Multiple sequence alignment - TraesCS2D01G306200

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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 TraesCS2D01G306200 chr2D 100.000 7321 0 0 1 7321 391849030 391856350 0.000000e+00 13520.0
1 TraesCS2D01G306200 chr2D 91.837 2401 146 25 1754 4137 392052528 392054895 0.000000e+00 3302.0
2 TraesCS2D01G306200 chr2D 91.806 2209 106 27 4187 6354 392054894 392057068 0.000000e+00 3007.0
3 TraesCS2D01G306200 chr2D 92.062 970 33 16 6393 7321 622502220 622503186 0.000000e+00 1325.0
4 TraesCS2D01G306200 chr2D 84.333 600 41 15 883 1460 392051780 392052348 8.360000e-149 538.0
5 TraesCS2D01G306200 chr2D 86.517 89 12 0 769 857 391867919 391868007 1.680000e-16 99.0
6 TraesCS2D01G306200 chr2B 96.392 5765 145 36 626 6354 463765449 463771186 0.000000e+00 9435.0
7 TraesCS2D01G306200 chr2B 92.918 2231 132 10 1918 4136 464021518 464023734 0.000000e+00 3221.0
8 TraesCS2D01G306200 chr2B 90.614 2461 151 43 1694 4137 463856119 463858516 0.000000e+00 3192.0
9 TraesCS2D01G306200 chr2B 92.978 2193 112 15 4189 6354 464023736 464025913 0.000000e+00 3158.0
10 TraesCS2D01G306200 chr2B 91.881 2217 112 19 4187 6354 463858515 463860712 0.000000e+00 3035.0
11 TraesCS2D01G306200 chr2B 83.253 1033 104 30 862 1866 464020299 464021290 0.000000e+00 885.0
12 TraesCS2D01G306200 chr2B 90.415 626 54 3 1 626 692476842 692476223 0.000000e+00 819.0
13 TraesCS2D01G306200 chr2B 89.052 612 54 9 17 626 39980297 39980897 0.000000e+00 747.0
14 TraesCS2D01G306200 chr2B 88.964 444 45 2 1 444 692482690 692482251 4.990000e-151 545.0
15 TraesCS2D01G306200 chr2B 80.940 766 72 34 883 1612 463855299 463856026 8.360000e-149 538.0
16 TraesCS2D01G306200 chr2A 96.515 5624 123 33 687 6259 528905109 528910710 0.000000e+00 9232.0
17 TraesCS2D01G306200 chr2A 90.909 2464 150 35 1690 4137 529792470 529794875 0.000000e+00 3241.0
18 TraesCS2D01G306200 chr2A 89.059 2541 165 43 1614 4137 529692131 529694575 0.000000e+00 3048.0
19 TraesCS2D01G306200 chr2A 91.302 2219 128 17 4187 6354 529794874 529797078 0.000000e+00 2968.0
20 TraesCS2D01G306200 chr2A 91.592 2129 112 15 4187 6263 529694574 529696687 0.000000e+00 2878.0
21 TraesCS2D01G306200 chr2A 83.148 629 50 22 852 1455 529791492 529792089 2.340000e-144 523.0
22 TraesCS2D01G306200 chr2A 84.318 491 52 13 1140 1612 529691601 529692084 2.410000e-124 457.0
23 TraesCS2D01G306200 chr2A 87.218 133 11 2 626 752 528905009 528905141 5.920000e-31 147.0
24 TraesCS2D01G306200 chr3D 92.380 958 40 4 6393 7321 293866575 293865622 0.000000e+00 1334.0
25 TraesCS2D01G306200 chr3D 91.327 957 26 4 6394 7321 402682762 402681834 0.000000e+00 1254.0
26 TraesCS2D01G306200 chr3D 90.121 496 26 9 6810 7286 152541015 152541506 2.240000e-174 623.0
27 TraesCS2D01G306200 chr3D 82.779 331 34 14 6592 6908 555535711 555535390 2.600000e-69 274.0
28 TraesCS2D01G306200 chr3D 96.875 32 1 0 6390 6421 275855925 275855956 4.000000e-03 54.7
29 TraesCS2D01G306200 chr5D 92.992 899 29 8 6384 7253 545339820 545340713 0.000000e+00 1280.0
30 TraesCS2D01G306200 chr5D 97.368 76 2 0 7246 7321 545342193 545342268 5.960000e-26 130.0
31 TraesCS2D01G306200 chr1D 91.536 957 24 4 6394 7321 253078615 253077687 0.000000e+00 1266.0
32 TraesCS2D01G306200 chr1B 92.173 626 49 0 1 626 401332560 401333185 0.000000e+00 885.0
33 TraesCS2D01G306200 chr1B 93.188 367 25 0 260 626 401331601 401331967 2.320000e-149 540.0
34 TraesCS2D01G306200 chr1B 89.811 265 27 0 1 265 401328703 401328967 2.530000e-89 340.0
35 TraesCS2D01G306200 chrUn 90.735 626 53 3 1 626 406960759 406960139 0.000000e+00 830.0
36 TraesCS2D01G306200 chrUn 88.964 444 45 2 1 444 290118551 290118990 4.990000e-151 545.0
37 TraesCS2D01G306200 chrUn 80.586 546 51 29 6393 6907 345161849 345162370 3.230000e-98 370.0
38 TraesCS2D01G306200 chr7A 88.084 621 72 2 1 621 444965356 444965974 0.000000e+00 736.0
39 TraesCS2D01G306200 chr6A 80.732 519 84 15 105 617 564591295 564590787 2.480000e-104 390.0
40 TraesCS2D01G306200 chr4D 80.435 552 53 29 6387 6907 490886076 490886603 3.230000e-98 370.0
41 TraesCS2D01G306200 chr5A 80.550 545 51 29 6394 6907 25128599 25129119 1.160000e-97 368.0
42 TraesCS2D01G306200 chr5A 96.970 33 1 0 2568 2600 444923498 444923530 1.000000e-03 56.5
43 TraesCS2D01G306200 chr6D 80.367 545 52 29 6394 6907 378805958 378805438 5.400000e-96 363.0
44 TraesCS2D01G306200 chr6D 95.614 228 5 3 6916 7143 312062136 312062358 1.940000e-95 361.0
45 TraesCS2D01G306200 chr6D 72.486 527 108 30 4324 4844 128257908 128258403 1.280000e-27 135.0
46 TraesCS2D01G306200 chr4B 95.614 228 5 3 6916 7143 311280379 311280157 1.940000e-95 361.0
47 TraesCS2D01G306200 chr4B 100.000 29 0 0 6393 6421 412035264 412035236 4.000000e-03 54.7
48 TraesCS2D01G306200 chr1A 95.614 228 5 3 6916 7143 343667790 343668012 1.940000e-95 361.0
49 TraesCS2D01G306200 chr1A 83.210 405 42 6 6394 6773 63750291 63750694 1.510000e-91 348.0
50 TraesCS2D01G306200 chr3A 87.946 224 17 5 6694 6908 748845435 748845657 9.430000e-64 255.0
51 TraesCS2D01G306200 chr7D 83.173 208 20 11 6697 6904 629594239 629594047 7.550000e-40 176.0
52 TraesCS2D01G306200 chr7D 88.889 72 8 0 573 644 602209125 602209196 1.010000e-13 89.8
53 TraesCS2D01G306200 chr7D 78.899 109 10 7 6540 6640 118220379 118220482 2.210000e-05 62.1
54 TraesCS2D01G306200 chr6B 72.727 528 104 32 4324 4844 227096126 227096620 2.750000e-29 141.0
55 TraesCS2D01G306200 chr7B 92.424 66 5 0 568 633 625972516 625972451 2.170000e-15 95.3
56 TraesCS2D01G306200 chr5B 83.951 81 13 0 2256 2336 62958498 62958578 2.190000e-10 78.7
57 TraesCS2D01G306200 chr5B 97.368 38 1 0 6384 6421 241199623 241199586 1.700000e-06 65.8
58 TraesCS2D01G306200 chr5B 94.118 34 2 0 6388 6421 246274345 246274378 1.300000e-02 52.8


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 TraesCS2D01G306200 chr2D 391849030 391856350 7320 False 13520.000000 13520 100.000000 1 7321 1 chr2D.!!$F1 7320
1 TraesCS2D01G306200 chr2D 392051780 392057068 5288 False 2282.333333 3302 89.325333 883 6354 3 chr2D.!!$F4 5471
2 TraesCS2D01G306200 chr2D 622502220 622503186 966 False 1325.000000 1325 92.062000 6393 7321 1 chr2D.!!$F3 928
3 TraesCS2D01G306200 chr2B 463765449 463771186 5737 False 9435.000000 9435 96.392000 626 6354 1 chr2B.!!$F2 5728
4 TraesCS2D01G306200 chr2B 464020299 464025913 5614 False 2421.333333 3221 89.716333 862 6354 3 chr2B.!!$F4 5492
5 TraesCS2D01G306200 chr2B 463855299 463860712 5413 False 2255.000000 3192 87.811667 883 6354 3 chr2B.!!$F3 5471
6 TraesCS2D01G306200 chr2B 692476223 692476842 619 True 819.000000 819 90.415000 1 626 1 chr2B.!!$R1 625
7 TraesCS2D01G306200 chr2B 39980297 39980897 600 False 747.000000 747 89.052000 17 626 1 chr2B.!!$F1 609
8 TraesCS2D01G306200 chr2A 528905009 528910710 5701 False 4689.500000 9232 91.866500 626 6259 2 chr2A.!!$F1 5633
9 TraesCS2D01G306200 chr2A 529791492 529797078 5586 False 2244.000000 3241 88.453000 852 6354 3 chr2A.!!$F3 5502
10 TraesCS2D01G306200 chr2A 529691601 529696687 5086 False 2127.666667 3048 88.323000 1140 6263 3 chr2A.!!$F2 5123
11 TraesCS2D01G306200 chr3D 293865622 293866575 953 True 1334.000000 1334 92.380000 6393 7321 1 chr3D.!!$R1 928
12 TraesCS2D01G306200 chr3D 402681834 402682762 928 True 1254.000000 1254 91.327000 6394 7321 1 chr3D.!!$R2 927
13 TraesCS2D01G306200 chr5D 545339820 545342268 2448 False 705.000000 1280 95.180000 6384 7321 2 chr5D.!!$F1 937
14 TraesCS2D01G306200 chr1D 253077687 253078615 928 True 1266.000000 1266 91.536000 6394 7321 1 chr1D.!!$R1 927
15 TraesCS2D01G306200 chr1B 401328703 401333185 4482 False 588.333333 885 91.724000 1 626 3 chr1B.!!$F1 625
16 TraesCS2D01G306200 chrUn 406960139 406960759 620 True 830.000000 830 90.735000 1 626 1 chrUn.!!$R1 625
17 TraesCS2D01G306200 chrUn 345161849 345162370 521 False 370.000000 370 80.586000 6393 6907 1 chrUn.!!$F2 514
18 TraesCS2D01G306200 chr7A 444965356 444965974 618 False 736.000000 736 88.084000 1 621 1 chr7A.!!$F1 620
19 TraesCS2D01G306200 chr6A 564590787 564591295 508 True 390.000000 390 80.732000 105 617 1 chr6A.!!$R1 512
20 TraesCS2D01G306200 chr4D 490886076 490886603 527 False 370.000000 370 80.435000 6387 6907 1 chr4D.!!$F1 520
21 TraesCS2D01G306200 chr5A 25128599 25129119 520 False 368.000000 368 80.550000 6394 6907 1 chr5A.!!$F1 513
22 TraesCS2D01G306200 chr6D 378805438 378805958 520 True 363.000000 363 80.367000 6394 6907 1 chr6D.!!$R1 513

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
75 76 0.031449 TACCCGTTGCAGCAAAAAGC 59.969 50.0 10.11 0.00 46.19 3.51 F
621 4490 0.031449 CCGCCGGTCACAAACATTTT 59.969 50.0 1.90 0.00 0.00 1.82 F
1389 5346 0.037734 TCGCTTTTCCCCTTCTTCCC 59.962 55.0 0.00 0.00 0.00 3.97 F
2746 7264 0.441533 GCTCGGCTCATGCATATTCG 59.558 55.0 0.00 1.63 41.91 3.34 F
3542 8064 0.251354 TGGAGATGGTGAGCAAGAGC 59.749 55.0 0.00 0.00 42.56 4.09 F
4270 8792 0.034186 TTCATGAGGATGGTGGTGCC 60.034 55.0 0.00 0.00 37.90 5.01 F
5099 9651 0.389817 TCAAAGAGCATCGTGGACGG 60.390 55.0 0.00 0.00 42.67 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 5723 0.464373 CGACTACCTACCTACCGCCA 60.464 60.000 0.00 0.00 0.00 5.69 R
2746 7264 2.099141 TACAGTCATGGCTGCTTGTC 57.901 50.000 26.95 0.00 39.96 3.18 R
3318 7840 8.358148 GGTCAATATTTTCTGCAGATGATGAAT 58.642 33.333 19.04 14.25 0.00 2.57 R
4068 8590 0.179045 ATCAATGCGCAGAGGGGTAC 60.179 55.000 18.32 0.00 0.00 3.34 R
4741 9264 1.134128 TCAGAACTTGCAGCCAACTCA 60.134 47.619 0.00 0.00 0.00 3.41 R
5431 10021 1.153289 CACGGCCCTCAATCTCAGG 60.153 63.158 0.00 0.00 0.00 3.86 R
6528 11187 0.741221 GAGTGATGGGGAACGAGTGC 60.741 60.000 0.00 0.00 0.00 4.40 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
74 75 2.124122 GTTACCCGTTGCAGCAAAAAG 58.876 47.619 10.11 4.49 0.00 2.27
75 76 0.031449 TACCCGTTGCAGCAAAAAGC 59.969 50.000 10.11 0.00 46.19 3.51
232 234 2.258013 CCTCGCCGGTTGCAGAAAA 61.258 57.895 1.90 0.00 41.33 2.29
243 245 3.128349 GTTGCAGAAAAGTACGACCTCA 58.872 45.455 0.00 0.00 0.00 3.86
292 2933 3.050089 GGTTGGAAGCAACCCATGA 57.950 52.632 0.00 0.00 46.62 3.07
298 2939 0.038166 GAAGCAACCCATGACCTCCA 59.962 55.000 0.00 0.00 0.00 3.86
321 2962 6.294675 CCATTTGCAAACACCTTTCTCTGATA 60.295 38.462 15.41 0.00 0.00 2.15
349 2991 3.288092 ACAAAACGGAGGAAAAGAGCTT 58.712 40.909 0.00 0.00 0.00 3.74
446 3095 0.930726 GAAGGAGAGAGAGGGGGAGA 59.069 60.000 0.00 0.00 0.00 3.71
617 4486 2.589442 GTCCGCCGGTCACAAACA 60.589 61.111 1.63 0.00 0.00 2.83
621 4490 0.031449 CCGCCGGTCACAAACATTTT 59.969 50.000 1.90 0.00 0.00 1.82
650 4519 4.211374 AGAAAACCATCGAAAACAGTCTCG 59.789 41.667 0.00 0.00 36.39 4.04
867 4777 3.174788 CGCCTAACGCCCTGAAAC 58.825 61.111 0.00 0.00 33.16 2.78
885 4796 0.769247 ACTTACCAAAACGCCCCTCT 59.231 50.000 0.00 0.00 0.00 3.69
1366 5307 3.518303 GTGTCCCTGTCTGGTACCTTTAT 59.482 47.826 14.36 0.00 0.00 1.40
1389 5346 0.037734 TCGCTTTTCCCCTTCTTCCC 59.962 55.000 0.00 0.00 0.00 3.97
1397 5354 1.918800 CCCTTCTTCCCCCTCACGT 60.919 63.158 0.00 0.00 0.00 4.49
1409 5366 0.871722 CCTCACGTTGGATTGCGAAA 59.128 50.000 0.00 0.00 0.00 3.46
1412 5369 2.147150 TCACGTTGGATTGCGAAATCA 58.853 42.857 17.95 1.58 0.00 2.57
1433 5393 1.464997 GAGGCGTGAACTGTGAATTCC 59.535 52.381 2.27 0.00 0.00 3.01
1440 5400 4.552767 CGTGAACTGTGAATTCCAAGTGTC 60.553 45.833 10.05 9.99 0.00 3.67
1462 5424 4.061596 CGAGGACTGCTTTTTCTTCTTCT 58.938 43.478 0.00 0.00 0.00 2.85
1463 5425 4.513318 CGAGGACTGCTTTTTCTTCTTCTT 59.487 41.667 0.00 0.00 0.00 2.52
1464 5426 5.333721 CGAGGACTGCTTTTTCTTCTTCTTC 60.334 44.000 0.00 0.00 0.00 2.87
1465 5427 4.824537 AGGACTGCTTTTTCTTCTTCTTCC 59.175 41.667 0.00 0.00 0.00 3.46
1466 5428 4.580580 GGACTGCTTTTTCTTCTTCTTCCA 59.419 41.667 0.00 0.00 0.00 3.53
1467 5429 5.242615 GGACTGCTTTTTCTTCTTCTTCCAT 59.757 40.000 0.00 0.00 0.00 3.41
1468 5430 6.431234 GGACTGCTTTTTCTTCTTCTTCCATA 59.569 38.462 0.00 0.00 0.00 2.74
1469 5431 7.121907 GGACTGCTTTTTCTTCTTCTTCCATAT 59.878 37.037 0.00 0.00 0.00 1.78
1470 5432 7.824672 ACTGCTTTTTCTTCTTCTTCCATATG 58.175 34.615 0.00 0.00 0.00 1.78
1471 5433 6.624423 TGCTTTTTCTTCTTCTTCCATATGC 58.376 36.000 0.00 0.00 0.00 3.14
1472 5434 6.435277 TGCTTTTTCTTCTTCTTCCATATGCT 59.565 34.615 0.00 0.00 0.00 3.79
1513 5493 2.841881 GTGGTTCCCATCCTTACTGGTA 59.158 50.000 0.00 0.00 35.28 3.25
1517 5497 5.015817 TGGTTCCCATCCTTACTGGTAAAAT 59.984 40.000 0.00 0.00 37.07 1.82
1524 5504 7.445402 CCCATCCTTACTGGTAAAATGATAGTG 59.555 40.741 12.88 0.00 37.07 2.74
1547 5527 1.740025 GTGTCCTGCTATTGAAGTGGC 59.260 52.381 0.00 0.00 0.00 5.01
1548 5528 1.009829 GTCCTGCTATTGAAGTGGCG 58.990 55.000 0.00 0.00 0.00 5.69
1612 5597 9.498176 TGAAGGATTTTACAGTAACTTTAGACC 57.502 33.333 0.00 0.00 0.00 3.85
1667 5709 2.289819 GGGGGTGTCGAAGTAACATTCA 60.290 50.000 0.00 0.00 0.00 2.57
1681 5723 9.271828 GAAGTAACATTCATTGGGAATTGTTTT 57.728 29.630 0.00 0.00 43.76 2.43
2746 7264 0.441533 GCTCGGCTCATGCATATTCG 59.558 55.000 0.00 1.63 41.91 3.34
2991 7511 1.335324 GCCGATTACATCAAGCATGCC 60.335 52.381 15.66 0.00 35.65 4.40
3025 7545 5.402398 CAAGAAAGCTTGCAAGGTATTACC 58.598 41.667 29.86 16.72 44.41 2.85
3093 7613 4.123276 TGCACGTTCGAGTTAATTGAAC 57.877 40.909 2.97 2.97 45.49 3.18
3542 8064 0.251354 TGGAGATGGTGAGCAAGAGC 59.749 55.000 0.00 0.00 42.56 4.09
3589 8111 3.391296 ACTTTGTCAGGGAGTTTGAGCTA 59.609 43.478 0.00 0.00 0.00 3.32
3691 8213 3.944015 AGAAGTCTTATGATGTTGCCAGC 59.056 43.478 0.00 0.00 0.00 4.85
4079 8601 2.277084 CAAACGTATGTACCCCTCTGC 58.723 52.381 0.00 0.00 0.00 4.26
4270 8792 0.034186 TTCATGAGGATGGTGGTGCC 60.034 55.000 0.00 0.00 37.90 5.01
4516 9038 6.782988 TCGAAATTCTATCCCAGGTAAGATCT 59.217 38.462 0.00 0.00 0.00 2.75
4741 9264 6.435277 AGGCAAGTCATGACAAATTATTGAGT 59.565 34.615 27.02 9.53 40.75 3.41
4767 9290 3.338249 TGGCTGCAAGTTCTGAAGATAC 58.662 45.455 0.50 0.00 31.15 2.24
4816 9339 2.825836 GTCATCAAGGGCCTGCGG 60.826 66.667 6.92 0.00 0.00 5.69
4844 9367 5.998363 ACTCTGGAAGAAATAAAGGTGTGTC 59.002 40.000 0.00 0.00 46.34 3.67
5099 9651 0.389817 TCAAAGAGCATCGTGGACGG 60.390 55.000 0.00 0.00 42.67 4.79
5212 9802 7.103641 TCTATTTGTTATCTGGTTCCTGACAC 58.896 38.462 0.72 2.78 0.00 3.67
5213 9803 4.974645 TTGTTATCTGGTTCCTGACACT 57.025 40.909 0.72 0.00 0.00 3.55
5214 9804 6.428083 TTTGTTATCTGGTTCCTGACACTA 57.572 37.500 0.72 0.00 0.00 2.74
5548 10139 7.150783 AGTCTGCAGGATTAAAACTTGAATC 57.849 36.000 15.13 0.00 0.00 2.52
6065 10659 5.368145 TCGCCTGAATGTGAATATAGCTTT 58.632 37.500 0.00 0.00 0.00 3.51
6354 11001 5.786401 ATATCTCGTTTGTTTGAGCAGTC 57.214 39.130 0.00 0.00 32.20 3.51
6355 11002 1.858458 TCTCGTTTGTTTGAGCAGTCG 59.142 47.619 0.00 0.00 32.20 4.18
6356 11003 0.303493 TCGTTTGTTTGAGCAGTCGC 59.697 50.000 0.00 0.00 38.99 5.19
6357 11004 0.027455 CGTTTGTTTGAGCAGTCGCA 59.973 50.000 0.00 0.00 42.27 5.10
6358 11005 1.334059 CGTTTGTTTGAGCAGTCGCAT 60.334 47.619 0.00 0.00 42.27 4.73
6359 11006 2.310577 GTTTGTTTGAGCAGTCGCATC 58.689 47.619 0.00 0.00 42.27 3.91
6360 11007 1.592064 TTGTTTGAGCAGTCGCATCA 58.408 45.000 0.00 0.00 42.27 3.07
6361 11008 1.812235 TGTTTGAGCAGTCGCATCAT 58.188 45.000 0.00 0.00 42.27 2.45
6362 11009 2.971307 TGTTTGAGCAGTCGCATCATA 58.029 42.857 0.00 0.00 42.27 2.15
6363 11010 3.534554 TGTTTGAGCAGTCGCATCATAT 58.465 40.909 0.00 0.00 42.27 1.78
6364 11011 3.310501 TGTTTGAGCAGTCGCATCATATG 59.689 43.478 0.00 0.00 42.27 1.78
6365 11012 2.159327 TGAGCAGTCGCATCATATGG 57.841 50.000 2.13 0.00 42.27 2.74
6366 11013 1.688197 TGAGCAGTCGCATCATATGGA 59.312 47.619 2.13 0.00 42.27 3.41
6367 11014 2.301009 TGAGCAGTCGCATCATATGGAT 59.699 45.455 2.13 0.00 42.27 3.41
6368 11015 3.244318 TGAGCAGTCGCATCATATGGATT 60.244 43.478 2.13 0.00 42.27 3.01
6369 11016 3.748083 AGCAGTCGCATCATATGGATTT 58.252 40.909 2.13 0.00 42.27 2.17
6370 11017 4.898320 AGCAGTCGCATCATATGGATTTA 58.102 39.130 2.13 0.00 42.27 1.40
6371 11018 5.494724 AGCAGTCGCATCATATGGATTTAT 58.505 37.500 2.13 0.00 42.27 1.40
6372 11019 5.583854 AGCAGTCGCATCATATGGATTTATC 59.416 40.000 2.13 0.00 42.27 1.75
6373 11020 5.583854 GCAGTCGCATCATATGGATTTATCT 59.416 40.000 2.13 0.00 38.36 1.98
6374 11021 6.456584 GCAGTCGCATCATATGGATTTATCTG 60.457 42.308 2.13 5.75 38.36 2.90
6375 11022 6.592994 CAGTCGCATCATATGGATTTATCTGT 59.407 38.462 2.13 0.00 32.57 3.41
6376 11023 7.118825 CAGTCGCATCATATGGATTTATCTGTT 59.881 37.037 2.13 0.00 32.57 3.16
6377 11024 8.314021 AGTCGCATCATATGGATTTATCTGTTA 58.686 33.333 2.13 0.00 32.57 2.41
6378 11025 8.935844 GTCGCATCATATGGATTTATCTGTTAA 58.064 33.333 2.13 0.00 32.57 2.01
6379 11026 9.500785 TCGCATCATATGGATTTATCTGTTAAA 57.499 29.630 2.13 0.00 32.57 1.52
6380 11027 9.764870 CGCATCATATGGATTTATCTGTTAAAG 57.235 33.333 2.13 0.00 33.40 1.85
6389 11036 8.303876 TGGATTTATCTGTTAAAGGCTCAAAAC 58.696 33.333 0.00 0.00 33.40 2.43
6390 11037 8.303876 GGATTTATCTGTTAAAGGCTCAAAACA 58.696 33.333 8.42 8.42 33.40 2.83
6456 11103 5.592688 TGCATACAAAATTTCCTAGGCTACC 59.407 40.000 2.96 0.00 0.00 3.18
6506 11165 1.447838 CGACCGACACATTCCCCTG 60.448 63.158 0.00 0.00 0.00 4.45
6511 11170 0.458543 CGACACATTCCCCTGTCTCG 60.459 60.000 0.00 0.00 35.58 4.04
6563 11222 3.163110 CTCGTCTCTCTCTCGCGCC 62.163 68.421 0.00 0.00 0.00 6.53
6619 11278 2.747460 GCATCTTGCTCCGCACCA 60.747 61.111 0.00 0.00 40.96 4.17
6909 11622 3.785859 GGAGCCGCATCTGGACCA 61.786 66.667 0.00 0.00 0.00 4.02
7089 11802 1.000359 GGGGCTGGGTAAACTGCAT 60.000 57.895 0.00 0.00 37.08 3.96
7125 11838 7.914427 ACTTCCCTAATTTGTTTTCCTCTTT 57.086 32.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.380410 GCTACAACCACGTGGCGAG 61.380 63.158 34.26 24.62 39.32 5.03
42 43 2.083167 CGGGTAACGGAAAAGCTACA 57.917 50.000 0.00 0.00 39.75 2.74
94 96 4.367023 AGGCGACGGCAAGCGTTA 62.367 61.111 24.23 0.00 42.47 3.18
101 103 3.583276 CTACAACCAGGCGACGGCA 62.583 63.158 24.23 0.00 42.47 5.69
232 234 1.075050 TCTCCTTGGTGAGGTCGTACT 59.925 52.381 0.00 0.00 46.39 2.73
243 245 1.296715 GGTCGTGCATCTCCTTGGT 59.703 57.895 0.00 0.00 0.00 3.67
292 2933 2.086610 AGGTGTTTGCAAATGGAGGT 57.913 45.000 16.21 0.00 0.00 3.85
298 2939 5.796424 ATCAGAGAAAGGTGTTTGCAAAT 57.204 34.783 16.21 0.00 0.00 2.32
321 2962 2.041251 TCCTCCGTTTTGTTTTCCGT 57.959 45.000 0.00 0.00 0.00 4.69
382 3027 1.150081 CCTCCCCTGTCATGGATGC 59.850 63.158 0.00 0.00 0.00 3.91
388 3033 0.690411 CTCTCTGCCTCCCCTGTCAT 60.690 60.000 0.00 0.00 0.00 3.06
446 3095 1.482593 GACCACTCGTTCAGATCCCAT 59.517 52.381 0.00 0.00 0.00 4.00
471 3120 3.702792 TCTCTTCCTCCGTTCAGATCTT 58.297 45.455 0.00 0.00 0.00 2.40
621 4490 6.544564 ACTGTTTTCGATGGTTTTCTTAAGGA 59.455 34.615 1.85 0.00 0.00 3.36
637 4506 6.744082 TGTATATGTGTACGAGACTGTTTTCG 59.256 38.462 12.20 12.20 42.26 3.46
650 4519 3.614159 TCGGAGCGTGTATATGTGTAC 57.386 47.619 0.00 0.00 0.00 2.90
788 4698 0.386731 CGTTGGGTTGACCGAATTGC 60.387 55.000 0.90 0.00 44.64 3.56
867 4777 1.003233 AGAGAGGGGCGTTTTGGTAAG 59.997 52.381 0.00 0.00 0.00 2.34
1286 5226 2.186903 GATTTCCTCGGCGCTGGA 59.813 61.111 17.88 14.40 0.00 3.86
1366 5307 3.069016 GGAAGAAGGGGAAAAGCGAAAAA 59.931 43.478 0.00 0.00 0.00 1.94
1389 5346 0.953471 TTCGCAATCCAACGTGAGGG 60.953 55.000 7.39 1.41 0.00 4.30
1397 5354 1.745087 GCCTCTGATTTCGCAATCCAA 59.255 47.619 5.32 0.00 38.50 3.53
1409 5366 0.969149 TCACAGTTCACGCCTCTGAT 59.031 50.000 0.00 0.00 33.93 2.90
1412 5369 2.417719 GAATTCACAGTTCACGCCTCT 58.582 47.619 0.00 0.00 0.00 3.69
1433 5393 1.871080 AAAGCAGTCCTCGACACTTG 58.129 50.000 0.00 0.00 33.63 3.16
1440 5400 4.061596 AGAAGAAGAAAAAGCAGTCCTCG 58.938 43.478 0.00 0.00 0.00 4.63
1462 5424 9.121658 CGAGGATAATAGTAGTAGCATATGGAA 57.878 37.037 4.56 0.00 0.00 3.53
1463 5425 8.272889 ACGAGGATAATAGTAGTAGCATATGGA 58.727 37.037 4.56 0.00 0.00 3.41
1464 5426 8.453238 ACGAGGATAATAGTAGTAGCATATGG 57.547 38.462 4.56 0.00 0.00 2.74
1465 5427 8.277018 CGACGAGGATAATAGTAGTAGCATATG 58.723 40.741 0.00 0.00 0.00 1.78
1466 5428 7.441760 CCGACGAGGATAATAGTAGTAGCATAT 59.558 40.741 0.00 0.00 45.00 1.78
1467 5429 6.760298 CCGACGAGGATAATAGTAGTAGCATA 59.240 42.308 0.00 0.00 45.00 3.14
1468 5430 5.585445 CCGACGAGGATAATAGTAGTAGCAT 59.415 44.000 0.00 0.00 45.00 3.79
1469 5431 4.934001 CCGACGAGGATAATAGTAGTAGCA 59.066 45.833 0.00 0.00 45.00 3.49
1470 5432 4.934602 ACCGACGAGGATAATAGTAGTAGC 59.065 45.833 8.56 0.00 45.00 3.58
1471 5433 5.350914 CCACCGACGAGGATAATAGTAGTAG 59.649 48.000 8.56 0.00 45.00 2.57
1472 5434 5.221722 ACCACCGACGAGGATAATAGTAGTA 60.222 44.000 12.38 0.00 45.00 1.82
1513 5493 3.009723 CAGGACACGCCACTATCATTTT 58.990 45.455 0.00 0.00 40.02 1.82
1517 5497 1.218047 GCAGGACACGCCACTATCA 59.782 57.895 0.00 0.00 40.02 2.15
1524 5504 1.009829 CTTCAATAGCAGGACACGCC 58.990 55.000 0.00 0.00 0.00 5.68
1612 5597 6.199719 GCTCAACCAAAAGAATTCTTTCACAG 59.800 38.462 28.87 20.16 44.69 3.66
1667 5709 1.696884 ACCGCCAAAACAATTCCCAAT 59.303 42.857 0.00 0.00 0.00 3.16
1681 5723 0.464373 CGACTACCTACCTACCGCCA 60.464 60.000 0.00 0.00 0.00 5.69
2746 7264 2.099141 TACAGTCATGGCTGCTTGTC 57.901 50.000 26.95 0.00 39.96 3.18
3093 7613 9.915629 AGCACCTATAATATACGAGAAGAAAAG 57.084 33.333 0.00 0.00 0.00 2.27
3318 7840 8.358148 GGTCAATATTTTCTGCAGATGATGAAT 58.642 33.333 19.04 14.25 0.00 2.57
3542 8064 1.479730 TGCTGACTCCATGAGTAGCTG 59.520 52.381 17.98 6.45 43.53 4.24
3589 8111 7.201893 GGTCCCTCGAGTATTGTCTTAACTAAT 60.202 40.741 12.31 0.00 0.00 1.73
3691 8213 7.141363 CCAACTGAGTCTTGAATTTACTTTGG 58.859 38.462 0.00 0.00 0.00 3.28
4068 8590 0.179045 ATCAATGCGCAGAGGGGTAC 60.179 55.000 18.32 0.00 0.00 3.34
4079 8601 3.066342 AGCTTTCCAGATGAATCAATGCG 59.934 43.478 0.00 0.00 31.67 4.73
4270 8792 4.447724 GCATCATTAGAATTGCCAGCAATG 59.552 41.667 18.02 6.82 44.86 2.82
4741 9264 1.134128 TCAGAACTTGCAGCCAACTCA 60.134 47.619 0.00 0.00 0.00 3.41
4767 9290 3.724508 ACGAGCTGACTCCATTATCAG 57.275 47.619 0.00 0.00 44.37 2.90
4816 9339 6.486993 ACACCTTTATTTCTTCCAGAGTGAAC 59.513 38.462 0.00 0.00 0.00 3.18
4844 9367 9.525007 GACAAGTTTAATGTATTAACACACTCG 57.475 33.333 0.00 0.00 38.78 4.18
5099 9651 2.208431 CCAGATGTTCGCTCCATTCTC 58.792 52.381 0.00 0.00 0.00 2.87
5212 9802 4.142381 GCCTGCCACAAAGGATTAAACTAG 60.142 45.833 0.00 0.00 41.22 2.57
5213 9803 3.761752 GCCTGCCACAAAGGATTAAACTA 59.238 43.478 0.00 0.00 41.22 2.24
5214 9804 2.562738 GCCTGCCACAAAGGATTAAACT 59.437 45.455 0.00 0.00 41.22 2.66
5431 10021 1.153289 CACGGCCCTCAATCTCAGG 60.153 63.158 0.00 0.00 0.00 3.86
5548 10139 6.037172 ACAAACAGTAAGTTCAGTTAGCACAG 59.963 38.462 0.00 0.00 40.26 3.66
6065 10659 6.261381 GTGTATTCACAGAACCAACCAAAGTA 59.739 38.462 0.00 0.00 43.37 2.24
6327 10974 8.177663 ACTGCTCAAACAAACGAGATATATTTG 58.822 33.333 0.00 0.00 38.89 2.32
6354 11001 9.764870 CTTTAACAGATAAATCCATATGATGCG 57.235 33.333 3.65 0.00 33.15 4.73
6358 11005 9.507329 GAGCCTTTAACAGATAAATCCATATGA 57.493 33.333 3.65 0.00 33.15 2.15
6359 11006 9.288576 TGAGCCTTTAACAGATAAATCCATATG 57.711 33.333 0.00 0.00 33.15 1.78
6360 11007 9.866655 TTGAGCCTTTAACAGATAAATCCATAT 57.133 29.630 0.00 0.00 33.15 1.78
6361 11008 9.693739 TTTGAGCCTTTAACAGATAAATCCATA 57.306 29.630 0.00 0.00 33.15 2.74
6362 11009 8.593945 TTTGAGCCTTTAACAGATAAATCCAT 57.406 30.769 0.00 0.00 33.15 3.41
6363 11010 8.303876 GTTTTGAGCCTTTAACAGATAAATCCA 58.696 33.333 0.00 0.00 33.15 3.41
6364 11011 8.303876 TGTTTTGAGCCTTTAACAGATAAATCC 58.696 33.333 0.00 0.00 33.15 3.01
6365 11012 9.860898 ATGTTTTGAGCCTTTAACAGATAAATC 57.139 29.630 0.00 0.00 34.37 2.17
6366 11013 9.860898 GATGTTTTGAGCCTTTAACAGATAAAT 57.139 29.630 0.00 0.00 34.37 1.40
6367 11014 9.077885 AGATGTTTTGAGCCTTTAACAGATAAA 57.922 29.630 0.00 0.00 34.37 1.40
6368 11015 8.635765 AGATGTTTTGAGCCTTTAACAGATAA 57.364 30.769 0.00 0.00 34.37 1.75
6369 11016 9.162764 GTAGATGTTTTGAGCCTTTAACAGATA 57.837 33.333 0.00 0.00 34.37 1.98
6370 11017 7.885399 AGTAGATGTTTTGAGCCTTTAACAGAT 59.115 33.333 0.00 0.00 34.37 2.90
6371 11018 7.224297 AGTAGATGTTTTGAGCCTTTAACAGA 58.776 34.615 0.00 0.00 34.37 3.41
6372 11019 7.361286 GGAGTAGATGTTTTGAGCCTTTAACAG 60.361 40.741 0.00 0.00 34.37 3.16
6373 11020 6.430000 GGAGTAGATGTTTTGAGCCTTTAACA 59.570 38.462 0.00 0.00 35.25 2.41
6374 11021 6.127980 GGGAGTAGATGTTTTGAGCCTTTAAC 60.128 42.308 0.00 0.00 0.00 2.01
6375 11022 5.944007 GGGAGTAGATGTTTTGAGCCTTTAA 59.056 40.000 0.00 0.00 0.00 1.52
6376 11023 5.250774 AGGGAGTAGATGTTTTGAGCCTTTA 59.749 40.000 0.00 0.00 0.00 1.85
6377 11024 4.043435 AGGGAGTAGATGTTTTGAGCCTTT 59.957 41.667 0.00 0.00 0.00 3.11
6378 11025 3.589288 AGGGAGTAGATGTTTTGAGCCTT 59.411 43.478 0.00 0.00 0.00 4.35
6379 11026 3.185455 AGGGAGTAGATGTTTTGAGCCT 58.815 45.455 0.00 0.00 0.00 4.58
6380 11027 3.198853 AGAGGGAGTAGATGTTTTGAGCC 59.801 47.826 0.00 0.00 0.00 4.70
6381 11028 4.187694 CAGAGGGAGTAGATGTTTTGAGC 58.812 47.826 0.00 0.00 0.00 4.26
6382 11029 5.413309 ACAGAGGGAGTAGATGTTTTGAG 57.587 43.478 0.00 0.00 0.00 3.02
6389 11036 2.656002 TCGGAACAGAGGGAGTAGATG 58.344 52.381 0.00 0.00 0.00 2.90
6390 11037 3.383698 TTCGGAACAGAGGGAGTAGAT 57.616 47.619 0.00 0.00 0.00 1.98
6456 11103 6.350629 AGAATGGGAAACTCAGGAAATTTG 57.649 37.500 0.00 0.00 0.00 2.32
6528 11187 0.741221 GAGTGATGGGGAACGAGTGC 60.741 60.000 0.00 0.00 0.00 4.40
6909 11622 3.369892 GGTCAGACCTTGATGCAGTACAT 60.370 47.826 12.94 0.00 38.29 2.29
6968 11681 4.519906 AGGTCTTGTTCAAAGGGAAGAA 57.480 40.909 0.00 0.00 36.51 2.52
7125 11838 1.570024 TCCATCCATCTGGCCAAATCA 59.430 47.619 7.01 0.00 36.16 2.57


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

AutoCloner maintained by Alex Coulton.