Multiple sequence alignment - TraesCS3D01G304000

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 TraesCS3D01G304000 chr3D 100.000 3112 0 0 1 3112 418483985 418480874 0.000000e+00 5747.0
1 TraesCS3D01G304000 chr3D 97.112 658 18 1 2456 3112 418704839 418704182 0.000000e+00 1109.0
2 TraesCS3D01G304000 chr3D 93.643 645 29 3 1359 1992 418705530 418704887 0.000000e+00 953.0
3 TraesCS3D01G304000 chr3D 85.065 462 36 10 1 440 418417559 418417109 1.020000e-119 440.0
4 TraesCS3D01G304000 chr3D 90.882 340 11 8 1740 2079 418410256 418409937 3.680000e-119 438.0
5 TraesCS3D01G304000 chr3D 88.705 363 30 7 1359 1710 418410726 418410364 1.710000e-117 433.0
6 TraesCS3D01G304000 chr3D 91.844 282 20 2 1429 1707 416404365 416404646 1.050000e-104 390.0
7 TraesCS3D01G304000 chr3D 87.398 246 16 5 671 910 418411103 418410867 5.120000e-68 268.0
8 TraesCS3D01G304000 chr3B 92.833 879 37 18 2079 2955 545001698 545000844 0.000000e+00 1251.0
9 TraesCS3D01G304000 chr3B 95.593 658 27 2 2456 3112 544898778 544898122 0.000000e+00 1053.0
10 TraesCS3D01G304000 chr3B 94.786 537 26 2 1359 1895 544922208 544921674 0.000000e+00 835.0
11 TraesCS3D01G304000 chr3B 93.110 537 35 2 1359 1895 545008853 545008319 0.000000e+00 785.0
12 TraesCS3D01G304000 chr3B 90.064 624 24 14 555 1155 544922812 544922204 0.000000e+00 774.0
13 TraesCS3D01G304000 chr3B 95.518 357 15 1 2079 2435 544899207 544898852 1.250000e-158 569.0
14 TraesCS3D01G304000 chr3B 93.460 367 18 4 1713 2079 544818780 544818420 9.820000e-150 540.0
15 TraesCS3D01G304000 chr3B 83.107 515 43 20 1 483 544923800 544923298 2.220000e-116 429.0
16 TraesCS3D01G304000 chr3B 88.154 363 32 9 1 363 544822544 544822193 3.710000e-114 422.0
17 TraesCS3D01G304000 chr3B 92.073 164 13 0 2949 3112 544999274 544999111 6.710000e-57 231.0
18 TraesCS3D01G304000 chr3B 96.063 127 3 2 1938 2064 545008318 545008194 4.070000e-49 206.0
19 TraesCS3D01G304000 chr3B 93.939 132 5 3 1938 2069 544921673 544921545 2.450000e-46 196.0
20 TraesCS3D01G304000 chr3B 89.865 148 11 3 1566 1710 544819027 544818881 1.470000e-43 187.0
21 TraesCS3D01G304000 chr3B 100.000 31 0 0 2431 2461 544898830 544898800 1.210000e-04 58.4
22 TraesCS3D01G304000 chrUn 95.593 658 27 2 2456 3112 351404279 351404935 0.000000e+00 1053.0
23 TraesCS3D01G304000 chrUn 95.518 357 15 1 2079 2435 351403850 351404205 1.250000e-158 569.0
24 TraesCS3D01G304000 chrUn 100.000 31 0 0 2431 2461 351404227 351404257 1.210000e-04 58.4
25 TraesCS3D01G304000 chr3A 92.890 436 26 3 1359 1790 532488343 532488777 2.040000e-176 628.0
26 TraesCS3D01G304000 chr3A 88.071 394 31 10 1 390 532641301 532641682 1.320000e-123 453.0
27 TraesCS3D01G304000 chr3A 83.570 493 62 9 673 1155 532487864 532488347 7.920000e-121 444.0
28 TraesCS3D01G304000 chr3A 88.618 369 21 9 1712 2079 532644944 532645292 2.220000e-116 429.0
29 TraesCS3D01G304000 chr3A 86.667 240 24 3 1359 1598 532644548 532644779 3.080000e-65 259.0
30 TraesCS3D01G304000 chr3A 91.860 172 11 3 26 196 534177412 534177243 1.440000e-58 237.0
31 TraesCS3D01G304000 chr3A 88.177 203 14 3 649 850 532644150 532644343 1.870000e-57 233.0
32 TraesCS3D01G304000 chr3A 85.253 217 16 8 612 821 534167933 534167726 3.140000e-50 209.0
33 TraesCS3D01G304000 chr3A 91.818 110 9 0 2994 3103 532490784 532490893 1.490000e-33 154.0
34 TraesCS3D01G304000 chr3A 84.000 150 15 6 128 277 532627267 532627407 5.410000e-28 135.0
35 TraesCS3D01G304000 chr5B 83.133 498 67 13 2471 2955 19743957 19744450 3.680000e-119 438.0
36 TraesCS3D01G304000 chr4A 82.157 510 75 13 2458 2955 666951736 666952241 1.030000e-114 424.0
37 TraesCS3D01G304000 chr4A 80.924 498 83 10 2468 2955 17897410 17897905 1.750000e-102 383.0
38 TraesCS3D01G304000 chr7D 81.781 494 77 12 2472 2955 52354407 52354897 4.830000e-108 401.0
39 TraesCS3D01G304000 chr7D 80.336 417 67 10 2472 2877 52474003 52474415 5.040000e-78 302.0
40 TraesCS3D01G304000 chr7D 97.917 48 1 0 504 551 6442863 6442910 1.990000e-12 84.2
41 TraesCS3D01G304000 chr7D 93.878 49 1 2 2951 2999 194802095 194802141 4.300000e-09 73.1
42 TraesCS3D01G304000 chr5D 81.452 496 76 14 2472 2955 27354487 27354978 2.910000e-105 392.0
43 TraesCS3D01G304000 chr5D 95.652 46 1 1 2954 2999 44636015 44636059 4.300000e-09 73.1
44 TraesCS3D01G304000 chr4D 96.985 199 6 0 1160 1358 455910586 455910388 4.970000e-88 335.0
45 TraesCS3D01G304000 chr4D 98.947 95 1 0 1264 1358 455914169 455914075 1.480000e-38 171.0
46 TraesCS3D01G304000 chr4D 93.478 46 2 1 2954 2999 96610228 96610272 2.000000e-07 67.6
47 TraesCS3D01G304000 chr7B 95.238 189 9 0 1158 1346 509602525 509602337 1.810000e-77 300.0
48 TraesCS3D01G304000 chr7B 100.000 35 0 0 1298 1332 509605109 509605143 7.200000e-07 65.8
49 TraesCS3D01G304000 chr7A 80.753 239 36 8 2472 2703 54851755 54851990 8.870000e-41 178.0
50 TraesCS3D01G304000 chr7A 90.291 103 6 2 1257 1358 1494110 1494011 7.000000e-27 132.0
51 TraesCS3D01G304000 chr2A 96.809 94 3 0 1265 1358 223510245 223510338 1.160000e-34 158.0
52 TraesCS3D01G304000 chr6B 88.889 99 7 2 1257 1355 713948638 713948544 5.450000e-23 119.0
53 TraesCS3D01G304000 chr1D 95.652 46 1 1 2954 2999 455634918 455634874 4.300000e-09 73.1
54 TraesCS3D01G304000 chr6D 88.136 59 4 3 2953 3010 60324343 60324399 2.000000e-07 67.6


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 TraesCS3D01G304000 chr3D 418480874 418483985 3111 True 5747.000000 5747 100.00000 1 3112 1 chr3D.!!$R2 3111
1 TraesCS3D01G304000 chr3D 418704182 418705530 1348 True 1031.000000 1109 95.37750 1359 3112 2 chr3D.!!$R4 1753
2 TraesCS3D01G304000 chr3D 418409937 418411103 1166 True 379.666667 438 88.99500 671 2079 3 chr3D.!!$R3 1408
3 TraesCS3D01G304000 chr3B 544999111 545001698 2587 True 741.000000 1251 92.45300 2079 3112 2 chr3B.!!$R4 1033
4 TraesCS3D01G304000 chr3B 544898122 544899207 1085 True 560.133333 1053 97.03700 2079 3112 3 chr3B.!!$R2 1033
5 TraesCS3D01G304000 chr3B 544921545 544923800 2255 True 558.500000 835 90.47400 1 2069 4 chr3B.!!$R3 2068
6 TraesCS3D01G304000 chr3B 545008194 545008853 659 True 495.500000 785 94.58650 1359 2064 2 chr3B.!!$R5 705
7 TraesCS3D01G304000 chr3B 544818420 544822544 4124 True 383.000000 540 90.49300 1 2079 3 chr3B.!!$R1 2078
8 TraesCS3D01G304000 chrUn 351403850 351404935 1085 False 560.133333 1053 97.03700 2079 3112 3 chrUn.!!$F1 1033
9 TraesCS3D01G304000 chr3A 532487864 532490893 3029 False 408.666667 628 89.42600 673 3103 3 chr3A.!!$F2 2430
10 TraesCS3D01G304000 chr3A 532641301 532645292 3991 False 343.500000 453 87.88325 1 2079 4 chr3A.!!$F3 2078
11 TraesCS3D01G304000 chr4A 666951736 666952241 505 False 424.000000 424 82.15700 2458 2955 1 chr4A.!!$F2 497
12 TraesCS3D01G304000 chr4D 455910388 455914169 3781 True 253.000000 335 97.96600 1160 1358 2 chr4D.!!$R1 198

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
791 3205 0.034896 TGGTTCTCGCCTCCAAGTTC 59.965 55.0 0.00 0.0 0.0 3.01 F
1222 3700 0.171455 CTCTACCAGGTGCTCACGTC 59.829 60.0 0.76 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 6325 1.594293 CCTGGCACTCGTCAACGTT 60.594 57.895 0.0 0.0 40.8 3.99 R
3045 13635 1.529438 CTTGCACTTTTTCGTCCGCTA 59.471 47.619 0.0 0.0 0.0 4.26 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
95 96 3.342627 CGCGTCAAACCGGCAGAA 61.343 61.111 0.00 0.00 0.00 3.02
96 97 2.887889 CGCGTCAAACCGGCAGAAA 61.888 57.895 0.00 0.00 0.00 2.52
116 117 5.655532 AGAAATCATGGAAAGAGACAATGGG 59.344 40.000 0.00 0.00 0.00 4.00
119 120 4.996793 TCATGGAAAGAGACAATGGGAAA 58.003 39.130 0.00 0.00 0.00 3.13
146 147 3.455910 ACATAGGCTCTATTGACTTGCCA 59.544 43.478 8.26 0.00 45.42 4.92
186 187 4.264543 CGCAAGTAGTGAGGCTAAATTG 57.735 45.455 0.00 0.00 34.38 2.32
192 193 7.096065 GCAAGTAGTGAGGCTAAATTGTTTTTG 60.096 37.037 0.00 0.00 34.05 2.44
193 194 7.582667 AGTAGTGAGGCTAAATTGTTTTTGT 57.417 32.000 0.00 0.00 0.00 2.83
194 195 7.425606 AGTAGTGAGGCTAAATTGTTTTTGTG 58.574 34.615 0.00 0.00 0.00 3.33
195 196 6.220726 AGTGAGGCTAAATTGTTTTTGTGT 57.779 33.333 0.00 0.00 0.00 3.72
196 197 6.042143 AGTGAGGCTAAATTGTTTTTGTGTG 58.958 36.000 0.00 0.00 0.00 3.82
197 198 5.810074 GTGAGGCTAAATTGTTTTTGTGTGT 59.190 36.000 0.00 0.00 0.00 3.72
198 199 5.809562 TGAGGCTAAATTGTTTTTGTGTGTG 59.190 36.000 0.00 0.00 0.00 3.82
199 200 5.729510 AGGCTAAATTGTTTTTGTGTGTGT 58.270 33.333 0.00 0.00 0.00 3.72
200 201 5.580297 AGGCTAAATTGTTTTTGTGTGTGTG 59.420 36.000 0.00 0.00 0.00 3.82
479 525 4.142838 TGAGAACAATTTATGTGCAGCGAG 60.143 41.667 0.00 0.00 42.99 5.03
492 538 3.114693 GCAGCGAGCATTAGATATTGC 57.885 47.619 0.00 0.00 44.79 3.56
494 540 3.126514 GCAGCGAGCATTAGATATTGCAT 59.873 43.478 8.85 0.00 44.79 3.96
495 541 4.648970 CAGCGAGCATTAGATATTGCATG 58.351 43.478 8.85 0.00 41.35 4.06
497 543 5.349543 CAGCGAGCATTAGATATTGCATGTA 59.650 40.000 8.85 0.00 41.35 2.29
498 544 5.579904 AGCGAGCATTAGATATTGCATGTAG 59.420 40.000 8.85 0.00 41.35 2.74
499 545 5.578336 GCGAGCATTAGATATTGCATGTAGA 59.422 40.000 8.85 0.00 41.35 2.59
500 546 6.091305 GCGAGCATTAGATATTGCATGTAGAA 59.909 38.462 8.85 0.00 41.35 2.10
502 548 8.167345 CGAGCATTAGATATTGCATGTAGAAAG 58.833 37.037 8.85 0.00 41.35 2.62
503 549 8.332996 AGCATTAGATATTGCATGTAGAAAGG 57.667 34.615 8.85 0.00 41.35 3.11
505 551 7.308770 GCATTAGATATTGCATGTAGAAAGGCA 60.309 37.037 0.00 0.00 38.72 4.75
506 552 7.734924 TTAGATATTGCATGTAGAAAGGCAG 57.265 36.000 0.00 0.00 37.59 4.85
508 554 0.804364 TTGCATGTAGAAAGGCAGCG 59.196 50.000 0.00 0.00 37.59 5.18
510 556 1.718757 GCATGTAGAAAGGCAGCGGG 61.719 60.000 0.00 0.00 0.00 6.13
511 557 1.097547 CATGTAGAAAGGCAGCGGGG 61.098 60.000 0.00 0.00 0.00 5.73
512 558 1.562672 ATGTAGAAAGGCAGCGGGGT 61.563 55.000 0.00 0.00 0.00 4.95
513 559 1.745489 GTAGAAAGGCAGCGGGGTG 60.745 63.158 0.00 0.00 0.00 4.61
514 560 3.622060 TAGAAAGGCAGCGGGGTGC 62.622 63.158 14.06 14.06 46.98 5.01
524 2846 3.319198 CGGGGTGCAGTACAGGGT 61.319 66.667 0.00 0.00 0.00 4.34
534 2856 2.015587 CAGTACAGGGTCCTCTACGAC 58.984 57.143 0.00 0.00 0.00 4.34
548 2870 4.098654 CCTCTACGACTTCATCATGGTCTT 59.901 45.833 0.00 0.00 0.00 3.01
551 2873 4.478206 ACGACTTCATCATGGTCTTCAT 57.522 40.909 0.00 0.00 36.31 2.57
553 2875 4.081476 ACGACTTCATCATGGTCTTCATCA 60.081 41.667 0.00 0.00 32.92 3.07
635 3044 1.402456 GCACGGTATATGTAGGAGGCG 60.402 57.143 0.00 0.00 0.00 5.52
729 3138 5.993748 AAAGAAGTTCACTGGGTCAAAAA 57.006 34.783 5.50 0.00 0.00 1.94
791 3205 0.034896 TGGTTCTCGCCTCCAAGTTC 59.965 55.000 0.00 0.00 0.00 3.01
939 3358 1.815817 AAACGCCATTCCCAGTTGCC 61.816 55.000 0.00 0.00 0.00 4.52
994 3416 1.267632 CGAAGAGCTAGTTCTCGACCG 60.268 57.143 9.78 7.69 38.12 4.79
1074 3552 0.886043 GTGAGCATGGCCGCATCATA 60.886 55.000 5.37 0.00 0.00 2.15
1105 3583 3.475774 GTGTTCGCGGCGTTCGAT 61.476 61.111 22.90 0.00 42.43 3.59
1155 3633 2.900838 GCTGCGGCTCTGCATGAT 60.901 61.111 11.21 0.00 45.26 2.45
1156 3634 3.023118 CTGCGGCTCTGCATGATG 58.977 61.111 3.60 0.00 45.26 3.07
1157 3635 1.818363 CTGCGGCTCTGCATGATGT 60.818 57.895 3.60 0.00 45.26 3.06
1158 3636 2.048312 CTGCGGCTCTGCATGATGTG 62.048 60.000 3.60 0.00 45.26 3.21
1159 3637 1.816679 GCGGCTCTGCATGATGTGA 60.817 57.895 0.00 0.00 34.15 3.58
1160 3638 1.371337 GCGGCTCTGCATGATGTGAA 61.371 55.000 0.00 0.00 34.15 3.18
1161 3639 0.656259 CGGCTCTGCATGATGTGAAG 59.344 55.000 0.00 0.00 34.45 3.02
1162 3640 1.747709 GGCTCTGCATGATGTGAAGT 58.252 50.000 0.00 0.00 34.78 3.01
1163 3641 2.089980 GGCTCTGCATGATGTGAAGTT 58.910 47.619 0.00 0.00 34.78 2.66
1164 3642 2.097142 GGCTCTGCATGATGTGAAGTTC 59.903 50.000 0.00 0.00 34.78 3.01
1165 3643 2.097142 GCTCTGCATGATGTGAAGTTCC 59.903 50.000 0.00 0.00 34.78 3.62
1166 3644 2.349590 TCTGCATGATGTGAAGTTCCG 58.650 47.619 0.00 0.00 34.78 4.30
1167 3645 2.079158 CTGCATGATGTGAAGTTCCGT 58.921 47.619 0.00 0.00 0.00 4.69
1168 3646 2.076100 TGCATGATGTGAAGTTCCGTC 58.924 47.619 0.00 3.85 0.00 4.79
1169 3647 2.289631 TGCATGATGTGAAGTTCCGTCT 60.290 45.455 0.00 0.00 0.00 4.18
1170 3648 3.056179 TGCATGATGTGAAGTTCCGTCTA 60.056 43.478 0.00 0.00 0.00 2.59
1171 3649 3.553511 GCATGATGTGAAGTTCCGTCTAG 59.446 47.826 0.00 2.22 0.00 2.43
1172 3650 4.678044 GCATGATGTGAAGTTCCGTCTAGA 60.678 45.833 0.00 0.00 0.00 2.43
1173 3651 5.595885 CATGATGTGAAGTTCCGTCTAGAT 58.404 41.667 0.00 0.00 0.00 1.98
1174 3652 5.250235 TGATGTGAAGTTCCGTCTAGATC 57.750 43.478 0.00 0.00 0.00 2.75
1175 3653 3.759527 TGTGAAGTTCCGTCTAGATCG 57.240 47.619 0.00 1.64 0.00 3.69
1176 3654 3.340928 TGTGAAGTTCCGTCTAGATCGA 58.659 45.455 13.90 0.00 0.00 3.59
1177 3655 3.945921 TGTGAAGTTCCGTCTAGATCGAT 59.054 43.478 13.90 0.00 0.00 3.59
1178 3656 4.398358 TGTGAAGTTCCGTCTAGATCGATT 59.602 41.667 13.90 0.00 0.00 3.34
1179 3657 4.971220 GTGAAGTTCCGTCTAGATCGATTC 59.029 45.833 13.90 12.04 0.00 2.52
1180 3658 3.881780 AGTTCCGTCTAGATCGATTCG 57.118 47.619 13.90 0.00 0.00 3.34
1181 3659 3.204526 AGTTCCGTCTAGATCGATTCGT 58.795 45.455 13.90 0.00 0.00 3.85
1182 3660 3.626670 AGTTCCGTCTAGATCGATTCGTT 59.373 43.478 13.90 0.00 0.00 3.85
1183 3661 3.874400 TCCGTCTAGATCGATTCGTTC 57.126 47.619 13.90 7.47 0.00 3.95
1184 3662 2.547211 TCCGTCTAGATCGATTCGTTCC 59.453 50.000 12.31 1.35 0.00 3.62
1185 3663 2.561922 CGTCTAGATCGATTCGTTCCG 58.438 52.381 12.31 6.39 0.00 4.30
1186 3664 2.220363 CGTCTAGATCGATTCGTTCCGA 59.780 50.000 12.31 7.72 39.25 4.55
1187 3665 3.120615 CGTCTAGATCGATTCGTTCCGAT 60.121 47.826 12.31 0.00 46.67 4.18
1191 3669 2.991434 ATCGATTCGTTCCGATCGAT 57.009 45.000 18.66 18.79 43.42 3.59
1192 3670 2.311450 TCGATTCGTTCCGATCGATC 57.689 50.000 18.66 15.68 39.15 3.69
1193 3671 1.600485 TCGATTCGTTCCGATCGATCA 59.400 47.619 24.40 3.68 39.15 2.92
1194 3672 2.032426 TCGATTCGTTCCGATCGATCAA 59.968 45.455 24.40 9.94 39.15 2.57
1195 3673 2.402049 CGATTCGTTCCGATCGATCAAG 59.598 50.000 24.40 15.07 38.27 3.02
1196 3674 3.629058 GATTCGTTCCGATCGATCAAGA 58.371 45.455 24.40 17.06 37.18 3.02
1197 3675 2.757686 TCGTTCCGATCGATCAAGAG 57.242 50.000 24.40 11.45 32.30 2.85
1198 3676 1.124462 CGTTCCGATCGATCAAGAGC 58.876 55.000 24.40 19.18 0.00 4.09
1199 3677 1.268794 CGTTCCGATCGATCAAGAGCT 60.269 52.381 24.40 0.00 0.00 4.09
1200 3678 2.031944 CGTTCCGATCGATCAAGAGCTA 60.032 50.000 24.40 4.06 0.00 3.32
1201 3679 3.560503 GTTCCGATCGATCAAGAGCTAG 58.439 50.000 24.40 6.01 0.00 3.42
1202 3680 1.537638 TCCGATCGATCAAGAGCTAGC 59.462 52.381 24.40 6.62 0.00 3.42
1203 3681 1.402194 CCGATCGATCAAGAGCTAGCC 60.402 57.143 24.40 2.81 0.00 3.93
1204 3682 1.539388 CGATCGATCAAGAGCTAGCCT 59.461 52.381 24.40 5.44 0.00 4.58
1205 3683 2.414029 CGATCGATCAAGAGCTAGCCTC 60.414 54.545 24.40 8.54 41.07 4.70
1213 3691 3.524346 GAGCTAGCCTCTACCAGGT 57.476 57.895 12.13 0.00 45.61 4.00
1214 3692 1.036707 GAGCTAGCCTCTACCAGGTG 58.963 60.000 12.13 0.00 45.61 4.00
1215 3693 1.045911 AGCTAGCCTCTACCAGGTGC 61.046 60.000 12.13 0.00 45.61 5.01
1216 3694 1.045911 GCTAGCCTCTACCAGGTGCT 61.046 60.000 2.29 4.73 45.61 4.40
1217 3695 1.036707 CTAGCCTCTACCAGGTGCTC 58.963 60.000 0.76 0.00 45.61 4.26
1218 3696 0.335019 TAGCCTCTACCAGGTGCTCA 59.665 55.000 0.76 0.00 45.61 4.26
1219 3697 1.219393 GCCTCTACCAGGTGCTCAC 59.781 63.158 0.76 0.00 45.61 3.51
1220 3698 1.513158 CCTCTACCAGGTGCTCACG 59.487 63.158 0.76 0.00 37.53 4.35
1221 3699 1.251527 CCTCTACCAGGTGCTCACGT 61.252 60.000 0.76 0.00 37.53 4.49
1222 3700 0.171455 CTCTACCAGGTGCTCACGTC 59.829 60.000 0.76 0.00 0.00 4.34
1223 3701 0.251209 TCTACCAGGTGCTCACGTCT 60.251 55.000 0.76 0.00 0.00 4.18
1224 3702 0.171455 CTACCAGGTGCTCACGTCTC 59.829 60.000 0.76 0.00 0.00 3.36
1225 3703 1.583495 TACCAGGTGCTCACGTCTCG 61.583 60.000 0.76 0.00 0.00 4.04
1226 3704 2.645567 CAGGTGCTCACGTCTCGT 59.354 61.111 0.00 0.00 42.36 4.18
1227 3705 1.583495 CCAGGTGCTCACGTCTCGTA 61.583 60.000 0.00 0.00 38.32 3.43
1228 3706 0.454620 CAGGTGCTCACGTCTCGTAC 60.455 60.000 0.00 0.00 38.32 3.67
1247 3725 3.784701 ACGTGAAGTACTGGCTAGATG 57.215 47.619 3.17 0.00 0.00 2.90
1248 3726 3.090037 ACGTGAAGTACTGGCTAGATGT 58.910 45.455 3.17 0.00 0.00 3.06
1249 3727 3.119459 ACGTGAAGTACTGGCTAGATGTG 60.119 47.826 3.17 0.00 0.00 3.21
1250 3728 3.119459 CGTGAAGTACTGGCTAGATGTGT 60.119 47.826 3.17 0.00 0.00 3.72
1251 3729 4.177026 GTGAAGTACTGGCTAGATGTGTG 58.823 47.826 3.17 0.00 0.00 3.82
1252 3730 2.969628 AGTACTGGCTAGATGTGTGC 57.030 50.000 3.17 0.00 0.00 4.57
1253 3731 1.482593 AGTACTGGCTAGATGTGTGCC 59.517 52.381 3.17 0.00 46.26 5.01
1254 3732 1.482593 GTACTGGCTAGATGTGTGCCT 59.517 52.381 3.17 0.00 46.23 4.75
1255 3733 0.251354 ACTGGCTAGATGTGTGCCTG 59.749 55.000 3.17 11.70 46.23 4.85
1256 3734 1.078214 TGGCTAGATGTGTGCCTGC 60.078 57.895 9.45 0.00 46.23 4.85
1257 3735 1.078214 GGCTAGATGTGTGCCTGCA 60.078 57.895 0.00 0.00 43.05 4.41
1258 3736 1.372087 GGCTAGATGTGTGCCTGCAC 61.372 60.000 15.15 15.15 46.33 4.57
1259 3737 0.392193 GCTAGATGTGTGCCTGCACT 60.392 55.000 21.62 3.08 46.30 4.40
1260 3738 1.366679 CTAGATGTGTGCCTGCACTG 58.633 55.000 21.62 2.00 46.30 3.66
1261 3739 0.686789 TAGATGTGTGCCTGCACTGT 59.313 50.000 21.62 8.71 46.30 3.55
1262 3740 0.686789 AGATGTGTGCCTGCACTGTA 59.313 50.000 21.62 9.41 46.30 2.74
1263 3741 1.081892 GATGTGTGCCTGCACTGTAG 58.918 55.000 21.62 0.00 46.30 2.74
1264 3742 0.686789 ATGTGTGCCTGCACTGTAGA 59.313 50.000 21.62 2.41 46.30 2.59
1265 3743 0.686789 TGTGTGCCTGCACTGTAGAT 59.313 50.000 21.62 0.00 46.30 1.98
1266 3744 1.338105 TGTGTGCCTGCACTGTAGATC 60.338 52.381 21.62 5.86 46.30 2.75
1267 3745 0.975887 TGTGCCTGCACTGTAGATCA 59.024 50.000 21.62 0.00 46.30 2.92
1457 6046 1.079750 GTTGCTGGACGAGGAGGAC 60.080 63.158 0.00 0.00 0.00 3.85
1532 6121 0.461339 GCAAAGAGGCGTTCGGGATA 60.461 55.000 0.00 0.00 0.00 2.59
1608 6325 3.402681 GGCTAGGGCTGCACCTGA 61.403 66.667 16.79 0.00 42.02 3.86
1613 6330 1.764571 TAGGGCTGCACCTGAACGTT 61.765 55.000 16.79 0.00 42.02 3.99
1694 7388 3.692593 TCGACGAGTTCAAGACCATGATA 59.307 43.478 0.00 0.00 0.00 2.15
2045 9269 4.771114 TCCAACATACCTGGTCCTAATG 57.229 45.455 0.63 3.99 35.30 1.90
2240 9464 6.614694 TCAGCTAGGAAATGGTACTTACAA 57.385 37.500 0.00 0.00 0.00 2.41
2330 9555 9.601397 CGCGTCGTAACATATTACAAATATATG 57.399 33.333 0.00 0.00 40.77 1.78
2507 9785 8.409825 TCAATATTAGGATATCCCTTCTCTCCA 58.590 37.037 18.56 0.00 44.85 3.86
2675 9959 8.561738 TCATACATAACAAAAGAGAGTTTCCC 57.438 34.615 0.00 0.00 0.00 3.97
2969 11834 9.285770 GATTTAGTATTTACCGAAAAAGGCTTG 57.714 33.333 0.00 0.00 33.69 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 5.197224 TCCCATTGTCTCTTTCCATGATT 57.803 39.130 0.00 0.00 0.00 2.57
96 97 4.868172 TCCCATTGTCTCTTTCCATGAT 57.132 40.909 0.00 0.00 0.00 2.45
116 117 8.950208 AGTCAATAGAGCCTATGTAAAGTTTC 57.050 34.615 0.00 0.00 0.00 2.78
119 120 6.763610 GCAAGTCAATAGAGCCTATGTAAAGT 59.236 38.462 0.00 0.00 0.00 2.66
155 156 3.813800 TCACTACTTGCGTGTAACTACG 58.186 45.455 0.00 0.00 46.28 3.51
174 175 5.809562 CACACACAAAAACAATTTAGCCTCA 59.190 36.000 0.00 0.00 0.00 3.86
178 179 6.128688 ACACACACACACAAAAACAATTTAGC 60.129 34.615 0.00 0.00 0.00 3.09
181 182 5.525378 ACACACACACACACAAAAACAATTT 59.475 32.000 0.00 0.00 0.00 1.82
184 185 4.046938 ACACACACACACACAAAAACAA 57.953 36.364 0.00 0.00 0.00 2.83
186 187 5.193936 CAAAACACACACACACACAAAAAC 58.806 37.500 0.00 0.00 0.00 2.43
192 193 2.057503 TGCAAAACACACACACACAC 57.942 45.000 0.00 0.00 0.00 3.82
193 194 2.800881 TTGCAAAACACACACACACA 57.199 40.000 0.00 0.00 0.00 3.72
194 195 5.769967 TTATTTGCAAAACACACACACAC 57.230 34.783 17.19 0.00 0.00 3.82
195 196 6.369890 ACATTTATTTGCAAAACACACACACA 59.630 30.769 17.19 0.00 0.00 3.72
196 197 6.770076 ACATTTATTTGCAAAACACACACAC 58.230 32.000 17.19 0.00 0.00 3.82
197 198 6.974932 ACATTTATTTGCAAAACACACACA 57.025 29.167 17.19 0.00 0.00 3.72
198 199 9.928236 AATTACATTTATTTGCAAAACACACAC 57.072 25.926 17.19 0.00 0.00 3.82
297 301 8.537223 CGATTATTGCAATCAATCAAGAAAAGG 58.463 33.333 24.93 12.88 41.68 3.11
479 525 7.025963 GCCTTTCTACATGCAATATCTAATGC 58.974 38.462 0.00 0.00 42.86 3.56
483 529 5.702670 GCTGCCTTTCTACATGCAATATCTA 59.297 40.000 0.00 0.00 32.58 1.98
487 533 2.613595 CGCTGCCTTTCTACATGCAATA 59.386 45.455 0.00 0.00 32.58 1.90
488 534 1.402968 CGCTGCCTTTCTACATGCAAT 59.597 47.619 0.00 0.00 32.58 3.56
489 535 0.804364 CGCTGCCTTTCTACATGCAA 59.196 50.000 0.00 0.00 32.58 4.08
490 536 1.026182 CCGCTGCCTTTCTACATGCA 61.026 55.000 0.00 0.00 0.00 3.96
491 537 1.718757 CCCGCTGCCTTTCTACATGC 61.719 60.000 0.00 0.00 0.00 4.06
492 538 1.097547 CCCCGCTGCCTTTCTACATG 61.098 60.000 0.00 0.00 0.00 3.21
494 540 2.221299 ACCCCGCTGCCTTTCTACA 61.221 57.895 0.00 0.00 0.00 2.74
495 541 1.745489 CACCCCGCTGCCTTTCTAC 60.745 63.158 0.00 0.00 0.00 2.59
503 549 4.697756 TGTACTGCACCCCGCTGC 62.698 66.667 0.00 0.00 43.01 5.25
505 551 3.706373 CCTGTACTGCACCCCGCT 61.706 66.667 0.00 0.00 43.06 5.52
506 552 4.778143 CCCTGTACTGCACCCCGC 62.778 72.222 0.00 0.00 42.89 6.13
508 554 2.669240 GACCCTGTACTGCACCCC 59.331 66.667 0.00 0.00 0.00 4.95
510 556 0.905337 AGAGGACCCTGTACTGCACC 60.905 60.000 0.00 0.00 0.00 5.01
511 557 1.477295 GTAGAGGACCCTGTACTGCAC 59.523 57.143 14.11 0.00 39.03 4.57
512 558 1.848652 GTAGAGGACCCTGTACTGCA 58.151 55.000 14.11 0.00 39.03 4.41
513 559 0.739561 CGTAGAGGACCCTGTACTGC 59.260 60.000 17.71 2.57 39.67 4.40
514 560 2.015587 GTCGTAGAGGACCCTGTACTG 58.984 57.143 17.71 12.53 39.67 2.74
524 2846 3.632333 ACCATGATGAAGTCGTAGAGGA 58.368 45.455 0.00 0.00 36.95 3.71
534 2856 4.023107 GCCATGATGAAGACCATGATGAAG 60.023 45.833 6.14 0.00 45.82 3.02
635 3044 0.100503 GCCGTGCCATGGATTTGTAC 59.899 55.000 18.40 2.92 0.00 2.90
664 3073 3.674682 GCTTCGATGAGTTCAGTAGCACT 60.675 47.826 1.89 0.00 0.00 4.40
669 3078 1.469251 GGCGCTTCGATGAGTTCAGTA 60.469 52.381 7.64 0.00 0.00 2.74
729 3138 6.368516 CCGTGCCATTTAAAATTGAACTTCAT 59.631 34.615 0.00 0.00 0.00 2.57
791 3205 9.173939 GAAATTCTTTGACGGAATATATTGCAG 57.826 33.333 16.12 11.16 33.65 4.41
939 3358 3.417069 TGAGAATATTGGTATGGGCGG 57.583 47.619 0.00 0.00 0.00 6.13
994 3416 1.130561 GATCGTAGCTGGTTTGTTGCC 59.869 52.381 0.00 0.00 0.00 4.52
1034 3482 0.745845 CACTCGGCTGGGAAGATTGG 60.746 60.000 0.00 0.00 0.00 3.16
1074 3552 1.291877 GAACACGCGCCTGAACTCAT 61.292 55.000 13.48 0.00 0.00 2.90
1150 3628 4.998788 TCTAGACGGAACTTCACATCATG 58.001 43.478 0.00 0.00 0.00 3.07
1151 3629 5.506483 CGATCTAGACGGAACTTCACATCAT 60.506 44.000 0.00 0.00 0.00 2.45
1152 3630 4.201920 CGATCTAGACGGAACTTCACATCA 60.202 45.833 0.00 0.00 0.00 3.07
1153 3631 4.035324 TCGATCTAGACGGAACTTCACATC 59.965 45.833 12.62 0.00 0.00 3.06
1154 3632 3.945921 TCGATCTAGACGGAACTTCACAT 59.054 43.478 12.62 0.00 0.00 3.21
1155 3633 3.340928 TCGATCTAGACGGAACTTCACA 58.659 45.455 12.62 0.00 0.00 3.58
1156 3634 4.555348 ATCGATCTAGACGGAACTTCAC 57.445 45.455 12.62 0.00 0.00 3.18
1157 3635 4.260661 CGAATCGATCTAGACGGAACTTCA 60.261 45.833 0.00 0.00 0.00 3.02
1158 3636 4.212911 CGAATCGATCTAGACGGAACTTC 58.787 47.826 0.00 6.54 0.00 3.01
1159 3637 3.626670 ACGAATCGATCTAGACGGAACTT 59.373 43.478 10.55 0.00 0.00 2.66
1160 3638 3.204526 ACGAATCGATCTAGACGGAACT 58.795 45.455 10.55 0.00 0.00 3.01
1161 3639 3.605743 ACGAATCGATCTAGACGGAAC 57.394 47.619 10.55 4.54 0.00 3.62
1162 3640 3.003068 GGAACGAATCGATCTAGACGGAA 59.997 47.826 10.55 0.00 0.00 4.30
1163 3641 2.547211 GGAACGAATCGATCTAGACGGA 59.453 50.000 10.55 6.07 0.00 4.69
1164 3642 2.918616 GGAACGAATCGATCTAGACGG 58.081 52.381 10.55 1.12 0.00 4.79
1180 3658 2.500509 AGCTCTTGATCGATCGGAAC 57.499 50.000 20.03 14.95 0.00 3.62
1181 3659 2.030717 GCTAGCTCTTGATCGATCGGAA 60.031 50.000 20.03 9.20 0.00 4.30
1182 3660 1.537638 GCTAGCTCTTGATCGATCGGA 59.462 52.381 20.03 17.94 0.00 4.55
1183 3661 1.402194 GGCTAGCTCTTGATCGATCGG 60.402 57.143 20.03 14.91 0.00 4.18
1184 3662 1.539388 AGGCTAGCTCTTGATCGATCG 59.461 52.381 20.03 9.36 0.00 3.69
1185 3663 2.819608 AGAGGCTAGCTCTTGATCGATC 59.180 50.000 18.72 18.72 0.00 3.69
1186 3664 2.875296 AGAGGCTAGCTCTTGATCGAT 58.125 47.619 15.72 0.00 0.00 3.59
1187 3665 2.356665 AGAGGCTAGCTCTTGATCGA 57.643 50.000 15.72 0.00 0.00 3.59
1188 3666 2.227865 GGTAGAGGCTAGCTCTTGATCG 59.772 54.545 15.72 0.00 32.79 3.69
1189 3667 3.226777 TGGTAGAGGCTAGCTCTTGATC 58.773 50.000 15.72 3.01 32.79 2.92
1190 3668 3.230134 CTGGTAGAGGCTAGCTCTTGAT 58.770 50.000 15.72 3.77 32.79 2.57
1191 3669 2.660572 CTGGTAGAGGCTAGCTCTTGA 58.339 52.381 15.72 0.00 32.79 3.02
1192 3670 1.686052 CCTGGTAGAGGCTAGCTCTTG 59.314 57.143 15.72 6.86 34.01 3.02
1193 3671 2.080654 CCTGGTAGAGGCTAGCTCTT 57.919 55.000 15.72 0.21 34.01 2.85
1194 3672 3.839979 CCTGGTAGAGGCTAGCTCT 57.160 57.895 15.72 16.63 34.01 4.09
1203 3681 0.171455 GACGTGAGCACCTGGTAGAG 59.829 60.000 0.00 0.00 0.00 2.43
1204 3682 0.251209 AGACGTGAGCACCTGGTAGA 60.251 55.000 0.00 0.00 0.00 2.59
1205 3683 0.171455 GAGACGTGAGCACCTGGTAG 59.829 60.000 0.00 0.00 0.00 3.18
1206 3684 1.583495 CGAGACGTGAGCACCTGGTA 61.583 60.000 0.00 0.00 0.00 3.25
1207 3685 2.920645 CGAGACGTGAGCACCTGGT 61.921 63.158 0.00 0.00 0.00 4.00
1208 3686 1.583495 TACGAGACGTGAGCACCTGG 61.583 60.000 0.00 0.00 41.39 4.45
1209 3687 0.454620 GTACGAGACGTGAGCACCTG 60.455 60.000 0.00 0.00 41.39 4.00
1210 3688 1.874562 GTACGAGACGTGAGCACCT 59.125 57.895 0.00 0.00 41.39 4.00
1211 3689 1.511464 CGTACGAGACGTGAGCACC 60.511 63.158 10.44 0.00 46.86 5.01
1212 3690 4.038036 CGTACGAGACGTGAGCAC 57.962 61.111 10.44 0.00 46.86 4.40
1226 3704 4.095932 CACATCTAGCCAGTACTTCACGTA 59.904 45.833 0.00 0.00 0.00 3.57
1227 3705 3.090037 ACATCTAGCCAGTACTTCACGT 58.910 45.455 0.00 0.00 0.00 4.49
1228 3706 3.119459 ACACATCTAGCCAGTACTTCACG 60.119 47.826 0.00 0.00 0.00 4.35
1229 3707 4.177026 CACACATCTAGCCAGTACTTCAC 58.823 47.826 0.00 0.00 0.00 3.18
1230 3708 3.368427 GCACACATCTAGCCAGTACTTCA 60.368 47.826 0.00 0.00 0.00 3.02
1231 3709 3.190874 GCACACATCTAGCCAGTACTTC 58.809 50.000 0.00 0.00 0.00 3.01
1232 3710 3.252974 GCACACATCTAGCCAGTACTT 57.747 47.619 0.00 0.00 0.00 2.24
1233 3711 2.969628 GCACACATCTAGCCAGTACT 57.030 50.000 0.00 0.00 0.00 2.73
1240 3718 2.093216 GTGCAGGCACACATCTAGC 58.907 57.895 18.84 0.00 45.53 3.42
1249 3727 2.099141 TTGATCTACAGTGCAGGCAC 57.901 50.000 16.29 16.29 46.50 5.01
1250 3728 2.236893 TGATTGATCTACAGTGCAGGCA 59.763 45.455 0.00 0.00 0.00 4.75
1251 3729 2.910199 TGATTGATCTACAGTGCAGGC 58.090 47.619 0.00 0.00 0.00 4.85
1252 3730 3.624861 GGTTGATTGATCTACAGTGCAGG 59.375 47.826 7.63 0.00 34.85 4.85
1253 3731 4.511527 AGGTTGATTGATCTACAGTGCAG 58.488 43.478 7.63 0.00 34.85 4.41
1254 3732 4.558226 AGGTTGATTGATCTACAGTGCA 57.442 40.909 7.63 0.00 34.85 4.57
1255 3733 5.665459 AGTAGGTTGATTGATCTACAGTGC 58.335 41.667 7.63 0.00 35.75 4.40
1256 3734 7.429633 CCTAGTAGGTTGATTGATCTACAGTG 58.570 42.308 8.17 0.00 35.75 3.66
1257 3735 6.041069 GCCTAGTAGGTTGATTGATCTACAGT 59.959 42.308 17.69 0.00 37.80 3.55
1258 3736 6.040955 TGCCTAGTAGGTTGATTGATCTACAG 59.959 42.308 17.69 0.00 37.80 2.74
1259 3737 5.897250 TGCCTAGTAGGTTGATTGATCTACA 59.103 40.000 17.69 0.00 37.80 2.74
1260 3738 6.406692 TGCCTAGTAGGTTGATTGATCTAC 57.593 41.667 17.69 0.00 37.80 2.59
1261 3739 5.011125 GCTGCCTAGTAGGTTGATTGATCTA 59.989 44.000 17.69 0.00 37.80 1.98
1262 3740 4.202305 GCTGCCTAGTAGGTTGATTGATCT 60.202 45.833 17.69 0.00 37.80 2.75
1263 3741 4.061596 GCTGCCTAGTAGGTTGATTGATC 58.938 47.826 17.69 0.00 37.80 2.92
1264 3742 3.713764 AGCTGCCTAGTAGGTTGATTGAT 59.286 43.478 17.69 0.00 37.80 2.57
1265 3743 3.107601 AGCTGCCTAGTAGGTTGATTGA 58.892 45.455 17.69 0.00 37.80 2.57
1266 3744 3.550437 AGCTGCCTAGTAGGTTGATTG 57.450 47.619 17.69 3.58 37.80 2.67
1267 3745 6.152589 AGCAAGCTGCCTAGTAGGTTGATT 62.153 45.833 26.98 12.09 46.18 2.57
1353 3831 2.953821 CGCCGCCTTCATGTGTTT 59.046 55.556 0.00 0.00 0.00 2.83
1457 6046 2.435586 CGCACCAGCCTCAGGAAG 60.436 66.667 0.00 0.00 37.52 3.46
1532 6121 1.483307 CCCCTCCCTTCCATCTCGTAT 60.483 57.143 0.00 0.00 0.00 3.06
1608 6325 1.594293 CCTGGCACTCGTCAACGTT 60.594 57.895 0.00 0.00 40.80 3.99
1613 6330 3.321648 ATGGCCTGGCACTCGTCA 61.322 61.111 22.05 8.32 0.00 4.35
1694 7388 6.814644 CAGTTTTTGTATGTCATGCCATCATT 59.185 34.615 0.00 0.00 0.00 2.57
2045 9269 2.485814 GTCTGCTGGTCCATCTGTTTTC 59.514 50.000 0.00 0.00 0.00 2.29
2147 9371 2.159014 TCGGTGTGTAGTTTCTGCTTGT 60.159 45.455 0.00 0.00 0.00 3.16
2304 9529 9.601397 CATATATTTGTAATATGTTACGACGCG 57.399 33.333 3.53 3.53 42.50 6.01
2330 9555 7.659799 TGTTACATAATGCATCTACATGGTACC 59.340 37.037 4.43 4.43 0.00 3.34
2370 9595 9.869757 AGGCAACCATAAAATTTCTAAATACAC 57.130 29.630 0.00 0.00 37.17 2.90
2675 9959 6.047870 ACTCTGTAAGCTTGCTATCAATCTG 58.952 40.000 15.83 0.00 29.94 2.90
2969 11834 4.779987 CTTTATTTATAAAGCGGGGCGTC 58.220 43.478 8.78 0.00 41.69 5.19
3045 13635 1.529438 CTTGCACTTTTTCGTCCGCTA 59.471 47.619 0.00 0.00 0.00 4.26
3087 13677 5.262588 TCTTTTCTCTTTTGGGCTTGTTC 57.737 39.130 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.