Multiple sequence alignment - TraesCS3D01G171300

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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 TraesCS3D01G171300 chr3D 100.000 2951 0 0 636 3586 151901144 151904094 0.000000e+00 5450
1 TraesCS3D01G171300 chr3D 86.450 369 40 8 3203 3564 355617323 355617688 2.590000e-106 396
2 TraesCS3D01G171300 chr3D 100.000 154 0 0 1 154 151900509 151900662 5.860000e-73 285
3 TraesCS3D01G171300 chr3B 94.491 2614 81 23 636 3199 222317832 222320432 0.000000e+00 3971
4 TraesCS3D01G171300 chr3B 94.340 159 3 2 1 154 222317626 222317783 4.630000e-59 239
5 TraesCS3D01G171300 chr3A 94.367 2219 83 14 767 2961 178987753 178985553 0.000000e+00 3367
6 TraesCS3D01G171300 chr3A 90.133 375 28 6 3195 3564 717009814 717009444 2.500000e-131 479
7 TraesCS3D01G171300 chr3A 93.561 264 10 2 2944 3200 178985527 178985264 1.560000e-103 387
8 TraesCS3D01G171300 chr3A 99.219 128 1 0 636 763 178988304 178988177 7.740000e-57 231
9 TraesCS3D01G171300 chr3A 93.082 159 5 2 1 154 178988511 178988354 1.000000e-55 228
10 TraesCS3D01G171300 chr4D 90.050 402 40 0 1234 1635 433393653 433393252 4.100000e-144 521
11 TraesCS3D01G171300 chr4B 90.050 402 40 0 1234 1635 531580985 531580584 4.100000e-144 521
12 TraesCS3D01G171300 chr4A 89.681 407 41 1 1229 1635 34787862 34787457 5.310000e-143 518
13 TraesCS3D01G171300 chr5D 89.578 403 42 0 1233 1635 442331797 442332199 2.470000e-141 512
14 TraesCS3D01G171300 chr5D 89.067 375 30 6 3197 3564 67871355 67871725 4.220000e-124 455
15 TraesCS3D01G171300 chr5B 89.578 403 42 0 1233 1635 538542404 538542806 2.470000e-141 512
16 TraesCS3D01G171300 chr5B 86.494 385 35 13 3195 3564 498698060 498697678 1.200000e-109 407
17 TraesCS3D01G171300 chr5A 88.586 403 46 0 1233 1635 558543702 558544104 1.160000e-134 490
18 TraesCS3D01G171300 chr5A 86.933 375 35 9 3198 3564 701884671 701885039 3.330000e-110 409
19 TraesCS3D01G171300 chr6D 88.060 402 45 3 1233 1631 332499020 332499421 1.170000e-129 473
20 TraesCS3D01G171300 chr1A 89.730 370 31 5 3199 3565 398115560 398115925 1.950000e-127 466
21 TraesCS3D01G171300 chr1A 86.737 377 34 12 3199 3566 496118986 496119355 4.310000e-109 405
22 TraesCS3D01G171300 chr2B 86.702 376 42 6 3196 3564 749825122 749824748 9.270000e-111 411
23 TraesCS3D01G171300 chr6B 87.500 368 26 14 3199 3560 156478723 156479076 1.200000e-109 407


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 TraesCS3D01G171300 chr3D 151900509 151904094 3585 False 2867.50 5450 100.00000 1 3586 2 chr3D.!!$F2 3585
1 TraesCS3D01G171300 chr3B 222317626 222320432 2806 False 2105.00 3971 94.41550 1 3199 2 chr3B.!!$F1 3198
2 TraesCS3D01G171300 chr3A 178985264 178988511 3247 True 1053.25 3367 95.05725 1 3200 4 chr3A.!!$R2 3199

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
938 1364 2.003301 GACTAGTTAAGCACCAGCAGC 58.997 52.381 0.0 0.0 45.49 5.25 F
2135 2575 1.402259 CTCTCGTCATCTAACGCCAGT 59.598 52.381 0.0 0.0 42.31 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 2718 0.108138 CATCGAGGTGTTGGAGGACC 60.108 60.0 0.0 0.0 0.00 4.46 R
3463 3985 0.107081 TTCTCGCCTCCGTCCAAAAA 59.893 50.0 0.0 0.0 35.54 1.94 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
938 1364 2.003301 GACTAGTTAAGCACCAGCAGC 58.997 52.381 0.00 0.00 45.49 5.25
975 1401 4.642437 ACAACAATCTCATCGAGAGCTAGA 59.358 41.667 0.00 0.00 42.26 2.43
977 1403 5.437289 ACAATCTCATCGAGAGCTAGAAG 57.563 43.478 0.00 0.00 42.26 2.85
1011 1442 2.874701 GAGCACAATAATGGCGAGTGAT 59.125 45.455 0.00 0.00 32.14 3.06
1022 1453 2.184830 CGAGTGATGCCATGGCCAG 61.185 63.158 33.44 12.71 41.09 4.85
1119 1553 3.682292 GAAGCGCAATCTCCCCGGT 62.682 63.158 11.47 0.00 0.00 5.28
1146 1583 4.192317 CAGGTAATAAGTCCAACCTCAGC 58.808 47.826 0.00 0.00 40.39 4.26
1319 1756 2.903357 GAGATCTGCGGCAAGGGA 59.097 61.111 0.00 0.00 0.00 4.20
1998 2438 2.033602 GTGGTGGTGGTACTGGCC 59.966 66.667 0.00 0.00 0.00 5.36
2135 2575 1.402259 CTCTCGTCATCTAACGCCAGT 59.598 52.381 0.00 0.00 42.31 4.00
2171 2611 1.680651 CTCCAGAGAGGCGGACAGT 60.681 63.158 0.00 0.00 36.39 3.55
2173 2613 2.279069 CCAGAGAGGCGGACAGTGT 61.279 63.158 0.00 0.00 0.00 3.55
2278 2718 1.874019 CGCAGATCGGTTCCGTCAG 60.874 63.158 11.04 6.52 33.78 3.51
2382 2822 1.880675 TCGACGACAGAGCTCTTTTCT 59.119 47.619 15.27 3.92 0.00 2.52
2420 2860 0.690762 ACAATGCTAACGTCCCCAGT 59.309 50.000 0.00 0.00 0.00 4.00
2447 2887 4.357947 GAGCTCACGACGGCCACA 62.358 66.667 9.40 0.00 0.00 4.17
2593 3033 4.398044 ACATGGGTGGATTTAGTTTAAGCG 59.602 41.667 0.00 0.00 0.00 4.68
2643 3088 4.442375 ACGAGGAGTAGTGTTTCATGAG 57.558 45.455 0.00 0.00 0.00 2.90
2661 3106 2.666190 CCATCCGCGGCCATGTAG 60.666 66.667 23.51 4.47 0.00 2.74
2768 3216 4.694509 CAGCTGTCATTTCTTGTCTTAGCT 59.305 41.667 5.25 0.00 39.35 3.32
2771 3219 5.293079 GCTGTCATTTCTTGTCTTAGCTAGG 59.707 44.000 0.00 0.00 0.00 3.02
2982 3497 3.267483 TCGCGAAGAAAAATAGAAGGGG 58.733 45.455 6.20 0.00 0.00 4.79
3105 3623 8.177663 CACCACTTTACAACTCTATTATTGCAG 58.822 37.037 0.00 0.00 0.00 4.41
3194 3716 5.997746 GCAATGTTATTCCTAGCCATAGTGA 59.002 40.000 0.00 0.00 0.00 3.41
3200 3722 5.636903 ATTCCTAGCCATAGTGACACATT 57.363 39.130 8.59 0.00 0.00 2.71
3201 3723 6.747414 ATTCCTAGCCATAGTGACACATTA 57.253 37.500 8.59 0.00 0.00 1.90
3202 3724 6.553953 TTCCTAGCCATAGTGACACATTAA 57.446 37.500 8.59 0.00 0.00 1.40
3203 3725 6.553953 TCCTAGCCATAGTGACACATTAAA 57.446 37.500 8.59 0.00 0.00 1.52
3204 3726 6.346096 TCCTAGCCATAGTGACACATTAAAC 58.654 40.000 8.59 0.00 0.00 2.01
3205 3727 6.156256 TCCTAGCCATAGTGACACATTAAACT 59.844 38.462 8.59 0.71 0.00 2.66
3206 3728 6.480320 CCTAGCCATAGTGACACATTAAACTC 59.520 42.308 8.59 0.00 0.00 3.01
3207 3729 5.804639 AGCCATAGTGACACATTAAACTCA 58.195 37.500 8.59 0.00 0.00 3.41
3208 3730 6.418101 AGCCATAGTGACACATTAAACTCAT 58.582 36.000 8.59 0.00 0.00 2.90
3209 3731 6.886459 AGCCATAGTGACACATTAAACTCATT 59.114 34.615 8.59 0.00 0.00 2.57
3210 3732 8.046708 AGCCATAGTGACACATTAAACTCATTA 58.953 33.333 8.59 0.00 0.00 1.90
3211 3733 8.673711 GCCATAGTGACACATTAAACTCATTAA 58.326 33.333 8.59 0.00 37.86 1.40
3213 3735 9.708222 CATAGTGACACATTAAACTCATTAAGC 57.292 33.333 8.59 0.00 36.94 3.09
3214 3736 7.986085 AGTGACACATTAAACTCATTAAGCT 57.014 32.000 8.59 0.00 36.94 3.74
3216 3738 8.936864 AGTGACACATTAAACTCATTAAGCTAC 58.063 33.333 8.59 0.00 36.94 3.58
3217 3739 7.898309 GTGACACATTAAACTCATTAAGCTACG 59.102 37.037 0.00 0.00 36.94 3.51
3218 3740 6.772078 ACACATTAAACTCATTAAGCTACGC 58.228 36.000 0.00 0.00 36.94 4.42
3219 3741 5.896432 CACATTAAACTCATTAAGCTACGCG 59.104 40.000 3.53 3.53 36.94 6.01
3220 3742 5.579511 ACATTAAACTCATTAAGCTACGCGT 59.420 36.000 19.17 19.17 36.94 6.01
3221 3743 3.991605 AAACTCATTAAGCTACGCGTG 57.008 42.857 24.59 13.17 0.00 5.34
3222 3744 2.933495 ACTCATTAAGCTACGCGTGA 57.067 45.000 24.59 6.82 0.00 4.35
3223 3745 3.226346 ACTCATTAAGCTACGCGTGAA 57.774 42.857 24.59 8.37 0.00 3.18
3224 3746 3.179830 ACTCATTAAGCTACGCGTGAAG 58.820 45.455 24.59 13.92 0.00 3.02
3225 3747 2.535984 CTCATTAAGCTACGCGTGAAGG 59.464 50.000 24.59 10.35 0.00 3.46
3226 3748 1.593006 CATTAAGCTACGCGTGAAGGG 59.407 52.381 24.59 7.77 38.93 3.95
3227 3749 0.738412 TTAAGCTACGCGTGAAGGGC 60.738 55.000 24.59 17.01 36.05 5.19
3245 3767 2.124736 GGCCAACGAGCTATGCCA 60.125 61.111 0.00 0.00 41.76 4.92
3246 3768 2.472909 GGCCAACGAGCTATGCCAC 61.473 63.158 0.00 0.00 41.76 5.01
3247 3769 2.813179 GCCAACGAGCTATGCCACG 61.813 63.158 0.00 0.00 35.71 4.94
3248 3770 1.447838 CCAACGAGCTATGCCACGT 60.448 57.895 0.00 6.58 41.65 4.49
3249 3771 1.695893 CCAACGAGCTATGCCACGTG 61.696 60.000 9.08 9.08 40.39 4.49
3250 3772 1.447838 AACGAGCTATGCCACGTGG 60.448 57.895 30.66 30.66 40.39 4.94
3268 3790 4.347453 CGCAAGCTGGTTGGCCAC 62.347 66.667 19.87 0.00 40.46 5.01
3269 3791 4.347453 GCAAGCTGGTTGGCCACG 62.347 66.667 19.87 0.00 40.46 4.94
3270 3792 3.673484 CAAGCTGGTTGGCCACGG 61.673 66.667 3.88 0.01 40.46 4.94
3271 3793 4.204028 AAGCTGGTTGGCCACGGT 62.204 61.111 3.88 0.00 40.46 4.83
3272 3794 4.954970 AGCTGGTTGGCCACGGTG 62.955 66.667 3.88 0.00 40.46 4.94
3273 3795 4.947147 GCTGGTTGGCCACGGTGA 62.947 66.667 3.88 0.00 40.46 4.02
3274 3796 2.669569 CTGGTTGGCCACGGTGAG 60.670 66.667 3.88 0.83 40.46 3.51
3275 3797 3.164977 TGGTTGGCCACGGTGAGA 61.165 61.111 3.88 0.00 40.46 3.27
3276 3798 2.112297 GGTTGGCCACGGTGAGAA 59.888 61.111 3.88 0.00 34.09 2.87
3277 3799 1.527380 GGTTGGCCACGGTGAGAAA 60.527 57.895 3.88 0.00 34.09 2.52
3278 3800 0.893727 GGTTGGCCACGGTGAGAAAT 60.894 55.000 3.88 0.00 34.09 2.17
3279 3801 0.521735 GTTGGCCACGGTGAGAAATC 59.478 55.000 3.88 0.00 0.00 2.17
3280 3802 0.400213 TTGGCCACGGTGAGAAATCT 59.600 50.000 3.88 0.00 0.00 2.40
3281 3803 0.400213 TGGCCACGGTGAGAAATCTT 59.600 50.000 10.28 0.00 0.00 2.40
3282 3804 1.202879 TGGCCACGGTGAGAAATCTTT 60.203 47.619 10.28 0.00 0.00 2.52
3283 3805 1.886542 GGCCACGGTGAGAAATCTTTT 59.113 47.619 10.28 0.00 0.00 2.27
3284 3806 2.351738 GGCCACGGTGAGAAATCTTTTG 60.352 50.000 10.28 0.00 0.00 2.44
3285 3807 2.293399 GCCACGGTGAGAAATCTTTTGT 59.707 45.455 10.28 0.00 0.00 2.83
3286 3808 3.243401 GCCACGGTGAGAAATCTTTTGTT 60.243 43.478 10.28 0.00 0.00 2.83
3287 3809 4.736464 GCCACGGTGAGAAATCTTTTGTTT 60.736 41.667 10.28 0.00 0.00 2.83
3288 3810 5.348164 CCACGGTGAGAAATCTTTTGTTTT 58.652 37.500 10.28 0.00 0.00 2.43
3289 3811 5.810074 CCACGGTGAGAAATCTTTTGTTTTT 59.190 36.000 10.28 0.00 0.00 1.94
3342 3864 8.767478 AATGCACATTTTCTTTTTAGATGGAG 57.233 30.769 0.00 0.00 0.00 3.86
3343 3865 6.690530 TGCACATTTTCTTTTTAGATGGAGG 58.309 36.000 0.00 0.00 0.00 4.30
3344 3866 6.267471 TGCACATTTTCTTTTTAGATGGAGGT 59.733 34.615 0.00 0.00 0.00 3.85
3345 3867 6.587608 GCACATTTTCTTTTTAGATGGAGGTG 59.412 38.462 0.00 0.00 0.00 4.00
3346 3868 7.523709 GCACATTTTCTTTTTAGATGGAGGTGA 60.524 37.037 0.00 0.00 0.00 4.02
3347 3869 8.025445 CACATTTTCTTTTTAGATGGAGGTGAG 58.975 37.037 0.00 0.00 0.00 3.51
3348 3870 7.177392 ACATTTTCTTTTTAGATGGAGGTGAGG 59.823 37.037 0.00 0.00 0.00 3.86
3349 3871 6.448369 TTTCTTTTTAGATGGAGGTGAGGA 57.552 37.500 0.00 0.00 0.00 3.71
3350 3872 5.422214 TCTTTTTAGATGGAGGTGAGGAC 57.578 43.478 0.00 0.00 0.00 3.85
3351 3873 4.225267 TCTTTTTAGATGGAGGTGAGGACC 59.775 45.833 0.00 0.00 43.52 4.46
3386 3908 8.600449 TTTTAAATGAAGGTTATGCAAAGTGG 57.400 30.769 0.00 0.00 0.00 4.00
3387 3909 3.874392 ATGAAGGTTATGCAAAGTGGC 57.126 42.857 0.00 0.00 0.00 5.01
3394 3916 2.203195 TGCAAAGTGGCACTCGCT 60.203 55.556 30.33 12.89 39.25 4.93
3395 3917 2.253452 GCAAAGTGGCACTCGCTG 59.747 61.111 26.14 21.11 38.60 5.18
3396 3918 2.949106 CAAAGTGGCACTCGCTGG 59.051 61.111 22.31 0.00 38.60 4.85
3397 3919 1.893808 CAAAGTGGCACTCGCTGGT 60.894 57.895 22.31 0.07 38.60 4.00
3398 3920 0.602638 CAAAGTGGCACTCGCTGGTA 60.603 55.000 22.31 0.00 38.60 3.25
3399 3921 0.320771 AAAGTGGCACTCGCTGGTAG 60.321 55.000 22.31 0.00 38.60 3.18
3400 3922 2.125512 GTGGCACTCGCTGGTAGG 60.126 66.667 11.13 0.00 38.60 3.18
3401 3923 2.603473 TGGCACTCGCTGGTAGGT 60.603 61.111 0.00 0.00 38.60 3.08
3402 3924 2.214216 TGGCACTCGCTGGTAGGTT 61.214 57.895 0.00 0.00 38.60 3.50
3403 3925 1.741770 GGCACTCGCTGGTAGGTTG 60.742 63.158 0.00 0.00 38.60 3.77
3404 3926 2.391389 GCACTCGCTGGTAGGTTGC 61.391 63.158 0.00 0.00 34.30 4.17
3408 3930 3.118454 CGCTGGTAGGTTGCGGTG 61.118 66.667 0.00 0.00 45.07 4.94
3409 3931 2.746277 GCTGGTAGGTTGCGGTGG 60.746 66.667 0.00 0.00 0.00 4.61
3410 3932 2.747686 CTGGTAGGTTGCGGTGGT 59.252 61.111 0.00 0.00 0.00 4.16
3411 3933 1.976898 CTGGTAGGTTGCGGTGGTA 59.023 57.895 0.00 0.00 0.00 3.25
3412 3934 0.322322 CTGGTAGGTTGCGGTGGTAA 59.678 55.000 0.00 0.00 0.00 2.85
3413 3935 0.985760 TGGTAGGTTGCGGTGGTAAT 59.014 50.000 0.00 0.00 0.00 1.89
3414 3936 1.351683 TGGTAGGTTGCGGTGGTAATT 59.648 47.619 0.00 0.00 0.00 1.40
3415 3937 2.224818 TGGTAGGTTGCGGTGGTAATTT 60.225 45.455 0.00 0.00 0.00 1.82
3416 3938 2.821378 GGTAGGTTGCGGTGGTAATTTT 59.179 45.455 0.00 0.00 0.00 1.82
3417 3939 3.256383 GGTAGGTTGCGGTGGTAATTTTT 59.744 43.478 0.00 0.00 0.00 1.94
3480 4002 4.371975 TTTTTGGACGGAGGCGAG 57.628 55.556 0.00 0.00 0.00 5.03
3481 4003 1.749665 TTTTTGGACGGAGGCGAGA 59.250 52.632 0.00 0.00 0.00 4.04
3482 4004 0.107081 TTTTTGGACGGAGGCGAGAA 59.893 50.000 0.00 0.00 0.00 2.87
3483 4005 0.601841 TTTTGGACGGAGGCGAGAAC 60.602 55.000 0.00 0.00 0.00 3.01
3484 4006 1.469335 TTTGGACGGAGGCGAGAACT 61.469 55.000 0.00 0.00 0.00 3.01
3485 4007 1.874345 TTGGACGGAGGCGAGAACTC 61.874 60.000 0.00 0.00 0.00 3.01
3486 4008 2.047443 GGACGGAGGCGAGAACTCT 61.047 63.158 0.00 0.00 35.34 3.24
3487 4009 0.747283 GGACGGAGGCGAGAACTCTA 60.747 60.000 0.00 0.00 35.34 2.43
3488 4010 1.310904 GACGGAGGCGAGAACTCTAT 58.689 55.000 0.00 0.00 35.34 1.98
3489 4011 1.002251 GACGGAGGCGAGAACTCTATG 60.002 57.143 0.00 0.00 35.34 2.23
3490 4012 1.025812 CGGAGGCGAGAACTCTATGT 58.974 55.000 0.00 0.00 35.34 2.29
3491 4013 2.219458 CGGAGGCGAGAACTCTATGTA 58.781 52.381 0.00 0.00 35.34 2.29
3492 4014 2.814919 CGGAGGCGAGAACTCTATGTAT 59.185 50.000 0.00 0.00 35.34 2.29
3493 4015 3.253677 CGGAGGCGAGAACTCTATGTATT 59.746 47.826 0.00 0.00 35.34 1.89
3494 4016 4.261656 CGGAGGCGAGAACTCTATGTATTT 60.262 45.833 0.00 0.00 35.34 1.40
3495 4017 5.602628 GGAGGCGAGAACTCTATGTATTTT 58.397 41.667 0.00 0.00 35.34 1.82
3496 4018 6.049790 GGAGGCGAGAACTCTATGTATTTTT 58.950 40.000 0.00 0.00 35.34 1.94
3517 4039 6.683090 TTTTGTAGATAAAAACATGCGCAC 57.317 33.333 14.90 0.00 0.00 5.34
3518 4040 5.363979 TTGTAGATAAAAACATGCGCACA 57.636 34.783 14.90 0.00 0.00 4.57
3519 4041 5.363979 TGTAGATAAAAACATGCGCACAA 57.636 34.783 14.90 0.00 0.00 3.33
3520 4042 5.150683 TGTAGATAAAAACATGCGCACAAC 58.849 37.500 14.90 0.00 0.00 3.32
3521 4043 4.503741 AGATAAAAACATGCGCACAACT 57.496 36.364 14.90 0.00 0.00 3.16
3522 4044 4.870363 AGATAAAAACATGCGCACAACTT 58.130 34.783 14.90 5.47 0.00 2.66
3523 4045 5.288804 AGATAAAAACATGCGCACAACTTT 58.711 33.333 14.90 13.14 0.00 2.66
3524 4046 3.923827 AAAAACATGCGCACAACTTTC 57.076 38.095 14.90 0.00 0.00 2.62
3525 4047 2.869233 AAACATGCGCACAACTTTCT 57.131 40.000 14.90 0.00 0.00 2.52
3526 4048 2.405892 AACATGCGCACAACTTTCTC 57.594 45.000 14.90 0.00 0.00 2.87
3527 4049 1.597742 ACATGCGCACAACTTTCTCT 58.402 45.000 14.90 0.00 0.00 3.10
3528 4050 1.949525 ACATGCGCACAACTTTCTCTT 59.050 42.857 14.90 0.00 0.00 2.85
3529 4051 3.138304 ACATGCGCACAACTTTCTCTTA 58.862 40.909 14.90 0.00 0.00 2.10
3530 4052 3.563808 ACATGCGCACAACTTTCTCTTAA 59.436 39.130 14.90 0.00 0.00 1.85
3531 4053 3.878086 TGCGCACAACTTTCTCTTAAG 57.122 42.857 5.66 0.00 0.00 1.85
3532 4054 2.032030 TGCGCACAACTTTCTCTTAAGC 60.032 45.455 5.66 0.00 0.00 3.09
3533 4055 2.827555 CGCACAACTTTCTCTTAAGCG 58.172 47.619 0.00 0.00 36.62 4.68
3534 4056 2.411547 CGCACAACTTTCTCTTAAGCGG 60.412 50.000 0.00 0.00 39.07 5.52
3535 4057 2.665794 GCACAACTTTCTCTTAAGCGGC 60.666 50.000 0.00 0.00 0.00 6.53
3536 4058 1.798813 ACAACTTTCTCTTAAGCGGCG 59.201 47.619 0.51 0.51 0.00 6.46
3537 4059 0.796927 AACTTTCTCTTAAGCGGCGC 59.203 50.000 26.86 26.86 0.00 6.53
3538 4060 1.019805 ACTTTCTCTTAAGCGGCGCC 61.020 55.000 30.40 19.07 0.00 6.53
3539 4061 1.004320 TTTCTCTTAAGCGGCGCCA 60.004 52.632 30.40 14.72 0.00 5.69
3540 4062 1.296056 TTTCTCTTAAGCGGCGCCAC 61.296 55.000 30.40 18.62 0.00 5.01
3541 4063 2.434185 CTCTTAAGCGGCGCCACA 60.434 61.111 30.40 11.30 0.00 4.17
3542 4064 2.434185 TCTTAAGCGGCGCCACAG 60.434 61.111 30.40 20.90 0.00 3.66
3543 4065 3.499737 CTTAAGCGGCGCCACAGG 61.500 66.667 30.40 11.41 0.00 4.00
3562 4084 4.028490 TGGCGCCCCAACCACTAG 62.028 66.667 26.77 0.00 38.46 2.57
3563 4085 4.029809 GGCGCCCCAACCACTAGT 62.030 66.667 18.11 0.00 0.00 2.57
3564 4086 2.662070 GGCGCCCCAACCACTAGTA 61.662 63.158 18.11 0.00 0.00 1.82
3565 4087 1.525442 GCGCCCCAACCACTAGTAT 59.475 57.895 0.00 0.00 0.00 2.12
3566 4088 0.754472 GCGCCCCAACCACTAGTATA 59.246 55.000 0.00 0.00 0.00 1.47
3567 4089 1.539712 GCGCCCCAACCACTAGTATAC 60.540 57.143 0.00 0.00 0.00 1.47
3568 4090 1.758280 CGCCCCAACCACTAGTATACA 59.242 52.381 5.50 0.00 0.00 2.29
3569 4091 2.367567 CGCCCCAACCACTAGTATACAT 59.632 50.000 5.50 0.00 0.00 2.29
3570 4092 3.575256 CGCCCCAACCACTAGTATACATA 59.425 47.826 5.50 0.00 0.00 2.29
3571 4093 4.039488 CGCCCCAACCACTAGTATACATAA 59.961 45.833 5.50 0.00 0.00 1.90
3572 4094 5.453621 CGCCCCAACCACTAGTATACATAAA 60.454 44.000 5.50 0.00 0.00 1.40
3573 4095 5.995897 GCCCCAACCACTAGTATACATAAAG 59.004 44.000 5.50 0.00 0.00 1.85
3574 4096 6.531021 CCCCAACCACTAGTATACATAAAGG 58.469 44.000 5.50 3.04 0.00 3.11
3575 4097 6.328148 CCCCAACCACTAGTATACATAAAGGA 59.672 42.308 5.50 0.00 0.00 3.36
3576 4098 7.442656 CCCAACCACTAGTATACATAAAGGAG 58.557 42.308 5.50 0.26 0.00 3.69
3577 4099 7.289317 CCCAACCACTAGTATACATAAAGGAGA 59.711 40.741 5.50 0.00 0.00 3.71
3578 4100 8.701895 CCAACCACTAGTATACATAAAGGAGAA 58.298 37.037 5.50 0.00 0.00 2.87
3581 4103 9.884814 ACCACTAGTATACATAAAGGAGAATCT 57.115 33.333 5.50 0.00 33.73 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
938 1364 0.722282 TGTTGTTGTTGGTCGACGTG 59.278 50.000 9.92 0.00 33.33 4.49
975 1401 1.140312 TGCTCCTTCTTGGTGTCCTT 58.860 50.000 0.00 0.00 37.07 3.36
977 1403 0.108585 TGTGCTCCTTCTTGGTGTCC 59.891 55.000 0.00 0.00 37.07 4.02
1011 1442 4.319949 AAAGGGCTGGCCATGGCA 62.320 61.111 36.56 21.67 44.11 4.92
1018 1449 4.416738 AGGAGCGAAAGGGCTGGC 62.417 66.667 0.00 0.00 44.93 4.85
1022 1453 1.448717 GTGAGAGGAGCGAAAGGGC 60.449 63.158 0.00 0.00 0.00 5.19
1119 1553 5.095809 AGGTTGGACTTATTACCTGGTGTA 58.904 41.667 10.23 0.00 39.47 2.90
1146 1583 0.392706 TGCTGCAGGGGATATACGTG 59.607 55.000 17.12 0.00 0.00 4.49
1319 1756 1.741770 GTTCTGGTCGCGCTGGAAT 60.742 57.895 5.56 0.00 0.00 3.01
1355 1792 3.579302 CAGGGGAGGTTGTGGCCA 61.579 66.667 0.00 0.00 0.00 5.36
1475 1912 1.568504 AGTGCTTCTTGATCCCGGTA 58.431 50.000 0.00 0.00 0.00 4.02
1556 1993 2.435059 GCCTTCCAGTCGGACTGC 60.435 66.667 28.50 15.69 44.63 4.40
1817 2254 4.729918 CCTCCCGCAGCAGGCTTT 62.730 66.667 0.00 0.00 41.67 3.51
2135 2575 2.085320 GAGGAGTTAGTCGTCAGCTCA 58.915 52.381 5.04 0.00 39.48 4.26
2171 2611 2.279851 CTGAACACGGACGGCACA 60.280 61.111 0.00 0.00 0.00 4.57
2216 2656 2.982130 GACATGTCGGTGGGAGCT 59.018 61.111 10.69 0.00 0.00 4.09
2270 2710 0.761323 TGTTGGAGGACCTGACGGAA 60.761 55.000 0.00 0.00 37.04 4.30
2278 2718 0.108138 CATCGAGGTGTTGGAGGACC 60.108 60.000 0.00 0.00 0.00 4.46
2439 2879 4.619227 CACGTTCCCTGTGGCCGT 62.619 66.667 0.00 0.00 38.81 5.68
2700 3145 4.244862 GGAATGCCTTGTGGTATTTTGTG 58.755 43.478 0.37 0.00 46.32 3.33
2768 3216 9.685276 AGTAACAAAATCATGAATGATGTCCTA 57.315 29.630 6.56 0.00 46.22 2.94
2771 3219 9.630098 ACAAGTAACAAAATCATGAATGATGTC 57.370 29.630 6.56 0.00 46.22 3.06
2887 3350 4.281688 CCCTTTTCTCTTCAATTTGCCTGA 59.718 41.667 0.00 0.00 0.00 3.86
2976 3491 1.290134 AGGATTCAGTGTCCCCCTTC 58.710 55.000 0.00 0.00 36.36 3.46
3105 3623 6.045955 TGCACTGAAAAGGTAATTTGGTTTC 58.954 36.000 0.00 0.00 0.00 2.78
3165 3687 4.398988 TGGCTAGGAATAACATTGCACAAG 59.601 41.667 0.00 0.00 33.32 3.16
3220 3742 4.697756 CTCGTTGGCCGCCCTTCA 62.698 66.667 7.03 0.00 36.19 3.02
3224 3746 4.547367 ATAGCTCGTTGGCCGCCC 62.547 66.667 7.03 0.00 36.19 6.13
3225 3747 3.272334 CATAGCTCGTTGGCCGCC 61.272 66.667 1.04 1.04 36.19 6.13
3226 3748 3.941836 GCATAGCTCGTTGGCCGC 61.942 66.667 0.00 0.00 36.19 6.53
3227 3749 3.272334 GGCATAGCTCGTTGGCCG 61.272 66.667 0.00 0.00 34.56 6.13
3228 3750 2.124736 TGGCATAGCTCGTTGGCC 60.125 61.111 13.08 0.00 44.82 5.36
3229 3751 2.813179 CGTGGCATAGCTCGTTGGC 61.813 63.158 9.90 9.90 38.77 4.52
3230 3752 1.447838 ACGTGGCATAGCTCGTTGG 60.448 57.895 0.00 0.00 36.32 3.77
3231 3753 1.695893 CCACGTGGCATAGCTCGTTG 61.696 60.000 24.02 0.00 37.12 4.10
3232 3754 1.447838 CCACGTGGCATAGCTCGTT 60.448 57.895 24.02 0.00 37.12 3.85
3233 3755 2.184322 CCACGTGGCATAGCTCGT 59.816 61.111 24.02 0.00 38.73 4.18
3246 3768 4.688419 CAACCAGCTTGCGCCACG 62.688 66.667 4.18 0.00 36.60 4.94
3247 3769 4.347453 CCAACCAGCTTGCGCCAC 62.347 66.667 4.18 0.00 36.60 5.01
3258 3780 2.272230 TTTCTCACCGTGGCCAACCA 62.272 55.000 7.24 0.00 46.51 3.67
3259 3781 0.893727 ATTTCTCACCGTGGCCAACC 60.894 55.000 7.24 0.00 0.00 3.77
3260 3782 0.521735 GATTTCTCACCGTGGCCAAC 59.478 55.000 7.24 0.15 0.00 3.77
3261 3783 0.400213 AGATTTCTCACCGTGGCCAA 59.600 50.000 7.24 0.00 0.00 4.52
3262 3784 0.400213 AAGATTTCTCACCGTGGCCA 59.600 50.000 0.00 0.00 0.00 5.36
3263 3785 1.534729 AAAGATTTCTCACCGTGGCC 58.465 50.000 0.00 0.00 0.00 5.36
3264 3786 2.293399 ACAAAAGATTTCTCACCGTGGC 59.707 45.455 0.00 0.00 0.00 5.01
3265 3787 4.568152 AACAAAAGATTTCTCACCGTGG 57.432 40.909 0.00 0.00 0.00 4.94
3266 3788 6.885735 AAAAACAAAAGATTTCTCACCGTG 57.114 33.333 0.00 0.00 0.00 4.94
3316 3838 9.211485 CTCCATCTAAAAAGAAAATGTGCATTT 57.789 29.630 4.48 4.48 42.35 2.32
3317 3839 7.820872 CCTCCATCTAAAAAGAAAATGTGCATT 59.179 33.333 0.00 0.00 0.00 3.56
3318 3840 7.038799 ACCTCCATCTAAAAAGAAAATGTGCAT 60.039 33.333 0.00 0.00 0.00 3.96
3319 3841 6.267471 ACCTCCATCTAAAAAGAAAATGTGCA 59.733 34.615 0.00 0.00 0.00 4.57
3320 3842 6.587608 CACCTCCATCTAAAAAGAAAATGTGC 59.412 38.462 0.00 0.00 0.00 4.57
3321 3843 7.885297 TCACCTCCATCTAAAAAGAAAATGTG 58.115 34.615 0.00 0.00 0.00 3.21
3322 3844 7.177392 CCTCACCTCCATCTAAAAAGAAAATGT 59.823 37.037 0.00 0.00 0.00 2.71
3323 3845 7.394359 TCCTCACCTCCATCTAAAAAGAAAATG 59.606 37.037 0.00 0.00 0.00 2.32
3324 3846 7.394641 GTCCTCACCTCCATCTAAAAAGAAAAT 59.605 37.037 0.00 0.00 0.00 1.82
3325 3847 6.715264 GTCCTCACCTCCATCTAAAAAGAAAA 59.285 38.462 0.00 0.00 0.00 2.29
3326 3848 6.238648 GTCCTCACCTCCATCTAAAAAGAAA 58.761 40.000 0.00 0.00 0.00 2.52
3327 3849 5.280521 GGTCCTCACCTCCATCTAAAAAGAA 60.281 44.000 0.00 0.00 40.00 2.52
3328 3850 4.225267 GGTCCTCACCTCCATCTAAAAAGA 59.775 45.833 0.00 0.00 40.00 2.52
3329 3851 4.518249 GGTCCTCACCTCCATCTAAAAAG 58.482 47.826 0.00 0.00 40.00 2.27
3330 3852 4.569719 GGTCCTCACCTCCATCTAAAAA 57.430 45.455 0.00 0.00 40.00 1.94
3360 3882 9.050601 CCACTTTGCATAACCTTCATTTAAAAA 57.949 29.630 0.00 0.00 0.00 1.94
3361 3883 7.172361 GCCACTTTGCATAACCTTCATTTAAAA 59.828 33.333 0.00 0.00 0.00 1.52
3362 3884 6.648725 GCCACTTTGCATAACCTTCATTTAAA 59.351 34.615 0.00 0.00 0.00 1.52
3363 3885 6.162777 GCCACTTTGCATAACCTTCATTTAA 58.837 36.000 0.00 0.00 0.00 1.52
3364 3886 5.244851 TGCCACTTTGCATAACCTTCATTTA 59.755 36.000 0.00 0.00 36.04 1.40
3365 3887 4.040217 TGCCACTTTGCATAACCTTCATTT 59.960 37.500 0.00 0.00 36.04 2.32
3366 3888 3.577848 TGCCACTTTGCATAACCTTCATT 59.422 39.130 0.00 0.00 36.04 2.57
3367 3889 3.056607 GTGCCACTTTGCATAACCTTCAT 60.057 43.478 0.00 0.00 44.30 2.57
3368 3890 2.295909 GTGCCACTTTGCATAACCTTCA 59.704 45.455 0.00 0.00 44.30 3.02
3369 3891 2.558359 AGTGCCACTTTGCATAACCTTC 59.442 45.455 0.00 0.00 44.30 3.46
3370 3892 2.558359 GAGTGCCACTTTGCATAACCTT 59.442 45.455 0.00 0.00 44.30 3.50
3371 3893 2.162681 GAGTGCCACTTTGCATAACCT 58.837 47.619 0.00 0.00 44.30 3.50
3372 3894 1.135689 CGAGTGCCACTTTGCATAACC 60.136 52.381 0.00 0.00 44.30 2.85
3373 3895 1.729149 GCGAGTGCCACTTTGCATAAC 60.729 52.381 15.52 0.00 44.30 1.89
3374 3896 0.521291 GCGAGTGCCACTTTGCATAA 59.479 50.000 15.52 0.00 44.30 1.90
3375 3897 0.321564 AGCGAGTGCCACTTTGCATA 60.322 50.000 20.52 0.00 44.30 3.14
3376 3898 1.601759 AGCGAGTGCCACTTTGCAT 60.602 52.632 20.52 7.23 44.30 3.96
3377 3899 2.203195 AGCGAGTGCCACTTTGCA 60.203 55.556 20.52 0.41 44.31 4.08
3378 3900 2.253452 CAGCGAGTGCCACTTTGC 59.747 61.111 13.31 13.31 44.31 3.68
3379 3901 0.602638 TACCAGCGAGTGCCACTTTG 60.603 55.000 0.00 0.00 44.31 2.77
3380 3902 0.320771 CTACCAGCGAGTGCCACTTT 60.321 55.000 0.00 0.00 44.31 2.66
3381 3903 1.293498 CTACCAGCGAGTGCCACTT 59.707 57.895 0.00 0.00 44.31 3.16
3382 3904 2.650116 CCTACCAGCGAGTGCCACT 61.650 63.158 0.00 0.00 44.31 4.00
3383 3905 2.125512 CCTACCAGCGAGTGCCAC 60.126 66.667 0.00 0.00 44.31 5.01
3384 3906 2.214216 AACCTACCAGCGAGTGCCA 61.214 57.895 0.00 0.00 44.31 4.92
3385 3907 1.741770 CAACCTACCAGCGAGTGCC 60.742 63.158 0.00 0.00 44.31 5.01
3386 3908 2.391389 GCAACCTACCAGCGAGTGC 61.391 63.158 0.00 0.00 43.24 4.40
3387 3909 3.876300 GCAACCTACCAGCGAGTG 58.124 61.111 0.00 0.00 0.00 3.51
3392 3914 2.175035 TACCACCGCAACCTACCAGC 62.175 60.000 0.00 0.00 0.00 4.85
3393 3915 0.322322 TTACCACCGCAACCTACCAG 59.678 55.000 0.00 0.00 0.00 4.00
3394 3916 0.985760 ATTACCACCGCAACCTACCA 59.014 50.000 0.00 0.00 0.00 3.25
3395 3917 2.118313 AATTACCACCGCAACCTACC 57.882 50.000 0.00 0.00 0.00 3.18
3396 3918 4.508461 AAAAATTACCACCGCAACCTAC 57.492 40.909 0.00 0.00 0.00 3.18
3463 3985 0.107081 TTCTCGCCTCCGTCCAAAAA 59.893 50.000 0.00 0.00 35.54 1.94
3464 3986 0.601841 GTTCTCGCCTCCGTCCAAAA 60.602 55.000 0.00 0.00 35.54 2.44
3465 3987 1.005394 GTTCTCGCCTCCGTCCAAA 60.005 57.895 0.00 0.00 35.54 3.28
3466 3988 1.874345 GAGTTCTCGCCTCCGTCCAA 61.874 60.000 0.00 0.00 35.54 3.53
3467 3989 2.282958 AGTTCTCGCCTCCGTCCA 60.283 61.111 0.00 0.00 35.54 4.02
3468 3990 0.747283 TAGAGTTCTCGCCTCCGTCC 60.747 60.000 0.00 0.00 35.54 4.79
3469 3991 1.002251 CATAGAGTTCTCGCCTCCGTC 60.002 57.143 0.00 0.00 35.54 4.79
3470 3992 1.025812 CATAGAGTTCTCGCCTCCGT 58.974 55.000 0.00 0.00 35.54 4.69
3471 3993 1.025812 ACATAGAGTTCTCGCCTCCG 58.974 55.000 0.00 0.00 0.00 4.63
3472 3994 4.857509 AATACATAGAGTTCTCGCCTCC 57.142 45.455 0.00 0.00 0.00 4.30
3493 4015 6.697455 TGTGCGCATGTTTTTATCTACAAAAA 59.303 30.769 15.91 0.00 35.56 1.94
3494 4016 6.209361 TGTGCGCATGTTTTTATCTACAAAA 58.791 32.000 15.91 0.00 0.00 2.44
3495 4017 5.763088 TGTGCGCATGTTTTTATCTACAAA 58.237 33.333 15.91 0.00 0.00 2.83
3496 4018 5.363979 TGTGCGCATGTTTTTATCTACAA 57.636 34.783 15.91 0.00 0.00 2.41
3497 4019 5.049060 AGTTGTGCGCATGTTTTTATCTACA 60.049 36.000 15.91 0.00 0.00 2.74
3498 4020 5.390613 AGTTGTGCGCATGTTTTTATCTAC 58.609 37.500 15.91 4.26 0.00 2.59
3499 4021 5.621197 AGTTGTGCGCATGTTTTTATCTA 57.379 34.783 15.91 0.00 0.00 1.98
3500 4022 4.503741 AGTTGTGCGCATGTTTTTATCT 57.496 36.364 15.91 0.00 0.00 1.98
3501 4023 5.402270 AGAAAGTTGTGCGCATGTTTTTATC 59.598 36.000 15.91 6.15 0.00 1.75
3502 4024 5.288804 AGAAAGTTGTGCGCATGTTTTTAT 58.711 33.333 15.91 7.51 0.00 1.40
3503 4025 4.677584 AGAAAGTTGTGCGCATGTTTTTA 58.322 34.783 15.91 0.00 0.00 1.52
3504 4026 3.520569 AGAAAGTTGTGCGCATGTTTTT 58.479 36.364 15.91 12.79 0.00 1.94
3505 4027 3.115554 GAGAAAGTTGTGCGCATGTTTT 58.884 40.909 15.91 12.41 0.00 2.43
3506 4028 2.358898 AGAGAAAGTTGTGCGCATGTTT 59.641 40.909 15.91 11.12 0.00 2.83
3507 4029 1.949525 AGAGAAAGTTGTGCGCATGTT 59.050 42.857 15.91 3.29 0.00 2.71
3508 4030 1.597742 AGAGAAAGTTGTGCGCATGT 58.402 45.000 15.91 0.00 0.00 3.21
3509 4031 2.693797 AAGAGAAAGTTGTGCGCATG 57.306 45.000 15.91 0.00 0.00 4.06
3510 4032 3.365364 GCTTAAGAGAAAGTTGTGCGCAT 60.365 43.478 15.91 0.00 0.00 4.73
3511 4033 2.032030 GCTTAAGAGAAAGTTGTGCGCA 60.032 45.455 5.66 5.66 0.00 6.09
3512 4034 2.575363 GCTTAAGAGAAAGTTGTGCGC 58.425 47.619 6.67 0.00 0.00 6.09
3513 4035 2.411547 CCGCTTAAGAGAAAGTTGTGCG 60.412 50.000 6.67 0.00 40.44 5.34
3514 4036 2.665794 GCCGCTTAAGAGAAAGTTGTGC 60.666 50.000 6.67 0.00 0.00 4.57
3515 4037 2.411547 CGCCGCTTAAGAGAAAGTTGTG 60.412 50.000 6.67 0.00 0.00 3.33
3516 4038 1.798813 CGCCGCTTAAGAGAAAGTTGT 59.201 47.619 6.67 0.00 0.00 3.32
3517 4039 1.464189 GCGCCGCTTAAGAGAAAGTTG 60.464 52.381 6.67 0.00 0.00 3.16
3518 4040 0.796927 GCGCCGCTTAAGAGAAAGTT 59.203 50.000 6.67 0.00 0.00 2.66
3519 4041 1.019805 GGCGCCGCTTAAGAGAAAGT 61.020 55.000 12.58 0.00 0.00 2.66
3520 4042 1.019278 TGGCGCCGCTTAAGAGAAAG 61.019 55.000 23.90 0.00 0.00 2.62
3521 4043 1.004320 TGGCGCCGCTTAAGAGAAA 60.004 52.632 23.90 0.00 0.00 2.52
3522 4044 1.740296 GTGGCGCCGCTTAAGAGAA 60.740 57.895 32.27 1.45 0.00 2.87
3523 4045 2.125673 GTGGCGCCGCTTAAGAGA 60.126 61.111 32.27 2.34 0.00 3.10
3524 4046 2.434185 TGTGGCGCCGCTTAAGAG 60.434 61.111 37.39 2.25 0.00 2.85
3525 4047 2.434185 CTGTGGCGCCGCTTAAGA 60.434 61.111 37.39 18.48 0.00 2.10
3526 4048 3.499737 CCTGTGGCGCCGCTTAAG 61.500 66.667 37.39 26.70 0.00 1.85
3545 4067 4.028490 CTAGTGGTTGGGGCGCCA 62.028 66.667 30.85 20.22 0.00 5.69
3546 4068 1.979619 ATACTAGTGGTTGGGGCGCC 61.980 60.000 21.18 21.18 0.00 6.53
3547 4069 0.754472 TATACTAGTGGTTGGGGCGC 59.246 55.000 5.39 0.00 0.00 6.53
3548 4070 1.758280 TGTATACTAGTGGTTGGGGCG 59.242 52.381 5.39 0.00 0.00 6.13
3549 4071 5.556006 TTATGTATACTAGTGGTTGGGGC 57.444 43.478 5.39 0.00 0.00 5.80
3550 4072 6.328148 TCCTTTATGTATACTAGTGGTTGGGG 59.672 42.308 5.39 0.00 0.00 4.96
3551 4073 7.289317 TCTCCTTTATGTATACTAGTGGTTGGG 59.711 40.741 5.39 0.00 0.00 4.12
3552 4074 8.246430 TCTCCTTTATGTATACTAGTGGTTGG 57.754 38.462 5.39 0.00 0.00 3.77
3555 4077 9.884814 AGATTCTCCTTTATGTATACTAGTGGT 57.115 33.333 5.39 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.