Multiple sequence alignment - TraesCS1D01G131000

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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 TraesCS1D01G131000 chr1D 100.000 4932 0 0 1 4932 147893826 147898757 0.000000e+00 9108
1 TraesCS1D01G131000 chr1D 88.927 289 23 6 630 909 198740361 198740073 1.020000e-91 348
2 TraesCS1D01G131000 chr1D 85.714 182 26 0 4201 4382 147897843 147898024 5.040000e-45 193
3 TraesCS1D01G131000 chr1D 85.714 182 26 0 4018 4199 147898026 147898207 5.040000e-45 193
4 TraesCS1D01G131000 chr1D 91.463 82 7 0 2413 2494 325484494 325484575 4.040000e-21 113
5 TraesCS1D01G131000 chr1A 97.050 3220 63 11 944 4159 201747182 201743991 0.000000e+00 5409
6 TraesCS1D01G131000 chr1A 91.954 957 58 13 10 952 201748355 201747404 0.000000e+00 1323
7 TraesCS1D01G131000 chr1A 93.758 785 33 6 4151 4932 201735729 201734958 0.000000e+00 1164
8 TraesCS1D01G131000 chr1A 95.918 196 8 0 3964 4159 201742339 201742144 7.970000e-83 318
9 TraesCS1D01G131000 chr1A 95.408 196 9 0 3964 4159 201743260 201743065 3.710000e-81 313
10 TraesCS1D01G131000 chr1A 84.906 159 20 3 4018 4174 201735679 201735523 1.840000e-34 158
11 TraesCS1D01G131000 chr1A 84.507 142 22 0 4201 4342 201742285 201742144 1.850000e-29 141
12 TraesCS1D01G131000 chr1A 84.507 142 22 0 4201 4342 201744132 201743991 1.850000e-29 141
13 TraesCS1D01G131000 chr1A 83.803 142 23 0 4201 4342 201743206 201743065 8.610000e-28 135
14 TraesCS1D01G131000 chr3D 89.895 287 20 7 631 908 255424392 255424678 1.310000e-95 361
15 TraesCS1D01G131000 chr3B 89.895 287 19 8 631 908 377115120 377115405 1.310000e-95 361
16 TraesCS1D01G131000 chr4D 89.860 286 18 9 633 908 32419110 32418826 1.690000e-94 357
17 TraesCS1D01G131000 chr3A 89.583 288 20 8 631 908 319962312 319962599 1.690000e-94 357
18 TraesCS1D01G131000 chr6D 88.591 298 23 10 631 918 327021869 327022165 7.850000e-93 351
19 TraesCS1D01G131000 chr6D 88.136 295 27 6 631 917 344056102 344056396 1.310000e-90 344
20 TraesCS1D01G131000 chr2D 88.581 289 24 8 631 911 62406580 62406293 4.730000e-90 342
21 TraesCS1D01G131000 chr2D 90.698 86 8 0 2413 2498 74975910 74975995 1.120000e-21 115
22 TraesCS1D01G131000 chr2B 91.765 85 7 0 2413 2497 247368622 247368538 8.670000e-23 119
23 TraesCS1D01G131000 chr2B 89.247 93 10 0 2409 2501 175632108 175632200 3.120000e-22 117
24 TraesCS1D01G131000 chr2A 89.474 95 9 1 2403 2497 182009060 182008967 8.670000e-23 119
25 TraesCS1D01G131000 chr2A 88.172 93 11 0 2409 2501 127200297 127200389 1.450000e-20 111
26 TraesCS1D01G131000 chr6A 87.500 96 11 1 2399 2494 263872788 263872882 5.220000e-20 110
27 TraesCS1D01G131000 chr5D 88.764 89 10 0 2412 2500 441906575 441906487 5.220000e-20 110


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 TraesCS1D01G131000 chr1D 147893826 147898757 4931 False 3164.666667 9108 90.476000 1 4932 3 chr1D.!!$F2 4931
1 TraesCS1D01G131000 chr1A 201742144 201748355 6211 True 1111.428571 5409 90.449571 10 4342 7 chr1A.!!$R2 4332
2 TraesCS1D01G131000 chr1A 201734958 201735729 771 True 661.000000 1164 89.332000 4018 4932 2 chr1A.!!$R1 914

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
698 709 0.328258 CCATCCCTTCGTCCAACCTT 59.672 55.000 0.00 0.00 0.00 3.50 F
1205 1451 0.038526 CTTGGTTCGTACGTCCTGCT 60.039 55.000 23.82 0.00 0.00 4.24 F
1448 1694 0.253327 GAGTCGGCCAGGGAGAATTT 59.747 55.000 2.24 0.00 0.00 1.82 F
3023 3269 1.072331 CTGGTCATATTTCCCCGGGAG 59.928 57.143 26.32 12.97 31.21 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2431 0.182061 TGATCTTGGCAGCCCTGATC 59.818 55.000 25.49 25.49 39.72 2.92 R
2663 2909 3.987547 GCTCATAGCTCAGCTGTTATCA 58.012 45.455 10.31 0.00 40.10 2.15 R
3251 3498 1.770294 TTCTCCCACAACAACCAACC 58.230 50.000 0.00 0.00 0.00 3.77 R
4178 4426 0.246360 ACACGAGCAATCGACATCCA 59.754 50.000 4.44 0.00 36.85 3.41 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
90 91 1.831736 ACCGGCCTATGATACTATGCC 59.168 52.381 0.00 0.00 35.55 4.40
91 92 1.139058 CCGGCCTATGATACTATGCCC 59.861 57.143 0.00 0.00 35.46 5.36
93 94 2.159043 CGGCCTATGATACTATGCCCTG 60.159 54.545 0.00 0.00 35.46 4.45
96 97 3.515502 GCCTATGATACTATGCCCTGTGA 59.484 47.826 0.00 0.00 0.00 3.58
235 243 2.675348 GTGGTCATGCTTACAGAAGAGC 59.325 50.000 0.00 0.00 39.33 4.09
279 287 7.869800 ACAAGAGTTTTCAATCTCAGATGTTC 58.130 34.615 0.00 0.00 33.63 3.18
281 289 6.226787 AGAGTTTTCAATCTCAGATGTTCGT 58.773 36.000 0.00 0.00 33.63 3.85
308 316 6.880529 GGTTTTTCAATCATCCAATCCACAAT 59.119 34.615 0.00 0.00 0.00 2.71
310 318 9.434420 GTTTTTCAATCATCCAATCCACAATAA 57.566 29.630 0.00 0.00 0.00 1.40
314 322 7.954835 TCAATCATCCAATCCACAATAAATCC 58.045 34.615 0.00 0.00 0.00 3.01
319 327 7.564292 TCATCCAATCCACAATAAATCCAATGA 59.436 33.333 0.00 0.00 0.00 2.57
321 329 7.555087 TCCAATCCACAATAAATCCAATGAAC 58.445 34.615 0.00 0.00 0.00 3.18
347 355 6.087291 CGCTTCAGATTTCTTTTGATGAACAC 59.913 38.462 0.00 0.00 0.00 3.32
362 370 0.396811 AACACCCTTGTTCCTCCGAG 59.603 55.000 0.00 0.00 42.67 4.63
368 376 1.537202 CCTTGTTCCTCCGAGCTTTTG 59.463 52.381 0.00 0.00 0.00 2.44
376 384 0.392998 TCCGAGCTTTTGGAGATGCC 60.393 55.000 0.00 0.00 37.10 4.40
381 389 1.635487 AGCTTTTGGAGATGCCCAGTA 59.365 47.619 0.00 0.00 37.53 2.74
396 404 6.449830 TGCCCAGTAGACTATCTCACTATA 57.550 41.667 0.00 0.00 0.00 1.31
412 420 9.927081 ATCTCACTATATCATTTCTTGGGTTTT 57.073 29.630 0.00 0.00 0.00 2.43
464 472 7.323420 TCTACATCAACATTCACTCGATTCTT 58.677 34.615 0.00 0.00 0.00 2.52
493 501 8.421784 TGAACTCATACCTTGTACTATCATTCC 58.578 37.037 0.00 0.00 0.00 3.01
496 504 7.015682 ACTCATACCTTGTACTATCATTCCCTG 59.984 40.741 0.00 0.00 0.00 4.45
513 521 3.391296 TCCCTGGTTTTAGCTAGCCATAG 59.609 47.826 12.13 0.67 0.00 2.23
514 522 3.136626 CCCTGGTTTTAGCTAGCCATAGT 59.863 47.826 12.13 0.00 0.00 2.12
530 538 9.520515 CTAGCCATAGTGGTATCCATAATTTTT 57.479 33.333 0.00 0.00 40.46 1.94
572 580 4.340950 TCATGTCGTCAATATGCCTAGTCA 59.659 41.667 0.00 0.00 0.00 3.41
578 586 6.700081 GTCGTCAATATGCCTAGTCAACATTA 59.300 38.462 0.00 0.00 0.00 1.90
672 682 6.051179 AGTAAGGTTCCTATGTCACCTTTC 57.949 41.667 8.08 3.81 46.85 2.62
681 692 5.070001 CCTATGTCACCTTTCTTTCAACCA 58.930 41.667 0.00 0.00 0.00 3.67
692 703 2.084546 CTTTCAACCATCCCTTCGTCC 58.915 52.381 0.00 0.00 0.00 4.79
698 709 0.328258 CCATCCCTTCGTCCAACCTT 59.672 55.000 0.00 0.00 0.00 3.50
766 777 9.757227 TGAACCAATTCCACTTTAATTTACTTG 57.243 29.630 0.00 0.00 33.49 3.16
810 821 6.180472 AGGTAATTCACGGTCAGAATTTGAT 58.820 36.000 10.52 0.00 41.54 2.57
864 878 8.418662 TGACAGGTAAATCATAAGCTAACGTAT 58.581 33.333 0.00 0.00 0.00 3.06
866 880 9.042008 ACAGGTAAATCATAAGCTAACGTATTG 57.958 33.333 0.00 0.00 0.00 1.90
867 881 9.256477 CAGGTAAATCATAAGCTAACGTATTGA 57.744 33.333 0.00 0.00 0.00 2.57
905 919 2.190170 AACGCACCGGCATTGTTCA 61.190 52.632 0.00 0.00 41.24 3.18
906 920 2.128853 AACGCACCGGCATTGTTCAG 62.129 55.000 0.00 0.00 41.24 3.02
917 932 4.026640 CGGCATTGTTCAGTTGACAAAAAG 60.027 41.667 0.00 0.00 0.00 2.27
990 1235 6.053005 TCAATAAAATCGTCCATCCACTACC 58.947 40.000 0.00 0.00 0.00 3.18
1095 1341 2.370633 GCTTCCCCTCCTCCTCCT 59.629 66.667 0.00 0.00 0.00 3.69
1096 1342 1.764454 GCTTCCCCTCCTCCTCCTC 60.764 68.421 0.00 0.00 0.00 3.71
1097 1343 1.074850 CTTCCCCTCCTCCTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
1098 1344 1.550374 TTCCCCTCCTCCTCCTCCT 60.550 63.158 0.00 0.00 0.00 3.69
1099 1345 1.595058 TTCCCCTCCTCCTCCTCCTC 61.595 65.000 0.00 0.00 0.00 3.71
1100 1346 2.612251 CCCTCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1196 1442 0.670546 GCTGCTGCTCTTGGTTCGTA 60.671 55.000 8.53 0.00 36.03 3.43
1205 1451 0.038526 CTTGGTTCGTACGTCCTGCT 60.039 55.000 23.82 0.00 0.00 4.24
1279 1525 4.974721 CTGCGGGGTTTGGCCTGT 62.975 66.667 3.32 0.00 37.43 4.00
1448 1694 0.253327 GAGTCGGCCAGGGAGAATTT 59.747 55.000 2.24 0.00 0.00 1.82
1588 1834 5.491323 TTTCTTTTTGGGTTTGGTGTCTT 57.509 34.783 0.00 0.00 0.00 3.01
1644 1890 2.631160 TTCCCGTTTCTCTGCTGAAA 57.369 45.000 0.00 0.00 34.05 2.69
1670 1916 8.908786 TTTCTCTTCATTTCTTGCTCTTTCTA 57.091 30.769 0.00 0.00 0.00 2.10
2065 2311 2.213499 CGCAAGAGAGTTGGTTTGACT 58.787 47.619 0.00 0.00 43.02 3.41
2152 2398 7.829725 ACTGCTCATTTGATTATAAAACTGCA 58.170 30.769 0.00 0.00 0.00 4.41
2261 2507 8.539544 TCAATCATCTTACATCTGGTCTGTAAA 58.460 33.333 0.00 0.00 38.30 2.01
2363 2609 9.507329 AAGATGTAAATCGCCATACTGAAATAT 57.493 29.630 0.00 0.00 0.00 1.28
2486 2732 8.730970 TGCAAAAACGTCTTATATTTTGGTAC 57.269 30.769 17.78 6.55 41.02 3.34
2494 2740 6.517864 CGTCTTATATTTTGGTACGGAGGGAT 60.518 42.308 0.00 0.00 0.00 3.85
2663 2909 5.032327 TGATGCTCTACTGATTTGCTCAT 57.968 39.130 0.00 0.00 32.10 2.90
2669 2915 6.481313 TGCTCTACTGATTTGCTCATGATAAC 59.519 38.462 0.00 0.00 32.10 1.89
2672 2918 5.496133 ACTGATTTGCTCATGATAACAGC 57.504 39.130 0.00 0.00 32.10 4.40
2698 2944 5.401033 GCTATGAGCTGTTATGTCACTTG 57.599 43.478 0.00 0.00 38.45 3.16
2730 2976 8.844244 GCTGTAGATTGTCAATGATTTCCTTAT 58.156 33.333 1.88 0.00 0.00 1.73
2733 2979 9.956720 GTAGATTGTCAATGATTTCCTTATTGG 57.043 33.333 1.88 0.00 33.70 3.16
2854 3100 1.100510 TGCATCAGATTTGCCTGAGC 58.899 50.000 0.00 0.00 45.27 4.26
2855 3101 1.340697 TGCATCAGATTTGCCTGAGCT 60.341 47.619 0.00 0.00 45.27 4.09
2856 3102 1.749634 GCATCAGATTTGCCTGAGCTT 59.250 47.619 0.00 0.00 45.27 3.74
2857 3103 2.947652 GCATCAGATTTGCCTGAGCTTA 59.052 45.455 0.00 0.00 45.27 3.09
2858 3104 3.379372 GCATCAGATTTGCCTGAGCTTAA 59.621 43.478 0.00 0.00 45.27 1.85
2971 3217 7.067737 GCTCTGTTAGTCAGTTATCTACTTCCT 59.932 40.741 0.00 0.00 43.97 3.36
3020 3266 2.092646 TGTTCTGGTCATATTTCCCCGG 60.093 50.000 0.00 0.00 0.00 5.73
3023 3269 1.072331 CTGGTCATATTTCCCCGGGAG 59.928 57.143 26.32 12.97 31.21 4.30
3189 3436 1.547372 GAAAGCATGACCACTGCCAAT 59.453 47.619 0.00 0.00 40.56 3.16
3251 3498 5.677091 GCATACAAACCTACATTGAGCAAGG 60.677 44.000 0.00 0.00 35.14 3.61
3293 3540 2.476997 GCTTCACTCTTGTTCTTCGTCC 59.523 50.000 0.00 0.00 0.00 4.79
3353 3600 9.987272 CATGAACACAGATGATAGAACCTATAA 57.013 33.333 0.00 0.00 0.00 0.98
3507 3754 4.654015 CTGAAGCTACTCAGTTCTCGTAC 58.346 47.826 7.18 0.00 38.43 3.67
3625 3872 2.488153 CCCTCCTTTTCCGTTGATTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3794 4041 7.341769 TGGTCAAATTGAAAACCTAGGGATATG 59.658 37.037 14.81 0.00 32.82 1.78
3863 4111 2.828877 TGTTTGTTACACCACCTCTCG 58.171 47.619 0.00 0.00 0.00 4.04
3866 4114 1.991121 TGTTACACCACCTCTCGTCT 58.009 50.000 0.00 0.00 0.00 4.18
3885 4133 3.058016 GTCTGACACCATGTTGATGTTGG 60.058 47.826 2.24 0.00 36.56 3.77
4003 4251 0.179001 GTTGGTGCTGGTGGTTAGGT 60.179 55.000 0.00 0.00 0.00 3.08
4004 4252 0.553819 TTGGTGCTGGTGGTTAGGTT 59.446 50.000 0.00 0.00 0.00 3.50
4107 4355 4.012374 GAGTCAATGATGAAAGGGCTTGA 58.988 43.478 0.00 0.00 37.30 3.02
4148 4396 3.181470 TGACGATGTGGTCTTTCAACAGA 60.181 43.478 0.00 0.00 37.81 3.41
4159 4407 6.589523 TGGTCTTTCAACAGAAAACAAATGTG 59.410 34.615 0.00 0.00 31.38 3.21
4160 4408 6.455513 GGTCTTTCAACAGAAAACAAATGTGC 60.456 38.462 0.00 0.00 31.38 4.57
4161 4409 5.580297 TCTTTCAACAGAAAACAAATGTGCC 59.420 36.000 0.00 0.00 31.38 5.01
4164 4412 4.629200 TCAACAGAAAACAAATGTGCCAAC 59.371 37.500 0.00 0.00 0.00 3.77
4165 4413 3.186119 ACAGAAAACAAATGTGCCAACG 58.814 40.909 0.00 0.00 0.00 4.10
4166 4414 2.539274 CAGAAAACAAATGTGCCAACGG 59.461 45.455 0.00 0.00 0.00 4.44
4167 4415 2.428890 AGAAAACAAATGTGCCAACGGA 59.571 40.909 0.00 0.00 0.00 4.69
4169 4417 0.673437 AACAAATGTGCCAACGGAGG 59.327 50.000 0.00 0.00 0.00 4.30
4184 4432 4.716025 AGGCGATCCTCTGGATGT 57.284 55.556 3.57 0.00 43.27 3.06
4185 4433 2.435418 AGGCGATCCTCTGGATGTC 58.565 57.895 3.57 0.00 43.27 3.06
4186 4434 1.006805 GGCGATCCTCTGGATGTCG 60.007 63.158 3.57 4.71 43.27 4.35
4187 4435 1.456196 GGCGATCCTCTGGATGTCGA 61.456 60.000 12.13 0.00 43.27 4.20
4189 4437 1.000283 GCGATCCTCTGGATGTCGATT 60.000 52.381 12.13 0.00 43.27 3.34
4190 4438 2.670479 CGATCCTCTGGATGTCGATTG 58.330 52.381 3.57 0.00 43.27 2.67
4191 4439 2.411904 GATCCTCTGGATGTCGATTGC 58.588 52.381 3.57 0.00 43.27 3.56
4192 4440 1.489481 TCCTCTGGATGTCGATTGCT 58.511 50.000 0.00 0.00 0.00 3.91
4195 4443 0.817654 TCTGGATGTCGATTGCTCGT 59.182 50.000 0.00 0.00 45.25 4.18
4196 4444 0.926155 CTGGATGTCGATTGCTCGTG 59.074 55.000 0.00 0.00 45.25 4.35
4198 4446 1.337728 TGGATGTCGATTGCTCGTGTT 60.338 47.619 0.00 0.00 45.25 3.32
4199 4447 1.061131 GGATGTCGATTGCTCGTGTTG 59.939 52.381 0.00 0.00 45.25 3.33
4207 6119 3.545633 GATTGCTCGTGTTGACTTGTTC 58.454 45.455 0.00 0.00 0.00 3.18
4217 6129 3.641436 TGTTGACTTGTTCTGAGCTAGGA 59.359 43.478 7.71 0.00 0.00 2.94
4225 6137 3.243873 TGTTCTGAGCTAGGATTATGGCG 60.244 47.826 0.00 0.00 0.00 5.69
4226 6138 1.895798 TCTGAGCTAGGATTATGGCGG 59.104 52.381 0.00 0.00 0.00 6.13
4227 6139 1.895798 CTGAGCTAGGATTATGGCGGA 59.104 52.381 0.00 0.00 0.00 5.54
4229 6141 1.205893 GAGCTAGGATTATGGCGGAGG 59.794 57.143 0.00 0.00 0.00 4.30
4245 6157 1.077716 AGGCGTCCCCAAGTTATGC 60.078 57.895 0.00 0.00 35.39 3.14
4271 6183 2.159170 GCGGATGAGCTAGAGTCAAAGT 60.159 50.000 0.00 0.00 0.00 2.66
4282 6194 6.817641 AGCTAGAGTCAAAGTCAATGATGAAG 59.182 38.462 0.00 0.00 37.30 3.02
4284 6196 6.119240 AGAGTCAAAGTCAATGATGAAGGA 57.881 37.500 0.00 0.00 37.30 3.36
4287 6199 4.699257 GTCAAAGTCAATGATGAAGGAGCT 59.301 41.667 0.00 0.00 37.30 4.09
4322 6234 5.877572 GGAGGATCTTGACGATGTGGTCG 62.878 56.522 0.00 0.00 45.94 4.79
4333 6245 2.672874 CGATGTGGTCGTTCAACATGAT 59.327 45.455 0.00 0.00 45.19 2.45
4364 6276 4.428294 CCAATGAAGGCAATCCTCTAGA 57.572 45.455 0.00 0.00 43.40 2.43
4365 6277 4.983053 CCAATGAAGGCAATCCTCTAGAT 58.017 43.478 0.00 0.00 43.40 1.98
4366 6278 4.760715 CCAATGAAGGCAATCCTCTAGATG 59.239 45.833 0.00 0.00 43.40 2.90
4473 6386 3.903090 CCTAGGAGGCAAAGATCAGATCT 59.097 47.826 7.15 7.15 42.61 2.75
4552 6465 1.354368 TGAAAGATGGACCTTGGACCC 59.646 52.381 5.77 1.60 0.00 4.46
4629 6542 6.486253 TTAATCTAGCTGCACAACTTTGAG 57.514 37.500 1.02 0.00 0.00 3.02
4634 6547 4.277515 AGCTGCACAACTTTGAGATCTA 57.722 40.909 1.02 0.00 0.00 1.98
4646 6559 5.757320 ACTTTGAGATCTAGATGCAAATCCG 59.243 40.000 21.50 15.77 0.00 4.18
4717 6630 5.717078 AGTTCGTGAGTTCATAAGTACCA 57.283 39.130 0.00 0.00 0.00 3.25
4772 6686 5.545658 TTAAGCCATTGAAGAATGTCGTC 57.454 39.130 0.00 0.00 37.82 4.20
4774 6688 3.679389 AGCCATTGAAGAATGTCGTCTT 58.321 40.909 0.00 0.00 40.62 3.01
4779 6693 2.672714 TGAAGAATGTCGTCTTGGTCG 58.327 47.619 0.00 0.00 37.98 4.79
4802 6717 1.467342 GTGGCGGTAAACATCAACTCC 59.533 52.381 0.00 0.00 0.00 3.85
4841 6756 0.455410 TTTGGCATATTGGTGCTCGC 59.545 50.000 0.00 0.00 44.45 5.03
4853 6768 0.670546 GTGCTCGCTGTGTGGTATGT 60.671 55.000 0.00 0.00 0.00 2.29
4854 6769 0.670239 TGCTCGCTGTGTGGTATGTG 60.670 55.000 0.00 0.00 0.00 3.21
4908 6823 2.751436 CATCCCCAAGTGCCCACG 60.751 66.667 0.00 0.00 36.20 4.94
4910 6825 2.840753 ATCCCCAAGTGCCCACGTT 61.841 57.895 0.00 0.00 36.20 3.99
4911 6826 3.294493 CCCCAAGTGCCCACGTTG 61.294 66.667 0.00 0.00 36.20 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 3.515502 TCACAGGGCATAGTATCATAGGC 59.484 47.826 0.00 0.00 0.00 3.93
279 287 5.348451 GGATTGGATGATTGAAAAACCAACG 59.652 40.000 0.00 0.00 39.60 4.10
281 289 6.183361 TGTGGATTGGATGATTGAAAAACCAA 60.183 34.615 0.00 0.00 40.74 3.67
308 316 4.584874 TCTGAAGCGGTTCATTGGATTTA 58.415 39.130 28.41 4.40 41.96 1.40
310 318 3.071874 TCTGAAGCGGTTCATTGGATT 57.928 42.857 28.41 0.00 41.96 3.01
314 322 4.691860 AGAAATCTGAAGCGGTTCATTG 57.308 40.909 28.41 18.50 41.96 2.82
319 327 5.241506 TCATCAAAAGAAATCTGAAGCGGTT 59.758 36.000 0.00 0.00 0.00 4.44
321 329 5.300969 TCATCAAAAGAAATCTGAAGCGG 57.699 39.130 0.00 0.00 0.00 5.52
347 355 0.036875 AAAGCTCGGAGGAACAAGGG 59.963 55.000 7.20 0.00 0.00 3.95
362 370 2.019984 CTACTGGGCATCTCCAAAAGC 58.980 52.381 0.00 0.00 36.21 3.51
368 376 3.761752 GAGATAGTCTACTGGGCATCTCC 59.238 52.174 8.50 0.00 34.78 3.71
396 404 6.610075 ATGCACTAAAACCCAAGAAATGAT 57.390 33.333 0.00 0.00 0.00 2.45
486 494 4.464947 GCTAGCTAAAACCAGGGAATGAT 58.535 43.478 7.70 0.00 0.00 2.45
493 501 4.130118 CACTATGGCTAGCTAAAACCAGG 58.870 47.826 15.72 11.22 35.20 4.45
496 504 4.152284 ACCACTATGGCTAGCTAAAACC 57.848 45.455 15.72 0.00 42.67 3.27
530 538 6.701340 ACATGATATAGCGCTAAATGAGGAA 58.299 36.000 22.98 0.00 0.00 3.36
532 540 5.230936 CGACATGATATAGCGCTAAATGAGG 59.769 44.000 22.98 12.46 0.00 3.86
598 606 6.169094 GCTAGCCATGACATGAGTAACATAT 58.831 40.000 17.24 0.00 37.46 1.78
617 625 4.321675 GCAGTAGAGATTCCTTAGGCTAGC 60.322 50.000 6.04 6.04 0.00 3.42
663 673 3.255888 GGGATGGTTGAAAGAAAGGTGAC 59.744 47.826 0.00 0.00 0.00 3.67
672 682 2.084546 GGACGAAGGGATGGTTGAAAG 58.915 52.381 0.00 0.00 0.00 2.62
681 692 0.618981 GGAAGGTTGGACGAAGGGAT 59.381 55.000 0.00 0.00 0.00 3.85
744 755 9.981114 AGTTCAAGTAAATTAAAGTGGAATTGG 57.019 29.630 0.00 0.00 0.00 3.16
792 803 4.819088 TGTTCATCAAATTCTGACCGTGAA 59.181 37.500 0.00 0.00 36.69 3.18
827 841 7.878547 TGATTTACCTGTCAATAATGATGCA 57.121 32.000 0.00 0.00 38.01 3.96
894 908 2.772568 TTGTCAACTGAACAATGCCG 57.227 45.000 0.00 0.00 0.00 5.69
961 1206 7.122650 AGTGGATGGACGATTTTATTGATGTTT 59.877 33.333 0.00 0.00 0.00 2.83
990 1235 0.695347 AGAGCCAAAGAAGGGTGGAG 59.305 55.000 0.00 0.00 40.02 3.86
1095 1341 1.607612 GAATTGGGAAGGCGGAGGA 59.392 57.895 0.00 0.00 0.00 3.71
1096 1342 1.453928 GGAATTGGGAAGGCGGAGG 60.454 63.158 0.00 0.00 0.00 4.30
1097 1343 1.453928 GGGAATTGGGAAGGCGGAG 60.454 63.158 0.00 0.00 0.00 4.63
1098 1344 2.680965 GGGAATTGGGAAGGCGGA 59.319 61.111 0.00 0.00 0.00 5.54
1099 1345 2.442087 GGGGAATTGGGAAGGCGG 60.442 66.667 0.00 0.00 0.00 6.13
1100 1346 0.687427 ATTGGGGAATTGGGAAGGCG 60.687 55.000 0.00 0.00 0.00 5.52
1205 1451 3.249189 AGACAAAGAGGCCGGCCA 61.249 61.111 45.13 0.00 38.92 5.36
1279 1525 4.298626 AGTATTTCCAGGCCAGATCAGTA 58.701 43.478 5.01 0.00 0.00 2.74
1581 1827 1.975680 TGGGTGAAGACCTAAGACACC 59.024 52.381 0.00 0.00 46.79 4.16
1644 1890 8.406730 AGAAAGAGCAAGAAATGAAGAGAAAT 57.593 30.769 0.00 0.00 0.00 2.17
1670 1916 1.196012 GATCAGGAAGAACCGAGGGT 58.804 55.000 0.00 0.00 44.74 4.34
1746 1992 1.986575 GCTCTCCTGCGCCATTTGAC 61.987 60.000 4.18 0.00 0.00 3.18
2152 2398 3.483869 GCAATCTCCTCCCGGCCT 61.484 66.667 0.00 0.00 0.00 5.19
2185 2431 0.182061 TGATCTTGGCAGCCCTGATC 59.818 55.000 25.49 25.49 39.72 2.92
2357 2603 8.158169 TCAGACCATGACTTTATGCATATTTC 57.842 34.615 7.36 5.15 31.12 2.17
2363 2609 6.233434 GGATATCAGACCATGACTTTATGCA 58.767 40.000 4.83 0.00 41.91 3.96
2486 2732 6.239345 GCCCATATTACTATCTAATCCCTCCG 60.239 46.154 0.00 0.00 0.00 4.63
2663 2909 3.987547 GCTCATAGCTCAGCTGTTATCA 58.012 45.455 10.31 0.00 40.10 2.15
2698 2944 5.118990 TCATTGACAATCTACAGCTAAGCC 58.881 41.667 0.00 0.00 0.00 4.35
2928 3174 4.344102 ACAGAGCACCAGACAGTAAAGTAA 59.656 41.667 0.00 0.00 0.00 2.24
2971 3217 4.905429 TCATTGAACTAGCAAGGCTGTAA 58.095 39.130 0.07 0.00 40.10 2.41
3189 3436 4.026744 TGTTTGGGGAATGTCTTCACAAA 58.973 39.130 0.00 0.00 36.44 2.83
3235 3482 2.555227 CCAACCCTTGCTCAATGTAGGT 60.555 50.000 0.00 0.00 0.00 3.08
3251 3498 1.770294 TTCTCCCACAACAACCAACC 58.230 50.000 0.00 0.00 0.00 3.77
3293 3540 3.255888 TGCTATAGAGTGAACCATAGCCG 59.744 47.826 3.21 0.00 43.33 5.52
3353 3600 7.721399 GGATCCAATAGAATTACAACTGGACAT 59.279 37.037 6.95 0.00 34.46 3.06
3504 3751 7.793902 ACAAGAAATGTTACAACAGATCGTAC 58.206 34.615 0.84 0.00 43.04 3.67
3507 3754 6.955963 GCTACAAGAAATGTTACAACAGATCG 59.044 38.462 0.84 0.00 43.04 3.69
3794 4041 6.560253 TGAACTAGATTCCTTTTCAGTTGC 57.440 37.500 0.00 0.00 36.36 4.17
3863 4111 3.058016 CCAACATCAACATGGTGTCAGAC 60.058 47.826 11.27 0.00 41.60 3.51
3866 4114 2.237643 CCCAACATCAACATGGTGTCA 58.762 47.619 11.27 0.00 41.60 3.58
3885 4133 2.035783 GCCAAGGGGAGGAACACC 59.964 66.667 0.00 0.00 43.70 4.16
4003 4251 1.757682 ACAAGTTCCAGGTTGCGAAA 58.242 45.000 0.00 0.00 0.00 3.46
4004 4252 1.757682 AACAAGTTCCAGGTTGCGAA 58.242 45.000 0.00 0.00 0.00 4.70
4107 4355 3.197549 GTCAAGATCCTCCTCTTCAAGCT 59.802 47.826 0.00 0.00 33.18 3.74
4148 4396 2.482839 CCTCCGTTGGCACATTTGTTTT 60.483 45.455 0.00 0.00 39.30 2.43
4169 4417 0.600557 ATCGACATCCAGAGGATCGC 59.399 55.000 4.60 0.00 40.98 4.58
4170 4418 2.670479 CAATCGACATCCAGAGGATCG 58.330 52.381 0.00 0.00 40.98 3.69
4171 4419 2.036992 AGCAATCGACATCCAGAGGATC 59.963 50.000 0.00 0.00 40.98 3.36
4173 4421 1.410517 GAGCAATCGACATCCAGAGGA 59.589 52.381 0.00 0.00 35.55 3.71
4174 4422 1.863267 GAGCAATCGACATCCAGAGG 58.137 55.000 0.00 0.00 0.00 3.69
4175 4423 1.202348 ACGAGCAATCGACATCCAGAG 60.202 52.381 4.44 0.00 36.85 3.35
4177 4425 0.926155 CACGAGCAATCGACATCCAG 59.074 55.000 4.44 0.00 36.85 3.86
4178 4426 0.246360 ACACGAGCAATCGACATCCA 59.754 50.000 4.44 0.00 36.85 3.41
4179 4427 1.061131 CAACACGAGCAATCGACATCC 59.939 52.381 4.44 0.00 36.85 3.51
4180 4428 1.992667 TCAACACGAGCAATCGACATC 59.007 47.619 4.44 0.00 36.85 3.06
4181 4429 1.726791 GTCAACACGAGCAATCGACAT 59.273 47.619 4.44 0.00 36.85 3.06
4182 4430 1.136690 GTCAACACGAGCAATCGACA 58.863 50.000 4.44 0.00 36.85 4.35
4183 4431 1.419374 AGTCAACACGAGCAATCGAC 58.581 50.000 4.44 0.00 36.85 4.20
4184 4432 1.792367 CAAGTCAACACGAGCAATCGA 59.208 47.619 4.44 0.00 36.85 3.59
4185 4433 1.526887 ACAAGTCAACACGAGCAATCG 59.473 47.619 0.00 0.00 39.31 3.34
4186 4434 3.248602 AGAACAAGTCAACACGAGCAATC 59.751 43.478 0.00 0.00 0.00 2.67
4187 4435 3.002656 CAGAACAAGTCAACACGAGCAAT 59.997 43.478 0.00 0.00 0.00 3.56
4189 4437 1.933181 CAGAACAAGTCAACACGAGCA 59.067 47.619 0.00 0.00 0.00 4.26
4190 4438 2.201732 TCAGAACAAGTCAACACGAGC 58.798 47.619 0.00 0.00 0.00 5.03
4191 4439 2.219674 GCTCAGAACAAGTCAACACGAG 59.780 50.000 0.00 0.00 0.00 4.18
4192 4440 2.159099 AGCTCAGAACAAGTCAACACGA 60.159 45.455 0.00 0.00 0.00 4.35
4195 4443 3.641436 TCCTAGCTCAGAACAAGTCAACA 59.359 43.478 0.00 0.00 0.00 3.33
4196 4444 4.258702 TCCTAGCTCAGAACAAGTCAAC 57.741 45.455 0.00 0.00 0.00 3.18
4198 4446 6.407412 CCATAATCCTAGCTCAGAACAAGTCA 60.407 42.308 0.00 0.00 0.00 3.41
4199 4447 5.988561 CCATAATCCTAGCTCAGAACAAGTC 59.011 44.000 0.00 0.00 0.00 3.01
4207 6119 1.895798 TCCGCCATAATCCTAGCTCAG 59.104 52.381 0.00 0.00 0.00 3.35
4217 6129 2.426023 GGACGCCTCCGCCATAAT 59.574 61.111 0.00 0.00 38.22 1.28
4225 6137 0.463833 CATAACTTGGGGACGCCTCC 60.464 60.000 10.28 0.00 35.50 4.30
4226 6138 1.095807 GCATAACTTGGGGACGCCTC 61.096 60.000 10.28 0.00 0.00 4.70
4227 6139 1.077716 GCATAACTTGGGGACGCCT 60.078 57.895 10.28 0.00 0.00 5.52
4229 6141 1.022451 TTCGCATAACTTGGGGACGC 61.022 55.000 0.00 0.00 38.74 5.19
4245 6157 1.066303 ACTCTAGCTCATCCGCTTTCG 59.934 52.381 0.00 0.00 41.30 3.46
4251 6163 3.129462 TGACTTTGACTCTAGCTCATCCG 59.871 47.826 0.00 0.00 0.00 4.18
4253 6165 6.336566 TCATTGACTTTGACTCTAGCTCATC 58.663 40.000 0.00 0.00 0.00 2.92
4256 6168 6.336566 TCATCATTGACTTTGACTCTAGCTC 58.663 40.000 0.00 0.00 0.00 4.09
4260 6172 7.244886 TCCTTCATCATTGACTTTGACTCTA 57.755 36.000 0.00 0.00 0.00 2.43
4265 6177 4.914983 AGCTCCTTCATCATTGACTTTGA 58.085 39.130 0.00 0.00 0.00 2.69
4266 6178 5.399858 CAAGCTCCTTCATCATTGACTTTG 58.600 41.667 0.00 0.00 0.00 2.77
4267 6179 4.461781 CCAAGCTCCTTCATCATTGACTTT 59.538 41.667 0.00 0.00 0.00 2.66
4268 6180 4.015084 CCAAGCTCCTTCATCATTGACTT 58.985 43.478 0.00 0.00 0.00 3.01
4271 6183 2.947243 GCCCAAGCTCCTTCATCATTGA 60.947 50.000 0.00 0.00 35.50 2.57
4287 6199 1.561542 GATCCTCCTCTTCAAGCCCAA 59.438 52.381 0.00 0.00 0.00 4.12
4322 6234 5.468592 TGGCACATTTGTATCATGTTGAAC 58.531 37.500 0.00 0.00 32.25 3.18
4330 6242 5.327616 CCTTCATTGGCACATTTGTATCA 57.672 39.130 0.00 0.00 39.30 2.15
4357 6269 2.292016 ACGAGCAATCGACATCTAGAGG 59.708 50.000 2.12 2.12 36.85 3.69
4358 6270 3.242903 ACACGAGCAATCGACATCTAGAG 60.243 47.826 4.44 0.00 36.85 2.43
4359 6271 2.683362 ACACGAGCAATCGACATCTAGA 59.317 45.455 4.44 0.00 36.85 2.43
4360 6272 3.071786 ACACGAGCAATCGACATCTAG 57.928 47.619 4.44 0.00 36.85 2.43
4361 6273 3.503827 AACACGAGCAATCGACATCTA 57.496 42.857 4.44 0.00 36.85 1.98
4362 6274 2.370281 AACACGAGCAATCGACATCT 57.630 45.000 4.44 0.00 36.85 2.90
4363 6275 3.366724 TGTTAACACGAGCAATCGACATC 59.633 43.478 3.59 0.00 36.85 3.06
4364 6276 3.122948 GTGTTAACACGAGCAATCGACAT 59.877 43.478 22.16 0.00 37.10 3.06
4365 6277 2.473609 GTGTTAACACGAGCAATCGACA 59.526 45.455 22.16 0.00 37.10 4.35
4366 6278 3.086298 GTGTTAACACGAGCAATCGAC 57.914 47.619 22.16 0.00 37.10 4.20
4509 6422 1.066645 GCCTTTTCCCAATCAGCAAGG 60.067 52.381 0.00 0.00 34.94 3.61
4617 6530 4.633126 TGCATCTAGATCTCAAAGTTGTGC 59.367 41.667 1.03 0.82 0.00 4.57
4629 6542 2.677199 TCGCGGATTTGCATCTAGATC 58.323 47.619 6.13 0.00 34.15 2.75
4634 6547 1.069823 AGAGATCGCGGATTTGCATCT 59.930 47.619 6.13 4.92 36.28 2.90
4646 6559 2.600731 CATAACCATCCGAGAGATCGC 58.399 52.381 0.00 0.00 30.59 4.58
4717 6630 4.880696 GGAGAAGTCATATGAAGCTTGCTT 59.119 41.667 2.10 7.65 0.00 3.91
4770 6684 3.103911 CGCCACGACGACCAAGAC 61.104 66.667 0.00 0.00 34.06 3.01
4772 6686 2.752322 TTACCGCCACGACGACCAAG 62.752 60.000 0.00 0.00 34.06 3.61
4774 6688 2.854401 TTTACCGCCACGACGACCA 61.854 57.895 0.00 0.00 34.06 4.02
4779 6693 1.136169 GTTGATGTTTACCGCCACGAC 60.136 52.381 0.00 0.00 0.00 4.34
4802 6717 5.343058 CCAAACGTTCATACTTGATGCAAAG 59.657 40.000 0.00 0.00 35.29 2.77
4841 6756 2.233676 TGTCCTAGCACATACCACACAG 59.766 50.000 0.00 0.00 0.00 3.66
4853 6768 8.511321 CATTTTATTTGTACACTTGTCCTAGCA 58.489 33.333 0.00 0.00 0.00 3.49
4854 6769 8.512138 ACATTTTATTTGTACACTTGTCCTAGC 58.488 33.333 0.00 0.00 0.00 3.42
4908 6823 0.889186 ACTCCATTGCGACCACCAAC 60.889 55.000 0.00 0.00 0.00 3.77
4910 6825 0.908910 ATACTCCATTGCGACCACCA 59.091 50.000 0.00 0.00 0.00 4.17
4911 6826 1.299541 CATACTCCATTGCGACCACC 58.700 55.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.