Multiple sequence alignment - TraesCS6B01G377300

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 TraesCS6B01G377300 chr6B 100.000 3853 0 0 1 3853 652523961 652520109 0.000000e+00 7116.0
1 TraesCS6B01G377300 chr6B 92.754 828 57 1 3029 3853 652508667 652507840 0.000000e+00 1194.0
2 TraesCS6B01G377300 chr6B 85.000 440 51 5 2490 2914 652902935 652903374 2.130000e-117 433.0
3 TraesCS6B01G377300 chr6B 87.805 82 10 0 2919 3000 652903418 652903499 3.170000e-16 97.1
4 TraesCS6B01G377300 chr6B 92.857 42 2 1 2990 3030 652903518 652903559 4.160000e-05 60.2
5 TraesCS6B01G377300 chr6A 94.806 1829 67 11 1141 2962 578701817 578700010 0.000000e+00 2826.0
6 TraesCS6B01G377300 chr6A 86.904 1657 174 20 1284 2914 578926053 578927692 0.000000e+00 1818.0
7 TraesCS6B01G377300 chr6A 88.935 723 47 13 1 718 578703420 578702726 0.000000e+00 861.0
8 TraesCS6B01G377300 chr6A 84.211 285 19 11 745 1023 578702464 578702200 1.780000e-63 254.0
9 TraesCS6B01G377300 chr6A 84.541 207 27 2 2713 2914 578931226 578931432 2.350000e-47 200.0
10 TraesCS6B01G377300 chr6A 85.859 99 14 0 2902 3000 578927712 578927810 5.260000e-19 106.0
11 TraesCS6B01G377300 chr6A 84.615 91 10 3 2606 2692 578931136 578931226 1.910000e-13 87.9
12 TraesCS6B01G377300 chr6A 82.418 91 14 2 693 783 338118931 338119019 1.150000e-10 78.7
13 TraesCS6B01G377300 chr6A 91.489 47 2 2 2985 3030 578699832 578699787 3.210000e-06 63.9
14 TraesCS6B01G377300 chr6D 92.519 1671 85 10 1304 2953 432672678 432671027 0.000000e+00 2357.0
15 TraesCS6B01G377300 chr6D 85.101 1725 179 29 1284 2987 432810579 432812246 0.000000e+00 1690.0
16 TraesCS6B01G377300 chr6D 92.821 390 21 2 182 568 432673343 432672958 3.360000e-155 558.0
17 TraesCS6B01G377300 chr6D 87.171 304 33 3 2617 2914 432815739 432816042 1.330000e-89 340.0
18 TraesCS6B01G377300 chr6D 97.810 137 3 0 1 137 432673476 432673340 1.790000e-58 237.0
19 TraesCS6B01G377300 chr6D 86.735 196 4 7 857 1035 432672946 432672756 8.440000e-47 198.0
20 TraesCS6B01G377300 chr6D 100.000 68 0 0 1022 1089 432672740 432672673 4.040000e-25 126.0
21 TraesCS6B01G377300 chr3B 80.344 1745 256 46 1284 3006 463458376 463456697 0.000000e+00 1242.0
22 TraesCS6B01G377300 chr3B 88.530 837 81 11 3029 3853 117804471 117803638 0.000000e+00 1000.0
23 TraesCS6B01G377300 chr3B 87.665 835 91 9 3029 3853 14200050 14199218 0.000000e+00 961.0
24 TraesCS6B01G377300 chr3B 82.614 903 116 26 1284 2180 455509540 455510407 0.000000e+00 760.0
25 TraesCS6B01G377300 chr1D 79.496 1746 253 54 1284 3000 198167298 198168967 0.000000e+00 1144.0
26 TraesCS6B01G377300 chr1D 88.608 395 33 7 171 564 328875965 328875582 1.620000e-128 470.0
27 TraesCS6B01G377300 chr1D 87.121 396 39 8 171 565 222737790 222737406 4.570000e-119 438.0
28 TraesCS6B01G377300 chr2B 90.264 832 74 5 3026 3853 528036891 528037719 0.000000e+00 1081.0
29 TraesCS6B01G377300 chr2B 87.154 397 38 10 171 565 772373414 772373029 4.570000e-119 438.0
30 TraesCS6B01G377300 chr1B 87.890 834 87 12 3029 3853 274576653 274575825 0.000000e+00 968.0
31 TraesCS6B01G377300 chr1B 87.066 835 95 11 3026 3853 529102535 529103363 0.000000e+00 931.0
32 TraesCS6B01G377300 chr1B 84.524 84 12 1 693 776 585242623 585242541 8.870000e-12 82.4
33 TraesCS6B01G377300 chr4B 87.500 832 91 9 3029 3853 126720506 126719681 0.000000e+00 948.0
34 TraesCS6B01G377300 chr4B 87.232 838 89 12 3026 3853 133642054 133642883 0.000000e+00 939.0
35 TraesCS6B01G377300 chr4B 87.216 837 90 12 3026 3853 476179305 476180133 0.000000e+00 937.0
36 TraesCS6B01G377300 chr4B 76.179 1272 242 41 1284 2540 477371617 477370392 7.070000e-172 614.0
37 TraesCS6B01G377300 chr4B 76.119 1273 241 43 1284 2540 477389556 477388331 3.290000e-170 608.0
38 TraesCS6B01G377300 chr4B 83.721 86 10 3 693 778 34574310 34574229 1.150000e-10 78.7
39 TraesCS6B01G377300 chr4B 82.759 87 14 1 693 779 552777639 552777554 4.130000e-10 76.8
40 TraesCS6B01G377300 chr4B 80.220 91 14 2 692 779 402764571 402764660 8.940000e-07 65.8
41 TraesCS6B01G377300 chr7A 81.003 1137 154 33 1231 2346 471814483 471813388 0.000000e+00 846.0
42 TraesCS6B01G377300 chr7A 88.342 386 35 7 180 564 651951151 651950775 4.540000e-124 455.0
43 TraesCS6B01G377300 chr2D 89.896 386 29 8 171 551 540321711 540321331 4.470000e-134 488.0
44 TraesCS6B01G377300 chr4D 89.717 389 29 6 178 565 310115941 310115563 1.610000e-133 486.0
45 TraesCS6B01G377300 chr4D 90.196 51 5 0 729 779 487289838 487289888 2.480000e-07 67.6
46 TraesCS6B01G377300 chr4D 86.538 52 7 0 2669 2720 442428646 442428697 1.500000e-04 58.4
47 TraesCS6B01G377300 chr1A 88.442 398 33 9 171 567 425711053 425710668 5.830000e-128 468.0
48 TraesCS6B01G377300 chr5B 84.270 89 11 3 692 779 325085902 325085816 2.470000e-12 84.2
49 TraesCS6B01G377300 chr5B 81.053 95 15 3 685 779 602243646 602243737 5.340000e-09 73.1


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 TraesCS6B01G377300 chr6B 652520109 652523961 3852 True 7116.000 7116 100.00000 1 3853 1 chr6B.!!$R2 3852
1 TraesCS6B01G377300 chr6B 652507840 652508667 827 True 1194.000 1194 92.75400 3029 3853 1 chr6B.!!$R1 824
2 TraesCS6B01G377300 chr6A 578699787 578703420 3633 True 1001.225 2826 89.86025 1 3030 4 chr6A.!!$R1 3029
3 TraesCS6B01G377300 chr6A 578926053 578931432 5379 False 552.975 1818 85.47975 1284 3000 4 chr6A.!!$F2 1716
4 TraesCS6B01G377300 chr6D 432810579 432816042 5463 False 1015.000 1690 86.13600 1284 2987 2 chr6D.!!$F1 1703
5 TraesCS6B01G377300 chr6D 432671027 432673476 2449 True 695.200 2357 93.97700 1 2953 5 chr6D.!!$R1 2952
6 TraesCS6B01G377300 chr3B 463456697 463458376 1679 True 1242.000 1242 80.34400 1284 3006 1 chr3B.!!$R3 1722
7 TraesCS6B01G377300 chr3B 117803638 117804471 833 True 1000.000 1000 88.53000 3029 3853 1 chr3B.!!$R2 824
8 TraesCS6B01G377300 chr3B 14199218 14200050 832 True 961.000 961 87.66500 3029 3853 1 chr3B.!!$R1 824
9 TraesCS6B01G377300 chr3B 455509540 455510407 867 False 760.000 760 82.61400 1284 2180 1 chr3B.!!$F1 896
10 TraesCS6B01G377300 chr1D 198167298 198168967 1669 False 1144.000 1144 79.49600 1284 3000 1 chr1D.!!$F1 1716
11 TraesCS6B01G377300 chr2B 528036891 528037719 828 False 1081.000 1081 90.26400 3026 3853 1 chr2B.!!$F1 827
12 TraesCS6B01G377300 chr1B 274575825 274576653 828 True 968.000 968 87.89000 3029 3853 1 chr1B.!!$R1 824
13 TraesCS6B01G377300 chr1B 529102535 529103363 828 False 931.000 931 87.06600 3026 3853 1 chr1B.!!$F1 827
14 TraesCS6B01G377300 chr4B 126719681 126720506 825 True 948.000 948 87.50000 3029 3853 1 chr4B.!!$R2 824
15 TraesCS6B01G377300 chr4B 133642054 133642883 829 False 939.000 939 87.23200 3026 3853 1 chr4B.!!$F1 827
16 TraesCS6B01G377300 chr4B 476179305 476180133 828 False 937.000 937 87.21600 3026 3853 1 chr4B.!!$F3 827
17 TraesCS6B01G377300 chr4B 477370392 477371617 1225 True 614.000 614 76.17900 1284 2540 1 chr4B.!!$R3 1256
18 TraesCS6B01G377300 chr4B 477388331 477389556 1225 True 608.000 608 76.11900 1284 2540 1 chr4B.!!$R4 1256
19 TraesCS6B01G377300 chr7A 471813388 471814483 1095 True 846.000 846 81.00300 1231 2346 1 chr7A.!!$R1 1115

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
162 164 0.377554 TTACCCAACAAACGTGCGTG 59.622 50.0 0.0 0.0 0.0 5.34 F
1114 1400 0.191064 TCTTCCACCCAGACAGACCT 59.809 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1123 1409 0.107703 TGAGAAATGAATCCGCCGCT 60.108 50.0 0.0 0.0 0.00 5.52 R
3067 3865 0.110678 TGGGTATGTTTTGCGTCCCA 59.889 50.0 0.0 0.0 41.96 4.37 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
112 113 9.959749 GTTTGATTTGTAGTGGAGTTCAATTTA 57.040 29.630 0.00 0.00 0.00 1.40
155 157 8.760569 CAAACATGACTATTTTACCCAACAAAC 58.239 33.333 0.00 0.00 0.00 2.93
156 158 6.674066 ACATGACTATTTTACCCAACAAACG 58.326 36.000 0.00 0.00 0.00 3.60
157 159 6.263617 ACATGACTATTTTACCCAACAAACGT 59.736 34.615 0.00 0.00 0.00 3.99
158 160 6.062434 TGACTATTTTACCCAACAAACGTG 57.938 37.500 0.00 0.00 0.00 4.49
159 161 4.862350 ACTATTTTACCCAACAAACGTGC 58.138 39.130 0.00 0.00 0.00 5.34
160 162 2.190325 TTTTACCCAACAAACGTGCG 57.810 45.000 0.00 0.00 0.00 5.34
161 163 1.093159 TTTACCCAACAAACGTGCGT 58.907 45.000 0.00 0.00 0.00 5.24
162 164 0.377554 TTACCCAACAAACGTGCGTG 59.622 50.000 0.00 0.00 0.00 5.34
212 216 1.487558 GGTTACCGCCCCAGAATTAGA 59.512 52.381 0.00 0.00 0.00 2.10
279 283 2.703536 AGGATTTTCAAGGGCCGTTTTT 59.296 40.909 8.25 0.00 0.00 1.94
328 332 1.862602 AACCAATTGCTTCGACGGCC 61.863 55.000 0.00 0.00 0.00 6.13
377 381 2.487934 CTGATATCAAGGAGTTGGCGG 58.512 52.381 6.90 0.00 34.09 6.13
408 412 2.987149 CGTCTGTTCGCTTTAGTCATGT 59.013 45.455 0.00 0.00 0.00 3.21
409 413 4.083164 TCGTCTGTTCGCTTTAGTCATGTA 60.083 41.667 0.00 0.00 0.00 2.29
433 437 4.637873 TCGTTTGTCGATGTCGCA 57.362 50.000 0.00 0.00 44.01 5.10
434 438 2.888218 TCGTTTGTCGATGTCGCAA 58.112 47.368 0.00 3.27 44.01 4.85
456 460 7.362142 CGCAACACATATCCTAGCTAGATCTTA 60.362 40.741 22.70 8.11 0.00 2.10
557 564 7.667043 TCAATAAAGCGCGATATTATTCCTT 57.333 32.000 12.10 0.00 29.24 3.36
588 597 6.827586 ACGTATATGTGTTGACCCAAAAAT 57.172 33.333 0.00 0.00 0.00 1.82
592 601 8.455682 CGTATATGTGTTGACCCAAAAATAACT 58.544 33.333 0.00 0.00 0.00 2.24
595 604 4.404073 TGTGTTGACCCAAAAATAACTGCT 59.596 37.500 0.00 0.00 0.00 4.24
598 607 7.151976 GTGTTGACCCAAAAATAACTGCTATT 58.848 34.615 0.00 0.00 0.00 1.73
599 608 7.655732 GTGTTGACCCAAAAATAACTGCTATTT 59.344 33.333 0.00 0.00 41.16 1.40
620 629 2.572209 TTTGAGGGGTAAAGGAACCG 57.428 50.000 0.00 0.00 40.73 4.44
625 634 2.723322 GGGGTAAAGGAACCGCTATT 57.277 50.000 3.09 0.00 46.23 1.73
626 635 3.008835 GGGGTAAAGGAACCGCTATTT 57.991 47.619 3.09 0.00 46.23 1.40
627 636 2.947652 GGGGTAAAGGAACCGCTATTTC 59.052 50.000 3.09 0.00 46.23 2.17
628 637 3.371273 GGGGTAAAGGAACCGCTATTTCT 60.371 47.826 3.09 0.00 46.23 2.52
629 638 4.141642 GGGGTAAAGGAACCGCTATTTCTA 60.142 45.833 3.09 0.00 46.23 2.10
630 639 5.055144 GGGTAAAGGAACCGCTATTTCTAG 58.945 45.833 0.00 0.00 40.73 2.43
631 640 5.055144 GGTAAAGGAACCGCTATTTCTAGG 58.945 45.833 0.00 0.00 0.00 3.02
632 641 5.163374 GGTAAAGGAACCGCTATTTCTAGGA 60.163 44.000 0.00 0.00 0.00 2.94
676 685 5.463724 CCAAGCAAGGAGACGTAGATATTTC 59.536 44.000 0.00 0.00 0.00 2.17
678 687 4.649674 AGCAAGGAGACGTAGATATTTCCA 59.350 41.667 0.00 0.00 0.00 3.53
680 689 5.635700 GCAAGGAGACGTAGATATTTCCATC 59.364 44.000 0.00 0.00 0.00 3.51
681 690 6.738731 GCAAGGAGACGTAGATATTTCCATCA 60.739 42.308 0.00 0.00 0.00 3.07
682 691 6.978674 AGGAGACGTAGATATTTCCATCAA 57.021 37.500 0.00 0.00 0.00 2.57
683 692 7.361457 AGGAGACGTAGATATTTCCATCAAA 57.639 36.000 0.00 0.00 0.00 2.69
684 693 7.792032 AGGAGACGTAGATATTTCCATCAAAA 58.208 34.615 0.00 0.00 0.00 2.44
772 1017 4.056050 CGTCTTAAATTATGGGACGGAGG 58.944 47.826 12.35 0.00 43.69 4.30
774 1019 4.102054 GTCTTAAATTATGGGACGGAGGGA 59.898 45.833 0.00 0.00 0.00 4.20
783 1028 1.904537 GGGACGGAGGGAGTAGAAAAA 59.095 52.381 0.00 0.00 0.00 1.94
837 1082 4.803426 GAGCGCTCCCACTCCGTG 62.803 72.222 27.22 0.00 0.00 4.94
885 1130 4.574527 TTTTGAATTGCACACAAACACG 57.425 36.364 10.33 0.00 39.77 4.49
894 1139 3.365220 TGCACACAAACACGTTTTAAAGC 59.635 39.130 0.00 0.00 0.00 3.51
941 1187 2.579787 CGATTCCGAGCGCGTCTT 60.580 61.111 8.43 0.00 38.22 3.01
942 1188 2.568912 CGATTCCGAGCGCGTCTTC 61.569 63.158 8.43 2.43 38.22 2.87
943 1189 1.226717 GATTCCGAGCGCGTCTTCT 60.227 57.895 8.43 0.00 35.23 2.85
944 1190 1.203600 GATTCCGAGCGCGTCTTCTC 61.204 60.000 8.43 4.52 35.23 2.87
945 1191 2.615262 ATTCCGAGCGCGTCTTCTCC 62.615 60.000 8.43 0.00 35.23 3.71
947 1193 2.578178 CGAGCGCGTCTTCTCCTG 60.578 66.667 8.43 0.00 0.00 3.86
948 1194 2.202676 GAGCGCGTCTTCTCCTGG 60.203 66.667 8.43 0.00 0.00 4.45
949 1195 2.676822 AGCGCGTCTTCTCCTGGA 60.677 61.111 8.43 0.00 0.00 3.86
951 1197 1.590259 GCGCGTCTTCTCCTGGATC 60.590 63.158 8.43 0.00 0.00 3.36
956 1203 2.275318 CGTCTTCTCCTGGATCTTTGC 58.725 52.381 0.00 0.00 0.00 3.68
1087 1373 1.369625 GGAGGCACACCGTCTAAATG 58.630 55.000 0.00 0.00 42.76 2.32
1088 1374 1.338769 GGAGGCACACCGTCTAAATGT 60.339 52.381 0.00 0.00 42.76 2.71
1089 1375 1.732259 GAGGCACACCGTCTAAATGTG 59.268 52.381 0.00 0.00 45.29 3.21
1090 1376 1.346395 AGGCACACCGTCTAAATGTGA 59.654 47.619 7.74 0.00 45.34 3.58
1091 1377 2.027192 AGGCACACCGTCTAAATGTGAT 60.027 45.455 7.74 0.00 45.34 3.06
1092 1378 2.747446 GGCACACCGTCTAAATGTGATT 59.253 45.455 7.74 0.00 45.34 2.57
1093 1379 3.190535 GGCACACCGTCTAAATGTGATTT 59.809 43.478 7.74 0.00 45.34 2.17
1094 1380 4.320935 GGCACACCGTCTAAATGTGATTTT 60.321 41.667 7.74 0.00 45.34 1.82
1095 1381 5.219633 GCACACCGTCTAAATGTGATTTTT 58.780 37.500 7.74 0.00 45.34 1.94
1096 1382 5.342259 GCACACCGTCTAAATGTGATTTTTC 59.658 40.000 7.74 0.00 45.34 2.29
1097 1383 6.668323 CACACCGTCTAAATGTGATTTTTCT 58.332 36.000 0.00 0.00 45.34 2.52
1098 1384 7.138736 CACACCGTCTAAATGTGATTTTTCTT 58.861 34.615 0.00 0.00 45.34 2.52
1099 1385 7.323656 CACACCGTCTAAATGTGATTTTTCTTC 59.676 37.037 0.00 0.00 45.34 2.87
1100 1386 6.801862 CACCGTCTAAATGTGATTTTTCTTCC 59.198 38.462 0.00 0.00 33.82 3.46
1101 1387 6.488683 ACCGTCTAAATGTGATTTTTCTTCCA 59.511 34.615 0.00 0.00 33.82 3.53
1102 1388 6.801862 CCGTCTAAATGTGATTTTTCTTCCAC 59.198 38.462 0.00 0.00 33.82 4.02
1103 1389 6.801862 CGTCTAAATGTGATTTTTCTTCCACC 59.198 38.462 0.00 0.00 33.82 4.61
1104 1390 7.090808 GTCTAAATGTGATTTTTCTTCCACCC 58.909 38.462 0.00 0.00 33.82 4.61
1105 1391 5.885449 AAATGTGATTTTTCTTCCACCCA 57.115 34.783 0.00 0.00 0.00 4.51
1106 1392 5.473066 AATGTGATTTTTCTTCCACCCAG 57.527 39.130 0.00 0.00 0.00 4.45
1107 1393 4.177537 TGTGATTTTTCTTCCACCCAGA 57.822 40.909 0.00 0.00 0.00 3.86
1108 1394 3.888930 TGTGATTTTTCTTCCACCCAGAC 59.111 43.478 0.00 0.00 0.00 3.51
1109 1395 3.888930 GTGATTTTTCTTCCACCCAGACA 59.111 43.478 0.00 0.00 0.00 3.41
1110 1396 4.022849 GTGATTTTTCTTCCACCCAGACAG 60.023 45.833 0.00 0.00 0.00 3.51
1111 1397 3.943671 TTTTTCTTCCACCCAGACAGA 57.056 42.857 0.00 0.00 0.00 3.41
1112 1398 2.930826 TTTCTTCCACCCAGACAGAC 57.069 50.000 0.00 0.00 0.00 3.51
1113 1399 1.056660 TTCTTCCACCCAGACAGACC 58.943 55.000 0.00 0.00 0.00 3.85
1114 1400 0.191064 TCTTCCACCCAGACAGACCT 59.809 55.000 0.00 0.00 0.00 3.85
1115 1401 0.322975 CTTCCACCCAGACAGACCTG 59.677 60.000 0.00 0.00 0.00 4.00
1121 1407 2.973899 CAGACAGACCTGGGACGG 59.026 66.667 0.00 0.00 34.19 4.79
1122 1408 2.997897 AGACAGACCTGGGACGGC 60.998 66.667 0.00 0.00 34.19 5.68
1123 1409 3.311110 GACAGACCTGGGACGGCA 61.311 66.667 0.00 0.00 34.19 5.69
1124 1410 3.302347 GACAGACCTGGGACGGCAG 62.302 68.421 0.00 0.00 34.19 4.85
1125 1411 4.767255 CAGACCTGGGACGGCAGC 62.767 72.222 0.00 0.00 0.00 5.25
1137 1423 3.211963 GGCAGCGGCGGATTCATT 61.212 61.111 9.78 0.00 42.47 2.57
1138 1424 2.774799 GGCAGCGGCGGATTCATTT 61.775 57.895 9.78 0.00 42.47 2.32
1139 1425 1.298638 GCAGCGGCGGATTCATTTC 60.299 57.895 9.78 0.00 0.00 2.17
1161 1683 0.689745 AATTCGATCTGGGGGTCGGA 60.690 55.000 0.00 0.00 38.34 4.55
1187 1709 2.120232 CGCCAGCGTGAGATTAAGTAG 58.880 52.381 3.35 0.00 34.35 2.57
1198 1720 4.344102 TGAGATTAAGTAGATTGGGGACGG 59.656 45.833 0.00 0.00 0.00 4.79
1199 1721 3.646637 AGATTAAGTAGATTGGGGACGGG 59.353 47.826 0.00 0.00 0.00 5.28
1864 2431 1.112113 GTCCTCCGCAGACTCCATTA 58.888 55.000 0.00 0.00 0.00 1.90
1924 2494 3.550431 CCGACCCGGGCTCATCAT 61.550 66.667 24.08 0.00 44.15 2.45
1925 2495 2.029666 CGACCCGGGCTCATCATC 59.970 66.667 24.08 7.81 0.00 2.92
1926 2496 2.796193 CGACCCGGGCTCATCATCA 61.796 63.158 24.08 0.00 0.00 3.07
1965 2535 3.758554 ACACAGGATTCTATGTTTGGTGC 59.241 43.478 0.00 0.00 23.05 5.01
2047 2626 2.287487 GCTATACCCTCCGAGACGAAAC 60.287 54.545 0.00 0.00 0.00 2.78
2068 2647 0.790814 GAAACGGACCGCAAGAGAAG 59.209 55.000 15.39 0.00 43.02 2.85
2118 2697 1.803519 CTGCTGACCGCGAAGTCTC 60.804 63.158 8.23 4.66 43.27 3.36
2192 2774 2.381911 CAGCTCCTTATGCAAATGGGT 58.618 47.619 0.00 0.00 0.00 4.51
2206 2792 2.832643 ATGGGTCAGAATGGAATGCA 57.167 45.000 0.00 0.00 36.16 3.96
2225 2811 2.149803 ATTGGACTGGTCGCGACGAA 62.150 55.000 30.99 21.09 37.72 3.85
2266 2855 0.684535 TGGATCTGAACAGCCAACGA 59.315 50.000 0.00 0.00 0.00 3.85
2268 2860 2.499693 TGGATCTGAACAGCCAACGATA 59.500 45.455 0.00 0.00 0.00 2.92
2274 2866 3.202906 TGAACAGCCAACGATATAAGCC 58.797 45.455 0.00 0.00 0.00 4.35
2281 2873 3.055385 GCCAACGATATAAGCCTATCCCA 60.055 47.826 0.00 0.00 0.00 4.37
2336 2928 2.583593 GCGACCGATGCCTGTCTC 60.584 66.667 0.00 0.00 0.00 3.36
2347 2939 1.304509 GCCTGTCTCTTTCAGCCAGC 61.305 60.000 0.00 0.00 0.00 4.85
2358 2950 1.523258 CAGCCAGCGATCTCCCTTG 60.523 63.158 0.00 0.00 0.00 3.61
2359 2951 2.203126 GCCAGCGATCTCCCTTGG 60.203 66.667 0.00 0.00 0.00 3.61
2360 2952 2.507944 CCAGCGATCTCCCTTGGG 59.492 66.667 0.00 0.00 0.00 4.12
2382 2974 3.126000 GTGAGCAGCAACTCCATTTACTC 59.874 47.826 0.00 0.00 35.72 2.59
2411 3003 1.351017 CACAGTACCCCATTCTGGTGT 59.649 52.381 0.00 0.00 36.57 4.16
2418 3010 1.308998 CCCATTCTGGTGTATTCGCC 58.691 55.000 0.00 0.00 43.87 5.54
2469 3061 2.552599 TCCTGCCAAATACACGACAA 57.447 45.000 0.00 0.00 0.00 3.18
2932 3575 2.358898 GGCACACTGTTTGTTGATCTGT 59.641 45.455 0.00 0.00 35.67 3.41
3067 3865 3.121030 GTTGGCATGAGCGAGCGT 61.121 61.111 0.00 0.00 43.41 5.07
3123 4422 3.271225 TGGAGAGATAACACCCCTAGTCA 59.729 47.826 0.00 0.00 0.00 3.41
3130 4429 0.691078 ACACCCCTAGTCATGCCGAT 60.691 55.000 0.00 0.00 0.00 4.18
3190 4489 2.103941 CTGTATGGAGGAAGAAGGGAGC 59.896 54.545 0.00 0.00 0.00 4.70
3238 4540 1.674057 GGTGTGCTCTACTGGCTGT 59.326 57.895 1.74 1.74 0.00 4.40
3285 4595 0.317160 CTTGCCCGTATATGCGAGGA 59.683 55.000 15.21 0.00 35.70 3.71
3500 5231 0.035881 AGTCGAGTCGGGTACAGTGA 59.964 55.000 13.54 0.00 0.00 3.41
3606 5583 4.374702 GCACTGTTGCCACGCTCG 62.375 66.667 0.00 0.00 43.66 5.03
3607 5584 2.661537 CACTGTTGCCACGCTCGA 60.662 61.111 0.00 0.00 0.00 4.04
3762 7161 1.328279 GTTGGGGAAGTCTTGGTTGG 58.672 55.000 0.00 0.00 0.00 3.77
3763 7162 0.930726 TTGGGGAAGTCTTGGTTGGT 59.069 50.000 0.00 0.00 0.00 3.67
3767 7166 0.395312 GGAAGTCTTGGTTGGTCCGA 59.605 55.000 0.00 0.00 39.52 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.320683 GGGATGGCAGGTTTTGTTGC 60.321 55.000 0.00 0.00 39.56 4.17
146 148 0.456995 AAACACGCACGTTTGTTGGG 60.457 50.000 7.52 0.00 37.69 4.12
176 180 0.033504 AACCTCGACAACATGCTCGT 59.966 50.000 7.64 0.00 0.00 4.18
212 216 2.511600 GTAGCGCCGGTGCTTCAT 60.512 61.111 44.16 25.03 44.46 2.57
377 381 0.703466 CGAACAGACGAGAAGAACGC 59.297 55.000 0.00 0.00 35.09 4.84
433 437 9.760926 TCATAAGATCTAGCTAGGATATGTGTT 57.239 33.333 20.58 7.57 0.00 3.32
434 438 9.407380 CTCATAAGATCTAGCTAGGATATGTGT 57.593 37.037 20.58 1.71 0.00 3.72
509 516 9.194972 TGATCAAGTATAATCAGAAGAGAGTGT 57.805 33.333 0.00 0.00 0.00 3.55
599 608 3.224269 CGGTTCCTTTACCCCTCAAAAA 58.776 45.455 0.00 0.00 34.56 1.94
601 610 1.546099 GCGGTTCCTTTACCCCTCAAA 60.546 52.381 0.00 0.00 34.56 2.69
602 611 0.037160 GCGGTTCCTTTACCCCTCAA 59.963 55.000 0.00 0.00 34.56 3.02
603 612 0.838987 AGCGGTTCCTTTACCCCTCA 60.839 55.000 0.00 0.00 34.56 3.86
604 613 1.197812 TAGCGGTTCCTTTACCCCTC 58.802 55.000 0.00 0.00 34.56 4.30
605 614 1.889174 ATAGCGGTTCCTTTACCCCT 58.111 50.000 0.00 0.00 34.56 4.79
606 615 2.723322 AATAGCGGTTCCTTTACCCC 57.277 50.000 0.00 0.00 34.56 4.95
607 616 3.882444 AGAAATAGCGGTTCCTTTACCC 58.118 45.455 0.00 0.00 34.56 3.69
608 617 5.055144 CCTAGAAATAGCGGTTCCTTTACC 58.945 45.833 0.00 0.00 34.72 2.85
609 618 5.910614 TCCTAGAAATAGCGGTTCCTTTAC 58.089 41.667 0.00 0.00 0.00 2.01
610 619 6.549433 TTCCTAGAAATAGCGGTTCCTTTA 57.451 37.500 0.00 0.00 0.00 1.85
611 620 5.431179 TTCCTAGAAATAGCGGTTCCTTT 57.569 39.130 0.00 0.00 0.00 3.11
612 621 5.189145 TCTTTCCTAGAAATAGCGGTTCCTT 59.811 40.000 0.00 0.00 0.00 3.36
613 622 4.715297 TCTTTCCTAGAAATAGCGGTTCCT 59.285 41.667 0.00 0.00 0.00 3.36
614 623 5.019785 TCTTTCCTAGAAATAGCGGTTCC 57.980 43.478 0.00 0.00 0.00 3.62
615 624 6.980051 TTTCTTTCCTAGAAATAGCGGTTC 57.020 37.500 0.00 0.00 45.60 3.62
625 634 6.927381 CGGACACTAGTTTTTCTTTCCTAGAA 59.073 38.462 0.00 0.00 41.11 2.10
626 635 6.266103 TCGGACACTAGTTTTTCTTTCCTAGA 59.734 38.462 0.00 0.00 32.93 2.43
627 636 6.365518 GTCGGACACTAGTTTTTCTTTCCTAG 59.634 42.308 2.62 0.00 34.44 3.02
628 637 6.218746 GTCGGACACTAGTTTTTCTTTCCTA 58.781 40.000 2.62 0.00 0.00 2.94
629 638 5.055144 GTCGGACACTAGTTTTTCTTTCCT 58.945 41.667 2.62 0.00 0.00 3.36
630 639 4.212847 GGTCGGACACTAGTTTTTCTTTCC 59.787 45.833 10.76 0.00 0.00 3.13
631 640 4.812626 TGGTCGGACACTAGTTTTTCTTTC 59.187 41.667 10.76 0.00 0.00 2.62
632 641 4.773013 TGGTCGGACACTAGTTTTTCTTT 58.227 39.130 10.76 0.00 0.00 2.52
749 994 4.442472 CCTCCGTCCCATAATTTAAGACGT 60.442 45.833 17.96 0.00 46.62 4.34
751 996 4.102054 TCCCTCCGTCCCATAATTTAAGAC 59.898 45.833 0.00 0.00 0.00 3.01
755 1000 3.660959 ACTCCCTCCGTCCCATAATTTA 58.339 45.455 0.00 0.00 0.00 1.40
757 1002 2.191981 ACTCCCTCCGTCCCATAATT 57.808 50.000 0.00 0.00 0.00 1.40
763 1008 1.565067 TTTTCTACTCCCTCCGTCCC 58.435 55.000 0.00 0.00 0.00 4.46
783 1028 3.570125 GCCTTTCTAAGTGTCCTTGCTTT 59.430 43.478 0.00 0.00 31.89 3.51
787 1032 2.437413 GGGCCTTTCTAAGTGTCCTTG 58.563 52.381 0.84 0.00 31.89 3.61
796 1041 1.988015 CTGGGTCGGGCCTTTCTAA 59.012 57.895 0.84 0.00 37.43 2.10
847 1092 2.629639 AAAAGATTTAACCCGCTGCG 57.370 45.000 16.34 16.34 0.00 5.18
848 1093 3.908213 TCAAAAAGATTTAACCCGCTGC 58.092 40.909 0.00 0.00 0.00 5.25
849 1094 6.618379 GCAATTCAAAAAGATTTAACCCGCTG 60.618 38.462 0.00 0.00 0.00 5.18
850 1095 5.408299 GCAATTCAAAAAGATTTAACCCGCT 59.592 36.000 0.00 0.00 0.00 5.52
851 1096 5.178438 TGCAATTCAAAAAGATTTAACCCGC 59.822 36.000 0.00 0.00 0.00 6.13
852 1097 6.201806 TGTGCAATTCAAAAAGATTTAACCCG 59.798 34.615 0.00 0.00 0.00 5.28
853 1098 7.011857 TGTGTGCAATTCAAAAAGATTTAACCC 59.988 33.333 0.00 0.00 0.00 4.11
854 1099 7.914465 TGTGTGCAATTCAAAAAGATTTAACC 58.086 30.769 0.00 0.00 0.00 2.85
855 1100 9.766277 TTTGTGTGCAATTCAAAAAGATTTAAC 57.234 25.926 8.91 0.00 34.18 2.01
885 1130 7.781548 TCCCGAGTATAATGAGCTTTAAAAC 57.218 36.000 0.00 0.00 0.00 2.43
941 1187 1.205655 CGTCTGCAAAGATCCAGGAGA 59.794 52.381 0.00 0.00 0.00 3.71
942 1188 1.649664 CGTCTGCAAAGATCCAGGAG 58.350 55.000 0.00 0.00 0.00 3.69
943 1189 0.250234 CCGTCTGCAAAGATCCAGGA 59.750 55.000 0.00 0.00 0.00 3.86
944 1190 0.745845 CCCGTCTGCAAAGATCCAGG 60.746 60.000 0.00 0.00 0.00 4.45
945 1191 0.250234 TCCCGTCTGCAAAGATCCAG 59.750 55.000 0.00 0.00 0.00 3.86
947 1193 1.740025 CTTTCCCGTCTGCAAAGATCC 59.260 52.381 0.00 0.00 29.96 3.36
948 1194 1.740025 CCTTTCCCGTCTGCAAAGATC 59.260 52.381 0.00 0.00 29.96 2.75
949 1195 1.073923 ACCTTTCCCGTCTGCAAAGAT 59.926 47.619 0.00 0.00 29.96 2.40
951 1197 0.875059 GACCTTTCCCGTCTGCAAAG 59.125 55.000 0.00 0.00 0.00 2.77
956 1203 3.335579 CCTTTAAGACCTTTCCCGTCTG 58.664 50.000 0.00 0.00 39.69 3.51
1087 1373 3.888930 TGTCTGGGTGGAAGAAAAATCAC 59.111 43.478 0.00 0.00 0.00 3.06
1088 1374 4.141274 TCTGTCTGGGTGGAAGAAAAATCA 60.141 41.667 0.00 0.00 0.00 2.57
1089 1375 4.216472 GTCTGTCTGGGTGGAAGAAAAATC 59.784 45.833 0.00 0.00 0.00 2.17
1090 1376 4.145052 GTCTGTCTGGGTGGAAGAAAAAT 58.855 43.478 0.00 0.00 0.00 1.82
1091 1377 3.551846 GTCTGTCTGGGTGGAAGAAAAA 58.448 45.455 0.00 0.00 0.00 1.94
1092 1378 2.158667 GGTCTGTCTGGGTGGAAGAAAA 60.159 50.000 0.00 0.00 0.00 2.29
1093 1379 1.420138 GGTCTGTCTGGGTGGAAGAAA 59.580 52.381 0.00 0.00 0.00 2.52
1094 1380 1.056660 GGTCTGTCTGGGTGGAAGAA 58.943 55.000 0.00 0.00 0.00 2.52
1095 1381 0.191064 AGGTCTGTCTGGGTGGAAGA 59.809 55.000 0.00 0.00 0.00 2.87
1096 1382 0.322975 CAGGTCTGTCTGGGTGGAAG 59.677 60.000 0.00 0.00 0.00 3.46
1097 1383 2.452116 CAGGTCTGTCTGGGTGGAA 58.548 57.895 0.00 0.00 0.00 3.53
1098 1384 4.215370 CAGGTCTGTCTGGGTGGA 57.785 61.111 0.00 0.00 0.00 4.02
1104 1390 2.973899 CCGTCCCAGGTCTGTCTG 59.026 66.667 0.00 0.00 34.70 3.51
1105 1391 2.997897 GCCGTCCCAGGTCTGTCT 60.998 66.667 0.00 0.00 0.00 3.41
1106 1392 3.302347 CTGCCGTCCCAGGTCTGTC 62.302 68.421 0.00 0.00 0.00 3.51
1107 1393 3.314331 CTGCCGTCCCAGGTCTGT 61.314 66.667 0.00 0.00 0.00 3.41
1108 1394 4.767255 GCTGCCGTCCCAGGTCTG 62.767 72.222 0.00 0.00 33.44 3.51
1120 1406 2.668261 GAAATGAATCCGCCGCTGCC 62.668 60.000 0.00 0.00 0.00 4.85
1121 1407 1.298638 GAAATGAATCCGCCGCTGC 60.299 57.895 0.00 0.00 0.00 5.25
1122 1408 0.305922 GAGAAATGAATCCGCCGCTG 59.694 55.000 0.00 0.00 0.00 5.18
1123 1409 0.107703 TGAGAAATGAATCCGCCGCT 60.108 50.000 0.00 0.00 0.00 5.52
1124 1410 0.732571 TTGAGAAATGAATCCGCCGC 59.267 50.000 0.00 0.00 0.00 6.53
1125 1411 3.621794 GAATTGAGAAATGAATCCGCCG 58.378 45.455 0.00 0.00 0.00 6.46
1126 1412 3.312421 TCGAATTGAGAAATGAATCCGCC 59.688 43.478 0.00 0.00 0.00 6.13
1127 1413 4.536364 TCGAATTGAGAAATGAATCCGC 57.464 40.909 0.00 0.00 0.00 5.54
1128 1414 6.361114 CAGATCGAATTGAGAAATGAATCCG 58.639 40.000 0.00 0.00 0.00 4.18
1129 1415 6.293845 CCCAGATCGAATTGAGAAATGAATCC 60.294 42.308 0.00 0.00 0.00 3.01
1130 1416 6.293845 CCCCAGATCGAATTGAGAAATGAATC 60.294 42.308 0.00 0.00 0.00 2.52
1131 1417 5.533903 CCCCAGATCGAATTGAGAAATGAAT 59.466 40.000 0.00 0.00 0.00 2.57
1132 1418 4.883585 CCCCAGATCGAATTGAGAAATGAA 59.116 41.667 0.00 0.00 0.00 2.57
1133 1419 4.454678 CCCCAGATCGAATTGAGAAATGA 58.545 43.478 0.00 0.00 0.00 2.57
1134 1420 3.567164 CCCCCAGATCGAATTGAGAAATG 59.433 47.826 0.00 0.00 0.00 2.32
1135 1421 3.203040 ACCCCCAGATCGAATTGAGAAAT 59.797 43.478 0.00 0.00 0.00 2.17
1136 1422 2.576191 ACCCCCAGATCGAATTGAGAAA 59.424 45.455 0.00 0.00 0.00 2.52
1137 1423 2.170607 GACCCCCAGATCGAATTGAGAA 59.829 50.000 0.00 0.00 0.00 2.87
1138 1424 1.762957 GACCCCCAGATCGAATTGAGA 59.237 52.381 0.00 0.00 0.00 3.27
1139 1425 1.539065 CGACCCCCAGATCGAATTGAG 60.539 57.143 0.00 0.00 40.86 3.02
1187 1709 0.981277 TCTCCTTCCCGTCCCCAATC 60.981 60.000 0.00 0.00 0.00 2.67
1198 1720 5.395879 GGACTTACTTGGATCTTCTCCTTCC 60.396 48.000 0.00 0.00 45.21 3.46
1199 1721 5.187967 TGGACTTACTTGGATCTTCTCCTTC 59.812 44.000 0.00 0.00 45.21 3.46
1357 1897 3.601685 CGCCCAGCCACCGTTTTT 61.602 61.111 0.00 0.00 0.00 1.94
1921 2491 2.402564 GAGGACCTCCCAATCTGATGA 58.597 52.381 10.74 0.00 37.41 2.92
1922 2492 1.419387 GGAGGACCTCCCAATCTGATG 59.581 57.143 28.16 0.00 44.36 3.07
1923 2493 1.813102 GGAGGACCTCCCAATCTGAT 58.187 55.000 28.16 0.00 44.36 2.90
1924 2494 3.324246 GGAGGACCTCCCAATCTGA 57.676 57.895 28.16 0.00 44.36 3.27
1946 2516 2.355756 CGGCACCAAACATAGAATCCTG 59.644 50.000 0.00 0.00 0.00 3.86
1965 2535 3.064324 CTTGGAAGGGCAAGGCGG 61.064 66.667 0.00 0.00 0.00 6.13
2051 2630 0.319641 GACTTCTCTTGCGGTCCGTT 60.320 55.000 13.94 0.00 0.00 4.44
2052 2631 1.179814 AGACTTCTCTTGCGGTCCGT 61.180 55.000 13.94 0.00 0.00 4.69
2068 2647 1.002430 TGAGCAATCACCACCAGAGAC 59.998 52.381 0.00 0.00 0.00 3.36
2118 2697 5.581085 CCAGACTCCACGAGGTAAAAATTAG 59.419 44.000 0.00 0.00 33.35 1.73
2192 2774 3.697542 CAGTCCAATGCATTCCATTCTGA 59.302 43.478 9.53 0.00 42.15 3.27
2206 2792 2.126071 CGTCGCGACCAGTCCAAT 60.126 61.111 31.84 0.00 0.00 3.16
2225 2811 2.323599 TGCATAGAGCCTGCAGACTAT 58.676 47.619 17.39 16.78 44.30 2.12
2266 2855 5.188751 GCTCTTCACTGGGATAGGCTTATAT 59.811 44.000 0.00 0.00 0.00 0.86
2268 2860 3.326297 GCTCTTCACTGGGATAGGCTTAT 59.674 47.826 0.00 0.00 0.00 1.73
2274 2866 3.900601 ACCTATGCTCTTCACTGGGATAG 59.099 47.826 0.00 0.00 33.30 2.08
2281 2873 1.478510 CGGTCACCTATGCTCTTCACT 59.521 52.381 0.00 0.00 0.00 3.41
2336 2928 0.813210 GGGAGATCGCTGGCTGAAAG 60.813 60.000 0.00 0.00 0.00 2.62
2347 2939 1.144936 GCTCACCCAAGGGAGATCG 59.855 63.158 13.15 0.00 38.96 3.69
2358 2950 0.610232 AATGGAGTTGCTGCTCACCC 60.610 55.000 0.00 2.77 37.24 4.61
2359 2951 1.251251 AAATGGAGTTGCTGCTCACC 58.749 50.000 0.00 3.29 37.24 4.02
2360 2952 3.077359 AGTAAATGGAGTTGCTGCTCAC 58.923 45.455 0.00 0.00 37.24 3.51
2382 2974 1.192428 GGGGTACTGTGGTAGAGTGG 58.808 60.000 0.00 0.00 0.00 4.00
2411 3003 1.555477 AAACCAGTCCCCGGCGAATA 61.555 55.000 9.30 0.00 0.00 1.75
2418 3010 0.320771 CTCAGACAAACCAGTCCCCG 60.321 60.000 0.00 0.00 39.34 5.73
2434 3026 0.543277 AGGAATCTGCCAATCGCTCA 59.457 50.000 0.00 0.00 38.78 4.26
3067 3865 0.110678 TGGGTATGTTTTGCGTCCCA 59.889 50.000 0.00 0.00 41.96 4.37
3123 4422 2.294233 GCATATCAACCACAATCGGCAT 59.706 45.455 0.00 0.00 0.00 4.40
3130 4429 7.066887 CCTTGTACTATTGCATATCAACCACAA 59.933 37.037 0.00 0.00 37.53 3.33
3238 4540 1.671054 GCGCACAGGAACTAGCCAA 60.671 57.895 0.30 0.00 36.02 4.52
3314 4624 4.938575 AACATTACCATTGTACCCCTGA 57.061 40.909 0.00 0.00 0.00 3.86
3500 5231 4.057428 GCCGACCTGACAGAGCGT 62.057 66.667 3.32 0.00 0.00 5.07
3606 5583 2.124403 CATGCCCCTGGTCAGCTC 60.124 66.667 0.00 0.00 0.00 4.09
3607 5584 3.736224 CCATGCCCCTGGTCAGCT 61.736 66.667 0.00 0.00 0.00 4.24
3762 7161 0.868406 CAAGACAGCCAAACTCGGAC 59.132 55.000 0.00 0.00 0.00 4.79
3763 7162 0.468226 ACAAGACAGCCAAACTCGGA 59.532 50.000 0.00 0.00 0.00 4.55
3767 7166 2.172717 ACCAGTACAAGACAGCCAAACT 59.827 45.455 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.