 0.00 34.50 2.71
2146 2258 6.202954 CCAATGATACTCCCTTCGTTTCATAC 59.797 42.308 0.00 0.00 33.78 2.39
2158 2270 4.816385 CACATGTACACCAATGATACTCCC 59.184 45.833 0.00 0.00 0.00 4.30
2165 2277 5.566429 GCATTTTCCACATGTACACCAATGA 60.566 40.000 15.74 0.00 0.00 2.57
2169 2281 3.225940 TGCATTTTCCACATGTACACCA 58.774 40.909 0.00 0.00 0.00 4.17
2170 2282 3.932545 TGCATTTTCCACATGTACACC 57.067 42.857 0.00 0.00 0.00 4.16
2191 2303 9.959749 GTTGAACACTTTATTTGGTTTCTCATA 57.040 29.630 0.00 0.00 0.00 2.15
2216 2328 5.386958 TCAAGCTGTAACTAGACGAATGT 57.613 39.130 0.00 0.00 0.00 2.71
2221 2333 6.807230 ACAAGTTATCAAGCTGTAACTAGACG 59.193 38.462 15.62 9.81 39.52 4.18
2342 2637 4.954118 TCCACCACGGCCACCTCT 62.954 66.667 2.24 0.00 33.14 3.69
2343 2638 3.268103 AATCCACCACGGCCACCTC 62.268 63.158 2.24 0.00 33.14 3.85
2344 2639 3.256960 AATCCACCACGGCCACCT 61.257 61.111 2.24 0.00 33.14 4.00
2462 2923 6.822667 TGTAGAGCATCATGTTTCAACAAT 57.177 33.333 0.00 0.00 43.03 2.71
2574 3035 5.067283 ACCAACATTAACTCAACACTTGACC 59.933 40.000 0.00 0.00 35.46 4.02
2599 3060 5.661759 GGGACGGAGGGAGTAATTATGATAT 59.338 44.000 0.00 0.00 0.00 1.63
2627 3088 7.656137 ACACTAGTGTCGAAAAATGTCTTACAT 59.344 33.333 22.95 0.00 40.24 2.29
2628 3089 6.982141 ACACTAGTGTCGAAAAATGTCTTACA 59.018 34.615 22.95 0.00 40.24 2.41
2629 3090 7.404139 ACACTAGTGTCGAAAAATGTCTTAC 57.596 36.000 22.95 0.00 40.24 2.34
2630 3091 8.355169 ACTACACTAGTGTCGAAAAATGTCTTA 58.645 33.333 31.11 8.36 43.74 2.10
2631 3092 7.208080 ACTACACTAGTGTCGAAAAATGTCTT 58.792 34.615 31.11 4.99 43.74 3.01
2632 3093 6.746120 ACTACACTAGTGTCGAAAAATGTCT 58.254 36.000 31.11 5.44 43.74 3.41
2661 3122 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2662 3123 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2663 3124 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2664 3125 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2665 3126 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2667 3128 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2668 3129 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2669 3130 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2670 3131 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2671 3132 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2672 3133 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2673 3134 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2674 3135 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2675 3136 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2676 3137 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2677 3138 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2678 3139 0.613853 CAAGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
2679 3140 0.614134 ACAAGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
2680 3141 0.531200 CACAAGTACTCCCTCCGTCC 59.469 60.000 0.00 0.00 0.00 4.79
2681 3142 1.542492 TCACAAGTACTCCCTCCGTC 58.458 55.000 0.00 0.00 0.00 4.79
2682 3143 1.893801 CTTCACAAGTACTCCCTCCGT 59.106 52.381 0.00 0.00 0.00 4.69
2683 3144 1.204941 CCTTCACAAGTACTCCCTCCG 59.795 57.143 0.00 0.00 0.00 4.63
2684 3145 2.028020 CACCTTCACAAGTACTCCCTCC 60.028 54.545 0.00 0.00 0.00 4.30
2685 3146 2.613223 GCACCTTCACAAGTACTCCCTC 60.613 54.545 0.00 0.00 0.00 4.30
2686 3147 1.348036 GCACCTTCACAAGTACTCCCT 59.652 52.381 0.00 0.00 0.00 4.20
2687 3148 1.348036 AGCACCTTCACAAGTACTCCC 59.652 52.381 0.00 0.00 0.00 4.30
2688 3149 2.841442 AGCACCTTCACAAGTACTCC 57.159 50.000 0.00 0.00 0.00 3.85
2689 3150 8.414778 ACTATATAAGCACCTTCACAAGTACTC 58.585 37.037 0.00 0.00 0.00 2.59
2690 3151 8.198109 CACTATATAAGCACCTTCACAAGTACT 58.802 37.037 0.00 0.00 0.00 2.73
2691 3152 8.195436 TCACTATATAAGCACCTTCACAAGTAC 58.805 37.037 0.00 0.00 0.00 2.73
2692 3153 8.301252 TCACTATATAAGCACCTTCACAAGTA 57.699 34.615 0.00 0.00 0.00 2.24
2693 3154 7.182817 TCACTATATAAGCACCTTCACAAGT 57.817 36.000 0.00 0.00 0.00 3.16
2694 3155 9.764363 TTATCACTATATAAGCACCTTCACAAG 57.236 33.333 0.00 0.00 0.00 3.16
2695 3156 9.542462 GTTATCACTATATAAGCACCTTCACAA 57.458 33.333 0.00 0.00 0.00 3.33
2696 3157 8.700973 TGTTATCACTATATAAGCACCTTCACA 58.299 33.333 0.00 0.00 0.00 3.58
2697 3158 9.712305 ATGTTATCACTATATAAGCACCTTCAC 57.288 33.333 0.00 0.00 0.00 3.18
2728 3189 6.202188 GCGTCCCGGATAATAATACCAATATG 59.798 42.308 0.73 0.00 0.00 1.78
2739 3200 2.079158 CTAGACGCGTCCCGGATAATA 58.921 52.381 34.08 16.72 42.52 0.98
2740 3201 0.879765 CTAGACGCGTCCCGGATAAT 59.120 55.000 34.08 16.48 42.52 1.28
2742 3203 1.598962 CCTAGACGCGTCCCGGATA 60.599 63.158 34.08 18.84 42.52 2.59
2743 3204 2.905880 CCTAGACGCGTCCCGGAT 60.906 66.667 34.08 18.72 42.52 4.18
2746 3207 3.584052 CTCCCTAGACGCGTCCCG 61.584 72.222 34.08 24.23 44.21 5.14
2866 3328 1.898574 GTGGTGGAGCAGGTTGTGG 60.899 63.158 0.00 0.00 0.00 4.17
2919 3381 1.584724 GAGGAGAGGTGGGGATGAAA 58.415 55.000 0.00 0.00 0.00 2.69
2921 3383 1.314867 GGAGGAGAGGTGGGGATGA 59.685 63.158 0.00 0.00 0.00 2.92
2984 3446 0.856982 TTGCCTCTTTCTTGGGGGAA 59.143 50.000 0.00 0.00 0.00 3.97
3048 3510 0.534203 ACAGTTTCATGGACGCCGTT 60.534 50.000 0.00 0.00 0.00 4.44
3216 3679 7.447374 AAATCGTTCATATGAAAACAGGACA 57.553 32.000 19.55 0.00 35.58 4.02
3247 3710 6.233434 AGAACTAGCAGATGATTCAACACAA 58.767 36.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.