Multiple sequence alignment - TraesCS5D01G323600

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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 TraesCS5D01G323600 chr5D 100.000 5479 0 0 1 5479 415651878 415646400 0.000000e+00 10118.0
1 TraesCS5D01G323600 chr5D 87.208 1157 115 19 4049 5194 46076335 46075201 0.000000e+00 1286.0
2 TraesCS5D01G323600 chr5D 98.925 186 1 1 2095 2279 295930131 295930316 1.140000e-86 331.0
3 TraesCS5D01G323600 chr5D 93.233 133 9 0 3322 3454 46076458 46076326 4.330000e-46 196.0
4 TraesCS5D01G323600 chr5D 96.667 90 3 0 3194 3283 62177256 62177167 3.420000e-32 150.0
5 TraesCS5D01G323600 chr5D 100.000 28 0 0 1548 1575 415650244 415650217 1.000000e-02 52.8
6 TraesCS5D01G323600 chr5D 100.000 28 0 0 1635 1662 415650331 415650304 1.000000e-02 52.8
7 TraesCS5D01G323600 chr5A 93.352 3204 119 42 14 3193 528277150 528274017 0.000000e+00 4650.0
8 TraesCS5D01G323600 chr5A 94.444 2214 79 18 3282 5479 528273979 528271794 0.000000e+00 3367.0
9 TraesCS5D01G323600 chr5A 89.210 899 75 5 4049 4945 37084898 37084020 0.000000e+00 1103.0
10 TraesCS5D01G323600 chr5A 88.281 256 15 9 5228 5475 37084028 37083780 5.370000e-75 292.0
11 TraesCS5D01G323600 chr5A 92.029 138 11 0 3317 3454 37085026 37084889 1.560000e-45 195.0
12 TraesCS5D01G323600 chr5A 100.000 30 0 0 2052 2081 528275007 528274978 7.670000e-04 56.5
13 TraesCS5D01G323600 chr5A 100.000 28 0 0 1548 1575 528275571 528275544 1.000000e-02 52.8
14 TraesCS5D01G323600 chr5A 100.000 28 0 0 1635 1662 528275658 528275631 1.000000e-02 52.8
15 TraesCS5D01G323600 chr5B 97.601 1459 32 1 3282 4740 502025761 502024306 0.000000e+00 2497.0
16 TraesCS5D01G323600 chr5B 88.491 1981 92 34 4 1935 502029088 502027195 0.000000e+00 2270.0
17 TraesCS5D01G323600 chr5B 95.272 1269 35 4 1927 3193 502027044 502025799 0.000000e+00 1988.0
18 TraesCS5D01G323600 chr5B 97.727 748 12 2 4737 5479 502024149 502023402 0.000000e+00 1282.0
19 TraesCS5D01G323600 chr5B 100.000 30 0 0 355 384 216400675 216400704 7.670000e-04 56.5
20 TraesCS5D01G323600 chr5B 100.000 28 0 0 1548 1575 502027495 502027468 1.000000e-02 52.8
21 TraesCS5D01G323600 chr3B 88.511 705 44 13 4 696 47169415 47168736 0.000000e+00 819.0
22 TraesCS5D01G323600 chr2B 91.500 200 14 2 438 637 759190187 759189991 6.990000e-69 272.0
23 TraesCS5D01G323600 chr2B 87.425 167 15 2 191 357 759190365 759190205 2.610000e-43 187.0
24 TraesCS5D01G323600 chr4D 97.778 90 2 0 3194 3283 482703602 482703513 7.350000e-34 156.0
25 TraesCS5D01G323600 chr4A 97.778 90 2 0 3194 3283 681712937 681713026 7.350000e-34 156.0
26 TraesCS5D01G323600 chr4A 96.667 90 3 0 3194 3283 40451895 40451806 3.420000e-32 150.0
27 TraesCS5D01G323600 chr4A 96.667 90 3 0 3194 3283 594012756 594012845 3.420000e-32 150.0
28 TraesCS5D01G323600 chr2D 95.789 95 4 0 3189 3283 395133884 395133790 2.640000e-33 154.0
29 TraesCS5D01G323600 chr3D 96.667 90 3 0 3194 3283 401175229 401175318 3.420000e-32 150.0
30 TraesCS5D01G323600 chr3D 96.667 90 3 0 3194 3283 422517771 422517682 3.420000e-32 150.0
31 TraesCS5D01G323600 chr1A 96.667 90 3 0 3194 3283 251336944 251337033 3.420000e-32 150.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G323600 chr5D 415646400 415651878 5478 True 3407.866667 10118 100.0000 1 5479 3 chr5D.!!$R3 5478
1 TraesCS5D01G323600 chr5D 46075201 46076458 1257 True 741.000000 1286 90.2205 3322 5194 2 chr5D.!!$R2 1872
2 TraesCS5D01G323600 chr5A 528271794 528277150 5356 True 1635.820000 4650 97.5592 14 5479 5 chr5A.!!$R2 5465
3 TraesCS5D01G323600 chr5A 37083780 37085026 1246 True 530.000000 1103 89.8400 3317 5475 3 chr5A.!!$R1 2158
4 TraesCS5D01G323600 chr5B 502023402 502029088 5686 True 1617.960000 2497 95.8182 4 5479 5 chr5B.!!$R1 5475
5 TraesCS5D01G323600 chr3B 47168736 47169415 679 True 819.000000 819 88.5110 4 696 1 chr3B.!!$R1 692

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
847 895 0.032117 ATAAAAAGGCCAGCCCCTCC 60.032 55.000 5.01 0.0 32.93 4.30 F
1169 1224 0.468400 GAGATAGACGAGGCCAGGGT 60.468 60.000 5.01 0.0 0.00 4.34 F
1224 1303 1.638467 GTCATCATCGCGGTCAAGC 59.362 57.895 6.13 0.0 0.00 4.01 F
3202 3457 0.534203 TTTCTTGTTCGCTCCCGCTT 60.534 50.000 0.00 0.0 0.00 4.68 F
3524 3779 0.824759 GGTGCCTCGACCACTCTAAT 59.175 55.000 10.32 0.0 35.88 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 1892 0.391793 GAAACGAGAGGGGCCAGAAG 60.392 60.00 4.39 0.0 0.00 2.85 R
3058 3313 0.887933 TCCTTGGAAGAAAATGGCGC 59.112 50.00 0.00 0.0 0.00 6.53 R
3215 3470 0.187606 AAAGTGGTTGGACCCTTCCC 59.812 55.00 0.00 0.0 42.01 3.97 R
4454 4709 1.058404 GGTTCTGTAACTGCGTCGTC 58.942 55.00 0.00 0.0 35.81 4.20 R
5137 5566 5.248870 TCAGCTTTTGGAAGAAGTTTCAC 57.751 39.13 0.00 0.0 34.71 3.18 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
189 204 0.528684 GGCTCTGTTCGATCGAAGGG 60.529 60.000 29.79 23.10 34.49 3.95
244 259 4.137872 CAATGCAAGGGGCTGCCG 62.138 66.667 13.40 0.00 45.15 5.69
271 286 0.807496 GTTGGGAGACAATGCTCTGC 59.193 55.000 5.07 1.56 41.95 4.26
272 287 0.694771 TTGGGAGACAATGCTCTGCT 59.305 50.000 5.07 0.00 35.26 4.24
273 288 0.251354 TGGGAGACAATGCTCTGCTC 59.749 55.000 5.07 0.00 35.26 4.26
274 289 0.809241 GGGAGACAATGCTCTGCTCG 60.809 60.000 5.07 0.00 35.26 5.03
275 290 0.809241 GGAGACAATGCTCTGCTCGG 60.809 60.000 5.07 0.00 35.26 4.63
276 291 1.427592 GAGACAATGCTCTGCTCGGC 61.428 60.000 0.00 0.00 32.16 5.54
277 292 1.449246 GACAATGCTCTGCTCGGCT 60.449 57.895 0.00 0.00 0.00 5.52
278 293 1.427592 GACAATGCTCTGCTCGGCTC 61.428 60.000 0.00 0.00 0.00 4.70
279 294 1.449070 CAATGCTCTGCTCGGCTCA 60.449 57.895 0.00 0.00 0.00 4.26
280 295 0.814410 CAATGCTCTGCTCGGCTCAT 60.814 55.000 0.00 0.00 0.00 2.90
357 387 0.603065 TCGTGCTGCAGACATGTACT 59.397 50.000 20.43 0.00 0.00 2.73
358 388 0.994995 CGTGCTGCAGACATGTACTC 59.005 55.000 20.43 0.00 0.00 2.59
359 389 1.363744 GTGCTGCAGACATGTACTCC 58.636 55.000 20.43 0.00 0.00 3.85
360 390 0.250234 TGCTGCAGACATGTACTCCC 59.750 55.000 20.43 0.00 0.00 4.30
363 393 1.137872 CTGCAGACATGTACTCCCTCC 59.862 57.143 8.42 0.00 0.00 4.30
364 394 0.103208 GCAGACATGTACTCCCTCCG 59.897 60.000 0.00 0.00 0.00 4.63
365 395 1.475403 CAGACATGTACTCCCTCCGT 58.525 55.000 0.00 0.00 0.00 4.69
366 396 1.825474 CAGACATGTACTCCCTCCGTT 59.175 52.381 0.00 0.00 0.00 4.44
367 397 2.100989 AGACATGTACTCCCTCCGTTC 58.899 52.381 0.00 0.00 0.00 3.95
368 398 1.136500 GACATGTACTCCCTCCGTTCC 59.864 57.143 0.00 0.00 0.00 3.62
369 399 1.191535 CATGTACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
370 400 1.762957 CATGTACTCCCTCCGTTCCAT 59.237 52.381 0.00 0.00 0.00 3.41
371 401 2.832643 TGTACTCCCTCCGTTCCATA 57.167 50.000 0.00 0.00 0.00 2.74
372 402 3.323774 TGTACTCCCTCCGTTCCATAT 57.676 47.619 0.00 0.00 0.00 1.78
373 403 3.649843 TGTACTCCCTCCGTTCCATATT 58.350 45.455 0.00 0.00 0.00 1.28
374 404 4.806892 TGTACTCCCTCCGTTCCATATTA 58.193 43.478 0.00 0.00 0.00 0.98
375 405 4.831155 TGTACTCCCTCCGTTCCATATTAG 59.169 45.833 0.00 0.00 0.00 1.73
376 406 2.633481 ACTCCCTCCGTTCCATATTAGC 59.367 50.000 0.00 0.00 0.00 3.09
377 407 2.900546 CTCCCTCCGTTCCATATTAGCT 59.099 50.000 0.00 0.00 0.00 3.32
378 408 2.632996 TCCCTCCGTTCCATATTAGCTG 59.367 50.000 0.00 0.00 0.00 4.24
379 409 2.368875 CCCTCCGTTCCATATTAGCTGT 59.631 50.000 0.00 0.00 0.00 4.40
380 410 3.555168 CCCTCCGTTCCATATTAGCTGTC 60.555 52.174 0.00 0.00 0.00 3.51
381 411 3.309388 CTCCGTTCCATATTAGCTGTCG 58.691 50.000 0.00 0.00 0.00 4.35
382 412 1.792949 CCGTTCCATATTAGCTGTCGC 59.207 52.381 0.00 0.00 0.00 5.19
384 414 2.726760 CGTTCCATATTAGCTGTCGCTC 59.273 50.000 0.00 0.00 45.15 5.03
385 415 3.717707 GTTCCATATTAGCTGTCGCTCA 58.282 45.455 0.00 0.00 45.15 4.26
386 416 4.119862 GTTCCATATTAGCTGTCGCTCAA 58.880 43.478 0.00 0.00 45.15 3.02
387 417 4.400529 TCCATATTAGCTGTCGCTCAAA 57.599 40.909 0.00 0.00 45.15 2.69
388 418 4.119862 TCCATATTAGCTGTCGCTCAAAC 58.880 43.478 0.00 0.00 45.15 2.93
422 452 0.461548 CGGACAGATAGCAGCTGGAA 59.538 55.000 17.12 0.00 37.69 3.53
423 453 1.537776 CGGACAGATAGCAGCTGGAAG 60.538 57.143 17.12 0.00 37.69 3.46
430 460 5.242838 ACAGATAGCAGCTGGAAGTACTATC 59.757 44.000 17.12 19.28 39.92 2.08
547 584 2.417719 GGAATGCTTGACAGAAGACGT 58.582 47.619 0.00 0.00 0.00 4.34
615 652 2.357009 GCTCGAGATCATTGCATTTGGT 59.643 45.455 18.75 0.00 0.00 3.67
616 653 3.791122 GCTCGAGATCATTGCATTTGGTG 60.791 47.826 18.75 0.00 0.00 4.17
640 677 0.880278 TGGTTCGTTCTGCAGACAGC 60.880 55.000 18.03 10.90 44.10 4.40
653 691 2.283298 CAGACAGCCATGTGTATCCAC 58.717 52.381 0.00 0.00 40.68 4.02
658 696 1.151777 GCCATGTGTATCCACCGTCG 61.152 60.000 0.00 0.00 41.09 5.12
701 739 2.286294 CGCAAGTCTATCAACAGATGGC 59.714 50.000 0.00 0.00 0.00 4.40
703 741 4.697514 GCAAGTCTATCAACAGATGGCTA 58.302 43.478 0.00 0.00 0.00 3.93
720 761 3.580895 TGGCTACAGACCTACAATGACAA 59.419 43.478 0.00 0.00 0.00 3.18
782 830 0.668401 GTTTGCACAGCATTGGGAGC 60.668 55.000 0.00 0.00 38.76 4.70
844 892 2.091830 AGACTATAAAAAGGCCAGCCCC 60.092 50.000 5.01 0.00 36.58 5.80
847 895 0.032117 ATAAAAAGGCCAGCCCCTCC 60.032 55.000 5.01 0.00 32.93 4.30
861 909 1.122019 CCCTCCCTCCTCCAATACCG 61.122 65.000 0.00 0.00 0.00 4.02
930 978 4.363138 CTCCCAAACTCAAAACAAGAAGC 58.637 43.478 0.00 0.00 0.00 3.86
931 979 3.132111 TCCCAAACTCAAAACAAGAAGCC 59.868 43.478 0.00 0.00 0.00 4.35
932 980 3.118811 CCCAAACTCAAAACAAGAAGCCA 60.119 43.478 0.00 0.00 0.00 4.75
933 981 4.443315 CCCAAACTCAAAACAAGAAGCCAT 60.443 41.667 0.00 0.00 0.00 4.40
934 982 4.746611 CCAAACTCAAAACAAGAAGCCATC 59.253 41.667 0.00 0.00 0.00 3.51
935 983 3.904136 ACTCAAAACAAGAAGCCATCG 57.096 42.857 0.00 0.00 0.00 3.84
936 984 2.030805 ACTCAAAACAAGAAGCCATCGC 60.031 45.455 0.00 0.00 0.00 4.58
940 988 0.539438 AACAAGAAGCCATCGCCCAA 60.539 50.000 0.00 0.00 34.57 4.12
1062 1117 3.732849 CTTGCCCCTCCTGGACCC 61.733 72.222 0.00 0.00 35.39 4.46
1169 1224 0.468400 GAGATAGACGAGGCCAGGGT 60.468 60.000 5.01 0.00 0.00 4.34
1224 1303 1.638467 GTCATCATCGCGGTCAAGC 59.362 57.895 6.13 0.00 0.00 4.01
1813 1892 6.311445 TGTTTCTAATCGAAGCTCATGTCTTC 59.689 38.462 15.62 15.62 37.25 2.87
2100 2353 2.681976 GCCAGTAGCATCATGGTGTTCT 60.682 50.000 8.00 0.00 42.97 3.01
2101 2354 3.614092 CCAGTAGCATCATGGTGTTCTT 58.386 45.455 8.00 0.00 0.00 2.52
2102 2355 4.012374 CCAGTAGCATCATGGTGTTCTTT 58.988 43.478 8.00 0.00 0.00 2.52
2103 2356 4.460382 CCAGTAGCATCATGGTGTTCTTTT 59.540 41.667 8.00 0.00 0.00 2.27
2104 2357 5.647658 CCAGTAGCATCATGGTGTTCTTTTA 59.352 40.000 8.00 0.00 0.00 1.52
2105 2358 6.403636 CCAGTAGCATCATGGTGTTCTTTTAC 60.404 42.308 8.00 0.00 0.00 2.01
2106 2359 6.149308 CAGTAGCATCATGGTGTTCTTTTACA 59.851 38.462 8.00 0.00 0.00 2.41
2107 2360 6.886459 AGTAGCATCATGGTGTTCTTTTACAT 59.114 34.615 8.00 0.00 0.00 2.29
2108 2361 5.957798 AGCATCATGGTGTTCTTTTACATG 58.042 37.500 8.00 0.00 40.06 3.21
2109 2362 5.104374 GCATCATGGTGTTCTTTTACATGG 58.896 41.667 8.00 0.00 39.39 3.66
2110 2363 5.336690 GCATCATGGTGTTCTTTTACATGGT 60.337 40.000 8.00 0.00 39.39 3.55
2111 2364 5.703978 TCATGGTGTTCTTTTACATGGTG 57.296 39.130 0.00 0.00 39.39 4.17
2112 2365 5.136828 TCATGGTGTTCTTTTACATGGTGT 58.863 37.500 0.00 0.00 39.39 4.16
2113 2366 5.596361 TCATGGTGTTCTTTTACATGGTGTT 59.404 36.000 0.00 0.00 39.39 3.32
2114 2367 5.508200 TGGTGTTCTTTTACATGGTGTTC 57.492 39.130 0.00 0.00 0.00 3.18
2454 2708 5.860941 TGTTTCCTGTTCTGCCAAATTTA 57.139 34.783 0.00 0.00 0.00 1.40
2668 2922 7.133133 TCCCTTTTTAGTCACTGAGTAGTTT 57.867 36.000 0.00 0.00 34.07 2.66
2720 2975 7.010697 TGCATCACATGTTTATAGTTAACGG 57.989 36.000 0.00 0.00 0.00 4.44
2862 3117 2.357075 GTTAAGCTAGTTGGCCAGGTC 58.643 52.381 5.11 0.52 0.00 3.85
2868 3123 2.170607 GCTAGTTGGCCAGGTCTGATAA 59.829 50.000 5.11 0.00 0.00 1.75
3193 3448 6.961554 GCTGTATTATGTCCTTTTCTTGTTCG 59.038 38.462 0.00 0.00 0.00 3.95
3194 3449 6.837992 TGTATTATGTCCTTTTCTTGTTCGC 58.162 36.000 0.00 0.00 0.00 4.70
3195 3450 6.653320 TGTATTATGTCCTTTTCTTGTTCGCT 59.347 34.615 0.00 0.00 0.00 4.93
3196 3451 5.607119 TTATGTCCTTTTCTTGTTCGCTC 57.393 39.130 0.00 0.00 0.00 5.03
3197 3452 2.218603 TGTCCTTTTCTTGTTCGCTCC 58.781 47.619 0.00 0.00 0.00 4.70
3198 3453 1.535896 GTCCTTTTCTTGTTCGCTCCC 59.464 52.381 0.00 0.00 0.00 4.30
3202 3457 0.534203 TTTCTTGTTCGCTCCCGCTT 60.534 50.000 0.00 0.00 0.00 4.68
3203 3458 1.227999 TTCTTGTTCGCTCCCGCTTG 61.228 55.000 0.00 0.00 0.00 4.01
3204 3459 3.314388 CTTGTTCGCTCCCGCTTGC 62.314 63.158 0.00 0.00 0.00 4.01
3224 3479 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
3234 3489 3.842069 GGAAGGGTCCAACCACTTT 57.158 52.632 0.00 0.00 44.26 2.66
3235 3490 1.328279 GGAAGGGTCCAACCACTTTG 58.672 55.000 0.00 0.00 44.26 2.77
3247 3502 5.684550 CAACCACTTTGGGTCTTTAGTAC 57.315 43.478 0.00 0.00 43.37 2.73
3248 3503 3.999046 ACCACTTTGGGTCTTTAGTACG 58.001 45.455 0.00 0.00 43.37 3.67
3249 3504 2.740447 CCACTTTGGGTCTTTAGTACGC 59.260 50.000 0.00 0.00 32.67 4.42
3250 3505 3.395639 CACTTTGGGTCTTTAGTACGCA 58.604 45.455 0.00 0.00 37.94 5.24
3251 3506 3.810941 CACTTTGGGTCTTTAGTACGCAA 59.189 43.478 0.00 0.00 44.85 4.85
3252 3507 3.811497 ACTTTGGGTCTTTAGTACGCAAC 59.189 43.478 5.36 0.00 45.77 4.17
3253 3508 2.460757 TGGGTCTTTAGTACGCAACC 57.539 50.000 0.00 0.00 36.92 3.77
3254 3509 1.972795 TGGGTCTTTAGTACGCAACCT 59.027 47.619 0.00 0.00 36.92 3.50
3255 3510 2.369532 TGGGTCTTTAGTACGCAACCTT 59.630 45.455 0.00 0.00 36.92 3.50
3256 3511 3.181452 TGGGTCTTTAGTACGCAACCTTT 60.181 43.478 0.00 0.00 36.92 3.11
3257 3512 3.434641 GGGTCTTTAGTACGCAACCTTTC 59.565 47.826 6.11 0.00 0.00 2.62
3258 3513 3.434641 GGTCTTTAGTACGCAACCTTTCC 59.565 47.826 0.00 0.00 0.00 3.13
3259 3514 3.434641 GTCTTTAGTACGCAACCTTTCCC 59.565 47.826 0.00 0.00 0.00 3.97
3260 3515 3.325716 TCTTTAGTACGCAACCTTTCCCT 59.674 43.478 0.00 0.00 0.00 4.20
3261 3516 4.527816 TCTTTAGTACGCAACCTTTCCCTA 59.472 41.667 0.00 0.00 0.00 3.53
3262 3517 2.756840 AGTACGCAACCTTTCCCTAC 57.243 50.000 0.00 0.00 0.00 3.18
3263 3518 1.972795 AGTACGCAACCTTTCCCTACA 59.027 47.619 0.00 0.00 0.00 2.74
3264 3519 2.570302 AGTACGCAACCTTTCCCTACAT 59.430 45.455 0.00 0.00 0.00 2.29
3265 3520 2.579410 ACGCAACCTTTCCCTACATT 57.421 45.000 0.00 0.00 0.00 2.71
3266 3521 2.871453 ACGCAACCTTTCCCTACATTT 58.129 42.857 0.00 0.00 0.00 2.32
3267 3522 2.817844 ACGCAACCTTTCCCTACATTTC 59.182 45.455 0.00 0.00 0.00 2.17
3268 3523 3.081804 CGCAACCTTTCCCTACATTTCT 58.918 45.455 0.00 0.00 0.00 2.52
3269 3524 3.119849 CGCAACCTTTCCCTACATTTCTG 60.120 47.826 0.00 0.00 0.00 3.02
3270 3525 3.367395 GCAACCTTTCCCTACATTTCTGC 60.367 47.826 0.00 0.00 0.00 4.26
3271 3526 3.806949 ACCTTTCCCTACATTTCTGCA 57.193 42.857 0.00 0.00 0.00 4.41
3272 3527 4.112634 ACCTTTCCCTACATTTCTGCAA 57.887 40.909 0.00 0.00 0.00 4.08
3273 3528 4.082125 ACCTTTCCCTACATTTCTGCAAG 58.918 43.478 0.00 0.00 0.00 4.01
3274 3529 4.202567 ACCTTTCCCTACATTTCTGCAAGA 60.203 41.667 0.00 0.00 44.68 3.02
3524 3779 0.824759 GGTGCCTCGACCACTCTAAT 59.175 55.000 10.32 0.00 35.88 1.73
3647 3902 1.626356 AAGAGGCCTTGCGGATGCTA 61.626 55.000 6.77 0.00 43.34 3.49
4400 4655 3.430790 CCAAGAGAATACCGATGCAGACA 60.431 47.826 0.00 0.00 0.00 3.41
4454 4709 2.160417 GTCAGAAATGTTTCCAGCTCCG 59.840 50.000 2.04 0.00 37.92 4.63
4525 4780 5.303078 AGCCACATGAATAGACGAGTCTTAT 59.697 40.000 11.27 0.88 40.93 1.73
4717 4975 8.349568 ACGAATCATCTAGCTACCATATGTAA 57.650 34.615 1.24 0.00 0.00 2.41
4763 5183 1.908619 AGCATGGAAATTTTGGGACCC 59.091 47.619 2.45 2.45 0.00 4.46
4981 5404 6.652205 ACATTTAGATCCCAGTTTCCCTTA 57.348 37.500 0.00 0.00 0.00 2.69
5151 5580 4.825085 GGTACATTGGTGAAACTTCTTCCA 59.175 41.667 0.00 3.90 36.74 3.53
5275 5709 2.133858 TGAAGGAGAAGAAAGGGGGT 57.866 50.000 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.767505 CTCGACCTAAACCTTGCTGTT 58.232 47.619 0.00 0.00 0.00 3.16
1 2 1.608283 GCTCGACCTAAACCTTGCTGT 60.608 52.381 0.00 0.00 0.00 4.40
2 3 1.079503 GCTCGACCTAAACCTTGCTG 58.920 55.000 0.00 0.00 0.00 4.41
119 126 1.289109 ATTTCGTCGAACACCTGCCG 61.289 55.000 7.29 0.00 0.00 5.69
189 204 2.511145 CGCTTCTCCTCTGCTGGC 60.511 66.667 0.00 0.00 0.00 4.85
244 259 2.450609 TTGTCTCCCAACTCGCTAAC 57.549 50.000 0.00 0.00 0.00 2.34
271 286 2.329690 CCGTCGAGATGAGCCGAG 59.670 66.667 0.00 0.00 35.31 4.63
272 287 3.889044 GCCGTCGAGATGAGCCGA 61.889 66.667 0.00 0.00 0.00 5.54
273 288 3.490793 ATGCCGTCGAGATGAGCCG 62.491 63.158 0.00 0.00 0.00 5.52
274 289 1.953138 CATGCCGTCGAGATGAGCC 60.953 63.158 0.00 0.00 0.00 4.70
275 290 2.593134 GCATGCCGTCGAGATGAGC 61.593 63.158 6.36 0.00 0.00 4.26
276 291 0.529337 AAGCATGCCGTCGAGATGAG 60.529 55.000 15.66 0.00 0.00 2.90
277 292 0.807275 CAAGCATGCCGTCGAGATGA 60.807 55.000 15.66 0.00 0.00 2.92
278 293 0.807275 TCAAGCATGCCGTCGAGATG 60.807 55.000 15.66 1.32 0.00 2.90
279 294 0.807667 GTCAAGCATGCCGTCGAGAT 60.808 55.000 15.66 0.00 0.00 2.75
280 295 1.446099 GTCAAGCATGCCGTCGAGA 60.446 57.895 15.66 0.49 0.00 4.04
357 387 2.632996 CAGCTAATATGGAACGGAGGGA 59.367 50.000 0.00 0.00 0.00 4.20
358 388 2.368875 ACAGCTAATATGGAACGGAGGG 59.631 50.000 0.00 0.00 0.00 4.30
359 389 3.654414 GACAGCTAATATGGAACGGAGG 58.346 50.000 0.00 0.00 0.00 4.30
360 390 3.309388 CGACAGCTAATATGGAACGGAG 58.691 50.000 0.00 0.00 0.00 4.63
375 405 2.551270 CCACGTTTGAGCGACAGC 59.449 61.111 0.00 0.00 45.58 4.40
376 406 1.956170 AGCCACGTTTGAGCGACAG 60.956 57.895 0.00 0.00 35.59 3.51
377 407 2.108157 AGCCACGTTTGAGCGACA 59.892 55.556 0.00 0.00 35.59 4.35
378 408 1.772063 AACAGCCACGTTTGAGCGAC 61.772 55.000 0.00 0.00 35.59 5.19
379 409 1.092921 AAACAGCCACGTTTGAGCGA 61.093 50.000 0.00 0.00 37.69 4.93
380 410 1.355210 AAACAGCCACGTTTGAGCG 59.645 52.632 0.00 0.00 37.69 5.03
385 415 0.098025 CGTGTCAAACAGCCACGTTT 59.902 50.000 0.00 0.00 45.00 3.60
386 416 1.719117 CGTGTCAAACAGCCACGTT 59.281 52.632 0.00 0.00 45.00 3.99
387 417 3.405464 CGTGTCAAACAGCCACGT 58.595 55.556 0.00 0.00 45.00 4.49
399 429 0.457851 AGCTGCTATCTGTCCGTGTC 59.542 55.000 0.00 0.00 0.00 3.67
422 452 5.873164 GTCAACCAACCAATTCGATAGTACT 59.127 40.000 0.00 0.00 37.40 2.73
423 453 5.640357 TGTCAACCAACCAATTCGATAGTAC 59.360 40.000 0.00 0.00 37.40 2.73
430 460 3.371168 CTTGTGTCAACCAACCAATTCG 58.629 45.455 0.00 0.00 0.00 3.34
615 652 2.037121 TCTGCAGAACGAACCATCTTCA 59.963 45.455 15.67 0.00 0.00 3.02
616 653 2.413453 GTCTGCAGAACGAACCATCTTC 59.587 50.000 20.19 0.00 0.00 2.87
653 691 3.253432 TGATAGAAGATGATCACCGACGG 59.747 47.826 13.61 13.61 0.00 4.79
658 696 5.218885 CGTGACTGATAGAAGATGATCACC 58.781 45.833 0.00 0.00 33.28 4.02
687 725 4.343526 AGGTCTGTAGCCATCTGTTGATAG 59.656 45.833 0.00 0.00 0.00 2.08
701 739 5.104941 TGGGATTGTCATTGTAGGTCTGTAG 60.105 44.000 0.00 0.00 0.00 2.74
703 741 3.587061 TGGGATTGTCATTGTAGGTCTGT 59.413 43.478 0.00 0.00 0.00 3.41
720 761 5.053978 ACTCTTTCTGTTTCTGTTGGGAT 57.946 39.130 0.00 0.00 0.00 3.85
782 830 4.740822 CCGGTCTGGGGGCAAAGG 62.741 72.222 0.00 0.00 0.00 3.11
844 892 1.041437 GACGGTATTGGAGGAGGGAG 58.959 60.000 0.00 0.00 0.00 4.30
847 895 1.408453 GGGGACGGTATTGGAGGAGG 61.408 65.000 0.00 0.00 0.00 4.30
849 897 0.935942 TAGGGGACGGTATTGGAGGA 59.064 55.000 0.00 0.00 0.00 3.71
861 909 5.400870 AGTGGTGGTAGTTATATAGGGGAC 58.599 45.833 0.00 0.00 0.00 4.46
931 979 3.585990 GATGGGCGTTGGGCGATG 61.586 66.667 0.00 0.00 44.92 3.84
970 1025 4.322385 GTTTCTTGCGCGGCGGTT 62.322 61.111 25.03 0.00 0.00 4.44
1183 1238 2.689034 GGAGGTGGAGTGGGAGGG 60.689 72.222 0.00 0.00 0.00 4.30
1184 1239 3.077556 CGGAGGTGGAGTGGGAGG 61.078 72.222 0.00 0.00 0.00 4.30
1207 1286 0.108186 AAGCTTGACCGCGATGATGA 60.108 50.000 8.23 0.00 34.40 2.92
1320 1399 2.577593 GTGGCCTCAGGTACCGTC 59.422 66.667 6.18 0.00 0.00 4.79
1529 1608 1.556911 ACGTCATTGCCTTCTCCATCT 59.443 47.619 0.00 0.00 0.00 2.90
1813 1892 0.391793 GAAACGAGAGGGGCCAGAAG 60.392 60.000 4.39 0.00 0.00 2.85
2100 2353 9.883142 AAATGAAGAAAAGAACACCATGTAAAA 57.117 25.926 0.00 0.00 0.00 1.52
2101 2354 9.311916 CAAATGAAGAAAAGAACACCATGTAAA 57.688 29.630 0.00 0.00 0.00 2.01
2102 2355 8.474025 ACAAATGAAGAAAAGAACACCATGTAA 58.526 29.630 0.00 0.00 0.00 2.41
2103 2356 8.006298 ACAAATGAAGAAAAGAACACCATGTA 57.994 30.769 0.00 0.00 0.00 2.29
2104 2357 6.877236 ACAAATGAAGAAAAGAACACCATGT 58.123 32.000 0.00 0.00 0.00 3.21
2105 2358 8.870160 TTACAAATGAAGAAAAGAACACCATG 57.130 30.769 0.00 0.00 0.00 3.66
2106 2359 8.912988 TCTTACAAATGAAGAAAAGAACACCAT 58.087 29.630 0.00 0.00 29.97 3.55
2107 2360 8.287439 TCTTACAAATGAAGAAAAGAACACCA 57.713 30.769 0.00 0.00 29.97 4.17
2108 2361 9.020813 GTTCTTACAAATGAAGAAAAGAACACC 57.979 33.333 16.68 0.00 46.07 4.16
2145 2398 3.081804 ACTGAGCAGGAAATTTTACCCG 58.918 45.455 2.20 0.00 0.00 5.28
2211 2464 6.259608 AGAGAGACGGCTTAATCAATTTGATG 59.740 38.462 12.50 2.21 37.15 3.07
2454 2708 1.415659 GGCTAGTGATGGTGAGCAGAT 59.584 52.381 0.00 0.00 36.63 2.90
2523 2777 5.826643 TCCTGGTTGTGGATAGCTTTTATT 58.173 37.500 0.00 0.00 0.00 1.40
2635 2889 5.649831 AGTGACTAAAAAGGGAATCTCATGC 59.350 40.000 0.00 0.00 0.00 4.06
2668 2922 6.098266 TCAAGAGGAAAGTCCATCGATAATCA 59.902 38.462 0.00 0.00 39.61 2.57
2718 2973 3.118775 TGCCCGATCTATTTGGATATCCG 60.119 47.826 17.04 2.32 39.43 4.18
2720 2975 6.115446 TCAATGCCCGATCTATTTGGATATC 58.885 40.000 0.00 0.00 0.00 1.63
2724 2979 3.855255 TCAATGCCCGATCTATTTGGA 57.145 42.857 0.00 0.00 0.00 3.53
3058 3313 0.887933 TCCTTGGAAGAAAATGGCGC 59.112 50.000 0.00 0.00 0.00 6.53
3207 3462 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
3210 3465 2.931649 TTGGACCCTTCCCCGGAC 60.932 66.667 0.73 0.00 42.01 4.79
3211 3466 2.931649 GTTGGACCCTTCCCCGGA 60.932 66.667 0.73 0.00 42.01 5.14
3212 3467 4.043100 GGTTGGACCCTTCCCCGG 62.043 72.222 0.00 0.00 42.01 5.73
3213 3468 3.253838 TGGTTGGACCCTTCCCCG 61.254 66.667 0.00 0.00 42.01 5.73
3214 3469 1.726192 AAGTGGTTGGACCCTTCCCC 61.726 60.000 0.00 0.00 42.01 4.81
3215 3470 0.187606 AAAGTGGTTGGACCCTTCCC 59.812 55.000 0.00 0.00 42.01 3.97
3225 3480 4.212636 CGTACTAAAGACCCAAAGTGGTTG 59.787 45.833 0.00 0.00 39.24 3.77
3226 3481 4.383173 CGTACTAAAGACCCAAAGTGGTT 58.617 43.478 0.00 0.00 39.24 3.67
3227 3482 3.804759 GCGTACTAAAGACCCAAAGTGGT 60.805 47.826 0.00 0.00 42.79 4.16
3228 3483 2.740447 GCGTACTAAAGACCCAAAGTGG 59.260 50.000 0.00 0.00 37.25 4.00
3229 3484 3.395639 TGCGTACTAAAGACCCAAAGTG 58.604 45.455 0.00 0.00 0.00 3.16
3230 3485 3.756933 TGCGTACTAAAGACCCAAAGT 57.243 42.857 0.00 0.00 0.00 2.66
3231 3486 3.187842 GGTTGCGTACTAAAGACCCAAAG 59.812 47.826 0.00 0.00 0.00 2.77
3232 3487 3.140623 GGTTGCGTACTAAAGACCCAAA 58.859 45.455 0.00 0.00 0.00 3.28
3234 3489 1.972795 AGGTTGCGTACTAAAGACCCA 59.027 47.619 0.00 0.00 0.00 4.51
3235 3490 2.756840 AGGTTGCGTACTAAAGACCC 57.243 50.000 0.00 0.00 0.00 4.46
3236 3491 3.434641 GGAAAGGTTGCGTACTAAAGACC 59.565 47.826 0.00 0.00 0.00 3.85
3237 3492 3.434641 GGGAAAGGTTGCGTACTAAAGAC 59.565 47.826 0.00 0.00 0.00 3.01
3238 3493 3.325716 AGGGAAAGGTTGCGTACTAAAGA 59.674 43.478 0.00 0.00 0.00 2.52
3239 3494 3.671716 AGGGAAAGGTTGCGTACTAAAG 58.328 45.455 0.00 0.00 0.00 1.85
3240 3495 3.775261 AGGGAAAGGTTGCGTACTAAA 57.225 42.857 0.00 0.00 0.00 1.85
3241 3496 3.577848 TGTAGGGAAAGGTTGCGTACTAA 59.422 43.478 11.74 0.00 41.15 2.24
3242 3497 3.164268 TGTAGGGAAAGGTTGCGTACTA 58.836 45.455 11.74 0.00 41.15 1.82
3243 3498 1.972795 TGTAGGGAAAGGTTGCGTACT 59.027 47.619 11.74 0.00 41.15 2.73
3244 3499 2.460757 TGTAGGGAAAGGTTGCGTAC 57.539 50.000 5.68 5.68 41.02 3.67
3245 3500 3.706600 AATGTAGGGAAAGGTTGCGTA 57.293 42.857 0.00 0.00 0.00 4.42
3246 3501 2.579410 AATGTAGGGAAAGGTTGCGT 57.421 45.000 0.00 0.00 0.00 5.24
3247 3502 3.081804 AGAAATGTAGGGAAAGGTTGCG 58.918 45.455 0.00 0.00 0.00 4.85
3248 3503 3.367395 GCAGAAATGTAGGGAAAGGTTGC 60.367 47.826 0.00 0.00 0.00 4.17
3249 3504 3.826157 TGCAGAAATGTAGGGAAAGGTTG 59.174 43.478 0.00 0.00 0.00 3.77
3250 3505 4.112634 TGCAGAAATGTAGGGAAAGGTT 57.887 40.909 0.00 0.00 0.00 3.50
3251 3506 3.806949 TGCAGAAATGTAGGGAAAGGT 57.193 42.857 0.00 0.00 0.00 3.50
3252 3507 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
3253 3508 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
3254 3509 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
3255 3510 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
3256 3511 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
3257 3512 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
3258 3513 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
3259 3514 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
3260 3515 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
3261 3516 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
3262 3517 3.655276 AAACAGCCTCTTGCAGAAATG 57.345 42.857 0.00 0.00 44.83 2.32
3263 3518 4.401925 AGTAAACAGCCTCTTGCAGAAAT 58.598 39.130 0.00 0.00 44.83 2.17
3264 3519 3.820557 AGTAAACAGCCTCTTGCAGAAA 58.179 40.909 0.00 0.00 44.83 2.52
3265 3520 3.492102 AGTAAACAGCCTCTTGCAGAA 57.508 42.857 0.00 0.00 44.83 3.02
3266 3521 4.826274 ATAGTAAACAGCCTCTTGCAGA 57.174 40.909 0.00 0.00 44.83 4.26
3267 3522 8.662781 TTATTATAGTAAACAGCCTCTTGCAG 57.337 34.615 0.00 0.00 44.83 4.41
3268 3523 9.627123 ATTTATTATAGTAAACAGCCTCTTGCA 57.373 29.630 2.84 0.00 44.83 4.08
3524 3779 3.272364 AATGCTGGAGCGGGCAAGA 62.272 57.895 0.00 0.00 45.83 3.02
4191 4446 3.430042 AGCCTTGTCACAGATCATGTT 57.570 42.857 0.00 0.00 41.41 2.71
4424 4679 4.451096 GGAAACATTTCTGACAGCGTCTTA 59.549 41.667 0.00 0.00 37.35 2.10
4430 4685 2.555757 AGCTGGAAACATTTCTGACAGC 59.444 45.455 18.63 18.63 43.79 4.40
4454 4709 1.058404 GGTTCTGTAACTGCGTCGTC 58.942 55.000 0.00 0.00 35.81 4.20
4525 4780 7.806487 CACGAACAACTATACAGAAAGACAGTA 59.194 37.037 0.00 0.00 0.00 2.74
4763 5183 8.628279 GCGTAGATCAAAACTATACTACAATCG 58.372 37.037 0.00 0.00 33.05 3.34
5137 5566 5.248870 TCAGCTTTTGGAAGAAGTTTCAC 57.751 39.130 0.00 0.00 34.71 3.18
5151 5580 6.534475 TTCTGAATAATGCCATCAGCTTTT 57.466 33.333 0.00 0.00 44.23 2.27


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

AutoCloner maintained by Alex Coulton.