Multiple sequence alignment - TraesCS5B01G307400

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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 TraesCS5B01G307400 chr5B 100.000 3923 0 0 1 3923 490742256 490746178 0.000000e+00 7245.0
1 TraesCS5B01G307400 chr5B 91.255 526 43 3 1055 1580 108841819 108841297 0.000000e+00 713.0
2 TraesCS5B01G307400 chr5B 78.027 223 35 8 716 925 597297158 597297379 1.140000e-25 128.0
3 TraesCS5B01G307400 chr5B 71.429 441 102 20 149 577 517780280 517779852 1.160000e-15 95.3
4 TraesCS5B01G307400 chr5A 93.170 3265 160 25 678 3913 519887198 519890428 0.000000e+00 4735.0
5 TraesCS5B01G307400 chr5A 76.033 242 36 21 677 906 631755995 631755764 5.360000e-19 106.0
6 TraesCS5B01G307400 chr5A 79.070 129 26 1 450 577 43251112 43251240 1.940000e-13 87.9
7 TraesCS5B01G307400 chr5A 77.953 127 13 11 677 799 345198307 345198422 9.100000e-07 65.8
8 TraesCS5B01G307400 chr5D 93.876 1388 52 14 678 2048 408793239 408794610 0.000000e+00 2061.0
9 TraesCS5B01G307400 chr7D 97.305 668 17 1 1 668 10976818 10976152 0.000000e+00 1133.0
10 TraesCS5B01G307400 chr2A 94.369 515 27 2 158 671 707990058 707990571 0.000000e+00 789.0
11 TraesCS5B01G307400 chr1D 91.969 523 40 2 1055 1577 418714243 418714763 0.000000e+00 732.0
12 TraesCS5B01G307400 chr3B 96.386 166 5 1 502 667 10217977 10217813 4.990000e-69 272.0
13 TraesCS5B01G307400 chr3B 82.400 125 14 5 678 796 572756906 572757028 6.930000e-18 102.0
14 TraesCS5B01G307400 chr7B 84.211 95 15 0 483 577 465593867 465593773 4.170000e-15 93.5
15 TraesCS5B01G307400 chr7B 100.000 29 0 0 682 710 200636564 200636592 2.000000e-03 54.7
16 TraesCS5B01G307400 chr3D 75.556 180 34 9 678 855 603263266 603263437 3.250000e-11 80.5
17 TraesCS5B01G307400 chrUn 77.236 123 15 9 681 798 101816346 101816460 4.230000e-05 60.2
18 TraesCS5B01G307400 chrUn 100.000 29 0 0 682 710 349254410 349254438 2.000000e-03 54.7
19 TraesCS5B01G307400 chr4B 85.246 61 2 7 682 737 141092349 141092291 5.480000e-04 56.5
20 TraesCS5B01G307400 chr2B 100.000 29 0 0 682 710 341259042 341259070 2.000000e-03 54.7
21 TraesCS5B01G307400 chr1B 94.444 36 1 1 682 717 319993206 319993172 2.000000e-03 54.7


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 TraesCS5B01G307400 chr5B 490742256 490746178 3922 False 7245 7245 100.000 1 3923 1 chr5B.!!$F1 3922
1 TraesCS5B01G307400 chr5B 108841297 108841819 522 True 713 713 91.255 1055 1580 1 chr5B.!!$R1 525
2 TraesCS5B01G307400 chr5A 519887198 519890428 3230 False 4735 4735 93.170 678 3913 1 chr5A.!!$F3 3235
3 TraesCS5B01G307400 chr5D 408793239 408794610 1371 False 2061 2061 93.876 678 2048 1 chr5D.!!$F1 1370
4 TraesCS5B01G307400 chr7D 10976152 10976818 666 True 1133 1133 97.305 1 668 1 chr7D.!!$R1 667
5 TraesCS5B01G307400 chr2A 707990058 707990571 513 False 789 789 94.369 158 671 1 chr2A.!!$F1 513
6 TraesCS5B01G307400 chr1D 418714243 418714763 520 False 732 732 91.969 1055 1577 1 chr1D.!!$F1 522

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
236 237 0.397114 GGGGGCCGGAATGATTCTTT 60.397 55.0 5.05 0.0 0.00 2.52 F
1635 1666 0.250124 TGTTCAACGAGATGCGGGTT 60.250 50.0 0.00 0.0 46.49 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1846 0.173708 ACTCGAAGATCTTGACGGCC 59.826 55.0 14.00 0.0 33.89 6.13 R
3080 3111 0.032952 TCAGTGCGTTCTAGGCGTTT 59.967 50.0 8.84 0.0 0.00 3.60 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
36 37 5.608437 TCAGATTCCTTCAAGGCTATATGGT 59.392 40.000 0.00 0.00 34.61 3.55
57 58 4.580580 GGTGTCCCTTCTGGCTATTAAATG 59.419 45.833 0.00 0.00 0.00 2.32
83 84 7.466996 GCAACACTCATATTGATCCAGAGAAAG 60.467 40.741 0.00 0.00 0.00 2.62
103 104 7.059156 AGAAAGGGAAATCATACATCTCCTTG 58.941 38.462 0.00 0.00 34.10 3.61
116 117 0.914417 CTCCTTGGCCCCTGGTAGAA 60.914 60.000 0.00 0.00 0.00 2.10
119 120 0.914417 CTTGGCCCCTGGTAGAAGGA 60.914 60.000 0.00 0.00 40.02 3.36
179 180 4.972568 AACCAAAGGAAGGTTGGGTAAAAT 59.027 37.500 8.01 0.00 44.44 1.82
236 237 0.397114 GGGGGCCGGAATGATTCTTT 60.397 55.000 5.05 0.00 0.00 2.52
246 247 6.365839 CCGGAATGATTCTTTGTAATGATCG 58.634 40.000 0.00 0.00 0.00 3.69
286 287 1.355916 GTGTAGGGCGCTCTACTCG 59.644 63.158 39.16 0.00 40.05 4.18
301 302 3.356639 CTCGTGCAGGGAAGCGCTA 62.357 63.158 12.05 0.00 42.62 4.26
395 396 1.595655 TTGGACGCGCAAGTTGCTA 60.596 52.632 24.61 2.50 42.25 3.49
422 423 7.950124 TGTCTATGATCATATGTGAGGGAACTA 59.050 37.037 15.71 0.00 44.43 2.24
625 627 4.318332 TCTCGCATGATGATTGTAATCCC 58.682 43.478 0.00 0.00 34.50 3.85
662 664 9.569122 AGTAATACAAGTATTTATCCCGCAAAT 57.431 29.630 10.41 0.00 37.07 2.32
786 788 6.899393 ATTTTCTTTGCCATGACTTCTACA 57.101 33.333 0.00 0.00 0.00 2.74
799 801 8.464404 CCATGACTTCTACAAATGTCATTTCAT 58.536 33.333 7.87 3.95 44.62 2.57
813 823 6.215121 TGTCATTTCATTTTACAGGCACTTG 58.785 36.000 0.00 0.00 34.60 3.16
817 827 7.984050 TCATTTCATTTTACAGGCACTTGAAAA 59.016 29.630 0.00 0.00 39.87 2.29
897 915 8.668510 ATTTTACTATTCATCACGAGCTCAAT 57.331 30.769 15.40 7.21 0.00 2.57
940 958 7.596995 AGATGACTTTCGAGAAAAACTCACTAG 59.403 37.037 0.00 0.00 45.14 2.57
942 960 6.696148 TGACTTTCGAGAAAAACTCACTAGTC 59.304 38.462 0.00 0.00 45.14 2.59
951 970 2.949451 ACTCACTAGTCCATTCAGCG 57.051 50.000 0.00 0.00 0.00 5.18
1261 1292 4.069232 CGCTGGACGCCTTCTCCA 62.069 66.667 0.00 0.00 36.34 3.86
1635 1666 0.250124 TGTTCAACGAGATGCGGGTT 60.250 50.000 0.00 0.00 46.49 4.11
1638 1669 0.672401 TCAACGAGATGCGGGTTTCC 60.672 55.000 0.00 0.00 46.49 3.13
1674 1705 4.759564 GCAACGCTCTGCATTCTG 57.240 55.556 2.28 0.00 42.17 3.02
1815 1846 5.519566 CAGTAAGTTCAGCTTGCTAGATCAG 59.480 44.000 0.00 0.00 46.14 2.90
1992 2023 2.024414 GGTTTTGCGAGGAATGGCTAT 58.976 47.619 0.00 0.00 0.00 2.97
2035 2066 2.049888 TGTCAAGATGTTGGCACACA 57.950 45.000 5.67 0.00 43.47 3.72
2067 2098 3.088532 TCCCGATGATTTCACTTTTGGG 58.911 45.455 0.17 0.17 35.40 4.12
2070 2101 2.417243 CGATGATTTCACTTTTGGGGCC 60.417 50.000 0.00 0.00 0.00 5.80
2085 2116 2.629656 GGCCGTGCTTCATGCTTGT 61.630 57.895 0.00 0.00 43.37 3.16
2108 2139 2.818714 CGCTGCTTCTCTGGCCAG 60.819 66.667 27.87 27.87 0.00 4.85
2190 2221 3.127548 CCAACAGCTTGATGGACATGTAC 59.872 47.826 0.00 0.00 42.23 2.90
2213 2244 3.188786 GTGTGGCGATGTCGAGGC 61.189 66.667 6.60 0.00 43.02 4.70
2236 2267 0.542467 AGGCAATGTGTTCCATGCCA 60.542 50.000 17.00 0.00 43.98 4.92
2244 2275 2.821378 TGTGTTCCATGCCATTCTTCAG 59.179 45.455 0.00 0.00 0.00 3.02
2314 2345 2.765699 GGATGGGCAAAGGAAGCATTTA 59.234 45.455 0.00 0.00 0.00 1.40
2316 2347 2.888212 TGGGCAAAGGAAGCATTTACT 58.112 42.857 0.00 0.00 0.00 2.24
2317 2348 2.562298 TGGGCAAAGGAAGCATTTACTG 59.438 45.455 0.00 0.00 0.00 2.74
2332 2363 6.886459 AGCATTTACTGTGTATGAAAGGATGT 59.114 34.615 7.79 0.00 0.00 3.06
2352 2383 1.303317 GTCCCACGATGTTTGCCCT 60.303 57.895 0.00 0.00 0.00 5.19
2374 2405 0.531974 TGAAGTCACGTTCACAGGCC 60.532 55.000 0.00 0.00 31.31 5.19
2400 2431 3.145551 GCCTGCAGCCATTCTGGG 61.146 66.667 8.66 0.00 43.06 4.45
2463 2494 0.770499 TCCATGGACTGAAGCCAACA 59.230 50.000 11.44 0.00 39.21 3.33
2473 2504 0.807496 GAAGCCAACACCAGAGCATC 59.193 55.000 0.00 0.00 0.00 3.91
2505 2536 6.385033 CATTCTCGACATGTATGCTAGATCA 58.615 40.000 0.00 0.00 0.00 2.92
2508 2539 4.145052 TCGACATGTATGCTAGATCAGGT 58.855 43.478 0.00 0.00 0.00 4.00
2514 2545 7.739825 ACATGTATGCTAGATCAGGTAACATT 58.260 34.615 0.00 0.00 41.41 2.71
2538 2569 1.760192 AAGCCATTGAGATGCTGGAC 58.240 50.000 0.00 0.00 31.38 4.02
2550 2581 3.776969 AGATGCTGGACCAATACTCTGAA 59.223 43.478 0.00 0.00 0.00 3.02
2553 2584 3.072330 TGCTGGACCAATACTCTGAAACA 59.928 43.478 0.00 0.00 0.00 2.83
2611 2642 3.868077 GCTTAGTGCCTACTCATCAGTTG 59.132 47.826 0.00 0.00 38.36 3.16
2620 2651 1.273606 ACTCATCAGTTGACCTGGACG 59.726 52.381 0.00 0.00 41.83 4.79
2649 2680 1.151810 AAGGAAGGTGGGGAGCAGA 60.152 57.895 0.00 0.00 0.00 4.26
2691 2722 1.552337 AGAGACACTGGCTATGTGGTG 59.448 52.381 9.71 0.00 39.52 4.17
2718 2749 2.124529 TTGTTGTGCGCCACTGGA 60.125 55.556 4.18 0.00 35.11 3.86
2733 2764 0.322008 CTGGACAGTGGAAGGAAGCC 60.322 60.000 0.00 0.00 0.00 4.35
2745 2776 2.683933 GAAGCCGAGGGGGTGAGA 60.684 66.667 0.00 0.00 45.20 3.27
2748 2779 3.787001 GCCGAGGGGGTGAGAAGG 61.787 72.222 0.00 0.00 38.44 3.46
2799 2830 0.179062 CTGGCTGTAGCTGGATCCAC 60.179 60.000 11.44 8.29 41.70 4.02
2854 2885 2.295885 GGCAGGAACTTGATCCATCAG 58.704 52.381 0.00 0.00 42.27 2.90
2895 2926 7.372714 TCATTCAGTTGTTGGATGAAGAAATG 58.627 34.615 0.00 0.00 46.59 2.32
2905 2936 9.958180 TGTTGGATGAAGAAATGAGAAATACTA 57.042 29.630 0.00 0.00 0.00 1.82
2955 2986 2.775856 TTTTGCGCGGCACCTTTGA 61.776 52.632 8.83 0.00 38.71 2.69
2965 2996 1.270550 GGCACCTTTGATGTGTGGAAG 59.729 52.381 0.00 0.00 36.11 3.46
3005 3036 7.452501 ACATATTGGTTAGCCATGCTCAAATAT 59.547 33.333 0.00 0.00 45.56 1.28
3012 3043 5.130292 AGCCATGCTCAAATATTACATGC 57.870 39.130 12.03 5.79 37.41 4.06
3035 3066 4.508124 CAGGAATTGCCGTAGTAAGATGAC 59.492 45.833 0.00 0.00 43.43 3.06
3040 3071 0.317603 CCGTAGTAAGATGACCGGCG 60.318 60.000 0.00 0.00 0.00 6.46
3044 3075 1.227556 GTAAGATGACCGGCGGCAT 60.228 57.895 28.71 28.04 0.00 4.40
3071 3102 4.115516 TCGAAGATGATTAGAACAGCAGC 58.884 43.478 0.00 0.00 0.00 5.25
3080 3111 5.238432 TGATTAGAACAGCAGCGAAAAGAAA 59.762 36.000 0.00 0.00 0.00 2.52
3093 3124 3.898361 CGAAAAGAAAAACGCCTAGAACG 59.102 43.478 0.00 0.00 0.00 3.95
3101 3132 0.388649 ACGCCTAGAACGCACTGAAG 60.389 55.000 5.20 0.00 0.00 3.02
3140 3171 2.248431 GCTGAAACACACGGCGTC 59.752 61.111 10.85 0.00 0.00 5.19
3144 3175 0.102663 TGAAACACACGGCGTCTACA 59.897 50.000 10.85 2.05 0.00 2.74
3163 3194 7.042725 CGTCTACACTGAAAAGATTGAAGAACA 60.043 37.037 0.00 0.00 0.00 3.18
3214 3245 6.649557 GGATATATTTTCTGTCCTTACGGGTG 59.350 42.308 0.00 0.00 36.25 4.61
3223 3254 2.169769 GTCCTTACGGGTGATCCAATGA 59.830 50.000 0.00 0.00 36.25 2.57
3279 3310 2.560105 GTCAGCAGCCAAAAAGGAGATT 59.440 45.455 0.00 0.00 41.22 2.40
3280 3311 3.006217 GTCAGCAGCCAAAAAGGAGATTT 59.994 43.478 0.00 0.00 41.22 2.17
3292 3323 5.956068 AAAGGAGATTTTCTTCTCAGTGC 57.044 39.130 4.07 0.00 43.28 4.40
3293 3324 4.906747 AGGAGATTTTCTTCTCAGTGCT 57.093 40.909 4.07 0.00 43.28 4.40
3294 3325 4.831107 AGGAGATTTTCTTCTCAGTGCTC 58.169 43.478 4.07 0.00 43.28 4.26
3295 3326 4.285517 AGGAGATTTTCTTCTCAGTGCTCA 59.714 41.667 4.07 0.00 43.28 4.26
3296 3327 4.999950 GGAGATTTTCTTCTCAGTGCTCAA 59.000 41.667 4.07 0.00 43.28 3.02
3297 3328 5.471456 GGAGATTTTCTTCTCAGTGCTCAAA 59.529 40.000 4.07 0.00 43.28 2.69
3298 3329 6.016777 GGAGATTTTCTTCTCAGTGCTCAAAA 60.017 38.462 4.07 0.00 43.28 2.44
3324 3355 5.048504 TCAAAAGACATCCATTGCAAGTCTC 60.049 40.000 16.05 1.22 38.51 3.36
3390 3421 0.028902 GTGTGTTGCTGGAAACCGAC 59.971 55.000 0.00 0.00 0.00 4.79
3399 3430 0.471211 TGGAAACCGACTCTCCTGGT 60.471 55.000 0.00 0.00 37.68 4.00
3412 3443 0.827507 TCCTGGTCTGGGCAAAAAGC 60.828 55.000 0.00 0.00 44.65 3.51
3444 3475 0.318699 TTCCTTCGTCGCTGACACAG 60.319 55.000 8.91 0.00 32.09 3.66
3469 3500 3.120304 GTTGCAAACGTGGAAGGATACTC 60.120 47.826 0.00 0.00 42.68 2.59
3496 3527 3.496160 GCCGGCCCCTATATGTATTATGG 60.496 52.174 18.11 0.00 0.00 2.74
3504 3535 9.774413 GCCCCTATATGTATTATGGTATTGTAC 57.226 37.037 0.00 0.00 0.00 2.90
3536 3567 9.461312 AGTCTATTTATCATTGTTTGGCTACAA 57.539 29.630 7.92 7.92 41.81 2.41
3571 3602 5.300752 CAGTTTTGGAGCGATATAGGACAT 58.699 41.667 0.00 0.00 0.00 3.06
3575 3606 1.202582 GGAGCGATATAGGACATGCGT 59.797 52.381 0.00 0.00 0.00 5.24
3597 3628 2.796651 GATGCGGGCTTGCTCTTG 59.203 61.111 4.09 0.00 35.36 3.02
3598 3629 3.407046 GATGCGGGCTTGCTCTTGC 62.407 63.158 4.09 0.00 40.20 4.01
3601 3632 2.564975 CGGGCTTGCTCTTGCTTG 59.435 61.111 0.00 0.00 40.48 4.01
3602 3633 2.968206 GGGCTTGCTCTTGCTTGG 59.032 61.111 0.00 0.00 40.48 3.61
3614 3645 1.628846 CTTGCTTGGGGGTAGTAGTGT 59.371 52.381 0.00 0.00 0.00 3.55
3621 3652 4.063851 TGGGGGTAGTAGTGTTATGTGA 57.936 45.455 0.00 0.00 0.00 3.58
3637 3669 6.477688 TGTTATGTGAGCGTTTTATACTAGCC 59.522 38.462 0.00 0.00 0.00 3.93
3642 3674 5.047847 TGAGCGTTTTATACTAGCCATGTC 58.952 41.667 0.00 0.00 0.00 3.06
3643 3675 5.018539 AGCGTTTTATACTAGCCATGTCA 57.981 39.130 0.00 0.00 0.00 3.58
3645 3677 5.047847 GCGTTTTATACTAGCCATGTCAGA 58.952 41.667 0.00 0.00 0.00 3.27
3647 3679 6.504398 CGTTTTATACTAGCCATGTCAGAGA 58.496 40.000 0.00 0.00 0.00 3.10
3649 3681 7.115520 CGTTTTATACTAGCCATGTCAGAGATG 59.884 40.741 0.24 0.24 0.00 2.90
3650 3682 6.596309 TTATACTAGCCATGTCAGAGATGG 57.404 41.667 20.37 20.37 43.01 3.51
3651 3683 3.037851 ACTAGCCATGTCAGAGATGGA 57.962 47.619 27.30 8.98 42.81 3.41
3652 3684 3.585360 ACTAGCCATGTCAGAGATGGAT 58.415 45.455 27.30 23.85 42.81 3.41
3654 3686 3.947612 AGCCATGTCAGAGATGGATTT 57.052 42.857 27.30 10.92 42.81 2.17
3655 3687 3.552875 AGCCATGTCAGAGATGGATTTG 58.447 45.455 27.30 3.88 42.81 2.32
3656 3688 3.053842 AGCCATGTCAGAGATGGATTTGT 60.054 43.478 27.30 5.59 42.81 2.83
3657 3689 3.066342 GCCATGTCAGAGATGGATTTGTG 59.934 47.826 27.30 2.54 42.81 3.33
3658 3690 4.267536 CCATGTCAGAGATGGATTTGTGT 58.732 43.478 20.08 0.00 42.81 3.72
3659 3691 5.430886 CCATGTCAGAGATGGATTTGTGTA 58.569 41.667 20.08 0.00 42.81 2.90
3660 3692 5.882000 CCATGTCAGAGATGGATTTGTGTAA 59.118 40.000 20.08 0.00 42.81 2.41
3661 3693 6.375174 CCATGTCAGAGATGGATTTGTGTAAA 59.625 38.462 20.08 0.00 42.81 2.01
3662 3694 7.067859 CCATGTCAGAGATGGATTTGTGTAAAT 59.932 37.037 20.08 0.00 42.81 1.40
3706 3738 1.639298 GCTTGTCGGTGTGCCAGATC 61.639 60.000 0.00 0.00 34.09 2.75
3707 3739 1.003839 TTGTCGGTGTGCCAGATCC 60.004 57.895 0.00 0.00 34.09 3.36
3708 3740 1.763546 TTGTCGGTGTGCCAGATCCA 61.764 55.000 0.00 0.00 34.09 3.41
3731 3769 7.898636 TCCATTTTGTAAGGATTAAACCCATCT 59.101 33.333 0.00 0.00 28.70 2.90
3738 3776 2.358195 GGATTAAACCCATCTGGCCTGT 60.358 50.000 3.32 0.00 37.83 4.00
3779 3817 7.286775 TCATGCCCTAAAAGGTGTAATTATTCC 59.713 37.037 0.00 0.00 31.93 3.01
3781 3819 7.874252 TGCCCTAAAAGGTGTAATTATTCCTA 58.126 34.615 10.45 0.00 31.93 2.94
3783 3821 8.215736 GCCCTAAAAGGTGTAATTATTCCTAGA 58.784 37.037 10.45 1.86 31.93 2.43
3787 3825 7.427989 AAAGGTGTAATTATTCCTAGACGGA 57.572 36.000 10.45 0.00 41.06 4.69
3796 3834 1.464734 TCCTAGACGGAGAAGCACTG 58.535 55.000 0.00 0.00 36.69 3.66
3800 3838 0.605589 AGACGGAGAAGCACTGAAGG 59.394 55.000 0.00 0.00 0.00 3.46
3827 3865 7.890127 TGATGAATTATTCTTTCAGTGGAAGGT 59.110 33.333 11.39 3.59 36.60 3.50
3851 3889 2.554806 TTACCGTCGATAGTGCACTG 57.445 50.000 29.57 13.02 37.40 3.66
3856 3894 1.914051 CGTCGATAGTGCACTGTCTTG 59.086 52.381 32.42 21.82 32.72 3.02
3860 3898 4.559251 GTCGATAGTGCACTGTCTTGTAAG 59.441 45.833 32.42 20.04 32.72 2.34
3861 3899 4.457949 TCGATAGTGCACTGTCTTGTAAGA 59.542 41.667 32.42 21.62 32.72 2.10
3863 3901 5.287274 CGATAGTGCACTGTCTTGTAAGAAG 59.713 44.000 32.42 15.63 36.68 2.85
3865 3903 5.220710 AGTGCACTGTCTTGTAAGAAGAT 57.779 39.130 20.97 0.00 36.68 2.40
3868 3906 7.217200 AGTGCACTGTCTTGTAAGAAGATTTA 58.783 34.615 20.97 0.00 36.68 1.40
3869 3907 7.880195 AGTGCACTGTCTTGTAAGAAGATTTAT 59.120 33.333 20.97 0.00 36.68 1.40
3870 3908 7.959651 GTGCACTGTCTTGTAAGAAGATTTATG 59.040 37.037 10.32 0.00 36.68 1.90
3871 3909 7.661437 TGCACTGTCTTGTAAGAAGATTTATGT 59.339 33.333 0.00 0.00 36.68 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.207165 GCATTTAATAGCCAGAAGGGACA 58.793 43.478 0.00 0.00 40.01 4.02
57 58 5.363101 TCTCTGGATCAATATGAGTGTTGC 58.637 41.667 0.00 0.00 0.00 4.17
83 84 3.823304 GCCAAGGAGATGTATGATTTCCC 59.177 47.826 0.00 0.00 0.00 3.97
103 104 0.256177 CTTTCCTTCTACCAGGGGCC 59.744 60.000 0.00 0.00 34.24 5.80
116 117 0.251832 TCGGTGCTCCTCTCTTTCCT 60.252 55.000 2.85 0.00 0.00 3.36
119 120 0.321996 GGTTCGGTGCTCCTCTCTTT 59.678 55.000 2.85 0.00 0.00 2.52
153 154 2.503765 ACCCAACCTTCCTTTGGTTTTG 59.496 45.455 0.00 0.00 44.54 2.44
179 180 6.176896 TCACAAAAGATCCATCCGTATTCAA 58.823 36.000 0.00 0.00 0.00 2.69
236 237 3.844640 TGATCTCCCCTCGATCATTACA 58.155 45.455 0.00 0.00 41.55 2.41
246 247 2.299867 GCTGAGAAGATGATCTCCCCTC 59.700 54.545 0.00 4.21 44.27 4.30
286 287 1.520342 CTCTAGCGCTTCCCTGCAC 60.520 63.158 18.68 0.00 0.00 4.57
301 302 0.833287 ATGCACATAACTCCGCCTCT 59.167 50.000 0.00 0.00 0.00 3.69
395 396 7.457218 AGTTCCCTCACATATGATCATAGACAT 59.543 37.037 19.73 2.37 33.22 3.06
422 423 2.880890 GGGCTGCATAAACAGATCGATT 59.119 45.455 0.00 0.00 40.25 3.34
550 552 3.375699 CCAGGTCATAGTTCTACCCTGT 58.624 50.000 14.90 0.00 38.20 4.00
673 675 8.735692 ACTTCCACAAATGTCATTTCATTTTT 57.264 26.923 7.87 0.00 42.88 1.94
674 676 7.986320 TGACTTCCACAAATGTCATTTCATTTT 59.014 29.630 7.87 0.00 42.88 1.82
675 677 7.499292 TGACTTCCACAAATGTCATTTCATTT 58.501 30.769 7.87 0.00 45.23 2.32
676 678 7.053316 TGACTTCCACAAATGTCATTTCATT 57.947 32.000 7.87 0.00 39.35 2.57
680 682 5.539574 TCCATGACTTCCACAAATGTCATTT 59.460 36.000 4.91 4.91 44.62 2.32
719 721 8.202745 TGCTTTCGAAAAATAACATTTTTGGT 57.797 26.923 12.41 0.00 35.35 3.67
799 801 5.233263 GCGAATTTTTCAAGTGCCTGTAAAA 59.767 36.000 0.00 0.00 32.41 1.52
813 823 4.039032 TGACGAACTTTGGCGAATTTTTC 58.961 39.130 0.00 0.00 0.00 2.29
817 827 1.944024 TGTGACGAACTTTGGCGAATT 59.056 42.857 0.00 0.00 0.00 2.17
940 958 3.869272 CGCTGGCGCTGAATGGAC 61.869 66.667 7.64 0.00 0.00 4.02
942 960 3.570638 CTCGCTGGCGCTGAATGG 61.571 66.667 7.64 0.00 39.59 3.16
992 1011 2.101415 GGGTTTAGGCTCATCAAATGGC 59.899 50.000 0.00 0.00 0.00 4.40
1261 1292 4.521062 GGAGAGCGCTGCGGTGAT 62.521 66.667 32.29 19.36 37.83 3.06
1635 1666 3.450507 TCGCAAGACAGTCCGGAA 58.549 55.556 5.23 0.00 45.01 4.30
1674 1705 2.506217 TCCGTGCAAGCGTCGATC 60.506 61.111 0.00 0.00 0.00 3.69
1815 1846 0.173708 ACTCGAAGATCTTGACGGCC 59.826 55.000 14.00 0.00 33.89 6.13
1992 2023 2.044650 GCAAGGGCCTCATCTGCA 60.045 61.111 20.34 0.00 0.00 4.41
2108 2139 1.144503 AGGCATGGATCATCCTTCCAC 59.855 52.381 4.96 0.00 45.71 4.02
2213 2244 2.343506 TGGAACACATTGCCTGCAG 58.656 52.632 6.78 6.78 0.00 4.41
2244 2275 3.259374 TGTTCCATGAGACAGAGTCCTTC 59.741 47.826 0.00 0.00 32.18 3.46
2314 2345 5.003804 GGACAACATCCTTTCATACACAGT 58.996 41.667 0.00 0.00 45.22 3.55
2332 2363 1.175983 GGGCAAACATCGTGGGACAA 61.176 55.000 0.00 0.00 44.16 3.18
2352 2383 2.754472 CCTGTGAACGTGACTTCATCA 58.246 47.619 0.00 0.00 32.78 3.07
2423 2454 3.997021 GACAGACACCATCGACTCAAAAT 59.003 43.478 0.00 0.00 0.00 1.82
2473 2504 3.193263 ACATGTCGAGAATGCAAGCTAG 58.807 45.455 7.73 0.00 0.00 3.42
2538 2569 6.455646 GCGTATGAACTGTTTCAGAGTATTGG 60.456 42.308 3.70 0.00 45.07 3.16
2550 2581 2.609459 GCTGCTATGCGTATGAACTGTT 59.391 45.455 0.00 0.00 0.00 3.16
2579 2610 2.659740 GCACTAAGCAGAGACTCGC 58.340 57.895 10.17 10.17 44.79 5.03
2611 2642 1.084370 CCGATTCTTGCGTCCAGGTC 61.084 60.000 0.00 0.00 0.00 3.85
2620 2651 1.740025 CACCTTCCTTCCGATTCTTGC 59.260 52.381 0.00 0.00 0.00 4.01
2649 2680 0.606401 CAGGCTCCGTTGACACCATT 60.606 55.000 0.00 0.00 0.00 3.16
2658 2689 0.827925 TGTCTCTCACAGGCTCCGTT 60.828 55.000 0.00 0.00 0.00 4.44
2679 2710 1.299648 GGACAGCACCACATAGCCA 59.700 57.895 0.00 0.00 0.00 4.75
2691 2722 0.592247 CGCACAACAAGTTGGACAGC 60.592 55.000 16.45 12.75 44.45 4.40
2718 2749 1.674057 CTCGGCTTCCTTCCACTGT 59.326 57.895 0.00 0.00 0.00 3.55
2730 2761 2.685380 CTTCTCACCCCCTCGGCT 60.685 66.667 0.00 0.00 33.26 5.52
2733 2764 3.787001 GCCCTTCTCACCCCCTCG 61.787 72.222 0.00 0.00 0.00 4.63
2745 2776 3.005148 ATGCTCTGCCATGGCCCTT 62.005 57.895 33.44 14.01 41.09 3.95
2799 2830 1.021390 CCTTAGCAGCACCCTTCACG 61.021 60.000 0.00 0.00 0.00 4.35
2895 2926 4.494199 GCACCGCAACACATAGTATTTCTC 60.494 45.833 0.00 0.00 0.00 2.87
2905 2936 4.916983 ATAATTATGCACCGCAACACAT 57.083 36.364 0.00 0.00 43.62 3.21
2955 2986 4.897509 TTCTCTGATGACTTCCACACAT 57.102 40.909 0.00 0.00 0.00 3.21
2965 2996 7.798596 AACCAATATGTGATTCTCTGATGAC 57.201 36.000 0.00 0.00 0.00 3.06
3012 3043 4.508124 GTCATCTTACTACGGCAATTCCTG 59.492 45.833 0.00 0.00 0.00 3.86
3035 3066 2.378945 CTTCGATTTCATGCCGCCGG 62.379 60.000 0.00 0.00 0.00 6.13
3040 3071 6.791887 TCTAATCATCTTCGATTTCATGCC 57.208 37.500 0.00 0.00 36.92 4.40
3044 3075 6.818142 TGCTGTTCTAATCATCTTCGATTTCA 59.182 34.615 0.00 0.00 36.92 2.69
3071 3102 3.898361 CGTTCTAGGCGTTTTTCTTTTCG 59.102 43.478 0.00 0.00 0.00 3.46
3080 3111 0.032952 TCAGTGCGTTCTAGGCGTTT 59.967 50.000 8.84 0.00 0.00 3.60
3140 3171 7.065894 CGTGTTCTTCAATCTTTTCAGTGTAG 58.934 38.462 0.00 0.00 0.00 2.74
3144 3175 5.220854 CCACGTGTTCTTCAATCTTTTCAGT 60.221 40.000 15.65 0.00 0.00 3.41
3163 3194 4.945543 AGTCTTTTAAACTGGAAACCACGT 59.054 37.500 0.00 0.00 0.00 4.49
3209 3240 3.832490 TCCTATACTCATTGGATCACCCG 59.168 47.826 0.00 0.00 37.93 5.28
3214 3245 5.221461 ACGGTTGTCCTATACTCATTGGATC 60.221 44.000 0.00 0.00 38.18 3.36
3223 3254 4.592942 TGACACTACGGTTGTCCTATACT 58.407 43.478 9.75 0.00 0.00 2.12
3279 3310 5.185454 TGAGTTTTGAGCACTGAGAAGAAA 58.815 37.500 0.00 0.00 0.00 2.52
3280 3311 4.769688 TGAGTTTTGAGCACTGAGAAGAA 58.230 39.130 0.00 0.00 0.00 2.52
3292 3323 6.145048 GCAATGGATGTCTTTTGAGTTTTGAG 59.855 38.462 0.00 0.00 0.00 3.02
3293 3324 5.984926 GCAATGGATGTCTTTTGAGTTTTGA 59.015 36.000 0.00 0.00 0.00 2.69
3294 3325 5.754406 TGCAATGGATGTCTTTTGAGTTTTG 59.246 36.000 0.00 0.00 0.00 2.44
3295 3326 5.916318 TGCAATGGATGTCTTTTGAGTTTT 58.084 33.333 0.00 0.00 0.00 2.43
3296 3327 5.534207 TGCAATGGATGTCTTTTGAGTTT 57.466 34.783 0.00 0.00 0.00 2.66
3297 3328 5.069516 ACTTGCAATGGATGTCTTTTGAGTT 59.930 36.000 0.00 0.00 0.00 3.01
3298 3329 4.586001 ACTTGCAATGGATGTCTTTTGAGT 59.414 37.500 0.00 0.00 0.00 3.41
3390 3421 0.401738 TTTTGCCCAGACCAGGAGAG 59.598 55.000 0.00 0.00 0.00 3.20
3399 3430 0.820871 AACGTTGCTTTTTGCCCAGA 59.179 45.000 0.00 0.00 42.00 3.86
3412 3443 0.234884 GAAGGAAGCACCGAACGTTG 59.765 55.000 5.00 0.00 44.74 4.10
3419 3450 3.479269 GCGACGAAGGAAGCACCG 61.479 66.667 0.00 0.00 44.74 4.94
3444 3475 0.310854 CCTTCCACGTTTGCAACTCC 59.689 55.000 0.00 0.00 0.00 3.85
3458 3489 2.222027 CCGGCAAATGAGTATCCTTCC 58.778 52.381 0.00 0.00 0.00 3.46
3469 3500 1.176527 CATATAGGGGCCGGCAAATG 58.823 55.000 30.85 16.74 0.00 2.32
3475 3506 3.714798 ACCATAATACATATAGGGGCCGG 59.285 47.826 0.00 0.00 0.00 6.13
3519 3550 6.403866 TCAAAGTTGTAGCCAAACAATGAT 57.596 33.333 0.83 0.00 41.18 2.45
3536 3567 4.082125 CTCCAAAACTGCCCTATCAAAGT 58.918 43.478 0.00 0.00 0.00 2.66
3597 3628 3.199289 ACATAACACTACTACCCCCAAGC 59.801 47.826 0.00 0.00 0.00 4.01
3598 3629 4.468510 TCACATAACACTACTACCCCCAAG 59.531 45.833 0.00 0.00 0.00 3.61
3601 3632 3.181468 GCTCACATAACACTACTACCCCC 60.181 52.174 0.00 0.00 0.00 5.40
3602 3633 3.490419 CGCTCACATAACACTACTACCCC 60.490 52.174 0.00 0.00 0.00 4.95
3614 3645 6.575267 TGGCTAGTATAAAACGCTCACATAA 58.425 36.000 0.00 0.00 0.00 1.90
3621 3652 5.018539 TGACATGGCTAGTATAAAACGCT 57.981 39.130 0.00 0.00 0.00 5.07
3637 3669 6.990341 TTACACAAATCCATCTCTGACATG 57.010 37.500 0.00 0.00 0.00 3.21
3642 3674 8.217131 TGATGATTTACACAAATCCATCTCTG 57.783 34.615 7.45 0.00 46.42 3.35
3643 3675 8.812513 TTGATGATTTACACAAATCCATCTCT 57.187 30.769 7.45 0.00 46.42 3.10
3649 3681 8.695456 ACCCTATTTGATGATTTACACAAATCC 58.305 33.333 0.00 0.00 46.42 3.01
3650 3682 9.520204 CACCCTATTTGATGATTTACACAAATC 57.480 33.333 0.00 3.66 46.91 2.17
3651 3683 7.981225 GCACCCTATTTGATGATTTACACAAAT 59.019 33.333 0.00 0.00 40.09 2.32
3652 3684 7.178274 AGCACCCTATTTGATGATTTACACAAA 59.822 33.333 0.00 0.00 35.65 2.83
3654 3686 6.095300 CAGCACCCTATTTGATGATTTACACA 59.905 38.462 0.00 0.00 31.85 3.72
3655 3687 6.318648 TCAGCACCCTATTTGATGATTTACAC 59.681 38.462 0.00 0.00 34.53 2.90
3656 3688 6.422333 TCAGCACCCTATTTGATGATTTACA 58.578 36.000 0.00 0.00 34.53 2.41
3657 3689 6.942532 TCAGCACCCTATTTGATGATTTAC 57.057 37.500 0.00 0.00 34.53 2.01
3662 3694 6.351202 CCAAAAATCAGCACCCTATTTGATGA 60.351 38.462 0.00 0.00 43.16 2.92
3663 3695 5.813672 CCAAAAATCAGCACCCTATTTGATG 59.186 40.000 0.00 0.00 31.11 3.07
3664 3696 5.627503 GCCAAAAATCAGCACCCTATTTGAT 60.628 40.000 0.00 0.00 31.93 2.57
3665 3697 4.322650 GCCAAAAATCAGCACCCTATTTGA 60.323 41.667 0.00 0.00 0.00 2.69
3666 3698 3.934579 GCCAAAAATCAGCACCCTATTTG 59.065 43.478 0.00 0.00 0.00 2.32
3667 3699 3.840078 AGCCAAAAATCAGCACCCTATTT 59.160 39.130 0.00 0.00 0.00 1.40
3674 3706 2.053627 CGACAAGCCAAAAATCAGCAC 58.946 47.619 0.00 0.00 0.00 4.40
3702 3734 7.898636 TGGGTTTAATCCTTACAAAATGGATCT 59.101 33.333 0.00 0.00 39.43 2.75
3706 3738 7.981225 CAGATGGGTTTAATCCTTACAAAATGG 59.019 37.037 0.00 0.00 0.00 3.16
3707 3739 7.981225 CCAGATGGGTTTAATCCTTACAAAATG 59.019 37.037 0.00 0.00 0.00 2.32
3708 3740 7.364673 GCCAGATGGGTTTAATCCTTACAAAAT 60.365 37.037 0.12 0.00 39.65 1.82
3731 3769 1.320344 CCGACTGCTAGTACAGGCCA 61.320 60.000 5.01 0.00 43.24 5.36
3738 3776 2.035961 GGCATGAATCCGACTGCTAGTA 59.964 50.000 0.00 0.00 35.03 1.82
3779 3817 2.159310 CCTTCAGTGCTTCTCCGTCTAG 60.159 54.545 0.00 0.00 0.00 2.43
3781 3819 0.605589 CCTTCAGTGCTTCTCCGTCT 59.394 55.000 0.00 0.00 0.00 4.18
3783 3821 0.034059 CACCTTCAGTGCTTCTCCGT 59.966 55.000 0.00 0.00 40.28 4.69
3787 3825 3.777106 TTCATCACCTTCAGTGCTTCT 57.223 42.857 0.00 0.00 46.81 2.85
3796 3834 8.186821 CCACTGAAAGAATAATTCATCACCTTC 58.813 37.037 0.00 0.00 36.30 3.46
3800 3838 8.186821 CCTTCCACTGAAAGAATAATTCATCAC 58.813 37.037 0.00 0.00 36.30 3.06
3804 3842 7.174946 GTCACCTTCCACTGAAAGAATAATTCA 59.825 37.037 0.00 0.00 37.43 2.57
3827 3865 2.424246 TGCACTATCGACGGTAATGTCA 59.576 45.455 0.00 0.00 38.84 3.58
3874 3912 8.668353 GCTCATTATTGACAAGAACATCACTAA 58.332 33.333 0.00 0.00 0.00 2.24
3878 3917 5.945191 TGGCTCATTATTGACAAGAACATCA 59.055 36.000 0.00 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.