Multiple sequence alignment - TraesCS7B01G116700

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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 TraesCS7B01G116700 chr7B 100.000 6198 0 0 1 6198 135583646 135577449 0.000000e+00 11446.0
1 TraesCS7B01G116700 chr7B 85.609 271 32 5 1201 1469 532275765 532276030 1.700000e-70 278.0
2 TraesCS7B01G116700 chr7A 93.010 4621 194 53 1 4540 172470331 172465759 0.000000e+00 6625.0
3 TraesCS7B01G116700 chr7A 92.000 925 46 12 4531 5453 172465716 172464818 0.000000e+00 1273.0
4 TraesCS7B01G116700 chr7A 87.160 514 34 9 5468 5957 172460748 172460243 7.020000e-154 555.0
5 TraesCS7B01G116700 chr7A 93.878 245 14 1 5955 6198 172461833 172461589 9.820000e-98 368.0
6 TraesCS7B01G116700 chr7A 90.984 244 20 2 5955 6198 172422545 172422304 1.670000e-85 327.0
7 TraesCS7B01G116700 chr7A 84.871 271 34 5 1201 1469 571701720 571701985 3.680000e-67 267.0
8 TraesCS7B01G116700 chr7A 90.323 93 9 0 5657 5749 172464452 172464360 8.440000e-24 122.0
9 TraesCS7B01G116700 chr7A 82.759 116 6 3 5844 5957 172462812 172462709 2.380000e-14 91.6
10 TraesCS7B01G116700 chr7D 92.747 2730 103 39 1 2682 169916492 169913810 0.000000e+00 3856.0
11 TraesCS7B01G116700 chr7D 94.832 1277 44 8 3283 4540 169913033 169911760 0.000000e+00 1973.0
12 TraesCS7B01G116700 chr7D 92.238 992 51 10 4525 5511 169911720 169910750 0.000000e+00 1382.0
13 TraesCS7B01G116700 chr7D 94.118 680 24 7 2613 3280 169913773 169913098 0.000000e+00 1020.0
14 TraesCS7B01G116700 chr7D 85.603 514 42 8 5468 5957 169833967 169833462 1.540000e-140 510.0
15 TraesCS7B01G116700 chr7D 95.082 244 12 0 5955 6198 169835018 169834775 9.750000e-103 385.0
16 TraesCS7B01G116700 chr7D 90.164 244 21 3 5955 6198 169832546 169832306 1.300000e-81 315.0
17 TraesCS7B01G116700 chr7D 85.978 271 31 5 1201 1469 504174825 504175090 3.660000e-72 283.0
18 TraesCS7B01G116700 chr7D 87.342 237 21 4 5516 5751 169908220 169907992 4.760000e-66 263.0
19 TraesCS7B01G116700 chr7D 85.185 108 4 5 5850 5957 169835955 169835860 3.950000e-17 100.0
20 TraesCS7B01G116700 chr7D 91.667 72 5 1 5736 5807 169836257 169836187 1.420000e-16 99.0
21 TraesCS7B01G116700 chr6D 83.264 478 64 12 1181 1644 381999852 381999377 5.740000e-115 425.0
22 TraesCS7B01G116700 chr6B 82.708 480 63 14 1181 1644 570982500 570982025 5.780000e-110 409.0
23 TraesCS7B01G116700 chr6A 82.365 482 64 16 1181 1644 523949646 523949168 3.480000e-107 399.0
24 TraesCS7B01G116700 chr1D 86.769 325 33 7 3529 3843 7919415 7919739 2.750000e-93 353.0
25 TraesCS7B01G116700 chr1B 83.041 342 36 9 3529 3848 10111920 10112261 2.190000e-74 291.0
26 TraesCS7B01G116700 chr2B 84.585 253 34 3 1196 1447 91257421 91257669 4.800000e-61 246.0


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 TraesCS7B01G116700 chr7B 135577449 135583646 6197 True 11446.000000 11446 100.0000 1 6198 1 chr7B.!!$R1 6197
1 TraesCS7B01G116700 chr7A 172460243 172470331 10088 True 1505.766667 6625 89.8550 1 6198 6 chr7A.!!$R2 6197
2 TraesCS7B01G116700 chr7D 169907992 169916492 8500 True 1698.800000 3856 92.2554 1 5751 5 chr7D.!!$R2 5750
3 TraesCS7B01G116700 chr7D 169832306 169836257 3951 True 281.800000 510 89.5402 5468 6198 5 chr7D.!!$R1 730

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
312 323 0.389025 AAAAGCAAGACCCGCCTTTG 59.611 50.000 0.00 0.0 0.00 2.77 F
1328 1412 0.179026 AGGAGATCTACGGCGTGCTA 60.179 55.000 24.86 8.1 0.00 3.49 F
2299 2396 0.322816 ATGTGCCATTTGACTCCGCT 60.323 50.000 0.00 0.0 0.00 5.52 F
2573 2671 1.468520 TGTTGAAATAAGAGGCGCTGC 59.531 47.619 7.64 0.0 0.00 5.25 F
2587 2685 1.521423 GCGCTGCGTGGTATAGTTAAG 59.479 52.381 24.04 0.0 0.00 1.85 F
3663 3947 2.028748 GCCTGTTCTGGTGATTGCAATT 60.029 45.455 14.33 0.0 0.00 2.32 F
4797 5153 0.107654 GGTGCCACAGACCATACCTC 60.108 60.000 0.00 0.0 33.25 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2283 2380 0.613260 AGTAGCGGAGTCAAATGGCA 59.387 50.000 0.00 0.0 0.00 4.92 R
3311 3593 1.079490 AGGTCACCAGAGGAAGGATGA 59.921 52.381 0.00 0.0 0.00 2.92 R
3663 3947 1.153449 CCCAATAACGGCTGCGAGA 60.153 57.895 0.00 0.0 0.00 4.04 R
3988 4291 2.740447 GGCACCTAAAGTTGACCGTAAG 59.260 50.000 0.00 0.0 0.00 2.34 R
4505 4808 4.487714 TTAGCAGAGTGTATTGGGGAAG 57.512 45.455 0.00 0.0 0.00 3.46 R
5116 5472 0.035458 CAGAACCTCGGCTGTTCCTT 59.965 55.000 8.38 0.0 42.41 3.36 R
6096 11531 0.668535 AGAAAGCCTTTGCAACCGTC 59.331 50.000 0.00 0.0 41.13 4.79 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
109 111 4.151417 CGCCATTTTCCAGCGTTG 57.849 55.556 0.00 0.00 44.65 4.10
177 187 6.877855 GCCTATCATCTAATTCATCTCAGCAA 59.122 38.462 0.00 0.00 0.00 3.91
230 240 6.729187 AGAGAATGACGTTTTCCTTTTGAAG 58.271 36.000 8.16 0.00 33.63 3.02
287 298 2.450476 GAAGTGGCAGGTGAATTCCAT 58.550 47.619 2.27 0.00 0.00 3.41
304 315 1.200020 CCATCGTGGAAAAGCAAGACC 59.800 52.381 0.00 0.00 40.96 3.85
305 316 1.200020 CATCGTGGAAAAGCAAGACCC 59.800 52.381 0.00 0.00 0.00 4.46
307 318 1.285950 GTGGAAAAGCAAGACCCGC 59.714 57.895 0.00 0.00 0.00 6.13
308 319 1.901464 TGGAAAAGCAAGACCCGCC 60.901 57.895 0.00 0.00 0.00 6.13
310 321 1.179174 GGAAAAGCAAGACCCGCCTT 61.179 55.000 0.00 0.00 0.00 4.35
312 323 0.389025 AAAAGCAAGACCCGCCTTTG 59.611 50.000 0.00 0.00 0.00 2.77
313 324 1.463553 AAAGCAAGACCCGCCTTTGG 61.464 55.000 0.00 0.00 0.00 3.28
490 533 2.137810 AAGTAGAAGCCTCGCTCTCT 57.862 50.000 0.00 0.00 38.25 3.10
524 567 2.092375 GGGATCAAAGGGGTTGGTAGAG 60.092 54.545 0.00 0.00 37.85 2.43
555 598 2.347322 GCAGGCAGTCGTCTCCTCT 61.347 63.158 0.00 0.00 0.00 3.69
556 599 1.806568 CAGGCAGTCGTCTCCTCTC 59.193 63.158 0.00 0.00 0.00 3.20
582 627 1.131883 CCTGCTCGCTTCTTCCAAATG 59.868 52.381 0.00 0.00 0.00 2.32
586 631 2.426522 CTCGCTTCTTCCAAATGGTCA 58.573 47.619 0.00 0.00 36.34 4.02
711 777 1.069668 GGGACACGAGTTGGTAGTTGT 59.930 52.381 0.00 0.00 0.00 3.32
799 865 2.927014 GCTACAAAGTCCACACCGAGAG 60.927 54.545 0.00 0.00 0.00 3.20
823 889 2.224354 CCTGCCAAAACAGAATTTGCCT 60.224 45.455 0.00 0.00 40.25 4.75
1084 1162 1.423845 CGCCGGTTTCTTGGATTCG 59.576 57.895 1.90 0.00 0.00 3.34
1085 1163 1.296056 CGCCGGTTTCTTGGATTCGT 61.296 55.000 1.90 0.00 0.00 3.85
1109 1188 3.067461 TGGAAGATTCGGTGTTTGTTTGG 59.933 43.478 0.00 0.00 0.00 3.28
1110 1189 3.067601 GGAAGATTCGGTGTTTGTTTGGT 59.932 43.478 0.00 0.00 0.00 3.67
1111 1190 3.982576 AGATTCGGTGTTTGTTTGGTC 57.017 42.857 0.00 0.00 0.00 4.02
1113 1192 3.315191 AGATTCGGTGTTTGTTTGGTCTG 59.685 43.478 0.00 0.00 0.00 3.51
1118 1197 3.517602 GGTGTTTGTTTGGTCTGGTTTC 58.482 45.455 0.00 0.00 0.00 2.78
1152 1235 3.740513 GGTGACGGCGGTTTCTTT 58.259 55.556 13.24 0.00 0.00 2.52
1298 1382 1.595382 CGGGGACATCGAGCATTCC 60.595 63.158 0.00 0.00 0.00 3.01
1328 1412 0.179026 AGGAGATCTACGGCGTGCTA 60.179 55.000 24.86 8.10 0.00 3.49
1586 1670 4.779966 ATGCTGCTGCTGCTCGCT 62.780 61.111 27.67 10.73 40.48 4.93
1706 1793 0.668401 GCTCTTGGTGTTGCATTGGC 60.668 55.000 0.00 0.00 41.68 4.52
1869 1956 3.637911 ATACCGATTTGTGGGTGCTAA 57.362 42.857 0.00 0.00 37.09 3.09
1870 1957 1.530323 ACCGATTTGTGGGTGCTAAC 58.470 50.000 0.00 0.00 34.58 2.34
1975 2067 5.964958 ATATTGTGTTGAGGGTTTGTGAG 57.035 39.130 0.00 0.00 0.00 3.51
1976 2068 2.799126 TGTGTTGAGGGTTTGTGAGT 57.201 45.000 0.00 0.00 0.00 3.41
2087 2182 1.512156 GGGTCGGCTTTCTTTTCGCA 61.512 55.000 0.00 0.00 0.00 5.10
2144 2239 5.894298 TCATAGGGCTCTACAACATCATT 57.106 39.130 0.00 0.00 0.00 2.57
2156 2251 4.665451 ACAACATCATTCACTGGAATCCA 58.335 39.130 0.48 0.48 41.78 3.41
2165 2260 3.937814 TCACTGGAATCCACATGTGTAC 58.062 45.455 23.79 7.62 0.00 2.90
2213 2308 6.423905 CGTACAAATTTCTCCAGAAGACTCAA 59.576 38.462 0.00 0.00 35.21 3.02
2215 2310 7.032377 ACAAATTTCTCCAGAAGACTCAAAC 57.968 36.000 0.00 0.00 35.21 2.93
2283 2380 4.755266 AAGGACCGAATAGCTGTTATGT 57.245 40.909 0.00 0.00 0.00 2.29
2299 2396 0.322816 ATGTGCCATTTGACTCCGCT 60.323 50.000 0.00 0.00 0.00 5.52
2415 2512 4.523173 TCTCAGTCTTCAATCAAGGTACGT 59.477 41.667 0.00 0.00 32.22 3.57
2560 2658 7.271511 AGATTACAAAAGCCACATTGTTGAAA 58.728 30.769 0.00 0.00 40.14 2.69
2573 2671 1.468520 TGTTGAAATAAGAGGCGCTGC 59.531 47.619 7.64 0.00 0.00 5.25
2587 2685 1.521423 GCGCTGCGTGGTATAGTTAAG 59.479 52.381 24.04 0.00 0.00 1.85
2716 2918 6.272318 TGGATAACACTGTTCAAGCAAAAAG 58.728 36.000 0.00 0.00 0.00 2.27
2786 2989 5.049198 TGAGTATAGCGGTAGTTGATTACGG 60.049 44.000 0.00 0.00 0.00 4.02
2863 3066 6.402118 GCTGATTTAGTTGCTGTGTTAATCGA 60.402 38.462 0.00 0.00 0.00 3.59
3057 3270 2.825532 GGGCAATGAAACTTAGAGCCAA 59.174 45.455 0.00 0.00 42.26 4.52
3058 3271 3.367395 GGGCAATGAAACTTAGAGCCAAC 60.367 47.826 0.00 0.00 42.26 3.77
3220 3439 8.753133 CAGATGCTCTGGTAATACCTATATCAA 58.247 37.037 11.16 0.00 40.71 2.57
3311 3593 7.620880 TCTTAGGAATTAATATGCGCTACCAT 58.379 34.615 9.73 0.00 0.00 3.55
3329 3611 2.158842 CCATCATCCTTCCTCTGGTGAC 60.159 54.545 0.00 0.00 0.00 3.67
3432 3714 6.136857 TCTTTAGTGTACCCAGCTCTGATAT 58.863 40.000 0.00 0.00 0.00 1.63
3467 3749 4.479619 GACAAGCTGCTTACATTTCAAGG 58.520 43.478 15.51 1.06 0.00 3.61
3663 3947 2.028748 GCCTGTTCTGGTGATTGCAATT 60.029 45.455 14.33 0.00 0.00 2.32
3947 4231 9.994432 CAGGAGAATACAACATATTTTCTTGTC 57.006 33.333 0.00 0.00 30.76 3.18
4012 4315 2.369532 ACGGTCAACTTTAGGTGCCTAA 59.630 45.455 6.60 6.60 36.81 2.69
4073 4376 4.040461 ACTGTAATGCTGGTCACTACTTGT 59.960 41.667 0.00 0.00 29.37 3.16
4505 4808 6.543831 ACACACCAATCTCTATTCTTTATGCC 59.456 38.462 0.00 0.00 0.00 4.40
4529 4832 4.780815 TCCCCAATACACTCTGCTAAATG 58.219 43.478 0.00 0.00 0.00 2.32
4597 4953 2.317040 CCTATACCACACATCCGACCT 58.683 52.381 0.00 0.00 0.00 3.85
4770 5126 2.248835 CCGACGACCAAAACGGCTT 61.249 57.895 0.00 0.00 38.98 4.35
4771 5127 0.945265 CCGACGACCAAAACGGCTTA 60.945 55.000 0.00 0.00 38.98 3.09
4786 5142 1.369692 CTTACTGGACGGTGCCACA 59.630 57.895 0.00 0.00 33.52 4.17
4793 5149 1.594833 GACGGTGCCACAGACCATA 59.405 57.895 0.92 0.00 32.45 2.74
4797 5153 0.107654 GGTGCCACAGACCATACCTC 60.108 60.000 0.00 0.00 33.25 3.85
4818 5174 1.552337 TGAGAGGCTGTCTTCCATCAC 59.448 52.381 13.27 0.00 34.71 3.06
4831 5187 1.760613 TCCATCACTAAAGGCCTACCG 59.239 52.381 5.16 0.00 42.76 4.02
4861 5217 3.703556 AGGACGATGACAGTGAGATCAAT 59.296 43.478 0.00 0.00 0.00 2.57
4864 5220 3.448660 ACGATGACAGTGAGATCAATGGA 59.551 43.478 14.08 1.70 45.21 3.41
4970 5326 2.867333 GAAGGACGCGCAGATCGACA 62.867 60.000 5.73 0.00 41.67 4.35
5089 5445 1.424493 GCCTGGTGAAGAAGATCGCG 61.424 60.000 0.00 0.00 0.00 5.87
5097 5453 4.026475 GGTGAAGAAGATCGCGATAAACTG 60.026 45.833 23.76 0.00 0.00 3.16
5116 5472 2.685388 CTGCATCTACGAGTTCCTGAGA 59.315 50.000 0.00 0.00 0.00 3.27
5136 5492 2.035442 GGAACAGCCGAGGTTCTGC 61.035 63.158 11.65 0.00 43.20 4.26
5213 5569 4.272991 AGGTCTGATACGATACGAAGTCAC 59.727 45.833 0.00 0.00 43.93 3.67
5253 5609 1.732941 ATGTCGTGTGTGTGTGTTGT 58.267 45.000 0.00 0.00 0.00 3.32
5254 5610 0.793250 TGTCGTGTGTGTGTGTTGTG 59.207 50.000 0.00 0.00 0.00 3.33
5255 5611 0.793861 GTCGTGTGTGTGTGTTGTGT 59.206 50.000 0.00 0.00 0.00 3.72
5256 5612 1.994074 GTCGTGTGTGTGTGTTGTGTA 59.006 47.619 0.00 0.00 0.00 2.90
5257 5613 2.605818 GTCGTGTGTGTGTGTTGTGTAT 59.394 45.455 0.00 0.00 0.00 2.29
5258 5614 3.797796 GTCGTGTGTGTGTGTTGTGTATA 59.202 43.478 0.00 0.00 0.00 1.47
5355 5712 6.541086 CAGATCAGAAGTGTGCATAGTTTTC 58.459 40.000 4.91 0.25 0.00 2.29
5360 5717 6.868864 TCAGAAGTGTGCATAGTTTTCTCTAC 59.131 38.462 4.91 0.00 0.00 2.59
5366 5723 5.416639 TGTGCATAGTTTTCTCTACGGTCTA 59.583 40.000 0.00 0.00 0.00 2.59
5369 5726 7.167801 GTGCATAGTTTTCTCTACGGTCTATTC 59.832 40.741 0.00 0.00 0.00 1.75
5371 5728 8.566260 GCATAGTTTTCTCTACGGTCTATTCTA 58.434 37.037 0.00 0.00 0.00 2.10
5375 5732 8.968969 AGTTTTCTCTACGGTCTATTCTATTGT 58.031 33.333 0.00 0.00 0.00 2.71
5393 5750 5.989551 ATTGTGTTGATCTTTGTTTTGGC 57.010 34.783 0.00 0.00 0.00 4.52
5394 5751 4.462508 TGTGTTGATCTTTGTTTTGGCA 57.537 36.364 0.00 0.00 0.00 4.92
5395 5752 5.021033 TGTGTTGATCTTTGTTTTGGCAT 57.979 34.783 0.00 0.00 0.00 4.40
5396 5753 5.426504 TGTGTTGATCTTTGTTTTGGCATT 58.573 33.333 0.00 0.00 0.00 3.56
5397 5754 5.879223 TGTGTTGATCTTTGTTTTGGCATTT 59.121 32.000 0.00 0.00 0.00 2.32
5398 5755 6.373774 TGTGTTGATCTTTGTTTTGGCATTTT 59.626 30.769 0.00 0.00 0.00 1.82
5399 5756 7.094463 TGTGTTGATCTTTGTTTTGGCATTTTT 60.094 29.630 0.00 0.00 0.00 1.94
5400 5757 8.394121 GTGTTGATCTTTGTTTTGGCATTTTTA 58.606 29.630 0.00 0.00 0.00 1.52
5401 5758 9.118300 TGTTGATCTTTGTTTTGGCATTTTTAT 57.882 25.926 0.00 0.00 0.00 1.40
5402 5759 9.597999 GTTGATCTTTGTTTTGGCATTTTTATC 57.402 29.630 0.00 0.00 0.00 1.75
5403 5760 8.321650 TGATCTTTGTTTTGGCATTTTTATCC 57.678 30.769 0.00 0.00 0.00 2.59
5404 5761 6.777526 TCTTTGTTTTGGCATTTTTATCCG 57.222 33.333 0.00 0.00 0.00 4.18
5405 5762 6.284459 TCTTTGTTTTGGCATTTTTATCCGT 58.716 32.000 0.00 0.00 0.00 4.69
5406 5763 6.763610 TCTTTGTTTTGGCATTTTTATCCGTT 59.236 30.769 0.00 0.00 0.00 4.44
5407 5764 5.914085 TGTTTTGGCATTTTTATCCGTTG 57.086 34.783 0.00 0.00 0.00 4.10
5411 5768 2.560542 TGGCATTTTTATCCGTTGCTGT 59.439 40.909 0.00 0.00 33.86 4.40
5448 5806 5.901884 CGATTTTGTATATTGGTCGTTGAGC 59.098 40.000 0.00 0.00 0.00 4.26
5455 5897 1.045407 TTGGTCGTTGAGCTGTAGGT 58.955 50.000 0.00 0.00 0.00 3.08
5492 5938 3.317993 GTGCATGACTTTGGTGTTTAGGT 59.682 43.478 0.00 0.00 0.00 3.08
5535 8507 1.989706 TACCCTGAAACTGTTTGCCC 58.010 50.000 11.03 0.00 0.00 5.36
5536 8508 0.261696 ACCCTGAAACTGTTTGCCCT 59.738 50.000 11.03 0.00 0.00 5.19
5552 8525 1.680249 GCCCTGCAGAAACTTAGAGGG 60.680 57.143 17.39 5.53 42.80 4.30
5556 8529 0.394488 GCAGAAACTTAGAGGGGGCC 60.394 60.000 0.00 0.00 0.00 5.80
5583 8557 3.870723 TGATACTTGTCACACGCAAAC 57.129 42.857 0.00 0.00 0.00 2.93
5703 8757 4.803098 TGTAAGCAGGGAGTACTTTCTC 57.197 45.455 0.00 0.00 0.00 2.87
5704 8758 4.157246 TGTAAGCAGGGAGTACTTTCTCA 58.843 43.478 0.00 0.00 36.30 3.27
5708 8762 5.248380 AGCAGGGAGTACTTTCTCAATTT 57.752 39.130 0.00 0.00 36.30 1.82
5807 10128 2.694628 GTGGCCATATGCAAAGGATCAA 59.305 45.455 9.72 0.00 43.89 2.57
5808 10129 3.132646 GTGGCCATATGCAAAGGATCAAA 59.867 43.478 9.72 0.00 43.89 2.69
5811 10132 3.796504 GCCATATGCAAAGGATCAAACGG 60.797 47.826 6.62 0.00 40.77 4.44
5812 10133 3.381272 CCATATGCAAAGGATCAAACGGT 59.619 43.478 0.00 0.00 0.00 4.83
5813 10134 4.578516 CCATATGCAAAGGATCAAACGGTA 59.421 41.667 0.00 0.00 0.00 4.02
5827 10171 8.905850 GGATCAAACGGTAATATTTTTAAGGGA 58.094 33.333 0.00 0.00 0.00 4.20
5971 11405 7.660208 TCCAAGTGTGAATTAGGTAAGACTTTC 59.340 37.037 0.00 0.00 0.00 2.62
6013 11447 5.329035 ACTTTTGGTCCATATGTGATTGC 57.671 39.130 1.24 0.00 0.00 3.56
6037 11471 4.836125 TTCAAAGATTCTGGTTGCTCAC 57.164 40.909 0.00 0.00 0.00 3.51
6040 11474 4.276678 TCAAAGATTCTGGTTGCTCACTTG 59.723 41.667 0.00 0.00 0.00 3.16
6096 11531 9.530129 GATGTTTATTTCTTCAGTAAACAGACG 57.470 33.333 13.26 0.00 45.76 4.18
6150 11585 7.148804 CGCTATATAAAGAAGTTGCGCTATGAA 60.149 37.037 9.73 0.00 35.98 2.57
6186 11621 3.247886 TCAACGCGTCTACTATAGAGCTG 59.752 47.826 14.44 1.64 35.04 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 187 1.338674 TGAAAGTCATGGCGGTCGAAT 60.339 47.619 0.00 0.00 0.00 3.34
230 240 2.012673 GTGTGATCTGGTGATGCCTTC 58.987 52.381 0.00 0.00 38.35 3.46
287 298 0.882927 CGGGTCTTGCTTTTCCACGA 60.883 55.000 0.00 0.00 0.00 4.35
313 324 3.275338 GGCTGTGGCTATCGCTGC 61.275 66.667 0.00 0.00 45.95 5.25
315 326 2.025767 CTCTGGCTGTGGCTATCGCT 62.026 60.000 0.00 0.00 38.73 4.93
490 533 4.517285 CTTTGATCCCTTCCGAGAATCAA 58.483 43.478 0.00 0.00 33.17 2.57
524 567 1.532868 CTGCCTGCGCAATTATACTCC 59.467 52.381 13.05 0.00 46.66 3.85
555 598 4.314440 AAGCGAGCAGGCCAACGA 62.314 61.111 5.01 0.00 0.00 3.85
556 599 3.793144 GAAGCGAGCAGGCCAACG 61.793 66.667 5.01 6.00 0.00 4.10
582 627 2.701107 GCTAGGACAGGAAAAGTGACC 58.299 52.381 0.00 0.00 0.00 4.02
586 631 0.036294 GCCGCTAGGACAGGAAAAGT 60.036 55.000 0.00 0.00 41.02 2.66
641 695 0.467290 AGAAAAGCAGCCCGAAACCA 60.467 50.000 0.00 0.00 0.00 3.67
799 865 3.681417 GCAAATTCTGTTTTGGCAGGATC 59.319 43.478 0.00 0.00 33.78 3.36
948 1014 2.972505 CGTCACGCTGCCCAACTT 60.973 61.111 0.00 0.00 0.00 2.66
1084 1162 4.301637 ACAAACACCGAATCTTCCAAAC 57.698 40.909 0.00 0.00 0.00 2.93
1085 1163 4.993029 AACAAACACCGAATCTTCCAAA 57.007 36.364 0.00 0.00 0.00 3.28
1109 1188 2.047560 CCCGACCCGAAACCAGAC 60.048 66.667 0.00 0.00 0.00 3.51
1110 1189 3.315949 CCCCGACCCGAAACCAGA 61.316 66.667 0.00 0.00 0.00 3.86
1111 1190 4.404098 CCCCCGACCCGAAACCAG 62.404 72.222 0.00 0.00 0.00 4.00
1152 1235 0.871722 CGCCGTCATGAAAGAAACCA 59.128 50.000 0.00 0.00 0.00 3.67
1298 1382 3.486252 GATCTCCTCGTTCCCCGCG 62.486 68.421 0.00 0.00 36.19 6.46
1598 1682 2.511373 TCGCCGATGACCATGCAC 60.511 61.111 0.00 0.00 0.00 4.57
1706 1793 2.364647 TCAGGCTCTGACATAGCATCAG 59.635 50.000 14.10 0.00 44.22 2.90
1869 1956 7.504924 TTATTCAGTCTGAATCCAAAAACGT 57.495 32.000 27.51 7.20 43.03 3.99
1870 1957 8.970691 ATTTATTCAGTCTGAATCCAAAAACG 57.029 30.769 27.51 0.00 43.03 3.60
2087 2182 1.805428 GCCACAAGCAAACGATGGGT 61.805 55.000 0.00 0.00 42.97 4.51
2144 2239 3.307410 GGTACACATGTGGATTCCAGTGA 60.307 47.826 28.64 9.65 33.34 3.41
2156 2251 2.299013 TGAAAGAGCTCGGTACACATGT 59.701 45.455 8.37 0.00 0.00 3.21
2165 2260 2.969628 AGTATGGTGAAAGAGCTCGG 57.030 50.000 8.37 0.00 0.00 4.63
2213 2308 1.003355 CGACATCCAGCCACCTGTT 60.003 57.895 0.00 0.00 37.38 3.16
2215 2310 2.821366 GCGACATCCAGCCACCTG 60.821 66.667 0.00 0.00 38.85 4.00
2283 2380 0.613260 AGTAGCGGAGTCAAATGGCA 59.387 50.000 0.00 0.00 0.00 4.92
2415 2512 3.872696 ACAAATATCCGCACACTCATCA 58.127 40.909 0.00 0.00 0.00 3.07
2500 2597 2.615447 AGACATTAATGCACATGCTCCG 59.385 45.455 15.48 0.00 42.66 4.63
2538 2636 8.948631 TTATTTCAACAATGTGGCTTTTGTAA 57.051 26.923 0.00 0.00 35.09 2.41
2545 2643 4.082026 GCCTCTTATTTCAACAATGTGGCT 60.082 41.667 0.00 0.00 33.45 4.75
2560 2658 1.672854 TACCACGCAGCGCCTCTTAT 61.673 55.000 16.61 0.00 0.00 1.73
2573 2671 7.862741 TGATTATTCGCTTAACTATACCACG 57.137 36.000 0.00 0.00 0.00 4.94
2786 2989 2.363359 CAAGCTGCCCCATCTAAATTCC 59.637 50.000 0.00 0.00 0.00 3.01
2863 3066 1.813862 CGGGGCAATATCCGTTGTCAT 60.814 52.381 0.00 0.00 41.23 3.06
2887 3090 5.487488 ACATGGGAGTACTTCCTTCATAACA 59.513 40.000 21.31 0.00 45.98 2.41
3038 3246 4.229876 GTGTTGGCTCTAAGTTTCATTGC 58.770 43.478 0.00 0.00 0.00 3.56
3166 3380 8.406297 GTTAACATAGAGAATTGGGGCTTAAAG 58.594 37.037 0.00 0.00 0.00 1.85
3220 3439 8.757982 AATTGAGACATCCTACAAAATGCTAT 57.242 30.769 0.00 0.00 0.00 2.97
3311 3593 1.079490 AGGTCACCAGAGGAAGGATGA 59.921 52.381 0.00 0.00 0.00 2.92
3347 3629 3.486383 GGATTCTGGACTCCACACAAAA 58.514 45.455 0.00 0.00 0.00 2.44
3355 3637 1.769465 GGGTAAGGGATTCTGGACTCC 59.231 57.143 0.00 0.00 0.00 3.85
3432 3714 3.489355 CAGCTTGTCCCATATATGCCAA 58.511 45.455 7.24 8.42 0.00 4.52
3663 3947 1.153449 CCCAATAACGGCTGCGAGA 60.153 57.895 0.00 0.00 0.00 4.04
3932 4216 8.161699 AGTTTACGGTGACAAGAAAATATGTT 57.838 30.769 0.00 0.00 0.00 2.71
3988 4291 2.740447 GGCACCTAAAGTTGACCGTAAG 59.260 50.000 0.00 0.00 0.00 2.34
4012 4315 5.473504 CCTGTACCAAGAAAAGCACATAAGT 59.526 40.000 0.00 0.00 0.00 2.24
4073 4376 7.581213 AAGAACAATAACCAGTGACATCAAA 57.419 32.000 0.00 0.00 0.00 2.69
4446 4749 9.533253 AAACAAAAATGTAGAAGTTGATGAAGG 57.467 29.630 0.00 0.00 0.00 3.46
4505 4808 4.487714 TTAGCAGAGTGTATTGGGGAAG 57.512 45.455 0.00 0.00 0.00 3.46
4529 4832 7.736447 CCAGAACCTGGTGAAAGATATAATC 57.264 40.000 0.00 0.00 45.82 1.75
4561 4917 6.207417 GTGGTATAGGCACTGATTTAATGCAT 59.793 38.462 0.00 0.00 41.52 3.96
4597 4953 0.391130 CGACCCAAAATCGCTCCTCA 60.391 55.000 0.00 0.00 31.96 3.86
4770 5126 1.532078 TCTGTGGCACCGTCCAGTA 60.532 57.895 16.26 0.00 36.67 2.74
4771 5127 2.842462 TCTGTGGCACCGTCCAGT 60.842 61.111 16.26 0.00 36.67 4.00
4797 5153 1.829849 TGATGGAAGACAGCCTCTCAG 59.170 52.381 0.00 0.00 33.62 3.35
4810 5166 2.169769 CGGTAGGCCTTTAGTGATGGAA 59.830 50.000 12.58 0.00 0.00 3.53
4818 5174 2.235402 TCCTGAAACGGTAGGCCTTTAG 59.765 50.000 12.58 4.84 34.00 1.85
4831 5187 2.028930 ACTGTCATCGTCCTCCTGAAAC 60.029 50.000 0.00 0.00 0.00 2.78
4861 5217 0.659427 GTATCGACGTGTCCGATCCA 59.341 55.000 13.15 0.00 44.50 3.41
4864 5220 1.329906 GACAGTATCGACGTGTCCGAT 59.670 52.381 14.06 14.06 46.82 4.18
4927 5283 1.004918 CGCGAACCTCACCCTCTTT 60.005 57.895 0.00 0.00 0.00 2.52
5089 5445 5.460419 CAGGAACTCGTAGATGCAGTTTATC 59.540 44.000 0.00 0.00 34.60 1.75
5097 5453 3.490078 CCTTCTCAGGAACTCGTAGATGC 60.490 52.174 0.00 0.00 44.19 3.91
5116 5472 0.035458 CAGAACCTCGGCTGTTCCTT 59.965 55.000 8.38 0.00 42.41 3.36
5136 5492 0.178068 AGGTATGTTAGCTGCCGTGG 59.822 55.000 0.00 0.00 34.78 4.94
5140 5496 1.876156 GCATGAGGTATGTTAGCTGCC 59.124 52.381 0.00 0.00 39.08 4.85
5213 5569 2.954753 GAACAACAGAGCGTGGCGG 61.955 63.158 0.00 0.00 0.00 6.13
5355 5712 7.704271 TCAACACAATAGAATAGACCGTAGAG 58.296 38.462 0.00 0.00 0.00 2.43
5360 5717 8.331022 CAAAGATCAACACAATAGAATAGACCG 58.669 37.037 0.00 0.00 0.00 4.79
5366 5723 9.480053 CCAAAACAAAGATCAACACAATAGAAT 57.520 29.630 0.00 0.00 0.00 2.40
5369 5726 6.700960 TGCCAAAACAAAGATCAACACAATAG 59.299 34.615 0.00 0.00 0.00 1.73
5371 5728 5.426504 TGCCAAAACAAAGATCAACACAAT 58.573 33.333 0.00 0.00 0.00 2.71
5375 5732 6.998968 AAAATGCCAAAACAAAGATCAACA 57.001 29.167 0.00 0.00 0.00 3.33
5393 5750 7.112009 CGATAATGACAGCAACGGATAAAAATG 59.888 37.037 0.00 0.00 0.00 2.32
5394 5751 7.132213 CGATAATGACAGCAACGGATAAAAAT 58.868 34.615 0.00 0.00 0.00 1.82
5395 5752 6.092944 ACGATAATGACAGCAACGGATAAAAA 59.907 34.615 0.00 0.00 0.00 1.94
5396 5753 5.583061 ACGATAATGACAGCAACGGATAAAA 59.417 36.000 0.00 0.00 0.00 1.52
5397 5754 5.113383 ACGATAATGACAGCAACGGATAAA 58.887 37.500 0.00 0.00 0.00 1.40
5398 5755 4.689071 ACGATAATGACAGCAACGGATAA 58.311 39.130 0.00 0.00 0.00 1.75
5399 5756 4.295870 GACGATAATGACAGCAACGGATA 58.704 43.478 0.00 0.00 0.00 2.59
5400 5757 3.123804 GACGATAATGACAGCAACGGAT 58.876 45.455 0.00 0.00 0.00 4.18
5401 5758 2.536365 GACGATAATGACAGCAACGGA 58.464 47.619 0.00 0.00 0.00 4.69
5402 5759 1.255342 CGACGATAATGACAGCAACGG 59.745 52.381 0.00 0.00 0.00 4.44
5403 5760 1.917955 ACGACGATAATGACAGCAACG 59.082 47.619 0.00 0.00 0.00 4.10
5404 5761 2.035674 CGACGACGATAATGACAGCAAC 60.036 50.000 0.00 0.00 42.66 4.17
5405 5762 2.159490 TCGACGACGATAATGACAGCAA 60.159 45.455 5.75 0.00 43.81 3.91
5406 5763 1.399089 TCGACGACGATAATGACAGCA 59.601 47.619 5.75 0.00 43.81 4.41
5407 5764 2.101053 TCGACGACGATAATGACAGC 57.899 50.000 5.75 0.00 43.81 4.40
5428 5785 5.242434 ACAGCTCAACGACCAATATACAAA 58.758 37.500 0.00 0.00 0.00 2.83
5448 5806 8.620416 TGCACAAAAATGCTATATTACCTACAG 58.380 33.333 0.00 0.00 46.28 2.74
5478 5924 7.490079 GGTTCTAAAACAACCTAAACACCAAAG 59.510 37.037 0.00 0.00 40.33 2.77
5506 5952 9.840427 CAAACAGTTTCAGGGTATAACTTATTG 57.160 33.333 0.00 0.00 30.08 1.90
5512 5959 4.082408 GGGCAAACAGTTTCAGGGTATAAC 60.082 45.833 0.00 0.00 0.00 1.89
5535 8507 1.680249 GCCCCCTCTAAGTTTCTGCAG 60.680 57.143 7.63 7.63 0.00 4.41
5536 8508 0.328258 GCCCCCTCTAAGTTTCTGCA 59.672 55.000 0.00 0.00 0.00 4.41
5552 8525 2.872858 GACAAGTATCATTTCTCGGCCC 59.127 50.000 0.00 0.00 0.00 5.80
5556 8529 4.490959 GCGTGTGACAAGTATCATTTCTCG 60.491 45.833 0.00 0.00 0.00 4.04
5583 8557 1.331214 ACCACCAGTTCTGGCAAATG 58.669 50.000 17.55 8.99 31.13 2.32
5599 8573 5.129815 ACTTTATCGAGCCTTACCAATACCA 59.870 40.000 0.00 0.00 0.00 3.25
5600 8574 5.608449 ACTTTATCGAGCCTTACCAATACC 58.392 41.667 0.00 0.00 0.00 2.73
5601 8575 7.279313 TCAAACTTTATCGAGCCTTACCAATAC 59.721 37.037 0.00 0.00 0.00 1.89
5602 8576 7.332557 TCAAACTTTATCGAGCCTTACCAATA 58.667 34.615 0.00 0.00 0.00 1.90
5603 8577 6.177610 TCAAACTTTATCGAGCCTTACCAAT 58.822 36.000 0.00 0.00 0.00 3.16
5604 8578 5.553123 TCAAACTTTATCGAGCCTTACCAA 58.447 37.500 0.00 0.00 0.00 3.67
5835 10179 8.349245 ACTCATACTGATATTTCTTGAGACTCG 58.651 37.037 4.21 0.00 34.62 4.18
5852 10362 4.022242 CCCGGGTACATTCTACTCATACTG 60.022 50.000 14.18 0.00 0.00 2.74
5885 10395 1.402787 AAAGTGAACCAACCTGCCAG 58.597 50.000 0.00 0.00 0.00 4.85
5888 10398 1.269723 GGCTAAAGTGAACCAACCTGC 59.730 52.381 0.00 0.00 0.00 4.85
5891 10401 1.989706 TGGGCTAAAGTGAACCAACC 58.010 50.000 0.00 0.00 0.00 3.77
5971 11405 5.779806 AGTTATTCGACGATCTTTTGGTG 57.220 39.130 0.00 0.00 0.00 4.17
6013 11447 4.222114 GAGCAACCAGAATCTTTGAAACG 58.778 43.478 0.00 0.00 0.00 3.60
6037 11471 6.700352 ACCAGAATCTCTCTCTCTTTTCAAG 58.300 40.000 0.00 0.00 29.07 3.02
6040 11474 5.351189 GCAACCAGAATCTCTCTCTCTTTTC 59.649 44.000 0.00 0.00 29.07 2.29
6096 11531 0.668535 AGAAAGCCTTTGCAACCGTC 59.331 50.000 0.00 0.00 41.13 4.79


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

AutoCloner maintained by Alex Coulton.