Multiple sequence alignment - TraesCS5D01G240500

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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 TraesCS5D01G240500 chr5D 100.000 4260 0 0 1 4260 348745111 348749370 0.000000e+00 7867.0
1 TraesCS5D01G240500 chr5D 93.467 199 9 4 3359 3555 410592129 410591933 4.170000e-75 292.0
2 TraesCS5D01G240500 chr5D 92.500 200 12 2 3354 3550 521487795 521487994 2.510000e-72 283.0
3 TraesCS5D01G240500 chr5D 92.308 65 4 1 4197 4260 63485462 63485526 1.630000e-14 91.6
4 TraesCS5D01G240500 chr5B 96.266 3374 91 16 1 3353 409058696 409062055 0.000000e+00 5500.0
5 TraesCS5D01G240500 chr5B 85.870 644 68 10 3554 4196 409062089 409062710 0.000000e+00 664.0
6 TraesCS5D01G240500 chr5A 95.805 2765 70 18 614 3360 448834996 448837732 0.000000e+00 4421.0
7 TraesCS5D01G240500 chr5A 88.567 621 34 14 1 609 448834348 448834943 0.000000e+00 719.0
8 TraesCS5D01G240500 chr5A 85.352 710 66 16 3554 4260 448837728 448838402 0.000000e+00 701.0
9 TraesCS5D01G240500 chr5A 83.333 84 12 2 2747 2829 560604103 560604021 4.570000e-10 76.8
10 TraesCS5D01G240500 chr6D 89.549 421 39 4 3774 4194 463532609 463533024 2.920000e-146 529.0
11 TraesCS5D01G240500 chr6D 80.739 379 62 10 3823 4197 448797218 448797589 6.970000e-73 285.0
12 TraesCS5D01G240500 chr6D 89.286 84 9 0 2747 2830 305275415 305275498 5.830000e-19 106.0
13 TraesCS5D01G240500 chr6D 89.286 84 9 0 2747 2830 394218356 394218439 5.830000e-19 106.0
14 TraesCS5D01G240500 chr3D 83.245 376 59 3 3822 4197 251397303 251397674 4.080000e-90 342.0
15 TraesCS5D01G240500 chr3D 93.651 189 10 2 3365 3551 506177312 506177124 9.020000e-72 281.0
16 TraesCS5D01G240500 chr3D 90.476 84 8 0 2747 2830 106680636 106680719 1.250000e-20 111.0
17 TraesCS5D01G240500 chr7D 81.963 377 54 10 3822 4196 463711083 463711447 1.490000e-79 307.0
18 TraesCS5D01G240500 chr7D 92.157 204 13 3 3347 3547 629623730 629623527 6.970000e-73 285.0
19 TraesCS5D01G240500 chr7D 81.481 270 30 13 2320 2588 585589793 585590043 2.010000e-48 204.0
20 TraesCS5D01G240500 chr7D 88.506 87 10 0 2747 2833 628183101 628183015 5.830000e-19 106.0
21 TraesCS5D01G240500 chr7D 89.610 77 8 0 2754 2830 274259836 274259912 9.750000e-17 99.0
22 TraesCS5D01G240500 chr1D 81.283 374 62 7 3823 4194 249582602 249582235 3.220000e-76 296.0
23 TraesCS5D01G240500 chr1D 92.462 199 13 2 3362 3560 375011913 375012109 2.510000e-72 283.0
24 TraesCS5D01G240500 chr4D 93.467 199 12 1 3355 3552 35722493 35722295 1.160000e-75 294.0
25 TraesCS5D01G240500 chr2B 95.628 183 7 1 3363 3544 771215135 771215317 4.170000e-75 292.0
26 TraesCS5D01G240500 chr2D 93.035 201 10 4 3355 3553 537187920 537187722 1.500000e-74 291.0
27 TraesCS5D01G240500 chr2D 92.929 198 13 1 3358 3554 48184303 48184500 1.940000e-73 287.0
28 TraesCS5D01G240500 chr7B 83.438 320 44 8 3886 4202 499934726 499935039 5.390000e-74 289.0
29 TraesCS5D01G240500 chr7B 96.970 33 0 1 4197 4228 60912362 60912394 2.000000e-03 54.7
30 TraesCS5D01G240500 chr7A 80.106 377 62 11 3823 4196 495429180 495428814 7.020000e-68 268.0
31 TraesCS5D01G240500 chr7A 79.683 379 67 9 3823 4198 507134175 507133804 9.080000e-67 265.0
32 TraesCS5D01G240500 chr7A 82.375 261 26 13 2329 2588 16124066 16123825 4.320000e-50 209.0
33 TraesCS5D01G240500 chr7A 94.444 54 3 0 2777 2830 719985299 719985352 2.730000e-12 84.2
34 TraesCS5D01G240500 chrUn 80.669 269 30 12 2323 2588 277340752 277340503 5.620000e-44 189.0
35 TraesCS5D01G240500 chr4A 80.515 272 31 12 2320 2588 714915947 714916199 5.620000e-44 189.0
36 TraesCS5D01G240500 chr2A 81.193 218 23 11 2372 2588 78535499 78535299 4.410000e-35 159.0
37 TraesCS5D01G240500 chr1B 87.500 80 9 1 3689 3767 342295027 342294948 1.630000e-14 91.6
38 TraesCS5D01G240500 chr4B 90.625 64 3 3 4197 4258 509764210 509764148 9.820000e-12 82.4
39 TraesCS5D01G240500 chr3B 90.476 63 5 1 4197 4258 2158479 2158417 9.820000e-12 82.4


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 TraesCS5D01G240500 chr5D 348745111 348749370 4259 False 7867 7867 100.000 1 4260 1 chr5D.!!$F2 4259
1 TraesCS5D01G240500 chr5B 409058696 409062710 4014 False 3082 5500 91.068 1 4196 2 chr5B.!!$F1 4195
2 TraesCS5D01G240500 chr5A 448834348 448838402 4054 False 1947 4421 89.908 1 4260 3 chr5A.!!$F1 4259

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
589 606 0.320073 TTTCCCTCGCGACGTTCATT 60.32 50.0 3.71 0.0 0.00 2.57 F
1400 1480 0.249531 TATGTGTGTCGTGCCGTGTT 60.25 50.0 0.00 0.0 0.00 3.32 F
1813 1903 0.529773 TCACGTGCACTCACTCAACC 60.53 55.0 16.19 0.0 40.99 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 1903 2.034432 TGCAACACACAGCATAGGTTTG 59.966 45.455 0.0 0.0 35.51 2.93 R
2704 2794 0.241749 CGACTACGCCACTGTTGGTA 59.758 55.000 0.0 0.0 45.98 3.25 R
3559 3681 1.037579 GGGGCAATCCTCCTTTTCGG 61.038 60.000 0.0 0.0 35.33 4.30 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
66 67 1.068333 GTCGCAGTACTCCACGGTAAA 60.068 52.381 9.00 0.00 0.00 2.01
138 139 5.606348 AGGTAGCAAGGACAGATAAGAAG 57.394 43.478 0.00 0.00 0.00 2.85
589 606 0.320073 TTTCCCTCGCGACGTTCATT 60.320 50.000 3.71 0.00 0.00 2.57
726 791 3.964909 AGATGGTCGTGCAAAGTTTTTC 58.035 40.909 0.00 0.00 0.00 2.29
782 848 4.213270 TGTGCAAAGTTTCAATAGGAGACG 59.787 41.667 0.00 0.00 35.83 4.18
792 858 2.625314 CAATAGGAGACGAGAGCCATGA 59.375 50.000 0.00 0.00 0.00 3.07
992 1062 2.506065 CCCGTCTTCTCTAGGGGTG 58.494 63.158 0.00 0.00 40.18 4.61
994 1064 0.324460 CCGTCTTCTCTAGGGGTGGT 60.324 60.000 0.00 0.00 0.00 4.16
1319 1399 6.569035 CGTGTCATCGGTACATATAGGCTTTA 60.569 42.308 0.00 0.00 0.00 1.85
1400 1480 0.249531 TATGTGTGTCGTGCCGTGTT 60.250 50.000 0.00 0.00 0.00 3.32
1481 1561 2.681591 TCCTCCGTGGAGACCGAT 59.318 61.111 17.52 0.00 44.53 4.18
1700 1780 3.166657 CTCAGCGTTACACGTAAGGTAC 58.833 50.000 10.37 0.00 44.73 3.34
1810 1900 0.744281 TTCTCACGTGCACTCACTCA 59.256 50.000 16.19 0.00 40.99 3.41
1811 1901 0.744281 TCTCACGTGCACTCACTCAA 59.256 50.000 16.19 0.00 40.99 3.02
1812 1902 0.855349 CTCACGTGCACTCACTCAAC 59.145 55.000 16.19 0.00 40.99 3.18
1813 1903 0.529773 TCACGTGCACTCACTCAACC 60.530 55.000 16.19 0.00 40.99 3.77
1814 1904 0.809636 CACGTGCACTCACTCAACCA 60.810 55.000 16.19 0.00 40.99 3.67
2704 2794 2.579201 CACGAAGGGATGACCGCT 59.421 61.111 0.00 0.00 46.96 5.52
2974 3064 3.376078 GTGGGGAGCACCGTCGTA 61.376 66.667 0.00 0.00 41.60 3.43
3009 3099 2.357517 CGAGCAGCAGGAACCGTT 60.358 61.111 0.00 0.00 0.00 4.44
3023 3113 4.831307 CGTTCGAGGAGGGCGACG 62.831 72.222 0.00 0.00 37.52 5.12
3040 3130 2.161486 CGAGAGGAAGAAAGCGGCG 61.161 63.158 0.51 0.51 0.00 6.46
3097 3187 1.167781 TCGTAGACTGCGTGTGTGGA 61.168 55.000 12.78 0.00 0.00 4.02
3387 3509 9.990360 TTACAGTTTGACTAATTCACATGTAGA 57.010 29.630 0.00 0.00 32.37 2.59
3389 3511 8.939929 ACAGTTTGACTAATTCACATGTAGATG 58.060 33.333 0.00 0.00 32.26 2.90
3390 3512 8.939929 CAGTTTGACTAATTCACATGTAGATGT 58.060 33.333 0.00 0.00 44.08 3.06
3391 3513 9.507329 AGTTTGACTAATTCACATGTAGATGTT 57.493 29.630 2.09 0.00 41.12 2.71
3416 3538 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
3417 3539 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
3418 3540 2.703007 AGGATGTCACATCTAAGCTCCC 59.297 50.000 17.46 0.00 0.00 4.30
3419 3541 2.435805 GGATGTCACATCTAAGCTCCCA 59.564 50.000 17.46 0.00 0.00 4.37
3420 3542 3.462021 GATGTCACATCTAAGCTCCCAC 58.538 50.000 10.81 0.00 0.00 4.61
3421 3543 2.256306 TGTCACATCTAAGCTCCCACA 58.744 47.619 0.00 0.00 0.00 4.17
3422 3544 2.637382 TGTCACATCTAAGCTCCCACAA 59.363 45.455 0.00 0.00 0.00 3.33
3423 3545 3.072330 TGTCACATCTAAGCTCCCACAAA 59.928 43.478 0.00 0.00 0.00 2.83
3424 3546 4.263462 TGTCACATCTAAGCTCCCACAAAT 60.263 41.667 0.00 0.00 0.00 2.32
3425 3547 5.045942 TGTCACATCTAAGCTCCCACAAATA 60.046 40.000 0.00 0.00 0.00 1.40
3426 3548 6.058183 GTCACATCTAAGCTCCCACAAATAT 58.942 40.000 0.00 0.00 0.00 1.28
3427 3549 7.147567 TGTCACATCTAAGCTCCCACAAATATA 60.148 37.037 0.00 0.00 0.00 0.86
3428 3550 7.880195 GTCACATCTAAGCTCCCACAAATATAT 59.120 37.037 0.00 0.00 0.00 0.86
3429 3551 9.100197 TCACATCTAAGCTCCCACAAATATATA 57.900 33.333 0.00 0.00 0.00 0.86
3430 3552 9.725019 CACATCTAAGCTCCCACAAATATATAA 57.275 33.333 0.00 0.00 0.00 0.98
3433 3555 8.792830 TCTAAGCTCCCACAAATATATAATGC 57.207 34.615 0.00 0.00 0.00 3.56
3434 3556 8.382405 TCTAAGCTCCCACAAATATATAATGCA 58.618 33.333 0.00 0.00 0.00 3.96
3435 3557 7.458409 AAGCTCCCACAAATATATAATGCAG 57.542 36.000 0.00 0.00 0.00 4.41
3436 3558 5.416952 AGCTCCCACAAATATATAATGCAGC 59.583 40.000 0.00 0.00 0.00 5.25
3437 3559 5.183713 GCTCCCACAAATATATAATGCAGCA 59.816 40.000 0.00 0.00 0.00 4.41
3438 3560 6.294675 GCTCCCACAAATATATAATGCAGCAA 60.295 38.462 0.00 0.00 0.00 3.91
3439 3561 6.980593 TCCCACAAATATATAATGCAGCAAC 58.019 36.000 0.00 0.00 0.00 4.17
3440 3562 6.548993 TCCCACAAATATATAATGCAGCAACA 59.451 34.615 0.00 0.00 0.00 3.33
3441 3563 7.069208 TCCCACAAATATATAATGCAGCAACAA 59.931 33.333 0.00 0.00 0.00 2.83
3442 3564 7.383029 CCCACAAATATATAATGCAGCAACAAG 59.617 37.037 0.00 0.00 0.00 3.16
3443 3565 8.136800 CCACAAATATATAATGCAGCAACAAGA 58.863 33.333 0.00 0.00 0.00 3.02
3444 3566 9.518906 CACAAATATATAATGCAGCAACAAGAA 57.481 29.630 0.00 0.00 0.00 2.52
3450 3572 8.830201 ATATAATGCAGCAACAAGAAACAAAA 57.170 26.923 0.00 0.00 0.00 2.44
3451 3573 5.876612 AATGCAGCAACAAGAAACAAAAA 57.123 30.435 0.00 0.00 0.00 1.94
3476 3598 8.934023 AAATTAGGACAGAAAAATAGACCACA 57.066 30.769 0.00 0.00 0.00 4.17
3477 3599 8.934023 AATTAGGACAGAAAAATAGACCACAA 57.066 30.769 0.00 0.00 0.00 3.33
3478 3600 8.934023 ATTAGGACAGAAAAATAGACCACAAA 57.066 30.769 0.00 0.00 0.00 2.83
3479 3601 8.934023 TTAGGACAGAAAAATAGACCACAAAT 57.066 30.769 0.00 0.00 0.00 2.32
3481 3603 8.567285 AGGACAGAAAAATAGACCACAAATAG 57.433 34.615 0.00 0.00 0.00 1.73
3482 3604 8.383175 AGGACAGAAAAATAGACCACAAATAGA 58.617 33.333 0.00 0.00 0.00 1.98
3483 3605 8.669243 GGACAGAAAAATAGACCACAAATAGAG 58.331 37.037 0.00 0.00 0.00 2.43
3484 3606 9.220767 GACAGAAAAATAGACCACAAATAGAGT 57.779 33.333 0.00 0.00 0.00 3.24
3485 3607 9.003658 ACAGAAAAATAGACCACAAATAGAGTG 57.996 33.333 0.00 0.00 36.76 3.51
3494 3616 4.871993 CACAAATAGAGTGGACATGAGC 57.128 45.455 0.00 0.00 33.43 4.26
3495 3617 4.511527 CACAAATAGAGTGGACATGAGCT 58.488 43.478 0.00 0.00 33.43 4.09
3496 3618 4.940046 CACAAATAGAGTGGACATGAGCTT 59.060 41.667 0.00 0.00 33.43 3.74
3497 3619 6.108687 CACAAATAGAGTGGACATGAGCTTA 58.891 40.000 0.00 0.00 33.43 3.09
3498 3620 6.257411 CACAAATAGAGTGGACATGAGCTTAG 59.743 42.308 0.00 0.00 33.43 2.18
3499 3621 6.155221 ACAAATAGAGTGGACATGAGCTTAGA 59.845 38.462 0.00 0.00 0.00 2.10
3500 3622 6.992664 AATAGAGTGGACATGAGCTTAGAT 57.007 37.500 0.00 0.00 0.00 1.98
3501 3623 4.669206 AGAGTGGACATGAGCTTAGATG 57.331 45.455 0.00 0.00 0.00 2.90
3502 3624 4.029520 AGAGTGGACATGAGCTTAGATGT 58.970 43.478 0.00 6.66 35.46 3.06
3503 3625 4.118410 GAGTGGACATGAGCTTAGATGTG 58.882 47.826 10.67 0.00 32.85 3.21
3504 3626 3.771479 AGTGGACATGAGCTTAGATGTGA 59.229 43.478 10.67 0.00 32.85 3.58
3505 3627 3.868077 GTGGACATGAGCTTAGATGTGAC 59.132 47.826 10.67 5.19 32.85 3.67
3506 3628 3.515104 TGGACATGAGCTTAGATGTGACA 59.485 43.478 10.67 7.59 32.85 3.58
3507 3629 4.162888 TGGACATGAGCTTAGATGTGACAT 59.837 41.667 0.00 0.00 32.85 3.06
3508 3630 5.363580 TGGACATGAGCTTAGATGTGACATA 59.636 40.000 10.67 0.00 32.85 2.29
3509 3631 6.127083 TGGACATGAGCTTAGATGTGACATAA 60.127 38.462 10.67 0.00 32.85 1.90
3510 3632 6.201806 GGACATGAGCTTAGATGTGACATAAC 59.798 42.308 10.67 0.00 32.85 1.89
3511 3633 6.882656 ACATGAGCTTAGATGTGACATAACT 58.117 36.000 0.00 0.00 31.47 2.24
3512 3634 8.011844 ACATGAGCTTAGATGTGACATAACTA 57.988 34.615 0.00 0.00 31.47 2.24
3513 3635 8.646004 ACATGAGCTTAGATGTGACATAACTAT 58.354 33.333 0.00 0.00 31.47 2.12
3514 3636 8.923683 CATGAGCTTAGATGTGACATAACTATG 58.076 37.037 0.00 0.92 39.55 2.23
3541 3663 6.312399 CATCTAGATGTGTCCTAGACAGAC 57.688 45.833 22.42 0.00 43.57 3.51
3542 3664 4.783055 TCTAGATGTGTCCTAGACAGACC 58.217 47.826 0.00 0.00 43.57 3.85
3543 3665 2.741145 AGATGTGTCCTAGACAGACCC 58.259 52.381 0.00 0.00 43.57 4.46
3544 3666 2.313342 AGATGTGTCCTAGACAGACCCT 59.687 50.000 0.00 0.00 43.57 4.34
3545 3667 2.696526 TGTGTCCTAGACAGACCCTT 57.303 50.000 0.00 0.00 43.57 3.95
3546 3668 2.972348 TGTGTCCTAGACAGACCCTTT 58.028 47.619 0.00 0.00 43.57 3.11
3547 3669 3.314693 TGTGTCCTAGACAGACCCTTTT 58.685 45.455 0.00 0.00 43.57 2.27
3548 3670 3.714798 TGTGTCCTAGACAGACCCTTTTT 59.285 43.478 0.00 0.00 43.57 1.94
3549 3671 4.903049 TGTGTCCTAGACAGACCCTTTTTA 59.097 41.667 0.00 0.00 43.57 1.52
3550 3672 5.546499 TGTGTCCTAGACAGACCCTTTTTAT 59.454 40.000 0.00 0.00 43.57 1.40
3551 3673 6.043938 TGTGTCCTAGACAGACCCTTTTTATT 59.956 38.462 0.00 0.00 43.57 1.40
3552 3674 7.236019 TGTGTCCTAGACAGACCCTTTTTATTA 59.764 37.037 0.00 0.00 43.57 0.98
3553 3675 8.265764 GTGTCCTAGACAGACCCTTTTTATTAT 58.734 37.037 0.00 0.00 43.57 1.28
3554 3676 8.832735 TGTCCTAGACAGACCCTTTTTATTATT 58.167 33.333 0.00 0.00 37.67 1.40
3664 3786 6.465465 GCAGTACGTTACAAAAACTCGAAAAA 59.535 34.615 0.00 0.00 0.00 1.94
3665 3787 7.304453 GCAGTACGTTACAAAAACTCGAAAAAG 60.304 37.037 0.00 0.00 0.00 2.27
3666 3788 7.689400 CAGTACGTTACAAAAACTCGAAAAAGT 59.311 33.333 0.00 0.00 0.00 2.66
3668 3790 7.255770 ACGTTACAAAAACTCGAAAAAGTTG 57.744 32.000 0.00 0.00 39.40 3.16
3669 3791 6.857451 ACGTTACAAAAACTCGAAAAAGTTGT 59.143 30.769 6.45 6.45 39.40 3.32
3670 3792 8.014517 ACGTTACAAAAACTCGAAAAAGTTGTA 58.985 29.630 0.00 0.00 39.40 2.41
3671 3793 8.838961 CGTTACAAAAACTCGAAAAAGTTGTAA 58.161 29.630 13.04 13.04 39.40 2.41
3744 3866 3.812053 CAGCTATCCTATTGTTGGACTGC 59.188 47.826 0.00 0.00 36.30 4.40
3767 3889 5.127031 GCCATCCAAACATGTTGTAGGTATT 59.873 40.000 12.82 2.76 30.50 1.89
3769 3891 6.603201 CCATCCAAACATGTTGTAGGTATTCT 59.397 38.462 12.82 0.00 30.50 2.40
3783 3905 5.994416 AGGTATTCTGTGGGGAATGTATT 57.006 39.130 0.00 0.00 36.69 1.89
3793 3915 1.064017 GGGAATGTATTGGGTGCTCCA 60.064 52.381 7.20 0.85 45.43 3.86
3818 3940 2.659610 GAGTGCTCCCGAGTGCTT 59.340 61.111 0.00 0.00 33.59 3.91
3883 4005 5.204409 AGCACATTCACACAACATCAATT 57.796 34.783 0.00 0.00 0.00 2.32
3949 4071 9.612620 ACTCGAGATACAAAAATGACAAATTTC 57.387 29.630 21.68 0.00 0.00 2.17
4052 4174 9.995379 GTTTTTCTCGAGCTATTTTTCAAATTC 57.005 29.630 7.81 0.00 0.00 2.17
4104 4226 6.141560 TGATGTTGTGTGAATGTGCTAAAA 57.858 33.333 0.00 0.00 0.00 1.52
4105 4227 6.567959 TGATGTTGTGTGAATGTGCTAAAAA 58.432 32.000 0.00 0.00 0.00 1.94
4157 4279 0.613260 TATGCCGAGTTTGGAGCACT 59.387 50.000 0.00 0.00 38.21 4.40
4195 4317 2.849294 GGAGCACCAGATATTCTCCC 57.151 55.000 0.00 0.00 37.85 4.30
4209 4331 0.820891 TCTCCCGTATCCCGTGCTAC 60.821 60.000 0.00 0.00 33.66 3.58
4232 4355 1.300971 CTCCCAACGGTGCACTCATG 61.301 60.000 17.98 12.40 0.00 3.07
4255 4378 1.133699 CCATATGCTCCTTGGCTTCCA 60.134 52.381 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 2.766263 CTGTCCTTGCTACCTACCATCA 59.234 50.000 0.00 0.00 0.00 3.07
138 139 0.242017 AAGCGGTGAAAATGCTGCTC 59.758 50.000 0.00 0.00 45.55 4.26
621 686 2.164422 GTCCTAAGCAAAACCAGCATCC 59.836 50.000 0.00 0.00 0.00 3.51
726 791 5.618561 GCGTTCTCACATGTAAAGTTTAGG 58.381 41.667 0.00 0.00 0.00 2.69
782 848 2.548904 GCTCATTCACATCATGGCTCTC 59.451 50.000 0.00 0.00 0.00 3.20
792 858 1.019673 GACATGGCGCTCATTCACAT 58.980 50.000 7.64 0.00 32.92 3.21
992 1062 1.709147 CTTAGCAGCCATGTCGCACC 61.709 60.000 0.00 0.00 0.00 5.01
994 1064 0.178767 ATCTTAGCAGCCATGTCGCA 59.821 50.000 0.00 0.00 0.00 5.10
1182 1257 3.236391 TGGAACGACCAGCACCTT 58.764 55.556 0.00 0.00 44.64 3.50
1311 1391 4.334203 CGTGCAATGGTTATGTAAAGCCTA 59.666 41.667 0.00 0.00 0.00 3.93
1319 1399 0.167908 CGTGCGTGCAATGGTTATGT 59.832 50.000 0.00 0.00 0.00 2.29
1347 1427 0.251608 TCCCCGTGACAGACTGATCA 60.252 55.000 10.08 6.55 0.00 2.92
1481 1561 2.687200 ATCCCGTAGCACAGCCCA 60.687 61.111 0.00 0.00 0.00 5.36
1532 1612 2.434359 GAGGTCGCCGTCCCTTTG 60.434 66.667 0.00 0.00 0.00 2.77
1572 1652 2.758770 TAGCCGTTGAGGTGCACGAC 62.759 60.000 11.45 7.84 43.70 4.34
1736 1816 6.690098 ACATACGTTTGCGATCGATATATACC 59.310 38.462 21.57 0.00 42.00 2.73
1810 1900 2.944129 ACACACAGCATAGGTTTGGTT 58.056 42.857 0.00 0.00 0.00 3.67
1811 1901 2.622942 CAACACACAGCATAGGTTTGGT 59.377 45.455 0.00 0.00 0.00 3.67
1812 1902 2.607771 GCAACACACAGCATAGGTTTGG 60.608 50.000 0.00 0.00 0.00 3.28
1813 1903 2.034432 TGCAACACACAGCATAGGTTTG 59.966 45.455 0.00 0.00 35.51 2.93
1814 1904 2.305928 TGCAACACACAGCATAGGTTT 58.694 42.857 0.00 0.00 35.51 3.27
2329 2419 2.581409 CCCGTGTCGCCGATGTAC 60.581 66.667 0.00 0.00 0.00 2.90
2588 2678 2.665000 CTGGCTCGGCTCCTTGAA 59.335 61.111 0.00 0.00 0.00 2.69
2704 2794 0.241749 CGACTACGCCACTGTTGGTA 59.758 55.000 0.00 0.00 45.98 3.25
2833 2923 1.673665 CTGCACCTCCCACTTGAGC 60.674 63.158 0.00 0.00 0.00 4.26
2947 3037 4.899239 CTCCCCACGCCGATCAGC 62.899 72.222 0.00 0.00 0.00 4.26
2974 3064 2.995574 CCGACCACCCCTTCGACT 60.996 66.667 0.00 0.00 37.43 4.18
3008 3098 3.132139 CTCGTCGCCCTCCTCGAA 61.132 66.667 0.00 0.00 37.73 3.71
3009 3099 4.091939 TCTCGTCGCCCTCCTCGA 62.092 66.667 0.00 0.00 0.00 4.04
3023 3113 1.811679 CCGCCGCTTTCTTCCTCTC 60.812 63.158 0.00 0.00 0.00 3.20
3091 3181 4.034258 TCGTCGTCCGCTCCACAC 62.034 66.667 0.00 0.00 36.19 3.82
3361 3483 9.990360 TCTACATGTGAATTAGTCAAACTGTAA 57.010 29.630 9.11 0.00 38.23 2.41
3363 3485 8.939929 CATCTACATGTGAATTAGTCAAACTGT 58.060 33.333 9.11 0.00 38.23 3.55
3364 3486 8.939929 ACATCTACATGTGAATTAGTCAAACTG 58.060 33.333 9.11 0.00 42.05 3.16
3365 3487 9.507329 AACATCTACATGTGAATTAGTCAAACT 57.493 29.630 9.11 0.00 42.89 2.66
3391 3513 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
3392 3514 6.823689 GGAGCTTAGATGTGACATCCTTAAAA 59.176 38.462 21.05 8.00 0.00 1.52
3393 3515 6.349300 GGAGCTTAGATGTGACATCCTTAAA 58.651 40.000 21.05 10.18 0.00 1.52
3394 3516 5.163301 GGGAGCTTAGATGTGACATCCTTAA 60.163 44.000 21.05 13.11 0.00 1.85
3395 3517 4.345257 GGGAGCTTAGATGTGACATCCTTA 59.655 45.833 21.05 6.22 0.00 2.69
3396 3518 3.135530 GGGAGCTTAGATGTGACATCCTT 59.864 47.826 21.05 7.22 0.00 3.36
3397 3519 2.703007 GGGAGCTTAGATGTGACATCCT 59.297 50.000 21.05 11.37 0.00 3.24
3398 3520 2.435805 TGGGAGCTTAGATGTGACATCC 59.564 50.000 21.05 6.28 0.00 3.51
3399 3521 3.118629 TGTGGGAGCTTAGATGTGACATC 60.119 47.826 17.46 17.46 0.00 3.06
3400 3522 2.840038 TGTGGGAGCTTAGATGTGACAT 59.160 45.455 0.00 0.00 0.00 3.06
3401 3523 2.256306 TGTGGGAGCTTAGATGTGACA 58.744 47.619 0.00 0.00 0.00 3.58
3402 3524 3.334583 TTGTGGGAGCTTAGATGTGAC 57.665 47.619 0.00 0.00 0.00 3.67
3403 3525 4.574674 ATTTGTGGGAGCTTAGATGTGA 57.425 40.909 0.00 0.00 0.00 3.58
3404 3526 9.725019 TTATATATTTGTGGGAGCTTAGATGTG 57.275 33.333 0.00 0.00 0.00 3.21
3407 3529 9.401058 GCATTATATATTTGTGGGAGCTTAGAT 57.599 33.333 0.00 0.00 0.00 1.98
3408 3530 8.382405 TGCATTATATATTTGTGGGAGCTTAGA 58.618 33.333 0.00 0.00 0.00 2.10
3409 3531 8.565896 TGCATTATATATTTGTGGGAGCTTAG 57.434 34.615 0.00 0.00 0.00 2.18
3410 3532 7.121168 GCTGCATTATATATTTGTGGGAGCTTA 59.879 37.037 0.00 0.00 0.00 3.09
3411 3533 6.071728 GCTGCATTATATATTTGTGGGAGCTT 60.072 38.462 0.00 0.00 0.00 3.74
3412 3534 5.416952 GCTGCATTATATATTTGTGGGAGCT 59.583 40.000 0.00 0.00 0.00 4.09
3413 3535 5.183713 TGCTGCATTATATATTTGTGGGAGC 59.816 40.000 0.00 0.00 0.00 4.70
3414 3536 6.822667 TGCTGCATTATATATTTGTGGGAG 57.177 37.500 0.00 0.00 0.00 4.30
3415 3537 6.548993 TGTTGCTGCATTATATATTTGTGGGA 59.451 34.615 1.84 0.00 0.00 4.37
3416 3538 6.747125 TGTTGCTGCATTATATATTTGTGGG 58.253 36.000 1.84 0.00 0.00 4.61
3417 3539 8.136800 TCTTGTTGCTGCATTATATATTTGTGG 58.863 33.333 1.84 0.00 0.00 4.17
3418 3540 9.518906 TTCTTGTTGCTGCATTATATATTTGTG 57.481 29.630 1.84 0.00 0.00 3.33
3424 3546 9.920133 TTTTGTTTCTTGTTGCTGCATTATATA 57.080 25.926 1.84 0.00 0.00 0.86
3425 3547 8.830201 TTTTGTTTCTTGTTGCTGCATTATAT 57.170 26.923 1.84 0.00 0.00 0.86
3426 3548 8.654230 TTTTTGTTTCTTGTTGCTGCATTATA 57.346 26.923 1.84 0.00 0.00 0.98
3427 3549 7.551035 TTTTTGTTTCTTGTTGCTGCATTAT 57.449 28.000 1.84 0.00 0.00 1.28
3428 3550 6.974932 TTTTTGTTTCTTGTTGCTGCATTA 57.025 29.167 1.84 0.00 0.00 1.90
3429 3551 5.876612 TTTTTGTTTCTTGTTGCTGCATT 57.123 30.435 1.84 0.00 0.00 3.56
3450 3572 9.362151 TGTGGTCTATTTTTCTGTCCTAATTTT 57.638 29.630 0.00 0.00 0.00 1.82
3451 3573 8.934023 TGTGGTCTATTTTTCTGTCCTAATTT 57.066 30.769 0.00 0.00 0.00 1.82
3452 3574 8.934023 TTGTGGTCTATTTTTCTGTCCTAATT 57.066 30.769 0.00 0.00 0.00 1.40
3453 3575 8.934023 TTTGTGGTCTATTTTTCTGTCCTAAT 57.066 30.769 0.00 0.00 0.00 1.73
3454 3576 8.934023 ATTTGTGGTCTATTTTTCTGTCCTAA 57.066 30.769 0.00 0.00 0.00 2.69
3455 3577 9.667107 CTATTTGTGGTCTATTTTTCTGTCCTA 57.333 33.333 0.00 0.00 0.00 2.94
3456 3578 8.383175 TCTATTTGTGGTCTATTTTTCTGTCCT 58.617 33.333 0.00 0.00 0.00 3.85
3457 3579 8.561738 TCTATTTGTGGTCTATTTTTCTGTCC 57.438 34.615 0.00 0.00 0.00 4.02
3458 3580 9.220767 ACTCTATTTGTGGTCTATTTTTCTGTC 57.779 33.333 0.00 0.00 0.00 3.51
3459 3581 9.003658 CACTCTATTTGTGGTCTATTTTTCTGT 57.996 33.333 0.00 0.00 0.00 3.41
3473 3595 4.511527 AGCTCATGTCCACTCTATTTGTG 58.488 43.478 0.00 0.00 35.39 3.33
3474 3596 4.833478 AGCTCATGTCCACTCTATTTGT 57.167 40.909 0.00 0.00 0.00 2.83
3475 3597 6.577103 TCTAAGCTCATGTCCACTCTATTTG 58.423 40.000 0.00 0.00 0.00 2.32
3476 3598 6.798427 TCTAAGCTCATGTCCACTCTATTT 57.202 37.500 0.00 0.00 0.00 1.40
3477 3599 6.326064 ACATCTAAGCTCATGTCCACTCTATT 59.674 38.462 0.00 0.00 0.00 1.73
3478 3600 5.837979 ACATCTAAGCTCATGTCCACTCTAT 59.162 40.000 0.00 0.00 0.00 1.98
3479 3601 5.068329 CACATCTAAGCTCATGTCCACTCTA 59.932 44.000 3.50 0.00 30.48 2.43
3480 3602 4.029520 ACATCTAAGCTCATGTCCACTCT 58.970 43.478 0.00 0.00 0.00 3.24
3481 3603 4.118410 CACATCTAAGCTCATGTCCACTC 58.882 47.826 3.50 0.00 30.48 3.51
3482 3604 3.771479 TCACATCTAAGCTCATGTCCACT 59.229 43.478 3.50 0.00 30.48 4.00
3483 3605 3.868077 GTCACATCTAAGCTCATGTCCAC 59.132 47.826 3.50 1.47 30.48 4.02
3484 3606 3.515104 TGTCACATCTAAGCTCATGTCCA 59.485 43.478 3.50 2.18 30.48 4.02
3485 3607 4.128925 TGTCACATCTAAGCTCATGTCC 57.871 45.455 3.50 0.09 30.48 4.02
3486 3608 6.983307 AGTTATGTCACATCTAAGCTCATGTC 59.017 38.462 0.00 0.00 30.48 3.06
3487 3609 6.882656 AGTTATGTCACATCTAAGCTCATGT 58.117 36.000 0.00 0.00 33.29 3.21
3488 3610 8.923683 CATAGTTATGTCACATCTAAGCTCATG 58.076 37.037 0.00 0.00 0.00 3.07
3489 3611 8.646004 ACATAGTTATGTCACATCTAAGCTCAT 58.354 33.333 0.00 0.00 42.96 2.90
3490 3612 8.011844 ACATAGTTATGTCACATCTAAGCTCA 57.988 34.615 0.00 0.00 42.96 4.26
3518 3640 5.240623 GGTCTGTCTAGGACACATCTAGATG 59.759 48.000 27.63 27.63 43.25 2.90
3519 3641 5.381757 GGTCTGTCTAGGACACATCTAGAT 58.618 45.833 0.00 0.00 43.25 1.98
3520 3642 4.385421 GGGTCTGTCTAGGACACATCTAGA 60.385 50.000 0.00 0.00 37.67 2.43
3521 3643 3.886505 GGGTCTGTCTAGGACACATCTAG 59.113 52.174 0.00 0.00 37.67 2.43
3522 3644 3.528078 AGGGTCTGTCTAGGACACATCTA 59.472 47.826 3.18 0.00 39.36 1.98
3523 3645 2.313342 AGGGTCTGTCTAGGACACATCT 59.687 50.000 3.18 0.00 39.36 2.90
3524 3646 2.741145 AGGGTCTGTCTAGGACACATC 58.259 52.381 3.18 0.00 39.36 3.06
3525 3647 2.930109 AGGGTCTGTCTAGGACACAT 57.070 50.000 3.18 0.00 39.36 3.21
3526 3648 2.696526 AAGGGTCTGTCTAGGACACA 57.303 50.000 3.18 0.00 39.36 3.72
3527 3649 4.353383 AAAAAGGGTCTGTCTAGGACAC 57.647 45.455 0.00 0.00 37.67 3.67
3528 3650 6.697641 AATAAAAAGGGTCTGTCTAGGACA 57.302 37.500 0.43 0.43 40.50 4.02
3535 3657 9.946165 CGGAAATAATAATAAAAAGGGTCTGTC 57.054 33.333 0.00 0.00 0.00 3.51
3536 3658 9.689501 TCGGAAATAATAATAAAAAGGGTCTGT 57.310 29.630 0.00 0.00 0.00 3.41
3549 3671 8.360390 GCAATCCTCCTTTTCGGAAATAATAAT 58.640 33.333 3.67 0.00 42.53 1.28
3550 3672 7.201875 GGCAATCCTCCTTTTCGGAAATAATAA 60.202 37.037 3.67 0.00 42.53 1.40
3551 3673 6.264518 GGCAATCCTCCTTTTCGGAAATAATA 59.735 38.462 3.67 0.00 42.53 0.98
3552 3674 5.069119 GGCAATCCTCCTTTTCGGAAATAAT 59.931 40.000 3.67 0.00 42.53 1.28
3553 3675 4.401202 GGCAATCCTCCTTTTCGGAAATAA 59.599 41.667 3.67 0.00 42.53 1.40
3554 3676 3.951680 GGCAATCCTCCTTTTCGGAAATA 59.048 43.478 3.67 0.00 42.53 1.40
3555 3677 2.760650 GGCAATCCTCCTTTTCGGAAAT 59.239 45.455 3.67 0.00 42.53 2.17
3559 3681 1.037579 GGGGCAATCCTCCTTTTCGG 61.038 60.000 0.00 0.00 35.33 4.30
3713 3835 6.287589 ACAATAGGATAGCTGTATAGGCAC 57.712 41.667 0.00 0.00 0.00 5.01
3724 3846 3.142174 GGCAGTCCAACAATAGGATAGC 58.858 50.000 0.00 0.00 37.52 2.97
3744 3866 6.603201 AGAATACCTACAACATGTTTGGATGG 59.397 38.462 21.76 15.78 30.76 3.51
3754 3876 4.108570 TCCCCACAGAATACCTACAACAT 58.891 43.478 0.00 0.00 0.00 2.71
3755 3877 3.522759 TCCCCACAGAATACCTACAACA 58.477 45.455 0.00 0.00 0.00 3.33
3767 3889 2.025416 CACCCAATACATTCCCCACAGA 60.025 50.000 0.00 0.00 0.00 3.41
3769 3891 1.618345 GCACCCAATACATTCCCCACA 60.618 52.381 0.00 0.00 0.00 4.17
3923 4045 9.612620 GAAATTTGTCATTTTTGTATCTCGAGT 57.387 29.630 13.13 2.46 0.00 4.18
3964 4086 1.893062 GGCTTGAGATTTGGCCCAC 59.107 57.895 0.00 0.00 38.77 4.61
4074 4196 7.121020 AGCACATTCACACAACATCAATGTATA 59.879 33.333 0.00 0.00 40.80 1.47
4139 4261 0.957395 CAGTGCTCCAAACTCGGCAT 60.957 55.000 0.00 0.00 37.05 4.40
4141 4263 2.328099 CCAGTGCTCCAAACTCGGC 61.328 63.158 0.00 0.00 0.00 5.54
4143 4265 0.671781 CTCCCAGTGCTCCAAACTCG 60.672 60.000 0.00 0.00 0.00 4.18
4149 4271 3.640407 GGTGCTCCCAGTGCTCCA 61.640 66.667 0.00 0.00 41.91 3.86
4182 4304 2.427453 CGGGATACGGGAGAATATCTGG 59.573 54.545 0.00 0.00 39.42 3.86


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

AutoCloner maintained by Alex Coulton.