Multiple sequence alignment - TraesCS7A01G450400

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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 TraesCS7A01G450400 chr7A 100.000 2378 0 0 1 2378 644105817 644103440 0.000000e+00 4392
1 TraesCS7A01G450400 chr7A 83.234 167 18 7 163 323 644105543 644105381 6.850000e-31 145
2 TraesCS7A01G450400 chr7A 83.234 167 18 7 275 437 644105655 644105495 6.850000e-31 145
3 TraesCS7A01G450400 chr7D 80.734 1526 159 78 280 1745 559394938 559393488 0.000000e+00 1064
4 TraesCS7A01G450400 chr7D 83.150 546 46 17 1855 2364 559393329 559392794 7.750000e-125 457
5 TraesCS7A01G450400 chr7B 84.729 812 74 33 815 1614 607530161 607529388 0.000000e+00 767
6 TraesCS7A01G450400 chr7B 80.669 807 95 32 1 769 607531060 607530277 9.540000e-159 569
7 TraesCS7A01G450400 chr7B 88.382 241 24 4 1 238 607532550 607532311 1.080000e-73 287
8 TraesCS7A01G450400 chr7B 87.554 233 16 4 2147 2378 607528865 607528645 8.430000e-65 257


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 TraesCS7A01G450400 chr7A 644103440 644105817 2377 True 1560.666667 4392 88.822667 1 2378 3 chr7A.!!$R1 2377
1 TraesCS7A01G450400 chr7D 559392794 559394938 2144 True 760.500000 1064 81.942000 280 2364 2 chr7D.!!$R1 2084
2 TraesCS7A01G450400 chr7B 607528645 607532550 3905 True 470.000000 767 85.333500 1 2378 4 chr7B.!!$R1 2377

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
938 2554 0.036577 CAGCGATCCATCCATCCTCC 60.037 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 3481 0.036732 AGAGAACGGGCATTTGCTCA 59.963 50.0 2.94 0.0 43.04 4.26 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
37 1527 8.614469 AAAAATGGTGAGACAAAACTTTGAAA 57.386 26.923 9.12 0.00 40.55 2.69
40 1530 8.424274 AATGGTGAGACAAAACTTTGAAATTC 57.576 30.769 9.12 0.00 40.55 2.17
77 1567 6.781014 TGGGTAGGTTTAGATGATACCACTAG 59.219 42.308 0.00 0.00 38.10 2.57
116 1607 9.474313 AAGATTAAATGCTACCAAAATCCTACA 57.526 29.630 0.00 0.00 0.00 2.74
125 1616 7.552687 TGCTACCAAAATCCTACAAATCTAGTG 59.447 37.037 0.00 0.00 0.00 2.74
126 1617 7.553044 GCTACCAAAATCCTACAAATCTAGTGT 59.447 37.037 0.00 0.00 0.00 3.55
129 1620 6.456988 CCAAAATCCTACAAATCTAGTGTCGC 60.457 42.308 0.00 0.00 0.00 5.19
178 1669 8.368668 GGTCACATAAACATATACTTAGAGGCT 58.631 37.037 0.00 0.00 0.00 4.58
187 1678 9.530633 AACATATACTTAGAGGCTAAGAAAACG 57.469 33.333 18.20 8.05 0.00 3.60
196 1688 5.875359 AGAGGCTAAGAAAACGTAGAAATGG 59.125 40.000 0.00 0.00 0.00 3.16
209 1701 3.967332 AGAAATGGGTGAAATTGGCTG 57.033 42.857 0.00 0.00 0.00 4.85
212 1704 0.544833 ATGGGTGAAATTGGCTGGCA 60.545 50.000 0.00 0.00 0.00 4.92
225 1717 2.103094 TGGCTGGCACTCACATATACTC 59.897 50.000 0.00 0.00 0.00 2.59
234 1726 8.700973 TGGCACTCACATATACTCAATACTTAA 58.299 33.333 0.00 0.00 0.00 1.85
239 1731 8.812147 TCACATATACTCAATACTTAAAGCCG 57.188 34.615 0.00 0.00 0.00 5.52
241 1733 8.916654 CACATATACTCAATACTTAAAGCCGAG 58.083 37.037 0.00 0.00 0.00 4.63
242 1734 8.639761 ACATATACTCAATACTTAAAGCCGAGT 58.360 33.333 0.00 0.00 36.33 4.18
245 1737 8.868635 ATACTCAATACTTAAAGCCGAGTTAC 57.131 34.615 0.00 0.00 34.33 2.50
246 1738 5.803967 ACTCAATACTTAAAGCCGAGTTACG 59.196 40.000 0.00 0.00 42.18 3.18
247 1739 5.713025 TCAATACTTAAAGCCGAGTTACGT 58.287 37.500 0.00 0.00 40.78 3.57
248 1740 6.851609 TCAATACTTAAAGCCGAGTTACGTA 58.148 36.000 0.00 0.00 40.78 3.57
250 1742 7.485913 TCAATACTTAAAGCCGAGTTACGTAAG 59.514 37.037 8.60 0.00 40.78 2.34
252 1744 4.218417 ACTTAAAGCCGAGTTACGTAAGGA 59.782 41.667 8.60 0.00 46.39 3.36
254 1746 3.881937 AAGCCGAGTTACGTAAGGAAT 57.118 42.857 8.60 0.00 45.79 3.01
255 1747 3.881937 AGCCGAGTTACGTAAGGAATT 57.118 42.857 8.60 0.00 45.79 2.17
256 1748 4.198028 AGCCGAGTTACGTAAGGAATTT 57.802 40.909 8.60 0.00 45.79 1.82
258 1750 3.681417 GCCGAGTTACGTAAGGAATTTGT 59.319 43.478 8.60 0.00 45.79 2.83
259 1751 4.201656 GCCGAGTTACGTAAGGAATTTGTC 60.202 45.833 8.60 0.00 45.79 3.18
261 1753 5.636543 CCGAGTTACGTAAGGAATTTGTCTT 59.363 40.000 8.60 0.00 45.79 3.01
262 1754 6.808212 CCGAGTTACGTAAGGAATTTGTCTTA 59.192 38.462 8.60 0.00 45.79 2.10
263 1755 7.490402 CCGAGTTACGTAAGGAATTTGTCTTAT 59.510 37.037 8.60 0.00 45.79 1.73
264 1756 8.529911 CGAGTTACGTAAGGAATTTGTCTTATC 58.470 37.037 8.60 0.00 45.79 1.75
265 1757 9.362539 GAGTTACGTAAGGAATTTGTCTTATCA 57.637 33.333 8.60 0.00 45.79 2.15
267 1759 9.750882 GTTACGTAAGGAATTTGTCTTATCAAC 57.249 33.333 8.60 0.00 45.79 3.18
270 1762 7.610305 ACGTAAGGAATTTGTCTTATCAACCAT 59.390 33.333 0.00 0.00 46.39 3.55
271 1763 8.458843 CGTAAGGAATTTGTCTTATCAACCATT 58.541 33.333 0.00 0.00 0.00 3.16
272 1764 9.573133 GTAAGGAATTTGTCTTATCAACCATTG 57.427 33.333 0.00 0.00 0.00 2.82
273 1765 7.781324 AGGAATTTGTCTTATCAACCATTGT 57.219 32.000 0.00 0.00 0.00 2.71
274 1766 8.877864 AGGAATTTGTCTTATCAACCATTGTA 57.122 30.769 0.00 0.00 0.00 2.41
276 1768 8.519526 GGAATTTGTCTTATCAACCATTGTACA 58.480 33.333 0.00 0.00 0.00 2.90
328 1824 0.746659 AGTGAAGTTTGGCTTGCACC 59.253 50.000 0.00 0.00 37.59 5.01
353 1868 4.272504 GCGCACATATACTTAGAAGCCAAA 59.727 41.667 0.30 0.00 0.00 3.28
359 1874 9.042008 CACATATACTTAGAAGCCAAATTACGT 57.958 33.333 0.00 0.00 0.00 3.57
363 1878 6.980051 ACTTAGAAGCCAAATTACGTAAGG 57.020 37.500 14.25 10.58 46.39 2.69
365 1880 7.336396 ACTTAGAAGCCAAATTACGTAAGGAT 58.664 34.615 14.25 5.61 46.39 3.24
368 1883 9.669887 TTAGAAGCCAAATTACGTAAGGATAAA 57.330 29.630 14.25 2.36 46.39 1.40
369 1884 8.747538 AGAAGCCAAATTACGTAAGGATAAAT 57.252 30.769 14.25 0.00 46.39 1.40
370 1885 9.185680 AGAAGCCAAATTACGTAAGGATAAATT 57.814 29.630 14.25 0.00 46.39 1.82
383 1898 9.931210 CGTAAGGATAAATTTGTCTTATCAACC 57.069 33.333 13.76 0.00 37.46 3.77
417 1932 6.681729 TTCTTAGAGGCTAAGAAAACTCCA 57.318 37.500 21.09 3.70 39.68 3.86
421 1936 5.568620 AGAGGCTAAGAAAACTCCAGAAA 57.431 39.130 0.00 0.00 0.00 2.52
423 1938 7.259088 AGAGGCTAAGAAAACTCCAGAAATA 57.741 36.000 0.00 0.00 0.00 1.40
437 1952 6.071728 ACTCCAGAAATAAGTGAAATTGGCTG 60.072 38.462 0.00 0.00 0.00 4.85
438 1953 5.774690 TCCAGAAATAAGTGAAATTGGCTGT 59.225 36.000 0.00 0.00 0.00 4.40
439 1954 5.865552 CCAGAAATAAGTGAAATTGGCTGTG 59.134 40.000 0.00 0.00 0.00 3.66
440 1955 5.865552 CAGAAATAAGTGAAATTGGCTGTGG 59.134 40.000 0.00 0.00 0.00 4.17
443 1969 0.542702 AGTGAAATTGGCTGTGGGGG 60.543 55.000 0.00 0.00 0.00 5.40
445 1971 0.541764 TGAAATTGGCTGTGGGGGTC 60.542 55.000 0.00 0.00 0.00 4.46
448 1974 2.484287 AATTGGCTGTGGGGGTCTCG 62.484 60.000 0.00 0.00 0.00 4.04
457 1983 2.647158 GGGGGTCTCGACGCTCTTT 61.647 63.158 12.85 0.00 41.06 2.52
458 1984 1.153804 GGGGTCTCGACGCTCTTTC 60.154 63.158 12.85 0.00 42.97 2.62
459 1985 1.596895 GGGGTCTCGACGCTCTTTCT 61.597 60.000 12.85 0.00 42.97 2.52
460 1986 0.244178 GGGTCTCGACGCTCTTTCTT 59.756 55.000 6.84 0.00 40.60 2.52
461 1987 1.471684 GGGTCTCGACGCTCTTTCTTA 59.528 52.381 6.84 0.00 40.60 2.10
462 1988 2.094854 GGGTCTCGACGCTCTTTCTTAA 60.095 50.000 6.84 0.00 40.60 1.85
463 1989 3.572584 GGTCTCGACGCTCTTTCTTAAA 58.427 45.455 0.00 0.00 0.00 1.52
487 2013 1.971149 AACCCAGTCATCCATCCTCA 58.029 50.000 0.00 0.00 0.00 3.86
513 2040 2.761559 CACACAACGAGACACCCATAA 58.238 47.619 0.00 0.00 0.00 1.90
514 2041 3.135225 CACACAACGAGACACCCATAAA 58.865 45.455 0.00 0.00 0.00 1.40
532 2059 1.458746 AACTTACGCGCAAACAAACG 58.541 45.000 5.73 0.00 0.00 3.60
540 2067 1.732528 CGCAAACAAACGAACGCTTA 58.267 45.000 0.00 0.00 0.00 3.09
631 2162 3.391382 AACCCGGGAGAGAAGCCG 61.391 66.667 32.02 0.00 0.00 5.52
681 2226 4.357279 GGCACCCAGGAAGCTGCT 62.357 66.667 0.00 0.00 0.00 4.24
682 2227 3.060615 GCACCCAGGAAGCTGCTG 61.061 66.667 1.35 0.00 35.43 4.41
683 2228 3.060615 CACCCAGGAAGCTGCTGC 61.061 66.667 1.35 7.62 34.22 5.25
769 2314 2.285144 TTCCTTCCCCGTCTCCCC 60.285 66.667 0.00 0.00 0.00 4.81
780 2363 3.399181 TCTCCCCCACACATCGCC 61.399 66.667 0.00 0.00 0.00 5.54
879 2495 3.330998 CCTCCCCACTATTTATTCCCTCC 59.669 52.174 0.00 0.00 0.00 4.30
880 2496 3.330998 CTCCCCACTATTTATTCCCTCCC 59.669 52.174 0.00 0.00 0.00 4.30
892 2508 4.354943 CCTCCCCTCCCCCACAGT 62.355 72.222 0.00 0.00 0.00 3.55
893 2509 2.689034 CTCCCCTCCCCCACAGTC 60.689 72.222 0.00 0.00 0.00 3.51
894 2510 3.208592 TCCCCTCCCCCACAGTCT 61.209 66.667 0.00 0.00 0.00 3.24
895 2511 2.204151 CCCCTCCCCCACAGTCTT 60.204 66.667 0.00 0.00 0.00 3.01
909 2525 2.439507 ACAGTCTTCTCCACAACCACAT 59.560 45.455 0.00 0.00 0.00 3.21
916 2532 0.178975 TCCACAACCACATCCCAACC 60.179 55.000 0.00 0.00 0.00 3.77
922 2538 2.345760 CCACATCCCAACCAGCAGC 61.346 63.158 0.00 0.00 0.00 5.25
923 2539 2.360350 ACATCCCAACCAGCAGCG 60.360 61.111 0.00 0.00 0.00 5.18
924 2540 2.046023 CATCCCAACCAGCAGCGA 60.046 61.111 0.00 0.00 0.00 4.93
925 2541 1.452651 CATCCCAACCAGCAGCGAT 60.453 57.895 0.00 0.00 0.00 4.58
926 2542 1.153086 ATCCCAACCAGCAGCGATC 60.153 57.895 0.00 0.00 0.00 3.69
927 2543 2.615227 ATCCCAACCAGCAGCGATCC 62.615 60.000 0.00 0.00 0.00 3.36
928 2544 2.046023 CCAACCAGCAGCGATCCA 60.046 61.111 0.00 0.00 0.00 3.41
929 2545 1.452651 CCAACCAGCAGCGATCCAT 60.453 57.895 0.00 0.00 0.00 3.41
930 2546 1.442526 CCAACCAGCAGCGATCCATC 61.443 60.000 0.00 0.00 0.00 3.51
931 2547 1.153086 AACCAGCAGCGATCCATCC 60.153 57.895 0.00 0.00 0.00 3.51
932 2548 1.913951 AACCAGCAGCGATCCATCCA 61.914 55.000 0.00 0.00 0.00 3.41
933 2549 1.072678 CCAGCAGCGATCCATCCAT 59.927 57.895 0.00 0.00 0.00 3.41
934 2550 0.954449 CCAGCAGCGATCCATCCATC 60.954 60.000 0.00 0.00 0.00 3.51
935 2551 0.954449 CAGCAGCGATCCATCCATCC 60.954 60.000 0.00 0.00 0.00 3.51
936 2552 1.126329 AGCAGCGATCCATCCATCCT 61.126 55.000 0.00 0.00 0.00 3.24
937 2553 0.673022 GCAGCGATCCATCCATCCTC 60.673 60.000 0.00 0.00 0.00 3.71
938 2554 0.036577 CAGCGATCCATCCATCCTCC 60.037 60.000 0.00 0.00 0.00 4.30
939 2555 0.472543 AGCGATCCATCCATCCTCCA 60.473 55.000 0.00 0.00 0.00 3.86
940 2556 0.321122 GCGATCCATCCATCCTCCAC 60.321 60.000 0.00 0.00 0.00 4.02
941 2557 1.051008 CGATCCATCCATCCTCCACA 58.949 55.000 0.00 0.00 0.00 4.17
942 2558 1.417517 CGATCCATCCATCCTCCACAA 59.582 52.381 0.00 0.00 0.00 3.33
943 2559 2.039480 CGATCCATCCATCCTCCACAAT 59.961 50.000 0.00 0.00 0.00 2.71
944 2560 3.683802 GATCCATCCATCCTCCACAATC 58.316 50.000 0.00 0.00 0.00 2.67
945 2561 2.490961 TCCATCCATCCTCCACAATCA 58.509 47.619 0.00 0.00 0.00 2.57
946 2562 2.440627 TCCATCCATCCTCCACAATCAG 59.559 50.000 0.00 0.00 0.00 2.90
947 2563 2.440627 CCATCCATCCTCCACAATCAGA 59.559 50.000 0.00 0.00 0.00 3.27
948 2564 3.496337 CCATCCATCCTCCACAATCAGAG 60.496 52.174 0.00 0.00 0.00 3.35
949 2565 1.487976 TCCATCCTCCACAATCAGAGC 59.512 52.381 0.00 0.00 0.00 4.09
950 2566 1.211212 CCATCCTCCACAATCAGAGCA 59.789 52.381 0.00 0.00 0.00 4.26
954 2570 0.725686 CTCCACAATCAGAGCAAGCG 59.274 55.000 0.00 0.00 0.00 4.68
958 2574 1.347564 CAATCAGAGCAAGCGAGCG 59.652 57.895 0.00 0.00 40.15 5.03
960 2576 1.080995 AATCAGAGCAAGCGAGCGAC 61.081 55.000 0.00 0.00 40.15 5.19
978 2594 1.197721 GACCAAGAAACCATCACAGCG 59.802 52.381 0.00 0.00 0.00 5.18
979 2595 1.202758 ACCAAGAAACCATCACAGCGA 60.203 47.619 0.00 0.00 0.00 4.93
983 2599 1.003580 AGAAACCATCACAGCGACCAT 59.996 47.619 0.00 0.00 0.00 3.55
984 2600 1.398390 GAAACCATCACAGCGACCATC 59.602 52.381 0.00 0.00 0.00 3.51
985 2601 0.324614 AACCATCACAGCGACCATCA 59.675 50.000 0.00 0.00 0.00 3.07
986 2602 0.543277 ACCATCACAGCGACCATCAT 59.457 50.000 0.00 0.00 0.00 2.45
987 2603 1.224075 CCATCACAGCGACCATCATC 58.776 55.000 0.00 0.00 0.00 2.92
988 2604 1.202615 CCATCACAGCGACCATCATCT 60.203 52.381 0.00 0.00 0.00 2.90
989 2605 2.558378 CATCACAGCGACCATCATCTT 58.442 47.619 0.00 0.00 0.00 2.40
990 2606 2.299993 TCACAGCGACCATCATCTTC 57.700 50.000 0.00 0.00 0.00 2.87
991 2607 1.827344 TCACAGCGACCATCATCTTCT 59.173 47.619 0.00 0.00 0.00 2.85
993 2609 2.106566 ACAGCGACCATCATCTTCTCT 58.893 47.619 0.00 0.00 0.00 3.10
995 2611 1.202510 AGCGACCATCATCTTCTCTGC 60.203 52.381 0.00 0.00 0.00 4.26
1025 2652 4.353437 GCACCAGCAGCAGCAACC 62.353 66.667 3.17 0.00 45.49 3.77
1380 3034 1.142748 CCTCTTCACCAGCTAGGCG 59.857 63.158 2.50 0.00 43.14 5.52
1382 3036 1.304962 TCTTCACCAGCTAGGCGGA 60.305 57.895 0.00 0.00 43.14 5.54
1399 3053 0.596083 GGAGCATCTGGTGTCGATCG 60.596 60.000 9.36 9.36 33.73 3.69
1424 3079 8.704234 CGGATAGGAAATTAATCTTCTTCTTCG 58.296 37.037 0.00 0.00 0.00 3.79
1482 3137 7.742556 AGAGTCAGGATTCAAGAAAAGAAAG 57.257 36.000 0.00 0.00 0.00 2.62
1507 3162 4.379813 GCACTGTCGATTGGTTGAATGATT 60.380 41.667 0.00 0.00 0.00 2.57
1510 3165 4.968626 TGTCGATTGGTTGAATGATTTCG 58.031 39.130 0.00 0.00 34.39 3.46
1517 3172 5.045668 TGGTTGAATGATTTCGATGTGTG 57.954 39.130 0.00 0.00 34.39 3.82
1520 3175 4.604843 TGAATGATTTCGATGTGTGCTC 57.395 40.909 0.00 0.00 34.39 4.26
1521 3176 4.256110 TGAATGATTTCGATGTGTGCTCT 58.744 39.130 0.00 0.00 34.39 4.09
1523 3178 2.621338 TGATTTCGATGTGTGCTCTCC 58.379 47.619 0.00 0.00 0.00 3.71
1524 3179 1.936547 GATTTCGATGTGTGCTCTCCC 59.063 52.381 0.00 0.00 0.00 4.30
1525 3180 0.389817 TTTCGATGTGTGCTCTCCCG 60.390 55.000 0.00 0.00 0.00 5.14
1527 3182 2.581354 GATGTGTGCTCTCCCGCT 59.419 61.111 0.00 0.00 0.00 5.52
1529 3184 1.954362 GATGTGTGCTCTCCCGCTCT 61.954 60.000 0.00 0.00 0.00 4.09
1531 3186 2.036414 TGTGCTCTCCCGCTCTCT 59.964 61.111 0.00 0.00 0.00 3.10
1532 3187 2.346541 TGTGCTCTCCCGCTCTCTG 61.347 63.158 0.00 0.00 0.00 3.35
1533 3188 2.049185 GTGCTCTCCCGCTCTCTGA 61.049 63.158 0.00 0.00 0.00 3.27
1534 3189 1.076412 TGCTCTCCCGCTCTCTGAT 60.076 57.895 0.00 0.00 0.00 2.90
1536 3191 1.391157 GCTCTCCCGCTCTCTGATGT 61.391 60.000 0.00 0.00 0.00 3.06
1537 3192 1.110442 CTCTCCCGCTCTCTGATGTT 58.890 55.000 0.00 0.00 0.00 2.71
1540 3195 0.537188 TCCCGCTCTCTGATGTTTCC 59.463 55.000 0.00 0.00 0.00 3.13
1542 3197 0.250234 CCGCTCTCTGATGTTTCCCA 59.750 55.000 0.00 0.00 0.00 4.37
1543 3198 1.134280 CCGCTCTCTGATGTTTCCCAT 60.134 52.381 0.00 0.00 36.13 4.00
1544 3199 1.938577 CGCTCTCTGATGTTTCCCATG 59.061 52.381 0.00 0.00 32.56 3.66
1546 3201 2.928334 CTCTCTGATGTTTCCCATGGG 58.072 52.381 26.30 26.30 32.56 4.00
1588 3243 8.359642 ACATAAGCTTCTAAATTTTCAGCACAA 58.640 29.630 0.00 4.24 32.58 3.33
1589 3244 8.642020 CATAAGCTTCTAAATTTTCAGCACAAC 58.358 33.333 0.00 0.00 32.58 3.32
1590 3245 6.396829 AGCTTCTAAATTTTCAGCACAACT 57.603 33.333 14.77 0.00 32.58 3.16
1591 3246 6.442112 AGCTTCTAAATTTTCAGCACAACTC 58.558 36.000 14.77 0.00 32.58 3.01
1602 3257 1.081242 CACAACTCGCCACATTGCC 60.081 57.895 0.00 0.00 0.00 4.52
1611 3266 0.895100 GCCACATTGCCCTGTTCTCA 60.895 55.000 0.00 0.00 0.00 3.27
1620 3275 3.782244 CTGTTCTCAGCCGCGCAC 61.782 66.667 8.75 0.00 34.79 5.34
1630 3285 3.869272 CCGCGCACCAGCAGAATC 61.869 66.667 8.75 0.00 42.27 2.52
1632 3287 1.519234 CGCGCACCAGCAGAATCTA 60.519 57.895 8.75 0.00 42.27 1.98
1633 3288 1.083806 CGCGCACCAGCAGAATCTAA 61.084 55.000 8.75 0.00 42.27 2.10
1634 3289 0.375106 GCGCACCAGCAGAATCTAAC 59.625 55.000 0.30 0.00 42.27 2.34
1635 3290 2.009042 GCGCACCAGCAGAATCTAACT 61.009 52.381 0.30 0.00 42.27 2.24
1639 3319 2.860735 CACCAGCAGAATCTAACTACGC 59.139 50.000 0.00 0.00 0.00 4.42
1652 3332 5.566623 TCTAACTACGCTATGAACGTTGAG 58.433 41.667 5.00 0.85 41.93 3.02
1656 3336 0.025513 CGCTATGAACGTTGAGCAGC 59.974 55.000 20.33 16.53 34.49 5.25
1680 3360 2.583520 CAGAGAGCCAGAGGGTGC 59.416 66.667 0.00 0.00 36.17 5.01
1684 3364 4.459089 GAGCCAGAGGGTGCGTCC 62.459 72.222 0.00 0.00 36.17 4.79
1704 3384 4.147449 CACCCTGATCGCTCCGCA 62.147 66.667 0.00 0.00 0.00 5.69
1706 3386 3.842923 CCCTGATCGCTCCGCACT 61.843 66.667 0.00 0.00 0.00 4.40
1717 3397 1.900351 TCCGCACTGGAATCTCTGG 59.100 57.895 0.00 0.00 46.38 3.86
1736 3416 5.052481 TCTGGATTAATCGACATGAGCTTG 58.948 41.667 9.32 0.00 0.00 4.01
1745 3425 3.805422 TCGACATGAGCTTGTACGTTTTT 59.195 39.130 0.00 0.00 0.00 1.94
1746 3426 4.084745 TCGACATGAGCTTGTACGTTTTTC 60.085 41.667 0.00 0.00 0.00 2.29
1748 3428 5.614668 CGACATGAGCTTGTACGTTTTTCAT 60.615 40.000 0.00 0.00 0.00 2.57
1749 3429 6.072112 ACATGAGCTTGTACGTTTTTCATT 57.928 33.333 0.00 0.00 0.00 2.57
1750 3430 6.503524 ACATGAGCTTGTACGTTTTTCATTT 58.496 32.000 0.00 0.00 0.00 2.32
1751 3431 6.978080 ACATGAGCTTGTACGTTTTTCATTTT 59.022 30.769 0.00 0.00 0.00 1.82
1752 3432 7.491048 ACATGAGCTTGTACGTTTTTCATTTTT 59.509 29.630 0.00 0.00 0.00 1.94
1753 3433 7.444558 TGAGCTTGTACGTTTTTCATTTTTC 57.555 32.000 0.00 0.00 0.00 2.29
1754 3434 7.030165 TGAGCTTGTACGTTTTTCATTTTTCA 58.970 30.769 0.00 0.00 0.00 2.69
1755 3435 7.542477 TGAGCTTGTACGTTTTTCATTTTTCAA 59.458 29.630 0.00 0.00 0.00 2.69
1756 3436 7.671827 AGCTTGTACGTTTTTCATTTTTCAAC 58.328 30.769 0.00 0.00 0.00 3.18
1757 3437 7.329717 AGCTTGTACGTTTTTCATTTTTCAACA 59.670 29.630 0.00 0.00 0.00 3.33
1758 3438 7.421331 GCTTGTACGTTTTTCATTTTTCAACAC 59.579 33.333 0.00 0.00 0.00 3.32
1759 3439 7.279470 TGTACGTTTTTCATTTTTCAACACC 57.721 32.000 0.00 0.00 0.00 4.16
1760 3440 5.443142 ACGTTTTTCATTTTTCAACACCG 57.557 34.783 0.00 0.00 0.00 4.94
1761 3441 4.201637 ACGTTTTTCATTTTTCAACACCGC 60.202 37.500 0.00 0.00 0.00 5.68
1762 3442 4.259889 GTTTTTCATTTTTCAACACCGCG 58.740 39.130 0.00 0.00 0.00 6.46
1763 3443 2.853731 TTCATTTTTCAACACCGCGT 57.146 40.000 4.92 0.00 0.00 6.01
1764 3444 2.112475 TCATTTTTCAACACCGCGTG 57.888 45.000 4.92 6.23 39.75 5.34
1765 3445 0.502275 CATTTTTCAACACCGCGTGC 59.498 50.000 4.92 0.00 36.98 5.34
1766 3446 0.932585 ATTTTTCAACACCGCGTGCG 60.933 50.000 4.92 7.38 36.98 5.34
1767 3447 1.978712 TTTTTCAACACCGCGTGCGA 61.979 50.000 16.91 1.60 42.83 5.10
1768 3448 1.777030 TTTTCAACACCGCGTGCGAT 61.777 50.000 16.91 0.00 42.83 4.58
1769 3449 2.436997 TTTCAACACCGCGTGCGATG 62.437 55.000 16.91 12.12 42.83 3.84
1778 3458 2.021793 CGTGCGATGCGACATTGG 59.978 61.111 8.52 0.55 0.00 3.16
1789 3469 1.372087 CGACATTGGCCCTTCTCTGC 61.372 60.000 0.00 0.00 0.00 4.26
1799 3481 3.153130 GCCCTTCTCTGCTTCTTTCTTT 58.847 45.455 0.00 0.00 0.00 2.52
1800 3482 3.057666 GCCCTTCTCTGCTTCTTTCTTTG 60.058 47.826 0.00 0.00 0.00 2.77
1809 3491 4.053295 TGCTTCTTTCTTTGAGCAAATGC 58.947 39.130 0.00 0.00 42.49 3.56
1812 3494 2.030007 TCTTTCTTTGAGCAAATGCCCG 60.030 45.455 0.94 0.00 43.38 6.13
1824 3506 0.460284 AATGCCCGTTCTCTGCTACG 60.460 55.000 0.00 0.00 37.50 3.51
1827 3509 1.139095 CCCGTTCTCTGCTACGACC 59.861 63.158 0.00 0.00 40.03 4.79
1828 3510 1.313812 CCCGTTCTCTGCTACGACCT 61.314 60.000 0.00 0.00 40.03 3.85
1831 3513 1.736126 CGTTCTCTGCTACGACCTACA 59.264 52.381 0.00 0.00 40.03 2.74
1832 3514 2.475852 CGTTCTCTGCTACGACCTACAC 60.476 54.545 0.00 0.00 40.03 2.90
1835 3517 0.800631 TCTGCTACGACCTACACACG 59.199 55.000 0.00 0.00 0.00 4.49
1837 3519 1.198408 CTGCTACGACCTACACACGAA 59.802 52.381 0.00 0.00 0.00 3.85
1838 3520 1.069022 TGCTACGACCTACACACGAAC 60.069 52.381 0.00 0.00 0.00 3.95
1842 3524 1.065401 ACGACCTACACACGAACGAAA 59.935 47.619 0.14 0.00 0.00 3.46
1843 3525 2.287788 ACGACCTACACACGAACGAAAT 60.288 45.455 0.14 0.00 0.00 2.17
1844 3526 2.340577 CGACCTACACACGAACGAAATC 59.659 50.000 0.14 0.00 0.00 2.17
1846 3528 2.036217 ACCTACACACGAACGAAATCCA 59.964 45.455 0.14 0.00 0.00 3.41
1847 3529 3.061322 CCTACACACGAACGAAATCCAA 58.939 45.455 0.14 0.00 0.00 3.53
1849 3531 2.557317 ACACACGAACGAAATCCAACT 58.443 42.857 0.14 0.00 0.00 3.16
1851 3533 1.263217 ACACGAACGAAATCCAACTGC 59.737 47.619 0.14 0.00 0.00 4.40
1852 3534 0.511221 ACGAACGAAATCCAACTGCG 59.489 50.000 0.14 0.00 0.00 5.18
1945 3697 2.477863 GCCGAAATCCTTTCACCGATTG 60.478 50.000 1.06 0.00 39.63 2.67
1947 3699 2.161410 CGAAATCCTTTCACCGATTGCA 59.839 45.455 1.06 0.00 39.63 4.08
1953 3705 2.351738 CCTTTCACCGATTGCAAGAACC 60.352 50.000 4.94 0.00 30.52 3.62
1954 3706 0.871722 TTCACCGATTGCAAGAACCG 59.128 50.000 4.94 5.86 0.00 4.44
1955 3707 0.250124 TCACCGATTGCAAGAACCGT 60.250 50.000 4.94 0.00 0.00 4.83
1977 3776 1.269778 CGTTGAGAAGAGTGGCTGACA 60.270 52.381 0.00 0.00 0.00 3.58
1979 3778 3.206150 GTTGAGAAGAGTGGCTGACAAA 58.794 45.455 0.00 0.00 0.00 2.83
1982 3781 2.810852 GAGAAGAGTGGCTGACAAAAGG 59.189 50.000 0.00 0.00 0.00 3.11
1983 3782 1.268079 GAAGAGTGGCTGACAAAAGGC 59.732 52.381 0.00 0.00 42.86 4.35
1993 3792 0.235926 GACAAAAGGCGTGCAGACTC 59.764 55.000 0.00 0.00 37.06 3.36
2050 3923 2.231235 TCGGTCGATCCATCCATACATG 59.769 50.000 0.00 0.00 35.57 3.21
2198 4114 4.675029 ACGAAGCAACCGTCCGGG 62.675 66.667 10.91 0.00 43.62 5.73
2204 4120 2.428622 CAACCGTCCGGGGAAACT 59.571 61.111 10.91 0.00 41.60 2.66
2205 4121 1.670083 CAACCGTCCGGGGAAACTC 60.670 63.158 10.91 0.00 41.60 3.01
2245 4174 1.135803 ACGCCCGAATTCAATTCAACG 60.136 47.619 10.76 11.73 39.22 4.10
2252 4181 0.179200 ATTCAATTCAACGCGGCGTC 60.179 50.000 29.53 0.00 39.99 5.19
2268 4197 1.742761 CGTCCATGTCAATTCCTGCT 58.257 50.000 0.00 0.00 0.00 4.24
2269 4198 2.905075 CGTCCATGTCAATTCCTGCTA 58.095 47.619 0.00 0.00 0.00 3.49
2270 4199 2.609459 CGTCCATGTCAATTCCTGCTAC 59.391 50.000 0.00 0.00 0.00 3.58
2271 4200 2.609459 GTCCATGTCAATTCCTGCTACG 59.391 50.000 0.00 0.00 0.00 3.51
2291 4220 2.031437 CGTACTACTAGTGCTCCGTTCC 59.969 54.545 5.39 0.00 0.00 3.62
2311 4240 1.012486 GCTGTGTTTACTCGGTCCGG 61.012 60.000 12.29 0.00 0.00 5.14
2333 4262 2.034001 GCCGTGAGAAATATCCGAAACG 60.034 50.000 0.00 0.00 0.00 3.60
2337 4266 4.331962 GTGAGAAATATCCGAAACGCAAC 58.668 43.478 0.00 0.00 0.00 4.17
2348 4278 1.779157 GAAACGCAACGAAAAGGAAGC 59.221 47.619 0.00 0.00 0.00 3.86
2358 4288 0.035820 AAAAGGAAGCCGCCGATGTA 60.036 50.000 0.00 0.00 0.00 2.29
2361 4291 0.754217 AGGAAGCCGCCGATGTACTA 60.754 55.000 0.00 0.00 0.00 1.82
2375 4305 5.208624 GATGTACTAGTACGTCGTTGTCA 57.791 43.478 30.10 11.73 40.80 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 1521 7.282585 ACCCATGATCTATCTCGAATTTCAAA 58.717 34.615 0.00 0.00 0.00 2.69
37 1527 5.584913 ACCTACCCATGATCTATCTCGAAT 58.415 41.667 0.00 0.00 0.00 3.34
40 1530 5.730296 AAACCTACCCATGATCTATCTCG 57.270 43.478 0.00 0.00 0.00 4.04
112 1603 2.852413 CACGGCGACACTAGATTTGTAG 59.148 50.000 16.62 0.00 0.00 2.74
116 1607 0.037697 TGCACGGCGACACTAGATTT 60.038 50.000 16.62 0.00 0.00 2.17
125 1616 1.146358 GGTCTAATCTGCACGGCGAC 61.146 60.000 16.62 5.70 0.00 5.19
126 1617 1.141019 GGTCTAATCTGCACGGCGA 59.859 57.895 16.62 0.00 0.00 5.54
129 1620 5.696724 CCTTATTTAGGTCTAATCTGCACGG 59.303 44.000 0.00 0.00 39.39 4.94
172 1663 5.875359 CCATTTCTACGTTTTCTTAGCCTCT 59.125 40.000 0.00 0.00 0.00 3.69
178 1669 7.804843 TTTCACCCATTTCTACGTTTTCTTA 57.195 32.000 0.00 0.00 0.00 2.10
181 1672 6.364976 CCAATTTCACCCATTTCTACGTTTTC 59.635 38.462 0.00 0.00 0.00 2.29
187 1678 4.381932 CCAGCCAATTTCACCCATTTCTAC 60.382 45.833 0.00 0.00 0.00 2.59
196 1688 0.244721 GAGTGCCAGCCAATTTCACC 59.755 55.000 0.00 0.00 0.00 4.02
209 1701 9.542462 TTTAAGTATTGAGTATATGTGAGTGCC 57.458 33.333 0.00 0.00 0.00 5.01
212 1704 9.765795 GGCTTTAAGTATTGAGTATATGTGAGT 57.234 33.333 0.00 0.00 0.00 3.41
225 1717 7.253883 CCTTACGTAACTCGGCTTTAAGTATTG 60.254 40.741 3.29 0.00 44.69 1.90
234 1726 3.881937 ATTCCTTACGTAACTCGGCTT 57.118 42.857 3.29 0.00 44.69 4.35
236 1728 3.681417 ACAAATTCCTTACGTAACTCGGC 59.319 43.478 3.29 0.00 44.69 5.54
237 1729 5.166398 AGACAAATTCCTTACGTAACTCGG 58.834 41.667 3.29 4.81 44.69 4.63
239 1731 9.362539 TGATAAGACAAATTCCTTACGTAACTC 57.637 33.333 3.29 0.00 0.00 3.01
241 1733 9.750882 GTTGATAAGACAAATTCCTTACGTAAC 57.249 33.333 3.29 0.00 0.00 2.50
242 1734 8.938906 GGTTGATAAGACAAATTCCTTACGTAA 58.061 33.333 7.94 7.94 0.00 3.18
244 1736 6.938030 TGGTTGATAAGACAAATTCCTTACGT 59.062 34.615 0.00 0.00 0.00 3.57
245 1737 7.372451 TGGTTGATAAGACAAATTCCTTACG 57.628 36.000 0.00 0.00 0.00 3.18
246 1738 9.573133 CAATGGTTGATAAGACAAATTCCTTAC 57.427 33.333 0.00 0.00 0.00 2.34
247 1739 9.308000 ACAATGGTTGATAAGACAAATTCCTTA 57.692 29.630 0.00 0.00 0.00 2.69
248 1740 8.193953 ACAATGGTTGATAAGACAAATTCCTT 57.806 30.769 0.00 0.00 0.00 3.36
250 1742 8.519526 TGTACAATGGTTGATAAGACAAATTCC 58.480 33.333 0.00 0.00 0.00 3.01
262 1754 9.784531 CCTCTAAGAATATGTACAATGGTTGAT 57.215 33.333 0.00 0.00 0.00 2.57
263 1755 7.715249 GCCTCTAAGAATATGTACAATGGTTGA 59.285 37.037 0.00 0.00 0.00 3.18
264 1756 7.716998 AGCCTCTAAGAATATGTACAATGGTTG 59.283 37.037 0.00 0.00 0.00 3.77
265 1757 7.806180 AGCCTCTAAGAATATGTACAATGGTT 58.194 34.615 0.00 0.00 0.00 3.67
267 1759 9.429359 CTTAGCCTCTAAGAATATGTACAATGG 57.571 37.037 0.00 0.00 0.00 3.16
274 1766 7.993758 GGGTTTTCTTAGCCTCTAAGAATATGT 59.006 37.037 22.26 0.00 41.47 2.29
276 1768 8.338418 AGGGTTTTCTTAGCCTCTAAGAATAT 57.662 34.615 22.26 9.79 42.16 1.28
279 1771 6.958192 TCTAGGGTTTTCTTAGCCTCTAAGAA 59.042 38.462 19.42 19.42 44.57 2.52
280 1772 6.500336 TCTAGGGTTTTCTTAGCCTCTAAGA 58.500 40.000 11.13 11.13 44.57 2.10
281 1773 6.793505 TCTAGGGTTTTCTTAGCCTCTAAG 57.206 41.667 7.16 7.16 44.57 2.18
282 1774 7.563724 TTTCTAGGGTTTTCTTAGCCTCTAA 57.436 36.000 0.00 0.00 44.57 2.10
328 1824 2.408704 GCTTCTAAGTATATGTGCGCCG 59.591 50.000 4.18 0.00 0.00 6.46
395 1910 6.017192 TCTGGAGTTTTCTTAGCCTCTAAGA 58.983 40.000 11.13 11.13 0.00 2.10
401 1916 7.391833 CACTTATTTCTGGAGTTTTCTTAGCCT 59.608 37.037 0.00 0.00 0.00 4.58
414 1929 5.774690 ACAGCCAATTTCACTTATTTCTGGA 59.225 36.000 0.00 0.00 0.00 3.86
417 1932 5.047092 CCCACAGCCAATTTCACTTATTTCT 60.047 40.000 0.00 0.00 0.00 2.52
421 1936 3.099141 CCCCACAGCCAATTTCACTTAT 58.901 45.455 0.00 0.00 0.00 1.73
423 1938 1.341080 CCCCACAGCCAATTTCACTT 58.659 50.000 0.00 0.00 0.00 3.16
437 1952 4.131088 GAGCGTCGAGACCCCCAC 62.131 72.222 0.00 0.00 0.00 4.61
438 1953 3.881019 AAGAGCGTCGAGACCCCCA 62.881 63.158 0.00 0.00 0.00 4.96
439 1954 2.560051 GAAAGAGCGTCGAGACCCCC 62.560 65.000 0.00 0.00 0.00 5.40
440 1955 1.153804 GAAAGAGCGTCGAGACCCC 60.154 63.158 0.00 0.00 0.00 4.95
443 1969 5.096849 AGATTTAAGAAAGAGCGTCGAGAC 58.903 41.667 0.00 0.00 0.00 3.36
445 1971 7.384886 GTTAAGATTTAAGAAAGAGCGTCGAG 58.615 38.462 0.00 0.00 0.00 4.04
448 1974 6.370718 TGGGTTAAGATTTAAGAAAGAGCGTC 59.629 38.462 0.00 0.00 0.00 5.19
457 1983 7.265599 TGGATGACTGGGTTAAGATTTAAGA 57.734 36.000 0.00 0.00 0.00 2.10
458 1984 7.229506 GGATGGATGACTGGGTTAAGATTTAAG 59.770 40.741 0.00 0.00 0.00 1.85
459 1985 7.060421 GGATGGATGACTGGGTTAAGATTTAA 58.940 38.462 0.00 0.00 0.00 1.52
460 1986 6.389869 AGGATGGATGACTGGGTTAAGATTTA 59.610 38.462 0.00 0.00 0.00 1.40
461 1987 5.194537 AGGATGGATGACTGGGTTAAGATTT 59.805 40.000 0.00 0.00 0.00 2.17
462 1988 4.728860 AGGATGGATGACTGGGTTAAGATT 59.271 41.667 0.00 0.00 0.00 2.40
463 1989 4.310740 AGGATGGATGACTGGGTTAAGAT 58.689 43.478 0.00 0.00 0.00 2.40
487 2013 0.249699 TGTCTCGTTGTGTGCCGAAT 60.250 50.000 0.00 0.00 31.92 3.34
513 2040 1.062294 TCGTTTGTTTGCGCGTAAGTT 59.938 42.857 10.10 0.00 41.68 2.66
514 2041 0.651551 TCGTTTGTTTGCGCGTAAGT 59.348 45.000 10.10 0.00 41.68 2.24
532 2059 5.835476 CTGAAAGAAAACGAGGTAAGCGTTC 60.835 44.000 0.00 0.00 43.92 3.95
540 2067 2.480419 CGATGCTGAAAGAAAACGAGGT 59.520 45.455 0.00 0.00 34.07 3.85
581 2108 1.515736 CCTCGTCTTCGCGGGTAAC 60.516 63.158 6.13 0.00 38.16 2.50
613 2140 2.269241 GGCTTCTCTCCCGGGTTG 59.731 66.667 22.86 15.12 0.00 3.77
619 2146 4.856607 CGCGTCGGCTTCTCTCCC 62.857 72.222 0.00 0.00 36.88 4.30
683 2228 2.794621 CATCAGCAGCAGCAGCAG 59.205 61.111 12.92 3.97 45.49 4.24
684 2229 3.440415 GCATCAGCAGCAGCAGCA 61.440 61.111 12.92 0.00 45.49 4.41
685 2230 4.194720 GGCATCAGCAGCAGCAGC 62.195 66.667 3.17 0.46 45.49 5.25
686 2231 3.518998 GGGCATCAGCAGCAGCAG 61.519 66.667 3.17 0.00 45.49 4.24
687 2232 4.354162 TGGGCATCAGCAGCAGCA 62.354 61.111 3.17 0.00 45.49 4.41
688 2233 3.518998 CTGGGCATCAGCAGCAGC 61.519 66.667 0.00 0.00 44.61 5.25
879 2495 1.229658 AGAAGACTGTGGGGGAGGG 60.230 63.158 0.00 0.00 0.00 4.30
880 2496 1.268283 GGAGAAGACTGTGGGGGAGG 61.268 65.000 0.00 0.00 0.00 4.30
891 2507 2.427506 GGATGTGGTTGTGGAGAAGAC 58.572 52.381 0.00 0.00 0.00 3.01
892 2508 1.351017 GGGATGTGGTTGTGGAGAAGA 59.649 52.381 0.00 0.00 0.00 2.87
893 2509 1.073763 TGGGATGTGGTTGTGGAGAAG 59.926 52.381 0.00 0.00 0.00 2.85
894 2510 1.144691 TGGGATGTGGTTGTGGAGAA 58.855 50.000 0.00 0.00 0.00 2.87
895 2511 1.144691 TTGGGATGTGGTTGTGGAGA 58.855 50.000 0.00 0.00 0.00 3.71
909 2525 2.268920 GATCGCTGCTGGTTGGGA 59.731 61.111 0.00 0.00 0.00 4.37
916 2532 0.954449 GGATGGATGGATCGCTGCTG 60.954 60.000 0.00 0.00 0.00 4.41
922 2538 1.051008 TGTGGAGGATGGATGGATCG 58.949 55.000 0.00 0.00 0.00 3.69
923 2539 3.073503 TGATTGTGGAGGATGGATGGATC 59.926 47.826 0.00 0.00 0.00 3.36
924 2540 3.058341 TGATTGTGGAGGATGGATGGAT 58.942 45.455 0.00 0.00 0.00 3.41
925 2541 2.440627 CTGATTGTGGAGGATGGATGGA 59.559 50.000 0.00 0.00 0.00 3.41
926 2542 2.440627 TCTGATTGTGGAGGATGGATGG 59.559 50.000 0.00 0.00 0.00 3.51
927 2543 3.741249 CTCTGATTGTGGAGGATGGATG 58.259 50.000 0.00 0.00 0.00 3.51
928 2544 2.106166 GCTCTGATTGTGGAGGATGGAT 59.894 50.000 0.00 0.00 0.00 3.41
929 2545 1.487976 GCTCTGATTGTGGAGGATGGA 59.512 52.381 0.00 0.00 0.00 3.41
930 2546 1.211212 TGCTCTGATTGTGGAGGATGG 59.789 52.381 0.00 0.00 0.00 3.51
931 2547 2.704464 TGCTCTGATTGTGGAGGATG 57.296 50.000 0.00 0.00 0.00 3.51
932 2548 2.683152 GCTTGCTCTGATTGTGGAGGAT 60.683 50.000 0.00 0.00 30.57 3.24
933 2549 1.339438 GCTTGCTCTGATTGTGGAGGA 60.339 52.381 0.00 0.00 0.00 3.71
934 2550 1.093159 GCTTGCTCTGATTGTGGAGG 58.907 55.000 0.00 0.00 0.00 4.30
935 2551 0.725686 CGCTTGCTCTGATTGTGGAG 59.274 55.000 0.00 0.00 0.00 3.86
936 2552 0.321346 TCGCTTGCTCTGATTGTGGA 59.679 50.000 0.00 0.00 0.00 4.02
937 2553 0.725686 CTCGCTTGCTCTGATTGTGG 59.274 55.000 0.00 0.00 0.00 4.17
938 2554 0.096628 GCTCGCTTGCTCTGATTGTG 59.903 55.000 0.00 0.00 0.00 3.33
939 2555 1.357258 CGCTCGCTTGCTCTGATTGT 61.357 55.000 0.00 0.00 0.00 2.71
940 2556 1.080435 TCGCTCGCTTGCTCTGATTG 61.080 55.000 0.00 0.00 0.00 2.67
941 2557 1.080995 GTCGCTCGCTTGCTCTGATT 61.081 55.000 0.00 0.00 0.00 2.57
942 2558 1.518133 GTCGCTCGCTTGCTCTGAT 60.518 57.895 0.00 0.00 0.00 2.90
943 2559 2.126307 GTCGCTCGCTTGCTCTGA 60.126 61.111 0.00 0.00 0.00 3.27
944 2560 3.184683 GGTCGCTCGCTTGCTCTG 61.185 66.667 0.00 0.00 0.00 3.35
945 2561 3.226429 TTGGTCGCTCGCTTGCTCT 62.226 57.895 0.00 0.00 0.00 4.09
946 2562 2.734673 CTTGGTCGCTCGCTTGCTC 61.735 63.158 0.00 0.00 0.00 4.26
947 2563 2.715532 TTCTTGGTCGCTCGCTTGCT 62.716 55.000 0.00 0.00 0.00 3.91
948 2564 1.841663 TTTCTTGGTCGCTCGCTTGC 61.842 55.000 0.00 0.00 0.00 4.01
949 2565 0.110644 GTTTCTTGGTCGCTCGCTTG 60.111 55.000 0.00 0.00 0.00 4.01
950 2566 1.228657 GGTTTCTTGGTCGCTCGCTT 61.229 55.000 0.00 0.00 0.00 4.68
954 2570 1.464997 GTGATGGTTTCTTGGTCGCTC 59.535 52.381 0.00 0.00 0.00 5.03
958 2574 1.197721 CGCTGTGATGGTTTCTTGGTC 59.802 52.381 0.00 0.00 0.00 4.02
960 2576 1.197721 GTCGCTGTGATGGTTTCTTGG 59.802 52.381 0.00 0.00 0.00 3.61
978 2594 2.224257 GGAGGCAGAGAAGATGATGGTC 60.224 54.545 0.00 0.00 0.00 4.02
979 2595 1.767681 GGAGGCAGAGAAGATGATGGT 59.232 52.381 0.00 0.00 0.00 3.55
983 2599 1.767088 CCATGGAGGCAGAGAAGATGA 59.233 52.381 5.56 0.00 0.00 2.92
984 2600 2.257691 CCATGGAGGCAGAGAAGATG 57.742 55.000 5.56 0.00 0.00 2.90
1089 2743 2.509916 GCCAGCTCCTCCATCAGG 59.490 66.667 0.00 0.00 45.15 3.86
1119 2773 4.864334 GCCGGGTCCATGAGCAGG 62.864 72.222 2.18 7.90 45.43 4.85
1196 2850 2.202570 GGTCGTCGTCGGACATGG 60.203 66.667 9.10 0.00 43.61 3.66
1260 2914 3.467776 GCAGAACTCCATCTGGGAC 57.532 57.895 6.46 0.00 45.60 4.46
1380 3034 0.596083 CGATCGACACCAGATGCTCC 60.596 60.000 10.26 0.00 0.00 4.70
1382 3036 1.037579 TCCGATCGACACCAGATGCT 61.038 55.000 18.66 0.00 0.00 3.79
1384 3038 2.095008 CCTATCCGATCGACACCAGATG 60.095 54.545 18.66 4.84 0.00 2.90
1385 3039 2.163509 CCTATCCGATCGACACCAGAT 58.836 52.381 18.66 11.80 0.00 2.90
1387 3041 1.605753 TCCTATCCGATCGACACCAG 58.394 55.000 18.66 5.98 0.00 4.00
1388 3042 2.061509 TTCCTATCCGATCGACACCA 57.938 50.000 18.66 0.00 0.00 4.17
1389 3043 3.662247 ATTTCCTATCCGATCGACACC 57.338 47.619 18.66 0.00 0.00 4.16
1390 3044 7.091443 AGATTAATTTCCTATCCGATCGACAC 58.909 38.462 18.66 0.00 0.00 3.67
1391 3045 7.228314 AGATTAATTTCCTATCCGATCGACA 57.772 36.000 18.66 2.45 0.00 4.35
1392 3046 8.030106 AGAAGATTAATTTCCTATCCGATCGAC 58.970 37.037 18.66 0.00 0.00 4.20
1399 3053 9.549078 ACGAAGAAGAAGATTAATTTCCTATCC 57.451 33.333 0.00 0.00 0.00 2.59
1433 3088 0.324943 CAGCGGGGGAGAGAAGAAAA 59.675 55.000 0.00 0.00 0.00 2.29
1482 3137 0.605319 TCAACCAATCGACAGTGCCC 60.605 55.000 0.00 0.00 0.00 5.36
1507 3162 1.215382 CGGGAGAGCACACATCGAA 59.785 57.895 0.00 0.00 0.00 3.71
1510 3165 1.520342 GAGCGGGAGAGCACACATC 60.520 63.158 0.00 0.00 40.15 3.06
1517 3172 1.363443 CATCAGAGAGCGGGAGAGC 59.637 63.158 0.00 0.00 37.41 4.09
1520 3175 1.472376 GGAAACATCAGAGAGCGGGAG 60.472 57.143 0.00 0.00 0.00 4.30
1521 3176 0.537188 GGAAACATCAGAGAGCGGGA 59.463 55.000 0.00 0.00 0.00 5.14
1523 3178 0.250234 TGGGAAACATCAGAGAGCGG 59.750 55.000 0.00 0.00 0.00 5.52
1524 3179 1.938577 CATGGGAAACATCAGAGAGCG 59.061 52.381 0.00 0.00 37.84 5.03
1525 3180 2.295885 CCATGGGAAACATCAGAGAGC 58.704 52.381 2.85 0.00 37.84 4.09
1527 3182 2.561187 TCCCATGGGAAACATCAGAGA 58.439 47.619 32.09 3.29 42.05 3.10
1540 3195 5.764686 TGTCGATTAATTCAGATTCCCATGG 59.235 40.000 4.14 4.14 0.00 3.66
1542 3197 9.224267 CTTATGTCGATTAATTCAGATTCCCAT 57.776 33.333 0.00 0.00 0.00 4.00
1543 3198 7.173218 GCTTATGTCGATTAATTCAGATTCCCA 59.827 37.037 0.00 0.00 0.00 4.37
1544 3199 7.389053 AGCTTATGTCGATTAATTCAGATTCCC 59.611 37.037 0.00 0.00 0.00 3.97
1546 3201 9.804547 GAAGCTTATGTCGATTAATTCAGATTC 57.195 33.333 0.00 0.00 0.00 2.52
1575 3230 1.680735 TGGCGAGTTGTGCTGAAAATT 59.319 42.857 0.00 0.00 0.00 1.82
1576 3231 1.001378 GTGGCGAGTTGTGCTGAAAAT 60.001 47.619 0.00 0.00 0.00 1.82
1577 3232 0.380378 GTGGCGAGTTGTGCTGAAAA 59.620 50.000 0.00 0.00 0.00 2.29
1588 3243 2.360350 CAGGGCAATGTGGCGAGT 60.360 61.111 0.00 0.00 44.78 4.18
1589 3244 1.926511 GAACAGGGCAATGTGGCGAG 61.927 60.000 0.00 0.00 44.78 5.03
1590 3245 1.971167 GAACAGGGCAATGTGGCGA 60.971 57.895 0.00 0.00 44.78 5.54
1591 3246 1.926511 GAGAACAGGGCAATGTGGCG 61.927 60.000 0.00 0.00 44.78 5.69
1617 3272 2.860735 CGTAGTTAGATTCTGCTGGTGC 59.139 50.000 0.00 0.00 40.20 5.01
1618 3273 2.860735 GCGTAGTTAGATTCTGCTGGTG 59.139 50.000 0.00 0.00 0.00 4.17
1619 3274 2.761208 AGCGTAGTTAGATTCTGCTGGT 59.239 45.455 0.00 0.00 0.00 4.00
1620 3275 3.444703 AGCGTAGTTAGATTCTGCTGG 57.555 47.619 0.00 0.00 0.00 4.85
1623 3278 5.115773 CGTTCATAGCGTAGTTAGATTCTGC 59.884 44.000 0.00 0.00 0.00 4.26
1624 3279 6.200100 ACGTTCATAGCGTAGTTAGATTCTG 58.800 40.000 0.00 0.00 41.06 3.02
1626 3281 6.690098 TCAACGTTCATAGCGTAGTTAGATTC 59.310 38.462 0.00 0.00 42.10 2.52
1627 3282 6.558009 TCAACGTTCATAGCGTAGTTAGATT 58.442 36.000 0.00 0.00 42.10 2.40
1629 3284 5.550232 TCAACGTTCATAGCGTAGTTAGA 57.450 39.130 0.00 0.00 42.10 2.10
1630 3285 4.204573 GCTCAACGTTCATAGCGTAGTTAG 59.795 45.833 0.00 0.00 42.10 2.34
1632 3287 2.921754 GCTCAACGTTCATAGCGTAGTT 59.078 45.455 0.00 0.00 42.10 2.24
1633 3288 2.094906 TGCTCAACGTTCATAGCGTAGT 60.095 45.455 17.30 0.00 42.10 2.73
1634 3289 2.526077 TGCTCAACGTTCATAGCGTAG 58.474 47.619 17.30 0.00 42.10 3.51
1635 3290 2.526077 CTGCTCAACGTTCATAGCGTA 58.474 47.619 17.30 5.11 42.10 4.42
1639 3319 1.350193 ACGCTGCTCAACGTTCATAG 58.650 50.000 0.00 0.00 40.09 2.23
1652 3332 2.243264 GCTCTCTGCCATACGCTGC 61.243 63.158 0.00 0.00 38.78 5.25
1680 3360 3.849951 CGATCAGGGTGGGGGACG 61.850 72.222 0.00 0.00 0.00 4.79
1684 3364 3.866582 GGAGCGATCAGGGTGGGG 61.867 72.222 1.84 0.00 0.00 4.96
1704 3384 5.363868 TGTCGATTAATCCAGAGATTCCAGT 59.636 40.000 9.87 0.00 41.91 4.00
1706 3386 5.869649 TGTCGATTAATCCAGAGATTCCA 57.130 39.130 9.87 0.00 41.91 3.53
1717 3397 5.459107 ACGTACAAGCTCATGTCGATTAATC 59.541 40.000 5.30 5.30 34.75 1.75
1736 3416 6.396450 CGGTGTTGAAAAATGAAAAACGTAC 58.604 36.000 0.00 0.00 0.00 3.67
1745 3425 1.862008 GCACGCGGTGTTGAAAAATGA 60.862 47.619 12.47 0.00 35.75 2.57
1746 3426 0.502275 GCACGCGGTGTTGAAAAATG 59.498 50.000 12.47 0.00 35.75 2.32
1748 3428 1.583967 CGCACGCGGTGTTGAAAAA 60.584 52.632 12.47 0.00 35.75 1.94
1749 3429 1.777030 ATCGCACGCGGTGTTGAAAA 61.777 50.000 12.47 0.00 40.25 2.29
1750 3430 2.248135 ATCGCACGCGGTGTTGAAA 61.248 52.632 12.47 0.00 40.25 2.69
1751 3431 2.663520 ATCGCACGCGGTGTTGAA 60.664 55.556 12.47 0.00 40.25 2.69
1752 3432 3.410516 CATCGCACGCGGTGTTGA 61.411 61.111 16.28 9.25 44.58 3.18
1760 3440 2.645628 CAATGTCGCATCGCACGC 60.646 61.111 0.00 0.00 0.00 5.34
1761 3441 2.021793 CCAATGTCGCATCGCACG 59.978 61.111 0.00 0.00 0.00 5.34
1762 3442 2.277501 GCCAATGTCGCATCGCAC 60.278 61.111 6.85 0.00 0.00 5.34
1763 3443 3.507924 GGCCAATGTCGCATCGCA 61.508 61.111 0.00 0.00 0.00 5.10
1764 3444 4.256090 GGGCCAATGTCGCATCGC 62.256 66.667 4.39 0.00 0.00 4.58
1765 3445 2.051804 GAAGGGCCAATGTCGCATCG 62.052 60.000 6.18 0.00 0.00 3.84
1766 3446 0.749454 AGAAGGGCCAATGTCGCATC 60.749 55.000 6.18 0.00 0.00 3.91
1767 3447 0.749454 GAGAAGGGCCAATGTCGCAT 60.749 55.000 6.18 0.00 0.00 4.73
1768 3448 1.377202 GAGAAGGGCCAATGTCGCA 60.377 57.895 6.18 0.00 0.00 5.10
1769 3449 1.078143 AGAGAAGGGCCAATGTCGC 60.078 57.895 6.18 0.00 0.00 5.19
1770 3450 1.372087 GCAGAGAAGGGCCAATGTCG 61.372 60.000 6.18 0.65 0.00 4.35
1778 3458 2.488204 AGAAAGAAGCAGAGAAGGGC 57.512 50.000 0.00 0.00 0.00 5.19
1789 3469 3.992427 GGGCATTTGCTCAAAGAAAGAAG 59.008 43.478 2.12 0.00 42.27 2.85
1799 3481 0.036732 AGAGAACGGGCATTTGCTCA 59.963 50.000 2.94 0.00 43.04 4.26
1800 3482 0.449388 CAGAGAACGGGCATTTGCTC 59.551 55.000 2.12 0.00 41.70 4.26
1809 3491 1.139095 GGTCGTAGCAGAGAACGGG 59.861 63.158 0.00 0.00 39.52 5.28
1812 3494 2.486982 TGTGTAGGTCGTAGCAGAGAAC 59.513 50.000 0.00 0.00 0.00 3.01
1824 3506 2.665052 GGATTTCGTTCGTGTGTAGGTC 59.335 50.000 0.00 0.00 0.00 3.85
1827 3509 3.739300 AGTTGGATTTCGTTCGTGTGTAG 59.261 43.478 0.00 0.00 0.00 2.74
1828 3510 3.491639 CAGTTGGATTTCGTTCGTGTGTA 59.508 43.478 0.00 0.00 0.00 2.90
1831 3513 1.263217 GCAGTTGGATTTCGTTCGTGT 59.737 47.619 0.00 0.00 0.00 4.49
1832 3514 1.721489 CGCAGTTGGATTTCGTTCGTG 60.721 52.381 0.00 0.00 0.00 4.35
1852 3534 1.521681 GGCTGCTGGTCGTATGGAC 60.522 63.158 0.00 0.00 45.31 4.02
1945 3697 1.774639 TCTCAACGTACGGTTCTTGC 58.225 50.000 21.06 0.00 36.49 4.01
1947 3699 3.317430 ACTCTTCTCAACGTACGGTTCTT 59.683 43.478 21.06 1.11 36.49 2.52
1953 3705 1.068472 AGCCACTCTTCTCAACGTACG 60.068 52.381 15.01 15.01 0.00 3.67
1954 3706 2.030185 TCAGCCACTCTTCTCAACGTAC 60.030 50.000 0.00 0.00 0.00 3.67
1955 3707 2.030185 GTCAGCCACTCTTCTCAACGTA 60.030 50.000 0.00 0.00 0.00 3.57
1977 3776 2.607892 GCGAGTCTGCACGCCTTTT 61.608 57.895 8.12 0.00 46.26 2.27
1995 3794 3.633094 CTGTGCGAGGACCGGAGTG 62.633 68.421 9.46 0.00 39.91 3.51
2011 3880 2.879942 GATTACGGCGTTGCGTGCTG 62.880 60.000 21.24 2.30 44.36 4.41
2042 3915 1.586422 CCTCGTGGAAGCATGTATGG 58.414 55.000 0.00 0.00 34.57 2.74
2089 3962 1.804151 CGAATTTCACCCATGACGTGT 59.196 47.619 0.00 0.00 33.38 4.49
2100 3973 3.120477 TGACGTATTGCACCGAATTTCAC 60.120 43.478 6.61 0.00 0.00 3.18
2198 4114 2.032808 GTGCTTCACGAGTTGAGTTTCC 60.033 50.000 0.00 0.00 34.94 3.13
2204 4120 0.927537 CGTTGTGCTTCACGAGTTGA 59.072 50.000 0.00 0.00 37.14 3.18
2205 4121 0.654472 GCGTTGTGCTTCACGAGTTG 60.654 55.000 6.35 0.00 41.73 3.16
2245 4174 1.062525 GAATTGACATGGACGCCGC 59.937 57.895 0.00 0.00 0.00 6.53
2252 4181 2.632377 ACGTAGCAGGAATTGACATGG 58.368 47.619 0.00 0.00 0.00 3.66
2268 4197 3.526931 ACGGAGCACTAGTAGTACGTA 57.473 47.619 11.31 0.00 0.00 3.57
2269 4198 2.393271 ACGGAGCACTAGTAGTACGT 57.607 50.000 7.88 7.88 0.00 3.57
2270 4199 2.031437 GGAACGGAGCACTAGTAGTACG 59.969 54.545 1.57 8.17 0.00 3.67
2271 4200 3.689309 GGAACGGAGCACTAGTAGTAC 57.311 52.381 1.57 0.00 0.00 2.73
2291 4220 1.342082 CGGACCGAGTAAACACAGCG 61.342 60.000 8.64 0.00 0.00 5.18
2311 4240 2.234300 TTCGGATATTTCTCACGGCC 57.766 50.000 0.00 0.00 0.00 6.13
2333 4262 1.729484 GCGGCTTCCTTTTCGTTGC 60.729 57.895 0.00 0.00 0.00 4.17
2337 4266 2.106683 ATCGGCGGCTTCCTTTTCG 61.107 57.895 7.21 0.00 0.00 3.46
2348 4278 0.940126 ACGTACTAGTACATCGGCGG 59.060 55.000 28.03 14.80 35.87 6.13
2358 4288 2.977405 GGTGACAACGACGTACTAGT 57.023 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.