Multiple sequence alignment - TraesCS1D01G381600

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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 TraesCS1D01G381600 chr1D 100.000 2297 0 0 1 2297 457032363 457034659 0.000000e+00 4242.0
1 TraesCS1D01G381600 chr1D 96.738 889 15 1 1 875 7321476 7320588 0.000000e+00 1469.0
2 TraesCS1D01G381600 chr1D 96.625 889 14 2 1 873 467136603 467135715 0.000000e+00 1461.0
3 TraesCS1D01G381600 chr1D 91.564 652 39 6 1013 1654 457044149 457044794 0.000000e+00 885.0
4 TraesCS1D01G381600 chr1D 88.889 504 31 13 874 1356 456251583 456252082 4.220000e-167 597.0
5 TraesCS1D01G381600 chr1D 90.596 436 25 8 874 1297 456202999 456203430 4.280000e-157 564.0
6 TraesCS1D01G381600 chr1D 94.915 236 9 1 638 873 491055156 491054924 1.300000e-97 366.0
7 TraesCS1D01G381600 chr3D 97.088 893 12 4 1 879 588095540 588096432 0.000000e+00 1493.0
8 TraesCS1D01G381600 chr3D 97.595 873 13 6 1 873 26320730 26321594 0.000000e+00 1489.0
9 TraesCS1D01G381600 chr3D 95.000 880 15 4 1 877 10267502 10268355 0.000000e+00 1354.0
10 TraesCS1D01G381600 chr6D 97.069 887 12 1 1 873 6071835 6070949 0.000000e+00 1482.0
11 TraesCS1D01G381600 chr6D 92.727 55 4 0 2241 2295 401172524 401172470 1.890000e-11 80.5
12 TraesCS1D01G381600 chr2D 97.069 887 12 1 1 873 5264089 5264975 0.000000e+00 1482.0
13 TraesCS1D01G381600 chr2D 94.700 283 11 2 594 874 12802259 12802539 9.740000e-119 436.0
14 TraesCS1D01G381600 chr4D 96.956 887 13 1 1 873 6994527 6995413 0.000000e+00 1476.0
15 TraesCS1D01G381600 chr4D 96.745 891 14 2 1 877 498542539 498541650 0.000000e+00 1471.0
16 TraesCS1D01G381600 chr4D 92.982 285 14 4 594 874 503443025 503443307 5.910000e-111 411.0
17 TraesCS1D01G381600 chr5D 97.885 851 14 3 1 851 439455188 439454342 0.000000e+00 1469.0
18 TraesCS1D01G381600 chr5D 95.339 236 8 1 638 873 9457684 9457452 2.790000e-99 372.0
19 TraesCS1D01G381600 chr5D 76.101 159 26 1 2127 2285 15503445 15503591 3.170000e-09 73.1
20 TraesCS1D01G381600 chr1A 91.576 736 37 4 1013 1742 549695451 549696167 0.000000e+00 992.0
21 TraesCS1D01G381600 chr1A 89.200 500 32 10 874 1356 549670516 549671010 2.520000e-169 604.0
22 TraesCS1D01G381600 chr1A 91.803 61 3 2 2147 2205 115431743 115431803 1.460000e-12 84.2
23 TraesCS1D01G381600 chr1B 90.483 662 33 15 1013 1654 626649127 626649778 0.000000e+00 846.0
24 TraesCS1D01G381600 chr1B 88.969 417 24 10 900 1297 626610183 626610596 1.590000e-136 496.0
25 TraesCS1D01G381600 chr1B 83.333 114 19 0 2103 2216 74952731 74952618 3.120000e-19 106.0
26 TraesCS1D01G381600 chr1B 83.784 111 18 0 2103 2213 426870859 426870969 3.120000e-19 106.0
27 TraesCS1D01G381600 chr5A 89.757 576 36 4 1741 2295 547819830 547819257 0.000000e+00 715.0
28 TraesCS1D01G381600 chr5A 91.525 59 5 0 2105 2163 231065713 231065655 5.260000e-12 82.4
29 TraesCS1D01G381600 chr5A 89.091 55 6 0 2127 2181 472474916 472474970 4.090000e-08 69.4
30 TraesCS1D01G381600 chr7D 94.979 239 9 1 638 876 63012197 63011962 2.790000e-99 372.0
31 TraesCS1D01G381600 chr7D 94.561 239 10 1 638 876 63010158 63009923 1.300000e-97 366.0
32 TraesCS1D01G381600 chr7B 80.781 333 46 10 1976 2292 689179108 689179438 6.340000e-61 244.0
33 TraesCS1D01G381600 chr7B 79.217 332 54 9 1975 2292 672661425 672661095 1.380000e-52 217.0
34 TraesCS1D01G381600 chr7B 78.354 328 53 12 1976 2287 689668513 689668838 1.800000e-46 196.0
35 TraesCS1D01G381600 chr7A 79.819 332 48 12 1978 2292 696994205 696994534 8.260000e-55 224.0
36 TraesCS1D01G381600 chr7A 79.341 334 50 13 1975 2292 688195515 688195185 1.380000e-52 217.0
37 TraesCS1D01G381600 chr2B 83.663 202 32 1 1999 2200 137443375 137443175 3.010000e-44 189.0
38 TraesCS1D01G381600 chr2A 80.952 189 32 3 2027 2213 39258394 39258208 1.840000e-31 147.0
39 TraesCS1D01G381600 chr4B 85.455 110 9 4 2103 2205 644331064 644330955 8.680000e-20 108.0
40 TraesCS1D01G381600 chr3B 84.685 111 8 9 2103 2205 18201115 18201006 4.040000e-18 102.0
41 TraesCS1D01G381600 chrUn 94.231 52 3 0 2241 2292 287940562 287940613 1.890000e-11 80.5
42 TraesCS1D01G381600 chrUn 94.231 52 3 0 2241 2292 287946631 287946682 1.890000e-11 80.5


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 TraesCS1D01G381600 chr1D 457032363 457034659 2296 False 4242 4242 100.000 1 2297 1 chr1D.!!$F3 2296
1 TraesCS1D01G381600 chr1D 7320588 7321476 888 True 1469 1469 96.738 1 875 1 chr1D.!!$R1 874
2 TraesCS1D01G381600 chr1D 467135715 467136603 888 True 1461 1461 96.625 1 873 1 chr1D.!!$R2 872
3 TraesCS1D01G381600 chr1D 457044149 457044794 645 False 885 885 91.564 1013 1654 1 chr1D.!!$F4 641
4 TraesCS1D01G381600 chr3D 588095540 588096432 892 False 1493 1493 97.088 1 879 1 chr3D.!!$F3 878
5 TraesCS1D01G381600 chr3D 26320730 26321594 864 False 1489 1489 97.595 1 873 1 chr3D.!!$F2 872
6 TraesCS1D01G381600 chr3D 10267502 10268355 853 False 1354 1354 95.000 1 877 1 chr3D.!!$F1 876
7 TraesCS1D01G381600 chr6D 6070949 6071835 886 True 1482 1482 97.069 1 873 1 chr6D.!!$R1 872
8 TraesCS1D01G381600 chr2D 5264089 5264975 886 False 1482 1482 97.069 1 873 1 chr2D.!!$F1 872
9 TraesCS1D01G381600 chr4D 6994527 6995413 886 False 1476 1476 96.956 1 873 1 chr4D.!!$F1 872
10 TraesCS1D01G381600 chr4D 498541650 498542539 889 True 1471 1471 96.745 1 877 1 chr4D.!!$R1 876
11 TraesCS1D01G381600 chr5D 439454342 439455188 846 True 1469 1469 97.885 1 851 1 chr5D.!!$R2 850
12 TraesCS1D01G381600 chr1A 549695451 549696167 716 False 992 992 91.576 1013 1742 1 chr1A.!!$F3 729
13 TraesCS1D01G381600 chr1B 626649127 626649778 651 False 846 846 90.483 1013 1654 1 chr1B.!!$F3 641
14 TraesCS1D01G381600 chr5A 547819257 547819830 573 True 715 715 89.757 1741 2295 1 chr5A.!!$R2 554
15 TraesCS1D01G381600 chr7D 63009923 63012197 2274 True 369 372 94.770 638 876 2 chr7D.!!$R1 238

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
940 2998 0.031716 ATCAGCCAGCTCCTCACCTA 60.032 55.0 0.0 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 4200 0.396695 GAGATCCGACACTACCCCCA 60.397 60.0 0.0 0.0 0.0 4.96 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
256 257 1.030488 TAGTGAACTCGCCGGAGAGG 61.030 60.000 34.27 18.92 43.27 3.69
498 499 8.579006 ACACTTCATATCATGTTTGTTTCATGT 58.421 29.630 5.94 0.00 42.03 3.21
851 2909 1.270678 GGGACTAATGGGGACGTATGC 60.271 57.143 0.00 0.00 0.00 3.14
879 2937 8.759782 AGCCTCTTTTTCTACTAGTGCTATAAA 58.240 33.333 5.39 0.00 0.00 1.40
880 2938 9.379791 GCCTCTTTTTCTACTAGTGCTATAAAA 57.620 33.333 5.39 4.71 0.00 1.52
886 2944 8.767478 TTTCTACTAGTGCTATAAAACACACC 57.233 34.615 5.39 0.00 39.30 4.16
887 2945 6.558009 TCTACTAGTGCTATAAAACACACCG 58.442 40.000 5.39 0.00 39.30 4.94
888 2946 5.143376 ACTAGTGCTATAAAACACACCGT 57.857 39.130 0.00 0.00 39.30 4.83
889 2947 5.166398 ACTAGTGCTATAAAACACACCGTC 58.834 41.667 0.00 0.00 39.30 4.79
890 2948 2.991190 AGTGCTATAAAACACACCGTCG 59.009 45.455 0.00 0.00 39.30 5.12
891 2949 2.988493 GTGCTATAAAACACACCGTCGA 59.012 45.455 0.00 0.00 36.77 4.20
892 2950 2.988493 TGCTATAAAACACACCGTCGAC 59.012 45.455 5.18 5.18 0.00 4.20
893 2951 2.346545 GCTATAAAACACACCGTCGACC 59.653 50.000 10.58 0.00 0.00 4.79
894 2952 1.421382 ATAAAACACACCGTCGACCG 58.579 50.000 10.58 6.12 0.00 4.79
895 2953 1.214373 TAAAACACACCGTCGACCGC 61.214 55.000 10.58 0.00 34.38 5.68
896 2954 2.911332 AAAACACACCGTCGACCGCT 62.911 55.000 10.58 0.00 34.38 5.52
897 2955 3.836176 AACACACCGTCGACCGCTC 62.836 63.158 10.58 0.00 34.38 5.03
903 2961 4.143333 CGTCGACCGCTCCCCATT 62.143 66.667 10.58 0.00 0.00 3.16
904 2962 2.202892 GTCGACCGCTCCCCATTC 60.203 66.667 3.51 0.00 0.00 2.67
905 2963 2.363795 TCGACCGCTCCCCATTCT 60.364 61.111 0.00 0.00 0.00 2.40
906 2964 2.107141 CGACCGCTCCCCATTCTC 59.893 66.667 0.00 0.00 0.00 2.87
907 2965 2.506472 GACCGCTCCCCATTCTCC 59.494 66.667 0.00 0.00 0.00 3.71
908 2966 2.285368 ACCGCTCCCCATTCTCCA 60.285 61.111 0.00 0.00 0.00 3.86
909 2967 2.190578 CCGCTCCCCATTCTCCAC 59.809 66.667 0.00 0.00 0.00 4.02
910 2968 2.669133 CCGCTCCCCATTCTCCACA 61.669 63.158 0.00 0.00 0.00 4.17
911 2969 1.299648 CGCTCCCCATTCTCCACAA 59.700 57.895 0.00 0.00 0.00 3.33
912 2970 1.026718 CGCTCCCCATTCTCCACAAC 61.027 60.000 0.00 0.00 0.00 3.32
913 2971 0.329596 GCTCCCCATTCTCCACAACT 59.670 55.000 0.00 0.00 0.00 3.16
914 2972 1.680249 GCTCCCCATTCTCCACAACTC 60.680 57.143 0.00 0.00 0.00 3.01
915 2973 1.630369 CTCCCCATTCTCCACAACTCA 59.370 52.381 0.00 0.00 0.00 3.41
916 2974 1.630369 TCCCCATTCTCCACAACTCAG 59.370 52.381 0.00 0.00 0.00 3.35
917 2975 1.630369 CCCCATTCTCCACAACTCAGA 59.370 52.381 0.00 0.00 0.00 3.27
918 2976 2.355513 CCCCATTCTCCACAACTCAGAG 60.356 54.545 0.00 0.00 0.00 3.35
919 2977 2.355513 CCCATTCTCCACAACTCAGAGG 60.356 54.545 1.53 0.00 0.00 3.69
920 2978 2.354259 CATTCTCCACAACTCAGAGGC 58.646 52.381 1.53 0.00 0.00 4.70
921 2979 1.423584 TTCTCCACAACTCAGAGGCA 58.576 50.000 1.53 0.00 0.00 4.75
922 2980 1.649321 TCTCCACAACTCAGAGGCAT 58.351 50.000 1.53 0.00 0.00 4.40
923 2981 1.552337 TCTCCACAACTCAGAGGCATC 59.448 52.381 1.53 0.00 0.00 3.91
924 2982 1.277273 CTCCACAACTCAGAGGCATCA 59.723 52.381 0.00 0.00 0.00 3.07
925 2983 1.277273 TCCACAACTCAGAGGCATCAG 59.723 52.381 0.00 0.00 0.00 2.90
926 2984 1.085091 CACAACTCAGAGGCATCAGC 58.915 55.000 0.00 0.00 41.10 4.26
936 2994 2.588439 GCATCAGCCAGCTCCTCA 59.412 61.111 0.00 0.00 33.58 3.86
937 2995 1.818785 GCATCAGCCAGCTCCTCAC 60.819 63.158 0.00 0.00 33.58 3.51
938 2996 1.153208 CATCAGCCAGCTCCTCACC 60.153 63.158 0.00 0.00 0.00 4.02
939 2997 1.306825 ATCAGCCAGCTCCTCACCT 60.307 57.895 0.00 0.00 0.00 4.00
940 2998 0.031716 ATCAGCCAGCTCCTCACCTA 60.032 55.000 0.00 0.00 0.00 3.08
941 2999 0.972983 TCAGCCAGCTCCTCACCTAC 60.973 60.000 0.00 0.00 0.00 3.18
942 3000 2.055042 AGCCAGCTCCTCACCTACG 61.055 63.158 0.00 0.00 0.00 3.51
943 3001 2.496817 CCAGCTCCTCACCTACGC 59.503 66.667 0.00 0.00 0.00 4.42
944 3002 2.351244 CCAGCTCCTCACCTACGCA 61.351 63.158 0.00 0.00 0.00 5.24
945 3003 1.153745 CAGCTCCTCACCTACGCAC 60.154 63.158 0.00 0.00 0.00 5.34
946 3004 1.606601 AGCTCCTCACCTACGCACA 60.607 57.895 0.00 0.00 0.00 4.57
947 3005 1.446272 GCTCCTCACCTACGCACAC 60.446 63.158 0.00 0.00 0.00 3.82
948 3006 1.215647 CTCCTCACCTACGCACACC 59.784 63.158 0.00 0.00 0.00 4.16
949 3007 2.126071 CCTCACCTACGCACACCG 60.126 66.667 0.00 0.00 44.21 4.94
950 3008 2.632544 CCTCACCTACGCACACCGA 61.633 63.158 0.00 0.00 41.02 4.69
951 3009 1.154016 CTCACCTACGCACACCGAG 60.154 63.158 0.00 0.00 41.02 4.63
952 3010 2.809601 CACCTACGCACACCGAGC 60.810 66.667 0.00 0.00 41.02 5.03
969 3027 3.867771 CGAGAGCAGCTTCACCAC 58.132 61.111 0.00 0.00 0.00 4.16
970 3028 1.291588 CGAGAGCAGCTTCACCACT 59.708 57.895 0.00 0.00 0.00 4.00
971 3029 0.320247 CGAGAGCAGCTTCACCACTT 60.320 55.000 0.00 0.00 0.00 3.16
972 3030 1.437625 GAGAGCAGCTTCACCACTTC 58.562 55.000 0.00 0.00 0.00 3.01
973 3031 0.036022 AGAGCAGCTTCACCACTTCC 59.964 55.000 0.00 0.00 0.00 3.46
974 3032 0.957888 GAGCAGCTTCACCACTTCCC 60.958 60.000 0.00 0.00 0.00 3.97
975 3033 1.073897 GCAGCTTCACCACTTCCCT 59.926 57.895 0.00 0.00 0.00 4.20
976 3034 0.957888 GCAGCTTCACCACTTCCCTC 60.958 60.000 0.00 0.00 0.00 4.30
977 3035 0.322008 CAGCTTCACCACTTCCCTCC 60.322 60.000 0.00 0.00 0.00 4.30
978 3036 1.002011 GCTTCACCACTTCCCTCCC 60.002 63.158 0.00 0.00 0.00 4.30
979 3037 1.779061 GCTTCACCACTTCCCTCCCA 61.779 60.000 0.00 0.00 0.00 4.37
980 3038 0.995024 CTTCACCACTTCCCTCCCAT 59.005 55.000 0.00 0.00 0.00 4.00
981 3039 0.991920 TTCACCACTTCCCTCCCATC 59.008 55.000 0.00 0.00 0.00 3.51
982 3040 0.914417 TCACCACTTCCCTCCCATCC 60.914 60.000 0.00 0.00 0.00 3.51
983 3041 1.995626 ACCACTTCCCTCCCATCCG 60.996 63.158 0.00 0.00 0.00 4.18
984 3042 1.689233 CCACTTCCCTCCCATCCGA 60.689 63.158 0.00 0.00 0.00 4.55
985 3043 1.690219 CCACTTCCCTCCCATCCGAG 61.690 65.000 0.00 0.00 0.00 4.63
986 3044 2.066999 ACTTCCCTCCCATCCGAGC 61.067 63.158 0.00 0.00 0.00 5.03
987 3045 2.768344 TTCCCTCCCATCCGAGCC 60.768 66.667 0.00 0.00 0.00 4.70
988 3046 4.880426 TCCCTCCCATCCGAGCCC 62.880 72.222 0.00 0.00 0.00 5.19
990 3048 3.089874 CCTCCCATCCGAGCCCAA 61.090 66.667 0.00 0.00 0.00 4.12
991 3049 2.455565 CCTCCCATCCGAGCCCAAT 61.456 63.158 0.00 0.00 0.00 3.16
992 3050 1.127567 CCTCCCATCCGAGCCCAATA 61.128 60.000 0.00 0.00 0.00 1.90
993 3051 0.764890 CTCCCATCCGAGCCCAATAA 59.235 55.000 0.00 0.00 0.00 1.40
994 3052 0.764890 TCCCATCCGAGCCCAATAAG 59.235 55.000 0.00 0.00 0.00 1.73
995 3053 0.890996 CCCATCCGAGCCCAATAAGC 60.891 60.000 0.00 0.00 0.00 3.09
996 3054 0.179020 CCATCCGAGCCCAATAAGCA 60.179 55.000 0.00 0.00 0.00 3.91
997 3055 1.679139 CATCCGAGCCCAATAAGCAA 58.321 50.000 0.00 0.00 0.00 3.91
998 3056 1.334869 CATCCGAGCCCAATAAGCAAC 59.665 52.381 0.00 0.00 0.00 4.17
999 3057 0.393808 TCCGAGCCCAATAAGCAACC 60.394 55.000 0.00 0.00 0.00 3.77
1000 3058 0.679640 CCGAGCCCAATAAGCAACCA 60.680 55.000 0.00 0.00 0.00 3.67
1001 3059 1.392589 CGAGCCCAATAAGCAACCAT 58.607 50.000 0.00 0.00 0.00 3.55
1002 3060 1.066002 CGAGCCCAATAAGCAACCATG 59.934 52.381 0.00 0.00 0.00 3.66
1003 3061 1.410153 GAGCCCAATAAGCAACCATGG 59.590 52.381 11.19 11.19 0.00 3.66
1004 3062 0.179076 GCCCAATAAGCAACCATGGC 60.179 55.000 13.04 0.00 0.00 4.40
1005 3063 0.102844 CCCAATAAGCAACCATGGCG 59.897 55.000 13.04 4.23 36.08 5.69
1006 3064 0.102844 CCAATAAGCAACCATGGCGG 59.897 55.000 13.04 5.11 42.50 6.13
1007 3065 0.528249 CAATAAGCAACCATGGCGGC 60.528 55.000 13.04 16.05 39.03 6.53
1008 3066 2.003658 AATAAGCAACCATGGCGGCG 62.004 55.000 13.04 0.51 39.03 6.46
1009 3067 3.910914 TAAGCAACCATGGCGGCGT 62.911 57.895 13.04 16.16 39.03 5.68
1257 3315 1.228429 CTCCCCCAACGGCAAGAAA 60.228 57.895 0.00 0.00 0.00 2.52
1313 3371 0.751643 TGAGCGATCGACCCATGAGA 60.752 55.000 21.57 0.00 0.00 3.27
1337 3409 2.356793 CATCCATCTCCCTCGCGC 60.357 66.667 0.00 0.00 0.00 6.86
1338 3410 3.983494 ATCCATCTCCCTCGCGCG 61.983 66.667 26.76 26.76 0.00 6.86
1352 3424 2.167684 CGCGTTGCACGTACACTG 59.832 61.111 0.00 0.00 44.73 3.66
1370 3450 2.124901 CGTGTGGTGTGGGTGTGT 60.125 61.111 0.00 0.00 0.00 3.72
1371 3451 2.468670 CGTGTGGTGTGGGTGTGTG 61.469 63.158 0.00 0.00 0.00 3.82
1372 3452 2.118404 GTGTGGTGTGGGTGTGTGG 61.118 63.158 0.00 0.00 0.00 4.17
1373 3453 3.216292 GTGGTGTGGGTGTGTGGC 61.216 66.667 0.00 0.00 0.00 5.01
1374 3454 3.732849 TGGTGTGGGTGTGTGGCA 61.733 61.111 0.00 0.00 0.00 4.92
1540 3624 1.520787 GGTATGGACCGAGTTGCCG 60.521 63.158 0.00 0.00 35.52 5.69
1601 3691 2.033299 GTGGCACCATATGATTGTTCCG 59.967 50.000 6.29 0.00 0.00 4.30
1611 3701 7.121168 ACCATATGATTGTTCCGGCTATAAATG 59.879 37.037 3.65 0.00 0.00 2.32
1672 3762 2.181021 GCCGATCCACTCGTCGTT 59.819 61.111 0.00 0.00 46.18 3.85
1696 3786 7.462109 TGTTTTCGTCAAAATGGAAAATGAG 57.538 32.000 2.07 0.00 40.51 2.90
1703 3793 6.514870 CGTCAAAATGGAAAATGAGTCTGGAA 60.515 38.462 0.00 0.00 0.00 3.53
1827 3938 2.346803 CCTCGTTGGTCCACTTGTATG 58.653 52.381 0.00 0.00 0.00 2.39
1835 3946 3.244630 TGGTCCACTTGTATGTTGGGTAC 60.245 47.826 0.00 0.00 0.00 3.34
1838 3949 1.735571 CACTTGTATGTTGGGTACGCC 59.264 52.381 7.55 0.31 0.00 5.68
1839 3950 1.003851 CTTGTATGTTGGGTACGCCG 58.996 55.000 7.55 0.00 34.97 6.46
1844 3955 3.428282 GTTGGGTACGCCGGCAAG 61.428 66.667 28.98 14.14 34.97 4.01
1875 3986 2.286772 ACAAAACATGGTTCGCTTCGTC 60.287 45.455 0.00 0.00 0.00 4.20
1876 3987 0.511221 AAACATGGTTCGCTTCGTCG 59.489 50.000 0.00 0.00 0.00 5.12
1877 3988 1.897398 AACATGGTTCGCTTCGTCGC 61.897 55.000 0.00 0.00 0.00 5.19
1968 4079 1.688884 GCAAGCCTCCTCCTCTCCT 60.689 63.158 0.00 0.00 0.00 3.69
1972 4083 1.228215 AGCCTCCTCCTCTCCTTCCT 61.228 60.000 0.00 0.00 0.00 3.36
1978 4089 2.115427 CCTCCTCTCCTTCCTTTCTCC 58.885 57.143 0.00 0.00 0.00 3.71
1986 4097 2.854187 CTTCCTTTCTCCGCCCGTCC 62.854 65.000 0.00 0.00 0.00 4.79
2015 4126 4.760047 GCCGATGACCGCACCACT 62.760 66.667 0.00 0.00 36.84 4.00
2025 4136 2.828868 GCACCACTGGAGACCACA 59.171 61.111 0.71 0.00 0.00 4.17
2034 4145 2.262915 GAGACCACAGGCCACTCG 59.737 66.667 5.01 0.00 0.00 4.18
2041 4152 1.597027 ACAGGCCACTCGGAAAACG 60.597 57.895 5.01 0.00 46.11 3.60
2065 4176 2.203788 ACGAGGAGGCTTGACCCA 60.204 61.111 0.00 0.00 40.58 4.51
2089 4200 4.680537 AGACCTGCGTCCCCGAGT 62.681 66.667 0.00 0.00 40.12 4.18
2116 4227 2.364632 AGTGTCGGATCTCTCTGTCTG 58.635 52.381 0.00 0.00 0.00 3.51
2219 4330 1.079438 GGTGAGGTCTCTGGGGACT 59.921 63.158 0.45 0.00 36.55 3.85
2225 4336 2.997315 TCTCTGGGGACTGCACGG 60.997 66.667 0.00 0.00 0.00 4.94
2247 4358 4.785453 GGACTGGCCTGGCTTCCG 62.785 72.222 19.68 7.04 0.00 4.30
2290 4401 2.565645 CCGTAGATCTGAGCCCCCG 61.566 68.421 5.18 0.00 0.00 5.73
2295 4406 0.896019 AGATCTGAGCCCCCGTATCG 60.896 60.000 0.00 0.00 0.00 2.92
2296 4407 2.493907 GATCTGAGCCCCCGTATCGC 62.494 65.000 0.00 0.00 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
498 499 2.006888 GTTCGATGAAATGCCCGAGAA 58.993 47.619 0.00 0.00 32.41 2.87
757 2815 1.515954 CGCGACCAACTATCTGGGT 59.484 57.895 0.00 0.00 41.16 4.51
814 2872 5.349061 AGTCCCTAAAATAATCGAACCGT 57.651 39.130 0.00 0.00 0.00 4.83
844 2902 3.412386 AGAAAAAGAGGCTTGCATACGT 58.588 40.909 0.00 0.00 0.00 3.57
851 2909 5.241662 AGCACTAGTAGAAAAAGAGGCTTG 58.758 41.667 3.59 0.00 0.00 4.01
887 2945 2.202892 GAATGGGGAGCGGTCGAC 60.203 66.667 7.13 7.13 0.00 4.20
888 2946 2.363795 AGAATGGGGAGCGGTCGA 60.364 61.111 8.77 0.00 0.00 4.20
889 2947 2.107141 GAGAATGGGGAGCGGTCG 59.893 66.667 8.77 0.00 0.00 4.79
890 2948 2.367202 TGGAGAATGGGGAGCGGTC 61.367 63.158 5.93 5.93 0.00 4.79
891 2949 2.285368 TGGAGAATGGGGAGCGGT 60.285 61.111 0.00 0.00 0.00 5.68
892 2950 2.190578 GTGGAGAATGGGGAGCGG 59.809 66.667 0.00 0.00 0.00 5.52
893 2951 1.026718 GTTGTGGAGAATGGGGAGCG 61.027 60.000 0.00 0.00 0.00 5.03
894 2952 0.329596 AGTTGTGGAGAATGGGGAGC 59.670 55.000 0.00 0.00 0.00 4.70
895 2953 1.630369 TGAGTTGTGGAGAATGGGGAG 59.370 52.381 0.00 0.00 0.00 4.30
896 2954 1.630369 CTGAGTTGTGGAGAATGGGGA 59.370 52.381 0.00 0.00 0.00 4.81
897 2955 1.630369 TCTGAGTTGTGGAGAATGGGG 59.370 52.381 0.00 0.00 0.00 4.96
898 2956 2.355513 CCTCTGAGTTGTGGAGAATGGG 60.356 54.545 3.66 0.00 0.00 4.00
899 2957 2.938756 GCCTCTGAGTTGTGGAGAATGG 60.939 54.545 3.66 0.00 0.00 3.16
900 2958 2.289882 TGCCTCTGAGTTGTGGAGAATG 60.290 50.000 3.66 0.00 0.00 2.67
901 2959 1.980765 TGCCTCTGAGTTGTGGAGAAT 59.019 47.619 3.66 0.00 0.00 2.40
902 2960 1.423584 TGCCTCTGAGTTGTGGAGAA 58.576 50.000 3.66 0.00 0.00 2.87
903 2961 1.552337 GATGCCTCTGAGTTGTGGAGA 59.448 52.381 3.66 0.00 0.00 3.71
904 2962 1.277273 TGATGCCTCTGAGTTGTGGAG 59.723 52.381 3.66 0.00 0.00 3.86
905 2963 1.277273 CTGATGCCTCTGAGTTGTGGA 59.723 52.381 3.66 0.00 0.00 4.02
906 2964 1.735386 CTGATGCCTCTGAGTTGTGG 58.265 55.000 3.66 0.00 0.00 4.17
907 2965 1.085091 GCTGATGCCTCTGAGTTGTG 58.915 55.000 3.66 0.00 0.00 3.33
908 2966 3.547567 GCTGATGCCTCTGAGTTGT 57.452 52.632 3.66 0.00 0.00 3.32
919 2977 1.818785 GTGAGGAGCTGGCTGATGC 60.819 63.158 0.00 0.00 38.76 3.91
920 2978 1.153208 GGTGAGGAGCTGGCTGATG 60.153 63.158 0.00 0.00 0.00 3.07
921 2979 0.031716 TAGGTGAGGAGCTGGCTGAT 60.032 55.000 0.00 0.00 0.00 2.90
922 2980 0.972983 GTAGGTGAGGAGCTGGCTGA 60.973 60.000 0.00 0.00 0.00 4.26
923 2981 1.519719 GTAGGTGAGGAGCTGGCTG 59.480 63.158 0.00 0.00 0.00 4.85
924 2982 2.055042 CGTAGGTGAGGAGCTGGCT 61.055 63.158 0.00 0.00 0.00 4.75
925 2983 2.496817 CGTAGGTGAGGAGCTGGC 59.503 66.667 0.00 0.00 0.00 4.85
926 2984 2.351244 TGCGTAGGTGAGGAGCTGG 61.351 63.158 0.00 0.00 0.00 4.85
927 2985 1.153745 GTGCGTAGGTGAGGAGCTG 60.154 63.158 0.00 0.00 0.00 4.24
928 2986 1.606601 TGTGCGTAGGTGAGGAGCT 60.607 57.895 0.00 0.00 0.00 4.09
929 2987 1.446272 GTGTGCGTAGGTGAGGAGC 60.446 63.158 0.00 0.00 0.00 4.70
930 2988 1.215647 GGTGTGCGTAGGTGAGGAG 59.784 63.158 0.00 0.00 0.00 3.69
931 2989 2.632544 CGGTGTGCGTAGGTGAGGA 61.633 63.158 0.00 0.00 0.00 3.71
932 2990 2.126071 CGGTGTGCGTAGGTGAGG 60.126 66.667 0.00 0.00 0.00 3.86
933 2991 1.154016 CTCGGTGTGCGTAGGTGAG 60.154 63.158 0.00 0.00 0.00 3.51
934 2992 2.959372 CTCGGTGTGCGTAGGTGA 59.041 61.111 0.00 0.00 0.00 4.02
935 2993 2.809601 GCTCGGTGTGCGTAGGTG 60.810 66.667 0.00 0.00 0.00 4.00
942 3000 4.724602 TGCTCTCGCTCGGTGTGC 62.725 66.667 0.00 0.00 36.97 4.57
943 3001 2.505777 CTGCTCTCGCTCGGTGTG 60.506 66.667 0.00 0.00 36.97 3.82
944 3002 4.427661 GCTGCTCTCGCTCGGTGT 62.428 66.667 0.00 0.00 36.97 4.16
945 3003 3.639541 AAGCTGCTCTCGCTCGGTG 62.640 63.158 1.00 0.00 36.56 4.94
946 3004 3.349481 GAAGCTGCTCTCGCTCGGT 62.349 63.158 1.00 0.00 36.56 4.69
947 3005 2.581953 GAAGCTGCTCTCGCTCGG 60.582 66.667 1.00 0.00 36.56 4.63
948 3006 2.157701 GTGAAGCTGCTCTCGCTCG 61.158 63.158 1.00 0.00 36.56 5.03
949 3007 1.809209 GGTGAAGCTGCTCTCGCTC 60.809 63.158 1.00 0.00 36.56 5.03
950 3008 2.264166 GGTGAAGCTGCTCTCGCT 59.736 61.111 1.00 0.00 39.94 4.93
951 3009 2.047844 TGGTGAAGCTGCTCTCGC 60.048 61.111 1.00 9.42 0.00 5.03
952 3010 0.320247 AAGTGGTGAAGCTGCTCTCG 60.320 55.000 1.00 0.00 0.00 4.04
953 3011 1.437625 GAAGTGGTGAAGCTGCTCTC 58.562 55.000 1.00 3.80 0.00 3.20
954 3012 0.036022 GGAAGTGGTGAAGCTGCTCT 59.964 55.000 1.00 0.00 0.00 4.09
955 3013 0.957888 GGGAAGTGGTGAAGCTGCTC 60.958 60.000 1.00 0.00 0.00 4.26
956 3014 1.073897 GGGAAGTGGTGAAGCTGCT 59.926 57.895 0.00 0.00 0.00 4.24
957 3015 0.957888 GAGGGAAGTGGTGAAGCTGC 60.958 60.000 0.00 0.00 0.00 5.25
958 3016 0.322008 GGAGGGAAGTGGTGAAGCTG 60.322 60.000 0.00 0.00 0.00 4.24
959 3017 1.492993 GGGAGGGAAGTGGTGAAGCT 61.493 60.000 0.00 0.00 0.00 3.74
960 3018 1.002011 GGGAGGGAAGTGGTGAAGC 60.002 63.158 0.00 0.00 0.00 3.86
961 3019 0.995024 ATGGGAGGGAAGTGGTGAAG 59.005 55.000 0.00 0.00 0.00 3.02
962 3020 0.991920 GATGGGAGGGAAGTGGTGAA 59.008 55.000 0.00 0.00 0.00 3.18
963 3021 0.914417 GGATGGGAGGGAAGTGGTGA 60.914 60.000 0.00 0.00 0.00 4.02
964 3022 1.609783 GGATGGGAGGGAAGTGGTG 59.390 63.158 0.00 0.00 0.00 4.17
965 3023 1.995626 CGGATGGGAGGGAAGTGGT 60.996 63.158 0.00 0.00 0.00 4.16
966 3024 1.689233 TCGGATGGGAGGGAAGTGG 60.689 63.158 0.00 0.00 0.00 4.00
967 3025 1.826024 CTCGGATGGGAGGGAAGTG 59.174 63.158 0.00 0.00 0.00 3.16
968 3026 2.066999 GCTCGGATGGGAGGGAAGT 61.067 63.158 0.00 0.00 34.56 3.01
969 3027 2.812619 GGCTCGGATGGGAGGGAAG 61.813 68.421 0.00 0.00 34.56 3.46
970 3028 2.768344 GGCTCGGATGGGAGGGAA 60.768 66.667 0.00 0.00 34.56 3.97
971 3029 4.880426 GGGCTCGGATGGGAGGGA 62.880 72.222 0.00 0.00 34.56 4.20
973 3031 1.127567 TATTGGGCTCGGATGGGAGG 61.128 60.000 0.00 0.00 34.56 4.30
974 3032 0.764890 TTATTGGGCTCGGATGGGAG 59.235 55.000 0.00 0.00 37.11 4.30
975 3033 0.764890 CTTATTGGGCTCGGATGGGA 59.235 55.000 0.00 0.00 0.00 4.37
976 3034 0.890996 GCTTATTGGGCTCGGATGGG 60.891 60.000 0.00 0.00 0.00 4.00
977 3035 0.179020 TGCTTATTGGGCTCGGATGG 60.179 55.000 0.00 0.00 0.00 3.51
978 3036 1.334869 GTTGCTTATTGGGCTCGGATG 59.665 52.381 0.00 0.00 0.00 3.51
979 3037 1.680338 GTTGCTTATTGGGCTCGGAT 58.320 50.000 0.00 0.00 0.00 4.18
980 3038 0.393808 GGTTGCTTATTGGGCTCGGA 60.394 55.000 0.00 0.00 0.00 4.55
981 3039 0.679640 TGGTTGCTTATTGGGCTCGG 60.680 55.000 0.00 0.00 0.00 4.63
982 3040 1.066002 CATGGTTGCTTATTGGGCTCG 59.934 52.381 0.00 0.00 0.00 5.03
983 3041 1.410153 CCATGGTTGCTTATTGGGCTC 59.590 52.381 2.57 0.00 0.00 4.70
984 3042 1.488390 CCATGGTTGCTTATTGGGCT 58.512 50.000 2.57 0.00 0.00 5.19
985 3043 0.179076 GCCATGGTTGCTTATTGGGC 60.179 55.000 14.67 0.00 0.00 5.36
986 3044 0.102844 CGCCATGGTTGCTTATTGGG 59.897 55.000 14.67 0.00 0.00 4.12
987 3045 0.102844 CCGCCATGGTTGCTTATTGG 59.897 55.000 14.67 0.00 0.00 3.16
988 3046 0.528249 GCCGCCATGGTTGCTTATTG 60.528 55.000 14.67 0.00 41.21 1.90
989 3047 1.815866 GCCGCCATGGTTGCTTATT 59.184 52.632 14.67 0.00 41.21 1.40
990 3048 2.480610 CGCCGCCATGGTTGCTTAT 61.481 57.895 20.63 0.00 41.21 1.73
991 3049 3.130819 CGCCGCCATGGTTGCTTA 61.131 61.111 20.63 0.00 41.21 3.09
996 3054 4.690719 TTCGACGCCGCCATGGTT 62.691 61.111 14.67 0.00 41.21 3.67
1011 3069 2.266055 CAGACGAGGGTGGCCTTC 59.734 66.667 3.32 0.00 0.00 3.46
1017 3075 0.742281 CCATGAAGCAGACGAGGGTG 60.742 60.000 0.00 0.00 0.00 4.61
1313 3371 2.560080 GAGGGAGATGGATGGATGGAT 58.440 52.381 0.00 0.00 0.00 3.41
1338 3410 3.315796 ACGCAGTGTACGTGCAAC 58.684 55.556 8.25 3.00 43.23 4.17
1352 3424 3.582120 CACACCCACACCACACGC 61.582 66.667 0.00 0.00 0.00 5.34
1370 3450 3.157949 CCATGCCATGCCATGCCA 61.158 61.111 11.13 0.00 40.92 4.92
1371 3451 4.619227 GCCATGCCATGCCATGCC 62.619 66.667 11.13 0.00 40.92 4.40
1372 3452 2.602746 AAAGCCATGCCATGCCATGC 62.603 55.000 11.13 7.00 40.92 4.06
1373 3453 0.813610 CAAAGCCATGCCATGCCATG 60.814 55.000 9.68 9.68 41.71 3.66
1374 3454 1.268992 ACAAAGCCATGCCATGCCAT 61.269 50.000 0.00 0.00 0.00 4.40
1540 3624 4.084066 TCACATTGACATAACACAAGTCGC 60.084 41.667 0.00 0.00 35.09 5.19
1601 3691 7.934120 AGACATTAGAACAGGACATTTATAGCC 59.066 37.037 0.00 0.00 0.00 3.93
1611 3701 6.109359 AGTATGCAAGACATTAGAACAGGAC 58.891 40.000 0.00 0.00 40.38 3.85
1664 3754 2.982919 TTGACGAAAACAACGACGAG 57.017 45.000 0.00 0.00 34.70 4.18
1672 3762 7.038659 ACTCATTTTCCATTTTGACGAAAACA 58.961 30.769 0.00 0.00 38.07 2.83
1703 3793 3.980775 CCATTTGTTCGTCGCTCATTTTT 59.019 39.130 0.00 0.00 0.00 1.94
1712 3802 1.126846 GACAGCTCCATTTGTTCGTCG 59.873 52.381 0.00 0.00 0.00 5.12
1724 3814 6.763135 TGTGTTTGATATTATCTGACAGCTCC 59.237 38.462 0.00 0.64 0.00 4.70
1820 3931 1.003851 CGGCGTACCCAACATACAAG 58.996 55.000 0.00 0.00 0.00 3.16
1827 3938 3.428282 CTTGCCGGCGTACCCAAC 61.428 66.667 23.90 0.00 0.00 3.77
1838 3949 1.737838 TTGTCTCATTAGCCTTGCCG 58.262 50.000 0.00 0.00 0.00 5.69
1839 3950 3.255642 TGTTTTGTCTCATTAGCCTTGCC 59.744 43.478 0.00 0.00 0.00 4.52
1844 3955 5.391312 AACCATGTTTTGTCTCATTAGCC 57.609 39.130 0.00 0.00 0.00 3.93
1848 3959 3.569701 AGCGAACCATGTTTTGTCTCATT 59.430 39.130 0.00 0.00 0.00 2.57
1875 3986 1.863454 CTTCCCATCTCTTTCATCGCG 59.137 52.381 0.00 0.00 0.00 5.87
1876 3987 3.129871 CTCTTCCCATCTCTTTCATCGC 58.870 50.000 0.00 0.00 0.00 4.58
1877 3988 4.662468 TCTCTTCCCATCTCTTTCATCG 57.338 45.455 0.00 0.00 0.00 3.84
1880 3991 5.006386 GCTTTTCTCTTCCCATCTCTTTCA 58.994 41.667 0.00 0.00 0.00 2.69
1931 4042 0.951040 CGTGTGTGAAAGGAGGAGGC 60.951 60.000 0.00 0.00 0.00 4.70
1968 4079 2.660802 GACGGGCGGAGAAAGGAA 59.339 61.111 0.00 0.00 0.00 3.36
2003 4114 2.523168 TCTCCAGTGGTGCGGTCA 60.523 61.111 9.54 0.00 0.00 4.02
2015 4126 2.122413 AGTGGCCTGTGGTCTCCA 60.122 61.111 3.32 0.00 0.00 3.86
2025 4136 2.032071 CCGTTTTCCGAGTGGCCT 59.968 61.111 3.32 0.00 39.56 5.19
2048 4159 1.613630 ATGGGTCAAGCCTCCTCGT 60.614 57.895 0.00 0.00 37.43 4.18
2049 4160 1.153289 CATGGGTCAAGCCTCCTCG 60.153 63.158 0.00 0.00 37.43 4.63
2089 4200 0.396695 GAGATCCGACACTACCCCCA 60.397 60.000 0.00 0.00 0.00 4.96
2092 4203 1.950909 CAGAGAGATCCGACACTACCC 59.049 57.143 0.00 0.00 0.00 3.69
2200 4311 1.229209 GTCCCCAGAGACCTCACCA 60.229 63.158 0.00 0.00 0.00 4.17
2219 4330 3.636231 CCAGTCCCTTCCCGTGCA 61.636 66.667 0.00 0.00 0.00 4.57
2225 4336 4.432741 GCCAGGCCAGTCCCTTCC 62.433 72.222 5.01 0.00 31.24 3.46
2247 4358 4.668118 TCGCCGAAACCCACGACC 62.668 66.667 0.00 0.00 0.00 4.79
2276 4387 0.896019 CGATACGGGGGCTCAGATCT 60.896 60.000 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.