Multiple sequence alignment - TraesCS5D01G388800

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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 TraesCS5D01G388800 chr5D 100.000 5567 0 0 1 5567 458184350 458178784 0.000000e+00 10281.0
1 TraesCS5D01G388800 chr5D 83.883 1061 114 38 1423 2452 458097591 458096557 0.000000e+00 959.0
2 TraesCS5D01G388800 chr5D 88.348 781 91 0 3520 4300 458095567 458094787 0.000000e+00 939.0
3 TraesCS5D01G388800 chr5D 82.935 879 131 13 2582 3450 458096554 458095685 0.000000e+00 774.0
4 TraesCS5D01G388800 chr5D 75.791 632 107 36 1815 2404 537224590 537223963 1.530000e-70 278.0
5 TraesCS5D01G388800 chr5D 84.071 226 28 5 1501 1722 537224914 537224693 1.570000e-50 211.0
6 TraesCS5D01G388800 chr5D 87.755 147 18 0 1178 1324 458098041 458097895 7.410000e-39 172.0
7 TraesCS5D01G388800 chr5D 100.000 58 0 0 5266 5323 458179027 458178970 2.120000e-19 108.0
8 TraesCS5D01G388800 chr5D 100.000 58 0 0 5324 5381 458179085 458179028 2.120000e-19 108.0
9 TraesCS5D01G388800 chr5B 93.379 2492 109 30 2561 5017 561063549 561061079 0.000000e+00 3637.0
10 TraesCS5D01G388800 chr5B 94.632 1863 49 19 613 2457 561065434 561063605 0.000000e+00 2839.0
11 TraesCS5D01G388800 chr5B 88.246 1693 178 17 2761 4435 560730781 560729092 0.000000e+00 2004.0
12 TraesCS5D01G388800 chr5B 84.428 1066 106 47 1423 2451 560444248 560443206 0.000000e+00 994.0
13 TraesCS5D01G388800 chr5B 88.633 783 87 2 3520 4301 560442217 560441436 0.000000e+00 952.0
14 TraesCS5D01G388800 chr5B 91.499 647 37 15 1816 2452 560731742 560731104 0.000000e+00 874.0
15 TraesCS5D01G388800 chr5B 88.000 525 45 5 1 515 561065976 561065460 6.170000e-169 604.0
16 TraesCS5D01G388800 chr5B 91.030 301 27 0 1422 1722 560732206 560731906 1.870000e-109 407.0
17 TraesCS5D01G388800 chr5B 81.507 292 43 7 1435 1722 677821660 677821376 4.340000e-56 230.0
18 TraesCS5D01G388800 chr5B 88.043 184 16 3 1141 1324 560732449 560732272 4.370000e-51 213.0
19 TraesCS5D01G388800 chr5B 87.755 147 18 0 1178 1324 560444634 560444488 7.410000e-39 172.0
20 TraesCS5D01G388800 chr5A 91.692 2323 137 36 2491 4796 576086671 576084388 0.000000e+00 3169.0
21 TraesCS5D01G388800 chr5A 91.754 2195 126 35 2491 4668 576270760 576272916 0.000000e+00 3000.0
22 TraesCS5D01G388800 chr5A 89.603 1712 152 17 2746 4438 575902597 575900893 0.000000e+00 2152.0
23 TraesCS5D01G388800 chr5A 90.490 1672 100 22 837 2484 576088423 576086787 0.000000e+00 2152.0
24 TraesCS5D01G388800 chr5A 83.936 1743 243 29 2583 4300 575707766 575706036 0.000000e+00 1633.0
25 TraesCS5D01G388800 chr5A 84.434 1060 116 39 1423 2452 575708810 575707770 0.000000e+00 998.0
26 TraesCS5D01G388800 chr5A 90.658 653 47 8 1816 2456 575903535 575902885 0.000000e+00 856.0
27 TraesCS5D01G388800 chr5A 90.654 642 32 8 980 1612 576268958 576269580 0.000000e+00 828.0
28 TraesCS5D01G388800 chr5A 91.466 539 34 5 4793 5323 576073221 576072687 0.000000e+00 730.0
29 TraesCS5D01G388800 chr5A 96.143 363 14 0 2122 2484 576270282 576270644 1.340000e-165 593.0
30 TraesCS5D01G388800 chr5A 78.049 697 78 34 309 969 576089478 576088821 2.450000e-98 370.0
31 TraesCS5D01G388800 chr5A 81.978 455 61 9 4203 4653 575900543 575900106 3.170000e-97 366.0
32 TraesCS5D01G388800 chr5A 89.388 245 23 3 1478 1722 575903854 575903613 7.010000e-79 305.0
33 TraesCS5D01G388800 chr5A 80.435 368 37 24 1141 1507 575904275 575903942 1.200000e-61 248.0
34 TraesCS5D01G388800 chr4A 85.038 782 117 0 3520 4301 632944753 632943972 0.000000e+00 797.0
35 TraesCS5D01G388800 chr4B 86.636 217 29 0 1814 2030 27249687 27249903 2.000000e-59 241.0
36 TraesCS5D01G388800 chr7B 86.076 79 9 1 170 248 477374835 477374759 3.570000e-12 84.2
37 TraesCS5D01G388800 chr7B 83.544 79 11 1 170 248 477380691 477380615 7.740000e-09 73.1


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 TraesCS5D01G388800 chr5D 458178784 458184350 5566 True 10281.000000 10281 100.000000 1 5567 1 chr5D.!!$R1 5566
1 TraesCS5D01G388800 chr5D 458094787 458098041 3254 True 711.000000 959 85.730250 1178 4300 4 chr5D.!!$R2 3122
2 TraesCS5D01G388800 chr5D 537223963 537224914 951 True 244.500000 278 79.931000 1501 2404 2 chr5D.!!$R4 903
3 TraesCS5D01G388800 chr5B 561061079 561065976 4897 True 2360.000000 3637 92.003667 1 5017 3 chr5B.!!$R4 5016
4 TraesCS5D01G388800 chr5B 560729092 560732449 3357 True 874.500000 2004 89.704500 1141 4435 4 chr5B.!!$R3 3294
5 TraesCS5D01G388800 chr5B 560441436 560444634 3198 True 706.000000 994 86.938667 1178 4301 3 chr5B.!!$R2 3123
6 TraesCS5D01G388800 chr5A 576084388 576089478 5090 True 1897.000000 3169 86.743667 309 4796 3 chr5A.!!$R4 4487
7 TraesCS5D01G388800 chr5A 576268958 576272916 3958 False 1473.666667 3000 92.850333 980 4668 3 chr5A.!!$F1 3688
8 TraesCS5D01G388800 chr5A 575706036 575708810 2774 True 1315.500000 1633 84.185000 1423 4300 2 chr5A.!!$R2 2877
9 TraesCS5D01G388800 chr5A 575900106 575904275 4169 True 785.400000 2152 86.412400 1141 4653 5 chr5A.!!$R3 3512
10 TraesCS5D01G388800 chr5A 576072687 576073221 534 True 730.000000 730 91.466000 4793 5323 1 chr5A.!!$R1 530
11 TraesCS5D01G388800 chr4A 632943972 632944753 781 True 797.000000 797 85.038000 3520 4301 1 chr4A.!!$R1 781


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
684 710 0.107508 ATGCAGAGGTCATTCCACCG 60.108 55.000 0.00 0.00 41.90 4.94 F
690 716 0.245539 AGGTCATTCCACCGTGTACG 59.754 55.000 0.00 0.00 41.90 3.67 F
1379 1947 1.079875 CTTCCCGTGCAATGCAATGC 61.080 55.000 19.99 19.99 46.58 3.56 F
2448 3553 0.542702 CCCCCAAGCCACAAGTCATT 60.543 55.000 0.00 0.00 0.00 2.57 F
2713 4008 3.568007 TCCATCGGCCAAATTATTAGTGC 59.432 43.478 2.24 0.00 0.00 4.40 F
4357 5711 0.185901 ATGTTGGGGTGTGTGCTTCT 59.814 50.000 0.00 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 2649 2.286294 GCATCCACTGAACACATCGATC 59.714 50.000 0.00 0.00 0.00 3.69 R
2076 3123 2.288825 CGTAAGTTCCAAGGAGAGTGCA 60.289 50.000 0.00 0.00 0.00 4.57 R
2815 4114 1.003355 CTCGGTGATGGTGCTGGTT 60.003 57.895 0.00 0.00 0.00 3.67 R
3510 4810 1.868713 TGCCCCTGCATTTCATTGAT 58.131 45.000 0.00 0.00 44.23 2.57 R
4438 6380 2.423538 GGAACATACATTGACCAGTGGC 59.576 50.000 9.78 2.56 0.00 5.01 R
5209 7164 0.464036 TGGACTCTCAACTGCGTGTT 59.536 50.000 0.00 0.00 39.92 3.32 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
64 65 6.690194 ATCATGTTCAGCTTGATAACTTCC 57.310 37.500 0.00 0.00 39.34 3.46
76 77 4.075682 TGATAACTTCCGCCAAACATCAA 58.924 39.130 0.00 0.00 0.00 2.57
136 137 1.152881 ATCAAGCCTTCCGCCATCC 60.153 57.895 0.00 0.00 38.78 3.51
152 162 2.227089 ATCCTGCACGGACGAACTCC 62.227 60.000 7.00 0.00 46.80 3.85
159 169 0.179067 ACGGACGAACTCCTGCAAAA 60.179 50.000 0.00 0.00 36.80 2.44
168 178 0.178992 CTCCTGCAAAACCCCTGACA 60.179 55.000 0.00 0.00 0.00 3.58
176 186 3.181466 GCAAAACCCCTGACATTTGTCTT 60.181 43.478 11.67 0.00 44.99 3.01
181 191 2.558359 CCCCTGACATTTGTCTTTGGTC 59.442 50.000 11.67 0.00 44.99 4.02
184 194 3.304928 CCTGACATTTGTCTTTGGTCTGC 60.305 47.826 11.67 0.00 44.99 4.26
185 195 2.290367 TGACATTTGTCTTTGGTCTGCG 59.710 45.455 11.67 0.00 44.99 5.18
186 196 1.608590 ACATTTGTCTTTGGTCTGCGG 59.391 47.619 0.00 0.00 0.00 5.69
187 197 1.068333 CATTTGTCTTTGGTCTGCGGG 60.068 52.381 0.00 0.00 0.00 6.13
215 225 2.125912 CTTCTGGACCACTCGGCG 60.126 66.667 0.00 0.00 34.57 6.46
219 229 3.432051 CTGGACCACTCGGCGGATC 62.432 68.421 7.21 0.00 34.57 3.36
224 234 1.081376 CCACTCGGCGGATCGATAC 60.081 63.158 7.21 0.00 38.55 2.24
225 235 1.652563 CACTCGGCGGATCGATACA 59.347 57.895 8.69 0.00 38.55 2.29
227 237 1.442857 CTCGGCGGATCGATACAGC 60.443 63.158 8.69 11.74 38.55 4.40
232 242 2.561956 CGGATCGATACAGCCCCGT 61.562 63.158 8.69 0.00 33.02 5.28
237 247 1.216977 CGATACAGCCCCGTGTTGA 59.783 57.895 0.00 0.00 31.46 3.18
240 250 1.670811 GATACAGCCCCGTGTTGAATG 59.329 52.381 0.00 0.00 31.46 2.67
254 264 1.213491 TGAATGACACAACACGTCCG 58.787 50.000 0.00 0.00 32.15 4.79
266 276 2.434359 CGTCCGAAAGCAGGGTCC 60.434 66.667 0.00 0.00 0.00 4.46
268 278 1.072505 GTCCGAAAGCAGGGTCCAA 59.927 57.895 0.00 0.00 0.00 3.53
273 283 1.874739 CGAAAGCAGGGTCCAAACGTA 60.875 52.381 0.00 0.00 0.00 3.57
287 297 0.319727 AACGTATGCGGACGGTTTGA 60.320 50.000 8.39 0.00 40.66 2.69
289 299 0.457166 CGTATGCGGACGGTTTGAGA 60.457 55.000 0.00 0.00 39.19 3.27
293 303 1.006571 GCGGACGGTTTGAGAGTCA 60.007 57.895 0.00 0.00 36.68 3.41
294 304 0.599204 GCGGACGGTTTGAGAGTCAA 60.599 55.000 0.00 0.00 36.68 3.18
296 306 1.537348 CGGACGGTTTGAGAGTCAACA 60.537 52.381 0.00 0.00 35.89 3.33
306 316 6.205464 GGTTTGAGAGTCAACATTGAAGATGA 59.795 38.462 0.00 0.00 39.21 2.92
337 347 5.859205 ATTTTACTCATCCAAATCCTGCC 57.141 39.130 0.00 0.00 0.00 4.85
447 458 2.103143 CGAGGCGCACGAATCTCT 59.897 61.111 18.59 0.00 0.00 3.10
448 459 1.941734 CGAGGCGCACGAATCTCTC 60.942 63.158 18.59 8.00 0.00 3.20
487 504 1.740380 CGTCTATGCTGGTCCCAAGTG 60.740 57.143 0.00 0.00 0.00 3.16
498 515 4.680237 CCAAGTGGCGCGGACAGA 62.680 66.667 8.83 0.00 0.00 3.41
499 516 3.114616 CAAGTGGCGCGGACAGAG 61.115 66.667 8.83 0.00 0.00 3.35
578 595 3.515286 GGTCGACGCCGGAGATCA 61.515 66.667 13.83 0.00 36.24 2.92
598 616 3.179265 CGCGCAGTCGACCGATTT 61.179 61.111 16.80 0.00 38.10 2.17
602 620 0.298707 CGCAGTCGACCGATTTGATG 59.701 55.000 13.01 2.12 38.10 3.07
605 623 1.012234 GTCGACCGATTTGATGCGC 60.012 57.895 3.51 0.00 0.00 6.09
610 628 1.867233 GACCGATTTGATGCGCATACT 59.133 47.619 25.40 0.84 0.00 2.12
635 653 1.656095 CCAAGCTTGAACTCGATCGAC 59.344 52.381 28.05 5.41 0.00 4.20
641 659 3.686128 CTTGAACTCGATCGACCTACTG 58.314 50.000 15.15 5.95 0.00 2.74
683 709 1.747355 CAATGCAGAGGTCATTCCACC 59.253 52.381 0.00 0.00 39.02 4.61
684 710 0.107508 ATGCAGAGGTCATTCCACCG 60.108 55.000 0.00 0.00 41.90 4.94
685 711 1.296715 GCAGAGGTCATTCCACCGT 59.703 57.895 0.00 0.00 41.90 4.83
687 713 0.321671 CAGAGGTCATTCCACCGTGT 59.678 55.000 0.00 0.00 41.90 4.49
688 714 1.548719 CAGAGGTCATTCCACCGTGTA 59.451 52.381 0.00 0.00 41.90 2.90
689 715 1.549170 AGAGGTCATTCCACCGTGTAC 59.451 52.381 0.00 0.00 41.90 2.90
690 716 0.245539 AGGTCATTCCACCGTGTACG 59.754 55.000 0.00 0.00 41.90 3.67
799 830 5.233902 CACGATTGAGATCTTGTCTTGATCC 59.766 44.000 0.00 0.00 40.69 3.36
857 900 6.239232 CGTAGCTACTCCCCTGTATACAATTT 60.239 42.308 21.20 0.00 0.00 1.82
858 901 5.930135 AGCTACTCCCCTGTATACAATTTG 58.070 41.667 7.06 0.00 0.00 2.32
859 902 5.428783 AGCTACTCCCCTGTATACAATTTGT 59.571 40.000 7.06 7.30 0.00 2.83
860 903 6.614087 AGCTACTCCCCTGTATACAATTTGTA 59.386 38.462 11.47 11.47 37.24 2.41
861 904 6.929606 GCTACTCCCCTGTATACAATTTGTAG 59.070 42.308 14.18 14.63 36.14 2.74
978 1536 3.883744 AACGCCAAGCTCACCGAGG 62.884 63.158 6.82 0.00 0.00 4.63
1065 1624 1.697432 AGCAAGCCACACTACCACTAA 59.303 47.619 0.00 0.00 0.00 2.24
1097 1656 3.321111 ACTGTTTCTCCGTCTTAGAAGCA 59.679 43.478 0.00 0.00 40.48 3.91
1101 1660 5.047590 TGTTTCTCCGTCTTAGAAGCATACA 60.048 40.000 0.00 0.00 38.68 2.29
1103 1662 6.954487 TTCTCCGTCTTAGAAGCATACATA 57.046 37.500 0.00 0.00 0.00 2.29
1104 1663 6.315091 TCTCCGTCTTAGAAGCATACATAC 57.685 41.667 0.00 0.00 0.00 2.39
1105 1664 5.826208 TCTCCGTCTTAGAAGCATACATACA 59.174 40.000 0.00 0.00 0.00 2.29
1106 1665 5.828747 TCCGTCTTAGAAGCATACATACAC 58.171 41.667 0.00 0.00 0.00 2.90
1107 1666 5.358725 TCCGTCTTAGAAGCATACATACACA 59.641 40.000 0.00 0.00 0.00 3.72
1174 1742 2.525629 TCACCGGGAGCAAGACCA 60.526 61.111 6.32 0.00 0.00 4.02
1334 1902 1.741770 GTGAGCACCATCGACCACC 60.742 63.158 0.00 0.00 0.00 4.61
1379 1947 1.079875 CTTCCCGTGCAATGCAATGC 61.080 55.000 19.99 19.99 46.58 3.56
1742 2649 1.945394 CGAGCTCTTCAATCCCCAATG 59.055 52.381 12.85 0.00 0.00 2.82
1788 2791 5.278604 ACGTTTTTGCTTGTCCACTTATTC 58.721 37.500 0.00 0.00 0.00 1.75
1807 2839 9.918630 ACTTATTCAAGTAAACGTGTATGTACT 57.081 29.630 0.00 0.00 43.33 2.73
2076 3123 5.260424 TCTCTCTTTCTCACTCACTAGCAT 58.740 41.667 0.00 0.00 0.00 3.79
2448 3553 0.542702 CCCCCAAGCCACAAGTCATT 60.543 55.000 0.00 0.00 0.00 2.57
2546 3761 6.209391 AGGATCATCAAACGTTGGAAGAAAAT 59.791 34.615 14.12 0.00 0.00 1.82
2708 4003 8.821686 TTCATATATCCATCGGCCAAATTATT 57.178 30.769 2.24 0.00 0.00 1.40
2711 4006 9.342308 CATATATCCATCGGCCAAATTATTAGT 57.658 33.333 2.24 0.00 0.00 2.24
2712 4007 5.964958 ATCCATCGGCCAAATTATTAGTG 57.035 39.130 2.24 0.00 0.00 2.74
2713 4008 3.568007 TCCATCGGCCAAATTATTAGTGC 59.432 43.478 2.24 0.00 0.00 4.40
4349 5703 1.542987 GCATGCAAAATGTTGGGGTGT 60.543 47.619 14.21 0.00 35.10 4.16
4357 5711 0.185901 ATGTTGGGGTGTGTGCTTCT 59.814 50.000 0.00 0.00 0.00 2.85
4365 5719 2.171448 GGGTGTGTGCTTCTAGGATCAT 59.829 50.000 0.00 0.00 0.00 2.45
4389 6331 7.534085 TTTGCTTGAATAATCTAGTACACCG 57.466 36.000 0.00 0.00 31.94 4.94
4438 6380 1.296715 GTGGGTAGCCACTGGTCAG 59.703 63.158 32.12 0.00 37.68 3.51
4439 6381 2.269241 GGGTAGCCACTGGTCAGC 59.731 66.667 5.96 0.00 0.00 4.26
4440 6382 2.269241 GGTAGCCACTGGTCAGCC 59.731 66.667 0.00 0.00 0.00 4.85
4441 6383 2.592993 GGTAGCCACTGGTCAGCCA 61.593 63.158 0.00 0.00 43.73 4.75
4442 6384 1.376037 GTAGCCACTGGTCAGCCAC 60.376 63.158 0.00 0.00 40.46 5.01
4445 6387 2.033141 CCACTGGTCAGCCACTGG 59.967 66.667 0.00 0.00 40.61 4.00
4446 6388 2.822637 CCACTGGTCAGCCACTGGT 61.823 63.158 0.00 0.00 41.20 4.00
4447 6389 1.302033 CACTGGTCAGCCACTGGTC 60.302 63.158 0.00 0.00 40.46 4.02
4448 6390 1.766059 ACTGGTCAGCCACTGGTCA 60.766 57.895 0.00 0.00 40.46 4.02
4449 6391 1.344953 ACTGGTCAGCCACTGGTCAA 61.345 55.000 0.00 0.00 40.46 3.18
4450 6392 0.037303 CTGGTCAGCCACTGGTCAAT 59.963 55.000 0.00 0.00 40.46 2.57
4451 6393 0.250858 TGGTCAGCCACTGGTCAATG 60.251 55.000 0.00 0.00 40.46 2.82
4452 6394 0.250901 GGTCAGCCACTGGTCAATGT 60.251 55.000 0.00 0.00 34.09 2.71
4455 6397 2.679837 GTCAGCCACTGGTCAATGTATG 59.320 50.000 0.00 0.00 31.51 2.39
4617 6563 0.388520 GGCATTGAAGGTGGTTTCGC 60.389 55.000 0.00 0.00 0.00 4.70
4657 6603 2.049433 CCGTCCGCCTATAAGCCG 60.049 66.667 0.00 0.00 0.00 5.52
4687 6633 2.672961 TGTGCCTAGAATTGGAGACG 57.327 50.000 0.00 0.00 0.00 4.18
4725 6671 6.710692 TGCAATGATATATCACTGTAAGCG 57.289 37.500 21.63 0.31 40.03 4.68
4927 6873 5.918426 TCATAATGCACACATCCACATTT 57.082 34.783 0.00 0.00 34.62 2.32
5018 6966 5.462034 TGCAACAAACAAAATGCTACAAC 57.538 34.783 0.00 0.00 39.49 3.32
5019 6967 4.331168 TGCAACAAACAAAATGCTACAACC 59.669 37.500 0.00 0.00 39.49 3.77
5021 6969 5.276820 GCAACAAACAAAATGCTACAACCTC 60.277 40.000 0.00 0.00 35.93 3.85
5033 6981 5.237815 TGCTACAACCTCAAATGTGTCTAG 58.762 41.667 0.00 0.00 0.00 2.43
5087 7035 2.205022 ATGTGTGATCACCAACTGGG 57.795 50.000 22.85 0.00 43.26 4.45
5089 7037 1.072173 TGTGTGATCACCAACTGGGAG 59.928 52.381 22.85 0.00 43.26 4.30
5098 7046 4.168101 TCACCAACTGGGAGAATAGTCTT 58.832 43.478 0.00 0.00 41.15 3.01
5105 7053 3.024547 TGGGAGAATAGTCTTGAGTCCG 58.975 50.000 0.00 0.00 32.80 4.79
5111 7059 4.767928 AGAATAGTCTTGAGTCCGTCAACT 59.232 41.667 0.00 0.00 40.45 3.16
5112 7060 4.705337 ATAGTCTTGAGTCCGTCAACTC 57.295 45.455 3.59 3.59 44.87 3.01
5137 7085 5.471556 TGAAAATGACCATTGCATTGTCT 57.528 34.783 7.75 0.00 39.58 3.41
5148 7096 2.300433 TGCATTGTCTGTTGAGCAGTT 58.700 42.857 0.00 0.00 45.23 3.16
5156 7104 3.991121 GTCTGTTGAGCAGTTAAGAGTCC 59.009 47.826 0.00 0.00 45.23 3.85
5170 7118 1.717077 AGAGTCCAGGTAAGACCCTCA 59.283 52.381 0.00 0.00 39.75 3.86
5177 7125 3.055747 CCAGGTAAGACCCTCAACTTCTC 60.056 52.174 0.00 0.00 39.75 2.87
5182 7130 2.104170 AGACCCTCAACTTCTCGGATC 58.896 52.381 0.00 0.00 0.00 3.36
5185 7133 0.173481 CCTCAACTTCTCGGATCGCA 59.827 55.000 0.00 0.00 0.00 5.10
5186 7134 1.202463 CCTCAACTTCTCGGATCGCAT 60.202 52.381 0.00 0.00 0.00 4.73
5206 7161 4.623167 GCATGCGACGACTTTATCATATCT 59.377 41.667 0.00 0.00 0.00 1.98
5209 7164 6.308371 TGCGACGACTTTATCATATCTGTA 57.692 37.500 0.00 0.00 0.00 2.74
5230 7185 0.668706 CACGCAGTTGAGAGTCCAGG 60.669 60.000 0.00 0.00 41.61 4.45
5236 7191 2.162608 CAGTTGAGAGTCCAGGTAGTCG 59.837 54.545 0.00 0.00 0.00 4.18
5254 7209 4.869451 AGTCGTCCTCCTCCTTTTATAGT 58.131 43.478 0.00 0.00 0.00 2.12
5261 7216 1.217882 CTCCTTTTATAGTGGCGCCG 58.782 55.000 23.90 3.23 0.00 6.46
5263 7218 0.179067 CCTTTTATAGTGGCGCCGGA 60.179 55.000 23.90 9.88 0.00 5.14
5290 7245 9.076781 CCTCCCCAAATTAACAATTTCAAAAAT 57.923 29.630 0.00 0.00 38.97 1.82
5317 7272 5.331980 CCGCAAATTTGTAAGAAAACGTTCC 60.332 40.000 19.03 0.00 33.92 3.62
5323 7278 8.797266 AATTTGTAAGAAAACGTTCCTGATTC 57.203 30.769 0.00 0.90 33.92 2.52
5324 7279 7.562454 TTTGTAAGAAAACGTTCCTGATTCT 57.438 32.000 0.00 3.60 33.92 2.40
5325 7280 6.780706 TGTAAGAAAACGTTCCTGATTCTC 57.219 37.500 11.49 3.10 33.92 2.87
5326 7281 5.699458 TGTAAGAAAACGTTCCTGATTCTCC 59.301 40.000 11.49 7.24 33.92 3.71
5327 7282 3.676093 AGAAAACGTTCCTGATTCTCCC 58.324 45.455 0.00 0.00 33.92 4.30
5328 7283 2.491675 AAACGTTCCTGATTCTCCCC 57.508 50.000 0.00 0.00 0.00 4.81
5329 7284 1.358152 AACGTTCCTGATTCTCCCCA 58.642 50.000 0.00 0.00 0.00 4.96
5330 7285 1.358152 ACGTTCCTGATTCTCCCCAA 58.642 50.000 0.00 0.00 0.00 4.12
5331 7286 1.702957 ACGTTCCTGATTCTCCCCAAA 59.297 47.619 0.00 0.00 0.00 3.28
5332 7287 2.308866 ACGTTCCTGATTCTCCCCAAAT 59.691 45.455 0.00 0.00 0.00 2.32
5333 7288 3.245264 ACGTTCCTGATTCTCCCCAAATT 60.245 43.478 0.00 0.00 0.00 1.82
5334 7289 4.018779 ACGTTCCTGATTCTCCCCAAATTA 60.019 41.667 0.00 0.00 0.00 1.40
5335 7290 4.947388 CGTTCCTGATTCTCCCCAAATTAA 59.053 41.667 0.00 0.00 0.00 1.40
5336 7291 5.163652 CGTTCCTGATTCTCCCCAAATTAAC 60.164 44.000 0.00 0.00 0.00 2.01
5337 7292 5.528600 TCCTGATTCTCCCCAAATTAACA 57.471 39.130 0.00 0.00 0.00 2.41
5338 7293 5.898120 TCCTGATTCTCCCCAAATTAACAA 58.102 37.500 0.00 0.00 0.00 2.83
5339 7294 6.502138 TCCTGATTCTCCCCAAATTAACAAT 58.498 36.000 0.00 0.00 0.00 2.71
5340 7295 6.959366 TCCTGATTCTCCCCAAATTAACAATT 59.041 34.615 0.00 0.00 0.00 2.32
5341 7296 7.457535 TCCTGATTCTCCCCAAATTAACAATTT 59.542 33.333 0.00 0.00 41.57 1.82
5342 7297 7.765819 CCTGATTCTCCCCAAATTAACAATTTC 59.234 37.037 0.00 0.00 38.97 2.17
5343 7298 8.200024 TGATTCTCCCCAAATTAACAATTTCA 57.800 30.769 0.00 0.00 38.97 2.69
5344 7299 8.654997 TGATTCTCCCCAAATTAACAATTTCAA 58.345 29.630 0.00 0.00 38.97 2.69
5345 7300 9.500785 GATTCTCCCCAAATTAACAATTTCAAA 57.499 29.630 0.00 0.00 38.97 2.69
5346 7301 9.859152 ATTCTCCCCAAATTAACAATTTCAAAA 57.141 25.926 0.00 0.00 38.97 2.44
5347 7302 9.686683 TTCTCCCCAAATTAACAATTTCAAAAA 57.313 25.926 0.00 0.00 38.97 1.94
5348 7303 9.859152 TCTCCCCAAATTAACAATTTCAAAAAT 57.141 25.926 0.00 0.00 38.97 1.82
5351 7306 8.976471 CCCCAAATTAACAATTTCAAAAATTGC 58.024 29.630 19.76 0.00 38.97 3.56
5352 7307 8.976471 CCCAAATTAACAATTTCAAAAATTGCC 58.024 29.630 19.76 0.00 38.97 4.52
5353 7308 8.689069 CCAAATTAACAATTTCAAAAATTGCCG 58.311 29.630 19.76 3.29 38.97 5.69
5354 7309 7.850268 AATTAACAATTTCAAAAATTGCCGC 57.150 28.000 19.76 0.00 40.35 6.53
5355 7310 4.889832 AACAATTTCAAAAATTGCCGCA 57.110 31.818 19.76 0.00 40.35 5.69
5356 7311 4.889832 ACAATTTCAAAAATTGCCGCAA 57.110 31.818 19.76 8.55 40.35 4.85
5357 7312 5.240713 ACAATTTCAAAAATTGCCGCAAA 57.759 30.435 19.76 0.00 40.35 3.68
5358 7313 5.829829 ACAATTTCAAAAATTGCCGCAAAT 58.170 29.167 19.76 0.00 40.35 2.32
5359 7314 6.271566 ACAATTTCAAAAATTGCCGCAAATT 58.728 28.000 19.76 5.10 40.35 1.82
5360 7315 6.755607 ACAATTTCAAAAATTGCCGCAAATTT 59.244 26.923 19.76 11.58 40.60 1.82
5361 7316 6.750775 ATTTCAAAAATTGCCGCAAATTTG 57.249 29.167 26.41 26.41 39.20 2.32
5362 7317 4.889832 TCAAAAATTGCCGCAAATTTGT 57.110 31.818 28.57 16.41 39.20 2.83
5363 7318 5.991328 TCAAAAATTGCCGCAAATTTGTA 57.009 30.435 28.57 19.90 39.20 2.41
5364 7319 6.363577 TCAAAAATTGCCGCAAATTTGTAA 57.636 29.167 28.57 17.88 39.20 2.41
5365 7320 6.425504 TCAAAAATTGCCGCAAATTTGTAAG 58.574 32.000 28.57 17.26 39.20 2.34
5366 7321 6.258727 TCAAAAATTGCCGCAAATTTGTAAGA 59.741 30.769 28.57 18.54 39.20 2.10
5367 7322 6.610741 AAAATTGCCGCAAATTTGTAAGAA 57.389 29.167 16.54 8.31 39.20 2.52
5368 7323 6.610741 AAATTGCCGCAAATTTGTAAGAAA 57.389 29.167 19.03 9.51 38.12 2.52
5369 7324 6.610741 AATTGCCGCAAATTTGTAAGAAAA 57.389 29.167 19.03 7.60 0.00 2.29
5370 7325 5.396750 TTGCCGCAAATTTGTAAGAAAAC 57.603 34.783 19.03 0.00 0.00 2.43
5371 7326 3.487574 TGCCGCAAATTTGTAAGAAAACG 59.512 39.130 19.03 10.97 0.00 3.60
5372 7327 3.487942 GCCGCAAATTTGTAAGAAAACGT 59.512 39.130 19.03 0.00 0.00 3.99
5373 7328 4.026393 GCCGCAAATTTGTAAGAAAACGTT 60.026 37.500 19.03 0.00 0.00 3.99
5374 7329 5.652699 CCGCAAATTTGTAAGAAAACGTTC 58.347 37.500 19.03 0.00 0.00 3.95
5375 7330 5.331980 CCGCAAATTTGTAAGAAAACGTTCC 60.332 40.000 19.03 0.00 33.92 3.62
5376 7331 5.457473 CGCAAATTTGTAAGAAAACGTTCCT 59.543 36.000 19.03 0.00 33.92 3.36
5377 7332 6.559521 CGCAAATTTGTAAGAAAACGTTCCTG 60.560 38.462 19.03 0.00 33.92 3.86
5378 7333 6.474102 GCAAATTTGTAAGAAAACGTTCCTGA 59.526 34.615 19.03 0.00 33.92 3.86
5379 7334 7.169140 GCAAATTTGTAAGAAAACGTTCCTGAT 59.831 33.333 19.03 0.00 33.92 2.90
5380 7335 9.030301 CAAATTTGTAAGAAAACGTTCCTGATT 57.970 29.630 10.15 0.00 33.92 2.57
5381 7336 9.594478 AAATTTGTAAGAAAACGTTCCTGATTT 57.406 25.926 0.00 0.00 33.92 2.17
5382 7337 9.594478 AATTTGTAAGAAAACGTTCCTGATTTT 57.406 25.926 0.00 0.00 33.92 1.82
5383 7338 8.989653 TTTGTAAGAAAACGTTCCTGATTTTT 57.010 26.923 0.00 0.00 33.92 1.94
5426 7381 5.950758 AAAATGTTAGCGGACAATGTACA 57.049 34.783 0.00 0.00 32.47 2.90
5427 7382 4.939509 AATGTTAGCGGACAATGTACAC 57.060 40.909 0.00 0.00 32.47 2.90
5428 7383 2.330286 TGTTAGCGGACAATGTACACG 58.670 47.619 0.00 0.00 0.00 4.49
5429 7384 2.030096 TGTTAGCGGACAATGTACACGA 60.030 45.455 0.00 0.00 0.00 4.35
5430 7385 2.988493 GTTAGCGGACAATGTACACGAA 59.012 45.455 0.00 0.00 0.00 3.85
5431 7386 2.380084 AGCGGACAATGTACACGAAT 57.620 45.000 0.00 0.00 0.00 3.34
5432 7387 2.695359 AGCGGACAATGTACACGAATT 58.305 42.857 0.00 0.00 0.00 2.17
5433 7388 2.415168 AGCGGACAATGTACACGAATTG 59.585 45.455 0.00 1.02 39.26 2.32
5434 7389 2.475519 GCGGACAATGTACACGAATTGG 60.476 50.000 10.75 0.00 37.96 3.16
5435 7390 2.997303 CGGACAATGTACACGAATTGGA 59.003 45.455 10.75 0.00 37.96 3.53
5436 7391 3.433957 CGGACAATGTACACGAATTGGAA 59.566 43.478 10.75 0.00 37.96 3.53
5437 7392 4.083749 CGGACAATGTACACGAATTGGAAA 60.084 41.667 10.75 0.00 37.96 3.13
5438 7393 5.151389 GGACAATGTACACGAATTGGAAAC 58.849 41.667 10.75 1.57 37.96 2.78
5439 7394 5.278071 GGACAATGTACACGAATTGGAAACA 60.278 40.000 10.75 0.00 37.96 2.83
5440 7395 6.325919 ACAATGTACACGAATTGGAAACAT 57.674 33.333 10.75 0.00 42.32 2.71
5441 7396 6.148948 ACAATGTACACGAATTGGAAACATG 58.851 36.000 10.75 0.00 42.32 3.21
5442 7397 5.957842 ATGTACACGAATTGGAAACATGT 57.042 34.783 0.00 0.00 42.32 3.21
5443 7398 5.759506 TGTACACGAATTGGAAACATGTT 57.240 34.783 4.92 4.92 42.32 2.71
5444 7399 5.753744 TGTACACGAATTGGAAACATGTTC 58.246 37.500 12.39 5.57 42.32 3.18
5450 7405 5.922546 CGAATTGGAAACATGTTCGTAAGA 58.077 37.500 12.39 0.00 45.68 2.10
5451 7406 6.542852 CGAATTGGAAACATGTTCGTAAGAT 58.457 36.000 12.39 0.00 45.68 2.40
5452 7407 6.465781 CGAATTGGAAACATGTTCGTAAGATG 59.534 38.462 12.39 0.00 45.68 2.90
5453 7408 7.447374 AATTGGAAACATGTTCGTAAGATGA 57.553 32.000 12.39 0.00 44.98 2.92
5454 7409 6.869315 TTGGAAACATGTTCGTAAGATGAA 57.131 33.333 12.39 0.00 44.98 2.57
5455 7410 6.869315 TGGAAACATGTTCGTAAGATGAAA 57.131 33.333 12.39 0.00 41.26 2.69
5456 7411 6.664515 TGGAAACATGTTCGTAAGATGAAAC 58.335 36.000 12.39 0.00 41.26 2.78
5457 7412 6.261158 TGGAAACATGTTCGTAAGATGAAACA 59.739 34.615 12.39 0.00 41.26 2.83
5458 7413 7.519809 TGGAAACATGTTCGTAAGATGAAACAG 60.520 37.037 12.39 0.00 41.26 3.16
5466 7421 5.860611 TCGTAAGATGAAACAGAAAAGGGA 58.139 37.500 0.00 0.00 45.01 4.20
5467 7422 6.292923 TCGTAAGATGAAACAGAAAAGGGAA 58.707 36.000 0.00 0.00 45.01 3.97
5468 7423 6.426937 TCGTAAGATGAAACAGAAAAGGGAAG 59.573 38.462 0.00 0.00 45.01 3.46
5469 7424 6.426937 CGTAAGATGAAACAGAAAAGGGAAGA 59.573 38.462 0.00 0.00 43.02 2.87
5470 7425 6.890979 AAGATGAAACAGAAAAGGGAAGAG 57.109 37.500 0.00 0.00 0.00 2.85
5471 7426 5.320277 AGATGAAACAGAAAAGGGAAGAGG 58.680 41.667 0.00 0.00 0.00 3.69
5472 7427 4.788925 TGAAACAGAAAAGGGAAGAGGA 57.211 40.909 0.00 0.00 0.00 3.71
5473 7428 5.124036 TGAAACAGAAAAGGGAAGAGGAA 57.876 39.130 0.00 0.00 0.00 3.36
5474 7429 5.515106 TGAAACAGAAAAGGGAAGAGGAAA 58.485 37.500 0.00 0.00 0.00 3.13
5475 7430 5.955355 TGAAACAGAAAAGGGAAGAGGAAAA 59.045 36.000 0.00 0.00 0.00 2.29
5476 7431 6.439058 TGAAACAGAAAAGGGAAGAGGAAAAA 59.561 34.615 0.00 0.00 0.00 1.94
5477 7432 7.125659 TGAAACAGAAAAGGGAAGAGGAAAAAT 59.874 33.333 0.00 0.00 0.00 1.82
5478 7433 8.547481 AAACAGAAAAGGGAAGAGGAAAAATA 57.453 30.769 0.00 0.00 0.00 1.40
5479 7434 8.547481 AACAGAAAAGGGAAGAGGAAAAATAA 57.453 30.769 0.00 0.00 0.00 1.40
5480 7435 8.547481 ACAGAAAAGGGAAGAGGAAAAATAAA 57.453 30.769 0.00 0.00 0.00 1.40
5481 7436 8.988060 ACAGAAAAGGGAAGAGGAAAAATAAAA 58.012 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.737838 TGGCGGAAGTTATCAAGCTG 58.262 50.000 0.00 0.00 34.76 4.24
64 65 3.127548 ACTGATTAGCTTGATGTTTGGCG 59.872 43.478 0.00 0.00 0.00 5.69
76 77 9.810545 GAGAACTTGATTAGTAACTGATTAGCT 57.189 33.333 0.00 0.00 35.54 3.32
152 162 2.102925 ACAAATGTCAGGGGTTTTGCAG 59.897 45.455 0.00 0.00 33.43 4.41
168 178 1.202879 TCCCGCAGACCAAAGACAAAT 60.203 47.619 0.00 0.00 0.00 2.32
199 209 3.691342 CCGCCGAGTGGTCCAGAA 61.691 66.667 0.00 0.00 37.67 3.02
203 213 4.570663 CGATCCGCCGAGTGGTCC 62.571 72.222 3.84 0.00 37.67 4.46
204 214 1.512996 TATCGATCCGCCGAGTGGTC 61.513 60.000 0.00 1.54 42.21 4.02
215 225 1.006102 CACGGGGCTGTATCGATCC 60.006 63.158 0.00 0.00 0.00 3.36
219 229 0.390603 TTCAACACGGGGCTGTATCG 60.391 55.000 0.00 0.00 0.00 2.92
224 234 0.888736 TGTCATTCAACACGGGGCTG 60.889 55.000 0.00 0.00 0.00 4.85
225 235 0.889186 GTGTCATTCAACACGGGGCT 60.889 55.000 0.00 0.00 40.09 5.19
237 247 1.942677 TTCGGACGTGTTGTGTCATT 58.057 45.000 0.00 0.00 38.10 2.57
240 250 0.042448 GCTTTCGGACGTGTTGTGTC 60.042 55.000 0.00 0.00 35.60 3.67
254 264 1.886886 TACGTTTGGACCCTGCTTTC 58.113 50.000 0.00 0.00 0.00 2.62
266 276 0.513820 AAACCGTCCGCATACGTTTG 59.486 50.000 0.00 0.00 41.27 2.93
268 278 0.319727 TCAAACCGTCCGCATACGTT 60.320 50.000 0.00 0.09 41.27 3.99
273 283 0.389948 GACTCTCAAACCGTCCGCAT 60.390 55.000 0.00 0.00 0.00 4.73
287 297 4.021104 TCGGTCATCTTCAATGTTGACTCT 60.021 41.667 0.00 0.00 36.83 3.24
289 299 4.248859 CTCGGTCATCTTCAATGTTGACT 58.751 43.478 0.00 0.00 36.83 3.41
293 303 2.290260 TGGCTCGGTCATCTTCAATGTT 60.290 45.455 0.00 0.00 0.00 2.71
294 304 1.278985 TGGCTCGGTCATCTTCAATGT 59.721 47.619 0.00 0.00 0.00 2.71
296 306 2.787473 TTGGCTCGGTCATCTTCAAT 57.213 45.000 0.00 0.00 0.00 2.57
306 316 3.279434 GGATGAGTAAAATTGGCTCGGT 58.721 45.455 0.00 0.00 32.32 4.69
337 347 0.109597 GTTGCTCGCATTCAACCCAG 60.110 55.000 0.00 0.00 37.26 4.45
400 411 4.796231 ATCACCGACGCCGAGCAC 62.796 66.667 0.00 0.00 38.22 4.40
487 504 2.485795 ATCTCTCTCTGTCCGCGCC 61.486 63.158 0.00 0.00 0.00 6.53
493 510 0.527385 GCGCACCATCTCTCTCTGTC 60.527 60.000 0.30 0.00 0.00 3.51
495 512 1.588403 CGCGCACCATCTCTCTCTG 60.588 63.158 8.75 0.00 0.00 3.35
496 513 2.804167 CGCGCACCATCTCTCTCT 59.196 61.111 8.75 0.00 0.00 3.10
497 514 2.959071 GCGCGCACCATCTCTCTC 60.959 66.667 29.10 0.00 0.00 3.20
498 515 4.862092 CGCGCGCACCATCTCTCT 62.862 66.667 32.61 0.00 0.00 3.10
499 516 3.751401 TACGCGCGCACCATCTCTC 62.751 63.158 32.58 0.00 0.00 3.20
582 599 1.421410 ATCAAATCGGTCGACTGCGC 61.421 55.000 19.89 0.00 37.46 6.09
598 616 1.039856 TGGAGCTAGTATGCGCATCA 58.960 50.000 29.11 13.28 38.13 3.07
602 620 2.229965 GCTTGGAGCTAGTATGCGC 58.770 57.895 0.00 0.00 38.45 6.09
635 653 0.647410 CGACGAAATGCAGCAGTAGG 59.353 55.000 0.00 0.00 0.00 3.18
683 709 2.357760 CACCAACCCCCGTACACG 60.358 66.667 0.00 0.00 39.44 4.49
684 710 1.004200 CTCACCAACCCCCGTACAC 60.004 63.158 0.00 0.00 0.00 2.90
685 711 2.218454 CCTCACCAACCCCCGTACA 61.218 63.158 0.00 0.00 0.00 2.90
687 713 2.608368 CCCTCACCAACCCCCGTA 60.608 66.667 0.00 0.00 0.00 4.02
763 794 1.482182 TCAATCGTGGGAGAGATGTGG 59.518 52.381 0.00 0.00 0.00 4.17
799 830 3.256631 GTGGGCTCATTAATTAGGGCATG 59.743 47.826 0.00 0.00 0.00 4.06
978 1536 0.608308 GGACCAAGGGTAAGGTGTGC 60.608 60.000 0.00 0.00 38.50 4.57
985 1543 7.256908 GGCTATTTATAGATGGACCAAGGGTAA 60.257 40.741 0.00 0.00 31.69 2.85
1065 1624 2.224209 CGGAGAAACAGTGGTACCAGTT 60.224 50.000 20.09 15.90 0.00 3.16
1097 1656 4.062293 GGTGTGTGTGTGTGTGTATGTAT 58.938 43.478 0.00 0.00 0.00 2.29
1101 1660 2.700722 TGGTGTGTGTGTGTGTGTAT 57.299 45.000 0.00 0.00 0.00 2.29
1103 1662 1.164411 CTTGGTGTGTGTGTGTGTGT 58.836 50.000 0.00 0.00 0.00 3.72
1104 1663 1.447945 TCTTGGTGTGTGTGTGTGTG 58.552 50.000 0.00 0.00 0.00 3.82
1105 1664 2.016318 CATCTTGGTGTGTGTGTGTGT 58.984 47.619 0.00 0.00 0.00 3.72
1106 1665 2.016318 ACATCTTGGTGTGTGTGTGTG 58.984 47.619 0.00 0.00 0.00 3.82
1107 1666 2.418368 ACATCTTGGTGTGTGTGTGT 57.582 45.000 0.00 0.00 0.00 3.72
1174 1742 3.322466 CACCGACCCCTTGAGCCT 61.322 66.667 0.00 0.00 0.00 4.58
1379 1947 2.969990 AGCTAGTCAGACACTGCATTG 58.030 47.619 2.66 1.95 36.43 2.82
1381 1949 2.301296 ACAAGCTAGTCAGACACTGCAT 59.699 45.455 2.66 0.00 36.43 3.96
1742 2649 2.286294 GCATCCACTGAACACATCGATC 59.714 50.000 0.00 0.00 0.00 3.69
2076 3123 2.288825 CGTAAGTTCCAAGGAGAGTGCA 60.289 50.000 0.00 0.00 0.00 4.57
2448 3553 7.954666 ATAAGTTGGTAGGTAGGTACGTTTA 57.045 36.000 0.00 0.00 0.00 2.01
2507 3721 9.601217 GTTTGATGATCCTATGTACTTGTAGTT 57.399 33.333 0.00 0.00 0.00 2.24
2508 3722 7.921214 CGTTTGATGATCCTATGTACTTGTAGT 59.079 37.037 0.00 0.00 0.00 2.73
2511 3725 6.640518 ACGTTTGATGATCCTATGTACTTGT 58.359 36.000 0.00 0.00 0.00 3.16
2512 3726 7.401860 CAACGTTTGATGATCCTATGTACTTG 58.598 38.462 0.00 0.00 0.00 3.16
2513 3727 6.538742 CCAACGTTTGATGATCCTATGTACTT 59.461 38.462 0.00 0.00 0.00 2.24
2514 3728 6.049149 CCAACGTTTGATGATCCTATGTACT 58.951 40.000 0.00 0.00 0.00 2.73
2674 3893 8.519526 GGCCGATGGATATATGAATTTGTTTAA 58.480 33.333 0.00 0.00 0.00 1.52
2713 4008 9.477484 ACCATTCGTTTAGTCTATGCTTAATAG 57.523 33.333 0.00 0.00 39.86 1.73
2815 4114 1.003355 CTCGGTGATGGTGCTGGTT 60.003 57.895 0.00 0.00 0.00 3.67
3505 4805 5.601729 TGCCCCTGCATTTCATTGATTTATA 59.398 36.000 0.00 0.00 44.23 0.98
3507 4807 3.773667 TGCCCCTGCATTTCATTGATTTA 59.226 39.130 0.00 0.00 44.23 1.40
3509 4809 2.189676 TGCCCCTGCATTTCATTGATT 58.810 42.857 0.00 0.00 44.23 2.57
3510 4810 1.868713 TGCCCCTGCATTTCATTGAT 58.131 45.000 0.00 0.00 44.23 2.57
3511 4811 3.377848 TGCCCCTGCATTTCATTGA 57.622 47.368 0.00 0.00 44.23 2.57
4349 5703 4.226427 AGCAAATGATCCTAGAAGCACA 57.774 40.909 0.00 0.00 0.00 4.57
4365 5719 6.537301 CCGGTGTACTAGATTATTCAAGCAAA 59.463 38.462 0.00 0.00 0.00 3.68
4438 6380 2.423538 GGAACATACATTGACCAGTGGC 59.576 50.000 9.78 2.56 0.00 5.01
4439 6381 3.684908 TGGAACATACATTGACCAGTGG 58.315 45.455 7.91 7.91 33.80 4.00
4455 6397 8.846943 ATTTGGAAGGAAAAATTACATGGAAC 57.153 30.769 0.00 0.00 0.00 3.62
4657 6603 2.888594 TCTAGGCACATTAGCGACAAC 58.111 47.619 0.00 0.00 34.64 3.32
4687 6633 6.754702 ATCATTGCATGCAGTTAGATATCC 57.245 37.500 21.50 0.00 0.00 2.59
4718 6664 1.275010 TCTCTCAATGCACCGCTTACA 59.725 47.619 0.00 0.00 0.00 2.41
4821 6767 4.584029 CGAAATACATGTCGTTCTGCTT 57.416 40.909 0.00 0.00 32.61 3.91
5057 7005 2.363680 TGATCACACATTGCCGGTTTTT 59.636 40.909 1.90 0.00 0.00 1.94
5087 7035 4.966965 TGACGGACTCAAGACTATTCTC 57.033 45.455 0.00 0.00 0.00 2.87
5089 7037 5.061920 AGTTGACGGACTCAAGACTATTC 57.938 43.478 0.00 0.00 39.69 1.75
5098 7046 3.812156 TTCAAAGAGTTGACGGACTCA 57.188 42.857 15.24 0.00 46.69 3.41
5105 7053 6.074142 GCAATGGTCATTTTCAAAGAGTTGAC 60.074 38.462 0.00 0.00 43.52 3.18
5111 7059 6.289834 ACAATGCAATGGTCATTTTCAAAGA 58.710 32.000 6.73 0.00 32.30 2.52
5112 7060 6.548441 ACAATGCAATGGTCATTTTCAAAG 57.452 33.333 6.73 0.00 32.30 2.77
5137 7085 3.244215 CCTGGACTCTTAACTGCTCAACA 60.244 47.826 0.00 0.00 0.00 3.33
5148 7096 3.335786 TGAGGGTCTTACCTGGACTCTTA 59.664 47.826 0.00 0.00 43.65 2.10
5156 7104 3.367498 CGAGAAGTTGAGGGTCTTACCTG 60.367 52.174 0.00 0.00 42.10 4.00
5170 7118 1.148157 CGCATGCGATCCGAGAAGTT 61.148 55.000 35.82 0.00 42.83 2.66
5182 7130 0.920664 TGATAAAGTCGTCGCATGCG 59.079 50.000 33.61 33.61 41.35 4.73
5185 7133 5.773575 ACAGATATGATAAAGTCGTCGCAT 58.226 37.500 0.00 0.00 0.00 4.73
5186 7134 5.183014 ACAGATATGATAAAGTCGTCGCA 57.817 39.130 0.00 0.00 0.00 5.10
5206 7161 2.545113 GGACTCTCAACTGCGTGTTACA 60.545 50.000 0.00 0.00 37.07 2.41
5209 7164 0.464036 TGGACTCTCAACTGCGTGTT 59.536 50.000 0.00 0.00 39.92 3.32
5230 7185 5.827267 ACTATAAAAGGAGGAGGACGACTAC 59.173 44.000 0.00 0.00 0.00 2.73
5236 7191 3.492829 CGCCACTATAAAAGGAGGAGGAC 60.493 52.174 0.00 0.00 0.00 3.85
5261 7216 5.247337 TGAAATTGTTAATTTGGGGAGGTCC 59.753 40.000 4.42 0.00 40.97 4.46
5263 7218 6.755542 TTGAAATTGTTAATTTGGGGAGGT 57.244 33.333 4.42 0.00 40.97 3.85
5290 7245 4.026475 CGTTTTCTTACAAATTTGCGGCAA 60.026 37.500 18.12 12.11 0.00 4.52
5317 7272 8.313292 TGAAATTGTTAATTTGGGGAGAATCAG 58.687 33.333 4.42 0.00 40.97 2.90
5325 7280 8.976471 GCAATTTTTGAAATTGTTAATTTGGGG 58.024 29.630 20.77 0.17 40.97 4.96
5326 7281 8.976471 GGCAATTTTTGAAATTGTTAATTTGGG 58.024 29.630 20.77 0.56 40.97 4.12
5327 7282 8.689069 CGGCAATTTTTGAAATTGTTAATTTGG 58.311 29.630 20.77 1.10 40.97 3.28
5328 7283 8.206600 GCGGCAATTTTTGAAATTGTTAATTTG 58.793 29.630 20.77 9.26 40.97 2.32
5329 7284 7.917505 TGCGGCAATTTTTGAAATTGTTAATTT 59.082 25.926 20.77 0.00 43.43 1.82
5330 7285 7.420800 TGCGGCAATTTTTGAAATTGTTAATT 58.579 26.923 20.77 1.36 39.25 1.40
5331 7286 6.963796 TGCGGCAATTTTTGAAATTGTTAAT 58.036 28.000 20.77 0.00 39.25 1.40
5332 7287 6.363577 TGCGGCAATTTTTGAAATTGTTAA 57.636 29.167 20.77 7.79 39.25 2.01
5333 7288 5.991328 TGCGGCAATTTTTGAAATTGTTA 57.009 30.435 20.77 8.04 39.25 2.41
5334 7289 4.889832 TGCGGCAATTTTTGAAATTGTT 57.110 31.818 20.77 0.00 39.25 2.83
5335 7290 4.889832 TTGCGGCAATTTTTGAAATTGT 57.110 31.818 20.77 0.00 39.25 2.71
5336 7291 6.750775 AATTTGCGGCAATTTTTGAAATTG 57.249 29.167 17.19 17.44 39.84 2.32
5337 7292 6.755607 ACAAATTTGCGGCAATTTTTGAAATT 59.244 26.923 34.16 20.94 34.23 1.82
5338 7293 6.271566 ACAAATTTGCGGCAATTTTTGAAAT 58.728 28.000 34.16 21.40 34.23 2.17
5339 7294 5.644644 ACAAATTTGCGGCAATTTTTGAAA 58.355 29.167 34.16 16.37 34.23 2.69
5340 7295 5.240713 ACAAATTTGCGGCAATTTTTGAA 57.759 30.435 34.16 16.94 34.23 2.69
5341 7296 4.889832 ACAAATTTGCGGCAATTTTTGA 57.110 31.818 34.16 17.50 34.23 2.69
5342 7297 6.425504 TCTTACAAATTTGCGGCAATTTTTG 58.574 32.000 30.05 30.05 35.21 2.44
5343 7298 6.610741 TCTTACAAATTTGCGGCAATTTTT 57.389 29.167 24.81 19.72 28.65 1.94
5344 7299 6.610741 TTCTTACAAATTTGCGGCAATTTT 57.389 29.167 22.78 22.78 30.40 1.82
5345 7300 6.610741 TTTCTTACAAATTTGCGGCAATTT 57.389 29.167 17.19 15.94 0.00 1.82
5346 7301 6.426327 GTTTTCTTACAAATTTGCGGCAATT 58.574 32.000 17.19 10.35 0.00 2.32
5347 7302 5.332959 CGTTTTCTTACAAATTTGCGGCAAT 60.333 36.000 17.19 3.49 0.00 3.56
5348 7303 4.026475 CGTTTTCTTACAAATTTGCGGCAA 60.026 37.500 18.12 12.11 0.00 4.52
5349 7304 3.487574 CGTTTTCTTACAAATTTGCGGCA 59.512 39.130 18.12 0.00 0.00 5.69
5350 7305 3.487942 ACGTTTTCTTACAAATTTGCGGC 59.512 39.130 18.12 0.00 0.00 6.53
5351 7306 5.331980 GGAACGTTTTCTTACAAATTTGCGG 60.332 40.000 18.12 8.44 31.71 5.69
5352 7307 5.457473 AGGAACGTTTTCTTACAAATTTGCG 59.543 36.000 18.12 12.54 31.71 4.85
5353 7308 6.474102 TCAGGAACGTTTTCTTACAAATTTGC 59.526 34.615 18.12 0.00 31.71 3.68
5354 7309 7.979115 TCAGGAACGTTTTCTTACAAATTTG 57.021 32.000 16.67 16.67 31.71 2.32
5355 7310 9.594478 AAATCAGGAACGTTTTCTTACAAATTT 57.406 25.926 0.46 2.76 31.71 1.82
5356 7311 9.594478 AAAATCAGGAACGTTTTCTTACAAATT 57.406 25.926 0.46 0.00 31.71 1.82
5357 7312 9.594478 AAAAATCAGGAACGTTTTCTTACAAAT 57.406 25.926 0.46 0.00 31.71 2.32
5358 7313 8.989653 AAAAATCAGGAACGTTTTCTTACAAA 57.010 26.923 0.46 0.00 31.71 2.83
5403 7358 6.146898 GTGTACATTGTCCGCTAACATTTTT 58.853 36.000 0.00 0.00 0.00 1.94
5404 7359 5.615984 CGTGTACATTGTCCGCTAACATTTT 60.616 40.000 0.00 0.00 0.00 1.82
5405 7360 4.142988 CGTGTACATTGTCCGCTAACATTT 60.143 41.667 0.00 0.00 0.00 2.32
5406 7361 3.369756 CGTGTACATTGTCCGCTAACATT 59.630 43.478 0.00 0.00 0.00 2.71
5407 7362 2.927477 CGTGTACATTGTCCGCTAACAT 59.073 45.455 0.00 0.00 0.00 2.71
5408 7363 2.030096 TCGTGTACATTGTCCGCTAACA 60.030 45.455 0.00 0.00 0.00 2.41
5409 7364 2.598589 TCGTGTACATTGTCCGCTAAC 58.401 47.619 0.00 0.00 0.00 2.34
5410 7365 3.300852 TTCGTGTACATTGTCCGCTAA 57.699 42.857 0.00 0.00 0.00 3.09
5411 7366 3.513680 ATTCGTGTACATTGTCCGCTA 57.486 42.857 0.00 0.00 0.00 4.26
5412 7367 2.380084 ATTCGTGTACATTGTCCGCT 57.620 45.000 0.00 0.00 0.00 5.52
5413 7368 2.475519 CCAATTCGTGTACATTGTCCGC 60.476 50.000 0.00 0.00 0.00 5.54
5414 7369 2.997303 TCCAATTCGTGTACATTGTCCG 59.003 45.455 0.00 0.00 0.00 4.79
5415 7370 5.151389 GTTTCCAATTCGTGTACATTGTCC 58.849 41.667 0.00 0.00 0.00 4.02
5416 7371 5.753744 TGTTTCCAATTCGTGTACATTGTC 58.246 37.500 0.00 0.00 0.00 3.18
5417 7372 5.759506 TGTTTCCAATTCGTGTACATTGT 57.240 34.783 0.00 0.00 0.00 2.71
5418 7373 6.148948 ACATGTTTCCAATTCGTGTACATTG 58.851 36.000 0.00 0.00 30.89 2.82
5419 7374 6.325919 ACATGTTTCCAATTCGTGTACATT 57.674 33.333 0.00 0.00 30.89 2.71
5420 7375 5.957842 ACATGTTTCCAATTCGTGTACAT 57.042 34.783 0.00 0.00 30.89 2.29
5421 7376 5.559225 CGAACATGTTTCCAATTCGTGTACA 60.559 40.000 13.36 0.00 37.95 2.90
5422 7377 4.843984 CGAACATGTTTCCAATTCGTGTAC 59.156 41.667 13.36 0.00 37.95 2.90
5423 7378 4.512198 ACGAACATGTTTCCAATTCGTGTA 59.488 37.500 16.30 0.00 46.27 2.90
5424 7379 3.314080 ACGAACATGTTTCCAATTCGTGT 59.686 39.130 16.30 0.00 46.27 4.49
5425 7380 3.884169 ACGAACATGTTTCCAATTCGTG 58.116 40.909 16.30 0.22 46.27 4.35
5427 7382 5.922546 TCTTACGAACATGTTTCCAATTCG 58.077 37.500 13.36 12.13 43.48 3.34
5428 7383 7.526608 TCATCTTACGAACATGTTTCCAATTC 58.473 34.615 13.36 0.00 0.00 2.17
5429 7384 7.447374 TCATCTTACGAACATGTTTCCAATT 57.553 32.000 13.36 0.00 0.00 2.32
5430 7385 7.447374 TTCATCTTACGAACATGTTTCCAAT 57.553 32.000 13.36 0.00 0.00 3.16
5431 7386 6.869315 TTCATCTTACGAACATGTTTCCAA 57.131 33.333 13.36 6.09 0.00 3.53
5432 7387 6.261158 TGTTTCATCTTACGAACATGTTTCCA 59.739 34.615 13.36 0.00 0.00 3.53
5433 7388 6.664515 TGTTTCATCTTACGAACATGTTTCC 58.335 36.000 13.36 0.00 0.00 3.13
5434 7389 7.572759 TCTGTTTCATCTTACGAACATGTTTC 58.427 34.615 13.36 5.34 32.23 2.78
5435 7390 7.490962 TCTGTTTCATCTTACGAACATGTTT 57.509 32.000 13.36 0.00 32.23 2.83
5436 7391 7.490962 TTCTGTTTCATCTTACGAACATGTT 57.509 32.000 11.78 11.78 32.23 2.71
5437 7392 7.490962 TTTCTGTTTCATCTTACGAACATGT 57.509 32.000 0.00 0.00 32.23 3.21
5438 7393 7.535258 CCTTTTCTGTTTCATCTTACGAACATG 59.465 37.037 0.00 0.00 32.23 3.21
5439 7394 7.308589 CCCTTTTCTGTTTCATCTTACGAACAT 60.309 37.037 0.00 0.00 32.23 2.71
5440 7395 6.017440 CCCTTTTCTGTTTCATCTTACGAACA 60.017 38.462 0.00 0.00 0.00 3.18
5441 7396 6.204108 TCCCTTTTCTGTTTCATCTTACGAAC 59.796 38.462 0.00 0.00 0.00 3.95
5442 7397 6.292923 TCCCTTTTCTGTTTCATCTTACGAA 58.707 36.000 0.00 0.00 0.00 3.85
5443 7398 5.860611 TCCCTTTTCTGTTTCATCTTACGA 58.139 37.500 0.00 0.00 0.00 3.43
5444 7399 6.426937 TCTTCCCTTTTCTGTTTCATCTTACG 59.573 38.462 0.00 0.00 0.00 3.18
5445 7400 7.094592 CCTCTTCCCTTTTCTGTTTCATCTTAC 60.095 40.741 0.00 0.00 0.00 2.34
5446 7401 6.942576 CCTCTTCCCTTTTCTGTTTCATCTTA 59.057 38.462 0.00 0.00 0.00 2.10
5447 7402 5.772169 CCTCTTCCCTTTTCTGTTTCATCTT 59.228 40.000 0.00 0.00 0.00 2.40
5448 7403 5.073691 TCCTCTTCCCTTTTCTGTTTCATCT 59.926 40.000 0.00 0.00 0.00 2.90
5449 7404 5.316987 TCCTCTTCCCTTTTCTGTTTCATC 58.683 41.667 0.00 0.00 0.00 2.92
5450 7405 5.324832 TCCTCTTCCCTTTTCTGTTTCAT 57.675 39.130 0.00 0.00 0.00 2.57
5451 7406 4.788925 TCCTCTTCCCTTTTCTGTTTCA 57.211 40.909 0.00 0.00 0.00 2.69
5452 7407 6.465439 TTTTCCTCTTCCCTTTTCTGTTTC 57.535 37.500 0.00 0.00 0.00 2.78
5453 7408 6.867519 TTTTTCCTCTTCCCTTTTCTGTTT 57.132 33.333 0.00 0.00 0.00 2.83
5454 7409 8.547481 TTATTTTTCCTCTTCCCTTTTCTGTT 57.453 30.769 0.00 0.00 0.00 3.16
5455 7410 8.547481 TTTATTTTTCCTCTTCCCTTTTCTGT 57.453 30.769 0.00 0.00 0.00 3.41



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

AutoCloner maintained by Alex Coulton.