Multiple sequence alignment - TraesCS2A01G516500

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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 TraesCS2A01G516500 chr2A 100.000 3533 0 0 1 3533 740080005 740076473 0.000000e+00 6525.0
1 TraesCS2A01G516500 chr2A 98.154 2654 37 7 1 2643 740144037 740141385 0.000000e+00 4619.0
2 TraesCS2A01G516500 chr2A 98.041 2654 40 7 1 2643 740119849 740117197 0.000000e+00 4602.0
3 TraesCS2A01G516500 chr2D 91.068 2407 174 20 647 3029 608559738 608557349 0.000000e+00 3216.0
4 TraesCS2A01G516500 chr2D 89.370 2192 165 35 480 2640 608578913 608576759 0.000000e+00 2695.0
5 TraesCS2A01G516500 chr2D 92.857 336 6 4 3025 3357 608557321 608557001 4.130000e-129 472.0
6 TraesCS2A01G516500 chr2B 91.525 2065 148 15 489 2546 742173242 742171198 0.000000e+00 2819.0
7 TraesCS2A01G516500 chr2B 90.168 2085 159 14 647 2719 742110633 742108583 0.000000e+00 2673.0
8 TraesCS2A01G516500 chr2B 95.808 334 13 1 3025 3357 742104760 742104427 4.010000e-149 538.0
9 TraesCS2A01G516500 chr2B 88.696 345 34 3 147 487 742174647 742174304 1.960000e-112 416.0
10 TraesCS2A01G516500 chr2B 86.970 330 27 6 2713 3026 742105120 742104791 1.210000e-94 357.0
11 TraesCS2A01G516500 chr7A 86.570 2070 222 28 986 3026 563246828 563244786 0.000000e+00 2231.0
12 TraesCS2A01G516500 chr7A 87.098 1961 214 25 1000 2942 563293364 563291425 0.000000e+00 2183.0
13 TraesCS2A01G516500 chr4A 84.932 2190 229 60 753 2887 702328055 702325912 0.000000e+00 2122.0
14 TraesCS2A01G516500 chr7D 87.688 1795 181 19 986 2769 497320731 497318966 0.000000e+00 2054.0
15 TraesCS2A01G516500 chr7D 93.182 44 3 0 2808 2851 497318671 497318628 8.190000e-07 65.8
16 TraesCS2A01G516500 chr1B 76.868 281 52 8 658 928 50900365 50900642 2.840000e-31 147.0
17 TraesCS2A01G516500 chr1B 76.512 281 50 11 658 928 50950267 50950541 4.760000e-29 139.0
18 TraesCS2A01G516500 chr5A 81.081 148 25 3 1 148 472707726 472707582 8.010000e-22 115.0
19 TraesCS2A01G516500 chr4D 80.420 143 16 5 3361 3493 494479094 494478954 8.070000e-17 99.0
20 TraesCS2A01G516500 chr4D 76.190 147 21 9 3358 3492 382336212 382336068 8.190000e-07 65.8
21 TraesCS2A01G516500 chr3A 88.889 63 4 2 3 65 510693759 510693818 1.360000e-09 75.0
22 TraesCS2A01G516500 chr3A 93.750 48 3 0 3445 3492 47844752 47844705 4.890000e-09 73.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G516500 chr2A 740076473 740080005 3532 True 6525.000000 6525 100.0000 1 3533 1 chr2A.!!$R1 3532
1 TraesCS2A01G516500 chr2A 740141385 740144037 2652 True 4619.000000 4619 98.1540 1 2643 1 chr2A.!!$R3 2642
2 TraesCS2A01G516500 chr2A 740117197 740119849 2652 True 4602.000000 4602 98.0410 1 2643 1 chr2A.!!$R2 2642
3 TraesCS2A01G516500 chr2D 608576759 608578913 2154 True 2695.000000 2695 89.3700 480 2640 1 chr2D.!!$R1 2160
4 TraesCS2A01G516500 chr2D 608557001 608559738 2737 True 1844.000000 3216 91.9625 647 3357 2 chr2D.!!$R2 2710
5 TraesCS2A01G516500 chr2B 742171198 742174647 3449 True 1617.500000 2819 90.1105 147 2546 2 chr2B.!!$R2 2399
6 TraesCS2A01G516500 chr2B 742104427 742110633 6206 True 1189.333333 2673 90.9820 647 3357 3 chr2B.!!$R1 2710
7 TraesCS2A01G516500 chr7A 563244786 563246828 2042 True 2231.000000 2231 86.5700 986 3026 1 chr7A.!!$R1 2040
8 TraesCS2A01G516500 chr7A 563291425 563293364 1939 True 2183.000000 2183 87.0980 1000 2942 1 chr7A.!!$R2 1942
9 TraesCS2A01G516500 chr4A 702325912 702328055 2143 True 2122.000000 2122 84.9320 753 2887 1 chr4A.!!$R1 2134
10 TraesCS2A01G516500 chr7D 497318628 497320731 2103 True 1059.900000 2054 90.4350 986 2851 2 chr7D.!!$R1 1865

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
2472 3583 0.458543 GATCGTCGCTGCAAGAGGAA 60.459 55.0 15.19 3.52 36.33 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3370 8325 0.036388 CGACCCCACAGCTTACACAT 60.036 55.0 0.0 0.0 0.0 3.21 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
2472 3583 0.458543 GATCGTCGCTGCAAGAGGAA 60.459 55.000 15.19 3.52 36.33 3.36
2765 7368 7.682628 TGTACACTGTAAAAGGGCTTATACTT 58.317 34.615 0.00 0.00 29.26 2.24
2983 7877 0.902531 TCCCATCTCCAAAGTCGGAC 59.097 55.000 0.00 0.00 0.00 4.79
3010 7915 4.094294 GCACGTCTGAATTAATGGCACTTA 59.906 41.667 0.00 0.00 0.00 2.24
3090 8029 7.745022 ATTTCATGTTTGAGTATGAAATGCG 57.255 32.000 18.84 0.00 38.28 4.73
3201 8142 4.579869 AGCGACTGTTTACTGAATGGAAT 58.420 39.130 0.00 0.00 0.00 3.01
3294 8249 4.036144 GGATCAGCTCTTTCAGGTTATTGC 59.964 45.833 0.00 0.00 0.00 3.56
3295 8250 4.019792 TCAGCTCTTTCAGGTTATTGCA 57.980 40.909 0.00 0.00 0.00 4.08
3296 8251 4.005650 TCAGCTCTTTCAGGTTATTGCAG 58.994 43.478 0.00 0.00 0.00 4.41
3297 8252 3.755378 CAGCTCTTTCAGGTTATTGCAGT 59.245 43.478 0.00 0.00 0.00 4.40
3298 8253 4.006319 AGCTCTTTCAGGTTATTGCAGTC 58.994 43.478 0.00 0.00 0.00 3.51
3299 8254 3.753272 GCTCTTTCAGGTTATTGCAGTCA 59.247 43.478 0.00 0.00 0.00 3.41
3300 8255 4.142730 GCTCTTTCAGGTTATTGCAGTCAG 60.143 45.833 0.00 0.00 0.00 3.51
3301 8256 4.973168 TCTTTCAGGTTATTGCAGTCAGT 58.027 39.130 0.00 0.00 0.00 3.41
3302 8257 5.376625 TCTTTCAGGTTATTGCAGTCAGTT 58.623 37.500 0.00 0.00 0.00 3.16
3303 8258 5.239306 TCTTTCAGGTTATTGCAGTCAGTTG 59.761 40.000 0.00 0.00 0.00 3.16
3304 8259 4.085357 TCAGGTTATTGCAGTCAGTTGT 57.915 40.909 0.00 0.00 0.00 3.32
3305 8260 4.460263 TCAGGTTATTGCAGTCAGTTGTT 58.540 39.130 0.00 0.00 0.00 2.83
3306 8261 4.887071 TCAGGTTATTGCAGTCAGTTGTTT 59.113 37.500 0.00 0.00 0.00 2.83
3307 8262 4.977963 CAGGTTATTGCAGTCAGTTGTTTG 59.022 41.667 0.00 0.00 0.00 2.93
3357 8312 7.987649 TGGATTTTAATTATGTTACGGTGGTC 58.012 34.615 0.00 0.00 0.00 4.02
3358 8313 7.610692 TGGATTTTAATTATGTTACGGTGGTCA 59.389 33.333 0.00 0.00 0.00 4.02
3359 8314 8.126700 GGATTTTAATTATGTTACGGTGGTCAG 58.873 37.037 0.00 0.00 0.00 3.51
3360 8315 8.795842 ATTTTAATTATGTTACGGTGGTCAGA 57.204 30.769 0.00 0.00 0.00 3.27
3361 8316 7.837202 TTTAATTATGTTACGGTGGTCAGAG 57.163 36.000 0.00 0.00 0.00 3.35
3362 8317 3.880047 TTATGTTACGGTGGTCAGAGG 57.120 47.619 0.00 0.00 0.00 3.69
3363 8318 0.249398 ATGTTACGGTGGTCAGAGGC 59.751 55.000 0.00 0.00 0.00 4.70
3364 8319 1.445582 GTTACGGTGGTCAGAGGCG 60.446 63.158 0.00 0.00 0.00 5.52
3365 8320 1.604308 TTACGGTGGTCAGAGGCGA 60.604 57.895 0.00 0.00 0.00 5.54
3366 8321 1.180456 TTACGGTGGTCAGAGGCGAA 61.180 55.000 0.00 0.00 0.00 4.70
3367 8322 0.968901 TACGGTGGTCAGAGGCGAAT 60.969 55.000 0.00 0.00 0.00 3.34
3368 8323 1.519455 CGGTGGTCAGAGGCGAATC 60.519 63.158 0.00 0.00 0.00 2.52
3369 8324 1.901085 GGTGGTCAGAGGCGAATCT 59.099 57.895 0.00 0.00 0.00 2.40
3370 8325 1.112113 GGTGGTCAGAGGCGAATCTA 58.888 55.000 0.00 0.00 0.00 1.98
3371 8326 1.689273 GGTGGTCAGAGGCGAATCTAT 59.311 52.381 0.00 0.00 0.00 1.98
3372 8327 2.546795 GGTGGTCAGAGGCGAATCTATG 60.547 54.545 0.00 0.00 0.00 2.23
3373 8328 2.101582 GTGGTCAGAGGCGAATCTATGT 59.898 50.000 0.00 0.00 0.00 2.29
3374 8329 2.101415 TGGTCAGAGGCGAATCTATGTG 59.899 50.000 0.00 0.00 0.00 3.21
3375 8330 2.101582 GGTCAGAGGCGAATCTATGTGT 59.898 50.000 0.00 0.00 0.00 3.72
3376 8331 3.318275 GGTCAGAGGCGAATCTATGTGTA 59.682 47.826 0.00 0.00 0.00 2.90
3377 8332 4.202121 GGTCAGAGGCGAATCTATGTGTAA 60.202 45.833 0.00 0.00 0.00 2.41
3378 8333 4.979197 GTCAGAGGCGAATCTATGTGTAAG 59.021 45.833 0.00 0.00 0.00 2.34
3379 8334 3.738282 CAGAGGCGAATCTATGTGTAAGC 59.262 47.826 0.00 0.00 0.00 3.09
3380 8335 3.639094 AGAGGCGAATCTATGTGTAAGCT 59.361 43.478 0.00 0.00 0.00 3.74
3381 8336 3.722147 AGGCGAATCTATGTGTAAGCTG 58.278 45.455 0.00 0.00 0.00 4.24
3382 8337 3.133003 AGGCGAATCTATGTGTAAGCTGT 59.867 43.478 0.00 0.00 0.00 4.40
3383 8338 3.246226 GGCGAATCTATGTGTAAGCTGTG 59.754 47.826 0.00 0.00 0.00 3.66
3384 8339 3.246226 GCGAATCTATGTGTAAGCTGTGG 59.754 47.826 0.00 0.00 0.00 4.17
3385 8340 3.804325 CGAATCTATGTGTAAGCTGTGGG 59.196 47.826 0.00 0.00 0.00 4.61
3386 8341 3.845781 ATCTATGTGTAAGCTGTGGGG 57.154 47.619 0.00 0.00 0.00 4.96
3387 8342 2.546899 TCTATGTGTAAGCTGTGGGGT 58.453 47.619 0.00 0.00 0.00 4.95
3388 8343 2.500098 TCTATGTGTAAGCTGTGGGGTC 59.500 50.000 0.00 0.00 0.00 4.46
3389 8344 0.036388 ATGTGTAAGCTGTGGGGTCG 60.036 55.000 0.00 0.00 0.00 4.79
3390 8345 1.375523 GTGTAAGCTGTGGGGTCGG 60.376 63.158 0.00 0.00 0.00 4.79
3391 8346 2.267961 GTAAGCTGTGGGGTCGGG 59.732 66.667 0.00 0.00 0.00 5.14
3392 8347 3.712907 TAAGCTGTGGGGTCGGGC 61.713 66.667 0.00 0.00 0.00 6.13
3395 8350 4.660938 GCTGTGGGGTCGGGCTTT 62.661 66.667 0.00 0.00 0.00 3.51
3396 8351 2.115266 CTGTGGGGTCGGGCTTTT 59.885 61.111 0.00 0.00 0.00 2.27
3397 8352 1.530655 CTGTGGGGTCGGGCTTTTT 60.531 57.895 0.00 0.00 0.00 1.94
3419 8374 6.959639 TTTGAAAAACAGCCTAGAATCACT 57.040 33.333 0.00 0.00 0.00 3.41
3420 8375 5.947228 TGAAAAACAGCCTAGAATCACTG 57.053 39.130 0.00 0.00 36.22 3.66
3421 8376 5.376625 TGAAAAACAGCCTAGAATCACTGT 58.623 37.500 0.00 0.00 44.96 3.55
3425 8380 3.931578 ACAGCCTAGAATCACTGTTCAC 58.068 45.455 0.00 0.00 40.35 3.18
3426 8381 3.580458 ACAGCCTAGAATCACTGTTCACT 59.420 43.478 0.00 0.00 40.35 3.41
3427 8382 4.040952 ACAGCCTAGAATCACTGTTCACTT 59.959 41.667 0.00 0.00 40.35 3.16
3428 8383 4.629200 CAGCCTAGAATCACTGTTCACTTC 59.371 45.833 0.00 0.00 0.00 3.01
3429 8384 3.935828 GCCTAGAATCACTGTTCACTTCC 59.064 47.826 0.00 0.00 0.00 3.46
3430 8385 4.323104 GCCTAGAATCACTGTTCACTTCCT 60.323 45.833 0.00 0.00 0.00 3.36
3431 8386 5.174395 CCTAGAATCACTGTTCACTTCCTG 58.826 45.833 0.00 0.00 0.00 3.86
3432 8387 4.696479 AGAATCACTGTTCACTTCCTGT 57.304 40.909 0.00 0.00 0.00 4.00
3433 8388 5.041191 AGAATCACTGTTCACTTCCTGTT 57.959 39.130 0.00 0.00 0.00 3.16
3434 8389 5.059833 AGAATCACTGTTCACTTCCTGTTC 58.940 41.667 0.00 0.00 0.00 3.18
3435 8390 3.904800 TCACTGTTCACTTCCTGTTCA 57.095 42.857 0.00 0.00 0.00 3.18
3436 8391 3.531538 TCACTGTTCACTTCCTGTTCAC 58.468 45.455 0.00 0.00 0.00 3.18
3437 8392 2.614057 CACTGTTCACTTCCTGTTCACC 59.386 50.000 0.00 0.00 0.00 4.02
3438 8393 1.867233 CTGTTCACTTCCTGTTCACCG 59.133 52.381 0.00 0.00 0.00 4.94
3439 8394 1.208535 TGTTCACTTCCTGTTCACCGT 59.791 47.619 0.00 0.00 0.00 4.83
3440 8395 1.597663 GTTCACTTCCTGTTCACCGTG 59.402 52.381 0.00 0.00 0.00 4.94
3441 8396 1.116308 TCACTTCCTGTTCACCGTGA 58.884 50.000 0.00 0.00 0.00 4.35
3442 8397 1.483004 TCACTTCCTGTTCACCGTGAA 59.517 47.619 9.99 9.99 33.32 3.18
3443 8398 1.867233 CACTTCCTGTTCACCGTGAAG 59.133 52.381 14.35 3.82 37.00 3.02
3444 8399 1.760613 ACTTCCTGTTCACCGTGAAGA 59.239 47.619 14.35 12.26 37.00 2.87
3445 8400 2.169769 ACTTCCTGTTCACCGTGAAGAA 59.830 45.455 14.35 12.77 37.00 2.52
3446 8401 2.992124 TCCTGTTCACCGTGAAGAAA 57.008 45.000 14.35 2.07 37.00 2.52
3447 8402 3.269538 TCCTGTTCACCGTGAAGAAAA 57.730 42.857 14.35 1.73 37.00 2.29
3448 8403 3.611970 TCCTGTTCACCGTGAAGAAAAA 58.388 40.909 14.35 0.00 37.00 1.94
3467 8422 3.541242 AAAATCCATTGACCCCACAGA 57.459 42.857 0.00 0.00 0.00 3.41
3468 8423 3.763557 AAATCCATTGACCCCACAGAT 57.236 42.857 0.00 0.00 0.00 2.90
3469 8424 3.763557 AATCCATTGACCCCACAGATT 57.236 42.857 0.00 0.00 0.00 2.40
3470 8425 2.806945 TCCATTGACCCCACAGATTC 57.193 50.000 0.00 0.00 0.00 2.52
3471 8426 2.278245 TCCATTGACCCCACAGATTCT 58.722 47.619 0.00 0.00 0.00 2.40
3472 8427 2.649312 TCCATTGACCCCACAGATTCTT 59.351 45.455 0.00 0.00 0.00 2.52
3473 8428 2.756760 CCATTGACCCCACAGATTCTTG 59.243 50.000 0.00 0.00 0.00 3.02
3474 8429 3.561960 CCATTGACCCCACAGATTCTTGA 60.562 47.826 0.00 0.00 0.00 3.02
3475 8430 3.423539 TTGACCCCACAGATTCTTGAG 57.576 47.619 0.00 0.00 0.00 3.02
3476 8431 1.630369 TGACCCCACAGATTCTTGAGG 59.370 52.381 0.00 0.00 0.00 3.86
3477 8432 0.329596 ACCCCACAGATTCTTGAGGC 59.670 55.000 0.00 0.00 0.00 4.70
3478 8433 0.622665 CCCCACAGATTCTTGAGGCT 59.377 55.000 0.00 0.00 0.00 4.58
3479 8434 1.681166 CCCCACAGATTCTTGAGGCTG 60.681 57.143 0.00 0.00 34.65 4.85
3480 8435 1.681166 CCCACAGATTCTTGAGGCTGG 60.681 57.143 0.00 0.00 32.82 4.85
3481 8436 1.093159 CACAGATTCTTGAGGCTGGC 58.907 55.000 0.00 0.00 32.82 4.85
3482 8437 0.392193 ACAGATTCTTGAGGCTGGCG 60.392 55.000 0.00 0.00 32.82 5.69
3483 8438 1.451028 AGATTCTTGAGGCTGGCGC 60.451 57.895 0.00 0.00 0.00 6.53
3499 8454 4.643387 GCCGCCACTGGTGTTCCT 62.643 66.667 7.86 0.00 34.23 3.36
3500 8455 2.113139 CCGCCACTGGTGTTCCTT 59.887 61.111 7.86 0.00 34.23 3.36
3501 8456 1.528309 CCGCCACTGGTGTTCCTTT 60.528 57.895 7.86 0.00 34.23 3.11
3502 8457 1.515521 CCGCCACTGGTGTTCCTTTC 61.516 60.000 7.86 0.00 34.23 2.62
3503 8458 0.817634 CGCCACTGGTGTTCCTTTCA 60.818 55.000 0.00 0.00 34.23 2.69
3504 8459 1.620822 GCCACTGGTGTTCCTTTCAT 58.379 50.000 0.00 0.00 34.23 2.57
3505 8460 1.963515 GCCACTGGTGTTCCTTTCATT 59.036 47.619 0.00 0.00 34.23 2.57
3506 8461 2.365293 GCCACTGGTGTTCCTTTCATTT 59.635 45.455 0.00 0.00 34.23 2.32
3507 8462 3.799917 GCCACTGGTGTTCCTTTCATTTG 60.800 47.826 0.00 0.00 34.23 2.32
3508 8463 3.383761 CACTGGTGTTCCTTTCATTTGC 58.616 45.455 0.00 0.00 34.23 3.68
3509 8464 3.030291 ACTGGTGTTCCTTTCATTTGCA 58.970 40.909 0.00 0.00 34.23 4.08
3510 8465 3.642848 ACTGGTGTTCCTTTCATTTGCAT 59.357 39.130 0.00 0.00 34.23 3.96
3511 8466 4.832266 ACTGGTGTTCCTTTCATTTGCATA 59.168 37.500 0.00 0.00 34.23 3.14
3512 8467 5.481473 ACTGGTGTTCCTTTCATTTGCATAT 59.519 36.000 0.00 0.00 34.23 1.78
3513 8468 5.964758 TGGTGTTCCTTTCATTTGCATATC 58.035 37.500 0.00 0.00 34.23 1.63
3514 8469 5.036737 GGTGTTCCTTTCATTTGCATATCG 58.963 41.667 0.00 0.00 0.00 2.92
3515 8470 5.393027 GGTGTTCCTTTCATTTGCATATCGT 60.393 40.000 0.00 0.00 0.00 3.73
3516 8471 5.512788 GTGTTCCTTTCATTTGCATATCGTG 59.487 40.000 0.00 0.00 0.00 4.35
3517 8472 5.414144 TGTTCCTTTCATTTGCATATCGTGA 59.586 36.000 0.00 0.00 0.00 4.35
3518 8473 6.095300 TGTTCCTTTCATTTGCATATCGTGAT 59.905 34.615 0.00 0.00 0.00 3.06
3519 8474 6.063640 TCCTTTCATTTGCATATCGTGATG 57.936 37.500 0.00 0.00 0.00 3.07
3520 8475 5.008911 TCCTTTCATTTGCATATCGTGATGG 59.991 40.000 0.00 0.00 0.00 3.51
3521 8476 4.834357 TTCATTTGCATATCGTGATGGG 57.166 40.909 0.00 0.00 0.00 4.00
3522 8477 2.553602 TCATTTGCATATCGTGATGGGC 59.446 45.455 0.00 0.00 0.00 5.36
3523 8478 2.346766 TTTGCATATCGTGATGGGCT 57.653 45.000 0.00 0.00 0.00 5.19
3524 8479 1.596603 TTGCATATCGTGATGGGCTG 58.403 50.000 0.00 0.00 0.00 4.85
3525 8480 0.886043 TGCATATCGTGATGGGCTGC 60.886 55.000 0.00 0.00 0.00 5.25
3526 8481 0.886043 GCATATCGTGATGGGCTGCA 60.886 55.000 0.50 0.00 0.00 4.41
3527 8482 1.154197 CATATCGTGATGGGCTGCAG 58.846 55.000 10.11 10.11 0.00 4.41
3528 8483 0.761187 ATATCGTGATGGGCTGCAGT 59.239 50.000 16.64 0.00 0.00 4.40
3529 8484 0.541392 TATCGTGATGGGCTGCAGTT 59.459 50.000 16.64 0.00 0.00 3.16
3530 8485 1.028330 ATCGTGATGGGCTGCAGTTG 61.028 55.000 16.64 0.00 0.00 3.16
3531 8486 1.672030 CGTGATGGGCTGCAGTTGA 60.672 57.895 16.64 0.00 0.00 3.18
3532 8487 1.642037 CGTGATGGGCTGCAGTTGAG 61.642 60.000 16.64 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2472 3583 1.816835 CATGCACTTCTCACATGCCTT 59.183 47.619 0.00 0.00 38.63 4.35
2641 3768 9.762381 AGAACCCCATGTCTAAATAAATAACAA 57.238 29.630 0.00 0.00 0.00 2.83
2642 3769 9.762381 AAGAACCCCATGTCTAAATAAATAACA 57.238 29.630 0.00 0.00 0.00 2.41
2647 3774 9.416284 GGAATAAGAACCCCATGTCTAAATAAA 57.584 33.333 0.00 0.00 0.00 1.40
2648 3775 8.787818 AGGAATAAGAACCCCATGTCTAAATAA 58.212 33.333 0.00 0.00 0.00 1.40
2654 3781 5.536497 AAAGGAATAAGAACCCCATGTCT 57.464 39.130 0.00 0.00 0.00 3.41
2680 3807 5.619220 ACCCTCGGTCGGTATATATAGATC 58.381 45.833 0.00 0.00 0.00 2.75
2738 7341 6.812879 ATAAGCCCTTTTACAGTGTACAAC 57.187 37.500 1.43 0.00 0.00 3.32
2741 7344 9.657419 TTAAGTATAAGCCCTTTTACAGTGTAC 57.343 33.333 1.43 0.00 32.04 2.90
2917 7811 8.954350 ACCAAATAATTGATGAGAAGTTGAGAG 58.046 33.333 0.00 0.00 38.94 3.20
2951 7845 1.768275 AGATGGGATTGTACGGCATGA 59.232 47.619 0.00 0.00 0.00 3.07
2983 7877 2.223021 CCATTAATTCAGACGTGCACGG 60.223 50.000 39.21 23.79 44.95 4.94
3010 7915 3.496131 CCGTTAATGCTGCGGCGT 61.496 61.111 13.96 10.37 42.25 5.68
3220 8161 1.615124 TGGGTGACGGATGGGTGAT 60.615 57.895 0.00 0.00 0.00 3.06
3294 8249 4.186856 ACCAAAACCAAACAACTGACTG 57.813 40.909 0.00 0.00 0.00 3.51
3295 8250 4.882842 AACCAAAACCAAACAACTGACT 57.117 36.364 0.00 0.00 0.00 3.41
3296 8251 5.933187 AAAACCAAAACCAAACAACTGAC 57.067 34.783 0.00 0.00 0.00 3.51
3297 8252 8.622948 AAATAAAACCAAAACCAAACAACTGA 57.377 26.923 0.00 0.00 0.00 3.41
3298 8253 9.762062 GTAAATAAAACCAAAACCAAACAACTG 57.238 29.630 0.00 0.00 0.00 3.16
3299 8254 8.657729 CGTAAATAAAACCAAAACCAAACAACT 58.342 29.630 0.00 0.00 0.00 3.16
3300 8255 8.441608 ACGTAAATAAAACCAAAACCAAACAAC 58.558 29.630 0.00 0.00 0.00 3.32
3301 8256 8.543862 ACGTAAATAAAACCAAAACCAAACAA 57.456 26.923 0.00 0.00 0.00 2.83
3302 8257 8.440833 CAACGTAAATAAAACCAAAACCAAACA 58.559 29.630 0.00 0.00 0.00 2.83
3303 8258 7.903946 CCAACGTAAATAAAACCAAAACCAAAC 59.096 33.333 0.00 0.00 0.00 2.93
3304 8259 7.413767 GCCAACGTAAATAAAACCAAAACCAAA 60.414 33.333 0.00 0.00 0.00 3.28
3305 8260 6.036844 GCCAACGTAAATAAAACCAAAACCAA 59.963 34.615 0.00 0.00 0.00 3.67
3306 8261 5.522824 GCCAACGTAAATAAAACCAAAACCA 59.477 36.000 0.00 0.00 0.00 3.67
3307 8262 5.754406 AGCCAACGTAAATAAAACCAAAACC 59.246 36.000 0.00 0.00 0.00 3.27
3357 8312 3.738282 GCTTACACATAGATTCGCCTCTG 59.262 47.826 0.00 0.00 0.00 3.35
3358 8313 3.639094 AGCTTACACATAGATTCGCCTCT 59.361 43.478 0.00 0.00 0.00 3.69
3359 8314 3.738282 CAGCTTACACATAGATTCGCCTC 59.262 47.826 0.00 0.00 0.00 4.70
3360 8315 3.133003 ACAGCTTACACATAGATTCGCCT 59.867 43.478 0.00 0.00 0.00 5.52
3361 8316 3.246226 CACAGCTTACACATAGATTCGCC 59.754 47.826 0.00 0.00 0.00 5.54
3362 8317 3.246226 CCACAGCTTACACATAGATTCGC 59.754 47.826 0.00 0.00 0.00 4.70
3363 8318 3.804325 CCCACAGCTTACACATAGATTCG 59.196 47.826 0.00 0.00 0.00 3.34
3364 8319 4.130118 CCCCACAGCTTACACATAGATTC 58.870 47.826 0.00 0.00 0.00 2.52
3365 8320 3.523564 ACCCCACAGCTTACACATAGATT 59.476 43.478 0.00 0.00 0.00 2.40
3366 8321 3.115390 ACCCCACAGCTTACACATAGAT 58.885 45.455 0.00 0.00 0.00 1.98
3367 8322 2.500098 GACCCCACAGCTTACACATAGA 59.500 50.000 0.00 0.00 0.00 1.98
3368 8323 2.738643 CGACCCCACAGCTTACACATAG 60.739 54.545 0.00 0.00 0.00 2.23
3369 8324 1.206132 CGACCCCACAGCTTACACATA 59.794 52.381 0.00 0.00 0.00 2.29
3370 8325 0.036388 CGACCCCACAGCTTACACAT 60.036 55.000 0.00 0.00 0.00 3.21
3371 8326 1.369692 CGACCCCACAGCTTACACA 59.630 57.895 0.00 0.00 0.00 3.72
3372 8327 1.375523 CCGACCCCACAGCTTACAC 60.376 63.158 0.00 0.00 0.00 2.90
3373 8328 2.589157 CCCGACCCCACAGCTTACA 61.589 63.158 0.00 0.00 0.00 2.41
3374 8329 2.267961 CCCGACCCCACAGCTTAC 59.732 66.667 0.00 0.00 0.00 2.34
3375 8330 3.712907 GCCCGACCCCACAGCTTA 61.713 66.667 0.00 0.00 0.00 3.09
3378 8333 4.660938 AAAGCCCGACCCCACAGC 62.661 66.667 0.00 0.00 0.00 4.40
3379 8334 1.530655 AAAAAGCCCGACCCCACAG 60.531 57.895 0.00 0.00 0.00 3.66
3380 8335 2.604152 AAAAAGCCCGACCCCACA 59.396 55.556 0.00 0.00 0.00 4.17
3394 8349 7.706179 CAGTGATTCTAGGCTGTTTTTCAAAAA 59.294 33.333 0.00 0.00 0.00 1.94
3395 8350 7.147915 ACAGTGATTCTAGGCTGTTTTTCAAAA 60.148 33.333 0.00 0.00 38.86 2.44
3396 8351 6.321181 ACAGTGATTCTAGGCTGTTTTTCAAA 59.679 34.615 0.00 0.00 38.86 2.69
3397 8352 5.827797 ACAGTGATTCTAGGCTGTTTTTCAA 59.172 36.000 0.00 0.00 38.86 2.69
3398 8353 5.376625 ACAGTGATTCTAGGCTGTTTTTCA 58.623 37.500 0.00 0.00 38.86 2.69
3399 8354 5.948992 ACAGTGATTCTAGGCTGTTTTTC 57.051 39.130 0.00 0.00 38.86 2.29
3404 8359 3.580458 AGTGAACAGTGATTCTAGGCTGT 59.420 43.478 0.00 0.00 43.13 4.40
3405 8360 4.199432 AGTGAACAGTGATTCTAGGCTG 57.801 45.455 0.00 0.00 35.31 4.85
3406 8361 4.323104 GGAAGTGAACAGTGATTCTAGGCT 60.323 45.833 0.00 0.00 0.00 4.58
3407 8362 3.935828 GGAAGTGAACAGTGATTCTAGGC 59.064 47.826 0.00 0.00 0.00 3.93
3408 8363 5.174395 CAGGAAGTGAACAGTGATTCTAGG 58.826 45.833 0.00 0.00 0.00 3.02
3409 8364 5.788450 ACAGGAAGTGAACAGTGATTCTAG 58.212 41.667 0.00 0.00 0.00 2.43
3410 8365 5.808366 ACAGGAAGTGAACAGTGATTCTA 57.192 39.130 0.00 0.00 0.00 2.10
3411 8366 4.696479 ACAGGAAGTGAACAGTGATTCT 57.304 40.909 0.00 0.00 0.00 2.40
3412 8367 4.816385 TGAACAGGAAGTGAACAGTGATTC 59.184 41.667 0.00 0.00 0.00 2.52
3413 8368 4.576463 GTGAACAGGAAGTGAACAGTGATT 59.424 41.667 0.00 0.00 0.00 2.57
3414 8369 4.130118 GTGAACAGGAAGTGAACAGTGAT 58.870 43.478 0.00 0.00 0.00 3.06
3415 8370 3.531538 GTGAACAGGAAGTGAACAGTGA 58.468 45.455 0.00 0.00 0.00 3.41
3416 8371 2.614057 GGTGAACAGGAAGTGAACAGTG 59.386 50.000 0.00 0.00 0.00 3.66
3417 8372 2.741878 CGGTGAACAGGAAGTGAACAGT 60.742 50.000 0.00 0.00 0.00 3.55
3418 8373 1.867233 CGGTGAACAGGAAGTGAACAG 59.133 52.381 0.00 0.00 0.00 3.16
3419 8374 1.208535 ACGGTGAACAGGAAGTGAACA 59.791 47.619 0.00 0.00 0.00 3.18
3420 8375 1.597663 CACGGTGAACAGGAAGTGAAC 59.402 52.381 0.74 0.00 0.00 3.18
3421 8376 1.483004 TCACGGTGAACAGGAAGTGAA 59.517 47.619 8.68 0.00 35.94 3.18
3422 8377 1.116308 TCACGGTGAACAGGAAGTGA 58.884 50.000 8.68 0.00 36.43 3.41
3423 8378 1.867233 CTTCACGGTGAACAGGAAGTG 59.133 52.381 19.07 4.01 32.21 3.16
3424 8379 1.760613 TCTTCACGGTGAACAGGAAGT 59.239 47.619 19.07 0.00 37.02 3.01
3425 8380 2.526304 TCTTCACGGTGAACAGGAAG 57.474 50.000 19.07 8.97 37.03 3.46
3426 8381 2.992124 TTCTTCACGGTGAACAGGAA 57.008 45.000 19.07 17.15 32.21 3.36
3427 8382 2.992124 TTTCTTCACGGTGAACAGGA 57.008 45.000 19.07 12.49 32.21 3.86
3446 8401 3.855668 TCTGTGGGGTCAATGGATTTTT 58.144 40.909 0.00 0.00 0.00 1.94
3447 8402 3.541242 TCTGTGGGGTCAATGGATTTT 57.459 42.857 0.00 0.00 0.00 1.82
3448 8403 3.763557 ATCTGTGGGGTCAATGGATTT 57.236 42.857 0.00 0.00 0.00 2.17
3449 8404 3.270433 AGAATCTGTGGGGTCAATGGATT 59.730 43.478 0.00 0.00 0.00 3.01
3450 8405 2.854967 AGAATCTGTGGGGTCAATGGAT 59.145 45.455 0.00 0.00 0.00 3.41
3451 8406 2.278245 AGAATCTGTGGGGTCAATGGA 58.722 47.619 0.00 0.00 0.00 3.41
3452 8407 2.756760 CAAGAATCTGTGGGGTCAATGG 59.243 50.000 0.00 0.00 0.00 3.16
3453 8408 3.689347 TCAAGAATCTGTGGGGTCAATG 58.311 45.455 0.00 0.00 0.00 2.82
3454 8409 3.308688 CCTCAAGAATCTGTGGGGTCAAT 60.309 47.826 4.00 0.00 0.00 2.57
3455 8410 2.040278 CCTCAAGAATCTGTGGGGTCAA 59.960 50.000 4.00 0.00 0.00 3.18
3456 8411 1.630369 CCTCAAGAATCTGTGGGGTCA 59.370 52.381 4.00 0.00 0.00 4.02
3457 8412 1.680249 GCCTCAAGAATCTGTGGGGTC 60.680 57.143 11.22 3.23 31.80 4.46
3458 8413 0.329596 GCCTCAAGAATCTGTGGGGT 59.670 55.000 11.22 0.00 31.80 4.95
3459 8414 0.622665 AGCCTCAAGAATCTGTGGGG 59.377 55.000 6.89 6.89 31.80 4.96
3460 8415 1.681166 CCAGCCTCAAGAATCTGTGGG 60.681 57.143 0.00 0.00 31.80 4.61
3461 8416 1.747709 CCAGCCTCAAGAATCTGTGG 58.252 55.000 0.00 0.00 33.85 4.17
3462 8417 1.093159 GCCAGCCTCAAGAATCTGTG 58.907 55.000 0.00 0.00 0.00 3.66
3463 8418 0.392193 CGCCAGCCTCAAGAATCTGT 60.392 55.000 0.00 0.00 0.00 3.41
3464 8419 1.712977 GCGCCAGCCTCAAGAATCTG 61.713 60.000 0.00 0.00 37.42 2.90
3465 8420 1.451028 GCGCCAGCCTCAAGAATCT 60.451 57.895 0.00 0.00 37.42 2.40
3466 8421 3.105659 GCGCCAGCCTCAAGAATC 58.894 61.111 0.00 0.00 37.42 2.52
3482 8437 4.643387 AGGAACACCAGTGGCGGC 62.643 66.667 9.78 0.00 34.19 6.53
3483 8438 1.515521 GAAAGGAACACCAGTGGCGG 61.516 60.000 9.78 4.24 34.19 6.13
3484 8439 0.817634 TGAAAGGAACACCAGTGGCG 60.818 55.000 9.78 1.17 34.19 5.69
3485 8440 1.620822 ATGAAAGGAACACCAGTGGC 58.379 50.000 9.78 0.00 34.19 5.01
3486 8441 3.799917 GCAAATGAAAGGAACACCAGTGG 60.800 47.826 7.91 7.91 34.19 4.00
3487 8442 3.181477 TGCAAATGAAAGGAACACCAGTG 60.181 43.478 0.00 0.00 0.00 3.66
3488 8443 3.030291 TGCAAATGAAAGGAACACCAGT 58.970 40.909 0.00 0.00 0.00 4.00
3489 8444 3.731652 TGCAAATGAAAGGAACACCAG 57.268 42.857 0.00 0.00 0.00 4.00
3490 8445 5.392919 CGATATGCAAATGAAAGGAACACCA 60.393 40.000 0.00 0.00 0.00 4.17
3491 8446 5.036737 CGATATGCAAATGAAAGGAACACC 58.963 41.667 0.00 0.00 0.00 4.16
3492 8447 5.512788 CACGATATGCAAATGAAAGGAACAC 59.487 40.000 0.00 0.00 0.00 3.32
3493 8448 5.414144 TCACGATATGCAAATGAAAGGAACA 59.586 36.000 0.00 0.00 0.00 3.18
3494 8449 5.879237 TCACGATATGCAAATGAAAGGAAC 58.121 37.500 0.00 0.00 0.00 3.62
3495 8450 6.459985 CCATCACGATATGCAAATGAAAGGAA 60.460 38.462 0.00 0.00 0.00 3.36
3496 8451 5.008911 CCATCACGATATGCAAATGAAAGGA 59.991 40.000 0.00 0.00 0.00 3.36
3497 8452 5.217393 CCATCACGATATGCAAATGAAAGG 58.783 41.667 0.00 0.00 0.00 3.11
3498 8453 5.217393 CCCATCACGATATGCAAATGAAAG 58.783 41.667 0.00 0.00 0.00 2.62
3499 8454 4.499526 GCCCATCACGATATGCAAATGAAA 60.500 41.667 0.00 0.00 0.00 2.69
3500 8455 3.004629 GCCCATCACGATATGCAAATGAA 59.995 43.478 0.00 0.00 0.00 2.57
3501 8456 2.553602 GCCCATCACGATATGCAAATGA 59.446 45.455 0.00 0.00 0.00 2.57
3502 8457 2.555325 AGCCCATCACGATATGCAAATG 59.445 45.455 0.00 0.00 0.00 2.32
3503 8458 2.555325 CAGCCCATCACGATATGCAAAT 59.445 45.455 0.00 0.00 0.00 2.32
3504 8459 1.948834 CAGCCCATCACGATATGCAAA 59.051 47.619 0.00 0.00 0.00 3.68
3505 8460 1.596603 CAGCCCATCACGATATGCAA 58.403 50.000 0.00 0.00 0.00 4.08
3506 8461 0.886043 GCAGCCCATCACGATATGCA 60.886 55.000 0.00 0.00 32.58 3.96
3507 8462 0.886043 TGCAGCCCATCACGATATGC 60.886 55.000 0.00 0.00 0.00 3.14
3508 8463 1.154197 CTGCAGCCCATCACGATATG 58.846 55.000 0.00 0.00 0.00 1.78
3509 8464 0.761187 ACTGCAGCCCATCACGATAT 59.239 50.000 15.27 0.00 0.00 1.63
3510 8465 0.541392 AACTGCAGCCCATCACGATA 59.459 50.000 15.27 0.00 0.00 2.92
3511 8466 1.028330 CAACTGCAGCCCATCACGAT 61.028 55.000 15.27 0.00 0.00 3.73
3512 8467 1.672030 CAACTGCAGCCCATCACGA 60.672 57.895 15.27 0.00 0.00 4.35
3513 8468 1.642037 CTCAACTGCAGCCCATCACG 61.642 60.000 15.27 0.00 0.00 4.35
3514 8469 2.177950 CTCAACTGCAGCCCATCAC 58.822 57.895 15.27 0.00 0.00 3.06
3515 8470 4.728409 CTCAACTGCAGCCCATCA 57.272 55.556 15.27 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.