Multiple sequence alignment - TraesCS2D01G016100

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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 TraesCS2D01G016100 chr2D 100.000 3280 0 0 1 3280 7833403 7836682 0.000000e+00 6058
1 TraesCS2D01G016100 chr2D 91.697 1096 84 3 1246 2341 7646156 7645068 0.000000e+00 1513
2 TraesCS2D01G016100 chr2D 79.972 719 103 23 507 1207 7646961 7646266 2.940000e-135 492
3 TraesCS2D01G016100 chr2B 92.020 3158 185 28 1 3137 4376423 4379534 0.000000e+00 4373
4 TraesCS2D01G016100 chr2B 92.023 3159 183 27 1 3137 4424264 4427375 0.000000e+00 4373
5 TraesCS2D01G016100 chr2B 91.894 3158 187 28 1 3137 4283030 4286139 0.000000e+00 4349
6 TraesCS2D01G016100 chr2B 91.799 3158 188 28 1 3137 4013529 4016636 0.000000e+00 4331
7 TraesCS2D01G016100 chr2B 87.299 1803 162 38 566 2344 3796301 3794542 0.000000e+00 1999
8 TraesCS2D01G016100 chr2B 83.586 859 80 34 566 1400 3709441 3708620 0.000000e+00 749
9 TraesCS2D01G016100 chr2B 91.946 149 12 0 3132 3280 4048776 4048924 3.320000e-50 209
10 TraesCS2D01G016100 chr2B 91.946 149 12 0 3132 3280 4459511 4459659 3.320000e-50 209
11 TraesCS2D01G016100 chr2B 91.275 149 13 0 3132 3280 4312976 4313124 1.540000e-48 204
12 TraesCS2D01G016100 chr2A 80.680 1382 218 25 928 2280 5910874 5912235 0.000000e+00 1027
13 TraesCS2D01G016100 chr2A 77.575 602 83 30 1 582 5707297 5707866 1.900000e-82 316
14 TraesCS2D01G016100 chrUn 93.891 311 17 1 1 311 438604620 438604928 4.960000e-128 468
15 TraesCS2D01G016100 chrUn 89.846 325 27 3 2017 2341 446626984 446627302 2.360000e-111 412
16 TraesCS2D01G016100 chr4A 73.887 1011 235 25 1281 2279 668442189 668441196 8.590000e-101 377
17 TraesCS2D01G016100 chr4A 95.385 65 3 0 3212 3276 591696540 591696476 1.610000e-18 104
18 TraesCS2D01G016100 chr4D 95.385 65 3 0 3212 3276 10928205 10928141 1.610000e-18 104
19 TraesCS2D01G016100 chr4B 95.385 65 3 0 3212 3276 20583561 20583497 1.610000e-18 104


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 TraesCS2D01G016100 chr2D 7833403 7836682 3279 False 6058.0 6058 100.0000 1 3280 1 chr2D.!!$F1 3279
1 TraesCS2D01G016100 chr2D 7645068 7646961 1893 True 1002.5 1513 85.8345 507 2341 2 chr2D.!!$R1 1834
2 TraesCS2D01G016100 chr2B 4376423 4379534 3111 False 4373.0 4373 92.0200 1 3137 1 chr2B.!!$F5 3136
3 TraesCS2D01G016100 chr2B 4424264 4427375 3111 False 4373.0 4373 92.0230 1 3137 1 chr2B.!!$F6 3136
4 TraesCS2D01G016100 chr2B 4283030 4286139 3109 False 4349.0 4349 91.8940 1 3137 1 chr2B.!!$F3 3136
5 TraesCS2D01G016100 chr2B 4013529 4016636 3107 False 4331.0 4331 91.7990 1 3137 1 chr2B.!!$F1 3136
6 TraesCS2D01G016100 chr2B 3794542 3796301 1759 True 1999.0 1999 87.2990 566 2344 1 chr2B.!!$R2 1778
7 TraesCS2D01G016100 chr2B 3708620 3709441 821 True 749.0 749 83.5860 566 1400 1 chr2B.!!$R1 834
8 TraesCS2D01G016100 chr2A 5910874 5912235 1361 False 1027.0 1027 80.6800 928 2280 1 chr2A.!!$F2 1352
9 TraesCS2D01G016100 chr2A 5707297 5707866 569 False 316.0 316 77.5750 1 582 1 chr2A.!!$F1 581
10 TraesCS2D01G016100 chr4A 668441196 668442189 993 True 377.0 377 73.8870 1281 2279 1 chr4A.!!$R2 998

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
376 386 0.472471 ACCTTCCTGCGAAAGACCAA 59.528 50.000 0.0 0.0 0.00 3.67 F
1104 1185 1.000274 GCAAATCCTGCGAACAAGGTT 60.000 47.619 0.0 0.0 42.37 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 1920 0.893270 CTGCCCCATCACCGAACAAA 60.893 55.0 0.00 0.0 0.00 2.83 R
2534 2714 0.328258 ACAAACCCGGATGGAGGAAG 59.672 55.0 0.73 0.0 37.49 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
69 70 4.263572 CCCAACCGTCCACCTGCA 62.264 66.667 0.00 0.00 0.00 4.41
70 71 2.203280 CCAACCGTCCACCTGCAA 60.203 61.111 0.00 0.00 0.00 4.08
72 73 1.178534 CCAACCGTCCACCTGCAATT 61.179 55.000 0.00 0.00 0.00 2.32
152 161 2.094597 TGCATAATTGTTGTCTGCTGCC 60.095 45.455 0.00 0.00 34.02 4.85
159 168 2.494059 TGTTGTCTGCTGCCTAGTTTC 58.506 47.619 0.00 0.00 0.00 2.78
204 214 8.630917 GCTCTTATCTACCTGTGTATTAAGACA 58.369 37.037 0.00 0.00 33.06 3.41
216 226 5.915758 GTGTATTAAGACATAGCAGGTCGAG 59.084 44.000 6.16 0.00 40.20 4.04
244 254 6.158169 CCAGAAGGTAAGTCCCTAAACCTATT 59.842 42.308 0.00 0.00 41.51 1.73
373 383 2.479275 GTGTAACCTTCCTGCGAAAGAC 59.521 50.000 0.00 0.00 0.00 3.01
376 386 0.472471 ACCTTCCTGCGAAAGACCAA 59.528 50.000 0.00 0.00 0.00 3.67
440 452 9.109393 ACTAATAAGTTCATTCGTTATGCACAT 57.891 29.630 0.00 0.00 33.45 3.21
491 506 1.342496 TGCGCAATGGGTGATTCAAAA 59.658 42.857 8.16 0.00 0.00 2.44
500 515 7.469732 GCAATGGGTGATTCAAAATTTCCAAAA 60.470 33.333 0.00 0.00 0.00 2.44
616 641 5.240183 GCCATAATTCAAGCTAAGCATCTCA 59.760 40.000 0.00 0.00 0.00 3.27
663 689 4.983671 CAGAAAGTTACTTTATGCCCCC 57.016 45.455 17.59 1.61 36.21 5.40
686 712 6.017934 CCCATATATAGTGTGCAGTGACAAAC 60.018 42.308 0.00 0.00 0.00 2.93
770 823 8.832521 TCTTAGTTTTATTCACGTCACAACATT 58.167 29.630 0.00 0.00 0.00 2.71
771 824 9.445786 CTTAGTTTTATTCACGTCACAACATTT 57.554 29.630 0.00 0.00 0.00 2.32
773 826 8.776680 AGTTTTATTCACGTCACAACATTTAC 57.223 30.769 0.00 0.00 0.00 2.01
774 827 8.617809 AGTTTTATTCACGTCACAACATTTACT 58.382 29.630 0.00 0.00 0.00 2.24
775 828 9.866936 GTTTTATTCACGTCACAACATTTACTA 57.133 29.630 0.00 0.00 0.00 1.82
778 831 6.384178 TTCACGTCACAACATTTACTATCG 57.616 37.500 0.00 0.00 0.00 2.92
779 832 5.463286 TCACGTCACAACATTTACTATCGT 58.537 37.500 0.00 0.00 0.00 3.73
812 881 5.641783 TTGTTCACATTGATACCCATGTG 57.358 39.130 6.02 6.02 44.01 3.21
852 926 2.928801 TGTGCTGCTTTCTTGGAGTA 57.071 45.000 0.00 0.00 0.00 2.59
859 933 4.142513 GCTGCTTTCTTGGAGTATTTGAGG 60.143 45.833 0.00 0.00 0.00 3.86
952 1026 4.943705 CACACAATATACAGTGCTTCCCTT 59.056 41.667 6.35 0.00 39.30 3.95
953 1027 4.943705 ACACAATATACAGTGCTTCCCTTG 59.056 41.667 6.35 0.00 39.30 3.61
962 1036 1.876156 GTGCTTCCCTTGTGTCTTCAG 59.124 52.381 0.00 0.00 0.00 3.02
963 1037 1.768275 TGCTTCCCTTGTGTCTTCAGA 59.232 47.619 0.00 0.00 0.00 3.27
1011 1086 2.673523 GAGACCATGGCAGGCAGT 59.326 61.111 13.04 0.00 0.00 4.40
1017 1098 2.036256 ATGGCAGGCAGTTCACCC 59.964 61.111 1.89 0.00 0.00 4.61
1071 1152 3.885521 GGCTCAGCGGCAATGCTC 61.886 66.667 4.82 0.00 45.23 4.26
1104 1185 1.000274 GCAAATCCTGCGAACAAGGTT 60.000 47.619 0.00 0.00 42.37 3.50
1219 1382 7.716998 AGCACCCAAACATACTGAAATATCTAG 59.283 37.037 0.00 0.00 0.00 2.43
1514 1680 1.069765 CACCAACTCTGACGCTGGT 59.930 57.895 0.00 0.00 43.01 4.00
1748 1920 3.110705 AGACACCCTCATTACTCATGCT 58.889 45.455 0.00 0.00 32.13 3.79
1853 2025 1.979155 CTCTCAGACCCTCGTGCCA 60.979 63.158 0.00 0.00 0.00 4.92
1898 2070 2.676121 TTGGGGAGCAATGGCACG 60.676 61.111 0.00 0.00 44.61 5.34
1931 2103 0.751643 ACACCAAACTGCCCACACTC 60.752 55.000 0.00 0.00 0.00 3.51
2360 2532 9.249053 TGCCCAACTATTTTAATTGTTCTCATA 57.751 29.630 0.38 0.00 33.25 2.15
2396 2568 9.527157 TTTTGATTGGATCTGTAACCTATTTGA 57.473 29.630 0.00 0.00 0.00 2.69
2475 2655 8.531146 TGACAGCCATTAATGAATCTATATCGA 58.469 33.333 17.23 0.00 0.00 3.59
2479 2659 9.388506 AGCCATTAATGAATCTATATCGAAAGG 57.611 33.333 17.23 0.00 0.00 3.11
2484 2664 7.897575 AATGAATCTATATCGAAAGGCAGTC 57.102 36.000 0.00 0.00 0.00 3.51
2502 2682 5.181245 GGCAGTCTAAAAGTATTGCTCACAA 59.819 40.000 0.00 0.00 40.87 3.33
2545 2725 1.141657 TGCATGCTACTTCCTCCATCC 59.858 52.381 20.33 0.00 0.00 3.51
2554 2734 0.037590 TTCCTCCATCCGGGTTTGTG 59.962 55.000 0.00 0.00 38.11 3.33
2582 2763 4.637977 GGGCACAGATTTTTGGTTTTTCAA 59.362 37.500 0.00 0.00 0.00 2.69
2622 2803 4.508492 TGTGTACAACATCCGTTTAGTGTG 59.492 41.667 0.00 0.00 32.36 3.82
2646 2827 7.712797 TGTAGATACACTCATTTCTGCGATAA 58.287 34.615 0.00 0.00 0.00 1.75
2658 2839 5.917541 TTCTGCGATAATTAATTCCGGAC 57.082 39.130 1.83 8.35 0.00 4.79
2663 2844 3.924686 CGATAATTAATTCCGGACGGAGG 59.075 47.826 13.64 0.00 46.06 4.30
2750 2931 7.023575 CACATTTTGCTAGTCAAATAGGTGAC 58.976 38.462 19.50 0.00 46.90 3.67
2763 2944 9.357652 GTCAAATAGGTGACGTAAATAACAGTA 57.642 33.333 0.00 0.00 38.68 2.74
2764 2945 9.577110 TCAAATAGGTGACGTAAATAACAGTAG 57.423 33.333 0.00 0.00 0.00 2.57
2769 2950 5.166398 GTGACGTAAATAACAGTAGCCACT 58.834 41.667 0.00 0.00 34.42 4.00
2771 2952 6.808212 GTGACGTAAATAACAGTAGCCACTTA 59.192 38.462 0.00 0.00 30.46 2.24
2772 2953 7.008992 GTGACGTAAATAACAGTAGCCACTTAG 59.991 40.741 0.00 0.00 30.46 2.18
2792 2974 8.573035 CACTTAGAAACCCAGATAGAGATAGTC 58.427 40.741 0.00 0.00 0.00 2.59
2807 2989 5.008415 AGAGATAGTCGTATTTACCCACACG 59.992 44.000 0.00 0.00 35.78 4.49
2810 2992 3.319755 AGTCGTATTTACCCACACGTTG 58.680 45.455 0.00 0.00 35.91 4.10
2820 3002 4.877378 ACCCACACGTTGATAAGTAAGA 57.123 40.909 0.00 0.00 0.00 2.10
2821 3003 4.817517 ACCCACACGTTGATAAGTAAGAG 58.182 43.478 0.00 0.00 0.00 2.85
2874 3056 2.437651 TGGAATCACAGTGTCTGAACCA 59.562 45.455 0.00 1.28 35.18 3.67
2883 3065 4.156008 ACAGTGTCTGAACCAAACTTTCAC 59.844 41.667 3.70 0.00 35.18 3.18
2987 3171 6.484288 TCAGTTCAGACCATGTAATTCCATT 58.516 36.000 0.00 0.00 0.00 3.16
2989 3173 8.106462 TCAGTTCAGACCATGTAATTCCATTTA 58.894 33.333 0.00 0.00 0.00 1.40
3019 3203 7.795272 GGTTTAACATATATAGTTTTCCGTGCG 59.205 37.037 0.00 0.00 0.00 5.34
3053 3237 5.007385 ACGCTTACAATCCAGTTACCTAG 57.993 43.478 0.00 0.00 0.00 3.02
3063 3248 3.762288 TCCAGTTACCTAGTGTACAGCTG 59.238 47.826 13.48 13.48 0.00 4.24
3093 3278 1.518325 TTATTCCACACACGCCACTG 58.482 50.000 0.00 0.00 0.00 3.66
3149 3334 8.743085 AAATGATATCCTTTCCATCCATATCG 57.257 34.615 0.00 0.00 31.60 2.92
3150 3335 6.874278 TGATATCCTTTCCATCCATATCGT 57.126 37.500 0.00 0.00 31.60 3.73
3151 3336 6.878317 TGATATCCTTTCCATCCATATCGTC 58.122 40.000 0.00 0.00 31.60 4.20
3152 3337 3.660501 TCCTTTCCATCCATATCGTCG 57.339 47.619 0.00 0.00 0.00 5.12
3153 3338 2.963101 TCCTTTCCATCCATATCGTCGT 59.037 45.455 0.00 0.00 0.00 4.34
3154 3339 3.386726 TCCTTTCCATCCATATCGTCGTT 59.613 43.478 0.00 0.00 0.00 3.85
3155 3340 3.741344 CCTTTCCATCCATATCGTCGTTC 59.259 47.826 0.00 0.00 0.00 3.95
3156 3341 4.501571 CCTTTCCATCCATATCGTCGTTCT 60.502 45.833 0.00 0.00 0.00 3.01
3157 3342 4.665833 TTCCATCCATATCGTCGTTCTT 57.334 40.909 0.00 0.00 0.00 2.52
3158 3343 3.977427 TCCATCCATATCGTCGTTCTTG 58.023 45.455 0.00 0.00 0.00 3.02
3159 3344 3.634910 TCCATCCATATCGTCGTTCTTGA 59.365 43.478 0.00 0.00 0.00 3.02
3160 3345 4.280929 TCCATCCATATCGTCGTTCTTGAT 59.719 41.667 0.00 0.00 0.00 2.57
3161 3346 4.991056 CCATCCATATCGTCGTTCTTGATT 59.009 41.667 0.00 0.00 0.00 2.57
3162 3347 5.107337 CCATCCATATCGTCGTTCTTGATTG 60.107 44.000 0.00 0.00 0.00 2.67
3163 3348 3.802139 TCCATATCGTCGTTCTTGATTGC 59.198 43.478 0.00 0.00 0.00 3.56
3164 3349 3.555547 CCATATCGTCGTTCTTGATTGCA 59.444 43.478 0.00 0.00 0.00 4.08
3165 3350 4.318333 CCATATCGTCGTTCTTGATTGCAG 60.318 45.833 0.00 0.00 0.00 4.41
3166 3351 0.790207 TCGTCGTTCTTGATTGCAGC 59.210 50.000 0.00 0.00 0.00 5.25
3167 3352 0.179215 CGTCGTTCTTGATTGCAGCC 60.179 55.000 0.00 0.00 0.00 4.85
3168 3353 0.169009 GTCGTTCTTGATTGCAGCCC 59.831 55.000 0.00 0.00 0.00 5.19
3169 3354 0.250684 TCGTTCTTGATTGCAGCCCA 60.251 50.000 0.00 0.00 0.00 5.36
3170 3355 0.597568 CGTTCTTGATTGCAGCCCAA 59.402 50.000 0.00 0.00 37.94 4.12
3171 3356 1.666888 CGTTCTTGATTGCAGCCCAAC 60.667 52.381 0.00 0.00 35.99 3.77
3172 3357 0.968405 TTCTTGATTGCAGCCCAACC 59.032 50.000 0.00 0.00 35.99 3.77
3173 3358 0.112995 TCTTGATTGCAGCCCAACCT 59.887 50.000 0.00 0.00 35.99 3.50
3174 3359 0.245539 CTTGATTGCAGCCCAACCTG 59.754 55.000 0.00 0.00 35.99 4.00
3180 3365 4.308526 CAGCCCAACCTGCAGTAG 57.691 61.111 13.81 0.00 0.00 2.57
3181 3366 1.376466 CAGCCCAACCTGCAGTAGT 59.624 57.895 13.81 0.70 0.00 2.73
3182 3367 0.957395 CAGCCCAACCTGCAGTAGTG 60.957 60.000 13.81 7.23 0.00 2.74
3183 3368 1.073199 GCCCAACCTGCAGTAGTGT 59.927 57.895 13.81 0.00 0.00 3.55
3184 3369 0.323629 GCCCAACCTGCAGTAGTGTA 59.676 55.000 13.81 0.00 0.00 2.90
3185 3370 1.944430 GCCCAACCTGCAGTAGTGTAC 60.944 57.143 13.81 0.00 0.00 2.90
3186 3371 1.623811 CCCAACCTGCAGTAGTGTACT 59.376 52.381 13.81 0.00 40.28 2.73
3187 3372 2.829720 CCCAACCTGCAGTAGTGTACTA 59.170 50.000 13.81 0.00 37.23 1.82
3188 3373 3.119101 CCCAACCTGCAGTAGTGTACTAG 60.119 52.174 13.81 0.00 37.23 2.57
3189 3374 3.510360 CCAACCTGCAGTAGTGTACTAGT 59.490 47.826 13.81 0.00 37.23 2.57
3190 3375 4.703575 CCAACCTGCAGTAGTGTACTAGTA 59.296 45.833 13.81 0.00 37.23 1.82
3191 3376 5.360144 CCAACCTGCAGTAGTGTACTAGTAT 59.640 44.000 13.81 0.00 37.23 2.12
3192 3377 6.127423 CCAACCTGCAGTAGTGTACTAGTATT 60.127 42.308 13.81 0.00 37.23 1.89
3193 3378 6.452494 ACCTGCAGTAGTGTACTAGTATTG 57.548 41.667 13.81 0.00 37.23 1.90
3194 3379 6.185511 ACCTGCAGTAGTGTACTAGTATTGA 58.814 40.000 13.81 0.00 37.23 2.57
3195 3380 6.095160 ACCTGCAGTAGTGTACTAGTATTGAC 59.905 42.308 13.81 3.98 37.23 3.18
3196 3381 6.095021 CCTGCAGTAGTGTACTAGTATTGACA 59.905 42.308 13.81 0.00 37.23 3.58
3197 3382 7.201830 CCTGCAGTAGTGTACTAGTATTGACAT 60.202 40.741 13.81 0.00 37.23 3.06
3198 3383 8.063200 TGCAGTAGTGTACTAGTATTGACATT 57.937 34.615 5.75 1.46 37.23 2.71
3199 3384 8.188799 TGCAGTAGTGTACTAGTATTGACATTC 58.811 37.037 5.75 0.00 37.23 2.67
3200 3385 7.648510 GCAGTAGTGTACTAGTATTGACATTCC 59.351 40.741 5.75 0.00 37.23 3.01
3201 3386 8.904834 CAGTAGTGTACTAGTATTGACATTCCT 58.095 37.037 5.75 0.00 37.23 3.36
3204 3389 8.466617 AGTGTACTAGTATTGACATTCCTAGG 57.533 38.462 5.75 0.82 31.50 3.02
3205 3390 8.060075 AGTGTACTAGTATTGACATTCCTAGGT 58.940 37.037 9.08 0.00 31.50 3.08
3206 3391 8.351461 GTGTACTAGTATTGACATTCCTAGGTC 58.649 40.741 9.08 0.00 35.68 3.85
3207 3392 6.636562 ACTAGTATTGACATTCCTAGGTCG 57.363 41.667 9.08 0.86 37.88 4.79
3208 3393 4.939052 AGTATTGACATTCCTAGGTCGG 57.061 45.455 9.08 1.70 37.88 4.79
3209 3394 4.543689 AGTATTGACATTCCTAGGTCGGA 58.456 43.478 9.08 0.00 37.88 4.55
3210 3395 5.148502 AGTATTGACATTCCTAGGTCGGAT 58.851 41.667 9.08 0.57 37.88 4.18
3211 3396 3.819564 TTGACATTCCTAGGTCGGATG 57.180 47.619 9.08 11.26 37.88 3.51
3212 3397 2.039418 TGACATTCCTAGGTCGGATGG 58.961 52.381 9.08 0.00 37.88 3.51
3213 3398 2.040178 GACATTCCTAGGTCGGATGGT 58.960 52.381 9.08 0.00 32.02 3.55
3214 3399 1.762957 ACATTCCTAGGTCGGATGGTG 59.237 52.381 9.08 0.55 32.02 4.17
3215 3400 1.070758 CATTCCTAGGTCGGATGGTGG 59.929 57.143 9.08 0.00 32.02 4.61
3216 3401 0.689745 TTCCTAGGTCGGATGGTGGG 60.690 60.000 9.08 0.00 32.02 4.61
3217 3402 1.382695 CCTAGGTCGGATGGTGGGT 60.383 63.158 0.00 0.00 0.00 4.51
3218 3403 1.686325 CCTAGGTCGGATGGTGGGTG 61.686 65.000 0.00 0.00 0.00 4.61
3219 3404 2.311688 CTAGGTCGGATGGTGGGTGC 62.312 65.000 0.00 0.00 0.00 5.01
3221 3406 4.388499 GTCGGATGGTGGGTGCGT 62.388 66.667 0.00 0.00 0.00 5.24
3222 3407 4.386951 TCGGATGGTGGGTGCGTG 62.387 66.667 0.00 0.00 0.00 5.34
3225 3410 4.344865 GATGGTGGGTGCGTGGGT 62.345 66.667 0.00 0.00 0.00 4.51
3226 3411 4.659172 ATGGTGGGTGCGTGGGTG 62.659 66.667 0.00 0.00 0.00 4.61
3237 3422 4.717313 GTGGGTGGCCGGGAAGTC 62.717 72.222 2.18 0.00 0.00 3.01
3247 3432 4.867599 GGGAAGTCGCGGCCGTAG 62.868 72.222 28.70 21.14 35.54 3.51
3269 3454 4.980805 GGAAGTCGGCGTGCACCA 62.981 66.667 12.15 0.00 0.00 4.17
3270 3455 3.414700 GAAGTCGGCGTGCACCAG 61.415 66.667 12.15 5.22 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.877168 AGGTATACCTCTACGTTGCTCG 59.123 50.000 19.27 0.84 44.77 5.03
15 16 1.964223 CACCGATGCAGGTATACCTCT 59.036 52.381 22.09 9.51 46.65 3.69
49 50 3.246880 AGGTGGACGGTTGGGGAC 61.247 66.667 0.00 0.00 0.00 4.46
69 70 4.813750 ATTTAAAGGCAGCAGCAGAATT 57.186 36.364 2.65 0.00 44.61 2.17
70 71 6.475596 AATATTTAAAGGCAGCAGCAGAAT 57.524 33.333 2.65 0.00 44.61 2.40
72 73 5.394443 CCAAATATTTAAAGGCAGCAGCAGA 60.394 40.000 2.65 0.00 44.61 4.26
159 168 1.139853 GCTTCCTCCTGTGTATGGGAG 59.860 57.143 0.00 0.00 46.22 4.30
216 226 3.111741 TAGGGACTTACCTTCTGGTCC 57.888 52.381 0.00 0.00 43.16 4.46
244 254 5.604231 AGGCCACTGATGAATAGACATAGAA 59.396 40.000 5.01 0.00 0.00 2.10
352 362 2.479275 GTCTTTCGCAGGAAGGTTACAC 59.521 50.000 0.00 0.00 32.80 2.90
354 364 2.074576 GGTCTTTCGCAGGAAGGTTAC 58.925 52.381 0.00 0.00 32.80 2.50
373 383 8.908903 TGCAGGTTAGGTTATACATAAATTTGG 58.091 33.333 0.00 0.00 0.00 3.28
376 386 8.899771 GTGTGCAGGTTAGGTTATACATAAATT 58.100 33.333 0.00 0.00 0.00 1.82
473 485 4.093261 GGAAATTTTGAATCACCCATTGCG 59.907 41.667 0.00 0.00 0.00 4.85
582 607 5.533903 AGCTTGAATTATGGCTAACATGGAG 59.466 40.000 0.00 0.00 40.82 3.86
616 641 7.468494 GCTTTTGTTTTTCTTATTGGCAATGGT 60.468 33.333 22.57 0.00 0.00 3.55
663 689 7.776933 AGTTTGTCACTGCACACTATATATG 57.223 36.000 0.00 0.00 32.83 1.78
773 826 5.569059 GTGAACAAAAGAAATGCCACGATAG 59.431 40.000 0.00 0.00 46.19 2.08
774 827 5.009110 TGTGAACAAAAGAAATGCCACGATA 59.991 36.000 0.00 0.00 31.41 2.92
775 828 4.202101 TGTGAACAAAAGAAATGCCACGAT 60.202 37.500 0.00 0.00 31.41 3.73
776 829 3.129462 TGTGAACAAAAGAAATGCCACGA 59.871 39.130 0.00 0.00 31.41 4.35
777 830 3.443037 TGTGAACAAAAGAAATGCCACG 58.557 40.909 0.00 0.00 31.41 4.94
778 831 5.523188 TCAATGTGAACAAAAGAAATGCCAC 59.477 36.000 0.00 0.00 0.00 5.01
779 832 5.668471 TCAATGTGAACAAAAGAAATGCCA 58.332 33.333 0.00 0.00 0.00 4.92
962 1036 6.552445 AACCTGCTACATATATCAGGGATC 57.448 41.667 17.92 0.00 45.44 3.36
963 1037 7.124901 CAGTAACCTGCTACATATATCAGGGAT 59.875 40.741 17.92 11.16 45.44 3.85
1011 1086 1.344065 TCTCGCTAACCTTGGGTGAA 58.656 50.000 0.00 0.00 35.34 3.18
1017 1098 0.460311 ACCGGATCTCGCTAACCTTG 59.540 55.000 9.46 0.00 37.59 3.61
1071 1152 1.261619 GGATTTGCTGTTCCGATAGCG 59.738 52.381 0.00 0.00 42.36 4.26
1104 1185 2.904434 GTCAGGGTACTCTTCTTGGGAA 59.096 50.000 0.00 0.00 0.00 3.97
1219 1382 4.063998 TGTCAGATCATATGTGTCTGCC 57.936 45.455 23.93 18.25 39.30 4.85
1301 1467 4.323868 GTGTGGTAGAAGAAACGATTCTCG 59.676 45.833 8.51 0.00 45.19 4.04
1424 1590 1.524863 CCTTCTTTGCTGCTGCTGCT 61.525 55.000 27.67 0.00 40.48 4.24
1709 1878 2.564553 CTAAGCAGTCGCCTTCGCCT 62.565 60.000 0.00 0.00 39.83 5.52
1748 1920 0.893270 CTGCCCCATCACCGAACAAA 60.893 55.000 0.00 0.00 0.00 2.83
1898 2070 2.810439 TGGTGTAAACTTTGCCATGC 57.190 45.000 0.00 0.00 0.00 4.06
1931 2103 1.670811 GGTTCCATGTTATCTGCCACG 59.329 52.381 0.00 0.00 0.00 4.94
1940 2112 5.450453 TCCAAAAGACAAGGTTCCATGTTA 58.550 37.500 1.32 0.00 0.00 2.41
1994 2166 1.680249 GCCCAGAAGAGGTCATTCCAC 60.680 57.143 0.00 0.00 39.02 4.02
2473 2653 5.122396 AGCAATACTTTTAGACTGCCTTTCG 59.878 40.000 0.00 0.00 0.00 3.46
2475 2655 6.003950 TGAGCAATACTTTTAGACTGCCTTT 58.996 36.000 0.00 0.00 0.00 3.11
2479 2659 5.862924 TGTGAGCAATACTTTTAGACTGC 57.137 39.130 0.00 0.00 0.00 4.40
2502 2682 6.261826 GCATAGTGCAGTGGAGAAATAAATCT 59.738 38.462 3.69 0.00 44.26 2.40
2534 2714 0.328258 ACAAACCCGGATGGAGGAAG 59.672 55.000 0.73 0.00 37.49 3.46
2545 2725 1.826054 TGCCCACTTCACAAACCCG 60.826 57.895 0.00 0.00 0.00 5.28
2554 2734 2.365293 ACCAAAAATCTGTGCCCACTTC 59.635 45.455 0.00 0.00 0.00 3.01
2582 2763 7.270757 TGTACACACATTTTGCTAGTCAAAT 57.729 32.000 11.44 4.82 43.53 2.32
2591 2772 3.668191 CGGATGTTGTACACACATTTTGC 59.332 43.478 18.45 10.00 38.61 3.68
2622 2803 8.749841 ATTATCGCAGAAATGAGTGTATCTAC 57.250 34.615 0.00 0.00 43.58 2.59
2642 2823 4.020839 TCCCTCCGTCCGGAATTAATTATC 60.021 45.833 5.23 0.00 44.66 1.75
2646 2827 1.692519 CTCCCTCCGTCCGGAATTAAT 59.307 52.381 5.23 0.00 44.66 1.40
2658 2839 5.449314 CGATGCTTCTAATATACTCCCTCCG 60.449 48.000 0.00 0.00 0.00 4.63
2663 2844 7.148950 CGTCAAACGATGCTTCTAATATACTCC 60.149 40.741 0.00 0.00 46.05 3.85
2750 2931 8.378421 GTTTCTAAGTGGCTACTGTTATTTACG 58.622 37.037 2.40 0.00 37.19 3.18
2755 2936 5.249852 TGGGTTTCTAAGTGGCTACTGTTAT 59.750 40.000 2.40 0.00 37.19 1.89
2756 2937 4.594062 TGGGTTTCTAAGTGGCTACTGTTA 59.406 41.667 2.40 0.00 37.19 2.41
2760 2941 3.517612 TCTGGGTTTCTAAGTGGCTACT 58.482 45.455 0.00 0.00 39.32 2.57
2763 2944 4.362677 TCTATCTGGGTTTCTAAGTGGCT 58.637 43.478 0.00 0.00 0.00 4.75
2764 2945 4.406003 TCTCTATCTGGGTTTCTAAGTGGC 59.594 45.833 0.00 0.00 0.00 5.01
2769 2950 7.288560 ACGACTATCTCTATCTGGGTTTCTAA 58.711 38.462 0.00 0.00 0.00 2.10
2771 2952 5.697067 ACGACTATCTCTATCTGGGTTTCT 58.303 41.667 0.00 0.00 0.00 2.52
2772 2953 7.690952 ATACGACTATCTCTATCTGGGTTTC 57.309 40.000 0.00 0.00 0.00 2.78
2792 2974 5.577945 ACTTATCAACGTGTGGGTAAATACG 59.422 40.000 0.00 0.00 41.86 3.06
2820 3002 9.836864 TGATTTAACACATGAGCATATAGTTCT 57.163 29.630 0.00 0.00 0.00 3.01
2834 3016 9.253832 TGATTCCATTTACCTGATTTAACACAT 57.746 29.630 0.00 0.00 0.00 3.21
2836 3018 8.519526 TGTGATTCCATTTACCTGATTTAACAC 58.480 33.333 0.00 0.00 0.00 3.32
2874 3056 5.066968 ACCACGTGAAATTGTGAAAGTTT 57.933 34.783 19.30 0.00 38.36 2.66
2914 3098 2.100584 TCCACAATTTGTGTTGCCACTC 59.899 45.455 24.01 0.00 46.45 3.51
2916 3100 2.593346 TCCACAATTTGTGTTGCCAC 57.407 45.000 24.01 0.00 46.45 5.01
2944 3128 6.124088 ACTGAACTTTCACAGTTTCATGAC 57.876 37.500 0.00 0.00 46.53 3.06
2953 3137 4.191544 TGGTCTGAACTGAACTTTCACAG 58.808 43.478 0.00 0.00 39.65 3.66
2989 3173 9.333724 CGGAAAACTATATATGTTAAACCAGGT 57.666 33.333 0.00 0.00 0.00 4.00
3009 3193 2.068837 ACTCGATAACGCACGGAAAA 57.931 45.000 0.00 0.00 39.58 2.29
3019 3203 5.624491 GGATTGTAAGCGTCTACTCGATAAC 59.376 44.000 0.00 0.00 0.00 1.89
3053 3237 5.924475 AATGTCAGTAAACAGCTGTACAC 57.076 39.130 22.01 19.87 35.60 2.90
3063 3248 6.304126 CGTGTGTGGAATAATGTCAGTAAAC 58.696 40.000 0.00 0.00 0.00 2.01
3123 3308 9.836864 CGATATGGATGGAAAGGATATCATTTA 57.163 33.333 14.87 1.81 29.27 1.40
3127 3312 6.405842 CGACGATATGGATGGAAAGGATATCA 60.406 42.308 4.83 0.00 0.00 2.15
3128 3313 5.980116 CGACGATATGGATGGAAAGGATATC 59.020 44.000 0.00 0.00 0.00 1.63
3129 3314 5.422331 ACGACGATATGGATGGAAAGGATAT 59.578 40.000 0.00 0.00 0.00 1.63
3130 3315 4.770531 ACGACGATATGGATGGAAAGGATA 59.229 41.667 0.00 0.00 0.00 2.59
3131 3316 3.578716 ACGACGATATGGATGGAAAGGAT 59.421 43.478 0.00 0.00 0.00 3.24
3132 3317 2.963101 ACGACGATATGGATGGAAAGGA 59.037 45.455 0.00 0.00 0.00 3.36
3133 3318 3.386768 ACGACGATATGGATGGAAAGG 57.613 47.619 0.00 0.00 0.00 3.11
3134 3319 4.621991 AGAACGACGATATGGATGGAAAG 58.378 43.478 0.00 0.00 0.00 2.62
3135 3320 4.665833 AGAACGACGATATGGATGGAAA 57.334 40.909 0.00 0.00 0.00 3.13
3138 3323 3.977427 TCAAGAACGACGATATGGATGG 58.023 45.455 0.00 0.00 0.00 3.51
3139 3324 5.613360 GCAATCAAGAACGACGATATGGATG 60.613 44.000 0.00 0.00 0.00 3.51
3140 3325 4.449068 GCAATCAAGAACGACGATATGGAT 59.551 41.667 0.00 0.00 0.00 3.41
3141 3326 3.802139 GCAATCAAGAACGACGATATGGA 59.198 43.478 0.00 0.00 0.00 3.41
3142 3327 3.555547 TGCAATCAAGAACGACGATATGG 59.444 43.478 0.00 0.00 0.00 2.74
3143 3328 4.755388 CTGCAATCAAGAACGACGATATG 58.245 43.478 0.00 0.00 0.00 1.78
3144 3329 3.246226 GCTGCAATCAAGAACGACGATAT 59.754 43.478 0.00 0.00 0.00 1.63
3145 3330 2.603110 GCTGCAATCAAGAACGACGATA 59.397 45.455 0.00 0.00 0.00 2.92
3146 3331 1.394917 GCTGCAATCAAGAACGACGAT 59.605 47.619 0.00 0.00 0.00 3.73
3147 3332 0.790207 GCTGCAATCAAGAACGACGA 59.210 50.000 0.00 0.00 0.00 4.20
3148 3333 0.179215 GGCTGCAATCAAGAACGACG 60.179 55.000 0.50 0.00 0.00 5.12
3149 3334 0.169009 GGGCTGCAATCAAGAACGAC 59.831 55.000 0.50 0.00 0.00 4.34
3150 3335 0.250684 TGGGCTGCAATCAAGAACGA 60.251 50.000 0.50 0.00 0.00 3.85
3151 3336 0.597568 TTGGGCTGCAATCAAGAACG 59.402 50.000 0.50 0.00 0.00 3.95
3152 3337 1.337167 GGTTGGGCTGCAATCAAGAAC 60.337 52.381 0.50 0.00 0.00 3.01
3153 3338 0.968405 GGTTGGGCTGCAATCAAGAA 59.032 50.000 0.50 0.00 0.00 2.52
3154 3339 0.112995 AGGTTGGGCTGCAATCAAGA 59.887 50.000 0.50 0.00 0.00 3.02
3155 3340 0.245539 CAGGTTGGGCTGCAATCAAG 59.754 55.000 0.50 0.00 0.00 3.02
3156 3341 1.818959 GCAGGTTGGGCTGCAATCAA 61.819 55.000 0.50 0.00 45.11 2.57
3157 3342 2.277591 GCAGGTTGGGCTGCAATCA 61.278 57.895 0.50 0.00 45.11 2.57
3158 3343 2.575461 GCAGGTTGGGCTGCAATC 59.425 61.111 0.50 0.00 45.11 2.67
3162 3347 2.034066 TACTGCAGGTTGGGCTGC 59.966 61.111 19.93 0.00 45.89 5.25
3163 3348 0.957395 CACTACTGCAGGTTGGGCTG 60.957 60.000 19.93 0.00 36.43 4.85
3164 3349 1.376466 CACTACTGCAGGTTGGGCT 59.624 57.895 19.93 0.00 0.00 5.19
3165 3350 0.323629 TACACTACTGCAGGTTGGGC 59.676 55.000 19.93 0.00 0.00 5.36
3166 3351 1.623811 AGTACACTACTGCAGGTTGGG 59.376 52.381 19.93 10.96 37.69 4.12
3167 3352 3.510360 ACTAGTACACTACTGCAGGTTGG 59.490 47.826 19.93 7.40 39.81 3.77
3168 3353 4.785511 ACTAGTACACTACTGCAGGTTG 57.214 45.455 19.93 13.77 39.81 3.77
3169 3354 6.662234 TCAATACTAGTACACTACTGCAGGTT 59.338 38.462 19.93 0.00 39.81 3.50
3170 3355 6.095160 GTCAATACTAGTACACTACTGCAGGT 59.905 42.308 19.93 8.65 39.81 4.00
3171 3356 6.095021 TGTCAATACTAGTACACTACTGCAGG 59.905 42.308 19.93 3.21 39.81 4.85
3172 3357 7.085052 TGTCAATACTAGTACACTACTGCAG 57.915 40.000 13.48 13.48 39.81 4.41
3173 3358 7.640597 ATGTCAATACTAGTACACTACTGCA 57.359 36.000 4.31 0.00 39.81 4.41
3174 3359 7.648510 GGAATGTCAATACTAGTACACTACTGC 59.351 40.741 4.31 0.00 39.81 4.40
3175 3360 8.904834 AGGAATGTCAATACTAGTACACTACTG 58.095 37.037 4.31 0.00 39.81 2.74
3178 3363 9.570468 CCTAGGAATGTCAATACTAGTACACTA 57.430 37.037 1.05 0.00 31.50 2.74
3179 3364 8.060075 ACCTAGGAATGTCAATACTAGTACACT 58.940 37.037 17.98 0.00 31.50 3.55
3180 3365 8.235359 ACCTAGGAATGTCAATACTAGTACAC 57.765 38.462 17.98 3.33 31.50 2.90
3181 3366 7.228108 CGACCTAGGAATGTCAATACTAGTACA 59.772 40.741 17.98 1.26 31.50 2.90
3182 3367 7.308469 CCGACCTAGGAATGTCAATACTAGTAC 60.308 44.444 17.98 0.00 31.50 2.73
3183 3368 6.713903 CCGACCTAGGAATGTCAATACTAGTA 59.286 42.308 17.98 4.77 31.50 1.82
3184 3369 5.535406 CCGACCTAGGAATGTCAATACTAGT 59.465 44.000 17.98 0.00 31.50 2.57
3185 3370 5.768662 TCCGACCTAGGAATGTCAATACTAG 59.231 44.000 17.98 0.54 37.36 2.57
3186 3371 5.698104 TCCGACCTAGGAATGTCAATACTA 58.302 41.667 17.98 0.00 37.36 1.82
3187 3372 4.543689 TCCGACCTAGGAATGTCAATACT 58.456 43.478 17.98 0.00 37.36 2.12
3188 3373 4.931661 TCCGACCTAGGAATGTCAATAC 57.068 45.455 17.98 0.00 37.36 1.89
3189 3374 4.283467 CCATCCGACCTAGGAATGTCAATA 59.717 45.833 17.98 0.00 44.50 1.90
3190 3375 3.071602 CCATCCGACCTAGGAATGTCAAT 59.928 47.826 17.98 0.00 44.50 2.57
3191 3376 2.434336 CCATCCGACCTAGGAATGTCAA 59.566 50.000 17.98 0.00 44.50 3.18
3192 3377 2.039418 CCATCCGACCTAGGAATGTCA 58.961 52.381 17.98 0.00 44.50 3.58
3193 3378 2.040178 ACCATCCGACCTAGGAATGTC 58.960 52.381 17.98 0.71 44.50 3.06
3194 3379 1.762957 CACCATCCGACCTAGGAATGT 59.237 52.381 17.98 0.00 44.50 2.71
3195 3380 1.070758 CCACCATCCGACCTAGGAATG 59.929 57.143 17.98 12.59 44.50 2.67
3196 3381 1.424638 CCACCATCCGACCTAGGAAT 58.575 55.000 17.98 0.00 44.50 3.01
3197 3382 0.689745 CCCACCATCCGACCTAGGAA 60.690 60.000 17.98 0.00 44.50 3.36
3198 3383 1.075525 CCCACCATCCGACCTAGGA 60.076 63.158 17.98 0.00 45.54 2.94
3199 3384 1.382695 ACCCACCATCCGACCTAGG 60.383 63.158 7.41 7.41 0.00 3.02
3200 3385 1.823295 CACCCACCATCCGACCTAG 59.177 63.158 0.00 0.00 0.00 3.02
3201 3386 2.363975 GCACCCACCATCCGACCTA 61.364 63.158 0.00 0.00 0.00 3.08
3202 3387 3.717294 GCACCCACCATCCGACCT 61.717 66.667 0.00 0.00 0.00 3.85
3204 3389 4.388499 ACGCACCCACCATCCGAC 62.388 66.667 0.00 0.00 0.00 4.79
3205 3390 4.386951 CACGCACCCACCATCCGA 62.387 66.667 0.00 0.00 0.00 4.55
3208 3393 4.344865 ACCCACGCACCCACCATC 62.345 66.667 0.00 0.00 0.00 3.51
3209 3394 4.659172 CACCCACGCACCCACCAT 62.659 66.667 0.00 0.00 0.00 3.55
3220 3405 4.717313 GACTTCCCGGCCACCCAC 62.717 72.222 2.24 0.00 0.00 4.61
3230 3415 4.867599 CTACGGCCGCGACTTCCC 62.868 72.222 28.58 0.00 0.00 3.97
3252 3437 4.980805 TGGTGCACGCCGACTTCC 62.981 66.667 11.45 0.00 0.00 3.46
3253 3438 3.414700 CTGGTGCACGCCGACTTC 61.415 66.667 11.45 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.