Multiple sequence alignment - TraesCS2A01G459800

Loading Multiple Alignment...

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 TraesCS2A01G459800 chr2A 100.000 3589 0 0 1 3589 706646254 706642666 0.000000e+00 6628.0
1 TraesCS2A01G459800 chr2A 91.656 755 38 10 1635 2389 706742072 706741343 0.000000e+00 1022.0
2 TraesCS2A01G459800 chr2A 87.228 689 65 14 588 1261 706743329 706742649 0.000000e+00 763.0
3 TraesCS2A01G459800 chr2A 97.917 48 1 0 2801 2848 706643348 706643301 2.300000e-12 84.2
4 TraesCS2A01G459800 chr2A 97.917 48 1 0 2907 2954 706643454 706643407 2.300000e-12 84.2
5 TraesCS2A01G459800 chr2D 93.342 1472 83 8 1 1461 566838857 566837390 0.000000e+00 2161.0
6 TraesCS2A01G459800 chr2D 95.309 1002 29 7 1627 2617 566836058 566835064 0.000000e+00 1574.0
7 TraesCS2A01G459800 chr2D 91.398 744 41 7 1635 2377 566980592 566979871 0.000000e+00 998.0
8 TraesCS2A01G459800 chr2D 86.744 694 58 19 581 1261 566982000 566981328 0.000000e+00 741.0
9 TraesCS2A01G459800 chr2D 93.548 124 3 4 2639 2762 566835082 566834964 2.850000e-41 180.0
10 TraesCS2A01G459800 chr2B 93.869 1207 60 7 212 1405 679819896 679818691 0.000000e+00 1807.0
11 TraesCS2A01G459800 chr2B 93.739 1182 40 11 1627 2800 679816102 679814947 0.000000e+00 1742.0
12 TraesCS2A01G459800 chr2B 90.897 758 44 10 1632 2389 679885942 679885210 0.000000e+00 994.0
13 TraesCS2A01G459800 chr2B 87.572 692 65 16 581 1261 679887198 679886517 0.000000e+00 782.0
14 TraesCS2A01G459800 chr6A 95.963 644 18 2 2943 3586 158406809 158407444 0.000000e+00 1038.0
15 TraesCS2A01G459800 chr6A 86.798 659 61 19 2943 3585 26818977 26818329 0.000000e+00 712.0
16 TraesCS2A01G459800 chr6A 92.157 51 1 3 2992 3041 578931040 578931088 6.430000e-08 69.4
17 TraesCS2A01G459800 chr4D 89.291 663 43 20 2943 3589 507782539 507783189 0.000000e+00 806.0
18 TraesCS2A01G459800 chr3A 97.216 467 12 1 2943 3409 50955695 50956160 0.000000e+00 789.0
19 TraesCS2A01G459800 chr3A 97.714 175 3 1 3412 3586 50959425 50959598 2.090000e-77 300.0
20 TraesCS2A01G459800 chr3D 88.754 658 48 10 2950 3589 29284293 29283644 0.000000e+00 782.0
21 TraesCS2A01G459800 chr5B 88.225 569 38 17 2989 3538 610111005 610110447 0.000000e+00 652.0
22 TraesCS2A01G459800 chr5B 86.557 610 50 12 2950 3539 40095995 40095398 0.000000e+00 643.0
23 TraesCS2A01G459800 chr5B 95.455 66 2 1 3524 3589 610110438 610110374 1.760000e-18 104.0
24 TraesCS2A01G459800 chr6D 86.891 595 43 27 2944 3522 414709684 414710259 5.060000e-178 634.0


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 TraesCS2A01G459800 chr2A 706642666 706646254 3588 True 2265.466667 6628 98.611333 1 3589 3 chr2A.!!$R1 3588
1 TraesCS2A01G459800 chr2A 706741343 706743329 1986 True 892.500000 1022 89.442000 588 2389 2 chr2A.!!$R2 1801
2 TraesCS2A01G459800 chr2D 566834964 566838857 3893 True 1305.000000 2161 94.066333 1 2762 3 chr2D.!!$R1 2761
3 TraesCS2A01G459800 chr2D 566979871 566982000 2129 True 869.500000 998 89.071000 581 2377 2 chr2D.!!$R2 1796
4 TraesCS2A01G459800 chr2B 679814947 679819896 4949 True 1774.500000 1807 93.804000 212 2800 2 chr2B.!!$R1 2588
5 TraesCS2A01G459800 chr2B 679885210 679887198 1988 True 888.000000 994 89.234500 581 2389 2 chr2B.!!$R2 1808
6 TraesCS2A01G459800 chr6A 158406809 158407444 635 False 1038.000000 1038 95.963000 2943 3586 1 chr6A.!!$F1 643
7 TraesCS2A01G459800 chr6A 26818329 26818977 648 True 712.000000 712 86.798000 2943 3585 1 chr6A.!!$R1 642
8 TraesCS2A01G459800 chr4D 507782539 507783189 650 False 806.000000 806 89.291000 2943 3589 1 chr4D.!!$F1 646
9 TraesCS2A01G459800 chr3A 50955695 50959598 3903 False 544.500000 789 97.465000 2943 3586 2 chr3A.!!$F1 643
10 TraesCS2A01G459800 chr3D 29283644 29284293 649 True 782.000000 782 88.754000 2950 3589 1 chr3D.!!$R1 639
11 TraesCS2A01G459800 chr5B 40095398 40095995 597 True 643.000000 643 86.557000 2950 3539 1 chr5B.!!$R1 589
12 TraesCS2A01G459800 chr5B 610110374 610111005 631 True 378.000000 652 91.840000 2989 3589 2 chr5B.!!$R2 600
13 TraesCS2A01G459800 chr6D 414709684 414710259 575 False 634.000000 634 86.891000 2944 3522 1 chr6D.!!$F1 578

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
652 660 0.532862 CACTCCCCACCATCATACGC 60.533 60.0 0.0 0.0 0.0 4.42 F
1819 5047 0.038159 GTGACGGTGAAGCAGCTAGT 60.038 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 5381 0.387202 CGAGGATGAGGTCGCTGATT 59.613 55.0 0.0 0.0 0.00 2.57 R
2860 6100 0.107214 GGGTGCTGATCAATCGGGAA 60.107 55.0 0.0 0.0 35.22 3.97 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
83 84 5.066893 AGTTGACGTGTACAAGTTCTAGTGA 59.933 40.000 15.70 0.00 0.00 3.41
96 97 8.322828 ACAAGTTCTAGTGACTAGTCTCTATGA 58.677 37.037 26.72 22.49 35.80 2.15
104 105 7.450074 AGTGACTAGTCTCTATGATTCTCGAT 58.550 38.462 22.69 0.00 32.33 3.59
146 147 8.252624 AGGAGAGGAATACTAGGATGTTTAAC 57.747 38.462 0.00 0.00 0.00 2.01
147 148 7.844779 AGGAGAGGAATACTAGGATGTTTAACA 59.155 37.037 0.00 0.00 0.00 2.41
204 205 9.793259 GAAACACTCATTAATGGGGATTAGATA 57.207 33.333 19.43 0.00 30.76 1.98
288 289 5.705905 CCGGACCAAAGAAACTAAGAAAGAT 59.294 40.000 0.00 0.00 0.00 2.40
308 309 7.763172 AAGATGATCAAAGTAGAATCGACAC 57.237 36.000 0.00 0.00 0.00 3.67
335 336 2.039818 TCACCTAGCTAGTCGTCTGG 57.960 55.000 19.31 5.73 0.00 3.86
337 338 2.026542 TCACCTAGCTAGTCGTCTGGAA 60.027 50.000 19.31 0.00 0.00 3.53
382 383 2.195727 TGATGGCATCTACCCAGTTGA 58.804 47.619 26.49 0.93 35.48 3.18
395 396 1.535462 CCAGTTGAAGTTTACGGCCAG 59.465 52.381 2.24 0.00 0.00 4.85
439 440 7.851387 TGATAGCGGTGTAACATTTGAATAA 57.149 32.000 0.00 0.00 39.98 1.40
442 443 6.811253 AGCGGTGTAACATTTGAATAAGAA 57.189 33.333 0.00 0.00 39.98 2.52
476 480 5.691754 AGGCTCGCTTTGTTTTTCTATTTTG 59.308 36.000 0.00 0.00 0.00 2.44
499 503 9.778741 TTTGTGTAGAAAGATGTCACTCTATTT 57.221 29.630 0.00 0.00 0.00 1.40
509 513 3.371898 TGTCACTCTATTTGCTCATTGCG 59.628 43.478 0.00 0.00 46.63 4.85
643 651 3.192103 AAGGCGTTCACTCCCCACC 62.192 63.158 0.00 0.00 0.00 4.61
652 660 0.532862 CACTCCCCACCATCATACGC 60.533 60.000 0.00 0.00 0.00 4.42
656 664 1.525995 CCCACCATCATACGCACCC 60.526 63.158 0.00 0.00 0.00 4.61
663 671 0.755698 ATCATACGCACCCTCCTCGT 60.756 55.000 0.00 0.00 39.88 4.18
1094 1132 5.297547 TGACAGACATTGTTAGGTCTTGTC 58.702 41.667 13.79 1.71 42.39 3.18
1097 1135 4.692625 CAGACATTGTTAGGTCTTGTCAGG 59.307 45.833 4.42 0.00 42.39 3.86
1250 1290 6.484643 ACTTCTGCGTTGCTGATATAATGAAT 59.515 34.615 0.00 0.00 36.48 2.57
1481 4709 5.530519 TCACAAGCGTCAATCATTAGAAC 57.469 39.130 0.00 0.00 0.00 3.01
1489 4717 5.685954 GCGTCAATCATTAGAACTCGTCATA 59.314 40.000 0.00 0.00 0.00 2.15
1498 4726 8.737175 TCATTAGAACTCGTCATAAGTTGTAGT 58.263 33.333 0.00 0.00 37.10 2.73
1499 4727 9.355215 CATTAGAACTCGTCATAAGTTGTAGTT 57.645 33.333 0.00 0.00 37.10 2.24
1500 4728 9.924650 ATTAGAACTCGTCATAAGTTGTAGTTT 57.075 29.630 0.00 0.00 37.10 2.66
1501 4729 9.754382 TTAGAACTCGTCATAAGTTGTAGTTTT 57.246 29.630 0.00 0.00 37.10 2.43
1503 4731 9.924650 AGAACTCGTCATAAGTTGTAGTTTTAT 57.075 29.630 0.00 0.00 37.10 1.40
1571 4799 7.730364 ACTTGGTCAGAGTATGTAAAGTTTG 57.270 36.000 0.00 0.00 0.00 2.93
1572 4800 7.506114 ACTTGGTCAGAGTATGTAAAGTTTGA 58.494 34.615 0.00 0.00 0.00 2.69
1573 4801 7.441458 ACTTGGTCAGAGTATGTAAAGTTTGAC 59.559 37.037 0.00 0.00 34.66 3.18
1574 4802 7.062749 TGGTCAGAGTATGTAAAGTTTGACT 57.937 36.000 0.00 0.00 35.37 3.41
1575 4803 7.506114 TGGTCAGAGTATGTAAAGTTTGACTT 58.494 34.615 0.00 0.00 40.80 3.01
1577 4805 9.485206 GGTCAGAGTATGTAAAGTTTGACTTTA 57.515 33.333 8.72 8.72 45.75 1.85
1686 4914 3.181507 GCAACTGTGTATACATGCAGTGG 60.182 47.826 22.78 21.19 40.71 4.00
1730 4958 0.324614 ACATGAAGATGGTGACGGCA 59.675 50.000 0.00 0.00 33.39 5.69
1817 5045 1.292223 GGTGACGGTGAAGCAGCTA 59.708 57.895 0.00 0.00 0.00 3.32
1819 5047 0.038159 GTGACGGTGAAGCAGCTAGT 60.038 55.000 0.00 0.00 0.00 2.57
1832 5060 1.127567 AGCTAGTGGGGCTGAACACA 61.128 55.000 0.00 0.00 39.99 3.72
2138 5366 2.358247 ATCGCCAACGCCGTCTTT 60.358 55.556 0.00 0.00 39.84 2.52
2264 5492 2.285969 AGCAGCATGGGAGGAGGT 60.286 61.111 0.00 0.00 35.86 3.85
2267 5495 2.693864 AGCATGGGAGGAGGTGGG 60.694 66.667 0.00 0.00 0.00 4.61
2279 5507 1.895020 GAGGTGGGTACGACATGCCA 61.895 60.000 0.00 0.00 39.40 4.92
2399 5627 2.633657 GCCATCCACGCGCTTATG 59.366 61.111 5.73 7.12 0.00 1.90
2471 5701 8.033038 TGCATCAAACCAGTACTTAGTACTTAG 58.967 37.037 21.03 17.22 45.68 2.18
2472 5702 8.033626 GCATCAAACCAGTACTTAGTACTTAGT 58.966 37.037 21.03 17.85 45.68 2.24
2523 5753 5.106555 TGGTGTAGTTACTAGTAAGTCGTGC 60.107 44.000 23.24 13.81 37.15 5.34
2526 5756 5.702670 TGTAGTTACTAGTAAGTCGTGCACT 59.297 40.000 23.24 13.75 37.15 4.40
2715 5955 7.944729 AGCCATCTGTGTTTTAATCTTGTAT 57.055 32.000 0.00 0.00 0.00 2.29
2732 5972 9.449719 AATCTTGTATATTTTCCGAGTGTTTCT 57.550 29.630 0.00 0.00 0.00 2.52
2756 5996 2.849007 GCATCATGGCGTCGATCG 59.151 61.111 9.36 9.36 43.12 3.69
2757 5997 1.661509 GCATCATGGCGTCGATCGA 60.662 57.895 15.15 15.15 42.86 3.59
2764 6004 1.283181 GGCGTCGATCGACTAGCAT 59.717 57.895 37.12 0.00 45.28 3.79
2789 6029 3.579586 AGCCATGATCACCAAACACAATT 59.420 39.130 0.00 0.00 0.00 2.32
2800 6040 8.121305 TCACCAAACACAATTAAAGCAGATAT 57.879 30.769 0.00 0.00 0.00 1.63
2801 6041 9.237187 TCACCAAACACAATTAAAGCAGATATA 57.763 29.630 0.00 0.00 0.00 0.86
2807 6047 8.547967 ACACAATTAAAGCAGATATATACGGG 57.452 34.615 0.00 0.00 0.00 5.28
2808 6048 7.606456 ACACAATTAAAGCAGATATATACGGGG 59.394 37.037 0.00 0.00 0.00 5.73
2809 6049 7.065803 CACAATTAAAGCAGATATATACGGGGG 59.934 40.741 0.00 0.00 0.00 5.40
2810 6050 7.037873 ACAATTAAAGCAGATATATACGGGGGA 60.038 37.037 0.00 0.00 0.00 4.81
2811 6051 6.938698 TTAAAGCAGATATATACGGGGGAA 57.061 37.500 0.00 0.00 0.00 3.97
2812 6052 5.836024 AAAGCAGATATATACGGGGGAAA 57.164 39.130 0.00 0.00 0.00 3.13
2813 6053 6.388619 AAAGCAGATATATACGGGGGAAAT 57.611 37.500 0.00 0.00 0.00 2.17
2814 6054 7.504926 AAAGCAGATATATACGGGGGAAATA 57.495 36.000 0.00 0.00 0.00 1.40
2815 6055 6.481434 AGCAGATATATACGGGGGAAATAC 57.519 41.667 0.00 0.00 0.00 1.89
2816 6056 5.365895 AGCAGATATATACGGGGGAAATACC 59.634 44.000 0.00 0.00 38.08 2.73
2851 6091 4.478206 GACATCTGTCCCTTGAATCTCA 57.522 45.455 0.00 0.00 39.07 3.27
2852 6092 4.187694 GACATCTGTCCCTTGAATCTCAC 58.812 47.826 0.00 0.00 39.07 3.51
2853 6093 3.054802 ACATCTGTCCCTTGAATCTCACC 60.055 47.826 0.00 0.00 0.00 4.02
2854 6094 1.550524 TCTGTCCCTTGAATCTCACCG 59.449 52.381 0.00 0.00 0.00 4.94
2855 6095 1.276421 CTGTCCCTTGAATCTCACCGT 59.724 52.381 0.00 0.00 0.00 4.83
2856 6096 1.697432 TGTCCCTTGAATCTCACCGTT 59.303 47.619 0.00 0.00 0.00 4.44
2857 6097 2.289444 TGTCCCTTGAATCTCACCGTTC 60.289 50.000 0.00 0.00 0.00 3.95
2858 6098 1.974957 TCCCTTGAATCTCACCGTTCA 59.025 47.619 0.00 0.00 32.86 3.18
2859 6099 2.571653 TCCCTTGAATCTCACCGTTCAT 59.428 45.455 0.00 0.00 34.60 2.57
2860 6100 3.009033 TCCCTTGAATCTCACCGTTCATT 59.991 43.478 0.00 0.00 34.60 2.57
2861 6101 3.758554 CCCTTGAATCTCACCGTTCATTT 59.241 43.478 0.00 0.00 34.60 2.32
2862 6102 4.142600 CCCTTGAATCTCACCGTTCATTTC 60.143 45.833 0.00 0.00 34.60 2.17
2863 6103 4.142600 CCTTGAATCTCACCGTTCATTTCC 60.143 45.833 0.00 0.00 34.60 3.13
2864 6104 3.343617 TGAATCTCACCGTTCATTTCCC 58.656 45.455 0.00 0.00 29.93 3.97
2865 6105 2.024176 ATCTCACCGTTCATTTCCCG 57.976 50.000 0.00 0.00 0.00 5.14
2866 6106 0.970640 TCTCACCGTTCATTTCCCGA 59.029 50.000 0.00 0.00 0.00 5.14
2867 6107 1.553248 TCTCACCGTTCATTTCCCGAT 59.447 47.619 0.00 0.00 0.00 4.18
2868 6108 2.027561 TCTCACCGTTCATTTCCCGATT 60.028 45.455 0.00 0.00 0.00 3.34
2869 6109 2.080693 TCACCGTTCATTTCCCGATTG 58.919 47.619 0.00 0.00 0.00 2.67
2870 6110 2.080693 CACCGTTCATTTCCCGATTGA 58.919 47.619 0.00 0.00 0.00 2.57
2871 6111 2.682856 CACCGTTCATTTCCCGATTGAT 59.317 45.455 0.00 0.00 0.00 2.57
2872 6112 2.943033 ACCGTTCATTTCCCGATTGATC 59.057 45.455 0.00 0.00 0.00 2.92
2873 6113 2.942376 CCGTTCATTTCCCGATTGATCA 59.058 45.455 0.00 0.00 0.00 2.92
2874 6114 3.002656 CCGTTCATTTCCCGATTGATCAG 59.997 47.826 0.00 0.00 0.00 2.90
2875 6115 3.546815 CGTTCATTTCCCGATTGATCAGC 60.547 47.826 0.00 0.00 0.00 4.26
2876 6116 3.280197 TCATTTCCCGATTGATCAGCA 57.720 42.857 0.00 0.00 0.00 4.41
2877 6117 2.945008 TCATTTCCCGATTGATCAGCAC 59.055 45.455 0.00 0.00 0.00 4.40
2878 6118 1.750193 TTTCCCGATTGATCAGCACC 58.250 50.000 0.00 0.00 0.00 5.01
2879 6119 0.107214 TTCCCGATTGATCAGCACCC 60.107 55.000 0.00 0.00 0.00 4.61
2880 6120 1.526917 CCCGATTGATCAGCACCCC 60.527 63.158 0.00 0.00 0.00 4.95
2881 6121 1.889105 CCGATTGATCAGCACCCCG 60.889 63.158 0.00 0.00 0.00 5.73
2882 6122 2.537560 CGATTGATCAGCACCCCGC 61.538 63.158 0.00 0.00 42.91 6.13
2894 6134 3.543680 GCACCCCGCTATATGTATCAT 57.456 47.619 0.00 0.00 37.77 2.45
2895 6135 3.198068 GCACCCCGCTATATGTATCATG 58.802 50.000 0.00 0.00 37.77 3.07
2896 6136 3.369471 GCACCCCGCTATATGTATCATGT 60.369 47.826 0.00 0.00 37.77 3.21
2897 6137 4.433615 CACCCCGCTATATGTATCATGTC 58.566 47.826 0.00 0.00 0.00 3.06
2898 6138 4.160439 CACCCCGCTATATGTATCATGTCT 59.840 45.833 0.00 0.00 0.00 3.41
2899 6139 4.777896 ACCCCGCTATATGTATCATGTCTT 59.222 41.667 0.00 0.00 0.00 3.01
2900 6140 5.248477 ACCCCGCTATATGTATCATGTCTTT 59.752 40.000 0.00 0.00 0.00 2.52
2901 6141 6.173339 CCCCGCTATATGTATCATGTCTTTT 58.827 40.000 0.00 0.00 0.00 2.27
2902 6142 6.313905 CCCCGCTATATGTATCATGTCTTTTC 59.686 42.308 0.00 0.00 0.00 2.29
2903 6143 7.099764 CCCGCTATATGTATCATGTCTTTTCT 58.900 38.462 0.00 0.00 0.00 2.52
2904 6144 7.063898 CCCGCTATATGTATCATGTCTTTTCTG 59.936 40.741 0.00 0.00 0.00 3.02
2905 6145 7.412346 CCGCTATATGTATCATGTCTTTTCTGC 60.412 40.741 0.00 0.00 0.00 4.26
2906 6146 7.330454 CGCTATATGTATCATGTCTTTTCTGCT 59.670 37.037 0.00 0.00 0.00 4.24
2907 6147 9.645059 GCTATATGTATCATGTCTTTTCTGCTA 57.355 33.333 0.00 0.00 0.00 3.49
2911 6151 7.930513 TGTATCATGTCTTTTCTGCTATACG 57.069 36.000 0.00 0.00 0.00 3.06
2912 6152 6.923508 TGTATCATGTCTTTTCTGCTATACGG 59.076 38.462 0.00 0.00 0.00 4.02
2913 6153 4.693283 TCATGTCTTTTCTGCTATACGGG 58.307 43.478 0.00 0.00 0.00 5.28
2914 6154 3.536956 TGTCTTTTCTGCTATACGGGG 57.463 47.619 0.00 0.00 0.00 5.73
2915 6155 2.169769 TGTCTTTTCTGCTATACGGGGG 59.830 50.000 0.00 0.00 0.00 5.40
2916 6156 2.433239 GTCTTTTCTGCTATACGGGGGA 59.567 50.000 0.00 0.00 0.00 4.81
2917 6157 3.109151 TCTTTTCTGCTATACGGGGGAA 58.891 45.455 0.00 0.00 0.00 3.97
2918 6158 3.520317 TCTTTTCTGCTATACGGGGGAAA 59.480 43.478 0.00 0.00 0.00 3.13
2919 6159 4.165372 TCTTTTCTGCTATACGGGGGAAAT 59.835 41.667 0.00 0.00 0.00 2.17
2920 6160 5.367352 TCTTTTCTGCTATACGGGGGAAATA 59.633 40.000 0.00 0.00 0.00 1.40
2921 6161 4.612264 TTCTGCTATACGGGGGAAATAC 57.388 45.455 0.00 0.00 0.00 1.89
2922 6162 2.901839 TCTGCTATACGGGGGAAATACC 59.098 50.000 0.00 0.00 38.08 2.73
3098 6340 8.783999 ATGTATACGAGTATGAAAGAAAGTCG 57.216 34.615 6.04 0.00 40.88 4.18
3307 6566 9.146984 GCTTTAAAAGTTTGTTTGGTCTTTACT 57.853 29.630 0.00 0.00 31.24 2.24
3324 6583 6.146021 GTCTTTACTACCGTTCAAAATTCCGA 59.854 38.462 0.00 0.00 0.00 4.55
3499 10028 3.404564 CAGCTGTGTATAACGCGTTTTC 58.595 45.455 31.50 19.62 34.73 2.29
3522 10052 1.834822 AGCAGGAGCCTCCCGTATC 60.835 63.158 7.26 0.00 43.56 2.24
3546 10099 7.033791 TCTCCTAATTCACTACTTTAGCAACG 58.966 38.462 0.00 0.00 0.00 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 5.762218 ACTAGTCACTAGAACTTGTACACGT 59.238 40.000 19.25 0.00 37.49 4.49
83 84 8.154203 TCAAGATCGAGAATCATAGAGACTAGT 58.846 37.037 0.00 0.00 36.79 2.57
104 105 9.883293 TTCCTCTCCTAGATAATATGTTCAAGA 57.117 33.333 0.00 0.00 0.00 3.02
121 122 7.844779 TGTTAAACATCCTAGTATTCCTCTCCT 59.155 37.037 0.00 0.00 0.00 3.69
131 132 7.924541 ACAAATCCCTGTTAAACATCCTAGTA 58.075 34.615 0.00 0.00 0.00 1.82
139 140 6.546428 TTTTGGACAAATCCCTGTTAAACA 57.454 33.333 0.00 0.00 45.59 2.83
146 147 6.345096 ACAACTATTTTGGACAAATCCCTG 57.655 37.500 0.00 0.00 45.59 4.45
147 148 8.485578 TTTACAACTATTTTGGACAAATCCCT 57.514 30.769 0.00 0.00 45.59 4.20
204 205 9.246670 TGATTTCCTTCATCAATCAATGTAGTT 57.753 29.630 0.00 0.00 34.66 2.24
253 254 1.202099 TTGGTCCGGACTATTGGGCA 61.202 55.000 32.52 17.92 0.00 5.36
288 289 5.047306 ACTGGTGTCGATTCTACTTTGATCA 60.047 40.000 0.00 0.00 0.00 2.92
304 305 2.009042 GCTAGGTGATGCACTGGTGTC 61.009 57.143 0.00 0.00 34.40 3.67
308 309 1.759445 ACTAGCTAGGTGATGCACTGG 59.241 52.381 24.35 0.00 34.40 4.00
335 336 2.198304 ATCCTGCCCACCGGACTTTC 62.198 60.000 9.46 0.00 30.90 2.62
337 338 2.610859 ATCCTGCCCACCGGACTT 60.611 61.111 9.46 0.00 30.90 3.01
382 383 5.949952 AGAAAATATTCCTGGCCGTAAACTT 59.050 36.000 0.00 0.00 36.12 2.66
395 396 9.852091 GCTATCAATGATGGAAGAAAATATTCC 57.148 33.333 10.89 0.00 45.45 3.01
439 440 1.410882 GCGAGCCTAAGATGGAGTTCT 59.589 52.381 0.00 0.00 0.00 3.01
442 443 1.490574 AAGCGAGCCTAAGATGGAGT 58.509 50.000 0.00 0.00 0.00 3.85
476 480 7.547370 AGCAAATAGAGTGACATCTTTCTACAC 59.453 37.037 0.00 0.00 0.00 2.90
499 503 2.106477 TGATACAACCGCAATGAGCA 57.894 45.000 0.00 0.00 46.13 4.26
509 513 8.495949 CATTCGTTATATGGAGTTGATACAACC 58.504 37.037 10.38 3.62 0.00 3.77
562 569 2.936498 CACTCACAGTCGACCAACTTTT 59.064 45.455 13.01 0.00 0.00 2.27
643 651 0.319040 CGAGGAGGGTGCGTATGATG 60.319 60.000 0.00 0.00 0.00 3.07
652 660 0.105039 GCTGGAATACGAGGAGGGTG 59.895 60.000 0.00 0.00 0.00 4.61
656 664 2.801342 GCAGAAGCTGGAATACGAGGAG 60.801 54.545 0.00 0.00 37.91 3.69
663 671 4.261801 GGTAACTTGCAGAAGCTGGAATA 58.738 43.478 1.90 0.00 40.71 1.75
1094 1132 3.567397 TCTTACCTAGCTAGCTTCCCTG 58.433 50.000 24.88 9.58 0.00 4.45
1097 1135 5.585445 GGTTTTTCTTACCTAGCTAGCTTCC 59.415 44.000 24.88 0.00 32.75 3.46
1438 2797 8.094798 TGTGATTGGTGACTTAAACATAAGAC 57.905 34.615 2.80 0.00 0.00 3.01
1455 3356 3.770263 ATGATTGACGCTTGTGATTGG 57.230 42.857 0.00 0.00 0.00 3.16
1544 4772 9.841295 AAACTTTACATACTCTGACCAAGTTTA 57.159 29.630 5.18 0.00 38.55 2.01
1545 4773 8.621286 CAAACTTTACATACTCTGACCAAGTTT 58.379 33.333 0.00 0.00 39.57 2.66
1686 4914 1.599419 GCACACGAACCCATTCACAAC 60.599 52.381 0.00 0.00 34.14 3.32
1730 4958 1.226746 CGGGCAAGAAGAAGTCGTTT 58.773 50.000 0.00 0.00 0.00 3.60
1817 5045 1.149174 CAGTGTGTTCAGCCCCACT 59.851 57.895 0.00 0.00 38.64 4.00
1819 5047 2.515398 CCAGTGTGTTCAGCCCCA 59.485 61.111 0.00 0.00 0.00 4.96
1832 5060 1.452651 CGCCATTGAGATGCCCAGT 60.453 57.895 0.00 0.00 31.67 4.00
1994 5222 1.153269 GCCCTCCACTAGCTGCTTC 60.153 63.158 7.79 0.00 0.00 3.86
2111 5339 1.018752 CGTTGGCGATGGTGATCACA 61.019 55.000 26.47 13.45 41.33 3.58
2153 5381 0.387202 CGAGGATGAGGTCGCTGATT 59.613 55.000 0.00 0.00 0.00 2.57
2264 5492 2.666207 GGTGGCATGTCGTACCCA 59.334 61.111 0.00 0.00 0.00 4.51
2267 5495 2.510691 CCGGGTGGCATGTCGTAC 60.511 66.667 0.00 0.00 0.00 3.67
2473 5703 9.609346 ACATCGTAAATTAAGCCAGTATTAAGT 57.391 29.630 0.00 0.00 0.00 2.24
2474 5704 9.864034 CACATCGTAAATTAAGCCAGTATTAAG 57.136 33.333 0.00 0.00 0.00 1.85
2475 5705 8.832521 CCACATCGTAAATTAAGCCAGTATTAA 58.167 33.333 0.00 0.00 0.00 1.40
2476 5706 7.988599 ACCACATCGTAAATTAAGCCAGTATTA 59.011 33.333 0.00 0.00 0.00 0.98
2477 5707 6.826741 ACCACATCGTAAATTAAGCCAGTATT 59.173 34.615 0.00 0.00 0.00 1.89
2478 5708 6.260050 CACCACATCGTAAATTAAGCCAGTAT 59.740 38.462 0.00 0.00 0.00 2.12
2523 5753 2.682856 ACAAACACACTTGCTGGTAGTG 59.317 45.455 0.00 0.00 46.56 2.74
2526 5756 2.020720 CCACAAACACACTTGCTGGTA 58.979 47.619 0.00 0.00 0.00 3.25
2631 5871 8.915871 TTTCATATTGAAGTTTAGCAGCATTC 57.084 30.769 0.00 0.00 37.70 2.67
2674 5914 6.810182 CAGATGGCTAAAGAAAACAGGAATTG 59.190 38.462 0.00 0.00 0.00 2.32
2725 5965 1.432514 TGATGCGCAGAGAGAAACAC 58.567 50.000 18.32 0.00 0.00 3.32
2754 5994 0.531311 CATGGCTGCATGCTAGTCGA 60.531 55.000 20.33 7.59 42.39 4.20
2755 5995 0.531311 TCATGGCTGCATGCTAGTCG 60.531 55.000 20.33 5.01 42.39 4.18
2756 5996 1.805345 GATCATGGCTGCATGCTAGTC 59.195 52.381 20.33 15.96 42.39 2.59
2757 5997 1.142262 TGATCATGGCTGCATGCTAGT 59.858 47.619 20.33 0.00 42.39 2.57
2764 6004 0.889994 GTTTGGTGATCATGGCTGCA 59.110 50.000 0.00 0.00 0.00 4.41
2789 6029 6.938698 TTTCCCCCGTATATATCTGCTTTA 57.061 37.500 0.00 0.00 0.00 1.85
2816 6056 3.137176 ACAGATGTCCCATAGACCATTGG 59.863 47.826 0.00 0.00 45.68 3.16
2817 6057 4.384056 GACAGATGTCCCATAGACCATTG 58.616 47.826 1.33 0.00 45.68 2.82
2818 6058 4.696479 GACAGATGTCCCATAGACCATT 57.304 45.455 1.33 0.00 45.68 3.16
2830 6070 4.187694 GTGAGATTCAAGGGACAGATGTC 58.812 47.826 4.33 4.33 44.04 3.06
2831 6071 3.054802 GGTGAGATTCAAGGGACAGATGT 60.055 47.826 0.00 0.00 0.00 3.06
2832 6072 3.539604 GGTGAGATTCAAGGGACAGATG 58.460 50.000 0.00 0.00 0.00 2.90
2833 6073 2.169352 CGGTGAGATTCAAGGGACAGAT 59.831 50.000 0.00 0.00 0.00 2.90
2834 6074 1.550524 CGGTGAGATTCAAGGGACAGA 59.449 52.381 0.00 0.00 0.00 3.41
2835 6075 1.276421 ACGGTGAGATTCAAGGGACAG 59.724 52.381 0.00 0.00 0.00 3.51
2836 6076 1.348064 ACGGTGAGATTCAAGGGACA 58.652 50.000 0.00 0.00 0.00 4.02
2837 6077 2.289444 TGAACGGTGAGATTCAAGGGAC 60.289 50.000 0.00 0.00 31.95 4.46
2838 6078 1.974957 TGAACGGTGAGATTCAAGGGA 59.025 47.619 0.00 0.00 31.95 4.20
2839 6079 2.472695 TGAACGGTGAGATTCAAGGG 57.527 50.000 0.00 0.00 31.95 3.95
2840 6080 4.142600 GGAAATGAACGGTGAGATTCAAGG 60.143 45.833 0.00 0.00 38.29 3.61
2841 6081 4.142600 GGGAAATGAACGGTGAGATTCAAG 60.143 45.833 0.00 0.00 38.29 3.02
2842 6082 3.756434 GGGAAATGAACGGTGAGATTCAA 59.244 43.478 0.00 0.00 38.29 2.69
2843 6083 3.343617 GGGAAATGAACGGTGAGATTCA 58.656 45.455 0.00 0.00 39.09 2.57
2844 6084 2.351726 CGGGAAATGAACGGTGAGATTC 59.648 50.000 0.00 0.00 0.00 2.52
2845 6085 2.027561 TCGGGAAATGAACGGTGAGATT 60.028 45.455 0.00 0.00 0.00 2.40
2846 6086 1.553248 TCGGGAAATGAACGGTGAGAT 59.447 47.619 0.00 0.00 0.00 2.75
2847 6087 0.970640 TCGGGAAATGAACGGTGAGA 59.029 50.000 0.00 0.00 0.00 3.27
2848 6088 2.024176 ATCGGGAAATGAACGGTGAG 57.976 50.000 0.00 0.00 0.00 3.51
2849 6089 2.080693 CAATCGGGAAATGAACGGTGA 58.919 47.619 0.00 0.00 0.00 4.02
2850 6090 2.080693 TCAATCGGGAAATGAACGGTG 58.919 47.619 0.00 0.00 0.00 4.94
2851 6091 2.483014 TCAATCGGGAAATGAACGGT 57.517 45.000 0.00 0.00 0.00 4.83
2852 6092 2.942376 TGATCAATCGGGAAATGAACGG 59.058 45.455 0.00 0.00 0.00 4.44
2853 6093 3.546815 GCTGATCAATCGGGAAATGAACG 60.547 47.826 0.00 0.00 33.75 3.95
2854 6094 3.378112 TGCTGATCAATCGGGAAATGAAC 59.622 43.478 0.00 0.00 33.75 3.18
2855 6095 3.378112 GTGCTGATCAATCGGGAAATGAA 59.622 43.478 0.00 0.00 35.22 2.57
2856 6096 2.945008 GTGCTGATCAATCGGGAAATGA 59.055 45.455 0.00 0.00 35.22 2.57
2857 6097 2.033801 GGTGCTGATCAATCGGGAAATG 59.966 50.000 0.00 0.00 35.22 2.32
2858 6098 2.301346 GGTGCTGATCAATCGGGAAAT 58.699 47.619 0.00 0.00 35.22 2.17
2859 6099 1.681780 GGGTGCTGATCAATCGGGAAA 60.682 52.381 0.00 0.00 35.22 3.13
2860 6100 0.107214 GGGTGCTGATCAATCGGGAA 60.107 55.000 0.00 0.00 35.22 3.97
2861 6101 1.526887 GGGTGCTGATCAATCGGGA 59.473 57.895 0.00 0.00 33.75 5.14
2862 6102 1.526917 GGGGTGCTGATCAATCGGG 60.527 63.158 0.00 0.00 33.75 5.14
2863 6103 1.889105 CGGGGTGCTGATCAATCGG 60.889 63.158 0.00 0.00 36.26 4.18
2864 6104 2.537560 GCGGGGTGCTGATCAATCG 61.538 63.158 0.00 0.00 41.73 3.34
2865 6105 3.425422 GCGGGGTGCTGATCAATC 58.575 61.111 0.00 0.00 41.73 2.67
2874 6114 3.198068 CATGATACATATAGCGGGGTGC 58.802 50.000 0.00 0.00 46.98 5.01
2875 6115 4.160439 AGACATGATACATATAGCGGGGTG 59.840 45.833 0.00 0.00 0.00 4.61
2876 6116 4.353777 AGACATGATACATATAGCGGGGT 58.646 43.478 0.00 0.00 0.00 4.95
2877 6117 5.344743 AAGACATGATACATATAGCGGGG 57.655 43.478 0.00 0.00 0.00 5.73
2878 6118 7.063898 CAGAAAAGACATGATACATATAGCGGG 59.936 40.741 0.00 0.00 0.00 6.13
2879 6119 7.412346 GCAGAAAAGACATGATACATATAGCGG 60.412 40.741 0.00 0.00 0.00 5.52
2880 6120 7.330454 AGCAGAAAAGACATGATACATATAGCG 59.670 37.037 0.00 0.00 0.00 4.26
2881 6121 8.545229 AGCAGAAAAGACATGATACATATAGC 57.455 34.615 0.00 0.00 0.00 2.97
2885 6125 9.626045 CGTATAGCAGAAAAGACATGATACATA 57.374 33.333 0.00 0.00 0.00 2.29
2886 6126 7.600375 CCGTATAGCAGAAAAGACATGATACAT 59.400 37.037 0.00 0.00 0.00 2.29
2887 6127 6.923508 CCGTATAGCAGAAAAGACATGATACA 59.076 38.462 0.00 0.00 0.00 2.29
2888 6128 6.366332 CCCGTATAGCAGAAAAGACATGATAC 59.634 42.308 0.00 0.00 0.00 2.24
2889 6129 6.455647 CCCGTATAGCAGAAAAGACATGATA 58.544 40.000 0.00 0.00 0.00 2.15
2890 6130 5.300752 CCCGTATAGCAGAAAAGACATGAT 58.699 41.667 0.00 0.00 0.00 2.45
2891 6131 4.442893 CCCCGTATAGCAGAAAAGACATGA 60.443 45.833 0.00 0.00 0.00 3.07
2892 6132 3.809832 CCCCGTATAGCAGAAAAGACATG 59.190 47.826 0.00 0.00 0.00 3.21
2893 6133 3.181454 CCCCCGTATAGCAGAAAAGACAT 60.181 47.826 0.00 0.00 0.00 3.06
2894 6134 2.169769 CCCCCGTATAGCAGAAAAGACA 59.830 50.000 0.00 0.00 0.00 3.41
2895 6135 2.433239 TCCCCCGTATAGCAGAAAAGAC 59.567 50.000 0.00 0.00 0.00 3.01
2896 6136 2.754465 TCCCCCGTATAGCAGAAAAGA 58.246 47.619 0.00 0.00 0.00 2.52
2897 6137 3.553828 TTCCCCCGTATAGCAGAAAAG 57.446 47.619 0.00 0.00 0.00 2.27
2898 6138 4.513406 ATTTCCCCCGTATAGCAGAAAA 57.487 40.909 0.00 0.00 0.00 2.29
2899 6139 4.202388 GGTATTTCCCCCGTATAGCAGAAA 60.202 45.833 0.00 0.00 0.00 2.52
2900 6140 3.325716 GGTATTTCCCCCGTATAGCAGAA 59.674 47.826 0.00 0.00 0.00 3.02
2901 6141 2.901839 GGTATTTCCCCCGTATAGCAGA 59.098 50.000 0.00 0.00 0.00 4.26
2902 6142 3.329929 GGTATTTCCCCCGTATAGCAG 57.670 52.381 0.00 0.00 0.00 4.24
2922 6162 3.137176 ACAGATGTCCCATAGACCATTGG 59.863 47.826 0.00 0.00 45.68 3.16
2923 6163 4.384056 GACAGATGTCCCATAGACCATTG 58.616 47.826 1.33 0.00 45.68 2.82
2924 6164 4.696479 GACAGATGTCCCATAGACCATT 57.304 45.455 1.33 0.00 45.68 3.16
2935 6175 6.665992 TGTATATACAAGGGACAGATGTCC 57.334 41.667 21.48 21.48 46.94 4.02
2936 6176 7.291411 AGTGTATATACAAGGGACAGATGTC 57.709 40.000 17.07 4.33 39.95 3.06
2937 6177 7.676683 AAGTGTATATACAAGGGACAGATGT 57.323 36.000 17.07 0.00 38.04 3.06
3241 6500 8.428186 TTCGGTCGTAAAGCTATATCAAAATT 57.572 30.769 0.00 0.00 0.00 1.82
3307 6566 3.075884 CCCTTCGGAATTTTGAACGGTA 58.924 45.455 0.00 0.00 0.00 4.02
3522 10052 6.255887 CCGTTGCTAAAGTAGTGAATTAGGAG 59.744 42.308 0.00 0.00 30.34 3.69
3546 10099 1.463444 GTGTAAGTGTGTTGCGATCCC 59.537 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.