Multiple sequence alignment - TraesCS1A01G247300

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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 TraesCS1A01G247300 chr1A 100.000 7370 0 0 1 7370 438692581 438699950 0.000000e+00 13610
1 TraesCS1A01G247300 chr1A 75.573 262 54 7 5203 5459 16917986 16918242 3.610000e-23 121
2 TraesCS1A01G247300 chr1B 96.116 4686 132 26 877 5545 453874539 453879191 0.000000e+00 7600
3 TraesCS1A01G247300 chr1B 93.204 1442 57 18 5545 6957 453879437 453880866 0.000000e+00 2082
4 TraesCS1A01G247300 chr1B 97.895 570 12 0 6801 7370 453881115 453881684 0.000000e+00 987
5 TraesCS1A01G247300 chr1B 86.053 760 40 27 21 750 453873689 453874412 0.000000e+00 756
6 TraesCS1A01G247300 chr1D 96.067 3585 110 17 877 4447 339107164 339110731 0.000000e+00 5810
7 TraesCS1A01G247300 chr1D 95.148 2947 72 11 4487 7370 339110732 339113670 0.000000e+00 4584
8 TraesCS1A01G247300 chr1D 89.375 800 41 26 43 818 339106298 339107077 0.000000e+00 966
9 TraesCS1A01G247300 chr1D 96.429 84 3 0 4660 4743 301353511 301353594 9.970000e-29 139
10 TraesCS1A01G247300 chr1D 74.333 300 71 6 5209 5505 16404237 16403941 1.000000e-23 122
11 TraesCS1A01G247300 chr2D 86.571 350 47 0 3562 3911 318331103 318330754 3.230000e-103 387
12 TraesCS1A01G247300 chr2D 76.786 616 117 22 5767 6367 318329704 318329100 9.220000e-84 322
13 TraesCS1A01G247300 chr2D 88.235 187 20 1 2494 2680 318332332 318332148 9.620000e-54 222
14 TraesCS1A01G247300 chr2D 84.375 160 23 2 2813 2970 318331896 318331737 9.900000e-34 156
15 TraesCS1A01G247300 chr2A 77.073 615 117 21 5767 6367 413332121 413332725 4.260000e-87 333
16 TraesCS1A01G247300 chr2A 90.798 163 15 0 2494 2656 413329300 413329462 1.240000e-52 219
17 TraesCS1A01G247300 chr2A 85.294 170 22 3 2803 2970 413329689 413329857 9.830000e-39 172
18 TraesCS1A01G247300 chr2B 91.566 166 14 0 2494 2659 386309636 386309471 5.750000e-56 230
19 TraesCS1A01G247300 chr2B 84.375 160 23 2 2813 2970 386309215 386309056 9.900000e-34 156
20 TraesCS1A01G247300 chr7A 95.349 86 4 0 4660 4745 477234926 477234841 3.590000e-28 137
21 TraesCS1A01G247300 chr6D 95.349 86 4 0 4660 4745 309072510 309072595 3.590000e-28 137
22 TraesCS1A01G247300 chr6D 96.386 83 2 1 4660 4741 78083085 78083167 1.290000e-27 135
23 TraesCS1A01G247300 chr5D 95.349 86 4 0 4660 4745 111788722 111788637 3.590000e-28 137
24 TraesCS1A01G247300 chr3D 97.500 80 2 0 4659 4738 179456725 179456646 3.590000e-28 137
25 TraesCS1A01G247300 chr3D 96.341 82 3 0 4660 4741 54370491 54370410 1.290000e-27 135


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 TraesCS1A01G247300 chr1A 438692581 438699950 7369 False 13610.000000 13610 100.000000 1 7370 1 chr1A.!!$F2 7369
1 TraesCS1A01G247300 chr1B 453873689 453881684 7995 False 2856.250000 7600 93.317000 21 7370 4 chr1B.!!$F1 7349
2 TraesCS1A01G247300 chr1D 339106298 339113670 7372 False 3786.666667 5810 93.530000 43 7370 3 chr1D.!!$F2 7327
3 TraesCS1A01G247300 chr2D 318329100 318332332 3232 True 271.750000 387 83.991750 2494 6367 4 chr2D.!!$R1 3873
4 TraesCS1A01G247300 chr2A 413329300 413332725 3425 False 241.333333 333 84.388333 2494 6367 3 chr2A.!!$F1 3873

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
529 565 0.033228 CGGCAAACCAAAATGGAGCA 59.967 50.000 2.85 0.0 40.96 4.26 F
1251 1357 0.729116 CAGCACTACAAATGCCGGAG 59.271 55.000 5.05 0.0 44.53 4.63 F
1765 1872 3.004315 GGAGTGTTCCAAGATCGCAAAAA 59.996 43.478 0.00 0.0 43.45 1.94 F
2492 2611 2.146342 CGTCTTCACTTGGCTGACAAT 58.854 47.619 0.00 0.0 38.65 2.71 F
4018 4588 1.754803 TGCCATCCTACTACTCCAACG 59.245 52.381 0.00 0.0 0.00 4.10 F
4189 4763 0.534877 GTCCACATGCCAGTGACACA 60.535 55.000 8.59 0.0 42.05 3.72 F
5276 5891 2.197577 GGTATCGCTGCTGAAGTTCTC 58.802 52.381 4.17 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2160 1.059006 AGAGGGAGCTGCATAAGGGG 61.059 60.000 7.79 0.00 0.00 4.79 R
2087 2203 3.191371 GTGAGGCCCTGACAGTAAAATTG 59.809 47.826 0.00 0.00 0.00 2.32 R
2795 3071 5.971493 ACCTAAATAGAGCAGGATAGGAGT 58.029 41.667 3.80 0.00 35.12 3.85 R
4171 4745 0.250424 CTGTGTCACTGGCATGTGGA 60.250 55.000 14.28 2.89 38.40 4.02 R
5276 5891 0.817634 TGACCAACGGCTTCAACCTG 60.818 55.000 0.00 0.00 0.00 4.00 R
6079 6974 1.743394 GTAAGTGTATGCACCAAGGCC 59.257 52.381 10.59 0.00 46.35 5.19 R
6408 7306 2.861462 TTCCTTTTTGCTCCAACGTG 57.139 45.000 0.00 0.00 0.00 4.49 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
71 72 3.287312 ACAGTGCATGAAATTTGGTCG 57.713 42.857 0.00 0.00 0.00 4.79
156 162 3.961414 GAAACCGCCACCCCTCCA 61.961 66.667 0.00 0.00 0.00 3.86
161 167 3.151710 CGCCACCCCTCCATCGTA 61.152 66.667 0.00 0.00 0.00 3.43
290 315 1.824230 CCGGCAAAATCCAAATCTCCA 59.176 47.619 0.00 0.00 0.00 3.86
291 316 2.431782 CCGGCAAAATCCAAATCTCCAT 59.568 45.455 0.00 0.00 0.00 3.41
292 317 3.491447 CCGGCAAAATCCAAATCTCCATC 60.491 47.826 0.00 0.00 0.00 3.51
293 318 3.130869 CGGCAAAATCCAAATCTCCATCA 59.869 43.478 0.00 0.00 0.00 3.07
294 319 4.436332 GGCAAAATCCAAATCTCCATCAC 58.564 43.478 0.00 0.00 0.00 3.06
295 320 4.081531 GGCAAAATCCAAATCTCCATCACA 60.082 41.667 0.00 0.00 0.00 3.58
296 321 5.481105 GCAAAATCCAAATCTCCATCACAA 58.519 37.500 0.00 0.00 0.00 3.33
297 322 5.933463 GCAAAATCCAAATCTCCATCACAAA 59.067 36.000 0.00 0.00 0.00 2.83
298 323 6.596497 GCAAAATCCAAATCTCCATCACAAAT 59.404 34.615 0.00 0.00 0.00 2.32
299 324 7.201582 GCAAAATCCAAATCTCCATCACAAATC 60.202 37.037 0.00 0.00 0.00 2.17
300 325 7.729124 AAATCCAAATCTCCATCACAAATCT 57.271 32.000 0.00 0.00 0.00 2.40
301 326 6.956202 ATCCAAATCTCCATCACAAATCTC 57.044 37.500 0.00 0.00 0.00 2.75
302 327 6.070951 TCCAAATCTCCATCACAAATCTCT 57.929 37.500 0.00 0.00 0.00 3.10
303 328 6.118170 TCCAAATCTCCATCACAAATCTCTC 58.882 40.000 0.00 0.00 0.00 3.20
304 329 6.069789 TCCAAATCTCCATCACAAATCTCTCT 60.070 38.462 0.00 0.00 0.00 3.10
305 330 6.038382 CCAAATCTCCATCACAAATCTCTCTG 59.962 42.308 0.00 0.00 0.00 3.35
315 346 2.393271 AATCTCTCTGCGTTTCCCTG 57.607 50.000 0.00 0.00 0.00 4.45
431 467 1.057471 GAGGTAATGCCCTCCTACCC 58.943 60.000 0.00 0.00 44.49 3.69
432 468 0.401541 AGGTAATGCCCTCCTACCCC 60.402 60.000 0.00 0.00 36.52 4.95
433 469 1.752833 GTAATGCCCTCCTACCCCG 59.247 63.158 0.00 0.00 0.00 5.73
434 470 1.052694 GTAATGCCCTCCTACCCCGT 61.053 60.000 0.00 0.00 0.00 5.28
435 471 0.761702 TAATGCCCTCCTACCCCGTC 60.762 60.000 0.00 0.00 0.00 4.79
440 476 0.481567 CCCTCCTACCCCGTCTCATA 59.518 60.000 0.00 0.00 0.00 2.15
469 505 0.678048 GCCCAATCTCGAGTGCCTTT 60.678 55.000 13.13 0.00 0.00 3.11
479 515 1.328680 CGAGTGCCTTTGATTCATCCG 59.671 52.381 0.00 0.00 0.00 4.18
480 516 1.672881 GAGTGCCTTTGATTCATCCGG 59.327 52.381 0.00 0.00 0.00 5.14
481 517 1.004745 AGTGCCTTTGATTCATCCGGT 59.995 47.619 0.00 0.00 0.00 5.28
483 519 0.740737 GCCTTTGATTCATCCGGTGG 59.259 55.000 0.00 0.00 0.00 4.61
484 520 1.955208 GCCTTTGATTCATCCGGTGGT 60.955 52.381 0.00 0.00 0.00 4.16
485 521 1.745087 CCTTTGATTCATCCGGTGGTG 59.255 52.381 0.00 0.00 0.00 4.17
486 522 2.617788 CCTTTGATTCATCCGGTGGTGA 60.618 50.000 0.00 1.75 0.00 4.02
487 523 3.282021 CTTTGATTCATCCGGTGGTGAT 58.718 45.455 0.00 0.00 0.00 3.06
488 524 4.450976 CTTTGATTCATCCGGTGGTGATA 58.549 43.478 0.00 0.00 0.00 2.15
489 525 4.705110 TTGATTCATCCGGTGGTGATAT 57.295 40.909 0.00 2.25 0.00 1.63
490 526 4.705110 TGATTCATCCGGTGGTGATATT 57.295 40.909 0.00 0.00 0.00 1.28
491 527 4.388485 TGATTCATCCGGTGGTGATATTG 58.612 43.478 0.00 0.00 0.00 1.90
492 528 2.928801 TCATCCGGTGGTGATATTGG 57.071 50.000 0.00 0.00 0.00 3.16
493 529 2.123589 TCATCCGGTGGTGATATTGGT 58.876 47.619 0.00 0.00 0.00 3.67
494 530 2.104111 TCATCCGGTGGTGATATTGGTC 59.896 50.000 0.00 0.00 0.00 4.02
495 531 1.574263 TCCGGTGGTGATATTGGTCA 58.426 50.000 0.00 0.00 0.00 4.02
496 532 1.909986 TCCGGTGGTGATATTGGTCAA 59.090 47.619 0.00 0.00 0.00 3.18
497 533 2.093181 TCCGGTGGTGATATTGGTCAAG 60.093 50.000 0.00 0.00 0.00 3.02
498 534 2.288666 CGGTGGTGATATTGGTCAAGG 58.711 52.381 0.00 0.00 0.00 3.61
499 535 2.024414 GGTGGTGATATTGGTCAAGGC 58.976 52.381 0.00 0.00 0.00 4.35
500 536 2.620367 GGTGGTGATATTGGTCAAGGCA 60.620 50.000 0.00 0.00 0.00 4.75
501 537 3.290710 GTGGTGATATTGGTCAAGGCAT 58.709 45.455 0.00 0.00 0.00 4.40
508 544 5.597594 TGATATTGGTCAAGGCATGCATTTA 59.402 36.000 21.36 7.56 0.00 1.40
526 562 4.873746 TTTATCGGCAAACCAAAATGGA 57.126 36.364 2.85 0.00 40.96 3.41
528 564 0.316841 TCGGCAAACCAAAATGGAGC 59.683 50.000 2.85 4.32 40.96 4.70
529 565 0.033228 CGGCAAACCAAAATGGAGCA 59.967 50.000 2.85 0.00 40.96 4.26
530 566 1.338011 CGGCAAACCAAAATGGAGCAT 60.338 47.619 2.85 0.00 40.96 3.79
531 567 2.078392 GGCAAACCAAAATGGAGCATG 58.922 47.619 2.85 0.00 40.96 4.06
532 568 2.550639 GGCAAACCAAAATGGAGCATGT 60.551 45.455 2.85 0.00 40.96 3.21
533 569 3.140623 GCAAACCAAAATGGAGCATGTT 58.859 40.909 2.85 0.00 40.96 2.71
534 570 3.187022 GCAAACCAAAATGGAGCATGTTC 59.813 43.478 2.85 0.04 40.96 3.18
535 571 4.634199 CAAACCAAAATGGAGCATGTTCT 58.366 39.130 9.57 0.00 40.96 3.01
536 572 3.947910 ACCAAAATGGAGCATGTTCTG 57.052 42.857 9.57 0.00 40.96 3.02
631 667 2.892374 GCACCTAACATGCATTTTCCC 58.108 47.619 0.33 0.00 42.88 3.97
693 731 5.007626 CACGTGTTATTGCTATATTGGCTGT 59.992 40.000 7.58 0.00 0.00 4.40
711 764 7.391148 TGGCTGTATCTAGGTTTTCATTTTC 57.609 36.000 0.00 0.00 0.00 2.29
728 781 6.924111 TCATTTTCTATCCTGCTGGTTTTTC 58.076 36.000 9.73 0.00 34.23 2.29
751 804 4.755123 CCGGTATGGAATTCTGGTATGAAC 59.245 45.833 5.23 0.00 42.00 3.18
770 823 4.889409 TGAACTGCAGAAATCTTTCCAAGT 59.111 37.500 23.35 0.00 37.92 3.16
776 831 4.037923 GCAGAAATCTTTCCAAGTTGTCCA 59.962 41.667 1.45 0.00 37.92 4.02
793 848 6.708054 AGTTGTCCAGAAGAATTACTCACAAG 59.292 38.462 0.00 0.00 0.00 3.16
813 868 6.147821 CACAAGGATTTGATGTTCGTACTCTT 59.852 38.462 0.00 0.00 37.73 2.85
814 869 7.330946 CACAAGGATTTGATGTTCGTACTCTTA 59.669 37.037 0.00 0.00 37.73 2.10
815 870 8.041323 ACAAGGATTTGATGTTCGTACTCTTAT 58.959 33.333 0.00 0.00 37.73 1.73
816 871 8.543774 CAAGGATTTGATGTTCGTACTCTTATC 58.456 37.037 0.00 0.00 36.36 1.75
824 930 5.891451 TGTTCGTACTCTTATCATGACCAG 58.109 41.667 0.00 0.00 0.00 4.00
843 949 1.974236 AGCAGATGGCCATCCTACTAC 59.026 52.381 36.81 21.42 46.50 2.73
844 950 1.974236 GCAGATGGCCATCCTACTACT 59.026 52.381 36.81 17.76 38.58 2.57
845 951 3.165875 GCAGATGGCCATCCTACTACTA 58.834 50.000 36.81 0.00 38.58 1.82
847 953 4.322349 GCAGATGGCCATCCTACTACTAAG 60.322 50.000 36.81 17.00 38.58 2.18
848 954 4.835615 CAGATGGCCATCCTACTACTAAGT 59.164 45.833 36.81 15.09 38.58 2.24
852 958 8.570470 AGATGGCCATCCTACTACTAAGTATAT 58.430 37.037 36.81 13.46 38.58 0.86
853 959 9.203163 GATGGCCATCCTACTACTAAGTATATT 57.797 37.037 32.15 0.00 37.57 1.28
872 978 9.881649 AGTATATTATTACAGCAGATGACCATG 57.118 33.333 0.00 0.00 0.00 3.66
873 979 9.102757 GTATATTATTACAGCAGATGACCATGG 57.897 37.037 11.19 11.19 0.00 3.66
874 980 3.939740 ATTACAGCAGATGACCATGGT 57.060 42.857 19.89 19.89 0.00 3.55
875 981 3.719268 TTACAGCAGATGACCATGGTT 57.281 42.857 20.85 3.15 0.00 3.67
894 1000 9.892130 CCATGGTTTTATTAACTCTAAGAGACT 57.108 33.333 2.57 0.00 33.32 3.24
957 1063 2.225727 GCCTTGCAGTTAACTACGCTTT 59.774 45.455 16.32 0.00 0.00 3.51
1095 1201 3.620488 TGCAATTCTGAGGATACAACCC 58.380 45.455 0.00 0.00 41.41 4.11
1176 1282 1.201429 ACATCGGGGCTGGTTTCTCT 61.201 55.000 0.00 0.00 0.00 3.10
1188 1294 5.383130 GCTGGTTTCTCTAAATTCGTGAAC 58.617 41.667 0.00 0.00 0.00 3.18
1195 1301 3.255725 TCTAAATTCGTGAACGCCGATT 58.744 40.909 0.00 0.00 39.60 3.34
1197 1303 2.520686 AATTCGTGAACGCCGATTTC 57.479 45.000 0.00 0.00 39.60 2.17
1212 1318 1.448677 GATTTCTCGACGTATCTGCGC 59.551 52.381 0.00 0.00 34.88 6.09
1248 1354 1.226101 CGCAGCACTACAAATGCCG 60.226 57.895 0.00 0.00 44.53 5.69
1251 1357 0.729116 CAGCACTACAAATGCCGGAG 59.271 55.000 5.05 0.00 44.53 4.63
1429 1536 5.456173 GCTCTCGACTGCTAGTATAAAACAC 59.544 44.000 0.00 0.00 0.00 3.32
1668 1775 3.747529 ACGGTATGGTTTTGTTTACTCCG 59.252 43.478 0.00 0.00 40.00 4.63
1684 1791 7.988599 TGTTTACTCCGCCTATATGTTGTATTT 59.011 33.333 0.00 0.00 0.00 1.40
1688 1795 7.959175 ACTCCGCCTATATGTTGTATTTCTTA 58.041 34.615 0.00 0.00 0.00 2.10
1725 1832 5.860716 GGATCATGTTGTTTCTTTGAAGAGC 59.139 40.000 0.00 0.00 36.22 4.09
1765 1872 3.004315 GGAGTGTTCCAAGATCGCAAAAA 59.996 43.478 0.00 0.00 43.45 1.94
1857 1964 7.067728 GCTTAATTATAGCTAAACCGAAACCG 58.932 38.462 0.00 0.00 35.74 4.44
1859 1966 6.990341 AATTATAGCTAAACCGAAACCGTT 57.010 33.333 0.00 0.00 0.00 4.44
2078 2194 5.071115 AGCTCCCTCTTGTATTTATGTCTCC 59.929 44.000 0.00 0.00 0.00 3.71
2191 2307 3.951663 AGTTAGGACTTATGGTGCAACC 58.048 45.455 0.00 0.00 46.82 3.77
2210 2326 8.432359 GTGCAACCTACAATAACTTAATTTTGC 58.568 33.333 0.00 0.00 32.24 3.68
2259 2375 8.154856 ACCTAGCTGTAGAGTGTTGAAAAATAA 58.845 33.333 0.00 0.00 0.00 1.40
2406 2524 4.512944 TCTGCAACTGAAACTGAATGACTC 59.487 41.667 0.00 0.00 0.00 3.36
2492 2611 2.146342 CGTCTTCACTTGGCTGACAAT 58.854 47.619 0.00 0.00 38.65 2.71
2775 3010 6.780706 TTTTAGCAGACTTACTAGTGTTGC 57.219 37.500 5.39 8.03 39.82 4.17
2804 3080 6.948589 AGTTTCCTACTTTTCACTCCTATCC 58.051 40.000 0.00 0.00 31.29 2.59
2975 3253 9.915629 TGGTATTGTTATGGTGAATACAAAAAC 57.084 29.630 0.00 0.00 35.24 2.43
2996 3274 8.989653 AAAACATTAACGAGAACCAAGAAAAA 57.010 26.923 0.00 0.00 0.00 1.94
3967 4537 7.928307 ATAAGAGAAAAGAGCATTTACAGCA 57.072 32.000 0.00 0.00 0.00 4.41
4013 4583 3.898123 TGAATCCTGCCATCCTACTACTC 59.102 47.826 0.00 0.00 0.00 2.59
4018 4588 1.754803 TGCCATCCTACTACTCCAACG 59.245 52.381 0.00 0.00 0.00 4.10
4171 4745 1.545651 GCTTACAAGAGGGCAACAGGT 60.546 52.381 0.00 0.00 39.74 4.00
4189 4763 0.534877 GTCCACATGCCAGTGACACA 60.535 55.000 8.59 0.00 42.05 3.72
5276 5891 2.197577 GGTATCGCTGCTGAAGTTCTC 58.802 52.381 4.17 0.00 0.00 2.87
6056 6951 7.127955 ACCCTTCATTAAGATCTTCACCATAGT 59.872 37.037 12.24 0.00 34.37 2.12
6273 7171 0.670546 AGAATCCCACTGTTGCGACG 60.671 55.000 0.00 0.00 0.00 5.12
6302 7200 2.126734 GCGCATGAACACACCAGC 60.127 61.111 0.30 0.00 0.00 4.85
6345 7243 2.703536 TGTTGGCACTAGTGAAGGAGAA 59.296 45.455 27.08 5.90 0.00 2.87
6436 7334 3.244181 GGAGCAAAAAGGAAATGCAGGAA 60.244 43.478 0.00 0.00 42.45 3.36
6583 7507 4.020218 TCGAGTCCTTCCATCAGTTGAATT 60.020 41.667 0.00 0.00 0.00 2.17
6584 7508 4.697352 CGAGTCCTTCCATCAGTTGAATTT 59.303 41.667 0.00 0.00 0.00 1.82
6585 7509 5.874810 CGAGTCCTTCCATCAGTTGAATTTA 59.125 40.000 0.00 0.00 0.00 1.40
6752 7885 7.764331 ACTTTCAAGCCTTAAACTTACGAAAA 58.236 30.769 0.00 0.00 0.00 2.29
6787 7920 5.753716 AGAGGCTCTGCTCATAAAGAAAAT 58.246 37.500 17.96 0.00 0.00 1.82
6874 8201 8.928448 AGAGATCTTGGAAAGTACAATATAGCA 58.072 33.333 0.00 0.00 46.34 3.49
6893 8220 5.444663 AGCAACAGAACTGGAATTTCTTC 57.555 39.130 6.76 0.00 30.56 2.87
6952 8280 8.929260 TGAGCATTCTTTCCAATATATGACAT 57.071 30.769 0.00 0.00 0.00 3.06
7063 8391 3.541242 TGTCCAAGAATCCACCCAATT 57.459 42.857 0.00 0.00 0.00 2.32
7186 8514 4.637534 CAGCTAAGAGCAGCCAAGAATTTA 59.362 41.667 0.64 0.00 45.56 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.412286 TCATGCACTGTACGTACTTAGTGTA 59.588 40.000 30.91 29.04 41.84 2.90
39 40 4.729595 TCATGCACTGTACGTACTTAGTG 58.270 43.478 28.70 28.70 42.51 2.74
40 41 5.381174 TTCATGCACTGTACGTACTTAGT 57.619 39.130 25.12 18.14 0.00 2.24
41 42 6.887376 ATTTCATGCACTGTACGTACTTAG 57.113 37.500 25.12 17.52 0.00 2.18
42 43 7.360522 CCAAATTTCATGCACTGTACGTACTTA 60.361 37.037 25.12 6.43 0.00 2.24
43 44 6.370593 CAAATTTCATGCACTGTACGTACTT 58.629 36.000 25.12 10.56 0.00 2.24
44 45 5.106712 CCAAATTTCATGCACTGTACGTACT 60.107 40.000 25.12 4.41 0.00 2.73
45 46 5.086058 CCAAATTTCATGCACTGTACGTAC 58.914 41.667 18.90 18.90 0.00 3.67
46 47 4.757657 ACCAAATTTCATGCACTGTACGTA 59.242 37.500 0.00 0.00 0.00 3.57
47 48 3.568007 ACCAAATTTCATGCACTGTACGT 59.432 39.130 0.00 0.00 0.00 3.57
48 49 4.158384 GACCAAATTTCATGCACTGTACG 58.842 43.478 0.00 0.00 0.00 3.67
110 116 2.070783 GTCCTCGTCGGTTAAATTGCA 58.929 47.619 0.00 0.00 0.00 4.08
156 162 3.491581 GGCGGAATGACGATACGAT 57.508 52.632 0.00 0.00 35.47 3.73
273 298 5.075858 TGTGATGGAGATTTGGATTTTGC 57.924 39.130 0.00 0.00 0.00 3.68
290 315 3.686726 GGAAACGCAGAGAGATTTGTGAT 59.313 43.478 0.00 0.00 0.00 3.06
291 316 3.067106 GGAAACGCAGAGAGATTTGTGA 58.933 45.455 0.00 0.00 0.00 3.58
292 317 2.160417 GGGAAACGCAGAGAGATTTGTG 59.840 50.000 0.00 0.00 0.00 3.33
293 318 2.039084 AGGGAAACGCAGAGAGATTTGT 59.961 45.455 0.00 0.00 0.00 2.83
294 319 2.417933 CAGGGAAACGCAGAGAGATTTG 59.582 50.000 0.00 0.00 0.00 2.32
295 320 2.704572 CAGGGAAACGCAGAGAGATTT 58.295 47.619 0.00 0.00 0.00 2.17
296 321 1.677217 GCAGGGAAACGCAGAGAGATT 60.677 52.381 0.00 0.00 0.00 2.40
297 322 0.107945 GCAGGGAAACGCAGAGAGAT 60.108 55.000 0.00 0.00 0.00 2.75
298 323 1.293498 GCAGGGAAACGCAGAGAGA 59.707 57.895 0.00 0.00 0.00 3.10
299 324 1.743252 GGCAGGGAAACGCAGAGAG 60.743 63.158 0.00 0.00 0.00 3.20
300 325 2.347490 GGCAGGGAAACGCAGAGA 59.653 61.111 0.00 0.00 0.00 3.10
301 326 3.121030 CGGCAGGGAAACGCAGAG 61.121 66.667 0.00 0.00 0.00 3.35
302 327 3.876589 GACGGCAGGGAAACGCAGA 62.877 63.158 0.00 0.00 0.00 4.26
303 328 3.423154 GACGGCAGGGAAACGCAG 61.423 66.667 0.00 0.00 0.00 5.18
304 329 3.876589 GAGACGGCAGGGAAACGCA 62.877 63.158 0.00 0.00 0.00 5.24
305 330 3.119096 GAGACGGCAGGGAAACGC 61.119 66.667 0.00 0.00 0.00 4.84
431 467 1.575244 CACAGCCATGTATGAGACGG 58.425 55.000 1.70 0.00 37.65 4.79
432 468 0.933097 GCACAGCCATGTATGAGACG 59.067 55.000 1.70 0.00 37.65 4.18
469 505 4.388485 CAATATCACCACCGGATGAATCA 58.612 43.478 9.46 0.00 0.00 2.57
479 515 2.024414 GCCTTGACCAATATCACCACC 58.976 52.381 0.00 0.00 0.00 4.61
480 516 2.722094 TGCCTTGACCAATATCACCAC 58.278 47.619 0.00 0.00 0.00 4.16
481 517 3.289836 CATGCCTTGACCAATATCACCA 58.710 45.455 0.00 0.00 0.00 4.17
483 519 2.689471 TGCATGCCTTGACCAATATCAC 59.311 45.455 16.68 0.00 0.00 3.06
484 520 3.015675 TGCATGCCTTGACCAATATCA 57.984 42.857 16.68 0.00 0.00 2.15
485 521 4.595762 AATGCATGCCTTGACCAATATC 57.404 40.909 16.68 0.00 0.00 1.63
486 522 6.570957 CGATAAATGCATGCCTTGACCAATAT 60.571 38.462 16.68 5.23 0.00 1.28
487 523 5.278414 CGATAAATGCATGCCTTGACCAATA 60.278 40.000 16.68 0.12 0.00 1.90
488 524 4.500205 CGATAAATGCATGCCTTGACCAAT 60.500 41.667 16.68 0.00 0.00 3.16
489 525 3.181488 CGATAAATGCATGCCTTGACCAA 60.181 43.478 16.68 0.00 0.00 3.67
490 526 2.358582 CGATAAATGCATGCCTTGACCA 59.641 45.455 16.68 0.00 0.00 4.02
491 527 2.287788 CCGATAAATGCATGCCTTGACC 60.288 50.000 16.68 0.00 0.00 4.02
492 528 2.859806 GCCGATAAATGCATGCCTTGAC 60.860 50.000 16.68 6.17 0.00 3.18
493 529 1.337703 GCCGATAAATGCATGCCTTGA 59.662 47.619 16.68 5.04 0.00 3.02
494 530 1.067364 TGCCGATAAATGCATGCCTTG 59.933 47.619 16.68 0.36 31.31 3.61
495 531 1.401761 TGCCGATAAATGCATGCCTT 58.598 45.000 16.68 9.11 31.31 4.35
496 532 1.401761 TTGCCGATAAATGCATGCCT 58.598 45.000 16.68 1.31 37.33 4.75
497 533 1.860326 GTTTGCCGATAAATGCATGCC 59.140 47.619 16.68 0.00 37.33 4.40
498 534 1.860326 GGTTTGCCGATAAATGCATGC 59.140 47.619 11.82 11.82 37.33 4.06
499 535 3.162202 TGGTTTGCCGATAAATGCATG 57.838 42.857 0.00 0.00 37.33 4.06
500 536 3.883830 TTGGTTTGCCGATAAATGCAT 57.116 38.095 0.00 0.00 37.33 3.96
501 537 3.667497 TTTGGTTTGCCGATAAATGCA 57.333 38.095 0.00 0.00 37.67 3.96
508 544 1.066929 GCTCCATTTTGGTTTGCCGAT 60.067 47.619 0.00 0.00 39.03 4.18
693 731 9.561069 GCAGGATAGAAAATGAAAACCTAGATA 57.439 33.333 0.00 0.00 0.00 1.98
711 764 2.017049 CCGGAAAAACCAGCAGGATAG 58.983 52.381 0.35 0.00 38.90 2.08
728 781 4.617253 TCATACCAGAATTCCATACCGG 57.383 45.455 0.00 0.00 0.00 5.28
770 823 5.997746 CCTTGTGAGTAATTCTTCTGGACAA 59.002 40.000 0.00 0.00 0.00 3.18
776 831 8.954350 CATCAAATCCTTGTGAGTAATTCTTCT 58.046 33.333 0.00 0.00 33.94 2.85
793 848 8.491152 CATGATAAGAGTACGAACATCAAATCC 58.509 37.037 0.00 0.00 0.00 3.01
824 930 1.974236 AGTAGTAGGATGGCCATCTGC 59.026 52.381 37.94 27.36 37.92 4.26
847 953 9.102757 CCATGGTCATCTGCTGTAATAATATAC 57.897 37.037 2.57 0.00 0.00 1.47
848 954 8.825774 ACCATGGTCATCTGCTGTAATAATATA 58.174 33.333 13.00 0.00 0.00 0.86
852 958 5.372343 ACCATGGTCATCTGCTGTAATAA 57.628 39.130 13.00 0.00 0.00 1.40
853 959 5.372343 AACCATGGTCATCTGCTGTAATA 57.628 39.130 20.07 0.00 0.00 0.98
854 960 3.939740 ACCATGGTCATCTGCTGTAAT 57.060 42.857 13.00 0.00 0.00 1.89
855 961 3.719268 AACCATGGTCATCTGCTGTAA 57.281 42.857 20.07 0.00 0.00 2.41
856 962 3.719268 AAACCATGGTCATCTGCTGTA 57.281 42.857 20.07 0.00 0.00 2.74
857 963 2.592102 AAACCATGGTCATCTGCTGT 57.408 45.000 20.07 0.00 0.00 4.40
858 964 5.587388 AATAAAACCATGGTCATCTGCTG 57.413 39.130 20.07 0.00 0.00 4.41
859 965 6.891908 AGTTAATAAAACCATGGTCATCTGCT 59.108 34.615 20.07 7.35 0.00 4.24
860 966 7.067494 AGAGTTAATAAAACCATGGTCATCTGC 59.933 37.037 20.07 5.10 0.00 4.26
861 967 8.511604 AGAGTTAATAAAACCATGGTCATCTG 57.488 34.615 20.07 0.00 0.00 2.90
865 971 9.667107 CTCTTAGAGTTAATAAAACCATGGTCA 57.333 33.333 20.07 7.07 0.00 4.02
866 972 9.886132 TCTCTTAGAGTTAATAAAACCATGGTC 57.114 33.333 20.07 2.44 0.00 4.02
867 973 9.668497 GTCTCTTAGAGTTAATAAAACCATGGT 57.332 33.333 13.00 13.00 0.00 3.55
868 974 9.892130 AGTCTCTTAGAGTTAATAAAACCATGG 57.108 33.333 11.19 11.19 0.00 3.66
957 1063 1.344438 ACTCCAGAACACGCTTCATCA 59.656 47.619 0.00 0.00 0.00 3.07
1095 1201 5.820423 TGGAAAGTACACCCGATCATTAATG 59.180 40.000 9.29 9.29 0.00 1.90
1176 1282 3.680937 AGAAATCGGCGTTCACGAATTTA 59.319 39.130 6.85 0.00 44.20 1.40
1195 1301 0.450583 AAGCGCAGATACGTCGAGAA 59.549 50.000 11.47 0.00 34.88 2.87
1197 1303 0.840729 GAAAGCGCAGATACGTCGAG 59.159 55.000 11.47 0.00 34.88 4.04
1212 1318 1.202336 GCGGGCATCCAATTCAGAAAG 60.202 52.381 0.00 0.00 0.00 2.62
1236 1342 0.392998 CTGGCTCCGGCATTTGTAGT 60.393 55.000 0.00 0.00 40.87 2.73
1429 1536 4.856487 GTCTGTCATCTCAAGAAAGAGTCG 59.144 45.833 0.00 0.00 36.97 4.18
1607 1714 6.279227 AGATTTGATATCGAAAGCTTGTCG 57.721 37.500 18.78 18.78 39.88 4.35
1668 1775 8.283291 GTGCTGTAAGAAATACAACATATAGGC 58.717 37.037 0.00 0.00 43.75 3.93
1684 1791 3.455543 TGATCCATGGATGTGCTGTAAGA 59.544 43.478 32.05 0.00 32.39 2.10
1688 1795 2.092049 ACATGATCCATGGATGTGCTGT 60.092 45.455 32.05 22.62 45.16 4.40
1696 1803 5.774184 TCAAAGAAACAACATGATCCATGGA 59.226 36.000 18.88 18.88 45.16 3.41
1697 1804 6.028146 TCAAAGAAACAACATGATCCATGG 57.972 37.500 4.97 4.97 45.16 3.66
1725 1832 5.694910 ACACTCCGTAATAGAAAACACACAG 59.305 40.000 0.00 0.00 0.00 3.66
1818 1925 7.955864 GCTATAATTAAGCCATTACTGCGTAAC 59.044 37.037 3.80 0.00 35.93 2.50
1822 1929 6.727824 AGCTATAATTAAGCCATTACTGCG 57.272 37.500 12.92 0.00 41.02 5.18
1857 1964 8.192110 TCAACTTAAACCAGTTCAATTACCAAC 58.808 33.333 0.00 0.00 34.60 3.77
1859 1966 7.883391 TCAACTTAAACCAGTTCAATTACCA 57.117 32.000 0.00 0.00 34.60 3.25
2044 2160 1.059006 AGAGGGAGCTGCATAAGGGG 61.059 60.000 7.79 0.00 0.00 4.79
2078 2194 7.968405 GCCCTGACAGTAAAATTGTATGTAAAG 59.032 37.037 0.93 0.00 0.00 1.85
2087 2203 3.191371 GTGAGGCCCTGACAGTAAAATTG 59.809 47.826 0.00 0.00 0.00 2.32
2210 2326 9.581099 AGGTTTTTCTGTTTGTTAAGTACAATG 57.419 29.630 0.00 0.00 45.72 2.82
2259 2375 5.710567 GGCTTACTCCCAACTCTTAACATTT 59.289 40.000 0.00 0.00 0.00 2.32
2292 2408 8.894768 AAGCATTACAGTTCAGTATTATCTCC 57.105 34.615 0.00 0.00 0.00 3.71
2795 3071 5.971493 ACCTAAATAGAGCAGGATAGGAGT 58.029 41.667 3.80 0.00 35.12 3.85
2798 3074 7.233757 ACAAGTACCTAAATAGAGCAGGATAGG 59.766 40.741 0.00 0.00 36.75 2.57
2800 3076 7.783119 TCACAAGTACCTAAATAGAGCAGGATA 59.217 37.037 0.00 0.00 33.44 2.59
2801 3077 6.611642 TCACAAGTACCTAAATAGAGCAGGAT 59.388 38.462 0.00 0.00 33.44 3.24
2803 3079 6.096987 TCTCACAAGTACCTAAATAGAGCAGG 59.903 42.308 0.00 0.00 35.45 4.85
2804 3080 7.101652 TCTCACAAGTACCTAAATAGAGCAG 57.898 40.000 0.00 0.00 0.00 4.24
2978 3256 9.724839 CAGTTTTATTTTTCTTGGTTCTCGTTA 57.275 29.630 0.00 0.00 0.00 3.18
3967 4537 7.047460 AGAAGATGCTTCTTGTGAAAAACAT 57.953 32.000 18.72 0.00 42.34 2.71
4013 4583 4.414852 CAGTCATTGCCTTAAATCGTTGG 58.585 43.478 0.00 0.00 0.00 3.77
4018 4588 4.427312 CAAGCCAGTCATTGCCTTAAATC 58.573 43.478 0.00 0.00 0.00 2.17
4102 4672 4.630111 TGCACATCTTTTTGATTGAACCC 58.370 39.130 0.00 0.00 32.05 4.11
4171 4745 0.250424 CTGTGTCACTGGCATGTGGA 60.250 55.000 14.28 2.89 38.40 4.02
4189 4763 2.273538 AGTCGGAGTATACCATCGCT 57.726 50.000 0.00 1.38 0.00 4.93
4398 4972 8.764287 CATTTATTTGAGGTTCTTGTTTTCCAC 58.236 33.333 0.00 0.00 0.00 4.02
5105 5720 1.560611 CATTGGCCCCATCCATTGTTT 59.439 47.619 0.00 0.00 35.77 2.83
5114 5729 1.194218 GCAGTAAACATTGGCCCCAT 58.806 50.000 0.00 0.00 0.00 4.00
5276 5891 0.817634 TGACCAACGGCTTCAACCTG 60.818 55.000 0.00 0.00 0.00 4.00
5647 6518 6.324819 CAGTTGTTTACTAAGAATGGCATGG 58.675 40.000 0.00 0.00 34.56 3.66
5683 6554 6.095440 AGCATGCAGGGTATTTTAGTTTACTG 59.905 38.462 21.98 0.00 0.00 2.74
6020 6894 9.232473 AGATCTTAATGAAGGGTAAGTTTCAAC 57.768 33.333 0.00 0.00 36.93 3.18
6079 6974 1.743394 GTAAGTGTATGCACCAAGGCC 59.257 52.381 10.59 0.00 46.35 5.19
6302 7200 4.980434 CACTGGAATTGAACTTGCTTTCTG 59.020 41.667 0.00 0.00 0.00 3.02
6394 7292 3.135225 CCAACGTGTACAAGATCACCAA 58.865 45.455 16.00 0.00 0.00 3.67
6408 7306 2.861462 TTCCTTTTTGCTCCAACGTG 57.139 45.000 0.00 0.00 0.00 4.49
6496 7394 3.243168 GGCTCAAATCATAATCTTGCGCA 60.243 43.478 5.66 5.66 33.51 6.09
6548 7472 5.186992 TGGAAGGACTCGATTCAACTAATGA 59.813 40.000 5.06 0.00 35.85 2.57
6585 7509 8.703336 CGCATGCGCTAGTATCATAATATTAAT 58.297 33.333 29.09 0.00 35.30 1.40
6752 7885 6.942576 TGAGCAGAGCCTCTAATTTACTTTTT 59.057 34.615 0.00 0.00 33.02 1.94
6757 7890 7.928706 TCTTTATGAGCAGAGCCTCTAATTTAC 59.071 37.037 0.00 0.00 33.02 2.01
6758 7891 8.023021 TCTTTATGAGCAGAGCCTCTAATTTA 57.977 34.615 0.00 0.00 33.02 1.40
6769 7902 8.239314 TGTTGCTTATTTTCTTTATGAGCAGAG 58.761 33.333 0.00 0.00 42.93 3.35
6787 7920 6.701145 TCCAGTTGTTGTTTATGTTGCTTA 57.299 33.333 0.00 0.00 0.00 3.09
6802 7936 4.536765 AGTGTCATCCTTTTTCCAGTTGT 58.463 39.130 0.00 0.00 0.00 3.32
6874 8201 4.275936 CACGGAAGAAATTCCAGTTCTGTT 59.724 41.667 7.72 0.00 41.16 3.16
6893 8220 6.920758 TGATTTTTCTCCAACAATTAACACGG 59.079 34.615 0.00 0.00 0.00 4.94
6952 8280 6.017440 GTCAAGGCACAGAAATGTACAAAGTA 60.017 38.462 0.00 0.00 0.00 2.24
7186 8514 8.584157 GTGATTGATTGTCTATGTAGAGAGGAT 58.416 37.037 0.00 0.00 32.01 3.24


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

AutoCloner maintained by Alex Coulton.