Multiple sequence alignment - TraesCS6B01G017600

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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 TraesCS6B01G017600 chr6B 100.000 3396 0 0 1 3396 11262349 11258954 0.000000e+00 6272.0
1 TraesCS6B01G017600 chr6B 100.000 1753 0 0 3784 5536 11258566 11256814 0.000000e+00 3238.0
2 TraesCS6B01G017600 chr6B 77.888 1411 233 53 2035 3394 11210517 11209135 0.000000e+00 804.0
3 TraesCS6B01G017600 chr6B 84.277 795 70 18 2615 3394 11242198 11241444 0.000000e+00 725.0
4 TraesCS6B01G017600 chr6B 85.962 634 70 9 3784 4411 11241410 11240790 0.000000e+00 660.0
5 TraesCS6B01G017600 chr6B 77.438 687 115 30 2610 3269 174567302 174567975 1.880000e-99 374.0
6 TraesCS6B01G017600 chr6B 89.474 266 25 3 2228 2491 11242480 11242216 3.200000e-87 333.0
7 TraesCS6B01G017600 chr6B 80.000 475 70 17 3803 4263 98519847 98520310 1.490000e-85 327.0
8 TraesCS6B01G017600 chr6B 79.618 471 78 11 3803 4263 97818464 97818926 6.920000e-84 322.0
9 TraesCS6B01G017600 chr6B 79.579 475 72 17 3803 4263 98451856 98452319 3.220000e-82 316.0
10 TraesCS6B01G017600 chr6B 76.936 594 106 28 1332 1908 98659245 98659824 5.390000e-80 309.0
11 TraesCS6B01G017600 chr6B 76.557 610 113 22 1332 1924 98605373 98605969 1.940000e-79 307.0
12 TraesCS6B01G017600 chr6B 75.767 619 128 14 1339 1940 174566049 174566662 5.420000e-75 292.0
13 TraesCS6B01G017600 chr6B 86.328 256 30 3 4473 4724 11240487 11240233 1.960000e-69 274.0
14 TraesCS6B01G017600 chr6B 76.289 485 75 18 3813 4263 98691214 98691692 7.220000e-54 222.0
15 TraesCS6B01G017600 chr6B 80.220 273 42 10 1332 1593 98516201 98516472 1.570000e-45 195.0
16 TraesCS6B01G017600 chr6B 78.000 250 44 9 3027 3269 98518818 98519063 4.470000e-31 147.0
17 TraesCS6B01G017600 chr6B 77.481 262 48 9 3015 3269 98606886 98607143 4.470000e-31 147.0
18 TraesCS6B01G017600 chr6B 92.000 50 3 1 4579 4627 174569832 174569881 9.950000e-08 69.4
19 TraesCS6B01G017600 chr6A 91.472 3424 195 35 1 3377 5298529 5295156 0.000000e+00 4615.0
20 TraesCS6B01G017600 chr6A 94.744 780 34 3 3799 4573 5294915 5294138 0.000000e+00 1206.0
21 TraesCS6B01G017600 chr6A 81.779 461 72 6 2054 2509 5239825 5239372 5.240000e-100 375.0
22 TraesCS6B01G017600 chr6D 93.347 2360 114 19 1067 3396 5913014 5910668 0.000000e+00 3448.0
23 TraesCS6B01G017600 chr6D 92.842 950 52 7 3784 4724 5910635 5909693 0.000000e+00 1363.0
24 TraesCS6B01G017600 chr6D 91.002 878 70 7 2522 3396 5948301 5947430 0.000000e+00 1175.0
25 TraesCS6B01G017600 chr6D 87.407 810 51 13 4720 5526 5946284 5945523 0.000000e+00 883.0
26 TraesCS6B01G017600 chr6D 92.550 604 33 8 230 833 5913637 5913046 0.000000e+00 856.0
27 TraesCS6B01G017600 chr6D 88.269 699 67 4 3803 4489 5947422 5946727 0.000000e+00 822.0
28 TraesCS6B01G017600 chr6D 86.024 737 68 22 2667 3394 5889071 5888361 0.000000e+00 758.0
29 TraesCS6B01G017600 chr6D 88.036 560 62 2 3784 4339 5888329 5887771 0.000000e+00 658.0
30 TraesCS6B01G017600 chr6D 90.769 325 28 2 4706 5028 5909487 5909163 3.060000e-117 433.0
31 TraesCS6B01G017600 chr6D 84.091 440 49 11 5095 5534 5907759 5907341 6.680000e-109 405.0
32 TraesCS6B01G017600 chr6D 86.592 358 38 7 4376 4724 5887774 5887418 2.420000e-103 387.0
33 TraesCS6B01G017600 chr6D 87.037 324 36 6 2171 2491 5902578 5902258 1.470000e-95 361.0
34 TraesCS6B01G017600 chr6D 78.395 324 32 27 4438 4727 5946728 5946409 5.700000e-40 176.0
35 TraesCS6B01G017600 chr6D 89.873 79 5 2 4443 4521 5946605 5946530 1.270000e-16 99.0
36 TraesCS6B01G017600 chrUn 77.888 1411 233 53 2035 3394 231207607 231208989 0.000000e+00 804.0
37 TraesCS6B01G017600 chrUn 77.924 607 104 20 1339 1924 21369777 21369180 8.820000e-93 351.0
38 TraesCS6B01G017600 chrUn 76.338 355 55 22 2600 2928 170381442 170381091 4.440000e-36 163.0
39 TraesCS6B01G017600 chrUn 76.338 355 55 22 2600 2928 174089771 174090122 4.440000e-36 163.0
40 TraesCS6B01G017600 chrUn 76.338 355 55 22 2600 2928 255569604 255569955 4.440000e-36 163.0
41 TraesCS6B01G017600 chr7A 72.512 422 98 15 1516 1926 31115596 31116010 2.710000e-23 121.0
42 TraesCS6B01G017600 chr4B 82.143 84 11 3 1498 1580 36001627 36001707 9.950000e-08 69.4


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 TraesCS6B01G017600 chr6B 11256814 11262349 5535 True 4755.000000 6272 100.000000 1 5536 2 chr6B.!!$R3 5535
1 TraesCS6B01G017600 chr6B 11209135 11210517 1382 True 804.000000 804 77.888000 2035 3394 1 chr6B.!!$R1 1359
2 TraesCS6B01G017600 chr6B 11240233 11242480 2247 True 498.000000 725 86.510250 2228 4724 4 chr6B.!!$R2 2496
3 TraesCS6B01G017600 chr6B 98659245 98659824 579 False 309.000000 309 76.936000 1332 1908 1 chr6B.!!$F3 576
4 TraesCS6B01G017600 chr6B 174566049 174569881 3832 False 245.133333 374 81.735000 1339 4627 3 chr6B.!!$F7 3288
5 TraesCS6B01G017600 chr6B 98605373 98607143 1770 False 227.000000 307 77.019000 1332 3269 2 chr6B.!!$F6 1937
6 TraesCS6B01G017600 chr6B 98516201 98520310 4109 False 223.000000 327 79.406667 1332 4263 3 chr6B.!!$F5 2931
7 TraesCS6B01G017600 chr6A 5294138 5298529 4391 True 2910.500000 4615 93.108000 1 4573 2 chr6A.!!$R2 4572
8 TraesCS6B01G017600 chr6D 5907341 5913637 6296 True 1301.000000 3448 90.719800 230 5534 5 chr6D.!!$R3 5304
9 TraesCS6B01G017600 chr6D 5945523 5948301 2778 True 631.000000 1175 86.989200 2522 5526 5 chr6D.!!$R4 3004
10 TraesCS6B01G017600 chr6D 5887418 5889071 1653 True 601.000000 758 86.884000 2667 4724 3 chr6D.!!$R2 2057
11 TraesCS6B01G017600 chrUn 231207607 231208989 1382 False 804.000000 804 77.888000 2035 3394 1 chrUn.!!$F2 1359
12 TraesCS6B01G017600 chrUn 21369180 21369777 597 True 351.000000 351 77.924000 1339 1924 1 chrUn.!!$R1 585

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
112 113 0.035820 TGGCCGTTAGATCCGCTTTT 60.036 50.00 0.00 0.0 0.00 2.27 F
747 764 0.175760 ATCAGATGGCTTGCGTACGT 59.824 50.00 17.90 0.0 0.00 3.57 F
1107 1133 0.391793 GCGTTTGAGGGGAGAAGGAG 60.392 60.00 0.00 0.0 0.00 3.69 F
1971 3136 0.254178 CTCCCATGGCACTAGCAAGT 59.746 55.00 6.09 0.0 44.61 3.16 F
3132 4363 0.605319 CGTGGCTACTCCCAAAAGCA 60.605 55.00 0.00 0.0 38.01 3.91 F
3868 5752 5.033078 GTTTGTTAACTCAAACGTTTCGC 57.967 39.13 11.37 0.0 44.47 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1139 0.324614 TCCTTCTCCGCTGATGCAAA 59.675 50.000 0.00 0.00 39.64 3.68 R
1928 3093 0.521291 CGGACGATGGTTTGTGCAAT 59.479 50.000 0.00 0.00 0.00 3.56 R
3062 4284 1.002502 AAAGGAAGTAGGGCCGCAC 60.003 57.895 0.00 0.00 0.00 5.34 R
3868 5752 0.107312 ACTATGGCAGGCTGCTTGAG 60.107 55.000 35.73 28.84 44.28 3.02 R
4131 6037 0.466007 TGTGCTGCCAACACATGAGT 60.466 50.000 0.00 0.00 42.88 3.41 R
5407 9916 0.167908 TTTGCTTGCGCTACCATTCG 59.832 50.000 9.73 0.00 36.97 3.34 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
25 26 8.874744 CCTTTTCGTTACTTTTTGGGAAATTA 57.125 30.769 0.00 0.00 0.00 1.40
65 66 9.778741 TTATTTTTCGAATATGCCTCTACTCAT 57.221 29.630 0.00 0.00 0.00 2.90
112 113 0.035820 TGGCCGTTAGATCCGCTTTT 60.036 50.000 0.00 0.00 0.00 2.27
133 134 0.601841 ATCGGACGACCCACAACAAC 60.602 55.000 0.00 0.00 34.14 3.32
190 191 4.082949 CCTTGTTGTAAATCCCTTCGAACC 60.083 45.833 0.00 0.00 0.00 3.62
196 197 4.286549 TGTAAATCCCTTCGAACCCAACTA 59.713 41.667 0.00 0.00 0.00 2.24
197 198 3.629142 AATCCCTTCGAACCCAACTAG 57.371 47.619 0.00 0.00 0.00 2.57
198 199 1.272807 TCCCTTCGAACCCAACTAGG 58.727 55.000 0.00 0.00 37.03 3.02
224 225 0.901580 TTGTAGACCGACCAGGGGAC 60.902 60.000 0.00 0.00 46.96 4.46
285 287 2.413765 GGTAGGAAGCCGAGCTCG 59.586 66.667 29.06 29.06 38.25 5.03
437 451 2.125326 CGGGAGCTCGGTGTGGATA 61.125 63.158 7.83 0.00 0.00 2.59
463 477 1.076777 AATTGGCAGGGACGATGGG 60.077 57.895 0.00 0.00 0.00 4.00
483 497 0.472471 GACAGAGGTCCCCAACAACA 59.528 55.000 0.00 0.00 38.12 3.33
530 544 1.806542 GCGGAGATTCTTTCTGCAACA 59.193 47.619 1.42 0.00 42.63 3.33
600 614 2.460918 CATGAGTCAACGACGGATACC 58.539 52.381 0.00 0.00 37.67 2.73
601 615 1.536940 TGAGTCAACGACGGATACCA 58.463 50.000 0.00 0.00 37.67 3.25
630 644 2.221169 GCGATATTGATGGCCACAAGA 58.779 47.619 8.16 12.69 30.96 3.02
648 662 3.305398 AGACGAAGGTGCTTTCTACAG 57.695 47.619 0.00 0.00 0.00 2.74
675 689 2.287915 GTCCTATTGCAATTGCGACGAT 59.712 45.455 22.61 15.96 45.83 3.73
734 751 7.075851 ACATGGTGAACATCATAGATCAGAT 57.924 36.000 0.00 0.00 37.84 2.90
744 761 3.573967 TCATAGATCAGATGGCTTGCGTA 59.426 43.478 7.54 0.00 0.00 4.42
745 762 2.231215 AGATCAGATGGCTTGCGTAC 57.769 50.000 0.00 0.00 0.00 3.67
746 763 0.855349 GATCAGATGGCTTGCGTACG 59.145 55.000 11.84 11.84 0.00 3.67
747 764 0.175760 ATCAGATGGCTTGCGTACGT 59.824 50.000 17.90 0.00 0.00 3.57
779 796 4.722194 TCTCTTTCAAAAATCAATCGGCG 58.278 39.130 0.00 0.00 0.00 6.46
781 798 2.645730 TTCAAAAATCAATCGGCGGG 57.354 45.000 7.21 0.00 0.00 6.13
833 850 6.127730 ACACGGTTCTCAAATCTTCTTTGTTT 60.128 34.615 0.00 0.00 0.00 2.83
867 884 5.607477 ACTTCACACGGTTCTCAAATCTTA 58.393 37.500 0.00 0.00 0.00 2.10
874 891 6.073222 ACACGGTTCTCAAATCTTATGTGTTC 60.073 38.462 0.00 0.00 33.45 3.18
875 892 5.411669 ACGGTTCTCAAATCTTATGTGTTCC 59.588 40.000 0.00 0.00 0.00 3.62
876 893 5.411361 CGGTTCTCAAATCTTATGTGTTCCA 59.589 40.000 0.00 0.00 0.00 3.53
877 894 6.072728 CGGTTCTCAAATCTTATGTGTTCCAA 60.073 38.462 0.00 0.00 0.00 3.53
878 895 7.521423 CGGTTCTCAAATCTTATGTGTTCCAAA 60.521 37.037 0.00 0.00 0.00 3.28
879 896 8.141268 GGTTCTCAAATCTTATGTGTTCCAAAA 58.859 33.333 0.00 0.00 0.00 2.44
880 897 9.696917 GTTCTCAAATCTTATGTGTTCCAAAAT 57.303 29.630 0.00 0.00 0.00 1.82
939 956 3.062639 CGGAATCGAACAGTCAATCCAAG 59.937 47.826 0.00 0.00 39.00 3.61
955 972 2.317594 TCCAAGCCCTAAATTTCCCCAT 59.682 45.455 0.00 0.00 0.00 4.00
961 978 1.410932 CCTAAATTTCCCCATCGCCCA 60.411 52.381 0.00 0.00 0.00 5.36
962 979 1.956477 CTAAATTTCCCCATCGCCCAG 59.044 52.381 0.00 0.00 0.00 4.45
963 980 1.329913 AAATTTCCCCATCGCCCAGC 61.330 55.000 0.00 0.00 0.00 4.85
964 981 3.738745 ATTTCCCCATCGCCCAGCC 62.739 63.158 0.00 0.00 0.00 4.85
969 986 4.528039 CCATCGCCCAGCCCCAAT 62.528 66.667 0.00 0.00 0.00 3.16
970 987 2.515398 CATCGCCCAGCCCCAATA 59.485 61.111 0.00 0.00 0.00 1.90
971 988 1.152777 CATCGCCCAGCCCCAATAA 60.153 57.895 0.00 0.00 0.00 1.40
972 989 1.152756 ATCGCCCAGCCCCAATAAC 60.153 57.895 0.00 0.00 0.00 1.89
973 990 1.932156 ATCGCCCAGCCCCAATAACA 61.932 55.000 0.00 0.00 0.00 2.41
974 991 2.414785 CGCCCAGCCCCAATAACAC 61.415 63.158 0.00 0.00 0.00 3.32
975 992 2.058001 GCCCAGCCCCAATAACACC 61.058 63.158 0.00 0.00 0.00 4.16
976 993 1.386155 CCCAGCCCCAATAACACCA 59.614 57.895 0.00 0.00 0.00 4.17
977 994 0.970427 CCCAGCCCCAATAACACCAC 60.970 60.000 0.00 0.00 0.00 4.16
978 995 0.970427 CCAGCCCCAATAACACCACC 60.970 60.000 0.00 0.00 0.00 4.61
979 996 1.001393 AGCCCCAATAACACCACCG 60.001 57.895 0.00 0.00 0.00 4.94
980 997 2.706834 GCCCCAATAACACCACCGC 61.707 63.158 0.00 0.00 0.00 5.68
981 998 2.403378 CCCCAATAACACCACCGCG 61.403 63.158 0.00 0.00 0.00 6.46
982 999 2.483288 CCAATAACACCACCGCGC 59.517 61.111 0.00 0.00 0.00 6.86
983 1000 2.483288 CAATAACACCACCGCGCC 59.517 61.111 0.00 0.00 0.00 6.53
984 1001 2.748647 AATAACACCACCGCGCCC 60.749 61.111 0.00 0.00 0.00 6.13
997 1014 1.976474 GCGCCCAAACCCTCAATCA 60.976 57.895 0.00 0.00 0.00 2.57
1008 1025 1.668419 CCTCAATCAATCCCCGACAC 58.332 55.000 0.00 0.00 0.00 3.67
1052 1069 3.394836 GCTCTGAACCCTCCCGCT 61.395 66.667 0.00 0.00 0.00 5.52
1056 1073 2.038975 TGAACCCTCCCGCTAGCT 59.961 61.111 13.93 0.00 0.00 3.32
1101 1127 3.423154 GTGCGCGTTTGAGGGGAG 61.423 66.667 8.43 0.00 0.00 4.30
1102 1128 3.621805 TGCGCGTTTGAGGGGAGA 61.622 61.111 8.43 0.00 0.00 3.71
1103 1129 2.358247 GCGCGTTTGAGGGGAGAA 60.358 61.111 8.43 0.00 0.00 2.87
1104 1130 2.391389 GCGCGTTTGAGGGGAGAAG 61.391 63.158 8.43 0.00 0.00 2.85
1106 1132 1.677552 GCGTTTGAGGGGAGAAGGA 59.322 57.895 0.00 0.00 0.00 3.36
1107 1133 0.391793 GCGTTTGAGGGGAGAAGGAG 60.392 60.000 0.00 0.00 0.00 3.69
1108 1134 0.977395 CGTTTGAGGGGAGAAGGAGT 59.023 55.000 0.00 0.00 0.00 3.85
1109 1135 1.348036 CGTTTGAGGGGAGAAGGAGTT 59.652 52.381 0.00 0.00 0.00 3.01
1110 1136 2.784347 GTTTGAGGGGAGAAGGAGTTG 58.216 52.381 0.00 0.00 0.00 3.16
1111 1137 0.693049 TTGAGGGGAGAAGGAGTTGC 59.307 55.000 0.00 0.00 0.00 4.17
1112 1138 0.473694 TGAGGGGAGAAGGAGTTGCA 60.474 55.000 0.00 0.00 0.00 4.08
1113 1139 0.915364 GAGGGGAGAAGGAGTTGCAT 59.085 55.000 0.00 0.00 0.00 3.96
1137 1163 4.069232 CAGCGGAGAAGGACGGCA 62.069 66.667 0.00 0.00 36.34 5.69
1157 1183 4.619227 CCGGCTGGTTCACCACGT 62.619 66.667 2.29 0.00 42.01 4.49
1158 1184 3.041940 CGGCTGGTTCACCACGTC 61.042 66.667 0.00 0.00 42.01 4.34
1175 1210 1.251251 GTCCTGTGCAAGCAAGGAAT 58.749 50.000 20.00 0.00 0.00 3.01
1320 1355 0.682209 CCCACCTTCATTCCCTGCTG 60.682 60.000 0.00 0.00 0.00 4.41
1790 2949 3.765381 TGGCATGAAGAGGTTTGATGAA 58.235 40.909 0.00 0.00 0.00 2.57
1864 3029 2.929477 GTACCCCAACCCCGACCA 60.929 66.667 0.00 0.00 0.00 4.02
1928 3093 1.381191 TCTGCACCTCCTCGCCATA 60.381 57.895 0.00 0.00 0.00 2.74
1971 3136 0.254178 CTCCCATGGCACTAGCAAGT 59.746 55.000 6.09 0.00 44.61 3.16
2226 3394 2.210424 CCAGCAGGCTCTAGCTTCT 58.790 57.895 0.00 0.00 39.50 2.85
2454 3624 1.745087 GCTTCGATTTCCATCAAGCCA 59.255 47.619 0.00 0.00 37.46 4.75
2538 3708 3.434167 CGATCCCAACATTGATCCTTCCT 60.434 47.826 0.00 0.00 35.09 3.36
3031 4253 0.855349 CAGGATCCGAAATTCGAGCG 59.145 55.000 17.75 0.05 43.74 5.03
3033 4255 1.134788 AGGATCCGAAATTCGAGCGTT 60.135 47.619 17.75 0.00 43.74 4.84
3062 4284 2.142319 TGTGGTGTGAATGATCGTGTG 58.858 47.619 0.00 0.00 0.00 3.82
3132 4363 0.605319 CGTGGCTACTCCCAAAAGCA 60.605 55.000 0.00 0.00 38.01 3.91
3258 4504 7.522542 TGGTATGCTATAACCAAACCATATGT 58.477 34.615 1.24 0.00 42.74 2.29
3868 5752 5.033078 GTTTGTTAACTCAAACGTTTCGC 57.967 39.130 11.37 0.00 44.47 4.70
4112 6014 7.425577 TCTATGCACATGTAGTTTATGATGC 57.574 36.000 0.00 0.00 35.30 3.91
4280 6187 1.202336 CCCCGTAACGGTGACTATGTC 60.202 57.143 0.00 0.00 46.80 3.06
4325 6232 3.192001 ACAGCAACTCGCAAATCATCAAT 59.808 39.130 0.00 0.00 46.13 2.57
4507 7442 9.628500 AGTATGATGTGTAGTTCTGTGACTATA 57.372 33.333 0.00 0.00 34.84 1.31
4520 7455 9.098355 GTTCTGTGACTATATGCAAGACAATTA 57.902 33.333 0.00 0.00 0.00 1.40
4551 7486 6.323210 TGTTGTCTCAGAGGTAGGATAGTA 57.677 41.667 0.00 0.00 0.00 1.82
4555 7492 5.072058 TGTCTCAGAGGTAGGATAGTACTCC 59.928 48.000 0.00 0.00 35.37 3.85
4570 7507 8.145122 GGATAGTACTCCTGAAATCTAACAAGG 58.855 40.741 0.00 0.00 32.18 3.61
4576 7513 5.070001 TCCTGAAATCTAACAAGGTGGTTG 58.930 41.667 0.00 0.00 42.48 3.77
4585 7525 6.694447 TCTAACAAGGTGGTTGATGTACTAC 58.306 40.000 0.00 0.00 38.60 2.73
4617 7557 6.826668 TCCTATGATGTGTGTTAGTAATGGG 58.173 40.000 0.00 0.00 0.00 4.00
4628 7568 7.968405 GTGTGTTAGTAATGGGATTTGAATGAC 59.032 37.037 0.00 0.00 0.00 3.06
4667 7607 0.106708 TGAGTGTGGGAACTGCAGTC 59.893 55.000 21.95 13.39 37.10 3.51
4678 7622 4.563580 GGGAACTGCAGTCTAATCTGAACA 60.564 45.833 21.95 0.00 37.61 3.18
4748 7918 0.532862 CTTGACGTCAACCCTGTGCT 60.533 55.000 26.53 0.00 0.00 4.40
4852 8022 2.488937 AGTGCATGATTGTTGCGAATGA 59.511 40.909 0.00 0.00 43.10 2.57
4854 8024 2.488937 TGCATGATTGTTGCGAATGACT 59.511 40.909 0.00 0.00 43.10 3.41
4889 8059 5.875359 GCTACATTTGCTCTAGTTTGTAGGT 59.125 40.000 9.25 0.00 37.86 3.08
4895 8065 8.564574 CATTTGCTCTAGTTTGTAGGTTAAACA 58.435 33.333 0.00 0.00 39.78 2.83
4951 8121 2.409975 CAAGCATTGCCAACCTTTCAG 58.590 47.619 4.70 0.00 40.39 3.02
4952 8122 1.708341 AGCATTGCCAACCTTTCAGT 58.292 45.000 4.70 0.00 0.00 3.41
4977 8148 0.250901 AAGGTTGGCGCTGTTGATCT 60.251 50.000 7.64 0.00 0.00 2.75
5028 8199 2.773661 TGGAAAGAGCATCAGCCATCTA 59.226 45.455 0.00 0.00 43.56 1.98
5029 8200 3.393609 TGGAAAGAGCATCAGCCATCTAT 59.606 43.478 0.00 0.00 43.56 1.98
5129 9638 1.336887 GCTTCAGTTAGCAGTCACGGA 60.337 52.381 0.00 0.00 40.89 4.69
5140 9649 2.106074 GTCACGGATTGCGGCATCA 61.106 57.895 2.28 0.00 0.00 3.07
5170 9679 8.659925 TTATTTTTGAGTTTGTCAACATGCAT 57.340 26.923 0.00 0.00 45.23 3.96
5171 9680 6.586868 TTTTTGAGTTTGTCAACATGCATC 57.413 33.333 0.00 0.00 45.23 3.91
5172 9681 4.915158 TTGAGTTTGTCAACATGCATCA 57.085 36.364 0.00 0.00 40.45 3.07
5173 9682 4.492791 TGAGTTTGTCAACATGCATCAG 57.507 40.909 0.00 0.00 35.05 2.90
5174 9683 3.884693 TGAGTTTGTCAACATGCATCAGT 59.115 39.130 0.00 0.00 35.05 3.41
5175 9684 4.224433 GAGTTTGTCAACATGCATCAGTG 58.776 43.478 0.00 0.00 35.05 3.66
5176 9685 2.727798 GTTTGTCAACATGCATCAGTGC 59.272 45.455 0.00 0.00 41.13 4.40
5177 9686 4.686559 GTTTGTCAACATGCATCAGTGCG 61.687 47.826 0.00 0.00 42.42 5.34
5236 9745 6.751514 ATTTGCTATGTGTTTATCCGTTGA 57.248 33.333 0.00 0.00 0.00 3.18
5247 9756 6.795114 GTGTTTATCCGTTGACACATGTTTAG 59.205 38.462 0.00 0.00 41.42 1.85
5262 9771 3.838565 TGTTTAGCAGACCCAATTTCCA 58.161 40.909 0.00 0.00 0.00 3.53
5390 9899 6.751514 ATAGTTTCATTCGTACCAATTGCA 57.248 33.333 0.00 0.00 0.00 4.08
5407 9916 3.648339 TGCACTCTTCCAAGCAAAATC 57.352 42.857 0.00 0.00 33.48 2.17
5418 9927 3.100817 CAAGCAAAATCGAATGGTAGCG 58.899 45.455 0.00 0.00 0.00 4.26
5465 9974 4.925054 CGAAGTTTTCATGCAACCATTGAT 59.075 37.500 0.00 0.00 0.00 2.57
5466 9975 5.164031 CGAAGTTTTCATGCAACCATTGATG 60.164 40.000 0.00 0.00 0.00 3.07
5477 9986 4.689812 GCAACCATTGATGTAATTGCACAA 59.310 37.500 0.00 6.24 38.26 3.33
5484 9993 5.268118 TGATGTAATTGCACAAAACCACA 57.732 34.783 0.00 0.00 30.84 4.17
5526 10035 9.736023 TTTGCAGAAAAGAGAGTTTTCTATTTC 57.264 29.630 11.39 3.47 42.41 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 7.722728 AGAGGCAGCATGAAAATAATAATCAGA 59.277 33.333 0.00 0.00 39.69 3.27
112 113 1.290955 GTTGTGGGTCGTCCGATGA 59.709 57.895 0.00 0.00 38.76 2.92
120 121 0.107081 TGGTAGGTTGTTGTGGGTCG 59.893 55.000 0.00 0.00 0.00 4.79
163 164 4.154195 CGAAGGGATTTACAACAAGGACAG 59.846 45.833 0.00 0.00 0.00 3.51
164 165 4.069304 CGAAGGGATTTACAACAAGGACA 58.931 43.478 0.00 0.00 0.00 4.02
190 191 4.141779 GGTCTACAACATACCCCTAGTTGG 60.142 50.000 9.05 0.00 45.08 3.77
196 197 2.105766 GTCGGTCTACAACATACCCCT 58.894 52.381 0.00 0.00 0.00 4.79
197 198 1.137675 GGTCGGTCTACAACATACCCC 59.862 57.143 0.00 0.00 31.26 4.95
198 199 1.826720 TGGTCGGTCTACAACATACCC 59.173 52.381 0.00 0.00 34.73 3.69
285 287 1.134401 TGCAGATCTCCGAAACCATCC 60.134 52.381 0.00 0.00 0.00 3.51
287 289 1.833630 TCTGCAGATCTCCGAAACCAT 59.166 47.619 13.74 0.00 0.00 3.55
437 451 2.102578 GTCCCTGCCAATTGTAAGCAT 58.897 47.619 8.09 0.00 35.64 3.79
483 497 2.038975 TAAGACCAGGAGGCGGCT 59.961 61.111 13.09 13.09 39.06 5.52
530 544 2.733956 TGTTGCAACAAGAGGACCTTT 58.266 42.857 29.36 0.00 35.67 3.11
559 573 1.534595 GTCTAGTCCGTCGCCGATAAT 59.465 52.381 0.00 0.00 35.63 1.28
575 589 1.471287 CCGTCGTTGACTCATGGTCTA 59.529 52.381 13.32 5.48 44.74 2.59
576 590 0.243907 CCGTCGTTGACTCATGGTCT 59.756 55.000 13.32 0.00 44.74 3.85
578 592 0.895530 ATCCGTCGTTGACTCATGGT 59.104 50.000 0.00 0.00 0.00 3.55
600 614 4.796830 GCCATCAATATCGCAATTGCTATG 59.203 41.667 26.86 17.14 36.89 2.23
601 615 4.142315 GGCCATCAATATCGCAATTGCTAT 60.142 41.667 26.86 23.20 36.89 2.97
630 644 1.797025 GCTGTAGAAAGCACCTTCGT 58.203 50.000 0.00 0.00 43.01 3.85
648 662 2.931969 GCAATTGCAATAGGACCTTTGC 59.068 45.455 25.36 23.53 46.53 3.68
675 689 8.471609 TGTACGTGTTCATATTCTCTATTTCCA 58.528 33.333 0.00 0.00 0.00 3.53
734 751 0.604243 ATTTGGACGTACGCAAGCCA 60.604 50.000 16.72 14.78 45.62 4.75
744 761 6.633500 TTTGAAAGAGATTGATTTGGACGT 57.367 33.333 0.00 0.00 0.00 4.34
745 762 7.928908 TTTTTGAAAGAGATTGATTTGGACG 57.071 32.000 0.00 0.00 0.00 4.79
746 763 9.480053 TGATTTTTGAAAGAGATTGATTTGGAC 57.520 29.630 0.00 0.00 0.00 4.02
833 850 2.355310 CCGTGTGAAGTATAAGGGGCAA 60.355 50.000 0.00 0.00 0.00 4.52
939 956 0.673985 GCGATGGGGAAATTTAGGGC 59.326 55.000 0.00 0.00 0.00 5.19
955 972 2.274104 GTTATTGGGGCTGGGCGA 59.726 61.111 0.00 0.00 0.00 5.54
961 978 1.001393 CGGTGGTGTTATTGGGGCT 60.001 57.895 0.00 0.00 0.00 5.19
962 979 2.706834 GCGGTGGTGTTATTGGGGC 61.707 63.158 0.00 0.00 0.00 5.80
963 980 2.403378 CGCGGTGGTGTTATTGGGG 61.403 63.158 0.00 0.00 0.00 4.96
964 981 3.046497 GCGCGGTGGTGTTATTGGG 62.046 63.158 8.83 0.00 0.00 4.12
965 982 2.483288 GCGCGGTGGTGTTATTGG 59.517 61.111 8.83 0.00 0.00 3.16
966 983 2.483288 GGCGCGGTGGTGTTATTG 59.517 61.111 8.83 0.00 0.00 1.90
967 984 2.748647 GGGCGCGGTGGTGTTATT 60.749 61.111 8.83 0.00 0.00 1.40
968 985 3.554696 TTGGGCGCGGTGGTGTTAT 62.555 57.895 8.83 0.00 0.00 1.89
969 986 3.769369 TTTGGGCGCGGTGGTGTTA 62.769 57.895 8.83 0.00 0.00 2.41
978 995 3.051392 GATTGAGGGTTTGGGCGCG 62.051 63.158 0.00 0.00 0.00 6.86
979 996 1.531739 TTGATTGAGGGTTTGGGCGC 61.532 55.000 0.00 0.00 0.00 6.53
980 997 1.134946 GATTGATTGAGGGTTTGGGCG 59.865 52.381 0.00 0.00 0.00 6.13
981 998 1.482182 GGATTGATTGAGGGTTTGGGC 59.518 52.381 0.00 0.00 0.00 5.36
982 999 2.110578 GGGATTGATTGAGGGTTTGGG 58.889 52.381 0.00 0.00 0.00 4.12
983 1000 2.110578 GGGGATTGATTGAGGGTTTGG 58.889 52.381 0.00 0.00 0.00 3.28
984 1001 1.750778 CGGGGATTGATTGAGGGTTTG 59.249 52.381 0.00 0.00 0.00 2.93
988 1005 0.546122 TGTCGGGGATTGATTGAGGG 59.454 55.000 0.00 0.00 0.00 4.30
1032 1049 4.475135 GGGAGGGTTCAGAGCGGC 62.475 72.222 0.00 0.00 0.00 6.53
1062 1079 3.132139 CGTCCTCGAAGGCTCCGA 61.132 66.667 0.00 0.00 39.71 4.55
1063 1080 3.114647 CTCGTCCTCGAAGGCTCCG 62.115 68.421 0.00 0.00 45.61 4.63
1064 1081 2.802106 CTCGTCCTCGAAGGCTCC 59.198 66.667 0.00 0.00 45.61 4.70
1065 1082 2.103340 GCTCGTCCTCGAAGGCTC 59.897 66.667 0.00 0.00 45.61 4.70
1098 1124 2.643933 GCAAATGCAACTCCTTCTCC 57.356 50.000 0.00 0.00 41.59 3.71
1110 1136 0.452987 TTCTCCGCTGATGCAAATGC 59.547 50.000 0.00 0.00 39.64 3.56
1111 1137 1.065102 CCTTCTCCGCTGATGCAAATG 59.935 52.381 0.00 0.00 39.64 2.32
1112 1138 1.065199 TCCTTCTCCGCTGATGCAAAT 60.065 47.619 0.00 0.00 39.64 2.32
1113 1139 0.324614 TCCTTCTCCGCTGATGCAAA 59.675 50.000 0.00 0.00 39.64 3.68
1148 1174 0.813610 CTTGCACAGGACGTGGTGAA 60.814 55.000 13.89 2.52 46.45 3.18
1152 1178 2.121564 CTTGCTTGCACAGGACGTGG 62.122 60.000 0.00 0.00 46.45 4.94
1155 1181 1.165907 TTCCTTGCTTGCACAGGACG 61.166 55.000 18.80 0.00 0.00 4.79
1156 1182 1.068055 CATTCCTTGCTTGCACAGGAC 60.068 52.381 18.80 0.00 0.00 3.85
1157 1183 1.202915 TCATTCCTTGCTTGCACAGGA 60.203 47.619 16.63 16.63 0.00 3.86
1158 1184 1.250328 TCATTCCTTGCTTGCACAGG 58.750 50.000 13.70 13.70 0.00 4.00
1168 1203 3.681897 CACCTTCGAGACTTCATTCCTTG 59.318 47.826 0.00 0.00 0.00 3.61
1175 1210 2.558795 CCTTCTCACCTTCGAGACTTCA 59.441 50.000 0.00 0.00 41.72 3.02
1594 1656 2.420022 CCCTCGCAACAACTAAATCCAG 59.580 50.000 0.00 0.00 0.00 3.86
1763 2922 0.700564 ACCTCTTCATGCCATGGTGT 59.299 50.000 14.67 0.00 0.00 4.16
1897 3062 1.502231 GTGCAGAGTGTCGTCAATGT 58.498 50.000 0.00 0.00 0.00 2.71
1928 3093 0.521291 CGGACGATGGTTTGTGCAAT 59.479 50.000 0.00 0.00 0.00 3.56
1971 3136 1.277842 TGTCTTAAGCATCCTGGCGAA 59.722 47.619 0.00 0.00 39.27 4.70
2454 3624 1.380785 CCTGGACCAGGCATTGCAT 60.381 57.895 27.72 0.00 45.13 3.96
2538 3708 3.635836 CACCTCATCAGCACATAGAGAGA 59.364 47.826 0.00 0.00 0.00 3.10
3031 4253 7.067532 TCATTCACACCACAAATCGTATAAC 57.932 36.000 0.00 0.00 0.00 1.89
3033 4255 6.200097 CGATCATTCACACCACAAATCGTATA 59.800 38.462 0.00 0.00 32.38 1.47
3062 4284 1.002502 AAAGGAAGTAGGGCCGCAC 60.003 57.895 0.00 0.00 0.00 5.34
3132 4363 1.525995 CCGCAGAACCACCACAAGT 60.526 57.895 0.00 0.00 0.00 3.16
3276 4523 8.918202 TTTACAGCAAAATATACCAGATAGGG 57.082 34.615 0.00 0.00 43.89 3.53
3868 5752 0.107312 ACTATGGCAGGCTGCTTGAG 60.107 55.000 35.73 28.84 44.28 3.02
4131 6037 0.466007 TGTGCTGCCAACACATGAGT 60.466 50.000 0.00 0.00 42.88 3.41
4325 6232 2.590575 GCCAAGCCGCGCCTATTA 60.591 61.111 0.00 0.00 0.00 0.98
4507 7442 9.762933 ACAACATAAACTTTAATTGTCTTGCAT 57.237 25.926 8.00 0.00 0.00 3.96
4508 7443 9.243637 GACAACATAAACTTTAATTGTCTTGCA 57.756 29.630 21.45 0.00 41.61 4.08
4520 7455 7.016268 TCCTACCTCTGAGACAACATAAACTTT 59.984 37.037 6.17 0.00 0.00 2.66
4551 7486 4.351111 ACCACCTTGTTAGATTTCAGGAGT 59.649 41.667 0.00 0.00 0.00 3.85
4555 7492 6.207417 ACATCAACCACCTTGTTAGATTTCAG 59.793 38.462 0.00 0.00 0.00 3.02
4570 7507 9.080097 AGGATATTCTAGTAGTACATCAACCAC 57.920 37.037 2.52 0.00 0.00 4.16
4617 7557 6.223138 TCACTAACACACGTCATTCAAATC 57.777 37.500 0.00 0.00 0.00 2.17
4628 7568 7.009440 CACTCAAATAACATCACTAACACACG 58.991 38.462 0.00 0.00 0.00 4.49
4667 7607 8.032952 TGAAGCAGTTACATTGTTCAGATTAG 57.967 34.615 0.00 0.00 0.00 1.73
4698 7642 2.453521 AGATGCAGCACCATGTGATTT 58.546 42.857 4.07 0.00 35.23 2.17
4819 7989 3.683365 TCATGCACTCAAAGCTCACTA 57.317 42.857 0.00 0.00 0.00 2.74
4852 8022 5.888161 AGCAAATGTAGCTATTTTAGGCAGT 59.112 36.000 0.00 0.00 41.32 4.40
4854 8024 6.122277 AGAGCAAATGTAGCTATTTTAGGCA 58.878 36.000 0.00 0.00 43.58 4.75
4895 8065 7.881142 TCGTTTCAAATACATCTTCAAACCAT 58.119 30.769 0.00 0.00 0.00 3.55
4951 8121 1.599797 AGCGCCAACCTTGTACCAC 60.600 57.895 2.29 0.00 0.00 4.16
4952 8122 1.599518 CAGCGCCAACCTTGTACCA 60.600 57.895 2.29 0.00 0.00 3.25
4977 8148 1.468506 TAGAGTGCCGCAAGTGACCA 61.469 55.000 0.00 0.00 0.00 4.02
5129 9638 6.370994 TCAAAAATAAACAATGATGCCGCAAT 59.629 30.769 0.00 0.00 0.00 3.56
5229 9738 2.805671 CTGCTAAACATGTGTCAACGGA 59.194 45.455 0.00 0.00 0.00 4.69
5236 9745 2.949177 TGGGTCTGCTAAACATGTGT 57.051 45.000 0.00 0.00 0.00 3.72
5241 9750 3.838565 TGGAAATTGGGTCTGCTAAACA 58.161 40.909 0.00 0.00 0.00 2.83
5247 9756 2.415893 CGACAATGGAAATTGGGTCTGC 60.416 50.000 3.70 0.00 35.93 4.26
5262 9771 5.527582 AGAACAAAACAGCTAGAACGACAAT 59.472 36.000 0.00 0.00 0.00 2.71
5313 9822 9.958180 ATTGACCCCCAAATTAGAAAATTAAAG 57.042 29.630 0.00 0.00 38.43 1.85
5327 9836 3.008485 GCACCATAAAATTGACCCCCAAA 59.992 43.478 0.00 0.00 38.43 3.28
5343 9852 2.495155 TTACATGAGCTGTGCACCAT 57.505 45.000 15.69 7.46 38.92 3.55
5369 9878 4.518970 AGTGCAATTGGTACGAATGAAACT 59.481 37.500 7.72 5.43 37.18 2.66
5386 9895 3.550639 CGATTTTGCTTGGAAGAGTGCAA 60.551 43.478 0.00 0.00 42.60 4.08
5390 9899 4.082571 CCATTCGATTTTGCTTGGAAGAGT 60.083 41.667 0.00 0.00 0.00 3.24
5407 9916 0.167908 TTTGCTTGCGCTACCATTCG 59.832 50.000 9.73 0.00 36.97 3.34
5418 9927 5.734035 GTCAAACAAGAACAATTTTGCTTGC 59.266 36.000 11.58 0.00 40.94 4.01
5465 9974 4.820897 TGTTGTGGTTTTGTGCAATTACA 58.179 34.783 0.00 0.00 0.00 2.41
5466 9975 5.982465 ATGTTGTGGTTTTGTGCAATTAC 57.018 34.783 0.00 0.00 0.00 1.89
5484 9993 3.806380 TGCAAATGAAGCCACAAATGTT 58.194 36.364 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.