Multiple sequence alignment - TraesCS2B01G514500

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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 TraesCS2B01G514500 chr2B 100.000 3299 0 0 1 3299 709427312 709424014 0.000000e+00 6093.0
1 TraesCS2B01G514500 chr2B 98.276 116 2 0 2405 2520 89498950 89499065 1.550000e-48 204.0
2 TraesCS2B01G514500 chr2B 93.443 122 8 0 2405 2526 142446640 142446761 7.270000e-42 182.0
3 TraesCS2B01G514500 chr6D 93.373 1660 62 11 745 2394 8967212 8968833 0.000000e+00 2412.0
4 TraesCS2B01G514500 chr6D 90.141 1704 128 12 616 2311 8553300 8551629 0.000000e+00 2180.0
5 TraesCS2B01G514500 chr6D 97.311 781 18 2 2519 3299 8968849 8969626 0.000000e+00 1323.0
6 TraesCS2B01G514500 chr6D 92.513 748 43 6 4 741 8923250 8923994 0.000000e+00 1059.0
7 TraesCS2B01G514500 chr6D 80.596 1242 229 10 1120 2355 8659844 8658609 0.000000e+00 948.0
8 TraesCS2B01G514500 chr6D 94.167 120 7 0 2405 2524 36114517 36114636 2.020000e-42 183.0
9 TraesCS2B01G514500 chr6D 93.443 122 7 1 2405 2525 108860650 108860771 2.620000e-41 180.0
10 TraesCS2B01G514500 chr6D 93.443 122 7 1 2405 2525 302751876 302751997 2.620000e-41 180.0
11 TraesCS2B01G514500 chr6A 94.888 1389 45 5 1022 2394 9473004 9474382 0.000000e+00 2148.0
12 TraesCS2B01G514500 chr6A 88.846 1031 72 13 4 1019 9469516 9470518 0.000000e+00 1227.0
13 TraesCS2B01G514500 chr6A 99.482 193 1 0 2519 2711 9474398 9474590 5.240000e-93 351.0
14 TraesCS2B01G514500 chr6A 84.733 262 33 4 2758 3013 7989365 7989625 4.220000e-64 255.0
15 TraesCS2B01G514500 chr6B 85.306 1191 161 14 1121 2305 52981067 52979885 0.000000e+00 1218.0
16 TraesCS2B01G514500 chr6B 84.859 1202 169 12 1120 2316 16433126 16434319 0.000000e+00 1199.0
17 TraesCS2B01G514500 chr6B 84.818 1100 164 1 1209 2305 53062443 53061344 0.000000e+00 1103.0
18 TraesCS2B01G514500 chr6B 91.700 747 50 6 4 741 15377042 15376299 0.000000e+00 1026.0
19 TraesCS2B01G514500 chr6B 94.737 57 2 1 2829 2884 14547673 14547617 1.630000e-13 87.9
20 TraesCS2B01G514500 chr5D 81.265 1281 219 19 1120 2387 524577505 524578777 0.000000e+00 1016.0
21 TraesCS2B01G514500 chr5D 85.388 219 26 4 2808 3022 524579815 524580031 4.280000e-54 222.0
22 TraesCS2B01G514500 chr5A 81.109 1281 221 19 1120 2387 650824531 650825803 0.000000e+00 1005.0
23 TraesCS2B01G514500 chr5A 88.172 186 20 2 2525 2709 650825828 650826012 1.540000e-53 220.0
24 TraesCS2B01G514500 chr3A 91.874 443 34 2 79 520 7203908 7204349 4.680000e-173 617.0
25 TraesCS2B01G514500 chr1D 90.541 444 39 3 79 520 113599498 113599940 4.740000e-163 584.0
26 TraesCS2B01G514500 chr3B 90.200 449 36 6 79 526 4198909 4198468 2.210000e-161 579.0
27 TraesCS2B01G514500 chr3B 89.532 449 39 5 79 526 5055323 5054882 2.220000e-156 562.0
28 TraesCS2B01G514500 chrUn 89.616 443 40 6 79 520 222087748 222087311 2.880000e-155 558.0
29 TraesCS2B01G514500 chr7A 89.318 440 42 4 82 520 26168609 26168174 6.220000e-152 547.0
30 TraesCS2B01G514500 chr7B 92.000 125 10 0 2396 2520 567885454 567885578 3.380000e-40 176.0
31 TraesCS2B01G514500 chr1B 90.370 135 11 2 2405 2538 630918556 630918423 3.380000e-40 176.0
32 TraesCS2B01G514500 chr1B 91.463 82 6 1 2829 2909 27750514 27750433 9.680000e-21 111.0
33 TraesCS2B01G514500 chr7D 90.152 132 13 0 2397 2528 443163219 443163350 4.380000e-39 172.0
34 TraesCS2B01G514500 chr3D 90.769 130 11 1 2396 2524 498226119 498226248 4.380000e-39 172.0


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 TraesCS2B01G514500 chr2B 709424014 709427312 3298 True 6093.0 6093 100.000000 1 3299 1 chr2B.!!$R1 3298
1 TraesCS2B01G514500 chr6D 8551629 8553300 1671 True 2180.0 2180 90.141000 616 2311 1 chr6D.!!$R1 1695
2 TraesCS2B01G514500 chr6D 8967212 8969626 2414 False 1867.5 2412 95.342000 745 3299 2 chr6D.!!$F5 2554
3 TraesCS2B01G514500 chr6D 8923250 8923994 744 False 1059.0 1059 92.513000 4 741 1 chr6D.!!$F1 737
4 TraesCS2B01G514500 chr6D 8658609 8659844 1235 True 948.0 948 80.596000 1120 2355 1 chr6D.!!$R2 1235
5 TraesCS2B01G514500 chr6A 9469516 9474590 5074 False 1242.0 2148 94.405333 4 2711 3 chr6A.!!$F2 2707
6 TraesCS2B01G514500 chr6B 52979885 52981067 1182 True 1218.0 1218 85.306000 1121 2305 1 chr6B.!!$R3 1184
7 TraesCS2B01G514500 chr6B 16433126 16434319 1193 False 1199.0 1199 84.859000 1120 2316 1 chr6B.!!$F1 1196
8 TraesCS2B01G514500 chr6B 53061344 53062443 1099 True 1103.0 1103 84.818000 1209 2305 1 chr6B.!!$R4 1096
9 TraesCS2B01G514500 chr6B 15376299 15377042 743 True 1026.0 1026 91.700000 4 741 1 chr6B.!!$R2 737
10 TraesCS2B01G514500 chr5D 524577505 524580031 2526 False 619.0 1016 83.326500 1120 3022 2 chr5D.!!$F1 1902
11 TraesCS2B01G514500 chr5A 650824531 650826012 1481 False 612.5 1005 84.640500 1120 2709 2 chr5A.!!$F1 1589

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
912 927 0.107654 GGAACCGCCTAACTCAGCAT 60.108 55.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2497 5047 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 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
49 51 6.398095 AGAAGTCACTTTGTTTTCCCTTTTG 58.602 36.000 0.00 0.00 0.00 2.44
50 52 4.503910 AGTCACTTTGTTTTCCCTTTTGC 58.496 39.130 0.00 0.00 0.00 3.68
52 54 4.329801 GTCACTTTGTTTTCCCTTTTGCTG 59.670 41.667 0.00 0.00 0.00 4.41
53 55 4.221703 TCACTTTGTTTTCCCTTTTGCTGA 59.778 37.500 0.00 0.00 0.00 4.26
54 56 4.567959 CACTTTGTTTTCCCTTTTGCTGAG 59.432 41.667 0.00 0.00 0.00 3.35
55 57 3.817709 TTGTTTTCCCTTTTGCTGAGG 57.182 42.857 0.00 0.00 0.00 3.86
76 80 7.458397 TGAGGGGTATAACTATGCTTTATTGG 58.542 38.462 0.00 0.00 0.00 3.16
158 171 8.072567 CCTGATCAAGAGTGTTTGAAAACTTAG 58.927 37.037 7.39 0.00 40.21 2.18
204 217 4.764823 TGATGTCCGCCTTCAAAAGTAAAT 59.235 37.500 0.00 0.00 0.00 1.40
280 293 4.020543 AGTGCTACTAGACCCTCTTTCAG 58.979 47.826 0.00 0.00 0.00 3.02
283 296 3.764972 GCTACTAGACCCTCTTTCAGTGT 59.235 47.826 0.00 0.00 0.00 3.55
285 298 2.820787 ACTAGACCCTCTTTCAGTGTCG 59.179 50.000 0.00 0.00 0.00 4.35
307 320 1.071542 TCACCACCTGCTTTGAATCGA 59.928 47.619 0.00 0.00 0.00 3.59
355 368 1.163554 GTCTTCTGCCAGAGCCAAAG 58.836 55.000 0.00 0.00 38.69 2.77
407 420 0.393077 ACATCGATGATTCCCCGGAC 59.607 55.000 31.33 0.00 0.00 4.79
411 424 0.107897 CGATGATTCCCCGGACAACA 60.108 55.000 0.73 0.00 0.00 3.33
424 437 1.338579 GGACAACAAGAGAGGAGCTGG 60.339 57.143 0.00 0.00 0.00 4.85
449 462 4.732442 CGAATATCGTCCATCATCATCTCG 59.268 45.833 0.00 0.00 34.72 4.04
504 517 4.505217 GCCACGCTTGCATCGACG 62.505 66.667 14.56 6.30 0.00 5.12
506 519 2.667318 CCACGCTTGCATCGACGTT 61.667 57.895 14.56 0.00 36.45 3.99
514 527 3.181550 GCTTGCATCGACGTTGATTTTTG 60.182 43.478 15.89 7.61 0.00 2.44
567 580 5.416639 TCTGCAATCAAAACAGAGCACATAT 59.583 36.000 0.00 0.00 35.58 1.78
649 662 4.649692 CCATGCATGTTTAGCTAGGAGAT 58.350 43.478 24.58 0.00 0.00 2.75
678 691 4.861102 AAGAAGTTCAAAATCAGCCCAG 57.139 40.909 5.50 0.00 0.00 4.45
707 720 3.865745 CGCCGTTGTTCTTCTAATCTCAT 59.134 43.478 0.00 0.00 0.00 2.90
747 761 5.407995 CCTTCTCTGTTGTCATCTTCAGTTC 59.592 44.000 0.00 0.00 0.00 3.01
829 843 2.027625 CACTTTCCTCCGCGTCCAC 61.028 63.158 4.92 0.00 0.00 4.02
909 924 4.934989 GGGAACCGCCTAACTCAG 57.065 61.111 0.00 0.00 40.86 3.35
910 925 1.449778 GGGAACCGCCTAACTCAGC 60.450 63.158 0.00 0.00 40.86 4.26
911 926 1.295423 GGAACCGCCTAACTCAGCA 59.705 57.895 0.00 0.00 0.00 4.41
912 927 0.107654 GGAACCGCCTAACTCAGCAT 60.108 55.000 0.00 0.00 0.00 3.79
913 928 1.679032 GGAACCGCCTAACTCAGCATT 60.679 52.381 0.00 0.00 0.00 3.56
914 929 2.084546 GAACCGCCTAACTCAGCATTT 58.915 47.619 0.00 0.00 0.00 2.32
915 930 1.453155 ACCGCCTAACTCAGCATTTG 58.547 50.000 0.00 0.00 0.00 2.32
916 931 0.734889 CCGCCTAACTCAGCATTTGG 59.265 55.000 0.00 0.00 0.00 3.28
917 932 1.453155 CGCCTAACTCAGCATTTGGT 58.547 50.000 0.00 0.00 0.00 3.67
918 933 1.812571 CGCCTAACTCAGCATTTGGTT 59.187 47.619 0.00 0.00 0.00 3.67
919 934 2.414559 CGCCTAACTCAGCATTTGGTTG 60.415 50.000 0.00 0.00 0.00 3.77
920 935 2.819608 GCCTAACTCAGCATTTGGTTGA 59.180 45.455 0.00 0.00 35.29 3.18
921 936 3.445096 GCCTAACTCAGCATTTGGTTGAT 59.555 43.478 0.00 0.00 36.07 2.57
922 937 4.082026 GCCTAACTCAGCATTTGGTTGATT 60.082 41.667 0.00 0.00 36.07 2.57
923 938 5.644644 CCTAACTCAGCATTTGGTTGATTC 58.355 41.667 0.00 0.00 36.07 2.52
924 939 3.837213 ACTCAGCATTTGGTTGATTCG 57.163 42.857 0.00 0.00 36.07 3.34
932 947 4.179579 GGTTGATTCGCCGCTGCC 62.180 66.667 0.00 0.00 0.00 4.85
1201 3734 0.746563 CTCGTCTCTCTCCGCCTCTT 60.747 60.000 0.00 0.00 0.00 2.85
1359 3895 3.636231 CACCTCAAGTCCCCCGCA 61.636 66.667 0.00 0.00 0.00 5.69
1370 3906 4.770874 CCCCGCAAATCCCGACGT 62.771 66.667 0.00 0.00 0.00 4.34
1377 3913 1.005394 AAATCCCGACGTCGTGCTT 60.005 52.632 33.49 19.57 37.74 3.91
1391 3927 4.760047 GCTTGCCTTCCTCGCCGA 62.760 66.667 0.00 0.00 0.00 5.54
1550 4099 3.955101 CGCCTCGCTCTCCCGTAG 61.955 72.222 0.00 0.00 0.00 3.51
1750 4299 3.280197 TTGCCAAGCTATGCATCAGTA 57.720 42.857 0.19 0.00 37.33 2.74
2308 4857 7.523293 TTCAGATTTACATGAAGCAAGGAAA 57.477 32.000 0.00 0.00 31.93 3.13
2394 4944 5.973565 GCAATTCACATTAGTGTATTCTGCC 59.026 40.000 0.00 0.00 41.82 4.85
2395 4945 6.183360 GCAATTCACATTAGTGTATTCTGCCT 60.183 38.462 0.00 0.00 41.82 4.75
2396 4946 7.012327 GCAATTCACATTAGTGTATTCTGCCTA 59.988 37.037 0.00 0.00 41.82 3.93
2397 4947 8.892723 CAATTCACATTAGTGTATTCTGCCTAA 58.107 33.333 0.00 0.00 41.82 2.69
2398 4948 9.461312 AATTCACATTAGTGTATTCTGCCTAAA 57.539 29.630 0.00 0.00 40.38 1.85
2399 4949 7.843490 TCACATTAGTGTATTCTGCCTAAAC 57.157 36.000 0.00 0.00 46.01 2.01
2400 4950 7.390823 TCACATTAGTGTATTCTGCCTAAACA 58.609 34.615 0.00 0.00 46.01 2.83
2401 4951 7.549134 TCACATTAGTGTATTCTGCCTAAACAG 59.451 37.037 0.00 0.00 46.01 3.16
2402 4952 7.549134 CACATTAGTGTATTCTGCCTAAACAGA 59.451 37.037 0.00 0.00 41.58 3.41
2403 4953 7.549488 ACATTAGTGTATTCTGCCTAAACAGAC 59.451 37.037 0.00 0.00 40.64 3.51
2404 4954 5.483685 AGTGTATTCTGCCTAAACAGACA 57.516 39.130 0.00 0.00 46.13 3.41
2405 4955 5.238583 AGTGTATTCTGCCTAAACAGACAC 58.761 41.667 6.80 6.80 46.13 3.67
2406 4956 5.012148 AGTGTATTCTGCCTAAACAGACACT 59.988 40.000 10.14 10.14 46.13 3.55
2407 4957 5.348997 GTGTATTCTGCCTAAACAGACACTC 59.651 44.000 7.39 1.88 46.13 3.51
2408 4958 3.402628 TTCTGCCTAAACAGACACTCC 57.597 47.619 0.00 0.00 46.13 3.85
2409 4959 1.623811 TCTGCCTAAACAGACACTCCC 59.376 52.381 0.00 0.00 41.72 4.30
2410 4960 1.625818 CTGCCTAAACAGACACTCCCT 59.374 52.381 0.00 0.00 40.25 4.20
2411 4961 1.623811 TGCCTAAACAGACACTCCCTC 59.376 52.381 0.00 0.00 0.00 4.30
2412 4962 1.066071 GCCTAAACAGACACTCCCTCC 60.066 57.143 0.00 0.00 0.00 4.30
2413 4963 2.257207 CCTAAACAGACACTCCCTCCA 58.743 52.381 0.00 0.00 0.00 3.86
2414 4964 2.840651 CCTAAACAGACACTCCCTCCAT 59.159 50.000 0.00 0.00 0.00 3.41
2415 4965 3.118592 CCTAAACAGACACTCCCTCCATC 60.119 52.174 0.00 0.00 0.00 3.51
2416 4966 2.334006 AACAGACACTCCCTCCATCT 57.666 50.000 0.00 0.00 0.00 2.90
2417 4967 1.566211 ACAGACACTCCCTCCATCTG 58.434 55.000 0.00 0.00 42.07 2.90
2418 4968 0.829333 CAGACACTCCCTCCATCTGG 59.171 60.000 0.00 0.00 34.43 3.86
2419 4969 0.415429 AGACACTCCCTCCATCTGGT 59.585 55.000 0.00 0.00 36.34 4.00
2420 4970 1.646447 AGACACTCCCTCCATCTGGTA 59.354 52.381 0.00 0.00 36.34 3.25
2421 4971 2.044492 AGACACTCCCTCCATCTGGTAA 59.956 50.000 0.00 0.00 36.34 2.85
2422 4972 3.041946 GACACTCCCTCCATCTGGTAAT 58.958 50.000 0.00 0.00 36.34 1.89
2423 4973 4.078571 AGACACTCCCTCCATCTGGTAATA 60.079 45.833 0.00 0.00 36.34 0.98
2424 4974 3.967987 ACACTCCCTCCATCTGGTAATAC 59.032 47.826 0.00 0.00 36.34 1.89
2425 4975 4.227197 CACTCCCTCCATCTGGTAATACT 58.773 47.826 0.00 0.00 36.34 2.12
2426 4976 4.656112 CACTCCCTCCATCTGGTAATACTT 59.344 45.833 0.00 0.00 36.34 2.24
2427 4977 4.656112 ACTCCCTCCATCTGGTAATACTTG 59.344 45.833 0.00 0.00 36.34 3.16
2428 4978 4.631234 TCCCTCCATCTGGTAATACTTGT 58.369 43.478 0.00 0.00 36.34 3.16
2429 4979 4.654262 TCCCTCCATCTGGTAATACTTGTC 59.346 45.833 0.00 0.00 36.34 3.18
2430 4980 4.501571 CCCTCCATCTGGTAATACTTGTCG 60.502 50.000 0.00 0.00 36.34 4.35
2431 4981 4.501571 CCTCCATCTGGTAATACTTGTCGG 60.502 50.000 0.00 0.00 36.34 4.79
2432 4982 4.283337 TCCATCTGGTAATACTTGTCGGA 58.717 43.478 0.00 0.00 36.34 4.55
2433 4983 4.341235 TCCATCTGGTAATACTTGTCGGAG 59.659 45.833 0.00 0.00 36.34 4.63
2434 4984 4.341235 CCATCTGGTAATACTTGTCGGAGA 59.659 45.833 0.00 0.00 0.00 3.71
2435 4985 5.163447 CCATCTGGTAATACTTGTCGGAGAA 60.163 44.000 0.00 0.00 39.69 2.87
2436 4986 5.988310 TCTGGTAATACTTGTCGGAGAAA 57.012 39.130 0.00 0.00 39.69 2.52
2437 4987 6.540438 TCTGGTAATACTTGTCGGAGAAAT 57.460 37.500 0.00 0.00 39.69 2.17
2438 4988 6.338146 TCTGGTAATACTTGTCGGAGAAATG 58.662 40.000 0.00 0.00 39.69 2.32
2439 4989 5.424757 TGGTAATACTTGTCGGAGAAATGG 58.575 41.667 0.00 0.00 39.69 3.16
2440 4990 5.188163 TGGTAATACTTGTCGGAGAAATGGA 59.812 40.000 0.00 0.00 39.69 3.41
2441 4991 6.126883 TGGTAATACTTGTCGGAGAAATGGAT 60.127 38.462 0.00 0.00 39.69 3.41
2442 4992 6.202954 GGTAATACTTGTCGGAGAAATGGATG 59.797 42.308 0.00 0.00 39.69 3.51
2443 4993 3.703001 ACTTGTCGGAGAAATGGATGT 57.297 42.857 0.00 0.00 39.69 3.06
2444 4994 4.819105 ACTTGTCGGAGAAATGGATGTA 57.181 40.909 0.00 0.00 39.69 2.29
2445 4995 5.359194 ACTTGTCGGAGAAATGGATGTAT 57.641 39.130 0.00 0.00 39.69 2.29
2446 4996 5.360591 ACTTGTCGGAGAAATGGATGTATC 58.639 41.667 0.00 0.00 39.69 2.24
2447 4997 5.129485 ACTTGTCGGAGAAATGGATGTATCT 59.871 40.000 0.00 0.00 39.69 1.98
2448 4998 6.323996 ACTTGTCGGAGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 39.69 1.98
2449 4999 6.332735 TGTCGGAGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 39.69 2.43
2450 5000 6.068670 TGTCGGAGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 39.69 2.43
2451 5001 6.016192 TGTCGGAGAAATGGATGTATCTAGAC 60.016 42.308 0.00 0.00 39.69 2.59
2452 5002 5.181433 TCGGAGAAATGGATGTATCTAGACG 59.819 44.000 0.00 0.00 0.00 4.18
2453 5003 5.048643 CGGAGAAATGGATGTATCTAGACGT 60.049 44.000 0.00 0.00 0.00 4.34
2454 5004 6.148976 CGGAGAAATGGATGTATCTAGACGTA 59.851 42.308 0.00 0.00 0.00 3.57
2494 5044 8.545229 ACATCCATTTTTATTCATTTTTGCGA 57.455 26.923 0.00 0.00 0.00 5.10
2495 5045 8.442384 ACATCCATTTTTATTCATTTTTGCGAC 58.558 29.630 0.00 0.00 0.00 5.19
2496 5046 7.953158 TCCATTTTTATTCATTTTTGCGACA 57.047 28.000 0.00 0.00 0.00 4.35
2497 5047 8.370493 TCCATTTTTATTCATTTTTGCGACAA 57.630 26.923 0.00 0.00 0.00 3.18
2498 5048 8.494347 TCCATTTTTATTCATTTTTGCGACAAG 58.506 29.630 0.00 0.00 0.00 3.16
2499 5049 8.281893 CCATTTTTATTCATTTTTGCGACAAGT 58.718 29.630 0.00 0.00 0.00 3.16
2505 5055 7.581011 ATTCATTTTTGCGACAAGTATTTCC 57.419 32.000 0.00 0.00 0.00 3.13
2506 5056 5.150683 TCATTTTTGCGACAAGTATTTCCG 58.849 37.500 0.00 0.00 0.00 4.30
2507 5057 3.546002 TTTTGCGACAAGTATTTCCGG 57.454 42.857 0.00 0.00 0.00 5.14
2508 5058 2.459060 TTGCGACAAGTATTTCCGGA 57.541 45.000 0.00 0.00 0.00 5.14
2509 5059 1.717194 TGCGACAAGTATTTCCGGAC 58.283 50.000 1.83 0.00 0.00 4.79
2510 5060 0.643820 GCGACAAGTATTTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79
2511 5061 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2512 5062 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2513 5063 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2514 5064 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2515 5065 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2516 5066 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2517 5067 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2713 5264 2.176798 TGTGTTTCCAACCTCCAATCCT 59.823 45.455 0.00 0.00 0.00 3.24
2910 6192 6.046593 TGTAGCATGACTAGGTTTAATTCCG 58.953 40.000 0.00 0.00 0.00 4.30
3022 6307 3.834489 AGGGCTCATCAGTAACATCAG 57.166 47.619 0.00 0.00 0.00 2.90
3027 6312 3.064545 GCTCATCAGTAACATCAGTTGCC 59.935 47.826 0.00 0.00 40.70 4.52
3073 6358 4.217334 TGTTTGCACTGTCTGAAACAAAGA 59.783 37.500 0.00 0.00 37.45 2.52
3076 6361 3.206150 GCACTGTCTGAAACAAAGAGGA 58.794 45.455 0.00 0.00 37.45 3.71
3090 6375 3.889520 AAGAGGAAAGATACCCGTCAC 57.110 47.619 0.00 0.00 0.00 3.67
3142 6427 3.709141 TCGTGATTACCTGATCCCATTCA 59.291 43.478 0.00 0.00 0.00 2.57
3219 6504 5.643777 GTGTGTCTAATTCTGTATGCCAACT 59.356 40.000 0.00 0.00 0.00 3.16
3238 6523 5.509670 CCAACTAGAGAAGACATGTCACACA 60.510 44.000 27.02 6.66 0.00 3.72
3239 6524 5.991933 ACTAGAGAAGACATGTCACACAT 57.008 39.130 27.02 12.43 39.91 3.21
3243 6528 4.774726 AGAGAAGACATGTCACACATAGGT 59.225 41.667 27.02 0.42 36.53 3.08
3246 6531 4.623932 AGACATGTCACACATAGGTTGT 57.376 40.909 27.02 0.00 36.53 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.948034 TCTAGAAAAAGGGAAAACAAAGTGA 57.052 32.000 0.00 0.00 0.00 3.41
1 2 8.466798 TCTTCTAGAAAAAGGGAAAACAAAGTG 58.533 33.333 6.63 0.00 0.00 3.16
2 3 8.589701 TCTTCTAGAAAAAGGGAAAACAAAGT 57.410 30.769 6.63 0.00 0.00 2.66
20 22 6.768381 AGGGAAAACAAAGTGACTTCTTCTAG 59.232 38.462 0.00 0.00 0.00 2.43
49 51 4.625607 AAGCATAGTTATACCCCTCAGC 57.374 45.455 0.00 0.00 0.00 4.26
50 52 7.607991 CCAATAAAGCATAGTTATACCCCTCAG 59.392 40.741 0.00 0.00 0.00 3.35
52 54 7.459234 ACCAATAAAGCATAGTTATACCCCTC 58.541 38.462 0.00 0.00 0.00 4.30
53 55 7.073215 TGACCAATAAAGCATAGTTATACCCCT 59.927 37.037 0.00 0.00 0.00 4.79
54 56 7.228590 TGACCAATAAAGCATAGTTATACCCC 58.771 38.462 0.00 0.00 0.00 4.95
55 57 8.730680 CATGACCAATAAAGCATAGTTATACCC 58.269 37.037 0.00 0.00 0.00 3.69
62 66 8.267894 ACTACTTCATGACCAATAAAGCATAGT 58.732 33.333 0.00 0.00 0.00 2.12
130 143 2.783135 TCAAACACTCTTGATCAGGGC 58.217 47.619 4.83 0.00 30.31 5.19
158 171 1.331756 CACCGATGCAGATAGTTTGGC 59.668 52.381 0.00 0.00 0.00 4.52
204 217 9.982291 CAGCGAGCTAGTTTAATTAATTGTAAA 57.018 29.630 11.05 1.76 0.00 2.01
283 296 0.179234 TCAAAGCAGGTGGTGAACGA 59.821 50.000 0.00 0.00 0.00 3.85
285 298 2.350772 CGATTCAAAGCAGGTGGTGAAC 60.351 50.000 1.98 0.00 33.09 3.18
355 368 1.647629 CGATGGCATGCAGAGAAGC 59.352 57.895 21.36 0.00 0.00 3.86
407 420 0.676151 GGCCAGCTCCTCTCTTGTTG 60.676 60.000 0.00 0.00 0.00 3.33
411 424 0.980231 ATTCGGCCAGCTCCTCTCTT 60.980 55.000 2.24 0.00 0.00 2.85
460 473 2.026449 CCAAGTTGAGAGGAGAGGCATT 60.026 50.000 3.87 0.00 0.00 3.56
504 517 4.485163 AGCCAGATTACGCAAAAATCAAC 58.515 39.130 5.71 0.00 36.09 3.18
506 519 4.484236 CAAGCCAGATTACGCAAAAATCA 58.516 39.130 5.71 0.00 36.09 2.57
514 527 5.106673 GGTAATTATCCAAGCCAGATTACGC 60.107 44.000 0.00 0.00 33.16 4.42
592 605 8.366401 TCAAAATCCAGAATCAATAAGTGCAAA 58.634 29.630 0.00 0.00 0.00 3.68
649 662 7.872483 GGCTGATTTTGAACTTCTTAATTTGGA 59.128 33.333 0.00 0.00 0.00 3.53
678 691 0.865769 AAGAACAACGGCGACACATC 59.134 50.000 16.62 5.10 0.00 3.06
747 761 8.393366 ACGAGTTCATTGAAATGTTCATATCAG 58.607 33.333 3.76 0.00 39.84 2.90
798 812 5.468746 CGGAGGAAAGTGATACACAAAGAAA 59.531 40.000 4.75 0.00 36.74 2.52
799 813 4.994852 CGGAGGAAAGTGATACACAAAGAA 59.005 41.667 4.75 0.00 36.74 2.52
829 843 8.147058 GCTATAGATCACTTATGGACCATATGG 58.853 40.741 24.10 20.68 42.17 2.74
848 863 7.919091 CACACGAGGTATTTGTTAAGCTATAGA 59.081 37.037 3.21 0.00 0.00 1.98
850 865 7.774134 TCACACGAGGTATTTGTTAAGCTATA 58.226 34.615 0.00 0.00 0.00 1.31
852 867 6.028146 TCACACGAGGTATTTGTTAAGCTA 57.972 37.500 0.00 0.00 0.00 3.32
865 880 6.348498 TGATTGATTCATTATCACACGAGGT 58.652 36.000 0.00 0.00 42.88 3.85
898 913 1.453155 ACCAAATGCTGAGTTAGGCG 58.547 50.000 0.00 0.00 0.00 5.52
900 915 5.644644 GAATCAACCAAATGCTGAGTTAGG 58.355 41.667 0.00 0.00 0.00 2.69
901 916 5.327091 CGAATCAACCAAATGCTGAGTTAG 58.673 41.667 0.00 0.00 0.00 2.34
902 917 4.379394 GCGAATCAACCAAATGCTGAGTTA 60.379 41.667 0.00 0.00 0.00 2.24
903 918 3.612479 GCGAATCAACCAAATGCTGAGTT 60.612 43.478 0.00 0.00 0.00 3.01
904 919 2.095059 GCGAATCAACCAAATGCTGAGT 60.095 45.455 0.00 0.00 0.00 3.41
905 920 2.523015 GCGAATCAACCAAATGCTGAG 58.477 47.619 0.00 0.00 0.00 3.35
906 921 1.202114 GGCGAATCAACCAAATGCTGA 59.798 47.619 0.00 0.00 0.00 4.26
907 922 1.632422 GGCGAATCAACCAAATGCTG 58.368 50.000 0.00 0.00 0.00 4.41
908 923 0.171007 CGGCGAATCAACCAAATGCT 59.829 50.000 0.00 0.00 0.00 3.79
909 924 1.413008 GCGGCGAATCAACCAAATGC 61.413 55.000 12.98 0.00 0.00 3.56
910 925 0.171007 AGCGGCGAATCAACCAAATG 59.829 50.000 12.98 0.00 0.00 2.32
911 926 0.171007 CAGCGGCGAATCAACCAAAT 59.829 50.000 12.98 0.00 0.00 2.32
912 927 1.578926 CAGCGGCGAATCAACCAAA 59.421 52.632 12.98 0.00 0.00 3.28
913 928 2.976840 GCAGCGGCGAATCAACCAA 61.977 57.895 12.98 0.00 0.00 3.67
914 929 3.430862 GCAGCGGCGAATCAACCA 61.431 61.111 12.98 0.00 0.00 3.67
915 930 4.179579 GGCAGCGGCGAATCAACC 62.180 66.667 12.98 0.00 42.47 3.77
916 931 3.127533 AGGCAGCGGCGAATCAAC 61.128 61.111 12.98 0.00 42.47 3.18
917 932 3.126879 CAGGCAGCGGCGAATCAA 61.127 61.111 12.98 0.00 42.47 2.57
932 947 1.392589 ACAACTCAACCAAGTGCCAG 58.607 50.000 0.00 0.00 0.00 4.85
975 999 2.208132 TCCGCTCAAATGCCCTTAAA 57.792 45.000 0.00 0.00 0.00 1.52
978 1002 0.753111 GGATCCGCTCAAATGCCCTT 60.753 55.000 0.00 0.00 0.00 3.95
1201 3734 2.361771 GTGGAGAGGGGGTACGGA 59.638 66.667 0.00 0.00 0.00 4.69
1370 3906 2.048222 CGAGGAAGGCAAGCACGA 60.048 61.111 0.00 0.00 0.00 4.35
1444 3980 4.827087 CACGCTGGCGCAGAGGAT 62.827 66.667 10.83 0.00 44.19 3.24
1836 4385 1.509463 CAGCGCATGCCTGAACATT 59.491 52.632 23.86 0.00 44.31 2.71
2073 4622 1.074167 CCTCCCCTCCAGGCTGTAT 60.074 63.158 14.43 0.00 0.00 2.29
2278 4827 8.442632 TTGCTTCATGTAAATCTGAATCTAGG 57.557 34.615 0.00 0.00 31.39 3.02
2308 4857 4.949856 CACAGTTACCAATTTCCATAGCCT 59.050 41.667 0.00 0.00 0.00 4.58
2394 4944 3.772025 AGATGGAGGGAGTGTCTGTTTAG 59.228 47.826 0.00 0.00 0.00 1.85
2395 4945 3.515502 CAGATGGAGGGAGTGTCTGTTTA 59.484 47.826 0.00 0.00 33.42 2.01
2396 4946 2.304180 CAGATGGAGGGAGTGTCTGTTT 59.696 50.000 0.00 0.00 33.42 2.83
2397 4947 1.905215 CAGATGGAGGGAGTGTCTGTT 59.095 52.381 0.00 0.00 33.42 3.16
2398 4948 1.566211 CAGATGGAGGGAGTGTCTGT 58.434 55.000 0.00 0.00 33.42 3.41
2399 4949 0.829333 CCAGATGGAGGGAGTGTCTG 59.171 60.000 0.00 0.00 37.39 3.51
2400 4950 0.415429 ACCAGATGGAGGGAGTGTCT 59.585 55.000 5.72 0.00 38.94 3.41
2401 4951 2.160721 TACCAGATGGAGGGAGTGTC 57.839 55.000 5.72 0.00 38.94 3.67
2402 4952 2.642171 TTACCAGATGGAGGGAGTGT 57.358 50.000 5.72 0.00 38.94 3.55
2403 4953 4.227197 AGTATTACCAGATGGAGGGAGTG 58.773 47.826 5.72 0.00 38.94 3.51
2404 4954 4.561254 AGTATTACCAGATGGAGGGAGT 57.439 45.455 5.72 0.00 38.94 3.85
2405 4955 4.656112 ACAAGTATTACCAGATGGAGGGAG 59.344 45.833 5.72 0.00 38.94 4.30
2406 4956 4.631234 ACAAGTATTACCAGATGGAGGGA 58.369 43.478 5.72 0.00 38.94 4.20
2407 4957 4.501571 CGACAAGTATTACCAGATGGAGGG 60.502 50.000 5.72 0.00 38.94 4.30
2408 4958 4.501571 CCGACAAGTATTACCAGATGGAGG 60.502 50.000 5.72 0.00 38.94 4.30
2409 4959 4.341235 TCCGACAAGTATTACCAGATGGAG 59.659 45.833 5.72 0.00 38.94 3.86
2410 4960 4.283337 TCCGACAAGTATTACCAGATGGA 58.717 43.478 5.72 0.00 38.94 3.41
2411 4961 4.341235 TCTCCGACAAGTATTACCAGATGG 59.659 45.833 0.00 0.00 42.17 3.51
2412 4962 5.515797 TCTCCGACAAGTATTACCAGATG 57.484 43.478 0.00 0.00 0.00 2.90
2413 4963 6.540438 TTTCTCCGACAAGTATTACCAGAT 57.460 37.500 0.00 0.00 0.00 2.90
2414 4964 5.988310 TTTCTCCGACAAGTATTACCAGA 57.012 39.130 0.00 0.00 0.00 3.86
2415 4965 5.523916 CCATTTCTCCGACAAGTATTACCAG 59.476 44.000 0.00 0.00 0.00 4.00
2416 4966 5.188163 TCCATTTCTCCGACAAGTATTACCA 59.812 40.000 0.00 0.00 0.00 3.25
2417 4967 5.667466 TCCATTTCTCCGACAAGTATTACC 58.333 41.667 0.00 0.00 0.00 2.85
2418 4968 6.761714 ACATCCATTTCTCCGACAAGTATTAC 59.238 38.462 0.00 0.00 0.00 1.89
2419 4969 6.884832 ACATCCATTTCTCCGACAAGTATTA 58.115 36.000 0.00 0.00 0.00 0.98
2420 4970 5.745227 ACATCCATTTCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
2421 4971 5.359194 ACATCCATTTCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
2422 4972 4.819105 ACATCCATTTCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
2423 4973 3.703001 ACATCCATTTCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
2424 4974 5.605534 AGATACATCCATTTCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
2425 4975 5.614324 AGATACATCCATTTCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
2426 4976 6.016192 GTCTAGATACATCCATTTCTCCGACA 60.016 42.308 0.00 0.00 0.00 4.35
2427 4977 6.383415 GTCTAGATACATCCATTTCTCCGAC 58.617 44.000 0.00 0.00 0.00 4.79
2428 4978 5.181433 CGTCTAGATACATCCATTTCTCCGA 59.819 44.000 0.00 0.00 0.00 4.55
2429 4979 5.048643 ACGTCTAGATACATCCATTTCTCCG 60.049 44.000 0.00 0.00 0.00 4.63
2430 4980 6.334102 ACGTCTAGATACATCCATTTCTCC 57.666 41.667 0.00 0.00 0.00 3.71
2431 4981 9.915629 AAATACGTCTAGATACATCCATTTCTC 57.084 33.333 0.00 0.00 0.00 2.87
2470 5020 8.441608 TGTCGCAAAAATGAATAAAAATGGATG 58.558 29.630 0.00 0.00 0.00 3.51
2472 5022 7.953158 TGTCGCAAAAATGAATAAAAATGGA 57.047 28.000 0.00 0.00 0.00 3.41
2473 5023 8.281893 ACTTGTCGCAAAAATGAATAAAAATGG 58.718 29.630 0.00 0.00 0.00 3.16
2479 5029 9.134734 GGAAATACTTGTCGCAAAAATGAATAA 57.865 29.630 0.00 0.00 0.00 1.40
2480 5030 7.483375 CGGAAATACTTGTCGCAAAAATGAATA 59.517 33.333 0.00 0.00 0.00 1.75
2481 5031 6.307800 CGGAAATACTTGTCGCAAAAATGAAT 59.692 34.615 0.00 0.00 0.00 2.57
2482 5032 5.627367 CGGAAATACTTGTCGCAAAAATGAA 59.373 36.000 0.00 0.00 0.00 2.57
2483 5033 5.150683 CGGAAATACTTGTCGCAAAAATGA 58.849 37.500 0.00 0.00 0.00 2.57
2484 5034 4.323336 CCGGAAATACTTGTCGCAAAAATG 59.677 41.667 0.00 0.00 0.00 2.32
2485 5035 4.216687 TCCGGAAATACTTGTCGCAAAAAT 59.783 37.500 0.00 0.00 0.00 1.82
2486 5036 3.564644 TCCGGAAATACTTGTCGCAAAAA 59.435 39.130 0.00 0.00 0.00 1.94
2487 5037 3.058777 GTCCGGAAATACTTGTCGCAAAA 60.059 43.478 5.23 0.00 0.00 2.44
2488 5038 2.481185 GTCCGGAAATACTTGTCGCAAA 59.519 45.455 5.23 0.00 0.00 3.68
2489 5039 2.070783 GTCCGGAAATACTTGTCGCAA 58.929 47.619 5.23 0.00 0.00 4.85
2490 5040 1.717194 GTCCGGAAATACTTGTCGCA 58.283 50.000 5.23 0.00 0.00 5.10
2491 5041 0.643820 CGTCCGGAAATACTTGTCGC 59.356 55.000 5.23 0.00 0.00 5.19
2492 5042 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2493 5043 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2494 5044 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2495 5045 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2496 5046 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2497 5047 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2498 5048 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2499 5049 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2500 5050 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2501 5051 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2502 5052 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
2503 5053 0.846015 TAATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
2504 5054 1.245732 CTAATACTCCCTCCGTCCGG 58.754 60.000 0.00 0.00 0.00 5.14
2505 5055 1.978454 ACTAATACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
2506 5056 4.405036 AGAAAACTAATACTCCCTCCGTCC 59.595 45.833 0.00 0.00 0.00 4.79
2507 5057 5.349809 CAGAAAACTAATACTCCCTCCGTC 58.650 45.833 0.00 0.00 0.00 4.79
2508 5058 4.382793 GCAGAAAACTAATACTCCCTCCGT 60.383 45.833 0.00 0.00 0.00 4.69
2509 5059 4.120589 GCAGAAAACTAATACTCCCTCCG 58.879 47.826 0.00 0.00 0.00 4.63
2510 5060 5.119694 CAGCAGAAAACTAATACTCCCTCC 58.880 45.833 0.00 0.00 0.00 4.30
2511 5061 5.735766 ACAGCAGAAAACTAATACTCCCTC 58.264 41.667 0.00 0.00 0.00 4.30
2512 5062 5.763876 ACAGCAGAAAACTAATACTCCCT 57.236 39.130 0.00 0.00 0.00 4.20
2513 5063 6.641474 AGTACAGCAGAAAACTAATACTCCC 58.359 40.000 0.00 0.00 0.00 4.30
2514 5064 9.250624 CATAGTACAGCAGAAAACTAATACTCC 57.749 37.037 0.00 0.00 0.00 3.85
2515 5065 9.804758 ACATAGTACAGCAGAAAACTAATACTC 57.195 33.333 0.00 0.00 0.00 2.59
2516 5066 9.804758 GACATAGTACAGCAGAAAACTAATACT 57.195 33.333 0.00 0.00 0.00 2.12
2517 5067 9.804758 AGACATAGTACAGCAGAAAACTAATAC 57.195 33.333 0.00 0.00 0.00 1.89
2713 5264 4.017958 TGGATACATAGGGTTTTCCTTGCA 60.018 41.667 0.00 0.00 43.45 4.08
2737 5288 8.880991 AAGAAAGAGTTCAGTCCTAGTATGTA 57.119 34.615 0.00 0.00 36.09 2.29
2910 6192 7.012327 ACTGATATGTTGTACCATGCATGTAAC 59.988 37.037 24.58 20.55 0.00 2.50
3027 6312 1.699634 TCACAGAGAACCCCAGAAAGG 59.300 52.381 0.00 0.00 37.03 3.11
3038 6323 2.092968 AGTGCAAACAGGTCACAGAGAA 60.093 45.455 0.00 0.00 33.44 2.87
3073 6358 2.496470 GACTGTGACGGGTATCTTTCCT 59.504 50.000 0.00 0.00 0.00 3.36
3076 6361 5.670792 TTATGACTGTGACGGGTATCTTT 57.329 39.130 0.00 0.00 0.00 2.52
3142 6427 2.622436 GCGACTGCTACCTGAAAGAAT 58.378 47.619 0.00 0.00 38.39 2.40
3219 6504 5.952347 ACCTATGTGTGACATGTCTTCTCTA 59.048 40.000 25.55 11.37 39.53 2.43
3238 6523 6.379133 TCACCTATTCGACAAGTACAACCTAT 59.621 38.462 0.00 0.00 0.00 2.57
3239 6524 5.711506 TCACCTATTCGACAAGTACAACCTA 59.288 40.000 0.00 0.00 0.00 3.08
3243 6528 5.456548 TGTCACCTATTCGACAAGTACAA 57.543 39.130 0.00 0.00 39.14 2.41
3246 6531 7.037438 GGTAAATGTCACCTATTCGACAAGTA 58.963 38.462 0.00 0.00 44.78 2.24


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

AutoCloner maintained by Alex Coulton.