Multiple sequence alignment - TraesCS1B01G165300

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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 TraesCS1B01G165300 chr1B 100.000 6948 0 0 1 6948 288643296 288650243 0.000000e+00 12831.0
1 TraesCS1B01G165300 chr1B 78.443 167 25 6 5303 5460 14509062 14508898 1.590000e-16 99.0
2 TraesCS1B01G165300 chr1D 93.873 6267 292 45 758 6948 200710967 200717217 0.000000e+00 9361.0
3 TraesCS1B01G165300 chr1A 90.595 2754 174 35 2632 5326 254185228 254187955 0.000000e+00 3572.0
4 TraesCS1B01G165300 chr1A 96.796 1904 52 6 753 2653 254182953 254184850 0.000000e+00 3169.0
5 TraesCS1B01G165300 chr1A 91.412 1572 110 18 5383 6946 254187955 254189509 0.000000e+00 2132.0
6 TraesCS1B01G165300 chr1A 91.599 619 51 1 1 618 579577557 579578175 0.000000e+00 854.0
7 TraesCS1B01G165300 chr3D 88.804 786 82 4 1 783 424650360 424649578 0.000000e+00 959.0
8 TraesCS1B01G165300 chr3D 73.540 291 55 20 4409 4689 543916781 543917059 2.670000e-14 91.6
9 TraesCS1B01G165300 chr5D 86.897 809 77 14 1 785 404491578 404490775 0.000000e+00 880.0
10 TraesCS1B01G165300 chr5D 85.995 814 86 13 1 792 404103885 404104692 0.000000e+00 846.0
11 TraesCS1B01G165300 chr5D 74.306 288 55 16 4410 4689 412463647 412463371 3.430000e-18 104.0
12 TraesCS1B01G165300 chr5D 76.761 142 27 5 4468 4606 344541761 344541623 2.690000e-09 75.0
13 TraesCS1B01G165300 chr6D 86.156 809 84 11 1 785 412489454 412488650 0.000000e+00 848.0
14 TraesCS1B01G165300 chr3A 88.177 702 75 6 1 698 81665450 81666147 0.000000e+00 830.0
15 TraesCS1B01G165300 chr3A 88.287 683 68 5 1 679 59957001 59956327 0.000000e+00 808.0
16 TraesCS1B01G165300 chr3A 85.542 83 9 2 2567 2646 22549390 22549472 4.470000e-12 84.2
17 TraesCS1B01G165300 chr3A 78.358 134 19 7 2483 2607 703915936 703915804 2.080000e-10 78.7
18 TraesCS1B01G165300 chr7B 87.701 683 78 5 1 680 1476779 1476100 0.000000e+00 791.0
19 TraesCS1B01G165300 chr7B 82.143 196 21 10 2456 2640 40917457 40917265 9.330000e-34 156.0
20 TraesCS1B01G165300 chr7B 96.774 31 1 0 5530 5560 689935316 689935346 1.300000e-02 52.8
21 TraesCS1B01G165300 chr4B 87.408 683 83 2 1 680 569015414 569016096 0.000000e+00 782.0
22 TraesCS1B01G165300 chr4A 80.303 264 46 6 1168 1428 330084988 330085248 1.980000e-45 195.0
23 TraesCS1B01G165300 chr4A 77.419 217 34 12 5342 5548 2154984 2154773 1.580000e-21 115.0
24 TraesCS1B01G165300 chr4A 75.421 297 39 22 5259 5524 714070781 714071074 5.700000e-21 113.0
25 TraesCS1B01G165300 chr6B 81.579 190 22 8 2475 2653 516082804 516082991 2.020000e-30 145.0
26 TraesCS1B01G165300 chr6B 78.519 135 17 9 4558 4689 135949097 135949222 2.080000e-10 78.7
27 TraesCS1B01G165300 chr7A 78.512 242 35 15 5312 5545 85159320 85159552 7.260000e-30 143.0
28 TraesCS1B01G165300 chr5B 77.982 218 36 9 2455 2661 55187025 55186809 7.320000e-25 126.0
29 TraesCS1B01G165300 chr3B 74.825 286 55 16 4412 4689 452458850 452458574 5.700000e-21 113.0
30 TraesCS1B01G165300 chrUn 76.190 231 41 10 4464 4689 29748480 29748701 7.370000e-20 110.0
31 TraesCS1B01G165300 chr7D 86.869 99 10 2 2567 2662 614354649 614354747 2.650000e-19 108.0
32 TraesCS1B01G165300 chr7D 81.513 119 15 5 5266 5381 538824837 538824723 2.670000e-14 91.6
33 TraesCS1B01G165300 chr7D 79.787 94 13 6 2519 2609 56982242 56982332 5.820000e-06 63.9
34 TraesCS1B01G165300 chr2B 80.000 130 19 7 5305 5430 63219562 63219688 9.600000e-14 89.8
35 TraesCS1B01G165300 chr2B 84.932 73 9 2 5346 5416 63246964 63247036 9.670000e-09 73.1
36 TraesCS1B01G165300 chr2A 83.673 98 13 3 4543 4639 1319364 1319269 9.600000e-14 89.8
37 TraesCS1B01G165300 chr2A 90.164 61 5 1 2554 2613 84947317 84947257 2.080000e-10 78.7
38 TraesCS1B01G165300 chr2D 81.818 88 13 3 5346 5430 36787277 36787364 3.480000e-08 71.3


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 TraesCS1B01G165300 chr1B 288643296 288650243 6947 False 12831.000000 12831 100.000000 1 6948 1 chr1B.!!$F1 6947
1 TraesCS1B01G165300 chr1D 200710967 200717217 6250 False 9361.000000 9361 93.873000 758 6948 1 chr1D.!!$F1 6190
2 TraesCS1B01G165300 chr1A 254182953 254189509 6556 False 2957.666667 3572 92.934333 753 6946 3 chr1A.!!$F2 6193
3 TraesCS1B01G165300 chr1A 579577557 579578175 618 False 854.000000 854 91.599000 1 618 1 chr1A.!!$F1 617
4 TraesCS1B01G165300 chr3D 424649578 424650360 782 True 959.000000 959 88.804000 1 783 1 chr3D.!!$R1 782
5 TraesCS1B01G165300 chr5D 404490775 404491578 803 True 880.000000 880 86.897000 1 785 1 chr5D.!!$R2 784
6 TraesCS1B01G165300 chr5D 404103885 404104692 807 False 846.000000 846 85.995000 1 792 1 chr5D.!!$F1 791
7 TraesCS1B01G165300 chr6D 412488650 412489454 804 True 848.000000 848 86.156000 1 785 1 chr6D.!!$R1 784
8 TraesCS1B01G165300 chr3A 81665450 81666147 697 False 830.000000 830 88.177000 1 698 1 chr3A.!!$F2 697
9 TraesCS1B01G165300 chr3A 59956327 59957001 674 True 808.000000 808 88.287000 1 679 1 chr3A.!!$R1 678
10 TraesCS1B01G165300 chr7B 1476100 1476779 679 True 791.000000 791 87.701000 1 680 1 chr7B.!!$R1 679
11 TraesCS1B01G165300 chr4B 569015414 569016096 682 False 782.000000 782 87.408000 1 680 1 chr4B.!!$F1 679

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
748 785 0.397564 AAGGAAAGTTTACCCCGCGA 59.602 50.0 8.23 0.0 0.00 5.87 F
1081 1118 0.037303 CACCACCAGCACCATCTCTT 59.963 55.0 0.00 0.0 0.00 2.85 F
1086 1123 0.179936 CCAGCACCATCTCTTCCTCC 59.820 60.0 0.00 0.0 0.00 4.30 F
1584 1621 0.460635 GCTATTACCCACCGTTGCGA 60.461 55.0 0.00 0.0 0.00 5.10 F
1695 1732 0.672401 TCTCCAACCGCGTCCAAATC 60.672 55.0 4.92 0.0 0.00 2.17 F
3136 3583 0.815213 TTCATAGGTGGCGCTGCATC 60.815 55.0 7.64 0.0 0.00 3.91 F
4378 4839 0.112995 AGGTGAACATGGGTGCATGT 59.887 50.0 0.00 0.0 46.63 3.21 F
5391 5898 1.130955 CAAGGTGCGTGCATTTTCAC 58.869 50.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1631 1.663379 GGGTGGTCATTAAAGCGGCC 61.663 60.000 0.00 0.0 0.00 6.13 R
2949 3394 1.024271 TTCACAACCAGCAAGCTGAC 58.976 50.000 22.76 0.0 46.30 3.51 R
2981 3426 2.628178 CCTTCTCGGGTATAGATGTGCA 59.372 50.000 0.00 0.0 0.00 4.57 R
3444 3891 1.175983 GGTGGATGACGGTTTGGCAA 61.176 55.000 0.00 0.0 0.00 4.52 R
3554 4001 1.269448 GGTTCATCGGCTGAAAAGCAA 59.731 47.619 14.82 0.0 45.27 3.91 R
4691 5170 0.878416 TTTTGGAAGATGGTTCCGCG 59.122 50.000 0.00 0.0 41.43 6.46 R
5483 5992 0.400213 GTGGTTGGACATGTGAGGGA 59.600 55.000 1.15 0.0 0.00 4.20 R
6666 7183 0.546598 GGAGGGGTGTCGAATGGAAT 59.453 55.000 0.00 0.0 0.00 3.01 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
41 42 2.231716 TCCTCAAAGATCGACTCCCA 57.768 50.000 0.00 0.00 0.00 4.37
66 67 1.258982 GCTTCAACGATATCGCACTGG 59.741 52.381 24.59 13.10 44.43 4.00
74 75 3.784701 GATATCGCACTGGGATATCGT 57.215 47.619 27.49 11.82 46.72 3.73
86 87 1.412710 GGATATCGTCAGTGCCTTCCA 59.587 52.381 0.00 0.00 0.00 3.53
227 230 4.148825 GTGATGAGGAGGCGGCGT 62.149 66.667 9.37 0.00 0.00 5.68
410 413 2.040544 GGTCCCGAACGTACCGAGA 61.041 63.158 11.21 1.53 0.00 4.04
417 420 1.642952 GAACGTACCGAGACCGAGCT 61.643 60.000 0.00 0.00 38.22 4.09
628 640 1.440353 GGCAATTTATAGGCGCGCG 60.440 57.895 28.44 28.44 0.00 6.86
657 669 3.564027 GCCAAATCTAGCGCGCGT 61.564 61.111 32.35 20.00 0.00 6.01
659 671 2.321060 CAAATCTAGCGCGCGTGG 59.679 61.111 32.35 20.48 0.00 4.94
730 765 3.416382 GTCCCGCACGCGCTAAAA 61.416 61.111 5.73 0.00 38.24 1.52
731 766 3.115892 TCCCGCACGCGCTAAAAG 61.116 61.111 5.73 0.00 38.24 2.27
743 780 3.668757 CGCGCTAAAAGGAAAGTTTACCC 60.669 47.826 5.56 0.00 0.00 3.69
748 785 0.397564 AAGGAAAGTTTACCCCGCGA 59.602 50.000 8.23 0.00 0.00 5.87
749 786 0.397564 AGGAAAGTTTACCCCGCGAA 59.602 50.000 8.23 0.00 0.00 4.70
752 789 0.532640 AAAGTTTACCCCGCGAACGT 60.533 50.000 8.23 2.30 37.70 3.99
755 792 1.227497 TTTACCCCGCGAACGTGTT 60.227 52.632 8.23 0.00 37.70 3.32
1081 1118 0.037303 CACCACCAGCACCATCTCTT 59.963 55.000 0.00 0.00 0.00 2.85
1086 1123 0.179936 CCAGCACCATCTCTTCCTCC 59.820 60.000 0.00 0.00 0.00 4.30
1584 1621 0.460635 GCTATTACCCACCGTTGCGA 60.461 55.000 0.00 0.00 0.00 5.10
1594 1631 0.796312 ACCGTTGCGATGCTTTAGTG 59.204 50.000 0.00 0.00 0.00 2.74
1695 1732 0.672401 TCTCCAACCGCGTCCAAATC 60.672 55.000 4.92 0.00 0.00 2.17
2173 2210 3.426615 CAACATTACTACAAGGGGGCAA 58.573 45.455 0.00 0.00 0.00 4.52
2372 2409 6.983307 CCGCCAATTCAAACATGGATTTTATA 59.017 34.615 0.00 0.00 36.27 0.98
2500 2538 4.637483 ACCATGGCAAATTATGTTCTCG 57.363 40.909 13.04 0.00 0.00 4.04
2532 2570 5.700373 GCAAATTTAGTTGGCAGAAAATCCA 59.300 36.000 0.00 0.00 36.71 3.41
2613 2653 5.403166 CGCACCAATATAAATTGCCATGAAG 59.597 40.000 0.00 0.00 41.06 3.02
2614 2654 5.178067 GCACCAATATAAATTGCCATGAAGC 59.822 40.000 0.00 0.00 41.06 3.86
2627 2668 3.065233 GCCATGAAGCGTCATATTTGTCA 59.935 43.478 14.96 0.00 42.88 3.58
2663 2704 8.883789 TCTGACGTTAGTTTTAAAGTGTTTTG 57.116 30.769 7.27 0.00 32.70 2.44
2664 2705 7.964011 TCTGACGTTAGTTTTAAAGTGTTTTGG 59.036 33.333 7.27 0.00 32.70 3.28
2665 2706 7.814642 TGACGTTAGTTTTAAAGTGTTTTGGA 58.185 30.769 0.00 0.00 32.70 3.53
2666 2707 8.460428 TGACGTTAGTTTTAAAGTGTTTTGGAT 58.540 29.630 0.00 0.00 32.70 3.41
2747 3192 9.463443 ACACAAGAGTTGTTATTGCTTTATTTC 57.537 29.630 0.00 0.00 43.23 2.17
2814 3259 3.648545 ACCTATCCCTGCCTAATTCTCAC 59.351 47.826 0.00 0.00 0.00 3.51
2900 3345 2.840651 ACTCCCTCATGTAAACTCCCAG 59.159 50.000 0.00 0.00 0.00 4.45
2981 3426 5.048713 GCTGGTTGTGAAATACTTACTGCTT 60.049 40.000 0.00 0.00 0.00 3.91
3095 3540 9.088987 TCTTGTCATTACATACTATCATAGCCA 57.911 33.333 0.00 0.00 34.97 4.75
3109 3554 8.307483 ACTATCATAGCCAAGTATCATACACAC 58.693 37.037 0.00 0.00 0.00 3.82
3136 3583 0.815213 TTCATAGGTGGCGCTGCATC 60.815 55.000 7.64 0.00 0.00 3.91
3137 3584 1.524393 CATAGGTGGCGCTGCATCA 60.524 57.895 7.64 0.00 0.00 3.07
3239 3686 4.098960 AGTGCCATGGATTCATCATGTTTC 59.901 41.667 18.40 0.00 40.07 2.78
3273 3720 7.611770 AGGAGTTAATGCCATTTTACCTTTTC 58.388 34.615 0.00 0.00 0.00 2.29
3288 3735 5.499004 ACCTTTTCAGAATAGTAGCCACA 57.501 39.130 0.56 0.00 0.00 4.17
3317 3764 7.033530 TCATTAAACAACAAGGGTTACACAG 57.966 36.000 0.00 0.00 34.87 3.66
3444 3891 4.593206 TCACTCTTGGAGAACCTTGTACAT 59.407 41.667 0.00 0.00 37.04 2.29
3538 3985 5.586243 GCCACAACAAGATCTATAAGAGCAA 59.414 40.000 0.00 0.00 31.99 3.91
3596 4043 1.293179 CCACTGCACATGACGGAGA 59.707 57.895 13.51 0.00 0.00 3.71
3650 4097 1.270839 CCCATGTCGCTAAATCCCGAT 60.271 52.381 0.00 0.00 35.76 4.18
3651 4098 1.800586 CCATGTCGCTAAATCCCGATG 59.199 52.381 0.00 0.00 35.76 3.84
3723 4170 0.178068 GTATGTCGGATGCCACCACT 59.822 55.000 0.00 0.00 0.00 4.00
3736 4185 1.482593 CCACCACTGTAGAGATGGACC 59.517 57.143 13.13 0.00 36.94 4.46
3762 4211 3.136443 TGAATGTGACTCCTCCTGTTGTT 59.864 43.478 0.00 0.00 0.00 2.83
3786 4235 7.451731 TGATTAGAGGACTACCAAATTGGAT 57.548 36.000 20.25 5.71 40.96 3.41
3795 4244 5.324409 ACTACCAAATTGGATGAGAAGCAA 58.676 37.500 20.25 0.00 40.96 3.91
3820 4269 8.472007 AAGACAATTTATTTAAGGTGGTGTCA 57.528 30.769 0.00 0.00 36.24 3.58
3833 4282 3.083349 TGTCATCCCTGCCCTCGG 61.083 66.667 0.00 0.00 0.00 4.63
3924 4373 3.326900 GGGGCCAAGAATACCCGA 58.673 61.111 4.39 0.00 45.27 5.14
3928 4377 0.255033 GGCCAAGAATACCCGACCTT 59.745 55.000 0.00 0.00 0.00 3.50
3967 4416 4.755123 GGAAATATGTCACCACCCTAATCG 59.245 45.833 0.00 0.00 0.00 3.34
3991 4440 0.687757 TGTAGGAGGCAGCGGAGATT 60.688 55.000 0.00 0.00 0.00 2.40
3992 4441 0.249657 GTAGGAGGCAGCGGAGATTG 60.250 60.000 0.00 0.00 0.00 2.67
4004 4453 1.511613 GGAGATTGTGGGGGATCTGA 58.488 55.000 0.00 0.00 32.96 3.27
4009 4458 2.879103 TTGTGGGGGATCTGAAACTC 57.121 50.000 0.00 0.00 0.00 3.01
4132 4581 5.536497 AGGTTGGTATTCCCTGAGAATTT 57.464 39.130 0.00 0.00 42.86 1.82
4152 4601 4.929819 TTCCAGGCTACTTTGTTTTTCC 57.070 40.909 0.00 0.00 0.00 3.13
4164 4613 5.712917 ACTTTGTTTTTCCGATAGCCCATTA 59.287 36.000 0.00 0.00 0.00 1.90
4219 4680 5.335127 CATGTTAAGCTTGATGGCAGTAAC 58.665 41.667 9.86 2.55 36.45 2.50
4223 4684 6.712998 TGTTAAGCTTGATGGCAGTAACTAAA 59.287 34.615 9.86 0.00 36.65 1.85
4259 4720 7.503230 ACATGTGTATCCATATTTGATCAGCAA 59.497 33.333 0.00 0.00 33.88 3.91
4268 4729 9.358406 TCCATATTTGATCAGCAATAATCTGTT 57.642 29.630 4.38 0.00 36.15 3.16
4341 4802 5.992729 TGTTGCTTGTTCGTTTACCTATTC 58.007 37.500 0.00 0.00 0.00 1.75
4378 4839 0.112995 AGGTGAACATGGGTGCATGT 59.887 50.000 0.00 0.00 46.63 3.21
4453 4932 5.680619 AGTCCACTCACATGTCAAGTTTTA 58.319 37.500 7.52 0.00 0.00 1.52
4455 4934 5.527582 GTCCACTCACATGTCAAGTTTTACT 59.472 40.000 7.52 0.00 0.00 2.24
4479 4958 7.993183 ACTAAGAAATACACCCATGGTATTCTG 59.007 37.037 11.73 0.00 39.77 3.02
4571 5050 8.825667 TTAATTTGTTTCCAAGAATACCAAGC 57.174 30.769 0.00 0.00 0.00 4.01
4609 5088 7.643214 CGTGAAACTTCATACGCGAGTAGAAT 61.643 42.308 15.93 0.00 42.77 2.40
4713 5192 3.613910 CGCGGAACCATCTTCCAAAAATT 60.614 43.478 0.00 0.00 38.49 1.82
4733 5212 6.436843 AATTCGTGTCTGTTTTGTTCTCTT 57.563 33.333 0.00 0.00 0.00 2.85
4787 5283 1.798813 GCGTGCATTTACATTGGCTCC 60.799 52.381 0.00 0.00 0.00 4.70
4788 5284 1.472082 CGTGCATTTACATTGGCTCCA 59.528 47.619 0.00 0.00 0.00 3.86
4907 5403 6.634805 TGCAATTTCACAAGTTTAGTTCCAA 58.365 32.000 0.00 0.00 0.00 3.53
4934 5430 5.059161 TGCTCTGGCTATAGCTATGTTTTG 58.941 41.667 23.53 5.63 41.70 2.44
4938 5434 7.226720 GCTCTGGCTATAGCTATGTTTTGTTTA 59.773 37.037 23.53 0.00 41.70 2.01
4974 5470 3.543680 ACATTACCAACCTCTCCATCG 57.456 47.619 0.00 0.00 0.00 3.84
5020 5516 7.122353 TGAGAACTAGTCTTAACATGGGTAGTC 59.878 40.741 0.00 0.00 36.41 2.59
5025 5521 6.786967 AGTCTTAACATGGGTAGTCGTAAT 57.213 37.500 0.00 0.00 0.00 1.89
5149 5648 6.964807 TCAATGTATCCCATTTGAAGGATG 57.035 37.500 1.78 0.00 41.93 3.51
5151 5650 3.213506 TGTATCCCATTTGAAGGATGCG 58.786 45.455 1.78 0.00 45.30 4.73
5240 5739 3.557185 CAGCCCTTTTGTCAAAAGCTTTC 59.443 43.478 26.22 16.14 45.05 2.62
5298 5798 2.708051 AGTGTCCATGTTCATCTGCAG 58.292 47.619 7.63 7.63 0.00 4.41
5314 5814 3.568007 TCTGCAGTTGGTGAATGGTAAAC 59.432 43.478 14.67 0.00 0.00 2.01
5363 5870 6.550163 AGAATATTTAGGCATCCAAGATGCT 58.450 36.000 24.33 14.93 44.02 3.79
5391 5898 1.130955 CAAGGTGCGTGCATTTTCAC 58.869 50.000 0.00 0.00 0.00 3.18
5393 5900 1.890876 AGGTGCGTGCATTTTCACTA 58.109 45.000 0.00 0.00 34.92 2.74
5397 5904 3.163594 GTGCGTGCATTTTCACTATGTC 58.836 45.455 0.00 0.00 34.92 3.06
5465 5973 5.516696 GCTCTTTTTCAAAGTTTCTCACACC 59.483 40.000 0.00 0.00 0.00 4.16
5467 5975 5.478679 TCTTTTTCAAAGTTTCTCACACCCA 59.521 36.000 0.00 0.00 0.00 4.51
5468 5976 5.730296 TTTTCAAAGTTTCTCACACCCAA 57.270 34.783 0.00 0.00 0.00 4.12
5469 5977 5.930837 TTTCAAAGTTTCTCACACCCAAT 57.069 34.783 0.00 0.00 0.00 3.16
5490 5999 1.153353 TTTTTCGCACGATCCCTCAC 58.847 50.000 0.00 0.00 0.00 3.51
5640 6150 1.075374 AGTCTGGGTGCAAAATAGCCA 59.925 47.619 0.00 0.00 42.93 4.75
5673 6183 3.837355 ACCTTGCTTTTGATCTCCTTGT 58.163 40.909 0.00 0.00 0.00 3.16
5696 6206 0.241481 GGGTCGCATCTATCGTCTCC 59.759 60.000 0.00 0.00 0.00 3.71
5790 6301 5.346822 GCATCTTGATTTAGCTTTGGTGTTG 59.653 40.000 0.00 0.00 0.00 3.33
5801 6312 1.040646 TTGGTGTTGCCCGCAAAATA 58.959 45.000 3.19 0.00 37.70 1.40
5899 6410 0.104855 TGTTGCTGCTCGACAAGTCT 59.895 50.000 0.00 0.00 36.18 3.24
5906 6417 3.058639 GCTGCTCGACAAGTCTTCAAAAT 60.059 43.478 0.00 0.00 0.00 1.82
6050 6561 2.868583 GCATGCTCTTTCGCTGATCTTA 59.131 45.455 11.37 0.00 0.00 2.10
6087 6598 5.292589 GCTTACAAATGGAAGCCATCAATTG 59.707 40.000 17.78 0.00 44.40 2.32
6092 6603 5.750352 AATGGAAGCCATCAATTGTTCTT 57.250 34.783 5.13 4.89 44.40 2.52
6181 6693 7.350382 TGATGTTTTATGGCCTTATACCTTCA 58.650 34.615 3.32 1.57 0.00 3.02
6182 6694 7.836685 TGATGTTTTATGGCCTTATACCTTCAA 59.163 33.333 3.32 0.00 0.00 2.69
6236 6749 5.523916 CCACTAGTTGAGTAATGTACATGGC 59.476 44.000 9.63 5.49 35.64 4.40
6304 6817 7.610305 GGGAACAATCATAGTTTCCAAGTTAGA 59.390 37.037 0.00 0.00 42.99 2.10
6319 6832 6.017440 TCCAAGTTAGAAATGTGTGCAACTAC 60.017 38.462 0.00 0.00 38.04 2.73
6331 6844 4.976116 GTGTGCAACTACTGGTTCATTTTC 59.024 41.667 0.00 0.00 38.04 2.29
6332 6845 4.642437 TGTGCAACTACTGGTTCATTTTCA 59.358 37.500 0.00 0.00 38.04 2.69
6376 6892 6.183361 GGACCACCCATAGATGCATATCATAT 60.183 42.308 0.00 0.00 32.97 1.78
6453 6969 7.781324 AACAAGGATGTCTCAACCAAATTAT 57.219 32.000 0.00 0.00 39.40 1.28
6533 7049 6.992063 AAAAATGTAGCTCATGTCGAGAAT 57.008 33.333 0.00 0.00 45.45 2.40
6544 7060 5.240891 TCATGTCGAGAATCAGAAGCTTTT 58.759 37.500 0.00 0.00 33.17 2.27
6661 7178 8.602424 TCATTTACTAAATCCAGAAGTTCCTCA 58.398 33.333 0.00 0.00 0.00 3.86
6691 7208 2.439701 CGACACCCCTCCTCGCTA 60.440 66.667 0.00 0.00 0.00 4.26
6787 7304 9.539194 AGATCTTAACCAAAAAGATGGAGAATT 57.461 29.630 3.20 0.00 42.38 2.17
6863 7380 6.785337 TTCTAAAACATCCGATAGTCCTCA 57.215 37.500 0.00 0.00 0.00 3.86
6875 7392 5.419542 CGATAGTCCTCACAAATTCTCCAA 58.580 41.667 0.00 0.00 0.00 3.53
6883 7400 5.750067 CCTCACAAATTCTCCAAACAAACAG 59.250 40.000 0.00 0.00 0.00 3.16
6886 7403 7.555087 TCACAAATTCTCCAAACAAACAGATT 58.445 30.769 0.00 0.00 0.00 2.40
6896 7413 8.804688 TCCAAACAAACAGATTAATTTTACCG 57.195 30.769 0.00 0.00 0.00 4.02
6899 7416 6.334102 ACAAACAGATTAATTTTACCGGCA 57.666 33.333 0.00 0.00 0.00 5.69
6911 7428 3.897141 TTACCGGCACATATGAACTCA 57.103 42.857 10.38 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.567504 CGATATCGTTGAAGCCGGTT 58.432 50.000 17.06 0.00 34.11 4.44
66 67 1.412710 TGGAAGGCACTGACGATATCC 59.587 52.381 0.00 0.00 40.86 2.59
74 75 2.741092 GTCGGTGGAAGGCACTGA 59.259 61.111 0.00 0.00 40.86 3.41
86 87 4.309950 GGTTGGACAGGCGTCGGT 62.310 66.667 0.00 0.00 43.61 4.69
112 114 1.305930 GGAAATGACGGAAAGGCGCT 61.306 55.000 7.64 0.00 0.00 5.92
404 407 3.063084 GTCCAGCTCGGTCTCGGT 61.063 66.667 2.68 0.00 36.95 4.69
554 561 1.454847 CTCCCCGCTCTACTCTGCT 60.455 63.158 0.00 0.00 0.00 4.24
730 765 0.397564 TTCGCGGGGTAAACTTTCCT 59.602 50.000 6.13 0.00 0.00 3.36
731 766 0.518636 GTTCGCGGGGTAAACTTTCC 59.481 55.000 6.13 0.00 0.00 3.13
755 792 1.030488 TCCAACACCGGCGTCAAAAA 61.030 50.000 6.01 0.00 0.00 1.94
913 950 0.677098 GAGAGGAAAAACGGGAGGGC 60.677 60.000 0.00 0.00 0.00 5.19
1081 1118 4.458829 AGACGATGGGCGGGAGGA 62.459 66.667 0.00 0.00 46.49 3.71
1409 1446 2.851071 GCGATGGTCTCCTCGAGGG 61.851 68.421 30.80 20.79 37.05 4.30
1584 1621 2.122783 TAAAGCGGCCACTAAAGCAT 57.877 45.000 2.24 0.00 0.00 3.79
1594 1631 1.663379 GGGTGGTCATTAAAGCGGCC 61.663 60.000 0.00 0.00 0.00 6.13
2263 2300 7.963532 ACCTTGACTACAGTAGAAAAGAATGA 58.036 34.615 14.94 0.00 0.00 2.57
2298 2335 6.983307 ACTGCTCTTAACATGAGATCATACAC 59.017 38.462 0.00 0.00 34.26 2.90
2299 2336 7.117285 ACTGCTCTTAACATGAGATCATACA 57.883 36.000 0.00 0.00 34.26 2.29
2449 2486 9.699410 AAATCTGACATTGGATTTATAGTGGAA 57.301 29.630 0.00 0.00 39.45 3.53
2500 2538 4.183865 GCCAACTAAATTTGCCATTCTCC 58.816 43.478 0.00 0.00 0.00 3.71
2551 2590 4.935352 TTGCAAGTGCTACAATTTTCCT 57.065 36.364 4.69 0.00 42.66 3.36
2552 2591 4.808364 TGTTTGCAAGTGCTACAATTTTCC 59.192 37.500 0.00 0.00 42.66 3.13
2613 2653 8.841444 ATTTTTAGACATGACAAATATGACGC 57.159 30.769 0.00 0.00 0.00 5.19
2670 2711 7.102993 GGCAAACAATATTCTACACCCATTTT 58.897 34.615 0.00 0.00 0.00 1.82
2794 3239 3.574396 TCGTGAGAATTAGGCAGGGATAG 59.426 47.826 0.00 0.00 37.03 2.08
2814 3259 7.072177 TCTTATTTCCTTGTTTAGCACATCG 57.928 36.000 0.00 0.00 34.43 3.84
2949 3394 1.024271 TTCACAACCAGCAAGCTGAC 58.976 50.000 22.76 0.00 46.30 3.51
2981 3426 2.628178 CCTTCTCGGGTATAGATGTGCA 59.372 50.000 0.00 0.00 0.00 4.57
3014 3459 6.315091 TGAGTTTATGATACTACTCGCTCC 57.685 41.667 8.51 0.00 39.83 4.70
3136 3583 9.932207 TCACGGTATTGTATTATAAGGGTATTG 57.068 33.333 0.00 0.00 0.00 1.90
3214 3661 3.383505 ACATGATGAATCCATGGCACTTG 59.616 43.478 6.96 5.99 44.11 3.16
3239 3686 4.016444 TGGCATTAACTCCTAAAAGGCTG 58.984 43.478 0.00 0.00 34.61 4.85
3273 3720 6.932356 ATGAAACATGTGGCTACTATTCTG 57.068 37.500 0.00 0.00 0.00 3.02
3317 3764 2.329379 GGAGAGTGATCGTGTGTGTTC 58.671 52.381 0.00 0.00 0.00 3.18
3390 3837 5.630415 TTTTCTTCTTCTTCCAGAGTCCA 57.370 39.130 0.00 0.00 0.00 4.02
3444 3891 1.175983 GGTGGATGACGGTTTGGCAA 61.176 55.000 0.00 0.00 0.00 4.52
3538 3985 4.660789 AAGCAAGATTCACTGCAAAAGT 57.339 36.364 11.83 0.00 40.93 2.66
3545 3992 3.572584 GGCTGAAAAGCAAGATTCACTG 58.427 45.455 0.00 0.00 36.33 3.66
3553 4000 2.589014 GTTCATCGGCTGAAAAGCAAG 58.411 47.619 0.00 0.00 45.27 4.01
3554 4001 1.269448 GGTTCATCGGCTGAAAAGCAA 59.731 47.619 14.82 0.00 45.27 3.91
3596 4043 3.716601 CCAACAAGCCAAAAATTCTCGT 58.283 40.909 0.00 0.00 0.00 4.18
3650 4097 7.552458 ACTATGTTGCATGAAAACGATATCA 57.448 32.000 3.12 0.00 0.00 2.15
3651 4098 7.376866 CCAACTATGTTGCATGAAAACGATATC 59.623 37.037 0.00 0.00 0.00 1.63
3663 4110 5.316167 TGTTCTTCTCCAACTATGTTGCAT 58.684 37.500 5.04 0.00 0.00 3.96
3671 4118 3.635331 CGACGTTGTTCTTCTCCAACTA 58.365 45.455 0.00 0.00 38.99 2.24
3711 4158 1.195115 TCTCTACAGTGGTGGCATCC 58.805 55.000 0.00 0.00 0.00 3.51
3723 4170 4.964897 ACATTCATCTGGTCCATCTCTACA 59.035 41.667 0.00 0.00 0.00 2.74
3736 4185 3.197333 ACAGGAGGAGTCACATTCATCTG 59.803 47.826 0.00 0.00 0.00 2.90
3762 4211 6.884472 TCCAATTTGGTAGTCCTCTAATCA 57.116 37.500 14.98 0.00 39.03 2.57
3786 4235 9.912634 CCTTAAATAAATTGTCTTTGCTTCTCA 57.087 29.630 0.00 0.00 0.00 3.27
3795 4244 8.472007 TGACACCACCTTAAATAAATTGTCTT 57.528 30.769 0.00 0.00 33.54 3.01
3809 4258 1.380302 GCAGGGATGACACCACCTT 59.620 57.895 0.00 0.00 0.00 3.50
3820 4269 3.402681 CACACCGAGGGCAGGGAT 61.403 66.667 0.00 0.00 0.00 3.85
3833 4282 2.751259 TGACGTGTAGATAGGGTCACAC 59.249 50.000 0.00 0.00 36.43 3.82
3896 4345 3.460478 TTGGCCCCTTTGTCCACCC 62.460 63.158 0.00 0.00 0.00 4.61
3924 4373 1.566231 CCCTCCCTTCATTAGCAAGGT 59.434 52.381 0.00 0.00 39.15 3.50
3928 4377 1.979809 TTCCCCTCCCTTCATTAGCA 58.020 50.000 0.00 0.00 0.00 3.49
3967 4416 1.153549 CGCTGCCTCCTACAAGGAC 60.154 63.158 0.00 0.00 40.06 3.85
3991 4440 2.044793 AGAGTTTCAGATCCCCCACA 57.955 50.000 0.00 0.00 0.00 4.17
3992 4441 3.456277 ACATAGAGTTTCAGATCCCCCAC 59.544 47.826 0.00 0.00 0.00 4.61
4035 4484 9.996554 TTAATGGATGATCGTATTACTTGTCAT 57.003 29.630 0.00 5.63 0.00 3.06
4132 4581 2.882137 CGGAAAAACAAAGTAGCCTGGA 59.118 45.455 0.00 0.00 0.00 3.86
4164 4613 5.570320 ACTATGAAACCTAATGTTGCCAGT 58.430 37.500 0.00 0.00 37.23 4.00
4288 4749 4.373156 AGGTCAAAGTAGCAATGTCCTT 57.627 40.909 0.00 0.00 30.04 3.36
4341 4802 5.551233 TCACCTTTGTATTCTCCAGAACAG 58.449 41.667 0.00 0.00 36.80 3.16
4453 4932 7.993183 CAGAATACCATGGGTGTATTTCTTAGT 59.007 37.037 18.09 0.00 38.63 2.24
4455 4934 7.990886 GTCAGAATACCATGGGTGTATTTCTTA 59.009 37.037 18.09 3.99 38.63 2.10
4479 4958 7.321745 AGATCCAATTATGTTTTCTTCCGTC 57.678 36.000 0.00 0.00 0.00 4.79
4553 5032 4.747810 CCATGCTTGGTATTCTTGGAAAC 58.252 43.478 10.48 0.00 38.30 2.78
4670 5149 7.041712 TCCGCGCATATGAATAGTAAAATCAAA 60.042 33.333 8.75 0.00 0.00 2.69
4691 5170 0.878416 TTTTGGAAGATGGTTCCGCG 59.122 50.000 0.00 0.00 41.43 6.46
4693 5172 4.165779 CGAATTTTTGGAAGATGGTTCCG 58.834 43.478 0.00 0.00 41.43 4.30
4713 5192 5.873179 AAAAGAGAACAAAACAGACACGA 57.127 34.783 0.00 0.00 0.00 4.35
4907 5403 6.805016 ACATAGCTATAGCCAGAGCAATAT 57.195 37.500 21.17 7.03 41.64 1.28
4974 5470 6.513180 TCTCATTCGATACATTACTGGGAAC 58.487 40.000 0.00 0.00 0.00 3.62
5025 5521 7.047271 GGGCAATCCAATGCTAAATTTTCTAA 58.953 34.615 0.00 0.00 45.68 2.10
5149 5648 2.197577 GAGAGCCAATCTAGAACACGC 58.802 52.381 0.00 0.00 38.84 5.34
5151 5650 3.895232 TGGAGAGCCAATCTAGAACAC 57.105 47.619 0.00 0.00 42.49 3.32
5278 5778 2.039480 ACTGCAGATGAACATGGACACT 59.961 45.455 23.35 0.00 0.00 3.55
5282 5782 2.224843 ACCAACTGCAGATGAACATGGA 60.225 45.455 24.19 0.00 0.00 3.41
5334 5841 8.435931 TCTTGGATGCCTAAATATTCTAGCTA 57.564 34.615 0.00 0.00 0.00 3.32
5344 5851 4.174704 TGAGCATCTTGGATGCCTAAAT 57.825 40.909 23.37 9.24 45.59 1.40
5397 5904 1.066573 ACGAGCTCCTCAAATGTCCAG 60.067 52.381 8.47 0.00 0.00 3.86
5429 5937 4.385825 TGAAAAAGAGCACTATTCGGTGT 58.614 39.130 0.00 0.00 39.21 4.16
5431 5939 5.531287 ACTTTGAAAAAGAGCACTATTCGGT 59.469 36.000 6.73 2.98 0.00 4.69
5442 5950 6.036470 GGGTGTGAGAAACTTTGAAAAAGAG 58.964 40.000 6.73 0.00 0.00 2.85
5483 5992 0.400213 GTGGTTGGACATGTGAGGGA 59.600 55.000 1.15 0.00 0.00 4.20
5490 5999 1.908344 TCATGGTGTGGTTGGACATG 58.092 50.000 0.00 0.00 40.06 3.21
5600 6109 3.769844 ACTCATTACTCCCGAGTGTGAAT 59.230 43.478 7.63 0.00 42.52 2.57
5640 6150 8.814038 ATCAAAAGCAAGGTAATTATGAGAGT 57.186 30.769 0.00 0.00 0.00 3.24
5673 6183 1.878088 GACGATAGATGCGACCCACTA 59.122 52.381 0.00 0.00 41.38 2.74
5790 6301 8.203937 AGGTAAATAATTTTTATTTTGCGGGC 57.796 30.769 9.73 0.00 0.00 6.13
5801 6312 9.705290 ATGAAAGCACGAAGGTAAATAATTTTT 57.295 25.926 0.00 0.00 0.00 1.94
5899 6410 1.000385 CCGTTGCCTGCAGATTTTGAA 60.000 47.619 17.39 0.00 0.00 2.69
5906 6417 4.349503 ATGCCCGTTGCCTGCAGA 62.350 61.111 17.39 0.00 38.58 4.26
5971 6482 7.117523 CCTTGTTTTTCACAAACAAATCAGTCA 59.882 33.333 12.59 0.00 45.11 3.41
6031 6542 4.989797 CAGATAAGATCAGCGAAAGAGCAT 59.010 41.667 0.00 0.00 40.15 3.79
6050 6561 9.851686 TTCCATTTGTAAGCTACATTATCAGAT 57.148 29.630 0.00 0.00 38.68 2.90
6114 6626 3.369451 GTCACGGCAACAAAAACAACAAT 59.631 39.130 0.00 0.00 0.00 2.71
6181 6693 7.640852 TGTGTACTACGCAATTGTTTTGTATT 58.359 30.769 7.40 3.12 35.42 1.89
6182 6694 7.041644 ACTGTGTACTACGCAATTGTTTTGTAT 60.042 33.333 7.40 0.47 38.24 2.29
6236 6749 4.475944 CTCTTGCCCATTCTTAACAAACG 58.524 43.478 0.00 0.00 0.00 3.60
6304 6817 3.951037 TGAACCAGTAGTTGCACACATTT 59.049 39.130 0.00 0.00 39.40 2.32
6376 6892 9.935241 AATATGTGGTATTTGTTGCATTTTACA 57.065 25.926 0.00 0.00 28.44 2.41
6661 7178 4.867086 AGGGGTGTCGAATGGAATTAAAT 58.133 39.130 0.00 0.00 36.07 1.40
6666 7183 0.546598 GGAGGGGTGTCGAATGGAAT 59.453 55.000 0.00 0.00 0.00 3.01
6691 7208 4.568956 CGGGAAAAGATTTGCCAAAGATT 58.431 39.130 12.83 0.00 37.63 2.40
6845 7362 4.819105 TTGTGAGGACTATCGGATGTTT 57.181 40.909 0.00 0.00 0.00 2.83
6875 7392 6.643360 GTGCCGGTAAAATTAATCTGTTTGTT 59.357 34.615 1.90 0.00 0.00 2.83
6883 7400 8.349983 AGTTCATATGTGCCGGTAAAATTAATC 58.650 33.333 1.90 0.00 0.00 1.75
6886 7403 6.824196 TGAGTTCATATGTGCCGGTAAAATTA 59.176 34.615 1.90 0.00 0.00 1.40
6896 7413 6.514048 GCCTTCTTATTGAGTTCATATGTGCC 60.514 42.308 1.90 0.00 0.00 5.01
6899 7416 6.480320 GTCGCCTTCTTATTGAGTTCATATGT 59.520 38.462 1.90 0.00 0.00 2.29
6911 7428 2.433436 GGTGTTGGTCGCCTTCTTATT 58.567 47.619 0.00 0.00 42.91 1.40


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

AutoCloner maintained by Alex Coulton.