Multiple sequence alignment - TraesCS2A01G041500

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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 TraesCS2A01G041500 chr2A 100.000 2672 0 0 1 2672 16744853 16747524 0.000000e+00 4935.0
1 TraesCS2A01G041500 chr2A 82.189 539 81 9 1142 1671 16771394 16771926 1.460000e-122 449.0
2 TraesCS2A01G041500 chr2A 80.952 168 25 5 2307 2472 377137399 377137237 2.790000e-25 126.0
3 TraesCS2A01G041500 chr2A 98.485 66 1 0 1109 1174 16745928 16745993 1.680000e-22 117.0
4 TraesCS2A01G041500 chr2A 98.485 66 1 0 1076 1141 16745961 16746026 1.680000e-22 117.0
5 TraesCS2A01G041500 chr2A 80.583 103 15 4 2507 2609 674018489 674018586 1.030000e-09 75.0
6 TraesCS2A01G041500 chr2D 84.596 1584 145 45 1142 2669 14642343 14643883 0.000000e+00 1482.0
7 TraesCS2A01G041500 chr2D 87.011 1278 88 37 1142 2374 14437460 14438704 0.000000e+00 1369.0
8 TraesCS2A01G041500 chr2D 83.920 852 60 29 36 865 14436485 14437281 0.000000e+00 743.0
9 TraesCS2A01G041500 chr2D 88.126 539 54 7 1142 1679 14591381 14591910 1.350000e-177 632.0
10 TraesCS2A01G041500 chr2D 81.383 752 72 31 337 1072 14641631 14642330 3.890000e-153 551.0
11 TraesCS2A01G041500 chr2D 80.127 790 79 45 340 1108 14590681 14591413 3.940000e-143 518.0
12 TraesCS2A01G041500 chr2D 83.734 541 69 13 1142 1671 14647746 14648278 6.650000e-136 494.0
13 TraesCS2A01G041500 chr2D 82.430 535 65 17 1150 1671 14711858 14712376 8.780000e-120 440.0
14 TraesCS2A01G041500 chr2D 81.400 543 78 14 1142 1671 14443282 14443814 3.180000e-114 422.0
15 TraesCS2A01G041500 chr2D 83.011 465 70 7 1207 1671 14694540 14694995 1.910000e-111 412.0
16 TraesCS2A01G041500 chr2D 80.891 539 73 19 1142 1671 14704241 14704758 5.360000e-107 398.0
17 TraesCS2A01G041500 chr2D 79.963 539 93 7 1142 1671 14565792 14566324 1.500000e-102 383.0
18 TraesCS2A01G041500 chr2D 91.852 270 15 4 3 271 14434204 14434467 1.170000e-98 370.0
19 TraesCS2A01G041500 chr2D 88.168 262 18 8 40 299 14590419 14590669 1.550000e-77 300.0
20 TraesCS2A01G041500 chr2D 84.375 256 24 9 1785 2032 14592099 14592346 1.240000e-58 237.0
21 TraesCS2A01G041500 chr2D 86.420 162 12 7 955 1108 14437333 14437492 4.570000e-38 169.0
22 TraesCS2A01G041500 chr2D 78.853 279 27 10 2414 2672 14438705 14438971 2.750000e-35 159.0
23 TraesCS2A01G041500 chr2D 81.579 152 20 7 2321 2470 376370088 376370233 4.670000e-23 119.0
24 TraesCS2A01G041500 chr2D 85.057 87 8 5 2114 2198 577331431 577331514 1.700000e-12 84.2
25 TraesCS2A01G041500 chr2D 85.897 78 7 2 1 78 14590318 14590391 2.210000e-11 80.5
26 TraesCS2A01G041500 chr2D 87.500 64 8 0 15 78 14436398 14436461 1.030000e-09 75.0
27 TraesCS2A01G041500 chr2B 82.848 1510 164 50 1142 2622 26348958 26350401 0.000000e+00 1266.0
28 TraesCS2A01G041500 chr2B 93.607 829 29 4 3 809 26347894 26348720 0.000000e+00 1216.0
29 TraesCS2A01G041500 chr2B 82.222 540 79 10 1142 1671 26354522 26355054 1.460000e-122 449.0
30 TraesCS2A01G041500 chr2B 81.218 197 25 11 2321 2510 733098787 733098978 5.960000e-32 148.0
31 TraesCS2A01G041500 chr2B 88.983 118 13 0 955 1072 26348825 26348942 2.140000e-31 147.0
32 TraesCS2A01G041500 chr2B 90.909 55 5 0 2617 2671 486591274 486591328 1.030000e-09 75.0
33 TraesCS2A01G041500 chr2B 95.652 46 1 1 2616 2661 733465836 733465880 3.690000e-09 73.1
34 TraesCS2A01G041500 chr5B 80.000 290 45 11 2338 2624 620004109 620003830 4.510000e-48 202.0
35 TraesCS2A01G041500 chr5B 79.535 215 36 8 2356 2566 293246104 293245894 2.140000e-31 147.0
36 TraesCS2A01G041500 chr5B 92.982 57 3 1 2615 2671 488715622 488715677 6.130000e-12 82.4
37 TraesCS2A01G041500 chr5B 91.071 56 4 1 2616 2671 590394545 590394599 1.030000e-09 75.0
38 TraesCS2A01G041500 chr1B 78.689 305 52 9 2321 2619 334434200 334434497 9.760000e-45 191.0
39 TraesCS2A01G041500 chr1D 77.108 332 46 19 2145 2462 259265045 259265360 5.920000e-37 165.0
40 TraesCS2A01G041500 chr7D 84.000 175 21 6 2357 2527 183797609 183797438 7.650000e-36 161.0
41 TraesCS2A01G041500 chr7D 92.727 55 4 0 2617 2671 133394725 133394779 2.210000e-11 80.5
42 TraesCS2A01G041500 chr3B 77.931 290 42 15 2297 2571 160696236 160695954 7.650000e-36 161.0
43 TraesCS2A01G041500 chr3B 91.071 56 4 1 2616 2671 448311466 448311412 1.030000e-09 75.0
44 TraesCS2A01G041500 chr3B 88.462 52 6 0 2523 2574 73302884 73302833 2.220000e-06 63.9
45 TraesCS2A01G041500 chr6A 78.661 239 39 10 2340 2566 94217686 94217924 5.960000e-32 148.0
46 TraesCS2A01G041500 chr5A 80.676 207 27 11 2357 2553 616543435 616543232 5.960000e-32 148.0
47 TraesCS2A01G041500 chr3D 81.761 159 20 8 2324 2477 104342926 104342772 1.000000e-24 124.0
48 TraesCS2A01G041500 chr4D 92.727 55 4 0 2617 2671 500412606 500412552 2.210000e-11 80.5
49 TraesCS2A01G041500 chr7A 87.273 55 7 0 2617 2671 119781853 119781799 2.220000e-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 TraesCS2A01G041500 chr2A 16744853 16747524 2671 False 1723.000000 4935 98.990000 1 2672 3 chr2A.!!$F3 2671
1 TraesCS2A01G041500 chr2A 16771394 16771926 532 False 449.000000 449 82.189000 1142 1671 1 chr2A.!!$F1 529
2 TraesCS2A01G041500 chr2D 14641631 14648278 6647 False 842.333333 1482 83.237667 337 2669 3 chr2D.!!$F10 2332
3 TraesCS2A01G041500 chr2D 14434204 14438971 4767 False 480.833333 1369 85.926000 3 2672 6 chr2D.!!$F8 2669
4 TraesCS2A01G041500 chr2D 14711858 14712376 518 False 440.000000 440 82.430000 1150 1671 1 chr2D.!!$F5 521
5 TraesCS2A01G041500 chr2D 14443282 14443814 532 False 422.000000 422 81.400000 1142 1671 1 chr2D.!!$F1 529
6 TraesCS2A01G041500 chr2D 14704241 14704758 517 False 398.000000 398 80.891000 1142 1671 1 chr2D.!!$F4 529
7 TraesCS2A01G041500 chr2D 14565792 14566324 532 False 383.000000 383 79.963000 1142 1671 1 chr2D.!!$F2 529
8 TraesCS2A01G041500 chr2D 14590318 14592346 2028 False 353.500000 632 85.338600 1 2032 5 chr2D.!!$F9 2031
9 TraesCS2A01G041500 chr2B 26347894 26350401 2507 False 876.333333 1266 88.479333 3 2622 3 chr2B.!!$F5 2619
10 TraesCS2A01G041500 chr2B 26354522 26355054 532 False 449.000000 449 82.222000 1142 1671 1 chr2B.!!$F1 529

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
879 3236 0.105224 TATATTGTGACCCACCCGCG 59.895 55.0 0.0 0.0 32.73 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 10004 0.74299 CCATTACGAGGCTGCCGAAA 60.743 55.0 13.96 6.76 0.0 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
42 43 8.858094 CCCTAGTAGATACTAAAAGAAACGGAT 58.142 37.037 0.00 0.00 38.24 4.18
177 246 2.122769 TGGACGACCCTGAACCCA 60.123 61.111 0.34 0.00 35.38 4.51
310 2624 0.981277 CCAGATACCACCCCTCCGTT 60.981 60.000 0.00 0.00 0.00 4.44
322 2636 6.788957 ACCACCCCTCCGTTCTATAATATAAA 59.211 38.462 0.00 0.00 0.00 1.40
325 2639 7.330208 CACCCCTCCGTTCTATAATATAAAACG 59.670 40.741 10.86 10.86 41.60 3.60
339 2653 6.704512 ATATAAAACGTTTTTGCAAGCCAG 57.295 33.333 29.42 0.00 0.00 4.85
383 2697 2.152016 GGTTTTGTCTACAGGTGAGGC 58.848 52.381 0.00 0.00 0.00 4.70
612 2961 1.379977 CCCTACGTGAGCCCTCTCA 60.380 63.158 0.00 0.00 46.43 3.27
622 2971 0.919710 AGCCCTCTCACCCATTTACC 59.080 55.000 0.00 0.00 0.00 2.85
689 3039 0.657659 CATCTCACGTACCGCTAGCG 60.658 60.000 29.93 29.93 39.44 4.26
811 3167 3.951775 TTTGTCAGCACAAAGTTTGGT 57.048 38.095 19.45 3.03 45.73 3.67
812 3168 3.951775 TTGTCAGCACAAAGTTTGGTT 57.048 38.095 19.45 4.37 39.69 3.67
813 3169 3.951775 TGTCAGCACAAAGTTTGGTTT 57.048 38.095 19.45 1.78 34.12 3.27
814 3170 5.392767 TTGTCAGCACAAAGTTTGGTTTA 57.607 34.783 19.45 0.00 39.69 2.01
815 3171 4.739195 TGTCAGCACAAAGTTTGGTTTAC 58.261 39.130 19.45 10.84 34.12 2.01
819 3175 7.030768 GTCAGCACAAAGTTTGGTTTACTTTA 58.969 34.615 19.45 0.00 42.32 1.85
833 3189 6.037391 TGGTTTACTTTACTCTTGTCAAACCG 59.963 38.462 0.00 0.00 44.16 4.44
837 3193 2.163818 TACTCTTGTCAAACCGCCAG 57.836 50.000 0.00 0.00 0.00 4.85
846 3203 3.976701 AAACCGCCAGGCTCCATCG 62.977 63.158 10.54 0.00 42.76 3.84
850 3207 3.550431 GCCAGGCTCCATCGGCTA 61.550 66.667 3.29 0.00 41.50 3.93
851 3208 2.739784 CCAGGCTCCATCGGCTAG 59.260 66.667 0.00 0.00 37.76 3.42
852 3209 2.030262 CAGGCTCCATCGGCTAGC 59.970 66.667 6.04 6.04 37.76 3.42
853 3210 2.123077 AGGCTCCATCGGCTAGCT 60.123 61.111 15.72 0.00 38.12 3.32
873 3230 3.009033 GCTGCCCTATATATTGTGACCCA 59.991 47.826 0.00 0.00 0.00 4.51
875 3232 3.329520 TGCCCTATATATTGTGACCCACC 59.670 47.826 0.00 0.00 32.73 4.61
879 3236 0.105224 TATATTGTGACCCACCCGCG 59.895 55.000 0.00 0.00 32.73 6.46
898 3255 1.660333 CGCAGCTTCTGAACGAAAACC 60.660 52.381 0.00 0.00 32.44 3.27
902 3259 1.975660 CTTCTGAACGAAAACCCCCA 58.024 50.000 0.00 0.00 0.00 4.96
904 3261 0.533308 TCTGAACGAAAACCCCCACG 60.533 55.000 0.00 0.00 0.00 4.94
907 3264 3.717924 AACGAAAACCCCCACGGCA 62.718 57.895 0.00 0.00 33.26 5.69
913 3270 2.150014 AAACCCCCACGGCAATAGCT 62.150 55.000 0.00 0.00 41.70 3.32
919 3276 2.297701 CCCACGGCAATAGCTAATTGT 58.702 47.619 0.00 0.00 45.78 2.71
923 3287 1.949525 CGGCAATAGCTAATTGTGCCT 59.050 47.619 25.88 0.00 45.78 4.75
924 3288 2.287188 CGGCAATAGCTAATTGTGCCTG 60.287 50.000 25.88 19.31 45.78 4.85
947 3311 2.821366 GGAGCACGCCCACTGATG 60.821 66.667 0.00 0.00 0.00 3.07
948 3312 2.265739 GAGCACGCCCACTGATGA 59.734 61.111 0.00 0.00 0.00 2.92
949 3313 2.046892 AGCACGCCCACTGATGAC 60.047 61.111 0.00 0.00 0.00 3.06
950 3314 2.358615 GCACGCCCACTGATGACA 60.359 61.111 0.00 0.00 0.00 3.58
951 3315 2.680913 GCACGCCCACTGATGACAC 61.681 63.158 0.00 0.00 0.00 3.67
952 3316 2.034879 CACGCCCACTGATGACACC 61.035 63.158 0.00 0.00 0.00 4.16
953 3317 2.436646 CGCCCACTGATGACACCC 60.437 66.667 0.00 0.00 0.00 4.61
969 3333 4.373116 CCACACCCACCGTCTCCG 62.373 72.222 0.00 0.00 0.00 4.63
1007 3373 2.174107 CAACACGCGCATGGACAG 59.826 61.111 8.88 0.00 0.00 3.51
1072 3438 4.862823 CCGACCCCTCCTCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
1073 3439 3.756783 CGACCCCTCCTCCTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
1077 8846 2.197324 CCCTCCTCCTCCCTCTCG 59.803 72.222 0.00 0.00 0.00 4.04
1082 8851 1.454847 CCTCCTCCCTCTCGTCCTG 60.455 68.421 0.00 0.00 0.00 3.86
1084 8853 2.443016 CCTCCCTCTCGTCCTGGG 60.443 72.222 0.00 0.00 42.20 4.45
1085 8854 2.684104 CTCCCTCTCGTCCTGGGA 59.316 66.667 0.00 0.00 46.78 4.37
1086 8855 1.755008 CTCCCTCTCGTCCTGGGAC 60.755 68.421 9.55 9.55 44.37 4.46
1087 8856 2.218115 CTCCCTCTCGTCCTGGGACT 62.218 65.000 16.44 0.00 44.37 3.85
1088 8857 1.755008 CCCTCTCGTCCTGGGACTC 60.755 68.421 16.44 0.00 43.47 3.36
1089 8858 1.000771 CCTCTCGTCCTGGGACTCA 60.001 63.158 16.44 3.71 42.54 3.41
1090 8859 0.396417 CCTCTCGTCCTGGGACTCAT 60.396 60.000 16.44 0.00 42.54 2.90
1091 8860 1.479709 CTCTCGTCCTGGGACTCATT 58.520 55.000 16.44 0.00 42.54 2.57
1092 8861 1.827969 CTCTCGTCCTGGGACTCATTT 59.172 52.381 16.44 0.00 42.54 2.32
1093 8862 1.825474 TCTCGTCCTGGGACTCATTTC 59.175 52.381 16.44 0.00 42.54 2.17
1094 8863 0.902531 TCGTCCTGGGACTCATTTCC 59.097 55.000 16.44 0.00 42.54 3.13
1095 8864 0.613260 CGTCCTGGGACTCATTTCCA 59.387 55.000 16.44 0.00 42.54 3.53
1096 8865 1.676014 CGTCCTGGGACTCATTTCCAC 60.676 57.143 16.44 0.00 42.54 4.02
1097 8866 0.991920 TCCTGGGACTCATTTCCACC 59.008 55.000 0.00 0.00 37.40 4.61
1098 8867 0.034089 CCTGGGACTCATTTCCACCC 60.034 60.000 0.00 0.00 37.40 4.61
1099 8868 0.392998 CTGGGACTCATTTCCACCCG 60.393 60.000 0.00 0.00 43.04 5.28
1100 8869 0.838554 TGGGACTCATTTCCACCCGA 60.839 55.000 0.00 0.00 43.04 5.14
1101 8870 0.392595 GGGACTCATTTCCACCCGAC 60.393 60.000 0.00 0.00 37.40 4.79
1102 8871 0.613777 GGACTCATTTCCACCCGACT 59.386 55.000 0.00 0.00 35.49 4.18
1103 8872 1.003233 GGACTCATTTCCACCCGACTT 59.997 52.381 0.00 0.00 35.49 3.01
1104 8873 2.076863 GACTCATTTCCACCCGACTTG 58.923 52.381 0.00 0.00 0.00 3.16
1105 8874 1.697432 ACTCATTTCCACCCGACTTGA 59.303 47.619 0.00 0.00 0.00 3.02
1106 8875 2.289694 ACTCATTTCCACCCGACTTGAG 60.290 50.000 0.00 0.00 36.47 3.02
1107 8876 1.697432 TCATTTCCACCCGACTTGAGT 59.303 47.619 0.00 0.00 0.00 3.41
1108 8877 2.105821 TCATTTCCACCCGACTTGAGTT 59.894 45.455 0.00 0.00 0.00 3.01
1109 8878 2.249844 TTTCCACCCGACTTGAGTTC 57.750 50.000 0.00 0.00 0.00 3.01
1110 8879 0.032952 TTCCACCCGACTTGAGTTCG 59.967 55.000 0.00 0.00 0.00 3.95
1111 8880 1.111116 TCCACCCGACTTGAGTTCGT 61.111 55.000 0.00 0.00 0.00 3.85
1112 8881 0.666577 CCACCCGACTTGAGTTCGTC 60.667 60.000 0.00 0.00 0.00 4.20
1113 8882 0.666577 CACCCGACTTGAGTTCGTCC 60.667 60.000 0.00 0.00 0.00 4.79
1114 8883 0.826672 ACCCGACTTGAGTTCGTCCT 60.827 55.000 0.00 0.00 0.00 3.85
1115 8884 0.388649 CCCGACTTGAGTTCGTCCTG 60.389 60.000 0.00 0.00 0.00 3.86
1116 8885 0.388649 CCGACTTGAGTTCGTCCTGG 60.389 60.000 0.00 0.00 0.00 4.45
1117 8886 0.388649 CGACTTGAGTTCGTCCTGGG 60.389 60.000 0.00 0.00 0.00 4.45
1118 8887 0.966920 GACTTGAGTTCGTCCTGGGA 59.033 55.000 0.00 0.00 0.00 4.37
1119 8888 0.680061 ACTTGAGTTCGTCCTGGGAC 59.320 55.000 9.55 9.55 41.40 4.46
1120 8889 0.969894 CTTGAGTTCGTCCTGGGACT 59.030 55.000 16.44 0.00 42.54 3.85
1121 8890 0.966920 TTGAGTTCGTCCTGGGACTC 59.033 55.000 16.44 8.54 42.54 3.36
1122 8891 0.178973 TGAGTTCGTCCTGGGACTCA 60.179 55.000 16.44 14.59 44.36 3.41
1123 8892 1.187087 GAGTTCGTCCTGGGACTCAT 58.813 55.000 16.44 1.68 42.54 2.90
1124 8893 1.550976 GAGTTCGTCCTGGGACTCATT 59.449 52.381 16.44 1.42 42.54 2.57
1125 8894 1.978580 AGTTCGTCCTGGGACTCATTT 59.021 47.619 16.44 0.00 42.54 2.32
1126 8895 2.028020 AGTTCGTCCTGGGACTCATTTC 60.028 50.000 16.44 3.26 42.54 2.17
1127 8896 0.902531 TCGTCCTGGGACTCATTTCC 59.097 55.000 16.44 0.00 42.54 3.13
1128 8897 0.613260 CGTCCTGGGACTCATTTCCA 59.387 55.000 16.44 0.00 42.54 3.53
1129 8898 1.210478 CGTCCTGGGACTCATTTCCAT 59.790 52.381 16.44 0.00 42.54 3.41
1130 8899 2.743183 CGTCCTGGGACTCATTTCCATC 60.743 54.545 16.44 0.00 42.54 3.51
1131 8900 1.846439 TCCTGGGACTCATTTCCATCC 59.154 52.381 0.00 0.00 37.40 3.51
1132 8901 1.475751 CCTGGGACTCATTTCCATCCG 60.476 57.143 0.00 0.00 37.40 4.18
1133 8902 1.486310 CTGGGACTCATTTCCATCCGA 59.514 52.381 0.00 0.00 37.40 4.55
1134 8903 1.209504 TGGGACTCATTTCCATCCGAC 59.790 52.381 0.00 0.00 37.40 4.79
1135 8904 1.486726 GGGACTCATTTCCATCCGACT 59.513 52.381 0.00 0.00 37.40 4.18
1136 8905 2.092914 GGGACTCATTTCCATCCGACTT 60.093 50.000 0.00 0.00 37.40 3.01
1137 8906 2.939103 GGACTCATTTCCATCCGACTTG 59.061 50.000 0.00 0.00 35.49 3.16
1138 8907 3.369471 GGACTCATTTCCATCCGACTTGA 60.369 47.826 0.00 0.00 35.49 3.02
1139 8908 3.866651 ACTCATTTCCATCCGACTTGAG 58.133 45.455 0.00 0.00 36.47 3.02
1140 8909 3.261897 ACTCATTTCCATCCGACTTGAGT 59.738 43.478 0.00 0.00 37.80 3.41
1211 8986 0.600255 ACGGAAACAAGGAGTCAGCG 60.600 55.000 0.00 0.00 0.00 5.18
1428 9212 2.626780 CGAGCACGTCCAGGAGTCA 61.627 63.158 0.00 0.00 34.56 3.41
1446 9231 4.880537 CTCCAGGCACTAGGCGCG 62.881 72.222 0.00 0.00 46.16 6.86
1530 9321 3.570638 CGCAGCAAGGCCGAGATG 61.571 66.667 10.80 10.80 0.00 2.90
1559 9356 4.124351 CGCGGTAGGCACGAGGAA 62.124 66.667 0.00 0.00 43.84 3.36
1578 9375 2.100605 AGAAGAACAAGACGATGGCC 57.899 50.000 0.00 0.00 0.00 5.36
1686 9544 6.660887 ACAGCTTAGTTACTACGTACTCTC 57.339 41.667 0.00 0.00 0.00 3.20
1733 9597 1.376037 GCTAGCTTTGAGGCGGTGT 60.376 57.895 7.70 0.00 37.29 4.16
1819 9716 3.812609 CGCCCAACTTTTTAAAGCCAATT 59.187 39.130 2.23 0.00 39.63 2.32
1820 9717 4.991687 CGCCCAACTTTTTAAAGCCAATTA 59.008 37.500 2.23 0.00 39.63 1.40
1821 9718 5.641636 CGCCCAACTTTTTAAAGCCAATTAT 59.358 36.000 2.23 0.00 39.63 1.28
1914 9815 3.181487 ACGAAGCAAGCAAACAAACTGAT 60.181 39.130 0.00 0.00 0.00 2.90
2045 9954 0.239347 CTGCTTTGCTTCAGGGAACG 59.761 55.000 0.00 0.00 0.00 3.95
2073 9983 3.848353 AGCCTTGCTTTCCCAAGAA 57.152 47.368 3.65 0.00 43.79 2.52
2083 9993 5.686753 TGCTTTCCCAAGAACAACTAGTTA 58.313 37.500 8.04 0.00 41.51 2.24
2092 10002 1.706443 ACAACTAGTTAACGAGCGCC 58.294 50.000 14.82 0.00 0.00 6.53
2094 10004 0.893447 AACTAGTTAACGAGCGCCCT 59.107 50.000 14.82 0.00 0.00 5.19
2113 10023 0.742990 TTTCGGCAGCCTCGTAATGG 60.743 55.000 10.54 0.00 0.00 3.16
2117 10027 0.179045 GGCAGCCTCGTAATGGTCAT 60.179 55.000 3.29 0.00 0.00 3.06
2184 10104 0.951558 GTTCTGGGCGCTTTCTTTGA 59.048 50.000 7.64 0.00 0.00 2.69
2189 10111 3.069443 TCTGGGCGCTTTCTTTGAATTTT 59.931 39.130 7.64 0.00 0.00 1.82
2190 10112 3.129871 TGGGCGCTTTCTTTGAATTTTG 58.870 40.909 7.64 0.00 0.00 2.44
2213 10135 0.232816 TTTTCGTACGCGTTTCCTGC 59.767 50.000 20.78 0.00 39.49 4.85
2224 10156 3.120338 CGCGTTTCCTGCTTTTTAGATGA 60.120 43.478 0.00 0.00 0.00 2.92
2251 10183 4.911514 TCCCTTTTTCTCAACTTTTCGG 57.088 40.909 0.00 0.00 0.00 4.30
2259 10191 4.625972 TCTCAACTTTTCGGTTTTCACC 57.374 40.909 0.00 0.00 40.16 4.02
2272 10204 3.633525 GGTTTTCACCGGGTTTTCTTAGT 59.366 43.478 6.32 0.00 31.60 2.24
2316 10248 2.776312 TTTGTGCGGAAAAATGCGTA 57.224 40.000 0.00 0.00 0.00 4.42
2319 10251 2.590073 TGTGCGGAAAAATGCGTATTG 58.410 42.857 0.00 0.00 0.00 1.90
2322 10254 3.427193 GTGCGGAAAAATGCGTATTGTTT 59.573 39.130 3.00 4.94 0.00 2.83
2353 10285 6.524101 TCCTTAGAACACAGTTTTGCTTTT 57.476 33.333 0.00 0.00 0.00 2.27
2379 10311 2.088178 GCATGGTTTTGCTTCCGCG 61.088 57.895 0.00 0.00 39.57 6.46
2407 10339 2.442188 GCCGTGCCTCTCGTAAACG 61.442 63.158 0.00 0.00 41.45 3.60
2409 10341 1.804326 CGTGCCTCTCGTAAACGGG 60.804 63.158 2.24 0.00 42.17 5.28
2469 10401 0.802494 ACATAGTTTTGCTTCCGCGG 59.198 50.000 22.12 22.12 39.65 6.46
2598 10546 3.633418 TCCGGAAAGGGAAAAAGAAACA 58.367 40.909 0.00 0.00 41.52 2.83
2638 10599 3.979948 TCGTCAAAACCTATCAACACGA 58.020 40.909 0.00 0.00 32.91 4.35
2667 10628 4.338118 AGTTTTGAAGATTTTGACGCCAGA 59.662 37.500 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.230472 TCCGTTTCTTTTAGTATCTACTAGGG 57.770 38.462 0.00 0.00 39.69 3.53
42 43 2.011122 ACCCCTCTTCTTCGTCTTGA 57.989 50.000 0.00 0.00 0.00 3.02
322 2636 0.108424 TGCTGGCTTGCAAAAACGTT 60.108 45.000 0.00 0.00 40.29 3.99
325 2639 1.501337 GGCTGCTGGCTTGCAAAAAC 61.501 55.000 10.05 0.00 42.83 2.43
339 2653 6.257193 CCATTCAGATTAAAATCAAAGGCTGC 59.743 38.462 5.55 0.00 37.89 5.25
383 2697 1.334599 GCTAGCTAGCTAGTGCAGTCG 60.335 57.143 39.05 21.44 45.67 4.18
612 2961 0.868186 TTGGGGTTGGGTAAATGGGT 59.132 50.000 0.00 0.00 0.00 4.51
616 2965 4.288366 CCTTCATTTTGGGGTTGGGTAAAT 59.712 41.667 0.00 0.00 0.00 1.40
622 2971 0.324614 GGCCTTCATTTTGGGGTTGG 59.675 55.000 0.00 0.00 0.00 3.77
652 3001 0.606944 TGGATTGGGGGTCGTTTTCG 60.607 55.000 0.00 0.00 45.64 3.46
689 3039 6.668541 TCAGCTCTATAAATGACAAGTTGC 57.331 37.500 1.81 0.00 0.00 4.17
809 3165 6.424683 CGGTTTGACAAGAGTAAAGTAAACC 58.575 40.000 0.00 0.00 41.27 3.27
810 3166 5.905733 GCGGTTTGACAAGAGTAAAGTAAAC 59.094 40.000 0.00 0.00 0.00 2.01
811 3167 5.007921 GGCGGTTTGACAAGAGTAAAGTAAA 59.992 40.000 0.00 0.00 0.00 2.01
812 3168 4.512571 GGCGGTTTGACAAGAGTAAAGTAA 59.487 41.667 0.00 0.00 0.00 2.24
813 3169 4.060205 GGCGGTTTGACAAGAGTAAAGTA 58.940 43.478 0.00 0.00 0.00 2.24
814 3170 2.876550 GGCGGTTTGACAAGAGTAAAGT 59.123 45.455 0.00 0.00 0.00 2.66
815 3171 2.875933 TGGCGGTTTGACAAGAGTAAAG 59.124 45.455 0.00 0.00 26.81 1.85
819 3175 0.535102 CCTGGCGGTTTGACAAGAGT 60.535 55.000 0.00 0.00 32.78 3.24
837 3193 2.030262 CAGCTAGCCGATGGAGCC 59.970 66.667 12.13 0.00 36.87 4.70
850 3207 3.264450 GGGTCACAATATATAGGGCAGCT 59.736 47.826 0.00 0.00 0.00 4.24
851 3208 3.009033 TGGGTCACAATATATAGGGCAGC 59.991 47.826 0.00 0.00 0.00 5.25
852 3209 4.565652 GGTGGGTCACAATATATAGGGCAG 60.566 50.000 0.38 0.00 35.86 4.85
853 3210 3.329520 GGTGGGTCACAATATATAGGGCA 59.670 47.826 0.38 0.00 35.86 5.36
873 3230 4.314440 TTCAGAAGCTGCGCGGGT 62.314 61.111 16.70 16.70 0.00 5.28
875 3232 4.139420 CGTTCAGAAGCTGCGCGG 62.139 66.667 13.18 13.18 0.00 6.46
879 3236 1.335051 GGGTTTTCGTTCAGAAGCTGC 60.335 52.381 0.00 0.00 40.40 5.25
886 3243 1.512156 CCGTGGGGGTTTTCGTTCAG 61.512 60.000 0.00 0.00 0.00 3.02
892 3249 0.815095 CTATTGCCGTGGGGGTTTTC 59.185 55.000 0.00 0.00 38.44 2.29
896 3253 1.276140 TTAGCTATTGCCGTGGGGGT 61.276 55.000 0.00 0.00 40.80 4.95
898 3255 1.608590 CAATTAGCTATTGCCGTGGGG 59.391 52.381 0.00 0.00 37.42 4.96
902 3259 1.676006 GGCACAATTAGCTATTGCCGT 59.324 47.619 16.16 1.69 46.21 5.68
904 3261 2.544486 GCAGGCACAATTAGCTATTGCC 60.544 50.000 20.63 20.63 46.21 4.52
940 3304 0.606401 GGGTGTGGGTGTCATCAGTG 60.606 60.000 0.00 0.00 0.00 3.66
945 3309 2.843545 GGTGGGTGTGGGTGTCAT 59.156 61.111 0.00 0.00 0.00 3.06
946 3310 3.867783 CGGTGGGTGTGGGTGTCA 61.868 66.667 0.00 0.00 0.00 3.58
947 3311 3.819877 GACGGTGGGTGTGGGTGTC 62.820 68.421 0.00 0.00 0.00 3.67
948 3312 3.868985 GACGGTGGGTGTGGGTGT 61.869 66.667 0.00 0.00 0.00 4.16
949 3313 3.530910 GAGACGGTGGGTGTGGGTG 62.531 68.421 0.00 0.00 0.00 4.61
950 3314 3.239253 GAGACGGTGGGTGTGGGT 61.239 66.667 0.00 0.00 0.00 4.51
951 3315 4.016706 GGAGACGGTGGGTGTGGG 62.017 72.222 0.00 0.00 0.00 4.61
1007 3373 1.202533 AGTAGCACATATCACCGTGGC 60.203 52.381 0.00 0.00 33.62 5.01
1077 8846 1.340114 GGTGGAAATGAGTCCCAGGAC 60.340 57.143 8.88 8.88 44.86 3.85
1082 8851 0.392595 GTCGGGTGGAAATGAGTCCC 60.393 60.000 0.00 0.00 36.80 4.46
1084 8853 2.076863 CAAGTCGGGTGGAAATGAGTC 58.923 52.381 0.00 0.00 0.00 3.36
1085 8854 1.697432 TCAAGTCGGGTGGAAATGAGT 59.303 47.619 0.00 0.00 0.00 3.41
1086 8855 2.289694 ACTCAAGTCGGGTGGAAATGAG 60.290 50.000 0.00 0.00 41.73 2.90
1087 8856 1.697432 ACTCAAGTCGGGTGGAAATGA 59.303 47.619 0.00 0.00 0.00 2.57
1088 8857 2.185004 ACTCAAGTCGGGTGGAAATG 57.815 50.000 0.00 0.00 0.00 2.32
1089 8858 2.779506 GAACTCAAGTCGGGTGGAAAT 58.220 47.619 0.00 0.00 0.00 2.17
1090 8859 1.539496 CGAACTCAAGTCGGGTGGAAA 60.539 52.381 0.00 0.00 0.00 3.13
1091 8860 0.032952 CGAACTCAAGTCGGGTGGAA 59.967 55.000 0.00 0.00 0.00 3.53
1092 8861 1.111116 ACGAACTCAAGTCGGGTGGA 61.111 55.000 0.00 0.00 0.00 4.02
1093 8862 0.666577 GACGAACTCAAGTCGGGTGG 60.667 60.000 0.00 0.00 0.00 4.61
1094 8863 0.666577 GGACGAACTCAAGTCGGGTG 60.667 60.000 0.00 0.00 38.20 4.61
1095 8864 0.826672 AGGACGAACTCAAGTCGGGT 60.827 55.000 0.00 0.00 38.20 5.28
1096 8865 0.388649 CAGGACGAACTCAAGTCGGG 60.389 60.000 0.00 0.00 38.20 5.14
1097 8866 0.388649 CCAGGACGAACTCAAGTCGG 60.389 60.000 0.00 0.00 38.20 4.79
1098 8867 0.388649 CCCAGGACGAACTCAAGTCG 60.389 60.000 0.00 0.00 38.20 4.18
1099 8868 0.966920 TCCCAGGACGAACTCAAGTC 59.033 55.000 0.00 0.00 36.70 3.01
1100 8869 0.680061 GTCCCAGGACGAACTCAAGT 59.320 55.000 0.05 0.00 35.30 3.16
1101 8870 3.516578 GTCCCAGGACGAACTCAAG 57.483 57.895 0.05 0.00 35.30 3.02
1110 8879 2.422093 GGATGGAAATGAGTCCCAGGAC 60.422 54.545 8.88 8.88 44.86 3.85
1111 8880 1.846439 GGATGGAAATGAGTCCCAGGA 59.154 52.381 0.00 0.00 36.80 3.86
1112 8881 1.475751 CGGATGGAAATGAGTCCCAGG 60.476 57.143 0.00 0.00 36.80 4.45
1113 8882 1.486310 TCGGATGGAAATGAGTCCCAG 59.514 52.381 0.00 0.00 36.80 4.45
1114 8883 1.209504 GTCGGATGGAAATGAGTCCCA 59.790 52.381 0.00 0.00 36.80 4.37
1115 8884 1.486726 AGTCGGATGGAAATGAGTCCC 59.513 52.381 0.00 0.00 36.80 4.46
1116 8885 2.939103 CAAGTCGGATGGAAATGAGTCC 59.061 50.000 0.00 0.00 38.27 3.85
1117 8886 3.861840 TCAAGTCGGATGGAAATGAGTC 58.138 45.455 0.00 0.00 0.00 3.36
1118 8887 3.261897 ACTCAAGTCGGATGGAAATGAGT 59.738 43.478 0.00 0.00 43.02 3.41
1119 8888 3.866651 ACTCAAGTCGGATGGAAATGAG 58.133 45.455 0.00 0.00 41.73 2.90
1120 8889 3.981071 ACTCAAGTCGGATGGAAATGA 57.019 42.857 0.00 0.00 0.00 2.57
1121 8890 3.062639 CGAACTCAAGTCGGATGGAAATG 59.937 47.826 0.00 0.00 0.00 2.32
1122 8891 3.262420 CGAACTCAAGTCGGATGGAAAT 58.738 45.455 0.00 0.00 0.00 2.17
1123 8892 2.036733 ACGAACTCAAGTCGGATGGAAA 59.963 45.455 0.00 0.00 0.00 3.13
1124 8893 1.616865 ACGAACTCAAGTCGGATGGAA 59.383 47.619 0.00 0.00 0.00 3.53
1125 8894 1.201647 GACGAACTCAAGTCGGATGGA 59.798 52.381 0.00 0.00 0.00 3.41
1126 8895 1.630148 GACGAACTCAAGTCGGATGG 58.370 55.000 0.00 0.00 0.00 3.51
1127 8896 1.202582 AGGACGAACTCAAGTCGGATG 59.797 52.381 0.00 0.00 38.20 3.51
1128 8897 1.202582 CAGGACGAACTCAAGTCGGAT 59.797 52.381 0.00 0.00 38.20 4.18
1129 8898 0.596577 CAGGACGAACTCAAGTCGGA 59.403 55.000 0.00 0.00 38.20 4.55
1130 8899 0.388649 CCAGGACGAACTCAAGTCGG 60.389 60.000 0.00 0.00 38.20 4.79
1131 8900 0.388649 CCCAGGACGAACTCAAGTCG 60.389 60.000 0.00 0.00 38.20 4.18
1132 8901 0.966920 TCCCAGGACGAACTCAAGTC 59.033 55.000 0.00 0.00 36.70 3.01
1133 8902 0.680061 GTCCCAGGACGAACTCAAGT 59.320 55.000 0.05 0.00 35.30 3.16
1134 8903 3.516578 GTCCCAGGACGAACTCAAG 57.483 57.895 0.05 0.00 35.30 3.02
1428 9212 3.775654 GCGCCTAGTGCCTGGAGT 61.776 66.667 0.00 0.00 36.24 3.85
1446 9231 3.443045 CCCATGCCTGTTGCGGTC 61.443 66.667 0.00 0.00 45.60 4.79
1452 9237 2.124151 GATCCGCCCATGCCTGTT 60.124 61.111 0.00 0.00 0.00 3.16
1559 9356 1.347707 TGGCCATCGTCTTGTTCTTCT 59.652 47.619 0.00 0.00 0.00 2.85
1733 9597 2.886523 CAGGTGCTCCAACTTGAAATGA 59.113 45.455 7.70 0.00 35.89 2.57
1836 9733 7.438160 TGTTCATCGTCCTTGTACATATCATTC 59.562 37.037 0.00 0.00 0.00 2.67
1839 9736 6.215495 TGTTCATCGTCCTTGTACATATCA 57.785 37.500 0.00 0.00 0.00 2.15
1914 9815 6.037720 TCGTCAAGTTGCACTTTGATTTTCTA 59.962 34.615 13.43 0.00 36.03 2.10
2045 9954 3.027419 AGCAAGGCTTGGTGTCTTC 57.973 52.632 29.29 10.58 38.78 2.87
2073 9983 1.670967 GGGCGCTCGTTAACTAGTTGT 60.671 52.381 18.56 0.00 0.00 3.32
2094 10004 0.742990 CCATTACGAGGCTGCCGAAA 60.743 55.000 13.96 6.76 0.00 3.46
2100 10010 2.223340 GCAAATGACCATTACGAGGCTG 60.223 50.000 0.00 0.00 0.00 4.85
2113 10023 0.798776 CTCAGTCCACCGCAAATGAC 59.201 55.000 0.00 0.00 0.00 3.06
2117 10027 1.301716 GCTCTCAGTCCACCGCAAA 60.302 57.895 0.00 0.00 0.00 3.68
2165 10085 0.951558 TCAAAGAAAGCGCCCAGAAC 59.048 50.000 2.29 0.00 0.00 3.01
2200 10122 3.391965 TCTAAAAAGCAGGAAACGCGTA 58.608 40.909 14.46 0.00 35.50 4.42
2231 10163 4.649088 ACCGAAAAGTTGAGAAAAAGGG 57.351 40.909 0.00 0.00 0.00 3.95
2232 10164 6.588373 TGAAAACCGAAAAGTTGAGAAAAAGG 59.412 34.615 0.00 0.00 0.00 3.11
2233 10165 7.411480 GGTGAAAACCGAAAAGTTGAGAAAAAG 60.411 37.037 0.00 0.00 0.00 2.27
2234 10166 6.366604 GGTGAAAACCGAAAAGTTGAGAAAAA 59.633 34.615 0.00 0.00 0.00 1.94
2235 10167 5.865013 GGTGAAAACCGAAAAGTTGAGAAAA 59.135 36.000 0.00 0.00 0.00 2.29
2236 10168 5.404096 GGTGAAAACCGAAAAGTTGAGAAA 58.596 37.500 0.00 0.00 0.00 2.52
2237 10169 4.989044 GGTGAAAACCGAAAAGTTGAGAA 58.011 39.130 0.00 0.00 0.00 2.87
2238 10170 4.625972 GGTGAAAACCGAAAAGTTGAGA 57.374 40.909 0.00 0.00 0.00 3.27
2251 10183 4.906065 ACTAAGAAAACCCGGTGAAAAC 57.094 40.909 0.00 0.00 0.00 2.43
2286 10218 6.727824 TTTTCCGCACAAAAAGATCAAAAA 57.272 29.167 0.00 0.00 0.00 1.94
2287 10219 6.727824 TTTTTCCGCACAAAAAGATCAAAA 57.272 29.167 0.00 0.00 31.65 2.44
2289 10221 5.277250 GCATTTTTCCGCACAAAAAGATCAA 60.277 36.000 8.15 0.00 38.36 2.57
2290 10222 4.210955 GCATTTTTCCGCACAAAAAGATCA 59.789 37.500 8.15 0.00 38.36 2.92
2292 10224 3.184178 CGCATTTTTCCGCACAAAAAGAT 59.816 39.130 8.15 0.00 38.36 2.40
2294 10226 2.283884 ACGCATTTTTCCGCACAAAAAG 59.716 40.909 8.15 3.38 38.36 2.27
2301 10233 2.999507 ACAATACGCATTTTTCCGCA 57.000 40.000 0.00 0.00 0.00 5.69
2322 10254 6.524101 AACTGTGTTCTAAGGAAGCAAAAA 57.476 33.333 0.00 0.00 31.46 1.94
2327 10259 4.036852 AGCAAAACTGTGTTCTAAGGAAGC 59.963 41.667 0.00 0.00 31.46 3.86
2328 10260 5.757850 AGCAAAACTGTGTTCTAAGGAAG 57.242 39.130 0.00 0.00 31.46 3.46
2330 10262 6.524101 AAAAGCAAAACTGTGTTCTAAGGA 57.476 33.333 0.00 0.00 0.00 3.36
2331 10263 6.413818 CGTAAAAGCAAAACTGTGTTCTAAGG 59.586 38.462 0.00 0.00 0.00 2.69
2332 10264 7.184106 TCGTAAAAGCAAAACTGTGTTCTAAG 58.816 34.615 0.00 0.00 0.00 2.18
2333 10265 7.064847 TCTCGTAAAAGCAAAACTGTGTTCTAA 59.935 33.333 0.00 0.00 0.00 2.10
2334 10266 6.535865 TCTCGTAAAAGCAAAACTGTGTTCTA 59.464 34.615 0.00 0.00 0.00 2.10
2337 10269 5.448632 CCTCTCGTAAAAGCAAAACTGTGTT 60.449 40.000 0.00 0.00 0.00 3.32
2353 10285 1.448985 GCAAAACCATGCCTCTCGTA 58.551 50.000 0.00 0.00 40.49 3.43
2391 10323 1.804326 CCCGTTTACGAGAGGCACG 60.804 63.158 3.46 0.00 43.02 5.34
2519 10467 4.451096 GGAAGCAAAAACGTATCTCTCACA 59.549 41.667 0.00 0.00 0.00 3.58
2598 10546 3.765968 AAAAAGGAACCGGGAGCAT 57.234 47.368 6.32 0.00 0.00 3.79
2638 10599 7.361286 GGCGTCAAAATCTTCAAAACTAGATCT 60.361 37.037 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.