Multiple sequence alignment - TraesCS7A01G254500

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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 TraesCS7A01G254500 chr7A 100.000 3349 0 0 1 3349 240958681 240955333 0.000000e+00 6185.0
1 TraesCS7A01G254500 chr7A 97.143 35 1 0 1969 2003 617949478 617949512 3.610000e-05 60.2
2 TraesCS7A01G254500 chr7D 91.310 2923 131 39 6 2858 228987840 228984971 0.000000e+00 3877.0
3 TraesCS7A01G254500 chr7D 96.739 92 2 1 3047 3137 228984815 228984724 5.790000e-33 152.0
4 TraesCS7A01G254500 chr7D 81.481 81 13 2 1969 2048 535658825 535658746 7.760000e-07 65.8
5 TraesCS7A01G254500 chr7B 90.960 2832 120 41 14 2791 199857678 199854929 0.000000e+00 3687.0
6 TraesCS7A01G254500 chr7B 81.481 81 13 2 1969 2048 577372462 577372383 7.760000e-07 65.8
7 TraesCS7A01G254500 chr6B 98.131 214 4 0 3136 3349 514694413 514694626 1.130000e-99 374.0
8 TraesCS7A01G254500 chr6B 97.685 216 5 0 3134 3349 538304471 538304686 4.080000e-99 372.0
9 TraesCS7A01G254500 chr6B 97.685 216 4 1 3135 3349 589123479 589123264 1.470000e-98 370.0
10 TraesCS7A01G254500 chr2B 97.696 217 4 1 3134 3349 546951878 546952094 4.080000e-99 372.0
11 TraesCS7A01G254500 chr3A 97.685 216 4 1 3135 3349 464322228 464322013 1.470000e-98 370.0
12 TraesCS7A01G254500 chr3A 97.235 217 6 0 3133 3349 632556808 632556592 5.280000e-98 368.0
13 TraesCS7A01G254500 chr1A 97.235 217 6 0 3133 3349 341181115 341181331 5.280000e-98 368.0
14 TraesCS7A01G254500 chr3B 96.818 220 6 1 3130 3349 736494081 736493863 1.900000e-97 366.0
15 TraesCS7A01G254500 chr2A 96.396 222 7 1 3128 3349 369213789 369214009 6.830000e-97 364.0
16 TraesCS7A01G254500 chr5B 83.590 195 26 3 1897 2088 462883340 462883149 9.550000e-41 178.0
17 TraesCS7A01G254500 chr5D 80.465 215 36 3 1877 2088 385604671 385604460 3.460000e-35 159.0
18 TraesCS7A01G254500 chr5A 80.465 215 36 3 1877 2088 487365619 487365408 3.460000e-35 159.0


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 TraesCS7A01G254500 chr7A 240955333 240958681 3348 True 6185.0 6185 100.0000 1 3349 1 chr7A.!!$R1 3348
1 TraesCS7A01G254500 chr7D 228984724 228987840 3116 True 2014.5 3877 94.0245 6 3137 2 chr7D.!!$R2 3131
2 TraesCS7A01G254500 chr7B 199854929 199857678 2749 True 3687.0 3687 90.9600 14 2791 1 chr7B.!!$R1 2777

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
251 276 0.035915 TTTGTTGGATCGATGCCGGA 60.036 50.0 14.82 0.0 36.24 5.14 F
1665 1732 0.179081 GCATTCTACCAGGACGGACC 60.179 60.0 0.00 0.0 38.63 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 2187 0.105709 CTTCCTCCTCCTCCTCCTCC 60.106 65.0 0.00 0.0 0.0 4.30 R
3072 3190 0.029834 TTAACTAGTCCGGATCGCGC 59.970 55.0 7.81 0.0 0.0 6.86 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
65 66 0.385098 CAGCATGCACAGTTCACACG 60.385 55.000 21.98 0.00 0.00 4.49
79 80 3.357079 CACGGTGCAAGGTCAGCC 61.357 66.667 0.00 0.00 0.00 4.85
109 110 3.467374 TTCACCTTGAACCAAAATGCC 57.533 42.857 0.00 0.00 30.26 4.40
148 149 2.735126 GCATGATTACCCTTTTGCGGTG 60.735 50.000 0.00 0.00 34.66 4.94
217 241 2.914379 CCGGACACTTCTGGTTGAC 58.086 57.895 0.00 0.00 42.84 3.18
224 248 3.270877 ACACTTCTGGTTGACTGTGAAC 58.729 45.455 1.24 1.24 35.10 3.18
227 251 1.116308 TCTGGTTGACTGTGAACCGA 58.884 50.000 21.39 18.03 45.15 4.69
232 256 2.218603 GTTGACTGTGAACCGAACCAT 58.781 47.619 0.00 0.00 0.00 3.55
235 259 2.616376 TGACTGTGAACCGAACCATTTG 59.384 45.455 0.00 0.00 0.00 2.32
251 276 0.035915 TTTGTTGGATCGATGCCGGA 60.036 50.000 14.82 0.00 36.24 5.14
298 329 0.982852 TTGTCGGGCCATCCAGAGAT 60.983 55.000 4.39 0.00 37.24 2.75
334 366 0.537371 CTGGGTTTGGGTGGACAGAC 60.537 60.000 0.00 0.00 0.00 3.51
394 426 1.439353 ATCATCCATCCAACGCGTGC 61.439 55.000 14.98 0.00 0.00 5.34
395 427 3.195002 ATCCATCCAACGCGTGCG 61.195 61.111 14.98 13.39 46.03 5.34
518 550 2.342910 CGCCCACCGTATGTATACTC 57.657 55.000 4.17 0.00 0.00 2.59
761 794 4.145052 CCTGTTTTTCCTTTGCTAGTCCT 58.855 43.478 0.00 0.00 0.00 3.85
762 795 4.022849 CCTGTTTTTCCTTTGCTAGTCCTG 60.023 45.833 0.00 0.00 0.00 3.86
763 796 3.888930 TGTTTTTCCTTTGCTAGTCCTGG 59.111 43.478 0.00 0.00 0.00 4.45
764 797 2.200373 TTTCCTTTGCTAGTCCTGGC 57.800 50.000 0.00 0.00 37.60 4.85
765 798 0.328258 TTCCTTTGCTAGTCCTGGCC 59.672 55.000 0.00 0.00 36.12 5.36
766 799 0.547712 TCCTTTGCTAGTCCTGGCCT 60.548 55.000 3.32 0.00 36.12 5.19
767 800 1.204146 CCTTTGCTAGTCCTGGCCTA 58.796 55.000 3.32 0.00 36.12 3.93
768 801 1.139853 CCTTTGCTAGTCCTGGCCTAG 59.860 57.143 7.41 7.41 36.12 3.02
772 805 2.740121 CTAGTCCTGGCCTAGCTCC 58.260 63.158 3.32 0.00 0.00 4.70
773 806 0.830023 CTAGTCCTGGCCTAGCTCCC 60.830 65.000 3.32 0.00 0.00 4.30
774 807 1.590339 TAGTCCTGGCCTAGCTCCCA 61.590 60.000 3.32 0.00 0.00 4.37
775 808 2.041508 TCCTGGCCTAGCTCCCAG 60.042 66.667 16.95 16.95 46.49 4.45
776 809 3.871395 CCTGGCCTAGCTCCCAGC 61.871 72.222 17.99 5.74 45.75 4.85
777 810 3.085947 CTGGCCTAGCTCCCAGCA 61.086 66.667 3.32 0.00 45.56 4.41
778 811 2.610546 TGGCCTAGCTCCCAGCAA 60.611 61.111 3.32 0.00 45.56 3.91
779 812 2.202236 CTGGCCTAGCTCCCAGCAAA 62.202 60.000 3.32 0.00 45.56 3.68
780 813 1.000896 GGCCTAGCTCCCAGCAAAA 60.001 57.895 0.00 0.00 45.56 2.44
781 814 0.611896 GGCCTAGCTCCCAGCAAAAA 60.612 55.000 0.00 0.00 45.56 1.94
821 854 4.621274 GCTCAGCATCTCTATCCAATCCTC 60.621 50.000 0.00 0.00 0.00 3.71
890 932 1.865865 TTTCTTGTCCTCGTCTGTGC 58.134 50.000 0.00 0.00 0.00 4.57
993 1039 2.501610 GCTTAGCTAGCTGCGGGT 59.498 61.111 27.68 1.35 46.77 5.28
1072 1118 4.035102 GGAAGGGGAAGCAGCGGT 62.035 66.667 0.00 0.00 0.00 5.68
1185 1234 4.219999 GAGCTGGAGGAGGCGCTC 62.220 72.222 7.64 2.45 41.60 5.03
1305 1360 4.899239 GAGGCGCCGGTGGATGAG 62.899 72.222 23.20 0.00 0.00 2.90
1592 1650 8.349245 CAGTTGTGTTTTCTGGTGTAATCATTA 58.651 33.333 0.00 0.00 0.00 1.90
1593 1651 8.908903 AGTTGTGTTTTCTGGTGTAATCATTAA 58.091 29.630 0.00 0.00 0.00 1.40
1621 1686 5.183969 TGTAGATCACAGAACTAGCGTACT 58.816 41.667 0.00 0.00 31.89 2.73
1654 1721 6.976350 GTTCTGTTGAACTTTGCATTCTAC 57.024 37.500 6.27 6.27 46.56 2.59
1655 1722 5.689383 TCTGTTGAACTTTGCATTCTACC 57.311 39.130 9.56 0.00 32.82 3.18
1661 1728 2.699954 ACTTTGCATTCTACCAGGACG 58.300 47.619 0.00 0.00 0.00 4.79
1665 1732 0.179081 GCATTCTACCAGGACGGACC 60.179 60.000 0.00 0.00 38.63 4.46
1667 1734 1.762957 CATTCTACCAGGACGGACCAT 59.237 52.381 0.00 0.00 42.04 3.55
1678 1745 2.235402 GGACGGACCATGGAGAAAGTTA 59.765 50.000 21.47 0.00 38.79 2.24
1683 1750 3.629398 GGACCATGGAGAAAGTTAGCATG 59.371 47.826 21.47 0.00 0.00 4.06
1701 1768 4.858935 GCATGTTTCTGCTAGTCAAAACA 58.141 39.130 15.91 15.91 43.44 2.83
1747 1814 5.643379 ATTTGGTGTGTGTAATTAGCTGG 57.357 39.130 0.00 0.00 0.00 4.85
1774 1841 1.650912 GCATGTGAATAGCCCAGCG 59.349 57.895 0.00 0.00 0.00 5.18
1782 1849 3.814615 ATAGCCCAGCGGTGCATCG 62.815 63.158 16.79 16.79 0.00 3.84
1785 1852 4.457496 CCCAGCGGTGCATCGACT 62.457 66.667 26.37 16.97 0.00 4.18
1852 1925 3.320826 AGTGTTTGCCCTGAACATTAACC 59.679 43.478 0.00 0.00 39.03 2.85
1925 1998 2.238521 GGCAAGTCCAAATCCTTCACA 58.761 47.619 0.00 0.00 34.01 3.58
1934 2007 0.962356 AATCCTTCACAAGCCTGGCG 60.962 55.000 13.96 2.09 0.00 5.69
2109 2182 4.715130 TGGTGGAGGGGGACGAGG 62.715 72.222 0.00 0.00 0.00 4.63
2110 2183 4.393778 GGTGGAGGGGGACGAGGA 62.394 72.222 0.00 0.00 0.00 3.71
2111 2184 2.760385 GTGGAGGGGGACGAGGAG 60.760 72.222 0.00 0.00 0.00 3.69
2112 2185 4.075793 TGGAGGGGGACGAGGAGG 62.076 72.222 0.00 0.00 0.00 4.30
2113 2186 3.752167 GGAGGGGGACGAGGAGGA 61.752 72.222 0.00 0.00 0.00 3.71
2114 2187 2.123640 GAGGGGGACGAGGAGGAG 60.124 72.222 0.00 0.00 0.00 3.69
2166 2239 2.562912 GCGACGACGAGGGTAACA 59.437 61.111 12.29 0.00 42.66 2.41
2270 2343 1.204941 AGCGTCATGAGTAGGAACACC 59.795 52.381 0.00 0.00 0.00 4.16
2281 2354 2.698855 AGGAACACCATCAATCCGAG 57.301 50.000 0.00 0.00 37.05 4.63
2300 2373 1.218230 GCACGAGCTCATTCCGATCC 61.218 60.000 15.40 0.00 37.91 3.36
2517 2602 4.917474 GACATGGCAATGGCAACC 57.083 55.556 14.81 2.12 41.98 3.77
2534 2619 2.358737 CCGAAGTGGCCGCTTCTT 60.359 61.111 41.32 24.06 41.84 2.52
2540 2625 2.672996 TGGCCGCTTCTTTCAGCC 60.673 61.111 0.00 0.00 44.13 4.85
2627 2712 7.332430 CGTTGATGACAGGTTAGTGGTTTAATA 59.668 37.037 0.00 0.00 0.00 0.98
2669 2754 3.972971 CTGGTGGCAGCAGAGAGGC 62.973 68.421 36.47 0.00 45.98 4.70
2752 2841 2.793237 CGACTCGCTTTAGGCTCTCTTC 60.793 54.545 0.00 0.00 39.13 2.87
2795 2884 5.504830 GCCAGCTAATCTAAAAGCTTAGCAC 60.505 44.000 19.15 8.77 46.64 4.40
2896 2988 9.606631 AAGGATAAAGTTGAAGATCACATAGAC 57.393 33.333 0.00 0.00 0.00 2.59
2897 2989 7.923344 AGGATAAAGTTGAAGATCACATAGACG 59.077 37.037 0.00 0.00 0.00 4.18
2898 2990 7.921214 GGATAAAGTTGAAGATCACATAGACGA 59.079 37.037 0.00 0.00 0.00 4.20
2899 2991 9.302345 GATAAAGTTGAAGATCACATAGACGAA 57.698 33.333 0.00 0.00 0.00 3.85
2900 2992 9.823647 ATAAAGTTGAAGATCACATAGACGAAT 57.176 29.630 0.00 0.00 0.00 3.34
2906 2998 7.264947 TGAAGATCACATAGACGAATAGCAAA 58.735 34.615 0.00 0.00 0.00 3.68
2909 3001 3.550275 TCACATAGACGAATAGCAAACGC 59.450 43.478 0.00 0.00 0.00 4.84
2911 3003 4.738252 CACATAGACGAATAGCAAACGCTA 59.262 41.667 0.00 0.00 45.78 4.26
2931 3023 1.746470 TGCAGATCATCTGGCACAAG 58.254 50.000 16.70 0.00 44.43 3.16
2950 3042 0.462789 GCAATGGCTTCCAATGGAGG 59.537 55.000 7.08 7.08 35.17 4.30
2951 3043 1.117150 CAATGGCTTCCAATGGAGGG 58.883 55.000 13.46 6.74 36.95 4.30
2952 3044 0.031817 AATGGCTTCCAATGGAGGGG 60.032 55.000 13.46 4.32 36.95 4.79
2953 3045 0.925720 ATGGCTTCCAATGGAGGGGA 60.926 55.000 13.46 0.00 36.95 4.81
2954 3046 1.228510 GGCTTCCAATGGAGGGGAG 59.771 63.158 13.46 3.97 34.02 4.30
2955 3047 1.575447 GGCTTCCAATGGAGGGGAGT 61.575 60.000 13.46 0.00 34.02 3.85
2956 3048 1.213296 GCTTCCAATGGAGGGGAGTA 58.787 55.000 13.46 0.00 34.02 2.59
2957 3049 1.564348 GCTTCCAATGGAGGGGAGTAA 59.436 52.381 13.46 0.00 34.02 2.24
2958 3050 2.175715 GCTTCCAATGGAGGGGAGTAAT 59.824 50.000 13.46 0.00 34.02 1.89
2959 3051 3.373110 GCTTCCAATGGAGGGGAGTAATT 60.373 47.826 13.46 0.00 34.02 1.40
2960 3052 4.141251 GCTTCCAATGGAGGGGAGTAATTA 60.141 45.833 13.46 0.00 34.02 1.40
2961 3053 5.633854 GCTTCCAATGGAGGGGAGTAATTAA 60.634 44.000 13.46 0.00 34.02 1.40
2962 3054 5.382664 TCCAATGGAGGGGAGTAATTAAC 57.617 43.478 0.00 0.00 0.00 2.01
2963 3055 5.043762 TCCAATGGAGGGGAGTAATTAACT 58.956 41.667 0.00 0.00 42.80 2.24
2964 3056 5.494706 TCCAATGGAGGGGAGTAATTAACTT 59.505 40.000 0.00 0.00 39.07 2.66
2965 3057 5.828328 CCAATGGAGGGGAGTAATTAACTTC 59.172 44.000 0.00 0.00 39.07 3.01
2966 3058 6.423182 CAATGGAGGGGAGTAATTAACTTCA 58.577 40.000 0.00 0.00 39.07 3.02
2995 3088 3.001736 CGAGAGCAAAAGCTATAACTGCC 59.998 47.826 0.00 0.00 33.41 4.85
3003 3096 7.122650 AGCAAAAGCTATAACTGCCATAGAAAA 59.877 33.333 0.00 0.00 33.41 2.29
3030 3123 3.305398 AATCGAGAAGCTCTTTGACGT 57.695 42.857 0.00 0.00 0.00 4.34
3072 3190 3.254892 GGTTAACGAAGCAGGAGAGAAG 58.745 50.000 0.00 0.00 33.08 2.85
3080 3198 1.299773 CAGGAGAGAAGCGCGATCC 60.300 63.158 12.10 0.00 0.00 3.36
3131 3249 3.044059 GCAGCAGGCGGATCACAAC 62.044 63.158 0.00 0.00 0.00 3.32
3133 3251 2.045926 GCAGGCGGATCACAACCT 60.046 61.111 0.00 0.00 0.00 3.50
3135 3253 0.392461 GCAGGCGGATCACAACCTTA 60.392 55.000 0.00 0.00 0.00 2.69
3138 3256 2.420022 CAGGCGGATCACAACCTTAAAG 59.580 50.000 0.00 0.00 0.00 1.85
3139 3257 1.743394 GGCGGATCACAACCTTAAAGG 59.257 52.381 0.00 0.00 42.49 3.11
3140 3258 1.743394 GCGGATCACAACCTTAAAGGG 59.257 52.381 0.00 0.00 40.58 3.95
3141 3259 2.878526 GCGGATCACAACCTTAAAGGGT 60.879 50.000 0.00 0.00 40.58 4.34
3149 3267 3.542969 AACCTTAAAGGGTGCTTGGAT 57.457 42.857 0.00 0.00 40.58 3.41
3150 3268 4.668138 AACCTTAAAGGGTGCTTGGATA 57.332 40.909 0.00 0.00 40.58 2.59
3151 3269 3.964411 ACCTTAAAGGGTGCTTGGATAC 58.036 45.455 0.00 0.00 40.58 2.24
3152 3270 3.332485 ACCTTAAAGGGTGCTTGGATACA 59.668 43.478 0.00 0.00 43.26 2.29
3171 3289 8.664211 GGATACAAGGGACTATTTTTAGTCTG 57.336 38.462 11.69 6.32 44.35 3.51
3172 3290 8.483758 GGATACAAGGGACTATTTTTAGTCTGA 58.516 37.037 11.69 0.00 44.35 3.27
3173 3291 9.315525 GATACAAGGGACTATTTTTAGTCTGAC 57.684 37.037 11.69 0.00 44.35 3.51
3174 3292 7.317722 ACAAGGGACTATTTTTAGTCTGACT 57.682 36.000 15.57 15.57 44.35 3.41
3175 3293 8.431910 ACAAGGGACTATTTTTAGTCTGACTA 57.568 34.615 13.34 13.34 44.35 2.59
3176 3294 8.877195 ACAAGGGACTATTTTTAGTCTGACTAA 58.123 33.333 22.80 22.80 44.35 2.24
3177 3295 9.720769 CAAGGGACTATTTTTAGTCTGACTAAA 57.279 33.333 29.65 29.65 42.90 1.85
3212 3330 6.812879 TTAAAGGCTAAAGTTCTAAGCACC 57.187 37.500 0.00 0.00 38.01 5.01
3213 3331 3.351794 AGGCTAAAGTTCTAAGCACCC 57.648 47.619 7.02 0.00 38.01 4.61
3214 3332 2.026169 AGGCTAAAGTTCTAAGCACCCC 60.026 50.000 7.02 0.00 38.01 4.95
3215 3333 2.026169 GGCTAAAGTTCTAAGCACCCCT 60.026 50.000 7.02 0.00 38.01 4.79
3216 3334 3.010420 GCTAAAGTTCTAAGCACCCCTG 58.990 50.000 0.00 0.00 36.26 4.45
3217 3335 3.307480 GCTAAAGTTCTAAGCACCCCTGA 60.307 47.826 0.00 0.00 36.26 3.86
3218 3336 2.861147 AAGTTCTAAGCACCCCTGAC 57.139 50.000 0.00 0.00 0.00 3.51
3219 3337 2.031495 AGTTCTAAGCACCCCTGACT 57.969 50.000 0.00 0.00 0.00 3.41
3220 3338 3.185880 AGTTCTAAGCACCCCTGACTA 57.814 47.619 0.00 0.00 0.00 2.59
3221 3339 3.517612 AGTTCTAAGCACCCCTGACTAA 58.482 45.455 0.00 0.00 0.00 2.24
3222 3340 3.908103 AGTTCTAAGCACCCCTGACTAAA 59.092 43.478 0.00 0.00 0.00 1.85
3223 3341 4.020128 AGTTCTAAGCACCCCTGACTAAAG 60.020 45.833 0.00 0.00 0.00 1.85
3224 3342 3.786553 TCTAAGCACCCCTGACTAAAGA 58.213 45.455 0.00 0.00 0.00 2.52
3225 3343 3.769844 TCTAAGCACCCCTGACTAAAGAG 59.230 47.826 0.00 0.00 0.00 2.85
3226 3344 2.327325 AGCACCCCTGACTAAAGAGA 57.673 50.000 0.00 0.00 0.00 3.10
3227 3345 2.183679 AGCACCCCTGACTAAAGAGAG 58.816 52.381 0.00 0.00 0.00 3.20
3228 3346 1.208293 GCACCCCTGACTAAAGAGAGG 59.792 57.143 0.00 0.00 0.00 3.69
3229 3347 1.208293 CACCCCTGACTAAAGAGAGGC 59.792 57.143 0.00 0.00 0.00 4.70
3230 3348 1.079658 ACCCCTGACTAAAGAGAGGCT 59.920 52.381 0.00 0.00 0.00 4.58
3231 3349 2.315155 ACCCCTGACTAAAGAGAGGCTA 59.685 50.000 0.00 0.00 0.00 3.93
3232 3350 2.962421 CCCCTGACTAAAGAGAGGCTAG 59.038 54.545 0.00 0.00 0.00 3.42
3233 3351 2.962421 CCCTGACTAAAGAGAGGCTAGG 59.038 54.545 0.00 0.00 0.00 3.02
3234 3352 3.373220 CCCTGACTAAAGAGAGGCTAGGA 60.373 52.174 0.00 0.00 29.08 2.94
3235 3353 3.634910 CCTGACTAAAGAGAGGCTAGGAC 59.365 52.174 0.00 0.00 29.08 3.85
3236 3354 4.532834 CTGACTAAAGAGAGGCTAGGACT 58.467 47.826 0.00 0.00 0.00 3.85
3237 3355 5.398126 CCTGACTAAAGAGAGGCTAGGACTA 60.398 48.000 0.00 0.00 29.08 2.59
3238 3356 5.686753 TGACTAAAGAGAGGCTAGGACTAG 58.313 45.833 1.98 1.98 36.29 2.57
3239 3357 5.192121 TGACTAAAGAGAGGCTAGGACTAGT 59.808 44.000 0.00 0.00 35.65 2.57
3240 3358 5.687780 ACTAAAGAGAGGCTAGGACTAGTC 58.312 45.833 14.87 14.87 38.03 2.59
3246 3364 3.306472 AGGCTAGGACTAGTCTTGAGG 57.694 52.381 21.88 10.56 45.03 3.86
3247 3365 1.684450 GGCTAGGACTAGTCTTGAGGC 59.316 57.143 21.88 21.38 35.06 4.70
3248 3366 2.661718 GCTAGGACTAGTCTTGAGGCT 58.338 52.381 21.88 11.79 35.65 4.58
3249 3367 3.435313 GGCTAGGACTAGTCTTGAGGCTA 60.435 52.174 24.87 16.06 35.06 3.93
3250 3368 4.208746 GCTAGGACTAGTCTTGAGGCTAA 58.791 47.826 21.88 0.00 35.65 3.09
3251 3369 4.645588 GCTAGGACTAGTCTTGAGGCTAAA 59.354 45.833 21.88 0.00 35.65 1.85
3252 3370 5.127356 GCTAGGACTAGTCTTGAGGCTAAAA 59.873 44.000 21.88 0.00 35.65 1.52
3253 3371 6.183360 GCTAGGACTAGTCTTGAGGCTAAAAT 60.183 42.308 21.88 0.00 35.65 1.82
3254 3372 6.228616 AGGACTAGTCTTGAGGCTAAAATC 57.771 41.667 21.88 0.73 0.00 2.17
3255 3373 5.961421 AGGACTAGTCTTGAGGCTAAAATCT 59.039 40.000 21.88 3.06 0.00 2.40
3256 3374 6.442244 AGGACTAGTCTTGAGGCTAAAATCTT 59.558 38.462 21.88 0.00 0.00 2.40
3257 3375 7.037945 AGGACTAGTCTTGAGGCTAAAATCTTT 60.038 37.037 21.88 0.00 0.00 2.52
3258 3376 7.608376 GGACTAGTCTTGAGGCTAAAATCTTTT 59.392 37.037 21.88 0.00 0.00 2.27
3259 3377 9.654663 GACTAGTCTTGAGGCTAAAATCTTTTA 57.345 33.333 15.91 0.00 0.00 1.52
3303 3421 9.600432 AAAATATGTATTAGCTCTCTCTCTCCT 57.400 33.333 0.00 0.00 0.00 3.69
3304 3422 8.807948 AATATGTATTAGCTCTCTCTCTCCTC 57.192 38.462 0.00 0.00 0.00 3.71
3305 3423 5.638530 TGTATTAGCTCTCTCTCTCCTCA 57.361 43.478 0.00 0.00 0.00 3.86
3306 3424 6.199557 TGTATTAGCTCTCTCTCTCCTCAT 57.800 41.667 0.00 0.00 0.00 2.90
3307 3425 6.609876 TGTATTAGCTCTCTCTCTCCTCATT 58.390 40.000 0.00 0.00 0.00 2.57
3308 3426 7.066142 TGTATTAGCTCTCTCTCTCCTCATTT 58.934 38.462 0.00 0.00 0.00 2.32
3309 3427 8.221251 TGTATTAGCTCTCTCTCTCCTCATTTA 58.779 37.037 0.00 0.00 0.00 1.40
3310 3428 9.073475 GTATTAGCTCTCTCTCTCCTCATTTAA 57.927 37.037 0.00 0.00 0.00 1.52
3311 3429 8.725606 ATTAGCTCTCTCTCTCCTCATTTAAT 57.274 34.615 0.00 0.00 0.00 1.40
3312 3430 8.546083 TTAGCTCTCTCTCTCCTCATTTAATT 57.454 34.615 0.00 0.00 0.00 1.40
3313 3431 7.054491 AGCTCTCTCTCTCCTCATTTAATTC 57.946 40.000 0.00 0.00 0.00 2.17
3314 3432 6.041979 AGCTCTCTCTCTCCTCATTTAATTCC 59.958 42.308 0.00 0.00 0.00 3.01
3315 3433 6.041979 GCTCTCTCTCTCCTCATTTAATTCCT 59.958 42.308 0.00 0.00 0.00 3.36
3316 3434 7.595819 TCTCTCTCTCCTCATTTAATTCCTC 57.404 40.000 0.00 0.00 0.00 3.71
3317 3435 7.361438 TCTCTCTCTCCTCATTTAATTCCTCT 58.639 38.462 0.00 0.00 0.00 3.69
3318 3436 7.505585 TCTCTCTCTCCTCATTTAATTCCTCTC 59.494 40.741 0.00 0.00 0.00 3.20
3319 3437 6.553100 TCTCTCTCCTCATTTAATTCCTCTCC 59.447 42.308 0.00 0.00 0.00 3.71
3320 3438 6.448202 TCTCTCCTCATTTAATTCCTCTCCT 58.552 40.000 0.00 0.00 0.00 3.69
3321 3439 6.905776 TCTCTCCTCATTTAATTCCTCTCCTT 59.094 38.462 0.00 0.00 0.00 3.36
3322 3440 8.068110 TCTCTCCTCATTTAATTCCTCTCCTTA 58.932 37.037 0.00 0.00 0.00 2.69
3323 3441 8.256356 TCTCCTCATTTAATTCCTCTCCTTAG 57.744 38.462 0.00 0.00 0.00 2.18
3324 3442 7.846823 TCTCCTCATTTAATTCCTCTCCTTAGT 59.153 37.037 0.00 0.00 0.00 2.24
3325 3443 8.393959 TCCTCATTTAATTCCTCTCCTTAGTT 57.606 34.615 0.00 0.00 0.00 2.24
3326 3444 8.487028 TCCTCATTTAATTCCTCTCCTTAGTTC 58.513 37.037 0.00 0.00 0.00 3.01
3327 3445 8.490311 CCTCATTTAATTCCTCTCCTTAGTTCT 58.510 37.037 0.00 0.00 0.00 3.01
3328 3446 9.323985 CTCATTTAATTCCTCTCCTTAGTTCTG 57.676 37.037 0.00 0.00 0.00 3.02
3329 3447 9.046846 TCATTTAATTCCTCTCCTTAGTTCTGA 57.953 33.333 0.00 0.00 0.00 3.27
3330 3448 9.672673 CATTTAATTCCTCTCCTTAGTTCTGAA 57.327 33.333 0.00 0.00 0.00 3.02
3333 3451 9.672673 TTAATTCCTCTCCTTAGTTCTGAATTG 57.327 33.333 0.00 0.00 34.23 2.32
3334 3452 5.683876 TCCTCTCCTTAGTTCTGAATTGG 57.316 43.478 0.00 0.00 0.00 3.16
3335 3453 5.342017 TCCTCTCCTTAGTTCTGAATTGGA 58.658 41.667 0.00 0.00 0.00 3.53
3336 3454 5.423610 TCCTCTCCTTAGTTCTGAATTGGAG 59.576 44.000 17.13 17.13 40.47 3.86
3337 3455 5.396213 CCTCTCCTTAGTTCTGAATTGGAGG 60.396 48.000 20.18 15.31 39.80 4.30
3338 3456 4.471386 TCTCCTTAGTTCTGAATTGGAGGG 59.529 45.833 20.18 11.41 39.80 4.30
3339 3457 4.175962 TCCTTAGTTCTGAATTGGAGGGT 58.824 43.478 13.35 0.00 0.00 4.34
3340 3458 4.601857 TCCTTAGTTCTGAATTGGAGGGTT 59.398 41.667 13.35 0.00 0.00 4.11
3341 3459 5.074515 TCCTTAGTTCTGAATTGGAGGGTTT 59.925 40.000 13.35 0.00 0.00 3.27
3342 3460 5.183904 CCTTAGTTCTGAATTGGAGGGTTTG 59.816 44.000 0.00 0.00 0.00 2.93
3343 3461 3.500343 AGTTCTGAATTGGAGGGTTTGG 58.500 45.455 0.00 0.00 0.00 3.28
3344 3462 3.140144 AGTTCTGAATTGGAGGGTTTGGA 59.860 43.478 0.00 0.00 0.00 3.53
3345 3463 3.439857 TCTGAATTGGAGGGTTTGGAG 57.560 47.619 0.00 0.00 0.00 3.86
3346 3464 2.041620 TCTGAATTGGAGGGTTTGGAGG 59.958 50.000 0.00 0.00 0.00 4.30
3347 3465 2.041620 CTGAATTGGAGGGTTTGGAGGA 59.958 50.000 0.00 0.00 0.00 3.71
3348 3466 2.654385 TGAATTGGAGGGTTTGGAGGAT 59.346 45.455 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.000570 ACCTTGACCAGAGAAGTACTAGT 57.999 43.478 0.00 0.00 0.00 2.57
1 2 7.648039 ATTACCTTGACCAGAGAAGTACTAG 57.352 40.000 0.00 0.00 0.00 2.57
2 3 9.537852 TTAATTACCTTGACCAGAGAAGTACTA 57.462 33.333 0.00 0.00 0.00 1.82
3 4 6.936968 AATTACCTTGACCAGAGAAGTACT 57.063 37.500 0.00 0.00 0.00 2.73
4 5 7.548427 GGTTAATTACCTTGACCAGAGAAGTAC 59.452 40.741 0.00 0.00 41.90 2.73
58 59 0.813610 CTGACCTTGCACCGTGTGAA 60.814 55.000 8.04 0.00 35.23 3.18
65 66 2.124507 TACTGGGCTGACCTTGCACC 62.125 60.000 0.00 0.00 41.11 5.01
109 110 3.467119 CTGGCGTTCGGTTCGACG 61.467 66.667 0.00 0.00 39.39 5.12
148 149 1.491563 CGCAACGTACTCCACTTGC 59.508 57.895 0.00 0.00 37.65 4.01
212 236 1.658994 TGGTTCGGTTCACAGTCAAC 58.341 50.000 0.00 0.00 0.00 3.18
217 241 3.371168 CAACAAATGGTTCGGTTCACAG 58.629 45.455 0.00 0.00 37.72 3.66
227 251 5.279472 CGGCATCGATCCAACAAATGGTT 62.279 47.826 0.00 0.00 43.93 3.67
232 256 0.035915 TCCGGCATCGATCCAACAAA 60.036 50.000 0.00 0.00 39.00 2.83
235 259 2.247437 GCTCCGGCATCGATCCAAC 61.247 63.158 0.00 0.00 39.00 3.77
251 276 4.957684 CCGATCGGCGATGCTGCT 62.958 66.667 29.20 1.61 44.57 4.24
298 329 2.033141 GTTCAGCTGGCTGCAGGA 59.967 61.111 17.12 12.24 45.94 3.86
512 544 5.185454 CGTATGGTATACGGGGTGAGTATA 58.815 45.833 12.23 0.00 36.36 1.47
513 545 4.012374 CGTATGGTATACGGGGTGAGTAT 58.988 47.826 12.23 0.00 38.27 2.12
514 546 3.411446 CGTATGGTATACGGGGTGAGTA 58.589 50.000 12.23 0.00 37.29 2.59
518 550 0.963962 AGCGTATGGTATACGGGGTG 59.036 55.000 19.22 0.00 40.86 4.61
706 739 1.315257 TAGTTACAGGACGACCCCGC 61.315 60.000 0.00 0.00 39.95 6.13
710 743 5.741040 CGTTTTCTATAGTTACAGGACGACC 59.259 44.000 0.00 0.00 0.00 4.79
761 794 1.788518 TTTTGCTGGGAGCTAGGCCA 61.789 55.000 5.01 0.00 42.97 5.36
762 795 0.611896 TTTTTGCTGGGAGCTAGGCC 60.612 55.000 0.00 0.00 42.97 5.19
763 796 2.961424 TTTTTGCTGGGAGCTAGGC 58.039 52.632 0.00 0.00 42.97 3.93
780 813 3.523564 TGAGCTAGGCCAGGACTATTTTT 59.476 43.478 1.05 0.00 0.00 1.94
781 814 3.115390 TGAGCTAGGCCAGGACTATTTT 58.885 45.455 1.05 0.00 0.00 1.82
782 815 2.703007 CTGAGCTAGGCCAGGACTATTT 59.297 50.000 1.05 0.00 0.00 1.40
783 816 2.324541 CTGAGCTAGGCCAGGACTATT 58.675 52.381 1.05 0.00 0.00 1.73
784 817 2.008242 CTGAGCTAGGCCAGGACTAT 57.992 55.000 1.05 0.00 0.00 2.12
785 818 0.757188 GCTGAGCTAGGCCAGGACTA 60.757 60.000 5.01 0.66 31.12 2.59
786 819 2.063378 GCTGAGCTAGGCCAGGACT 61.063 63.158 5.01 0.00 31.12 3.85
787 820 1.694133 ATGCTGAGCTAGGCCAGGAC 61.694 60.000 5.01 0.00 32.63 3.85
821 854 1.199615 GTGGAGAGAGAAGGGAAGGG 58.800 60.000 0.00 0.00 0.00 3.95
953 999 1.594862 GATCCAGCGAAAATCACGGAG 59.405 52.381 0.00 0.00 0.00 4.63
1305 1360 3.816367 GAGCCCCATAGCGAGCACC 62.816 68.421 0.00 0.00 38.01 5.01
1614 1673 1.473278 GAACAGGCAGACTAGTACGCT 59.527 52.381 13.94 0.00 0.00 5.07
1616 1675 2.488545 ACAGAACAGGCAGACTAGTACG 59.511 50.000 0.00 0.00 0.00 3.67
1618 1677 4.149598 TCAACAGAACAGGCAGACTAGTA 58.850 43.478 0.00 0.00 0.00 1.82
1621 1686 3.388024 AGTTCAACAGAACAGGCAGACTA 59.612 43.478 10.56 0.00 43.18 2.59
1630 1697 5.581126 AGAATGCAAAGTTCAACAGAACA 57.419 34.783 10.56 0.00 43.18 3.18
1651 1718 0.686441 TCCATGGTCCGTCCTGGTAG 60.686 60.000 12.58 0.00 39.52 3.18
1652 1719 0.686441 CTCCATGGTCCGTCCTGGTA 60.686 60.000 12.58 0.00 39.52 3.25
1653 1720 1.990060 CTCCATGGTCCGTCCTGGT 60.990 63.158 12.58 0.00 39.52 4.00
1654 1721 1.264749 TTCTCCATGGTCCGTCCTGG 61.265 60.000 12.58 0.00 36.50 4.45
1655 1722 0.613260 TTTCTCCATGGTCCGTCCTG 59.387 55.000 12.58 0.00 37.07 3.86
1661 1728 3.350219 TGCTAACTTTCTCCATGGTCC 57.650 47.619 12.58 0.00 0.00 4.46
1665 1732 6.320171 CAGAAACATGCTAACTTTCTCCATG 58.680 40.000 5.52 0.00 39.23 3.66
1667 1734 4.216257 GCAGAAACATGCTAACTTTCTCCA 59.784 41.667 5.52 0.00 43.07 3.86
1683 1750 8.774586 TCTTTATCTGTTTTGACTAGCAGAAAC 58.225 33.333 0.00 7.93 40.71 2.78
1696 1763 9.430399 AATCCATCCATGATCTTTATCTGTTTT 57.570 29.630 0.00 0.00 32.93 2.43
1747 1814 2.154462 CTATTCACATGCCCGGGATTC 58.846 52.381 29.31 7.28 0.00 2.52
1770 1837 1.142185 CTGTAGTCGATGCACCGCTG 61.142 60.000 0.00 0.00 0.00 5.18
1774 1841 1.521681 GGCCTGTAGTCGATGCACC 60.522 63.158 0.00 0.00 0.00 5.01
1782 1849 3.198872 GCAGAGTATTTGGCCTGTAGTC 58.801 50.000 3.32 6.81 0.00 2.59
1785 1852 3.712016 TTGCAGAGTATTTGGCCTGTA 57.288 42.857 3.32 0.00 0.00 2.74
1814 1884 5.570034 GCAAACACTCCATGGGTACTAGTAA 60.570 44.000 13.02 0.00 0.00 2.24
1852 1925 6.358030 GCGATTAATTTCATTCATCTTGGTCG 59.642 38.462 0.00 0.00 0.00 4.79
1955 2028 1.078214 CTTGGCGATCTCCTTGGCA 60.078 57.895 2.88 0.00 41.86 4.92
2109 2182 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
2110 2183 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
2111 2184 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
2112 2185 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
2113 2186 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
2114 2187 0.105709 CTTCCTCCTCCTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
2270 2343 1.930100 GCTCGTGCTCGGATTGATG 59.070 57.895 8.49 0.00 37.69 3.07
2281 2354 1.218230 GGATCGGAATGAGCTCGTGC 61.218 60.000 9.75 7.40 40.05 5.34
2300 2373 1.488393 GAGAGGGAGAATGACCTTGGG 59.512 57.143 0.00 0.00 37.18 4.12
2540 2625 5.875930 ACACGGTTAAGAACTTTCAGTTTG 58.124 37.500 0.00 0.00 38.80 2.93
2560 2645 9.261180 TCATTATCCTTTAATCGATGAGAACAC 57.739 33.333 0.00 0.00 0.00 3.32
2613 2698 7.148457 GGTCAGAGCAACTATTAAACCACTAAC 60.148 40.741 0.00 0.00 0.00 2.34
2627 2712 2.345244 CCGCTGGTCAGAGCAACT 59.655 61.111 3.41 0.00 39.07 3.16
2665 2750 0.038166 TCACCCACCATTTCTGCCTC 59.962 55.000 0.00 0.00 0.00 4.70
2669 2754 3.012518 GACTCATCACCCACCATTTCTG 58.987 50.000 0.00 0.00 0.00 3.02
2870 2962 9.606631 GTCTATGTGATCTTCAACTTTATCCTT 57.393 33.333 0.00 0.00 0.00 3.36
2871 2963 7.923344 CGTCTATGTGATCTTCAACTTTATCCT 59.077 37.037 0.00 0.00 0.00 3.24
2872 2964 7.921214 TCGTCTATGTGATCTTCAACTTTATCC 59.079 37.037 0.00 0.00 0.00 2.59
2873 2965 8.858003 TCGTCTATGTGATCTTCAACTTTATC 57.142 34.615 0.00 0.00 0.00 1.75
2874 2966 9.823647 ATTCGTCTATGTGATCTTCAACTTTAT 57.176 29.630 0.00 0.00 0.00 1.40
2876 2968 9.307121 CTATTCGTCTATGTGATCTTCAACTTT 57.693 33.333 0.00 0.00 0.00 2.66
2877 2969 7.436673 GCTATTCGTCTATGTGATCTTCAACTT 59.563 37.037 0.00 0.00 0.00 2.66
2878 2970 6.920758 GCTATTCGTCTATGTGATCTTCAACT 59.079 38.462 0.00 0.00 0.00 3.16
2879 2971 6.697455 TGCTATTCGTCTATGTGATCTTCAAC 59.303 38.462 0.00 0.00 0.00 3.18
2880 2972 6.805713 TGCTATTCGTCTATGTGATCTTCAA 58.194 36.000 0.00 0.00 0.00 2.69
2881 2973 6.391227 TGCTATTCGTCTATGTGATCTTCA 57.609 37.500 0.00 0.00 0.00 3.02
2882 2974 7.559845 GTTTGCTATTCGTCTATGTGATCTTC 58.440 38.462 0.00 0.00 0.00 2.87
2883 2975 6.199154 CGTTTGCTATTCGTCTATGTGATCTT 59.801 38.462 0.00 0.00 0.00 2.40
2884 2976 5.687730 CGTTTGCTATTCGTCTATGTGATCT 59.312 40.000 0.00 0.00 0.00 2.75
2885 2977 5.610552 GCGTTTGCTATTCGTCTATGTGATC 60.611 44.000 0.00 0.00 38.39 2.92
2886 2978 4.209288 GCGTTTGCTATTCGTCTATGTGAT 59.791 41.667 0.00 0.00 38.39 3.06
2887 2979 3.550275 GCGTTTGCTATTCGTCTATGTGA 59.450 43.478 0.00 0.00 38.39 3.58
2888 2980 3.850272 GCGTTTGCTATTCGTCTATGTG 58.150 45.455 0.00 0.00 38.39 3.21
2900 2992 6.529165 CAGATGATCTGCATAGCGTTTGCTA 61.529 44.000 9.82 0.00 46.50 3.49
2906 2998 1.607509 GCCAGATGATCTGCATAGCGT 60.608 52.381 16.81 0.00 42.98 5.07
2909 3001 3.121738 TGTGCCAGATGATCTGCATAG 57.878 47.619 16.81 4.62 42.98 2.23
2911 3003 2.298610 CTTGTGCCAGATGATCTGCAT 58.701 47.619 16.81 0.00 42.98 3.96
2914 3006 1.746470 TGCTTGTGCCAGATGATCTG 58.254 50.000 15.38 15.38 43.91 2.90
2931 3023 0.462789 CCTCCATTGGAAGCCATTGC 59.537 55.000 6.88 0.00 34.63 3.56
2940 3032 5.043762 AGTTAATTACTCCCCTCCATTGGA 58.956 41.667 5.05 5.05 28.23 3.53
2941 3033 5.388599 AGTTAATTACTCCCCTCCATTGG 57.611 43.478 0.00 0.00 28.23 3.16
2942 3034 6.423182 TGAAGTTAATTACTCCCCTCCATTG 58.577 40.000 0.00 0.00 35.54 2.82
2943 3035 6.652205 TGAAGTTAATTACTCCCCTCCATT 57.348 37.500 0.00 0.00 35.54 3.16
2944 3036 6.183361 GGATGAAGTTAATTACTCCCCTCCAT 60.183 42.308 0.00 0.00 35.54 3.41
2945 3037 5.132144 GGATGAAGTTAATTACTCCCCTCCA 59.868 44.000 0.00 0.00 35.54 3.86
2946 3038 5.369993 AGGATGAAGTTAATTACTCCCCTCC 59.630 44.000 0.00 0.00 35.54 4.30
2947 3039 6.099845 TGAGGATGAAGTTAATTACTCCCCTC 59.900 42.308 0.00 0.00 35.54 4.30
2948 3040 5.970640 TGAGGATGAAGTTAATTACTCCCCT 59.029 40.000 0.00 0.00 35.54 4.79
2949 3041 6.056236 GTGAGGATGAAGTTAATTACTCCCC 58.944 44.000 4.33 0.00 35.54 4.81
2950 3042 5.753921 CGTGAGGATGAAGTTAATTACTCCC 59.246 44.000 4.33 0.00 35.54 4.30
2951 3043 6.570692 TCGTGAGGATGAAGTTAATTACTCC 58.429 40.000 4.33 0.00 35.54 3.85
2952 3044 7.481642 TCTCGTGAGGATGAAGTTAATTACTC 58.518 38.462 0.00 0.00 35.54 2.59
2953 3045 7.406031 TCTCGTGAGGATGAAGTTAATTACT 57.594 36.000 0.00 0.00 39.32 2.24
2954 3046 6.199342 GCTCTCGTGAGGATGAAGTTAATTAC 59.801 42.308 15.74 0.00 40.53 1.89
2955 3047 6.127451 TGCTCTCGTGAGGATGAAGTTAATTA 60.127 38.462 15.74 0.00 40.53 1.40
2956 3048 5.112686 GCTCTCGTGAGGATGAAGTTAATT 58.887 41.667 15.74 0.00 40.53 1.40
2957 3049 4.160439 TGCTCTCGTGAGGATGAAGTTAAT 59.840 41.667 15.74 0.00 40.53 1.40
2958 3050 3.509967 TGCTCTCGTGAGGATGAAGTTAA 59.490 43.478 15.74 0.00 40.53 2.01
2959 3051 3.089284 TGCTCTCGTGAGGATGAAGTTA 58.911 45.455 15.74 0.00 40.53 2.24
2960 3052 1.895798 TGCTCTCGTGAGGATGAAGTT 59.104 47.619 15.74 0.00 40.53 2.66
2961 3053 1.550327 TGCTCTCGTGAGGATGAAGT 58.450 50.000 15.74 0.00 40.53 3.01
2962 3054 2.662006 TTGCTCTCGTGAGGATGAAG 57.338 50.000 15.74 0.00 40.32 3.02
2963 3055 3.329386 CTTTTGCTCTCGTGAGGATGAA 58.671 45.455 15.74 9.93 40.32 2.57
2964 3056 2.932622 GCTTTTGCTCTCGTGAGGATGA 60.933 50.000 15.74 3.04 40.32 2.92
2965 3057 1.396301 GCTTTTGCTCTCGTGAGGATG 59.604 52.381 15.74 7.88 40.32 3.51
2966 3058 1.731720 GCTTTTGCTCTCGTGAGGAT 58.268 50.000 15.74 0.00 40.32 3.24
2995 3088 6.963805 GCTTCTCGATTTCCACTTTTTCTATG 59.036 38.462 0.00 0.00 0.00 2.23
3003 3096 3.971245 AGAGCTTCTCGATTTCCACTT 57.029 42.857 0.00 0.00 35.36 3.16
3042 3135 0.881159 CTTCGTTAACCGGTGTGCCA 60.881 55.000 8.52 0.00 37.11 4.92
3043 3136 1.864176 CTTCGTTAACCGGTGTGCC 59.136 57.895 8.52 0.00 37.11 5.01
3044 3137 1.205820 GCTTCGTTAACCGGTGTGC 59.794 57.895 8.52 0.00 37.11 4.57
3072 3190 0.029834 TTAACTAGTCCGGATCGCGC 59.970 55.000 7.81 0.00 0.00 6.86
3080 3198 1.755380 CTCCCCAGGTTAACTAGTCCG 59.245 57.143 5.42 0.00 0.00 4.79
3131 3249 3.963129 TGTATCCAAGCACCCTTTAAGG 58.037 45.455 3.57 3.57 34.30 2.69
3133 3251 4.340617 CCTTGTATCCAAGCACCCTTTAA 58.659 43.478 0.00 0.00 45.57 1.52
3135 3253 2.557452 CCCTTGTATCCAAGCACCCTTT 60.557 50.000 0.00 0.00 45.57 3.11
3138 3256 0.623723 TCCCTTGTATCCAAGCACCC 59.376 55.000 0.00 0.00 45.57 4.61
3139 3257 1.282157 AGTCCCTTGTATCCAAGCACC 59.718 52.381 0.00 0.00 45.57 5.01
3140 3258 2.789409 AGTCCCTTGTATCCAAGCAC 57.211 50.000 0.00 0.00 45.57 4.40
3141 3259 5.450818 AAATAGTCCCTTGTATCCAAGCA 57.549 39.130 0.00 0.00 45.57 3.91
3142 3260 6.775594 AAAAATAGTCCCTTGTATCCAAGC 57.224 37.500 0.00 0.00 45.57 4.01
3143 3261 9.110502 GACTAAAAATAGTCCCTTGTATCCAAG 57.889 37.037 4.96 0.00 40.86 3.61
3144 3262 8.832735 AGACTAAAAATAGTCCCTTGTATCCAA 58.167 33.333 11.35 0.00 45.66 3.53
3145 3263 8.265055 CAGACTAAAAATAGTCCCTTGTATCCA 58.735 37.037 11.35 0.00 45.66 3.41
3146 3264 8.483758 TCAGACTAAAAATAGTCCCTTGTATCC 58.516 37.037 11.35 0.00 45.66 2.59
3147 3265 9.315525 GTCAGACTAAAAATAGTCCCTTGTATC 57.684 37.037 11.35 0.00 45.66 2.24
3148 3266 9.047947 AGTCAGACTAAAAATAGTCCCTTGTAT 57.952 33.333 0.00 0.00 45.66 2.29
3149 3267 8.431910 AGTCAGACTAAAAATAGTCCCTTGTA 57.568 34.615 0.00 0.00 45.66 2.41
3150 3268 7.317722 AGTCAGACTAAAAATAGTCCCTTGT 57.682 36.000 0.00 0.00 45.66 3.16
3151 3269 9.720769 TTTAGTCAGACTAAAAATAGTCCCTTG 57.279 33.333 26.93 5.29 44.84 3.61
3186 3304 8.139350 GGTGCTTAGAACTTTAGCCTTTAAAAA 58.861 33.333 0.00 0.00 34.03 1.94
3187 3305 7.255695 GGGTGCTTAGAACTTTAGCCTTTAAAA 60.256 37.037 0.00 0.00 34.03 1.52
3188 3306 6.208007 GGGTGCTTAGAACTTTAGCCTTTAAA 59.792 38.462 0.00 0.00 34.03 1.52
3189 3307 5.708697 GGGTGCTTAGAACTTTAGCCTTTAA 59.291 40.000 0.00 0.00 34.03 1.52
3190 3308 5.250982 GGGTGCTTAGAACTTTAGCCTTTA 58.749 41.667 0.00 0.00 34.03 1.85
3191 3309 4.079970 GGGTGCTTAGAACTTTAGCCTTT 58.920 43.478 0.00 0.00 34.03 3.11
3192 3310 3.561528 GGGGTGCTTAGAACTTTAGCCTT 60.562 47.826 0.00 0.00 34.03 4.35
3193 3311 2.026169 GGGGTGCTTAGAACTTTAGCCT 60.026 50.000 0.00 0.00 34.03 4.58
3194 3312 2.026169 AGGGGTGCTTAGAACTTTAGCC 60.026 50.000 0.00 0.00 34.03 3.93
3195 3313 3.010420 CAGGGGTGCTTAGAACTTTAGC 58.990 50.000 0.00 0.00 35.50 3.09
3196 3314 4.020128 AGTCAGGGGTGCTTAGAACTTTAG 60.020 45.833 0.00 0.00 0.00 1.85
3197 3315 3.908103 AGTCAGGGGTGCTTAGAACTTTA 59.092 43.478 0.00 0.00 0.00 1.85
3198 3316 2.711547 AGTCAGGGGTGCTTAGAACTTT 59.288 45.455 0.00 0.00 0.00 2.66
3199 3317 2.339769 AGTCAGGGGTGCTTAGAACTT 58.660 47.619 0.00 0.00 0.00 2.66
3200 3318 2.031495 AGTCAGGGGTGCTTAGAACT 57.969 50.000 0.00 0.00 0.00 3.01
3201 3319 3.975168 TTAGTCAGGGGTGCTTAGAAC 57.025 47.619 0.00 0.00 0.00 3.01
3202 3320 4.164981 TCTTTAGTCAGGGGTGCTTAGAA 58.835 43.478 0.00 0.00 0.00 2.10
3203 3321 3.769844 CTCTTTAGTCAGGGGTGCTTAGA 59.230 47.826 0.00 0.00 0.00 2.10
3204 3322 3.769844 TCTCTTTAGTCAGGGGTGCTTAG 59.230 47.826 0.00 0.00 0.00 2.18
3205 3323 3.769844 CTCTCTTTAGTCAGGGGTGCTTA 59.230 47.826 0.00 0.00 0.00 3.09
3206 3324 2.569404 CTCTCTTTAGTCAGGGGTGCTT 59.431 50.000 0.00 0.00 0.00 3.91
3207 3325 2.183679 CTCTCTTTAGTCAGGGGTGCT 58.816 52.381 0.00 0.00 0.00 4.40
3208 3326 1.208293 CCTCTCTTTAGTCAGGGGTGC 59.792 57.143 0.00 0.00 0.00 5.01
3209 3327 1.208293 GCCTCTCTTTAGTCAGGGGTG 59.792 57.143 0.00 0.00 0.00 4.61
3210 3328 1.079658 AGCCTCTCTTTAGTCAGGGGT 59.920 52.381 0.00 0.00 0.00 4.95
3211 3329 1.872773 AGCCTCTCTTTAGTCAGGGG 58.127 55.000 0.00 0.00 0.00 4.79
3212 3330 2.962421 CCTAGCCTCTCTTTAGTCAGGG 59.038 54.545 0.00 0.00 0.00 4.45
3213 3331 3.634910 GTCCTAGCCTCTCTTTAGTCAGG 59.365 52.174 0.00 0.00 0.00 3.86
3214 3332 4.532834 AGTCCTAGCCTCTCTTTAGTCAG 58.467 47.826 0.00 0.00 0.00 3.51
3215 3333 4.594675 AGTCCTAGCCTCTCTTTAGTCA 57.405 45.455 0.00 0.00 0.00 3.41
3216 3334 5.687780 ACTAGTCCTAGCCTCTCTTTAGTC 58.312 45.833 1.22 0.00 36.66 2.59
3217 3335 5.430745 AGACTAGTCCTAGCCTCTCTTTAGT 59.569 44.000 19.38 0.00 36.66 2.24
3218 3336 5.937111 AGACTAGTCCTAGCCTCTCTTTAG 58.063 45.833 19.38 0.00 36.66 1.85
3219 3337 5.979656 AGACTAGTCCTAGCCTCTCTTTA 57.020 43.478 19.38 0.00 36.66 1.85
3220 3338 4.873724 AGACTAGTCCTAGCCTCTCTTT 57.126 45.455 19.38 0.00 36.66 2.52
3221 3339 4.228666 TCAAGACTAGTCCTAGCCTCTCTT 59.771 45.833 19.38 0.17 36.66 2.85
3222 3340 3.783642 TCAAGACTAGTCCTAGCCTCTCT 59.216 47.826 19.38 0.00 36.66 3.10
3223 3341 4.134563 CTCAAGACTAGTCCTAGCCTCTC 58.865 52.174 19.38 0.00 36.66 3.20
3224 3342 3.117663 CCTCAAGACTAGTCCTAGCCTCT 60.118 52.174 19.38 0.00 36.66 3.69
3225 3343 3.219281 CCTCAAGACTAGTCCTAGCCTC 58.781 54.545 19.38 0.00 36.66 4.70
3226 3344 2.688515 GCCTCAAGACTAGTCCTAGCCT 60.689 54.545 19.38 0.00 36.66 4.58
3227 3345 1.684450 GCCTCAAGACTAGTCCTAGCC 59.316 57.143 19.38 0.89 36.66 3.93
3228 3346 2.661718 AGCCTCAAGACTAGTCCTAGC 58.338 52.381 19.38 14.54 36.66 3.42
3229 3347 6.777213 TTTTAGCCTCAAGACTAGTCCTAG 57.223 41.667 19.38 13.33 39.04 3.02
3230 3348 7.126733 AGATTTTAGCCTCAAGACTAGTCCTA 58.873 38.462 19.38 9.39 0.00 2.94
3231 3349 5.961421 AGATTTTAGCCTCAAGACTAGTCCT 59.039 40.000 19.38 10.36 0.00 3.85
3232 3350 6.228616 AGATTTTAGCCTCAAGACTAGTCC 57.771 41.667 19.38 2.89 0.00 3.85
3233 3351 8.554835 AAAAGATTTTAGCCTCAAGACTAGTC 57.445 34.615 15.41 15.41 0.00 2.59
3234 3352 9.660180 CTAAAAGATTTTAGCCTCAAGACTAGT 57.340 33.333 11.10 0.00 41.97 2.57
3277 3395 9.600432 AGGAGAGAGAGAGCTAATACATATTTT 57.400 33.333 0.00 0.00 0.00 1.82
3278 3396 9.243105 GAGGAGAGAGAGAGCTAATACATATTT 57.757 37.037 0.00 0.00 0.00 1.40
3279 3397 8.390143 TGAGGAGAGAGAGAGCTAATACATATT 58.610 37.037 0.00 0.00 0.00 1.28
3280 3398 7.927788 TGAGGAGAGAGAGAGCTAATACATAT 58.072 38.462 0.00 0.00 0.00 1.78
3281 3399 7.323052 TGAGGAGAGAGAGAGCTAATACATA 57.677 40.000 0.00 0.00 0.00 2.29
3282 3400 6.199557 TGAGGAGAGAGAGAGCTAATACAT 57.800 41.667 0.00 0.00 0.00 2.29
3283 3401 5.638530 TGAGGAGAGAGAGAGCTAATACA 57.361 43.478 0.00 0.00 0.00 2.29
3284 3402 7.524717 AAATGAGGAGAGAGAGAGCTAATAC 57.475 40.000 0.00 0.00 0.00 1.89
3285 3403 9.821240 ATTAAATGAGGAGAGAGAGAGCTAATA 57.179 33.333 0.00 0.00 0.00 0.98
3286 3404 8.725606 ATTAAATGAGGAGAGAGAGAGCTAAT 57.274 34.615 0.00 0.00 0.00 1.73
3287 3405 8.546083 AATTAAATGAGGAGAGAGAGAGCTAA 57.454 34.615 0.00 0.00 0.00 3.09
3288 3406 7.232534 GGAATTAAATGAGGAGAGAGAGAGCTA 59.767 40.741 0.00 0.00 0.00 3.32
3289 3407 6.041979 GGAATTAAATGAGGAGAGAGAGAGCT 59.958 42.308 0.00 0.00 0.00 4.09
3290 3408 6.041979 AGGAATTAAATGAGGAGAGAGAGAGC 59.958 42.308 0.00 0.00 0.00 4.09
3291 3409 7.506938 AGAGGAATTAAATGAGGAGAGAGAGAG 59.493 40.741 0.00 0.00 0.00 3.20
3292 3410 7.361438 AGAGGAATTAAATGAGGAGAGAGAGA 58.639 38.462 0.00 0.00 0.00 3.10
3293 3411 7.255942 GGAGAGGAATTAAATGAGGAGAGAGAG 60.256 44.444 0.00 0.00 0.00 3.20
3294 3412 6.553100 GGAGAGGAATTAAATGAGGAGAGAGA 59.447 42.308 0.00 0.00 0.00 3.10
3295 3413 6.554605 AGGAGAGGAATTAAATGAGGAGAGAG 59.445 42.308 0.00 0.00 0.00 3.20
3296 3414 6.448202 AGGAGAGGAATTAAATGAGGAGAGA 58.552 40.000 0.00 0.00 0.00 3.10
3297 3415 6.745794 AGGAGAGGAATTAAATGAGGAGAG 57.254 41.667 0.00 0.00 0.00 3.20
3298 3416 7.846823 ACTAAGGAGAGGAATTAAATGAGGAGA 59.153 37.037 0.00 0.00 0.00 3.71
3299 3417 8.028652 ACTAAGGAGAGGAATTAAATGAGGAG 57.971 38.462 0.00 0.00 0.00 3.69
3300 3418 7.996758 ACTAAGGAGAGGAATTAAATGAGGA 57.003 36.000 0.00 0.00 0.00 3.71
3301 3419 8.490311 AGAACTAAGGAGAGGAATTAAATGAGG 58.510 37.037 0.00 0.00 0.00 3.86
3302 3420 9.323985 CAGAACTAAGGAGAGGAATTAAATGAG 57.676 37.037 0.00 0.00 0.00 2.90
3303 3421 9.046846 TCAGAACTAAGGAGAGGAATTAAATGA 57.953 33.333 0.00 0.00 0.00 2.57
3304 3422 9.672673 TTCAGAACTAAGGAGAGGAATTAAATG 57.327 33.333 0.00 0.00 0.00 2.32
3307 3425 9.672673 CAATTCAGAACTAAGGAGAGGAATTAA 57.327 33.333 0.00 0.00 33.41 1.40
3308 3426 8.267894 CCAATTCAGAACTAAGGAGAGGAATTA 58.732 37.037 0.00 0.00 33.41 1.40
3309 3427 7.037297 TCCAATTCAGAACTAAGGAGAGGAATT 60.037 37.037 0.00 0.00 34.95 2.17
3310 3428 6.445139 TCCAATTCAGAACTAAGGAGAGGAAT 59.555 38.462 0.00 0.00 0.00 3.01
3311 3429 5.785423 TCCAATTCAGAACTAAGGAGAGGAA 59.215 40.000 0.00 0.00 0.00 3.36
3312 3430 5.342017 TCCAATTCAGAACTAAGGAGAGGA 58.658 41.667 0.00 0.00 0.00 3.71
3313 3431 5.396213 CCTCCAATTCAGAACTAAGGAGAGG 60.396 48.000 17.50 9.03 42.87 3.69
3314 3432 5.396213 CCCTCCAATTCAGAACTAAGGAGAG 60.396 48.000 17.50 6.44 42.87 3.20
3315 3433 4.471386 CCCTCCAATTCAGAACTAAGGAGA 59.529 45.833 17.50 0.00 42.87 3.71
3316 3434 4.226168 ACCCTCCAATTCAGAACTAAGGAG 59.774 45.833 12.13 12.13 40.58 3.69
3317 3435 4.175962 ACCCTCCAATTCAGAACTAAGGA 58.824 43.478 4.86 0.00 0.00 3.36
3318 3436 4.576330 ACCCTCCAATTCAGAACTAAGG 57.424 45.455 0.00 0.00 0.00 2.69
3319 3437 5.183904 CCAAACCCTCCAATTCAGAACTAAG 59.816 44.000 0.00 0.00 0.00 2.18
3320 3438 5.076873 CCAAACCCTCCAATTCAGAACTAA 58.923 41.667 0.00 0.00 0.00 2.24
3321 3439 4.352595 TCCAAACCCTCCAATTCAGAACTA 59.647 41.667 0.00 0.00 0.00 2.24
3322 3440 3.140144 TCCAAACCCTCCAATTCAGAACT 59.860 43.478 0.00 0.00 0.00 3.01
3323 3441 3.496331 TCCAAACCCTCCAATTCAGAAC 58.504 45.455 0.00 0.00 0.00 3.01
3324 3442 3.500289 CCTCCAAACCCTCCAATTCAGAA 60.500 47.826 0.00 0.00 0.00 3.02
3325 3443 2.041620 CCTCCAAACCCTCCAATTCAGA 59.958 50.000 0.00 0.00 0.00 3.27
3326 3444 2.041620 TCCTCCAAACCCTCCAATTCAG 59.958 50.000 0.00 0.00 0.00 3.02
3327 3445 2.069775 TCCTCCAAACCCTCCAATTCA 58.930 47.619 0.00 0.00 0.00 2.57
3328 3446 2.899303 TCCTCCAAACCCTCCAATTC 57.101 50.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.