Multiple sequence alignment - TraesCS4B01G114600

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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 TraesCS4B01G114600 chr4B 100.000 4940 0 0 931 5870 130622726 130627665 0.000000e+00 9123.0
1 TraesCS4B01G114600 chr4B 100.000 608 0 0 1 608 130621796 130622403 0.000000e+00 1123.0
2 TraesCS4B01G114600 chr4A 93.818 2572 97 31 931 3465 489436744 489434198 0.000000e+00 3812.0
3 TraesCS4B01G114600 chr4A 94.751 1886 48 20 3605 5456 489433796 489431928 0.000000e+00 2887.0
4 TraesCS4B01G114600 chr4A 97.020 302 3 2 6 301 489437714 489437413 2.440000e-138 503.0
5 TraesCS4B01G114600 chr4A 88.793 232 17 6 5647 5869 489431787 489431556 5.790000e-70 276.0
6 TraesCS4B01G114600 chr4A 94.286 140 2 2 465 603 489436938 489436804 5.960000e-50 209.0
7 TraesCS4B01G114600 chr4A 92.308 52 4 0 3555 3606 489434008 489433957 2.270000e-09 75.0
8 TraesCS4B01G114600 chr4D 91.545 2058 61 43 3465 5461 93069995 93072000 0.000000e+00 2732.0
9 TraesCS4B01G114600 chr4D 94.929 1617 45 17 1863 3465 93068367 93069960 0.000000e+00 2497.0
10 TraesCS4B01G114600 chr4D 97.225 865 24 0 931 1795 93067499 93068363 0.000000e+00 1465.0
11 TraesCS4B01G114600 chr4D 83.304 563 34 27 70 608 93066928 93067454 1.150000e-126 464.0
12 TraesCS4B01G114600 chr4D 96.413 223 8 0 5647 5869 93075685 93075907 9.290000e-98 368.0
13 TraesCS4B01G114600 chr4D 97.452 157 4 0 5475 5631 93075545 93075701 9.700000e-68 268.0
14 TraesCS4B01G114600 chr2D 93.333 330 15 3 1333 1656 81515467 81515139 1.140000e-131 481.0
15 TraesCS4B01G114600 chr2D 95.455 110 5 0 3160 3269 81515148 81515039 6.050000e-40 176.0
16 TraesCS4B01G114600 chr6B 91.104 326 16 3 1333 1655 615607840 615607525 4.200000e-116 429.0
17 TraesCS4B01G114600 chr6B 88.822 331 20 4 1333 1656 507373160 507373480 1.980000e-104 390.0
18 TraesCS4B01G114600 chr6B 95.327 107 5 0 3160 3266 507373471 507373577 2.810000e-38 171.0
19 TraesCS4B01G114600 chr6B 93.578 109 7 0 3161 3269 615607532 615607424 4.710000e-36 163.0
20 TraesCS4B01G114600 chr5B 91.104 326 16 3 1333 1655 625119812 625119497 4.200000e-116 429.0
21 TraesCS4B01G114600 chr5B 91.104 326 16 3 1333 1655 628699361 628699046 4.200000e-116 429.0
22 TraesCS4B01G114600 chr5B 93.578 109 7 0 3161 3269 625119504 625119396 4.710000e-36 163.0
23 TraesCS4B01G114600 chr5B 93.578 109 7 0 3161 3269 628699053 628698945 4.710000e-36 163.0
24 TraesCS4B01G114600 chr7A 90.654 321 17 3 1338 1655 487478230 487478540 1.180000e-111 414.0
25 TraesCS4B01G114600 chr7A 93.396 106 7 0 3161 3266 487478533 487478638 2.190000e-34 158.0
26 TraesCS4B01G114600 chr1D 85.841 113 9 4 4050 4160 269726486 269726379 4.810000e-21 113.0
27 TraesCS4B01G114600 chr1A 85.841 113 9 4 4050 4160 333135670 333135563 4.810000e-21 113.0
28 TraesCS4B01G114600 chr7D 98.333 60 1 0 4050 4109 477932153 477932212 8.050000e-19 106.0
29 TraesCS4B01G114600 chr3B 96.721 61 2 0 4050 4110 624317594 624317534 1.040000e-17 102.0
30 TraesCS4B01G114600 chr3A 96.721 61 2 0 4050 4110 612524273 612524213 1.040000e-17 102.0
31 TraesCS4B01G114600 chr2A 96.721 61 2 0 4050 4110 138533224 138533284 1.040000e-17 102.0
32 TraesCS4B01G114600 chr1B 84.071 113 11 4 4050 4160 342973261 342973154 1.040000e-17 102.0
33 TraesCS4B01G114600 chr2B 96.875 32 1 0 5535 5566 6045565 6045534 3.000000e-03 54.7
34 TraesCS4B01G114600 chr2B 96.875 32 1 0 5535 5566 6055324 6055293 3.000000e-03 54.7


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 TraesCS4B01G114600 chr4B 130621796 130627665 5869 False 5123.000000 9123 100.000 1 5870 2 chr4B.!!$F1 5869
1 TraesCS4B01G114600 chr4A 489431556 489437714 6158 True 1293.666667 3812 93.496 6 5869 6 chr4A.!!$R1 5863
2 TraesCS4B01G114600 chr4D 93066928 93075907 8979 False 1299.000000 2732 93.478 70 5869 6 chr4D.!!$F1 5799

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
402 430 0.793617 TCTCTTTCCTCCACCTCCCT 59.206 55.000 0.00 0.00 0.00 4.20 F
1242 1572 1.144936 CGGCATCCCTCTTCAGGTC 59.855 63.158 0.00 0.00 38.30 3.85 F
1461 1791 2.430465 CAGGTGGTGATGAACTCCAAG 58.570 52.381 0.00 0.00 42.63 3.61 F
2713 3071 1.062121 AGATAGGCCCTGCTTGTCCTA 60.062 52.381 0.00 0.00 35.83 2.94 F
3586 4063 0.109412 GTACAGGTGAACTCCGTCGG 60.109 60.000 4.39 4.39 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2511 2.129607 GGTGCAAGCTGACAAAACATG 58.870 47.619 0.00 0.00 0.00 3.21 R
2228 2566 7.921214 AGACAATACTGGTCAGTGTTTATATCG 59.079 37.037 13.32 3.59 40.13 2.92 R
3457 3828 1.003812 TGGCGGTAAAGTTAGCATGGT 59.996 47.619 1.62 1.62 0.00 3.55 R
4116 4786 0.103937 GATGCTCCTTGGTCTCCTCG 59.896 60.000 0.00 0.00 0.00 4.63 R
5465 6162 0.111253 CCTGTTTGGAGCAGAGGGTT 59.889 55.000 0.00 0.00 38.35 4.11 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
106 113 8.744652 GGAGAGAGATTACTTATATGCAAGCTA 58.255 37.037 0.00 0.00 0.00 3.32
315 333 4.229353 TCTCTCTCATCCTCTCTTCTTCCA 59.771 45.833 0.00 0.00 0.00 3.53
382 410 1.679139 TACATGCCATGCAGCTTACC 58.321 50.000 4.17 0.00 43.65 2.85
395 423 2.834549 CAGCTTACCTCTCTTTCCTCCA 59.165 50.000 0.00 0.00 0.00 3.86
397 425 2.093394 GCTTACCTCTCTTTCCTCCACC 60.093 54.545 0.00 0.00 0.00 4.61
402 430 0.793617 TCTCTTTCCTCCACCTCCCT 59.206 55.000 0.00 0.00 0.00 4.20
405 433 1.229853 TTTCCTCCACCTCCCTCCC 60.230 63.158 0.00 0.00 0.00 4.30
407 435 4.825679 CCTCCACCTCCCTCCCCC 62.826 77.778 0.00 0.00 0.00 5.40
431 459 6.836527 CCCTCTCTTTGTCTTTCCTCTATCTA 59.163 42.308 0.00 0.00 0.00 1.98
432 460 7.508977 CCCTCTCTTTGTCTTTCCTCTATCTAT 59.491 40.741 0.00 0.00 0.00 1.98
447 475 6.985645 CCTCTATCTATAATTCTGCATGGCTC 59.014 42.308 0.00 0.00 0.00 4.70
448 476 6.567959 TCTATCTATAATTCTGCATGGCTCG 58.432 40.000 0.00 0.00 0.00 5.03
461 489 2.214376 TGGCTCGTGGATCCAATTTT 57.786 45.000 18.20 0.00 0.00 1.82
462 490 2.524306 TGGCTCGTGGATCCAATTTTT 58.476 42.857 18.20 0.00 0.00 1.94
603 933 3.399440 ACAAGCTCCACTGAAGAAGAG 57.601 47.619 0.00 0.00 0.00 2.85
607 937 3.091545 AGCTCCACTGAAGAAGAGAGAG 58.908 50.000 5.81 0.00 33.99 3.20
974 1304 1.818060 CCAAGATTTTGCCATCGACCA 59.182 47.619 0.00 0.00 32.79 4.02
994 1324 2.661866 CTACATAGGTGCCGGCGC 60.662 66.667 31.86 31.86 0.00 6.53
1086 1416 1.275291 ACACTGTACCTCATGAACCCG 59.725 52.381 0.00 0.00 0.00 5.28
1236 1566 1.258445 ACTTCGTCGGCATCCCTCTT 61.258 55.000 0.00 0.00 0.00 2.85
1241 1571 1.306141 TCGGCATCCCTCTTCAGGT 60.306 57.895 0.00 0.00 38.30 4.00
1242 1572 1.144936 CGGCATCCCTCTTCAGGTC 59.855 63.158 0.00 0.00 38.30 3.85
1353 1683 2.653702 GTGCTCAGCCTGTCGTCT 59.346 61.111 0.00 0.00 0.00 4.18
1461 1791 2.430465 CAGGTGGTGATGAACTCCAAG 58.570 52.381 0.00 0.00 42.63 3.61
1791 2124 8.276252 TGTTAAGAAATGTCCTGCTTTATACC 57.724 34.615 0.00 0.00 0.00 2.73
1846 2179 5.492855 TTAATCTCTCAGTTTTCCCCGAA 57.507 39.130 0.00 0.00 0.00 4.30
1847 2180 4.367039 AATCTCTCAGTTTTCCCCGAAA 57.633 40.909 0.00 0.00 0.00 3.46
1853 2186 6.062258 TCTCAGTTTTCCCCGAAAATATCT 57.938 37.500 3.11 0.00 42.31 1.98
1857 2190 5.594317 CAGTTTTCCCCGAAAATATCTCCAT 59.406 40.000 3.11 0.00 42.31 3.41
1860 2193 7.180229 AGTTTTCCCCGAAAATATCTCCATTTT 59.820 33.333 3.11 0.00 42.31 1.82
1861 2194 7.489239 TTTCCCCGAAAATATCTCCATTTTT 57.511 32.000 0.00 0.00 38.04 1.94
1912 2245 6.608808 CCTCTGGAAAACAAGGGATATTTGAT 59.391 38.462 0.00 0.00 0.00 2.57
1940 2273 5.418310 AACCTGACGATTTTTGTAGTGTG 57.582 39.130 0.00 0.00 0.00 3.82
2170 2503 4.082845 CCTCCTCCCTTTTTCCTTTTCTC 58.917 47.826 0.00 0.00 0.00 2.87
2174 2507 6.858941 TCCTCCCTTTTTCCTTTTCTCAATA 58.141 36.000 0.00 0.00 0.00 1.90
2176 2509 7.232737 TCCTCCCTTTTTCCTTTTCTCAATAAC 59.767 37.037 0.00 0.00 0.00 1.89
2177 2510 7.015195 CCTCCCTTTTTCCTTTTCTCAATAACA 59.985 37.037 0.00 0.00 0.00 2.41
2178 2511 7.722363 TCCCTTTTTCCTTTTCTCAATAACAC 58.278 34.615 0.00 0.00 0.00 3.32
2349 2691 9.309516 CAGCTCTGGTAGTAATTAAATAAACGA 57.690 33.333 0.00 0.00 0.00 3.85
2370 2712 8.864069 AACGAAAATTATTTGTGAATGTGTGA 57.136 26.923 0.00 0.00 0.00 3.58
2371 2713 9.474920 AACGAAAATTATTTGTGAATGTGTGAT 57.525 25.926 0.00 0.00 0.00 3.06
2631 2989 9.338291 CTGATCAAATATGTGTCTCTTTTTGTG 57.662 33.333 0.00 0.00 0.00 3.33
2713 3071 1.062121 AGATAGGCCCTGCTTGTCCTA 60.062 52.381 0.00 0.00 35.83 2.94
2776 3134 2.354729 CCGGGTTTCCCTCATGCA 59.645 61.111 0.00 0.00 42.67 3.96
2822 3185 6.264518 TCTTTTTAGGGAGCTTTAGTTTGTGG 59.735 38.462 0.00 0.00 0.00 4.17
2886 3249 6.475504 TGCTAAAATCCACTTGATTCTCTCA 58.524 36.000 0.00 0.00 42.97 3.27
3023 3394 3.780294 TGTACTGGGATCTAATGTGGCTT 59.220 43.478 0.00 0.00 0.00 4.35
3440 3811 1.480137 CTCTTCGAGCACTTCCTCCAT 59.520 52.381 0.00 0.00 0.00 3.41
3449 3820 2.354805 GCACTTCCTCCATCCGTAAGTT 60.355 50.000 0.00 0.00 0.00 2.66
3450 3821 3.262420 CACTTCCTCCATCCGTAAGTTG 58.738 50.000 0.00 0.00 0.00 3.16
3456 3827 3.000727 CTCCATCCGTAAGTTGTTCACC 58.999 50.000 0.00 0.00 0.00 4.02
3457 3828 2.369203 TCCATCCGTAAGTTGTTCACCA 59.631 45.455 0.00 0.00 0.00 4.17
3459 3830 2.243602 TCCGTAAGTTGTTCACCACC 57.756 50.000 0.00 0.00 0.00 4.61
3460 3831 1.485480 TCCGTAAGTTGTTCACCACCA 59.515 47.619 0.00 0.00 0.00 4.17
3461 3832 2.105134 TCCGTAAGTTGTTCACCACCAT 59.895 45.455 0.00 0.00 0.00 3.55
3462 3833 2.225491 CCGTAAGTTGTTCACCACCATG 59.775 50.000 0.00 0.00 0.00 3.66
3482 3892 4.428615 TGCTAACTTTACCGCCATTTTC 57.571 40.909 0.00 0.00 0.00 2.29
3524 3937 4.768145 CACTGCATTGCTTGAATTGTTTG 58.232 39.130 10.49 0.00 0.00 2.93
3526 3939 4.059511 CTGCATTGCTTGAATTGTTTGGA 58.940 39.130 10.49 0.00 0.00 3.53
3539 3962 3.467374 TGTTTGGAAGGTTTTGCATCC 57.533 42.857 0.00 0.00 34.44 3.51
3582 4055 3.924686 GTGTATTGTACAGGTGAACTCCG 59.075 47.826 0.00 0.00 39.77 4.63
3586 4063 0.109412 GTACAGGTGAACTCCGTCGG 60.109 60.000 4.39 4.39 0.00 4.79
3634 4279 3.325293 TGCATTTCTCTCTCTGTCACC 57.675 47.619 0.00 0.00 0.00 4.02
3655 4300 2.539142 CGACGTGGTACAGATAGAGTGC 60.539 54.545 0.00 0.00 41.80 4.40
3666 4311 5.046529 ACAGATAGAGTGCGAAATGATGAC 58.953 41.667 0.00 0.00 0.00 3.06
3711 4361 3.881780 AGACATAGCACGAGATACGAC 57.118 47.619 0.00 0.00 45.77 4.34
3712 4362 3.203716 AGACATAGCACGAGATACGACA 58.796 45.455 0.00 0.00 45.77 4.35
3713 4363 3.002451 AGACATAGCACGAGATACGACAC 59.998 47.826 0.00 0.00 45.77 3.67
3714 4364 2.681344 ACATAGCACGAGATACGACACA 59.319 45.455 0.00 0.00 45.77 3.72
3715 4365 2.819422 TAGCACGAGATACGACACAC 57.181 50.000 0.00 0.00 45.77 3.82
3716 4366 0.879090 AGCACGAGATACGACACACA 59.121 50.000 0.00 0.00 45.77 3.72
3830 4492 2.273179 TACTCAGCGCCCTCGTGTT 61.273 57.895 2.29 0.00 38.14 3.32
3976 4638 5.065914 TCCTTCTTCAGTTTGATCCAGTTG 58.934 41.667 0.00 0.00 0.00 3.16
4041 4711 5.146482 TCCGTGAGAGTTTTTGTAAAACG 57.854 39.130 8.80 0.00 35.42 3.60
4176 4846 3.003763 GACAAGGGGAGGCCGTCT 61.004 66.667 0.00 0.00 0.00 4.18
4326 4996 3.947841 CTCGAGCTCGCCGGAGAG 61.948 72.222 30.97 28.81 43.27 3.20
4377 5047 2.372074 GGGTGAGGATGGCGGGTTA 61.372 63.158 0.00 0.00 0.00 2.85
4378 5048 1.605453 GGTGAGGATGGCGGGTTAA 59.395 57.895 0.00 0.00 0.00 2.01
4576 5264 4.016706 CGAGGGACCACCACCACC 62.017 72.222 0.00 0.00 43.89 4.61
4577 5265 2.852075 GAGGGACCACCACCACCA 60.852 66.667 0.00 0.00 43.89 4.17
4578 5266 2.369015 AGGGACCACCACCACCAA 60.369 61.111 0.00 0.00 43.89 3.67
4587 5275 0.968393 ACCACCACCAACACCAACAC 60.968 55.000 0.00 0.00 0.00 3.32
4672 5360 2.355481 ACCAGTCGTTCGCGTTCC 60.355 61.111 5.77 0.00 42.11 3.62
5024 5720 4.322567 CTGCCATTAATCCTAAGCCTCTC 58.677 47.826 0.00 0.00 0.00 3.20
5025 5721 3.976654 TGCCATTAATCCTAAGCCTCTCT 59.023 43.478 0.00 0.00 0.00 3.10
5026 5722 5.155161 TGCCATTAATCCTAAGCCTCTCTA 58.845 41.667 0.00 0.00 0.00 2.43
5028 5724 5.337975 GCCATTAATCCTAAGCCTCTCTAGG 60.338 48.000 0.00 0.00 46.76 3.02
5029 5725 5.782845 CCATTAATCCTAAGCCTCTCTAGGT 59.217 44.000 0.00 0.00 45.64 3.08
5030 5726 6.071051 CCATTAATCCTAAGCCTCTCTAGGTC 60.071 46.154 0.00 0.00 45.64 3.85
5031 5727 4.544564 AATCCTAAGCCTCTCTAGGTCA 57.455 45.455 0.00 0.00 45.64 4.02
5032 5728 4.757997 ATCCTAAGCCTCTCTAGGTCAT 57.242 45.455 0.00 0.00 45.64 3.06
5033 5729 4.544564 TCCTAAGCCTCTCTAGGTCATT 57.455 45.455 0.00 0.00 45.64 2.57
5172 5868 2.887152 GGTATACGATACGTGAAGGGGT 59.113 50.000 0.00 0.00 41.39 4.95
5173 5869 4.072131 GGTATACGATACGTGAAGGGGTA 58.928 47.826 0.00 0.00 41.39 3.69
5217 5913 5.449553 GAATTGGGGATCTTGGAAGTGTAT 58.550 41.667 0.00 0.00 0.00 2.29
5272 5968 8.040716 AGTATTGTTTTTGGATACTGTACTGC 57.959 34.615 0.00 0.00 35.78 4.40
5282 5978 6.649155 TGGATACTGTACTGCAATGTAATGT 58.351 36.000 0.00 0.00 37.61 2.71
5338 6035 3.453717 TCCAGTTCCATGGATGAAGAGAG 59.546 47.826 17.06 0.00 44.56 3.20
5339 6036 3.433314 CCAGTTCCATGGATGAAGAGAGG 60.433 52.174 17.06 5.75 43.57 3.69
5427 6124 9.730705 TCATGTGATTTTCTTTCTCTTCTACAT 57.269 29.630 0.00 0.00 0.00 2.29
5451 6148 2.417719 ACAGTTCATTTCTCGCAGGAC 58.582 47.619 0.00 0.00 0.00 3.85
5455 6152 3.882888 AGTTCATTTCTCGCAGGACAAAA 59.117 39.130 0.00 0.00 0.00 2.44
5456 6153 4.023707 AGTTCATTTCTCGCAGGACAAAAG 60.024 41.667 0.00 0.00 0.00 2.27
5457 6154 3.738982 TCATTTCTCGCAGGACAAAAGA 58.261 40.909 0.00 0.00 0.00 2.52
5461 6158 4.552166 TTCTCGCAGGACAAAAGAAAAG 57.448 40.909 0.00 0.00 0.00 2.27
5462 6159 3.804036 TCTCGCAGGACAAAAGAAAAGA 58.196 40.909 0.00 0.00 0.00 2.52
5464 6161 4.638421 TCTCGCAGGACAAAAGAAAAGAAA 59.362 37.500 0.00 0.00 0.00 2.52
5465 6162 5.124776 TCTCGCAGGACAAAAGAAAAGAAAA 59.875 36.000 0.00 0.00 0.00 2.29
5466 6163 5.715070 TCGCAGGACAAAAGAAAAGAAAAA 58.285 33.333 0.00 0.00 0.00 1.94
5467 6164 5.575218 TCGCAGGACAAAAGAAAAGAAAAAC 59.425 36.000 0.00 0.00 0.00 2.43
5468 6165 5.220397 CGCAGGACAAAAGAAAAGAAAAACC 60.220 40.000 0.00 0.00 0.00 3.27
5473 6170 6.535150 GGACAAAAGAAAAGAAAAACCCTCTG 59.465 38.462 0.00 0.00 0.00 3.35
5546 9774 7.591426 AGTTCAAAATCAGCGTCACTTATTTTC 59.409 33.333 0.00 0.00 39.21 2.29
5558 9786 5.294552 GTCACTTATTTTCGAATGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
5617 9852 3.341823 ACAAGACAAGATGATGGCAGAC 58.658 45.455 0.00 0.00 0.00 3.51
5631 9866 3.305720 TGGCAGACGGTAATAGAAGGAT 58.694 45.455 0.00 0.00 0.00 3.24
5634 9869 4.021016 GGCAGACGGTAATAGAAGGATCAT 60.021 45.833 0.00 0.00 0.00 2.45
5635 9870 5.511545 GGCAGACGGTAATAGAAGGATCATT 60.512 44.000 0.00 0.00 0.00 2.57
5636 9871 5.992217 GCAGACGGTAATAGAAGGATCATTT 59.008 40.000 0.00 0.00 0.00 2.32
5637 9872 6.146347 GCAGACGGTAATAGAAGGATCATTTC 59.854 42.308 0.00 0.00 0.00 2.17
5638 9873 7.210174 CAGACGGTAATAGAAGGATCATTTCA 58.790 38.462 10.64 0.00 0.00 2.69
5639 9874 7.710907 CAGACGGTAATAGAAGGATCATTTCAA 59.289 37.037 10.64 0.00 0.00 2.69
5640 9875 8.265055 AGACGGTAATAGAAGGATCATTTCAAA 58.735 33.333 10.64 1.20 0.00 2.69
5641 9876 8.801882 ACGGTAATAGAAGGATCATTTCAAAA 57.198 30.769 10.64 0.00 0.00 2.44
5642 9877 9.238368 ACGGTAATAGAAGGATCATTTCAAAAA 57.762 29.630 10.64 0.00 0.00 1.94
5671 9906 7.565680 AGACGGTAATAGAAGGAACAATCATT 58.434 34.615 0.00 0.00 31.01 2.57
5722 9966 1.550327 TTGCTGGACAACACACCAAA 58.450 45.000 0.00 0.00 35.67 3.28
5869 10113 6.424032 AGTTTGAAGAAGACTTACAAAGGGT 58.576 36.000 12.02 0.00 35.77 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.235372 AGAGGAAGGAGGAACAAGAAGAA 58.765 43.478 0.00 0.00 0.00 2.52
1 2 3.835395 GAGAGGAAGGAGGAACAAGAAGA 59.165 47.826 0.00 0.00 0.00 2.87
2 3 3.837731 AGAGAGGAAGGAGGAACAAGAAG 59.162 47.826 0.00 0.00 0.00 2.85
3 4 3.835395 GAGAGAGGAAGGAGGAACAAGAA 59.165 47.826 0.00 0.00 0.00 2.52
4 5 3.076785 AGAGAGAGGAAGGAGGAACAAGA 59.923 47.826 0.00 0.00 0.00 3.02
79 80 6.816140 GCTTGCATATAAGTAATCTCTCTCCC 59.184 42.308 0.00 0.00 0.00 4.30
106 113 4.873129 CGTGCTAGCCGTGCCGAT 62.873 66.667 13.29 0.00 0.00 4.18
363 381 1.212688 AGGTAAGCTGCATGGCATGTA 59.787 47.619 26.94 22.28 38.13 2.29
382 410 1.199615 GGGAGGTGGAGGAAAGAGAG 58.800 60.000 0.00 0.00 0.00 3.20
405 433 2.909662 AGAGGAAAGACAAAGAGAGGGG 59.090 50.000 0.00 0.00 0.00 4.79
407 435 6.790232 AGATAGAGGAAAGACAAAGAGAGG 57.210 41.667 0.00 0.00 0.00 3.69
414 442 9.988815 GCAGAATTATAGATAGAGGAAAGACAA 57.011 33.333 0.00 0.00 0.00 3.18
415 443 9.147732 TGCAGAATTATAGATAGAGGAAAGACA 57.852 33.333 0.00 0.00 0.00 3.41
431 459 2.158769 TCCACGAGCCATGCAGAATTAT 60.159 45.455 0.00 0.00 0.00 1.28
432 460 1.209261 TCCACGAGCCATGCAGAATTA 59.791 47.619 0.00 0.00 0.00 1.40
434 462 0.182061 ATCCACGAGCCATGCAGAAT 59.818 50.000 0.00 0.00 0.00 2.40
435 463 0.462581 GATCCACGAGCCATGCAGAA 60.463 55.000 0.00 0.00 0.00 3.02
436 464 1.144716 GATCCACGAGCCATGCAGA 59.855 57.895 0.00 0.00 0.00 4.26
437 465 1.890979 GGATCCACGAGCCATGCAG 60.891 63.158 6.95 0.00 38.12 4.41
463 491 3.513119 TCGGATGATTTGCCATGGAAAAA 59.487 39.130 22.09 17.30 0.00 1.94
473 802 9.476761 GTGATTTAAAATTTTCGGATGATTTGC 57.523 29.630 6.72 0.00 0.00 3.68
529 859 8.604890 GCCAAGAACTTAAGAACACATATACTC 58.395 37.037 10.09 0.00 0.00 2.59
530 860 8.100791 TGCCAAGAACTTAAGAACACATATACT 58.899 33.333 10.09 0.00 0.00 2.12
531 861 8.175716 GTGCCAAGAACTTAAGAACACATATAC 58.824 37.037 10.09 0.00 0.00 1.47
532 862 8.100791 AGTGCCAAGAACTTAAGAACACATATA 58.899 33.333 10.09 0.00 0.00 0.86
533 863 6.942576 AGTGCCAAGAACTTAAGAACACATAT 59.057 34.615 10.09 0.00 0.00 1.78
974 1304 1.735376 CGCCGGCACCTATGTAGACT 61.735 60.000 28.98 0.00 0.00 3.24
994 1324 0.380733 TAGTACGCTGCCATCGTGAG 59.619 55.000 3.50 0.00 40.69 3.51
1834 2167 5.187621 TGGAGATATTTTCGGGGAAAACT 57.812 39.130 5.74 0.02 42.98 2.66
1835 2168 6.465439 AATGGAGATATTTTCGGGGAAAAC 57.535 37.500 5.74 0.00 42.98 2.43
1876 2209 7.613411 CCTTGTTTTCCAGAGGAAGAAATATCT 59.387 37.037 0.00 0.00 43.06 1.98
1884 2217 3.508845 TCCCTTGTTTTCCAGAGGAAG 57.491 47.619 0.00 0.00 43.06 3.46
1940 2273 3.256631 AGAGGGCAATGTTGAATGTTCAC 59.743 43.478 0.00 0.00 36.83 3.18
2170 2503 6.562640 GCAAGCTGACAAAACATGTGTTATTG 60.563 38.462 0.00 6.66 44.12 1.90
2174 2507 3.189285 GCAAGCTGACAAAACATGTGTT 58.811 40.909 0.00 0.00 44.12 3.32
2176 2509 2.536803 GTGCAAGCTGACAAAACATGTG 59.463 45.455 0.00 0.00 44.12 3.21
2177 2510 4.994415 TGGTGCAAGCTGACAAAACATGT 61.994 43.478 0.00 0.00 39.53 3.21
2178 2511 2.129607 GGTGCAAGCTGACAAAACATG 58.870 47.619 0.00 0.00 0.00 3.21
2228 2566 7.921214 AGACAATACTGGTCAGTGTTTATATCG 59.079 37.037 13.32 3.59 40.13 2.92
2306 2648 8.515414 ACCAGAGCTGATTTGTAAATTTCTAAC 58.485 33.333 0.00 0.00 0.00 2.34
2372 2714 9.535878 GCTAGACTTGTCACTTTTATAATAGCT 57.464 33.333 0.00 0.00 0.00 3.32
2373 2715 9.535878 AGCTAGACTTGTCACTTTTATAATAGC 57.464 33.333 0.00 4.01 0.00 2.97
2662 3020 9.794719 TCTGTACTGATAGCATATACTTGTAGT 57.205 33.333 0.00 0.00 0.00 2.73
2665 3023 8.580720 CCTTCTGTACTGATAGCATATACTTGT 58.419 37.037 3.03 0.00 0.00 3.16
2666 3024 8.580720 ACCTTCTGTACTGATAGCATATACTTG 58.419 37.037 3.03 0.00 0.00 3.16
2667 3025 8.713708 ACCTTCTGTACTGATAGCATATACTT 57.286 34.615 3.03 0.00 0.00 2.24
2822 3185 9.294030 CTGCATTTCTTGTTTATATGGAGAAAC 57.706 33.333 0.00 0.00 38.65 2.78
2886 3249 8.099364 ACACGATTAATTGTCTTGTCAGATTT 57.901 30.769 5.29 0.00 0.00 2.17
3440 3811 1.485480 TGGTGGTGAACAACTTACGGA 59.515 47.619 0.00 0.00 37.78 4.69
3449 3820 2.949177 AGTTAGCATGGTGGTGAACA 57.051 45.000 7.89 0.00 0.00 3.18
3450 3821 4.082949 GGTAAAGTTAGCATGGTGGTGAAC 60.083 45.833 7.89 3.86 0.00 3.18
3456 3827 1.400494 GGCGGTAAAGTTAGCATGGTG 59.600 52.381 7.89 0.00 0.00 4.17
3457 3828 1.003812 TGGCGGTAAAGTTAGCATGGT 59.996 47.619 1.62 1.62 0.00 3.55
3459 3830 4.370364 AAATGGCGGTAAAGTTAGCATG 57.630 40.909 1.61 0.00 0.00 4.06
3460 3831 4.705023 AGAAAATGGCGGTAAAGTTAGCAT 59.295 37.500 1.61 0.00 0.00 3.79
3461 3832 4.076394 AGAAAATGGCGGTAAAGTTAGCA 58.924 39.130 1.61 0.00 0.00 3.49
3462 3833 4.696899 AGAAAATGGCGGTAAAGTTAGC 57.303 40.909 0.00 0.00 0.00 3.09
3504 3914 4.059511 TCCAAACAATTCAAGCAATGCAG 58.940 39.130 8.35 0.00 0.00 4.41
3509 3922 4.751767 ACCTTCCAAACAATTCAAGCAA 57.248 36.364 0.00 0.00 0.00 3.91
3539 3962 3.319291 CCTAGCTAGGTTGCATGTGCAG 61.319 54.545 28.90 1.25 42.63 4.41
3634 4279 2.539142 GCACTCTATCTGTACCACGTCG 60.539 54.545 0.00 0.00 0.00 5.12
3655 4300 1.556564 AGTACCGCGTCATCATTTCG 58.443 50.000 4.92 0.00 0.00 3.46
3666 4311 0.179137 TCTCTCATGCAAGTACCGCG 60.179 55.000 0.00 0.00 0.00 6.46
3711 4361 1.132834 AGCATTGTGTGTGTGTGTGTG 59.867 47.619 0.00 0.00 0.00 3.82
3712 4362 1.401552 GAGCATTGTGTGTGTGTGTGT 59.598 47.619 0.00 0.00 0.00 3.72
3713 4363 1.401199 TGAGCATTGTGTGTGTGTGTG 59.599 47.619 0.00 0.00 0.00 3.82
3714 4364 1.748950 TGAGCATTGTGTGTGTGTGT 58.251 45.000 0.00 0.00 0.00 3.72
3715 4365 2.291190 TCATGAGCATTGTGTGTGTGTG 59.709 45.455 0.00 0.00 0.00 3.82
3716 4366 2.574450 TCATGAGCATTGTGTGTGTGT 58.426 42.857 0.00 0.00 0.00 3.72
3830 4492 1.838112 GATCAACCAATGGGAGTGCA 58.162 50.000 3.55 0.00 38.05 4.57
3943 4605 5.511386 AACTGAAGAAGGATGGTTGAGAT 57.489 39.130 0.00 0.00 0.00 2.75
4041 4711 6.592607 TGAACCAGTTCGACACCTAATAATTC 59.407 38.462 6.08 0.00 42.28 2.17
4116 4786 0.103937 GATGCTCCTTGGTCTCCTCG 59.896 60.000 0.00 0.00 0.00 4.63
4377 5047 2.281484 TTCTTGAAGCCGCGCCTT 60.281 55.556 0.14 0.14 0.00 4.35
4378 5048 2.743928 CTTCTTGAAGCCGCGCCT 60.744 61.111 0.00 0.00 0.00 5.52
4576 5264 0.528901 TCCTCGTCGTGTTGGTGTTG 60.529 55.000 0.00 0.00 0.00 3.33
4577 5265 0.529119 GTCCTCGTCGTGTTGGTGTT 60.529 55.000 0.00 0.00 0.00 3.32
4578 5266 1.066918 GTCCTCGTCGTGTTGGTGT 59.933 57.895 0.00 0.00 0.00 4.16
4734 5422 1.215382 CATGAGGAACGCCGTCTGA 59.785 57.895 0.00 0.00 39.96 3.27
4797 5485 1.447140 GTTCATGTCGTAGCCGGCA 60.447 57.895 31.54 12.31 42.34 5.69
5024 5720 6.601332 ACATAATTACACCCCAATGACCTAG 58.399 40.000 0.00 0.00 0.00 3.02
5025 5721 6.584471 ACATAATTACACCCCAATGACCTA 57.416 37.500 0.00 0.00 0.00 3.08
5026 5722 5.466127 ACATAATTACACCCCAATGACCT 57.534 39.130 0.00 0.00 0.00 3.85
5028 5724 8.514330 TCTTTACATAATTACACCCCAATGAC 57.486 34.615 0.00 0.00 0.00 3.06
5029 5725 9.130661 CATCTTTACATAATTACACCCCAATGA 57.869 33.333 0.00 0.00 0.00 2.57
5030 5726 8.359642 CCATCTTTACATAATTACACCCCAATG 58.640 37.037 0.00 0.00 0.00 2.82
5031 5727 7.508977 CCCATCTTTACATAATTACACCCCAAT 59.491 37.037 0.00 0.00 0.00 3.16
5032 5728 6.836527 CCCATCTTTACATAATTACACCCCAA 59.163 38.462 0.00 0.00 0.00 4.12
5033 5729 6.369629 CCCATCTTTACATAATTACACCCCA 58.630 40.000 0.00 0.00 0.00 4.96
5080 5776 8.915813 TGGGTTTTAACTACCTAACCTATACT 57.084 34.615 0.00 0.00 39.90 2.12
5083 5779 8.447200 TGTTTGGGTTTTAACTACCTAACCTAT 58.553 33.333 0.00 0.00 39.90 2.57
5084 5780 7.810260 TGTTTGGGTTTTAACTACCTAACCTA 58.190 34.615 0.00 0.00 39.90 3.08
5085 5781 6.671605 TGTTTGGGTTTTAACTACCTAACCT 58.328 36.000 0.00 0.00 39.90 3.50
5086 5782 6.957920 TGTTTGGGTTTTAACTACCTAACC 57.042 37.500 4.73 0.00 36.09 2.85
5087 5783 9.467258 GAAATGTTTGGGTTTTAACTACCTAAC 57.533 33.333 4.73 9.34 36.09 2.34
5088 5784 8.640651 GGAAATGTTTGGGTTTTAACTACCTAA 58.359 33.333 6.04 3.93 34.75 2.69
5089 5785 7.040548 CGGAAATGTTTGGGTTTTAACTACCTA 60.041 37.037 6.04 0.00 35.92 3.08
5217 5913 5.498393 TCCAATAAACCAACTATACCGCAA 58.502 37.500 0.00 0.00 0.00 4.85
5338 6035 2.201921 ATGCCATCTCATGCATCTCC 57.798 50.000 0.00 0.00 44.58 3.71
5339 6036 3.556365 CGATATGCCATCTCATGCATCTC 59.444 47.826 0.00 0.50 44.58 2.75
5361 6058 5.898174 AGTTTTGGTTGCTAAAGGTAACAC 58.102 37.500 0.00 0.00 41.31 3.32
5427 6124 5.049680 GTCCTGCGAGAAATGAACTGTTTTA 60.050 40.000 0.00 0.00 0.00 1.52
5444 6141 5.220397 GGTTTTTCTTTTCTTTTGTCCTGCG 60.220 40.000 0.00 0.00 0.00 5.18
5451 6148 6.108687 AGCAGAGGGTTTTTCTTTTCTTTTG 58.891 36.000 0.00 0.00 0.00 2.44
5455 6152 3.891977 GGAGCAGAGGGTTTTTCTTTTCT 59.108 43.478 0.00 0.00 0.00 2.52
5456 6153 3.636764 TGGAGCAGAGGGTTTTTCTTTTC 59.363 43.478 0.00 0.00 0.00 2.29
5457 6154 3.642141 TGGAGCAGAGGGTTTTTCTTTT 58.358 40.909 0.00 0.00 0.00 2.27
5461 6158 2.693074 TGTTTGGAGCAGAGGGTTTTTC 59.307 45.455 0.00 0.00 0.00 2.29
5462 6159 2.695147 CTGTTTGGAGCAGAGGGTTTTT 59.305 45.455 0.00 0.00 36.12 1.94
5464 6161 1.479389 CCTGTTTGGAGCAGAGGGTTT 60.479 52.381 0.00 0.00 38.35 3.27
5465 6162 0.111253 CCTGTTTGGAGCAGAGGGTT 59.889 55.000 0.00 0.00 38.35 4.11
5466 6163 1.062488 ACCTGTTTGGAGCAGAGGGT 61.062 55.000 0.00 0.00 39.71 4.34
5467 6164 0.984230 TACCTGTTTGGAGCAGAGGG 59.016 55.000 0.00 0.00 39.71 4.30
5468 6165 1.347707 TGTACCTGTTTGGAGCAGAGG 59.652 52.381 0.00 0.00 39.71 3.69
5495 9723 4.569719 ACAGGGTCACTTATTTCCGAAT 57.430 40.909 0.00 0.00 0.00 3.34
5546 9774 5.531122 TTATCTTGTACTCCCTCCATTCG 57.469 43.478 0.00 0.00 0.00 3.34
5558 9786 7.190920 GGTAATCACCTGCATTATCTTGTAC 57.809 40.000 0.00 0.00 42.11 2.90
5642 9877 8.631480 ATTGTTCCTTCTATTACCGTCTTTTT 57.369 30.769 0.00 0.00 0.00 1.94
5643 9878 7.881232 TGATTGTTCCTTCTATTACCGTCTTTT 59.119 33.333 0.00 0.00 0.00 2.27
5644 9879 7.391620 TGATTGTTCCTTCTATTACCGTCTTT 58.608 34.615 0.00 0.00 0.00 2.52
5645 9880 6.942976 TGATTGTTCCTTCTATTACCGTCTT 58.057 36.000 0.00 0.00 0.00 3.01
5646 9881 6.540438 TGATTGTTCCTTCTATTACCGTCT 57.460 37.500 0.00 0.00 0.00 4.18
5647 9882 7.787725 AATGATTGTTCCTTCTATTACCGTC 57.212 36.000 0.00 0.00 0.00 4.79
5648 9883 8.483758 ACTAATGATTGTTCCTTCTATTACCGT 58.516 33.333 0.00 0.00 0.00 4.83
5649 9884 8.888579 ACTAATGATTGTTCCTTCTATTACCG 57.111 34.615 0.00 0.00 0.00 4.02
5653 9888 9.401058 CCAAGACTAATGATTGTTCCTTCTATT 57.599 33.333 0.00 0.00 0.00 1.73
5654 9889 8.552296 ACCAAGACTAATGATTGTTCCTTCTAT 58.448 33.333 0.00 0.00 0.00 1.98
5655 9890 7.918076 ACCAAGACTAATGATTGTTCCTTCTA 58.082 34.615 0.00 0.00 0.00 2.10
5656 9891 6.784031 ACCAAGACTAATGATTGTTCCTTCT 58.216 36.000 0.00 0.00 0.00 2.85
5657 9892 7.174946 TCAACCAAGACTAATGATTGTTCCTTC 59.825 37.037 0.00 0.00 0.00 3.46
5658 9893 7.004086 TCAACCAAGACTAATGATTGTTCCTT 58.996 34.615 0.00 0.00 0.00 3.36
5659 9894 6.431234 GTCAACCAAGACTAATGATTGTTCCT 59.569 38.462 0.00 0.00 35.65 3.36
5660 9895 6.206634 TGTCAACCAAGACTAATGATTGTTCC 59.793 38.462 0.00 0.00 39.27 3.62
5661 9896 7.173218 TCTGTCAACCAAGACTAATGATTGTTC 59.827 37.037 0.00 0.00 39.27 3.18
5662 9897 6.998074 TCTGTCAACCAAGACTAATGATTGTT 59.002 34.615 0.00 0.00 39.27 2.83
5663 9898 6.533730 TCTGTCAACCAAGACTAATGATTGT 58.466 36.000 0.00 0.00 39.27 2.71
5664 9899 6.875726 TCTCTGTCAACCAAGACTAATGATTG 59.124 38.462 0.00 0.00 39.27 2.67
5665 9900 7.009179 TCTCTGTCAACCAAGACTAATGATT 57.991 36.000 0.00 0.00 39.27 2.57
5671 9906 3.827302 GACCTCTCTGTCAACCAAGACTA 59.173 47.826 0.00 0.00 39.27 2.59


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

AutoCloner maintained by Alex Coulton.