Multiple sequence alignment - TraesCS2A01G462700

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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 TraesCS2A01G462700 chr2A 100.000 3641 0 0 1 3641 708190923 708187283 0.000000e+00 6724
1 TraesCS2A01G462700 chr2B 89.492 3664 219 71 4 3612 681544980 681541428 0.000000e+00 4481
2 TraesCS2A01G462700 chr2D 91.830 2558 140 20 384 2901 568945638 568943110 0.000000e+00 3502
3 TraesCS2A01G462700 chr2D 84.125 674 40 33 2961 3612 568943114 568942486 1.130000e-164 590
4 TraesCS2A01G462700 chr2D 86.056 251 22 5 32 277 568945903 568945661 1.300000e-64 257


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 TraesCS2A01G462700 chr2A 708187283 708190923 3640 True 6724.000000 6724 100.000 1 3641 1 chr2A.!!$R1 3640
1 TraesCS2A01G462700 chr2B 681541428 681544980 3552 True 4481.000000 4481 89.492 4 3612 1 chr2B.!!$R1 3608
2 TraesCS2A01G462700 chr2D 568942486 568945903 3417 True 1449.666667 3502 87.337 32 3612 3 chr2D.!!$R1 3580

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
21 22 0.096454 GTCGTTGTTTATCAGCCGGC 59.904 55.0 21.89 21.89 0.00 6.13 F
1397 1454 0.318699 TCGCAGTGAAGGTTCTGTCG 60.319 55.0 0.00 0.00 34.57 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1639 0.179179 GAACAGCAGAAATGCTCGGC 60.179 55.0 0.0 0.0 44.3 5.54 R
3067 3157 0.250338 AGCCCGTTTCAAGGTGAGAC 60.250 55.0 0.0 0.0 0.0 3.36 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
21 22 0.096454 GTCGTTGTTTATCAGCCGGC 59.904 55.000 21.89 21.89 0.00 6.13
148 150 0.749649 AGCTCCGGATTCAGCTAGTG 59.250 55.000 13.84 0.00 44.45 2.74
208 222 1.008767 CGCCGTCTTAGATCGGGAC 60.009 63.158 19.13 7.61 45.85 4.46
211 225 1.970092 CCGTCTTAGATCGGGACTCT 58.030 55.000 12.95 0.00 42.61 3.24
235 249 1.135575 CATGGCCGTCTTTGCTTCTTC 60.136 52.381 0.00 0.00 0.00 2.87
258 272 3.100671 CGGGATCTTATCTTAGGGGAGG 58.899 54.545 0.00 0.00 0.00 4.30
266 280 1.457831 CTTAGGGGAGGACGGGGAG 60.458 68.421 0.00 0.00 0.00 4.30
268 282 1.946063 TTAGGGGAGGACGGGGAGAG 61.946 65.000 0.00 0.00 0.00 3.20
277 291 1.835531 GGACGGGGAGAGGTTTTCATA 59.164 52.381 0.00 0.00 0.00 2.15
279 293 2.500504 GACGGGGAGAGGTTTTCATAGT 59.499 50.000 0.00 0.00 0.00 2.12
281 295 3.270877 CGGGGAGAGGTTTTCATAGTTG 58.729 50.000 0.00 0.00 0.00 3.16
288 313 6.043854 AGAGGTTTTCATAGTTGTCTCTCC 57.956 41.667 0.00 0.00 0.00 3.71
291 316 5.310857 AGGTTTTCATAGTTGTCTCTCCCTT 59.689 40.000 0.00 0.00 0.00 3.95
318 343 6.258230 TCTTTGTATTGCCATCAGTTTCTG 57.742 37.500 0.00 0.00 0.00 3.02
344 369 3.592059 CAAATCCAGGCTTTGATTGGTG 58.408 45.455 9.86 2.97 35.99 4.17
346 371 2.673775 TCCAGGCTTTGATTGGTGAA 57.326 45.000 0.00 0.00 33.65 3.18
348 373 2.158475 TCCAGGCTTTGATTGGTGAAGT 60.158 45.455 0.00 0.00 33.65 3.01
349 374 2.629617 CCAGGCTTTGATTGGTGAAGTT 59.370 45.455 0.00 0.00 0.00 2.66
359 384 6.155475 TGATTGGTGAAGTTTTTCCGATTT 57.845 33.333 0.00 0.00 32.09 2.17
374 399 3.970828 CGATTTCGGGTGCAATTTTTC 57.029 42.857 0.00 0.00 35.37 2.29
380 406 2.031508 TCGGGTGCAATTTTTCTCGAAC 60.032 45.455 0.00 0.00 0.00 3.95
402 428 3.066064 CCATTATTTCGGGTGCAATTCGA 59.934 43.478 0.00 0.00 0.00 3.71
405 431 0.871722 TTTCGGGTGCAATTCGACAG 59.128 50.000 6.77 0.00 32.39 3.51
406 432 1.573829 TTCGGGTGCAATTCGACAGC 61.574 55.000 6.77 0.00 32.39 4.40
418 444 6.132056 GCAATTCGACAGCTATAACAATCAG 58.868 40.000 0.00 0.00 0.00 2.90
421 447 6.887376 TTCGACAGCTATAACAATCAGTTC 57.113 37.500 0.00 0.00 41.64 3.01
461 491 4.788925 ATCCTCATTTCCGAATGGGTTA 57.211 40.909 0.00 0.00 41.33 2.85
463 493 3.778075 TCCTCATTTCCGAATGGGTTAGA 59.222 43.478 0.00 0.00 41.33 2.10
470 500 9.280174 TCATTTCCGAATGGGTTAGATTATTAC 57.720 33.333 0.00 0.00 42.36 1.89
482 514 9.088512 GGGTTAGATTATTACGATATTGCTGAG 57.911 37.037 0.00 0.00 0.00 3.35
544 583 4.213059 GGTGCTTGTTTCTTTCAGAGAGAG 59.787 45.833 0.00 0.00 35.37 3.20
660 712 9.316730 GCTTCAAAATTTCCATATTATCTTGCA 57.683 29.630 0.00 0.00 0.00 4.08
713 765 7.397761 AGTGAGTTAGGATAATATGGCTAGGTC 59.602 40.741 0.00 0.00 0.00 3.85
758 810 4.855937 GCTTCAGCTTTCTTTCTGTTATGC 59.144 41.667 0.00 0.00 38.21 3.14
760 812 5.618056 TCAGCTTTCTTTCTGTTATGCAG 57.382 39.130 0.00 0.00 46.34 4.41
772 824 4.701651 TCTGTTATGCAGTTTGGATTCCAG 59.298 41.667 5.36 0.00 45.23 3.86
776 828 6.663093 TGTTATGCAGTTTGGATTCCAGTAAT 59.337 34.615 5.36 0.00 33.81 1.89
786 838 9.435688 GTTTGGATTCCAGTAATTTAAAAGCAT 57.564 29.630 5.36 0.00 33.81 3.79
812 864 6.869421 CTGTTGTCCAGTTTGTGTTTTAAG 57.131 37.500 0.00 0.00 36.37 1.85
815 867 7.254852 TGTTGTCCAGTTTGTGTTTTAAGATC 58.745 34.615 0.00 0.00 0.00 2.75
847 899 7.643569 TGCTGTTCACACCAATAATTGATAT 57.356 32.000 0.00 0.00 0.00 1.63
918 971 9.585099 GTTTTGGATTCATCTATTGTTGCATTA 57.415 29.630 0.00 0.00 0.00 1.90
992 1046 6.998074 TCTTGCAGAAATTCCTTCTAGTTTGA 59.002 34.615 0.00 0.00 42.84 2.69
994 1048 8.862325 TTGCAGAAATTCCTTCTAGTTTGATA 57.138 30.769 0.00 0.00 42.84 2.15
1067 1121 1.233285 GGCGATGATGGTGAGCATCC 61.233 60.000 20.51 6.51 41.21 3.51
1133 1187 5.100259 TCCGTTCTTATACGCTTTCTTCTG 58.900 41.667 0.00 0.00 40.10 3.02
1135 1189 5.220228 CCGTTCTTATACGCTTTCTTCTGTG 60.220 44.000 0.00 0.00 40.10 3.66
1294 1348 1.058404 GTTACTGACCGCTTCGTCAC 58.942 55.000 0.00 0.00 37.85 3.67
1300 1354 3.114616 CCGCTTCGTCACTGCCTG 61.115 66.667 0.00 0.00 0.00 4.85
1397 1454 0.318699 TCGCAGTGAAGGTTCTGTCG 60.319 55.000 0.00 0.00 34.57 4.35
1478 1535 2.254546 AGCATGAAAACCTCGTCACA 57.745 45.000 0.00 0.00 0.00 3.58
1484 1541 3.340034 TGAAAACCTCGTCACACTTGTT 58.660 40.909 0.00 0.00 0.00 2.83
1487 1544 0.539986 ACCTCGTCACACTTGTTGGT 59.460 50.000 0.00 0.00 0.00 3.67
1493 1550 0.455410 TCACACTTGTTGGTTGCTGC 59.545 50.000 0.00 0.00 0.00 5.25
1526 1583 4.100498 TCCCATAGGATCCTCGTTTACAAC 59.900 45.833 20.22 0.00 37.19 3.32
1582 1639 5.169295 GCTAGGTACTAACACTTTGTCCTG 58.831 45.833 0.00 0.00 42.17 3.86
1624 1681 3.751175 GTCGATTCCTTCATTGGTTGTCA 59.249 43.478 0.00 0.00 0.00 3.58
1763 1820 2.990066 AGGAAATCCGTCCTCACATC 57.010 50.000 0.00 0.00 45.40 3.06
1772 1829 0.537188 GTCCTCACATCATCCACCGT 59.463 55.000 0.00 0.00 0.00 4.83
1847 1904 1.066152 GATTTTGGATTGGCGAGGCTC 59.934 52.381 3.87 3.87 0.00 4.70
1880 1937 1.943968 GCAACTCATGTTAGCACCCGA 60.944 52.381 0.00 0.00 34.60 5.14
1906 1963 3.129287 GCAGGCACATTGTAAGCATAACT 59.871 43.478 2.07 0.00 0.00 2.24
1916 1973 3.329520 TGTAAGCATAACTCAACCCCTGT 59.670 43.478 0.00 0.00 0.00 4.00
1920 1977 4.223144 AGCATAACTCAACCCCTGTTTTT 58.777 39.130 0.00 0.00 30.42 1.94
1934 1991 4.584743 CCCTGTTTTTACAGCCTTCTTTCT 59.415 41.667 0.00 0.00 36.46 2.52
1935 1992 5.069119 CCCTGTTTTTACAGCCTTCTTTCTT 59.931 40.000 0.00 0.00 36.46 2.52
1937 1994 7.363431 CCTGTTTTTACAGCCTTCTTTCTTAG 58.637 38.462 0.00 0.00 36.46 2.18
2243 2300 4.016113 ACTGAGCAAACGTTCAAAGAAC 57.984 40.909 0.00 0.00 0.00 3.01
2263 2320 7.237920 AGAACAATGCTGAATTTGACAAAAC 57.762 32.000 4.41 3.42 0.00 2.43
2272 2329 3.756933 ATTTGACAAAACCTGCTGCAT 57.243 38.095 1.31 0.00 0.00 3.96
2278 2335 3.460103 ACAAAACCTGCTGCATCTTTTG 58.540 40.909 26.91 26.91 37.67 2.44
2502 2559 1.226542 CAGGCCAGCCATGATCACT 59.773 57.895 12.03 0.00 38.92 3.41
2544 2601 4.555709 ACCAAACCGCACGGAGCA 62.556 61.111 17.40 0.00 46.13 4.26
2605 2662 1.633774 GGAGATATCGGAGCCCTTCA 58.366 55.000 0.00 0.00 0.00 3.02
2619 2676 0.728466 CCTTCACGTCGTCGGAGAAC 60.728 60.000 7.05 0.00 39.69 3.01
2662 2719 4.917906 AGAGTTGGACAGGAAATTAGCT 57.082 40.909 0.00 0.00 0.00 3.32
2663 2720 5.248380 AGAGTTGGACAGGAAATTAGCTT 57.752 39.130 0.00 0.00 0.00 3.74
2682 2739 3.538392 GCTTCGTTCGATTTGTACATTGC 59.462 43.478 0.00 0.00 0.00 3.56
2684 2741 3.331150 TCGTTCGATTTGTACATTGCCT 58.669 40.909 0.00 0.00 0.00 4.75
2685 2742 3.369756 TCGTTCGATTTGTACATTGCCTC 59.630 43.478 0.00 0.00 0.00 4.70
2890 2971 2.079925 GCTTCACATCTCTGAACCACC 58.920 52.381 0.00 0.00 0.00 4.61
2899 2980 1.942657 CTCTGAACCACCACTGTGTTG 59.057 52.381 7.08 2.33 41.09 3.33
2900 2981 1.024271 CTGAACCACCACTGTGTTGG 58.976 55.000 21.16 21.16 41.09 3.77
2901 2982 0.621082 TGAACCACCACTGTGTTGGA 59.379 50.000 28.20 5.80 41.09 3.53
2902 2983 1.308998 GAACCACCACTGTGTTGGAG 58.691 55.000 28.20 5.78 41.09 3.86
2903 2984 0.916086 AACCACCACTGTGTTGGAGA 59.084 50.000 28.20 0.00 41.09 3.71
2904 2985 0.469917 ACCACCACTGTGTTGGAGAG 59.530 55.000 28.20 4.74 41.09 3.20
2905 2986 0.758734 CCACCACTGTGTTGGAGAGA 59.241 55.000 18.50 0.00 41.09 3.10
2906 2987 1.270518 CCACCACTGTGTTGGAGAGAG 60.271 57.143 18.50 0.00 41.09 3.20
2907 2988 0.394565 ACCACTGTGTTGGAGAGAGC 59.605 55.000 7.08 0.00 39.24 4.09
2908 2989 0.683973 CCACTGTGTTGGAGAGAGCT 59.316 55.000 7.08 0.00 39.24 4.09
2909 2990 1.337635 CCACTGTGTTGGAGAGAGCTC 60.338 57.143 5.27 5.27 39.24 4.09
2943 3024 3.553511 GTCAGACTTCAGTGTTCACTGTG 59.446 47.826 25.52 21.51 38.75 3.66
2953 3034 5.243730 TCAGTGTTCACTGTGATGATGACTA 59.756 40.000 25.52 5.87 38.75 2.59
2984 3065 0.549950 CCTGCTGGTCTGGATGGATT 59.450 55.000 0.51 0.00 35.98 3.01
3002 3091 6.644248 TGGATTTCTAATCCAAGCATGATG 57.356 37.500 16.62 0.00 44.54 3.07
3049 3139 3.966665 ACAATTTGGAATGGACACACCTT 59.033 39.130 0.78 0.00 39.86 3.50
3067 3157 4.157289 CACCTTGACCAAATTCATCTCCAG 59.843 45.833 0.00 0.00 0.00 3.86
3118 3223 4.308458 CGCCTGACGGAACACCCA 62.308 66.667 0.00 0.00 38.44 4.51
3119 3224 2.668550 GCCTGACGGAACACCCAC 60.669 66.667 0.00 0.00 34.14 4.61
3120 3225 2.357034 CCTGACGGAACACCCACG 60.357 66.667 0.00 0.00 34.14 4.94
3178 3283 2.179018 GTGCAAATCACGCGCCAT 59.821 55.556 5.73 0.00 35.76 4.40
3179 3284 2.153945 GTGCAAATCACGCGCCATG 61.154 57.895 5.73 0.00 35.76 3.66
3180 3285 3.249605 GCAAATCACGCGCCATGC 61.250 61.111 5.73 6.61 41.47 4.06
3181 3286 2.486504 CAAATCACGCGCCATGCT 59.513 55.556 5.73 0.00 43.27 3.79
3182 3287 1.584483 CAAATCACGCGCCATGCTC 60.584 57.895 5.73 0.00 43.27 4.26
3187 3292 2.885644 ACGCGCCATGCTCTTACG 60.886 61.111 5.73 0.00 43.27 3.18
3203 3308 1.394266 TACGGGGATACGGTCAAGCC 61.394 60.000 0.00 0.00 38.39 4.35
3204 3309 2.727392 CGGGGATACGGTCAAGCCA 61.727 63.158 0.00 0.00 36.97 4.75
3205 3310 1.146263 GGGGATACGGTCAAGCCAG 59.854 63.158 0.00 0.00 36.97 4.85
3206 3311 1.523938 GGGATACGGTCAAGCCAGC 60.524 63.158 0.00 0.00 36.97 4.85
3207 3312 1.883084 GGATACGGTCAAGCCAGCG 60.883 63.158 0.00 0.00 42.99 5.18
3220 3325 2.505777 CAGCGAGCTCCACGTCTG 60.506 66.667 8.47 5.84 0.00 3.51
3227 3340 4.135153 CTCCACGTCTGGCTCGGG 62.135 72.222 0.00 0.00 37.49 5.14
3258 3371 4.767841 CTGAGCGAGCGAGCGTGT 62.768 66.667 0.00 0.00 43.00 4.49
3298 3411 4.515567 AGAAGTGGAGAACGGATCAAAAAC 59.484 41.667 0.00 0.00 0.00 2.43
3314 3427 6.729690 TCAAAAACTTCCAGAAATCACCAT 57.270 33.333 0.00 0.00 0.00 3.55
3315 3428 6.514947 TCAAAAACTTCCAGAAATCACCATG 58.485 36.000 0.00 0.00 0.00 3.66
3316 3429 6.098124 TCAAAAACTTCCAGAAATCACCATGT 59.902 34.615 0.00 0.00 0.00 3.21
3317 3430 5.712152 AAACTTCCAGAAATCACCATGTC 57.288 39.130 0.00 0.00 0.00 3.06
3318 3431 4.371624 ACTTCCAGAAATCACCATGTCA 57.628 40.909 0.00 0.00 0.00 3.58
3319 3432 4.728772 ACTTCCAGAAATCACCATGTCAA 58.271 39.130 0.00 0.00 0.00 3.18
3320 3433 5.327732 ACTTCCAGAAATCACCATGTCAAT 58.672 37.500 0.00 0.00 0.00 2.57
3329 3442 3.560105 TCACCATGTCAATTGTCAACCA 58.440 40.909 9.41 0.00 0.00 3.67
3382 3495 3.488489 GCGTGAACATGTCAAACCATAC 58.512 45.455 0.00 0.00 38.23 2.39
3383 3496 3.188460 GCGTGAACATGTCAAACCATACT 59.812 43.478 0.00 0.00 38.23 2.12
3387 3500 4.202514 TGAACATGTCAAACCATACTCCCA 60.203 41.667 0.00 0.00 31.51 4.37
3389 3502 3.330701 ACATGTCAAACCATACTCCCAGT 59.669 43.478 0.00 0.00 0.00 4.00
3434 3547 2.408110 CGTCGTCAACTCGTTAAAGTGC 60.408 50.000 0.00 0.00 0.00 4.40
3450 3563 3.318555 GCGAGACAGCGAGCGATG 61.319 66.667 6.59 6.59 37.56 3.84
3463 3576 1.062525 GCGATGGAACGGATTGCAC 59.937 57.895 0.00 0.00 39.19 4.57
3473 3586 1.787847 GGATTGCACCGTCAACTCG 59.212 57.895 0.00 0.00 0.00 4.18
3512 3625 1.273887 GAGCGATCGAACCAATGCG 59.726 57.895 21.57 0.00 0.00 4.73
3544 3657 0.033366 TCTCACACACATCCACACCG 59.967 55.000 0.00 0.00 0.00 4.94
3612 3730 0.785979 CGAAGTAAACCCGGTTGACG 59.214 55.000 11.60 6.37 43.80 4.35
3613 3731 0.514255 GAAGTAAACCCGGTTGACGC 59.486 55.000 11.60 5.29 42.52 5.19
3614 3732 0.886043 AAGTAAACCCGGTTGACGCC 60.886 55.000 11.60 0.00 42.52 5.68
3615 3733 1.597578 GTAAACCCGGTTGACGCCA 60.598 57.895 2.79 0.00 42.52 5.69
3616 3734 1.147824 TAAACCCGGTTGACGCCAA 59.852 52.632 2.79 0.00 42.52 4.52
3617 3735 0.465097 TAAACCCGGTTGACGCCAAA 60.465 50.000 2.79 0.00 42.52 3.28
3618 3736 1.321074 AAACCCGGTTGACGCCAAAA 61.321 50.000 2.79 0.00 42.52 2.44
3619 3737 1.110518 AACCCGGTTGACGCCAAAAT 61.111 50.000 0.69 0.00 42.52 1.82
3620 3738 1.080839 CCCGGTTGACGCCAAAATG 60.081 57.895 0.00 0.00 42.52 2.32
3621 3739 1.080839 CCGGTTGACGCCAAAATGG 60.081 57.895 0.00 0.00 42.52 3.16
3622 3740 1.519751 CCGGTTGACGCCAAAATGGA 61.520 55.000 0.00 0.00 39.92 3.41
3623 3741 0.386731 CGGTTGACGCCAAAATGGAC 60.387 55.000 0.00 0.00 40.96 4.02
3624 3742 0.038618 GGTTGACGCCAAAATGGACC 60.039 55.000 0.00 0.00 40.96 4.46
3625 3743 0.671251 GTTGACGCCAAAATGGACCA 59.329 50.000 0.00 0.00 40.96 4.02
3626 3744 1.067821 GTTGACGCCAAAATGGACCAA 59.932 47.619 0.00 0.00 40.96 3.67
3627 3745 1.403814 TGACGCCAAAATGGACCAAA 58.596 45.000 0.00 0.00 40.96 3.28
3628 3746 1.967066 TGACGCCAAAATGGACCAAAT 59.033 42.857 0.00 0.00 40.96 2.32
3629 3747 2.366916 TGACGCCAAAATGGACCAAATT 59.633 40.909 0.00 0.00 40.96 1.82
3630 3748 2.736192 GACGCCAAAATGGACCAAATTG 59.264 45.455 13.20 13.20 40.96 2.32
3631 3749 2.366916 ACGCCAAAATGGACCAAATTGA 59.633 40.909 19.13 0.00 40.96 2.57
3632 3750 3.007831 ACGCCAAAATGGACCAAATTGAT 59.992 39.130 19.13 6.31 40.96 2.57
3633 3751 3.618150 CGCCAAAATGGACCAAATTGATC 59.382 43.478 19.13 11.68 40.96 2.92
3634 3752 3.940852 GCCAAAATGGACCAAATTGATCC 59.059 43.478 19.13 0.00 40.96 3.36
3635 3753 4.323715 GCCAAAATGGACCAAATTGATCCT 60.324 41.667 19.13 0.00 40.96 3.24
3636 3754 5.804120 GCCAAAATGGACCAAATTGATCCTT 60.804 40.000 19.13 0.00 40.96 3.36
3637 3755 6.240145 CCAAAATGGACCAAATTGATCCTTT 58.760 36.000 19.13 4.80 40.96 3.11
3638 3756 6.716173 CCAAAATGGACCAAATTGATCCTTTT 59.284 34.615 12.88 12.88 38.60 2.27
3639 3757 7.094677 CCAAAATGGACCAAATTGATCCTTTTC 60.095 37.037 17.40 0.00 36.66 2.29
3640 3758 6.940430 AATGGACCAAATTGATCCTTTTCT 57.060 33.333 8.03 0.00 28.81 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.342555 CGGCTGATAAACAACGACGA 58.657 50.000 0.00 0.00 33.04 4.20
1 2 0.368907 CCGGCTGATAAACAACGACG 59.631 55.000 0.00 0.00 33.04 5.12
2 3 0.096454 GCCGGCTGATAAACAACGAC 59.904 55.000 22.15 0.00 33.04 4.34
115 117 2.615869 CGGAGCTGGAAGAAAGAAGAG 58.384 52.381 0.00 0.00 34.07 2.85
148 150 1.545841 GAACCAAACCCATCCAGACC 58.454 55.000 0.00 0.00 0.00 3.85
208 222 2.005451 CAAAGACGGCCATGAGAAGAG 58.995 52.381 2.24 0.00 0.00 2.85
211 225 0.036732 AGCAAAGACGGCCATGAGAA 59.963 50.000 2.24 0.00 0.00 2.87
235 249 2.188817 CCCCTAAGATAAGATCCCGGG 58.811 57.143 16.85 16.85 33.03 5.73
258 272 2.500504 ACTATGAAAACCTCTCCCCGTC 59.499 50.000 0.00 0.00 0.00 4.79
266 280 5.046231 AGGGAGAGACAACTATGAAAACCTC 60.046 44.000 0.00 0.00 0.00 3.85
268 282 5.167303 AGGGAGAGACAACTATGAAAACC 57.833 43.478 0.00 0.00 0.00 3.27
291 316 8.203485 AGAAACTGATGGCAATACAAAGAAAAA 58.797 29.630 0.00 0.00 0.00 1.94
296 321 6.017400 ACAGAAACTGATGGCAATACAAAG 57.983 37.500 5.76 0.00 35.18 2.77
297 322 6.349280 GCTACAGAAACTGATGGCAATACAAA 60.349 38.462 5.76 0.00 35.18 2.83
298 323 5.123820 GCTACAGAAACTGATGGCAATACAA 59.876 40.000 5.76 0.00 35.18 2.41
299 324 4.635765 GCTACAGAAACTGATGGCAATACA 59.364 41.667 5.76 0.00 35.18 2.29
301 326 4.199310 GGCTACAGAAACTGATGGCAATA 58.801 43.478 5.76 0.00 35.18 1.90
302 327 3.019564 GGCTACAGAAACTGATGGCAAT 58.980 45.455 5.76 0.00 35.18 3.56
303 328 2.224744 TGGCTACAGAAACTGATGGCAA 60.225 45.455 16.14 5.85 38.62 4.52
304 329 1.350684 TGGCTACAGAAACTGATGGCA 59.649 47.619 5.76 11.68 38.94 4.92
305 330 2.113860 TGGCTACAGAAACTGATGGC 57.886 50.000 5.76 9.62 35.18 4.40
306 331 4.096984 GGATTTGGCTACAGAAACTGATGG 59.903 45.833 5.76 0.00 35.18 3.51
307 332 4.701651 TGGATTTGGCTACAGAAACTGATG 59.298 41.667 5.76 0.00 35.18 3.07
308 333 4.922206 TGGATTTGGCTACAGAAACTGAT 58.078 39.130 5.76 0.00 35.18 2.90
333 358 5.587289 TCGGAAAAACTTCACCAATCAAAG 58.413 37.500 0.00 0.00 0.00 2.77
338 363 5.219633 CGAAATCGGAAAAACTTCACCAAT 58.780 37.500 0.00 0.00 35.37 3.16
359 384 1.885560 TCGAGAAAAATTGCACCCGA 58.114 45.000 0.00 0.00 0.00 5.14
380 406 3.066064 TCGAATTGCACCCGAAATAATGG 59.934 43.478 2.30 0.00 0.00 3.16
402 428 5.700402 AGGGAACTGATTGTTATAGCTGT 57.300 39.130 0.00 0.00 41.13 4.40
405 431 5.358160 AGCAAAGGGAACTGATTGTTATAGC 59.642 40.000 0.00 0.00 42.68 2.97
406 432 6.825721 AGAGCAAAGGGAACTGATTGTTATAG 59.174 38.462 0.00 0.00 42.68 1.31
418 444 1.239347 GGACACAGAGCAAAGGGAAC 58.761 55.000 0.00 0.00 0.00 3.62
421 447 1.691196 TTTGGACACAGAGCAAAGGG 58.309 50.000 0.00 0.00 0.00 3.95
461 491 8.090831 TGAAGCTCAGCAATATCGTAATAATCT 58.909 33.333 0.00 0.00 0.00 2.40
463 493 8.499162 GTTGAAGCTCAGCAATATCGTAATAAT 58.501 33.333 0.00 0.00 0.00 1.28
470 500 4.871993 AAGTTGAAGCTCAGCAATATCG 57.128 40.909 0.00 0.00 29.40 2.92
477 509 3.911661 ATCACAAAGTTGAAGCTCAGC 57.088 42.857 0.00 0.00 0.00 4.26
482 514 4.022849 ACCAGCTAATCACAAAGTTGAAGC 60.023 41.667 0.00 0.00 0.00 3.86
544 583 1.670083 ACAAGTAAACGCGGCCCTC 60.670 57.895 12.47 0.00 0.00 4.30
642 694 5.762045 GCACGTGCAAGATAATATGGAAAT 58.238 37.500 34.52 0.00 41.59 2.17
666 718 7.236529 TCACTAGGTTATGATTATCCCGTACT 58.763 38.462 0.00 0.00 0.00 2.73
748 800 5.183713 CTGGAATCCAAACTGCATAACAGAA 59.816 40.000 2.61 0.00 40.27 3.02
749 801 4.701651 CTGGAATCCAAACTGCATAACAGA 59.298 41.667 2.61 0.00 40.27 3.41
750 802 4.460382 ACTGGAATCCAAACTGCATAACAG 59.540 41.667 2.61 0.00 42.32 3.16
751 803 4.406456 ACTGGAATCCAAACTGCATAACA 58.594 39.130 2.61 0.00 30.80 2.41
752 804 6.509418 TTACTGGAATCCAAACTGCATAAC 57.491 37.500 2.61 0.00 30.80 1.89
757 809 8.825667 TTTTAAATTACTGGAATCCAAACTGC 57.174 30.769 2.61 0.00 30.80 4.40
758 810 8.925700 GCTTTTAAATTACTGGAATCCAAACTG 58.074 33.333 2.61 0.00 30.80 3.16
760 812 8.825667 TGCTTTTAAATTACTGGAATCCAAAC 57.174 30.769 2.61 0.00 30.80 2.93
772 824 9.685828 TGGACAACAGTTATGCTTTTAAATTAC 57.314 29.630 0.00 0.00 0.00 1.89
796 848 6.795399 ACACAGATCTTAAAACACAAACTGG 58.205 36.000 0.00 0.00 0.00 4.00
799 851 7.044052 GCAAGACACAGATCTTAAAACACAAAC 60.044 37.037 0.00 0.00 36.78 2.93
805 857 6.305693 ACAGCAAGACACAGATCTTAAAAC 57.694 37.500 0.00 0.00 36.78 2.43
812 864 3.059325 GTGTGAACAGCAAGACACAGATC 60.059 47.826 0.00 0.00 42.50 2.75
815 867 1.331756 GGTGTGAACAGCAAGACACAG 59.668 52.381 7.73 0.00 42.50 3.66
847 899 8.958119 ACTAACTTAGTGATTGTTGACTCAAA 57.042 30.769 0.33 0.00 37.69 2.69
928 981 8.928448 AGGCTGTCAGTCAGATAAGAATTATAA 58.072 33.333 7.30 0.00 42.35 0.98
929 982 8.363390 CAGGCTGTCAGTCAGATAAGAATTATA 58.637 37.037 7.30 0.00 42.35 0.98
931 984 6.577103 CAGGCTGTCAGTCAGATAAGAATTA 58.423 40.000 7.30 0.00 46.27 1.40
932 985 5.426504 CAGGCTGTCAGTCAGATAAGAATT 58.573 41.667 7.30 0.00 46.27 2.17
935 988 2.167281 GCAGGCTGTCAGTCAGATAAGA 59.833 50.000 17.16 0.00 46.27 2.10
937 990 2.182827 AGCAGGCTGTCAGTCAGATAA 58.817 47.619 17.16 0.00 46.27 1.75
938 991 1.857965 AGCAGGCTGTCAGTCAGATA 58.142 50.000 17.16 0.00 46.27 1.98
939 992 1.480137 GTAGCAGGCTGTCAGTCAGAT 59.520 52.381 17.16 0.00 46.27 2.90
943 996 3.742433 ATATGTAGCAGGCTGTCAGTC 57.258 47.619 17.16 0.00 0.00 3.51
992 1046 5.864418 AAAGCAGCAATCCATGTTGATAT 57.136 34.783 0.00 0.00 42.37 1.63
994 1048 5.128171 ACATAAAGCAGCAATCCATGTTGAT 59.872 36.000 0.00 0.00 42.37 2.57
1067 1121 3.514645 GACCAGGCAAATATGTGCAAAG 58.485 45.455 19.51 9.11 46.81 2.77
1133 1187 3.694566 ACCTGAGACAAAGAAACAACCAC 59.305 43.478 0.00 0.00 0.00 4.16
1135 1189 3.945285 TCACCTGAGACAAAGAAACAACC 59.055 43.478 0.00 0.00 0.00 3.77
1285 1339 1.294659 CCTTCAGGCAGTGACGAAGC 61.295 60.000 19.16 0.00 33.71 3.86
1294 1348 4.264253 TGATAATGTTGACCTTCAGGCAG 58.736 43.478 0.00 0.00 39.32 4.85
1300 1354 6.575162 AGGTGTTTGATAATGTTGACCTTC 57.425 37.500 0.00 0.00 0.00 3.46
1493 1550 1.048724 TCCTATGGGACCCTTCAGCG 61.049 60.000 13.00 1.32 36.57 5.18
1526 1583 7.080724 GTGAAAGGCTGTTTTTCTCAAGATAG 58.919 38.462 0.00 0.00 35.94 2.08
1582 1639 0.179179 GAACAGCAGAAATGCTCGGC 60.179 55.000 0.00 0.00 44.30 5.54
1624 1681 5.295292 GCACATGCAGAACATCTGTAAGTAT 59.705 40.000 8.97 0.00 45.94 2.12
1724 1781 3.181503 CCTCATGAAGAAATGCAAGTCCG 60.182 47.826 0.00 0.00 0.00 4.79
1763 1820 2.223021 CGCTTTTATGTCACGGTGGATG 60.223 50.000 8.50 0.00 0.00 3.51
1772 1829 4.455533 AGAATGTTGCTCGCTTTTATGTCA 59.544 37.500 0.00 0.00 0.00 3.58
1880 1937 1.538047 CTTACAATGTGCCTGCCACT 58.462 50.000 0.00 0.00 44.92 4.00
1906 1963 2.091555 AGGCTGTAAAAACAGGGGTTGA 60.092 45.455 7.57 0.00 37.30 3.18
1916 1973 8.154649 CAGTCTAAGAAAGAAGGCTGTAAAAA 57.845 34.615 0.00 0.00 39.95 1.94
1935 1992 9.298250 ACTAGTCAGAACAGAAAATACAGTCTA 57.702 33.333 0.00 0.00 0.00 2.59
1937 1994 9.909644 TTACTAGTCAGAACAGAAAATACAGTC 57.090 33.333 0.00 0.00 0.00 3.51
1967 2024 5.940470 GCCAAGTATCCTCTGAAAAGAAGAA 59.060 40.000 0.00 0.00 0.00 2.52
1968 2025 5.249393 AGCCAAGTATCCTCTGAAAAGAAGA 59.751 40.000 0.00 0.00 0.00 2.87
2210 2267 4.611355 CGTTTGCTCAGTCAACTTATGGTG 60.611 45.833 0.00 0.00 0.00 4.17
2221 2278 3.944422 TCTTTGAACGTTTGCTCAGTC 57.056 42.857 0.46 0.00 0.00 3.51
2243 2300 5.559417 GCAGGTTTTGTCAAATTCAGCATTG 60.559 40.000 0.00 0.00 0.00 2.82
2263 2320 3.076621 TCTGTACAAAAGATGCAGCAGG 58.923 45.455 4.07 0.00 0.00 4.85
2272 2329 3.500448 TGCCCATGTCTGTACAAAAGA 57.500 42.857 0.00 0.00 39.58 2.52
2278 2335 4.960938 TCATAGAATGCCCATGTCTGTAC 58.039 43.478 0.00 0.00 0.00 2.90
2502 2559 0.603707 CCTTGAGCTCCGCAAAGTCA 60.604 55.000 12.15 0.00 0.00 3.41
2544 2601 4.572571 TTGGACCGCGCCTGGTTT 62.573 61.111 8.45 0.00 44.01 3.27
2605 2662 2.188829 TGTGGTTCTCCGACGACGT 61.189 57.895 0.00 0.00 37.88 4.34
2662 2719 3.749088 AGGCAATGTACAAATCGAACGAA 59.251 39.130 0.00 0.00 0.00 3.85
2663 2720 3.331150 AGGCAATGTACAAATCGAACGA 58.669 40.909 0.00 0.00 0.00 3.85
2682 2739 2.417924 GCAGGCATATCTATCACCGAGG 60.418 54.545 0.00 0.00 0.00 4.63
2684 2741 2.247358 TGCAGGCATATCTATCACCGA 58.753 47.619 0.00 0.00 0.00 4.69
2685 2742 2.749280 TGCAGGCATATCTATCACCG 57.251 50.000 0.00 0.00 0.00 4.94
2758 2821 1.638589 CATTAACCCAACCCCTCCTCA 59.361 52.381 0.00 0.00 0.00 3.86
2792 2855 3.878086 ACATCGTACACAACAAGCAAG 57.122 42.857 0.00 0.00 0.00 4.01
2890 2971 2.077413 GAGCTCTCTCCAACACAGTG 57.923 55.000 6.43 0.00 33.19 3.66
2907 2988 2.125552 TGACGGCAATGCGAGGAG 60.126 61.111 0.00 0.00 0.00 3.69
2908 2989 2.125552 CTGACGGCAATGCGAGGA 60.126 61.111 0.00 0.00 0.00 3.71
2909 2990 2.125552 TCTGACGGCAATGCGAGG 60.126 61.111 0.00 0.00 0.00 4.63
2910 2991 1.016130 AAGTCTGACGGCAATGCGAG 61.016 55.000 0.00 0.00 0.00 5.03
2911 2992 1.005037 AAGTCTGACGGCAATGCGA 60.005 52.632 0.00 0.00 0.00 5.10
2912 2993 1.291184 TGAAGTCTGACGGCAATGCG 61.291 55.000 0.00 0.00 0.00 4.73
2943 3024 3.393800 CCGACCCATGTTAGTCATCATC 58.606 50.000 8.09 0.00 34.09 2.92
2953 3034 3.650950 AGCAGGCCGACCCATGTT 61.651 61.111 0.00 0.00 36.11 2.71
2984 3065 5.022282 TCGACATCATGCTTGGATTAGAA 57.978 39.130 0.00 0.00 0.00 2.10
3002 3091 1.448540 CACACCATGCCTCCTCGAC 60.449 63.158 0.00 0.00 0.00 4.20
3049 3139 4.286808 TGAGACTGGAGATGAATTTGGTCA 59.713 41.667 0.00 0.00 0.00 4.02
3067 3157 0.250338 AGCCCGTTTCAAGGTGAGAC 60.250 55.000 0.00 0.00 0.00 3.36
3131 3236 2.887568 CTCTGATGCCGACACCGC 60.888 66.667 0.00 0.00 0.00 5.68
3176 3281 1.336887 CCGTATCCCCGTAAGAGCATG 60.337 57.143 0.00 0.00 43.02 4.06
3178 3283 0.396139 ACCGTATCCCCGTAAGAGCA 60.396 55.000 0.00 0.00 43.02 4.26
3179 3284 0.313357 GACCGTATCCCCGTAAGAGC 59.687 60.000 0.00 0.00 43.02 4.09
3180 3285 1.683943 TGACCGTATCCCCGTAAGAG 58.316 55.000 0.00 0.00 43.02 2.85
3181 3286 2.026641 CTTGACCGTATCCCCGTAAGA 58.973 52.381 0.00 0.00 43.02 2.10
3182 3287 1.537562 GCTTGACCGTATCCCCGTAAG 60.538 57.143 0.00 0.00 0.00 2.34
3187 3292 1.146263 CTGGCTTGACCGTATCCCC 59.854 63.158 0.00 0.00 43.94 4.81
3203 3308 2.505777 CAGACGTGGAGCTCGCTG 60.506 66.667 7.83 6.25 0.00 5.18
3250 3363 4.068282 CTGCACTGCACACGCTCG 62.068 66.667 0.00 0.00 39.64 5.03
3251 3364 4.380628 GCTGCACTGCACACGCTC 62.381 66.667 0.00 0.00 39.64 5.03
3255 3368 3.720193 CTCGGCTGCACTGCACAC 61.720 66.667 0.00 0.00 33.79 3.82
3256 3369 2.939133 TTTCTCGGCTGCACTGCACA 62.939 55.000 0.00 0.00 33.79 4.57
3257 3370 2.180131 CTTTCTCGGCTGCACTGCAC 62.180 60.000 0.00 0.00 33.79 4.57
3258 3371 1.962822 CTTTCTCGGCTGCACTGCA 60.963 57.895 3.11 3.11 36.92 4.41
3259 3372 1.230635 TTCTTTCTCGGCTGCACTGC 61.231 55.000 0.50 0.00 0.00 4.40
3260 3373 0.795085 CTTCTTTCTCGGCTGCACTG 59.205 55.000 0.50 0.00 0.00 3.66
3261 3374 0.394565 ACTTCTTTCTCGGCTGCACT 59.605 50.000 0.50 0.00 0.00 4.40
3298 3411 5.909621 ATTGACATGGTGATTTCTGGAAG 57.090 39.130 0.00 0.00 0.00 3.46
3314 3427 0.950836 CGGCTGGTTGACAATTGACA 59.049 50.000 13.59 9.79 0.00 3.58
3315 3428 0.951558 ACGGCTGGTTGACAATTGAC 59.048 50.000 13.59 6.72 0.00 3.18
3316 3429 2.552599 TACGGCTGGTTGACAATTGA 57.447 45.000 13.59 0.00 0.00 2.57
3317 3430 2.552315 ACTTACGGCTGGTTGACAATTG 59.448 45.455 3.24 3.24 0.00 2.32
3318 3431 2.812011 GACTTACGGCTGGTTGACAATT 59.188 45.455 0.00 0.00 0.00 2.32
3319 3432 2.423577 GACTTACGGCTGGTTGACAAT 58.576 47.619 0.00 0.00 0.00 2.71
3320 3433 1.870580 CGACTTACGGCTGGTTGACAA 60.871 52.381 0.00 0.00 38.46 3.18
3359 3472 0.385473 GGTTTGACATGTTCACGCCG 60.385 55.000 0.00 0.00 32.26 6.46
3387 3500 2.593436 CGTTCAACGGGCCCAACT 60.593 61.111 24.92 1.05 38.08 3.16
3396 3509 3.047877 GACTGGGGCCGTTCAACG 61.048 66.667 1.89 1.89 42.11 4.10
3407 3520 1.442184 CGAGTTGACGACGACTGGG 60.442 63.158 12.62 1.03 40.46 4.45
3410 3523 3.242870 ACTTTAACGAGTTGACGACGACT 60.243 43.478 7.53 7.53 42.77 4.18
3411 3524 3.038710 ACTTTAACGAGTTGACGACGAC 58.961 45.455 0.00 0.00 37.03 4.34
3412 3525 3.038017 CACTTTAACGAGTTGACGACGA 58.962 45.455 0.00 0.00 37.03 4.20
3434 3547 2.598619 TTCCATCGCTCGCTGTCTCG 62.599 60.000 0.00 0.00 0.00 4.04
3473 3586 1.472480 GCTGTCTCTCACTGTCTCTCC 59.528 57.143 0.00 0.00 0.00 3.71
3474 3587 1.130373 CGCTGTCTCTCACTGTCTCTC 59.870 57.143 0.00 0.00 0.00 3.20
3475 3588 1.164411 CGCTGTCTCTCACTGTCTCT 58.836 55.000 0.00 0.00 0.00 3.10
3476 3589 1.130373 CTCGCTGTCTCTCACTGTCTC 59.870 57.143 0.00 0.00 0.00 3.36
3477 3590 1.164411 CTCGCTGTCTCTCACTGTCT 58.836 55.000 0.00 0.00 0.00 3.41
3478 3591 0.455972 GCTCGCTGTCTCTCACTGTC 60.456 60.000 0.00 0.00 0.00 3.51
3479 3592 1.583986 GCTCGCTGTCTCTCACTGT 59.416 57.895 0.00 0.00 0.00 3.55
3480 3593 1.513800 CGCTCGCTGTCTCTCACTG 60.514 63.158 0.00 0.00 0.00 3.66
3481 3594 1.029408 ATCGCTCGCTGTCTCTCACT 61.029 55.000 0.00 0.00 0.00 3.41
3482 3595 0.591236 GATCGCTCGCTGTCTCTCAC 60.591 60.000 0.00 0.00 0.00 3.51
3483 3596 1.724467 GATCGCTCGCTGTCTCTCA 59.276 57.895 0.00 0.00 0.00 3.27
3512 3625 4.301505 TGAGAATCACCGGCTTGC 57.698 55.556 0.00 0.00 42.56 4.01
3612 3730 3.940852 GGATCAATTTGGTCCATTTTGGC 59.059 43.478 21.46 6.86 46.88 4.52


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

AutoCloner maintained by Alex Coulton.