Multiple sequence alignment - TraesCS2A01G263000

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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 TraesCS2A01G263000 chr2A 100.000 3926 0 0 1 3926 416006508 416010433 0.000000e+00 7251
1 TraesCS2A01G263000 chr2A 92.931 962 46 9 1 942 62119348 62120307 0.000000e+00 1380
2 TraesCS2A01G263000 chr2A 92.910 945 60 7 2 943 759892235 759893175 0.000000e+00 1367
3 TraesCS2A01G263000 chr2A 86.340 571 58 12 371 938 416006723 416006170 4.340000e-169 604
4 TraesCS2A01G263000 chr2D 93.394 2861 119 14 1070 3926 317872129 317869335 0.000000e+00 4172
5 TraesCS2A01G263000 chr3A 94.597 944 48 3 1 942 99627028 99626086 0.000000e+00 1458
6 TraesCS2A01G263000 chr3A 94.198 948 48 7 1 942 488716048 488716994 0.000000e+00 1439
7 TraesCS2A01G263000 chr3A 95.670 739 26 6 1 736 688069602 688068867 0.000000e+00 1182
8 TraesCS2A01G263000 chr3A 93.204 309 19 2 1 307 93557907 93558215 1.660000e-123 453
9 TraesCS2A01G263000 chr7A 94.059 505 26 4 261 763 543826383 543826885 0.000000e+00 763
10 TraesCS2A01G263000 chr7A 93.663 505 22 9 6 507 431265032 431264535 0.000000e+00 747
11 TraesCS2A01G263000 chr4D 92.193 538 38 4 407 942 502885840 502886375 0.000000e+00 758
12 TraesCS2A01G263000 chr5B 92.673 505 29 7 6 507 78214421 78213922 0.000000e+00 721
13 TraesCS2A01G263000 chrUn 90.702 527 47 2 413 937 71596258 71596784 0.000000e+00 701
14 TraesCS2A01G263000 chr1D 89.815 540 45 9 407 942 356146738 356147271 0.000000e+00 684
15 TraesCS2A01G263000 chr1A 86.607 336 15 5 1 307 61262524 61262190 1.040000e-90 344


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 TraesCS2A01G263000 chr2A 416006508 416010433 3925 False 7251 7251 100.000 1 3926 1 chr2A.!!$F2 3925
1 TraesCS2A01G263000 chr2A 62119348 62120307 959 False 1380 1380 92.931 1 942 1 chr2A.!!$F1 941
2 TraesCS2A01G263000 chr2A 759892235 759893175 940 False 1367 1367 92.910 2 943 1 chr2A.!!$F3 941
3 TraesCS2A01G263000 chr2A 416006170 416006723 553 True 604 604 86.340 371 938 1 chr2A.!!$R1 567
4 TraesCS2A01G263000 chr2D 317869335 317872129 2794 True 4172 4172 93.394 1070 3926 1 chr2D.!!$R1 2856
5 TraesCS2A01G263000 chr3A 99626086 99627028 942 True 1458 1458 94.597 1 942 1 chr3A.!!$R1 941
6 TraesCS2A01G263000 chr3A 488716048 488716994 946 False 1439 1439 94.198 1 942 1 chr3A.!!$F2 941
7 TraesCS2A01G263000 chr3A 688068867 688069602 735 True 1182 1182 95.670 1 736 1 chr3A.!!$R2 735
8 TraesCS2A01G263000 chr7A 543826383 543826885 502 False 763 763 94.059 261 763 1 chr7A.!!$F1 502
9 TraesCS2A01G263000 chr4D 502885840 502886375 535 False 758 758 92.193 407 942 1 chr4D.!!$F1 535
10 TraesCS2A01G263000 chrUn 71596258 71596784 526 False 701 701 90.702 413 937 1 chrUn.!!$F1 524
11 TraesCS2A01G263000 chr1D 356146738 356147271 533 False 684 684 89.815 407 942 1 chr1D.!!$F1 535

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
965 1065 0.107654 AACTAGGCCCATCGTCTTGC 60.108 55.0 0.00 0.0 0.00 4.01 F
2088 2188 0.031857 TGTTTGTGCAATTGCGGGAG 59.968 50.0 24.58 0.0 45.83 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 2325 0.105760 AAGGTCCACCATGCAACCAA 60.106 50.0 5.81 0.0 38.89 3.67 R
2977 3077 0.107268 TCACAAGCAGCAGAGCAGAA 59.893 50.0 0.00 0.0 36.85 3.02 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
168 170 2.014033 TTTCCGCCAACCCTTTCCCT 62.014 55.000 0.00 0.00 0.00 4.20
479 511 1.304134 GGAAACGGGTGGCAGGAAT 60.304 57.895 0.00 0.00 0.00 3.01
658 726 1.069823 CGAAGAGTGGAGCCATGCTAT 59.930 52.381 0.00 0.00 39.88 2.97
697 795 0.471022 GAAAAGGTGGGCCCAAGGAA 60.471 55.000 30.64 0.00 34.66 3.36
766 865 2.287368 CCAAAAAGGTCTTTTCGGTCCG 60.287 50.000 4.39 4.39 41.45 4.79
784 883 3.932964 CCGAGTACGCACCTTTTCGGT 62.933 57.143 6.13 0.00 41.82 4.69
785 884 1.505425 GAGTACGCACCTTTTCGGTT 58.495 50.000 0.00 0.00 46.37 4.44
834 933 0.185175 AAAGGGAGGCCGAAAACACT 59.815 50.000 0.00 0.00 0.00 3.55
920 1020 5.826601 TTCCGAATTTGCTATAACATGCA 57.173 34.783 0.00 0.00 37.42 3.96
955 1055 2.247699 AAAATCCCCAAACTAGGCCC 57.752 50.000 0.00 0.00 0.00 5.80
956 1056 1.089123 AAATCCCCAAACTAGGCCCA 58.911 50.000 0.00 0.00 0.00 5.36
957 1057 1.318934 AATCCCCAAACTAGGCCCAT 58.681 50.000 0.00 0.00 0.00 4.00
958 1058 0.853530 ATCCCCAAACTAGGCCCATC 59.146 55.000 0.00 0.00 0.00 3.51
959 1059 1.152963 CCCCAAACTAGGCCCATCG 60.153 63.158 0.00 0.00 0.00 3.84
960 1060 1.607612 CCCAAACTAGGCCCATCGT 59.392 57.895 0.00 0.00 0.00 3.73
961 1061 0.463833 CCCAAACTAGGCCCATCGTC 60.464 60.000 0.00 0.00 0.00 4.20
962 1062 0.541863 CCAAACTAGGCCCATCGTCT 59.458 55.000 0.00 0.00 0.00 4.18
963 1063 1.065418 CCAAACTAGGCCCATCGTCTT 60.065 52.381 0.00 0.00 0.00 3.01
964 1064 2.009774 CAAACTAGGCCCATCGTCTTG 58.990 52.381 0.00 0.00 0.00 3.02
965 1065 0.107654 AACTAGGCCCATCGTCTTGC 60.108 55.000 0.00 0.00 0.00 4.01
966 1066 1.592669 CTAGGCCCATCGTCTTGCG 60.593 63.158 0.00 0.00 43.01 4.85
975 1075 3.642901 TCGTCTTGCGAGGATAAGC 57.357 52.632 0.00 0.00 45.68 3.09
976 1076 1.103803 TCGTCTTGCGAGGATAAGCT 58.896 50.000 0.00 0.00 45.68 3.74
977 1077 1.202302 TCGTCTTGCGAGGATAAGCTG 60.202 52.381 0.00 0.00 45.68 4.24
978 1078 0.933796 GTCTTGCGAGGATAAGCTGC 59.066 55.000 0.00 0.00 0.00 5.25
979 1079 0.528466 TCTTGCGAGGATAAGCTGCG 60.528 55.000 0.00 0.00 0.00 5.18
981 1081 2.586079 GCGAGGATAAGCTGCGCA 60.586 61.111 10.98 10.98 46.19 6.09
982 1082 2.593134 GCGAGGATAAGCTGCGCAG 61.593 63.158 32.83 32.83 46.19 5.18
983 1083 1.227089 CGAGGATAAGCTGCGCAGT 60.227 57.895 35.80 21.44 0.00 4.40
984 1084 1.485838 CGAGGATAAGCTGCGCAGTG 61.486 60.000 35.80 15.92 0.00 3.66
985 1085 0.179100 GAGGATAAGCTGCGCAGTGA 60.179 55.000 35.80 22.41 0.00 3.41
986 1086 0.179089 AGGATAAGCTGCGCAGTGAG 60.179 55.000 35.80 14.73 0.00 3.51
987 1087 0.179100 GGATAAGCTGCGCAGTGAGA 60.179 55.000 35.80 20.32 0.00 3.27
988 1088 0.926846 GATAAGCTGCGCAGTGAGAC 59.073 55.000 35.80 20.28 0.00 3.36
989 1089 0.534412 ATAAGCTGCGCAGTGAGACT 59.466 50.000 35.80 22.18 0.00 3.24
999 1099 3.446658 AGTGAGACTGAGCCAGTGA 57.553 52.632 11.89 0.00 45.44 3.41
1000 1100 1.709578 AGTGAGACTGAGCCAGTGAA 58.290 50.000 11.89 0.00 45.44 3.18
1001 1101 2.255406 AGTGAGACTGAGCCAGTGAAT 58.745 47.619 11.89 0.00 45.44 2.57
1002 1102 2.028294 AGTGAGACTGAGCCAGTGAATG 60.028 50.000 11.89 0.00 45.44 2.67
1003 1103 2.028658 GTGAGACTGAGCCAGTGAATGA 60.029 50.000 11.89 0.00 45.44 2.57
1004 1104 2.028658 TGAGACTGAGCCAGTGAATGAC 60.029 50.000 11.89 0.00 45.44 3.06
1005 1105 1.067283 AGACTGAGCCAGTGAATGACG 60.067 52.381 11.89 0.00 45.44 4.35
1006 1106 0.671781 ACTGAGCCAGTGAATGACGC 60.672 55.000 7.00 0.00 43.63 5.19
1007 1107 1.690283 CTGAGCCAGTGAATGACGCG 61.690 60.000 3.53 3.53 0.00 6.01
1008 1108 3.088500 GAGCCAGTGAATGACGCGC 62.089 63.158 5.73 0.00 0.00 6.86
1009 1109 4.166011 GCCAGTGAATGACGCGCC 62.166 66.667 5.73 0.00 0.00 6.53
1010 1110 2.741985 CCAGTGAATGACGCGCCA 60.742 61.111 5.73 0.00 0.00 5.69
1011 1111 2.476051 CAGTGAATGACGCGCCAC 59.524 61.111 5.73 7.05 0.00 5.01
1012 1112 2.029288 CAGTGAATGACGCGCCACT 61.029 57.895 5.73 9.39 40.15 4.00
1013 1113 1.738099 AGTGAATGACGCGCCACTC 60.738 57.895 5.73 0.00 35.15 3.51
1014 1114 2.434185 TGAATGACGCGCCACTCC 60.434 61.111 5.73 0.00 0.00 3.85
1015 1115 3.195698 GAATGACGCGCCACTCCC 61.196 66.667 5.73 0.00 0.00 4.30
1016 1116 3.665675 GAATGACGCGCCACTCCCT 62.666 63.158 5.73 0.00 0.00 4.20
1017 1117 3.665675 AATGACGCGCCACTCCCTC 62.666 63.158 5.73 0.00 0.00 4.30
1057 1157 4.838152 CGGCCTCCCACATGTCCG 62.838 72.222 0.00 6.97 0.00 4.79
1060 1160 4.838152 CCTCCCACATGTCCGCCG 62.838 72.222 0.00 0.00 0.00 6.46
1065 1165 3.792047 CACATGTCCGCCGCAGTG 61.792 66.667 0.00 0.00 0.00 3.66
1289 1389 1.448922 CTCTCGCTAACCCTCCTCCG 61.449 65.000 0.00 0.00 0.00 4.63
1395 1495 1.142748 CCTCTCCGACATGCTGTCC 59.857 63.158 9.71 0.00 44.20 4.02
1637 1737 2.233654 CGATGCTCACCTGCTACGC 61.234 63.158 0.00 0.00 0.00 4.42
1725 1825 1.636340 GAACGCGATGATTGACGGG 59.364 57.895 15.93 0.00 45.28 5.28
1752 1852 0.618458 AGCACGGGAAGCCTAATGAA 59.382 50.000 0.00 0.00 0.00 2.57
1761 1861 0.253044 AGCCTAATGAAGCGCTCCAA 59.747 50.000 12.06 0.00 28.93 3.53
1769 1869 0.179189 GAAGCGCTCCAATTGTTCCG 60.179 55.000 12.06 4.76 0.00 4.30
1772 1872 2.485122 GCTCCAATTGTTCCGGCG 59.515 61.111 0.00 0.00 0.00 6.46
1788 1888 2.021039 GCGGATGCTGAGATCGAGC 61.021 63.158 11.67 11.67 38.39 5.03
1790 1890 1.361993 GGATGCTGAGATCGAGCGT 59.638 57.895 12.72 12.72 39.47 5.07
1809 1909 1.112916 TTGAGCCTGACGAGGTGACA 61.113 55.000 0.00 0.00 42.15 3.58
1968 2068 2.815647 GGAAGCTTGGAGGACGCG 60.816 66.667 2.10 3.53 0.00 6.01
1984 2084 4.287580 CGGTTGCCGTATTCCACA 57.712 55.556 0.00 0.00 42.73 4.17
2088 2188 0.031857 TGTTTGTGCAATTGCGGGAG 59.968 50.000 24.58 0.00 45.83 4.30
2168 2268 4.785453 GCTGGTTGAGGAGGGCCG 62.785 72.222 0.00 0.00 39.96 6.13
2187 2287 1.466167 CGCAGGTTCTTCCAGTCAATG 59.534 52.381 0.00 0.00 39.02 2.82
2225 2325 2.611225 GATCCCAAGATCGAGCACTT 57.389 50.000 2.38 0.00 39.66 3.16
2291 2391 2.799017 AGCATTCCATCTTGTGCAGAA 58.201 42.857 0.00 0.00 39.94 3.02
2340 2440 0.250295 GGGTGTCACTACTTGCTGCA 60.250 55.000 0.00 0.00 0.00 4.41
2394 2494 1.534729 GGATTGCGGACTTCCTTGTT 58.465 50.000 0.00 0.00 0.00 2.83
2395 2495 1.200020 GGATTGCGGACTTCCTTGTTG 59.800 52.381 0.00 0.00 0.00 3.33
2505 2605 2.101582 GTCGATGATGAAGGCTAGTGGT 59.898 50.000 0.00 0.00 0.00 4.16
2526 2626 1.676967 CCAGAAAGAGCCTGGGTGC 60.677 63.158 1.59 0.00 45.66 5.01
2544 2644 4.054671 GGTGCAGTGCTATTGAGATAGAC 58.945 47.826 17.60 0.80 37.97 2.59
2607 2707 4.322198 CCCTGCACCAATGAAATATATGCC 60.322 45.833 0.00 0.00 0.00 4.40
2613 2713 7.015001 TGCACCAATGAAATATATGCCATGTTA 59.985 33.333 0.00 0.00 0.00 2.41
2798 2898 2.007608 GATTGTCAAGAACCTACGGGC 58.992 52.381 0.00 0.00 35.63 6.13
2907 3007 4.736896 GTCGACGGGTCCTGCACC 62.737 72.222 0.00 0.00 45.97 5.01
2935 3035 4.380531 AGATTACTGGTGATGCCGTTATG 58.619 43.478 0.00 0.00 41.21 1.90
2977 3077 6.285990 CACGGTAAATAGGGCTACTAACATT 58.714 40.000 0.00 0.00 34.79 2.71
2987 3087 3.311048 GGCTACTAACATTTCTGCTCTGC 59.689 47.826 0.00 0.00 0.00 4.26
2993 3093 1.540267 ACATTTCTGCTCTGCTGCTTG 59.460 47.619 0.00 0.00 0.00 4.01
2995 3095 0.949397 TTTCTGCTCTGCTGCTTGTG 59.051 50.000 0.00 0.00 0.00 3.33
3012 3112 4.434725 GCTTGTGAACTGATGTACGATGTG 60.435 45.833 0.00 0.00 0.00 3.21
3023 3123 3.258228 TGTACGATGTGCCTATGTGTTG 58.742 45.455 0.00 0.00 0.00 3.33
3046 3146 9.145865 GTTGTGGAGTTAATCTTAAAGAGAGAG 57.854 37.037 0.00 0.00 37.93 3.20
3079 3179 8.012957 AGAAGACAAATCGGTAGTTGAGATAT 57.987 34.615 0.00 0.00 34.79 1.63
3080 3180 7.923344 AGAAGACAAATCGGTAGTTGAGATATG 59.077 37.037 0.00 0.00 34.79 1.78
3124 3224 2.100418 GGGAGCAGCCAAGAATTTCATC 59.900 50.000 0.00 0.00 38.95 2.92
3134 3234 6.716628 AGCCAAGAATTTCATCTTTCACACTA 59.283 34.615 0.00 0.00 37.56 2.74
3163 3263 9.783256 CAAATTTACCCTTAATACACTGTTAGC 57.217 33.333 0.00 0.00 0.00 3.09
3164 3264 8.515695 AATTTACCCTTAATACACTGTTAGCC 57.484 34.615 0.00 0.00 0.00 3.93
3165 3265 6.623979 TTACCCTTAATACACTGTTAGCCA 57.376 37.500 0.00 0.00 0.00 4.75
3166 3266 5.710409 ACCCTTAATACACTGTTAGCCAT 57.290 39.130 0.00 0.00 0.00 4.40
3167 3267 6.818281 ACCCTTAATACACTGTTAGCCATA 57.182 37.500 0.00 0.00 0.00 2.74
3168 3268 7.202972 ACCCTTAATACACTGTTAGCCATAA 57.797 36.000 0.00 0.00 0.00 1.90
3169 3269 7.635648 ACCCTTAATACACTGTTAGCCATAAA 58.364 34.615 0.00 0.00 0.00 1.40
3170 3270 7.773690 ACCCTTAATACACTGTTAGCCATAAAG 59.226 37.037 0.00 0.00 0.00 1.85
3171 3271 7.773690 CCCTTAATACACTGTTAGCCATAAAGT 59.226 37.037 0.00 0.00 0.00 2.66
3172 3272 8.612619 CCTTAATACACTGTTAGCCATAAAGTG 58.387 37.037 0.00 0.00 43.07 3.16
3211 3311 6.899393 TGTCACTTGCAAAAATAGGAAGAT 57.101 33.333 0.00 0.00 37.78 2.40
3253 3353 7.789202 ATCTTGTCTGTATATCAGCCATAGT 57.211 36.000 0.00 0.00 43.32 2.12
3266 3366 5.381757 TCAGCCATAGTTTTGTGTTAGGTT 58.618 37.500 0.00 0.00 0.00 3.50
3285 3385 1.748122 GTGGCTCTGCAGGGACATG 60.748 63.158 28.55 4.49 0.00 3.21
3289 3389 1.684248 GGCTCTGCAGGGACATGAAAT 60.684 52.381 20.53 0.00 0.00 2.17
3327 3427 6.405278 TTCTTTCTTCCTTCCCATCAAAAC 57.595 37.500 0.00 0.00 0.00 2.43
3331 3431 6.552445 TTCTTCCTTCCCATCAAAACAAAA 57.448 33.333 0.00 0.00 0.00 2.44
3343 3443 7.272244 CCATCAAAACAAAAATATACCTCCCC 58.728 38.462 0.00 0.00 0.00 4.81
3351 3451 9.642343 AACAAAAATATACCTCCCCTAATTCTC 57.358 33.333 0.00 0.00 0.00 2.87
3352 3452 9.015146 ACAAAAATATACCTCCCCTAATTCTCT 57.985 33.333 0.00 0.00 0.00 3.10
3353 3453 9.289782 CAAAAATATACCTCCCCTAATTCTCTG 57.710 37.037 0.00 0.00 0.00 3.35
3354 3454 7.575499 AAATATACCTCCCCTAATTCTCTGG 57.425 40.000 0.00 0.00 0.00 3.86
3355 3455 2.972153 ACCTCCCCTAATTCTCTGGT 57.028 50.000 0.00 0.00 0.00 4.00
3356 3456 5.698369 ATACCTCCCCTAATTCTCTGGTA 57.302 43.478 0.00 0.00 34.01 3.25
3357 3457 3.655384 ACCTCCCCTAATTCTCTGGTAC 58.345 50.000 0.00 0.00 0.00 3.34
3358 3458 3.013648 ACCTCCCCTAATTCTCTGGTACA 59.986 47.826 0.00 0.00 0.00 2.90
3359 3459 4.235372 CCTCCCCTAATTCTCTGGTACAT 58.765 47.826 0.00 0.00 38.20 2.29
3360 3460 5.102783 ACCTCCCCTAATTCTCTGGTACATA 60.103 44.000 0.00 0.00 38.20 2.29
3361 3461 5.246429 CCTCCCCTAATTCTCTGGTACATAC 59.754 48.000 0.00 0.00 38.20 2.39
3362 3462 5.784023 TCCCCTAATTCTCTGGTACATACA 58.216 41.667 0.00 0.00 38.20 2.29
3363 3463 6.206787 TCCCCTAATTCTCTGGTACATACAA 58.793 40.000 0.00 0.00 38.20 2.41
3364 3464 6.326583 TCCCCTAATTCTCTGGTACATACAAG 59.673 42.308 0.00 0.00 38.20 3.16
3365 3465 6.099845 CCCCTAATTCTCTGGTACATACAAGT 59.900 42.308 0.00 0.00 38.20 3.16
3366 3466 7.365652 CCCCTAATTCTCTGGTACATACAAGTT 60.366 40.741 0.00 0.00 38.20 2.66
3367 3467 8.701895 CCCTAATTCTCTGGTACATACAAGTTA 58.298 37.037 0.00 0.00 38.20 2.24
3408 3508 6.333416 TGCACTCTAGATTGTGAACTGATAC 58.667 40.000 14.57 0.00 36.38 2.24
3415 3515 5.316167 AGATTGTGAACTGATACTTTGCCA 58.684 37.500 0.00 0.00 0.00 4.92
3467 3567 9.886132 ATTTCTTGTTACTGTTATACCTACAGG 57.114 33.333 7.73 0.00 45.67 4.00
3501 3601 3.811497 TCTTTCAGTGAACTGCATGAGTG 59.189 43.478 4.68 0.00 43.46 3.51
3511 3611 0.401356 TGCATGAGTGGGAAAGCTGA 59.599 50.000 0.00 0.00 0.00 4.26
3535 3639 8.149647 TGATTTATGACAAATTGGAGCAAGTTT 58.850 29.630 0.00 0.00 29.07 2.66
3556 3660 6.374333 AGTTTCTGTCAGTTCACAGCTTTTAA 59.626 34.615 0.00 0.00 43.18 1.52
3557 3661 6.751514 TTCTGTCAGTTCACAGCTTTTAAA 57.248 33.333 0.00 0.00 43.18 1.52
3559 3663 6.551736 TCTGTCAGTTCACAGCTTTTAAAAC 58.448 36.000 0.00 0.00 43.18 2.43
3591 3695 2.880268 CCGCAGATTATGAATTCAGCCA 59.120 45.455 14.54 0.41 0.00 4.75
3597 3701 7.308169 CGCAGATTATGAATTCAGCCAAGATTA 60.308 37.037 14.54 0.00 0.00 1.75
3630 3734 9.590451 CTCAATTATGATTTTATGTTTGTGGCT 57.410 29.630 0.00 0.00 34.37 4.75
3670 3774 2.949177 ATTCAGTGCAGTACCCAACA 57.051 45.000 0.00 0.00 0.00 3.33
3687 3791 3.066064 CCAACATTTTCCGTGTCACTTGA 59.934 43.478 0.65 0.00 0.00 3.02
3712 3816 8.986477 ACATATTTGACAGGTTTCAATTAAGC 57.014 30.769 0.00 0.00 35.42 3.09
3756 3860 4.678287 CACATGCACACTGATTTGAGAAAC 59.322 41.667 0.00 0.00 0.00 2.78
3781 3885 1.339055 TGCTGTTTCCTCGCTAGCAAT 60.339 47.619 16.45 0.00 40.99 3.56
3787 3891 4.757657 TGTTTCCTCGCTAGCAATTTTGTA 59.242 37.500 16.45 0.00 0.00 2.41
3804 3908 8.489559 CAATTTTGTATTTGTGATGTTCCACAG 58.510 33.333 0.00 0.00 46.32 3.66
3834 3938 3.455990 TGCAGCTTGCTGAATTTCAAA 57.544 38.095 24.67 0.00 45.31 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 130 0.180171 CGGGTGGCAGGAACATATGA 59.820 55.000 10.38 0.00 0.00 2.15
236 238 3.741388 CGTGAGGTCAGGTTTTTGACTCT 60.741 47.826 6.17 2.45 45.32 3.24
479 511 2.051692 CCAACCCCTTCCCGTCATATA 58.948 52.381 0.00 0.00 0.00 0.86
658 726 3.464907 TCACGTTAATGGTTGACCGAAA 58.535 40.909 0.00 0.00 39.43 3.46
697 795 1.275573 GTCAGGAGTAGGCCGAAAAGT 59.724 52.381 0.00 0.00 0.00 2.66
763 862 0.387622 CGAAAAGGTGCGTACTCGGA 60.388 55.000 3.01 0.00 37.56 4.55
834 933 2.110213 ACGCGTGGGCTGAAAAGA 59.890 55.556 12.93 0.00 36.88 2.52
943 1043 0.541863 AGACGATGGGCCTAGTTTGG 59.458 55.000 4.53 0.00 0.00 3.28
944 1044 2.009774 CAAGACGATGGGCCTAGTTTG 58.990 52.381 4.53 6.21 0.00 2.93
945 1045 1.679032 GCAAGACGATGGGCCTAGTTT 60.679 52.381 4.53 0.00 0.00 2.66
946 1046 0.107654 GCAAGACGATGGGCCTAGTT 60.108 55.000 4.53 0.00 0.00 2.24
947 1047 1.522569 GCAAGACGATGGGCCTAGT 59.477 57.895 4.53 1.34 0.00 2.57
948 1048 4.445699 GCAAGACGATGGGCCTAG 57.554 61.111 4.53 0.00 0.00 3.02
958 1058 1.203928 CAGCTTATCCTCGCAAGACG 58.796 55.000 0.00 0.00 45.01 4.18
959 1059 0.933796 GCAGCTTATCCTCGCAAGAC 59.066 55.000 0.00 0.00 45.01 3.01
961 1061 1.930100 CGCAGCTTATCCTCGCAAG 59.070 57.895 0.00 0.00 0.00 4.01
962 1062 4.108902 CGCAGCTTATCCTCGCAA 57.891 55.556 0.00 0.00 0.00 4.85
975 1075 4.165866 CTCAGTCTCACTGCGCAG 57.834 61.111 34.89 34.89 45.54 5.18
978 1078 1.445754 CTGGCTCAGTCTCACTGCG 60.446 63.158 0.00 0.00 45.54 5.18
979 1079 0.669932 CACTGGCTCAGTCTCACTGC 60.670 60.000 5.02 0.00 45.54 4.40
980 1080 0.964700 TCACTGGCTCAGTCTCACTG 59.035 55.000 5.02 0.00 43.43 3.66
981 1081 1.709578 TTCACTGGCTCAGTCTCACT 58.290 50.000 5.02 0.00 43.43 3.41
982 1082 2.028658 TCATTCACTGGCTCAGTCTCAC 60.029 50.000 5.02 0.00 43.43 3.51
983 1083 2.028658 GTCATTCACTGGCTCAGTCTCA 60.029 50.000 5.02 0.00 43.43 3.27
984 1084 2.615869 GTCATTCACTGGCTCAGTCTC 58.384 52.381 5.02 0.00 43.43 3.36
985 1085 1.067283 CGTCATTCACTGGCTCAGTCT 60.067 52.381 5.02 0.00 43.43 3.24
986 1086 1.354040 CGTCATTCACTGGCTCAGTC 58.646 55.000 5.02 0.00 43.43 3.51
987 1087 0.671781 GCGTCATTCACTGGCTCAGT 60.672 55.000 2.38 2.38 46.51 3.41
988 1088 1.690283 CGCGTCATTCACTGGCTCAG 61.690 60.000 0.00 1.16 37.52 3.35
989 1089 1.737735 CGCGTCATTCACTGGCTCA 60.738 57.895 0.00 0.00 0.00 4.26
990 1090 3.084579 CGCGTCATTCACTGGCTC 58.915 61.111 0.00 0.00 0.00 4.70
991 1091 3.121030 GCGCGTCATTCACTGGCT 61.121 61.111 8.43 0.00 0.00 4.75
992 1092 4.166011 GGCGCGTCATTCACTGGC 62.166 66.667 5.47 0.00 0.00 4.85
993 1093 2.741985 TGGCGCGTCATTCACTGG 60.742 61.111 10.57 0.00 0.00 4.00
994 1094 1.959899 GAGTGGCGCGTCATTCACTG 61.960 60.000 28.28 0.00 40.13 3.66
995 1095 1.738099 GAGTGGCGCGTCATTCACT 60.738 57.895 28.28 21.49 42.37 3.41
996 1096 2.740714 GGAGTGGCGCGTCATTCAC 61.741 63.158 32.50 20.22 0.00 3.18
997 1097 2.434185 GGAGTGGCGCGTCATTCA 60.434 61.111 32.50 10.69 0.00 2.57
998 1098 3.195698 GGGAGTGGCGCGTCATTC 61.196 66.667 25.86 25.86 0.00 2.67
999 1099 3.665675 GAGGGAGTGGCGCGTCATT 62.666 63.158 19.85 14.41 34.07 2.57
1000 1100 4.148825 GAGGGAGTGGCGCGTCAT 62.149 66.667 19.85 5.93 34.07 3.06
1040 1140 4.838152 CGGACATGTGGGAGGCCG 62.838 72.222 1.15 4.83 0.00 6.13
1043 1143 4.838152 CGGCGGACATGTGGGAGG 62.838 72.222 1.15 0.00 0.00 4.30
1048 1148 3.792047 CACTGCGGCGGACATGTG 61.792 66.667 17.15 6.98 0.00 3.21
1060 1160 4.459089 GACGGAGGGGAGCACTGC 62.459 72.222 0.00 0.00 0.00 4.40
1061 1161 4.135153 CGACGGAGGGGAGCACTG 62.135 72.222 0.00 0.00 0.00 3.66
1275 1375 4.222847 CGGCGGAGGAGGGTTAGC 62.223 72.222 0.00 0.00 0.00 3.09
1395 1495 3.775654 GTGGGCAGGAGACCCTCG 61.776 72.222 0.00 0.00 45.14 4.63
1725 1825 2.356553 TTCCCGTGCTGCGTGTAC 60.357 61.111 0.00 0.00 39.32 2.90
1752 1852 2.040544 CCGGAACAATTGGAGCGCT 61.041 57.895 11.27 11.27 0.00 5.92
1761 1861 2.114670 CAGCATCCGCCGGAACAAT 61.115 57.895 11.19 0.00 39.83 2.71
1769 1869 1.372748 CTCGATCTCAGCATCCGCC 60.373 63.158 0.00 0.00 39.83 6.13
1772 1872 0.249238 AACGCTCGATCTCAGCATCC 60.249 55.000 12.56 0.00 36.61 3.51
1782 1882 1.153745 GTCAGGCTCAACGCTCGAT 60.154 57.895 0.00 0.00 39.13 3.59
1788 1888 1.734477 CACCTCGTCAGGCTCAACG 60.734 63.158 11.64 11.64 45.05 4.10
1790 1890 1.112916 TGTCACCTCGTCAGGCTCAA 61.113 55.000 0.00 0.00 45.05 3.02
1809 1909 0.816825 CAGACAGCACCAGCACAACT 60.817 55.000 0.00 0.00 45.49 3.16
1836 1936 1.119574 ACTCCACCGTACCAAGCTGT 61.120 55.000 0.00 0.00 0.00 4.40
1984 2084 6.015180 ACAACAATATCTTTGTCACCAATGCT 60.015 34.615 0.00 0.00 29.75 3.79
2141 2241 1.064166 CCTCAACCAGCCCAGAATGAT 60.064 52.381 0.00 0.00 39.69 2.45
2184 2284 1.152963 GCCGTACTCATGCCCCATT 60.153 57.895 0.00 0.00 0.00 3.16
2187 2287 1.152963 AATGCCGTACTCATGCCCC 60.153 57.895 0.00 0.00 0.00 5.80
2189 2289 1.532868 GATCAATGCCGTACTCATGCC 59.467 52.381 0.00 0.00 0.00 4.40
2225 2325 0.105760 AAGGTCCACCATGCAACCAA 60.106 50.000 5.81 0.00 38.89 3.67
2291 2391 2.742053 GCGTCAGGTGTTATTGTCATGT 59.258 45.455 0.00 0.00 0.00 3.21
2340 2440 0.537143 TGTTCTTGTGAAGCCGGCAT 60.537 50.000 31.54 19.26 32.15 4.40
2394 2494 1.228737 GTTGGCTAACCCCTTGGCA 60.229 57.895 0.62 0.00 35.60 4.92
2395 2495 0.965866 GAGTTGGCTAACCCCTTGGC 60.966 60.000 9.60 0.00 37.52 4.52
2484 2584 2.101582 ACCACTAGCCTTCATCATCGAC 59.898 50.000 0.00 0.00 0.00 4.20
2526 2626 3.243535 TGCGGTCTATCTCAATAGCACTG 60.244 47.826 0.00 0.00 35.73 3.66
2544 2644 2.572191 TGAACTCGTATACCTTGCGG 57.428 50.000 0.00 0.00 33.84 5.69
2556 2656 0.105964 TATCCCCCGCAATGAACTCG 59.894 55.000 0.00 0.00 0.00 4.18
2563 2663 1.380302 GGCTCATATCCCCCGCAAT 59.620 57.895 0.00 0.00 0.00 3.56
2607 2707 4.885907 AGGCCATTCATCTTGTCTAACATG 59.114 41.667 5.01 0.00 0.00 3.21
2613 2713 3.087031 CACAAGGCCATTCATCTTGTCT 58.913 45.455 5.01 0.00 46.20 3.41
2658 2758 1.072806 TCATGCAGAACCAGCTCTGTT 59.927 47.619 0.00 0.55 44.04 3.16
2694 2794 1.301677 CCGCAAGTGCCTTCTCCTTC 61.302 60.000 0.00 0.00 37.91 3.46
2766 2866 3.436704 TCTTGACAATCTTGATCGTTGCC 59.563 43.478 0.00 0.00 0.00 4.52
2769 2869 5.308825 AGGTTCTTGACAATCTTGATCGTT 58.691 37.500 0.00 0.00 0.00 3.85
2798 2898 2.747822 GCATGGCAGTCAGAGCACG 61.748 63.158 0.00 0.00 32.65 5.34
2907 3007 3.201290 GCATCACCAGTAATCTCCACAG 58.799 50.000 0.00 0.00 0.00 3.66
2935 3035 3.429085 CGTGCATAAAGTTTGAGATGCC 58.571 45.455 15.79 8.75 43.26 4.40
2977 3077 0.107268 TCACAAGCAGCAGAGCAGAA 59.893 50.000 0.00 0.00 36.85 3.02
2987 3087 3.317150 TCGTACATCAGTTCACAAGCAG 58.683 45.455 0.00 0.00 0.00 4.24
2993 3093 2.348666 GGCACATCGTACATCAGTTCAC 59.651 50.000 0.00 0.00 0.00 3.18
2995 3095 2.893637 AGGCACATCGTACATCAGTTC 58.106 47.619 0.00 0.00 0.00 3.01
3012 3112 5.186198 AGATTAACTCCACAACACATAGGC 58.814 41.667 0.00 0.00 0.00 3.93
3023 3123 9.930693 TTTCTCTCTCTTTAAGATTAACTCCAC 57.069 33.333 0.00 0.00 32.19 4.02
3046 3146 5.629079 ACCGATTTGTCTTCTCCATTTTC 57.371 39.130 0.00 0.00 0.00 2.29
3079 3179 1.808343 GCAGTTCACACATCAGCATCA 59.192 47.619 0.00 0.00 0.00 3.07
3080 3180 1.201998 CGCAGTTCACACATCAGCATC 60.202 52.381 0.00 0.00 0.00 3.91
3111 3211 9.565213 GAATAGTGTGAAAGATGAAATTCTTGG 57.435 33.333 0.00 0.00 36.12 3.61
3164 3264 8.956426 ACATTTATACTTGTCCACCACTTTATG 58.044 33.333 0.00 0.00 0.00 1.90
3165 3265 9.174166 GACATTTATACTTGTCCACCACTTTAT 57.826 33.333 3.76 0.00 36.98 1.40
3166 3266 8.158132 TGACATTTATACTTGTCCACCACTTTA 58.842 33.333 10.32 0.00 41.22 1.85
3167 3267 7.001674 TGACATTTATACTTGTCCACCACTTT 58.998 34.615 10.32 0.00 41.22 2.66
3168 3268 6.430000 GTGACATTTATACTTGTCCACCACTT 59.570 38.462 10.32 0.00 41.22 3.16
3169 3269 5.938125 GTGACATTTATACTTGTCCACCACT 59.062 40.000 10.32 0.00 41.22 4.00
3170 3270 5.938125 AGTGACATTTATACTTGTCCACCAC 59.062 40.000 10.32 0.00 41.22 4.16
3171 3271 6.121776 AGTGACATTTATACTTGTCCACCA 57.878 37.500 10.32 0.00 41.22 4.17
3172 3272 6.842163 CAAGTGACATTTATACTTGTCCACC 58.158 40.000 10.32 1.89 43.75 4.61
3251 3351 3.361786 AGCCACAACCTAACACAAAACT 58.638 40.909 0.00 0.00 0.00 2.66
3253 3353 3.380004 CAGAGCCACAACCTAACACAAAA 59.620 43.478 0.00 0.00 0.00 2.44
3266 3366 2.226315 ATGTCCCTGCAGAGCCACA 61.226 57.895 17.39 12.00 0.00 4.17
3296 3396 7.616528 TGGGAAGGAAGAAAGAATTCAAATT 57.383 32.000 8.44 0.00 38.06 1.82
3303 3403 6.554605 TGTTTTGATGGGAAGGAAGAAAGAAT 59.445 34.615 0.00 0.00 0.00 2.40
3316 3416 7.125053 GGGAGGTATATTTTTGTTTTGATGGGA 59.875 37.037 0.00 0.00 0.00 4.37
3317 3417 7.272244 GGGAGGTATATTTTTGTTTTGATGGG 58.728 38.462 0.00 0.00 0.00 4.00
3327 3427 9.289782 CAGAGAATTAGGGGAGGTATATTTTTG 57.710 37.037 0.00 0.00 0.00 2.44
3331 3431 6.644882 ACCAGAGAATTAGGGGAGGTATATT 58.355 40.000 0.00 0.00 0.00 1.28
3362 3462 7.649306 GTGCAATCACAGAAAACAAGATAACTT 59.351 33.333 0.00 0.00 42.66 2.66
3363 3463 7.013655 AGTGCAATCACAGAAAACAAGATAACT 59.986 33.333 0.00 0.00 45.49 2.24
3364 3464 7.141363 AGTGCAATCACAGAAAACAAGATAAC 58.859 34.615 0.00 0.00 45.49 1.89
3365 3465 7.229306 AGAGTGCAATCACAGAAAACAAGATAA 59.771 33.333 17.53 0.00 45.49 1.75
3366 3466 6.712095 AGAGTGCAATCACAGAAAACAAGATA 59.288 34.615 17.53 0.00 45.49 1.98
3367 3467 5.533903 AGAGTGCAATCACAGAAAACAAGAT 59.466 36.000 17.53 0.00 45.49 2.40
3371 3471 5.610398 TCTAGAGTGCAATCACAGAAAACA 58.390 37.500 17.53 0.00 45.49 2.83
3467 3567 7.329717 CAGTTCACTGAAAGAGTAATCCAGTAC 59.670 40.741 0.14 0.00 46.59 2.73
3474 3574 6.233434 TCATGCAGTTCACTGAAAGAGTAAT 58.767 36.000 11.29 0.00 46.59 1.89
3476 3576 5.213891 TCATGCAGTTCACTGAAAGAGTA 57.786 39.130 11.29 0.00 46.59 2.59
3501 3601 6.536224 CCAATTTGTCATAAATCAGCTTTCCC 59.464 38.462 0.00 0.00 0.00 3.97
3511 3611 8.370182 AGAAACTTGCTCCAATTTGTCATAAAT 58.630 29.630 0.00 0.00 0.00 1.40
3535 3639 6.374333 AGTTTTAAAAGCTGTGAACTGACAGA 59.626 34.615 10.08 0.00 45.39 3.41
3603 3707 9.369904 GCCACAAACATAAAATCATAATTGAGT 57.630 29.630 0.00 0.00 34.73 3.41
3604 3708 9.590451 AGCCACAAACATAAAATCATAATTGAG 57.410 29.630 0.00 0.00 34.73 3.02
3617 3721 9.906660 CAAGAAATAACTTAGCCACAAACATAA 57.093 29.630 0.00 0.00 0.00 1.90
3618 3722 9.290988 TCAAGAAATAACTTAGCCACAAACATA 57.709 29.630 0.00 0.00 0.00 2.29
3619 3723 8.082242 GTCAAGAAATAACTTAGCCACAAACAT 58.918 33.333 0.00 0.00 0.00 2.71
3620 3724 7.067615 TGTCAAGAAATAACTTAGCCACAAACA 59.932 33.333 0.00 0.00 0.00 2.83
3621 3725 7.422399 TGTCAAGAAATAACTTAGCCACAAAC 58.578 34.615 0.00 0.00 0.00 2.93
3622 3726 7.284489 ACTGTCAAGAAATAACTTAGCCACAAA 59.716 33.333 0.00 0.00 0.00 2.83
3623 3727 6.770785 ACTGTCAAGAAATAACTTAGCCACAA 59.229 34.615 0.00 0.00 0.00 3.33
3624 3728 6.296026 ACTGTCAAGAAATAACTTAGCCACA 58.704 36.000 0.00 0.00 0.00 4.17
3625 3729 6.803154 ACTGTCAAGAAATAACTTAGCCAC 57.197 37.500 0.00 0.00 0.00 5.01
3634 3738 9.665719 TGCACTGAATATACTGTCAAGAAATAA 57.334 29.630 0.00 0.00 0.00 1.40
3687 3791 8.806146 AGCTTAATTGAAACCTGTCAAATATGT 58.194 29.630 0.00 0.00 40.76 2.29
3690 3794 8.402798 TCAGCTTAATTGAAACCTGTCAAATA 57.597 30.769 0.00 0.00 40.76 1.40
3696 3800 6.006449 ACTCATCAGCTTAATTGAAACCTGT 58.994 36.000 0.00 0.00 0.00 4.00
3756 3860 2.781945 AGCGAGGAAACAGCAAAAAG 57.218 45.000 0.00 0.00 38.48 2.27
3771 3875 6.247727 TCACAAATACAAAATTGCTAGCGA 57.752 33.333 7.23 7.23 0.00 4.93
3772 3876 6.527722 ACATCACAAATACAAAATTGCTAGCG 59.472 34.615 10.77 0.00 0.00 4.26
3804 3908 1.353076 GCAAGCTGCAAAAGGTATGC 58.647 50.000 1.02 0.00 44.26 3.14


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

AutoCloner maintained by Alex Coulton.