Multiple sequence alignment - TraesCS7B01G017500

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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 TraesCS7B01G017500 chr7B 100.000 6826 0 0 1 6826 14995290 15002115 0.000000e+00 12606.0
1 TraesCS7B01G017500 chr7B 87.334 2337 227 36 873 3172 14068551 14066247 0.000000e+00 2612.0
2 TraesCS7B01G017500 chr7B 89.610 1694 152 17 795 2472 13117204 13115519 0.000000e+00 2132.0
3 TraesCS7B01G017500 chr7B 88.037 1630 174 18 807 2423 13879724 13878103 0.000000e+00 1910.0
4 TraesCS7B01G017500 chr7B 89.575 777 70 5 4 769 12538244 12537468 0.000000e+00 976.0
5 TraesCS7B01G017500 chr7B 88.500 800 82 6 4 793 13118097 13117298 0.000000e+00 959.0
6 TraesCS7B01G017500 chr7B 84.929 982 110 24 3322 4275 14065966 14064995 0.000000e+00 959.0
7 TraesCS7B01G017500 chr7B 82.635 979 121 29 3337 4275 12534414 12533445 0.000000e+00 821.0
8 TraesCS7B01G017500 chr7B 86.738 656 73 9 5226 5875 13873463 13872816 0.000000e+00 717.0
9 TraesCS7B01G017500 chr7B 87.963 540 54 7 2458 2992 13115472 13114939 1.620000e-175 627.0
10 TraesCS7B01G017500 chr7B 84.848 627 75 16 5216 5837 13859548 13858937 1.260000e-171 614.0
11 TraesCS7B01G017500 chr7B 85.487 503 69 3 3774 4275 13818464 13817965 7.850000e-144 521.0
12 TraesCS7B01G017500 chr7B 79.416 753 102 32 2503 3221 13805929 13805196 3.700000e-132 483.0
13 TraesCS7B01G017500 chr7B 75.784 574 93 29 5580 6127 13812991 13812438 1.470000e-61 248.0
14 TraesCS7B01G017500 chr7D 95.836 3650 116 10 3170 6810 72171691 72175313 0.000000e+00 5866.0
15 TraesCS7B01G017500 chr7D 94.828 2494 107 6 855 3346 72169215 72171688 0.000000e+00 3871.0
16 TraesCS7B01G017500 chr7D 84.650 2469 300 51 803 3221 71319069 71316630 0.000000e+00 2386.0
17 TraesCS7B01G017500 chr7D 87.968 1629 175 18 807 2423 71344894 71346513 0.000000e+00 1903.0
18 TraesCS7B01G017500 chr7D 86.465 1655 196 22 793 2436 71216268 71214631 0.000000e+00 1790.0
19 TraesCS7B01G017500 chr7D 92.848 797 46 4 1 787 72167956 72168751 0.000000e+00 1146.0
20 TraesCS7B01G017500 chr7D 89.826 806 69 7 1 793 70747786 70748591 0.000000e+00 1022.0
21 TraesCS7B01G017500 chr7D 90.347 777 65 6 4 770 69942618 69941842 0.000000e+00 1011.0
22 TraesCS7B01G017500 chr7D 88.462 806 79 9 1 793 70231043 70231847 0.000000e+00 961.0
23 TraesCS7B01G017500 chr7D 88.375 800 81 7 4 793 71550292 71549495 0.000000e+00 952.0
24 TraesCS7B01G017500 chr7D 87.702 805 87 5 1 793 71344029 71344833 0.000000e+00 928.0
25 TraesCS7B01G017500 chr7D 87.422 803 91 5 1 793 71354410 71355212 0.000000e+00 915.0
26 TraesCS7B01G017500 chr7D 87.579 789 88 5 4 782 71338913 71338125 0.000000e+00 905.0
27 TraesCS7B01G017500 chr7D 83.164 986 120 29 3327 4275 70751621 70752597 0.000000e+00 859.0
28 TraesCS7B01G017500 chr7D 83.078 981 131 19 3310 4260 71316532 71315557 0.000000e+00 859.0
29 TraesCS7B01G017500 chr7D 87.722 733 74 7 3456 4172 71546055 71545323 0.000000e+00 841.0
30 TraesCS7B01G017500 chr7D 82.353 986 128 25 3327 4275 69938854 69937878 0.000000e+00 815.0
31 TraesCS7B01G017500 chr7D 80.758 1055 161 21 2134 3172 71361791 71362819 0.000000e+00 785.0
32 TraesCS7B01G017500 chr7D 85.866 658 80 10 5223 5875 71349014 71349663 0.000000e+00 688.0
33 TraesCS7B01G017500 chr7D 85.762 604 71 10 5219 5818 71544800 71544208 5.810000e-175 625.0
34 TraesCS7B01G017500 chr7D 85.859 198 22 5 5653 5845 71313760 71313564 8.970000e-49 206.0
35 TraesCS7B01G017500 chr7D 100.000 28 0 0 4311 4338 60602991 60602964 1.200000e-02 52.8
36 TraesCS7B01G017500 chr7A 95.976 3131 107 8 1 3119 77158442 77161565 0.000000e+00 5066.0
37 TraesCS7B01G017500 chr7A 94.751 1810 84 7 4455 6261 77163053 77164854 0.000000e+00 2806.0
38 TraesCS7B01G017500 chr7A 96.560 1279 36 7 3196 4470 77161764 77163038 0.000000e+00 2111.0
39 TraesCS7B01G017500 chr7A 89.169 794 73 9 4 785 76516829 76516037 0.000000e+00 977.0
40 TraesCS7B01G017500 chr7A 95.722 561 17 1 6257 6810 77166681 77167241 0.000000e+00 896.0
41 TraesCS7B01G017500 chr7A 84.183 961 102 26 3307 4231 76982539 76981593 0.000000e+00 887.0
42 TraesCS7B01G017500 chr7A 83.985 793 100 15 3417 4184 77024698 77023908 0.000000e+00 736.0
43 TraesCS7B01G017500 chrUn 86.603 2187 261 25 803 2969 84435519 84437693 0.000000e+00 2386.0
44 TraesCS7B01G017500 chrUn 85.645 1644 186 30 794 2423 84286715 84285108 0.000000e+00 1683.0
45 TraesCS7B01G017500 chrUn 85.645 1644 186 30 794 2423 226940040 226938433 0.000000e+00 1683.0
46 TraesCS7B01G017500 chrUn 88.500 800 80 7 4 793 82530206 82529409 0.000000e+00 957.0
47 TraesCS7B01G017500 chrUn 87.625 800 89 5 4 793 82519713 82518914 0.000000e+00 920.0
48 TraesCS7B01G017500 chrUn 85.586 888 99 18 3307 4172 82526399 82525519 0.000000e+00 904.0
49 TraesCS7B01G017500 chrUn 85.522 891 100 16 3307 4172 84246851 84245965 0.000000e+00 904.0
50 TraesCS7B01G017500 chrUn 83.300 1006 125 22 3304 4270 82516097 82515096 0.000000e+00 887.0
51 TraesCS7B01G017500 chrUn 83.898 944 105 19 3307 4217 84284342 84283413 0.000000e+00 857.0
52 TraesCS7B01G017500 chrUn 85.540 657 75 10 5230 5877 84245432 84244787 0.000000e+00 669.0
53 TraesCS7B01G017500 chrUn 84.848 627 65 22 5216 5837 82514516 82513915 7.570000e-169 604.0
54 TraesCS7B01G017500 chrUn 82.271 643 74 21 5218 5855 329448565 329449172 2.820000e-143 520.0
55 TraesCS7B01G017500 chrUn 83.163 196 31 2 5652 5845 84440642 84440837 1.960000e-40 178.0
56 TraesCS7B01G017500 chrUn 79.605 152 23 7 5963 6107 329449194 329449344 1.210000e-17 102.0
57 TraesCS7B01G017500 chr2B 87.791 1630 178 18 807 2423 723403652 723402031 0.000000e+00 1888.0
58 TraesCS7B01G017500 chr2B 87.125 800 93 5 4 793 723396177 723395378 0.000000e+00 898.0
59 TraesCS7B01G017500 chr2B 86.533 646 76 8 5226 5867 723399397 723398759 0.000000e+00 701.0
60 TraesCS7B01G017500 chr1A 81.180 983 139 21 3319 4272 21773030 21772065 0.000000e+00 749.0
61 TraesCS7B01G017500 chr1A 96.774 31 1 0 6179 6209 394593071 394593101 1.200000e-02 52.8
62 TraesCS7B01G017500 chr5D 86.408 103 11 3 4285 4385 160067099 160067200 7.240000e-20 110.0
63 TraesCS7B01G017500 chr5A 86.408 103 11 3 4285 4385 260334577 260334476 7.240000e-20 110.0
64 TraesCS7B01G017500 chr3D 86.567 67 7 1 4311 4377 606304169 606304233 9.500000e-09 73.1
65 TraesCS7B01G017500 chr1D 95.122 41 1 1 4305 4344 480572417 480572377 5.720000e-06 63.9


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 TraesCS7B01G017500 chr7B 14995290 15002115 6825 False 12606.000000 12606 100.000000 1 6826 1 chr7B.!!$F1 6825
1 TraesCS7B01G017500 chr7B 13878103 13879724 1621 True 1910.000000 1910 88.037000 807 2423 1 chr7B.!!$R6 1616
2 TraesCS7B01G017500 chr7B 14064995 14068551 3556 True 1785.500000 2612 86.131500 873 4275 2 chr7B.!!$R9 3402
3 TraesCS7B01G017500 chr7B 13114939 13118097 3158 True 1239.333333 2132 88.691000 4 2992 3 chr7B.!!$R8 2988
4 TraesCS7B01G017500 chr7B 12533445 12538244 4799 True 898.500000 976 86.105000 4 4275 2 chr7B.!!$R7 4271
5 TraesCS7B01G017500 chr7B 13872816 13873463 647 True 717.000000 717 86.738000 5226 5875 1 chr7B.!!$R5 649
6 TraesCS7B01G017500 chr7B 13858937 13859548 611 True 614.000000 614 84.848000 5216 5837 1 chr7B.!!$R4 621
7 TraesCS7B01G017500 chr7B 13805196 13805929 733 True 483.000000 483 79.416000 2503 3221 1 chr7B.!!$R1 718
8 TraesCS7B01G017500 chr7B 13812438 13812991 553 True 248.000000 248 75.784000 5580 6127 1 chr7B.!!$R2 547
9 TraesCS7B01G017500 chr7D 72167956 72175313 7357 False 3627.666667 5866 94.504000 1 6810 3 chr7D.!!$F6 6809
10 TraesCS7B01G017500 chr7D 71214631 71216268 1637 True 1790.000000 1790 86.465000 793 2436 1 chr7D.!!$R2 1643
11 TraesCS7B01G017500 chr7D 71344029 71349663 5634 False 1173.000000 1903 87.178667 1 5875 3 chr7D.!!$F5 5874
12 TraesCS7B01G017500 chr7D 71313564 71319069 5505 True 1150.333333 2386 84.529000 803 5845 3 chr7D.!!$R5 5042
13 TraesCS7B01G017500 chr7D 70231043 70231847 804 False 961.000000 961 88.462000 1 793 1 chr7D.!!$F1 792
14 TraesCS7B01G017500 chr7D 70747786 70752597 4811 False 940.500000 1022 86.495000 1 4275 2 chr7D.!!$F4 4274
15 TraesCS7B01G017500 chr7D 71354410 71355212 802 False 915.000000 915 87.422000 1 793 1 chr7D.!!$F2 792
16 TraesCS7B01G017500 chr7D 69937878 69942618 4740 True 913.000000 1011 86.350000 4 4275 2 chr7D.!!$R4 4271
17 TraesCS7B01G017500 chr7D 71338125 71338913 788 True 905.000000 905 87.579000 4 782 1 chr7D.!!$R3 778
18 TraesCS7B01G017500 chr7D 71544208 71550292 6084 True 806.000000 952 87.286333 4 5818 3 chr7D.!!$R6 5814
19 TraesCS7B01G017500 chr7D 71361791 71362819 1028 False 785.000000 785 80.758000 2134 3172 1 chr7D.!!$F3 1038
20 TraesCS7B01G017500 chr7A 77158442 77167241 8799 False 2719.750000 5066 95.752250 1 6810 4 chr7A.!!$F1 6809
21 TraesCS7B01G017500 chr7A 76516037 76516829 792 True 977.000000 977 89.169000 4 785 1 chr7A.!!$R1 781
22 TraesCS7B01G017500 chr7A 76981593 76982539 946 True 887.000000 887 84.183000 3307 4231 1 chr7A.!!$R2 924
23 TraesCS7B01G017500 chr7A 77023908 77024698 790 True 736.000000 736 83.985000 3417 4184 1 chr7A.!!$R3 767
24 TraesCS7B01G017500 chrUn 226938433 226940040 1607 True 1683.000000 1683 85.645000 794 2423 1 chrUn.!!$R1 1629
25 TraesCS7B01G017500 chrUn 84435519 84440837 5318 False 1282.000000 2386 84.883000 803 5845 2 chrUn.!!$F1 5042
26 TraesCS7B01G017500 chrUn 84283413 84286715 3302 True 1270.000000 1683 84.771500 794 4217 2 chrUn.!!$R5 3423
27 TraesCS7B01G017500 chrUn 82525519 82530206 4687 True 930.500000 957 87.043000 4 4172 2 chrUn.!!$R3 4168
28 TraesCS7B01G017500 chrUn 82513915 82519713 5798 True 803.666667 920 85.257667 4 5837 3 chrUn.!!$R2 5833
29 TraesCS7B01G017500 chrUn 84244787 84246851 2064 True 786.500000 904 85.531000 3307 5877 2 chrUn.!!$R4 2570
30 TraesCS7B01G017500 chrUn 329448565 329449344 779 False 311.000000 520 80.938000 5218 6107 2 chrUn.!!$F2 889
31 TraesCS7B01G017500 chr2B 723395378 723403652 8274 True 1162.333333 1888 87.149667 4 5867 3 chr2B.!!$R1 5863
32 TraesCS7B01G017500 chr1A 21772065 21773030 965 True 749.000000 749 81.180000 3319 4272 1 chr1A.!!$R1 953

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
757 768 2.297701 GTCCTCAAAACTGAAGGCACA 58.702 47.619 0.00 0.00 0.00 4.57 F
1008 2070 1.470051 TTGGATCGTCGATGGACAGA 58.530 50.000 13.54 6.75 43.61 3.41 F
2635 4513 2.284190 GCTCTGGTGAATCACTTAGGC 58.716 52.381 13.53 12.43 34.40 3.93 F
2729 4607 1.511850 TGTCGACAAGAATGCCAGTG 58.488 50.000 17.62 0.00 0.00 3.66 F
3325 6629 4.103153 TCCAGGCAGAATAGGGTGAATAAG 59.897 45.833 0.00 0.00 0.00 1.73 F
4705 8251 2.840038 ACATGAGTGATTGCCTGGTAGA 59.160 45.455 0.00 0.00 0.00 2.59 F
5366 9832 0.798776 ACTTTTGAGAAGATGCCGCG 59.201 50.000 0.00 0.00 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2660 4538 0.702316 TCTTCCCCAAAGGCCCTTAC 59.298 55.000 0.00 0.00 35.54 2.34 R
2729 4607 4.803088 TGCGGCAAAATTACAGAAATATGC 59.197 37.500 0.00 0.00 38.71 3.14 R
4473 7924 3.879295 CTCCGCCCCATAATAATATGCAG 59.121 47.826 0.00 0.00 38.06 4.41 R
4695 8241 0.035317 CTGCACACTTCTACCAGGCA 59.965 55.000 0.00 0.00 0.00 4.75 R
5189 9654 0.042581 TGTCCATAGGCAGGTCTGGA 59.957 55.000 0.00 0.00 35.46 3.86 R
5720 10201 0.679002 TCTCCATGAGCTTTGCAGGC 60.679 55.000 0.00 5.73 0.00 4.85 R
6466 13708 3.302480 GGATGTGCATTAATCGTCGACAC 60.302 47.826 17.16 3.19 0.00 3.67 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
44 45 2.951101 GCTTTGCATTGCCCTGGCT 61.951 57.895 9.97 0.00 42.51 4.75
75 76 3.049674 CGGTCGGTGCTGCAATGT 61.050 61.111 2.77 0.00 0.00 2.71
233 234 5.356882 TGAAGGTCTTGAAACTTTATGCG 57.643 39.130 0.00 0.00 0.00 4.73
410 411 6.715280 TCTGAAAATTCCTCTTGATGCTAGT 58.285 36.000 0.00 0.00 0.00 2.57
488 489 2.747446 ACCCGATGTAATTGCAGTTGTC 59.253 45.455 4.47 0.00 0.00 3.18
559 560 3.437049 CCTGAGCTAAACAGGCAAGTTAC 59.563 47.826 6.99 0.00 46.30 2.50
590 591 8.489676 AATATTATGTTGGCATTGATTACCCA 57.510 30.769 0.00 0.00 36.58 4.51
757 768 2.297701 GTCCTCAAAACTGAAGGCACA 58.702 47.619 0.00 0.00 0.00 4.57
825 1879 6.485171 AGTTGTTATGAGAATTAGGCTTGGT 58.515 36.000 0.00 0.00 0.00 3.67
1008 2070 1.470051 TTGGATCGTCGATGGACAGA 58.530 50.000 13.54 6.75 43.61 3.41
1164 2226 2.350192 TCGTGCACTATACCAAAATGCG 59.650 45.455 16.19 0.00 39.18 4.73
1252 2314 7.876582 TCAATGTAAGGATCATATTCAGCAGAG 59.123 37.037 0.00 0.00 0.00 3.35
1526 2612 7.104264 GCGATAAATTTTTGCAGTTAATGTCG 58.896 34.615 0.00 2.19 0.00 4.35
1646 2732 8.177663 GGTGCATCGGATCTTAATAACAATATG 58.822 37.037 0.00 0.00 0.00 1.78
1809 2907 3.484229 GCCTTATATGCTTTATCTGCGCG 60.484 47.826 0.00 0.00 0.00 6.86
2054 3152 5.144100 TCCTTATTTTCCCAGTTGCTCAAA 58.856 37.500 0.00 0.00 0.00 2.69
2058 3156 5.549742 ATTTTCCCAGTTGCTCAAATCAA 57.450 34.783 0.00 0.00 0.00 2.57
2295 3393 2.629051 GTGTTTAGCCTTGGCGATACT 58.371 47.619 13.86 0.00 0.00 2.12
2302 3400 7.553402 TGTTTAGCCTTGGCGATACTTTAAATA 59.447 33.333 13.86 5.31 0.00 1.40
2403 3501 7.781056 CAATTAGGTTGCAGGTAATTGGTATT 58.219 34.615 19.82 0.00 39.15 1.89
2438 4213 6.690194 ATGGCTAATTCTCATTTCTGTCAC 57.310 37.500 0.00 0.00 0.00 3.67
2489 4347 2.489329 TCTGCTGCTATTTTTGTCTGGC 59.511 45.455 0.00 0.00 0.00 4.85
2635 4513 2.284190 GCTCTGGTGAATCACTTAGGC 58.716 52.381 13.53 12.43 34.40 3.93
2660 4538 4.336889 TCGATTTCAGGGGCTATAACAG 57.663 45.455 0.00 0.00 0.00 3.16
2729 4607 1.511850 TGTCGACAAGAATGCCAGTG 58.488 50.000 17.62 0.00 0.00 3.66
3107 5124 7.434897 ACTGTTACTTTTGTTATGTGCATGTTG 59.565 33.333 0.00 0.00 0.00 3.33
3315 6483 5.305644 AGGTAGTAATGTCCAGGCAGAATAG 59.694 44.000 0.00 0.00 0.00 1.73
3325 6629 4.103153 TCCAGGCAGAATAGGGTGAATAAG 59.897 45.833 0.00 0.00 0.00 1.73
3930 7319 5.950758 AGACAACGTTAATTGGTGCATTA 57.049 34.783 0.00 0.00 33.63 1.90
4043 7432 5.103558 TGGGTATCATTCCACAAGATCCAAT 60.104 40.000 0.00 0.00 0.00 3.16
4160 7556 6.921307 ACGTTGATTTTTCTCATTTTACCCAC 59.079 34.615 0.00 0.00 0.00 4.61
4473 7924 5.122396 AGCTTGACTTTCACGAATACCAATC 59.878 40.000 0.00 0.00 0.00 2.67
4478 7929 4.943705 ACTTTCACGAATACCAATCTGCAT 59.056 37.500 0.00 0.00 0.00 3.96
4705 8251 2.840038 ACATGAGTGATTGCCTGGTAGA 59.160 45.455 0.00 0.00 0.00 2.59
4986 9399 4.338379 AACAGAAAACTCCGCTCTAGTT 57.662 40.909 0.00 0.00 38.82 2.24
5170 9630 8.159344 TGTTCAATGTGTATGTGTTGAATGTA 57.841 30.769 3.15 0.00 41.11 2.29
5171 9631 8.624776 TGTTCAATGTGTATGTGTTGAATGTAA 58.375 29.630 3.15 0.00 41.11 2.41
5177 9642 8.389779 TGTGTATGTGTTGAATGTAATGTCTT 57.610 30.769 0.00 0.00 0.00 3.01
5189 9654 8.511321 TGAATGTAATGTCTTTAGAAATTGCGT 58.489 29.630 5.58 3.23 37.23 5.24
5224 9689 7.255801 GCCTATGGACAGAGCTATATATCCTTC 60.256 44.444 6.93 0.00 0.00 3.46
5366 9832 0.798776 ACTTTTGAGAAGATGCCGCG 59.201 50.000 0.00 0.00 0.00 6.46
5720 10201 4.037446 GGGAGAGTAGCAGAGTATGACAAG 59.963 50.000 0.00 0.00 0.00 3.16
5774 10255 0.756294 TTCGTGAGCTGGTCAAGGAA 59.244 50.000 19.68 17.71 36.74 3.36
5903 10385 2.415168 CGCTTTCCAAAAGAGATACGCA 59.585 45.455 3.68 0.00 0.00 5.24
5972 10473 7.390718 AGGAAAAACAGTACCATCTGTATTGTC 59.609 37.037 0.00 2.96 46.21 3.18
5976 10477 5.978814 ACAGTACCATCTGTATTGTCTTCC 58.021 41.667 0.00 0.00 44.38 3.46
6038 11093 4.758674 GCAATACATGGTGAGCTGTCATAT 59.241 41.667 0.00 0.00 34.36 1.78
6142 11203 1.511768 GACCCTGCTGACCGTACTC 59.488 63.158 0.00 0.00 0.00 2.59
6378 13620 5.411977 CCAAGATATCTGAGAATGTCATGCC 59.588 44.000 5.86 0.00 33.51 4.40
6397 13639 3.244422 TGCCTCCACACACTAAAGTAAGG 60.244 47.826 0.00 0.00 0.00 2.69
6403 13645 4.443739 CCACACACTAAAGTAAGGACCACA 60.444 45.833 0.00 0.00 0.00 4.17
6443 13685 6.214615 TCAGGTGGATAACTTACAAGGAATCA 59.785 38.462 7.62 0.00 0.00 2.57
6461 13703 6.927381 AGGAATCAGAAAATCTTTTGCTGTTG 59.073 34.615 7.64 0.00 32.36 3.33
6466 13708 8.188531 TCAGAAAATCTTTTGCTGTTGAAAAG 57.811 30.769 7.64 0.00 40.38 2.27
6471 13713 4.411327 TCTTTTGCTGTTGAAAAGTGTCG 58.589 39.130 0.00 0.00 40.08 4.35
6482 13724 4.953269 TGAAAAGTGTCGACGATTAATGC 58.047 39.130 11.62 0.00 0.00 3.56
6486 13728 3.521560 AGTGTCGACGATTAATGCACAT 58.478 40.909 11.62 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.166870 ACCGACCGCATTGTACAGAATA 59.833 45.455 0.00 0.00 0.00 1.75
75 76 5.703978 ATGATGACAACCAATGACGAAAA 57.296 34.783 0.00 0.00 0.00 2.29
559 560 9.467258 AATCAATGCCAACATAATATTTCTTCG 57.533 29.630 0.00 0.00 34.62 3.79
788 1083 6.690957 TCTCATAACAACTTTGCAAACTTTCG 59.309 34.615 8.05 0.37 0.00 3.46
1008 2070 5.290493 TCAGTGTGTTGTGGTATCTTTCT 57.710 39.130 0.00 0.00 0.00 2.52
1164 2226 7.243604 AGGATCATCAAGAAGATAGATGTCC 57.756 40.000 0.57 0.57 39.96 4.02
1252 2314 7.915397 CACAACCAAATAGTAATACAATCTGCC 59.085 37.037 0.00 0.00 0.00 4.85
1506 2592 6.368516 CCATCCGACATTAACTGCAAAAATTT 59.631 34.615 0.00 0.00 0.00 1.82
1508 2594 5.184864 TCCATCCGACATTAACTGCAAAAAT 59.815 36.000 0.00 0.00 0.00 1.82
1526 2612 3.323403 CAGACTGGATAACCTCTCCATCC 59.677 52.174 0.00 0.00 41.83 3.51
1646 2732 2.127708 TCCTTAGATCTTTGAGGGGGC 58.872 52.381 15.49 0.00 0.00 5.80
1809 2907 5.707764 AGAAATACAGGAAGCCTTTGTTCTC 59.292 40.000 0.00 0.00 0.00 2.87
2054 3152 1.614996 TTGGTGCACGGAACATTGAT 58.385 45.000 11.45 0.00 0.00 2.57
2058 3156 0.881118 GACATTGGTGCACGGAACAT 59.119 50.000 11.45 0.00 0.00 2.71
2228 3326 7.226325 GGTCAATGATACTCAAATCTGAAGAGG 59.774 40.741 9.09 0.00 33.76 3.69
2302 3400 6.735704 ACCAATACCCCTAGATTGCTATATGT 59.264 38.462 0.00 0.00 32.69 2.29
2489 4347 3.498397 ACAAAACTGTAGGCTCATTCACG 59.502 43.478 0.00 0.00 0.00 4.35
2635 4513 2.526304 TAGCCCCTGAAATCGATTCG 57.474 50.000 11.83 0.00 41.18 3.34
2660 4538 0.702316 TCTTCCCCAAAGGCCCTTAC 59.298 55.000 0.00 0.00 35.54 2.34
2729 4607 4.803088 TGCGGCAAAATTACAGAAATATGC 59.197 37.500 0.00 0.00 38.71 3.14
3272 6401 7.328737 ACTACCTCAATTAGTAAACGCAAGAT 58.671 34.615 0.00 0.00 43.62 2.40
3325 6629 5.291971 AGTTTGAGAAATGCATGGTGTTTC 58.708 37.500 0.00 0.06 33.24 2.78
3930 7319 5.063204 TCATCAGGTTCAACAAGACGAAAT 58.937 37.500 0.00 0.00 0.00 2.17
4379 7799 9.874205 AATAAATTTCGTGATGAATCAAATGGT 57.126 25.926 0.00 0.00 38.75 3.55
4473 7924 3.879295 CTCCGCCCCATAATAATATGCAG 59.121 47.826 0.00 0.00 38.06 4.41
4478 7929 4.164981 ACTCACTCCGCCCCATAATAATA 58.835 43.478 0.00 0.00 0.00 0.98
4695 8241 0.035317 CTGCACACTTCTACCAGGCA 59.965 55.000 0.00 0.00 0.00 4.75
4830 8664 2.665165 TGACATTTGCCAAGAACCTGT 58.335 42.857 0.00 0.00 0.00 4.00
4986 9399 9.527157 TTCACACCTATTTGAATTTCTGGAATA 57.473 29.630 0.00 0.66 0.00 1.75
5100 9536 4.153475 CCCGTTGGTGTATTTGAAGTACTG 59.847 45.833 0.00 0.00 0.00 2.74
5170 9630 5.705441 TCTGGACGCAATTTCTAAAGACATT 59.295 36.000 0.00 0.00 0.00 2.71
5171 9631 5.122396 GTCTGGACGCAATTTCTAAAGACAT 59.878 40.000 0.00 0.00 33.41 3.06
5177 9642 3.334691 CAGGTCTGGACGCAATTTCTAA 58.665 45.455 0.00 0.00 0.00 2.10
5189 9654 0.042581 TGTCCATAGGCAGGTCTGGA 59.957 55.000 0.00 0.00 35.46 3.86
5224 9689 1.179152 TCCAAACATCATGCTGGCAG 58.821 50.000 10.94 10.94 0.00 4.85
5366 9832 4.923871 TGTCGCTTCATCAAGAACTAAGAC 59.076 41.667 0.00 0.00 31.61 3.01
5682 10157 1.081892 CTCCCTGAAGTGTTCATGCG 58.918 55.000 0.00 0.00 39.30 4.73
5720 10201 0.679002 TCTCCATGAGCTTTGCAGGC 60.679 55.000 0.00 5.73 0.00 4.85
5774 10255 4.391830 GTGTTTGATGTGTGTGACCGATAT 59.608 41.667 0.00 0.00 0.00 1.63
5903 10385 5.848921 ACTCCTCCAAGGAATATAGCTTCAT 59.151 40.000 0.00 0.00 45.28 2.57
6074 11135 4.532126 TCTGACTTCTGGAGCAAGGAAATA 59.468 41.667 0.00 0.00 0.00 1.40
6142 11203 7.405175 TGAGCTCTCATTTAGCCTTGCTAATG 61.405 42.308 16.19 9.56 41.30 1.90
6356 13598 6.436738 AGGCATGACATTCTCAGATATCTT 57.563 37.500 0.00 0.00 30.20 2.40
6378 13620 4.039973 TGGTCCTTACTTTAGTGTGTGGAG 59.960 45.833 0.00 0.00 0.00 3.86
6397 13639 6.114187 TGACTATTGGATCCATATGTGGTC 57.886 41.667 17.06 17.90 46.16 4.02
6403 13645 5.415065 TCCACCTGACTATTGGATCCATAT 58.585 41.667 17.06 14.02 34.35 1.78
6443 13685 7.603784 ACACTTTTCAACAGCAAAAGATTTTCT 59.396 29.630 11.83 0.00 41.52 2.52
6461 13703 4.781528 GTGCATTAATCGTCGACACTTTTC 59.218 41.667 17.16 0.00 0.00 2.29
6466 13708 3.302480 GGATGTGCATTAATCGTCGACAC 60.302 47.826 17.16 3.19 0.00 3.67
6471 13713 4.732285 AATCGGATGTGCATTAATCGTC 57.268 40.909 0.00 0.00 0.00 4.20
6482 13724 7.603784 TCCATGTAGATCATAAAATCGGATGTG 59.396 37.037 0.00 0.00 34.67 3.21
6486 13728 7.303182 ACTCCATGTAGATCATAAAATCGGA 57.697 36.000 0.00 0.00 34.67 4.55


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

AutoCloner maintained by Alex Coulton.