Multiple sequence alignment - TraesCS5D01G076500

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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 TraesCS5D01G076500 chr5D 100.000 3104 0 0 1 3104 75999355 75996252 0.000000e+00 5733.0
1 TraesCS5D01G076500 chr5D 95.341 279 13 0 2794 3072 533579560 533579282 7.900000e-121 444.0
2 TraesCS5D01G076500 chr5D 83.582 67 11 0 2724 2790 75920603 75920537 2.580000e-06 63.9
3 TraesCS5D01G076500 chr5A 93.116 2179 118 18 11 2181 71455125 71452971 0.000000e+00 3164.0
4 TraesCS5D01G076500 chr5A 92.628 624 32 10 2180 2797 71452771 71452156 0.000000e+00 885.0
5 TraesCS5D01G076500 chr5A 74.328 335 55 22 8 326 579919003 579918684 2.530000e-21 113.0
6 TraesCS5D01G076500 chr5B 95.135 1336 52 10 1469 2799 84657363 84656036 0.000000e+00 2095.0
7 TraesCS5D01G076500 chr5B 93.066 1370 79 11 88 1447 84658934 84657571 0.000000e+00 1989.0
8 TraesCS5D01G076500 chr5B 96.774 62 1 1 1 62 84658994 84658934 5.480000e-18 102.0
9 TraesCS5D01G076500 chr2A 88.505 983 67 16 1285 2258 23948857 23949802 0.000000e+00 1147.0
10 TraesCS5D01G076500 chr2A 85.424 295 21 6 271 544 23939859 23940152 1.410000e-73 287.0
11 TraesCS5D01G076500 chr6B 84.140 599 82 5 1520 2105 204124518 204123920 4.490000e-158 568.0
12 TraesCS5D01G076500 chr6B 83.250 603 80 11 1520 2105 204114946 204114348 4.560000e-148 534.0
13 TraesCS5D01G076500 chr6B 80.707 368 69 2 1073 1439 204115664 204115298 5.070000e-73 285.0
14 TraesCS5D01G076500 chr6D 83.806 599 84 5 1520 2105 114848139 114847541 9.720000e-155 556.0
15 TraesCS5D01G076500 chr6D 84.516 310 48 0 2794 3103 3220887 3220578 1.080000e-79 307.0
16 TraesCS5D01G076500 chr6D 76.000 650 123 22 813 1439 114844351 114843712 3.890000e-79 305.0
17 TraesCS5D01G076500 chr6D 76.380 326 58 13 8 321 139381379 139381061 1.150000e-34 158.0
18 TraesCS5D01G076500 chr6A 83.167 600 82 10 1520 2103 143066174 143065578 5.890000e-147 531.0
19 TraesCS5D01G076500 chr6A 84.061 458 63 5 1655 2105 143071375 143070921 1.710000e-117 433.0
20 TraesCS5D01G076500 chr6A 79.587 387 73 5 1056 1439 143066917 143066534 3.940000e-69 272.0
21 TraesCS5D01G076500 chr2D 96.141 311 12 0 2794 3104 68932876 68933186 2.760000e-140 508.0
22 TraesCS5D01G076500 chr2D 91.447 304 23 1 1041 1344 21913097 21913397 6.190000e-112 414.0
23 TraesCS5D01G076500 chr2D 83.562 73 12 0 2718 2790 22109394 22109466 5.550000e-08 69.4
24 TraesCS5D01G076500 chr3B 89.389 311 32 1 2794 3104 167454327 167454636 1.040000e-104 390.0
25 TraesCS5D01G076500 chr3B 75.167 600 104 36 1528 2095 686524942 686525528 1.110000e-59 241.0
26 TraesCS5D01G076500 chr3B 74.155 592 115 30 1528 2095 686492638 686493215 8.720000e-51 211.0
27 TraesCS5D01G076500 chr3D 86.452 310 42 0 2794 3103 477962950 477963259 1.070000e-89 340.0
28 TraesCS5D01G076500 chr3D 74.707 597 106 33 1528 2092 520824707 520825290 1.120000e-54 224.0
29 TraesCS5D01G076500 chr3D 78.902 346 41 19 5 326 39932672 39933009 4.060000e-49 206.0
30 TraesCS5D01G076500 chr3A 74.242 594 114 30 1528 2092 656135303 656135886 2.420000e-51 213.0
31 TraesCS5D01G076500 chr1D 78.723 329 48 13 5 330 371630247 371629938 1.890000e-47 200.0
32 TraesCS5D01G076500 chr1B 76.074 326 54 17 8 320 556968171 556968485 6.940000e-32 148.0
33 TraesCS5D01G076500 chr2B 76.817 289 32 22 46 316 751298259 751298530 2.510000e-26 130.0
34 TraesCS5D01G076500 chr2B 77.295 207 29 12 118 316 751287692 751287888 4.230000e-19 106.0
35 TraesCS5D01G076500 chr2B 97.143 35 1 0 505 539 50193457 50193491 3.340000e-05 60.2
36 TraesCS5D01G076500 chr2B 90.698 43 4 0 2752 2794 35125564 35125522 1.200000e-04 58.4
37 TraesCS5D01G076500 chr2B 94.286 35 2 0 505 539 49910793 49910759 2.000000e-03 54.7
38 TraesCS5D01G076500 chrUn 80.870 115 15 5 2429 2539 16310527 16310638 1.980000e-12 84.2
39 TraesCS5D01G076500 chrUn 80.870 115 15 6 2429 2539 381114665 381114554 1.980000e-12 84.2


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 TraesCS5D01G076500 chr5D 75996252 75999355 3103 True 5733.000000 5733 100.000000 1 3104 1 chr5D.!!$R2 3103
1 TraesCS5D01G076500 chr5A 71452156 71455125 2969 True 2024.500000 3164 92.872000 11 2797 2 chr5A.!!$R2 2786
2 TraesCS5D01G076500 chr5B 84656036 84658994 2958 True 1395.333333 2095 94.991667 1 2799 3 chr5B.!!$R1 2798
3 TraesCS5D01G076500 chr2A 23948857 23949802 945 False 1147.000000 1147 88.505000 1285 2258 1 chr2A.!!$F2 973
4 TraesCS5D01G076500 chr6B 204123920 204124518 598 True 568.000000 568 84.140000 1520 2105 1 chr6B.!!$R1 585
5 TraesCS5D01G076500 chr6B 204114348 204115664 1316 True 409.500000 534 81.978500 1073 2105 2 chr6B.!!$R2 1032
6 TraesCS5D01G076500 chr6D 114843712 114848139 4427 True 430.500000 556 79.903000 813 2105 2 chr6D.!!$R3 1292
7 TraesCS5D01G076500 chr6A 143065578 143066917 1339 True 401.500000 531 81.377000 1056 2103 2 chr6A.!!$R2 1047
8 TraesCS5D01G076500 chr3B 686524942 686525528 586 False 241.000000 241 75.167000 1528 2095 1 chr3B.!!$F3 567
9 TraesCS5D01G076500 chr3B 686492638 686493215 577 False 211.000000 211 74.155000 1528 2095 1 chr3B.!!$F2 567
10 TraesCS5D01G076500 chr3D 520824707 520825290 583 False 224.000000 224 74.707000 1528 2092 1 chr3D.!!$F3 564
11 TraesCS5D01G076500 chr3A 656135303 656135886 583 False 213.000000 213 74.242000 1528 2092 1 chr3A.!!$F1 564

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
771 788 0.250467 GTTCTCACCAAGCCAGCTCA 60.25 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 2903 0.459237 CATGTGAGGACGAGAGGTGC 60.459 60.0 0.0 0.0 37.22 5.01 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
91 92 6.774354 ATGTTAAAATGAGTGCTGCAAAAG 57.226 33.333 2.77 0.00 0.00 2.27
181 183 3.624861 AGCTCGCATTCAAGGTATTTCAG 59.375 43.478 0.00 0.00 0.00 3.02
192 194 6.977213 TCAAGGTATTTCAGCCAAAAGTAAC 58.023 36.000 0.00 0.00 0.00 2.50
207 209 6.855914 CCAAAAGTAACACACACATACACATC 59.144 38.462 0.00 0.00 0.00 3.06
217 219 5.528690 ACACACATACACATCATATCCTTGC 59.471 40.000 0.00 0.00 0.00 4.01
238 240 9.638239 CCTTGCATACATACTTGTACAATTTTT 57.362 29.630 9.13 0.00 41.02 1.94
336 342 3.922910 ACGCCCTACTCTTCTTACAAAC 58.077 45.455 0.00 0.00 0.00 2.93
337 343 2.921754 CGCCCTACTCTTCTTACAAACG 59.078 50.000 0.00 0.00 0.00 3.60
551 557 5.703978 TTGCATATATTATGTGGGTGTGC 57.296 39.130 3.04 0.00 0.00 4.57
555 561 5.649395 GCATATATTATGTGGGTGTGCTGAT 59.351 40.000 3.04 0.00 0.00 2.90
562 568 2.504996 TGTGGGTGTGCTGATGATGATA 59.495 45.455 0.00 0.00 0.00 2.15
670 681 8.316046 CAGTATTTATTTTACAGGTCGTGTACG 58.684 37.037 4.89 0.00 41.58 3.67
771 788 0.250467 GTTCTCACCAAGCCAGCTCA 60.250 55.000 0.00 0.00 0.00 4.26
785 802 0.901580 AGCTCACCCCCAAAGCAATG 60.902 55.000 0.00 0.00 38.51 2.82
788 805 2.996734 ACCCCCAAAGCAATGCCG 60.997 61.111 0.00 0.00 0.00 5.69
949 966 3.877559 ACACCCACATGTATCATCACAG 58.122 45.455 0.00 0.00 0.00 3.66
987 1004 3.828875 ACTTTCTCCATCGATCTTCCC 57.171 47.619 0.00 0.00 0.00 3.97
1012 1029 4.021016 CCCTACTGACCATGGCTAGTTATC 60.021 50.000 22.22 7.87 0.00 1.75
1221 1238 3.697747 TCCACGAACGCCGGGAAT 61.698 61.111 2.18 0.00 46.66 3.01
1257 1274 3.723348 GCCAACCAGTTCGCCGAC 61.723 66.667 0.00 0.00 0.00 4.79
1283 1300 1.404843 GAGGACGAGTTCAGGGCTAT 58.595 55.000 0.00 0.00 0.00 2.97
1290 1307 1.834263 GAGTTCAGGGCTATCCACACT 59.166 52.381 0.00 0.00 38.24 3.55
1398 1418 0.544357 TCGACTGGAGGACCAATGGT 60.544 55.000 3.74 3.74 46.32 3.55
1436 1456 1.173913 GACCAAGGCCAATGTGGTAC 58.826 55.000 17.44 9.68 45.72 3.34
1462 1482 1.082104 GCACTACGCAGCACAAACC 60.082 57.895 0.00 0.00 41.79 3.27
1518 1929 6.315274 GAGTATGCTTACTCGTTTGTACAC 57.685 41.667 20.28 0.00 43.59 2.90
2096 2546 0.995675 ATGCAGCCTTCCTACCCCAT 60.996 55.000 0.00 0.00 0.00 4.00
2121 2571 1.807886 GCCAGCTGCTTCATTCCTG 59.192 57.895 8.66 0.00 36.87 3.86
2140 2590 6.869206 TCCTGTCCTACTAGCTTGTAAATT 57.131 37.500 9.31 0.00 0.00 1.82
2200 2851 6.318648 TGGATGTACAACCTGCATTATTCTTC 59.681 38.462 21.41 0.00 0.00 2.87
2250 2903 9.521503 TCTTCAATCAGAAATCTACTATTCACG 57.478 33.333 0.00 0.00 35.40 4.35
2258 2911 4.839668 ATCTACTATTCACGCACCTCTC 57.160 45.455 0.00 0.00 0.00 3.20
2280 2933 3.487711 CGTCCTCACATGAGTACTAGTGC 60.488 52.174 5.39 3.75 40.48 4.40
2294 2948 6.060136 AGTACTAGTGCACTACCATAATCGA 58.940 40.000 22.67 0.17 0.00 3.59
2299 2953 9.239551 ACTAGTGCACTACCATAATCGAATATA 57.760 33.333 22.67 0.00 0.00 0.86
2368 3024 9.921637 TTTACAACAAAAGAGACTCAAATGTTT 57.078 25.926 13.74 9.86 0.00 2.83
2445 3102 4.660168 TGATATACTCCCTTCGTCCCTAC 58.340 47.826 0.00 0.00 0.00 3.18
2497 3154 4.814771 AGTCAACGGTTTCTAAGTTTGAGG 59.185 41.667 0.00 0.00 0.00 3.86
2795 5133 0.039618 GGCCTTCAACATCCCCTTGA 59.960 55.000 0.00 0.00 0.00 3.02
2800 5138 4.347607 CCTTCAACATCCCCTTGAAAGAT 58.652 43.478 0.00 0.00 37.22 2.40
2803 5141 4.996793 TCAACATCCCCTTGAAAGATCAA 58.003 39.130 0.00 0.00 43.18 2.57
2806 5144 6.497954 TCAACATCCCCTTGAAAGATCAATTT 59.502 34.615 0.00 0.00 44.29 1.82
2807 5145 6.290294 ACATCCCCTTGAAAGATCAATTTG 57.710 37.500 0.00 0.00 44.29 2.32
2808 5146 6.018469 ACATCCCCTTGAAAGATCAATTTGA 58.982 36.000 0.75 0.75 44.29 2.69
2810 5148 5.018809 TCCCCTTGAAAGATCAATTTGAGG 58.981 41.667 5.21 1.96 44.29 3.86
2811 5149 5.018809 CCCCTTGAAAGATCAATTTGAGGA 58.981 41.667 5.21 0.00 44.29 3.71
2812 5150 5.105595 CCCCTTGAAAGATCAATTTGAGGAC 60.106 44.000 5.21 0.00 44.29 3.85
2813 5151 5.477984 CCCTTGAAAGATCAATTTGAGGACA 59.522 40.000 5.21 0.00 44.29 4.02
2828 5166 6.834168 TTGAGGACAAATATTTGGGACTTC 57.166 37.500 27.43 21.93 42.34 3.01
2829 5167 5.261216 TGAGGACAAATATTTGGGACTTCC 58.739 41.667 27.43 23.26 42.34 3.46
2839 5177 0.472471 TGGGACTTCCAACACCAGAC 59.528 55.000 0.00 0.00 43.84 3.51
2841 5179 1.543429 GGGACTTCCAACACCAGACAG 60.543 57.143 0.00 0.00 37.91 3.51
2843 5181 2.484889 GACTTCCAACACCAGACAGTC 58.515 52.381 0.00 0.00 0.00 3.51
2844 5182 1.202533 ACTTCCAACACCAGACAGTCG 60.203 52.381 0.00 0.00 0.00 4.18
2846 5184 1.694844 TCCAACACCAGACAGTCGTA 58.305 50.000 0.00 0.00 0.00 3.43
2847 5185 2.244695 TCCAACACCAGACAGTCGTAT 58.755 47.619 0.00 0.00 0.00 3.06
2848 5186 2.029380 TCCAACACCAGACAGTCGTATG 60.029 50.000 0.00 0.00 34.00 2.39
2849 5187 1.726791 CAACACCAGACAGTCGTATGC 59.273 52.381 0.00 0.00 32.82 3.14
2850 5188 0.966179 ACACCAGACAGTCGTATGCA 59.034 50.000 0.00 0.00 32.82 3.96
2852 5190 2.758423 ACACCAGACAGTCGTATGCATA 59.242 45.455 1.16 1.16 32.82 3.14
2855 5193 4.268644 CACCAGACAGTCGTATGCATAAAG 59.731 45.833 8.28 6.06 32.82 1.85
2856 5194 3.804325 CCAGACAGTCGTATGCATAAAGG 59.196 47.826 8.28 1.17 32.82 3.11
2857 5195 3.246226 CAGACAGTCGTATGCATAAAGGC 59.754 47.826 8.28 7.44 0.00 4.35
2869 5207 5.226194 TGCATAAAGGCAAGTTCCAAAAT 57.774 34.783 0.00 0.00 41.65 1.82
2871 5209 6.060788 TGCATAAAGGCAAGTTCCAAAATTT 58.939 32.000 0.00 0.00 41.65 1.82
2872 5210 6.017275 TGCATAAAGGCAAGTTCCAAAATTTG 60.017 34.615 0.00 0.00 41.65 2.32
2880 5218 6.419980 CAAGTTCCAAAATTTGCAAGTGAA 57.580 33.333 0.00 0.00 0.00 3.18
2881 5219 6.480285 CAAGTTCCAAAATTTGCAAGTGAAG 58.520 36.000 0.00 0.00 0.00 3.02
2887 5225 8.140677 TCCAAAATTTGCAAGTGAAGTTAATG 57.859 30.769 0.00 0.00 0.00 1.90
2888 5226 7.984050 TCCAAAATTTGCAAGTGAAGTTAATGA 59.016 29.630 0.00 0.00 0.00 2.57
2889 5227 8.610896 CCAAAATTTGCAAGTGAAGTTAATGAA 58.389 29.630 0.00 0.00 0.00 2.57
2890 5228 9.985318 CAAAATTTGCAAGTGAAGTTAATGAAA 57.015 25.926 0.00 0.00 0.00 2.69
2891 5229 9.986833 AAAATTTGCAAGTGAAGTTAATGAAAC 57.013 25.926 0.00 0.00 38.46 2.78
2892 5230 6.804534 TTTGCAAGTGAAGTTAATGAAACG 57.195 33.333 0.00 0.00 43.29 3.60
2894 5232 4.201960 TGCAAGTGAAGTTAATGAAACGCA 60.202 37.500 0.00 0.00 43.29 5.24
2895 5233 4.917415 GCAAGTGAAGTTAATGAAACGCAT 59.083 37.500 0.00 0.00 43.29 4.73
2896 5234 5.059710 GCAAGTGAAGTTAATGAAACGCATC 59.940 40.000 0.00 0.00 43.29 3.91
2897 5235 6.373779 CAAGTGAAGTTAATGAAACGCATCT 58.626 36.000 0.00 0.00 43.29 2.90
2898 5236 5.931532 AGTGAAGTTAATGAAACGCATCTG 58.068 37.500 0.00 0.00 43.29 2.90
2899 5237 5.470098 AGTGAAGTTAATGAAACGCATCTGT 59.530 36.000 0.00 0.00 43.29 3.41
2900 5238 6.649141 AGTGAAGTTAATGAAACGCATCTGTA 59.351 34.615 0.00 0.00 43.29 2.74
2901 5239 7.334421 AGTGAAGTTAATGAAACGCATCTGTAT 59.666 33.333 0.00 0.00 43.29 2.29
2902 5240 8.600625 GTGAAGTTAATGAAACGCATCTGTATA 58.399 33.333 0.00 0.00 43.29 1.47
2903 5241 9.325198 TGAAGTTAATGAAACGCATCTGTATAT 57.675 29.630 0.00 0.00 43.29 0.86
2904 5242 9.586150 GAAGTTAATGAAACGCATCTGTATATG 57.414 33.333 0.00 0.00 43.29 1.78
2914 5252 5.447478 GCATCTGTATATGCGAAGATGTC 57.553 43.478 16.96 9.55 45.09 3.06
2915 5253 5.167121 GCATCTGTATATGCGAAGATGTCT 58.833 41.667 16.96 0.00 45.09 3.41
2916 5254 6.325596 GCATCTGTATATGCGAAGATGTCTA 58.674 40.000 16.96 0.00 45.09 2.59
2917 5255 6.252441 GCATCTGTATATGCGAAGATGTCTAC 59.748 42.308 16.96 3.48 45.09 2.59
2918 5256 6.877611 TCTGTATATGCGAAGATGTCTACA 57.122 37.500 0.00 0.00 0.00 2.74
2919 5257 7.454260 TCTGTATATGCGAAGATGTCTACAT 57.546 36.000 0.00 0.00 39.70 2.29
2920 5258 7.308435 TCTGTATATGCGAAGATGTCTACATG 58.692 38.462 0.00 0.00 36.57 3.21
2921 5259 6.389906 TGTATATGCGAAGATGTCTACATGG 58.610 40.000 0.00 0.00 36.57 3.66
2922 5260 1.939974 TGCGAAGATGTCTACATGGC 58.060 50.000 0.00 0.08 36.57 4.40
2923 5261 1.221414 GCGAAGATGTCTACATGGCC 58.779 55.000 0.00 0.00 36.57 5.36
2924 5262 1.491670 CGAAGATGTCTACATGGCCG 58.508 55.000 0.00 0.00 36.57 6.13
2925 5263 1.067060 CGAAGATGTCTACATGGCCGA 59.933 52.381 0.00 0.00 36.57 5.54
2926 5264 2.481276 CGAAGATGTCTACATGGCCGAA 60.481 50.000 0.00 0.00 36.57 4.30
2927 5265 2.898729 AGATGTCTACATGGCCGAAG 57.101 50.000 0.00 0.00 36.57 3.79
2928 5266 1.202580 AGATGTCTACATGGCCGAAGC 60.203 52.381 0.00 0.00 36.57 3.86
2929 5267 0.833287 ATGTCTACATGGCCGAAGCT 59.167 50.000 0.00 0.00 39.73 3.74
2930 5268 0.108186 TGTCTACATGGCCGAAGCTG 60.108 55.000 0.00 0.00 39.73 4.24
2931 5269 0.811616 GTCTACATGGCCGAAGCTGG 60.812 60.000 0.00 0.00 39.73 4.85
2932 5270 1.524621 CTACATGGCCGAAGCTGGG 60.525 63.158 0.00 0.00 39.73 4.45
2933 5271 1.971505 CTACATGGCCGAAGCTGGGA 61.972 60.000 8.22 0.00 39.73 4.37
2934 5272 1.971505 TACATGGCCGAAGCTGGGAG 61.972 60.000 8.22 0.00 39.73 4.30
2935 5273 2.688666 ATGGCCGAAGCTGGGAGA 60.689 61.111 8.22 0.00 39.73 3.71
2936 5274 2.739996 ATGGCCGAAGCTGGGAGAG 61.740 63.158 8.22 0.00 39.73 3.20
2937 5275 3.077556 GGCCGAAGCTGGGAGAGA 61.078 66.667 8.22 0.00 39.73 3.10
2938 5276 2.660064 GGCCGAAGCTGGGAGAGAA 61.660 63.158 8.22 0.00 39.73 2.87
2939 5277 1.153469 GCCGAAGCTGGGAGAGAAG 60.153 63.158 8.22 0.00 35.50 2.85
2940 5278 1.893919 GCCGAAGCTGGGAGAGAAGT 61.894 60.000 8.22 0.00 35.50 3.01
2941 5279 1.475403 CCGAAGCTGGGAGAGAAGTA 58.525 55.000 0.00 0.00 0.00 2.24
2942 5280 2.035632 CCGAAGCTGGGAGAGAAGTAT 58.964 52.381 0.00 0.00 0.00 2.12
2943 5281 2.432510 CCGAAGCTGGGAGAGAAGTATT 59.567 50.000 0.00 0.00 0.00 1.89
2944 5282 3.452474 CGAAGCTGGGAGAGAAGTATTG 58.548 50.000 0.00 0.00 0.00 1.90
2945 5283 3.131223 CGAAGCTGGGAGAGAAGTATTGA 59.869 47.826 0.00 0.00 0.00 2.57
2946 5284 4.202202 CGAAGCTGGGAGAGAAGTATTGAT 60.202 45.833 0.00 0.00 0.00 2.57
2947 5285 4.953940 AGCTGGGAGAGAAGTATTGATC 57.046 45.455 0.00 0.00 0.00 2.92
2948 5286 4.293494 AGCTGGGAGAGAAGTATTGATCA 58.707 43.478 0.00 0.00 0.00 2.92
2949 5287 4.718774 AGCTGGGAGAGAAGTATTGATCAA 59.281 41.667 11.26 11.26 0.00 2.57
2950 5288 5.055812 GCTGGGAGAGAAGTATTGATCAAG 58.944 45.833 14.54 0.00 0.00 3.02
2951 5289 5.609423 CTGGGAGAGAAGTATTGATCAAGG 58.391 45.833 14.54 0.00 0.00 3.61
2952 5290 4.141620 TGGGAGAGAAGTATTGATCAAGGC 60.142 45.833 14.54 8.89 0.00 4.35
2953 5291 4.054671 GGAGAGAAGTATTGATCAAGGCG 58.945 47.826 14.54 0.00 0.00 5.52
2954 5292 4.054671 GAGAGAAGTATTGATCAAGGCGG 58.945 47.826 14.54 0.00 0.00 6.13
2955 5293 3.452627 AGAGAAGTATTGATCAAGGCGGT 59.547 43.478 14.54 0.00 0.00 5.68
2956 5294 3.535561 AGAAGTATTGATCAAGGCGGTG 58.464 45.455 14.54 0.00 0.00 4.94
2957 5295 2.332063 AGTATTGATCAAGGCGGTGG 57.668 50.000 14.54 0.00 0.00 4.61
2958 5296 0.663153 GTATTGATCAAGGCGGTGGC 59.337 55.000 14.54 0.00 38.90 5.01
2959 5297 0.813610 TATTGATCAAGGCGGTGGCG 60.814 55.000 14.54 0.00 41.24 5.69
2964 5302 4.481112 CAAGGCGGTGGCGCAATC 62.481 66.667 10.83 0.00 41.24 2.67
2968 5306 4.256090 GCGGTGGCGCAATCCATC 62.256 66.667 10.83 0.00 38.57 3.51
2969 5307 3.585990 CGGTGGCGCAATCCATCC 61.586 66.667 10.83 0.00 38.57 3.51
2970 5308 3.219198 GGTGGCGCAATCCATCCC 61.219 66.667 10.83 0.00 38.57 3.85
2971 5309 2.124151 GTGGCGCAATCCATCCCT 60.124 61.111 10.83 0.00 38.57 4.20
2972 5310 1.148273 GTGGCGCAATCCATCCCTA 59.852 57.895 10.83 0.00 38.57 3.53
2973 5311 1.148273 TGGCGCAATCCATCCCTAC 59.852 57.895 10.83 0.00 0.00 3.18
2974 5312 1.961277 GGCGCAATCCATCCCTACG 60.961 63.158 10.83 0.00 0.00 3.51
2975 5313 1.227556 GCGCAATCCATCCCTACGT 60.228 57.895 0.30 0.00 0.00 3.57
2976 5314 0.032952 GCGCAATCCATCCCTACGTA 59.967 55.000 0.30 0.00 0.00 3.57
2977 5315 1.779569 CGCAATCCATCCCTACGTAC 58.220 55.000 0.00 0.00 0.00 3.67
2978 5316 1.067974 CGCAATCCATCCCTACGTACA 59.932 52.381 0.00 0.00 0.00 2.90
2979 5317 2.288825 CGCAATCCATCCCTACGTACAT 60.289 50.000 0.00 0.00 0.00 2.29
2980 5318 3.326747 GCAATCCATCCCTACGTACATC 58.673 50.000 0.00 0.00 0.00 3.06
2981 5319 3.244078 GCAATCCATCCCTACGTACATCA 60.244 47.826 0.00 0.00 0.00 3.07
2982 5320 4.563580 GCAATCCATCCCTACGTACATCAT 60.564 45.833 0.00 0.00 0.00 2.45
2983 5321 4.808414 ATCCATCCCTACGTACATCATG 57.192 45.455 0.00 0.00 0.00 3.07
2984 5322 2.897326 TCCATCCCTACGTACATCATGG 59.103 50.000 10.09 10.09 0.00 3.66
2985 5323 2.028112 CCATCCCTACGTACATCATGGG 60.028 54.545 8.66 8.66 36.14 4.00
2986 5324 2.759839 TCCCTACGTACATCATGGGA 57.240 50.000 12.69 12.69 40.99 4.37
2987 5325 2.594131 TCCCTACGTACATCATGGGAG 58.406 52.381 12.69 0.00 38.67 4.30
2988 5326 2.091499 TCCCTACGTACATCATGGGAGT 60.091 50.000 12.69 0.00 38.67 3.85
2989 5327 3.138839 TCCCTACGTACATCATGGGAGTA 59.861 47.826 12.69 0.00 38.67 2.59
2990 5328 4.087182 CCCTACGTACATCATGGGAGTAT 58.913 47.826 9.22 0.00 36.90 2.12
2991 5329 4.527038 CCCTACGTACATCATGGGAGTATT 59.473 45.833 9.22 0.00 36.90 1.89
2992 5330 5.011738 CCCTACGTACATCATGGGAGTATTT 59.988 44.000 9.22 0.00 36.90 1.40
2993 5331 6.209986 CCCTACGTACATCATGGGAGTATTTA 59.790 42.308 9.22 0.00 36.90 1.40
2994 5332 7.256048 CCCTACGTACATCATGGGAGTATTTAA 60.256 40.741 9.22 0.00 36.90 1.52
2995 5333 8.145767 CCTACGTACATCATGGGAGTATTTAAA 58.854 37.037 0.00 0.00 0.00 1.52
3007 6129 7.514721 TGGGAGTATTTAAACTGTTGTTCTCT 58.485 34.615 0.00 0.00 34.96 3.10
3009 6131 7.444487 GGGAGTATTTAAACTGTTGTTCTCTGT 59.556 37.037 0.00 0.00 34.96 3.41
3010 6132 9.485206 GGAGTATTTAAACTGTTGTTCTCTGTA 57.515 33.333 0.00 0.00 34.96 2.74
3015 6137 8.725405 TTTAAACTGTTGTTCTCTGTATGTGA 57.275 30.769 0.00 0.00 34.96 3.58
3016 6138 8.902540 TTAAACTGTTGTTCTCTGTATGTGAT 57.097 30.769 0.00 0.00 34.96 3.06
3017 6139 6.791887 AACTGTTGTTCTCTGTATGTGATG 57.208 37.500 0.00 0.00 0.00 3.07
3018 6140 6.101650 ACTGTTGTTCTCTGTATGTGATGA 57.898 37.500 0.00 0.00 0.00 2.92
3019 6141 6.705302 ACTGTTGTTCTCTGTATGTGATGAT 58.295 36.000 0.00 0.00 0.00 2.45
3020 6142 6.815641 ACTGTTGTTCTCTGTATGTGATGATC 59.184 38.462 0.00 0.00 0.00 2.92
3021 6143 6.939622 TGTTGTTCTCTGTATGTGATGATCT 58.060 36.000 0.00 0.00 0.00 2.75
3022 6144 7.389232 TGTTGTTCTCTGTATGTGATGATCTT 58.611 34.615 0.00 0.00 0.00 2.40
3023 6145 8.531146 TGTTGTTCTCTGTATGTGATGATCTTA 58.469 33.333 0.00 0.00 0.00 2.10
3024 6146 8.812329 GTTGTTCTCTGTATGTGATGATCTTAC 58.188 37.037 0.00 0.00 0.00 2.34
3025 6147 8.298729 TGTTCTCTGTATGTGATGATCTTACT 57.701 34.615 0.00 0.00 0.00 2.24
3026 6148 8.409371 TGTTCTCTGTATGTGATGATCTTACTC 58.591 37.037 0.00 0.00 0.00 2.59
3027 6149 7.195839 TCTCTGTATGTGATGATCTTACTCG 57.804 40.000 0.00 0.00 0.00 4.18
3028 6150 6.205658 TCTCTGTATGTGATGATCTTACTCGG 59.794 42.308 0.00 0.00 0.00 4.63
3031 6153 6.681777 TGTATGTGATGATCTTACTCGGATG 58.318 40.000 0.00 0.00 0.00 3.51
3032 6154 4.590850 TGTGATGATCTTACTCGGATGG 57.409 45.455 0.00 0.00 0.00 3.51
3033 6155 3.960755 TGTGATGATCTTACTCGGATGGT 59.039 43.478 0.00 0.00 0.00 3.55
3034 6156 4.038042 TGTGATGATCTTACTCGGATGGTC 59.962 45.833 0.00 0.00 0.00 4.02
3035 6157 3.574396 TGATGATCTTACTCGGATGGTCC 59.426 47.826 0.00 0.00 0.00 4.46
3047 6169 3.223674 GGATGGTCCGGAATTATTGGT 57.776 47.619 5.23 0.00 0.00 3.67
3048 6170 2.884639 GGATGGTCCGGAATTATTGGTG 59.115 50.000 5.23 0.00 0.00 4.17
3049 6171 2.428544 TGGTCCGGAATTATTGGTGG 57.571 50.000 5.23 0.00 0.00 4.61
3050 6172 1.064314 TGGTCCGGAATTATTGGTGGG 60.064 52.381 5.23 0.00 0.00 4.61
3051 6173 1.687563 GTCCGGAATTATTGGTGGGG 58.312 55.000 5.23 0.00 0.00 4.96
3052 6174 1.064240 GTCCGGAATTATTGGTGGGGT 60.064 52.381 5.23 0.00 0.00 4.95
3053 6175 1.064314 TCCGGAATTATTGGTGGGGTG 60.064 52.381 0.00 0.00 0.00 4.61
3055 6177 0.744281 GGAATTATTGGTGGGGTGCG 59.256 55.000 0.00 0.00 0.00 5.34
3057 6179 0.333312 AATTATTGGTGGGGTGCGGA 59.667 50.000 0.00 0.00 0.00 5.54
3058 6180 0.106719 ATTATTGGTGGGGTGCGGAG 60.107 55.000 0.00 0.00 0.00 4.63
3059 6181 1.202099 TTATTGGTGGGGTGCGGAGA 61.202 55.000 0.00 0.00 0.00 3.71
3060 6182 1.202099 TATTGGTGGGGTGCGGAGAA 61.202 55.000 0.00 0.00 0.00 2.87
3062 6184 2.359975 GGTGGGGTGCGGAGAAAG 60.360 66.667 0.00 0.00 0.00 2.62
3064 6186 3.646715 TGGGGTGCGGAGAAAGGG 61.647 66.667 0.00 0.00 0.00 3.95
3065 6187 3.327404 GGGGTGCGGAGAAAGGGA 61.327 66.667 0.00 0.00 0.00 4.20
3066 6188 2.754375 GGGTGCGGAGAAAGGGAA 59.246 61.111 0.00 0.00 0.00 3.97
3067 6189 1.074248 GGGTGCGGAGAAAGGGAAA 59.926 57.895 0.00 0.00 0.00 3.13
3069 6191 1.574702 GGTGCGGAGAAAGGGAAACG 61.575 60.000 0.00 0.00 0.00 3.60
3070 6192 1.302192 TGCGGAGAAAGGGAAACGG 60.302 57.895 0.00 0.00 0.00 4.44
3072 6194 0.604511 GCGGAGAAAGGGAAACGGAA 60.605 55.000 0.00 0.00 0.00 4.30
3073 6195 1.886886 CGGAGAAAGGGAAACGGAAA 58.113 50.000 0.00 0.00 0.00 3.13
3074 6196 2.223745 CGGAGAAAGGGAAACGGAAAA 58.776 47.619 0.00 0.00 0.00 2.29
3076 6198 2.295349 GGAGAAAGGGAAACGGAAAACC 59.705 50.000 0.00 0.00 0.00 3.27
3078 6200 2.033372 GAAAGGGAAACGGAAAACCCA 58.967 47.619 0.00 0.00 44.25 4.51
3079 6201 2.391926 AAGGGAAACGGAAAACCCAT 57.608 45.000 0.00 0.00 44.25 4.00
3080 6202 2.391926 AGGGAAACGGAAAACCCATT 57.608 45.000 0.00 0.00 44.25 3.16
3082 6204 1.001520 GGGAAACGGAAAACCCATTGG 59.998 52.381 0.00 0.00 41.72 3.16
3084 6206 2.565391 GGAAACGGAAAACCCATTGGAT 59.435 45.455 3.62 0.00 34.81 3.41
3085 6207 3.584834 GAAACGGAAAACCCATTGGATG 58.415 45.455 3.62 0.00 34.81 3.51
3094 6216 3.545003 CCATTGGATGGCTTGGGAT 57.455 52.632 0.00 0.00 44.70 3.85
3095 6217 1.045407 CCATTGGATGGCTTGGGATG 58.955 55.000 0.00 0.00 44.70 3.51
3096 6218 1.411930 CCATTGGATGGCTTGGGATGA 60.412 52.381 0.00 0.00 44.70 2.92
3097 6219 1.961394 CATTGGATGGCTTGGGATGAG 59.039 52.381 0.00 0.00 0.00 2.90
3098 6220 1.297968 TTGGATGGCTTGGGATGAGA 58.702 50.000 0.00 0.00 0.00 3.27
3100 6222 1.422781 TGGATGGCTTGGGATGAGATC 59.577 52.381 0.00 0.00 0.00 2.75
3101 6223 1.422781 GGATGGCTTGGGATGAGATCA 59.577 52.381 0.00 0.00 0.00 2.92
3102 6224 2.041350 GGATGGCTTGGGATGAGATCAT 59.959 50.000 0.00 0.00 39.70 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 3.155093 AGGCGCATAATTCTTTTGCAG 57.845 42.857 10.83 0.00 36.15 4.41
91 92 9.352784 TGCATATAATAAAAAGGCGCATAATTC 57.647 29.630 10.83 0.00 0.00 2.17
181 183 4.973663 GTGTATGTGTGTGTTACTTTTGGC 59.026 41.667 0.00 0.00 0.00 4.52
192 194 6.512253 GCAAGGATATGATGTGTATGTGTGTG 60.512 42.308 0.00 0.00 0.00 3.82
207 209 8.831715 TGTACAAGTATGTATGCAAGGATATG 57.168 34.615 0.00 0.00 43.60 1.78
336 342 3.932710 AGAGTGCCACATGTAACAATACG 59.067 43.478 0.00 0.00 34.60 3.06
337 343 5.880054 AAGAGTGCCACATGTAACAATAC 57.120 39.130 0.00 0.00 0.00 1.89
443 449 1.597854 CACTTTGTGCGAGGCCTGA 60.598 57.895 12.00 0.00 0.00 3.86
482 488 7.888250 AAACAGGAAATGAGAAAGAAGAAGT 57.112 32.000 0.00 0.00 0.00 3.01
493 499 3.321682 TCCAAGCCAAAACAGGAAATGAG 59.678 43.478 0.00 0.00 0.00 2.90
555 561 8.070034 AGCAAAACAGGAATTCAATATCATCA 57.930 30.769 7.93 0.00 0.00 3.07
562 568 6.226052 GGAAGAAGCAAAACAGGAATTCAAT 58.774 36.000 7.93 0.00 0.00 2.57
743 754 2.423538 GCTTGGTGAGAACAACACTTGT 59.576 45.455 0.00 0.00 43.86 3.16
744 755 2.223572 GGCTTGGTGAGAACAACACTTG 60.224 50.000 0.00 0.00 43.86 3.16
771 788 2.996734 CGGCATTGCTTTGGGGGT 60.997 61.111 8.82 0.00 0.00 4.95
785 802 0.382515 TGTTAAACAAGTGCACCGGC 59.617 50.000 14.63 0.00 41.68 6.13
788 805 6.902224 AATCTTTTGTTAAACAAGTGCACC 57.098 33.333 14.63 0.00 39.53 5.01
949 966 4.574599 AAGTTGTGCTGGATCTTGTTTC 57.425 40.909 0.00 0.00 0.00 2.78
987 1004 0.399949 TAGCCATGGTCAGTAGGGGG 60.400 60.000 14.67 0.00 0.00 5.40
995 1012 3.134623 CCAGTGATAACTAGCCATGGTCA 59.865 47.826 14.67 4.10 0.00 4.02
997 1014 2.439507 CCCAGTGATAACTAGCCATGGT 59.560 50.000 14.67 2.69 0.00 3.55
1012 1029 2.806244 CCAAAACGAGAACTACCCAGTG 59.194 50.000 0.00 0.00 34.36 3.66
1104 1121 1.750399 GCCCATCCATTGCTCGTGT 60.750 57.895 0.00 0.00 0.00 4.49
1113 1130 0.178953 GGCCATACTTGCCCATCCAT 60.179 55.000 0.00 0.00 43.33 3.41
1150 1167 3.127533 CCGCCTTGCTTTCTCGGG 61.128 66.667 0.00 0.00 36.73 5.14
1221 1238 0.615331 CCTCCAGCCAGAACTTGCTA 59.385 55.000 0.27 0.00 35.69 3.49
1257 1274 0.526211 TGAACTCGTCCTCGGTGATG 59.474 55.000 0.00 0.00 37.69 3.07
1290 1307 4.643795 GCAGCTGGCTTGTATCCA 57.356 55.556 17.12 0.00 40.25 3.41
1310 1330 3.965539 CTCCGGCCCTTGTCAGCTG 62.966 68.421 7.63 7.63 35.04 4.24
1311 1331 3.710722 CTCCGGCCCTTGTCAGCT 61.711 66.667 0.00 0.00 0.00 4.24
1462 1482 7.255242 CCATAGGTTCAGGCAAACATAATGTAG 60.255 40.741 5.35 0.00 30.19 2.74
1477 1854 2.834549 ACTCCAGTGTCCATAGGTTCAG 59.165 50.000 0.00 0.00 0.00 3.02
1518 1929 2.360852 CCCAGCAGCACCCTGAAG 60.361 66.667 0.00 0.00 41.77 3.02
2121 2571 7.224949 GTGGATCAATTTACAAGCTAGTAGGAC 59.775 40.741 0.00 0.00 0.00 3.85
2140 2590 2.270352 AACGCTTCAAAGGTGGATCA 57.730 45.000 0.00 0.00 0.00 2.92
2200 2851 8.462016 AGAATCATTTTTCGAAAAGGGTGATAG 58.538 33.333 28.64 15.32 31.85 2.08
2250 2903 0.459237 CATGTGAGGACGAGAGGTGC 60.459 60.000 0.00 0.00 37.22 5.01
2299 2953 7.130681 ACTGCTGCTTACTAGGAGAAATAAT 57.869 36.000 0.00 0.00 42.01 1.28
2368 3024 6.845758 TTCTAAGTTGCTAAGCCTACACTA 57.154 37.500 0.00 0.00 0.00 2.74
2445 3102 4.304110 ACTCGGTTTATACGCCATGTATG 58.696 43.478 0.00 0.00 43.63 2.39
2475 3132 4.812626 TCCTCAAACTTAGAAACCGTTGAC 59.187 41.667 0.00 0.00 0.00 3.18
2482 3139 6.723131 ATACGCTTCCTCAAACTTAGAAAC 57.277 37.500 0.00 0.00 0.00 2.78
2497 3154 9.204570 ACCTTCACATATTTGTATATACGCTTC 57.795 33.333 8.33 0.00 33.76 3.86
2803 5141 7.093333 GGAAGTCCCAAATATTTGTCCTCAAAT 60.093 37.037 23.24 10.31 43.71 2.32
2806 5144 5.222233 TGGAAGTCCCAAATATTTGTCCTCA 60.222 40.000 24.26 13.36 43.29 3.86
2807 5145 5.261216 TGGAAGTCCCAAATATTTGTCCTC 58.739 41.667 24.26 15.12 43.29 3.71
2808 5146 5.269554 TGGAAGTCCCAAATATTTGTCCT 57.730 39.130 24.26 15.90 43.29 3.85
2820 5158 0.472471 GTCTGGTGTTGGAAGTCCCA 59.528 55.000 0.00 0.00 44.93 4.37
2821 5159 0.472471 TGTCTGGTGTTGGAAGTCCC 59.528 55.000 0.00 0.00 34.29 4.46
2822 5160 1.141053 ACTGTCTGGTGTTGGAAGTCC 59.859 52.381 0.00 0.00 0.00 3.85
2823 5161 2.484889 GACTGTCTGGTGTTGGAAGTC 58.515 52.381 0.00 0.00 0.00 3.01
2825 5163 1.202533 ACGACTGTCTGGTGTTGGAAG 60.203 52.381 6.21 0.00 0.00 3.46
2826 5164 0.828022 ACGACTGTCTGGTGTTGGAA 59.172 50.000 6.21 0.00 0.00 3.53
2827 5165 1.694844 TACGACTGTCTGGTGTTGGA 58.305 50.000 6.21 0.00 0.00 3.53
2828 5166 2.337583 CATACGACTGTCTGGTGTTGG 58.662 52.381 6.21 0.00 0.00 3.77
2829 5167 1.726791 GCATACGACTGTCTGGTGTTG 59.273 52.381 6.21 2.27 0.00 3.33
2832 5170 2.299993 ATGCATACGACTGTCTGGTG 57.700 50.000 0.00 2.97 0.00 4.17
2833 5171 4.433615 CTTTATGCATACGACTGTCTGGT 58.566 43.478 5.74 0.00 0.00 4.00
2834 5172 3.804325 CCTTTATGCATACGACTGTCTGG 59.196 47.826 5.74 0.00 0.00 3.86
2835 5173 3.246226 GCCTTTATGCATACGACTGTCTG 59.754 47.826 5.74 2.43 0.00 3.51
2836 5174 3.118775 TGCCTTTATGCATACGACTGTCT 60.119 43.478 5.74 0.00 36.04 3.41
2837 5175 3.194861 TGCCTTTATGCATACGACTGTC 58.805 45.455 5.74 0.00 36.04 3.51
2839 5177 3.623060 ACTTGCCTTTATGCATACGACTG 59.377 43.478 5.74 0.00 41.70 3.51
2841 5179 4.495844 GGAACTTGCCTTTATGCATACGAC 60.496 45.833 5.74 0.00 41.70 4.34
2843 5181 3.376859 TGGAACTTGCCTTTATGCATACG 59.623 43.478 5.74 0.44 41.70 3.06
2844 5182 4.981806 TGGAACTTGCCTTTATGCATAC 57.018 40.909 5.74 0.00 41.70 2.39
2846 5184 4.888326 TTTGGAACTTGCCTTTATGCAT 57.112 36.364 3.79 3.79 41.70 3.96
2847 5185 4.679373 TTTTGGAACTTGCCTTTATGCA 57.321 36.364 0.00 0.00 40.07 3.96
2848 5186 6.372981 CAAATTTTGGAACTTGCCTTTATGC 58.627 36.000 0.97 0.00 0.00 3.14
2849 5187 6.017275 TGCAAATTTTGGAACTTGCCTTTATG 60.017 34.615 10.96 0.00 42.77 1.90
2850 5188 6.060788 TGCAAATTTTGGAACTTGCCTTTAT 58.939 32.000 10.96 0.00 42.77 1.40
2852 5190 4.268359 TGCAAATTTTGGAACTTGCCTTT 58.732 34.783 10.96 0.00 42.77 3.11
2855 5193 3.627123 ACTTGCAAATTTTGGAACTTGCC 59.373 39.130 11.48 0.00 42.77 4.52
2856 5194 4.332268 TCACTTGCAAATTTTGGAACTTGC 59.668 37.500 11.48 0.00 43.52 4.01
2857 5195 6.092533 ACTTCACTTGCAAATTTTGGAACTTG 59.907 34.615 11.48 11.35 36.01 3.16
2860 5198 6.421377 AACTTCACTTGCAAATTTTGGAAC 57.579 33.333 11.48 0.00 36.01 3.62
2862 5200 7.984050 TCATTAACTTCACTTGCAAATTTTGGA 59.016 29.630 10.96 5.24 0.00 3.53
2863 5201 8.140677 TCATTAACTTCACTTGCAAATTTTGG 57.859 30.769 10.96 0.00 0.00 3.28
2864 5202 9.985318 TTTCATTAACTTCACTTGCAAATTTTG 57.015 25.926 0.00 4.72 0.00 2.44
2869 5207 5.231147 GCGTTTCATTAACTTCACTTGCAAA 59.769 36.000 0.00 0.00 34.46 3.68
2871 5209 4.201960 TGCGTTTCATTAACTTCACTTGCA 60.202 37.500 0.00 0.00 34.46 4.08
2872 5210 4.286910 TGCGTTTCATTAACTTCACTTGC 58.713 39.130 0.00 0.00 34.46 4.01
2873 5211 6.303970 CAGATGCGTTTCATTAACTTCACTTG 59.696 38.462 0.00 0.00 35.05 3.16
2874 5212 6.017109 ACAGATGCGTTTCATTAACTTCACTT 60.017 34.615 0.00 0.00 35.05 3.16
2876 5214 5.689819 ACAGATGCGTTTCATTAACTTCAC 58.310 37.500 0.00 0.00 35.05 3.18
2877 5215 5.940192 ACAGATGCGTTTCATTAACTTCA 57.060 34.783 0.00 0.00 35.05 3.02
2878 5216 9.586150 CATATACAGATGCGTTTCATTAACTTC 57.414 33.333 0.00 0.00 35.05 3.01
2880 5218 7.576236 GCATATACAGATGCGTTTCATTAACT 58.424 34.615 0.00 0.00 42.63 2.24
2881 5219 7.766723 GCATATACAGATGCGTTTCATTAAC 57.233 36.000 0.00 0.00 42.63 2.01
2892 5230 5.167121 AGACATCTTCGCATATACAGATGC 58.833 41.667 7.73 0.00 44.44 3.91
2894 5232 7.454260 TGTAGACATCTTCGCATATACAGAT 57.546 36.000 0.00 0.00 0.00 2.90
2895 5233 6.877611 TGTAGACATCTTCGCATATACAGA 57.122 37.500 0.00 0.00 0.00 3.41
2896 5234 6.529477 CCATGTAGACATCTTCGCATATACAG 59.471 42.308 0.00 0.00 33.61 2.74
2897 5235 6.389906 CCATGTAGACATCTTCGCATATACA 58.610 40.000 0.00 0.00 33.61 2.29
2898 5236 5.289675 GCCATGTAGACATCTTCGCATATAC 59.710 44.000 0.00 0.00 33.61 1.47
2899 5237 5.410924 GCCATGTAGACATCTTCGCATATA 58.589 41.667 0.00 0.00 33.61 0.86
2900 5238 4.248859 GCCATGTAGACATCTTCGCATAT 58.751 43.478 0.00 0.00 33.61 1.78
2901 5239 3.554960 GGCCATGTAGACATCTTCGCATA 60.555 47.826 0.00 0.00 33.61 3.14
2902 5240 2.487934 GCCATGTAGACATCTTCGCAT 58.512 47.619 0.00 0.00 33.61 4.73
2903 5241 1.473257 GGCCATGTAGACATCTTCGCA 60.473 52.381 0.00 0.00 33.61 5.10
2904 5242 1.221414 GGCCATGTAGACATCTTCGC 58.779 55.000 0.00 0.00 33.61 4.70
2905 5243 1.067060 TCGGCCATGTAGACATCTTCG 59.933 52.381 2.24 0.00 33.61 3.79
2906 5244 2.890808 TCGGCCATGTAGACATCTTC 57.109 50.000 2.24 0.00 33.61 2.87
2907 5245 2.743183 GCTTCGGCCATGTAGACATCTT 60.743 50.000 2.24 0.00 33.61 2.40
2908 5246 1.202580 GCTTCGGCCATGTAGACATCT 60.203 52.381 2.24 0.00 33.61 2.90
2909 5247 1.202580 AGCTTCGGCCATGTAGACATC 60.203 52.381 2.24 0.00 43.01 3.06
2910 5248 0.833287 AGCTTCGGCCATGTAGACAT 59.167 50.000 2.24 0.00 43.01 3.06
2911 5249 0.108186 CAGCTTCGGCCATGTAGACA 60.108 55.000 2.24 0.00 43.01 3.41
2912 5250 0.811616 CCAGCTTCGGCCATGTAGAC 60.812 60.000 2.24 0.00 43.01 2.59
2913 5251 1.522092 CCAGCTTCGGCCATGTAGA 59.478 57.895 2.24 0.00 43.01 2.59
2914 5252 1.524621 CCCAGCTTCGGCCATGTAG 60.525 63.158 2.24 0.00 43.01 2.74
2915 5253 1.971505 CTCCCAGCTTCGGCCATGTA 61.972 60.000 2.24 0.00 43.01 2.29
2916 5254 3.329889 TCCCAGCTTCGGCCATGT 61.330 61.111 2.24 0.00 43.01 3.21
2917 5255 2.515523 CTCCCAGCTTCGGCCATG 60.516 66.667 2.24 0.00 43.01 3.66
2918 5256 2.688666 TCTCCCAGCTTCGGCCAT 60.689 61.111 2.24 0.00 43.01 4.40
2919 5257 3.393970 CTCTCCCAGCTTCGGCCA 61.394 66.667 2.24 0.00 43.01 5.36
2920 5258 2.585791 CTTCTCTCCCAGCTTCGGCC 62.586 65.000 0.00 0.00 43.01 6.13
2921 5259 1.153469 CTTCTCTCCCAGCTTCGGC 60.153 63.158 0.00 0.00 42.17 5.54
2922 5260 1.475403 TACTTCTCTCCCAGCTTCGG 58.525 55.000 0.00 0.00 0.00 4.30
2923 5261 3.131223 TCAATACTTCTCTCCCAGCTTCG 59.869 47.826 0.00 0.00 0.00 3.79
2924 5262 4.744795 TCAATACTTCTCTCCCAGCTTC 57.255 45.455 0.00 0.00 0.00 3.86
2925 5263 4.718774 TGATCAATACTTCTCTCCCAGCTT 59.281 41.667 0.00 0.00 0.00 3.74
2926 5264 4.293494 TGATCAATACTTCTCTCCCAGCT 58.707 43.478 0.00 0.00 0.00 4.24
2927 5265 4.679373 TGATCAATACTTCTCTCCCAGC 57.321 45.455 0.00 0.00 0.00 4.85
2928 5266 5.609423 CCTTGATCAATACTTCTCTCCCAG 58.391 45.833 8.96 0.00 0.00 4.45
2929 5267 4.141620 GCCTTGATCAATACTTCTCTCCCA 60.142 45.833 8.96 0.00 0.00 4.37
2930 5268 4.384940 GCCTTGATCAATACTTCTCTCCC 58.615 47.826 8.96 0.00 0.00 4.30
2931 5269 4.054671 CGCCTTGATCAATACTTCTCTCC 58.945 47.826 8.96 0.00 0.00 3.71
2932 5270 4.054671 CCGCCTTGATCAATACTTCTCTC 58.945 47.826 8.96 0.00 0.00 3.20
2933 5271 3.452627 ACCGCCTTGATCAATACTTCTCT 59.547 43.478 8.96 0.00 0.00 3.10
2934 5272 3.557595 CACCGCCTTGATCAATACTTCTC 59.442 47.826 8.96 0.00 0.00 2.87
2935 5273 3.535561 CACCGCCTTGATCAATACTTCT 58.464 45.455 8.96 0.00 0.00 2.85
2936 5274 2.614057 CCACCGCCTTGATCAATACTTC 59.386 50.000 8.96 0.00 0.00 3.01
2937 5275 2.643551 CCACCGCCTTGATCAATACTT 58.356 47.619 8.96 0.00 0.00 2.24
2938 5276 1.747206 GCCACCGCCTTGATCAATACT 60.747 52.381 8.96 0.00 0.00 2.12
2939 5277 0.663153 GCCACCGCCTTGATCAATAC 59.337 55.000 8.96 3.22 0.00 1.89
2940 5278 0.813610 CGCCACCGCCTTGATCAATA 60.814 55.000 8.96 0.00 0.00 1.90
2941 5279 2.114670 CGCCACCGCCTTGATCAAT 61.115 57.895 8.96 0.00 0.00 2.57
2942 5280 2.745884 CGCCACCGCCTTGATCAA 60.746 61.111 8.12 8.12 0.00 2.57
2952 5290 3.585990 GGATGGATTGCGCCACCG 61.586 66.667 4.18 0.00 41.56 4.94
2953 5291 2.337879 TAGGGATGGATTGCGCCACC 62.338 60.000 4.18 6.28 41.56 4.61
2954 5292 1.148273 TAGGGATGGATTGCGCCAC 59.852 57.895 4.18 0.00 41.56 5.01
2955 5293 1.148273 GTAGGGATGGATTGCGCCA 59.852 57.895 4.18 0.00 43.23 5.69
2956 5294 1.961277 CGTAGGGATGGATTGCGCC 60.961 63.158 4.18 0.00 0.00 6.53
2957 5295 0.032952 TACGTAGGGATGGATTGCGC 59.967 55.000 0.00 0.00 0.00 6.09
2958 5296 1.067974 TGTACGTAGGGATGGATTGCG 59.932 52.381 0.00 0.00 0.00 4.85
2959 5297 2.902705 TGTACGTAGGGATGGATTGC 57.097 50.000 0.00 0.00 0.00 3.56
2960 5298 4.600692 TGATGTACGTAGGGATGGATTG 57.399 45.455 0.00 0.00 0.00 2.67
2961 5299 4.020218 CCATGATGTACGTAGGGATGGATT 60.020 45.833 13.82 0.00 32.20 3.01
2962 5300 3.515502 CCATGATGTACGTAGGGATGGAT 59.484 47.826 13.82 0.00 32.20 3.41
2963 5301 2.897326 CCATGATGTACGTAGGGATGGA 59.103 50.000 13.82 0.00 32.20 3.41
2964 5302 2.028112 CCCATGATGTACGTAGGGATGG 60.028 54.545 9.22 11.24 38.60 3.51
2965 5303 2.897326 TCCCATGATGTACGTAGGGATG 59.103 50.000 12.69 5.64 40.26 3.51
2966 5304 3.165875 CTCCCATGATGTACGTAGGGAT 58.834 50.000 16.05 0.62 43.86 3.85
2967 5305 2.091499 ACTCCCATGATGTACGTAGGGA 60.091 50.000 15.17 15.17 42.76 4.20
2968 5306 2.317040 ACTCCCATGATGTACGTAGGG 58.683 52.381 8.66 8.66 37.65 3.53
2969 5307 5.723672 AATACTCCCATGATGTACGTAGG 57.276 43.478 0.00 0.00 0.00 3.18
2970 5308 8.975439 GTTTAAATACTCCCATGATGTACGTAG 58.025 37.037 0.00 0.00 0.00 3.51
2971 5309 8.698210 AGTTTAAATACTCCCATGATGTACGTA 58.302 33.333 0.00 0.00 0.00 3.57
2972 5310 7.494625 CAGTTTAAATACTCCCATGATGTACGT 59.505 37.037 0.00 0.00 0.00 3.57
2973 5311 7.494625 ACAGTTTAAATACTCCCATGATGTACG 59.505 37.037 0.00 0.00 0.00 3.67
2974 5312 8.732746 ACAGTTTAAATACTCCCATGATGTAC 57.267 34.615 0.00 0.00 0.00 2.90
2975 5313 9.173021 CAACAGTTTAAATACTCCCATGATGTA 57.827 33.333 0.00 0.00 0.00 2.29
2976 5314 7.669722 ACAACAGTTTAAATACTCCCATGATGT 59.330 33.333 0.00 0.00 0.00 3.06
2977 5315 8.055279 ACAACAGTTTAAATACTCCCATGATG 57.945 34.615 0.00 0.00 0.00 3.07
2978 5316 8.650143 AACAACAGTTTAAATACTCCCATGAT 57.350 30.769 0.00 0.00 0.00 2.45
2979 5317 7.942341 AGAACAACAGTTTAAATACTCCCATGA 59.058 33.333 0.00 0.00 0.00 3.07
2980 5318 8.110860 AGAACAACAGTTTAAATACTCCCATG 57.889 34.615 0.00 0.00 0.00 3.66
2981 5319 8.164070 AGAGAACAACAGTTTAAATACTCCCAT 58.836 33.333 0.00 0.00 0.00 4.00
2982 5320 7.444183 CAGAGAACAACAGTTTAAATACTCCCA 59.556 37.037 0.00 0.00 0.00 4.37
2983 5321 7.444487 ACAGAGAACAACAGTTTAAATACTCCC 59.556 37.037 0.00 0.00 0.00 4.30
2984 5322 8.379457 ACAGAGAACAACAGTTTAAATACTCC 57.621 34.615 0.00 0.00 0.00 3.85
2989 5327 9.337396 TCACATACAGAGAACAACAGTTTAAAT 57.663 29.630 0.00 0.00 0.00 1.40
2990 5328 8.725405 TCACATACAGAGAACAACAGTTTAAA 57.275 30.769 0.00 0.00 0.00 1.52
2991 5329 8.773645 CATCACATACAGAGAACAACAGTTTAA 58.226 33.333 0.00 0.00 0.00 1.52
2992 5330 8.147704 TCATCACATACAGAGAACAACAGTTTA 58.852 33.333 0.00 0.00 0.00 2.01
2993 5331 6.992123 TCATCACATACAGAGAACAACAGTTT 59.008 34.615 0.00 0.00 0.00 2.66
2994 5332 6.524734 TCATCACATACAGAGAACAACAGTT 58.475 36.000 0.00 0.00 0.00 3.16
2995 5333 6.101650 TCATCACATACAGAGAACAACAGT 57.898 37.500 0.00 0.00 0.00 3.55
3007 6129 6.294731 CCATCCGAGTAAGATCATCACATACA 60.295 42.308 0.00 0.00 0.00 2.29
3009 6131 5.775195 ACCATCCGAGTAAGATCATCACATA 59.225 40.000 0.00 0.00 0.00 2.29
3010 6132 4.590647 ACCATCCGAGTAAGATCATCACAT 59.409 41.667 0.00 0.00 0.00 3.21
3011 6133 3.960755 ACCATCCGAGTAAGATCATCACA 59.039 43.478 0.00 0.00 0.00 3.58
3012 6134 4.551388 GACCATCCGAGTAAGATCATCAC 58.449 47.826 0.00 0.00 0.00 3.06
3013 6135 3.574396 GGACCATCCGAGTAAGATCATCA 59.426 47.826 0.00 0.00 0.00 3.07
3014 6136 4.181309 GGACCATCCGAGTAAGATCATC 57.819 50.000 0.00 0.00 0.00 2.92
3027 6149 2.884639 CACCAATAATTCCGGACCATCC 59.115 50.000 1.83 0.00 0.00 3.51
3028 6150 2.884639 CCACCAATAATTCCGGACCATC 59.115 50.000 1.83 0.00 0.00 3.51
3031 6153 1.687563 CCCACCAATAATTCCGGACC 58.312 55.000 1.83 0.00 0.00 4.46
3032 6154 1.064240 ACCCCACCAATAATTCCGGAC 60.064 52.381 1.83 0.00 0.00 4.79
3033 6155 1.064314 CACCCCACCAATAATTCCGGA 60.064 52.381 0.00 0.00 0.00 5.14
3034 6156 1.398692 CACCCCACCAATAATTCCGG 58.601 55.000 0.00 0.00 0.00 5.14
3035 6157 0.744281 GCACCCCACCAATAATTCCG 59.256 55.000 0.00 0.00 0.00 4.30
3036 6158 0.744281 CGCACCCCACCAATAATTCC 59.256 55.000 0.00 0.00 0.00 3.01
3038 6160 0.333312 TCCGCACCCCACCAATAATT 59.667 50.000 0.00 0.00 0.00 1.40
3039 6161 0.106719 CTCCGCACCCCACCAATAAT 60.107 55.000 0.00 0.00 0.00 1.28
3041 6163 1.202099 TTCTCCGCACCCCACCAATA 61.202 55.000 0.00 0.00 0.00 1.90
3043 6165 2.690653 CTTTCTCCGCACCCCACCAA 62.691 60.000 0.00 0.00 0.00 3.67
3044 6166 3.172106 TTTCTCCGCACCCCACCA 61.172 61.111 0.00 0.00 0.00 4.17
3045 6167 2.359975 CTTTCTCCGCACCCCACC 60.360 66.667 0.00 0.00 0.00 4.61
3047 6169 3.646715 CCCTTTCTCCGCACCCCA 61.647 66.667 0.00 0.00 0.00 4.96
3048 6170 2.420466 TTTCCCTTTCTCCGCACCCC 62.420 60.000 0.00 0.00 0.00 4.95
3049 6171 1.074248 TTTCCCTTTCTCCGCACCC 59.926 57.895 0.00 0.00 0.00 4.61
3050 6172 1.574702 CGTTTCCCTTTCTCCGCACC 61.575 60.000 0.00 0.00 0.00 5.01
3051 6173 1.574702 CCGTTTCCCTTTCTCCGCAC 61.575 60.000 0.00 0.00 0.00 5.34
3052 6174 1.302192 CCGTTTCCCTTTCTCCGCA 60.302 57.895 0.00 0.00 0.00 5.69
3053 6175 0.604511 TTCCGTTTCCCTTTCTCCGC 60.605 55.000 0.00 0.00 0.00 5.54
3055 6177 2.295349 GGTTTTCCGTTTCCCTTTCTCC 59.705 50.000 0.00 0.00 0.00 3.71
3057 6179 2.313317 GGGTTTTCCGTTTCCCTTTCT 58.687 47.619 0.00 0.00 41.82 2.52
3058 6180 2.033372 TGGGTTTTCCGTTTCCCTTTC 58.967 47.619 0.00 0.00 41.82 2.62
3059 6181 2.162264 TGGGTTTTCCGTTTCCCTTT 57.838 45.000 0.00 0.00 41.82 3.11
3060 6182 2.367241 CAATGGGTTTTCCGTTTCCCTT 59.633 45.455 0.00 0.00 42.63 3.95
3062 6184 1.001520 CCAATGGGTTTTCCGTTTCCC 59.998 52.381 0.00 0.00 42.63 3.97
3064 6186 3.584834 CATCCAATGGGTTTTCCGTTTC 58.415 45.455 0.00 0.00 42.63 2.78
3065 6187 2.301583 CCATCCAATGGGTTTTCCGTTT 59.698 45.455 0.00 0.00 46.86 3.60
3066 6188 1.899142 CCATCCAATGGGTTTTCCGTT 59.101 47.619 0.00 0.00 46.86 4.44
3067 6189 1.555967 CCATCCAATGGGTTTTCCGT 58.444 50.000 0.00 0.00 46.86 4.69
3078 6200 1.854939 TCTCATCCCAAGCCATCCAAT 59.145 47.619 0.00 0.00 0.00 3.16
3079 6201 1.297968 TCTCATCCCAAGCCATCCAA 58.702 50.000 0.00 0.00 0.00 3.53
3080 6202 1.422781 GATCTCATCCCAAGCCATCCA 59.577 52.381 0.00 0.00 0.00 3.41
3082 6204 2.945080 TGATCTCATCCCAAGCCATC 57.055 50.000 0.00 0.00 0.00 3.51
3084 6206 2.945080 GATGATCTCATCCCAAGCCA 57.055 50.000 8.69 0.00 45.24 4.75


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

AutoCloner maintained by Alex Coulton.