Multiple sequence alignment - TraesCS7D01G443400

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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 TraesCS7D01G443400 chr7D 100.000 4359 0 0 1 4359 563530144 563525786 0.000000e+00 8050.0
1 TraesCS7D01G443400 chr7D 85.274 1331 131 33 2722 4015 563480029 563478727 0.000000e+00 1312.0
2 TraesCS7D01G443400 chr7D 85.393 534 64 10 3273 3800 563516486 563515961 3.830000e-150 542.0
3 TraesCS7D01G443400 chr7D 78.049 492 62 28 1388 1857 563481393 563480926 7.190000e-68 268.0
4 TraesCS7D01G443400 chr7D 76.692 532 64 31 1920 2413 563480774 563480265 1.570000e-59 241.0
5 TraesCS7D01G443400 chr7B 92.832 3669 184 35 608 4229 613179365 613175729 0.000000e+00 5245.0
6 TraesCS7D01G443400 chr7B 82.601 1069 135 29 3193 4231 613151062 613150015 0.000000e+00 896.0
7 TraesCS7D01G443400 chr7B 85.314 606 69 14 3209 3800 613159830 613159231 3.730000e-170 608.0
8 TraesCS7D01G443400 chr7B 79.502 522 57 26 3148 3661 613237676 613237197 4.200000e-85 326.0
9 TraesCS7D01G443400 chr7B 78.947 513 59 24 3148 3655 613253575 613253107 1.970000e-78 303.0
10 TraesCS7D01G443400 chr7B 88.889 81 9 0 2326 2406 613152725 613152645 2.770000e-17 100.0
11 TraesCS7D01G443400 chr7A 90.531 1637 114 15 714 2320 649074671 649073046 0.000000e+00 2126.0
12 TraesCS7D01G443400 chr7A 88.244 1412 119 19 2331 3719 649072998 649071611 0.000000e+00 1644.0
13 TraesCS7D01G443400 chr7A 90.677 901 72 7 2807 3696 649060073 649059174 0.000000e+00 1188.0
14 TraesCS7D01G443400 chr7A 77.020 1114 129 59 1501 2554 649061264 649060218 5.000000e-144 521.0
15 TraesCS7D01G443400 chr7A 88.764 267 21 3 248 513 649075504 649075246 7.030000e-83 318.0
16 TraesCS7D01G443400 chr7A 92.233 206 10 5 511 711 649075215 649075011 1.980000e-73 287.0
17 TraesCS7D01G443400 chr7A 87.698 252 16 6 3 254 649076810 649076574 3.320000e-71 279.0
18 TraesCS7D01G443400 chr7A 96.226 53 2 0 1016 1068 649154025 649153973 2.160000e-13 87.9
19 TraesCS7D01G443400 chr3D 93.548 124 8 0 2647 2770 304329114 304328991 7.440000e-43 185.0
20 TraesCS7D01G443400 chr3D 95.652 69 3 0 999 1067 304331358 304331290 1.280000e-20 111.0
21 TraesCS7D01G443400 chr3D 75.843 178 21 13 1502 1674 304330736 304330576 2.170000e-08 71.3
22 TraesCS7D01G443400 chr3A 92.742 124 9 0 2647 2770 430336330 430336453 3.460000e-41 180.0
23 TraesCS7D01G443400 chr3A 95.652 69 3 0 999 1067 430333993 430334061 1.280000e-20 111.0
24 TraesCS7D01G443400 chr3A 93.333 45 2 1 2087 2130 430335317 430335361 1.010000e-06 65.8
25 TraesCS7D01G443400 chr3B 91.935 124 10 0 2647 2770 417264175 417264298 1.610000e-39 174.0
26 TraesCS7D01G443400 chr3B 95.652 69 3 0 999 1067 417261918 417261986 1.280000e-20 111.0
27 TraesCS7D01G443400 chr3B 75.691 181 22 13 1499 1674 417262553 417262716 2.170000e-08 71.3
28 TraesCS7D01G443400 chr3B 85.938 64 7 2 2087 2148 417263222 417263285 2.810000e-07 67.6
29 TraesCS7D01G443400 chr6D 85.714 126 12 6 1 124 291144563 291144684 1.270000e-25 128.0
30 TraesCS7D01G443400 chr6A 83.721 129 15 6 1 127 432523145 432523021 2.750000e-22 117.0


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 TraesCS7D01G443400 chr7D 563525786 563530144 4358 True 8050.0 8050 100.0000 1 4359 1 chr7D.!!$R2 4358
1 TraesCS7D01G443400 chr7D 563478727 563481393 2666 True 607.0 1312 80.0050 1388 4015 3 chr7D.!!$R3 2627
2 TraesCS7D01G443400 chr7D 563515961 563516486 525 True 542.0 542 85.3930 3273 3800 1 chr7D.!!$R1 527
3 TraesCS7D01G443400 chr7B 613175729 613179365 3636 True 5245.0 5245 92.8320 608 4229 1 chr7B.!!$R2 3621
4 TraesCS7D01G443400 chr7B 613159231 613159830 599 True 608.0 608 85.3140 3209 3800 1 chr7B.!!$R1 591
5 TraesCS7D01G443400 chr7B 613150015 613152725 2710 True 498.0 896 85.7450 2326 4231 2 chr7B.!!$R5 1905
6 TraesCS7D01G443400 chr7A 649071611 649076810 5199 True 930.8 2126 89.4940 3 3719 5 chr7A.!!$R3 3716
7 TraesCS7D01G443400 chr7A 649059174 649061264 2090 True 854.5 1188 83.8485 1501 3696 2 chr7A.!!$R2 2195

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
470 1547 0.035630 ATCACAAGCCCAGCTCACTC 60.036 55.0 0.00 0.0 38.25 3.51 F
2089 3721 0.529337 CCTGCCGCTCTGAGTACATG 60.529 60.0 6.53 0.0 0.00 3.21 F
2892 4767 0.615850 CCCTCCTCAACCTCAAGGAC 59.384 60.0 2.30 0.0 36.75 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 4225 0.027455 TGCACGTTTCTGAAACAGCG 59.973 50.0 27.24 18.33 41.89 5.18 R
3010 5370 1.395826 CGATCCTGACCCAGTCCTCC 61.396 65.0 0.00 0.00 0.00 4.30 R
4336 7020 0.035820 TCCTGTGTAACCCGGATTGC 60.036 55.0 0.73 0.00 31.55 3.56 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
21 22 1.638388 TTGAGCGCTCGCCATTGAAG 61.638 55.000 30.75 0.00 43.17 3.02
33 34 2.919229 GCCATTGAAGCAATCTTTGTCG 59.081 45.455 0.00 0.00 31.05 4.35
52 53 4.759183 TGTCGTTGGATTGACATGAATTGA 59.241 37.500 0.00 0.00 40.02 2.57
55 56 5.647225 TCGTTGGATTGACATGAATTGATCA 59.353 36.000 0.00 0.00 43.67 2.92
57 58 5.840243 TGGATTGACATGAATTGATCACC 57.160 39.130 0.00 0.00 41.93 4.02
70 71 4.976224 TTGATCACCGAGATTAGTTCGA 57.024 40.909 0.00 0.00 40.36 3.71
84 85 0.391263 GTTCGATCCGCCCTTTGAGT 60.391 55.000 0.00 0.00 0.00 3.41
85 86 0.323629 TTCGATCCGCCCTTTGAGTT 59.676 50.000 0.00 0.00 0.00 3.01
131 132 9.532494 AGATATAGATAGATAGATGCATGGACC 57.468 37.037 2.46 0.00 0.00 4.46
200 201 5.692204 AGATATCATCTTTGCGAGTAAACCG 59.308 40.000 5.32 0.00 35.76 4.44
214 215 6.426025 GCGAGTAAACCGGGAAAGATATTATT 59.574 38.462 6.32 0.00 0.00 1.40
224 225 5.469084 GGGAAAGATATTATTGTGTCCCGAC 59.531 44.000 0.00 0.00 34.50 4.79
227 228 3.640029 AGATATTATTGTGTCCCGACGGT 59.360 43.478 13.94 0.00 0.00 4.83
243 244 3.374058 CGACGGTAAATGCAGGAAGAATT 59.626 43.478 0.00 0.00 0.00 2.17
329 1405 6.650807 TCAATCCTAGAGTGTTTAGCTTTGTG 59.349 38.462 0.00 0.00 0.00 3.33
339 1415 5.003121 GTGTTTAGCTTTGTGTTTTCGTGAC 59.997 40.000 0.00 0.00 0.00 3.67
391 1468 5.957910 TTTTTGCAGTGTTGAATTTACCG 57.042 34.783 0.00 0.00 0.00 4.02
405 1482 4.920640 ATTTACCGTCAGATGATCGACT 57.079 40.909 12.84 2.11 0.00 4.18
411 1488 2.350293 CGTCAGATGATCGACTGCTAGG 60.350 54.545 12.24 1.87 34.57 3.02
422 1499 7.952671 TGATCGACTGCTAGGATTAAATTACT 58.047 34.615 0.00 0.00 0.00 2.24
423 1500 9.074576 TGATCGACTGCTAGGATTAAATTACTA 57.925 33.333 0.00 0.00 0.00 1.82
428 1505 9.478768 GACTGCTAGGATTAAATTACTAAGGAC 57.521 37.037 0.00 0.00 0.00 3.85
462 1539 1.988293 TTTCCGAAATCACAAGCCCA 58.012 45.000 0.00 0.00 0.00 5.36
465 1542 0.962356 CCGAAATCACAAGCCCAGCT 60.962 55.000 0.00 0.00 42.56 4.24
469 1546 0.403271 AATCACAAGCCCAGCTCACT 59.597 50.000 0.00 0.00 38.25 3.41
470 1547 0.035630 ATCACAAGCCCAGCTCACTC 60.036 55.000 0.00 0.00 38.25 3.51
480 1557 4.314440 GCTCACTCGGCCACACCA 62.314 66.667 2.24 0.00 39.03 4.17
486 1563 3.925630 CTCGGCCACACCATTGCCT 62.926 63.158 2.24 0.00 43.12 4.75
487 1564 2.045438 CGGCCACACCATTGCCTA 60.045 61.111 2.24 0.00 43.12 3.93
506 1583 3.192422 CCTATATTCTGGCACCTCTCTCG 59.808 52.174 0.00 0.00 0.00 4.04
530 1640 5.835113 TTCCCACAAGAGTTTCTCAAAAG 57.165 39.130 0.00 0.00 32.06 2.27
558 1672 3.324993 AGAAGAAGAAGAAGAAGCAGCG 58.675 45.455 0.00 0.00 0.00 5.18
641 1759 1.185618 CCACCGTCTTCTCACCTCCA 61.186 60.000 0.00 0.00 0.00 3.86
645 1763 1.618837 CCGTCTTCTCACCTCCAAAGA 59.381 52.381 0.00 0.00 0.00 2.52
712 2168 5.125097 TCCGATCAAACAGGAGTACTACTTC 59.875 44.000 4.33 0.00 0.00 3.01
789 2246 3.120991 CCTTTCACGTGTCGTCATCTTTC 60.121 47.826 16.51 0.00 38.32 2.62
867 2339 4.928520 GCCCCTATGCCTCCCCCT 62.929 72.222 0.00 0.00 0.00 4.79
872 2344 3.049288 TATGCCTCCCCCTCCCCT 61.049 66.667 0.00 0.00 0.00 4.79
876 2348 3.779083 CCTCCCCCTCCCCTGCTA 61.779 72.222 0.00 0.00 0.00 3.49
885 2357 4.290942 CCCCTCCCCTGCTACTATATAAG 58.709 52.174 0.00 0.00 0.00 1.73
895 2367 6.270231 CCTGCTACTATATAAGTGGACCCTTT 59.730 42.308 1.19 0.00 38.95 3.11
915 2387 4.833478 TTCCTCCTCCAGATTTCAGAAG 57.167 45.455 0.00 0.00 0.00 2.85
943 2415 3.300962 ATCCTCCCCCACCCTCCA 61.301 66.667 0.00 0.00 0.00 3.86
944 2416 3.353689 ATCCTCCCCCACCCTCCAG 62.354 68.421 0.00 0.00 0.00 3.86
957 2429 0.538057 CCTCCAGCAAGCAAGTTCCA 60.538 55.000 0.00 0.00 0.00 3.53
1119 2599 2.149578 CCTCCTCGATCATGATTTGGC 58.850 52.381 10.14 0.00 0.00 4.52
1131 2611 5.883661 TCATGATTTGGCTCGATTTTCTTC 58.116 37.500 0.00 0.00 0.00 2.87
1146 2626 7.495934 TCGATTTTCTTCAGATTATCCAGTTCC 59.504 37.037 0.00 0.00 0.00 3.62
1237 2721 2.569853 CACCAGTCACCCAAGGTATACA 59.430 50.000 5.01 0.00 32.11 2.29
1238 2722 3.199946 CACCAGTCACCCAAGGTATACAT 59.800 47.826 5.01 0.00 32.11 2.29
1239 2723 4.407621 CACCAGTCACCCAAGGTATACATA 59.592 45.833 5.01 0.00 32.11 2.29
1240 2724 5.071788 CACCAGTCACCCAAGGTATACATAT 59.928 44.000 5.01 0.00 32.11 1.78
1288 2772 3.845625 CAACGAACTCTTGGTTGCC 57.154 52.632 0.00 0.00 41.29 4.52
1366 2851 2.646930 TGCCATAGCATTTCCTGTCAG 58.353 47.619 0.00 0.00 46.52 3.51
1410 2895 1.039856 ATGGAAACGGCTGCTTTGTT 58.960 45.000 0.00 0.00 0.00 2.83
1419 2904 3.189287 ACGGCTGCTTTGTTCTAATTGAG 59.811 43.478 0.00 0.00 0.00 3.02
1473 2958 4.682778 TGTACTGTGAAACCAACTAGCT 57.317 40.909 0.00 0.00 34.36 3.32
1474 2959 5.794726 TGTACTGTGAAACCAACTAGCTA 57.205 39.130 0.00 0.00 34.36 3.32
1475 2960 5.779922 TGTACTGTGAAACCAACTAGCTAG 58.220 41.667 19.44 19.44 34.36 3.42
1476 2961 4.273148 ACTGTGAAACCAACTAGCTAGG 57.727 45.455 24.35 10.67 34.36 3.02
1490 2979 3.697190 AGCTAGGAAGAGGGAGAATCA 57.303 47.619 0.00 0.00 36.25 2.57
1517 3007 5.657745 TGATGCAATACAATTGTGGATTCCT 59.342 36.000 21.42 0.49 36.01 3.36
1522 3012 6.340522 CAATACAATTGTGGATTCCTTTCCC 58.659 40.000 21.42 0.00 36.01 3.97
1537 3027 3.449918 CTTTCCCATTTAACCCCCACAT 58.550 45.455 0.00 0.00 0.00 3.21
1552 3044 1.683938 CCACATGTCATGCACCTCCAT 60.684 52.381 12.91 0.00 0.00 3.41
1574 3066 3.181470 TGAAATTGGATCATGCATGCTGG 60.181 43.478 22.25 11.00 0.00 4.85
1711 3220 9.987272 AAGGAATATTGTTCTTTTCTTTCCTTG 57.013 29.630 11.64 0.00 45.70 3.61
1724 3233 3.138283 TCTTTCCTTGCTCCTTTTCCTGA 59.862 43.478 0.00 0.00 0.00 3.86
1765 3274 5.802956 CAGCTAGCTAGGATAACTTATTCGC 59.197 44.000 18.86 3.43 0.00 4.70
1902 3446 1.700739 TGTTGAATTACCGGTCCCACT 59.299 47.619 12.40 0.00 0.00 4.00
2089 3721 0.529337 CCTGCCGCTCTGAGTACATG 60.529 60.000 6.53 0.00 0.00 3.21
2188 3832 7.821359 TCTTCCATTCTTGATAACTCACAGAAG 59.179 37.037 0.00 0.00 34.75 2.85
2192 3836 2.672961 TGATAACTCACAGAAGGGCG 57.327 50.000 0.00 0.00 0.00 6.13
2287 3934 3.384014 CTCTGGTCGAGCGACGGAC 62.384 68.421 15.76 4.22 45.41 4.79
2329 4013 3.084536 TGCCTGCCTTTTATGATGTCA 57.915 42.857 0.00 0.00 0.00 3.58
2409 4225 2.669364 CAGAATGTCAAAAGTGGCAGC 58.331 47.619 0.00 0.00 44.15 5.25
2436 4252 1.227853 AGAAACGTGCACTCCACCC 60.228 57.895 16.19 0.00 41.53 4.61
2502 4341 0.815615 GCTGGCTAATGCGGCTAAGT 60.816 55.000 0.00 0.00 40.82 2.24
2555 4394 5.526115 CAGCAACTGTGAAATGTTCTCATT 58.474 37.500 0.00 0.00 44.94 2.57
2575 4414 7.875041 TCTCATTTTCTGGTGTCTTTTCTAGAG 59.125 37.037 0.00 0.00 32.23 2.43
2644 4489 8.616942 TGAAATGTTGTCAACTAAAAGATTCGA 58.383 29.630 16.45 0.00 0.00 3.71
2781 4626 1.462616 ACTGCAAGAACAAGCACACA 58.537 45.000 0.00 0.00 37.43 3.72
2847 4722 1.134367 GAGTTCATCGTGGTGATCGGA 59.866 52.381 0.00 0.00 34.13 4.55
2892 4767 0.615850 CCCTCCTCAACCTCAAGGAC 59.384 60.000 2.30 0.00 36.75 3.85
2896 5247 1.371183 CTCAACCTCAAGGACGGCA 59.629 57.895 2.30 0.00 38.94 5.69
3010 5370 3.068165 TGGTATCTATCAGCCACTTCGTG 59.932 47.826 0.00 0.00 0.00 4.35
3132 5492 2.258286 GTTCGCACCATTGGCCAC 59.742 61.111 3.88 0.00 0.00 5.01
3669 6319 6.762333 AGTTTACCTTCGTATTACCTTGTGT 58.238 36.000 0.00 0.00 0.00 3.72
3704 6354 4.824537 TCTTTTAGCTATGTTGTGTGGCAA 59.175 37.500 0.00 0.00 34.16 4.52
3785 6440 1.788258 CGATCTGCGCATTCATAGGT 58.212 50.000 12.24 0.00 0.00 3.08
3803 6458 6.498303 TCATAGGTGCATATGGACTGTTAGAT 59.502 38.462 24.30 8.32 36.56 1.98
3874 6543 5.016831 CCTAAGGTTTTGCTTTCCCTATGT 58.983 41.667 0.00 0.00 0.00 2.29
3907 6576 5.048434 ACTGGCTAGCTGTTTCAGATTTTTC 60.048 40.000 20.47 0.00 32.44 2.29
4043 6725 4.595781 ACACCACTATACCCAACTGAAAGA 59.404 41.667 0.00 0.00 37.43 2.52
4102 6784 4.921470 AAATGACAGTCGGTGATTTACG 57.079 40.909 0.00 0.00 40.80 3.18
4155 6839 5.836024 TTTACAAAGGGATGGTGTCTAGT 57.164 39.130 0.00 0.00 0.00 2.57
4179 6863 0.462225 TTTCGTCGGTGCCTCACAAA 60.462 50.000 0.00 0.00 35.86 2.83
4187 6871 2.722094 GGTGCCTCACAAATGGTATGA 58.278 47.619 0.00 0.00 35.86 2.15
4224 6908 6.560003 TTTATGTAGTCATGGGATGTCACT 57.440 37.500 0.00 0.00 35.70 3.41
4231 6915 8.713971 TGTAGTCATGGGATGTCACTTTATATT 58.286 33.333 0.00 0.00 0.00 1.28
4232 6916 9.209175 GTAGTCATGGGATGTCACTTTATATTC 57.791 37.037 0.00 0.00 0.00 1.75
4233 6917 7.805163 AGTCATGGGATGTCACTTTATATTCA 58.195 34.615 0.00 0.00 0.00 2.57
4234 6918 7.935755 AGTCATGGGATGTCACTTTATATTCAG 59.064 37.037 0.00 0.00 0.00 3.02
4235 6919 7.933577 GTCATGGGATGTCACTTTATATTCAGA 59.066 37.037 0.00 0.00 0.00 3.27
4236 6920 7.933577 TCATGGGATGTCACTTTATATTCAGAC 59.066 37.037 0.00 0.00 0.00 3.51
4237 6921 7.194112 TGGGATGTCACTTTATATTCAGACA 57.806 36.000 0.00 0.00 39.90 3.41
4238 6922 7.629157 TGGGATGTCACTTTATATTCAGACAA 58.371 34.615 0.00 0.00 39.17 3.18
4239 6923 8.106462 TGGGATGTCACTTTATATTCAGACAAA 58.894 33.333 0.00 0.00 39.17 2.83
4240 6924 8.956426 GGGATGTCACTTTATATTCAGACAAAA 58.044 33.333 0.00 0.00 39.17 2.44
4241 6925 9.994432 GGATGTCACTTTATATTCAGACAAAAG 57.006 33.333 0.00 0.00 39.17 2.27
4242 6926 9.994432 GATGTCACTTTATATTCAGACAAAAGG 57.006 33.333 0.00 0.00 39.17 3.11
4243 6927 9.739276 ATGTCACTTTATATTCAGACAAAAGGA 57.261 29.630 0.00 0.00 39.17 3.36
4244 6928 9.739276 TGTCACTTTATATTCAGACAAAAGGAT 57.261 29.630 0.00 0.00 33.55 3.24
4255 6939 8.737168 TTCAGACAAAAGGATTGTGATATAGG 57.263 34.615 0.00 0.00 31.96 2.57
4256 6940 6.767902 TCAGACAAAAGGATTGTGATATAGGC 59.232 38.462 0.00 0.00 31.96 3.93
4257 6941 6.543465 CAGACAAAAGGATTGTGATATAGGCA 59.457 38.462 0.00 0.00 31.96 4.75
4258 6942 7.230108 CAGACAAAAGGATTGTGATATAGGCAT 59.770 37.037 0.00 0.00 31.96 4.40
4259 6943 8.439971 AGACAAAAGGATTGTGATATAGGCATA 58.560 33.333 0.00 0.00 31.96 3.14
4260 6944 8.396272 ACAAAAGGATTGTGATATAGGCATAC 57.604 34.615 0.00 0.00 0.00 2.39
4261 6945 7.998383 ACAAAAGGATTGTGATATAGGCATACA 59.002 33.333 0.00 0.00 0.00 2.29
4262 6946 9.017509 CAAAAGGATTGTGATATAGGCATACAT 57.982 33.333 0.00 0.00 0.00 2.29
4292 6976 2.531522 AGTTTGGTCTTTTGCATGGC 57.468 45.000 0.00 0.00 0.00 4.40
4293 6977 1.070601 AGTTTGGTCTTTTGCATGGCC 59.929 47.619 0.00 0.00 0.00 5.36
4294 6978 1.126488 TTTGGTCTTTTGCATGGCCA 58.874 45.000 8.56 8.56 0.00 5.36
4295 6979 0.392336 TTGGTCTTTTGCATGGCCAC 59.608 50.000 8.16 0.00 0.00 5.01
4296 6980 0.469705 TGGTCTTTTGCATGGCCACT 60.470 50.000 8.16 0.00 0.00 4.00
4297 6981 0.244721 GGTCTTTTGCATGGCCACTC 59.755 55.000 8.16 2.67 0.00 3.51
4298 6982 0.244721 GTCTTTTGCATGGCCACTCC 59.755 55.000 8.16 0.00 0.00 3.85
4299 6983 1.213537 CTTTTGCATGGCCACTCCG 59.786 57.895 8.16 0.00 37.80 4.63
4300 6984 2.216750 CTTTTGCATGGCCACTCCGG 62.217 60.000 8.16 0.00 37.80 5.14
4327 7011 3.915437 GGTATGCCCATGTTTAATCGG 57.085 47.619 0.00 0.00 0.00 4.18
4328 7012 2.556622 GGTATGCCCATGTTTAATCGGG 59.443 50.000 0.00 0.00 42.03 5.14
4329 7013 2.746279 ATGCCCATGTTTAATCGGGA 57.254 45.000 0.00 0.00 41.62 5.14
4330 7014 2.746279 TGCCCATGTTTAATCGGGAT 57.254 45.000 0.00 0.00 41.62 3.85
4331 7015 3.866703 TGCCCATGTTTAATCGGGATA 57.133 42.857 0.00 0.00 41.62 2.59
4332 7016 4.380843 TGCCCATGTTTAATCGGGATAT 57.619 40.909 0.00 0.00 41.62 1.63
4333 7017 5.506730 TGCCCATGTTTAATCGGGATATA 57.493 39.130 0.00 0.00 41.62 0.86
4334 7018 5.496556 TGCCCATGTTTAATCGGGATATAG 58.503 41.667 0.00 0.00 41.62 1.31
4335 7019 5.013704 TGCCCATGTTTAATCGGGATATAGT 59.986 40.000 0.00 0.00 41.62 2.12
4336 7020 5.354234 GCCCATGTTTAATCGGGATATAGTG 59.646 44.000 0.00 0.00 41.62 2.74
4337 7021 5.354234 CCCATGTTTAATCGGGATATAGTGC 59.646 44.000 0.00 0.00 41.62 4.40
4338 7022 5.937540 CCATGTTTAATCGGGATATAGTGCA 59.062 40.000 0.00 0.00 0.00 4.57
4339 7023 6.429692 CCATGTTTAATCGGGATATAGTGCAA 59.570 38.462 0.00 0.00 0.00 4.08
4340 7024 7.121168 CCATGTTTAATCGGGATATAGTGCAAT 59.879 37.037 0.00 0.00 0.00 3.56
4341 7025 7.667043 TGTTTAATCGGGATATAGTGCAATC 57.333 36.000 0.00 0.00 0.00 2.67
4342 7026 6.653320 TGTTTAATCGGGATATAGTGCAATCC 59.347 38.462 6.60 6.60 40.89 3.01
4343 7027 3.526931 ATCGGGATATAGTGCAATCCG 57.473 47.619 8.68 6.93 42.28 4.18
4344 7028 1.548719 TCGGGATATAGTGCAATCCGG 59.451 52.381 13.78 13.78 42.28 5.14
4345 7029 1.405526 CGGGATATAGTGCAATCCGGG 60.406 57.143 12.62 3.58 42.28 5.73
4346 7030 1.628846 GGGATATAGTGCAATCCGGGT 59.371 52.381 0.00 0.00 42.28 5.28
4347 7031 2.039879 GGGATATAGTGCAATCCGGGTT 59.960 50.000 0.00 0.00 42.28 4.11
4348 7032 3.262405 GGGATATAGTGCAATCCGGGTTA 59.738 47.826 0.00 0.00 42.28 2.85
4349 7033 4.251268 GGATATAGTGCAATCCGGGTTAC 58.749 47.826 0.00 0.00 32.79 2.50
4350 7034 4.262721 GGATATAGTGCAATCCGGGTTACA 60.263 45.833 0.00 0.00 32.79 2.41
4351 7035 2.389962 TAGTGCAATCCGGGTTACAC 57.610 50.000 21.24 21.24 0.00 2.90
4352 7036 0.398696 AGTGCAATCCGGGTTACACA 59.601 50.000 28.37 12.47 29.63 3.72
4353 7037 0.802494 GTGCAATCCGGGTTACACAG 59.198 55.000 23.35 1.55 0.00 3.66
4354 7038 0.322098 TGCAATCCGGGTTACACAGG 60.322 55.000 0.00 0.00 0.00 4.00
4355 7039 0.035820 GCAATCCGGGTTACACAGGA 60.036 55.000 0.00 1.22 37.17 3.86
4356 7040 1.408266 GCAATCCGGGTTACACAGGAT 60.408 52.381 0.00 5.42 44.64 3.24
4357 7041 2.288666 CAATCCGGGTTACACAGGATG 58.711 52.381 0.00 3.83 42.17 3.51
4358 7042 1.874129 ATCCGGGTTACACAGGATGA 58.126 50.000 0.00 0.00 41.51 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.358615 AATGGCGAGCGCTCAACA 60.359 55.556 34.69 30.34 41.60 3.33
1 2 1.911293 TTCAATGGCGAGCGCTCAAC 61.911 55.000 34.69 26.12 41.60 3.18
21 22 3.914364 GTCAATCCAACGACAAAGATTGC 59.086 43.478 6.69 0.33 43.33 3.56
33 34 6.038356 GGTGATCAATTCATGTCAATCCAAC 58.962 40.000 0.00 0.00 36.54 3.77
52 53 3.058155 CGGATCGAACTAATCTCGGTGAT 60.058 47.826 0.00 0.00 36.93 3.06
55 56 1.001597 GCGGATCGAACTAATCTCGGT 60.002 52.381 0.00 0.00 36.93 4.69
57 58 1.666311 GGGCGGATCGAACTAATCTCG 60.666 57.143 0.00 0.00 37.66 4.04
199 200 5.941948 GGGACACAATAATATCTTTCCCG 57.058 43.478 0.00 0.00 32.44 5.14
200 201 5.469084 GTCGGGACACAATAATATCTTTCCC 59.531 44.000 0.00 0.00 38.51 3.97
214 215 0.671163 GCATTTACCGTCGGGACACA 60.671 55.000 17.28 0.00 36.97 3.72
310 1386 6.846283 CGAAAACACAAAGCTAAACACTCTAG 59.154 38.462 0.00 0.00 0.00 2.43
381 1458 5.041287 GTCGATCATCTGACGGTAAATTCA 58.959 41.667 0.00 0.00 0.00 2.57
385 1462 3.733988 GCAGTCGATCATCTGACGGTAAA 60.734 47.826 15.43 0.00 40.05 2.01
391 1468 2.881513 TCCTAGCAGTCGATCATCTGAC 59.118 50.000 15.43 4.68 34.02 3.51
405 1482 7.070322 ACCGTCCTTAGTAATTTAATCCTAGCA 59.930 37.037 0.00 0.00 0.00 3.49
411 1488 6.913873 TGCACCGTCCTTAGTAATTTAATC 57.086 37.500 0.00 0.00 0.00 1.75
422 1499 3.410631 TTTTGAGATGCACCGTCCTTA 57.589 42.857 0.00 0.00 0.00 2.69
423 1500 2.270352 TTTTGAGATGCACCGTCCTT 57.730 45.000 0.00 0.00 0.00 3.36
428 1505 2.161410 TCGGAAATTTTGAGATGCACCG 59.839 45.455 0.00 0.00 39.30 4.94
462 1539 4.008933 GGTGTGGCCGAGTGAGCT 62.009 66.667 0.00 0.00 0.00 4.09
465 1542 1.302431 CAATGGTGTGGCCGAGTGA 60.302 57.895 0.00 0.00 41.21 3.41
486 1563 3.833732 ACGAGAGAGGTGCCAGAATATA 58.166 45.455 0.00 0.00 0.00 0.86
487 1564 2.672098 ACGAGAGAGGTGCCAGAATAT 58.328 47.619 0.00 0.00 0.00 1.28
506 1583 5.576447 TTTGAGAAACTCTTGTGGGAAAC 57.424 39.130 0.00 0.00 0.00 2.78
530 1640 7.924940 TGCTTCTTCTTCTTCTTCTTTCTTTC 58.075 34.615 0.00 0.00 0.00 2.62
534 1644 5.614449 CGCTGCTTCTTCTTCTTCTTCTTTC 60.614 44.000 0.00 0.00 0.00 2.62
538 1648 2.414825 CCGCTGCTTCTTCTTCTTCTTC 59.585 50.000 0.00 0.00 0.00 2.87
539 1649 2.421619 CCGCTGCTTCTTCTTCTTCTT 58.578 47.619 0.00 0.00 0.00 2.52
540 1650 1.943507 GCCGCTGCTTCTTCTTCTTCT 60.944 52.381 0.00 0.00 33.53 2.85
541 1651 0.445829 GCCGCTGCTTCTTCTTCTTC 59.554 55.000 0.00 0.00 33.53 2.87
542 1652 0.250467 TGCCGCTGCTTCTTCTTCTT 60.250 50.000 0.70 0.00 38.71 2.52
543 1653 0.673022 CTGCCGCTGCTTCTTCTTCT 60.673 55.000 0.70 0.00 38.71 2.85
544 1654 1.792941 CTGCCGCTGCTTCTTCTTC 59.207 57.895 0.70 0.00 38.71 2.87
558 1672 1.153168 TCGCTATTCTTGGGCTGCC 60.153 57.895 11.05 11.05 0.00 4.85
641 1759 0.887836 GGCGACCGGACCTTTTCTTT 60.888 55.000 9.46 0.00 0.00 2.52
645 1763 1.376812 GATGGCGACCGGACCTTTT 60.377 57.895 9.46 0.00 0.00 2.27
712 2168 5.631992 GCCGTTTCTGATTTCTCTTTTAGG 58.368 41.667 0.00 0.00 0.00 2.69
789 2246 2.470821 CCGGATTAGTAGCGGTCAAAG 58.529 52.381 0.00 0.00 0.00 2.77
867 2339 5.331069 GTCCACTTATATAGTAGCAGGGGA 58.669 45.833 0.00 0.00 34.56 4.81
872 2344 6.269307 GGAAAGGGTCCACTTATATAGTAGCA 59.731 42.308 0.00 0.00 46.97 3.49
895 2367 2.503356 GCTTCTGAAATCTGGAGGAGGA 59.497 50.000 0.00 0.00 0.00 3.71
915 2387 2.043953 GGAGGATGTTGGGTGGGC 60.044 66.667 0.00 0.00 0.00 5.36
943 2415 2.305343 AGAGAGATGGAACTTGCTTGCT 59.695 45.455 0.00 0.00 0.00 3.91
944 2416 2.677337 GAGAGAGATGGAACTTGCTTGC 59.323 50.000 0.00 0.00 0.00 4.01
945 2417 4.205065 AGAGAGAGATGGAACTTGCTTG 57.795 45.455 0.00 0.00 0.00 4.01
946 2418 4.323409 GGAAGAGAGAGATGGAACTTGCTT 60.323 45.833 0.00 0.00 0.00 3.91
957 2429 2.858768 AGGAGGTGAGGAAGAGAGAGAT 59.141 50.000 0.00 0.00 0.00 2.75
1086 2566 1.756430 GAGGAGGAGGATTTGTTGCC 58.244 55.000 0.00 0.00 0.00 4.52
1119 2599 8.430801 AACTGGATAATCTGAAGAAAATCGAG 57.569 34.615 12.03 12.03 34.44 4.04
1131 2611 5.269505 AGAAGACGGAACTGGATAATCTG 57.730 43.478 0.00 0.00 0.00 2.90
1146 2626 7.377397 CGAGAGAATAATCAGGTTAAGAAGACG 59.623 40.741 0.00 0.00 0.00 4.18
1254 2738 3.081061 TCGTTGCCAGCAAGATACAATT 58.919 40.909 5.07 0.00 36.52 2.32
1260 2744 1.160137 GAGTTCGTTGCCAGCAAGAT 58.840 50.000 5.07 0.00 36.52 2.40
1410 2895 1.679139 CAATGGCCCGCTCAATTAGA 58.321 50.000 0.00 0.00 0.00 2.10
1440 2925 9.871175 TGGTTTCACAGTACATATCCTAGTATA 57.129 33.333 0.00 0.00 0.00 1.47
1473 2958 6.155910 GCATCATATGATTCTCCCTCTTCCTA 59.844 42.308 15.74 0.00 31.21 2.94
1474 2959 5.045724 GCATCATATGATTCTCCCTCTTCCT 60.046 44.000 15.74 0.00 31.21 3.36
1475 2960 5.184711 GCATCATATGATTCTCCCTCTTCC 58.815 45.833 15.74 0.00 31.21 3.46
1476 2961 5.802465 TGCATCATATGATTCTCCCTCTTC 58.198 41.667 15.74 0.00 31.21 2.87
1490 2979 8.308931 GGAATCCACAATTGTATTGCATCATAT 58.691 33.333 11.53 0.00 0.00 1.78
1517 3007 3.177228 CATGTGGGGGTTAAATGGGAAA 58.823 45.455 0.00 0.00 0.00 3.13
1522 3012 3.430651 GCATGACATGTGGGGGTTAAATG 60.431 47.826 16.62 0.00 0.00 2.32
1537 3027 2.583024 TTTCATGGAGGTGCATGACA 57.417 45.000 13.14 5.06 37.53 3.58
1552 3044 3.181470 CCAGCATGCATGATCCAATTTCA 60.181 43.478 30.64 0.00 31.97 2.69
1724 3233 6.334202 GCTAGCTGCTATTCGTCCTTTATAT 58.666 40.000 10.23 0.00 38.95 0.86
2082 3714 2.780010 AGGGCCTGCTTAATCATGTACT 59.220 45.455 4.50 0.00 0.00 2.73
2089 3721 1.141185 AGGGTAGGGCCTGCTTAATC 58.859 55.000 21.36 3.94 37.43 1.75
2188 3832 0.322975 ATCATCTATCAGCCACGCCC 59.677 55.000 0.00 0.00 0.00 6.13
2192 3836 4.564041 ACGATTGATCATCTATCAGCCAC 58.436 43.478 9.40 0.00 45.32 5.01
2287 3934 1.787847 CAAGTAGCGGCAAGGTTCG 59.212 57.895 1.45 0.00 0.00 3.95
2329 4013 7.561021 AACCGGAAATAAATTTTGCTTTTGT 57.439 28.000 9.46 0.00 0.00 2.83
2409 4225 0.027455 TGCACGTTTCTGAAACAGCG 59.973 50.000 27.24 18.33 41.89 5.18
2644 4489 2.483877 CGAACACCATGTACTGCACAAT 59.516 45.455 0.00 0.00 41.55 2.71
2691 4536 1.002868 CAGGCCCAAGGTCACTGAG 60.003 63.158 0.00 0.00 0.00 3.35
2892 4767 2.047274 AAGGTGTCATCGGTGCCG 60.047 61.111 3.94 3.94 41.35 5.69
2896 5247 3.764237 AACTTACAAGGTGTCATCGGT 57.236 42.857 0.00 0.00 0.00 4.69
3010 5370 1.395826 CGATCCTGACCCAGTCCTCC 61.396 65.000 0.00 0.00 0.00 4.30
3132 5492 4.394920 ACATGCAAAGTACGAAATGGTAGG 59.605 41.667 0.00 0.00 0.00 3.18
3704 6354 7.112452 AGAAAAGTTTGAAACAACTAGCCAT 57.888 32.000 11.02 0.00 0.00 4.40
3785 6440 6.686484 ATACCATCTAACAGTCCATATGCA 57.314 37.500 0.00 0.00 0.00 3.96
3803 6458 5.429681 ACAGCCATGTACTGTTTATACCA 57.570 39.130 11.73 0.00 46.01 3.25
3921 6590 1.991121 TGGCGGGTCTAGAACGATAT 58.009 50.000 18.94 0.00 0.00 1.63
4043 6725 6.094603 GTCAATAGTCATGCAAGACCTCAAAT 59.905 38.462 17.95 1.71 39.34 2.32
4131 6813 6.238648 ACTAGACACCATCCCTTTGTAAAAG 58.761 40.000 0.00 0.00 0.00 2.27
4155 6839 1.546923 TGAGGCACCGACGAAATTAGA 59.453 47.619 0.00 0.00 0.00 2.10
4179 6863 7.554959 AAATCCCGTAGAACTATCATACCAT 57.445 36.000 0.00 0.00 0.00 3.55
4187 6871 8.701908 TGACTACATAAATCCCGTAGAACTAT 57.298 34.615 0.00 0.00 36.84 2.12
4231 6915 6.767902 GCCTATATCACAATCCTTTTGTCTGA 59.232 38.462 0.00 0.00 0.00 3.27
4232 6916 6.543465 TGCCTATATCACAATCCTTTTGTCTG 59.457 38.462 0.00 0.00 0.00 3.51
4233 6917 6.662755 TGCCTATATCACAATCCTTTTGTCT 58.337 36.000 0.00 0.00 0.00 3.41
4234 6918 6.942532 TGCCTATATCACAATCCTTTTGTC 57.057 37.500 0.00 0.00 0.00 3.18
4235 6919 7.998383 TGTATGCCTATATCACAATCCTTTTGT 59.002 33.333 0.00 0.00 0.00 2.83
4236 6920 8.394971 TGTATGCCTATATCACAATCCTTTTG 57.605 34.615 0.00 0.00 0.00 2.44
4266 6950 7.978975 GCCATGCAAAAGACCAAACTATAAATA 59.021 33.333 0.00 0.00 0.00 1.40
4267 6951 6.818142 GCCATGCAAAAGACCAAACTATAAAT 59.182 34.615 0.00 0.00 0.00 1.40
4268 6952 6.162777 GCCATGCAAAAGACCAAACTATAAA 58.837 36.000 0.00 0.00 0.00 1.40
4269 6953 5.337169 GGCCATGCAAAAGACCAAACTATAA 60.337 40.000 0.00 0.00 0.00 0.98
4270 6954 4.159506 GGCCATGCAAAAGACCAAACTATA 59.840 41.667 0.00 0.00 0.00 1.31
4271 6955 3.055891 GGCCATGCAAAAGACCAAACTAT 60.056 43.478 0.00 0.00 0.00 2.12
4272 6956 2.298729 GGCCATGCAAAAGACCAAACTA 59.701 45.455 0.00 0.00 0.00 2.24
4273 6957 1.070601 GGCCATGCAAAAGACCAAACT 59.929 47.619 0.00 0.00 0.00 2.66
4274 6958 1.202627 TGGCCATGCAAAAGACCAAAC 60.203 47.619 0.00 0.00 0.00 2.93
4275 6959 1.126488 TGGCCATGCAAAAGACCAAA 58.874 45.000 0.00 0.00 0.00 3.28
4276 6960 0.392336 GTGGCCATGCAAAAGACCAA 59.608 50.000 9.72 0.00 0.00 3.67
4277 6961 0.469705 AGTGGCCATGCAAAAGACCA 60.470 50.000 9.72 0.00 0.00 4.02
4278 6962 0.244721 GAGTGGCCATGCAAAAGACC 59.755 55.000 9.72 0.00 0.00 3.85
4279 6963 0.244721 GGAGTGGCCATGCAAAAGAC 59.755 55.000 9.72 0.00 36.34 3.01
4280 6964 1.243342 CGGAGTGGCCATGCAAAAGA 61.243 55.000 9.72 0.00 35.94 2.52
4281 6965 1.213537 CGGAGTGGCCATGCAAAAG 59.786 57.895 9.72 0.00 35.94 2.27
4282 6966 2.274645 CCGGAGTGGCCATGCAAAA 61.275 57.895 9.72 0.00 35.94 2.44
4283 6967 2.676121 CCGGAGTGGCCATGCAAA 60.676 61.111 9.72 0.00 35.94 3.68
4307 6991 2.556622 CCCGATTAAACATGGGCATACC 59.443 50.000 0.00 0.00 40.81 2.73
4308 6992 3.482436 TCCCGATTAAACATGGGCATAC 58.518 45.455 0.00 0.00 41.65 2.39
4309 6993 3.866703 TCCCGATTAAACATGGGCATA 57.133 42.857 0.00 0.00 41.65 3.14
4310 6994 2.746279 TCCCGATTAAACATGGGCAT 57.254 45.000 0.00 0.00 41.65 4.40
4311 6995 2.746279 ATCCCGATTAAACATGGGCA 57.254 45.000 0.00 0.00 41.65 5.36
4312 6996 5.354234 CACTATATCCCGATTAAACATGGGC 59.646 44.000 0.00 0.00 41.65 5.36
4313 6997 5.354234 GCACTATATCCCGATTAAACATGGG 59.646 44.000 0.00 0.00 43.36 4.00
4314 6998 5.937540 TGCACTATATCCCGATTAAACATGG 59.062 40.000 0.00 0.00 0.00 3.66
4315 6999 7.433708 TTGCACTATATCCCGATTAAACATG 57.566 36.000 0.00 0.00 0.00 3.21
4316 7000 7.336931 GGATTGCACTATATCCCGATTAAACAT 59.663 37.037 4.05 0.00 35.33 2.71
4317 7001 6.653320 GGATTGCACTATATCCCGATTAAACA 59.347 38.462 4.05 0.00 35.33 2.83
4318 7002 6.183360 CGGATTGCACTATATCCCGATTAAAC 60.183 42.308 9.14 0.00 37.60 2.01
4319 7003 5.872617 CGGATTGCACTATATCCCGATTAAA 59.127 40.000 9.14 0.00 37.60 1.52
4320 7004 5.416083 CGGATTGCACTATATCCCGATTAA 58.584 41.667 9.14 0.00 37.60 1.40
4321 7005 4.142026 CCGGATTGCACTATATCCCGATTA 60.142 45.833 9.14 0.00 37.60 1.75
4322 7006 3.369471 CCGGATTGCACTATATCCCGATT 60.369 47.826 9.14 0.00 37.60 3.34
4323 7007 2.168521 CCGGATTGCACTATATCCCGAT 59.831 50.000 9.14 0.00 37.60 4.18
4324 7008 1.548719 CCGGATTGCACTATATCCCGA 59.451 52.381 9.14 0.00 37.60 5.14
4325 7009 1.405526 CCCGGATTGCACTATATCCCG 60.406 57.143 0.73 2.41 37.60 5.14
4326 7010 1.628846 ACCCGGATTGCACTATATCCC 59.371 52.381 0.73 0.00 37.60 3.85
4327 7011 3.418684 AACCCGGATTGCACTATATCC 57.581 47.619 0.73 5.22 37.54 2.59
4328 7012 4.689345 GTGTAACCCGGATTGCACTATATC 59.311 45.833 21.49 0.00 40.72 1.63
4329 7013 4.101898 TGTGTAACCCGGATTGCACTATAT 59.898 41.667 27.44 0.00 43.30 0.86
4330 7014 3.451540 TGTGTAACCCGGATTGCACTATA 59.548 43.478 27.44 7.70 43.30 1.31
4331 7015 2.237643 TGTGTAACCCGGATTGCACTAT 59.762 45.455 27.44 0.00 43.30 2.12
4332 7016 1.624312 TGTGTAACCCGGATTGCACTA 59.376 47.619 27.44 13.31 43.30 2.74
4333 7017 0.398696 TGTGTAACCCGGATTGCACT 59.601 50.000 27.44 0.00 43.30 4.40
4334 7018 0.802494 CTGTGTAACCCGGATTGCAC 59.198 55.000 21.91 21.91 43.23 4.57
4335 7019 0.322098 CCTGTGTAACCCGGATTGCA 60.322 55.000 0.73 0.00 34.36 4.08
4336 7020 0.035820 TCCTGTGTAACCCGGATTGC 60.036 55.000 0.73 0.00 31.55 3.56
4337 7021 2.093181 TCATCCTGTGTAACCCGGATTG 60.093 50.000 0.73 0.00 41.53 2.67
4338 7022 2.193127 TCATCCTGTGTAACCCGGATT 58.807 47.619 0.73 0.00 41.53 3.01
4339 7023 1.874129 TCATCCTGTGTAACCCGGAT 58.126 50.000 0.73 0.00 44.00 4.18
4340 7024 3.384937 TCATCCTGTGTAACCCGGA 57.615 52.632 0.73 0.00 39.31 5.14


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

AutoCloner maintained by Alex Coulton.