Multiple sequence alignment - TraesCS7D01G530700

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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 TraesCS7D01G530700 chr7D 100.000 4069 0 0 1 4069 625338638 625334570 0.000000e+00 7515.0
1 TraesCS7D01G530700 chr7B 84.191 3264 290 101 318 3451 724844493 724841326 0.000000e+00 2961.0
2 TraesCS7D01G530700 chr7B 85.431 2725 221 101 816 3451 724818418 724815781 0.000000e+00 2671.0
3 TraesCS7D01G530700 chr7B 87.899 1504 110 34 1967 3412 724915857 724914368 0.000000e+00 1703.0
4 TraesCS7D01G530700 chr7B 86.237 792 79 8 20 794 724819274 724818496 0.000000e+00 832.0
5 TraesCS7D01G530700 chr7B 79.615 780 108 31 408 1170 724917966 724917221 2.800000e-141 512.0
6 TraesCS7D01G530700 chr7B 82.927 533 51 12 2335 2863 724839722 724839226 1.040000e-120 444.0
7 TraesCS7D01G530700 chr7B 89.474 342 30 3 2532 2869 724813885 724813546 1.050000e-115 427.0
8 TraesCS7D01G530700 chr7B 82.364 533 54 12 2335 2863 724880893 724880397 1.050000e-115 427.0
9 TraesCS7D01G530700 chr7B 91.429 175 14 1 1176 1349 724021383 724021209 5.260000e-59 239.0
10 TraesCS7D01G530700 chr7B 88.034 117 13 1 3812 3927 724840825 724840709 1.970000e-28 137.0
11 TraesCS7D01G530700 chr7B 88.034 117 13 1 3812 3927 724913786 724913670 1.970000e-28 137.0
12 TraesCS7D01G530700 chr7B 86.325 117 14 2 3812 3927 724815334 724815219 4.270000e-25 126.0
13 TraesCS7D01G530700 chr7B 87.234 94 6 1 318 405 724918171 724918078 7.200000e-18 102.0
14 TraesCS7D01G530700 chrUn 85.897 2340 167 64 1177 3412 332791153 332793433 0.000000e+00 2342.0
15 TraesCS7D01G530700 chrUn 87.899 1504 110 34 1967 3412 223478283 223476794 0.000000e+00 1703.0
16 TraesCS7D01G530700 chrUn 91.422 443 30 3 447 886 93245444 93245007 5.820000e-168 601.0
17 TraesCS7D01G530700 chrUn 82.111 682 69 38 2425 3069 93243118 93242453 5.990000e-148 534.0
18 TraesCS7D01G530700 chrUn 82.364 533 54 12 2335 2863 223475325 223474829 1.050000e-115 427.0
19 TraesCS7D01G530700 chrUn 82.364 533 54 12 2335 2863 436762788 436763284 1.050000e-115 427.0
20 TraesCS7D01G530700 chrUn 86.224 196 17 4 3255 3443 93244986 93244794 1.920000e-48 204.0
21 TraesCS7D01G530700 chrUn 87.234 94 6 1 318 405 434843283 434843376 7.200000e-18 102.0
22 TraesCS7D01G530700 chr1D 94.444 36 2 0 598 633 62157687 62157722 5.680000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G530700 chr7D 625334570 625338638 4068 True 7515.000000 7515 100.000000 1 4069 1 chr7D.!!$R1 4068
1 TraesCS7D01G530700 chr7B 724839226 724844493 5267 True 1180.666667 2961 85.050667 318 3927 3 chr7B.!!$R4 3609
2 TraesCS7D01G530700 chr7B 724813546 724819274 5728 True 1014.000000 2671 86.866750 20 3927 4 chr7B.!!$R3 3907
3 TraesCS7D01G530700 chr7B 724913670 724918171 4501 True 613.500000 1703 85.695500 318 3927 4 chr7B.!!$R5 3609
4 TraesCS7D01G530700 chrUn 332791153 332793433 2280 False 2342.000000 2342 85.897000 1177 3412 1 chrUn.!!$F1 2235
5 TraesCS7D01G530700 chrUn 223474829 223478283 3454 True 1065.000000 1703 85.131500 1967 3412 2 chrUn.!!$R2 1445
6 TraesCS7D01G530700 chrUn 93242453 93245444 2991 True 446.333333 601 86.585667 447 3443 3 chrUn.!!$R1 2996

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
854 1043 0.462225 TAGGTCGCTGTCCTCTCTCG 60.462 60.0 0.0 0.0 36.6 4.04 F
1479 2712 0.107017 ACGGGATGGAAAGGCATGAG 60.107 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 3143 0.259938 GGGCTCATCTCAAACCCCAT 59.740 55.0 0.0 0.0 34.23 4.00 R
3469 5198 0.035739 TGGCCGAGTTGTTACTTCCC 59.964 55.0 0.0 0.0 33.84 3.97 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
34 35 5.654497 AGAATTTTTGCCTGTTATGCTAGC 58.346 37.500 8.10 8.10 0.00 3.42
36 37 4.862902 TTTTTGCCTGTTATGCTAGCAA 57.137 36.364 23.54 8.51 41.39 3.91
57 58 0.539051 AGCCTCGATGAAACCCAGAG 59.461 55.000 0.00 0.00 0.00 3.35
73 74 2.092753 CCAGAGACATTATGCCACCACT 60.093 50.000 0.00 0.00 0.00 4.00
74 75 3.134623 CCAGAGACATTATGCCACCACTA 59.865 47.826 0.00 0.00 0.00 2.74
90 91 5.123979 CCACCACTAAGAAGGAATTACTTGC 59.876 44.000 7.92 0.00 0.00 4.01
97 98 9.740710 ACTAAGAAGGAATTACTTGCTATTGTT 57.259 29.630 7.92 0.00 32.05 2.83
156 158 7.682787 ACTCCAAAGTGATAGTTCTATGGAT 57.317 36.000 0.00 0.00 35.35 3.41
161 163 8.152898 CCAAAGTGATAGTTCTATGGATCATCA 58.847 37.037 0.00 0.00 31.35 3.07
174 176 8.829746 TCTATGGATCATCAAGCTTTATGGTAT 58.170 33.333 18.24 7.47 0.00 2.73
181 183 7.795047 TCATCAAGCTTTATGGTATCTTCTCA 58.205 34.615 18.24 0.00 0.00 3.27
197 199 2.816411 TCTCACCAAGAAGGACGGTAT 58.184 47.619 0.00 0.00 41.22 2.73
212 214 2.631062 ACGGTATGCCTCGATTAATCCA 59.369 45.455 9.87 2.51 0.00 3.41
223 225 7.552687 TGCCTCGATTAATCCATTGGATATTAC 59.447 37.037 18.49 9.87 42.27 1.89
261 263 1.368641 TGCAAATCGTCGATGGGAAG 58.631 50.000 8.83 0.00 0.00 3.46
262 264 1.338674 TGCAAATCGTCGATGGGAAGT 60.339 47.619 8.83 0.00 0.00 3.01
263 265 1.327764 GCAAATCGTCGATGGGAAGTC 59.672 52.381 8.83 0.00 0.00 3.01
282 284 1.003580 TCTGAAGACAATCCTGTGGCC 59.996 52.381 0.00 0.00 35.30 5.36
291 293 1.972872 ATCCTGTGGCCGATCATTTC 58.027 50.000 0.00 0.00 0.00 2.17
301 303 3.004106 GGCCGATCATTTCTCAAGAATGG 59.996 47.826 0.00 0.00 33.54 3.16
388 396 3.495983 CCACTTCAGATGTTGGGTGTGTA 60.496 47.826 0.00 0.00 32.82 2.90
421 545 1.228124 CCGGTGGTTTCTCAAGGCA 60.228 57.895 0.00 0.00 0.00 4.75
425 549 1.600636 TGGTTTCTCAAGGCAGCGG 60.601 57.895 0.00 0.00 0.00 5.52
470 594 4.816385 TCTCAGTTGCTTCTGTTTAAGTGG 59.184 41.667 8.15 0.00 36.85 4.00
490 618 3.137544 TGGGGTGACTTGTGTAATCTTGT 59.862 43.478 0.00 0.00 0.00 3.16
492 620 4.583073 GGGGTGACTTGTGTAATCTTGTTT 59.417 41.667 0.00 0.00 0.00 2.83
498 626 7.640240 GTGACTTGTGTAATCTTGTTTGACTTC 59.360 37.037 0.00 0.00 0.00 3.01
509 637 1.002792 GTTTGACTTCGAGTTGGTGGC 60.003 52.381 0.00 0.00 0.00 5.01
515 643 1.868498 CTTCGAGTTGGTGGCGTTTTA 59.132 47.619 0.00 0.00 0.00 1.52
529 657 6.019762 GTGGCGTTTTAGCTACTATTTTGAC 58.980 40.000 0.00 0.00 43.87 3.18
551 681 4.767409 ACCATCCTTTCTTTTAACCTGCTC 59.233 41.667 0.00 0.00 0.00 4.26
552 682 4.766891 CCATCCTTTCTTTTAACCTGCTCA 59.233 41.667 0.00 0.00 0.00 4.26
644 774 3.242739 CCTGTTTCGAGGAAATAATGCGG 60.243 47.826 0.00 0.00 33.97 5.69
648 778 1.021202 CGAGGAAATAATGCGGCCAA 58.979 50.000 2.24 0.00 0.00 4.52
672 804 2.247699 TACACACACTAGGGCCAGAT 57.752 50.000 6.18 0.00 0.00 2.90
678 810 0.463295 CACTAGGGCCAGATGTGCAG 60.463 60.000 6.18 0.00 0.00 4.41
679 811 1.147824 CTAGGGCCAGATGTGCAGG 59.852 63.158 6.18 0.00 0.00 4.85
854 1043 0.462225 TAGGTCGCTGTCCTCTCTCG 60.462 60.000 0.00 0.00 36.60 4.04
855 1044 2.101380 GTCGCTGTCCTCTCTCGC 59.899 66.667 0.00 0.00 0.00 5.03
856 1045 2.359975 TCGCTGTCCTCTCTCGCA 60.360 61.111 0.00 0.00 0.00 5.10
857 1046 1.750780 TCGCTGTCCTCTCTCGCAT 60.751 57.895 0.00 0.00 0.00 4.73
889 1078 1.815421 ATGTGTTCCTCGCATCGCC 60.815 57.895 0.00 0.00 42.76 5.54
953 1401 1.352404 GTCAGACTCGGACGATCGG 59.648 63.158 20.98 3.20 0.00 4.18
1013 1461 2.749621 GCATCCTCACACCAAAACCTAG 59.250 50.000 0.00 0.00 0.00 3.02
1016 1464 2.154462 CCTCACACCAAAACCTAGCTG 58.846 52.381 0.00 0.00 0.00 4.24
1017 1465 1.537202 CTCACACCAAAACCTAGCTGC 59.463 52.381 0.00 0.00 0.00 5.25
1033 1481 1.336125 GCTGCCTTTGCCTATTGCTAG 59.664 52.381 0.00 0.00 42.00 3.42
1038 1486 2.357009 CCTTTGCCTATTGCTAGCACAG 59.643 50.000 19.17 17.00 42.00 3.66
1357 2039 3.665323 CGTCATCTGTAAGTGTTTGCAGC 60.665 47.826 1.22 0.00 43.97 5.25
1358 2040 2.480037 TCATCTGTAAGTGTTTGCAGCG 59.520 45.455 1.22 0.00 43.97 5.18
1359 2041 2.232756 TCTGTAAGTGTTTGCAGCGA 57.767 45.000 1.22 0.00 43.97 4.93
1361 2043 2.736721 TCTGTAAGTGTTTGCAGCGATC 59.263 45.455 1.22 0.00 43.97 3.69
1364 2046 1.538047 AAGTGTTTGCAGCGATCCAT 58.462 45.000 0.00 0.00 0.00 3.41
1365 2047 0.806868 AGTGTTTGCAGCGATCCATG 59.193 50.000 0.00 0.00 0.00 3.66
1385 2392 2.073117 CACCACTACGTGCATGTACA 57.927 50.000 14.85 0.00 31.34 2.90
1389 2396 4.069304 ACCACTACGTGCATGTACATTTT 58.931 39.130 14.85 0.00 31.34 1.82
1390 2397 4.083537 ACCACTACGTGCATGTACATTTTG 60.084 41.667 14.85 6.91 31.34 2.44
1391 2398 3.845775 CACTACGTGCATGTACATTTTGC 59.154 43.478 14.85 9.36 36.91 3.68
1397 2404 6.847400 ACGTGCATGTACATTTTGCTATTAA 58.153 32.000 18.13 0.00 37.28 1.40
1399 2406 7.643764 ACGTGCATGTACATTTTGCTATTAATC 59.356 33.333 18.13 3.28 37.28 1.75
1400 2407 7.149303 CGTGCATGTACATTTTGCTATTAATCG 60.149 37.037 18.13 9.29 37.28 3.34
1402 2409 7.138736 GCATGTACATTTTGCTATTAATCGGT 58.861 34.615 5.37 0.00 33.61 4.69
1405 2412 5.418310 ACATTTTGCTATTAATCGGTCGG 57.582 39.130 0.00 0.00 0.00 4.79
1408 2415 2.605837 TGCTATTAATCGGTCGGCAA 57.394 45.000 0.00 0.00 0.00 4.52
1410 2417 2.101750 TGCTATTAATCGGTCGGCAAGA 59.898 45.455 0.00 0.00 0.00 3.02
1427 2654 5.999483 GCAAGAAGCAAGCTTAATGTTAC 57.001 39.130 7.37 0.00 44.79 2.50
1436 2669 3.750371 AGCTTAATGTTACAGTGCACCA 58.250 40.909 14.63 3.95 0.00 4.17
1479 2712 0.107017 ACGGGATGGAAAGGCATGAG 60.107 55.000 0.00 0.00 0.00 2.90
1600 2926 5.172232 GTCAACATCGAGATATGAACGACAG 59.828 44.000 0.00 0.00 38.79 3.51
1603 2929 4.820173 ACATCGAGATATGAACGACAGGTA 59.180 41.667 0.00 0.00 38.79 3.08
1605 2931 6.653740 ACATCGAGATATGAACGACAGGTATA 59.346 38.462 0.00 0.00 38.79 1.47
1606 2932 7.337184 ACATCGAGATATGAACGACAGGTATAT 59.663 37.037 0.00 0.00 38.79 0.86
1607 2933 8.827677 CATCGAGATATGAACGACAGGTATATA 58.172 37.037 0.00 0.00 38.79 0.86
1608 2934 8.959705 TCGAGATATGAACGACAGGTATATAT 57.040 34.615 0.00 0.00 0.00 0.86
1659 2985 0.179171 AACGAGTACGGCATGACGAG 60.179 55.000 31.27 15.02 44.46 4.18
1677 3019 3.192633 ACGAGATTAACAATGCAAACCCC 59.807 43.478 0.00 0.00 0.00 4.95
1680 3022 3.260632 AGATTAACAATGCAAACCCCCAC 59.739 43.478 0.00 0.00 0.00 4.61
1681 3023 2.088104 TAACAATGCAAACCCCCACA 57.912 45.000 0.00 0.00 0.00 4.17
1682 3024 0.758123 AACAATGCAAACCCCCACAG 59.242 50.000 0.00 0.00 0.00 3.66
1683 3025 1.004679 CAATGCAAACCCCCACAGC 60.005 57.895 0.00 0.00 0.00 4.40
1684 3026 1.152269 AATGCAAACCCCCACAGCT 60.152 52.632 0.00 0.00 0.00 4.24
1685 3027 0.763986 AATGCAAACCCCCACAGCTT 60.764 50.000 0.00 0.00 0.00 3.74
1686 3028 1.474332 ATGCAAACCCCCACAGCTTG 61.474 55.000 0.00 0.00 0.00 4.01
1687 3029 2.871253 GCAAACCCCCACAGCTTGG 61.871 63.158 7.69 7.69 46.47 3.61
1697 3039 2.486951 CACAGCTTGGATTATGCAGC 57.513 50.000 0.00 0.00 32.18 5.25
1698 3040 1.019673 ACAGCTTGGATTATGCAGCG 58.980 50.000 0.00 0.00 32.18 5.18
1728 3079 9.389570 GCACAATAACAAACGAATTAAGTAAGT 57.610 29.630 0.00 0.00 0.00 2.24
1752 3103 8.697292 AGTAGATAGGTAACCAAGTTTCTCATC 58.303 37.037 0.00 0.00 37.17 2.92
1792 3143 0.248949 TGTACGTGCAGCACAACGTA 60.249 50.000 25.19 17.92 37.28 3.57
1800 3151 1.243902 CAGCACAACGTATGGGGTTT 58.756 50.000 0.00 0.00 41.36 3.27
1818 3169 2.194326 GAGATGAGCCCCAAGCCC 59.806 66.667 0.00 0.00 45.47 5.19
1849 3200 1.421485 CTGCCGCACGACAAGATTC 59.579 57.895 0.00 0.00 0.00 2.52
1851 3202 1.291184 TGCCGCACGACAAGATTCTG 61.291 55.000 0.00 0.00 0.00 3.02
1854 3205 0.094216 CGCACGACAAGATTCTGCTG 59.906 55.000 0.00 0.00 0.00 4.41
1911 3262 1.739338 GATCCGGCATCCTCGACACT 61.739 60.000 0.00 0.00 0.00 3.55
1918 3269 1.607628 GCATCCTCGACACTACGGTAT 59.392 52.381 0.00 0.00 0.00 2.73
1921 3272 4.082895 GCATCCTCGACACTACGGTATATT 60.083 45.833 0.00 0.00 0.00 1.28
1925 3276 5.470098 TCCTCGACACTACGGTATATTAACC 59.530 44.000 0.00 0.00 36.08 2.85
1938 3291 7.392393 ACGGTATATTAACCAACTTCAAGCTTT 59.608 33.333 0.00 0.00 39.71 3.51
1939 3292 8.241367 CGGTATATTAACCAACTTCAAGCTTTT 58.759 33.333 0.00 0.00 39.71 2.27
1949 3302 9.350951 ACCAACTTCAAGCTTTTAATTACTACT 57.649 29.630 0.00 0.00 0.00 2.57
1970 3323 8.147058 ACTACTATTCCACTCAAGAGCATAATG 58.853 37.037 0.00 0.00 0.00 1.90
1973 3339 7.928706 ACTATTCCACTCAAGAGCATAATGTAC 59.071 37.037 0.00 0.00 0.00 2.90
1976 3342 7.360113 TCCACTCAAGAGCATAATGTACATA 57.640 36.000 9.21 0.00 0.00 2.29
2054 3420 0.599060 TCACGATGCGGACACAAGTA 59.401 50.000 0.00 0.00 0.00 2.24
2090 3456 0.521291 CGGCGGACAACATGATTTGT 59.479 50.000 0.00 0.00 42.55 2.83
2276 3642 1.749033 GATGGTGGGGATCCTCGAC 59.251 63.158 12.58 8.61 0.00 4.20
2378 3744 2.668550 GCGTTCAACGGCCTCCTT 60.669 61.111 12.81 0.00 42.82 3.36
2393 3759 2.892425 CTTAGGGCCAAGCTCGCG 60.892 66.667 6.18 0.00 32.17 5.87
2460 3858 3.146066 GCCAACTACAACATCCTCAACA 58.854 45.455 0.00 0.00 0.00 3.33
2512 3911 3.043586 CGTACGCAGATAAGCTAACCAG 58.956 50.000 0.52 0.00 0.00 4.00
2535 3934 7.759886 CCAGTTTATATGCTTATTCGCTAGCTA 59.240 37.037 13.93 0.00 38.22 3.32
2559 3965 2.710220 TCTTGTACGTACGTGCATGT 57.290 45.000 34.21 17.19 40.18 3.21
2579 3985 6.761242 GCATGTACTAATTCATGTGGACTGTA 59.239 38.462 6.69 0.00 42.09 2.74
2839 4250 0.460311 CGGGCAAGAACGTATCTCCT 59.540 55.000 0.00 0.00 37.42 3.69
2871 4282 2.370885 TCGTCGACGAGCAGTAGAG 58.629 57.895 34.97 4.96 44.22 2.43
2884 4298 1.513586 GTAGAGGGCGACGTTCGTG 60.514 63.158 1.74 0.00 42.81 4.35
3033 4477 2.880890 GCTCCATCTTGTGTTGTGTTCT 59.119 45.455 0.00 0.00 0.00 3.01
3034 4478 3.058639 GCTCCATCTTGTGTTGTGTTCTC 60.059 47.826 0.00 0.00 0.00 2.87
3040 4484 2.325583 TGTGTTGTGTTCTCTGTCCC 57.674 50.000 0.00 0.00 0.00 4.46
3050 4494 5.044558 GTGTTCTCTGTCCCTCGATTATTC 58.955 45.833 0.00 0.00 0.00 1.75
3100 4544 8.494016 AAGTAACTAAATCTTGTCCTATGTGC 57.506 34.615 0.00 0.00 0.00 4.57
3101 4545 7.852263 AGTAACTAAATCTTGTCCTATGTGCT 58.148 34.615 0.00 0.00 0.00 4.40
3102 4546 8.978472 AGTAACTAAATCTTGTCCTATGTGCTA 58.022 33.333 0.00 0.00 0.00 3.49
3103 4547 9.765795 GTAACTAAATCTTGTCCTATGTGCTAT 57.234 33.333 0.00 0.00 0.00 2.97
3106 4550 4.694760 ATCTTGTCCTATGTGCTATGCA 57.305 40.909 0.00 0.00 35.60 3.96
3107 4551 4.486125 TCTTGTCCTATGTGCTATGCAA 57.514 40.909 0.00 0.00 41.47 4.08
3108 4552 5.039920 TCTTGTCCTATGTGCTATGCAAT 57.960 39.130 0.00 0.00 41.47 3.56
3109 4553 4.818005 TCTTGTCCTATGTGCTATGCAATG 59.182 41.667 0.00 0.00 41.47 2.82
3110 4554 2.880268 TGTCCTATGTGCTATGCAATGC 59.120 45.455 0.00 0.00 41.47 3.56
3133 4602 6.830838 TGCATCCTATATCTGACACGATCTAT 59.169 38.462 0.00 0.00 0.00 1.98
3134 4603 7.138081 GCATCCTATATCTGACACGATCTATG 58.862 42.308 0.00 0.00 0.00 2.23
3138 4607 8.731605 TCCTATATCTGACACGATCTATGAAAC 58.268 37.037 0.00 0.00 0.00 2.78
3171 4640 5.824429 TGCTCAATTATCAGCTGCATAAAC 58.176 37.500 9.47 4.73 36.53 2.01
3174 4643 6.581542 GCTCAATTATCAGCTGCATAAACATC 59.418 38.462 9.47 2.21 32.48 3.06
3175 4644 6.661669 TCAATTATCAGCTGCATAAACATCG 58.338 36.000 9.47 3.87 0.00 3.84
3176 4645 6.482973 TCAATTATCAGCTGCATAAACATCGA 59.517 34.615 9.47 0.00 0.00 3.59
3177 4646 7.173735 TCAATTATCAGCTGCATAAACATCGAT 59.826 33.333 9.47 0.00 0.00 3.59
3178 4647 6.471976 TTATCAGCTGCATAAACATCGATC 57.528 37.500 9.47 0.00 0.00 3.69
3179 4648 3.795877 TCAGCTGCATAAACATCGATCA 58.204 40.909 9.47 0.00 0.00 2.92
3230 4699 8.918202 AGAAAAAGAAACTGTACATGGATGTA 57.082 30.769 0.00 0.00 41.97 2.29
3248 4717 0.892755 TAAGTCGTCCTTGCGGTCAT 59.107 50.000 1.23 0.00 34.46 3.06
3249 4718 0.389948 AAGTCGTCCTTGCGGTCATC 60.390 55.000 0.00 0.00 30.18 2.92
3250 4719 1.080093 GTCGTCCTTGCGGTCATCA 60.080 57.895 0.00 0.00 0.00 3.07
3253 4722 1.078759 CGTCCTTGCGGTCATCAGTC 61.079 60.000 0.00 0.00 0.00 3.51
3306 4801 4.021894 GTGCCGTGAGAAGATGGATAGTAT 60.022 45.833 0.00 0.00 0.00 2.12
3309 4804 5.621104 GCCGTGAGAAGATGGATAGTATCTG 60.621 48.000 9.97 0.00 35.20 2.90
3313 4808 4.756564 AGAAGATGGATAGTATCTGGCCA 58.243 43.478 4.71 4.71 35.20 5.36
3314 4809 4.776837 AGAAGATGGATAGTATCTGGCCAG 59.223 45.833 27.87 27.87 35.20 4.85
3333 4828 3.384668 CAGGCCAATCACTCATACTACG 58.615 50.000 5.01 0.00 0.00 3.51
3357 4854 3.498397 ACACACATAGCACAGTAGTTTGC 59.502 43.478 0.13 0.13 39.16 3.68
3359 4856 2.993220 CACATAGCACAGTAGTTTGCGA 59.007 45.455 3.11 0.00 43.87 5.10
3364 4861 1.201812 GCACAGTAGTTTGCGATCACG 60.202 52.381 0.00 0.00 42.93 4.35
3413 4910 8.879759 GCTTTGCTAGCCGACAAATATATAATA 58.120 33.333 13.29 0.00 44.48 0.98
3432 4972 9.725019 ATATAATATGATCATGTCCACACGTTT 57.275 29.630 18.72 0.00 0.00 3.60
3451 4991 1.610554 TTCGGCAGCCCTACTACACC 61.611 60.000 5.63 0.00 0.00 4.16
3469 5198 0.531532 CCAGCTGTCCATAAGAGGCG 60.532 60.000 13.81 0.00 31.78 5.52
3475 5204 0.831307 GTCCATAAGAGGCGGGAAGT 59.169 55.000 0.00 0.00 0.00 3.01
3481 5210 2.180432 AAGAGGCGGGAAGTAACAAC 57.820 50.000 0.00 0.00 0.00 3.32
3483 5212 1.275573 AGAGGCGGGAAGTAACAACTC 59.724 52.381 0.00 0.00 0.00 3.01
3485 5214 1.017701 GGCGGGAAGTAACAACTCGG 61.018 60.000 0.00 0.00 0.00 4.63
3494 5223 2.000447 GTAACAACTCGGCCATGACTC 59.000 52.381 2.24 0.00 0.00 3.36
3499 5228 1.198713 ACTCGGCCATGACTCAAGAT 58.801 50.000 2.24 0.00 0.00 2.40
3515 5244 2.022718 AGATAGATGGGCCAGACCTC 57.977 55.000 13.78 4.26 39.10 3.85
3550 5303 0.451783 GGCCGAACACATGGTGATTC 59.548 55.000 2.98 3.18 36.96 2.52
3613 5366 4.744795 TGTATGGTTTTGGTTTGCTTGT 57.255 36.364 0.00 0.00 0.00 3.16
3614 5367 4.688021 TGTATGGTTTTGGTTTGCTTGTC 58.312 39.130 0.00 0.00 0.00 3.18
3620 5373 5.123027 TGGTTTTGGTTTGCTTGTCAAATTC 59.877 36.000 0.00 0.00 45.43 2.17
3621 5374 5.123027 GGTTTTGGTTTGCTTGTCAAATTCA 59.877 36.000 0.00 0.00 45.43 2.57
3630 5383 5.417811 TGCTTGTCAAATTCACATGTTTGT 58.582 33.333 0.00 0.00 36.83 2.83
3647 5400 5.441500 TGTTTGTGTTGGAGAGGTTCATTA 58.558 37.500 0.00 0.00 0.00 1.90
3648 5401 5.888724 TGTTTGTGTTGGAGAGGTTCATTAA 59.111 36.000 0.00 0.00 0.00 1.40
3649 5402 6.549364 TGTTTGTGTTGGAGAGGTTCATTAAT 59.451 34.615 0.00 0.00 0.00 1.40
3650 5403 7.069331 TGTTTGTGTTGGAGAGGTTCATTAATT 59.931 33.333 0.00 0.00 0.00 1.40
3652 5405 5.710099 TGTGTTGGAGAGGTTCATTAATTCC 59.290 40.000 0.00 0.00 0.00 3.01
3654 5407 5.710099 TGTTGGAGAGGTTCATTAATTCCAC 59.290 40.000 2.86 1.12 33.31 4.02
3655 5408 4.855340 TGGAGAGGTTCATTAATTCCACC 58.145 43.478 0.00 0.23 0.00 4.61
3656 5409 4.207955 GGAGAGGTTCATTAATTCCACCC 58.792 47.826 4.48 0.00 0.00 4.61
3657 5410 4.325030 GGAGAGGTTCATTAATTCCACCCA 60.325 45.833 4.48 0.00 0.00 4.51
3658 5411 5.449553 GAGAGGTTCATTAATTCCACCCAT 58.550 41.667 4.48 0.00 0.00 4.00
3659 5412 5.449553 AGAGGTTCATTAATTCCACCCATC 58.550 41.667 4.48 0.00 0.00 3.51
3665 5418 6.575244 TCATTAATTCCACCCATCTGTAGT 57.425 37.500 0.00 0.00 0.00 2.73
3670 5423 9.936329 ATTAATTCCACCCATCTGTAGTAATTT 57.064 29.630 0.00 0.00 0.00 1.82
3706 5459 2.930682 GGAGCGATTCACCTTGTTCTAC 59.069 50.000 0.00 0.00 0.00 2.59
3707 5460 3.585862 GAGCGATTCACCTTGTTCTACA 58.414 45.455 0.00 0.00 0.00 2.74
3722 5475 3.577649 TCTACAAGAGGAAGCTTCACG 57.422 47.619 27.02 12.44 0.00 4.35
3806 5559 2.452600 AAAACCTGGGAAGTCAAGCA 57.547 45.000 0.00 0.00 0.00 3.91
3807 5560 2.452600 AAACCTGGGAAGTCAAGCAA 57.547 45.000 0.00 0.00 0.00 3.91
3808 5561 2.452600 AACCTGGGAAGTCAAGCAAA 57.547 45.000 0.00 0.00 0.00 3.68
3809 5562 1.692411 ACCTGGGAAGTCAAGCAAAC 58.308 50.000 0.00 0.00 0.00 2.93
3810 5563 1.215423 ACCTGGGAAGTCAAGCAAACT 59.785 47.619 0.00 0.00 0.00 2.66
3811 5564 2.441750 ACCTGGGAAGTCAAGCAAACTA 59.558 45.455 0.00 0.00 0.00 2.24
3812 5565 3.117663 ACCTGGGAAGTCAAGCAAACTAA 60.118 43.478 0.00 0.00 0.00 2.24
3813 5566 3.888930 CCTGGGAAGTCAAGCAAACTAAA 59.111 43.478 0.00 0.00 0.00 1.85
3814 5567 4.261614 CCTGGGAAGTCAAGCAAACTAAAC 60.262 45.833 0.00 0.00 0.00 2.01
3856 5609 3.708451 AGAAGTCACAAGTTTGGGGTTT 58.292 40.909 0.00 0.00 30.87 3.27
3865 5618 4.148838 CAAGTTTGGGGTTTAGACATGGA 58.851 43.478 0.00 0.00 0.00 3.41
3867 5620 4.810345 AGTTTGGGGTTTAGACATGGAAA 58.190 39.130 0.00 0.00 0.00 3.13
3868 5621 5.402630 AGTTTGGGGTTTAGACATGGAAAT 58.597 37.500 0.00 0.00 0.00 2.17
3876 5629 6.070824 GGGTTTAGACATGGAAATGTTTGGAT 60.071 38.462 0.00 0.00 34.45 3.41
3906 5659 6.575162 AAATACCAAAGAGTTCATCACACC 57.425 37.500 0.00 0.00 0.00 4.16
3919 5672 3.317711 TCATCACACCACGAAAAAGCAAT 59.682 39.130 0.00 0.00 0.00 3.56
3927 5680 4.023193 ACCACGAAAAAGCAATAGAAGGTG 60.023 41.667 0.00 0.00 0.00 4.00
3937 5948 9.836864 AAAAGCAATAGAAGGTGAAAAAGAAAT 57.163 25.926 0.00 0.00 0.00 2.17
3940 5951 9.077885 AGCAATAGAAGGTGAAAAAGAAATACA 57.922 29.630 0.00 0.00 0.00 2.29
3951 5962 9.020813 GTGAAAAAGAAATACAAGAAGTTCACC 57.979 33.333 5.50 0.00 36.66 4.02
3959 5970 2.681344 ACAAGAAGTTCACCGGACAAAC 59.319 45.455 9.46 9.40 0.00 2.93
3976 5988 5.305139 ACAAACGCTAAAAGTTCAGTTGT 57.695 34.783 0.00 0.00 0.00 3.32
3981 5993 5.329493 ACGCTAAAAGTTCAGTTGTTGTTC 58.671 37.500 0.00 0.00 0.00 3.18
3982 5994 5.123344 ACGCTAAAAGTTCAGTTGTTGTTCT 59.877 36.000 0.00 0.00 0.00 3.01
3994 6006 3.804786 TGTTGTTCTGACGACAGGTTA 57.195 42.857 14.76 0.00 43.60 2.85
3997 6009 3.637998 TGTTCTGACGACAGGTTAGTC 57.362 47.619 14.76 0.00 43.60 2.59
4004 6016 2.295349 GACGACAGGTTAGTCTGGTTCA 59.705 50.000 0.00 0.00 38.98 3.18
4008 6020 4.755123 CGACAGGTTAGTCTGGTTCAAATT 59.245 41.667 0.00 0.00 38.98 1.82
4009 6021 5.107065 CGACAGGTTAGTCTGGTTCAAATTC 60.107 44.000 0.00 0.00 38.98 2.17
4012 6024 6.263168 ACAGGTTAGTCTGGTTCAAATTCAAG 59.737 38.462 0.00 0.00 38.98 3.02
4016 6028 7.355778 GTTAGTCTGGTTCAAATTCAAGTGAG 58.644 38.462 0.00 0.00 0.00 3.51
4017 6029 5.440610 AGTCTGGTTCAAATTCAAGTGAGT 58.559 37.500 0.00 0.00 0.00 3.41
4061 6073 8.807667 AAAGAATGCAGAAGTTCACATTAAAG 57.192 30.769 18.68 0.00 33.07 1.85
4067 6079 9.630098 ATGCAGAAGTTCACATTAAAGTAAATG 57.370 29.630 5.50 0.00 41.65 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.758715 GCATAACAGGCAAAAATTCTTATCATC 58.241 33.333 0.00 0.00 0.00 2.92
5 6 8.480501 AGCATAACAGGCAAAAATTCTTATCAT 58.519 29.630 0.00 0.00 0.00 2.45
6 7 7.839907 AGCATAACAGGCAAAAATTCTTATCA 58.160 30.769 0.00 0.00 0.00 2.15
7 8 9.455847 CTAGCATAACAGGCAAAAATTCTTATC 57.544 33.333 0.00 0.00 0.00 1.75
8 9 7.922811 GCTAGCATAACAGGCAAAAATTCTTAT 59.077 33.333 10.63 0.00 0.00 1.73
9 10 7.093988 TGCTAGCATAACAGGCAAAAATTCTTA 60.094 33.333 14.93 0.00 0.00 2.10
10 11 6.101997 GCTAGCATAACAGGCAAAAATTCTT 58.898 36.000 10.63 0.00 0.00 2.52
11 12 5.185635 TGCTAGCATAACAGGCAAAAATTCT 59.814 36.000 14.93 0.00 0.00 2.40
12 13 5.410067 TGCTAGCATAACAGGCAAAAATTC 58.590 37.500 14.93 0.00 0.00 2.17
13 14 5.404466 TGCTAGCATAACAGGCAAAAATT 57.596 34.783 14.93 0.00 0.00 1.82
14 15 5.404466 TTGCTAGCATAACAGGCAAAAAT 57.596 34.783 20.13 0.00 39.45 1.82
15 16 4.862902 TTGCTAGCATAACAGGCAAAAA 57.137 36.364 20.13 0.00 39.45 1.94
16 17 4.862902 TTTGCTAGCATAACAGGCAAAA 57.137 36.364 20.13 2.37 45.60 2.44
17 18 4.808558 CTTTTGCTAGCATAACAGGCAAA 58.191 39.130 20.13 12.07 46.45 3.68
18 19 3.367292 GCTTTTGCTAGCATAACAGGCAA 60.367 43.478 20.13 3.99 43.35 4.52
24 25 2.936498 TCGAGGCTTTTGCTAGCATAAC 59.064 45.455 20.13 13.60 46.54 1.89
28 29 1.066215 TCATCGAGGCTTTTGCTAGCA 60.066 47.619 14.93 14.93 46.54 3.49
34 35 1.885887 TGGGTTTCATCGAGGCTTTTG 59.114 47.619 0.00 0.00 0.00 2.44
36 37 1.351017 TCTGGGTTTCATCGAGGCTTT 59.649 47.619 0.00 0.00 0.00 3.51
57 58 4.576463 CCTTCTTAGTGGTGGCATAATGTC 59.424 45.833 0.00 0.00 0.00 3.06
135 136 8.152898 TGATGATCCATAGAACTATCACTTTGG 58.847 37.037 0.00 0.00 36.86 3.28
150 151 8.829746 AGATACCATAAAGCTTGATGATCCATA 58.170 33.333 23.45 9.04 0.00 2.74
151 152 7.696981 AGATACCATAAAGCTTGATGATCCAT 58.303 34.615 23.45 11.05 0.00 3.41
152 153 7.083062 AGATACCATAAAGCTTGATGATCCA 57.917 36.000 23.45 7.11 0.00 3.41
156 158 7.712639 GTGAGAAGATACCATAAAGCTTGATGA 59.287 37.037 23.45 6.51 0.00 2.92
161 163 6.313519 TGGTGAGAAGATACCATAAAGCTT 57.686 37.500 0.00 0.00 41.80 3.74
181 183 0.252197 GGCATACCGTCCTTCTTGGT 59.748 55.000 0.00 0.00 39.80 3.67
193 195 4.396166 CCAATGGATTAATCGAGGCATACC 59.604 45.833 9.32 0.00 0.00 2.73
194 196 5.245531 TCCAATGGATTAATCGAGGCATAC 58.754 41.667 9.32 0.00 0.00 2.39
197 199 3.855255 TCCAATGGATTAATCGAGGCA 57.145 42.857 9.32 2.30 0.00 4.75
254 256 3.848975 AGGATTGTCTTCAGACTTCCCAT 59.151 43.478 18.46 6.00 43.13 4.00
256 258 3.008485 ACAGGATTGTCTTCAGACTTCCC 59.992 47.826 18.46 12.01 43.13 3.97
261 263 2.079925 GCCACAGGATTGTCTTCAGAC 58.920 52.381 0.00 0.00 44.97 3.51
262 264 1.003580 GGCCACAGGATTGTCTTCAGA 59.996 52.381 0.00 0.00 34.62 3.27
263 265 1.457346 GGCCACAGGATTGTCTTCAG 58.543 55.000 0.00 0.00 34.62 3.02
275 277 2.028420 TGAGAAATGATCGGCCACAG 57.972 50.000 2.24 0.00 0.00 3.66
282 284 6.279123 TCTCTCCATTCTTGAGAAATGATCG 58.721 40.000 0.00 0.00 38.34 3.69
291 293 4.815533 TGGTCTTCTCTCCATTCTTGAG 57.184 45.455 0.00 0.00 0.00 3.02
301 303 9.092876 CAAACTAAGTTCATATGGTCTTCTCTC 57.907 37.037 13.60 0.00 0.00 3.20
365 373 0.883833 CACCCAACATCTGAAGTGGC 59.116 55.000 0.00 0.00 0.00 5.01
425 549 1.534729 ATCAAGCAAGAACGGAACCC 58.465 50.000 0.00 0.00 0.00 4.11
470 594 5.298276 TCAAACAAGATTACACAAGTCACCC 59.702 40.000 0.00 0.00 0.00 4.61
490 618 1.305201 GCCACCAACTCGAAGTCAAA 58.695 50.000 0.00 0.00 0.00 2.69
492 620 1.300620 CGCCACCAACTCGAAGTCA 60.301 57.895 0.00 0.00 0.00 3.41
498 626 0.110373 GCTAAAACGCCACCAACTCG 60.110 55.000 0.00 0.00 0.00 4.18
509 637 7.280205 AGGATGGTCAAAATAGTAGCTAAAACG 59.720 37.037 0.00 0.00 0.00 3.60
515 643 6.963322 AGAAAGGATGGTCAAAATAGTAGCT 58.037 36.000 0.00 0.00 0.00 3.32
529 657 4.766891 TGAGCAGGTTAAAAGAAAGGATGG 59.233 41.667 0.00 0.00 0.00 3.51
601 731 4.525100 AGGTTTTCGCCCAGCTTTATTAAA 59.475 37.500 0.00 0.00 0.00 1.52
633 763 5.856455 GTGTATGTATTGGCCGCATTATTTC 59.144 40.000 0.00 0.00 0.00 2.17
644 774 4.127171 CCCTAGTGTGTGTATGTATTGGC 58.873 47.826 0.00 0.00 0.00 4.52
648 778 3.380393 TGGCCCTAGTGTGTGTATGTAT 58.620 45.455 0.00 0.00 0.00 2.29
855 1044 3.642981 ATGCGGTGCGATGCGATG 61.643 61.111 0.00 0.00 0.00 3.84
856 1045 3.642981 CATGCGGTGCGATGCGAT 61.643 61.111 0.00 0.00 0.00 4.58
889 1078 3.490759 GTCGGTGCATGCGTCCAG 61.491 66.667 24.50 18.42 0.00 3.86
910 1330 2.126580 CGGACGGACGTTCACTCC 60.127 66.667 3.84 0.00 0.00 3.85
953 1401 1.963172 ATTTAAAGGGCCGGATCGAC 58.037 50.000 5.05 0.00 0.00 4.20
991 1439 1.145738 AGGTTTTGGTGTGAGGATGCT 59.854 47.619 0.00 0.00 0.00 3.79
1013 1461 4.821177 GCAATAGGCAAAGGCAGC 57.179 55.556 0.00 0.00 43.71 5.25
1038 1486 2.155194 CACTCTAGCTCGTGCGTGC 61.155 63.158 10.14 10.14 45.42 5.34
1357 2039 0.179111 ACGTAGTGGTGCATGGATCG 60.179 55.000 0.00 0.00 42.51 3.69
1358 2040 3.760693 ACGTAGTGGTGCATGGATC 57.239 52.632 0.00 0.00 42.51 3.36
1384 2391 4.219033 GCCGACCGATTAATAGCAAAATG 58.781 43.478 0.00 0.00 0.00 2.32
1385 2392 3.880490 TGCCGACCGATTAATAGCAAAAT 59.120 39.130 0.00 0.00 0.00 1.82
1389 2396 2.101750 TCTTGCCGACCGATTAATAGCA 59.898 45.455 0.00 0.00 0.00 3.49
1390 2397 2.750948 TCTTGCCGACCGATTAATAGC 58.249 47.619 0.00 0.00 0.00 2.97
1391 2398 3.184581 GCTTCTTGCCGACCGATTAATAG 59.815 47.826 0.00 0.00 35.15 1.73
1397 2404 1.003839 TTGCTTCTTGCCGACCGAT 60.004 52.632 0.00 0.00 42.00 4.18
1399 2406 2.863153 CTTGCTTCTTGCCGACCG 59.137 61.111 0.00 0.00 42.00 4.79
1400 2407 1.518903 AAGCTTGCTTCTTGCCGACC 61.519 55.000 0.00 0.00 42.00 4.79
1402 2409 1.890876 TTAAGCTTGCTTCTTGCCGA 58.109 45.000 9.86 0.00 42.00 5.54
1405 2412 5.460646 TGTAACATTAAGCTTGCTTCTTGC 58.539 37.500 9.86 4.27 43.25 4.01
1408 2415 5.335191 GCACTGTAACATTAAGCTTGCTTCT 60.335 40.000 9.86 0.00 0.00 2.85
1410 2417 4.278170 TGCACTGTAACATTAAGCTTGCTT 59.722 37.500 9.86 12.65 0.00 3.91
1422 2649 2.409012 CACGTATGGTGCACTGTAACA 58.591 47.619 17.98 5.96 40.33 2.41
1444 2677 1.459592 CCCGTTCAACGTCAAGATGAC 59.540 52.381 9.52 0.39 43.65 3.06
1449 2682 0.796312 CCATCCCGTTCAACGTCAAG 59.204 55.000 9.52 0.00 40.58 3.02
1457 2690 0.331278 ATGCCTTTCCATCCCGTTCA 59.669 50.000 0.00 0.00 0.00 3.18
1570 2896 8.015658 CGTTCATATCTCGATGTTGACATACTA 58.984 37.037 0.00 0.00 36.57 1.82
1571 2897 6.858478 CGTTCATATCTCGATGTTGACATACT 59.142 38.462 0.00 0.00 36.57 2.12
1572 2898 6.856426 TCGTTCATATCTCGATGTTGACATAC 59.144 38.462 0.00 0.00 36.57 2.39
1581 2907 4.230314 ACCTGTCGTTCATATCTCGATG 57.770 45.455 0.00 0.00 36.08 3.84
1659 2985 3.007398 TGTGGGGGTTTGCATTGTTAATC 59.993 43.478 0.00 0.00 0.00 1.75
1680 3022 0.317603 GCGCTGCATAATCCAAGCTG 60.318 55.000 0.00 0.00 0.00 4.24
1681 3023 0.749091 TGCGCTGCATAATCCAAGCT 60.749 50.000 9.73 0.00 31.71 3.74
1682 3024 1.729276 TGCGCTGCATAATCCAAGC 59.271 52.632 9.73 0.00 31.71 4.01
1694 3036 1.979897 TTGTTATTGTGCATGCGCTG 58.020 45.000 29.79 5.66 39.64 5.18
1695 3037 2.327568 GTTTGTTATTGTGCATGCGCT 58.672 42.857 29.79 14.88 39.64 5.92
1696 3038 1.057566 CGTTTGTTATTGTGCATGCGC 59.942 47.619 24.25 24.25 39.24 6.09
1697 3039 2.579541 TCGTTTGTTATTGTGCATGCG 58.420 42.857 14.09 0.00 0.00 4.73
1698 3040 5.514059 AATTCGTTTGTTATTGTGCATGC 57.486 34.783 11.82 11.82 0.00 4.06
1728 3079 7.622081 TGGATGAGAAACTTGGTTACCTATCTA 59.378 37.037 2.07 0.00 0.00 1.98
1731 3082 6.636454 TGGATGAGAAACTTGGTTACCTAT 57.364 37.500 2.07 0.00 0.00 2.57
1792 3143 0.259938 GGGCTCATCTCAAACCCCAT 59.740 55.000 0.00 0.00 34.23 4.00
1800 3151 2.683465 GGGCTTGGGGCTCATCTCA 61.683 63.158 0.00 0.00 42.01 3.27
1818 3169 1.068753 CGGCAGCATGGAGAGGTAG 59.931 63.158 0.00 0.00 35.86 3.18
1849 3200 2.553765 ATCTTGCAGAGGCCCAGCAG 62.554 60.000 13.21 8.83 39.72 4.24
1851 3202 1.823041 GATCTTGCAGAGGCCCAGC 60.823 63.158 0.00 0.95 40.13 4.85
1854 3205 2.203126 CCGATCTTGCAGAGGCCC 60.203 66.667 0.00 0.00 40.13 5.80
1911 3262 7.558604 AGCTTGAAGTTGGTTAATATACCGTA 58.441 34.615 0.00 0.00 41.28 4.02
1939 3292 9.197306 TGCTCTTGAGTGGAATAGTAGTAATTA 57.803 33.333 0.00 0.00 0.00 1.40
1940 3293 8.079211 TGCTCTTGAGTGGAATAGTAGTAATT 57.921 34.615 0.00 0.00 0.00 1.40
1941 3294 7.661536 TGCTCTTGAGTGGAATAGTAGTAAT 57.338 36.000 0.00 0.00 0.00 1.89
1949 3302 7.791029 TGTACATTATGCTCTTGAGTGGAATA 58.209 34.615 0.00 0.00 0.00 1.75
1952 3305 5.675684 TGTACATTATGCTCTTGAGTGGA 57.324 39.130 0.00 0.00 0.00 4.02
1976 3342 9.874205 GCCATGCATATATTAACCAACAAATAT 57.126 29.630 0.00 0.00 33.82 1.28
1985 3351 5.418524 TCCATGTGCCATGCATATATTAACC 59.581 40.000 0.00 0.00 38.26 2.85
1986 3352 6.513806 TCCATGTGCCATGCATATATTAAC 57.486 37.500 0.00 0.00 38.26 2.01
1988 3354 6.665695 AGATCCATGTGCCATGCATATATTA 58.334 36.000 0.00 0.00 38.26 0.98
2013 3379 2.624364 GCGTCCCTTTTCCCTACAAAAA 59.376 45.455 0.00 0.00 0.00 1.94
2054 3420 1.066787 GCCGCCTTCTTGAAGTACTCT 60.067 52.381 0.00 0.00 0.00 3.24
2090 3456 0.328258 GCTCCTCCTTGCTTGGGTAA 59.672 55.000 0.00 0.00 0.00 2.85
2117 3483 1.000612 GAGGAGGAAGAGGGACCGT 59.999 63.158 0.00 0.00 0.00 4.83
2363 3729 0.392595 CCCTAAGGAGGCCGTTGAAC 60.393 60.000 0.00 0.00 42.21 3.18
2402 3768 0.747255 GCTCCTTCATAGTCGCCTCA 59.253 55.000 0.00 0.00 0.00 3.86
2404 3770 1.036707 GAGCTCCTTCATAGTCGCCT 58.963 55.000 0.87 0.00 0.00 5.52
2408 3774 5.221165 GGAGTACTTGAGCTCCTTCATAGTC 60.221 48.000 12.15 8.66 45.78 2.59
2460 3858 2.350522 GAGCGAGTTGTCCATCATGTT 58.649 47.619 0.00 0.00 0.00 2.71
2512 3911 8.543774 CCATAGCTAGCGAATAAGCATATAAAC 58.456 37.037 9.55 0.00 41.32 2.01
2535 3934 2.288334 TGCACGTACGTACAAGAACCAT 60.288 45.455 22.34 0.00 0.00 3.55
2559 3965 6.883744 TGCATACAGTCCACATGAATTAGTA 58.116 36.000 0.00 0.00 0.00 1.82
2819 4230 1.152383 GGAGATACGTTCTTGCCCGC 61.152 60.000 0.00 0.00 33.74 6.13
2825 4236 2.688446 TGATCGCAGGAGATACGTTCTT 59.312 45.455 0.00 0.00 33.74 2.52
2839 4250 0.525455 CGACGACCATCTTGATCGCA 60.525 55.000 0.00 0.00 36.72 5.10
2967 4407 8.622948 ATTAACGGGAAAATCATCCTCTTATC 57.377 34.615 0.00 0.00 39.57 1.75
3050 4494 7.605410 AACCACTTTATTAGTTCCACATACG 57.395 36.000 0.00 0.00 33.85 3.06
3081 4525 6.707608 TGCATAGCACATAGGACAAGATTTAG 59.292 38.462 0.00 0.00 31.71 1.85
3103 4547 4.999311 GTGTCAGATATAGGATGCATTGCA 59.001 41.667 14.72 14.72 44.86 4.08
3106 4550 5.728637 TCGTGTCAGATATAGGATGCATT 57.271 39.130 0.00 0.00 0.00 3.56
3107 4551 5.655974 AGATCGTGTCAGATATAGGATGCAT 59.344 40.000 0.00 0.00 0.00 3.96
3108 4552 5.012893 AGATCGTGTCAGATATAGGATGCA 58.987 41.667 0.00 0.00 0.00 3.96
3109 4553 5.574891 AGATCGTGTCAGATATAGGATGC 57.425 43.478 0.00 0.00 0.00 3.91
3110 4554 8.443953 TCATAGATCGTGTCAGATATAGGATG 57.556 38.462 1.86 0.00 32.49 3.51
3113 4582 8.735315 AGTTTCATAGATCGTGTCAGATATAGG 58.265 37.037 1.86 0.00 29.30 2.57
3117 4586 6.697455 GCAAGTTTCATAGATCGTGTCAGATA 59.303 38.462 1.86 0.00 0.00 1.98
3205 4674 7.823745 ACATCCATGTACAGTTTCTTTTTCT 57.176 32.000 0.33 0.00 39.68 2.52
3206 4675 9.612620 CTTACATCCATGTACAGTTTCTTTTTC 57.387 33.333 0.33 0.00 42.48 2.29
3210 4679 6.590292 CGACTTACATCCATGTACAGTTTCTT 59.410 38.462 0.33 0.00 42.48 2.52
3224 4693 1.278238 CGCAAGGACGACTTACATCC 58.722 55.000 0.00 0.00 37.29 3.51
3242 4711 1.596260 GCATGTGATGACTGATGACCG 59.404 52.381 0.00 0.00 0.00 4.79
3285 4765 4.461081 AGATACTATCCATCTTCTCACGGC 59.539 45.833 0.00 0.00 28.01 5.68
3313 4808 2.365617 CCGTAGTATGAGTGATTGGCCT 59.634 50.000 3.32 0.00 0.00 5.19
3314 4809 2.364324 TCCGTAGTATGAGTGATTGGCC 59.636 50.000 0.00 0.00 0.00 5.36
3324 4819 3.949113 TGCTATGTGTGTCCGTAGTATGA 59.051 43.478 0.00 0.00 0.00 2.15
3333 4828 3.594603 ACTACTGTGCTATGTGTGTCC 57.405 47.619 0.00 0.00 0.00 4.02
3357 4854 3.120511 TCTCAAGAGATATCGCGTGATCG 60.121 47.826 21.26 13.12 34.42 3.69
3373 4870 6.392353 CTAGCAAAGCATATCGATCTCAAG 57.608 41.667 0.00 0.00 0.00 3.02
3413 4910 3.125146 CGAAAACGTGTGGACATGATCAT 59.875 43.478 1.18 1.18 36.72 2.45
3414 4911 2.478514 CGAAAACGTGTGGACATGATCA 59.521 45.455 0.00 0.00 36.72 2.92
3415 4912 2.159707 CCGAAAACGTGTGGACATGATC 60.160 50.000 0.00 0.00 36.72 2.92
3427 4967 1.670083 GTAGGGCTGCCGAAAACGT 60.670 57.895 13.40 0.00 0.00 3.99
3428 4968 0.108520 TAGTAGGGCTGCCGAAAACG 60.109 55.000 13.40 0.00 0.00 3.60
3432 4972 1.610554 GGTGTAGTAGGGCTGCCGAA 61.611 60.000 13.40 0.00 0.00 4.30
3435 4975 1.522569 CTGGTGTAGTAGGGCTGCC 59.477 63.158 11.05 11.05 0.00 4.85
3451 4991 0.531532 CCGCCTCTTATGGACAGCTG 60.532 60.000 13.48 13.48 0.00 4.24
3469 5198 0.035739 TGGCCGAGTTGTTACTTCCC 59.964 55.000 0.00 0.00 33.84 3.97
3475 5204 1.621317 TGAGTCATGGCCGAGTTGTTA 59.379 47.619 0.00 0.00 0.00 2.41
3481 5210 2.625314 TCTATCTTGAGTCATGGCCGAG 59.375 50.000 0.00 0.00 0.00 4.63
3483 5212 3.324117 CATCTATCTTGAGTCATGGCCG 58.676 50.000 0.00 0.00 0.00 6.13
3485 5214 3.672808 CCCATCTATCTTGAGTCATGGC 58.327 50.000 6.21 0.00 31.10 4.40
3494 5223 2.038295 GAGGTCTGGCCCATCTATCTTG 59.962 54.545 0.00 0.00 38.26 3.02
3499 5228 0.755698 GTCGAGGTCTGGCCCATCTA 60.756 60.000 0.00 0.00 38.26 1.98
3527 5280 2.034066 CCATGTGTTCGGCCTGGT 59.966 61.111 0.00 0.00 0.00 4.00
3529 5282 0.677731 ATCACCATGTGTTCGGCCTG 60.678 55.000 0.00 0.00 34.79 4.85
3535 5288 7.775120 AGGAAAATATGAATCACCATGTGTTC 58.225 34.615 0.00 0.00 33.63 3.18
3578 5331 9.331282 CCAAAACCATACAAACAAATAGGAAAA 57.669 29.630 0.00 0.00 0.00 2.29
3579 5332 8.487028 ACCAAAACCATACAAACAAATAGGAAA 58.513 29.630 0.00 0.00 0.00 3.13
3580 5333 8.024145 ACCAAAACCATACAAACAAATAGGAA 57.976 30.769 0.00 0.00 0.00 3.36
3581 5334 7.604657 ACCAAAACCATACAAACAAATAGGA 57.395 32.000 0.00 0.00 0.00 2.94
3582 5335 8.555361 CAAACCAAAACCATACAAACAAATAGG 58.445 33.333 0.00 0.00 0.00 2.57
3583 5336 8.067189 GCAAACCAAAACCATACAAACAAATAG 58.933 33.333 0.00 0.00 0.00 1.73
3584 5337 7.770897 AGCAAACCAAAACCATACAAACAAATA 59.229 29.630 0.00 0.00 0.00 1.40
3585 5338 6.601217 AGCAAACCAAAACCATACAAACAAAT 59.399 30.769 0.00 0.00 0.00 2.32
3586 5339 5.940470 AGCAAACCAAAACCATACAAACAAA 59.060 32.000 0.00 0.00 0.00 2.83
3587 5340 5.491982 AGCAAACCAAAACCATACAAACAA 58.508 33.333 0.00 0.00 0.00 2.83
3588 5341 5.091261 AGCAAACCAAAACCATACAAACA 57.909 34.783 0.00 0.00 0.00 2.83
3589 5342 5.352846 ACAAGCAAACCAAAACCATACAAAC 59.647 36.000 0.00 0.00 0.00 2.93
3590 5343 5.491982 ACAAGCAAACCAAAACCATACAAA 58.508 33.333 0.00 0.00 0.00 2.83
3613 5366 5.970592 TCCAACACAAACATGTGAATTTGA 58.029 33.333 15.26 0.19 42.02 2.69
3614 5367 6.041511 TCTCCAACACAAACATGTGAATTTG 58.958 36.000 15.26 2.41 42.02 2.32
3620 5373 2.951642 ACCTCTCCAACACAAACATGTG 59.048 45.455 0.00 7.38 44.74 3.21
3621 5374 3.297134 ACCTCTCCAACACAAACATGT 57.703 42.857 0.00 0.00 0.00 3.21
3630 5383 5.710099 GTGGAATTAATGAACCTCTCCAACA 59.290 40.000 4.69 0.00 33.46 3.33
3647 5400 9.936329 AATAAATTACTACAGATGGGTGGAATT 57.064 29.630 0.00 0.00 0.00 2.17
3665 5418 9.179909 TCGCTCCCTGACAAAAATAATAAATTA 57.820 29.630 0.00 0.00 0.00 1.40
3670 5423 6.826231 TGAATCGCTCCCTGACAAAAATAATA 59.174 34.615 0.00 0.00 0.00 0.98
3671 5424 5.652014 TGAATCGCTCCCTGACAAAAATAAT 59.348 36.000 0.00 0.00 0.00 1.28
3706 5459 1.801178 GTTCCGTGAAGCTTCCTCTTG 59.199 52.381 23.42 8.48 0.00 3.02
3707 5460 1.270893 GGTTCCGTGAAGCTTCCTCTT 60.271 52.381 23.42 0.00 37.13 2.85
3710 5463 1.375326 GGGTTCCGTGAAGCTTCCT 59.625 57.895 23.42 0.00 39.61 3.36
3716 5469 1.336755 CCAAACTTGGGTTCCGTGAAG 59.663 52.381 0.09 0.00 44.70 3.02
3786 5539 2.745968 TGCTTGACTTCCCAGGTTTTT 58.254 42.857 0.00 0.00 0.00 1.94
3787 5540 2.452600 TGCTTGACTTCCCAGGTTTT 57.547 45.000 0.00 0.00 0.00 2.43
3788 5541 2.430694 GTTTGCTTGACTTCCCAGGTTT 59.569 45.455 0.00 0.00 0.00 3.27
3789 5542 2.031870 GTTTGCTTGACTTCCCAGGTT 58.968 47.619 0.00 0.00 0.00 3.50
3790 5543 1.215423 AGTTTGCTTGACTTCCCAGGT 59.785 47.619 0.00 0.00 0.00 4.00
3791 5544 1.986882 AGTTTGCTTGACTTCCCAGG 58.013 50.000 0.00 0.00 0.00 4.45
3792 5545 4.261614 GGTTTAGTTTGCTTGACTTCCCAG 60.262 45.833 0.00 0.00 0.00 4.45
3793 5546 3.634910 GGTTTAGTTTGCTTGACTTCCCA 59.365 43.478 0.00 0.00 0.00 4.37
3794 5547 3.889538 AGGTTTAGTTTGCTTGACTTCCC 59.110 43.478 0.00 0.00 0.00 3.97
3795 5548 5.995897 TCTAGGTTTAGTTTGCTTGACTTCC 59.004 40.000 0.00 0.00 0.00 3.46
3796 5549 6.147985 CCTCTAGGTTTAGTTTGCTTGACTTC 59.852 42.308 0.00 0.00 0.00 3.01
3797 5550 5.998363 CCTCTAGGTTTAGTTTGCTTGACTT 59.002 40.000 0.00 0.00 0.00 3.01
3798 5551 5.552178 CCTCTAGGTTTAGTTTGCTTGACT 58.448 41.667 0.00 0.00 0.00 3.41
3799 5552 5.864628 CCTCTAGGTTTAGTTTGCTTGAC 57.135 43.478 0.00 0.00 0.00 3.18
3814 5567 7.665974 ACTTCTTTTAACCATGAAACCTCTAGG 59.334 37.037 0.00 0.00 42.17 3.02
3879 5632 9.959749 GTGTGATGAACTCTTTGGTATTTTTAA 57.040 29.630 0.00 0.00 0.00 1.52
3891 5644 3.469008 TTCGTGGTGTGATGAACTCTT 57.531 42.857 0.00 0.00 0.00 2.85
3901 5654 4.481930 TCTATTGCTTTTTCGTGGTGTG 57.518 40.909 0.00 0.00 0.00 3.82
3906 5659 5.356882 TCACCTTCTATTGCTTTTTCGTG 57.643 39.130 0.00 0.00 0.00 4.35
3927 5680 7.378728 CCGGTGAACTTCTTGTATTTCTTTTTC 59.621 37.037 0.00 0.00 0.00 2.29
3937 5948 3.823281 TTGTCCGGTGAACTTCTTGTA 57.177 42.857 0.00 0.00 0.00 2.41
3938 5949 2.681344 GTTTGTCCGGTGAACTTCTTGT 59.319 45.455 0.00 0.00 0.00 3.16
3940 5951 1.937899 CGTTTGTCCGGTGAACTTCTT 59.062 47.619 0.00 0.00 0.00 2.52
3951 5962 3.001939 ACTGAACTTTTAGCGTTTGTCCG 59.998 43.478 0.00 0.00 0.00 4.79
3959 5970 5.452302 CAGAACAACAACTGAACTTTTAGCG 59.548 40.000 0.00 0.00 36.38 4.26
3976 5988 3.635373 AGACTAACCTGTCGTCAGAACAA 59.365 43.478 11.41 0.00 43.76 2.83
3981 5993 1.887198 ACCAGACTAACCTGTCGTCAG 59.113 52.381 2.40 2.40 41.47 3.51
3982 5994 1.991121 ACCAGACTAACCTGTCGTCA 58.009 50.000 0.00 0.00 41.47 4.35
3994 6006 5.440610 ACTCACTTGAATTTGAACCAGACT 58.559 37.500 0.00 0.00 0.00 3.24
3997 6009 8.925161 TTTTAACTCACTTGAATTTGAACCAG 57.075 30.769 0.00 0.00 0.00 4.00
4037 6049 7.945134 ACTTTAATGTGAACTTCTGCATTCTT 58.055 30.769 12.33 0.00 34.05 2.52
4039 6051 9.677567 TTTACTTTAATGTGAACTTCTGCATTC 57.322 29.630 12.33 0.00 34.05 2.67


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

AutoCloner maintained by Alex Coulton.