Multiple sequence alignment - TraesCS5B01G358200

Loading Multiple Alignment...

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 TraesCS5B01G358200 chr5B 100.000 3167 0 0 1 3167 537907724 537904558 0.000000e+00 5849
1 TraesCS5B01G358200 chr5D 94.820 1448 60 3 960 2399 441887651 441886211 0.000000e+00 2244
2 TraesCS5B01G358200 chr5D 89.037 675 48 13 2517 3167 441886212 441885540 0.000000e+00 813
3 TraesCS5B01G358200 chr5D 83.200 625 42 23 16 625 441890261 441889685 6.060000e-142 514
4 TraesCS5B01G358200 chr5D 95.604 182 7 1 656 837 441889318 441889138 1.110000e-74 291
5 TraesCS5B01G358200 chr5A 93.883 1455 67 4 959 2404 558252171 558250730 0.000000e+00 2174
6 TraesCS5B01G358200 chr5A 89.843 699 51 8 2480 3167 558250727 558250038 0.000000e+00 880
7 TraesCS5B01G358200 chr5A 84.185 626 50 21 16 625 558253402 558252810 2.130000e-156 562
8 TraesCS5B01G358200 chr5A 94.118 136 5 1 793 928 558252283 558252151 1.490000e-48 204
9 TraesCS5B01G358200 chr6A 91.954 87 6 1 2393 2478 615393785 615393871 1.540000e-23 121
10 TraesCS5B01G358200 chr6A 92.500 80 4 1 2401 2478 158316547 158316626 2.580000e-21 113
11 TraesCS5B01G358200 chr3B 93.590 78 5 0 2401 2478 59325929 59326006 2.000000e-22 117
12 TraesCS5B01G358200 chr3B 91.463 82 7 0 2401 2482 59326006 59325925 2.580000e-21 113
13 TraesCS5B01G358200 chr3B 90.244 82 7 1 2401 2481 438545537 438545456 4.320000e-19 106
14 TraesCS5B01G358200 chr7D 88.889 90 8 2 2401 2488 199127703 199127614 3.340000e-20 110
15 TraesCS5B01G358200 chr7D 88.298 94 5 2 2401 2488 351410571 351410478 1.200000e-19 108
16 TraesCS5B01G358200 chr1B 90.476 84 6 2 2401 2482 187002150 187002233 3.340000e-20 110
17 TraesCS5B01G358200 chr6B 89.412 85 9 0 2401 2485 561275760 561275676 1.200000e-19 108


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 TraesCS5B01G358200 chr5B 537904558 537907724 3166 True 5849.0 5849 100.00000 1 3167 1 chr5B.!!$R1 3166
1 TraesCS5B01G358200 chr5D 441885540 441890261 4721 True 965.5 2244 90.66525 16 3167 4 chr5D.!!$R1 3151
2 TraesCS5B01G358200 chr5A 558250038 558253402 3364 True 955.0 2174 90.50725 16 3167 4 chr5A.!!$R1 3151

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
106 107 0.460284 CCAATCGCAAGTCGCCTACT 60.460 55.0 0.0 0.0 41.49 2.57 F
1115 2945 0.179073 GTGGATGGCTACTCACGCAT 60.179 55.0 0.0 0.0 0.00 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1223 3053 0.179468 GGTAATAGAAGCGTGGCCCA 59.821 55.0 0.0 0.0 0.0 5.36 R
2460 4298 0.113776 AGTACTCCCTTCGTCCCACA 59.886 55.0 0.0 0.0 0.0 4.17 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
28 29 5.144100 AGGAGTAGAGATATGGAACCACAG 58.856 45.833 0.00 0.00 0.00 3.66
44 45 3.004629 ACCACAGATGTTAACGTGTACGA 59.995 43.478 11.79 0.00 43.02 3.43
66 67 0.887933 CCATGTTCCCGGTTTCCTTG 59.112 55.000 0.00 0.00 0.00 3.61
99 100 1.336795 CCAAAACCCCAATCGCAAGTC 60.337 52.381 0.00 0.00 39.48 3.01
100 101 0.596082 AAAACCCCAATCGCAAGTCG 59.404 50.000 0.00 0.00 40.15 4.18
101 102 1.862602 AAACCCCAATCGCAAGTCGC 61.863 55.000 0.00 0.00 38.27 5.19
102 103 3.508840 CCCCAATCGCAAGTCGCC 61.509 66.667 0.00 0.00 37.30 5.54
103 104 2.436646 CCCAATCGCAAGTCGCCT 60.437 61.111 0.00 0.00 37.30 5.52
104 105 1.153449 CCCAATCGCAAGTCGCCTA 60.153 57.895 0.00 0.00 37.30 3.93
105 106 1.429148 CCCAATCGCAAGTCGCCTAC 61.429 60.000 0.00 0.00 37.30 3.18
106 107 0.460284 CCAATCGCAAGTCGCCTACT 60.460 55.000 0.00 0.00 41.49 2.57
107 108 0.924090 CAATCGCAAGTCGCCTACTC 59.076 55.000 0.00 0.00 37.50 2.59
108 109 0.525668 AATCGCAAGTCGCCTACTCG 60.526 55.000 0.00 0.00 37.50 4.18
109 110 1.374343 ATCGCAAGTCGCCTACTCGA 61.374 55.000 1.70 1.70 38.40 4.04
115 116 3.188011 TCGCCTACTCGACTGCTG 58.812 61.111 0.00 0.00 33.02 4.41
116 117 2.103143 CGCCTACTCGACTGCTGG 59.897 66.667 0.00 0.00 0.00 4.85
117 118 2.496817 GCCTACTCGACTGCTGGG 59.503 66.667 0.00 0.00 0.00 4.45
118 119 2.496817 CCTACTCGACTGCTGGGC 59.503 66.667 0.00 0.00 0.00 5.36
119 120 2.351244 CCTACTCGACTGCTGGGCA 61.351 63.158 0.00 0.00 36.92 5.36
120 121 1.153745 CTACTCGACTGCTGGGCAC 60.154 63.158 0.00 0.00 33.79 5.01
121 122 2.874010 CTACTCGACTGCTGGGCACG 62.874 65.000 0.00 0.00 33.79 5.34
122 123 4.363990 CTCGACTGCTGGGCACGT 62.364 66.667 0.00 0.00 33.79 4.49
123 124 4.662961 TCGACTGCTGGGCACGTG 62.663 66.667 12.28 12.28 33.79 4.49
143 144 1.227002 GTACTGCTCACGGCTAGGC 60.227 63.158 6.15 6.15 42.39 3.93
301 311 2.022129 GTCGATATTCCCCGCTGCG 61.022 63.158 16.34 16.34 0.00 5.18
315 325 1.427592 GCTGCGTCATCTCTTCAGGC 61.428 60.000 0.00 0.00 0.00 4.85
392 406 6.260050 GCATATGTATTCTCCTTCCGTTTCAA 59.740 38.462 4.29 0.00 0.00 2.69
399 415 6.509418 TTCTCCTTCCGTTTCAAAATATGG 57.491 37.500 0.00 0.00 0.00 2.74
405 421 6.373216 CCTTCCGTTTCAAAATATGGAGTGTA 59.627 38.462 0.00 0.00 0.00 2.90
434 450 8.862325 ATTTTTCCAAAAGGGTGAATATTTCC 57.138 30.769 0.00 0.00 38.11 3.13
498 516 8.801299 TCTAACACTGAATAAAATTGGAATGCA 58.199 29.630 0.00 0.00 0.00 3.96
513 531 5.649557 TGGAATGCATGCTTTATGTGTAAC 58.350 37.500 20.33 4.24 39.08 2.50
537 555 1.474478 CAGTGCAGATACGTGAGGTCT 59.526 52.381 0.00 0.00 0.00 3.85
545 563 0.596577 TACGTGAGGTCTGCAGACAC 59.403 55.000 39.71 32.15 46.47 3.67
554 572 1.261619 GTCTGCAGACACGAGTTTTGG 59.738 52.381 36.23 0.00 44.18 3.28
572 590 1.759236 GGGTCGGTTTGAGAGGGTT 59.241 57.895 0.00 0.00 0.00 4.11
628 646 4.724279 ACCTTTGGGTTGATCACTACTT 57.276 40.909 0.00 0.00 44.73 2.24
629 647 4.398319 ACCTTTGGGTTGATCACTACTTG 58.602 43.478 0.00 0.00 44.73 3.16
630 648 4.141251 ACCTTTGGGTTGATCACTACTTGT 60.141 41.667 0.00 0.00 44.73 3.16
631 649 5.072600 ACCTTTGGGTTGATCACTACTTGTA 59.927 40.000 0.00 0.00 44.73 2.41
697 1068 9.605275 ATCATTACTCCACATATTCATATTCCG 57.395 33.333 0.00 0.00 0.00 4.30
763 1134 4.157840 ACAACGTGTAGAGTATCATCTGCA 59.842 41.667 0.00 0.00 39.26 4.41
768 1139 5.061721 TGTAGAGTATCATCTGCACCCTA 57.938 43.478 0.00 0.00 37.06 3.53
862 2691 2.223688 GCATGGCATTGGCGTGTTAATA 60.224 45.455 27.18 0.16 45.15 0.98
871 2700 6.427150 CATTGGCGTGTTAATAAGTGGTATC 58.573 40.000 0.00 0.00 0.00 2.24
925 2755 6.472887 CACTCTAAAATCCTAACTCCACCAA 58.527 40.000 0.00 0.00 0.00 3.67
928 2758 7.037586 ACTCTAAAATCCTAACTCCACCAATGA 60.038 37.037 0.00 0.00 0.00 2.57
929 2759 7.872138 TCTAAAATCCTAACTCCACCAATGAT 58.128 34.615 0.00 0.00 0.00 2.45
930 2760 8.998814 TCTAAAATCCTAACTCCACCAATGATA 58.001 33.333 0.00 0.00 0.00 2.15
931 2761 9.627123 CTAAAATCCTAACTCCACCAATGATAA 57.373 33.333 0.00 0.00 0.00 1.75
932 2762 7.881775 AAATCCTAACTCCACCAATGATAAC 57.118 36.000 0.00 0.00 0.00 1.89
933 2763 6.575244 ATCCTAACTCCACCAATGATAACA 57.425 37.500 0.00 0.00 0.00 2.41
934 2764 5.741011 TCCTAACTCCACCAATGATAACAC 58.259 41.667 0.00 0.00 0.00 3.32
935 2765 5.249622 TCCTAACTCCACCAATGATAACACA 59.750 40.000 0.00 0.00 0.00 3.72
936 2766 5.586243 CCTAACTCCACCAATGATAACACAG 59.414 44.000 0.00 0.00 0.00 3.66
937 2767 4.640771 ACTCCACCAATGATAACACAGT 57.359 40.909 0.00 0.00 0.00 3.55
938 2768 4.985538 ACTCCACCAATGATAACACAGTT 58.014 39.130 0.00 0.00 0.00 3.16
939 2769 6.121776 ACTCCACCAATGATAACACAGTTA 57.878 37.500 0.00 0.00 0.00 2.24
940 2770 6.721318 ACTCCACCAATGATAACACAGTTAT 58.279 36.000 2.28 2.28 0.00 1.89
941 2771 6.823689 ACTCCACCAATGATAACACAGTTATC 59.176 38.462 18.32 18.32 33.25 1.75
942 2772 6.119536 TCCACCAATGATAACACAGTTATCC 58.880 40.000 20.90 8.84 31.99 2.59
943 2773 5.299279 CCACCAATGATAACACAGTTATCCC 59.701 44.000 20.90 5.07 31.99 3.85
944 2774 5.299279 CACCAATGATAACACAGTTATCCCC 59.701 44.000 20.90 4.51 31.99 4.81
945 2775 5.193728 ACCAATGATAACACAGTTATCCCCT 59.806 40.000 20.90 8.36 31.99 4.79
946 2776 6.129179 CCAATGATAACACAGTTATCCCCTT 58.871 40.000 20.90 12.35 31.99 3.95
947 2777 6.607198 CCAATGATAACACAGTTATCCCCTTT 59.393 38.462 20.90 10.72 31.99 3.11
948 2778 7.124147 CCAATGATAACACAGTTATCCCCTTTT 59.876 37.037 20.90 9.00 31.99 2.27
949 2779 7.881775 ATGATAACACAGTTATCCCCTTTTC 57.118 36.000 20.90 2.92 31.99 2.29
950 2780 5.878116 TGATAACACAGTTATCCCCTTTTCG 59.122 40.000 20.90 0.00 31.99 3.46
951 2781 4.360951 AACACAGTTATCCCCTTTTCGA 57.639 40.909 0.00 0.00 0.00 3.71
952 2782 4.360951 ACACAGTTATCCCCTTTTCGAA 57.639 40.909 0.00 0.00 0.00 3.71
953 2783 4.324267 ACACAGTTATCCCCTTTTCGAAG 58.676 43.478 0.00 0.00 0.00 3.79
954 2784 4.041198 ACACAGTTATCCCCTTTTCGAAGA 59.959 41.667 0.00 0.00 0.00 2.87
955 2785 5.001232 CACAGTTATCCCCTTTTCGAAGAA 58.999 41.667 0.00 0.00 45.90 2.52
956 2786 5.472137 CACAGTTATCCCCTTTTCGAAGAAA 59.528 40.000 0.00 0.00 45.90 2.52
957 2787 6.016610 CACAGTTATCCCCTTTTCGAAGAAAA 60.017 38.462 0.00 7.58 45.90 2.29
958 2788 6.548251 ACAGTTATCCCCTTTTCGAAGAAAAA 59.452 34.615 8.92 0.00 45.90 1.94
979 2809 2.736670 AATCCTACCTCCACCAATGC 57.263 50.000 0.00 0.00 0.00 3.56
980 2810 0.469917 ATCCTACCTCCACCAATGCG 59.530 55.000 0.00 0.00 0.00 4.73
1115 2945 0.179073 GTGGATGGCTACTCACGCAT 60.179 55.000 0.00 0.00 0.00 4.73
1199 3029 1.327690 TGGGTCATCCTGTACTCGCC 61.328 60.000 0.00 0.00 36.20 5.54
1245 3075 1.540580 GGCCACGCTTCTATTACCCTC 60.541 57.143 0.00 0.00 0.00 4.30
1287 3117 0.675633 GCCATGTCAAGGTGCAGTTT 59.324 50.000 0.00 0.00 0.00 2.66
1344 3174 1.142185 CGTCACGCATTCGCTCATCT 61.142 55.000 0.00 0.00 39.84 2.90
1398 3228 2.158623 TGGCCATCATAGGTGGATGAAC 60.159 50.000 0.00 0.00 43.80 3.18
1458 3288 1.134401 AGTTTCATCATCCGGTGCGAT 60.134 47.619 0.00 0.00 0.00 4.58
1473 3303 0.996727 GCGATGTGTTTGTTGCGACC 60.997 55.000 0.45 0.00 0.00 4.79
1602 3432 2.355481 GTCGGTGGCGAGACGTTT 60.355 61.111 0.00 0.00 0.00 3.60
1604 3434 2.355363 CGGTGGCGAGACGTTTGA 60.355 61.111 0.00 0.00 0.00 2.69
1816 3646 1.241990 TGAAGGAGACACGGACGAGG 61.242 60.000 0.00 0.00 0.00 4.63
1817 3647 0.959372 GAAGGAGACACGGACGAGGA 60.959 60.000 0.00 0.00 0.00 3.71
1818 3648 1.242665 AAGGAGACACGGACGAGGAC 61.243 60.000 0.00 0.00 0.00 3.85
1819 3649 2.479650 GAGACACGGACGAGGACG 59.520 66.667 0.00 0.00 45.75 4.79
1820 3650 2.031516 GAGACACGGACGAGGACGA 61.032 63.158 0.00 0.00 42.66 4.20
1821 3651 2.175322 GACACGGACGAGGACGAC 59.825 66.667 0.00 0.00 42.66 4.34
1881 3711 1.332375 GAACAAGTAACGTGGCTGCAA 59.668 47.619 0.50 0.00 0.00 4.08
1951 3781 1.065851 TGTGCGAAGACGAGTTGTGTA 59.934 47.619 0.00 0.00 42.66 2.90
1963 3793 3.305131 CGAGTTGTGTAAGCACCTAGACA 60.305 47.826 0.00 0.00 44.65 3.41
2053 3883 3.044305 AGTTTGCGCGACTCCTGC 61.044 61.111 12.10 0.00 0.00 4.85
2082 3912 6.248420 CCGCAAAGTTACAAATCTTATTGTCG 59.752 38.462 0.00 0.00 42.33 4.35
2169 3999 5.124457 GCTTGCTTCCAAATTCTACTGATCA 59.876 40.000 0.00 0.00 0.00 2.92
2283 4121 2.632643 GCGCATGGCTCCATTGATA 58.367 52.632 0.30 0.00 39.11 2.15
2299 4137 5.174398 CCATTGATATGCATTCGTTCAAAGC 59.826 40.000 3.54 0.00 30.81 3.51
2325 4163 5.763876 AGTTCCCTTAGCAAGTACTCATT 57.236 39.130 0.00 0.00 0.00 2.57
2326 4164 5.491982 AGTTCCCTTAGCAAGTACTCATTG 58.508 41.667 0.00 0.00 0.00 2.82
2335 4173 9.774742 CTTAGCAAGTACTCATTGTTTTATTCC 57.225 33.333 0.00 0.00 0.00 3.01
2341 4179 8.472007 AGTACTCATTGTTTTATTCCCAACAA 57.528 30.769 0.00 0.27 44.78 2.83
2384 4222 0.401356 ACCATGTGCTGATGTGACCA 59.599 50.000 0.00 0.00 0.00 4.02
2391 4229 3.253921 TGTGCTGATGTGACCATGAAAAG 59.746 43.478 0.00 0.00 0.00 2.27
2404 4242 7.750903 GTGACCATGAAAAGCAGTTTTATACTC 59.249 37.037 0.00 0.00 35.94 2.59
2405 4243 7.094377 TGACCATGAAAAGCAGTTTTATACTCC 60.094 37.037 0.00 0.00 35.94 3.85
2406 4244 6.152831 ACCATGAAAAGCAGTTTTATACTCCC 59.847 38.462 0.00 0.00 35.94 4.30
2407 4245 6.378280 CCATGAAAAGCAGTTTTATACTCCCT 59.622 38.462 0.00 0.00 35.94 4.20
2408 4246 7.415653 CCATGAAAAGCAGTTTTATACTCCCTC 60.416 40.741 0.00 0.00 35.94 4.30
2409 4247 5.944007 TGAAAAGCAGTTTTATACTCCCTCC 59.056 40.000 0.00 0.00 35.94 4.30
2410 4248 3.821421 AGCAGTTTTATACTCCCTCCG 57.179 47.619 0.00 0.00 33.85 4.63
2411 4249 3.105283 AGCAGTTTTATACTCCCTCCGT 58.895 45.455 0.00 0.00 33.85 4.69
2412 4250 3.132467 AGCAGTTTTATACTCCCTCCGTC 59.868 47.826 0.00 0.00 33.85 4.79
2413 4251 3.740452 GCAGTTTTATACTCCCTCCGTCC 60.740 52.174 0.00 0.00 33.85 4.79
2414 4252 3.036819 AGTTTTATACTCCCTCCGTCCC 58.963 50.000 0.00 0.00 28.23 4.46
2415 4253 2.767960 GTTTTATACTCCCTCCGTCCCA 59.232 50.000 0.00 0.00 0.00 4.37
2416 4254 3.339713 TTTATACTCCCTCCGTCCCAT 57.660 47.619 0.00 0.00 0.00 4.00
2417 4255 4.474303 TTTATACTCCCTCCGTCCCATA 57.526 45.455 0.00 0.00 0.00 2.74
2418 4256 4.474303 TTATACTCCCTCCGTCCCATAA 57.526 45.455 0.00 0.00 0.00 1.90
2419 4257 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2420 4258 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
2421 4259 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2422 4260 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2423 4261 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2424 4262 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2425 4263 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2426 4264 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2427 4265 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
2428 4266 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
2429 4267 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
2430 4268 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
2431 4269 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
2432 4270 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
2433 4271 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
2468 4306 5.789710 AAACGTTCTTATATTGTGGGACG 57.210 39.130 0.00 0.00 0.00 4.79
2469 4307 4.724074 ACGTTCTTATATTGTGGGACGA 57.276 40.909 0.00 0.00 0.00 4.20
2470 4308 5.075858 ACGTTCTTATATTGTGGGACGAA 57.924 39.130 0.00 0.00 0.00 3.85
2471 4309 5.107133 ACGTTCTTATATTGTGGGACGAAG 58.893 41.667 0.00 0.00 0.00 3.79
2472 4310 4.506654 CGTTCTTATATTGTGGGACGAAGG 59.493 45.833 0.00 0.00 0.00 3.46
2473 4311 4.682778 TCTTATATTGTGGGACGAAGGG 57.317 45.455 0.00 0.00 0.00 3.95
2474 4312 4.291792 TCTTATATTGTGGGACGAAGGGA 58.708 43.478 0.00 0.00 0.00 4.20
2475 4313 4.344102 TCTTATATTGTGGGACGAAGGGAG 59.656 45.833 0.00 0.00 0.00 4.30
2476 4314 1.946984 TATTGTGGGACGAAGGGAGT 58.053 50.000 0.00 0.00 0.00 3.85
2477 4315 1.946984 ATTGTGGGACGAAGGGAGTA 58.053 50.000 0.00 0.00 0.00 2.59
2478 4316 0.971386 TTGTGGGACGAAGGGAGTAC 59.029 55.000 0.00 0.00 0.00 2.73
2528 4366 8.784043 AGTATTGTCTGTGGTTGAAATTACTTC 58.216 33.333 0.00 0.00 34.31 3.01
2533 4371 7.132863 GTCTGTGGTTGAAATTACTTCTTCAC 58.867 38.462 0.00 0.00 34.86 3.18
2535 4373 5.818336 TGTGGTTGAAATTACTTCTTCACGA 59.182 36.000 0.00 0.00 34.59 4.35
2638 4492 4.486125 TGTATGGAGATTGCAGCAACTA 57.514 40.909 10.85 0.00 0.00 2.24
2657 4511 7.040478 AGCAACTATTTCTTACAATGTGCTTCA 60.040 33.333 0.00 0.00 0.00 3.02
2663 4517 7.754069 TTTCTTACAATGTGCTTCAAAACAG 57.246 32.000 0.00 0.00 0.00 3.16
2705 4560 4.258702 AGAAACTCTACGCAGTTGACAT 57.741 40.909 0.00 0.00 37.78 3.06
2712 4567 5.105716 ACTCTACGCAGTTGACATACAAGAT 60.106 40.000 0.00 0.00 37.78 2.40
2714 4569 6.263344 TCTACGCAGTTGACATACAAGATAC 58.737 40.000 0.00 0.00 37.78 2.24
2841 4704 2.290260 ACAATTCGCTTCTCATCCCACA 60.290 45.455 0.00 0.00 0.00 4.17
2944 4807 1.143838 CCGGATCGACATTGCTGGA 59.856 57.895 0.00 0.00 0.00 3.86
3009 4872 0.601057 TGCTTCTTCGTCGACATCCA 59.399 50.000 17.16 0.00 0.00 3.41
3047 4910 2.344872 TCGTCGTCCTCGAGGTGA 59.655 61.111 30.17 24.69 46.96 4.02
3109 4972 0.179169 GCTCCGTCTTCGTGAGGTAC 60.179 60.000 0.00 0.00 36.04 3.34
3111 4974 1.538512 CTCCGTCTTCGTGAGGTACAA 59.461 52.381 0.00 0.00 33.81 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.726299 TGGTTCCATATCTCTACTCCTAATGG 59.274 42.308 0.00 0.00 34.91 3.16
1 2 7.233553 TGTGGTTCCATATCTCTACTCCTAATG 59.766 40.741 0.00 0.00 0.00 1.90
4 5 6.102762 TCTGTGGTTCCATATCTCTACTCCTA 59.897 42.308 0.00 0.00 0.00 2.94
5 6 5.103473 TCTGTGGTTCCATATCTCTACTCCT 60.103 44.000 0.00 0.00 0.00 3.69
6 7 5.141182 TCTGTGGTTCCATATCTCTACTCC 58.859 45.833 0.00 0.00 0.00 3.85
7 8 6.266558 ACATCTGTGGTTCCATATCTCTACTC 59.733 42.308 0.00 0.00 0.00 2.59
8 9 6.139671 ACATCTGTGGTTCCATATCTCTACT 58.860 40.000 0.00 0.00 0.00 2.57
9 10 6.412362 ACATCTGTGGTTCCATATCTCTAC 57.588 41.667 0.00 0.00 0.00 2.59
10 11 8.421784 GTTAACATCTGTGGTTCCATATCTCTA 58.578 37.037 0.00 0.00 0.00 2.43
11 12 5.965033 AACATCTGTGGTTCCATATCTCT 57.035 39.130 0.00 0.00 0.00 3.10
12 13 6.201044 CGTTAACATCTGTGGTTCCATATCTC 59.799 42.308 6.39 0.00 0.00 2.75
13 14 6.049149 CGTTAACATCTGTGGTTCCATATCT 58.951 40.000 6.39 0.00 0.00 1.98
14 15 5.815740 ACGTTAACATCTGTGGTTCCATATC 59.184 40.000 6.39 0.00 0.00 1.63
15 16 5.584649 CACGTTAACATCTGTGGTTCCATAT 59.415 40.000 6.39 0.00 0.00 1.78
16 17 4.932799 CACGTTAACATCTGTGGTTCCATA 59.067 41.667 6.39 0.00 0.00 2.74
17 18 3.751175 CACGTTAACATCTGTGGTTCCAT 59.249 43.478 6.39 0.00 0.00 3.41
18 19 3.135225 CACGTTAACATCTGTGGTTCCA 58.865 45.455 6.39 0.00 0.00 3.53
19 20 3.135994 ACACGTTAACATCTGTGGTTCC 58.864 45.455 13.61 0.00 36.67 3.62
20 21 4.143473 CGTACACGTTAACATCTGTGGTTC 60.143 45.833 13.61 5.20 36.67 3.62
28 29 3.825308 TGGACTCGTACACGTTAACATC 58.175 45.455 6.39 0.00 40.80 3.06
44 45 0.037734 GGAAACCGGGAACATGGACT 59.962 55.000 6.32 0.00 0.00 3.85
75 76 0.966179 GCGATTGGGGTTTTGGAACT 59.034 50.000 0.00 0.00 36.03 3.01
99 100 2.103143 CCAGCAGTCGAGTAGGCG 59.897 66.667 0.00 0.00 0.00 5.52
100 101 2.496817 CCCAGCAGTCGAGTAGGC 59.503 66.667 0.00 0.00 0.00 3.93
101 102 2.351244 TGCCCAGCAGTCGAGTAGG 61.351 63.158 0.00 0.00 33.32 3.18
102 103 1.153745 GTGCCCAGCAGTCGAGTAG 60.154 63.158 0.00 0.00 40.08 2.57
103 104 2.970639 GTGCCCAGCAGTCGAGTA 59.029 61.111 0.00 0.00 40.08 2.59
104 105 4.363990 CGTGCCCAGCAGTCGAGT 62.364 66.667 0.00 0.00 40.08 4.18
105 106 4.363990 ACGTGCCCAGCAGTCGAG 62.364 66.667 6.59 0.00 40.08 4.04
106 107 4.662961 CACGTGCCCAGCAGTCGA 62.663 66.667 0.82 0.00 40.08 4.20
113 114 3.112075 CAGTACGCACGTGCCCAG 61.112 66.667 33.23 22.10 37.91 4.45
116 117 3.479269 GAGCAGTACGCACGTGCC 61.479 66.667 33.23 20.11 46.13 5.01
117 118 2.733218 TGAGCAGTACGCACGTGC 60.733 61.111 30.42 30.42 46.13 5.34
118 119 3.147294 GTGAGCAGTACGCACGTG 58.853 61.111 12.28 12.28 46.13 4.49
121 122 3.479269 GCCGTGAGCAGTACGCAC 61.479 66.667 11.30 6.38 46.13 5.34
151 152 2.102553 GTCGCTACTCCGGCAGTC 59.897 66.667 9.44 0.00 36.43 3.51
279 280 0.178958 AGCGGGGAATATCGACTCCT 60.179 55.000 9.28 0.00 31.88 3.69
289 291 2.203070 GATGACGCAGCGGGGAAT 60.203 61.111 21.15 6.62 0.00 3.01
301 311 2.363683 CAAAGGGCCTGAAGAGATGAC 58.636 52.381 6.92 0.00 0.00 3.06
399 415 7.384932 CACCCTTTTGGAAAAATCAATACACTC 59.615 37.037 0.00 0.00 44.07 3.51
434 450 9.932699 TTTTTACAGCAAATTTGATCAAACATG 57.067 25.926 22.71 22.27 32.51 3.21
490 508 5.418524 AGTTACACATAAAGCATGCATTCCA 59.581 36.000 21.98 0.00 38.29 3.53
492 510 5.678483 CGAGTTACACATAAAGCATGCATTC 59.322 40.000 21.98 0.00 38.29 2.67
493 511 5.572211 CGAGTTACACATAAAGCATGCATT 58.428 37.500 21.98 17.42 38.29 3.56
498 516 4.093408 CACTGCGAGTTACACATAAAGCAT 59.907 41.667 0.00 0.00 31.41 3.79
513 531 0.179163 TCACGTATCTGCACTGCGAG 60.179 55.000 8.65 1.98 0.00 5.03
537 555 0.817634 CCCCAAAACTCGTGTCTGCA 60.818 55.000 0.00 0.00 0.00 4.41
539 557 1.226746 GACCCCAAAACTCGTGTCTG 58.773 55.000 0.00 0.00 0.00 3.51
545 563 0.309612 CAAACCGACCCCAAAACTCG 59.690 55.000 0.00 0.00 0.00 4.18
554 572 0.605589 CAACCCTCTCAAACCGACCC 60.606 60.000 0.00 0.00 0.00 4.46
572 590 2.290641 ACAAACTCACAACACCTGACCA 60.291 45.455 0.00 0.00 0.00 4.02
643 981 9.296400 GAACTAATACTGAAACAGTTGCAAAAA 57.704 29.630 0.00 0.00 42.59 1.94
763 1134 9.528489 AATGTCTTACATTTGTTTACATAGGGT 57.472 29.630 0.00 0.00 45.80 4.34
791 1162 7.516198 TCACCGTTCTAAAACTACTACTTCT 57.484 36.000 0.00 0.00 32.95 2.85
891 2720 9.910267 GTTAGGATTTTAGAGTGGGGTAATTAA 57.090 33.333 0.00 0.00 0.00 1.40
892 2721 9.287818 AGTTAGGATTTTAGAGTGGGGTAATTA 57.712 33.333 0.00 0.00 0.00 1.40
893 2722 8.171337 AGTTAGGATTTTAGAGTGGGGTAATT 57.829 34.615 0.00 0.00 0.00 1.40
894 2723 7.147355 GGAGTTAGGATTTTAGAGTGGGGTAAT 60.147 40.741 0.00 0.00 0.00 1.89
925 2755 6.542370 CGAAAAGGGGATAACTGTGTTATCAT 59.458 38.462 23.36 11.73 34.06 2.45
928 2758 6.057321 TCGAAAAGGGGATAACTGTGTTAT 57.943 37.500 3.00 3.00 0.00 1.89
929 2759 5.486735 TCGAAAAGGGGATAACTGTGTTA 57.513 39.130 0.00 0.00 0.00 2.41
930 2760 4.360951 TCGAAAAGGGGATAACTGTGTT 57.639 40.909 0.00 0.00 0.00 3.32
931 2761 4.041198 TCTTCGAAAAGGGGATAACTGTGT 59.959 41.667 0.00 0.00 33.03 3.72
932 2762 4.575885 TCTTCGAAAAGGGGATAACTGTG 58.424 43.478 0.00 0.00 33.03 3.66
933 2763 4.903045 TCTTCGAAAAGGGGATAACTGT 57.097 40.909 0.00 0.00 33.03 3.55
934 2764 6.569179 TTTTCTTCGAAAAGGGGATAACTG 57.431 37.500 0.00 0.00 33.03 3.16
957 2787 3.769300 GCATTGGTGGAGGTAGGATTTTT 59.231 43.478 0.00 0.00 0.00 1.94
958 2788 3.365472 GCATTGGTGGAGGTAGGATTTT 58.635 45.455 0.00 0.00 0.00 1.82
959 2789 2.683742 CGCATTGGTGGAGGTAGGATTT 60.684 50.000 0.00 0.00 0.00 2.17
960 2790 1.134098 CGCATTGGTGGAGGTAGGATT 60.134 52.381 0.00 0.00 0.00 3.01
961 2791 0.469917 CGCATTGGTGGAGGTAGGAT 59.530 55.000 0.00 0.00 0.00 3.24
962 2792 0.907704 ACGCATTGGTGGAGGTAGGA 60.908 55.000 0.00 0.00 0.00 2.94
963 2793 0.744414 CACGCATTGGTGGAGGTAGG 60.744 60.000 0.00 0.00 34.27 3.18
964 2794 1.369091 GCACGCATTGGTGGAGGTAG 61.369 60.000 7.19 0.00 38.36 3.18
965 2795 1.376683 GCACGCATTGGTGGAGGTA 60.377 57.895 7.19 0.00 38.36 3.08
966 2796 2.672996 GCACGCATTGGTGGAGGT 60.673 61.111 7.19 0.00 38.36 3.85
967 2797 2.672651 TGCACGCATTGGTGGAGG 60.673 61.111 7.19 0.00 38.36 4.30
969 2799 2.672651 CCTGCACGCATTGGTGGA 60.673 61.111 0.00 4.17 38.36 4.02
970 2800 2.981560 GACCTGCACGCATTGGTGG 61.982 63.158 7.61 0.55 38.36 4.61
971 2801 2.562912 GACCTGCACGCATTGGTG 59.437 61.111 7.61 0.00 40.89 4.17
972 2802 2.672996 GGACCTGCACGCATTGGT 60.673 61.111 2.81 2.81 35.23 3.67
973 2803 2.360350 AGGACCTGCACGCATTGG 60.360 61.111 0.00 0.00 0.00 3.16
974 2804 2.693762 CCAGGACCTGCACGCATTG 61.694 63.158 16.72 0.00 0.00 2.82
975 2805 2.360350 CCAGGACCTGCACGCATT 60.360 61.111 16.72 0.00 0.00 3.56
976 2806 4.415150 CCCAGGACCTGCACGCAT 62.415 66.667 16.72 0.00 0.00 4.73
979 2809 4.767255 GAGCCCAGGACCTGCACG 62.767 72.222 16.72 6.54 0.00 5.34
980 2810 4.767255 CGAGCCCAGGACCTGCAC 62.767 72.222 16.72 9.79 0.00 4.57
1115 2945 1.474320 CGTTGGGTGTGTTCTCCTTGA 60.474 52.381 0.00 0.00 0.00 3.02
1223 3053 0.179468 GGTAATAGAAGCGTGGCCCA 59.821 55.000 0.00 0.00 0.00 5.36
1231 3061 2.350964 CGAGAGCGAGGGTAATAGAAGC 60.351 54.545 0.00 0.00 40.82 3.86
1245 3075 2.123342 GAAACATCCTGATCGAGAGCG 58.877 52.381 0.00 0.00 39.35 5.03
1287 3117 3.320826 TCTGGTCGATGAAACTGAACTCA 59.679 43.478 0.00 0.00 0.00 3.41
1344 3174 3.191581 CAGTCGAAAGAGAGGCTACTTCA 59.808 47.826 6.84 0.00 43.49 3.02
1383 3213 1.138859 CCGCTGTTCATCCACCTATGA 59.861 52.381 0.00 0.00 34.07 2.15
1398 3228 2.747855 GCCTCAAAGTCCCCGCTG 60.748 66.667 0.00 0.00 0.00 5.18
1458 3288 2.405594 GCGGTCGCAACAAACACA 59.594 55.556 10.67 0.00 41.49 3.72
1473 3303 3.925238 GCAATGCTACCGACGGCG 61.925 66.667 15.39 1.94 37.24 6.46
1602 3432 4.656117 ACACACCGATGCGCGTCA 62.656 61.111 27.92 6.86 38.67 4.35
1816 3646 2.277382 GACTCGTCCTCGTCGTCGTC 62.277 65.000 1.33 0.00 38.33 4.20
1817 3647 2.356793 ACTCGTCCTCGTCGTCGT 60.357 61.111 1.33 0.00 38.33 4.34
1818 3648 2.394912 GACTCGTCCTCGTCGTCG 59.605 66.667 0.00 0.00 38.33 5.12
1819 3649 2.394912 CGACTCGTCCTCGTCGTC 59.605 66.667 3.88 0.00 45.64 4.20
1881 3711 2.317609 CGCCGCTACAAGCAAGTGT 61.318 57.895 0.00 0.00 42.58 3.55
1951 3781 1.135915 CGAGCTCATGTCTAGGTGCTT 59.864 52.381 15.40 0.00 37.53 3.91
1963 3793 1.109920 ATAGTCGCCACCGAGCTCAT 61.110 55.000 15.40 0.00 45.38 2.90
2053 3883 3.081804 AGATTTGTAACTTTGCGGGAGG 58.918 45.455 0.00 0.00 0.00 4.30
2082 3912 5.812436 GCTATATGCTTCCAGCCTTTGGTC 61.812 50.000 0.00 0.00 41.51 4.02
2169 3999 3.662247 AAGTAGCTAGCAAGACGTGTT 57.338 42.857 18.83 0.00 0.00 3.32
2283 4121 0.523072 AGCGCTTTGAACGAATGCAT 59.477 45.000 2.64 0.00 34.99 3.96
2299 4137 2.674796 ACTTGCTAAGGGAACTAGCG 57.325 50.000 0.00 0.00 42.68 4.26
2325 4163 7.437748 ACGATCATTTTGTTGGGAATAAAACA 58.562 30.769 0.00 0.00 34.92 2.83
2326 4164 7.883229 ACGATCATTTTGTTGGGAATAAAAC 57.117 32.000 0.00 0.00 34.92 2.43
2335 4173 7.095695 ACCCTAAATACGATCATTTTGTTGG 57.904 36.000 0.00 0.00 30.84 3.77
2341 4179 8.248253 GGTTCAAAACCCTAAATACGATCATTT 58.752 33.333 0.00 0.00 46.12 2.32
2384 4222 6.603599 GGAGGGAGTATAAAACTGCTTTTCAT 59.396 38.462 0.00 0.00 45.39 2.57
2391 4229 3.455327 GACGGAGGGAGTATAAAACTGC 58.545 50.000 0.00 0.00 45.35 4.40
2404 4242 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
2405 4243 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
2406 4244 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
2407 4245 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
2408 4246 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
2444 4282 6.427547 TCGTCCCACAATATAAGAACGTTTTT 59.572 34.615 9.22 9.22 0.00 1.94
2445 4283 5.933463 TCGTCCCACAATATAAGAACGTTTT 59.067 36.000 0.46 0.00 0.00 2.43
2446 4284 5.481105 TCGTCCCACAATATAAGAACGTTT 58.519 37.500 0.46 0.00 0.00 3.60
2447 4285 5.075858 TCGTCCCACAATATAAGAACGTT 57.924 39.130 0.00 0.00 0.00 3.99
2448 4286 4.724074 TCGTCCCACAATATAAGAACGT 57.276 40.909 0.00 0.00 0.00 3.99
2449 4287 4.506654 CCTTCGTCCCACAATATAAGAACG 59.493 45.833 0.00 0.00 0.00 3.95
2450 4288 4.814771 CCCTTCGTCCCACAATATAAGAAC 59.185 45.833 0.00 0.00 0.00 3.01
2451 4289 4.717778 TCCCTTCGTCCCACAATATAAGAA 59.282 41.667 0.00 0.00 0.00 2.52
2452 4290 4.291792 TCCCTTCGTCCCACAATATAAGA 58.708 43.478 0.00 0.00 0.00 2.10
2453 4291 4.101119 ACTCCCTTCGTCCCACAATATAAG 59.899 45.833 0.00 0.00 0.00 1.73
2454 4292 4.035112 ACTCCCTTCGTCCCACAATATAA 58.965 43.478 0.00 0.00 0.00 0.98
2455 4293 3.649843 ACTCCCTTCGTCCCACAATATA 58.350 45.455 0.00 0.00 0.00 0.86
2456 4294 2.478292 ACTCCCTTCGTCCCACAATAT 58.522 47.619 0.00 0.00 0.00 1.28
2457 4295 1.946984 ACTCCCTTCGTCCCACAATA 58.053 50.000 0.00 0.00 0.00 1.90
2458 4296 1.553704 GTACTCCCTTCGTCCCACAAT 59.446 52.381 0.00 0.00 0.00 2.71
2459 4297 0.971386 GTACTCCCTTCGTCCCACAA 59.029 55.000 0.00 0.00 0.00 3.33
2460 4298 0.113776 AGTACTCCCTTCGTCCCACA 59.886 55.000 0.00 0.00 0.00 4.17
2461 4299 2.022934 CTAGTACTCCCTTCGTCCCAC 58.977 57.143 0.00 0.00 0.00 4.61
2462 4300 1.918262 TCTAGTACTCCCTTCGTCCCA 59.082 52.381 0.00 0.00 0.00 4.37
2463 4301 2.725221 TCTAGTACTCCCTTCGTCCC 57.275 55.000 0.00 0.00 0.00 4.46
2464 4302 4.971939 ACTATCTAGTACTCCCTTCGTCC 58.028 47.826 0.00 0.00 34.13 4.79
2476 4314 9.448438 TTGTGAAACGTAAGGTACTATCTAGTA 57.552 33.333 0.00 0.00 42.39 1.82
2477 4315 7.928307 TGTGAAACGTAAGGTACTATCTAGT 57.072 36.000 0.00 0.00 42.39 2.57
2478 4316 8.457261 ACTTGTGAAACGTAAGGTACTATCTAG 58.543 37.037 0.00 0.00 42.39 2.43
2490 4328 6.018588 CCACAGACAATACTTGTGAAACGTAA 60.019 38.462 5.49 0.00 45.52 3.18
2495 4333 5.883115 TCAACCACAGACAATACTTGTGAAA 59.117 36.000 5.49 0.00 45.52 2.69
2508 4346 7.132863 GTGAAGAAGTAATTTCAACCACAGAC 58.867 38.462 0.00 0.00 38.31 3.51
2509 4347 6.018262 CGTGAAGAAGTAATTTCAACCACAGA 60.018 38.462 0.00 0.00 38.31 3.41
2589 4435 7.897920 ACAATACATATTCGCTTGCATTTTTG 58.102 30.769 0.00 0.00 0.00 2.44
2594 4440 7.874940 ACATTACAATACATATTCGCTTGCAT 58.125 30.769 0.00 0.00 0.00 3.96
2638 4492 7.981225 ACTGTTTTGAAGCACATTGTAAGAAAT 59.019 29.630 0.00 0.00 0.00 2.17
2657 4511 6.377146 AGTTGACATCTTGTTGGTACTGTTTT 59.623 34.615 0.00 0.00 0.00 2.43
2663 4517 7.724305 TTCTTAGTTGACATCTTGTTGGTAC 57.276 36.000 0.00 0.00 0.00 3.34
2705 4560 9.280174 GAAATCCAATTAATCCCGTATCTTGTA 57.720 33.333 0.00 0.00 0.00 2.41
2712 4567 4.746115 CGACGAAATCCAATTAATCCCGTA 59.254 41.667 0.00 0.00 0.00 4.02
2714 4569 3.805422 TCGACGAAATCCAATTAATCCCG 59.195 43.478 0.00 0.00 0.00 5.14
2841 4704 1.974236 GATCGAGATGGGTGGGAGATT 59.026 52.381 0.00 0.00 0.00 2.40
3009 4872 0.745468 TTTTACGGGCGCTTTTTGGT 59.255 45.000 7.64 0.00 0.00 3.67
3045 4908 1.948721 ATGCTCTCGTCGCACCATCA 61.949 55.000 0.00 0.00 40.65 3.07
3047 4910 1.227089 GATGCTCTCGTCGCACCAT 60.227 57.895 0.00 0.00 40.65 3.55


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

AutoCloner maintained by Alex Coulton.