Multiple sequence alignment - TraesCS7D01G079100

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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 TraesCS7D01G079100 chr7D 100.000 5751 0 0 1 5751 46803577 46797827 0.000000e+00 10621.0
1 TraesCS7D01G079100 chr7D 84.539 2018 220 54 3024 4987 46836867 46834888 0.000000e+00 1914.0
2 TraesCS7D01G079100 chr7D 78.295 1032 187 28 803 1806 46837998 46836976 1.050000e-176 630.0
3 TraesCS7D01G079100 chr7A 93.420 2994 135 30 2232 5196 48889630 48886670 0.000000e+00 4381.0
4 TraesCS7D01G079100 chr7A 84.226 2016 231 56 3024 4987 49045109 49043129 0.000000e+00 1881.0
5 TraesCS7D01G079100 chr7A 91.165 1245 78 13 1 1230 48902980 48901753 0.000000e+00 1661.0
6 TraesCS7D01G079100 chr7A 94.678 714 36 2 1265 1977 48890500 48889788 0.000000e+00 1107.0
7 TraesCS7D01G079100 chr7A 85.005 967 99 23 3955 4895 48943297 48942351 0.000000e+00 941.0
8 TraesCS7D01G079100 chr7A 86.727 663 68 13 3194 3846 48944248 48943596 0.000000e+00 719.0
9 TraesCS7D01G079100 chr7A 77.096 1157 196 38 687 1806 49046340 49045216 6.370000e-169 604.0
10 TraesCS7D01G079100 chr7A 77.169 968 175 27 907 1836 48947100 48946141 6.600000e-144 521.0
11 TraesCS7D01G079100 chr7A 83.403 476 52 16 5263 5715 48886541 48886070 3.210000e-112 416.0
12 TraesCS7D01G079100 chr7A 86.174 311 24 8 1990 2291 48889809 48889509 9.300000e-83 318.0
13 TraesCS7D01G079100 chr7A 78.622 421 62 18 468 884 48947803 48947407 2.660000e-63 254.0
14 TraesCS7D01G079100 chr4A 92.403 2343 126 24 2693 5003 660748194 660745872 0.000000e+00 3293.0
15 TraesCS7D01G079100 chr4A 92.173 1827 106 18 415 2226 660750303 660748499 0.000000e+00 2547.0
16 TraesCS7D01G079100 chr4A 90.937 1313 92 15 3580 4877 660780547 660779247 0.000000e+00 1740.0
17 TraesCS7D01G079100 chr4A 85.308 1511 154 45 3455 4939 660924970 660926438 0.000000e+00 1498.0
18 TraesCS7D01G079100 chr4A 88.022 1269 103 22 3942 5196 660740582 660739349 0.000000e+00 1456.0
19 TraesCS7D01G079100 chr4A 85.530 1009 96 27 3950 4936 660786357 660785377 0.000000e+00 1009.0
20 TraesCS7D01G079100 chr4A 77.507 1396 257 39 441 1798 660743996 660742620 0.000000e+00 785.0
21 TraesCS7D01G079100 chr4A 77.064 1369 238 48 519 1836 660922549 660923892 0.000000e+00 719.0
22 TraesCS7D01G079100 chr4A 86.971 614 66 12 3236 3846 660787190 660786588 0.000000e+00 678.0
23 TraesCS7D01G079100 chr4A 95.349 430 10 4 1 428 660750743 660750322 0.000000e+00 675.0
24 TraesCS7D01G079100 chr4A 95.796 333 14 0 2296 2628 660748545 660748213 6.560000e-149 538.0
25 TraesCS7D01G079100 chr4A 76.574 1080 189 47 512 1555 660790221 660789170 8.480000e-148 534.0
26 TraesCS7D01G079100 chr4A 79.825 570 87 16 2994 3544 660781441 660780881 1.940000e-104 390.0
27 TraesCS7D01G079100 chr4A 80.222 450 51 16 5303 5720 660739194 660738751 2.600000e-78 303.0
28 TraesCS7D01G079100 chr4A 84.071 113 18 0 2826 2938 556759286 556759174 6.090000e-20 110.0
29 TraesCS7D01G079100 chr4A 96.491 57 2 0 2235 2291 660748545 660748489 1.710000e-15 95.3
30 TraesCS7D01G079100 chrUn 92.488 1491 92 13 452 1928 49214011 49212527 0.000000e+00 2115.0
31 TraesCS7D01G079100 chrUn 92.488 1491 92 13 452 1928 273544403 273542919 0.000000e+00 2115.0
32 TraesCS7D01G079100 chrUn 94.899 941 43 4 3503 4438 49210926 49209986 0.000000e+00 1467.0
33 TraesCS7D01G079100 chrUn 94.899 941 43 4 3503 4438 273541318 273540378 0.000000e+00 1467.0
34 TraesCS7D01G079100 chrUn 95.592 794 27 6 2685 3478 49211705 49210920 0.000000e+00 1266.0
35 TraesCS7D01G079100 chrUn 95.592 794 27 6 2685 3478 273542097 273541312 0.000000e+00 1266.0
36 TraesCS7D01G079100 chrUn 87.832 1093 76 15 4440 5510 49209914 49208857 0.000000e+00 1229.0
37 TraesCS7D01G079100 chrUn 89.094 651 47 12 4440 5073 273540306 273539663 0.000000e+00 787.0
38 TraesCS7D01G079100 chrUn 95.075 467 22 1 2232 2698 49212186 49211721 0.000000e+00 734.0
39 TraesCS7D01G079100 chrUn 95.075 467 22 1 2232 2698 273542578 273542113 0.000000e+00 734.0
40 TraesCS7D01G079100 chrUn 89.286 224 12 5 198 421 49214644 49214433 2.640000e-68 270.0
41 TraesCS7D01G079100 chrUn 89.286 224 12 5 198 421 273545036 273544825 2.640000e-68 270.0
42 TraesCS7D01G079100 chrUn 93.976 166 8 2 5512 5676 49208772 49208608 3.440000e-62 250.0
43 TraesCS7D01G079100 chrUn 89.899 99 3 5 73 164 49214738 49214640 2.810000e-23 121.0
44 TraesCS7D01G079100 chrUn 89.899 99 3 5 73 164 273545130 273545032 2.810000e-23 121.0
45 TraesCS7D01G079100 chrUn 84.348 115 5 8 1929 2032 49212444 49212332 3.670000e-17 100.0
46 TraesCS7D01G079100 chrUn 84.348 115 5 8 1929 2032 273542836 273542724 3.670000e-17 100.0
47 TraesCS7D01G079100 chrUn 90.000 60 6 0 2293 2352 49212186 49212127 1.720000e-10 78.7
48 TraesCS7D01G079100 chrUn 90.000 60 6 0 2293 2352 273542578 273542519 1.720000e-10 78.7


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 TraesCS7D01G079100 chr7D 46797827 46803577 5750 True 10621.000000 10621 100.000000 1 5751 1 chr7D.!!$R1 5750
1 TraesCS7D01G079100 chr7D 46834888 46837998 3110 True 1272.000000 1914 81.417000 803 4987 2 chr7D.!!$R2 4184
2 TraesCS7D01G079100 chr7A 48901753 48902980 1227 True 1661.000000 1661 91.165000 1 1230 1 chr7A.!!$R1 1229
3 TraesCS7D01G079100 chr7A 48886070 48890500 4430 True 1555.500000 4381 89.418750 1265 5715 4 chr7A.!!$R2 4450
4 TraesCS7D01G079100 chr7A 49043129 49046340 3211 True 1242.500000 1881 80.661000 687 4987 2 chr7A.!!$R4 4300
5 TraesCS7D01G079100 chr7A 48942351 48947803 5452 True 608.750000 941 81.880750 468 4895 4 chr7A.!!$R3 4427
6 TraesCS7D01G079100 chr4A 660738751 660750743 11992 True 1211.537500 3293 89.745375 1 5720 8 chr4A.!!$R2 5719
7 TraesCS7D01G079100 chr4A 660922549 660926438 3889 False 1108.500000 1498 81.186000 519 4939 2 chr4A.!!$F1 4420
8 TraesCS7D01G079100 chr4A 660779247 660790221 10974 True 870.200000 1740 83.967400 512 4936 5 chr4A.!!$R3 4424
9 TraesCS7D01G079100 chrUn 273539663 273545130 5467 True 770.966667 2115 91.186778 73 5073 9 chrUn.!!$R2 5000
10 TraesCS7D01G079100 chrUn 49208608 49214738 6130 True 763.070000 2115 91.339500 73 5676 10 chrUn.!!$R1 5603

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
432 497 1.833860 ACAAACAACAAACGATGCCG 58.166 45.000 0.00 0.0 42.50 5.69 F
1159 1933 1.676746 CAGGAATGCCTCATCCACAG 58.323 55.000 0.00 0.0 44.80 3.66 F
2533 3713 1.104577 TCCAAAACCGGTTGTGCTCC 61.105 55.000 29.12 0.0 0.00 4.70 F
2658 3839 3.380637 TCCAATCTCGGTAGCTTGAGTAC 59.619 47.826 0.00 0.0 31.77 2.73 F
4242 12843 4.854173 TCCTGCATAAGTCAGCCAAATAA 58.146 39.130 0.00 0.0 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 2364 0.179111 TGCACTGCGCCATAGAGTAC 60.179 55.0 4.18 0.00 41.33 2.73 R
2757 4447 0.389426 CCTTGCCATGTTTGCAGCTC 60.389 55.0 0.00 0.00 40.35 4.09 R
4263 12869 2.224042 CCACTGAAAAGGCAGGGAAAAC 60.224 50.0 0.00 0.00 41.90 2.43 R
4272 12878 2.623416 GCCATATACCCACTGAAAAGGC 59.377 50.0 0.00 0.00 0.00 4.35 R
5727 20996 0.251073 ACAGGTAACCCGGGATTTCG 59.749 55.0 32.02 13.25 35.12 3.46 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
284 297 2.816087 CAAGCCACATTGCACTTCTACT 59.184 45.455 0.00 0.00 0.00 2.57
285 298 3.146104 AGCCACATTGCACTTCTACTT 57.854 42.857 0.00 0.00 0.00 2.24
286 299 3.490348 AGCCACATTGCACTTCTACTTT 58.510 40.909 0.00 0.00 0.00 2.66
287 300 3.503748 AGCCACATTGCACTTCTACTTTC 59.496 43.478 0.00 0.00 0.00 2.62
288 301 3.253188 GCCACATTGCACTTCTACTTTCA 59.747 43.478 0.00 0.00 0.00 2.69
289 302 4.614535 GCCACATTGCACTTCTACTTTCAG 60.615 45.833 0.00 0.00 0.00 3.02
290 303 4.470462 CACATTGCACTTCTACTTTCAGC 58.530 43.478 0.00 0.00 0.00 4.26
386 399 4.843516 ACCCACCCACATCATTATTGTTTT 59.156 37.500 0.00 0.00 0.00 2.43
429 494 6.964370 TCAGTAGAAACAAACAACAAACGATG 59.036 34.615 0.00 0.00 0.00 3.84
432 497 1.833860 ACAAACAACAAACGATGCCG 58.166 45.000 0.00 0.00 42.50 5.69
456 892 6.195798 CGGTCAAAACTTAGTTAACAAACTGC 59.804 38.462 8.61 0.00 34.37 4.40
676 1132 4.142816 CGCAAGAGAATCACCTTCGATTTT 60.143 41.667 0.00 0.00 38.98 1.82
681 1137 4.074970 AGAATCACCTTCGATTTTGCTGT 58.925 39.130 0.00 0.00 38.98 4.40
772 1239 6.954944 TCTAATTTTTGTTCTCCACTTGTCG 58.045 36.000 0.00 0.00 0.00 4.35
848 1319 2.613595 CGGCAGCAGCATTGTATTCTAA 59.386 45.455 2.65 0.00 44.61 2.10
893 1367 6.717997 TGCAGGCAGATGTTATCATTAATCAT 59.282 34.615 0.00 0.00 34.06 2.45
894 1368 7.231925 TGCAGGCAGATGTTATCATTAATCATT 59.768 33.333 0.00 0.00 34.06 2.57
895 1369 8.733458 GCAGGCAGATGTTATCATTAATCATTA 58.267 33.333 0.00 0.00 34.06 1.90
961 1722 5.939883 CCAAATGATGCCGATAATAAGGAGA 59.060 40.000 0.00 0.00 0.00 3.71
994 1756 3.534357 TGGGCTGAATAACCTTTTGGA 57.466 42.857 0.00 0.00 44.07 3.53
1159 1933 1.676746 CAGGAATGCCTCATCCACAG 58.323 55.000 0.00 0.00 44.80 3.66
1353 2127 1.883732 CATCGTCCACGTCTCCACT 59.116 57.895 0.00 0.00 40.80 4.00
1439 2213 4.342951 GGATCCCAGCATTCAATTCATTGA 59.657 41.667 0.00 0.00 44.42 2.57
1701 2495 1.895131 GGTGAATGGATTGCTGGTGTT 59.105 47.619 0.00 0.00 0.00 3.32
1886 2869 3.072476 CCCCAAAACTAGTCTGTCTTCCA 59.928 47.826 0.00 0.00 0.00 3.53
1893 2876 7.511959 AAACTAGTCTGTCTTCCATTTTTCC 57.488 36.000 0.00 0.00 0.00 3.13
2056 3154 8.213518 TCATTAGGCTTGATGAAATTGACTAC 57.786 34.615 0.42 0.00 29.82 2.73
2205 3363 7.420800 AGATCTAATGACCGCAAATCAATTTC 58.579 34.615 0.00 0.00 0.00 2.17
2237 3395 8.547481 TCTGAAAGACATAACACCCATATAGA 57.453 34.615 0.00 0.00 38.67 1.98
2238 3396 9.159254 TCTGAAAGACATAACACCCATATAGAT 57.841 33.333 0.00 0.00 38.67 1.98
2239 3397 9.429359 CTGAAAGACATAACACCCATATAGATC 57.571 37.037 0.00 0.00 34.07 2.75
2240 3398 9.159254 TGAAAGACATAACACCCATATAGATCT 57.841 33.333 0.00 0.00 0.00 2.75
2247 3405 9.823647 CATAACACCCATATAGATCTAATGACC 57.176 37.037 18.66 0.00 0.00 4.02
2248 3406 6.531503 ACACCCATATAGATCTAATGACCG 57.468 41.667 18.66 11.93 0.00 4.79
2249 3407 5.105310 ACACCCATATAGATCTAATGACCGC 60.105 44.000 18.66 0.00 0.00 5.68
2250 3408 5.023452 ACCCATATAGATCTAATGACCGCA 58.977 41.667 18.66 0.00 0.00 5.69
2251 3409 5.483937 ACCCATATAGATCTAATGACCGCAA 59.516 40.000 18.66 0.00 0.00 4.85
2252 3410 6.013725 ACCCATATAGATCTAATGACCGCAAA 60.014 38.462 18.66 0.00 0.00 3.68
2253 3411 6.313905 CCCATATAGATCTAATGACCGCAAAC 59.686 42.308 18.66 0.00 0.00 2.93
2254 3412 6.313905 CCATATAGATCTAATGACCGCAAACC 59.686 42.308 18.66 0.00 0.00 3.27
2255 3413 3.627395 AGATCTAATGACCGCAAACCA 57.373 42.857 0.00 0.00 0.00 3.67
2256 3414 3.950397 AGATCTAATGACCGCAAACCAA 58.050 40.909 0.00 0.00 0.00 3.67
2257 3415 4.526970 AGATCTAATGACCGCAAACCAAT 58.473 39.130 0.00 0.00 0.00 3.16
2258 3416 4.949856 AGATCTAATGACCGCAAACCAATT 59.050 37.500 0.00 0.00 0.00 2.32
2259 3417 5.418840 AGATCTAATGACCGCAAACCAATTT 59.581 36.000 0.00 0.00 0.00 1.82
2260 3418 5.054390 TCTAATGACCGCAAACCAATTTC 57.946 39.130 0.00 0.00 0.00 2.17
2261 3419 2.346099 ATGACCGCAAACCAATTTCG 57.654 45.000 0.00 0.00 0.00 3.46
2262 3420 1.309950 TGACCGCAAACCAATTTCGA 58.690 45.000 0.00 0.00 0.00 3.71
2263 3421 1.883275 TGACCGCAAACCAATTTCGAT 59.117 42.857 0.00 0.00 0.00 3.59
2264 3422 2.250188 GACCGCAAACCAATTTCGATG 58.750 47.619 0.00 0.00 0.00 3.84
2265 3423 1.883275 ACCGCAAACCAATTTCGATGA 59.117 42.857 0.00 0.00 0.00 2.92
2266 3424 2.491693 ACCGCAAACCAATTTCGATGAT 59.508 40.909 0.00 0.00 0.00 2.45
2267 3425 3.056891 ACCGCAAACCAATTTCGATGATT 60.057 39.130 0.00 0.00 0.00 2.57
2268 3426 3.547468 CCGCAAACCAATTTCGATGATTC 59.453 43.478 0.00 0.00 0.00 2.52
2269 3427 4.414852 CGCAAACCAATTTCGATGATTCT 58.585 39.130 0.00 0.00 0.00 2.40
2270 3428 4.263677 CGCAAACCAATTTCGATGATTCTG 59.736 41.667 0.00 0.00 0.00 3.02
2271 3429 5.401550 GCAAACCAATTTCGATGATTCTGA 58.598 37.500 0.00 0.00 0.00 3.27
2272 3430 5.863397 GCAAACCAATTTCGATGATTCTGAA 59.137 36.000 0.00 0.00 0.00 3.02
2273 3431 6.365789 GCAAACCAATTTCGATGATTCTGAAA 59.634 34.615 0.00 0.00 36.19 2.69
2326 3484 4.244066 TGACCGCAAATCAATTTTGATGG 58.756 39.130 6.56 6.27 46.60 3.51
2533 3713 1.104577 TCCAAAACCGGTTGTGCTCC 61.105 55.000 29.12 0.00 0.00 4.70
2635 3816 5.647589 CTGTACCTCTATACGTCAGCAAAA 58.352 41.667 0.00 0.00 0.00 2.44
2639 3820 4.161565 ACCTCTATACGTCAGCAAAATCCA 59.838 41.667 0.00 0.00 0.00 3.41
2658 3839 3.380637 TCCAATCTCGGTAGCTTGAGTAC 59.619 47.826 0.00 0.00 31.77 2.73
2932 4623 8.841300 AGATCTTAAGGTTGAAAAGTGAACTTC 58.159 33.333 1.85 0.00 34.61 3.01
3043 4797 7.448748 AATCAACTAACCACCTATGTTTGTC 57.551 36.000 0.00 0.00 31.98 3.18
3127 4883 5.972107 ACTAGCATCATTTTTGTGCTTCT 57.028 34.783 4.31 0.00 46.29 2.85
3145 4901 7.604927 TGTGCTTCTTCGTATGGTTTAAACTAT 59.395 33.333 19.46 19.46 34.34 2.12
3468 5501 8.474025 TCCATGTACACAAAGAGAACAAAAATT 58.526 29.630 0.00 0.00 0.00 1.82
3488 5586 5.741388 ATTGAACCTAGTTTGCATCGATC 57.259 39.130 0.00 0.00 0.00 3.69
4014 12615 4.991687 AGAAAAGCGATTATCGAAGGGATC 59.008 41.667 19.40 7.90 43.74 3.36
4050 12651 9.249457 CTTCTATATTTGCATAAACACTCTCGA 57.751 33.333 0.00 0.00 0.00 4.04
4089 12690 6.434018 AGAGATCTTAAAGCAAGCAACATC 57.566 37.500 0.00 0.00 33.94 3.06
4113 12714 5.876460 CCTTTTGGACATTGAAATGAATCCC 59.124 40.000 9.94 5.99 44.07 3.85
4227 12828 6.662755 TCTTACAAATTAGTCCATCCTGCAT 58.337 36.000 0.00 0.00 0.00 3.96
4242 12843 4.854173 TCCTGCATAAGTCAGCCAAATAA 58.146 39.130 0.00 0.00 0.00 1.40
4272 12878 7.229506 ACTGAGATAGAAGTTTTGTTTTCCCTG 59.770 37.037 0.00 0.00 0.00 4.45
4773 19818 5.942236 AGTGCTAATGATGTGACAATGTCTT 59.058 36.000 14.97 1.96 33.15 3.01
4907 19967 6.312672 CACAAACCTTTGGACTTTGGTTAAAG 59.687 38.462 2.94 0.00 43.77 1.85
5042 20116 3.939592 GGTAGAGTACATTTCAGGTTGGC 59.060 47.826 0.00 0.00 0.00 4.52
5047 20121 2.507339 ACATTTCAGGTTGGCGTTTG 57.493 45.000 0.00 0.00 0.00 2.93
5058 20132 4.130857 GCGTTTGCCTTTGCGTAG 57.869 55.556 0.00 0.00 41.78 3.51
5088 20163 6.592207 AAAAGGGTGGTAGGCTAAGATTAT 57.408 37.500 0.00 0.00 0.00 1.28
5094 20176 7.684619 AGGGTGGTAGGCTAAGATTATGATTAT 59.315 37.037 0.00 0.00 0.00 1.28
5095 20177 8.329502 GGGTGGTAGGCTAAGATTATGATTATT 58.670 37.037 0.00 0.00 0.00 1.40
5096 20178 9.384764 GGTGGTAGGCTAAGATTATGATTATTC 57.615 37.037 0.00 0.00 0.00 1.75
5097 20179 9.944376 GTGGTAGGCTAAGATTATGATTATTCA 57.056 33.333 0.00 0.00 36.00 2.57
5107 20189 9.645128 AAGATTATGATTATTCATCCAACCACA 57.355 29.630 3.43 0.00 41.73 4.17
5108 20190 9.818270 AGATTATGATTATTCATCCAACCACAT 57.182 29.630 3.43 0.00 41.73 3.21
5113 20195 8.993404 TGATTATTCATCCAACCACATAATCA 57.007 30.769 7.87 7.87 39.55 2.57
5136 20218 8.579850 TCAAGCCTTTGTACAGAAATCATAAT 57.420 30.769 0.00 0.00 35.73 1.28
5152 20234 8.876275 AAATCATAATCATAAACACACATGGC 57.124 30.769 0.00 0.00 0.00 4.40
5187 20269 4.908156 GCATATGCACTGAATCGATTCAAC 59.092 41.667 33.76 26.48 42.37 3.18
5314 20464 1.952102 TTAGTGTCTTAGGGGGCGCG 61.952 60.000 0.00 0.00 0.00 6.86
5322 20472 1.517210 TTAGGGGGCGCGTTTTGTTC 61.517 55.000 8.43 0.00 0.00 3.18
5324 20474 3.652000 GGGGCGCGTTTTGTTCGA 61.652 61.111 8.43 0.00 0.00 3.71
5325 20475 2.426261 GGGCGCGTTTTGTTCGAC 60.426 61.111 8.43 0.00 0.00 4.20
5329 20479 1.517718 GCGCGTTTTGTTCGACACAC 61.518 55.000 8.43 0.00 33.98 3.82
5331 20481 1.176838 GCGTTTTGTTCGACACACAC 58.823 50.000 0.00 0.00 33.98 3.82
5333 20483 2.789779 GCGTTTTGTTCGACACACACAT 60.790 45.455 0.00 0.00 33.98 3.21
5351 20501 5.001232 ACACATACACACATACCTTTGGTC 58.999 41.667 0.00 0.00 37.09 4.02
5437 20587 2.755836 AATTTGCATATCGTGACGCC 57.244 45.000 0.00 0.00 0.00 5.68
5444 20594 0.309922 ATATCGTGACGCCGAATCGT 59.690 50.000 0.00 0.00 46.38 3.73
5469 20621 2.084546 GCTCACCTCGGTTGCTAATTT 58.915 47.619 4.25 0.00 0.00 1.82
5487 20643 3.299340 TTTCTAGTGACGACTTCCTGC 57.701 47.619 0.00 0.00 33.21 4.85
5489 20645 2.085320 TCTAGTGACGACTTCCTGCTC 58.915 52.381 0.00 0.00 33.21 4.26
5490 20646 1.813178 CTAGTGACGACTTCCTGCTCA 59.187 52.381 0.00 0.00 33.21 4.26
5493 20649 0.390340 TGACGACTTCCTGCTCATGC 60.390 55.000 0.00 0.00 40.20 4.06
5494 20650 1.078848 ACGACTTCCTGCTCATGCC 60.079 57.895 0.00 0.00 38.71 4.40
5495 20651 1.078918 CGACTTCCTGCTCATGCCA 60.079 57.895 0.00 0.00 38.71 4.92
5499 20656 1.005097 ACTTCCTGCTCATGCCAATGA 59.995 47.619 0.00 0.00 40.61 2.57
5546 20786 0.871057 GGAGTGTCTCTTTGTGCAGC 59.129 55.000 0.00 0.00 0.00 5.25
5552 20792 0.599558 TCTCTTTGTGCAGCAATGGC 59.400 50.000 0.00 0.00 36.89 4.40
5634 20902 0.874390 TGCACTGAAATCCGAAGCAC 59.126 50.000 0.00 0.00 0.00 4.40
5635 20903 0.179215 GCACTGAAATCCGAAGCACG 60.179 55.000 0.00 0.00 42.18 5.34
5642 20911 2.093306 AATCCGAAGCACGAACATCA 57.907 45.000 4.96 0.00 45.77 3.07
5720 20989 2.224744 CCCCAACAAAAATCCCCAAAGG 60.225 50.000 0.00 0.00 0.00 3.11
5742 21011 1.875009 GGATCGAAATCCCGGGTTAC 58.125 55.000 22.86 9.35 45.11 2.50
5743 21012 1.541889 GGATCGAAATCCCGGGTTACC 60.542 57.143 22.86 10.04 45.11 2.85
5744 21013 1.415289 GATCGAAATCCCGGGTTACCT 59.585 52.381 22.86 1.20 33.28 3.08
5745 21014 0.538118 TCGAAATCCCGGGTTACCTG 59.462 55.000 22.86 2.61 33.28 4.00
5746 21015 0.251073 CGAAATCCCGGGTTACCTGT 59.749 55.000 22.86 0.00 33.28 4.00
5747 21016 1.741394 CGAAATCCCGGGTTACCTGTC 60.741 57.143 22.86 8.52 33.28 3.51
5748 21017 1.279846 GAAATCCCGGGTTACCTGTCA 59.720 52.381 22.86 0.00 33.28 3.58
5749 21018 1.591768 AATCCCGGGTTACCTGTCAT 58.408 50.000 22.86 0.00 33.28 3.06
5750 21019 1.129058 ATCCCGGGTTACCTGTCATC 58.871 55.000 22.86 0.00 33.28 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
363 376 3.756082 ACAATAATGATGTGGGTGGGT 57.244 42.857 0.00 0.00 0.00 4.51
366 379 6.572519 CCCTAAAACAATAATGATGTGGGTG 58.427 40.000 0.00 0.00 0.00 4.61
367 380 5.128663 GCCCTAAAACAATAATGATGTGGGT 59.871 40.000 0.00 0.00 32.82 4.51
370 383 8.299570 GGATAGCCCTAAAACAATAATGATGTG 58.700 37.037 0.00 0.00 0.00 3.21
374 387 7.350382 TGTGGATAGCCCTAAAACAATAATGA 58.650 34.615 0.00 0.00 35.38 2.57
386 399 3.300388 CTGAACTCTGTGGATAGCCCTA 58.700 50.000 0.00 0.00 35.38 3.53
429 494 4.816786 TGTTAACTAAGTTTTGACCGGC 57.183 40.909 0.00 0.00 0.00 6.13
432 497 6.474427 GGCAGTTTGTTAACTAAGTTTTGACC 59.526 38.462 7.22 2.00 42.67 4.02
456 892 5.345702 TGTAAACCAAGTTCGATATCTCGG 58.654 41.667 0.34 0.00 45.10 4.63
596 1051 4.142293 GCTGGATCCAGAAAGATTGTTTCC 60.142 45.833 40.29 17.05 46.30 3.13
666 1122 2.969443 ACGAACAGCAAAATCGAAGG 57.031 45.000 7.96 0.00 39.73 3.46
676 1132 1.495584 GCGACCTTGAACGAACAGCA 61.496 55.000 0.00 0.00 0.00 4.41
681 1137 3.430895 GTCTTATTGCGACCTTGAACGAA 59.569 43.478 0.00 0.00 0.00 3.85
772 1239 9.649167 AATTAGTTGGTAGTACAAGTGATACAC 57.351 33.333 2.06 0.00 35.70 2.90
961 1722 1.913762 AGCCCAACCTCTGTAGCGT 60.914 57.895 0.00 0.00 0.00 5.07
994 1756 5.292765 CAGTAAGACGATGAACATGGCTAT 58.707 41.667 0.00 0.00 0.00 2.97
1075 1843 4.263506 GCTATTATAGGGGATGCTGGTGTT 60.264 45.833 1.12 0.00 0.00 3.32
1159 1933 1.908299 CCTTGGGCTGGTTGGTTCC 60.908 63.158 0.00 0.00 0.00 3.62
1186 1960 0.324943 ATGGGGTCTTGGTCAGTTCG 59.675 55.000 0.00 0.00 0.00 3.95
1353 2127 2.897969 GGAGTTGTAGACAAGGTCCTCA 59.102 50.000 13.24 0.00 37.27 3.86
1439 2213 1.336887 CGTCGGTGAAGTTGGTGATCT 60.337 52.381 0.00 0.00 0.00 2.75
1569 2355 0.598680 CCATAGAGTACAGCAGCGGC 60.599 60.000 0.00 0.00 41.61 6.53
1578 2364 0.179111 TGCACTGCGCCATAGAGTAC 60.179 55.000 4.18 0.00 41.33 2.73
1701 2495 4.517453 GTGCTGTACCTGAAATTACACCAA 59.483 41.667 0.00 0.00 0.00 3.67
1893 2876 7.219484 TGGGAAAAATGCTCTTTAGAAGAAG 57.781 36.000 0.00 0.00 37.02 2.85
2056 3154 6.524586 GCATCGAGTTAAATGAAGTTTTGGAG 59.475 38.462 0.00 0.00 0.00 3.86
2205 3363 6.238211 GGGTGTTATGTCTTTCAGAATCATCG 60.238 42.308 0.00 0.00 29.85 3.84
2223 3381 7.363530 GCGGTCATTAGATCTATATGGGTGTTA 60.364 40.741 17.49 0.00 0.00 2.41
2224 3382 6.574465 GCGGTCATTAGATCTATATGGGTGTT 60.574 42.308 17.49 0.00 0.00 3.32
2225 3383 5.105310 GCGGTCATTAGATCTATATGGGTGT 60.105 44.000 17.49 0.00 0.00 4.16
2226 3384 5.105351 TGCGGTCATTAGATCTATATGGGTG 60.105 44.000 17.49 11.71 0.00 4.61
2227 3385 5.023452 TGCGGTCATTAGATCTATATGGGT 58.977 41.667 17.49 0.00 0.00 4.51
2228 3386 5.598416 TGCGGTCATTAGATCTATATGGG 57.402 43.478 17.49 11.81 0.00 4.00
2229 3387 6.313905 GGTTTGCGGTCATTAGATCTATATGG 59.686 42.308 17.49 8.70 0.00 2.74
2230 3388 6.873605 TGGTTTGCGGTCATTAGATCTATATG 59.126 38.462 2.58 10.16 0.00 1.78
2231 3389 7.004555 TGGTTTGCGGTCATTAGATCTATAT 57.995 36.000 2.58 0.00 0.00 0.86
2232 3390 6.413783 TGGTTTGCGGTCATTAGATCTATA 57.586 37.500 2.58 0.00 0.00 1.31
2233 3391 5.290493 TGGTTTGCGGTCATTAGATCTAT 57.710 39.130 2.58 0.00 0.00 1.98
2234 3392 4.746535 TGGTTTGCGGTCATTAGATCTA 57.253 40.909 0.00 0.00 0.00 1.98
2235 3393 3.627395 TGGTTTGCGGTCATTAGATCT 57.373 42.857 0.00 0.00 0.00 2.75
2236 3394 4.900635 ATTGGTTTGCGGTCATTAGATC 57.099 40.909 0.00 0.00 0.00 2.75
2237 3395 5.650543 GAAATTGGTTTGCGGTCATTAGAT 58.349 37.500 0.00 0.00 0.00 1.98
2238 3396 4.378978 CGAAATTGGTTTGCGGTCATTAGA 60.379 41.667 0.00 0.00 0.00 2.10
2239 3397 3.851403 CGAAATTGGTTTGCGGTCATTAG 59.149 43.478 0.00 0.00 0.00 1.73
2240 3398 3.502595 TCGAAATTGGTTTGCGGTCATTA 59.497 39.130 0.00 0.00 0.00 1.90
2241 3399 2.294791 TCGAAATTGGTTTGCGGTCATT 59.705 40.909 0.00 0.00 0.00 2.57
2242 3400 1.883275 TCGAAATTGGTTTGCGGTCAT 59.117 42.857 0.00 0.00 0.00 3.06
2243 3401 1.309950 TCGAAATTGGTTTGCGGTCA 58.690 45.000 0.00 0.00 0.00 4.02
2244 3402 2.095466 TCATCGAAATTGGTTTGCGGTC 60.095 45.455 0.00 0.00 0.00 4.79
2245 3403 1.883275 TCATCGAAATTGGTTTGCGGT 59.117 42.857 0.00 0.00 0.00 5.68
2246 3404 2.627863 TCATCGAAATTGGTTTGCGG 57.372 45.000 0.00 0.00 0.00 5.69
2247 3405 4.263677 CAGAATCATCGAAATTGGTTTGCG 59.736 41.667 0.00 0.00 0.00 4.85
2248 3406 5.401550 TCAGAATCATCGAAATTGGTTTGC 58.598 37.500 0.00 0.00 0.00 3.68
2249 3407 7.809331 TCTTTCAGAATCATCGAAATTGGTTTG 59.191 33.333 0.00 0.00 32.10 2.93
2250 3408 7.809806 GTCTTTCAGAATCATCGAAATTGGTTT 59.190 33.333 0.00 0.00 32.10 3.27
2251 3409 7.040478 TGTCTTTCAGAATCATCGAAATTGGTT 60.040 33.333 0.00 0.00 32.10 3.67
2252 3410 6.430925 TGTCTTTCAGAATCATCGAAATTGGT 59.569 34.615 0.00 0.00 32.10 3.67
2253 3411 6.845302 TGTCTTTCAGAATCATCGAAATTGG 58.155 36.000 0.00 0.00 32.10 3.16
2254 3412 9.992910 TTATGTCTTTCAGAATCATCGAAATTG 57.007 29.630 0.00 0.00 32.10 2.32
2266 3424 9.527157 TGGGTGAATTAATTATGTCTTTCAGAA 57.473 29.630 0.00 0.00 0.00 3.02
2267 3425 9.699410 ATGGGTGAATTAATTATGTCTTTCAGA 57.301 29.630 0.00 0.00 0.00 3.27
2533 3713 2.878406 ACGGATTCAACAGTTCAAGGTG 59.122 45.455 0.00 0.00 0.00 4.00
2635 3816 3.034635 ACTCAAGCTACCGAGATTGGAT 58.965 45.455 13.13 0.00 46.87 3.41
2639 3820 5.401531 TTTGTACTCAAGCTACCGAGATT 57.598 39.130 13.13 0.00 34.88 2.40
2757 4447 0.389426 CCTTGCCATGTTTGCAGCTC 60.389 55.000 0.00 0.00 40.35 4.09
2862 4553 7.939039 ACCTTGAAAGATTGAATCTGTTCACTA 59.061 33.333 21.34 13.20 43.72 2.74
2992 4743 7.719633 AGACAAATCAACCAATGTAACTACACT 59.280 33.333 0.00 0.00 39.30 3.55
3043 4797 5.371115 TGCCCTAAAACGAAAGATTTCAG 57.629 39.130 6.16 1.92 37.31 3.02
3263 5293 5.123027 CCTGAGAGCTCACTTTACCAAATTC 59.877 44.000 17.77 0.00 35.46 2.17
3265 5295 4.287067 TCCTGAGAGCTCACTTTACCAAAT 59.713 41.667 17.77 0.00 35.46 2.32
3468 5501 3.932710 GTGATCGATGCAAACTAGGTTCA 59.067 43.478 0.54 0.00 0.00 3.18
3488 5586 5.957798 TCCACTAGGTCGTACAAATTAGTG 58.042 41.667 13.51 13.51 38.32 2.74
4014 12615 4.332543 TGCAAATATAGAAGTCCTTGTGCG 59.667 41.667 0.00 0.00 0.00 5.34
4089 12690 5.876460 GGGATTCATTTCAATGTCCAAAAGG 59.124 40.000 10.02 0.00 34.77 3.11
4113 12714 5.875910 TGCAAGCCCAAAATCTGATATTTTG 59.124 36.000 13.65 13.65 44.32 2.44
4251 12854 5.243954 AGGCAGGGAAAACAAAACTTCTATC 59.756 40.000 0.00 0.00 0.00 2.08
4263 12869 2.224042 CCACTGAAAAGGCAGGGAAAAC 60.224 50.000 0.00 0.00 41.90 2.43
4272 12878 2.623416 GCCATATACCCACTGAAAAGGC 59.377 50.000 0.00 0.00 0.00 4.35
4773 19818 5.584551 TGATACTATCTGCCCTGTAGAGA 57.415 43.478 0.00 0.00 0.00 3.10
4907 19967 1.737838 TGTCTTCCGTTCATGCCATC 58.262 50.000 0.00 0.00 0.00 3.51
5042 20116 1.144969 TCTCTACGCAAAGGCAAACG 58.855 50.000 0.00 0.00 41.24 3.60
5047 20121 5.332707 CCTTTTATTTCTCTACGCAAAGGC 58.667 41.667 0.00 0.00 34.14 4.35
5054 20128 6.047231 CCTACCACCCTTTTATTTCTCTACG 58.953 44.000 0.00 0.00 0.00 3.51
5057 20131 4.540502 AGCCTACCACCCTTTTATTTCTCT 59.459 41.667 0.00 0.00 0.00 3.10
5058 20132 4.856509 AGCCTACCACCCTTTTATTTCTC 58.143 43.478 0.00 0.00 0.00 2.87
5088 20163 8.993404 TGATTATGTGGTTGGATGAATAATCA 57.007 30.769 10.36 10.36 41.32 2.57
5094 20176 4.402155 GGCTTGATTATGTGGTTGGATGAA 59.598 41.667 0.00 0.00 0.00 2.57
5095 20177 3.953612 GGCTTGATTATGTGGTTGGATGA 59.046 43.478 0.00 0.00 0.00 2.92
5096 20178 3.956199 AGGCTTGATTATGTGGTTGGATG 59.044 43.478 0.00 0.00 0.00 3.51
5097 20179 4.255510 AGGCTTGATTATGTGGTTGGAT 57.744 40.909 0.00 0.00 0.00 3.41
5098 20180 3.737559 AGGCTTGATTATGTGGTTGGA 57.262 42.857 0.00 0.00 0.00 3.53
5099 20181 4.021192 ACAAAGGCTTGATTATGTGGTTGG 60.021 41.667 0.00 0.00 36.33 3.77
5100 20182 5.138125 ACAAAGGCTTGATTATGTGGTTG 57.862 39.130 0.00 0.00 36.33 3.77
5101 20183 5.772672 TGTACAAAGGCTTGATTATGTGGTT 59.227 36.000 10.89 0.00 36.33 3.67
5102 20184 5.321102 TGTACAAAGGCTTGATTATGTGGT 58.679 37.500 10.89 0.00 36.33 4.16
5103 20185 5.647658 TCTGTACAAAGGCTTGATTATGTGG 59.352 40.000 10.89 3.19 36.33 4.17
5104 20186 6.741992 TCTGTACAAAGGCTTGATTATGTG 57.258 37.500 10.89 2.05 36.33 3.21
5105 20187 7.759489 TTTCTGTACAAAGGCTTGATTATGT 57.241 32.000 0.00 3.40 36.33 2.29
5106 20188 8.461222 TGATTTCTGTACAAAGGCTTGATTATG 58.539 33.333 0.00 0.00 36.33 1.90
5107 20189 8.579850 TGATTTCTGTACAAAGGCTTGATTAT 57.420 30.769 0.00 0.00 36.33 1.28
5108 20190 7.994425 TGATTTCTGTACAAAGGCTTGATTA 57.006 32.000 0.00 0.00 36.33 1.75
5109 20191 6.899393 TGATTTCTGTACAAAGGCTTGATT 57.101 33.333 0.00 0.00 36.33 2.57
5110 20192 8.579850 TTATGATTTCTGTACAAAGGCTTGAT 57.420 30.769 0.00 0.00 36.33 2.57
5111 20193 7.994425 TTATGATTTCTGTACAAAGGCTTGA 57.006 32.000 0.00 0.00 36.33 3.02
5112 20194 8.461222 TGATTATGATTTCTGTACAAAGGCTTG 58.539 33.333 0.00 0.00 38.61 4.01
5113 20195 8.579850 TGATTATGATTTCTGTACAAAGGCTT 57.420 30.769 0.00 0.00 0.00 4.35
5136 20218 9.806448 AAATATATAGGCCATGTGTGTTTATGA 57.194 29.630 5.01 0.00 0.00 2.15
5152 20234 8.510243 TTCAGTGCATATGCCAAATATATAGG 57.490 34.615 24.54 2.06 41.18 2.57
5187 20269 0.391927 TCGGGGATTTTACCACTGCG 60.392 55.000 0.00 0.00 0.00 5.18
5276 20421 0.877071 AGTGAATCAGCGGCACAAAG 59.123 50.000 1.45 0.00 35.08 2.77
5314 20464 4.726704 GTGTATGTGTGTGTCGAACAAAAC 59.273 41.667 0.00 0.00 41.57 2.43
5322 20472 3.366724 GGTATGTGTGTATGTGTGTGTCG 59.633 47.826 0.00 0.00 0.00 4.35
5324 20474 4.617253 AGGTATGTGTGTATGTGTGTGT 57.383 40.909 0.00 0.00 0.00 3.72
5325 20475 5.334802 CCAAAGGTATGTGTGTATGTGTGTG 60.335 44.000 0.00 0.00 0.00 3.82
5329 20479 5.000591 TGACCAAAGGTATGTGTGTATGTG 58.999 41.667 0.00 0.00 35.25 3.21
5331 20481 6.016693 TGTTTGACCAAAGGTATGTGTGTATG 60.017 38.462 0.00 0.00 35.25 2.39
5333 20483 5.437946 TGTTTGACCAAAGGTATGTGTGTA 58.562 37.500 0.00 0.00 35.25 2.90
5351 20501 4.202141 TGTCTTCCTTTCTTGCCATGTTTG 60.202 41.667 0.00 0.00 0.00 2.93
5419 20569 0.581529 CGGCGTCACGATATGCAAAT 59.418 50.000 0.00 0.00 35.47 2.32
5437 20587 2.565394 GGTGAGCGCGTACGATTCG 61.565 63.158 21.65 14.43 43.93 3.34
5444 20594 3.367743 AACCGAGGTGAGCGCGTA 61.368 61.111 8.43 0.00 0.00 4.42
5450 20602 3.600388 AGAAATTAGCAACCGAGGTGAG 58.400 45.455 0.00 0.00 0.00 3.51
5469 20621 2.085320 GAGCAGGAAGTCGTCACTAGA 58.915 52.381 0.00 0.00 30.14 2.43
5487 20643 4.862574 CACTTCACAATTCATTGGCATGAG 59.137 41.667 0.00 0.00 40.66 2.90
5489 20645 3.369756 GCACTTCACAATTCATTGGCATG 59.630 43.478 4.58 0.00 41.96 4.06
5490 20646 3.007074 TGCACTTCACAATTCATTGGCAT 59.993 39.130 4.58 0.00 41.96 4.40
5493 20649 4.247267 ACTGCACTTCACAATTCATTGG 57.753 40.909 4.58 0.00 41.96 3.16
5494 20650 5.761003 TGTACTGCACTTCACAATTCATTG 58.239 37.500 0.00 0.00 43.26 2.82
5495 20651 6.579666 ATGTACTGCACTTCACAATTCATT 57.420 33.333 0.00 0.00 0.00 2.57
5499 20656 6.389830 TGAAATGTACTGCACTTCACAATT 57.610 33.333 0.00 0.00 38.26 2.32
5552 20792 4.522789 AGGTTTGTTTGTAGGTAGGCATTG 59.477 41.667 0.00 0.00 0.00 2.82
5628 20896 0.949105 ACCGGTGATGTTCGTGCTTC 60.949 55.000 6.12 0.00 0.00 3.86
5634 20902 3.168271 CAGCACCGGTGATGTTCG 58.832 61.111 38.18 18.29 41.62 3.95
5642 20911 2.360350 CCATTCTGCAGCACCGGT 60.360 61.111 9.47 0.00 0.00 5.28
5720 20989 0.396811 ACCCGGGATTTCGATCCATC 59.603 55.000 32.02 0.00 42.49 3.51
5721 20990 0.843984 AACCCGGGATTTCGATCCAT 59.156 50.000 32.02 0.00 42.49 3.41
5722 20991 1.139455 GTAACCCGGGATTTCGATCCA 59.861 52.381 32.02 0.00 42.49 3.41
5723 20992 1.541889 GGTAACCCGGGATTTCGATCC 60.542 57.143 32.02 13.32 39.99 3.36
5724 20993 1.415289 AGGTAACCCGGGATTTCGATC 59.585 52.381 32.02 0.00 35.12 3.69
5725 20994 1.140252 CAGGTAACCCGGGATTTCGAT 59.860 52.381 32.02 0.00 35.12 3.59
5726 20995 0.538118 CAGGTAACCCGGGATTTCGA 59.462 55.000 32.02 0.00 35.12 3.71
5727 20996 0.251073 ACAGGTAACCCGGGATTTCG 59.749 55.000 32.02 13.25 35.12 3.46
5728 20997 1.279846 TGACAGGTAACCCGGGATTTC 59.720 52.381 32.02 15.07 35.12 2.17
5729 20998 1.364269 TGACAGGTAACCCGGGATTT 58.636 50.000 32.02 15.43 35.12 2.17
5730 20999 1.489230 GATGACAGGTAACCCGGGATT 59.511 52.381 32.02 20.02 35.12 3.01
5731 21000 1.129058 GATGACAGGTAACCCGGGAT 58.871 55.000 32.02 20.40 35.12 3.85
5732 21001 2.599216 GATGACAGGTAACCCGGGA 58.401 57.895 32.02 1.07 35.12 5.14


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

AutoCloner maintained by Alex Coulton.