Multiple sequence alignment - TraesCS2D01G362300

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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 TraesCS2D01G362300 chr2D 100.000 3695 0 0 1 3695 468162699 468166393 0.000000e+00 6824.0
1 TraesCS2D01G362300 chr2D 82.390 159 25 2 1584 1742 111000339 111000494 6.440000e-28 135.0
2 TraesCS2D01G362300 chr2D 77.723 202 41 3 2328 2527 111001751 111001950 1.800000e-23 121.0
3 TraesCS2D01G362300 chr2B 92.469 2151 89 31 623 2728 546628663 546630785 0.000000e+00 3007.0
4 TraesCS2D01G362300 chr2B 93.246 844 20 15 1390 2218 546830342 546831163 0.000000e+00 1208.0
5 TraesCS2D01G362300 chr2B 87.077 650 54 18 1 632 546627772 546628409 0.000000e+00 708.0
6 TraesCS2D01G362300 chr2B 92.191 397 19 6 902 1287 546822880 546823275 5.390000e-153 551.0
7 TraesCS2D01G362300 chr2B 86.220 508 39 19 2211 2696 546780102 546780600 4.230000e-144 521.0
8 TraesCS2D01G362300 chr2B 86.842 456 36 13 2256 2696 546831158 546831604 4.290000e-134 488.0
9 TraesCS2D01G362300 chr2B 77.128 188 37 5 2328 2512 160754797 160754981 1.820000e-18 104.0
10 TraesCS2D01G362300 chr2A 89.360 1485 98 32 1316 2758 608250638 608252104 0.000000e+00 1812.0
11 TraesCS2D01G362300 chr2A 85.079 1327 104 36 1 1269 608249110 608250400 0.000000e+00 1267.0
12 TraesCS2D01G362300 chr2A 92.506 427 31 1 1822 2247 608258050 608258476 8.770000e-171 610.0
13 TraesCS2D01G362300 chr2A 95.000 40 2 0 1275 1314 608250581 608250620 3.080000e-06 63.9
14 TraesCS2D01G362300 chr5D 90.409 563 51 1 2793 3355 464405781 464405222 0.000000e+00 737.0
15 TraesCS2D01G362300 chr5D 91.118 304 22 2 3393 3695 464405222 464404923 1.240000e-109 407.0
16 TraesCS2D01G362300 chr6B 89.928 556 51 3 2798 3352 163946866 163947417 0.000000e+00 712.0
17 TraesCS2D01G362300 chr6B 88.948 561 54 5 2795 3352 567544117 567543562 0.000000e+00 686.0
18 TraesCS2D01G362300 chr6B 92.715 302 21 1 3395 3695 163947420 163947721 5.670000e-118 435.0
19 TraesCS2D01G362300 chr6B 90.132 304 29 1 3393 3695 155266650 155266347 9.620000e-106 394.0
20 TraesCS2D01G362300 chr3B 89.558 565 52 3 2792 3353 112905721 112905161 0.000000e+00 710.0
21 TraesCS2D01G362300 chr3B 89.520 563 54 3 2792 3353 422314422 422314980 0.000000e+00 708.0
22 TraesCS2D01G362300 chr3B 92.384 302 22 1 3395 3695 112905159 112904858 2.640000e-116 429.0
23 TraesCS2D01G362300 chr3A 88.752 569 54 7 2789 3352 472764925 472765488 0.000000e+00 688.0
24 TraesCS2D01G362300 chr3A 90.492 305 28 1 3392 3695 472765491 472765795 5.750000e-108 401.0
25 TraesCS2D01G362300 chr1A 88.830 564 56 4 2792 3352 562118218 562118777 0.000000e+00 686.0
26 TraesCS2D01G362300 chr1D 88.770 561 58 3 2792 3352 361101768 361102323 0.000000e+00 682.0
27 TraesCS2D01G362300 chr1D 91.722 302 21 2 3395 3695 478744077 478744375 2.050000e-112 416.0
28 TraesCS2D01G362300 chr1B 88.632 563 58 4 2792 3352 381500426 381500984 0.000000e+00 680.0
29 TraesCS2D01G362300 chr1B 91.262 309 25 2 3389 3695 668207537 668207229 1.590000e-113 420.0
30 TraesCS2D01G362300 chr7A 92.440 291 21 1 3406 3695 538983904 538983614 7.380000e-112 414.0
31 TraesCS2D01G362300 chr7D 92.226 283 20 2 3414 3695 264477218 264476937 2.070000e-107 399.0


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 TraesCS2D01G362300 chr2D 468162699 468166393 3694 False 6824.000000 6824 100.0000 1 3695 1 chr2D.!!$F1 3694
1 TraesCS2D01G362300 chr2B 546627772 546630785 3013 False 1857.500000 3007 89.7730 1 2728 2 chr2B.!!$F4 2727
2 TraesCS2D01G362300 chr2B 546830342 546831604 1262 False 848.000000 1208 90.0440 1390 2696 2 chr2B.!!$F5 1306
3 TraesCS2D01G362300 chr2A 608249110 608252104 2994 False 1047.633333 1812 89.8130 1 2758 3 chr2A.!!$F2 2757
4 TraesCS2D01G362300 chr5D 464404923 464405781 858 True 572.000000 737 90.7635 2793 3695 2 chr5D.!!$R1 902
5 TraesCS2D01G362300 chr6B 567543562 567544117 555 True 686.000000 686 88.9480 2795 3352 1 chr6B.!!$R2 557
6 TraesCS2D01G362300 chr6B 163946866 163947721 855 False 573.500000 712 91.3215 2798 3695 2 chr6B.!!$F1 897
7 TraesCS2D01G362300 chr3B 422314422 422314980 558 False 708.000000 708 89.5200 2792 3353 1 chr3B.!!$F1 561
8 TraesCS2D01G362300 chr3B 112904858 112905721 863 True 569.500000 710 90.9710 2792 3695 2 chr3B.!!$R1 903
9 TraesCS2D01G362300 chr3A 472764925 472765795 870 False 544.500000 688 89.6220 2789 3695 2 chr3A.!!$F1 906
10 TraesCS2D01G362300 chr1A 562118218 562118777 559 False 686.000000 686 88.8300 2792 3352 1 chr1A.!!$F1 560
11 TraesCS2D01G362300 chr1D 361101768 361102323 555 False 682.000000 682 88.7700 2792 3352 1 chr1D.!!$F1 560
12 TraesCS2D01G362300 chr1B 381500426 381500984 558 False 680.000000 680 88.6320 2792 3352 1 chr1B.!!$F1 560

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
466 488 0.108585 GTCTCCTGGGCACTGACAAA 59.891 55.0 0.0 0.0 0.00 2.83 F
601 647 0.252467 AGAGGGAGTGGAAGGACAGG 60.252 60.0 0.0 0.0 0.00 4.00 F
797 1111 0.523546 CCATCTCGTTCTCGTCCGTG 60.524 60.0 0.0 0.0 38.33 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2309 2914 0.321346 TGTCGATGCTGGTGATGTGT 59.679 50.0 0.00 0.00 0.00 3.72 R
2528 3133 0.104487 CTCACGAGATGATGCTGGCT 59.896 55.0 0.00 0.00 36.48 4.75 R
2699 3335 0.666274 CACTTGGAACGCAGCGTCTA 60.666 55.0 23.22 10.04 39.99 2.59 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
153 156 6.471146 AGATCATTGACTACATTGATAGGGC 58.529 40.000 0.00 0.00 42.96 5.19
154 157 4.631131 TCATTGACTACATTGATAGGGCG 58.369 43.478 0.00 0.00 33.40 6.13
190 193 8.830580 CCAATCTGTACAACAAAGGATAGTATG 58.169 37.037 0.00 0.00 0.00 2.39
271 277 3.485463 TGTACTTTCCTCAACCCACTG 57.515 47.619 0.00 0.00 0.00 3.66
385 407 6.458210 ACAAAATGTTTATGGCTTCCTTGAG 58.542 36.000 0.00 0.00 0.00 3.02
408 430 2.273619 AGTTGAGATCCCAGGCTTTCT 58.726 47.619 0.00 0.00 0.00 2.52
419 441 4.010349 CCCAGGCTTTCTACTTTGTTAGG 58.990 47.826 0.00 0.00 0.00 2.69
445 467 4.582869 AGATCATTGCAGCAAGTAGACAA 58.417 39.130 14.47 0.00 0.00 3.18
454 476 2.564947 AGCAAGTAGACAAGGTCTCCTG 59.435 50.000 1.55 0.89 42.40 3.86
460 482 1.462238 ACAAGGTCTCCTGGGCACT 60.462 57.895 0.00 0.00 32.13 4.40
461 483 1.002868 CAAGGTCTCCTGGGCACTG 60.003 63.158 0.00 0.00 32.13 3.66
462 484 1.152030 AAGGTCTCCTGGGCACTGA 60.152 57.895 0.00 0.00 32.13 3.41
464 486 2.217038 GGTCTCCTGGGCACTGACA 61.217 63.158 0.00 0.00 0.00 3.58
465 487 1.754745 GTCTCCTGGGCACTGACAA 59.245 57.895 0.00 0.00 0.00 3.18
466 488 0.108585 GTCTCCTGGGCACTGACAAA 59.891 55.000 0.00 0.00 0.00 2.83
467 489 0.843309 TCTCCTGGGCACTGACAAAA 59.157 50.000 0.00 0.00 0.00 2.44
468 490 1.425066 TCTCCTGGGCACTGACAAAAT 59.575 47.619 0.00 0.00 0.00 1.82
469 491 2.158475 TCTCCTGGGCACTGACAAAATT 60.158 45.455 0.00 0.00 0.00 1.82
470 492 2.629617 CTCCTGGGCACTGACAAAATTT 59.370 45.455 0.00 0.00 0.00 1.82
471 493 2.364970 TCCTGGGCACTGACAAAATTTG 59.635 45.455 3.89 3.89 0.00 2.32
473 495 3.432046 CCTGGGCACTGACAAAATTTGTT 60.432 43.478 13.00 0.00 45.52 2.83
474 496 4.190772 CTGGGCACTGACAAAATTTGTTT 58.809 39.130 13.00 0.00 45.52 2.83
476 498 3.559655 GGGCACTGACAAAATTTGTTTCC 59.440 43.478 13.00 9.31 45.52 3.13
477 499 3.245048 GGCACTGACAAAATTTGTTTCCG 59.755 43.478 13.00 4.23 45.52 4.30
478 500 3.245048 GCACTGACAAAATTTGTTTCCGG 59.755 43.478 13.00 7.89 45.52 5.14
479 501 3.245048 CACTGACAAAATTTGTTTCCGGC 59.755 43.478 13.00 0.00 45.52 6.13
480 502 3.118956 ACTGACAAAATTTGTTTCCGGCA 60.119 39.130 13.00 4.39 45.52 5.69
490 535 0.671251 GTTTCCGGCACAACCATTGA 59.329 50.000 0.00 0.00 39.03 2.57
499 544 2.607771 GCACAACCATTGACCATGACAC 60.608 50.000 0.00 0.00 34.31 3.67
503 548 1.339055 ACCATTGACCATGACACGAGG 60.339 52.381 0.00 0.00 34.31 4.63
504 549 1.066215 CCATTGACCATGACACGAGGA 60.066 52.381 0.00 0.00 34.31 3.71
505 550 2.420547 CCATTGACCATGACACGAGGAT 60.421 50.000 0.00 0.00 34.31 3.24
506 551 3.181466 CCATTGACCATGACACGAGGATA 60.181 47.826 0.00 0.00 34.31 2.59
507 552 4.441792 CATTGACCATGACACGAGGATAA 58.558 43.478 0.00 0.00 34.31 1.75
508 553 4.545208 TTGACCATGACACGAGGATAAA 57.455 40.909 0.00 0.00 0.00 1.40
509 554 4.545208 TGACCATGACACGAGGATAAAA 57.455 40.909 0.00 0.00 0.00 1.52
510 555 4.503910 TGACCATGACACGAGGATAAAAG 58.496 43.478 0.00 0.00 0.00 2.27
513 558 4.164221 ACCATGACACGAGGATAAAAGGAT 59.836 41.667 0.00 0.00 0.00 3.24
514 559 5.365605 ACCATGACACGAGGATAAAAGGATA 59.634 40.000 0.00 0.00 0.00 2.59
515 560 5.928839 CCATGACACGAGGATAAAAGGATAG 59.071 44.000 0.00 0.00 0.00 2.08
516 561 6.463049 CCATGACACGAGGATAAAAGGATAGT 60.463 42.308 0.00 0.00 0.00 2.12
591 636 3.086600 GGGCCAGGAGAGGGAGTG 61.087 72.222 4.39 0.00 0.00 3.51
601 647 0.252467 AGAGGGAGTGGAAGGACAGG 60.252 60.000 0.00 0.00 0.00 4.00
697 1005 8.284945 TGTATGTACTTGTAGAACTTACGGAT 57.715 34.615 0.00 0.00 30.45 4.18
698 1006 9.394767 TGTATGTACTTGTAGAACTTACGGATA 57.605 33.333 0.00 0.00 30.45 2.59
787 1101 4.410883 TGGGTTAACCATATCCATCTCGTT 59.589 41.667 25.71 0.00 46.80 3.85
789 1103 5.221661 GGGTTAACCATATCCATCTCGTTCT 60.222 44.000 25.71 0.00 39.85 3.01
790 1104 5.927115 GGTTAACCATATCCATCTCGTTCTC 59.073 44.000 20.12 0.00 35.64 2.87
792 1106 3.223435 ACCATATCCATCTCGTTCTCGT 58.777 45.455 0.00 0.00 38.33 4.18
793 1107 3.253677 ACCATATCCATCTCGTTCTCGTC 59.746 47.826 0.00 0.00 38.33 4.20
794 1108 3.366476 CCATATCCATCTCGTTCTCGTCC 60.366 52.174 0.00 0.00 38.33 4.79
796 1110 0.675837 TCCATCTCGTTCTCGTCCGT 60.676 55.000 0.00 0.00 38.33 4.69
797 1111 0.523546 CCATCTCGTTCTCGTCCGTG 60.524 60.000 0.00 0.00 38.33 4.94
981 1324 1.433837 GCCGCTACAAATACCCGTGG 61.434 60.000 0.00 0.00 0.00 4.94
1011 1354 2.134287 TCTAGCCATCGCCTCCACC 61.134 63.158 0.00 0.00 34.57 4.61
1035 1378 2.355513 GCTCTCTTCTCCATCCAGCAAA 60.356 50.000 0.00 0.00 0.00 3.68
1114 1460 2.280524 TTGTTAGCGCGCTGGTGT 60.281 55.556 41.85 19.86 0.00 4.16
1170 1516 1.078143 GCACTCGCCAAAGGAGGAT 60.078 57.895 0.00 0.00 35.82 3.24
1365 1902 7.101054 CACCTACTTACAAACTATTGGTGCTA 58.899 38.462 0.00 0.00 41.01 3.49
1800 2358 5.460091 TCTCTTCTCGATCACAAATAATGCG 59.540 40.000 0.00 0.00 0.00 4.73
1932 2498 3.138304 CAACAAGTCCTTCATCGTGGAA 58.862 45.455 0.00 0.00 33.72 3.53
2248 2841 0.603065 GACCATGGCCAACACTTTCC 59.397 55.000 10.96 0.00 0.00 3.13
2309 2914 2.186160 CCACGACCACTGCTTGCAA 61.186 57.895 0.00 0.00 0.00 4.08
2311 2916 1.451207 ACGACCACTGCTTGCAACA 60.451 52.632 0.00 0.00 0.00 3.33
2317 2922 1.601162 CCACTGCTTGCAACACATCAC 60.601 52.381 0.00 0.00 0.00 3.06
2450 3055 1.153489 CCTGTCCATGGAGCTCACG 60.153 63.158 16.81 0.00 0.00 4.35
2528 3133 4.680237 CTCACCAAGTCGGCGCCA 62.680 66.667 28.98 11.20 39.03 5.69
2543 3148 2.252346 GCCAGCCAGCATCATCTCG 61.252 63.158 0.00 0.00 0.00 4.04
2550 3160 1.489574 CAGCATCATCTCGTGAGCTC 58.510 55.000 6.82 6.82 40.92 4.09
2556 3166 4.308265 CATCATCTCGTGAGCTCATCAAT 58.692 43.478 21.47 8.71 40.43 2.57
2566 3188 1.143838 CTCATCAATGGGCCGACGA 59.856 57.895 0.00 0.00 0.00 4.20
2567 3189 1.153449 TCATCAATGGGCCGACGAC 60.153 57.895 0.00 0.00 0.00 4.34
2568 3190 2.202878 ATCAATGGGCCGACGACG 60.203 61.111 0.00 0.00 39.43 5.12
2605 3237 2.073816 ACCAGCTGTTTAAACCGATCG 58.926 47.619 15.59 8.51 0.00 3.69
2606 3238 2.289195 ACCAGCTGTTTAAACCGATCGA 60.289 45.455 18.66 0.00 0.00 3.59
2607 3239 2.936498 CCAGCTGTTTAAACCGATCGAT 59.064 45.455 18.66 0.00 0.00 3.59
2608 3240 3.001330 CCAGCTGTTTAAACCGATCGATC 59.999 47.826 18.66 15.68 0.00 3.69
2626 3258 1.234821 TCGGACGCAAATGCTTTCTT 58.765 45.000 3.63 0.00 39.32 2.52
2627 3259 1.606668 TCGGACGCAAATGCTTTCTTT 59.393 42.857 3.63 0.00 39.32 2.52
2628 3260 2.034053 TCGGACGCAAATGCTTTCTTTT 59.966 40.909 3.63 0.00 39.32 2.27
2629 3261 2.794350 CGGACGCAAATGCTTTCTTTTT 59.206 40.909 3.63 0.00 39.32 1.94
2681 3317 3.907894 TGTTCCTCCGTAACAAAATGC 57.092 42.857 0.00 0.00 34.04 3.56
2699 3335 8.891720 ACAAAATGCCATGCGAAATAAATTAAT 58.108 25.926 0.00 0.00 0.00 1.40
2728 3364 4.320023 TGCGTTCCAAGTGTATGTATGTT 58.680 39.130 0.00 0.00 0.00 2.71
2731 3367 5.064707 GCGTTCCAAGTGTATGTATGTTCAT 59.935 40.000 0.00 0.00 0.00 2.57
2732 3368 6.256975 GCGTTCCAAGTGTATGTATGTTCATA 59.743 38.462 0.00 0.00 0.00 2.15
2758 3394 3.068307 GCATCTATACAACGACTCCCACT 59.932 47.826 0.00 0.00 0.00 4.00
2759 3395 4.277672 GCATCTATACAACGACTCCCACTA 59.722 45.833 0.00 0.00 0.00 2.74
2760 3396 5.563085 GCATCTATACAACGACTCCCACTAG 60.563 48.000 0.00 0.00 0.00 2.57
2761 3397 3.881688 TCTATACAACGACTCCCACTAGC 59.118 47.826 0.00 0.00 0.00 3.42
2762 3398 1.913778 TACAACGACTCCCACTAGCA 58.086 50.000 0.00 0.00 0.00 3.49
2763 3399 0.317479 ACAACGACTCCCACTAGCAC 59.683 55.000 0.00 0.00 0.00 4.40
2764 3400 0.732880 CAACGACTCCCACTAGCACG 60.733 60.000 0.00 0.00 0.00 5.34
2765 3401 2.202623 CGACTCCCACTAGCACGC 60.203 66.667 0.00 0.00 0.00 5.34
2766 3402 2.970639 GACTCCCACTAGCACGCA 59.029 61.111 0.00 0.00 0.00 5.24
2767 3403 1.292223 GACTCCCACTAGCACGCAA 59.708 57.895 0.00 0.00 0.00 4.85
2769 3405 1.185618 ACTCCCACTAGCACGCAAGA 61.186 55.000 0.00 0.00 43.62 3.02
2770 3406 0.176680 CTCCCACTAGCACGCAAGAT 59.823 55.000 0.00 0.00 43.62 2.40
2771 3407 1.409064 CTCCCACTAGCACGCAAGATA 59.591 52.381 0.00 0.00 43.62 1.98
2772 3408 1.136305 TCCCACTAGCACGCAAGATAC 59.864 52.381 0.00 0.00 43.62 2.24
2773 3409 1.137086 CCCACTAGCACGCAAGATACT 59.863 52.381 0.00 0.00 43.62 2.12
2774 3410 2.361119 CCCACTAGCACGCAAGATACTA 59.639 50.000 0.00 0.00 43.62 1.82
2775 3411 3.551046 CCCACTAGCACGCAAGATACTAG 60.551 52.174 0.00 0.00 40.67 2.57
2776 3412 3.315470 CCACTAGCACGCAAGATACTAGA 59.685 47.826 0.00 0.00 39.31 2.43
2777 3413 4.202020 CCACTAGCACGCAAGATACTAGAA 60.202 45.833 0.00 0.00 39.31 2.10
2778 3414 5.508153 CCACTAGCACGCAAGATACTAGAAT 60.508 44.000 0.00 0.00 39.31 2.40
2779 3415 5.400782 CACTAGCACGCAAGATACTAGAATG 59.599 44.000 0.00 0.00 39.31 2.67
2780 3416 4.655762 AGCACGCAAGATACTAGAATGA 57.344 40.909 0.00 0.00 43.62 2.57
2781 3417 5.207110 AGCACGCAAGATACTAGAATGAT 57.793 39.130 0.00 0.00 43.62 2.45
2782 3418 5.605534 AGCACGCAAGATACTAGAATGATT 58.394 37.500 0.00 0.00 43.62 2.57
2783 3419 6.051717 AGCACGCAAGATACTAGAATGATTT 58.948 36.000 0.00 0.00 43.62 2.17
2784 3420 6.540189 AGCACGCAAGATACTAGAATGATTTT 59.460 34.615 0.00 0.00 43.62 1.82
2785 3421 6.630443 GCACGCAAGATACTAGAATGATTTTG 59.370 38.462 0.00 0.00 43.62 2.44
2786 3422 7.465916 GCACGCAAGATACTAGAATGATTTTGA 60.466 37.037 0.00 0.00 43.62 2.69
2787 3423 8.060679 CACGCAAGATACTAGAATGATTTTGAG 58.939 37.037 0.00 1.34 43.62 3.02
2788 3424 7.068341 CGCAAGATACTAGAATGATTTTGAGC 58.932 38.462 0.00 0.00 43.02 4.26
2789 3425 7.042187 CGCAAGATACTAGAATGATTTTGAGCT 60.042 37.037 0.00 0.00 43.02 4.09
2790 3426 8.281893 GCAAGATACTAGAATGATTTTGAGCTC 58.718 37.037 6.82 6.82 0.00 4.09
2850 3486 9.846248 ATTTCATTGATTAAGAAGGAAGTTTCG 57.154 29.630 0.00 0.00 32.33 3.46
2867 3503 0.030101 TCGAACAAAAGCCGCAAAGG 59.970 50.000 0.00 0.00 44.97 3.11
2914 3556 4.388773 TGTCTACTTTCGCAGCATTACAAG 59.611 41.667 0.00 0.00 0.00 3.16
2954 3596 1.513158 CATCGCCCGAAGAGACACT 59.487 57.895 0.00 0.00 0.00 3.55
2973 3615 3.372206 CACTTCCGCTTTGATCTTACTGG 59.628 47.826 0.00 0.00 0.00 4.00
3066 3708 2.281345 GCATCATCAGGGAGGCGG 60.281 66.667 0.00 0.00 34.70 6.13
3105 3747 1.425428 CGAATCTGAAGGTTGCCGC 59.575 57.895 0.00 0.00 0.00 6.53
3150 3793 4.010224 TCTGCCAAGCCGCCGTAA 62.010 61.111 0.00 0.00 0.00 3.18
3170 3813 5.220912 CGTAATGATGTGATGCATTCCAAGT 60.221 40.000 0.00 0.00 38.06 3.16
3186 3829 3.118408 TCCAAGTCACGGAAGAATATGGG 60.118 47.826 0.00 0.00 0.00 4.00
3234 3877 2.837031 GAAAAGGAGATGGGCGGCCA 62.837 60.000 34.65 34.65 0.00 5.36
3260 3903 0.109735 GGCGTTGCTTACAAAGAGGC 60.110 55.000 0.00 0.00 37.44 4.70
3315 3958 1.927174 GTCGATCCAGTGTCCAAATCG 59.073 52.381 0.00 0.00 40.30 3.34
3336 3982 3.252215 CGTATTTTGAAGGACAAGCCACA 59.748 43.478 0.00 0.00 39.77 4.17
3339 3985 2.363306 TTGAAGGACAAGCCACACAT 57.637 45.000 0.00 0.00 40.02 3.21
3355 4001 0.320421 ACATAGAACTTGCACCGCGT 60.320 50.000 4.92 0.00 0.00 6.01
3356 4002 0.095245 CATAGAACTTGCACCGCGTG 59.905 55.000 4.92 4.73 36.51 5.34
3357 4003 0.320421 ATAGAACTTGCACCGCGTGT 60.320 50.000 4.92 0.00 35.75 4.49
3368 4014 3.935872 CGCGTGTGTGTGGGTGTG 61.936 66.667 0.00 0.00 0.00 3.82
3369 4015 2.822255 GCGTGTGTGTGGGTGTGT 60.822 61.111 0.00 0.00 0.00 3.72
3370 4016 3.097672 CGTGTGTGTGGGTGTGTG 58.902 61.111 0.00 0.00 0.00 3.82
3371 4017 1.743623 CGTGTGTGTGGGTGTGTGT 60.744 57.895 0.00 0.00 0.00 3.72
3372 4018 1.800032 GTGTGTGTGGGTGTGTGTG 59.200 57.895 0.00 0.00 0.00 3.82
3373 4019 0.958382 GTGTGTGTGGGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
3374 4020 0.957888 TGTGTGTGGGTGTGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
3375 4021 0.958382 GTGTGTGGGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
3376 4022 0.613777 TGTGTGGGTGTGTGTGTGTA 59.386 50.000 0.00 0.00 0.00 2.90
3377 4023 1.210722 TGTGTGGGTGTGTGTGTGTAT 59.789 47.619 0.00 0.00 0.00 2.29
3378 4024 1.601903 GTGTGGGTGTGTGTGTGTATG 59.398 52.381 0.00 0.00 0.00 2.39
3379 4025 1.210722 TGTGGGTGTGTGTGTGTATGT 59.789 47.619 0.00 0.00 0.00 2.29
3380 4026 1.601903 GTGGGTGTGTGTGTGTATGTG 59.398 52.381 0.00 0.00 0.00 3.21
3381 4027 1.210722 TGGGTGTGTGTGTGTATGTGT 59.789 47.619 0.00 0.00 0.00 3.72
3382 4028 1.601903 GGGTGTGTGTGTGTATGTGTG 59.398 52.381 0.00 0.00 0.00 3.82
3383 4029 2.285083 GGTGTGTGTGTGTATGTGTGT 58.715 47.619 0.00 0.00 0.00 3.72
3384 4030 2.031560 GGTGTGTGTGTGTATGTGTGTG 59.968 50.000 0.00 0.00 0.00 3.82
3385 4031 2.675844 GTGTGTGTGTGTATGTGTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
3386 4032 2.675348 TGTGTGTGTGTATGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
3387 4033 2.675844 GTGTGTGTGTATGTGTGTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
3388 4034 2.675348 TGTGTGTGTATGTGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
3389 4035 2.675844 GTGTGTGTATGTGTGTGTGTGT 59.324 45.455 0.00 0.00 0.00 3.72
3390 4036 2.675348 TGTGTGTATGTGTGTGTGTGTG 59.325 45.455 0.00 0.00 0.00 3.82
3416 4062 4.021925 GGGCAGACCTTCCGCACT 62.022 66.667 0.00 0.00 35.85 4.40
3427 4073 1.939934 CTTCCGCACTGAGTGAACAAA 59.060 47.619 18.18 3.58 35.23 2.83
3463 4109 0.111253 CCCTCAAACTGAGCCCTGTT 59.889 55.000 0.00 0.00 42.98 3.16
3486 4132 3.764972 GGCTGAGAAAGTAGAGTACACCT 59.235 47.826 0.00 0.00 0.00 4.00
3557 4204 6.179040 CAAAGAGTCATGGAAATCTTCTCCT 58.821 40.000 0.00 0.00 33.77 3.69
3618 4269 2.479566 TTGGAGGTGTCAATGAGAGC 57.520 50.000 1.02 1.02 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 147 2.158667 GGGAGGAAAATCGCCCTATCAA 60.159 50.000 0.00 0.00 37.59 2.57
148 151 1.291109 TTGGGAGGAAAATCGCCCTA 58.709 50.000 0.00 0.00 41.28 3.53
153 156 4.513442 TGTACAGATTGGGAGGAAAATCG 58.487 43.478 0.00 0.00 37.77 3.34
154 157 5.710099 TGTTGTACAGATTGGGAGGAAAATC 59.290 40.000 0.00 0.00 33.77 2.17
190 193 6.040054 TCCCTAACCTACTTTTGAAAAGTTGC 59.960 38.462 26.04 0.00 0.00 4.17
288 294 3.391506 AGGCATTGGAGCTTTGTTTTC 57.608 42.857 0.00 0.00 34.17 2.29
385 407 0.915364 AGCCTGGGATCTCAACTTCC 59.085 55.000 0.00 0.00 0.00 3.46
408 430 8.856153 TGCAATGATCTTAACCTAACAAAGTA 57.144 30.769 0.00 0.00 0.00 2.24
419 441 6.092670 TGTCTACTTGCTGCAATGATCTTAAC 59.907 38.462 16.38 7.12 0.00 2.01
445 467 1.915769 GTCAGTGCCCAGGAGACCT 60.916 63.158 0.00 0.00 0.00 3.85
454 476 3.559655 GGAAACAAATTTTGTCAGTGCCC 59.440 43.478 14.80 6.92 44.59 5.36
460 482 3.190874 GTGCCGGAAACAAATTTTGTCA 58.809 40.909 14.80 5.30 44.59 3.58
461 483 3.190874 TGTGCCGGAAACAAATTTTGTC 58.809 40.909 14.80 4.11 44.59 3.18
464 486 2.939756 GGTTGTGCCGGAAACAAATTTT 59.060 40.909 20.75 0.00 39.14 1.82
465 487 2.093447 TGGTTGTGCCGGAAACAAATTT 60.093 40.909 20.75 0.00 39.14 1.82
466 488 1.482593 TGGTTGTGCCGGAAACAAATT 59.517 42.857 20.75 0.00 39.14 1.82
467 489 1.115467 TGGTTGTGCCGGAAACAAAT 58.885 45.000 20.75 0.00 39.14 2.32
468 490 1.115467 ATGGTTGTGCCGGAAACAAA 58.885 45.000 20.75 10.05 39.14 2.83
469 491 1.115467 AATGGTTGTGCCGGAAACAA 58.885 45.000 16.62 16.62 41.21 2.83
470 492 0.387202 CAATGGTTGTGCCGGAAACA 59.613 50.000 5.05 5.85 41.21 2.83
471 493 0.671251 TCAATGGTTGTGCCGGAAAC 59.329 50.000 5.05 6.05 41.21 2.78
473 495 1.175983 GGTCAATGGTTGTGCCGGAA 61.176 55.000 5.05 0.00 41.21 4.30
474 496 1.602323 GGTCAATGGTTGTGCCGGA 60.602 57.895 5.05 0.00 41.21 5.14
476 498 0.109179 CATGGTCAATGGTTGTGCCG 60.109 55.000 0.00 0.00 41.21 5.69
477 499 1.067635 GTCATGGTCAATGGTTGTGCC 60.068 52.381 0.00 0.00 36.86 5.01
478 500 1.612950 TGTCATGGTCAATGGTTGTGC 59.387 47.619 0.00 0.00 36.86 4.57
479 501 2.350676 CGTGTCATGGTCAATGGTTGTG 60.351 50.000 0.00 0.00 36.86 3.33
480 502 1.879380 CGTGTCATGGTCAATGGTTGT 59.121 47.619 0.00 0.00 36.86 3.32
490 535 3.517901 TCCTTTTATCCTCGTGTCATGGT 59.482 43.478 0.00 0.00 0.00 3.55
499 544 4.039245 TGGCTCACTATCCTTTTATCCTCG 59.961 45.833 0.00 0.00 0.00 4.63
503 548 3.495001 GCGTGGCTCACTATCCTTTTATC 59.505 47.826 4.21 0.00 31.34 1.75
504 549 3.467803 GCGTGGCTCACTATCCTTTTAT 58.532 45.455 4.21 0.00 31.34 1.40
505 550 2.419574 GGCGTGGCTCACTATCCTTTTA 60.420 50.000 4.21 0.00 31.34 1.52
506 551 1.679032 GGCGTGGCTCACTATCCTTTT 60.679 52.381 4.21 0.00 31.34 2.27
507 552 0.107654 GGCGTGGCTCACTATCCTTT 60.108 55.000 4.21 0.00 31.34 3.11
508 553 1.522569 GGCGTGGCTCACTATCCTT 59.477 57.895 4.21 0.00 31.34 3.36
509 554 2.435693 GGGCGTGGCTCACTATCCT 61.436 63.158 4.21 0.00 31.34 3.24
510 555 2.109181 GGGCGTGGCTCACTATCC 59.891 66.667 4.21 3.01 31.34 2.59
513 558 3.075005 GGAGGGCGTGGCTCACTA 61.075 66.667 4.21 0.00 31.34 2.74
515 560 4.101448 ATGGAGGGCGTGGCTCAC 62.101 66.667 0.00 0.00 0.00 3.51
516 561 3.785859 GATGGAGGGCGTGGCTCA 61.786 66.667 0.00 0.00 0.00 4.26
591 636 0.540597 AAGCAAAGCCCTGTCCTTCC 60.541 55.000 0.00 0.00 0.00 3.46
601 647 2.429739 GCACGCTCAAGCAAAGCC 60.430 61.111 2.50 0.00 42.21 4.35
699 1007 9.214962 GCCTAGGTATCCCTCAAGTTATATATT 57.785 37.037 11.31 0.00 41.45 1.28
700 1008 8.579259 AGCCTAGGTATCCCTCAAGTTATATAT 58.421 37.037 11.31 0.00 41.45 0.86
701 1009 7.839705 CAGCCTAGGTATCCCTCAAGTTATATA 59.160 40.741 11.31 0.00 41.45 0.86
721 1029 1.079127 GCTTGCGGAGAACAGCCTA 60.079 57.895 0.00 0.00 36.45 3.93
787 1101 1.301322 TTGCATTGCACGGACGAGA 60.301 52.632 11.66 0.00 38.71 4.04
789 1103 2.942879 GTTGCATTGCACGGACGA 59.057 55.556 11.66 0.00 38.71 4.20
790 1104 2.499520 CGTTGCATTGCACGGACG 60.500 61.111 17.00 17.00 38.71 4.79
792 1106 4.382114 CGCGTTGCATTGCACGGA 62.382 61.111 24.44 6.59 38.71 4.69
894 1232 2.021457 CACCCCCAATGATTTACGTCC 58.979 52.381 0.00 0.00 0.00 4.79
920 1258 2.202058 GCGTTCGAGCTTGCGTTC 60.202 61.111 0.00 0.00 0.00 3.95
1011 1354 2.742530 GCTGGATGGAGAAGAGAGCAAG 60.743 54.545 0.00 0.00 0.00 4.01
1035 1378 1.339610 CTAGGCGACTTGAGCTGCTAT 59.660 52.381 0.00 0.00 43.67 2.97
1161 1507 1.630878 GTGAGTGACCCATCCTCCTTT 59.369 52.381 0.00 0.00 0.00 3.11
1665 2212 1.593209 GAAGGCCGTGTCGTTGTCA 60.593 57.895 0.00 0.00 0.00 3.58
1932 2498 1.261480 AGAAGTCCACGATGTCTGCT 58.739 50.000 0.00 0.00 0.00 4.24
2213 2800 2.737544 TGGTCAGCCACAATAATGCAT 58.262 42.857 0.00 0.00 40.46 3.96
2214 2801 2.212812 TGGTCAGCCACAATAATGCA 57.787 45.000 0.00 0.00 40.46 3.96
2304 2909 1.270274 GATGCTGGTGATGTGTTGCAA 59.730 47.619 0.00 0.00 34.07 4.08
2309 2914 0.321346 TGTCGATGCTGGTGATGTGT 59.679 50.000 0.00 0.00 0.00 3.72
2311 2916 0.742281 GCTGTCGATGCTGGTGATGT 60.742 55.000 6.18 0.00 0.00 3.06
2528 3133 0.104487 CTCACGAGATGATGCTGGCT 59.896 55.000 0.00 0.00 36.48 4.75
2543 3148 1.442526 CGGCCCATTGATGAGCTCAC 61.443 60.000 20.97 13.56 31.62 3.51
2550 3160 2.525248 CGTCGTCGGCCCATTGATG 61.525 63.158 0.00 0.00 0.00 3.07
2568 3190 4.770874 TTAGCAACGGCCGGCTCC 62.771 66.667 28.66 14.65 42.56 4.70
2569 3191 3.497031 GTTAGCAACGGCCGGCTC 61.497 66.667 28.66 17.00 42.56 4.70
2572 3194 3.124921 CTGGTTAGCAACGGCCGG 61.125 66.667 31.76 14.21 42.56 6.13
2628 3260 3.244345 CGACACGCAGAAGACACTAAAAA 59.756 43.478 0.00 0.00 0.00 1.94
2629 3261 2.792674 CGACACGCAGAAGACACTAAAA 59.207 45.455 0.00 0.00 0.00 1.52
2630 3262 2.223641 ACGACACGCAGAAGACACTAAA 60.224 45.455 0.00 0.00 0.00 1.85
2658 3294 4.732784 CATTTTGTTACGGAGGAACATGG 58.267 43.478 0.00 0.00 36.71 3.66
2681 3317 7.269084 CAGCGTCTATTAATTTATTTCGCATGG 59.731 37.037 16.34 7.37 42.79 3.66
2699 3335 0.666274 CACTTGGAACGCAGCGTCTA 60.666 55.000 23.22 10.04 39.99 2.59
2728 3364 6.981722 AGTCGTTGTATAGATGCATGTATGA 58.018 36.000 22.98 10.70 0.00 2.15
2731 3367 5.278808 GGGAGTCGTTGTATAGATGCATGTA 60.279 44.000 2.46 4.50 0.00 2.29
2732 3368 4.501571 GGGAGTCGTTGTATAGATGCATGT 60.502 45.833 2.46 1.37 0.00 3.21
2737 3373 4.920640 AGTGGGAGTCGTTGTATAGATG 57.079 45.455 0.00 0.00 0.00 2.90
2738 3374 4.519730 GCTAGTGGGAGTCGTTGTATAGAT 59.480 45.833 0.00 0.00 0.00 1.98
2740 3376 3.630769 TGCTAGTGGGAGTCGTTGTATAG 59.369 47.826 0.00 0.00 0.00 1.31
2758 3394 5.767816 TCATTCTAGTATCTTGCGTGCTA 57.232 39.130 0.00 0.00 0.00 3.49
2759 3395 4.655762 TCATTCTAGTATCTTGCGTGCT 57.344 40.909 0.00 0.00 0.00 4.40
2760 3396 5.914085 AATCATTCTAGTATCTTGCGTGC 57.086 39.130 0.00 0.00 0.00 5.34
2761 3397 7.909267 TCAAAATCATTCTAGTATCTTGCGTG 58.091 34.615 0.00 0.00 0.00 5.34
2762 3398 7.254590 GCTCAAAATCATTCTAGTATCTTGCGT 60.255 37.037 0.00 0.00 0.00 5.24
2763 3399 7.042187 AGCTCAAAATCATTCTAGTATCTTGCG 60.042 37.037 0.00 0.00 0.00 4.85
2764 3400 8.152309 AGCTCAAAATCATTCTAGTATCTTGC 57.848 34.615 0.00 0.00 0.00 4.01
2765 3401 9.545105 AGAGCTCAAAATCATTCTAGTATCTTG 57.455 33.333 17.77 0.00 0.00 3.02
2850 3486 1.221466 GCCCTTTGCGGCTTTTGTTC 61.221 55.000 0.00 0.00 46.10 3.18
2899 3541 3.038788 TGAGTCTTGTAATGCTGCGAA 57.961 42.857 0.00 0.00 0.00 4.70
2954 3596 3.695830 ACCAGTAAGATCAAAGCGGAA 57.304 42.857 0.00 0.00 0.00 4.30
2973 3615 2.629051 CATCCCTTCCACGGTTCTAAC 58.371 52.381 0.00 0.00 0.00 2.34
3066 3708 2.682582 CTTGGATCCCCTAAGGCGCC 62.683 65.000 21.89 21.89 34.51 6.53
3105 3747 1.153489 CGGTGAGAGCATGGTGGAG 60.153 63.158 0.00 0.00 0.00 3.86
3150 3793 4.097437 GTGACTTGGAATGCATCACATCAT 59.903 41.667 0.00 0.00 38.34 2.45
3170 3813 5.943349 TTTAGACCCATATTCTTCCGTGA 57.057 39.130 0.00 0.00 0.00 4.35
3186 3829 2.277084 CTACACCACCCGCATTTAGAC 58.723 52.381 0.00 0.00 0.00 2.59
3210 3853 1.886222 CGCCCATCTCCTTTTCCAACA 60.886 52.381 0.00 0.00 0.00 3.33
3211 3854 0.811281 CGCCCATCTCCTTTTCCAAC 59.189 55.000 0.00 0.00 0.00 3.77
3234 3877 1.961793 TGTAAGCAACGCCAAGAGTT 58.038 45.000 0.00 0.00 0.00 3.01
3244 3887 2.485814 CTCTGGCCTCTTTGTAAGCAAC 59.514 50.000 3.32 0.00 33.82 4.17
3260 3903 4.085876 CCAAACTGTGGCCTCTGG 57.914 61.111 15.10 6.54 41.72 3.86
3292 3935 1.338107 TTGGACACTGGATCGACTGT 58.662 50.000 0.00 0.00 0.00 3.55
3304 3947 6.084277 GTCCTTCAAAATACGATTTGGACAC 58.916 40.000 15.06 4.41 40.04 3.67
3315 3958 4.037446 TGTGTGGCTTGTCCTTCAAAATAC 59.963 41.667 0.00 0.00 35.48 1.89
3336 3982 0.320421 ACGCGGTGCAAGTTCTATGT 60.320 50.000 12.47 0.00 0.00 2.29
3339 3985 1.068417 ACACGCGGTGCAAGTTCTA 59.932 52.632 12.47 0.00 36.98 2.10
3355 4001 0.957888 CACACACACACCCACACACA 60.958 55.000 0.00 0.00 0.00 3.72
3356 4002 0.958382 ACACACACACACCCACACAC 60.958 55.000 0.00 0.00 0.00 3.82
3357 4003 0.613777 TACACACACACACCCACACA 59.386 50.000 0.00 0.00 0.00 3.72
3358 4004 1.601903 CATACACACACACACCCACAC 59.398 52.381 0.00 0.00 0.00 3.82
3359 4005 1.210722 ACATACACACACACACCCACA 59.789 47.619 0.00 0.00 0.00 4.17
3360 4006 1.601903 CACATACACACACACACCCAC 59.398 52.381 0.00 0.00 0.00 4.61
3361 4007 1.210722 ACACATACACACACACACCCA 59.789 47.619 0.00 0.00 0.00 4.51
3362 4008 1.601903 CACACATACACACACACACCC 59.398 52.381 0.00 0.00 0.00 4.61
3363 4009 2.031560 CACACACATACACACACACACC 59.968 50.000 0.00 0.00 0.00 4.16
3364 4010 2.675844 ACACACACATACACACACACAC 59.324 45.455 0.00 0.00 0.00 3.82
3365 4011 2.675348 CACACACACATACACACACACA 59.325 45.455 0.00 0.00 0.00 3.72
3366 4012 2.675844 ACACACACACATACACACACAC 59.324 45.455 0.00 0.00 0.00 3.82
3367 4013 2.675348 CACACACACACATACACACACA 59.325 45.455 0.00 0.00 0.00 3.72
3368 4014 2.675844 ACACACACACACATACACACAC 59.324 45.455 0.00 0.00 0.00 3.82
3369 4015 2.675348 CACACACACACACATACACACA 59.325 45.455 0.00 0.00 0.00 3.72
3370 4016 2.031560 CCACACACACACACATACACAC 59.968 50.000 0.00 0.00 0.00 3.82
3371 4017 2.284190 CCACACACACACACATACACA 58.716 47.619 0.00 0.00 0.00 3.72
3372 4018 1.601903 CCCACACACACACACATACAC 59.398 52.381 0.00 0.00 0.00 2.90
3373 4019 1.475930 CCCCACACACACACACATACA 60.476 52.381 0.00 0.00 0.00 2.29
3374 4020 1.234821 CCCCACACACACACACATAC 58.765 55.000 0.00 0.00 0.00 2.39
3375 4021 0.109532 CCCCCACACACACACACATA 59.890 55.000 0.00 0.00 0.00 2.29
3376 4022 1.152777 CCCCCACACACACACACAT 60.153 57.895 0.00 0.00 0.00 3.21
3377 4023 2.273776 CCCCCACACACACACACA 59.726 61.111 0.00 0.00 0.00 3.72
3404 4050 0.033504 TTCACTCAGTGCGGAAGGTC 59.966 55.000 0.00 0.00 32.98 3.85
3412 4058 2.548057 TCGGATTTTGTTCACTCAGTGC 59.452 45.455 0.00 0.00 32.98 4.40
3416 4062 3.100658 TCGTCGGATTTTGTTCACTCA 57.899 42.857 0.00 0.00 0.00 3.41
3427 4073 0.531200 GGGACTCACTTCGTCGGATT 59.469 55.000 0.00 0.00 32.24 3.01
3463 4109 3.510360 GGTGTACTCTACTTTCTCAGCCA 59.490 47.826 0.00 0.00 0.00 4.75
3471 4117 5.187967 CCAAGGATGAGGTGTACTCTACTTT 59.812 44.000 0.00 0.00 46.72 2.66
3486 4132 3.874383 TTGGAAGTTCACCAAGGATGA 57.126 42.857 5.01 0.00 41.64 2.92
3532 4178 5.163673 GGAGAAGATTTCCATGACTCTTTGC 60.164 44.000 0.00 0.00 34.74 3.68
3618 4269 4.261994 CCCTTACCAACAACAACTGGATTG 60.262 45.833 0.00 0.00 44.60 2.67


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

AutoCloner maintained by Alex Coulton.