Multiple sequence alignment - TraesCS5B01G161700

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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 TraesCS5B01G161700 chr5B 100.000 3494 0 0 1 3494 298677913 298681406 0.000000e+00 6453.0
1 TraesCS5B01G161700 chr5D 93.108 2786 83 28 1 2715 265540011 265542758 0.000000e+00 3980.0
2 TraesCS5B01G161700 chr5D 96.154 364 11 3 3131 3494 265543462 265543822 3.000000e-165 592.0
3 TraesCS5B01G161700 chr5D 91.813 171 8 3 2752 2919 265542760 265542927 2.100000e-57 233.0
4 TraesCS5B01G161700 chr5A 91.911 2077 80 42 632 2673 353053933 353055956 0.000000e+00 2824.0
5 TraesCS5B01G161700 chr5A 92.033 364 24 3 25 387 353052554 353052913 1.120000e-139 507.0
6 TraesCS5B01G161700 chr5A 91.643 347 18 7 3131 3473 353056736 353057075 1.470000e-128 470.0
7 TraesCS5B01G161700 chr5A 90.000 190 9 6 429 613 353052904 353053088 1.620000e-58 237.0
8 TraesCS5B01G161700 chr5A 81.818 165 10 8 2664 2825 353056141 353056288 1.700000e-23 121.0
9 TraesCS5B01G161700 chr6A 94.915 118 2 3 2943 3059 422165576 422165690 7.700000e-42 182.0
10 TraesCS5B01G161700 chr6A 90.299 134 7 5 2943 3076 313301001 313301128 1.670000e-38 171.0
11 TraesCS5B01G161700 chr6A 93.478 46 1 1 3059 3102 220691023 220690978 2.250000e-07 67.6
12 TraesCS5B01G161700 chr7D 92.248 129 6 3 2949 3075 2337972 2337846 2.770000e-41 180.0
13 TraesCS5B01G161700 chr7D 100.000 31 0 0 2899 2929 46759388 46759358 1.350000e-04 58.4
14 TraesCS5B01G161700 chr6B 94.828 116 4 1 2942 3057 214085162 214085049 2.770000e-41 180.0
15 TraesCS5B01G161700 chr2D 94.017 117 5 1 2943 3059 396667749 396667635 3.580000e-40 176.0
16 TraesCS5B01G161700 chr2D 84.337 166 19 6 2895 3057 312363679 312363840 4.670000e-34 156.0
17 TraesCS5B01G161700 chr4B 91.935 124 6 3 2949 3071 529838358 529838238 1.670000e-38 171.0
18 TraesCS5B01G161700 chr2B 91.406 128 6 3 2933 3058 17431109 17430985 1.670000e-38 171.0
19 TraesCS5B01G161700 chr2B 91.870 123 6 3 2949 3070 662882248 662882129 6.000000e-38 169.0
20 TraesCS5B01G161700 chr3B 85.714 140 2 12 374 513 253503313 253503434 7.870000e-27 132.0
21 TraesCS5B01G161700 chr3B 95.000 40 1 1 2896 2934 1356651 1356612 1.050000e-05 62.1
22 TraesCS5B01G161700 chr6D 97.619 42 1 0 2867 2908 12138817 12138776 4.840000e-09 73.1
23 TraesCS5B01G161700 chr3A 72.628 274 53 17 1511 1776 7790203 7789944 1.740000e-08 71.3
24 TraesCS5B01G161700 chrUn 100.000 34 0 0 1511 1544 281635398 281635365 2.910000e-06 63.9
25 TraesCS5B01G161700 chrUn 100.000 34 0 0 1511 1544 281642272 281642239 2.910000e-06 63.9
26 TraesCS5B01G161700 chrUn 100.000 34 0 0 1511 1544 312315256 312315223 2.910000e-06 63.9
27 TraesCS5B01G161700 chr1D 92.683 41 3 0 2898 2938 202354198 202354158 3.770000e-05 60.2
28 TraesCS5B01G161700 chr1D 97.222 36 0 1 2894 2929 280718955 280718989 3.770000e-05 60.2
29 TraesCS5B01G161700 chr1A 97.222 36 0 1 2894 2929 352872410 352872444 3.770000e-05 60.2
30 TraesCS5B01G161700 chr1A 92.683 41 2 1 2898 2938 256722988 256722949 1.350000e-04 58.4
31 TraesCS5B01G161700 chr7A 90.698 43 3 1 2899 2940 105168562 105168520 4.870000e-04 56.5


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 TraesCS5B01G161700 chr5B 298677913 298681406 3493 False 6453.000000 6453 100.000000 1 3494 1 chr5B.!!$F1 3493
1 TraesCS5B01G161700 chr5D 265540011 265543822 3811 False 1601.666667 3980 93.691667 1 3494 3 chr5D.!!$F1 3493
2 TraesCS5B01G161700 chr5A 353052554 353057075 4521 False 831.800000 2824 89.481000 25 3473 5 chr5A.!!$F1 3448

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
965 1850 0.455633 AGATCGTTCGTTCGTTCCCG 60.456 55.0 8.50 0.0 32.22 5.14 F
2018 2921 0.183492 GGGCCTAGGATGCATTCACA 59.817 55.0 14.75 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 3040 0.240145 CACTGTGCATGCAACAGGAG 59.760 55.0 33.6 26.5 35.93 3.69 R
3040 4524 2.306805 TGTACTACTCCCTCTGTTCGGA 59.693 50.0 0.0 0.0 0.00 4.55 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
42 51 1.134551 GTCTGGACTGGAATCCTCAGC 60.135 57.143 0.00 0.00 39.75 4.26
106 116 1.035932 CGACATACTCCTCCCACGGT 61.036 60.000 0.00 0.00 0.00 4.83
189 199 4.981812 TCGGCCTAGATCAGTACTAATGA 58.018 43.478 0.00 0.00 0.00 2.57
328 338 2.089980 CCTGATTTCCTGAAGGTGCTG 58.910 52.381 0.00 0.00 36.34 4.41
331 341 2.305635 TGATTTCCTGAAGGTGCTGCTA 59.694 45.455 0.00 0.00 36.34 3.49
333 343 3.439857 TTTCCTGAAGGTGCTGCTATT 57.560 42.857 0.00 0.00 36.34 1.73
354 364 3.343941 TTTTCACTAGGCGCCTTATGT 57.656 42.857 37.74 26.64 0.00 2.29
392 402 6.238842 GGAATACTACTACGGATGTACAGCAA 60.239 42.308 13.97 0.00 0.00 3.91
393 403 6.896021 ATACTACTACGGATGTACAGCAAT 57.104 37.500 13.97 2.43 0.00 3.56
394 404 5.593679 ACTACTACGGATGTACAGCAATT 57.406 39.130 13.97 0.00 0.00 2.32
395 405 6.704289 ACTACTACGGATGTACAGCAATTA 57.296 37.500 13.97 0.00 0.00 1.40
396 406 7.286215 ACTACTACGGATGTACAGCAATTAT 57.714 36.000 13.97 0.00 0.00 1.28
397 407 7.723324 ACTACTACGGATGTACAGCAATTATT 58.277 34.615 13.97 0.00 0.00 1.40
398 408 8.853126 ACTACTACGGATGTACAGCAATTATTA 58.147 33.333 13.97 0.00 0.00 0.98
399 409 7.941795 ACTACGGATGTACAGCAATTATTAC 57.058 36.000 13.97 0.00 0.00 1.89
401 411 7.866393 ACTACGGATGTACAGCAATTATTACTC 59.134 37.037 13.97 0.00 0.00 2.59
403 413 6.924060 ACGGATGTACAGCAATTATTACTCTC 59.076 38.462 13.97 0.00 0.00 3.20
413 438 8.077991 CAGCAATTATTACTCTCTCTCTCTCTG 58.922 40.741 0.00 0.00 0.00 3.35
421 446 2.703536 TCTCTCTCTCTCTGCCGAGTAT 59.296 50.000 4.97 0.00 38.45 2.12
492 520 6.978338 AGTGAGTACTACGTCAAAAGAATCA 58.022 36.000 0.00 0.00 34.74 2.57
506 534 6.607198 TCAAAAGAATCAAGACCTTGGAAGTT 59.393 34.615 9.59 1.48 40.78 2.66
538 566 5.246981 TGAGAATGGGAGGCCATAAATAG 57.753 43.478 5.01 0.00 0.00 1.73
540 568 5.221925 TGAGAATGGGAGGCCATAAATAGTC 60.222 44.000 5.01 0.00 0.00 2.59
624 1497 2.743928 GAAGGCACGCACAGAGGG 60.744 66.667 0.00 0.00 0.00 4.30
632 1505 2.649034 GCACAGAGGGACGAACGA 59.351 61.111 0.14 0.00 0.00 3.85
803 1682 3.127548 GTGCCACCATATATACATGCTGC 59.872 47.826 0.00 0.00 0.00 5.25
859 1739 4.286032 TCAGGCTTAGGCGTCCATATATTT 59.714 41.667 0.00 0.00 39.81 1.40
863 1743 4.154195 GCTTAGGCGTCCATATATTTGGTG 59.846 45.833 11.44 7.28 38.01 4.17
965 1850 0.455633 AGATCGTTCGTTCGTTCCCG 60.456 55.000 8.50 0.00 32.22 5.14
1014 1903 2.389059 CTATCAATGTCGTCGCTCCAG 58.611 52.381 0.00 0.00 0.00 3.86
1311 2203 2.577593 GCCTACCTCGACACCACC 59.422 66.667 0.00 0.00 0.00 4.61
1430 2322 1.134848 GGAGCAGCTGGACTACTTCAG 60.135 57.143 17.12 0.00 0.00 3.02
2002 2905 2.104170 ACAGAAGTGAGTAGCTAGGGC 58.896 52.381 0.00 0.00 39.06 5.19
2003 2906 1.410882 CAGAAGTGAGTAGCTAGGGCC 59.589 57.143 0.00 0.00 39.73 5.80
2004 2907 1.289530 AGAAGTGAGTAGCTAGGGCCT 59.710 52.381 12.58 12.58 39.73 5.19
2005 2908 2.514582 AGAAGTGAGTAGCTAGGGCCTA 59.485 50.000 13.73 13.73 39.73 3.93
2006 2909 2.668144 AGTGAGTAGCTAGGGCCTAG 57.332 55.000 32.12 32.12 39.73 3.02
2007 2910 1.146152 AGTGAGTAGCTAGGGCCTAGG 59.854 57.143 35.37 20.53 39.73 3.02
2018 2921 0.183492 GGGCCTAGGATGCATTCACA 59.817 55.000 14.75 0.00 0.00 3.58
2020 2923 1.133976 GGCCTAGGATGCATTCACACT 60.134 52.381 14.75 1.27 0.00 3.55
2118 3033 0.524862 GCCTTGTCTCCTGTTGCATG 59.475 55.000 0.00 0.00 0.00 4.06
2119 3034 0.524862 CCTTGTCTCCTGTTGCATGC 59.475 55.000 11.82 11.82 0.00 4.06
2120 3035 1.241165 CTTGTCTCCTGTTGCATGCA 58.759 50.000 18.46 18.46 0.00 3.96
2121 3036 0.953727 TTGTCTCCTGTTGCATGCAC 59.046 50.000 22.58 16.00 0.00 4.57
2122 3037 0.890542 TGTCTCCTGTTGCATGCACC 60.891 55.000 22.58 15.34 0.00 5.01
2123 3038 0.890542 GTCTCCTGTTGCATGCACCA 60.891 55.000 22.58 19.84 0.00 4.17
2124 3039 0.890542 TCTCCTGTTGCATGCACCAC 60.891 55.000 22.58 17.80 0.00 4.16
2125 3040 1.870055 CTCCTGTTGCATGCACCACC 61.870 60.000 22.58 9.33 0.00 4.61
2126 3041 1.904865 CCTGTTGCATGCACCACCT 60.905 57.895 22.58 0.00 0.00 4.00
2127 3042 1.582968 CTGTTGCATGCACCACCTC 59.417 57.895 22.58 7.47 0.00 3.85
2128 3043 1.870055 CTGTTGCATGCACCACCTCC 61.870 60.000 22.58 3.05 0.00 4.30
2129 3044 1.604593 GTTGCATGCACCACCTCCT 60.605 57.895 22.58 0.00 0.00 3.69
2130 3045 1.604308 TTGCATGCACCACCTCCTG 60.604 57.895 22.58 0.00 0.00 3.86
2131 3046 2.034687 GCATGCACCACCTCCTGT 59.965 61.111 14.21 0.00 0.00 4.00
2132 3047 1.604593 GCATGCACCACCTCCTGTT 60.605 57.895 14.21 0.00 0.00 3.16
2133 3048 1.870055 GCATGCACCACCTCCTGTTG 61.870 60.000 14.21 0.00 0.00 3.33
2134 3049 1.604593 ATGCACCACCTCCTGTTGC 60.605 57.895 0.00 0.00 0.00 4.17
2135 3050 2.203337 GCACCACCTCCTGTTGCA 60.203 61.111 0.00 0.00 0.00 4.08
2136 3051 1.604593 GCACCACCTCCTGTTGCAT 60.605 57.895 0.00 0.00 0.00 3.96
2189 3123 0.935196 ACGTCCGTTCAGACTTTTGC 59.065 50.000 0.00 0.00 34.46 3.68
2217 3151 6.914259 TCTCACTGTACACATTCTTAGACTG 58.086 40.000 0.00 0.00 0.00 3.51
2231 3177 5.003804 TCTTAGACTGCCTTTCACATTTCC 58.996 41.667 0.00 0.00 0.00 3.13
2451 3409 4.021894 ACGGAGAGGATGTACAATATGCTC 60.022 45.833 0.00 3.85 41.59 4.26
2514 3472 5.510671 TGAATTTCAGTTCAGTTTTCTCGC 58.489 37.500 0.00 0.00 33.41 5.03
2592 3550 7.525688 TGTTCTATGAAAACGAGACATCATC 57.474 36.000 0.00 0.00 34.54 2.92
2611 3569 1.138859 TCTTACACTGATCCATGGCGG 59.861 52.381 6.96 1.20 0.00 6.13
2655 3613 5.446143 ACGCAATGGACTGTAAATGAAAA 57.554 34.783 0.00 0.00 0.00 2.29
2722 3871 7.782897 AATATAAGATGATCCGAGGAAGTGA 57.217 36.000 0.00 0.00 0.00 3.41
2723 3872 3.810310 AAGATGATCCGAGGAAGTGAC 57.190 47.619 0.00 0.00 0.00 3.67
2724 3873 3.025322 AGATGATCCGAGGAAGTGACT 57.975 47.619 0.00 0.00 0.00 3.41
2725 3874 2.692557 AGATGATCCGAGGAAGTGACTG 59.307 50.000 0.00 0.00 0.00 3.51
2726 3875 1.186200 TGATCCGAGGAAGTGACTGG 58.814 55.000 0.00 0.00 0.00 4.00
2727 3876 0.461961 GATCCGAGGAAGTGACTGGG 59.538 60.000 0.00 0.00 35.41 4.45
2728 3877 0.041238 ATCCGAGGAAGTGACTGGGA 59.959 55.000 0.00 0.00 45.09 4.37
2729 3878 0.178944 TCCGAGGAAGTGACTGGGAA 60.179 55.000 0.00 0.00 39.47 3.97
2730 3879 0.685097 CCGAGGAAGTGACTGGGAAA 59.315 55.000 0.00 0.00 36.07 3.13
2737 3886 5.501156 AGGAAGTGACTGGGAAAATATGAC 58.499 41.667 0.00 0.00 0.00 3.06
2747 3896 6.096846 ACTGGGAAAATATGACTTTATGTGCC 59.903 38.462 0.00 0.00 0.00 5.01
2757 3906 1.393539 CTTTATGTGCCGTGGACGAAG 59.606 52.381 0.00 0.00 43.02 3.79
2772 3921 4.449743 TGGACGAAGAAAAACAATAGTCGG 59.550 41.667 0.00 0.00 0.00 4.79
2785 3934 8.617290 AAACAATAGTCGGGTCCATATAAATC 57.383 34.615 0.00 0.00 0.00 2.17
2786 3935 6.395629 ACAATAGTCGGGTCCATATAAATCG 58.604 40.000 0.00 0.00 0.00 3.34
2787 3936 6.014840 ACAATAGTCGGGTCCATATAAATCGT 60.015 38.462 0.00 0.00 0.00 3.73
2788 3937 7.177216 ACAATAGTCGGGTCCATATAAATCGTA 59.823 37.037 0.00 0.00 0.00 3.43
2806 3957 7.730364 AATCGTAGTGAGAGTTTTTGATGTT 57.270 32.000 0.00 0.00 0.00 2.71
2829 4254 2.012554 GCTGCTGCTCACATCTGATGT 61.013 52.381 17.24 17.24 39.16 3.06
2830 4255 2.740904 GCTGCTGCTCACATCTGATGTA 60.741 50.000 21.88 6.87 37.56 2.29
2831 4256 2.864946 CTGCTGCTCACATCTGATGTAC 59.135 50.000 21.88 14.79 42.70 2.90
2902 4327 7.125811 ACTTCAGTCTGGCTTTGGAATATACTA 59.874 37.037 0.00 0.00 0.00 1.82
2962 4446 3.505464 ATGAACTACTTCCTCCGTTCG 57.495 47.619 0.00 0.00 38.78 3.95
2963 4447 1.542915 TGAACTACTTCCTCCGTTCGG 59.457 52.381 4.74 4.74 38.78 4.30
2966 4450 2.454538 ACTACTTCCTCCGTTCGGAAT 58.545 47.619 14.79 2.09 39.64 3.01
2969 4453 3.242549 ACTTCCTCCGTTCGGAATTAC 57.757 47.619 14.79 0.00 39.64 1.89
2970 4454 2.830321 ACTTCCTCCGTTCGGAATTACT 59.170 45.455 14.79 0.00 39.64 2.24
2973 4457 2.564062 TCCTCCGTTCGGAATTACTTGT 59.436 45.455 14.79 0.00 33.41 3.16
2977 4461 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2979 4463 3.916172 CGTTCGGAATTACTTGTCTCGAA 59.084 43.478 0.00 0.00 33.66 3.71
2980 4464 4.383649 CGTTCGGAATTACTTGTCTCGAAA 59.616 41.667 0.00 0.00 37.00 3.46
2981 4465 5.107760 CGTTCGGAATTACTTGTCTCGAAAA 60.108 40.000 0.00 0.00 37.00 2.29
2984 4468 5.350365 TCGGAATTACTTGTCTCGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
2986 4470 6.037172 CGGAATTACTTGTCTCGAAAATGGAT 59.963 38.462 0.00 0.00 0.00 3.41
2987 4471 7.189512 GGAATTACTTGTCTCGAAAATGGATG 58.810 38.462 0.00 0.00 0.00 3.51
2988 4472 7.148239 GGAATTACTTGTCTCGAAAATGGATGT 60.148 37.037 0.00 0.00 0.00 3.06
2990 4474 8.964476 ATTACTTGTCTCGAAAATGGATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
2991 4475 6.910536 ACTTGTCTCGAAAATGGATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
2993 4477 6.758886 ACTTGTCTCGAAAATGGATGTATCTC 59.241 38.462 0.00 0.00 0.00 2.75
2994 4478 6.471233 TGTCTCGAAAATGGATGTATCTCT 57.529 37.500 0.00 0.00 0.00 3.10
2996 4480 7.652727 TGTCTCGAAAATGGATGTATCTCTAG 58.347 38.462 0.00 0.00 0.00 2.43
2998 4482 8.353684 GTCTCGAAAATGGATGTATCTCTAGAA 58.646 37.037 0.00 0.00 0.00 2.10
2999 4483 8.353684 TCTCGAAAATGGATGTATCTCTAGAAC 58.646 37.037 0.00 0.00 0.00 3.01
3000 4484 8.239038 TCGAAAATGGATGTATCTCTAGAACT 57.761 34.615 0.00 0.00 0.00 3.01
3029 4513 9.862371 AATACATCTAGATACATCCATTTCGAC 57.138 33.333 4.54 0.00 0.00 4.20
3032 4516 5.998553 TCTAGATACATCCATTTCGACGAC 58.001 41.667 0.00 0.00 0.00 4.34
3034 4518 5.006153 AGATACATCCATTTCGACGACAA 57.994 39.130 0.00 0.00 0.00 3.18
3036 4520 3.040147 ACATCCATTTCGACGACAAGT 57.960 42.857 0.00 0.00 0.00 3.16
3038 4522 4.562082 ACATCCATTTCGACGACAAGTAA 58.438 39.130 0.00 0.00 0.00 2.24
3039 4523 5.175859 ACATCCATTTCGACGACAAGTAAT 58.824 37.500 0.00 0.00 0.00 1.89
3040 4524 5.642063 ACATCCATTTCGACGACAAGTAATT 59.358 36.000 0.00 0.00 0.00 1.40
3041 4525 5.773239 TCCATTTCGACGACAAGTAATTC 57.227 39.130 0.00 0.00 0.00 2.17
3042 4526 4.628333 TCCATTTCGACGACAAGTAATTCC 59.372 41.667 0.00 0.00 0.00 3.01
3043 4527 4.491924 CCATTTCGACGACAAGTAATTCCG 60.492 45.833 0.00 0.00 0.00 4.30
3044 4528 3.557577 TTCGACGACAAGTAATTCCGA 57.442 42.857 0.00 0.00 0.00 4.55
3045 4529 3.557577 TCGACGACAAGTAATTCCGAA 57.442 42.857 0.00 0.00 0.00 4.30
3046 4530 3.236816 TCGACGACAAGTAATTCCGAAC 58.763 45.455 0.00 0.00 0.00 3.95
3047 4531 2.981805 CGACGACAAGTAATTCCGAACA 59.018 45.455 0.00 0.00 0.00 3.18
3048 4532 3.059044 CGACGACAAGTAATTCCGAACAG 59.941 47.826 0.00 0.00 0.00 3.16
3049 4533 4.232221 GACGACAAGTAATTCCGAACAGA 58.768 43.478 0.00 0.00 0.00 3.41
3050 4534 4.235360 ACGACAAGTAATTCCGAACAGAG 58.765 43.478 0.00 0.00 0.00 3.35
3051 4535 3.612860 CGACAAGTAATTCCGAACAGAGG 59.387 47.826 0.00 0.00 0.00 3.69
3052 4536 3.933332 GACAAGTAATTCCGAACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3053 4537 3.581332 ACAAGTAATTCCGAACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
3054 4538 4.184629 CAAGTAATTCCGAACAGAGGGAG 58.815 47.826 0.00 0.00 33.01 4.30
3055 4539 3.442076 AGTAATTCCGAACAGAGGGAGT 58.558 45.455 0.00 0.00 33.01 3.85
3065 4549 4.025061 CGAACAGAGGGAGTAGTACATACG 60.025 50.000 2.52 0.00 39.55 3.06
3070 4554 3.881688 GAGGGAGTAGTACATACGAAGCA 59.118 47.826 2.52 0.00 39.55 3.91
3075 4559 6.200475 GGGAGTAGTACATACGAAGCAAAATC 59.800 42.308 2.52 0.00 39.55 2.17
3121 4605 8.282455 TGTCTACTTCCAATACAAACAAAACA 57.718 30.769 0.00 0.00 0.00 2.83
3122 4606 8.185505 TGTCTACTTCCAATACAAACAAAACAC 58.814 33.333 0.00 0.00 0.00 3.32
3124 4608 6.538945 ACTTCCAATACAAACAAAACACCT 57.461 33.333 0.00 0.00 0.00 4.00
3126 4610 6.816140 ACTTCCAATACAAACAAAACACCTTG 59.184 34.615 0.00 0.00 0.00 3.61
3127 4611 6.531503 TCCAATACAAACAAAACACCTTGA 57.468 33.333 0.00 0.00 0.00 3.02
3128 4612 6.936279 TCCAATACAAACAAAACACCTTGAA 58.064 32.000 0.00 0.00 0.00 2.69
3259 5024 6.131544 TCTTTTGGCAGTTTGTACTCTTTC 57.868 37.500 0.00 0.00 30.26 2.62
3282 5047 7.654022 TCAAAAACCTCTTACTTCCAACAAT 57.346 32.000 0.00 0.00 0.00 2.71
3283 5048 8.073467 TCAAAAACCTCTTACTTCCAACAATT 57.927 30.769 0.00 0.00 0.00 2.32
3372 5137 9.247126 CAATGAATTCTATTTGTTCACACACAA 57.753 29.630 7.05 0.00 34.98 3.33
3425 5191 7.112122 TGAACATAGGACTTACATTTCTGCAT 58.888 34.615 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 51 0.036164 TCCTTGATGGAACCACACGG 59.964 55.000 0.00 4.55 42.94 4.94
66 75 2.911120 CGTCTACTCGCTGAAGCTATC 58.089 52.381 0.10 0.00 39.32 2.08
81 90 1.590932 GGAGGAGTATGTCGCGTCTA 58.409 55.000 5.77 0.00 32.82 2.59
93 102 0.836400 AACATCACCGTGGGAGGAGT 60.836 55.000 0.00 0.00 34.73 3.85
106 116 2.226674 TGAATTTAACGCGCCAACATCA 59.773 40.909 5.73 1.53 0.00 3.07
333 343 3.681593 ACATAAGGCGCCTAGTGAAAAA 58.318 40.909 34.60 14.86 0.00 1.94
346 356 2.104963 CCTTCCTCCAGGTACATAAGGC 59.895 54.545 3.80 0.00 30.55 4.35
349 359 3.788116 TCCCTTCCTCCAGGTACATAA 57.212 47.619 0.00 0.00 36.34 1.90
354 364 4.485021 AGTAGTATTCCCTTCCTCCAGGTA 59.515 45.833 0.00 0.00 36.34 3.08
392 402 5.705441 CGGCAGAGAGAGAGAGAGTAATAAT 59.295 44.000 0.00 0.00 0.00 1.28
393 403 5.060506 CGGCAGAGAGAGAGAGAGTAATAA 58.939 45.833 0.00 0.00 0.00 1.40
394 404 4.345547 TCGGCAGAGAGAGAGAGAGTAATA 59.654 45.833 0.00 0.00 0.00 0.98
395 405 3.135712 TCGGCAGAGAGAGAGAGAGTAAT 59.864 47.826 0.00 0.00 0.00 1.89
396 406 2.502130 TCGGCAGAGAGAGAGAGAGTAA 59.498 50.000 0.00 0.00 0.00 2.24
397 407 2.112190 TCGGCAGAGAGAGAGAGAGTA 58.888 52.381 0.00 0.00 0.00 2.59
398 408 0.908910 TCGGCAGAGAGAGAGAGAGT 59.091 55.000 0.00 0.00 0.00 3.24
399 409 3.778619 TCGGCAGAGAGAGAGAGAG 57.221 57.895 0.00 0.00 0.00 3.20
413 438 2.034305 ACCGTAGAATCACATACTCGGC 59.966 50.000 0.00 0.00 40.25 5.54
421 446 6.037940 GTGTAGAGATACACCGTAGAATCACA 59.962 42.308 7.20 0.00 43.24 3.58
492 520 2.091885 TGCTTCCAACTTCCAAGGTCTT 60.092 45.455 0.00 0.00 0.00 3.01
506 534 3.359033 CTCCCATTCTCATTTGCTTCCA 58.641 45.455 0.00 0.00 0.00 3.53
538 566 4.666253 TGCCCCTGCTTGCTGGAC 62.666 66.667 18.12 11.01 38.71 4.02
624 1497 1.403972 AAATCGCTCGCTCGTTCGTC 61.404 55.000 0.00 0.00 0.00 4.20
632 1505 0.304705 CCGCATTTAAATCGCTCGCT 59.695 50.000 15.72 0.00 0.00 4.93
762 1635 2.098233 CGTGGTGGCGTGGTGTATC 61.098 63.158 0.00 0.00 0.00 2.24
859 1739 0.389296 CGAATGGACGTACTGCACCA 60.389 55.000 0.00 0.00 36.83 4.17
863 1743 2.514013 CGCCGAATGGACGTACTGC 61.514 63.158 0.00 0.00 37.49 4.40
965 1850 0.103208 ACAGGCCGATCAATCTCGTC 59.897 55.000 0.00 0.00 36.93 4.20
1093 1985 4.162690 GATCGCCGGCACCTTCCT 62.163 66.667 28.98 1.23 0.00 3.36
1311 2203 1.433879 GAGGTCGTCGATGGTGAGG 59.566 63.158 4.48 0.00 0.00 3.86
1419 2311 3.119065 GCTTGTACTCCCTGAAGTAGTCC 60.119 52.174 0.00 0.00 32.52 3.85
1430 2322 2.820037 GCCGCAGCTTGTACTCCC 60.820 66.667 0.00 0.00 35.50 4.30
1500 2392 1.051008 TGCCGATGCTCCAGATGTAT 58.949 50.000 0.00 0.00 38.71 2.29
1755 2647 3.314388 CTTGGCGTTGAAGCTCCGC 62.314 63.158 10.44 10.44 46.28 5.54
1965 2866 1.449246 GTGCACCTCTGCTGGCTAG 60.449 63.158 5.22 0.00 44.57 3.42
1975 2876 2.928731 GCTACTCACTTCTGTGCACCTC 60.929 54.545 15.69 0.00 43.49 3.85
1986 2889 2.425102 CCTAGGCCCTAGCTACTCACTT 60.425 54.545 12.62 0.00 39.73 3.16
2001 2904 2.158842 AGAGTGTGAATGCATCCTAGGC 60.159 50.000 2.96 0.00 0.00 3.93
2002 2905 3.834489 AGAGTGTGAATGCATCCTAGG 57.166 47.619 0.82 0.82 0.00 3.02
2003 2906 3.801050 CGAAGAGTGTGAATGCATCCTAG 59.199 47.826 0.00 0.00 0.00 3.02
2004 2907 3.447229 TCGAAGAGTGTGAATGCATCCTA 59.553 43.478 0.00 0.00 0.00 2.94
2005 2908 2.234661 TCGAAGAGTGTGAATGCATCCT 59.765 45.455 0.00 0.00 0.00 3.24
2006 2909 2.621338 TCGAAGAGTGTGAATGCATCC 58.379 47.619 0.00 0.00 0.00 3.51
2007 2910 3.060674 CGATCGAAGAGTGTGAATGCATC 60.061 47.826 10.26 0.00 43.63 3.91
2120 3035 1.604593 GCATGCAACAGGAGGTGGT 60.605 57.895 14.21 0.00 0.00 4.16
2121 3036 1.604308 TGCATGCAACAGGAGGTGG 60.604 57.895 20.30 0.00 0.00 4.61
2122 3037 1.174078 TGTGCATGCAACAGGAGGTG 61.174 55.000 24.58 0.00 0.00 4.00
2123 3038 0.892358 CTGTGCATGCAACAGGAGGT 60.892 55.000 28.21 0.00 0.00 3.85
2124 3039 0.892358 ACTGTGCATGCAACAGGAGG 60.892 55.000 33.60 20.81 35.93 4.30
2125 3040 0.240145 CACTGTGCATGCAACAGGAG 59.760 55.000 33.60 26.50 35.93 3.69
2126 3041 1.798234 GCACTGTGCATGCAACAGGA 61.798 55.000 33.60 15.59 44.26 3.86
2127 3042 1.372499 GCACTGTGCATGCAACAGG 60.372 57.895 33.60 26.91 44.26 4.00
2128 3043 1.728074 CGCACTGTGCATGCAACAG 60.728 57.895 31.30 31.30 45.36 3.16
2129 3044 2.332159 CGCACTGTGCATGCAACA 59.668 55.556 29.86 20.42 45.36 3.33
2130 3045 2.012414 CACGCACTGTGCATGCAAC 61.012 57.895 29.86 16.87 45.36 4.17
2131 3046 2.332159 CACGCACTGTGCATGCAA 59.668 55.556 29.86 11.95 45.36 4.08
2162 3096 4.235360 AGTCTGAACGGACGTTAATTCAG 58.765 43.478 21.47 21.47 46.18 3.02
2189 3123 7.753132 GTCTAAGAATGTGTACAGTGAGAGAAG 59.247 40.741 0.00 0.00 0.00 2.85
2217 3151 3.335579 ACTACTCGGAAATGTGAAAGGC 58.664 45.455 0.00 0.00 0.00 4.35
2231 3177 7.909121 CAGGTAAAGTCACTACATAACTACTCG 59.091 40.741 0.00 0.00 0.00 4.18
2283 3232 3.834489 AAACCTGCGAGATCATCATCT 57.166 42.857 0.00 0.00 42.59 2.90
2451 3409 2.030457 GGTGTTCATGACTTTATCGGCG 59.970 50.000 0.00 0.00 0.00 6.46
2514 3472 7.308450 TCCCTCCATATATTGTCTTCTCAAG 57.692 40.000 0.00 0.00 0.00 3.02
2592 3550 1.138859 TCCGCCATGGATCAGTGTAAG 59.861 52.381 18.40 0.00 43.74 2.34
2720 3869 7.148086 GCACATAAAGTCATATTTTCCCAGTCA 60.148 37.037 0.00 0.00 0.00 3.41
2721 3870 7.196331 GCACATAAAGTCATATTTTCCCAGTC 58.804 38.462 0.00 0.00 0.00 3.51
2722 3871 6.096846 GGCACATAAAGTCATATTTTCCCAGT 59.903 38.462 0.00 0.00 0.00 4.00
2723 3872 6.507023 GGCACATAAAGTCATATTTTCCCAG 58.493 40.000 0.00 0.00 0.00 4.45
2724 3873 5.067153 CGGCACATAAAGTCATATTTTCCCA 59.933 40.000 0.00 0.00 0.00 4.37
2725 3874 5.067283 ACGGCACATAAAGTCATATTTTCCC 59.933 40.000 0.00 0.00 0.00 3.97
2726 3875 5.971202 CACGGCACATAAAGTCATATTTTCC 59.029 40.000 0.00 0.00 0.00 3.13
2727 3876 5.971202 CCACGGCACATAAAGTCATATTTTC 59.029 40.000 0.00 0.00 0.00 2.29
2728 3877 5.650266 TCCACGGCACATAAAGTCATATTTT 59.350 36.000 0.00 0.00 0.00 1.82
2729 3878 5.065988 GTCCACGGCACATAAAGTCATATTT 59.934 40.000 0.00 0.00 0.00 1.40
2730 3879 4.574828 GTCCACGGCACATAAAGTCATATT 59.425 41.667 0.00 0.00 0.00 1.28
2737 3886 1.393539 CTTCGTCCACGGCACATAAAG 59.606 52.381 0.00 0.00 40.29 1.85
2747 3896 5.338614 ACTATTGTTTTTCTTCGTCCACG 57.661 39.130 0.00 0.00 41.45 4.94
2757 3906 6.937436 ATATGGACCCGACTATTGTTTTTC 57.063 37.500 0.00 0.00 0.00 2.29
2772 3921 7.216973 ACTCTCACTACGATTTATATGGACC 57.783 40.000 0.00 0.00 0.00 4.46
2785 3934 6.955963 GCATAACATCAAAAACTCTCACTACG 59.044 38.462 0.00 0.00 0.00 3.51
2786 3935 7.959651 CAGCATAACATCAAAAACTCTCACTAC 59.040 37.037 0.00 0.00 0.00 2.73
2787 3936 7.361201 GCAGCATAACATCAAAAACTCTCACTA 60.361 37.037 0.00 0.00 0.00 2.74
2788 3937 6.569226 GCAGCATAACATCAAAAACTCTCACT 60.569 38.462 0.00 0.00 0.00 3.41
2806 3957 1.483415 TCAGATGTGAGCAGCAGCATA 59.517 47.619 3.17 0.00 45.49 3.14
2829 4254 8.429641 AGAAAGTCTGAGAATTGTTTGGTAGTA 58.570 33.333 0.00 0.00 0.00 1.82
2830 4255 7.283329 AGAAAGTCTGAGAATTGTTTGGTAGT 58.717 34.615 0.00 0.00 0.00 2.73
2831 4256 7.659390 AGAGAAAGTCTGAGAATTGTTTGGTAG 59.341 37.037 0.00 0.00 32.57 3.18
2883 4308 5.307196 GGAGGTAGTATATTCCAAAGCCAGA 59.693 44.000 0.00 0.00 30.32 3.86
2939 4423 4.096081 CGAACGGAGGAAGTAGTTCATAGT 59.904 45.833 12.31 6.24 42.01 2.12
2952 4436 2.564062 ACAAGTAATTCCGAACGGAGGA 59.436 45.455 15.34 3.20 46.06 3.71
2954 4438 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2962 4446 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
2963 4447 7.752695 ACATCCATTTTCGAGACAAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2966 4450 8.258007 AGATACATCCATTTTCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
2969 4453 6.983307 AGAGATACATCCATTTTCGAGACAAG 59.017 38.462 0.00 0.00 0.00 3.16
2970 4454 6.878317 AGAGATACATCCATTTTCGAGACAA 58.122 36.000 0.00 0.00 0.00 3.18
2973 4457 8.353684 GTTCTAGAGATACATCCATTTTCGAGA 58.646 37.037 0.00 0.00 0.00 4.04
3003 4487 9.862371 GTCGAAATGGATGTATCTAGATGTATT 57.138 33.333 15.79 4.32 0.00 1.89
3004 4488 8.184848 CGTCGAAATGGATGTATCTAGATGTAT 58.815 37.037 15.79 9.11 0.00 2.29
3005 4489 7.389607 TCGTCGAAATGGATGTATCTAGATGTA 59.610 37.037 15.79 4.44 0.00 2.29
3006 4490 6.206829 TCGTCGAAATGGATGTATCTAGATGT 59.793 38.462 15.79 1.25 0.00 3.06
3007 4491 6.524933 GTCGTCGAAATGGATGTATCTAGATG 59.475 42.308 15.79 0.00 0.00 2.90
3009 4493 5.529800 TGTCGTCGAAATGGATGTATCTAGA 59.470 40.000 0.00 0.00 0.00 2.43
3010 4494 5.758924 TGTCGTCGAAATGGATGTATCTAG 58.241 41.667 0.00 0.00 0.00 2.43
3011 4495 5.761165 TGTCGTCGAAATGGATGTATCTA 57.239 39.130 0.00 0.00 0.00 1.98
3014 4498 4.755411 ACTTGTCGTCGAAATGGATGTAT 58.245 39.130 0.00 0.00 0.00 2.29
3016 4500 3.040147 ACTTGTCGTCGAAATGGATGT 57.960 42.857 0.00 0.00 0.00 3.06
3017 4501 5.718649 ATTACTTGTCGTCGAAATGGATG 57.281 39.130 0.00 0.00 0.00 3.51
3018 4502 5.293569 GGAATTACTTGTCGTCGAAATGGAT 59.706 40.000 0.00 0.00 0.00 3.41
3021 4505 4.325204 TCGGAATTACTTGTCGTCGAAATG 59.675 41.667 0.00 0.00 0.00 2.32
3022 4506 4.487948 TCGGAATTACTTGTCGTCGAAAT 58.512 39.130 0.00 0.00 0.00 2.17
3023 4507 3.899734 TCGGAATTACTTGTCGTCGAAA 58.100 40.909 0.00 0.00 0.00 3.46
3025 4509 3.236816 GTTCGGAATTACTTGTCGTCGA 58.763 45.455 0.00 0.00 0.00 4.20
3026 4510 2.981805 TGTTCGGAATTACTTGTCGTCG 59.018 45.455 0.00 0.00 0.00 5.12
3027 4511 4.232221 TCTGTTCGGAATTACTTGTCGTC 58.768 43.478 0.00 0.00 0.00 4.20
3028 4512 4.235360 CTCTGTTCGGAATTACTTGTCGT 58.765 43.478 0.00 0.00 0.00 4.34
3029 4513 3.612860 CCTCTGTTCGGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
3032 4516 4.184629 CTCCCTCTGTTCGGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
3034 4518 3.442076 ACTCCCTCTGTTCGGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
3036 4520 4.607239 ACTACTCCCTCTGTTCGGAATTA 58.393 43.478 0.00 0.00 0.00 1.40
3038 4522 3.103080 ACTACTCCCTCTGTTCGGAAT 57.897 47.619 0.00 0.00 0.00 3.01
3039 4523 2.599408 ACTACTCCCTCTGTTCGGAA 57.401 50.000 0.00 0.00 0.00 4.30
3040 4524 2.306805 TGTACTACTCCCTCTGTTCGGA 59.693 50.000 0.00 0.00 0.00 4.55
3041 4525 2.719739 TGTACTACTCCCTCTGTTCGG 58.280 52.381 0.00 0.00 0.00 4.30
3042 4526 4.025061 CGTATGTACTACTCCCTCTGTTCG 60.025 50.000 0.00 0.00 0.00 3.95
3043 4527 5.121811 TCGTATGTACTACTCCCTCTGTTC 58.878 45.833 0.00 0.00 0.00 3.18
3044 4528 5.108187 TCGTATGTACTACTCCCTCTGTT 57.892 43.478 0.00 0.00 0.00 3.16
3045 4529 4.767578 TCGTATGTACTACTCCCTCTGT 57.232 45.455 0.00 0.00 0.00 3.41
3046 4530 4.023878 GCTTCGTATGTACTACTCCCTCTG 60.024 50.000 0.00 0.00 0.00 3.35
3047 4531 4.136051 GCTTCGTATGTACTACTCCCTCT 58.864 47.826 0.00 0.00 0.00 3.69
3048 4532 3.881688 TGCTTCGTATGTACTACTCCCTC 59.118 47.826 0.00 0.00 0.00 4.30
3049 4533 3.894759 TGCTTCGTATGTACTACTCCCT 58.105 45.455 0.00 0.00 0.00 4.20
3050 4534 4.644103 TTGCTTCGTATGTACTACTCCC 57.356 45.455 0.00 0.00 0.00 4.30
3051 4535 6.755141 TGATTTTGCTTCGTATGTACTACTCC 59.245 38.462 0.00 0.00 0.00 3.85
3052 4536 7.488471 ACTGATTTTGCTTCGTATGTACTACTC 59.512 37.037 0.00 0.00 0.00 2.59
3053 4537 7.321153 ACTGATTTTGCTTCGTATGTACTACT 58.679 34.615 0.00 0.00 0.00 2.57
3054 4538 7.521509 ACTGATTTTGCTTCGTATGTACTAC 57.478 36.000 0.00 0.00 0.00 2.73
3055 4539 9.642327 TTTACTGATTTTGCTTCGTATGTACTA 57.358 29.630 0.00 0.00 0.00 1.82
3097 4581 7.646526 GGTGTTTTGTTTGTATTGGAAGTAGAC 59.353 37.037 0.00 0.00 0.00 2.59
3099 4583 7.712797 AGGTGTTTTGTTTGTATTGGAAGTAG 58.287 34.615 0.00 0.00 0.00 2.57
3101 4585 6.538945 AGGTGTTTTGTTTGTATTGGAAGT 57.461 33.333 0.00 0.00 0.00 3.01
3102 4586 7.038659 TCAAGGTGTTTTGTTTGTATTGGAAG 58.961 34.615 0.00 0.00 0.00 3.46
3103 4587 6.936279 TCAAGGTGTTTTGTTTGTATTGGAA 58.064 32.000 0.00 0.00 0.00 3.53
3105 4589 6.257630 CCTTCAAGGTGTTTTGTTTGTATTGG 59.742 38.462 0.00 0.00 0.00 3.16
3106 4590 7.232945 CCTTCAAGGTGTTTTGTTTGTATTG 57.767 36.000 0.00 0.00 0.00 1.90
3122 4606 6.951062 AAGAAAGAAAGAGAACCTTCAAGG 57.049 37.500 0.22 0.22 42.49 3.61
3124 4608 7.547227 CCAAAAGAAAGAAAGAGAACCTTCAA 58.453 34.615 0.00 0.00 33.02 2.69
3126 4610 5.980116 GCCAAAAGAAAGAAAGAGAACCTTC 59.020 40.000 0.00 0.00 33.02 3.46
3127 4611 5.422012 TGCCAAAAGAAAGAAAGAGAACCTT 59.578 36.000 0.00 0.00 36.47 3.50
3128 4612 4.956075 TGCCAAAAGAAAGAAAGAGAACCT 59.044 37.500 0.00 0.00 0.00 3.50
3234 4999 5.757850 AGAGTACAAACTGCCAAAAGAAG 57.242 39.130 0.00 0.00 35.56 2.85
3259 5024 9.981114 ATAATTGTTGGAAGTAAGAGGTTTTTG 57.019 29.630 0.00 0.00 0.00 2.44
3282 5047 7.972832 TGCGAAATTGTTGATATGAGCAAATAA 59.027 29.630 0.00 0.00 0.00 1.40
3283 5048 7.431960 GTGCGAAATTGTTGATATGAGCAAATA 59.568 33.333 0.00 0.00 32.54 1.40
3361 5126 5.064452 TGGCAATCAATTTTTGTGTGTGAAC 59.936 36.000 0.00 0.00 0.00 3.18
3425 5191 6.751157 TGTAGAAGAAAACGTGACATCCTTA 58.249 36.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.