Multiple sequence alignment - TraesCS1B01G478000

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 TraesCS1B01G478000 chr1B 100.000 3025 0 0 1 3025 686749042 686746018 0.000000e+00 5587.0
1 TraesCS1B01G478000 chr1B 80.838 167 25 6 582 744 4873410 4873573 1.140000e-24 124.0
2 TraesCS1B01G478000 chr1B 100.000 37 0 0 2049 2085 304515107 304515071 5.410000e-08 69.4
3 TraesCS1B01G478000 chr1B 93.182 44 0 2 2041 2084 379424347 379424307 9.060000e-06 62.1
4 TraesCS1B01G478000 chr1D 88.095 1134 96 20 1 1122 493704678 493703572 0.000000e+00 1310.0
5 TraesCS1B01G478000 chr1D 93.757 865 41 9 1173 2035 493703588 493702735 0.000000e+00 1286.0
6 TraesCS1B01G478000 chr1D 94.712 416 21 1 1620 2035 493701618 493701204 0.000000e+00 645.0
7 TraesCS1B01G478000 chr1D 86.482 614 35 16 2324 2918 103328212 103327628 5.500000e-177 630.0
8 TraesCS1B01G478000 chr1D 97.786 271 6 0 1620 1890 493684154 493683884 4.570000e-128 468.0
9 TraesCS1B01G478000 chr1D 83.967 368 53 5 240 602 211476401 211476035 6.210000e-92 348.0
10 TraesCS1B01G478000 chr1D 96.923 130 0 1 2790 2919 493683885 493683760 6.570000e-52 215.0
11 TraesCS1B01G478000 chr1A 94.084 862 40 7 1164 2020 591948174 591947319 0.000000e+00 1299.0
12 TraesCS1B01G478000 chr1A 95.954 173 7 0 2016 2188 591947273 591947101 6.390000e-72 281.0
13 TraesCS1B01G478000 chr1A 96.117 103 4 0 2220 2322 591947111 591947009 5.190000e-38 169.0
14 TraesCS1B01G478000 chr1A 96.429 56 2 0 2970 3025 591945576 591945521 3.210000e-15 93.5
15 TraesCS1B01G478000 chr1A 90.000 50 3 2 2049 2096 10158790 10158741 2.520000e-06 63.9
16 TraesCS1B01G478000 chr3B 86.201 616 35 18 2324 2919 254017657 254017072 3.310000e-174 621.0
17 TraesCS1B01G478000 chr3B 80.443 767 92 34 2 744 596855594 596856326 1.600000e-147 532.0
18 TraesCS1B01G478000 chr3B 87.676 284 14 4 2310 2581 589567273 589566999 8.140000e-81 311.0
19 TraesCS1B01G478000 chr3B 85.761 309 17 15 2325 2612 89427716 89428018 4.900000e-78 302.0
20 TraesCS1B01G478000 chr3B 85.197 304 23 10 2325 2612 89429666 89429963 2.950000e-75 292.0
21 TraesCS1B01G478000 chr3B 96.429 56 2 0 2970 3025 253981229 253981174 3.210000e-15 93.5
22 TraesCS1B01G478000 chr3B 93.182 44 0 3 2041 2084 106829016 106828976 9.060000e-06 62.1
23 TraesCS1B01G478000 chr5A 82.438 763 77 19 1 733 338390864 338390129 5.540000e-172 614.0
24 TraesCS1B01G478000 chr5A 84.682 581 57 16 36 588 472280999 472280423 4.410000e-153 551.0
25 TraesCS1B01G478000 chr5A 90.000 50 3 2 2049 2096 686221962 686221913 2.520000e-06 63.9
26 TraesCS1B01G478000 chr2B 84.396 596 77 12 1 589 561262424 561263010 3.380000e-159 571.0
27 TraesCS1B01G478000 chr2B 84.135 624 38 24 2325 2919 644456064 644455473 5.700000e-152 547.0
28 TraesCS1B01G478000 chr2B 89.655 58 4 2 2041 2096 764060781 764060838 4.180000e-09 73.1
29 TraesCS1B01G478000 chr5B 81.496 762 80 23 5 741 330005388 330004663 1.220000e-158 569.0
30 TraesCS1B01G478000 chr5B 89.238 223 9 4 2383 2593 325157111 325156892 6.430000e-67 265.0
31 TraesCS1B01G478000 chr5B 91.667 48 0 3 2037 2084 685075612 685075569 2.520000e-06 63.9
32 TraesCS1B01G478000 chr4B 83.882 608 76 9 1 587 285585301 285584695 7.320000e-156 560.0
33 TraesCS1B01G478000 chr4B 80.713 757 87 34 1 732 348949173 348949895 4.440000e-148 534.0
34 TraesCS1B01G478000 chr4B 77.947 263 47 7 1752 2004 139134833 139135094 1.450000e-33 154.0
35 TraesCS1B01G478000 chr6A 80.713 757 88 26 1 730 25765928 25765203 1.230000e-148 536.0
36 TraesCS1B01G478000 chr6A 85.879 347 46 2 1 346 108199065 108198721 1.710000e-97 366.0
37 TraesCS1B01G478000 chr6A 95.161 62 2 1 2325 2386 570989836 570989776 2.480000e-16 97.1
38 TraesCS1B01G478000 chr2A 79.151 777 93 35 1 743 288989989 288989248 9.810000e-130 473.0
39 TraesCS1B01G478000 chr2A 84.104 346 44 6 1 346 508049390 508049724 1.050000e-84 324.0
40 TraesCS1B01G478000 chr2A 85.973 221 22 7 2325 2537 600519998 600520217 8.440000e-56 228.0
41 TraesCS1B01G478000 chr2A 82.222 90 9 1 2326 2408 380744659 380744570 1.500000e-08 71.3
42 TraesCS1B01G478000 chr7D 83.810 420 56 10 1 417 220307114 220307524 3.660000e-104 388.0
43 TraesCS1B01G478000 chr7D 88.477 243 9 9 2384 2611 180729555 180729317 2.970000e-70 276.0
44 TraesCS1B01G478000 chr7D 84.026 313 20 15 2326 2611 180734554 180734245 1.070000e-69 274.0
45 TraesCS1B01G478000 chr7D 86.885 244 13 12 2383 2611 180736846 180736607 3.870000e-64 255.0
46 TraesCS1B01G478000 chr7B 81.325 498 58 20 240 730 651202057 651201588 3.680000e-99 372.0
47 TraesCS1B01G478000 chr7B 84.080 402 35 11 2325 2699 422720556 422720955 7.970000e-96 361.0
48 TraesCS1B01G478000 chr7B 86.301 219 10 10 2701 2919 422721798 422721996 1.410000e-53 220.0
49 TraesCS1B01G478000 chr7B 93.333 60 3 1 2966 3025 422723437 422723495 1.490000e-13 87.9
50 TraesCS1B01G478000 chr4D 81.288 497 57 20 240 731 40220593 40221058 1.320000e-98 370.0
51 TraesCS1B01G478000 chr4D 78.327 263 46 7 1752 2004 97385961 97386222 3.120000e-35 159.0
52 TraesCS1B01G478000 chr5D 85.470 351 44 5 240 586 63263977 63264324 2.870000e-95 359.0
53 TraesCS1B01G478000 chr5D 86.381 257 14 12 2384 2623 297156777 297157029 8.320000e-66 261.0
54 TraesCS1B01G478000 chr5D 91.803 61 5 0 2325 2385 517972289 517972229 5.370000e-13 86.1
55 TraesCS1B01G478000 chr6B 77.500 640 92 31 100 731 191205445 191206040 1.340000e-88 337.0
56 TraesCS1B01G478000 chr6B 92.000 50 2 2 2049 2096 277158946 277158995 5.410000e-08 69.4
57 TraesCS1B01G478000 chr4A 88.435 294 10 6 2320 2591 637217438 637217147 1.740000e-87 333.0
58 TraesCS1B01G478000 chr4A 77.820 266 48 7 1752 2007 478746796 478746532 1.450000e-33 154.0
59 TraesCS1B01G478000 chr4A 91.935 62 4 1 2325 2386 614679283 614679223 5.370000e-13 86.1
60 TraesCS1B01G478000 chr3A 85.494 324 40 6 1 322 630041074 630040756 6.250000e-87 331.0
61 TraesCS1B01G478000 chr3A 83.908 348 52 3 1 347 492413418 492413762 2.250000e-86 329.0
62 TraesCS1B01G478000 chr3D 85.404 322 40 7 1 320 591197711 591197395 8.090000e-86 327.0
63 TraesCS1B01G478000 chr7A 80.422 332 32 14 405 732 694329357 694329659 3.930000e-54 222.0
64 TraesCS1B01G478000 chr2D 78.146 302 33 11 432 733 439434625 439434893 8.680000e-36 161.0
65 TraesCS1B01G478000 chr2D 85.185 135 5 4 2489 2611 61273828 61273697 1.140000e-24 124.0


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 TraesCS1B01G478000 chr1B 686746018 686749042 3024 True 5587.000000 5587 100.000000 1 3025 1 chr1B.!!$R3 3024
1 TraesCS1B01G478000 chr1D 493701204 493704678 3474 True 1080.333333 1310 92.188000 1 2035 3 chr1D.!!$R4 2034
2 TraesCS1B01G478000 chr1D 103327628 103328212 584 True 630.000000 630 86.482000 2324 2918 1 chr1D.!!$R1 594
3 TraesCS1B01G478000 chr1A 591945521 591948174 2653 True 460.625000 1299 95.646000 1164 3025 4 chr1A.!!$R2 1861
4 TraesCS1B01G478000 chr3B 254017072 254017657 585 True 621.000000 621 86.201000 2324 2919 1 chr3B.!!$R3 595
5 TraesCS1B01G478000 chr3B 596855594 596856326 732 False 532.000000 532 80.443000 2 744 1 chr3B.!!$F1 742
6 TraesCS1B01G478000 chr3B 89427716 89429963 2247 False 297.000000 302 85.479000 2325 2612 2 chr3B.!!$F2 287
7 TraesCS1B01G478000 chr5A 338390129 338390864 735 True 614.000000 614 82.438000 1 733 1 chr5A.!!$R1 732
8 TraesCS1B01G478000 chr5A 472280423 472280999 576 True 551.000000 551 84.682000 36 588 1 chr5A.!!$R2 552
9 TraesCS1B01G478000 chr2B 561262424 561263010 586 False 571.000000 571 84.396000 1 589 1 chr2B.!!$F1 588
10 TraesCS1B01G478000 chr2B 644455473 644456064 591 True 547.000000 547 84.135000 2325 2919 1 chr2B.!!$R1 594
11 TraesCS1B01G478000 chr5B 330004663 330005388 725 True 569.000000 569 81.496000 5 741 1 chr5B.!!$R2 736
12 TraesCS1B01G478000 chr4B 285584695 285585301 606 True 560.000000 560 83.882000 1 587 1 chr4B.!!$R1 586
13 TraesCS1B01G478000 chr4B 348949173 348949895 722 False 534.000000 534 80.713000 1 732 1 chr4B.!!$F2 731
14 TraesCS1B01G478000 chr6A 25765203 25765928 725 True 536.000000 536 80.713000 1 730 1 chr6A.!!$R1 729
15 TraesCS1B01G478000 chr2A 288989248 288989989 741 True 473.000000 473 79.151000 1 743 1 chr2A.!!$R1 742
16 TraesCS1B01G478000 chr7D 180734245 180736846 2601 True 264.500000 274 85.455500 2326 2611 2 chr7D.!!$R2 285
17 TraesCS1B01G478000 chr7B 422720556 422723495 2939 False 222.966667 361 87.904667 2325 3025 3 chr7B.!!$F1 700
18 TraesCS1B01G478000 chr6B 191205445 191206040 595 False 337.000000 337 77.500000 100 731 1 chr6B.!!$F1 631

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
886 1035 0.25382 AGAGGGGATGAATGGGTGGT 60.254 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2865 7268 0.038709 GCCGGAAGAGGATCGATGAG 60.039 60.0 5.05 0.0 42.67 2.9 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
29 30 7.687941 AAACTTGTCATGGTGGATTACTAAG 57.312 36.000 0.00 0.00 0.00 2.18
50 51 5.551760 AGATTTGTCATGATCCGTGAAAC 57.448 39.130 0.00 0.00 30.77 2.78
152 154 7.669427 TGCCATGAATCAGAAACTAAAATTGT 58.331 30.769 0.00 0.00 0.00 2.71
297 434 3.448301 TGATCCATGAATTGACTTTGCCC 59.552 43.478 0.00 0.00 0.00 5.36
322 460 9.665719 CCTGGTTAATTACTAAAAATTGCCATT 57.334 29.630 0.00 0.00 36.03 3.16
366 504 9.423061 GCCATGAAAAGTAGTTGAAATACAATT 57.577 29.630 5.56 0.00 40.76 2.32
522 671 6.250344 TCTAGTTTTGAAGATCTCGTCGAA 57.750 37.500 0.00 0.00 0.00 3.71
548 697 6.202954 ACGGATTTAATGATGAGAACGGATTC 59.797 38.462 0.00 0.00 34.78 2.52
673 822 4.092279 TGATGTGGCAAAATGGATGGTAA 58.908 39.130 0.00 0.00 0.00 2.85
674 823 4.160065 TGATGTGGCAAAATGGATGGTAAG 59.840 41.667 0.00 0.00 0.00 2.34
675 824 3.772387 TGTGGCAAAATGGATGGTAAGA 58.228 40.909 0.00 0.00 0.00 2.10
689 838 5.469084 GGATGGTAAGAAAGACGTTTGAACT 59.531 40.000 0.00 0.00 0.00 3.01
696 845 9.789029 GTAAGAAAGACGTTTGAACTATGTTAC 57.211 33.333 0.00 0.00 0.00 2.50
699 848 9.106070 AGAAAGACGTTTGAACTATGTTACTTT 57.894 29.630 0.00 0.00 0.00 2.66
703 852 7.279313 AGACGTTTGAACTATGTTACTTTGTGT 59.721 33.333 0.00 0.00 0.00 3.72
822 971 9.268268 ACAAGTTTGACTATCGTCTATTTTTGA 57.732 29.630 0.00 0.00 40.86 2.69
864 1013 7.966812 TCCATATATAGAAGAAGCAAGCAAGA 58.033 34.615 0.00 0.00 0.00 3.02
886 1035 0.253820 AGAGGGGATGAATGGGTGGT 60.254 55.000 0.00 0.00 0.00 4.16
903 1052 4.220602 GGGTGGTCACAAAATGATTTAGCT 59.779 41.667 3.40 0.00 40.28 3.32
904 1053 5.163513 GGTGGTCACAAAATGATTTAGCTG 58.836 41.667 0.00 0.00 40.28 4.24
911 1060 4.039004 ACAAAATGATTTAGCTGTGCCACA 59.961 37.500 0.00 0.00 0.00 4.17
929 1078 4.938226 GCCACACTATATATTGCTCCTTCC 59.062 45.833 0.22 0.00 0.00 3.46
968 1121 5.104067 CCTCCCTACCTATTTAAGCCACTTT 60.104 44.000 0.00 0.00 0.00 2.66
970 1123 5.104235 TCCCTACCTATTTAAGCCACTTTCC 60.104 44.000 0.00 0.00 0.00 3.13
988 1141 3.593442 TCCCTCAACAAACACCAATCT 57.407 42.857 0.00 0.00 0.00 2.40
998 1151 5.640732 ACAAACACCAATCTAATTCATCGC 58.359 37.500 0.00 0.00 0.00 4.58
1027 1180 1.024046 CCAAATGTCGTCGGCATGGA 61.024 55.000 14.01 0.00 0.00 3.41
1038 1191 3.188786 GCATGGACCGCTGTCGTC 61.189 66.667 1.95 0.00 42.73 4.20
1057 1210 1.352404 GTCATCGTCTCGTCCCTCG 59.648 63.158 0.00 0.00 41.41 4.63
1071 1224 3.199190 CTCGCCGTCGCTCTCTCT 61.199 66.667 0.00 0.00 35.26 3.10
1088 1241 6.576662 TCTCTCTCGTAAGTGAACATTTCT 57.423 37.500 0.00 0.00 39.65 2.52
1094 1247 5.227908 TCGTAAGTGAACATTTCTGACCTC 58.772 41.667 0.00 0.00 39.48 3.85
1101 1254 5.180304 GTGAACATTTCTGACCTCTCTTTCC 59.820 44.000 0.00 0.00 0.00 3.13
1218 1375 5.359009 AGTGGAATTGCGATGATGAAGAAAT 59.641 36.000 0.00 0.00 0.00 2.17
1219 1376 5.684626 GTGGAATTGCGATGATGAAGAAATC 59.315 40.000 0.00 0.00 0.00 2.17
1234 1391 7.966339 TGAAGAAATCATCAAGGATTGGATT 57.034 32.000 0.00 0.00 38.98 3.01
1235 1392 7.778083 TGAAGAAATCATCAAGGATTGGATTG 58.222 34.615 0.00 0.00 38.98 2.67
1236 1393 7.147794 TGAAGAAATCATCAAGGATTGGATTGG 60.148 37.037 0.00 0.00 38.98 3.16
1259 1424 0.743097 GGAATGCAGATGAAGGTGGC 59.257 55.000 0.00 0.00 0.00 5.01
1388 1553 2.167219 CATCGTCATCGCCAACGCT 61.167 57.895 0.00 0.00 38.72 5.07
1394 1559 3.706373 ATCGCCAACGCTGTCCCT 61.706 61.111 0.00 0.00 39.84 4.20
1439 1604 2.432300 CGTCTACGCCCCCTCCAAT 61.432 63.158 0.00 0.00 0.00 3.16
1456 1621 0.105760 AATGCCACCCTCCACAACAA 60.106 50.000 0.00 0.00 0.00 2.83
1477 1642 1.009829 GGCAAGGACATCGTCATGAC 58.990 55.000 16.21 16.21 33.68 3.06
1649 1814 2.332514 GTCCACGTCGACGACCAA 59.667 61.111 41.52 21.39 43.02 3.67
1727 1892 0.612174 ACCAGCTGACGGAGAAGCTA 60.612 55.000 17.39 0.00 45.84 3.32
1748 1913 2.569134 GAGCTCAAGACGACGCCT 59.431 61.111 9.40 0.00 0.00 5.52
2052 2267 5.000570 ACATAGTACATACTCCCTCCTCC 57.999 47.826 0.00 0.00 37.73 4.30
2055 2270 2.158638 AGTACATACTCCCTCCTCCGTC 60.159 54.545 0.00 0.00 0.00 4.79
2059 2274 1.294426 TACTCCCTCCTCCGTCCCAT 61.294 60.000 0.00 0.00 0.00 4.00
2066 2281 3.961408 CCCTCCTCCGTCCCATAATATAG 59.039 52.174 0.00 0.00 0.00 1.31
2372 5793 3.531538 TGAATAGTCCCATCACTTTCGC 58.468 45.455 0.00 0.00 0.00 4.70
2380 5801 2.432444 CCATCACTTTCGCCTGGTTTA 58.568 47.619 0.00 0.00 0.00 2.01
2408 5846 0.617535 TCCGTCTCACATCCCACCAT 60.618 55.000 0.00 0.00 0.00 3.55
2465 5903 9.161629 CACAATGAAAACTTTCCTAACCTTTTT 57.838 29.630 0.00 0.00 36.36 1.94
2579 6030 5.422970 TCCTAATGCATTGATCTTTGCCTTT 59.577 36.000 22.27 11.76 38.08 3.11
2590 6045 7.765695 TGATCTTTGCCTTTTTGTCTCTAAT 57.234 32.000 0.00 0.00 0.00 1.73
2591 6046 7.820648 TGATCTTTGCCTTTTTGTCTCTAATC 58.179 34.615 0.00 0.00 0.00 1.75
2592 6047 7.667219 TGATCTTTGCCTTTTTGTCTCTAATCT 59.333 33.333 0.00 0.00 0.00 2.40
2593 6048 7.440523 TCTTTGCCTTTTTGTCTCTAATCTC 57.559 36.000 0.00 0.00 0.00 2.75
2594 6049 7.227156 TCTTTGCCTTTTTGTCTCTAATCTCT 58.773 34.615 0.00 0.00 0.00 3.10
2595 6050 7.721399 TCTTTGCCTTTTTGTCTCTAATCTCTT 59.279 33.333 0.00 0.00 0.00 2.85
2596 6051 7.440523 TTGCCTTTTTGTCTCTAATCTCTTC 57.559 36.000 0.00 0.00 0.00 2.87
2597 6052 6.773638 TGCCTTTTTGTCTCTAATCTCTTCT 58.226 36.000 0.00 0.00 0.00 2.85
2616 6081 5.958987 TCTTCTTCTCTACTCCTAAAAGGGG 59.041 44.000 0.00 0.00 43.27 4.79
2617 6082 4.031611 TCTTCTCTACTCCTAAAAGGGGC 58.968 47.826 0.00 0.00 40.45 5.80
2618 6083 3.484953 TCTCTACTCCTAAAAGGGGCA 57.515 47.619 0.00 0.00 40.45 5.36
2725 7061 5.620738 ATCCTTTCTTGGAATGAGATCGA 57.379 39.130 0.00 0.00 39.85 3.59
2726 7062 5.620738 TCCTTTCTTGGAATGAGATCGAT 57.379 39.130 0.00 0.00 32.39 3.59
2727 7063 5.605534 TCCTTTCTTGGAATGAGATCGATC 58.394 41.667 17.91 17.91 32.39 3.69
2768 7171 3.746492 AGCGATTCTTTCCAACTGTGTAC 59.254 43.478 0.00 0.00 0.00 2.90
2792 7195 1.339535 CCCTCTCCTTCCTTCTTGCAC 60.340 57.143 0.00 0.00 0.00 4.57
2812 7215 7.312657 TGCACAAATCATATCTCTTTGTCTC 57.687 36.000 0.00 0.00 40.19 3.36
2813 7216 6.317140 TGCACAAATCATATCTCTTTGTCTCC 59.683 38.462 0.00 0.00 40.19 3.71
2861 7264 2.285668 TGCTCCTTCCCCTCCCTG 60.286 66.667 0.00 0.00 0.00 4.45
2865 7268 1.616628 TCCTTCCCCTCCCTGCTTC 60.617 63.158 0.00 0.00 0.00 3.86
2866 7269 1.617839 CCTTCCCCTCCCTGCTTCT 60.618 63.158 0.00 0.00 0.00 2.85
2867 7270 1.631071 CCTTCCCCTCCCTGCTTCTC 61.631 65.000 0.00 0.00 0.00 2.87
2868 7271 0.911525 CTTCCCCTCCCTGCTTCTCA 60.912 60.000 0.00 0.00 0.00 3.27
2869 7272 0.253347 TTCCCCTCCCTGCTTCTCAT 60.253 55.000 0.00 0.00 0.00 2.90
2870 7273 0.692419 TCCCCTCCCTGCTTCTCATC 60.692 60.000 0.00 0.00 0.00 2.92
2871 7274 1.445095 CCCTCCCTGCTTCTCATCG 59.555 63.158 0.00 0.00 0.00 3.84
2929 9895 4.383850 TTCCTCCATGTTGTTGTTGTTG 57.616 40.909 0.00 0.00 0.00 3.33
2931 9897 3.766591 TCCTCCATGTTGTTGTTGTTGTT 59.233 39.130 0.00 0.00 0.00 2.83
2932 9898 3.864583 CCTCCATGTTGTTGTTGTTGTTG 59.135 43.478 0.00 0.00 0.00 3.33
2935 9901 4.687948 TCCATGTTGTTGTTGTTGTTGTTG 59.312 37.500 0.00 0.00 0.00 3.33
2937 9903 5.049818 CCATGTTGTTGTTGTTGTTGTTGTT 60.050 36.000 0.00 0.00 0.00 2.83
2938 9904 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2941 9951 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2944 9954 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
2950 9960 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
3019 10052 8.742777 TCATTACCTCCTTTCTGAAAATGATTG 58.257 33.333 4.18 2.22 29.67 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.491152 CACGGATCATGACAAATCTTAGTAATC 58.509 37.037 0.00 0.00 0.00 1.75
29 30 5.295431 TGTTTCACGGATCATGACAAATC 57.705 39.130 0.00 0.00 0.00 2.17
174 176 7.201661 GGCAAAATTTTGTGCATGTATCATGAT 60.202 33.333 27.13 13.81 42.74 2.45
288 425 7.457024 TTTAGTAATTAACCAGGGCAAAGTC 57.543 36.000 0.00 0.00 0.00 3.01
322 460 9.770097 TTTCATGGCAAATTTTATTAGTTCACA 57.230 25.926 0.00 0.00 0.00 3.58
402 545 6.582295 GTGTTTACACTAAAGTTGCCATGATG 59.418 38.462 5.78 0.00 43.25 3.07
437 582 6.294453 CCAAAAGTTGCCATGATGTTACACTA 60.294 38.462 0.00 0.00 0.00 2.74
522 671 5.424757 TCCGTTCTCATCATTAAATCCGTT 58.575 37.500 0.00 0.00 0.00 4.44
659 808 6.254281 ACGTCTTTCTTACCATCCATTTTG 57.746 37.500 0.00 0.00 0.00 2.44
673 822 8.658499 AAGTAACATAGTTCAAACGTCTTTCT 57.342 30.769 0.00 0.00 0.00 2.52
674 823 9.155053 CAAAGTAACATAGTTCAAACGTCTTTC 57.845 33.333 0.00 0.00 0.00 2.62
675 824 8.671028 ACAAAGTAACATAGTTCAAACGTCTTT 58.329 29.630 0.00 0.00 0.00 2.52
689 838 5.110598 ACACGTGTGACACAAAGTAACATA 58.889 37.500 22.71 0.00 43.49 2.29
806 955 8.783833 ATGGATGGATCAAAAATAGACGATAG 57.216 34.615 0.00 0.00 46.19 2.08
808 957 8.156820 TGTATGGATGGATCAAAAATAGACGAT 58.843 33.333 0.00 0.00 0.00 3.73
864 1013 1.285962 CACCCATTCATCCCCTCTTGT 59.714 52.381 0.00 0.00 0.00 3.16
886 1035 4.280425 TGGCACAGCTAAATCATTTTGTGA 59.720 37.500 14.92 0.00 42.06 3.58
903 1052 4.347876 AGGAGCAATATATAGTGTGGCACA 59.652 41.667 17.96 17.96 36.74 4.57
904 1053 4.899502 AGGAGCAATATATAGTGTGGCAC 58.100 43.478 11.55 11.55 34.10 5.01
911 1060 8.773216 GGAAATAGGGAAGGAGCAATATATAGT 58.227 37.037 0.00 0.00 0.00 2.12
929 1078 2.058705 GGGAGGGAGGAAGGAAATAGG 58.941 57.143 0.00 0.00 0.00 2.57
968 1121 3.593442 AGATTGGTGTTTGTTGAGGGA 57.407 42.857 0.00 0.00 0.00 4.20
970 1123 6.980593 TGAATTAGATTGGTGTTTGTTGAGG 58.019 36.000 0.00 0.00 0.00 3.86
998 1151 0.179166 CGACATTTGGGACGCCATTG 60.179 55.000 0.00 0.00 0.00 2.82
1027 1180 2.178521 GATGACGACGACAGCGGT 59.821 61.111 0.00 0.00 43.17 5.68
1038 1191 1.352404 GAGGGACGAGACGATGACG 59.648 63.158 0.00 0.00 45.75 4.35
1057 1210 1.703438 TTACGAGAGAGAGCGACGGC 61.703 60.000 0.00 0.00 40.37 5.68
1071 1224 5.010719 AGAGGTCAGAAATGTTCACTTACGA 59.989 40.000 0.00 0.00 0.00 3.43
1179 1332 7.706179 CGCAATTCCACTCCACAAATTATTATT 59.294 33.333 0.00 0.00 0.00 1.40
1182 1335 5.184864 TCGCAATTCCACTCCACAAATTATT 59.815 36.000 0.00 0.00 0.00 1.40
1189 1342 1.003003 TCATCGCAATTCCACTCCACA 59.997 47.619 0.00 0.00 0.00 4.17
1218 1375 4.897076 CCATTCCAATCCAATCCTTGATGA 59.103 41.667 0.00 0.00 0.00 2.92
1219 1376 4.897076 TCCATTCCAATCCAATCCTTGATG 59.103 41.667 0.00 0.00 0.00 3.07
1221 1378 4.606476 TCCATTCCAATCCAATCCTTGA 57.394 40.909 0.00 0.00 0.00 3.02
1222 1379 5.607477 CATTCCATTCCAATCCAATCCTTG 58.393 41.667 0.00 0.00 0.00 3.61
1223 1380 4.102054 GCATTCCATTCCAATCCAATCCTT 59.898 41.667 0.00 0.00 0.00 3.36
1225 1382 3.388676 TGCATTCCATTCCAATCCAATCC 59.611 43.478 0.00 0.00 0.00 3.01
1226 1383 4.342951 TCTGCATTCCATTCCAATCCAATC 59.657 41.667 0.00 0.00 0.00 2.67
1228 1385 3.710724 TCTGCATTCCATTCCAATCCAA 58.289 40.909 0.00 0.00 0.00 3.53
1229 1386 3.385314 TCTGCATTCCATTCCAATCCA 57.615 42.857 0.00 0.00 0.00 3.41
1230 1387 3.893200 TCATCTGCATTCCATTCCAATCC 59.107 43.478 0.00 0.00 0.00 3.01
1231 1388 5.509163 CCTTCATCTGCATTCCATTCCAATC 60.509 44.000 0.00 0.00 0.00 2.67
1232 1389 4.344102 CCTTCATCTGCATTCCATTCCAAT 59.656 41.667 0.00 0.00 0.00 3.16
1233 1390 3.702548 CCTTCATCTGCATTCCATTCCAA 59.297 43.478 0.00 0.00 0.00 3.53
1234 1391 3.293337 CCTTCATCTGCATTCCATTCCA 58.707 45.455 0.00 0.00 0.00 3.53
1235 1392 3.067742 CACCTTCATCTGCATTCCATTCC 59.932 47.826 0.00 0.00 0.00 3.01
1236 1393 3.067742 CCACCTTCATCTGCATTCCATTC 59.932 47.826 0.00 0.00 0.00 2.67
1237 1394 3.028850 CCACCTTCATCTGCATTCCATT 58.971 45.455 0.00 0.00 0.00 3.16
1238 1395 2.662866 CCACCTTCATCTGCATTCCAT 58.337 47.619 0.00 0.00 0.00 3.41
1239 1396 1.956636 GCCACCTTCATCTGCATTCCA 60.957 52.381 0.00 0.00 0.00 3.53
1240 1397 0.743097 GCCACCTTCATCTGCATTCC 59.257 55.000 0.00 0.00 0.00 3.01
1241 1398 0.379669 CGCCACCTTCATCTGCATTC 59.620 55.000 0.00 0.00 0.00 2.67
1355 1520 1.676678 CGATGTCGATGGGGGACTGT 61.677 60.000 0.00 0.00 43.02 3.55
1388 1553 1.196104 CGAGGTTGGGGTTAGGGACA 61.196 60.000 0.00 0.00 0.00 4.02
1394 1559 1.482748 GGGTGTCGAGGTTGGGGTTA 61.483 60.000 0.00 0.00 0.00 2.85
1439 1604 1.454847 GTTGTTGTGGAGGGTGGCA 60.455 57.895 0.00 0.00 0.00 4.92
1456 1621 0.740868 CATGACGATGTCCTTGCCGT 60.741 55.000 0.00 0.00 38.01 5.68
1595 1760 2.892334 GAAGCGCTTGCCGTTGACA 61.892 57.895 30.47 0.00 40.41 3.58
1649 1814 1.296715 GATGACGGCCTTGTGGTCT 59.703 57.895 0.00 0.00 35.36 3.85
1727 1892 2.126812 GTCGTCTTGAGCTCGCGT 60.127 61.111 9.64 0.00 0.00 6.01
1763 1928 1.367471 CGACTTGAGCTCCACCACA 59.633 57.895 12.15 0.00 0.00 4.17
2039 2254 1.294426 TGGGACGGAGGAGGGAGTAT 61.294 60.000 0.00 0.00 0.00 2.12
2052 2267 7.225145 TCAAAAACGTTCCTATATTATGGGACG 59.775 37.037 19.49 19.49 39.88 4.79
2055 2270 8.126700 GTGTCAAAAACGTTCCTATATTATGGG 58.873 37.037 0.00 0.00 0.00 4.00
2066 2281 8.875803 TGATATGTATAGTGTCAAAAACGTTCC 58.124 33.333 0.00 0.00 0.00 3.62
2231 2500 9.915629 ACGGTTGCTACAAAATTGAAATTAATA 57.084 25.926 0.00 0.00 0.00 0.98
2232 2501 8.825667 ACGGTTGCTACAAAATTGAAATTAAT 57.174 26.923 0.00 0.00 0.00 1.40
2316 3520 9.469097 GTCCATTAGGAGTAGAGATACATACAT 57.531 37.037 0.00 0.00 46.92 2.29
2317 3521 7.606839 CGTCCATTAGGAGTAGAGATACATACA 59.393 40.741 0.00 0.00 46.92 2.29
2390 5828 0.179073 GATGGTGGGATGTGAGACGG 60.179 60.000 0.00 0.00 0.00 4.79
2408 5846 4.819105 AAACCAACGTGAGGAGATATGA 57.181 40.909 13.71 0.00 0.00 2.15
2579 6030 9.747898 AGTAGAGAAGAAGAGATTAGAGACAAA 57.252 33.333 0.00 0.00 0.00 2.83
2590 6045 6.893005 CCCTTTTAGGAGTAGAGAAGAAGAGA 59.107 42.308 0.00 0.00 37.67 3.10
2591 6046 6.097696 CCCCTTTTAGGAGTAGAGAAGAAGAG 59.902 46.154 0.00 0.00 37.67 2.85
2592 6047 5.958987 CCCCTTTTAGGAGTAGAGAAGAAGA 59.041 44.000 0.00 0.00 37.67 2.87
2593 6048 5.395879 GCCCCTTTTAGGAGTAGAGAAGAAG 60.396 48.000 0.00 0.00 37.67 2.85
2594 6049 4.470304 GCCCCTTTTAGGAGTAGAGAAGAA 59.530 45.833 0.00 0.00 37.67 2.52
2595 6050 4.031611 GCCCCTTTTAGGAGTAGAGAAGA 58.968 47.826 0.00 0.00 37.67 2.87
2596 6051 3.775316 TGCCCCTTTTAGGAGTAGAGAAG 59.225 47.826 0.00 0.00 37.67 2.85
2597 6052 3.775316 CTGCCCCTTTTAGGAGTAGAGAA 59.225 47.826 0.00 0.00 37.67 2.87
2616 6081 2.554462 GAGGTGAAAAGGAAGGAACTGC 59.446 50.000 0.00 0.00 40.86 4.40
2617 6082 3.149981 GGAGGTGAAAAGGAAGGAACTG 58.850 50.000 0.00 0.00 40.86 3.16
2710 7046 2.730404 CGCAGATCGATCTCATTCCAAG 59.270 50.000 25.00 12.25 41.67 3.61
2725 7061 2.425143 AACAATCATGACCCGCAGAT 57.575 45.000 0.00 0.00 0.00 2.90
2726 7062 2.198827 AAACAATCATGACCCGCAGA 57.801 45.000 0.00 0.00 0.00 4.26
2727 7063 2.223340 GCTAAACAATCATGACCCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
2768 7171 0.252927 AGAAGGAAGGAGAGGGGTGG 60.253 60.000 0.00 0.00 0.00 4.61
2792 7195 6.709846 GGAGGGAGACAAAGAGATATGATTTG 59.290 42.308 0.00 0.00 39.32 2.32
2812 7215 4.812091 CGATAGATATACGTGAGAGGAGGG 59.188 50.000 0.00 0.00 39.76 4.30
2813 7216 5.662456 TCGATAGATATACGTGAGAGGAGG 58.338 45.833 0.00 0.00 42.67 4.30
2861 7264 2.606795 CGGAAGAGGATCGATGAGAAGC 60.607 54.545 0.54 0.00 42.67 3.86
2865 7268 0.038709 GCCGGAAGAGGATCGATGAG 60.039 60.000 5.05 0.00 42.67 2.90
2866 7269 0.468214 AGCCGGAAGAGGATCGATGA 60.468 55.000 5.05 0.00 42.67 2.92
2867 7270 0.319383 CAGCCGGAAGAGGATCGATG 60.319 60.000 5.05 0.00 42.67 3.84
2868 7271 1.467678 CCAGCCGGAAGAGGATCGAT 61.468 60.000 5.05 0.00 42.67 3.59
2869 7272 2.127869 CCAGCCGGAAGAGGATCGA 61.128 63.158 5.05 0.00 42.67 3.59
2870 7273 2.356818 GACCAGCCGGAAGAGGATCG 62.357 65.000 5.05 0.00 36.53 3.69
2871 7274 1.045911 AGACCAGCCGGAAGAGGATC 61.046 60.000 5.05 1.46 35.59 3.36
2929 9895 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2931 9897 5.812642 AGAAACAACAACAACAACAACAACA 59.187 32.000 0.00 0.00 0.00 3.33
2932 9898 6.019479 TGAGAAACAACAACAACAACAACAAC 60.019 34.615 0.00 0.00 0.00 3.32
2935 9901 6.517914 TTGAGAAACAACAACAACAACAAC 57.482 33.333 0.00 0.00 33.18 3.32
2950 9960 9.880064 GTTTAATTACAAGGAGAGTTGAGAAAC 57.120 33.333 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.