Multiple sequence alignment - TraesCS4A01G130400

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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 TraesCS4A01G130400 chr4A 100.000 3513 0 0 1 3513 172016872 172013360 0.000000e+00 6488
1 TraesCS4A01G130400 chr4D 94.245 2085 64 17 444 2516 305378496 305380536 0.000000e+00 3134
2 TraesCS4A01G130400 chr4D 88.043 460 22 10 1 436 305377878 305378328 6.720000e-142 514
3 TraesCS4A01G130400 chr4D 83.955 536 36 22 2988 3513 305383465 305383960 5.310000e-128 468
4 TraesCS4A01G130400 chr4D 90.800 250 11 7 2510 2755 305380558 305380799 1.220000e-84 324
5 TraesCS4A01G130400 chr4B 93.031 2095 96 26 443 2516 381692340 381694405 0.000000e+00 3014
6 TraesCS4A01G130400 chr4B 88.104 538 45 12 2988 3513 381709864 381710394 3.850000e-174 621
7 TraesCS4A01G130400 chr4B 90.534 412 21 4 1 412 381687944 381688337 2.400000e-146 529
8 TraesCS4A01G130400 chr4B 89.493 276 16 7 2510 2777 381694427 381694697 1.560000e-88 337


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 TraesCS4A01G130400 chr4A 172013360 172016872 3512 True 6488.0 6488 100.00000 1 3513 1 chr4A.!!$R1 3512
1 TraesCS4A01G130400 chr4D 305377878 305383960 6082 False 1110.0 3134 89.26075 1 3513 4 chr4D.!!$F1 3512
2 TraesCS4A01G130400 chr4B 381692340 381694697 2357 False 1675.5 3014 91.26200 443 2777 2 chr4B.!!$F3 2334
3 TraesCS4A01G130400 chr4B 381709864 381710394 530 False 621.0 621 88.10400 2988 3513 1 chr4B.!!$F2 525

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
974 1177 0.035458 CGGCTTCTCCTCCTGTGTTT 59.965 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2889 3242 0.313672 GGAATGCAAGAACGCACCAA 59.686 50.0 0.0 0.0 46.56 3.67 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
38 39 2.805671 CGCTATCACTCAACCACACAAA 59.194 45.455 0.00 0.00 0.00 2.83
76 77 7.798486 CGAATTCGGTTACTATGAATAGGAG 57.202 40.000 20.16 0.00 32.32 3.69
116 117 7.446319 CACCGCATAATATCATCCATATCCAAT 59.554 37.037 0.00 0.00 0.00 3.16
117 118 8.659527 ACCGCATAATATCATCCATATCCAATA 58.340 33.333 0.00 0.00 0.00 1.90
118 119 9.676861 CCGCATAATATCATCCATATCCAATAT 57.323 33.333 0.00 0.00 0.00 1.28
247 248 3.370672 CACAACAGTGGTTTTCTTTTGCC 59.629 43.478 0.00 0.00 34.21 4.52
257 258 5.103687 GGTTTTCTTTTGCCAACTCGTTTA 58.896 37.500 0.00 0.00 0.00 2.01
258 259 5.577554 GGTTTTCTTTTGCCAACTCGTTTAA 59.422 36.000 0.00 0.00 0.00 1.52
259 260 6.091034 GGTTTTCTTTTGCCAACTCGTTTAAA 59.909 34.615 0.00 0.00 0.00 1.52
260 261 7.360185 GGTTTTCTTTTGCCAACTCGTTTAAAA 60.360 33.333 0.00 0.00 0.00 1.52
261 262 7.653767 TTTCTTTTGCCAACTCGTTTAAAAA 57.346 28.000 0.00 0.00 0.00 1.94
295 296 4.695455 TGAGATCAAGTCGATTTCCAAACC 59.305 41.667 0.00 0.00 34.93 3.27
296 297 4.651778 AGATCAAGTCGATTTCCAAACCA 58.348 39.130 0.00 0.00 33.17 3.67
297 298 4.697352 AGATCAAGTCGATTTCCAAACCAG 59.303 41.667 0.00 0.00 33.17 4.00
298 299 2.552315 TCAAGTCGATTTCCAAACCAGC 59.448 45.455 0.00 0.00 0.00 4.85
299 300 2.270352 AGTCGATTTCCAAACCAGCA 57.730 45.000 0.00 0.00 0.00 4.41
301 302 1.068541 GTCGATTTCCAAACCAGCACC 60.069 52.381 0.00 0.00 0.00 5.01
303 304 1.335872 CGATTTCCAAACCAGCACCAC 60.336 52.381 0.00 0.00 0.00 4.16
304 305 0.673437 ATTTCCAAACCAGCACCACG 59.327 50.000 0.00 0.00 0.00 4.94
337 361 6.236017 TCGCGAGAGTTTCAAAATTATTGT 57.764 33.333 3.71 0.00 34.84 2.71
343 367 7.504924 AGAGTTTCAAAATTATTGTCGTGGA 57.495 32.000 0.00 0.00 0.00 4.02
355 379 5.880054 ATTGTCGTGGATTTAGTTCAAGG 57.120 39.130 0.00 0.00 0.00 3.61
358 382 5.556915 TGTCGTGGATTTAGTTCAAGGAAT 58.443 37.500 0.00 0.00 0.00 3.01
360 384 5.411669 GTCGTGGATTTAGTTCAAGGAATGT 59.588 40.000 0.00 0.00 0.00 2.71
362 386 7.118680 GTCGTGGATTTAGTTCAAGGAATGTAA 59.881 37.037 0.00 0.00 0.00 2.41
424 449 7.726033 ATCTACTCTTTTGGTATCTCTGTGT 57.274 36.000 0.00 0.00 0.00 3.72
441 466 1.525619 GTGTGTGGCACTTAGTTCGTC 59.474 52.381 19.83 0.00 44.41 4.20
583 768 4.135153 CTGCCACGAGTCCCCGAG 62.135 72.222 0.00 0.00 0.00 4.63
695 880 3.254093 TCCGGTACATATCCATCCTGT 57.746 47.619 0.00 0.00 0.00 4.00
699 884 3.668447 GGTACATATCCATCCTGTGCAG 58.332 50.000 0.00 0.00 0.00 4.41
750 935 1.585521 GACTACGTGGCGACCATCG 60.586 63.158 0.00 14.19 43.89 3.84
778 963 2.648320 ATCGATGCGTCGGACGACTG 62.648 60.000 32.48 18.02 46.05 3.51
805 990 2.116533 CGGCGGGGGACATTTTACC 61.117 63.158 0.00 0.00 0.00 2.85
809 994 0.322997 CGGGGGACATTTTACCAGCA 60.323 55.000 0.00 0.00 0.00 4.41
810 995 1.888826 CGGGGGACATTTTACCAGCAA 60.889 52.381 0.00 0.00 0.00 3.91
824 1009 4.137116 ACCAGCAAAAAGGGAAGAAAAC 57.863 40.909 0.00 0.00 0.00 2.43
830 1015 1.104577 AAAGGGAAGAAAACGCGGCA 61.105 50.000 12.47 0.00 0.00 5.69
858 1048 0.317020 ACTTCGCGTTGCTTGCTTTC 60.317 50.000 5.77 0.00 0.00 2.62
932 1132 0.478507 CCCTCTCTCCTCTCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
933 1133 1.522900 CCTCTCTCCTCTCCTCTCCT 58.477 60.000 0.00 0.00 0.00 3.69
934 1134 1.421646 CCTCTCTCCTCTCCTCTCCTC 59.578 61.905 0.00 0.00 0.00 3.71
935 1135 2.412591 CTCTCTCCTCTCCTCTCCTCT 58.587 57.143 0.00 0.00 0.00 3.69
936 1136 2.370189 CTCTCTCCTCTCCTCTCCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
937 1137 2.022035 TCTCTCCTCTCCTCTCCTCTCT 60.022 54.545 0.00 0.00 0.00 3.10
968 1171 1.076339 CCTCTCGGCTTCTCCTCCT 60.076 63.158 0.00 0.00 0.00 3.69
969 1172 1.391157 CCTCTCGGCTTCTCCTCCTG 61.391 65.000 0.00 0.00 0.00 3.86
970 1173 0.682855 CTCTCGGCTTCTCCTCCTGT 60.683 60.000 0.00 0.00 0.00 4.00
971 1174 0.967887 TCTCGGCTTCTCCTCCTGTG 60.968 60.000 0.00 0.00 0.00 3.66
972 1175 1.228894 TCGGCTTCTCCTCCTGTGT 60.229 57.895 0.00 0.00 0.00 3.72
973 1176 0.832135 TCGGCTTCTCCTCCTGTGTT 60.832 55.000 0.00 0.00 0.00 3.32
974 1177 0.035458 CGGCTTCTCCTCCTGTGTTT 59.965 55.000 0.00 0.00 0.00 2.83
975 1178 1.814793 GGCTTCTCCTCCTGTGTTTC 58.185 55.000 0.00 0.00 0.00 2.78
976 1179 1.611936 GGCTTCTCCTCCTGTGTTTCC 60.612 57.143 0.00 0.00 0.00 3.13
1188 1391 2.134933 GGTCGGTCCCAGGAGATCC 61.135 68.421 0.00 0.00 0.00 3.36
1198 1401 1.065854 CCAGGAGATCCAAGCTCGTTT 60.066 52.381 0.92 0.00 38.89 3.60
1200 1403 1.208293 AGGAGATCCAAGCTCGTTTCC 59.792 52.381 0.92 0.00 38.89 3.13
1297 1500 1.710013 TCTCTTTTGATCGTCGGTGC 58.290 50.000 0.00 0.00 0.00 5.01
1301 1504 0.609151 TTTTGATCGTCGGTGCCCTA 59.391 50.000 0.00 0.00 0.00 3.53
1349 1562 7.703058 ATATTTTCCCTGACTTAACCTGTTG 57.297 36.000 0.00 0.00 0.00 3.33
1451 1664 5.294306 TCTGCTATTTTGCAACTAATCTCCG 59.706 40.000 0.00 0.00 42.83 4.63
1486 1699 1.152694 GGGCCAATATGCTGAGCCA 60.153 57.895 4.39 0.00 45.72 4.75
1580 1793 0.324738 TGAGGGAGATTGAGTCCGCT 60.325 55.000 0.00 0.00 34.56 5.52
1733 1946 2.300437 ACTACAGTTCTGAAGCTCCACC 59.700 50.000 6.83 0.00 0.00 4.61
1744 1957 2.094659 GCTCCACCGTCGTGTGATG 61.095 63.158 13.37 7.93 38.55 3.07
1854 2068 4.395959 AGTGAACTACGAGGAACACAAA 57.604 40.909 0.00 0.00 0.00 2.83
1906 2120 1.628846 TGCCCTTCTTCAGGTTCTACC 59.371 52.381 0.00 0.00 42.02 3.18
1979 2193 5.220710 AGATACTAATCTGGTCATGTGCC 57.779 43.478 0.00 0.00 41.08 5.01
2102 2316 4.150897 TGAAAGCCTTCCATATAGCGTT 57.849 40.909 0.00 0.00 0.00 4.84
2118 2332 2.000447 GCGTTACTTGGAGCTTACTGG 59.000 52.381 0.00 0.00 0.00 4.00
2366 2589 2.970974 GCTGCGAACAAGGACCTGC 61.971 63.158 0.00 0.00 0.00 4.85
2368 2591 1.572085 CTGCGAACAAGGACCTGCAG 61.572 60.000 14.40 14.40 43.08 4.41
2385 2608 1.605712 GCAGTTCACCTACACGAAGCT 60.606 52.381 0.00 0.00 0.00 3.74
2393 2616 1.406069 CCTACACGAAGCTGCCAGAAT 60.406 52.381 0.00 0.00 0.00 2.40
2467 2690 0.599728 CACCGGCAAAACCATTGGTG 60.600 55.000 9.62 0.00 39.97 4.17
2525 2776 2.546795 GGAAGATGAGATCGCGTCCATT 60.547 50.000 14.26 4.23 32.94 3.16
2542 2795 4.215613 GTCCATTGGTTCTGTACAGTTTCC 59.784 45.833 21.99 20.21 0.00 3.13
2565 2818 3.303725 CGATTGTTGTTGGTGTGTACAGG 60.304 47.826 0.00 0.00 0.00 4.00
2631 2884 1.059913 ACTACTTGTCAAGCCTGCCT 58.940 50.000 12.66 0.00 0.00 4.75
2632 2885 1.421646 ACTACTTGTCAAGCCTGCCTT 59.578 47.619 12.66 0.00 0.00 4.35
2633 2886 2.079925 CTACTTGTCAAGCCTGCCTTC 58.920 52.381 12.66 0.00 0.00 3.46
2636 2889 2.747855 GTCAAGCCTGCCTTCCCG 60.748 66.667 0.00 0.00 0.00 5.14
2637 2890 4.722700 TCAAGCCTGCCTTCCCGC 62.723 66.667 0.00 0.00 0.00 6.13
2642 2895 4.168291 CCTGCCTTCCCGCCTCTC 62.168 72.222 0.00 0.00 0.00 3.20
2643 2896 4.168291 CTGCCTTCCCGCCTCTCC 62.168 72.222 0.00 0.00 0.00 3.71
2668 2921 4.364415 AGAAGCGTAGAAGTAGAAGCAG 57.636 45.455 0.00 0.00 0.00 4.24
2673 2926 4.701171 AGCGTAGAAGTAGAAGCAGTACTT 59.299 41.667 0.00 5.38 42.26 2.24
2733 2986 6.710744 GCCAGTAAATTGTATGGTAGCTGTAT 59.289 38.462 0.00 0.00 35.17 2.29
2734 2987 7.307989 GCCAGTAAATTGTATGGTAGCTGTATG 60.308 40.741 0.00 0.00 35.17 2.39
2735 2988 7.173218 CCAGTAAATTGTATGGTAGCTGTATGG 59.827 40.741 0.00 0.00 0.00 2.74
2739 2992 6.757173 ATTGTATGGTAGCTGTATGGGTTA 57.243 37.500 0.00 0.00 0.00 2.85
2755 3008 4.415596 TGGGTTAAATCTGAGTGCCAATT 58.584 39.130 0.00 0.00 0.00 2.32
2756 3009 4.220382 TGGGTTAAATCTGAGTGCCAATTG 59.780 41.667 0.00 0.00 0.00 2.32
2757 3010 4.381932 GGGTTAAATCTGAGTGCCAATTGG 60.382 45.833 20.81 20.81 38.53 3.16
2758 3011 4.462483 GGTTAAATCTGAGTGCCAATTGGA 59.538 41.667 29.02 10.48 37.39 3.53
2759 3012 5.047377 GGTTAAATCTGAGTGCCAATTGGAA 60.047 40.000 29.02 16.26 37.39 3.53
2773 3031 1.388547 TTGGAATTATCGTGCCTGCC 58.611 50.000 0.00 0.00 0.00 4.85
2777 3035 2.017049 GAATTATCGTGCCTGCCTTGT 58.983 47.619 0.00 0.00 0.00 3.16
2780 3038 0.392461 TATCGTGCCTGCCTTGTTCC 60.392 55.000 0.00 0.00 0.00 3.62
2781 3039 3.365265 CGTGCCTGCCTTGTTCCC 61.365 66.667 0.00 0.00 0.00 3.97
2784 3042 2.118294 GCCTGCCTTGTTCCCCTT 59.882 61.111 0.00 0.00 0.00 3.95
2796 3149 5.278808 CCTTGTTCCCCTTTAGTAGTTTTGC 60.279 44.000 0.00 0.00 0.00 3.68
2798 3151 5.451354 TGTTCCCCTTTAGTAGTTTTGCTT 58.549 37.500 0.00 0.00 0.00 3.91
2799 3152 5.300792 TGTTCCCCTTTAGTAGTTTTGCTTG 59.699 40.000 0.00 0.00 0.00 4.01
2802 3155 5.533528 TCCCCTTTAGTAGTTTTGCTTGTTC 59.466 40.000 0.00 0.00 0.00 3.18
2805 3158 6.363473 CCTTTAGTAGTTTTGCTTGTTCGAG 58.637 40.000 0.00 0.00 0.00 4.04
2816 3169 5.947228 TGCTTGTTCGAGAATCTGAAATT 57.053 34.783 0.00 0.00 31.62 1.82
2819 3172 5.792468 GCTTGTTCGAGAATCTGAAATTCAC 59.208 40.000 0.00 0.00 31.62 3.18
2822 3175 2.930040 TCGAGAATCTGAAATTCACCGC 59.070 45.455 0.00 0.00 0.00 5.68
2830 3183 2.684881 CTGAAATTCACCGCCTGCTAAT 59.315 45.455 0.00 0.00 0.00 1.73
2831 3184 3.876914 CTGAAATTCACCGCCTGCTAATA 59.123 43.478 0.00 0.00 0.00 0.98
2832 3185 4.460263 TGAAATTCACCGCCTGCTAATAT 58.540 39.130 0.00 0.00 0.00 1.28
2833 3186 4.275689 TGAAATTCACCGCCTGCTAATATG 59.724 41.667 0.00 0.00 0.00 1.78
2834 3187 3.492102 ATTCACCGCCTGCTAATATGT 57.508 42.857 0.00 0.00 0.00 2.29
2835 3188 4.617253 ATTCACCGCCTGCTAATATGTA 57.383 40.909 0.00 0.00 0.00 2.29
2836 3189 3.380479 TCACCGCCTGCTAATATGTAC 57.620 47.619 0.00 0.00 0.00 2.90
2837 3190 2.963101 TCACCGCCTGCTAATATGTACT 59.037 45.455 0.00 0.00 0.00 2.73
2838 3191 3.005472 TCACCGCCTGCTAATATGTACTC 59.995 47.826 0.00 0.00 0.00 2.59
2839 3192 2.299297 ACCGCCTGCTAATATGTACTCC 59.701 50.000 0.00 0.00 0.00 3.85
2840 3193 2.353803 CCGCCTGCTAATATGTACTCCC 60.354 54.545 0.00 0.00 0.00 4.30
2841 3194 2.563179 CGCCTGCTAATATGTACTCCCT 59.437 50.000 0.00 0.00 0.00 4.20
2842 3195 3.367498 CGCCTGCTAATATGTACTCCCTC 60.367 52.174 0.00 0.00 0.00 4.30
2843 3196 3.578716 GCCTGCTAATATGTACTCCCTCA 59.421 47.826 0.00 0.00 0.00 3.86
2844 3197 4.561734 GCCTGCTAATATGTACTCCCTCAC 60.562 50.000 0.00 0.00 0.00 3.51
2845 3198 4.835615 CCTGCTAATATGTACTCCCTCACT 59.164 45.833 0.00 0.00 0.00 3.41
2846 3199 5.305644 CCTGCTAATATGTACTCCCTCACTT 59.694 44.000 0.00 0.00 0.00 3.16
2847 3200 6.406692 TGCTAATATGTACTCCCTCACTTC 57.593 41.667 0.00 0.00 0.00 3.01
2848 3201 5.897250 TGCTAATATGTACTCCCTCACTTCA 59.103 40.000 0.00 0.00 0.00 3.02
2849 3202 6.382859 TGCTAATATGTACTCCCTCACTTCAA 59.617 38.462 0.00 0.00 0.00 2.69
2850 3203 7.093068 TGCTAATATGTACTCCCTCACTTCAAA 60.093 37.037 0.00 0.00 0.00 2.69
2851 3204 7.769044 GCTAATATGTACTCCCTCACTTCAAAA 59.231 37.037 0.00 0.00 0.00 2.44
2852 3205 9.838339 CTAATATGTACTCCCTCACTTCAAAAT 57.162 33.333 0.00 0.00 0.00 1.82
2855 3208 9.784531 ATATGTACTCCCTCACTTCAAAATATG 57.215 33.333 0.00 0.00 0.00 1.78
2856 3209 7.016153 TGTACTCCCTCACTTCAAAATATGT 57.984 36.000 0.00 0.00 0.00 2.29
2857 3210 6.878923 TGTACTCCCTCACTTCAAAATATGTG 59.121 38.462 0.00 0.00 0.00 3.21
2858 3211 5.880901 ACTCCCTCACTTCAAAATATGTGT 58.119 37.500 0.00 0.00 0.00 3.72
2859 3212 5.940470 ACTCCCTCACTTCAAAATATGTGTC 59.060 40.000 0.00 0.00 0.00 3.67
2860 3213 4.935205 TCCCTCACTTCAAAATATGTGTCG 59.065 41.667 0.00 0.00 0.00 4.35
2861 3214 4.695455 CCCTCACTTCAAAATATGTGTCGT 59.305 41.667 0.00 0.00 0.00 4.34
2862 3215 5.390885 CCCTCACTTCAAAATATGTGTCGTG 60.391 44.000 0.00 0.00 0.00 4.35
2863 3216 5.390885 CCTCACTTCAAAATATGTGTCGTGG 60.391 44.000 0.00 0.00 0.00 4.94
2864 3217 5.060506 TCACTTCAAAATATGTGTCGTGGT 58.939 37.500 0.00 0.00 0.00 4.16
2865 3218 5.529430 TCACTTCAAAATATGTGTCGTGGTT 59.471 36.000 0.00 0.00 0.00 3.67
2866 3219 5.624900 CACTTCAAAATATGTGTCGTGGTTG 59.375 40.000 0.00 0.00 0.00 3.77
2867 3220 5.298276 ACTTCAAAATATGTGTCGTGGTTGT 59.702 36.000 0.00 0.00 0.00 3.32
2868 3221 6.483974 ACTTCAAAATATGTGTCGTGGTTGTA 59.516 34.615 0.00 0.00 0.00 2.41
2869 3222 6.474819 TCAAAATATGTGTCGTGGTTGTAG 57.525 37.500 0.00 0.00 0.00 2.74
2870 3223 5.992829 TCAAAATATGTGTCGTGGTTGTAGT 59.007 36.000 0.00 0.00 0.00 2.73
2871 3224 6.483974 TCAAAATATGTGTCGTGGTTGTAGTT 59.516 34.615 0.00 0.00 0.00 2.24
2872 3225 6.476243 AAATATGTGTCGTGGTTGTAGTTC 57.524 37.500 0.00 0.00 0.00 3.01
2873 3226 2.963548 TGTGTCGTGGTTGTAGTTCA 57.036 45.000 0.00 0.00 0.00 3.18
2874 3227 3.248495 TGTGTCGTGGTTGTAGTTCAA 57.752 42.857 0.00 0.00 0.00 2.69
2875 3228 3.597255 TGTGTCGTGGTTGTAGTTCAAA 58.403 40.909 0.00 0.00 37.81 2.69
2876 3229 3.371591 TGTGTCGTGGTTGTAGTTCAAAC 59.628 43.478 0.00 0.00 43.43 2.93
2887 3240 6.293790 GGTTGTAGTTCAAACAGGTACAATCC 60.294 42.308 8.52 8.23 42.74 3.01
2889 3242 6.597562 TGTAGTTCAAACAGGTACAATCCTT 58.402 36.000 0.00 0.00 35.37 3.36
2891 3244 6.391227 AGTTCAAACAGGTACAATCCTTTG 57.609 37.500 0.00 0.00 35.37 2.77
2892 3245 5.301805 AGTTCAAACAGGTACAATCCTTTGG 59.698 40.000 0.00 0.00 37.15 3.28
2896 3249 1.468520 CAGGTACAATCCTTTGGTGCG 59.531 52.381 0.00 0.00 37.15 5.34
2910 3263 4.819783 TGCGTTCTTGCATTCCCT 57.180 50.000 0.00 0.00 40.62 4.20
2921 3274 1.648467 GCATTCCCTTCTGCGTGGTC 61.648 60.000 0.00 0.00 0.00 4.02
2924 3277 1.118965 TTCCCTTCTGCGTGGTCAGA 61.119 55.000 0.00 0.00 40.99 3.27
2926 3279 0.951040 CCCTTCTGCGTGGTCAGAAC 60.951 60.000 2.43 0.00 45.21 3.01
2927 3280 0.034059 CCTTCTGCGTGGTCAGAACT 59.966 55.000 2.43 0.00 45.21 3.01
2930 3283 0.315251 TCTGCGTGGTCAGAACTCAG 59.685 55.000 0.00 0.00 39.89 3.35
2932 3285 1.112916 TGCGTGGTCAGAACTCAGGA 61.113 55.000 0.00 0.00 0.00 3.86
2934 3287 1.937108 GCGTGGTCAGAACTCAGGAAG 60.937 57.143 0.00 0.00 0.00 3.46
2937 3290 1.345741 TGGTCAGAACTCAGGAAGCAG 59.654 52.381 0.00 0.00 0.00 4.24
2938 3291 1.338579 GGTCAGAACTCAGGAAGCAGG 60.339 57.143 0.00 0.00 0.00 4.85
2940 3293 2.563179 GTCAGAACTCAGGAAGCAGGTA 59.437 50.000 0.00 0.00 0.00 3.08
2941 3294 2.563179 TCAGAACTCAGGAAGCAGGTAC 59.437 50.000 0.00 0.00 0.00 3.34
2943 3296 3.055530 CAGAACTCAGGAAGCAGGTACAT 60.056 47.826 0.00 0.00 0.00 2.29
2944 3297 4.160439 CAGAACTCAGGAAGCAGGTACATA 59.840 45.833 0.00 0.00 0.00 2.29
2945 3298 4.965532 AGAACTCAGGAAGCAGGTACATAT 59.034 41.667 0.00 0.00 0.00 1.78
2946 3299 6.040955 CAGAACTCAGGAAGCAGGTACATATA 59.959 42.308 0.00 0.00 0.00 0.86
2947 3300 6.266558 AGAACTCAGGAAGCAGGTACATATAG 59.733 42.308 0.00 0.00 0.00 1.31
2948 3301 4.282195 ACTCAGGAAGCAGGTACATATAGC 59.718 45.833 0.00 0.00 0.00 2.97
2949 3302 4.483950 TCAGGAAGCAGGTACATATAGCT 58.516 43.478 0.00 0.00 39.81 3.32
2951 3304 5.366768 TCAGGAAGCAGGTACATATAGCTTT 59.633 40.000 5.24 0.00 44.73 3.51
2952 3305 5.698545 CAGGAAGCAGGTACATATAGCTTTC 59.301 44.000 5.24 3.64 44.73 2.62
2953 3306 5.604650 AGGAAGCAGGTACATATAGCTTTCT 59.395 40.000 6.15 6.15 44.18 2.52
2954 3307 5.698545 GGAAGCAGGTACATATAGCTTTCTG 59.301 44.000 5.24 0.00 44.73 3.02
2955 3308 5.878406 AGCAGGTACATATAGCTTTCTGT 57.122 39.130 0.00 0.00 37.01 3.41
2956 3309 5.605534 AGCAGGTACATATAGCTTTCTGTG 58.394 41.667 5.61 0.00 37.01 3.66
2957 3310 4.752101 GCAGGTACATATAGCTTTCTGTGG 59.248 45.833 5.61 0.00 37.01 4.17
2958 3311 5.685075 GCAGGTACATATAGCTTTCTGTGGT 60.685 44.000 5.61 0.00 37.01 4.16
2960 3313 6.823689 CAGGTACATATAGCTTTCTGTGGTTT 59.176 38.462 5.61 0.00 37.01 3.27
2962 3315 6.821665 GGTACATATAGCTTTCTGTGGTTTGA 59.178 38.462 5.61 0.00 0.00 2.69
2963 3316 7.335924 GGTACATATAGCTTTCTGTGGTTTGAA 59.664 37.037 5.61 0.00 0.00 2.69
2964 3317 7.383102 ACATATAGCTTTCTGTGGTTTGAAG 57.617 36.000 0.00 0.00 0.00 3.02
2965 3318 4.773323 ATAGCTTTCTGTGGTTTGAAGC 57.227 40.909 0.00 0.00 0.00 3.86
2966 3319 2.378038 AGCTTTCTGTGGTTTGAAGCA 58.622 42.857 8.81 0.00 0.00 3.91
2967 3320 2.360165 AGCTTTCTGTGGTTTGAAGCAG 59.640 45.455 8.81 0.00 37.04 4.24
2968 3321 2.544486 GCTTTCTGTGGTTTGAAGCAGG 60.544 50.000 0.00 0.00 37.04 4.85
2970 3323 1.967319 TCTGTGGTTTGAAGCAGGAC 58.033 50.000 0.00 0.00 37.04 3.85
2971 3324 1.490490 TCTGTGGTTTGAAGCAGGACT 59.510 47.619 0.00 0.00 37.04 3.85
2985 3338 6.619329 AAGCAGGACTTCTCTTTTCTAGAT 57.381 37.500 0.00 0.00 30.77 1.98
2990 5726 7.440856 GCAGGACTTCTCTTTTCTAGATATTGG 59.559 40.741 0.00 0.00 30.92 3.16
2997 5733 6.042552 TCTCTTTTCTAGATATTGGAGCTGGG 59.957 42.308 0.00 0.00 30.92 4.45
3003 5739 2.243221 AGATATTGGAGCTGGGCTTTGT 59.757 45.455 0.00 0.00 39.88 2.83
3016 5752 3.829601 TGGGCTTTGTAATCGGACAAAAT 59.170 39.130 10.83 0.00 45.98 1.82
3024 5760 2.143876 ATCGGACAAAATGGGAAGGG 57.856 50.000 0.00 0.00 0.00 3.95
3027 5763 1.264749 GGACAAAATGGGAAGGGGGC 61.265 60.000 0.00 0.00 0.00 5.80
3028 5764 1.604147 GACAAAATGGGAAGGGGGCG 61.604 60.000 0.00 0.00 0.00 6.13
3031 5767 0.178918 AAAATGGGAAGGGGGCGAAA 60.179 50.000 0.00 0.00 0.00 3.46
3032 5768 0.614697 AAATGGGAAGGGGGCGAAAG 60.615 55.000 0.00 0.00 0.00 2.62
3033 5769 1.506028 AATGGGAAGGGGGCGAAAGA 61.506 55.000 0.00 0.00 0.00 2.52
3035 5771 1.076014 GGGAAGGGGGCGAAAGAAA 59.924 57.895 0.00 0.00 0.00 2.52
3037 5773 1.595993 GGAAGGGGGCGAAAGAAAGC 61.596 60.000 0.00 0.00 0.00 3.51
3038 5774 0.893727 GAAGGGGGCGAAAGAAAGCA 60.894 55.000 0.00 0.00 34.54 3.91
3054 5791 9.906111 GAAAGAAAGCATTTGAAACTTAACAAG 57.094 29.630 0.00 0.00 39.27 3.16
3060 5797 5.050159 GCATTTGAAACTTAACAAGCAAGGG 60.050 40.000 0.00 0.00 0.00 3.95
3063 5800 4.274147 TGAAACTTAACAAGCAAGGGACA 58.726 39.130 0.00 0.00 0.00 4.02
3066 5803 4.164843 ACTTAACAAGCAAGGGACAAGA 57.835 40.909 0.00 0.00 0.00 3.02
3083 5820 4.779475 ACCTTGTGGTTGCTCTCG 57.221 55.556 0.00 0.00 46.05 4.04
3125 5862 0.465642 TCCTGCCGAGCTAGATCGAA 60.466 55.000 30.59 17.21 45.56 3.71
3131 5868 2.219674 GCCGAGCTAGATCGAATTGTTG 59.780 50.000 30.59 13.40 45.56 3.33
3145 5882 7.405469 TCGAATTGTTGAACCATCAATTTTG 57.595 32.000 13.77 10.95 46.67 2.44
3150 5887 7.865875 TTGTTGAACCATCAATTTTGTATCG 57.134 32.000 0.00 0.00 46.67 2.92
3152 5889 4.657055 TGAACCATCAATTTTGTATCGCG 58.343 39.130 0.00 0.00 30.99 5.87
3191 5929 8.690203 TGATATACATTACTGGGAAAATGGTG 57.310 34.615 0.00 0.00 37.40 4.17
3209 5947 4.541705 TGGTGGGTATTACCAATTGGATG 58.458 43.478 31.22 4.98 44.79 3.51
3211 5949 5.205056 GGTGGGTATTACCAATTGGATGAA 58.795 41.667 31.22 19.96 43.34 2.57
3222 5960 4.539870 CAATTGGATGAACATCGTATGCC 58.460 43.478 8.41 0.00 38.69 4.40
3232 5970 3.930336 ACATCGTATGCCCTGTCATATG 58.070 45.455 0.00 0.00 37.31 1.78
3243 5981 4.142093 GCCCTGTCATATGATTGTTTTGCT 60.142 41.667 9.02 0.00 0.00 3.91
3245 5983 6.732154 CCCTGTCATATGATTGTTTTGCTAG 58.268 40.000 9.02 0.00 0.00 3.42
3246 5984 6.238842 CCCTGTCATATGATTGTTTTGCTAGG 60.239 42.308 9.02 3.71 0.00 3.02
3247 5985 6.543465 CCTGTCATATGATTGTTTTGCTAGGA 59.457 38.462 9.02 0.00 0.00 2.94
3248 5986 7.230108 CCTGTCATATGATTGTTTTGCTAGGAT 59.770 37.037 9.02 0.00 0.00 3.24
3249 5987 9.276590 CTGTCATATGATTGTTTTGCTAGGATA 57.723 33.333 9.02 0.00 0.00 2.59
3271 6009 8.624776 GGATAATAACAGGAACAAGAAATGAGG 58.375 37.037 0.00 0.00 0.00 3.86
3281 6019 3.094572 CAAGAAATGAGGAAGCATGGGT 58.905 45.455 0.00 0.00 0.00 4.51
3287 6026 1.280133 TGAGGAAGCATGGGTTCAGAG 59.720 52.381 9.96 0.00 41.18 3.35
3292 6031 4.101741 AGGAAGCATGGGTTCAGAGTATAC 59.898 45.833 9.96 0.00 41.18 1.47
3309 6048 9.764363 CAGAGTATACAATTAGGCAAGAACATA 57.236 33.333 5.50 0.00 0.00 2.29
3331 6075 3.748048 ACCATATCATCAAGCGTATGCAC 59.252 43.478 10.11 0.00 46.23 4.57
3362 6106 6.476243 TTCGTTATTTTCTTCTCCTTTCCG 57.524 37.500 0.00 0.00 0.00 4.30
3365 6109 5.585047 CGTTATTTTCTTCTCCTTTCCGGAT 59.415 40.000 4.15 0.00 42.12 4.18
3369 6113 1.066143 TCTTCTCCTTTCCGGATGCAC 60.066 52.381 4.15 0.00 42.12 4.57
3373 6117 2.094675 CTCCTTTCCGGATGCACAATT 58.905 47.619 4.15 0.00 42.12 2.32
3374 6118 1.818060 TCCTTTCCGGATGCACAATTG 59.182 47.619 4.15 3.24 36.69 2.32
3375 6119 1.736696 CCTTTCCGGATGCACAATTGC 60.737 52.381 4.15 0.00 41.94 3.56
3388 6132 4.987408 CACAATTGCATATCCTTGTCCA 57.013 40.909 5.05 0.00 29.74 4.02
3389 6133 4.675510 CACAATTGCATATCCTTGTCCAC 58.324 43.478 5.05 0.00 29.74 4.02
3390 6134 4.158209 CACAATTGCATATCCTTGTCCACA 59.842 41.667 5.05 0.00 29.74 4.17
3391 6135 4.158394 ACAATTGCATATCCTTGTCCACAC 59.842 41.667 5.05 0.00 0.00 3.82
3392 6136 2.022764 TGCATATCCTTGTCCACACG 57.977 50.000 0.00 0.00 0.00 4.49
3393 6137 1.299541 GCATATCCTTGTCCACACGG 58.700 55.000 0.00 0.00 36.69 4.94
3394 6138 1.299541 CATATCCTTGTCCACACGGC 58.700 55.000 0.00 0.00 35.46 5.68
3417 6183 2.365582 GCCTCCGGCTTTTCTTATCAA 58.634 47.619 0.00 0.00 46.69 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.403038 CGAATTCGGATAAAGGATGGCT 58.597 45.455 20.16 0.00 35.37 4.75
169 170 2.288763 ACGCAGGTGCTAAATTTTTGGG 60.289 45.455 0.00 0.00 39.32 4.12
280 281 1.880027 GTGCTGGTTTGGAAATCGACT 59.120 47.619 0.00 0.00 0.00 4.18
295 296 2.159707 CGAAGGTTAATTCGTGGTGCTG 60.160 50.000 3.55 0.00 45.37 4.41
296 297 2.073816 CGAAGGTTAATTCGTGGTGCT 58.926 47.619 3.55 0.00 45.37 4.40
297 298 2.520686 CGAAGGTTAATTCGTGGTGC 57.479 50.000 3.55 0.00 45.37 5.01
304 305 4.387862 TGAAACTCTCGCGAAGGTTAATTC 59.612 41.667 21.09 16.57 0.00 2.17
316 340 6.031417 CACGACAATAATTTTGAAACTCTCGC 59.969 38.462 0.00 0.00 0.00 5.03
318 342 7.581476 TCCACGACAATAATTTTGAAACTCTC 58.419 34.615 0.00 0.00 0.00 3.20
337 361 5.556915 ACATTCCTTGAACTAAATCCACGA 58.443 37.500 0.00 0.00 0.00 4.35
343 367 9.892130 CTACTCCTTACATTCCTTGAACTAAAT 57.108 33.333 0.00 0.00 0.00 1.40
347 371 7.554959 TTCTACTCCTTACATTCCTTGAACT 57.445 36.000 0.00 0.00 0.00 3.01
388 413 8.037758 ACCAAAAGAGTAGATTCTACTCACATG 58.962 37.037 37.24 31.20 44.66 3.21
394 419 9.930158 AGAGATACCAAAAGAGTAGATTCTACT 57.070 33.333 23.24 23.24 0.00 2.57
424 449 0.669619 TCGACGAACTAAGTGCCACA 59.330 50.000 0.00 0.00 0.00 4.17
436 461 0.385029 TTTCCTTCCACGTCGACGAA 59.615 50.000 41.52 24.96 43.02 3.85
437 462 0.039798 CTTTCCTTCCACGTCGACGA 60.040 55.000 41.52 19.40 43.02 4.20
438 463 0.039798 TCTTTCCTTCCACGTCGACG 60.040 55.000 34.58 34.58 46.33 5.12
441 466 0.317479 ACCTCTTTCCTTCCACGTCG 59.683 55.000 0.00 0.00 0.00 5.12
514 699 1.080705 ACGTTCAGCGAGTAGTGGC 60.081 57.895 0.00 0.00 44.77 5.01
583 768 2.300437 AGAGAGAGCTGGGTGTAAACAC 59.700 50.000 4.63 4.63 45.72 3.32
733 918 2.488355 CGATGGTCGCCACGTAGT 59.512 61.111 0.50 0.00 35.80 2.73
778 963 3.222121 CCCCCGCCGACTACTACC 61.222 72.222 0.00 0.00 0.00 3.18
805 990 2.539688 GCGTTTTCTTCCCTTTTTGCTG 59.460 45.455 0.00 0.00 0.00 4.41
809 994 1.537348 GCCGCGTTTTCTTCCCTTTTT 60.537 47.619 4.92 0.00 0.00 1.94
810 995 0.031585 GCCGCGTTTTCTTCCCTTTT 59.968 50.000 4.92 0.00 0.00 2.27
848 1038 1.243342 CCCACGGATGAAAGCAAGCA 61.243 55.000 0.00 0.00 0.00 3.91
858 1048 0.611896 AAAAAGGAGGCCCACGGATG 60.612 55.000 0.00 0.00 33.88 3.51
932 1132 2.739379 GAGGGAAGAAACGCAAAGAGAG 59.261 50.000 0.00 0.00 0.00 3.20
933 1133 2.368875 AGAGGGAAGAAACGCAAAGAGA 59.631 45.455 0.00 0.00 0.00 3.10
934 1134 2.739379 GAGAGGGAAGAAACGCAAAGAG 59.261 50.000 0.00 0.00 0.00 2.85
935 1135 2.767505 GAGAGGGAAGAAACGCAAAGA 58.232 47.619 0.00 0.00 0.00 2.52
936 1136 1.461127 CGAGAGGGAAGAAACGCAAAG 59.539 52.381 0.00 0.00 0.00 2.77
937 1137 1.508632 CGAGAGGGAAGAAACGCAAA 58.491 50.000 0.00 0.00 0.00 3.68
968 1171 2.035961 CGTCAAGAGAGAGGGAAACACA 59.964 50.000 0.00 0.00 0.00 3.72
969 1172 2.610727 CCGTCAAGAGAGAGGGAAACAC 60.611 54.545 0.00 0.00 44.32 3.32
970 1173 1.618837 CCGTCAAGAGAGAGGGAAACA 59.381 52.381 0.00 0.00 44.32 2.83
971 1174 1.673329 GCCGTCAAGAGAGAGGGAAAC 60.673 57.143 6.85 0.00 44.32 2.78
972 1175 0.608640 GCCGTCAAGAGAGAGGGAAA 59.391 55.000 6.85 0.00 44.32 3.13
973 1176 1.595993 CGCCGTCAAGAGAGAGGGAA 61.596 60.000 6.85 0.00 44.32 3.97
974 1177 2.046864 CGCCGTCAAGAGAGAGGGA 61.047 63.158 6.85 0.00 44.32 4.20
975 1178 1.999071 CTCGCCGTCAAGAGAGAGGG 61.999 65.000 0.00 0.00 44.37 4.30
976 1179 1.431440 CTCGCCGTCAAGAGAGAGG 59.569 63.158 0.00 0.00 36.65 3.69
1161 1364 2.753043 GGACCGACCGTGAGCCTA 60.753 66.667 0.00 0.00 0.00 3.93
1198 1401 0.822532 GAGGCGACTAGATTCCGGGA 60.823 60.000 0.00 0.00 44.43 5.14
1200 1403 0.030908 GTGAGGCGACTAGATTCCGG 59.969 60.000 0.00 0.00 44.43 5.14
1451 1664 1.024579 CCCCGCACACCACAATAGTC 61.025 60.000 0.00 0.00 0.00 2.59
1486 1699 4.456280 TTCATCTGCGACAGAACATACT 57.544 40.909 12.43 0.00 44.04 2.12
1580 1793 1.740664 CGAGTCGACGAGGTCCTGA 60.741 63.158 6.73 0.00 35.09 3.86
1733 1946 4.201261 CGCAAATTTTTACATCACACGACG 60.201 41.667 0.00 0.00 0.00 5.12
1854 2068 0.390860 GGAGGCTGTAGCACATCGAT 59.609 55.000 6.18 0.00 44.36 3.59
1979 2193 6.994496 TCTATAATTCACAGGAGCATGAAAGG 59.006 38.462 0.00 0.00 38.29 3.11
2087 2301 5.209818 TCCAAGTAACGCTATATGGAAGG 57.790 43.478 0.00 0.00 34.21 3.46
2089 2303 4.344102 AGCTCCAAGTAACGCTATATGGAA 59.656 41.667 4.70 0.00 36.59 3.53
2102 2316 4.413760 ACACTACCAGTAAGCTCCAAGTA 58.586 43.478 0.00 0.00 0.00 2.24
2118 2332 3.553904 AGACCTTCGATCCCTACACTAC 58.446 50.000 0.00 0.00 0.00 2.73
2203 2426 8.844244 AGTAAGCATCTCATCAAATGGTAAATC 58.156 33.333 0.00 0.00 33.50 2.17
2366 2589 2.061773 CAGCTTCGTGTAGGTGAACTG 58.938 52.381 7.91 0.00 44.37 3.16
2368 2591 0.790814 GCAGCTTCGTGTAGGTGAAC 59.209 55.000 14.84 0.00 44.37 3.18
2385 2608 0.976641 ACTCGGAACTGATTCTGGCA 59.023 50.000 0.00 0.00 41.03 4.92
2393 2616 1.535833 GAGTCTCCACTCGGAACTGA 58.464 55.000 0.00 0.00 42.21 3.41
2411 2634 1.617018 CCAGGAGCAATGACCTCGGA 61.617 60.000 0.00 0.00 33.91 4.55
2413 2636 1.153289 CCCAGGAGCAATGACCTCG 60.153 63.158 0.00 0.00 33.91 4.63
2476 2699 1.040339 CCAAGGTCCTCTCTCCGGAG 61.040 65.000 26.32 26.32 40.73 4.63
2525 2776 2.040939 TCGGGAAACTGTACAGAACCA 58.959 47.619 29.30 10.71 38.16 3.67
2542 2795 2.614520 TGTACACACCAACAACAATCGG 59.385 45.455 0.00 0.00 0.00 4.18
2565 2818 5.751243 ACACAACCATGAGAAAGTACAAC 57.249 39.130 0.00 0.00 0.00 3.32
2573 2826 3.070878 TGCACTCTACACAACCATGAGAA 59.929 43.478 0.00 0.00 0.00 2.87
2631 2884 2.833582 CTAGCGGAGAGGCGGGAA 60.834 66.667 0.00 0.00 38.18 3.97
2632 2885 3.354472 TTCTAGCGGAGAGGCGGGA 62.354 63.158 0.00 0.00 34.93 5.14
2633 2886 2.833582 TTCTAGCGGAGAGGCGGG 60.834 66.667 0.00 0.00 34.93 6.13
2673 2926 6.351541 CCCACAATACTTGCTGGTACTACTAA 60.352 42.308 0.00 0.00 33.08 2.24
2733 2986 3.517296 TTGGCACTCAGATTTAACCCA 57.483 42.857 0.00 0.00 0.00 4.51
2734 2987 4.381932 CCAATTGGCACTCAGATTTAACCC 60.382 45.833 12.53 0.00 0.00 4.11
2735 2988 4.462483 TCCAATTGGCACTCAGATTTAACC 59.538 41.667 20.33 0.00 34.44 2.85
2739 2992 5.750352 AATTCCAATTGGCACTCAGATTT 57.250 34.783 20.33 0.93 34.44 2.17
2755 3008 0.546122 AGGCAGGCACGATAATTCCA 59.454 50.000 0.00 0.00 0.00 3.53
2756 3009 1.334869 CAAGGCAGGCACGATAATTCC 59.665 52.381 0.00 0.00 0.00 3.01
2757 3010 2.017049 ACAAGGCAGGCACGATAATTC 58.983 47.619 0.00 0.00 0.00 2.17
2758 3011 2.128771 ACAAGGCAGGCACGATAATT 57.871 45.000 0.00 0.00 0.00 1.40
2759 3012 2.017049 GAACAAGGCAGGCACGATAAT 58.983 47.619 0.00 0.00 0.00 1.28
2773 3031 5.535030 AGCAAAACTACTAAAGGGGAACAAG 59.465 40.000 0.00 0.00 0.00 3.16
2777 3035 5.451354 ACAAGCAAAACTACTAAAGGGGAA 58.549 37.500 0.00 0.00 0.00 3.97
2780 3038 5.237779 TCGAACAAGCAAAACTACTAAAGGG 59.762 40.000 0.00 0.00 0.00 3.95
2781 3039 6.202188 TCTCGAACAAGCAAAACTACTAAAGG 59.798 38.462 0.00 0.00 0.00 3.11
2784 3042 7.656137 AGATTCTCGAACAAGCAAAACTACTAA 59.344 33.333 0.00 0.00 0.00 2.24
2796 3149 6.310197 GGTGAATTTCAGATTCTCGAACAAG 58.690 40.000 0.00 0.00 0.00 3.16
2798 3151 4.388773 CGGTGAATTTCAGATTCTCGAACA 59.611 41.667 0.00 0.00 32.11 3.18
2799 3152 4.725169 GCGGTGAATTTCAGATTCTCGAAC 60.725 45.833 0.00 1.21 32.11 3.95
2802 3155 2.030946 GGCGGTGAATTTCAGATTCTCG 59.969 50.000 0.00 5.82 0.00 4.04
2805 3158 2.478539 GCAGGCGGTGAATTTCAGATTC 60.479 50.000 0.00 0.00 0.00 2.52
2816 3169 2.963101 AGTACATATTAGCAGGCGGTGA 59.037 45.455 0.00 0.00 0.00 4.02
2819 3172 2.353803 GGGAGTACATATTAGCAGGCGG 60.354 54.545 0.00 0.00 0.00 6.13
2822 3175 4.835615 AGTGAGGGAGTACATATTAGCAGG 59.164 45.833 0.00 0.00 0.00 4.85
2830 3183 8.768397 ACATATTTTGAAGTGAGGGAGTACATA 58.232 33.333 0.00 0.00 0.00 2.29
2831 3184 7.554118 CACATATTTTGAAGTGAGGGAGTACAT 59.446 37.037 0.00 0.00 33.99 2.29
2832 3185 6.878923 CACATATTTTGAAGTGAGGGAGTACA 59.121 38.462 0.00 0.00 33.99 2.90
2833 3186 6.879458 ACACATATTTTGAAGTGAGGGAGTAC 59.121 38.462 0.00 0.00 35.97 2.73
2834 3187 7.016153 ACACATATTTTGAAGTGAGGGAGTA 57.984 36.000 0.00 0.00 35.97 2.59
2835 3188 5.880901 ACACATATTTTGAAGTGAGGGAGT 58.119 37.500 0.00 0.00 35.97 3.85
2836 3189 5.063944 CGACACATATTTTGAAGTGAGGGAG 59.936 44.000 0.00 0.00 35.97 4.30
2837 3190 4.935205 CGACACATATTTTGAAGTGAGGGA 59.065 41.667 0.00 0.00 35.97 4.20
2838 3191 4.695455 ACGACACATATTTTGAAGTGAGGG 59.305 41.667 0.00 0.00 35.97 4.30
2839 3192 5.390885 CCACGACACATATTTTGAAGTGAGG 60.391 44.000 0.00 0.00 35.97 3.86
2840 3193 5.179368 ACCACGACACATATTTTGAAGTGAG 59.821 40.000 0.00 0.00 35.97 3.51
2841 3194 5.060506 ACCACGACACATATTTTGAAGTGA 58.939 37.500 0.00 0.00 35.97 3.41
2842 3195 5.356882 ACCACGACACATATTTTGAAGTG 57.643 39.130 0.00 0.00 37.95 3.16
2843 3196 5.298276 ACAACCACGACACATATTTTGAAGT 59.702 36.000 0.00 0.00 0.00 3.01
2844 3197 5.757886 ACAACCACGACACATATTTTGAAG 58.242 37.500 0.00 0.00 0.00 3.02
2845 3198 5.759506 ACAACCACGACACATATTTTGAA 57.240 34.783 0.00 0.00 0.00 2.69
2846 3199 5.992829 ACTACAACCACGACACATATTTTGA 59.007 36.000 0.00 0.00 0.00 2.69
2847 3200 6.236017 ACTACAACCACGACACATATTTTG 57.764 37.500 0.00 0.00 0.00 2.44
2848 3201 6.483974 TGAACTACAACCACGACACATATTTT 59.516 34.615 0.00 0.00 0.00 1.82
2849 3202 5.992829 TGAACTACAACCACGACACATATTT 59.007 36.000 0.00 0.00 0.00 1.40
2850 3203 5.543714 TGAACTACAACCACGACACATATT 58.456 37.500 0.00 0.00 0.00 1.28
2851 3204 5.142061 TGAACTACAACCACGACACATAT 57.858 39.130 0.00 0.00 0.00 1.78
2852 3205 4.587584 TGAACTACAACCACGACACATA 57.412 40.909 0.00 0.00 0.00 2.29
2853 3206 3.462483 TGAACTACAACCACGACACAT 57.538 42.857 0.00 0.00 0.00 3.21
2854 3207 2.963548 TGAACTACAACCACGACACA 57.036 45.000 0.00 0.00 0.00 3.72
2855 3208 3.371591 TGTTTGAACTACAACCACGACAC 59.628 43.478 0.00 0.00 38.29 3.67
2856 3209 3.597255 TGTTTGAACTACAACCACGACA 58.403 40.909 0.00 0.00 38.29 4.35
2857 3210 3.001939 CCTGTTTGAACTACAACCACGAC 59.998 47.826 0.00 0.00 38.29 4.34
2858 3211 3.199677 CCTGTTTGAACTACAACCACGA 58.800 45.455 0.00 0.00 38.29 4.35
2859 3212 2.940410 ACCTGTTTGAACTACAACCACG 59.060 45.455 0.00 0.00 38.29 4.94
2860 3213 4.877251 TGTACCTGTTTGAACTACAACCAC 59.123 41.667 0.00 0.00 38.29 4.16
2861 3214 5.100344 TGTACCTGTTTGAACTACAACCA 57.900 39.130 0.00 0.00 38.29 3.67
2862 3215 6.293790 GGATTGTACCTGTTTGAACTACAACC 60.294 42.308 8.45 8.48 38.29 3.77
2863 3216 6.485648 AGGATTGTACCTGTTTGAACTACAAC 59.514 38.462 8.45 5.03 39.01 3.32
2864 3217 6.597562 AGGATTGTACCTGTTTGAACTACAA 58.402 36.000 8.62 8.62 39.01 2.41
2865 3218 6.182507 AGGATTGTACCTGTTTGAACTACA 57.817 37.500 0.00 0.00 39.01 2.74
2866 3219 7.360361 CAAAGGATTGTACCTGTTTGAACTAC 58.640 38.462 0.00 0.00 40.49 2.73
2867 3220 6.488683 CCAAAGGATTGTACCTGTTTGAACTA 59.511 38.462 0.00 0.00 40.49 2.24
2868 3221 5.301805 CCAAAGGATTGTACCTGTTTGAACT 59.698 40.000 0.00 0.00 40.49 3.01
2869 3222 5.068591 ACCAAAGGATTGTACCTGTTTGAAC 59.931 40.000 0.00 0.00 40.49 3.18
2870 3223 5.068460 CACCAAAGGATTGTACCTGTTTGAA 59.932 40.000 0.00 0.00 40.49 2.69
2871 3224 4.582656 CACCAAAGGATTGTACCTGTTTGA 59.417 41.667 0.00 0.00 40.49 2.69
2872 3225 4.795962 GCACCAAAGGATTGTACCTGTTTG 60.796 45.833 0.00 0.00 40.49 2.93
2873 3226 3.320826 GCACCAAAGGATTGTACCTGTTT 59.679 43.478 0.00 0.00 40.49 2.83
2874 3227 2.890945 GCACCAAAGGATTGTACCTGTT 59.109 45.455 0.00 0.00 40.49 3.16
2875 3228 2.514803 GCACCAAAGGATTGTACCTGT 58.485 47.619 0.00 0.00 40.49 4.00
2876 3229 1.468520 CGCACCAAAGGATTGTACCTG 59.531 52.381 0.00 0.00 40.49 4.00
2877 3230 1.073284 ACGCACCAAAGGATTGTACCT 59.927 47.619 0.00 0.00 42.69 3.08
2878 3231 1.530323 ACGCACCAAAGGATTGTACC 58.470 50.000 0.00 0.00 34.60 3.34
2879 3232 2.812011 AGAACGCACCAAAGGATTGTAC 59.188 45.455 0.00 0.00 34.60 2.90
2887 3240 2.053627 GAATGCAAGAACGCACCAAAG 58.946 47.619 0.00 0.00 46.56 2.77
2889 3242 0.313672 GGAATGCAAGAACGCACCAA 59.686 50.000 0.00 0.00 46.56 3.67
2891 3244 1.212751 GGGAATGCAAGAACGCACC 59.787 57.895 0.00 0.00 46.56 5.01
2892 3245 0.598065 AAGGGAATGCAAGAACGCAC 59.402 50.000 0.00 0.00 46.56 5.34
2896 3249 1.135575 CGCAGAAGGGAATGCAAGAAC 60.136 52.381 0.00 0.00 42.68 3.01
2921 3274 2.300152 TGTACCTGCTTCCTGAGTTCTG 59.700 50.000 0.00 0.00 0.00 3.02
2924 3277 5.221541 GCTATATGTACCTGCTTCCTGAGTT 60.222 44.000 0.00 0.00 0.00 3.01
2925 3278 4.282195 GCTATATGTACCTGCTTCCTGAGT 59.718 45.833 0.00 0.00 0.00 3.41
2926 3279 4.526262 AGCTATATGTACCTGCTTCCTGAG 59.474 45.833 0.00 0.00 0.00 3.35
2927 3280 4.483950 AGCTATATGTACCTGCTTCCTGA 58.516 43.478 0.00 0.00 0.00 3.86
2930 3283 5.698545 CAGAAAGCTATATGTACCTGCTTCC 59.301 44.000 0.00 0.00 42.23 3.46
2932 3285 6.051717 CACAGAAAGCTATATGTACCTGCTT 58.948 40.000 0.00 0.00 44.51 3.91
2934 3287 4.752101 CCACAGAAAGCTATATGTACCTGC 59.248 45.833 0.00 0.00 0.00 4.85
2937 3290 6.821665 TCAAACCACAGAAAGCTATATGTACC 59.178 38.462 0.00 0.00 0.00 3.34
2938 3291 7.843490 TCAAACCACAGAAAGCTATATGTAC 57.157 36.000 0.00 0.00 0.00 2.90
2940 3293 6.127897 GCTTCAAACCACAGAAAGCTATATGT 60.128 38.462 0.00 0.00 0.00 2.29
2941 3294 6.127925 TGCTTCAAACCACAGAAAGCTATATG 60.128 38.462 6.91 0.00 0.00 1.78
2943 3296 5.312895 TGCTTCAAACCACAGAAAGCTATA 58.687 37.500 6.91 0.00 0.00 1.31
2944 3297 4.144297 TGCTTCAAACCACAGAAAGCTAT 58.856 39.130 6.91 0.00 0.00 2.97
2945 3298 3.550820 TGCTTCAAACCACAGAAAGCTA 58.449 40.909 6.91 0.00 0.00 3.32
2946 3299 2.360165 CTGCTTCAAACCACAGAAAGCT 59.640 45.455 6.91 0.00 31.67 3.74
2947 3300 2.544486 CCTGCTTCAAACCACAGAAAGC 60.544 50.000 0.00 0.00 31.67 3.51
2948 3301 2.951642 TCCTGCTTCAAACCACAGAAAG 59.048 45.455 0.00 0.00 31.67 2.62
2949 3302 2.687935 GTCCTGCTTCAAACCACAGAAA 59.312 45.455 0.00 0.00 31.67 2.52
2950 3303 2.092429 AGTCCTGCTTCAAACCACAGAA 60.092 45.455 0.00 0.00 31.67 3.02
2951 3304 1.490490 AGTCCTGCTTCAAACCACAGA 59.510 47.619 0.00 0.00 31.67 3.41
2952 3305 1.972872 AGTCCTGCTTCAAACCACAG 58.027 50.000 0.00 0.00 0.00 3.66
2953 3306 2.435372 AAGTCCTGCTTCAAACCACA 57.565 45.000 0.00 0.00 30.06 4.17
2962 3315 6.619329 ATCTAGAAAAGAGAAGTCCTGCTT 57.381 37.500 0.00 0.00 37.74 3.91
2963 3316 7.912778 ATATCTAGAAAAGAGAAGTCCTGCT 57.087 36.000 0.00 0.00 37.74 4.24
2964 3317 7.440856 CCAATATCTAGAAAAGAGAAGTCCTGC 59.559 40.741 0.00 0.00 37.74 4.85
2965 3318 8.700051 TCCAATATCTAGAAAAGAGAAGTCCTG 58.300 37.037 0.00 0.00 37.74 3.86
2966 3319 8.846423 TCCAATATCTAGAAAAGAGAAGTCCT 57.154 34.615 0.00 0.00 37.74 3.85
2967 3320 7.655732 GCTCCAATATCTAGAAAAGAGAAGTCC 59.344 40.741 0.00 0.00 37.74 3.85
2968 3321 8.421002 AGCTCCAATATCTAGAAAAGAGAAGTC 58.579 37.037 0.00 0.00 37.74 3.01
2970 3323 7.656948 CCAGCTCCAATATCTAGAAAAGAGAAG 59.343 40.741 0.00 0.00 37.74 2.85
2971 3324 7.419518 CCCAGCTCCAATATCTAGAAAAGAGAA 60.420 40.741 0.00 0.00 37.74 2.87
2973 3326 6.229733 CCCAGCTCCAATATCTAGAAAAGAG 58.770 44.000 0.00 0.62 37.74 2.85
2974 3327 5.455326 GCCCAGCTCCAATATCTAGAAAAGA 60.455 44.000 0.00 0.00 39.02 2.52
2975 3328 4.759183 GCCCAGCTCCAATATCTAGAAAAG 59.241 45.833 0.00 0.00 0.00 2.27
2976 3329 4.413520 AGCCCAGCTCCAATATCTAGAAAA 59.586 41.667 0.00 0.00 30.62 2.29
2978 3331 3.591789 AGCCCAGCTCCAATATCTAGAA 58.408 45.455 0.00 0.00 30.62 2.10
2982 3335 2.243221 ACAAAGCCCAGCTCCAATATCT 59.757 45.455 0.00 0.00 38.25 1.98
2983 3336 2.659428 ACAAAGCCCAGCTCCAATATC 58.341 47.619 0.00 0.00 38.25 1.63
2985 3338 3.730215 TTACAAAGCCCAGCTCCAATA 57.270 42.857 0.00 0.00 38.25 1.90
2990 5726 1.017387 CCGATTACAAAGCCCAGCTC 58.983 55.000 0.00 0.00 38.25 4.09
2997 5733 4.082463 TCCCATTTTGTCCGATTACAAAGC 60.082 41.667 9.54 0.00 46.77 3.51
3003 5739 3.626222 CCCCTTCCCATTTTGTCCGATTA 60.626 47.826 0.00 0.00 0.00 1.75
3016 5752 1.721093 TTTCTTTCGCCCCCTTCCCA 61.721 55.000 0.00 0.00 0.00 4.37
3024 5760 2.723124 TCAAATGCTTTCTTTCGCCC 57.277 45.000 0.00 0.00 0.00 6.13
3027 5763 8.114359 TGTTAAGTTTCAAATGCTTTCTTTCG 57.886 30.769 0.00 0.00 0.00 3.46
3028 5764 9.906111 CTTGTTAAGTTTCAAATGCTTTCTTTC 57.094 29.630 0.00 0.00 0.00 2.62
3031 5767 7.041107 TGCTTGTTAAGTTTCAAATGCTTTCT 58.959 30.769 0.00 0.00 0.00 2.52
3032 5768 7.232945 TGCTTGTTAAGTTTCAAATGCTTTC 57.767 32.000 0.00 0.00 0.00 2.62
3033 5769 7.201635 CCTTGCTTGTTAAGTTTCAAATGCTTT 60.202 33.333 0.00 0.00 0.00 3.51
3035 5771 5.754890 CCTTGCTTGTTAAGTTTCAAATGCT 59.245 36.000 0.00 0.00 0.00 3.79
3037 5773 6.200854 GTCCCTTGCTTGTTAAGTTTCAAATG 59.799 38.462 0.00 0.00 0.00 2.32
3038 5774 6.127196 TGTCCCTTGCTTGTTAAGTTTCAAAT 60.127 34.615 0.00 0.00 0.00 2.32
3112 5849 4.026475 GGTTCAACAATTCGATCTAGCTCG 60.026 45.833 9.68 9.68 39.99 5.03
3125 5862 7.063308 GCGATACAAAATTGATGGTTCAACAAT 59.937 33.333 0.00 0.00 44.36 2.71
3131 5868 4.035017 CCGCGATACAAAATTGATGGTTC 58.965 43.478 8.23 0.00 0.00 3.62
3145 5882 1.822990 TCCATAAGATCCCCGCGATAC 59.177 52.381 8.23 0.00 0.00 2.24
3150 5887 4.696479 ATATCATCCATAAGATCCCCGC 57.304 45.455 0.00 0.00 30.59 6.13
3182 5920 6.155393 TCCAATTGGTAATACCCACCATTTTC 59.845 38.462 23.76 0.00 45.32 2.29
3191 5929 6.293955 CGATGTTCATCCAATTGGTAATACCC 60.294 42.308 23.76 8.08 37.50 3.69
3209 5947 2.309528 TGACAGGGCATACGATGTTC 57.690 50.000 0.00 0.00 0.00 3.18
3211 5949 3.578282 TCATATGACAGGGCATACGATGT 59.422 43.478 0.00 0.00 33.88 3.06
3222 5960 6.543465 TCCTAGCAAAACAATCATATGACAGG 59.457 38.462 7.78 3.12 0.00 4.00
3232 5970 9.120538 TCCTGTTATTATCCTAGCAAAACAATC 57.879 33.333 0.00 0.00 0.00 2.67
3245 5983 8.624776 CCTCATTTCTTGTTCCTGTTATTATCC 58.375 37.037 0.00 0.00 0.00 2.59
3246 5984 9.396022 TCCTCATTTCTTGTTCCTGTTATTATC 57.604 33.333 0.00 0.00 0.00 1.75
3247 5985 9.753674 TTCCTCATTTCTTGTTCCTGTTATTAT 57.246 29.630 0.00 0.00 0.00 1.28
3248 5986 9.231297 CTTCCTCATTTCTTGTTCCTGTTATTA 57.769 33.333 0.00 0.00 0.00 0.98
3249 5987 7.309438 GCTTCCTCATTTCTTGTTCCTGTTATT 60.309 37.037 0.00 0.00 0.00 1.40
3254 5992 3.822735 TGCTTCCTCATTTCTTGTTCCTG 59.177 43.478 0.00 0.00 0.00 3.86
3271 6009 5.023533 TGTATACTCTGAACCCATGCTTC 57.976 43.478 4.17 0.00 0.00 3.86
3281 6019 8.318412 TGTTCTTGCCTAATTGTATACTCTGAA 58.682 33.333 4.17 0.00 0.00 3.02
3287 6026 8.671384 TGGTATGTTCTTGCCTAATTGTATAC 57.329 34.615 0.00 0.00 0.00 1.47
3292 6031 8.394971 TGATATGGTATGTTCTTGCCTAATTG 57.605 34.615 0.00 0.00 0.00 2.32
3309 6048 3.748048 GTGCATACGCTTGATGATATGGT 59.252 43.478 0.00 0.00 39.64 3.55
3369 6113 4.675510 GTGTGGACAAGGATATGCAATTG 58.324 43.478 0.00 0.00 0.00 2.32
3373 6117 1.406751 CCGTGTGGACAAGGATATGCA 60.407 52.381 5.90 0.00 46.41 3.96
3374 6118 1.299541 CCGTGTGGACAAGGATATGC 58.700 55.000 5.90 0.00 46.41 3.14
3375 6119 1.134401 AGCCGTGTGGACAAGGATATG 60.134 52.381 15.02 0.00 46.41 1.78
3376 6120 1.134401 CAGCCGTGTGGACAAGGATAT 60.134 52.381 15.02 0.00 46.41 1.63
3377 6121 0.249120 CAGCCGTGTGGACAAGGATA 59.751 55.000 15.02 0.00 46.41 2.59
3378 6122 1.003355 CAGCCGTGTGGACAAGGAT 60.003 57.895 15.02 6.31 46.41 3.24
3379 6123 2.425592 CAGCCGTGTGGACAAGGA 59.574 61.111 15.02 0.00 46.41 3.36
3380 6124 2.669569 CCAGCCGTGTGGACAAGG 60.670 66.667 7.33 7.33 46.26 3.61
3381 6125 3.357079 GCCAGCCGTGTGGACAAG 61.357 66.667 4.49 0.00 40.44 3.16
3382 6126 4.947147 GGCCAGCCGTGTGGACAA 62.947 66.667 0.00 0.00 46.26 3.18
3405 6171 6.371389 GTCCTTGTCCGTTTGATAAGAAAAG 58.629 40.000 0.91 0.00 42.95 2.27
3409 6175 3.325425 TGGTCCTTGTCCGTTTGATAAGA 59.675 43.478 0.91 0.00 42.95 2.10
3417 6183 3.133003 CAGATCTATGGTCCTTGTCCGTT 59.867 47.826 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.