Multiple sequence alignment - TraesCS2D01G269500

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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 TraesCS2D01G269500 chr2D 100.000 4538 0 0 1 4538 331733082 331737619 0.000000e+00 8381.0
1 TraesCS2D01G269500 chr2D 88.278 546 37 11 45 587 64193079 64193600 2.980000e-176 628.0
2 TraesCS2D01G269500 chr2B 93.242 3448 130 37 1150 4538 399930806 399934209 0.000000e+00 4981.0
3 TraesCS2D01G269500 chr2B 90.722 97 2 4 954 1043 399930719 399930815 6.170000e-24 122.0
4 TraesCS2D01G269500 chr2A 90.506 2749 166 46 847 3556 439192643 439195335 0.000000e+00 3542.0
5 TraesCS2D01G269500 chr2A 89.388 245 14 5 4296 4538 439199528 439199762 9.540000e-77 298.0
6 TraesCS2D01G269500 chr2A 89.062 128 13 1 4151 4278 439199260 439199386 1.690000e-34 158.0
7 TraesCS2D01G269500 chr2A 84.091 88 8 6 1061 1147 439192946 439193028 3.760000e-11 80.5
8 TraesCS2D01G269500 chr7D 86.391 845 79 11 33 846 167591086 167590247 0.000000e+00 891.0
9 TraesCS2D01G269500 chr7D 87.054 448 52 6 42 486 458523178 458522734 6.780000e-138 501.0
10 TraesCS2D01G269500 chr7D 90.833 120 8 3 4034 4153 42212794 42212678 1.690000e-34 158.0
11 TraesCS2D01G269500 chr7D 90.000 120 9 3 4034 4153 41916841 41916957 7.860000e-33 152.0
12 TraesCS2D01G269500 chr3D 87.659 786 68 15 43 823 74327677 74326916 0.000000e+00 887.0
13 TraesCS2D01G269500 chr3D 85.956 826 98 12 34 846 573206236 573207056 0.000000e+00 867.0
14 TraesCS2D01G269500 chr3D 84.228 615 81 12 2099 2708 564929342 564929945 6.540000e-163 584.0
15 TraesCS2D01G269500 chr3D 88.503 461 42 5 397 846 178404439 178403979 8.580000e-152 547.0
16 TraesCS2D01G269500 chr3D 86.364 506 50 13 353 846 586568976 586569474 6.680000e-148 534.0
17 TraesCS2D01G269500 chr3D 89.831 118 10 2 4035 4152 537915012 537914897 2.830000e-32 150.0
18 TraesCS2D01G269500 chr3A 85.351 826 103 13 34 846 707834460 707835280 0.000000e+00 839.0
19 TraesCS2D01G269500 chr3A 83.670 643 87 10 2074 2708 699483027 699483659 1.410000e-164 590.0
20 TraesCS2D01G269500 chr3A 79.412 374 39 24 2965 3321 699484332 699484684 3.530000e-56 230.0
21 TraesCS2D01G269500 chrUn 84.752 846 89 16 39 845 162983273 162982429 0.000000e+00 811.0
22 TraesCS2D01G269500 chrUn 84.634 846 90 11 39 845 162957229 162956385 0.000000e+00 806.0
23 TraesCS2D01G269500 chrUn 84.634 846 90 11 39 845 375464096 375463252 0.000000e+00 806.0
24 TraesCS2D01G269500 chrUn 84.397 846 92 17 39 845 163042367 163041523 0.000000e+00 795.0
25 TraesCS2D01G269500 chrUn 87.731 432 41 6 426 845 163043566 163043135 1.130000e-135 494.0
26 TraesCS2D01G269500 chrUn 91.139 79 6 1 4035 4113 111701385 111701462 6.210000e-19 106.0
27 TraesCS2D01G269500 chrUn 91.026 78 6 1 4035 4112 81697232 81697156 2.230000e-18 104.0
28 TraesCS2D01G269500 chrUn 91.026 78 6 1 4035 4112 150796057 150795981 2.230000e-18 104.0
29 TraesCS2D01G269500 chrUn 89.286 84 7 2 4028 4111 190888311 190888230 2.230000e-18 104.0
30 TraesCS2D01G269500 chrUn 89.286 84 7 2 4028 4111 355878528 355878609 2.230000e-18 104.0
31 TraesCS2D01G269500 chrUn 90.909 77 6 1 4036 4112 328262880 328262805 8.030000e-18 102.0
32 TraesCS2D01G269500 chrUn 91.781 73 5 1 4034 4106 283389496 283389567 2.890000e-17 100.0
33 TraesCS2D01G269500 chrUn 89.744 78 7 1 4035 4112 355880601 355880525 1.040000e-16 99.0
34 TraesCS2D01G269500 chrUn 89.610 77 7 1 4036 4112 60521663 60521588 3.740000e-16 97.1
35 TraesCS2D01G269500 chrUn 87.952 83 7 3 4032 4112 82594830 82594749 1.340000e-15 95.3
36 TraesCS2D01G269500 chr3B 83.594 640 93 10 2074 2708 752491054 752491686 1.410000e-164 590.0
37 TraesCS2D01G269500 chr3B 87.041 463 47 6 394 845 267223327 267223787 1.130000e-140 510.0
38 TraesCS2D01G269500 chr3B 88.018 217 23 3 2901 3117 798221937 798221724 2.100000e-63 254.0
39 TraesCS2D01G269500 chr5B 85.972 499 52 11 357 844 67328147 67328638 6.730000e-143 518.0
40 TraesCS2D01G269500 chr7B 87.004 454 55 4 35 487 526233319 526232869 4.050000e-140 508.0
41 TraesCS2D01G269500 chr7B 87.603 121 12 3 4034 4153 627984713 627984595 2.200000e-28 137.0
42 TraesCS2D01G269500 chr1D 84.171 537 62 13 303 822 411227718 411227188 2.440000e-137 499.0
43 TraesCS2D01G269500 chr1D 88.983 118 13 0 4035 4152 216328885 216329002 3.660000e-31 147.0
44 TraesCS2D01G269500 chr1D 91.111 90 6 2 4024 4112 48024741 48024653 2.220000e-23 121.0
45 TraesCS2D01G269500 chr1D 92.405 79 5 1 4033 4111 411310686 411310763 1.330000e-20 111.0
46 TraesCS2D01G269500 chr1D 91.139 79 6 1 4035 4113 186442515 186442438 6.210000e-19 106.0
47 TraesCS2D01G269500 chr1D 91.139 79 6 1 4034 4112 349422924 349423001 6.210000e-19 106.0
48 TraesCS2D01G269500 chr1D 91.139 79 6 1 4035 4113 419809745 419809668 6.210000e-19 106.0
49 TraesCS2D01G269500 chr1D 87.640 89 9 2 4025 4112 476769123 476769036 8.030000e-18 102.0
50 TraesCS2D01G269500 chr6A 89.916 119 12 0 4034 4152 144266676 144266558 2.190000e-33 154.0
51 TraesCS2D01G269500 chr6D 89.831 118 9 1 4035 4152 87598710 87598596 1.020000e-31 148.0
52 TraesCS2D01G269500 chr6D 88.136 118 14 0 4035 4152 384220927 384221044 1.700000e-29 141.0
53 TraesCS2D01G269500 chr6D 83.471 121 20 0 4032 4152 30289896 30290016 3.710000e-21 113.0
54 TraesCS2D01G269500 chr6D 92.405 79 5 1 4034 4112 81674637 81674714 1.330000e-20 111.0
55 TraesCS2D01G269500 chr6D 92.308 78 5 1 4035 4112 112344482 112344406 4.800000e-20 110.0
56 TraesCS2D01G269500 chr6B 89.076 119 13 0 4034 4152 205267344 205267226 1.020000e-31 148.0
57 TraesCS2D01G269500 chr6B 86.667 120 11 4 4035 4152 130078157 130078041 1.330000e-25 128.0
58 TraesCS2D01G269500 chr5D 88.235 119 13 1 4034 4152 55856606 55856723 1.700000e-29 141.0
59 TraesCS2D01G269500 chr1A 87.603 121 13 2 4034 4152 463825330 463825450 6.120000e-29 139.0
60 TraesCS2D01G269500 chr1A 95.238 84 4 0 4035 4118 23967648 23967731 2.850000e-27 134.0
61 TraesCS2D01G269500 chr1A 93.671 79 4 1 4035 4113 513297970 513298047 2.870000e-22 117.0
62 TraesCS2D01G269500 chr4D 86.290 124 16 1 4035 4158 392514824 392514702 2.850000e-27 134.0
63 TraesCS2D01G269500 chr4D 84.167 120 18 1 4033 4152 373568412 373568530 1.030000e-21 115.0
64 TraesCS2D01G269500 chr7A 86.441 118 16 0 4035 4152 398917344 398917227 3.680000e-26 130.0


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 TraesCS2D01G269500 chr2D 331733082 331737619 4537 False 8381.00 8381 100.0000 1 4538 1 chr2D.!!$F2 4537
1 TraesCS2D01G269500 chr2D 64193079 64193600 521 False 628.00 628 88.2780 45 587 1 chr2D.!!$F1 542
2 TraesCS2D01G269500 chr2B 399930719 399934209 3490 False 2551.50 4981 91.9820 954 4538 2 chr2B.!!$F1 3584
3 TraesCS2D01G269500 chr2A 439192643 439195335 2692 False 1811.25 3542 87.2985 847 3556 2 chr2A.!!$F1 2709
4 TraesCS2D01G269500 chr2A 439199260 439199762 502 False 228.00 298 89.2250 4151 4538 2 chr2A.!!$F2 387
5 TraesCS2D01G269500 chr7D 167590247 167591086 839 True 891.00 891 86.3910 33 846 1 chr7D.!!$R2 813
6 TraesCS2D01G269500 chr3D 74326916 74327677 761 True 887.00 887 87.6590 43 823 1 chr3D.!!$R1 780
7 TraesCS2D01G269500 chr3D 573206236 573207056 820 False 867.00 867 85.9560 34 846 1 chr3D.!!$F2 812
8 TraesCS2D01G269500 chr3D 564929342 564929945 603 False 584.00 584 84.2280 2099 2708 1 chr3D.!!$F1 609
9 TraesCS2D01G269500 chr3A 707834460 707835280 820 False 839.00 839 85.3510 34 846 1 chr3A.!!$F1 812
10 TraesCS2D01G269500 chr3A 699483027 699484684 1657 False 410.00 590 81.5410 2074 3321 2 chr3A.!!$F2 1247
11 TraesCS2D01G269500 chrUn 162982429 162983273 844 True 811.00 811 84.7520 39 845 1 chrUn.!!$R6 806
12 TraesCS2D01G269500 chrUn 162956385 162957229 844 True 806.00 806 84.6340 39 845 1 chrUn.!!$R5 806
13 TraesCS2D01G269500 chrUn 375463252 375464096 844 True 806.00 806 84.6340 39 845 1 chrUn.!!$R10 806
14 TraesCS2D01G269500 chrUn 163041523 163043566 2043 True 644.50 795 86.0640 39 845 2 chrUn.!!$R11 806
15 TraesCS2D01G269500 chr3B 752491054 752491686 632 False 590.00 590 83.5940 2074 2708 1 chr3B.!!$F2 634
16 TraesCS2D01G269500 chr1D 411227188 411227718 530 True 499.00 499 84.1710 303 822 1 chr1D.!!$R3 519

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
897 2139 0.033109 GGGTGCCAGGAAGCCTATTT 60.033 55.0 8.70 0.00 29.64 1.40 F
1630 2931 0.112995 TGCCATGGAGCCATATTCCC 59.887 55.0 18.40 0.00 34.91 3.97 F
3227 5055 0.108396 TTGAGCAGTACAAGCTGGCA 59.892 50.0 16.31 7.42 43.58 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1721 3022 0.037512 CTAGCAGATCCATGGAGCCG 60.038 60.0 26.11 17.74 0.00 5.52 R
3401 5237 0.035176 TTTTTGGGCATGGAAGCTGC 59.965 50.0 0.00 0.00 38.93 5.25 R
4127 5983 0.333652 CCCCCGTCCCAAATTACCTT 59.666 55.0 0.00 0.00 0.00 3.50 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
51 1214 7.754924 ACAATATGTTTAATTTTGGACGCTGAG 59.245 33.333 0.00 0.00 0.00 3.35
91 1254 0.902984 ACTAGACATCCGCCCACACA 60.903 55.000 0.00 0.00 0.00 3.72
141 1304 1.749665 CACGGGTCTTGTGTGGGTA 59.250 57.895 0.00 0.00 32.68 3.69
296 1460 1.722011 CGGGATGACGCTTTAGTTGT 58.278 50.000 0.00 0.00 0.00 3.32
354 1518 5.241728 GGCAACTCTCTCTGTTTTGGTTAAT 59.758 40.000 0.00 0.00 0.00 1.40
410 1596 3.365868 GCGTGCAATCAAACCATAGTTGA 60.366 43.478 0.00 0.00 35.97 3.18
437 1648 3.262151 TGTGCTTACCTAGTTGCCATGTA 59.738 43.478 0.00 0.00 0.00 2.29
483 1697 8.214364 TGTATGGTTAATCATAGTTGCCATGTA 58.786 33.333 8.73 0.00 36.70 2.29
506 1720 0.757512 TTACCTGGTTGCCACGTACA 59.242 50.000 3.84 0.00 27.95 2.90
512 1726 1.083015 GTTGCCACGTACACGCAAG 60.083 57.895 10.52 0.00 42.77 4.01
541 1755 5.029807 TGCCATCTACCAACGAATCATAA 57.970 39.130 0.00 0.00 0.00 1.90
599 1817 3.261643 ACTGCAGTTGACATCTATCACCA 59.738 43.478 15.25 0.00 0.00 4.17
635 1859 2.533318 CGAAGAGCAGTTCACCCAC 58.467 57.895 0.00 0.00 0.00 4.61
636 1860 0.249868 CGAAGAGCAGTTCACCCACA 60.250 55.000 0.00 0.00 0.00 4.17
777 2012 1.667724 CACGTGGCATTCAGATTCCTC 59.332 52.381 7.95 0.00 0.00 3.71
780 2015 3.197766 ACGTGGCATTCAGATTCCTCTAA 59.802 43.478 0.00 0.00 0.00 2.10
782 2017 4.681781 CGTGGCATTCAGATTCCTCTAAGT 60.682 45.833 0.00 0.00 0.00 2.24
796 2031 6.707440 TCCTCTAAGTTTCATGCAAAACAA 57.293 33.333 14.70 3.69 40.77 2.83
855 2095 4.614306 GCCATACGTGTGGGTTACTTTTTC 60.614 45.833 29.62 7.84 39.73 2.29
894 2136 3.015145 GGGGTGCCAGGAAGCCTA 61.015 66.667 16.05 0.00 35.47 3.93
895 2137 2.386935 GGGGTGCCAGGAAGCCTAT 61.387 63.158 16.05 0.00 35.47 2.57
896 2138 1.615262 GGGTGCCAGGAAGCCTATT 59.385 57.895 8.70 0.00 29.64 1.73
897 2139 0.033109 GGGTGCCAGGAAGCCTATTT 60.033 55.000 8.70 0.00 29.64 1.40
898 2140 1.619704 GGGTGCCAGGAAGCCTATTTT 60.620 52.381 8.70 0.00 29.64 1.82
899 2141 2.357777 GGGTGCCAGGAAGCCTATTTTA 60.358 50.000 8.70 0.00 29.64 1.52
900 2142 2.688446 GGTGCCAGGAAGCCTATTTTAC 59.312 50.000 0.00 0.00 29.64 2.01
901 2143 2.688446 GTGCCAGGAAGCCTATTTTACC 59.312 50.000 0.00 0.00 29.64 2.85
902 2144 2.580783 TGCCAGGAAGCCTATTTTACCT 59.419 45.455 0.00 0.00 29.64 3.08
903 2145 3.011257 TGCCAGGAAGCCTATTTTACCTT 59.989 43.478 0.00 0.00 29.64 3.50
904 2146 4.023980 GCCAGGAAGCCTATTTTACCTTT 58.976 43.478 0.00 0.00 29.64 3.11
905 2147 4.466370 GCCAGGAAGCCTATTTTACCTTTT 59.534 41.667 0.00 0.00 29.64 2.27
906 2148 5.046591 GCCAGGAAGCCTATTTTACCTTTTT 60.047 40.000 0.00 0.00 29.64 1.94
930 2172 7.379059 TTTAGGTAGCCTATTTTACCTACCC 57.621 40.000 9.33 0.00 46.78 3.69
984 2255 0.261991 AATAGACGGCCCAGAGAGGA 59.738 55.000 0.00 0.00 41.22 3.71
1136 2424 2.022240 CTCTAACTCCGGCCCTGCTC 62.022 65.000 0.00 0.00 0.00 4.26
1137 2425 3.432051 CTAACTCCGGCCCTGCTCG 62.432 68.421 0.00 0.00 0.00 5.03
1152 2440 1.862147 CTCGACTGCGTACGTTCCG 60.862 63.158 17.90 14.70 38.98 4.30
1161 2449 3.384532 TACGTTCCGGTGCTCCCC 61.385 66.667 0.00 0.00 0.00 4.81
1173 2461 0.832135 TGCTCCCCCGCCTCTATTAG 60.832 60.000 0.00 0.00 0.00 1.73
1174 2462 0.832559 GCTCCCCCGCCTCTATTAGT 60.833 60.000 0.00 0.00 0.00 2.24
1215 2503 3.522731 CCGGCTCCTCTCGACCTG 61.523 72.222 0.00 0.00 0.00 4.00
1216 2504 4.200283 CGGCTCCTCTCGACCTGC 62.200 72.222 0.00 0.00 0.00 4.85
1217 2505 2.757917 GGCTCCTCTCGACCTGCT 60.758 66.667 0.00 0.00 0.00 4.24
1218 2506 2.493973 GCTCCTCTCGACCTGCTG 59.506 66.667 0.00 0.00 0.00 4.41
1220 2508 3.408501 CTCCTCTCGACCTGCTGCG 62.409 68.421 0.00 0.00 0.00 5.18
1222 2510 4.127040 CTCTCGACCTGCTGCGCT 62.127 66.667 9.73 0.00 0.00 5.92
1223 2511 4.426112 TCTCGACCTGCTGCGCTG 62.426 66.667 9.73 10.04 0.00 5.18
1248 2545 0.737219 GATTCTGCGAGCTTGCCATT 59.263 50.000 23.34 6.31 0.00 3.16
1283 2583 2.038813 CCCAACCCCAATCCCCAC 59.961 66.667 0.00 0.00 0.00 4.61
1285 2585 2.857889 CAACCCCAATCCCCACCA 59.142 61.111 0.00 0.00 0.00 4.17
1365 2666 5.336102 AGGTGATTTCCCTGATTTGTCAAT 58.664 37.500 0.00 0.00 0.00 2.57
1376 2677 8.485392 TCCCTGATTTGTCAATTTTTCTTTCTT 58.515 29.630 0.00 0.00 0.00 2.52
1377 2678 9.762933 CCCTGATTTGTCAATTTTTCTTTCTTA 57.237 29.630 0.00 0.00 0.00 2.10
1466 2767 5.367945 TCAAGGTGTAGGTTCTTTCTGTT 57.632 39.130 0.00 0.00 0.00 3.16
1467 2768 5.365619 TCAAGGTGTAGGTTCTTTCTGTTC 58.634 41.667 0.00 0.00 0.00 3.18
1468 2769 5.130477 TCAAGGTGTAGGTTCTTTCTGTTCT 59.870 40.000 0.00 0.00 0.00 3.01
1469 2770 4.962155 AGGTGTAGGTTCTTTCTGTTCTG 58.038 43.478 0.00 0.00 0.00 3.02
1470 2771 4.409247 AGGTGTAGGTTCTTTCTGTTCTGT 59.591 41.667 0.00 0.00 0.00 3.41
1599 2900 5.694231 TTGTTGGATCATCAAGTGTTGAG 57.306 39.130 0.00 0.00 43.98 3.02
1630 2931 0.112995 TGCCATGGAGCCATATTCCC 59.887 55.000 18.40 0.00 34.91 3.97
1642 2943 6.015940 GGAGCCATATTCCCTTAATCTGTTTG 60.016 42.308 0.00 0.00 0.00 2.93
1680 2981 6.600822 GGGTACTTTTTGGGATAGTTCTAACC 59.399 42.308 0.00 0.00 0.00 2.85
1731 3032 2.281070 CGAATCCCGGCTCCATGG 60.281 66.667 4.97 4.97 33.91 3.66
1741 3046 0.321475 GGCTCCATGGATCTGCTAGC 60.321 60.000 16.63 13.08 0.00 3.42
1742 3047 0.686224 GCTCCATGGATCTGCTAGCT 59.314 55.000 16.63 0.00 0.00 3.32
1743 3048 1.898472 GCTCCATGGATCTGCTAGCTA 59.102 52.381 16.63 4.41 0.00 3.32
1744 3049 2.500910 GCTCCATGGATCTGCTAGCTAT 59.499 50.000 16.63 9.55 0.00 2.97
1749 3054 4.694509 CCATGGATCTGCTAGCTATTGTTC 59.305 45.833 17.23 7.90 0.00 3.18
1762 3067 3.060895 GCTATTGTTCTGTCGAGTTTCCG 59.939 47.826 0.00 0.00 0.00 4.30
1797 3102 5.359756 TCTGATTATGAGAACGGAACATGG 58.640 41.667 0.00 0.00 0.00 3.66
1853 3158 3.764972 AGTTAGGACTTAGCAGTGAGGAC 59.235 47.826 0.00 0.00 31.22 3.85
1988 3295 1.950909 TGAAATCGTGGGTGGTGTTTC 59.049 47.619 0.00 0.00 0.00 2.78
1997 3304 4.202070 CGTGGGTGGTGTTTCTTTTATGTT 60.202 41.667 0.00 0.00 0.00 2.71
2003 3310 8.145122 GGGTGGTGTTTCTTTTATGTTTATTGA 58.855 33.333 0.00 0.00 0.00 2.57
2006 3313 9.743057 TGGTGTTTCTTTTATGTTTATTGACTG 57.257 29.630 0.00 0.00 0.00 3.51
2108 3427 4.589216 ACTGTAGCGGTGTGTACTTTTA 57.411 40.909 0.00 0.00 0.00 1.52
2606 3929 2.565394 CGTAATCCGAGTGTCGCGC 61.565 63.158 0.00 0.00 38.82 6.86
2812 4625 8.015185 TGAGTGTAAGGTAAAGTTCAGTTAGT 57.985 34.615 0.00 0.00 0.00 2.24
2927 4741 1.331756 GATGTATTCCCTGCACAAGCG 59.668 52.381 0.00 0.00 46.23 4.68
3011 4825 0.877213 CTGCACAAACTTTGGCCTGC 60.877 55.000 3.32 2.86 32.63 4.85
3027 4841 1.415289 CCTGCTGATGCTACTCCATGA 59.585 52.381 0.00 0.00 40.48 3.07
3058 4872 6.345096 TGATGCTCATCCTCATATCGTTTA 57.655 37.500 7.34 0.00 37.02 2.01
3080 4908 8.500773 GTTTAGTGTACTAGTTATTTTGCTGCA 58.499 33.333 0.00 0.00 0.00 4.41
3137 4965 1.739562 GGCACTTCAGAGCTGACCG 60.740 63.158 0.00 0.00 39.66 4.79
3227 5055 0.108396 TTGAGCAGTACAAGCTGGCA 59.892 50.000 16.31 7.42 43.58 4.92
3336 5168 0.321919 TGTTCCATGCCAGCAGTCTC 60.322 55.000 0.00 0.00 0.00 3.36
3387 5223 0.249868 TGTCGTTGCTCTGTCCAAGG 60.250 55.000 0.00 0.00 0.00 3.61
3537 5373 4.725790 AAAGAATGATGCAGTTTAGCCC 57.274 40.909 0.00 0.00 0.00 5.19
3569 5405 6.269307 TCCTGTTTCTTTAAGCTGGTACTACT 59.731 38.462 0.00 0.00 36.63 2.57
3630 5466 2.489329 ACGCTTTGCAACAAGAGCATAT 59.511 40.909 18.29 3.33 42.33 1.78
3649 5485 6.835914 GCATATGCTACATGATAGTTTCACC 58.164 40.000 20.64 0.00 36.08 4.02
3709 5549 9.097257 TCAAAGGAAGCAAAGAGTAAAATTTTG 57.903 29.630 13.76 0.00 35.47 2.44
3729 5569 4.805140 TGCCAGGTCAATAAATATGGGA 57.195 40.909 0.00 0.00 0.00 4.37
3745 5585 3.726557 TGGGACATGAGAAGCAAATCT 57.273 42.857 0.00 0.00 0.00 2.40
3747 5587 4.774124 TGGGACATGAGAAGCAAATCTAG 58.226 43.478 0.00 0.00 0.00 2.43
3748 5588 4.471025 TGGGACATGAGAAGCAAATCTAGA 59.529 41.667 0.00 0.00 0.00 2.43
3749 5589 5.131642 TGGGACATGAGAAGCAAATCTAGAT 59.868 40.000 0.00 0.00 0.00 1.98
3751 5591 6.648725 GGGACATGAGAAGCAAATCTAGATAC 59.351 42.308 5.46 0.00 0.00 2.24
3753 5593 7.384660 GGACATGAGAAGCAAATCTAGATACAG 59.615 40.741 5.46 0.25 0.00 2.74
3754 5594 7.790027 ACATGAGAAGCAAATCTAGATACAGT 58.210 34.615 5.46 0.00 0.00 3.55
3755 5595 8.918116 ACATGAGAAGCAAATCTAGATACAGTA 58.082 33.333 5.46 0.00 0.00 2.74
3796 5652 2.706190 AGGTTAACCAGCTAGCCTATGG 59.294 50.000 26.26 17.58 40.10 2.74
3838 5694 5.177326 TGCTGAAGTGCAAACTTTTTCATT 58.823 33.333 0.00 0.00 40.29 2.57
3844 5700 9.429359 TGAAGTGCAAACTTTTTCATTTCTTAA 57.571 25.926 9.67 0.00 33.59 1.85
3937 5793 2.673775 TTGTGCAAGAGGGAATGGAA 57.326 45.000 0.00 0.00 0.00 3.53
3982 5838 0.751277 CAGTCCCACAAGCCACAACA 60.751 55.000 0.00 0.00 0.00 3.33
4008 5864 8.948631 ATGCATACCTATCAATTATCTTACCG 57.051 34.615 0.00 0.00 0.00 4.02
4039 5895 8.753497 ATTCAGTCCCTTCAAATTAATACTCC 57.247 34.615 0.00 0.00 0.00 3.85
4061 5917 1.426041 CCGCCCCGAATTACTTGTCG 61.426 60.000 0.00 0.00 37.01 4.35
4079 5935 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
4080 5936 6.101650 TGTCGCAGAAATGGATGTATCTAT 57.898 37.500 0.00 0.00 39.69 1.98
4082 5938 7.090808 TGTCGCAGAAATGGATGTATCTATAC 58.909 38.462 0.00 0.00 39.69 1.47
4127 5983 8.805175 ACATCAATTTCTATCCATTTGTGTGAA 58.195 29.630 0.00 0.00 0.00 3.18
4129 5985 9.865321 ATCAATTTCTATCCATTTGTGTGAAAG 57.135 29.630 0.00 0.00 0.00 2.62
4142 5998 3.566322 TGTGTGAAAGGTAATTTGGGACG 59.434 43.478 0.00 0.00 0.00 4.79
4207 6063 1.524355 CACAACGACTGAGCACAAGAG 59.476 52.381 0.00 0.00 0.00 2.85
4282 6141 4.456222 CCGTGTTTACCACAAATACCATCA 59.544 41.667 0.00 0.00 44.78 3.07
4379 6360 4.400884 TGAATCCCATACGTTGATTTTGGG 59.599 41.667 0.00 1.57 46.99 4.12
4398 6379 2.955660 GGGTGACAGGAACATTCAACAA 59.044 45.455 0.00 0.00 31.63 2.83
4454 6435 2.906389 AGGGCATCTTACAACTGAGACA 59.094 45.455 0.00 0.00 0.00 3.41
4455 6436 3.055530 AGGGCATCTTACAACTGAGACAG 60.056 47.826 0.00 0.00 37.52 3.51
4456 6437 3.265791 GGCATCTTACAACTGAGACAGG 58.734 50.000 0.00 0.00 35.51 4.00
4457 6438 2.675348 GCATCTTACAACTGAGACAGGC 59.325 50.000 0.00 0.00 35.51 4.85
4458 6439 3.866066 GCATCTTACAACTGAGACAGGCA 60.866 47.826 0.00 0.00 35.51 4.75
4459 6440 4.318332 CATCTTACAACTGAGACAGGCAA 58.682 43.478 0.00 0.00 35.51 4.52
4460 6441 4.415881 TCTTACAACTGAGACAGGCAAA 57.584 40.909 0.00 0.00 35.51 3.68
4461 6442 4.973168 TCTTACAACTGAGACAGGCAAAT 58.027 39.130 0.00 0.00 35.51 2.32
4462 6443 6.109156 TCTTACAACTGAGACAGGCAAATA 57.891 37.500 0.00 0.00 35.51 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.185505 GCGTCCAAAATTAAACATATTGTCCTA 58.814 33.333 0.00 0.00 0.00 2.94
22 23 7.033185 GCGTCCAAAATTAAACATATTGTCCT 58.967 34.615 0.00 0.00 0.00 3.85
23 24 7.009174 CAGCGTCCAAAATTAAACATATTGTCC 59.991 37.037 0.00 0.00 0.00 4.02
24 25 7.753132 TCAGCGTCCAAAATTAAACATATTGTC 59.247 33.333 0.00 0.00 0.00 3.18
26 27 7.967854 TCTCAGCGTCCAAAATTAAACATATTG 59.032 33.333 0.00 0.00 0.00 1.90
27 28 8.050778 TCTCAGCGTCCAAAATTAAACATATT 57.949 30.769 0.00 0.00 0.00 1.28
28 29 7.624360 TCTCAGCGTCCAAAATTAAACATAT 57.376 32.000 0.00 0.00 0.00 1.78
29 30 7.302524 GTTCTCAGCGTCCAAAATTAAACATA 58.697 34.615 0.00 0.00 0.00 2.29
30 31 5.957842 TCTCAGCGTCCAAAATTAAACAT 57.042 34.783 0.00 0.00 0.00 2.71
31 32 5.516090 GTTCTCAGCGTCCAAAATTAAACA 58.484 37.500 0.00 0.00 0.00 2.83
32 33 4.611366 CGTTCTCAGCGTCCAAAATTAAAC 59.389 41.667 0.00 0.00 0.00 2.01
34 35 3.810941 ACGTTCTCAGCGTCCAAAATTAA 59.189 39.130 0.00 0.00 38.23 1.40
37 38 1.878953 ACGTTCTCAGCGTCCAAAAT 58.121 45.000 0.00 0.00 38.23 1.82
38 39 3.372795 ACGTTCTCAGCGTCCAAAA 57.627 47.368 0.00 0.00 38.23 2.44
67 1230 0.969894 GGGCGGATGTCTAGTATGCT 59.030 55.000 0.00 0.00 0.00 3.79
91 1254 0.388659 TACTTACGCCACACACGGTT 59.611 50.000 0.00 0.00 34.00 4.44
131 1294 5.009210 GCAGTTCTAATGTTTACCCACACAA 59.991 40.000 0.00 0.00 0.00 3.33
141 1304 3.561143 TGTGTGGGCAGTTCTAATGTTT 58.439 40.909 0.00 0.00 0.00 2.83
296 1460 2.142356 ACATTTGCCATCCCGAATGA 57.858 45.000 8.64 0.00 38.37 2.57
410 1596 3.074412 GCAACTAGGTAAGCACACATGT 58.926 45.455 0.00 0.00 0.00 3.21
437 1648 7.177216 CCATACATGGCAACTATGATTAACCAT 59.823 37.037 13.62 0.00 41.75 3.55
483 1697 1.243902 CGTGGCAACCAGGTAAACAT 58.756 50.000 0.00 0.00 35.03 2.71
506 1720 2.133742 GATGGCAACTGCACTTGCGT 62.134 55.000 20.26 13.60 46.43 5.24
512 1726 1.200020 GTTGGTAGATGGCAACTGCAC 59.800 52.381 14.23 2.47 44.36 4.57
541 1755 4.662278 ACTAGGTAAACACACATGGCAAT 58.338 39.130 0.00 0.00 0.00 3.56
587 1805 2.885266 ACGCTCGTATGGTGATAGATGT 59.115 45.455 0.00 0.00 0.00 3.06
633 1857 2.587753 AACCAGTCCACGCGTGTG 60.588 61.111 34.81 26.20 46.00 3.82
634 1858 2.587753 CAACCAGTCCACGCGTGT 60.588 61.111 34.81 16.67 0.00 4.49
635 1859 3.345808 CCAACCAGTCCACGCGTG 61.346 66.667 31.77 31.77 0.00 5.34
636 1860 3.857038 ACCAACCAGTCCACGCGT 61.857 61.111 5.58 5.58 0.00 6.01
766 1991 6.475504 TGCATGAAACTTAGAGGAATCTGAA 58.524 36.000 0.00 0.00 0.00 3.02
777 2012 9.640974 CTTGATTTTGTTTTGCATGAAACTTAG 57.359 29.630 13.62 0.56 39.62 2.18
780 2015 6.598850 ACCTTGATTTTGTTTTGCATGAAACT 59.401 30.769 13.62 0.00 39.62 2.66
782 2017 6.183360 CCACCTTGATTTTGTTTTGCATGAAA 60.183 34.615 0.00 0.00 0.00 2.69
796 2031 3.753272 CACGTCTTGATCCACCTTGATTT 59.247 43.478 0.00 0.00 0.00 2.17
836 2076 4.571580 CACAGAAAAAGTAACCCACACGTA 59.428 41.667 0.00 0.00 0.00 3.57
855 2095 2.430332 GGGGTCAATCTCTCTCTCACAG 59.570 54.545 0.00 0.00 0.00 3.66
908 2150 6.299227 AGGGTAGGTAAAATAGGCTACCTA 57.701 41.667 8.70 8.70 44.96 3.08
910 2152 5.901413 AAGGGTAGGTAAAATAGGCTACC 57.099 43.478 0.00 0.00 38.30 3.18
1109 2397 2.491022 CGGAGTTAGAGAGGGGCCG 61.491 68.421 0.00 0.00 0.00 6.13
1120 2408 3.458163 CGAGCAGGGCCGGAGTTA 61.458 66.667 5.05 0.00 0.00 2.24
1161 2449 1.604185 GCAGCAGACTAATAGAGGCGG 60.604 57.143 0.00 0.00 38.79 6.13
1203 2491 3.443925 CGCAGCAGGTCGAGAGGA 61.444 66.667 0.00 0.00 0.00 3.71
1283 2583 1.021390 CGACCAGGCTAGTGCTTTGG 61.021 60.000 0.00 9.33 43.94 3.28
1285 2585 0.396811 AACGACCAGGCTAGTGCTTT 59.603 50.000 0.00 0.00 39.59 3.51
1365 2666 9.239551 GCCCTAAGTCCTAATAAGAAAGAAAAA 57.760 33.333 0.00 0.00 0.00 1.94
1376 2677 5.131977 TCAATGCAAGCCCTAAGTCCTAATA 59.868 40.000 0.00 0.00 0.00 0.98
1377 2678 4.079787 TCAATGCAAGCCCTAAGTCCTAAT 60.080 41.667 0.00 0.00 0.00 1.73
1378 2679 3.265737 TCAATGCAAGCCCTAAGTCCTAA 59.734 43.478 0.00 0.00 0.00 2.69
1379 2680 2.843730 TCAATGCAAGCCCTAAGTCCTA 59.156 45.455 0.00 0.00 0.00 2.94
1380 2681 1.635487 TCAATGCAAGCCCTAAGTCCT 59.365 47.619 0.00 0.00 0.00 3.85
1381 2682 2.128771 TCAATGCAAGCCCTAAGTCC 57.871 50.000 0.00 0.00 0.00 3.85
1382 2683 6.656693 ACATATATCAATGCAAGCCCTAAGTC 59.343 38.462 0.00 0.00 0.00 3.01
1383 2684 6.546484 ACATATATCAATGCAAGCCCTAAGT 58.454 36.000 0.00 0.00 0.00 2.24
1384 2685 7.392673 AGAACATATATCAATGCAAGCCCTAAG 59.607 37.037 0.00 0.00 0.00 2.18
1385 2686 7.233632 AGAACATATATCAATGCAAGCCCTAA 58.766 34.615 0.00 0.00 0.00 2.69
1466 2767 5.939764 ATGAGCTTTACATGACCTACAGA 57.060 39.130 0.00 0.00 0.00 3.41
1467 2768 7.436933 TGATATGAGCTTTACATGACCTACAG 58.563 38.462 0.00 0.00 0.00 2.74
1468 2769 7.360113 TGATATGAGCTTTACATGACCTACA 57.640 36.000 0.00 0.00 0.00 2.74
1469 2770 8.552034 GTTTGATATGAGCTTTACATGACCTAC 58.448 37.037 0.00 0.00 0.00 3.18
1470 2771 8.264347 TGTTTGATATGAGCTTTACATGACCTA 58.736 33.333 0.00 0.00 0.00 3.08
1630 2931 4.619973 TGGCAAAGCACAAACAGATTAAG 58.380 39.130 0.00 0.00 0.00 1.85
1642 2943 0.611896 AGTACCCCATGGCAAAGCAC 60.612 55.000 6.09 0.00 33.59 4.40
1680 2981 3.428589 GGCCAAAATTCAAGCAGCTAGAG 60.429 47.826 0.00 0.00 0.00 2.43
1721 3022 0.037512 CTAGCAGATCCATGGAGCCG 60.038 60.000 26.11 17.74 0.00 5.52
1731 3032 4.679197 CGACAGAACAATAGCTAGCAGATC 59.321 45.833 18.83 7.92 0.00 2.75
1741 3046 3.060895 GCGGAAACTCGACAGAACAATAG 59.939 47.826 0.00 0.00 0.00 1.73
1742 3047 2.991190 GCGGAAACTCGACAGAACAATA 59.009 45.455 0.00 0.00 0.00 1.90
1743 3048 1.798813 GCGGAAACTCGACAGAACAAT 59.201 47.619 0.00 0.00 0.00 2.71
1744 3049 1.214367 GCGGAAACTCGACAGAACAA 58.786 50.000 0.00 0.00 0.00 2.83
1749 3054 2.049433 ACGGCGGAAACTCGACAG 60.049 61.111 13.24 0.00 38.22 3.51
1762 3067 4.876125 TCATAATCAGATTCTCAGACGGC 58.124 43.478 0.00 0.00 0.00 5.68
1797 3102 6.265196 TGAATCAATGGGCTGTTATAATGGAC 59.735 38.462 0.00 0.00 0.00 4.02
1961 3268 3.078097 CCACCCACGATTTCATGTGTTA 58.922 45.455 0.00 0.00 34.28 2.41
2019 3326 4.928615 CCTTGTTCTTCTGTTTTGCAAACA 59.071 37.500 12.39 12.14 0.00 2.83
2108 3427 8.540507 AGATATATCTTCGCCACTATACCATT 57.459 34.615 9.57 0.00 31.97 3.16
2469 3789 6.096705 CCCCAAACACTTATGATGCAATCTAA 59.903 38.462 0.00 0.00 45.81 2.10
2473 3793 4.081531 CACCCCAAACACTTATGATGCAAT 60.082 41.667 0.00 0.00 0.00 3.56
2606 3929 2.738846 CCACACTTTCTGGTGATCTTCG 59.261 50.000 1.52 0.00 40.13 3.79
2812 4625 9.753674 AAAATTAGAAAGGAGGTCATGTGATTA 57.246 29.630 0.00 0.00 0.00 1.75
2927 4741 4.989279 AAACATACATCATCAGGCCAAC 57.011 40.909 5.01 0.00 0.00 3.77
3011 4825 7.496920 TCAAAACTATTCATGGAGTAGCATCAG 59.503 37.037 0.00 0.00 0.00 2.90
3058 4872 7.530010 CATTGCAGCAAAATAACTAGTACACT 58.470 34.615 12.97 0.00 0.00 3.55
3080 4908 6.670695 AAACATTCCTTTCTGTTAGGCATT 57.329 33.333 0.00 0.00 34.61 3.56
3137 4965 5.046231 ACTTCCTGGAAAGGAGTAGATTGAC 60.046 44.000 10.86 0.00 39.43 3.18
3227 5055 0.249073 GCGTCATACGATCACCAGCT 60.249 55.000 3.22 0.00 46.05 4.24
3336 5168 7.884816 TTGTCTAGATTACTGGTTCTTTTCG 57.115 36.000 0.00 0.00 0.00 3.46
3393 5229 0.172803 CATGGAAGCTGCCTTCTTGC 59.827 55.000 13.40 0.00 45.44 4.01
3401 5237 0.035176 TTTTTGGGCATGGAAGCTGC 59.965 50.000 0.00 0.00 38.93 5.25
3537 5373 6.421801 CCAGCTTAAAGAAACAGGAAAACATG 59.578 38.462 0.00 0.00 0.00 3.21
3569 5405 7.648142 AGAAACATGAAAACGCTTGATAAAGA 58.352 30.769 0.00 0.00 0.00 2.52
3630 5466 4.729227 TCGGTGAAACTATCATGTAGCA 57.271 40.909 0.00 0.00 40.97 3.49
3649 5485 9.530129 GTACTATTCACTTTCTGTTTTTCATCG 57.470 33.333 0.00 0.00 0.00 3.84
3658 5494 7.680730 AGGACATTGTACTATTCACTTTCTGT 58.319 34.615 0.00 0.00 0.00 3.41
3680 5516 3.864789 ACTCTTTGCTTCCTTTGAGGA 57.135 42.857 0.00 0.00 44.10 3.71
3709 5549 4.469657 TGTCCCATATTTATTGACCTGGC 58.530 43.478 0.00 0.00 0.00 4.85
3711 5551 7.226441 TCTCATGTCCCATATTTATTGACCTG 58.774 38.462 0.00 0.00 0.00 4.00
3729 5569 7.790027 ACTGTATCTAGATTTGCTTCTCATGT 58.210 34.615 11.25 0.00 0.00 3.21
3759 5615 2.746803 TAACCTCTGTTCCGCTTTTGCA 60.747 45.455 0.00 0.00 39.62 4.08
3796 5652 2.610232 GCAAATGATGTGGGTTGTGTCC 60.610 50.000 0.00 0.00 0.00 4.02
3937 5793 3.202097 CGCCAACCAAATTTTGTTTCCT 58.798 40.909 4.96 0.00 0.00 3.36
3982 5838 9.383519 CGGTAAGATAATTGATAGGTATGCATT 57.616 33.333 3.54 0.00 0.00 3.56
4008 5864 6.535963 AATTTGAAGGGACTGAATTGATCC 57.464 37.500 0.00 0.00 40.86 3.36
4039 5895 0.814010 CAAGTAATTCGGGGCGGAGG 60.814 60.000 0.00 0.00 0.00 4.30
4061 5917 9.587772 AATACGTATAGATACATCCATTTCTGC 57.412 33.333 8.83 0.00 32.87 4.26
4127 5983 0.333652 CCCCCGTCCCAAATTACCTT 59.666 55.000 0.00 0.00 0.00 3.50
4129 5985 4.670199 CCCCCGTCCCAAATTACC 57.330 61.111 0.00 0.00 0.00 2.85
4207 6063 2.670509 GCCAGATTGTTGCTTGAGCTTC 60.671 50.000 4.44 0.00 42.66 3.86
4282 6141 4.408182 AGTGACTTGCTTACACAGAACT 57.592 40.909 0.00 0.00 37.05 3.01
4379 6360 5.519927 CCTTTTTGTTGAATGTTCCTGTCAC 59.480 40.000 0.00 0.00 0.00 3.67
4398 6379 7.148306 GGATACATGTAACATTCGTGACCTTTT 60.148 37.037 10.14 0.00 0.00 2.27
4440 6421 6.128172 CCTTATTTGCCTGTCTCAGTTGTAAG 60.128 42.308 0.00 0.00 0.00 2.34
4454 6435 5.419239 TGCTTTATTTGCCTTATTTGCCT 57.581 34.783 0.00 0.00 0.00 4.75
4455 6436 6.018507 CAGATGCTTTATTTGCCTTATTTGCC 60.019 38.462 0.00 0.00 0.00 4.52
4456 6437 6.510638 GCAGATGCTTTATTTGCCTTATTTGC 60.511 38.462 0.00 0.00 40.13 3.68
4457 6438 6.535865 TGCAGATGCTTTATTTGCCTTATTTG 59.464 34.615 6.35 0.00 44.10 2.32
4458 6439 6.642430 TGCAGATGCTTTATTTGCCTTATTT 58.358 32.000 6.35 0.00 44.10 1.40
4459 6440 6.224665 TGCAGATGCTTTATTTGCCTTATT 57.775 33.333 6.35 0.00 44.10 1.40
4460 6441 5.857471 TGCAGATGCTTTATTTGCCTTAT 57.143 34.783 6.35 0.00 44.10 1.73
4461 6442 5.657826 TTGCAGATGCTTTATTTGCCTTA 57.342 34.783 6.35 0.00 44.10 2.69
4462 6443 4.540359 TTGCAGATGCTTTATTTGCCTT 57.460 36.364 6.35 0.00 44.10 4.35


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

AutoCloner maintained by Alex Coulton.