Multiple sequence alignment - TraesCS2D01G387300

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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 TraesCS2D01G387300 chr2D 100.000 2833 0 0 1 2833 492675386 492678218 0.000000e+00 5232.0
1 TraesCS2D01G387300 chr2A 87.858 2726 151 64 170 2776 637983679 637986343 0.000000e+00 3035.0
2 TraesCS2D01G387300 chr2B 90.614 1907 73 39 1 1850 578604155 578606012 0.000000e+00 2433.0
3 TraesCS2D01G387300 chr2B 83.716 436 45 10 2337 2757 578607030 578607454 3.420000e-104 388.0
4 TraesCS2D01G387300 chr2B 93.689 206 13 0 2109 2314 578606646 578606851 2.740000e-80 309.0
5 TraesCS2D01G387300 chr2B 90.361 249 3 7 1865 2101 578606112 578606351 9.860000e-80 307.0
6 TraesCS2D01G387300 chr2B 96.491 57 2 0 2777 2833 526764687 526764743 8.360000e-16 95.3
7 TraesCS2D01G387300 chr6A 89.226 297 29 3 1110 1406 451660052 451660345 4.460000e-98 368.0
8 TraesCS2D01G387300 chr6A 98.276 58 1 0 2776 2833 600393461 600393518 4.990000e-18 102.0
9 TraesCS2D01G387300 chr6D 90.288 278 27 0 1129 1406 314056259 314056536 5.770000e-97 364.0
10 TraesCS2D01G387300 chr6B 90.288 278 27 0 1129 1406 512448211 512447934 5.770000e-97 364.0
11 TraesCS2D01G387300 chr6B 96.364 55 2 0 2776 2830 645271026 645271080 1.080000e-14 91.6
12 TraesCS2D01G387300 chr5B 80.989 263 45 3 1133 1394 501464953 501464695 1.330000e-48 204.0
13 TraesCS2D01G387300 chr5A 81.423 253 42 3 1134 1385 527905747 527905499 4.790000e-48 202.0
14 TraesCS2D01G387300 chr5A 96.552 58 2 0 2776 2833 482515738 482515795 2.320000e-16 97.1
15 TraesCS2D01G387300 chr5D 81.176 255 41 5 1133 1385 415273199 415272950 6.190000e-47 198.0
16 TraesCS2D01G387300 chr4D 76.444 225 45 7 1126 1348 457075099 457075317 6.410000e-22 115.0
17 TraesCS2D01G387300 chr7D 98.246 57 1 0 2777 2833 34070158 34070102 1.800000e-17 100.0
18 TraesCS2D01G387300 chr7B 98.246 57 1 0 2777 2833 739440850 739440906 1.800000e-17 100.0
19 TraesCS2D01G387300 chr7A 96.610 59 2 0 2775 2833 575457890 575457948 6.460000e-17 99.0
20 TraesCS2D01G387300 chr7A 94.828 58 3 0 2776 2833 696929537 696929480 1.080000e-14 91.6
21 TraesCS2D01G387300 chr3A 96.491 57 2 0 2777 2833 695866863 695866807 8.360000e-16 95.3


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 TraesCS2D01G387300 chr2D 492675386 492678218 2832 False 5232.00 5232 100.000 1 2833 1 chr2D.!!$F1 2832
1 TraesCS2D01G387300 chr2A 637983679 637986343 2664 False 3035.00 3035 87.858 170 2776 1 chr2A.!!$F1 2606
2 TraesCS2D01G387300 chr2B 578604155 578607454 3299 False 859.25 2433 89.595 1 2757 4 chr2B.!!$F2 2756

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
131 132 0.179124 AGCTAGCTTGCACTCGTAGC 60.179 55.0 22.05 7.07 37.05 3.58 F
307 321 0.252558 TGGTCCTACCTGTTCCTCCC 60.253 60.0 0.00 0.00 39.58 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 1463 0.720590 CGAGCTTCTCTTGCTTGAGC 59.279 55.0 0.0 0.0 42.84 4.26 R
2245 2757 0.039978 CCTACTGCCGATGCTCTACG 60.040 60.0 0.0 0.0 38.71 3.51 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
30 31 4.696479 ATCCTGAGTTACCATGATGTCC 57.304 45.455 0.00 0.00 0.00 4.02
31 32 2.771943 TCCTGAGTTACCATGATGTCCC 59.228 50.000 0.00 0.00 0.00 4.46
32 33 2.774234 CCTGAGTTACCATGATGTCCCT 59.226 50.000 0.00 0.00 0.00 4.20
33 34 3.200825 CCTGAGTTACCATGATGTCCCTT 59.799 47.826 0.00 0.00 0.00 3.95
34 35 4.446371 CTGAGTTACCATGATGTCCCTTC 58.554 47.826 0.00 0.00 0.00 3.46
52 53 3.055385 CCTTCCTTCCTGGTAAACGATCA 60.055 47.826 0.00 0.00 37.07 2.92
77 78 1.616865 AGTAAACTAGTGGAGCGCACA 59.383 47.619 11.47 5.21 0.00 4.57
79 80 1.226746 AAACTAGTGGAGCGCACAAC 58.773 50.000 11.47 7.36 0.00 3.32
116 117 4.789075 GGCCAACGCGACGAGCTA 62.789 66.667 15.93 0.00 45.59 3.32
118 119 3.248171 CCAACGCGACGAGCTAGC 61.248 66.667 15.93 6.62 45.59 3.42
119 120 2.202492 CAACGCGACGAGCTAGCT 60.202 61.111 19.45 19.45 45.59 3.32
120 121 1.801913 CAACGCGACGAGCTAGCTT 60.802 57.895 20.42 3.03 45.59 3.74
121 122 1.801913 AACGCGACGAGCTAGCTTG 60.802 57.895 27.42 27.42 45.59 4.01
122 123 3.611792 CGCGACGAGCTAGCTTGC 61.612 66.667 28.68 22.26 45.59 4.01
123 124 2.507102 GCGACGAGCTAGCTTGCA 60.507 61.111 28.68 0.00 44.04 4.08
124 125 2.793322 GCGACGAGCTAGCTTGCAC 61.793 63.158 28.68 21.37 44.04 4.57
125 126 1.153939 CGACGAGCTAGCTTGCACT 60.154 57.895 28.68 12.21 34.99 4.40
126 127 1.136872 CGACGAGCTAGCTTGCACTC 61.137 60.000 28.68 18.61 34.99 3.51
127 128 3.685592 CGAGCTAGCTTGCACTCG 58.314 61.111 20.42 18.17 45.02 4.18
130 131 1.833860 GAGCTAGCTTGCACTCGTAG 58.166 55.000 20.42 0.00 34.99 3.51
131 132 0.179124 AGCTAGCTTGCACTCGTAGC 60.179 55.000 22.05 7.07 37.05 3.58
132 133 0.179124 GCTAGCTTGCACTCGTAGCT 60.179 55.000 15.53 13.97 46.33 3.32
133 134 1.065701 GCTAGCTTGCACTCGTAGCTA 59.934 52.381 15.53 14.65 43.08 3.32
138 139 3.634568 CTTGCACTCGTAGCTAGCTAT 57.365 47.619 26.59 8.74 0.00 2.97
143 144 3.633235 CACTCGTAGCTAGCTATTGTGG 58.367 50.000 26.59 18.76 0.00 4.17
145 146 3.066900 ACTCGTAGCTAGCTATTGTGGTG 59.933 47.826 26.59 15.55 0.00 4.17
307 321 0.252558 TGGTCCTACCTGTTCCTCCC 60.253 60.000 0.00 0.00 39.58 4.30
465 488 4.634991 GATCGGTTCGTGTACATGAAAAC 58.365 43.478 27.75 21.99 37.99 2.43
513 558 7.691158 AGAAAATAAACGAAAAGAACACGTCT 58.309 30.769 0.00 0.00 39.31 4.18
524 569 2.818432 AGAACACGTCTGGTCGACTTAT 59.182 45.455 16.46 0.00 39.36 1.73
525 570 4.005650 AGAACACGTCTGGTCGACTTATA 58.994 43.478 16.46 0.00 39.36 0.98
535 580 7.126398 GTCTGGTCGACTTATAATTTGCAATC 58.874 38.462 16.46 0.00 39.61 2.67
925 975 0.321021 CCAACAGAGCAGAGCAGAGT 59.679 55.000 0.00 0.00 0.00 3.24
1077 1142 1.544982 GGCATGGACATGGAGATGGAG 60.545 57.143 13.63 0.00 39.16 3.86
1368 1463 4.813526 CACTCCCGCGTCGAGTCG 62.814 72.222 19.76 6.09 38.54 4.18
1377 1472 1.729484 CGTCGAGTCGCTCAAGCAA 60.729 57.895 7.92 0.00 42.21 3.91
1405 1500 4.077184 CCCTCGCCGCACAGGTAA 62.077 66.667 4.94 0.00 43.70 2.85
1406 1501 2.047655 CCTCGCCGCACAGGTAAA 60.048 61.111 0.00 0.00 43.70 2.01
1407 1502 1.449601 CCTCGCCGCACAGGTAAAT 60.450 57.895 0.00 0.00 43.70 1.40
1408 1503 0.179094 CCTCGCCGCACAGGTAAATA 60.179 55.000 0.00 0.00 43.70 1.40
1409 1504 1.540363 CCTCGCCGCACAGGTAAATAT 60.540 52.381 0.00 0.00 43.70 1.28
1410 1505 2.288579 CCTCGCCGCACAGGTAAATATA 60.289 50.000 0.00 0.00 43.70 0.86
1411 1506 3.585862 CTCGCCGCACAGGTAAATATAT 58.414 45.455 0.00 0.00 43.70 0.86
1412 1507 3.581755 TCGCCGCACAGGTAAATATATC 58.418 45.455 0.00 0.00 43.70 1.63
1413 1508 2.671396 CGCCGCACAGGTAAATATATCC 59.329 50.000 0.00 0.00 43.70 2.59
1414 1509 2.671396 GCCGCACAGGTAAATATATCCG 59.329 50.000 0.00 0.00 43.70 4.18
1415 1510 3.259064 CCGCACAGGTAAATATATCCGG 58.741 50.000 0.00 0.00 34.51 5.14
1416 1511 2.671396 CGCACAGGTAAATATATCCGGC 59.329 50.000 0.00 0.00 0.00 6.13
1417 1512 3.670625 GCACAGGTAAATATATCCGGCA 58.329 45.455 0.00 0.00 0.00 5.69
1418 1513 4.069304 GCACAGGTAAATATATCCGGCAA 58.931 43.478 0.00 0.00 0.00 4.52
1419 1514 4.517453 GCACAGGTAAATATATCCGGCAAA 59.483 41.667 0.00 0.00 0.00 3.68
1447 1547 3.234596 GCTTCGCGCGTATTCTTAATT 57.765 42.857 30.98 0.00 0.00 1.40
1449 1549 3.414422 GCTTCGCGCGTATTCTTAATTTG 59.586 43.478 30.98 5.13 0.00 2.32
1450 1550 4.780946 GCTTCGCGCGTATTCTTAATTTGA 60.781 41.667 30.98 1.00 0.00 2.69
1458 1558 6.363473 GCGTATTCTTAATTTGATCTTCCCG 58.637 40.000 0.00 0.00 0.00 5.14
1459 1559 6.202188 GCGTATTCTTAATTTGATCTTCCCGA 59.798 38.462 0.00 0.00 0.00 5.14
1928 2141 1.596727 GTGCTCGATTTCTCATCTGGC 59.403 52.381 0.00 0.00 0.00 4.85
1941 2154 1.422781 CATCTGGCTGGGGATACATGT 59.577 52.381 2.69 2.69 39.74 3.21
1986 2210 3.931247 CGGGTGGGTCCGTGTGAA 61.931 66.667 0.00 0.00 44.60 3.18
1987 2211 2.754375 GGGTGGGTCCGTGTGAAT 59.246 61.111 0.00 0.00 37.00 2.57
1988 2212 1.674322 GGGTGGGTCCGTGTGAATG 60.674 63.158 0.00 0.00 37.00 2.67
2000 2224 5.067413 GTCCGTGTGAATGTAAGATAGAGGA 59.933 44.000 0.00 0.00 0.00 3.71
2016 2240 2.141517 GAGGATGATGCACCTGAATCG 58.858 52.381 0.00 0.00 36.57 3.34
2017 2241 1.764723 AGGATGATGCACCTGAATCGA 59.235 47.619 0.00 0.00 32.57 3.59
2102 2326 2.543641 GGATGCTGCTAAAATGTTGCC 58.456 47.619 0.00 0.00 0.00 4.52
2104 2328 2.437200 TGCTGCTAAAATGTTGCCAC 57.563 45.000 0.00 0.00 0.00 5.01
2141 2653 2.977914 TGGTAGAGTTTGCATCAGCTC 58.022 47.619 0.00 0.00 42.74 4.09
2152 2664 2.810274 TGCATCAGCTCTTCTGTTTGTC 59.190 45.455 0.00 0.00 43.32 3.18
2175 2687 0.449388 GCTCCCGCTGTGAATTCAAG 59.551 55.000 10.35 10.88 0.00 3.02
2245 2757 6.127786 ACTGCTTCTCAATTTTAGGATCTTGC 60.128 38.462 0.00 0.00 0.00 4.01
2278 2790 3.131400 GGCAGTAGGTTCTTGTCTAGGAG 59.869 52.174 0.00 0.00 0.00 3.69
2336 2968 1.406903 AACTTTCTGCAGCCTGCTTT 58.593 45.000 18.96 0.00 45.31 3.51
2344 3012 3.636300 TCTGCAGCCTGCTTTTAGAAAAA 59.364 39.130 18.96 0.00 45.31 1.94
2396 3064 5.761165 TTTTAGGGTGTGCAACTTTAGAC 57.239 39.130 0.00 0.00 38.04 2.59
2478 3147 4.651503 TGGTTAAAGCCTGATTCAAAACCA 59.348 37.500 0.00 0.00 41.98 3.67
2507 3176 8.579682 AAATGTGACTGATTTAAGCAAAGTTC 57.420 30.769 0.00 0.00 0.00 3.01
2513 3182 6.729187 ACTGATTTAAGCAAAGTTCAGACAC 58.271 36.000 11.44 0.00 34.86 3.67
2515 3184 4.545823 TTTAAGCAAAGTTCAGACACCG 57.454 40.909 0.00 0.00 0.00 4.94
2561 3244 6.595716 TCAAATTTCAACGGTTTTGATTGGTT 59.404 30.769 1.82 0.00 34.20 3.67
2600 3283 6.423776 AATCATCCTGGAAAAACAACATGT 57.576 33.333 0.00 0.00 0.00 3.21
2606 3289 5.304101 TCCTGGAAAAACAACATGTTGCTAT 59.696 36.000 33.23 19.56 40.14 2.97
2617 3300 6.806249 ACAACATGTTGCTATTATGTTTTCCG 59.194 34.615 33.23 8.51 41.60 4.30
2619 3302 6.551736 ACATGTTGCTATTATGTTTTCCGTC 58.448 36.000 0.00 0.00 31.38 4.79
2629 3312 3.859411 TGTTTTCCGTCACTTTTGCTT 57.141 38.095 0.00 0.00 0.00 3.91
2666 3358 1.274167 TGTTAGGGCAACACTAGTCGG 59.726 52.381 0.00 0.00 42.29 4.79
2678 3370 3.244112 ACACTAGTCGGTCCCTCAAAAAG 60.244 47.826 0.00 0.00 0.00 2.27
2725 3417 4.967084 TCAAGGAGTTAACTGCACCTAA 57.033 40.909 26.40 10.28 36.72 2.69
2726 3418 5.298989 TCAAGGAGTTAACTGCACCTAAA 57.701 39.130 26.40 9.98 36.72 1.85
2727 3419 5.061179 TCAAGGAGTTAACTGCACCTAAAC 58.939 41.667 26.40 3.52 36.72 2.01
2775 3467 6.493189 AAAAATTTCAGGAGTTAAGCCCAA 57.507 33.333 0.00 0.00 0.00 4.12
2776 3468 5.728637 AAATTTCAGGAGTTAAGCCCAAG 57.271 39.130 0.00 0.00 0.00 3.61
2777 3469 2.879103 TTCAGGAGTTAAGCCCAAGG 57.121 50.000 0.00 0.00 0.00 3.61
2778 3470 0.991920 TCAGGAGTTAAGCCCAAGGG 59.008 55.000 0.00 0.00 38.57 3.95
2779 3471 0.698818 CAGGAGTTAAGCCCAAGGGT 59.301 55.000 7.05 0.00 37.65 4.34
2780 3472 0.698818 AGGAGTTAAGCCCAAGGGTG 59.301 55.000 7.05 0.00 37.65 4.61
2781 3473 0.696501 GGAGTTAAGCCCAAGGGTGA 59.303 55.000 7.05 0.00 37.65 4.02
2782 3474 1.074889 GGAGTTAAGCCCAAGGGTGAA 59.925 52.381 7.05 0.00 37.65 3.18
2783 3475 2.291605 GGAGTTAAGCCCAAGGGTGAAT 60.292 50.000 7.05 0.00 37.65 2.57
2784 3476 3.431415 GAGTTAAGCCCAAGGGTGAATT 58.569 45.455 7.05 0.26 37.65 2.17
2785 3477 3.431415 AGTTAAGCCCAAGGGTGAATTC 58.569 45.455 7.05 0.00 37.65 2.17
2786 3478 2.496070 GTTAAGCCCAAGGGTGAATTCC 59.504 50.000 7.05 0.00 37.65 3.01
2787 3479 0.486879 AAGCCCAAGGGTGAATTCCA 59.513 50.000 7.05 0.00 37.65 3.53
2788 3480 0.712380 AGCCCAAGGGTGAATTCCAT 59.288 50.000 7.05 0.00 37.65 3.41
2789 3481 1.929494 AGCCCAAGGGTGAATTCCATA 59.071 47.619 7.05 0.00 37.65 2.74
2790 3482 2.519691 AGCCCAAGGGTGAATTCCATAT 59.480 45.455 7.05 0.00 37.65 1.78
2791 3483 3.726859 AGCCCAAGGGTGAATTCCATATA 59.273 43.478 7.05 0.00 37.65 0.86
2792 3484 4.358006 AGCCCAAGGGTGAATTCCATATAT 59.642 41.667 7.05 0.00 37.65 0.86
2793 3485 4.463891 GCCCAAGGGTGAATTCCATATATG 59.536 45.833 7.05 5.68 37.65 1.78
2794 3486 4.463891 CCCAAGGGTGAATTCCATATATGC 59.536 45.833 7.24 0.00 0.00 3.14
2795 3487 4.463891 CCAAGGGTGAATTCCATATATGCC 59.536 45.833 7.24 1.33 0.00 4.40
2796 3488 5.078949 CAAGGGTGAATTCCATATATGCCA 58.921 41.667 7.24 0.00 0.00 4.92
2797 3489 4.666512 AGGGTGAATTCCATATATGCCAC 58.333 43.478 7.24 8.85 0.00 5.01
2798 3490 4.354987 AGGGTGAATTCCATATATGCCACT 59.645 41.667 7.24 0.00 0.00 4.00
2799 3491 4.702131 GGGTGAATTCCATATATGCCACTC 59.298 45.833 7.24 6.02 0.00 3.51
2800 3492 5.316167 GGTGAATTCCATATATGCCACTCA 58.684 41.667 7.24 4.78 0.00 3.41
2801 3493 5.769662 GGTGAATTCCATATATGCCACTCAA 59.230 40.000 7.24 0.00 0.00 3.02
2802 3494 6.265196 GGTGAATTCCATATATGCCACTCAAA 59.735 38.462 7.24 0.00 0.00 2.69
2803 3495 7.201902 GGTGAATTCCATATATGCCACTCAAAA 60.202 37.037 7.24 0.00 0.00 2.44
2804 3496 7.649306 GTGAATTCCATATATGCCACTCAAAAC 59.351 37.037 7.24 0.00 0.00 2.43
2805 3497 7.560991 TGAATTCCATATATGCCACTCAAAACT 59.439 33.333 7.24 0.00 0.00 2.66
2806 3498 7.902920 ATTCCATATATGCCACTCAAAACTT 57.097 32.000 7.24 0.00 0.00 2.66
2807 3499 6.698008 TCCATATATGCCACTCAAAACTTG 57.302 37.500 7.24 0.00 0.00 3.16
2808 3500 5.067674 TCCATATATGCCACTCAAAACTTGC 59.932 40.000 7.24 0.00 0.00 4.01
2809 3501 3.874392 ATATGCCACTCAAAACTTGCC 57.126 42.857 0.00 0.00 0.00 4.52
2810 3502 0.681175 ATGCCACTCAAAACTTGCCC 59.319 50.000 0.00 0.00 0.00 5.36
2811 3503 1.007387 GCCACTCAAAACTTGCCCG 60.007 57.895 0.00 0.00 0.00 6.13
2812 3504 1.734388 GCCACTCAAAACTTGCCCGT 61.734 55.000 0.00 0.00 0.00 5.28
2813 3505 1.600023 CCACTCAAAACTTGCCCGTA 58.400 50.000 0.00 0.00 0.00 4.02
2814 3506 1.265905 CCACTCAAAACTTGCCCGTAC 59.734 52.381 0.00 0.00 0.00 3.67
2815 3507 1.265905 CACTCAAAACTTGCCCGTACC 59.734 52.381 0.00 0.00 0.00 3.34
2816 3508 1.142262 ACTCAAAACTTGCCCGTACCT 59.858 47.619 0.00 0.00 0.00 3.08
2817 3509 2.227194 CTCAAAACTTGCCCGTACCTT 58.773 47.619 0.00 0.00 0.00 3.50
2818 3510 2.223745 TCAAAACTTGCCCGTACCTTC 58.776 47.619 0.00 0.00 0.00 3.46
2819 3511 1.950909 CAAAACTTGCCCGTACCTTCA 59.049 47.619 0.00 0.00 0.00 3.02
2820 3512 2.556622 CAAAACTTGCCCGTACCTTCAT 59.443 45.455 0.00 0.00 0.00 2.57
2821 3513 2.109425 AACTTGCCCGTACCTTCATC 57.891 50.000 0.00 0.00 0.00 2.92
2822 3514 1.276622 ACTTGCCCGTACCTTCATCT 58.723 50.000 0.00 0.00 0.00 2.90
2823 3515 1.066143 ACTTGCCCGTACCTTCATCTG 60.066 52.381 0.00 0.00 0.00 2.90
2824 3516 0.392461 TTGCCCGTACCTTCATCTGC 60.392 55.000 0.00 0.00 0.00 4.26
2825 3517 1.523938 GCCCGTACCTTCATCTGCC 60.524 63.158 0.00 0.00 0.00 4.85
2826 3518 1.904771 CCCGTACCTTCATCTGCCA 59.095 57.895 0.00 0.00 0.00 4.92
2827 3519 0.469917 CCCGTACCTTCATCTGCCAT 59.530 55.000 0.00 0.00 0.00 4.40
2828 3520 1.134098 CCCGTACCTTCATCTGCCATT 60.134 52.381 0.00 0.00 0.00 3.16
2829 3521 1.942657 CCGTACCTTCATCTGCCATTG 59.057 52.381 0.00 0.00 0.00 2.82
2830 3522 1.942657 CGTACCTTCATCTGCCATTGG 59.057 52.381 0.00 0.00 0.00 3.16
2831 3523 2.419990 CGTACCTTCATCTGCCATTGGA 60.420 50.000 6.95 0.00 0.00 3.53
2832 3524 2.905415 ACCTTCATCTGCCATTGGAA 57.095 45.000 6.95 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.055385 TGATCGTTTACCAGGAAGGAAGG 60.055 47.826 0.00 0.00 41.22 3.46
31 32 4.202245 TGATCGTTTACCAGGAAGGAAG 57.798 45.455 0.00 0.00 41.22 3.46
32 33 4.627284 TTGATCGTTTACCAGGAAGGAA 57.373 40.909 0.00 0.00 41.22 3.36
33 34 4.513442 CATTGATCGTTTACCAGGAAGGA 58.487 43.478 0.00 0.00 41.22 3.36
34 35 3.627577 CCATTGATCGTTTACCAGGAAGG 59.372 47.826 0.00 0.00 45.67 3.46
52 53 3.679083 GCGCTCCACTAGTTTACTCCATT 60.679 47.826 0.00 0.00 0.00 3.16
77 78 0.179094 TCTTGTCGCCTGTTGTCGTT 60.179 50.000 0.00 0.00 0.00 3.85
79 80 1.557443 GGTCTTGTCGCCTGTTGTCG 61.557 60.000 0.00 0.00 0.00 4.35
109 110 1.153939 CGAGTGCAAGCTAGCTCGT 60.154 57.895 19.65 0.00 43.79 4.18
110 111 3.685592 CGAGTGCAAGCTAGCTCG 58.314 61.111 19.65 8.33 43.42 5.03
111 112 1.833860 CTACGAGTGCAAGCTAGCTC 58.166 55.000 19.65 7.13 34.99 4.09
112 113 0.179124 GCTACGAGTGCAAGCTAGCT 60.179 55.000 12.68 12.68 33.40 3.32
115 116 1.065701 GCTAGCTACGAGTGCAAGCTA 59.934 52.381 14.65 14.65 44.55 3.32
118 119 3.634568 ATAGCTAGCTACGAGTGCAAG 57.365 47.619 26.41 0.00 0.00 4.01
119 120 3.130516 ACAATAGCTAGCTACGAGTGCAA 59.869 43.478 26.41 3.34 0.00 4.08
120 121 2.688446 ACAATAGCTAGCTACGAGTGCA 59.312 45.455 26.41 4.14 0.00 4.57
121 122 3.046390 CACAATAGCTAGCTACGAGTGC 58.954 50.000 26.41 0.00 0.00 4.40
122 123 3.066900 ACCACAATAGCTAGCTACGAGTG 59.933 47.826 28.76 28.76 32.54 3.51
123 124 3.066900 CACCACAATAGCTAGCTACGAGT 59.933 47.826 26.41 20.25 0.00 4.18
124 125 3.066900 ACACCACAATAGCTAGCTACGAG 59.933 47.826 26.41 19.64 0.00 4.18
125 126 3.021695 ACACCACAATAGCTAGCTACGA 58.978 45.455 26.41 7.44 0.00 3.43
126 127 3.116300 CACACCACAATAGCTAGCTACG 58.884 50.000 26.41 21.29 0.00 3.51
127 128 3.865745 CACACACCACAATAGCTAGCTAC 59.134 47.826 26.41 0.00 0.00 3.58
130 131 1.398390 GCACACACCACAATAGCTAGC 59.602 52.381 6.62 6.62 0.00 3.42
131 132 2.698803 TGCACACACCACAATAGCTAG 58.301 47.619 0.00 0.00 0.00 3.42
132 133 2.849294 TGCACACACCACAATAGCTA 57.151 45.000 0.00 0.00 0.00 3.32
133 134 2.086869 GATGCACACACCACAATAGCT 58.913 47.619 0.00 0.00 0.00 3.32
134 135 1.202065 CGATGCACACACCACAATAGC 60.202 52.381 0.00 0.00 0.00 2.97
135 136 1.398041 CCGATGCACACACCACAATAG 59.602 52.381 0.00 0.00 0.00 1.73
138 139 2.551006 GCCGATGCACACACCACAA 61.551 57.895 0.00 0.00 37.47 3.33
448 462 2.097299 TCGCGTTTTCATGTACACGAAC 60.097 45.455 14.18 3.55 34.49 3.95
465 488 0.730834 CTGTCTGTCCACTTCTCGCG 60.731 60.000 0.00 0.00 0.00 5.87
513 558 5.007234 CGGATTGCAAATTATAAGTCGACCA 59.993 40.000 13.01 0.02 0.00 4.02
524 569 1.944024 CGGCCTACGGATTGCAAATTA 59.056 47.619 1.71 0.00 39.42 1.40
525 570 0.738389 CGGCCTACGGATTGCAAATT 59.262 50.000 1.71 0.00 39.42 1.82
617 665 3.299190 CCTCCCGCCTCGAGATCC 61.299 72.222 15.71 0.55 0.00 3.36
746 794 1.676746 GATAAAGAAACCTCCCCGCC 58.323 55.000 0.00 0.00 0.00 6.13
747 795 1.676746 GGATAAAGAAACCTCCCCGC 58.323 55.000 0.00 0.00 0.00 6.13
857 905 1.404851 CGTTCCTTCCTCTTCCTCTGC 60.405 57.143 0.00 0.00 0.00 4.26
909 958 0.817013 GCTACTCTGCTCTGCTCTGT 59.183 55.000 0.00 0.00 0.00 3.41
957 1010 0.392461 AATCCATGTCAACCGACCCG 60.392 55.000 0.00 0.00 41.85 5.28
966 1019 1.632920 TGCTGGTGGTAATCCATGTCA 59.367 47.619 0.00 0.00 46.20 3.58
1077 1142 1.818785 GCACAGCTGCTCCTCCATC 60.819 63.158 15.27 0.00 40.63 3.51
1368 1463 0.720590 CGAGCTTCTCTTGCTTGAGC 59.279 55.000 0.00 0.00 42.84 4.26
1377 1472 3.832492 GCGAGGGCGAGCTTCTCT 61.832 66.667 13.48 0.00 40.82 3.10
1405 1500 4.332819 GCGATTAGCTTTGCCGGATATATT 59.667 41.667 5.05 0.00 44.04 1.28
1406 1501 3.871594 GCGATTAGCTTTGCCGGATATAT 59.128 43.478 5.05 0.00 44.04 0.86
1407 1502 3.259064 GCGATTAGCTTTGCCGGATATA 58.741 45.455 5.05 0.00 44.04 0.86
1408 1503 2.076863 GCGATTAGCTTTGCCGGATAT 58.923 47.619 5.05 0.00 44.04 1.63
1409 1504 1.508632 GCGATTAGCTTTGCCGGATA 58.491 50.000 5.05 0.00 44.04 2.59
1410 1505 2.321213 GCGATTAGCTTTGCCGGAT 58.679 52.632 5.05 0.00 44.04 4.18
1411 1506 3.808036 GCGATTAGCTTTGCCGGA 58.192 55.556 5.05 0.00 44.04 5.14
1430 1530 4.743151 AGATCAAATTAAGAATACGCGCGA 59.257 37.500 39.36 20.78 0.00 5.87
1434 1534 6.202188 TCGGGAAGATCAAATTAAGAATACGC 59.798 38.462 0.00 0.00 0.00 4.42
1447 1547 6.740944 TGGATTAAGTATCGGGAAGATCAA 57.259 37.500 0.00 0.00 40.66 2.57
1449 1549 5.046950 AGCTGGATTAAGTATCGGGAAGATC 60.047 44.000 0.00 0.00 40.66 2.75
1450 1550 4.841246 AGCTGGATTAAGTATCGGGAAGAT 59.159 41.667 0.00 0.00 43.19 2.40
1458 1558 6.284459 ACAGTTAGCAGCTGGATTAAGTATC 58.716 40.000 17.12 0.00 38.22 2.24
1459 1559 6.240549 ACAGTTAGCAGCTGGATTAAGTAT 57.759 37.500 17.12 0.00 38.22 2.12
1838 1963 7.594015 GGTTCACAACATGTATATACTACTCCG 59.406 40.741 13.89 1.78 0.00 4.63
1928 2141 1.071385 GCCTCTCACATGTATCCCCAG 59.929 57.143 0.00 0.00 0.00 4.45
1941 2154 3.379445 GTCCCCGTTCGCCTCTCA 61.379 66.667 0.00 0.00 0.00 3.27
1983 2207 7.157347 GTGCATCATCCTCTATCTTACATTCA 58.843 38.462 0.00 0.00 0.00 2.57
1984 2208 6.593382 GGTGCATCATCCTCTATCTTACATTC 59.407 42.308 0.00 0.00 0.00 2.67
1985 2209 6.271857 AGGTGCATCATCCTCTATCTTACATT 59.728 38.462 0.00 0.00 0.00 2.71
1986 2210 5.784390 AGGTGCATCATCCTCTATCTTACAT 59.216 40.000 0.00 0.00 0.00 2.29
1987 2211 5.011431 CAGGTGCATCATCCTCTATCTTACA 59.989 44.000 0.00 0.00 30.91 2.41
1988 2212 5.244851 TCAGGTGCATCATCCTCTATCTTAC 59.755 44.000 0.00 0.00 30.91 2.34
2000 2224 3.875727 CTCTTTCGATTCAGGTGCATCAT 59.124 43.478 0.00 0.00 0.00 2.45
2016 2240 3.978687 TCACTTCGGTCACTTCTCTTTC 58.021 45.455 0.00 0.00 0.00 2.62
2017 2241 4.039245 TCATCACTTCGGTCACTTCTCTTT 59.961 41.667 0.00 0.00 0.00 2.52
2102 2326 9.743057 CTCTACCAATGATCTCTACTAAAAGTG 57.257 37.037 0.00 0.00 0.00 3.16
2141 2653 1.264288 GGGAGCAACGACAAACAGAAG 59.736 52.381 0.00 0.00 0.00 2.85
2175 2687 0.179000 ATCGATCCTGCCTCCAACAC 59.821 55.000 0.00 0.00 0.00 3.32
2245 2757 0.039978 CCTACTGCCGATGCTCTACG 60.040 60.000 0.00 0.00 38.71 3.51
2278 2790 3.074412 ACCATGATGAACGTTTGGAGAC 58.926 45.455 20.08 0.00 0.00 3.36
2344 3012 6.364976 GCAATTTCAGGCGTTAATGTTAAGTT 59.635 34.615 0.00 0.00 0.00 2.66
2432 3100 8.623030 ACCAAACTTATCTCTAAGTCGATCTAC 58.377 37.037 0.00 0.00 45.40 2.59
2478 3147 9.252962 CTTTGCTTAAATCAGTCACATTTCTTT 57.747 29.630 0.00 0.00 0.00 2.52
2513 3182 9.374787 TTGAACTCAAATTAAACGATGGGTCGG 62.375 40.741 2.76 0.00 41.48 4.79
2515 3184 6.249035 TGAACTCAAATTAAACGATGGGTC 57.751 37.500 0.00 0.00 0.00 4.46
2547 3230 5.465056 ACAATTAGCAAACCAATCAAAACCG 59.535 36.000 0.00 0.00 0.00 4.44
2549 3232 9.040939 ACTAACAATTAGCAAACCAATCAAAAC 57.959 29.630 0.00 0.00 36.71 2.43
2561 3244 8.902806 CCAGGATGATTTACTAACAATTAGCAA 58.097 33.333 0.00 0.00 39.69 3.91
2576 3259 6.829849 ACATGTTGTTTTTCCAGGATGATTT 58.170 32.000 0.00 0.00 39.69 2.17
2600 3283 6.811253 AAGTGACGGAAAACATAATAGCAA 57.189 33.333 0.00 0.00 0.00 3.91
2606 3289 5.508200 AGCAAAAGTGACGGAAAACATAA 57.492 34.783 0.00 0.00 0.00 1.90
2654 3346 1.254026 TGAGGGACCGACTAGTGTTG 58.746 55.000 0.00 0.00 0.00 3.33
2658 3350 2.302157 CCTTTTTGAGGGACCGACTAGT 59.698 50.000 0.00 0.00 42.26 2.57
2678 3370 9.682465 AAAGAGGATATTTTGAGTAGTTAACCC 57.318 33.333 0.88 0.00 0.00 4.11
2687 3379 7.694093 ACTCCTTGAAAGAGGATATTTTGAGT 58.306 34.615 0.00 0.00 44.56 3.41
2698 3390 4.214332 GTGCAGTTAACTCCTTGAAAGAGG 59.786 45.833 4.77 0.00 35.58 3.69
2710 3402 5.298527 GGAGTTTGTTTAGGTGCAGTTAACT 59.701 40.000 1.12 1.12 0.00 2.24
2725 3417 3.518303 AGTTAGCCGGATAGGAGTTTGTT 59.482 43.478 5.05 0.00 45.00 2.83
2726 3418 3.105283 AGTTAGCCGGATAGGAGTTTGT 58.895 45.455 5.05 0.00 45.00 2.83
2727 3419 3.492829 GGAGTTAGCCGGATAGGAGTTTG 60.493 52.174 5.05 0.00 45.00 2.93
2757 3449 2.225017 CCCTTGGGCTTAACTCCTGAAA 60.225 50.000 0.00 0.00 0.00 2.69
2760 3452 0.698818 ACCCTTGGGCTTAACTCCTG 59.301 55.000 5.46 0.00 0.00 3.86
2764 3456 3.431415 GAATTCACCCTTGGGCTTAACT 58.569 45.455 5.46 0.00 0.00 2.24
2770 3462 2.452600 TATGGAATTCACCCTTGGGC 57.547 50.000 7.93 0.00 0.00 5.36
2773 3465 5.047802 GTGGCATATATGGAATTCACCCTTG 60.048 44.000 14.51 0.00 0.00 3.61
2775 3467 4.354987 AGTGGCATATATGGAATTCACCCT 59.645 41.667 14.51 2.74 0.00 4.34
2776 3468 4.666512 AGTGGCATATATGGAATTCACCC 58.333 43.478 14.51 5.04 0.00 4.61
2777 3469 5.316167 TGAGTGGCATATATGGAATTCACC 58.684 41.667 14.51 5.71 0.00 4.02
2778 3470 6.882610 TTGAGTGGCATATATGGAATTCAC 57.117 37.500 14.51 0.00 0.00 3.18
2779 3471 7.560991 AGTTTTGAGTGGCATATATGGAATTCA 59.439 33.333 14.51 0.00 0.00 2.57
2780 3472 7.945134 AGTTTTGAGTGGCATATATGGAATTC 58.055 34.615 14.51 0.00 0.00 2.17
2781 3473 7.902920 AGTTTTGAGTGGCATATATGGAATT 57.097 32.000 14.51 0.00 0.00 2.17
2782 3474 7.685155 GCAAGTTTTGAGTGGCATATATGGAAT 60.685 37.037 14.51 0.00 0.00 3.01
2783 3475 6.405731 GCAAGTTTTGAGTGGCATATATGGAA 60.406 38.462 14.51 0.00 0.00 3.53
2784 3476 5.067674 GCAAGTTTTGAGTGGCATATATGGA 59.932 40.000 14.51 0.00 0.00 3.41
2785 3477 5.284079 GCAAGTTTTGAGTGGCATATATGG 58.716 41.667 14.51 0.00 0.00 2.74
2786 3478 5.284079 GGCAAGTTTTGAGTGGCATATATG 58.716 41.667 8.45 8.45 37.73 1.78
2787 3479 4.342092 GGGCAAGTTTTGAGTGGCATATAT 59.658 41.667 0.00 0.00 39.46 0.86
2788 3480 3.699038 GGGCAAGTTTTGAGTGGCATATA 59.301 43.478 0.00 0.00 39.46 0.86
2789 3481 2.497273 GGGCAAGTTTTGAGTGGCATAT 59.503 45.455 0.00 0.00 39.46 1.78
2790 3482 1.892474 GGGCAAGTTTTGAGTGGCATA 59.108 47.619 0.00 0.00 39.46 3.14
2791 3483 0.681175 GGGCAAGTTTTGAGTGGCAT 59.319 50.000 0.00 0.00 39.46 4.40
2792 3484 1.733402 CGGGCAAGTTTTGAGTGGCA 61.733 55.000 0.00 0.00 39.46 4.92
2793 3485 1.007387 CGGGCAAGTTTTGAGTGGC 60.007 57.895 0.00 0.00 37.12 5.01
2794 3486 1.265905 GTACGGGCAAGTTTTGAGTGG 59.734 52.381 0.00 0.00 0.00 4.00
2795 3487 1.265905 GGTACGGGCAAGTTTTGAGTG 59.734 52.381 0.00 0.00 0.00 3.51
2796 3488 1.142262 AGGTACGGGCAAGTTTTGAGT 59.858 47.619 0.00 0.00 0.00 3.41
2797 3489 1.892209 AGGTACGGGCAAGTTTTGAG 58.108 50.000 0.00 0.00 0.00 3.02
2798 3490 2.223745 GAAGGTACGGGCAAGTTTTGA 58.776 47.619 0.00 0.00 0.00 2.69
2799 3491 1.950909 TGAAGGTACGGGCAAGTTTTG 59.049 47.619 0.00 0.00 0.00 2.44
2800 3492 2.351706 TGAAGGTACGGGCAAGTTTT 57.648 45.000 0.00 0.00 0.00 2.43
2801 3493 2.039879 AGATGAAGGTACGGGCAAGTTT 59.960 45.455 0.00 0.00 0.00 2.66
2802 3494 1.628846 AGATGAAGGTACGGGCAAGTT 59.371 47.619 0.00 0.00 0.00 2.66
2803 3495 1.066143 CAGATGAAGGTACGGGCAAGT 60.066 52.381 0.00 0.00 0.00 3.16
2804 3496 1.656652 CAGATGAAGGTACGGGCAAG 58.343 55.000 0.00 0.00 0.00 4.01
2805 3497 0.392461 GCAGATGAAGGTACGGGCAA 60.392 55.000 0.00 0.00 0.00 4.52
2806 3498 1.220749 GCAGATGAAGGTACGGGCA 59.779 57.895 0.00 0.00 0.00 5.36
2807 3499 1.523938 GGCAGATGAAGGTACGGGC 60.524 63.158 0.00 0.00 0.00 6.13
2808 3500 0.469917 ATGGCAGATGAAGGTACGGG 59.530 55.000 0.00 0.00 0.00 5.28
2809 3501 1.942657 CAATGGCAGATGAAGGTACGG 59.057 52.381 0.00 0.00 0.00 4.02
2810 3502 1.942657 CCAATGGCAGATGAAGGTACG 59.057 52.381 4.76 0.00 0.00 3.67
2811 3503 3.281727 TCCAATGGCAGATGAAGGTAC 57.718 47.619 0.00 0.00 0.00 3.34
2813 3505 2.905415 TTCCAATGGCAGATGAAGGT 57.095 45.000 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.