Multiple sequence alignment - TraesCS3D01G349700

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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 TraesCS3D01G349700 chr3D 100.000 4455 0 0 1 4455 461198453 461202907 0.000000e+00 8227.0
1 TraesCS3D01G349700 chr3D 96.610 59 0 2 530 588 549002220 549002164 3.670000e-16 97.1
2 TraesCS3D01G349700 chr3A 96.146 2932 83 8 593 3506 603789642 603792561 0.000000e+00 4761.0
3 TraesCS3D01G349700 chr3A 86.601 1015 53 15 3507 4452 603792719 603793719 0.000000e+00 1044.0
4 TraesCS3D01G349700 chr3A 91.699 518 37 4 1 514 603750160 603750675 0.000000e+00 713.0
5 TraesCS3D01G349700 chr3A 86.180 521 46 10 1 504 20396009 20396520 1.410000e-149 540.0
6 TraesCS3D01G349700 chr3B 96.080 2908 90 10 587 3490 611676076 611678963 0.000000e+00 4717.0
7 TraesCS3D01G349700 chr3B 88.783 419 26 11 3825 4231 611679003 611679412 1.110000e-135 494.0
8 TraesCS3D01G349700 chr3B 87.586 145 6 4 4318 4454 611679427 611679567 1.660000e-34 158.0
9 TraesCS3D01G349700 chr3B 96.154 52 1 1 529 580 786989526 786989576 2.860000e-12 84.2
10 TraesCS3D01G349700 chr1D 90.478 2699 188 28 1122 3790 471303057 471300398 0.000000e+00 3496.0
11 TraesCS3D01G349700 chr1D 85.749 414 33 12 2945 3332 471432555 471432968 8.920000e-112 414.0
12 TraesCS3D01G349700 chr1D 81.749 263 24 13 3539 3790 471297172 471296923 9.770000e-47 198.0
13 TraesCS3D01G349700 chr1D 92.857 70 5 0 3827 3896 303318900 303318969 7.880000e-18 102.0
14 TraesCS3D01G349700 chr1D 100.000 34 0 0 1028 1061 471303091 471303058 3.720000e-06 63.9
15 TraesCS3D01G349700 chr1B 90.063 2707 206 40 1122 3790 655104327 655101646 0.000000e+00 3450.0
16 TraesCS3D01G349700 chr1B 86.368 1049 109 21 2389 3410 655271553 655272594 0.000000e+00 1114.0
17 TraesCS3D01G349700 chr1B 92.857 70 5 0 3827 3896 410798095 410798164 7.880000e-18 102.0
18 TraesCS3D01G349700 chr1B 97.619 42 1 0 1020 1061 655104369 655104328 6.180000e-09 73.1
19 TraesCS3D01G349700 chr7D 95.798 1904 55 6 1916 3811 29536560 29534674 0.000000e+00 3049.0
20 TraesCS3D01G349700 chr7D 94.416 591 24 2 1329 1919 29537521 29536940 0.000000e+00 900.0
21 TraesCS3D01G349700 chr7D 81.701 623 58 17 3189 3789 613450060 613449472 6.750000e-128 468.0
22 TraesCS3D01G349700 chr7D 88.325 197 6 2 4049 4229 29534676 29534481 2.090000e-53 220.0
23 TraesCS3D01G349700 chr7D 96.610 59 2 0 530 588 189429408 189429350 1.020000e-16 99.0
24 TraesCS3D01G349700 chr7A 95.151 763 32 1 1329 2086 29781385 29780623 0.000000e+00 1199.0
25 TraesCS3D01G349700 chr7A 87.597 516 48 10 1 504 506276092 506275581 6.420000e-163 584.0
26 TraesCS3D01G349700 chr7A 87.403 516 49 10 1 504 620403864 620404375 2.990000e-161 579.0
27 TraesCS3D01G349700 chr7A 82.448 621 50 21 3189 3789 704893838 704893257 5.180000e-134 488.0
28 TraesCS3D01G349700 chr7A 93.750 64 3 1 526 588 579549958 579550021 1.320000e-15 95.3
29 TraesCS3D01G349700 chr6A 90.154 518 29 7 1 504 276308416 276308925 0.000000e+00 654.0
30 TraesCS3D01G349700 chr6A 84.942 259 31 5 3535 3790 607955813 607956066 5.720000e-64 255.0
31 TraesCS3D01G349700 chr6D 88.868 521 33 7 1 504 206552069 206551557 6.330000e-173 617.0
32 TraesCS3D01G349700 chr6D 85.821 268 28 7 3535 3797 461358576 461358838 4.390000e-70 276.0
33 TraesCS3D01G349700 chr7B 88.372 516 44 7 1 504 667284510 667285021 1.370000e-169 606.0
34 TraesCS3D01G349700 chr7B 96.262 107 4 0 3099 3205 703302127 703302021 4.580000e-40 176.0
35 TraesCS3D01G349700 chr7B 92.920 113 8 0 2947 3059 703302238 703302126 9.910000e-37 165.0
36 TraesCS3D01G349700 chrUn 87.037 540 55 8 1248 1787 1368158 1368682 2.970000e-166 595.0
37 TraesCS3D01G349700 chrUn 86.996 446 38 10 1342 1787 396328458 396328033 6.700000e-133 484.0
38 TraesCS3D01G349700 chrUn 85.542 83 7 2 981 1058 1366257 1366339 1.030000e-11 82.4
39 TraesCS3D01G349700 chrUn 84.884 86 8 2 981 1061 349798125 349798040 1.030000e-11 82.4
40 TraesCS3D01G349700 chrUn 89.062 64 1 2 530 588 337364392 337364454 1.720000e-09 75.0
41 TraesCS3D01G349700 chr5B 87.984 516 46 7 1 504 520852713 520853224 2.970000e-166 595.0
42 TraesCS3D01G349700 chr5B 87.984 516 46 7 1 504 585479453 585479964 2.970000e-166 595.0
43 TraesCS3D01G349700 chr5B 87.597 516 48 7 1 504 253188534 253189045 6.420000e-163 584.0
44 TraesCS3D01G349700 chr5B 90.625 64 3 1 528 591 486001420 486001360 1.030000e-11 82.4
45 TraesCS3D01G349700 chr1A 87.037 540 55 8 1248 1787 565571868 565572392 2.970000e-166 595.0
46 TraesCS3D01G349700 chr1A 91.045 67 6 0 3827 3893 380951208 380951274 1.710000e-14 91.6
47 TraesCS3D01G349700 chr1A 90.741 54 4 1 1006 1058 565569995 565570048 2.220000e-08 71.3
48 TraesCS3D01G349700 chr2A 85.687 517 52 11 1 504 142692440 142691933 3.950000e-145 525.0
49 TraesCS3D01G349700 chr6B 88.725 408 28 5 108 504 320407498 320407098 2.410000e-132 483.0
50 TraesCS3D01G349700 chr6B 84.556 259 32 5 3535 3790 702829277 702829530 2.660000e-62 250.0
51 TraesCS3D01G349700 chr4B 92.857 70 5 0 3827 3896 283728920 283728851 7.880000e-18 102.0
52 TraesCS3D01G349700 chr4B 91.803 61 4 1 527 586 273649173 273649113 2.860000e-12 84.2
53 TraesCS3D01G349700 chr2D 91.176 68 1 1 528 590 367592369 367592302 2.210000e-13 87.9
54 TraesCS3D01G349700 chr2D 90.000 70 2 3 527 591 367592301 367592370 7.940000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G349700 chr3D 461198453 461202907 4454 False 8227.000000 8227 100.000000 1 4455 1 chr3D.!!$F1 4454
1 TraesCS3D01G349700 chr3A 603789642 603793719 4077 False 2902.500000 4761 91.373500 593 4452 2 chr3A.!!$F3 3859
2 TraesCS3D01G349700 chr3A 603750160 603750675 515 False 713.000000 713 91.699000 1 514 1 chr3A.!!$F2 513
3 TraesCS3D01G349700 chr3A 20396009 20396520 511 False 540.000000 540 86.180000 1 504 1 chr3A.!!$F1 503
4 TraesCS3D01G349700 chr3B 611676076 611679567 3491 False 1789.666667 4717 90.816333 587 4454 3 chr3B.!!$F2 3867
5 TraesCS3D01G349700 chr1D 471296923 471303091 6168 True 1252.633333 3496 90.742333 1028 3790 3 chr1D.!!$R1 2762
6 TraesCS3D01G349700 chr1B 655101646 655104369 2723 True 1761.550000 3450 93.841000 1020 3790 2 chr1B.!!$R1 2770
7 TraesCS3D01G349700 chr1B 655271553 655272594 1041 False 1114.000000 1114 86.368000 2389 3410 1 chr1B.!!$F2 1021
8 TraesCS3D01G349700 chr7D 29534481 29537521 3040 True 1389.666667 3049 92.846333 1329 4229 3 chr7D.!!$R3 2900
9 TraesCS3D01G349700 chr7D 613449472 613450060 588 True 468.000000 468 81.701000 3189 3789 1 chr7D.!!$R2 600
10 TraesCS3D01G349700 chr7A 29780623 29781385 762 True 1199.000000 1199 95.151000 1329 2086 1 chr7A.!!$R1 757
11 TraesCS3D01G349700 chr7A 506275581 506276092 511 True 584.000000 584 87.597000 1 504 1 chr7A.!!$R2 503
12 TraesCS3D01G349700 chr7A 620403864 620404375 511 False 579.000000 579 87.403000 1 504 1 chr7A.!!$F2 503
13 TraesCS3D01G349700 chr7A 704893257 704893838 581 True 488.000000 488 82.448000 3189 3789 1 chr7A.!!$R3 600
14 TraesCS3D01G349700 chr6A 276308416 276308925 509 False 654.000000 654 90.154000 1 504 1 chr6A.!!$F1 503
15 TraesCS3D01G349700 chr6D 206551557 206552069 512 True 617.000000 617 88.868000 1 504 1 chr6D.!!$R1 503
16 TraesCS3D01G349700 chr7B 667284510 667285021 511 False 606.000000 606 88.372000 1 504 1 chr7B.!!$F1 503
17 TraesCS3D01G349700 chrUn 1366257 1368682 2425 False 338.700000 595 86.289500 981 1787 2 chrUn.!!$F2 806
18 TraesCS3D01G349700 chr5B 520852713 520853224 511 False 595.000000 595 87.984000 1 504 1 chr5B.!!$F2 503
19 TraesCS3D01G349700 chr5B 585479453 585479964 511 False 595.000000 595 87.984000 1 504 1 chr5B.!!$F3 503
20 TraesCS3D01G349700 chr5B 253188534 253189045 511 False 584.000000 584 87.597000 1 504 1 chr5B.!!$F1 503
21 TraesCS3D01G349700 chr1A 565569995 565572392 2397 False 333.150000 595 88.889000 1006 1787 2 chr1A.!!$F2 781
22 TraesCS3D01G349700 chr2A 142691933 142692440 507 True 525.000000 525 85.687000 1 504 1 chr2A.!!$R1 503

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
163 172 0.815213 GCATCATTGCCCAGCGTAGA 60.815 55.0 0.0 0.0 43.38 2.59 F
999 1036 0.108396 GCCACAGCCAAACCCAAATT 59.892 50.0 0.0 0.0 0.00 1.82 F
1796 3554 0.251474 TTGCAGCCAATGAGGAGCTT 60.251 50.0 0.0 0.0 41.22 3.74 F
2375 4516 0.681175 AAGCAATGTCAAAGGCCCAC 59.319 50.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1002 1039 0.095417 GAGAAGAACGGCGATGTTGC 59.905 55.0 16.62 1.11 30.75 4.17 R
1838 3596 1.470051 TCTCGTTGTCATCGGGATCA 58.530 50.0 1.65 0.00 32.69 2.92 R
3299 5454 2.490328 TTCTTCTGCAAACCAAAGCG 57.510 45.0 0.00 0.00 0.00 4.68 R
4202 8724 0.322975 GTGGATCTGACACTGCTGGT 59.677 55.0 0.00 0.00 35.98 4.00 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
40 41 7.118723 TGAGCATTATGAGGATTTGTAAAGGT 58.881 34.615 0.00 0.00 0.00 3.50
47 48 7.797121 ATGAGGATTTGTAAAGGTTTTGGAT 57.203 32.000 0.00 0.00 0.00 3.41
133 142 6.802608 ACATGTGCTTTCATCATATCAAAGG 58.197 36.000 0.00 0.00 0.00 3.11
140 149 7.496920 TGCTTTCATCATATCAAAGGTCTACAG 59.503 37.037 0.00 0.00 0.00 2.74
163 172 0.815213 GCATCATTGCCCAGCGTAGA 60.815 55.000 0.00 0.00 43.38 2.59
259 279 7.451566 TCATCCAGTGCAGCTAAGTATATCTAA 59.548 37.037 0.00 0.00 0.00 2.10
408 428 4.269844 TGCTTTTCTTGGTTCGATTTTTGC 59.730 37.500 0.00 0.00 0.00 3.68
410 430 3.972950 TTCTTGGTTCGATTTTTGCGA 57.027 38.095 0.00 0.00 35.76 5.10
416 436 2.515912 GTTCGATTTTTGCGATGTCCC 58.484 47.619 0.00 0.00 37.64 4.46
433 453 2.836981 GTCCCTCCTCCATGATATCAGG 59.163 54.545 11.78 11.09 0.00 3.86
466 486 3.544684 AGAATAAATGTCGCTCCATGCA 58.455 40.909 0.00 0.00 43.06 3.96
506 529 7.526192 GCCAAGAAGCTCAGTTAGGATATATCA 60.526 40.741 14.60 0.00 0.00 2.15
507 530 8.538701 CCAAGAAGCTCAGTTAGGATATATCAT 58.461 37.037 14.60 10.02 0.00 2.45
508 531 9.368674 CAAGAAGCTCAGTTAGGATATATCATG 57.631 37.037 14.60 5.24 0.00 3.07
510 533 8.530311 AGAAGCTCAGTTAGGATATATCATGTG 58.470 37.037 14.60 7.31 0.00 3.21
511 534 7.789202 AGCTCAGTTAGGATATATCATGTGT 57.211 36.000 14.60 0.00 0.00 3.72
512 535 8.200024 AGCTCAGTTAGGATATATCATGTGTT 57.800 34.615 14.60 2.25 0.00 3.32
513 536 8.093307 AGCTCAGTTAGGATATATCATGTGTTG 58.907 37.037 14.60 6.01 0.00 3.33
514 537 7.148507 GCTCAGTTAGGATATATCATGTGTTGC 60.149 40.741 14.60 10.97 0.00 4.17
515 538 7.734942 TCAGTTAGGATATATCATGTGTTGCA 58.265 34.615 14.60 0.00 0.00 4.08
516 539 7.657354 TCAGTTAGGATATATCATGTGTTGCAC 59.343 37.037 14.60 0.00 34.56 4.57
517 540 6.646653 AGTTAGGATATATCATGTGTTGCACG 59.353 38.462 14.60 0.00 37.14 5.34
518 541 4.960938 AGGATATATCATGTGTTGCACGT 58.039 39.130 14.60 0.00 37.14 4.49
519 542 6.096673 AGGATATATCATGTGTTGCACGTA 57.903 37.500 14.60 0.00 37.14 3.57
520 543 5.926542 AGGATATATCATGTGTTGCACGTAC 59.073 40.000 14.60 0.00 37.14 3.67
521 544 5.694458 GGATATATCATGTGTTGCACGTACA 59.306 40.000 14.60 0.00 37.14 2.90
522 545 6.368791 GGATATATCATGTGTTGCACGTACAT 59.631 38.462 14.60 4.34 37.14 2.29
524 547 1.196581 TCATGTGTTGCACGTACATGC 59.803 47.619 22.73 7.04 46.88 4.06
525 548 1.197492 CATGTGTTGCACGTACATGCT 59.803 47.619 15.74 0.00 46.28 3.79
526 549 1.304254 TGTGTTGCACGTACATGCTT 58.696 45.000 15.74 0.00 46.28 3.91
527 550 2.484889 TGTGTTGCACGTACATGCTTA 58.515 42.857 15.74 0.21 46.28 3.09
528 551 2.222213 TGTGTTGCACGTACATGCTTAC 59.778 45.455 15.74 13.07 46.28 2.34
529 552 2.478894 GTGTTGCACGTACATGCTTACT 59.521 45.455 15.74 0.00 46.28 2.24
530 553 3.676172 GTGTTGCACGTACATGCTTACTA 59.324 43.478 15.74 2.57 46.28 1.82
531 554 3.676172 TGTTGCACGTACATGCTTACTAC 59.324 43.478 15.74 6.19 46.28 2.73
532 555 3.861276 TGCACGTACATGCTTACTACT 57.139 42.857 15.74 0.00 46.28 2.57
533 556 3.766151 TGCACGTACATGCTTACTACTC 58.234 45.455 15.74 0.00 46.28 2.59
534 557 3.114065 GCACGTACATGCTTACTACTCC 58.886 50.000 6.68 0.00 42.62 3.85
535 558 3.703420 CACGTACATGCTTACTACTCCC 58.297 50.000 0.00 0.00 0.00 4.30
536 559 3.380637 CACGTACATGCTTACTACTCCCT 59.619 47.826 0.00 0.00 0.00 4.20
537 560 3.631227 ACGTACATGCTTACTACTCCCTC 59.369 47.826 0.00 0.00 0.00 4.30
538 561 3.004524 CGTACATGCTTACTACTCCCTCC 59.995 52.174 0.00 0.00 0.00 4.30
539 562 2.032620 ACATGCTTACTACTCCCTCCG 58.967 52.381 0.00 0.00 0.00 4.63
540 563 2.032620 CATGCTTACTACTCCCTCCGT 58.967 52.381 0.00 0.00 0.00 4.69
541 564 2.226962 TGCTTACTACTCCCTCCGTT 57.773 50.000 0.00 0.00 0.00 4.44
542 565 2.532843 TGCTTACTACTCCCTCCGTTT 58.467 47.619 0.00 0.00 0.00 3.60
543 566 2.494870 TGCTTACTACTCCCTCCGTTTC 59.505 50.000 0.00 0.00 0.00 2.78
544 567 2.494870 GCTTACTACTCCCTCCGTTTCA 59.505 50.000 0.00 0.00 0.00 2.69
545 568 3.056322 GCTTACTACTCCCTCCGTTTCAA 60.056 47.826 0.00 0.00 0.00 2.69
546 569 4.562143 GCTTACTACTCCCTCCGTTTCAAA 60.562 45.833 0.00 0.00 0.00 2.69
547 570 5.544650 CTTACTACTCCCTCCGTTTCAAAA 58.455 41.667 0.00 0.00 0.00 2.44
548 571 4.635699 ACTACTCCCTCCGTTTCAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
549 572 5.750352 ACTACTCCCTCCGTTTCAAAATA 57.250 39.130 0.00 0.00 0.00 1.40
550 573 5.731591 ACTACTCCCTCCGTTTCAAAATAG 58.268 41.667 0.00 0.00 0.00 1.73
551 574 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
552 575 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
553 576 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
554 577 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
555 578 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
556 579 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
557 580 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
558 581 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
559 582 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
560 583 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
561 584 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
562 585 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
563 586 6.801862 CGTTTCAAAATAGATGACCCAACTTC 59.198 38.462 0.00 0.00 0.00 3.01
564 587 7.521423 CGTTTCAAAATAGATGACCCAACTTCA 60.521 37.037 0.00 0.00 0.00 3.02
565 588 8.306761 GTTTCAAAATAGATGACCCAACTTCAT 58.693 33.333 0.00 0.00 36.37 2.57
566 589 7.630242 TCAAAATAGATGACCCAACTTCATC 57.370 36.000 4.48 4.48 46.71 2.92
574 597 7.630242 GATGACCCAACTTCATCTATTTTGA 57.370 36.000 5.29 0.00 44.12 2.69
575 598 8.055279 GATGACCCAACTTCATCTATTTTGAA 57.945 34.615 5.29 0.00 44.12 2.69
576 599 7.831691 TGACCCAACTTCATCTATTTTGAAA 57.168 32.000 0.00 0.00 32.98 2.69
577 600 7.657336 TGACCCAACTTCATCTATTTTGAAAC 58.343 34.615 0.00 0.00 32.98 2.78
578 601 6.677913 ACCCAACTTCATCTATTTTGAAACG 58.322 36.000 0.00 0.00 32.98 3.60
579 602 6.092748 CCCAACTTCATCTATTTTGAAACGG 58.907 40.000 0.00 0.00 32.98 4.44
580 603 6.072175 CCCAACTTCATCTATTTTGAAACGGA 60.072 38.462 0.00 0.00 32.98 4.69
581 604 7.023575 CCAACTTCATCTATTTTGAAACGGAG 58.976 38.462 0.00 0.00 32.98 4.63
582 605 6.743575 ACTTCATCTATTTTGAAACGGAGG 57.256 37.500 0.00 0.00 32.98 4.30
583 606 5.648092 ACTTCATCTATTTTGAAACGGAGGG 59.352 40.000 0.00 0.00 32.98 4.30
584 607 5.429681 TCATCTATTTTGAAACGGAGGGA 57.570 39.130 0.00 0.00 0.00 4.20
585 608 5.428253 TCATCTATTTTGAAACGGAGGGAG 58.572 41.667 0.00 0.00 0.00 4.30
625 648 7.876936 ATTGAATTCATAACTGACTCAGCAT 57.123 32.000 9.40 0.00 34.37 3.79
706 733 1.006922 GCAGTTTGCCAGCACTTCC 60.007 57.895 0.00 0.00 37.42 3.46
801 836 1.202698 CCGATCCAAAGAGGCCCTTAG 60.203 57.143 0.00 0.00 37.29 2.18
819 855 6.460261 GCCCTTAGAAGCCATATTTTGACTTC 60.460 42.308 0.00 0.00 37.58 3.01
820 856 6.830838 CCCTTAGAAGCCATATTTTGACTTCT 59.169 38.462 9.77 9.77 46.50 2.85
880 917 2.923035 CCTGTCCTCACACCCCGT 60.923 66.667 0.00 0.00 0.00 5.28
905 942 1.777941 CGGAGCTCTAACCCTAACCT 58.222 55.000 14.64 0.00 0.00 3.50
906 943 2.941480 CGGAGCTCTAACCCTAACCTA 58.059 52.381 14.64 0.00 0.00 3.08
908 945 3.067883 CGGAGCTCTAACCCTAACCTAAC 59.932 52.174 14.64 0.00 0.00 2.34
910 947 3.382278 AGCTCTAACCCTAACCTAACCC 58.618 50.000 0.00 0.00 0.00 4.11
911 948 3.013763 AGCTCTAACCCTAACCTAACCCT 59.986 47.826 0.00 0.00 0.00 4.34
912 949 4.233755 AGCTCTAACCCTAACCTAACCCTA 59.766 45.833 0.00 0.00 0.00 3.53
913 950 4.588106 GCTCTAACCCTAACCTAACCCTAG 59.412 50.000 0.00 0.00 0.00 3.02
914 951 4.550669 TCTAACCCTAACCTAACCCTAGC 58.449 47.826 0.00 0.00 0.00 3.42
915 952 1.785647 ACCCTAACCTAACCCTAGCG 58.214 55.000 0.00 0.00 0.00 4.26
999 1036 0.108396 GCCACAGCCAAACCCAAATT 59.892 50.000 0.00 0.00 0.00 1.82
1002 1039 0.678950 ACAGCCAAACCCAAATTCCG 59.321 50.000 0.00 0.00 0.00 4.30
1026 1071 0.684805 ATCGCCGTTCTTCTCCTCCT 60.685 55.000 0.00 0.00 0.00 3.69
1796 3554 0.251474 TTGCAGCCAATGAGGAGCTT 60.251 50.000 0.00 0.00 41.22 3.74
1836 3594 1.593296 GGCAAAGCTTGAGGCCTCTG 61.593 60.000 32.28 24.40 43.09 3.35
1838 3596 1.954258 GCAAAGCTTGAGGCCTCTGAT 60.954 52.381 32.28 20.82 43.05 2.90
1895 3653 5.127693 ACGAGAAGCTAAATCTATGCGAT 57.872 39.130 0.00 0.00 0.00 4.58
2375 4516 0.681175 AAGCAATGTCAAAGGCCCAC 59.319 50.000 0.00 0.00 0.00 4.61
2543 4684 3.499338 TCAGCTCATTGATGTGGGTTTT 58.501 40.909 0.00 0.00 33.14 2.43
3273 5428 4.218312 AGCTGGTTTGTTCTCCTGAAATT 58.782 39.130 0.00 0.00 33.52 1.82
3299 5454 8.405531 TCCATGTATTATTAGCAGCTTTTGTTC 58.594 33.333 0.00 0.00 0.00 3.18
3314 5473 1.098869 TGTTCGCTTTGGTTTGCAGA 58.901 45.000 0.00 0.00 0.00 4.26
3315 5474 1.474478 TGTTCGCTTTGGTTTGCAGAA 59.526 42.857 0.00 0.00 0.00 3.02
3316 5475 2.119457 GTTCGCTTTGGTTTGCAGAAG 58.881 47.619 0.00 0.00 0.00 2.85
3468 5645 2.980541 CCAATGCATCTTGGGTGGT 58.019 52.632 10.73 0.00 41.71 4.16
3469 5646 2.142356 CCAATGCATCTTGGGTGGTA 57.858 50.000 10.73 0.00 41.71 3.25
3470 5647 2.669781 CCAATGCATCTTGGGTGGTAT 58.330 47.619 10.73 0.00 41.71 2.73
3471 5648 3.831323 CCAATGCATCTTGGGTGGTATA 58.169 45.455 10.73 0.00 41.71 1.47
3697 6044 4.878397 ACTGGCTACATGAATTTAGCTGTC 59.122 41.667 11.54 0.00 40.57 3.51
3784 6132 8.702163 ATGTTTTGAGGAACTTAAGTTGTTTG 57.298 30.769 25.17 0.00 41.55 2.93
4197 8719 1.797025 ACCGTAGCTCTTTTGCACTC 58.203 50.000 0.00 0.00 34.99 3.51
4201 8723 1.727335 GTAGCTCTTTTGCACTCGTCC 59.273 52.381 0.00 0.00 34.99 4.79
4202 8724 0.106708 AGCTCTTTTGCACTCGTCCA 59.893 50.000 0.00 0.00 34.99 4.02
4231 8753 2.289257 TGTCAGATCCACAGCTGAACAG 60.289 50.000 23.35 6.98 46.59 3.16
4248 8770 6.569226 GCTGAACAGTGTCTATTGCAAATCTT 60.569 38.462 1.71 0.00 0.00 2.40
4272 8794 9.167311 CTTATTACTATTCTTGTTGCTCTTGGT 57.833 33.333 0.00 0.00 0.00 3.67
4274 8796 4.327680 ACTATTCTTGTTGCTCTTGGTCC 58.672 43.478 0.00 0.00 0.00 4.46
4276 8798 2.260844 TCTTGTTGCTCTTGGTCCTG 57.739 50.000 0.00 0.00 0.00 3.86
4282 8804 5.235850 TGTTGCTCTTGGTCCTGTAATTA 57.764 39.130 0.00 0.00 0.00 1.40
4294 8816 9.778741 TTGGTCCTGTAATTATTCTTATAGCTG 57.221 33.333 0.00 0.00 0.00 4.24
4316 8838 2.685897 TGGTTGCACACTTCCTTTGTAC 59.314 45.455 0.00 0.00 0.00 2.90
4327 8849 7.008941 ACACTTCCTTTGTACTAGGTAGAAGA 58.991 38.462 20.18 0.13 34.74 2.87
4328 8850 7.039853 ACACTTCCTTTGTACTAGGTAGAAGAC 60.040 40.741 20.18 0.00 34.74 3.01
4447 8988 1.897802 AGGGAAAAGCATGGAAGCAAG 59.102 47.619 0.00 0.00 36.85 4.01
4454 8995 2.089980 AGCATGGAAGCAAGTTAGCTG 58.910 47.619 0.00 0.00 45.89 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.928492 GGTTGTTCAGATTAGCAAATCCAAAA 59.072 34.615 0.00 0.00 42.20 2.44
47 48 8.347004 TCATAATGGTTGTTCAGATTAGCAAA 57.653 30.769 0.00 0.00 0.00 3.68
163 172 5.193679 GGACAAACCCAAGCAGATATAACT 58.806 41.667 0.00 0.00 0.00 2.24
206 226 7.878495 ACAAATACATGGACTAATTAAGGGGA 58.122 34.615 0.00 0.00 0.00 4.81
259 279 6.039941 TCAATAACCCATTCACACTCGTTTTT 59.960 34.615 0.00 0.00 0.00 1.94
264 284 4.094887 CCTTCAATAACCCATTCACACTCG 59.905 45.833 0.00 0.00 0.00 4.18
270 290 2.374184 CCGCCTTCAATAACCCATTCA 58.626 47.619 0.00 0.00 0.00 2.57
408 428 1.346062 ATCATGGAGGAGGGACATCG 58.654 55.000 0.00 0.00 0.00 3.84
410 430 4.102598 CTGATATCATGGAGGAGGGACAT 58.897 47.826 5.72 0.00 0.00 3.06
416 436 2.636403 TGCACCTGATATCATGGAGGAG 59.364 50.000 21.15 12.65 0.00 3.69
433 453 5.470845 ACATTTATTCTTCGTAGCTGCAC 57.529 39.130 1.02 0.00 0.00 4.57
466 486 0.314935 CTTGGCACCAGCGTTTTCAT 59.685 50.000 0.00 0.00 43.41 2.57
513 536 3.114065 GGAGTAGTAAGCATGTACGTGC 58.886 50.000 28.92 28.92 45.38 5.34
514 537 3.380637 AGGGAGTAGTAAGCATGTACGTG 59.619 47.826 10.89 10.89 0.00 4.49
515 538 3.629087 AGGGAGTAGTAAGCATGTACGT 58.371 45.455 0.00 0.00 0.00 3.57
516 539 3.004524 GGAGGGAGTAGTAAGCATGTACG 59.995 52.174 0.00 0.00 0.00 3.67
517 540 3.004524 CGGAGGGAGTAGTAAGCATGTAC 59.995 52.174 0.00 0.00 0.00 2.90
518 541 3.220110 CGGAGGGAGTAGTAAGCATGTA 58.780 50.000 0.00 0.00 0.00 2.29
519 542 2.032620 CGGAGGGAGTAGTAAGCATGT 58.967 52.381 0.00 0.00 0.00 3.21
520 543 2.032620 ACGGAGGGAGTAGTAAGCATG 58.967 52.381 0.00 0.00 0.00 4.06
521 544 2.456073 ACGGAGGGAGTAGTAAGCAT 57.544 50.000 0.00 0.00 0.00 3.79
522 545 2.226962 AACGGAGGGAGTAGTAAGCA 57.773 50.000 0.00 0.00 0.00 3.91
523 546 2.494870 TGAAACGGAGGGAGTAGTAAGC 59.505 50.000 0.00 0.00 0.00 3.09
524 547 4.796038 TTGAAACGGAGGGAGTAGTAAG 57.204 45.455 0.00 0.00 0.00 2.34
525 548 5.549742 TTTTGAAACGGAGGGAGTAGTAA 57.450 39.130 0.00 0.00 0.00 2.24
526 549 5.750352 ATTTTGAAACGGAGGGAGTAGTA 57.250 39.130 0.00 0.00 0.00 1.82
527 550 4.635699 ATTTTGAAACGGAGGGAGTAGT 57.364 40.909 0.00 0.00 0.00 2.73
528 551 5.974108 TCTATTTTGAAACGGAGGGAGTAG 58.026 41.667 0.00 0.00 0.00 2.57
529 552 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
530 553 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
531 554 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
532 555 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
533 556 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
534 557 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
535 558 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
536 559 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
537 560 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
538 561 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
539 562 7.657336 TGAAGTTGGGTCATCTATTTTGAAAC 58.343 34.615 0.00 0.00 0.00 2.78
540 563 7.831691 TGAAGTTGGGTCATCTATTTTGAAA 57.168 32.000 0.00 0.00 0.00 2.69
541 564 8.055279 GATGAAGTTGGGTCATCTATTTTGAA 57.945 34.615 7.07 0.00 45.28 2.69
542 565 7.630242 GATGAAGTTGGGTCATCTATTTTGA 57.370 36.000 7.07 0.00 45.28 2.69
551 574 8.306761 GTTTCAAAATAGATGAAGTTGGGTCAT 58.693 33.333 0.00 0.00 38.01 3.06
552 575 7.521423 CGTTTCAAAATAGATGAAGTTGGGTCA 60.521 37.037 0.00 0.00 38.01 4.02
553 576 6.801862 CGTTTCAAAATAGATGAAGTTGGGTC 59.198 38.462 0.00 0.00 38.01 4.46
554 577 6.294508 CCGTTTCAAAATAGATGAAGTTGGGT 60.295 38.462 0.00 0.00 38.01 4.51
555 578 6.072175 TCCGTTTCAAAATAGATGAAGTTGGG 60.072 38.462 0.00 0.00 38.01 4.12
556 579 6.908825 TCCGTTTCAAAATAGATGAAGTTGG 58.091 36.000 0.00 0.00 38.01 3.77
557 580 7.023575 CCTCCGTTTCAAAATAGATGAAGTTG 58.976 38.462 0.00 0.00 38.01 3.16
558 581 6.151144 CCCTCCGTTTCAAAATAGATGAAGTT 59.849 38.462 0.00 0.00 38.01 2.66
559 582 5.648092 CCCTCCGTTTCAAAATAGATGAAGT 59.352 40.000 0.00 0.00 38.01 3.01
560 583 5.880332 TCCCTCCGTTTCAAAATAGATGAAG 59.120 40.000 0.00 0.00 38.01 3.02
561 584 5.811190 TCCCTCCGTTTCAAAATAGATGAA 58.189 37.500 0.00 0.00 35.11 2.57
562 585 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
563 586 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
564 587 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
565 588 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
566 589 5.731591 ACTACTCCCTCCGTTTCAAAATAG 58.268 41.667 0.00 0.00 0.00 1.73
567 590 5.750352 ACTACTCCCTCCGTTTCAAAATA 57.250 39.130 0.00 0.00 0.00 1.40
568 591 4.635699 ACTACTCCCTCCGTTTCAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
569 592 4.426736 AACTACTCCCTCCGTTTCAAAA 57.573 40.909 0.00 0.00 0.00 2.44
570 593 4.102054 AGAAACTACTCCCTCCGTTTCAAA 59.898 41.667 13.93 0.00 44.55 2.69
571 594 3.644738 AGAAACTACTCCCTCCGTTTCAA 59.355 43.478 13.93 0.00 44.55 2.69
572 595 3.236896 AGAAACTACTCCCTCCGTTTCA 58.763 45.455 13.93 0.00 44.55 2.69
573 596 3.957591 AGAAACTACTCCCTCCGTTTC 57.042 47.619 0.00 0.00 43.24 2.78
574 597 4.670765 TCTAGAAACTACTCCCTCCGTTT 58.329 43.478 0.00 0.00 32.76 3.60
575 598 4.313020 TCTAGAAACTACTCCCTCCGTT 57.687 45.455 0.00 0.00 0.00 4.44
576 599 4.523168 ATCTAGAAACTACTCCCTCCGT 57.477 45.455 0.00 0.00 0.00 4.69
577 600 6.956202 TTTATCTAGAAACTACTCCCTCCG 57.044 41.667 0.00 0.00 0.00 4.63
578 601 9.549078 CAATTTTATCTAGAAACTACTCCCTCC 57.451 37.037 0.00 0.00 0.00 4.30
633 660 0.449388 GCATAGCAGTGCTTGTGGAC 59.551 55.000 25.23 7.40 41.82 4.02
639 666 0.389817 TCGTTCGCATAGCAGTGCTT 60.390 50.000 25.23 8.49 42.88 3.91
706 733 2.313717 TACTCGAATCGACCGCGGTG 62.314 60.000 39.65 26.80 38.28 4.94
734 769 0.804544 CGACGCTTCCTTGCCGATAA 60.805 55.000 0.00 0.00 0.00 1.75
781 816 0.837272 TAAGGGCCTCTTTGGATCGG 59.163 55.000 6.46 0.00 38.35 4.18
880 917 4.189188 GTTAGAGCTCCGCGCGGA 62.189 66.667 45.07 45.07 45.59 5.54
999 1036 3.115892 GAACGGCGATGTTGCGGA 61.116 61.111 16.62 0.00 38.43 5.54
1002 1039 0.095417 GAGAAGAACGGCGATGTTGC 59.905 55.000 16.62 1.11 30.75 4.17
1836 3594 2.034685 TCTCGTTGTCATCGGGATCATC 59.965 50.000 1.65 0.00 32.69 2.92
1838 3596 1.470051 TCTCGTTGTCATCGGGATCA 58.530 50.000 1.65 0.00 32.69 2.92
2114 4255 4.351111 ACAATTAGGGTCTTCTTCCACTGT 59.649 41.667 0.00 0.00 0.00 3.55
2375 4516 1.703411 TCCCCTTGGCAACTTCTTTG 58.297 50.000 0.00 0.00 38.37 2.77
2543 4684 3.324108 GGACGGTTGGGGTAGCCA 61.324 66.667 14.06 0.00 0.00 4.75
2627 4768 4.917906 AGTAGACTTTCCTGCTCCATTT 57.082 40.909 0.00 0.00 0.00 2.32
3062 5204 4.082408 TCACAAACTCGAGATATCAACCGT 60.082 41.667 21.68 0.00 0.00 4.83
3273 5428 7.880160 ACAAAAGCTGCTAATAATACATGGA 57.120 32.000 0.90 0.00 0.00 3.41
3299 5454 2.490328 TTCTTCTGCAAACCAAAGCG 57.510 45.000 0.00 0.00 0.00 4.68
3410 5587 6.553524 CAAAATTGCACAAAAGAAACACCAT 58.446 32.000 0.00 0.00 0.00 3.55
3537 5877 8.896744 CAAGCATTTCAATAGTTAGAATCTGGA 58.103 33.333 0.00 0.00 0.00 3.86
3697 6044 4.380841 AATTCAGCAGCCATAACACATG 57.619 40.909 0.00 0.00 0.00 3.21
3784 6132 5.874810 TCTGAGTTAGTTACATTGTCATGCC 59.125 40.000 0.00 0.00 33.05 4.40
4009 7259 4.019174 CAGAAGGGTGTCAAATATTGGCT 58.981 43.478 0.00 0.00 35.94 4.75
4010 7260 3.429410 GCAGAAGGGTGTCAAATATTGGC 60.429 47.826 0.00 0.00 35.37 4.52
4202 8724 0.322975 GTGGATCTGACACTGCTGGT 59.677 55.000 0.00 0.00 35.98 4.00
4248 8770 7.769044 GGACCAAGAGCAACAAGAATAGTAATA 59.231 37.037 0.00 0.00 0.00 0.98
4272 8794 8.934697 ACCACAGCTATAAGAATAATTACAGGA 58.065 33.333 0.00 0.00 0.00 3.86
4276 8798 8.836413 TGCAACCACAGCTATAAGAATAATTAC 58.164 33.333 0.00 0.00 0.00 1.89
4282 8804 4.588899 TGTGCAACCACAGCTATAAGAAT 58.411 39.130 0.00 0.00 46.51 2.40
4294 8816 1.476488 ACAAAGGAAGTGTGCAACCAC 59.524 47.619 0.00 0.00 42.40 4.16
4341 8863 6.519679 AGCAAAATCAGACATGCAATAGAA 57.480 33.333 0.00 0.00 41.18 2.10
4342 8864 6.071784 ACAAGCAAAATCAGACATGCAATAGA 60.072 34.615 0.00 0.00 41.18 1.98


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

AutoCloner maintained by Alex Coulton.